MICR2011

Regarding the viral membrane of an enveloped virus, the lipids are derived from the ________, and the proteins are encoded by ________.

host's cell membrane / viral genes

Haloarchaea characteristics...

hypersaline environments

A common mechanism in fungal diseases is... - red blood cell lysis. - hypersensitivity reactions. - endotoxin production. - intracellular invasion.

hypersensitivity reactions.

Laguage/terms for classifying viruses

Family and species level mossti mportant. Family ends in viridae, subfamily ends in virinae, genus ends in virus, species e.g. tobacco mosaic virus Over 100 families

What is the effect of healthy gut microbiota on the immune system?

'peace keeping' bacteria release anti-inflammatory products which participate in runing the host responses towards tolerance. Helps to prevent the pro-inflammatory effects of any pathobions present in the microbiota, thus manitaining intestinal homeostasis.

What is the function of pili?

- Twitching mobility - Attach to surfaces - Transfer DNA

Fts proteins are essential for bacterial cell division because they __________.

- are responsible for forming the divisive - are responsible for peptidoglycan synthesis - are responsible for pulling apart the two copies of the chromosome

What lives in 1ml seawater?

1 ml seawater contains around: 10^7 viruses 10^6 bacteria/archaea 10^3 fungi 10^3 microalgae 10^-18 whales

fungal diversity

1.5 million species of fungi on Earth, and 600-1000 are known to cause human and animal disease and even more than that cause disease in plants.

DNA in endospores is stabilised by _________.

10% dipicolinic acid

What temperature is most commonly used for autoclaves to sterilize growth media and other devices prior to experimentation?

121°C

Bacterial rRNA

16S

Mitochondria and Chloroplast rRNA

16S

Eucaryotic rRNA

18S

History of bacteriphages

1915-1917: discovered by Twort and d'Herelle independently 1920: combat pathogenic bacteria, bacterial strain typing. Not only to kill infections but also used to type strains 1940-1970: foundation of molecular biology. Restriction enzymes, cloning, plasmids all sorts of things, mapping of E. Coli chromosomes. Many nobel przies won by people working with these phages Phages found in over 140 bacterial genera, pretty much every bacteria has a few and iscovring more all the time Over 5100 phages examined by EM Bacteriophage is derived from Greek - Bacteria eater

Who discovered bacteriophages? how did they discover them?

1915-1917: discovered by Twort and d'Herelle independentlyHe discovered bacteriophages is 1918: This guy travelled all over the world and tried to kill locuses with bacteria The nobel prize of immunilogy told him that he was crazy and there was no such thing as a bacteriophage, and he wasn't even a properly trained scientistl Acientist acedemia establishemnet poo pood him for a while But he proved them wrong Was the first person to think about using bacteriophages to treat bacterial infections

What makes up healthy gut microbiota?

A healthy gut microbiota contains a balanced composition of many different types of salmon. Immunological equilibrium: Symbionts (regulation) - (organisms with known health-promoting functions) Commensals - permanent residents of a complex ecosystem. Provide no benefit or harm to the host. Pathobionts- - premenant residents of the complex ecosystem which have potential to induce pathology If things change in the environment it will increase potential to cause disease and cause pathology

Using examples of two papers, show how technology in biology has changed the data we get over a short period of time.

1980 - difficult to get data. In nature study published. These people sequenced bit of E. Coli genome, one bit of one gene. They sequenced 150 nucleotides and also sequenced a few different strains and looked at a few differences. They used a method by SANGA who had published this method a few years earlier and he went on to get the noble prize for that work. Was important because it lead on to more subsequent work. In those days difficult to get the data. These days don't see pics like this in scientific articles. In those days was very difficult to obtain even one picture like this where you can see a little bit of a sequence. These are four lanes coresponding to different bases, and you can read sequence as you go down. Even getting a 150 nucleotides got a page in nature in 1980 . Here's another figure from that paper where you can see sequence written out, this is in a protein coding gene, so you can see what each tripplet codon responds to in the protein (amino acid). This picture also shows where there is some differences. Sometimes these lead to different amino acids. So the protein sequence is different cause the DNA sequence is different. Fast Forward to 2016 - Infection genetics and evolution is a good journal is a pretty good journal, not as fancy as nature, but it's okay. In this journal, a short communication was published ( a minor paper) in the paper, we sequenced 14 isolates of this bacterial species (salmonaella enterica) the entire sequence was done for 14 isolates. A lot more info compared to 150 nucleotides in a handful of isolates. A lot more data and even so it was only published in a modest journal as a short communication.

How was penicilin discovered?

1982: the silver bullet In 1928 alexander fleming reported the discovery of penicilin. Left petri dish out on the bench, left window open and went on holidays, then when he came back found this fungus penicillium was growing on the plate, and where it was growing it was inhibitting the growth of staphyloccus aerus. Original isolate penicillium chryosogenum was only producing in tiny amounts, and really difficult to get more at that stage. Put on hold for about 16 years.

What lives in 1g soil of soil?

1g of soil contains around: 10^9 viruses 10^10 bacteria/archaea 10^5 fungi 10^4 protozoa

burden of antibiotic resistance

2016 US government prioritised combatting antibiotic resistance with USD $1.2 billion investment in research. Preventative research and development of new antimicrobials. UK government predictions indicate 700,000 death annually Predict 10 million deaths by 2050 - more than cancer, from spreading resistance

Explain the 'mosaic' genome of Enterohaemorrhagic E. Coli

24 bacteriophage elements (many cryptic) 1-2 plasmids Many transposons and IS In outer ring is the genome it shares with comensal e. coli. (what we have in gastrointestinal tract which doesn't cause disease) The red and orange bits are mobile genetic elements or horizontal transfer events where it has inserted predominantly bacterial phage elements, a couple of transposons and plasmids that have inserted into this genome and carry all of the virulence genes that it requires for causing disease. It causes a very severe disease which leads to renal failure. The acquisition of two bacteria phage that encode sugar toxins and molecular syringe, have been inserted into the genome and now we have a pathogen. E. Coli is thought to be 150 years old.

What are some Characteristics of Bacterial phyla?

3.5 billion hyears has given rise to incredible diversity of microorganisms. Microorganims have become extreely genotypically and phenotypically diverse Some phyla have been characterised much better than others. E.g. proteobacteria contains most of the bacteria that have been characterised. They culture very well in labs, grow very fast. Very easy for us to study, and a number of human disease microorganisms in here.

HIV epidemiology

36 million people infected. Mostly outside africa you get more men than women. In subsaharan africa, because it's heterosexually transmitted, it's pretty equal in distribution, maybe women are a bit more common. Sub-saharan africa though is by far the biggest chunk. 25/36 million in Africa. 33 million (similar estmate from 2007) if you look at Pi charts, red bit means how many people were infected in one year, purple is amount of people infected in total. If you put rest of the world together, it still wont be the same amount of those infected in Africa. This is population life-expectancy over time. In these countries with low HIV the life expectancy is still miserable but getting better, up to 50 in 2000. the Botswana population life expectancy was going up quite nicely, could live until 60 on average, but then it plummeted and crashed to around 35. it was absolutely devestating. Was caused sleeping sickness there. Wiped out many people in Africa from 1990-2000 (that period)

Provide a timeline of Life on Earth

4.5 billion years ago earth is formed , conditions on earth very harsh not condusive to life First signs of life - the first evidence we had of microbial life on earth was 3.5 billion years ago Microbial stromatilites and chemical signatures in rocks that indicate the presence of compounds present in microbial membranes. Cyanobacteria like microorganisms thought to be responsible for generating the oxygenic atmosphere which we now have today Higher organisms emerging in the last 50 million years Microorganisms had run of the planet for 3.5 billion years Long time to diversify and adapt to niche environments. Today we think there are about 1 trillion species of microbial cells.

What is used to classify a phage

4900 tailed phages, 5100 phages in total, so only 190 other (non tailed viruses) Pahge for salmonella will only affect salmonella, phage for E. Coli will only infect E. Coli. That's how they are used for typing - one phage per species. The classification is worked out by: What bacteria does it infect What genome does it have Its morphology Ability to lysogenize A temperate virus is also a lysogenic virus. Got over 110 families of virus now to infect animals. A lot less here, but still a lot of viruses out there When he did sequencing of bacterial genes they had to clone genes in M13 vector so that you can have nice single strand which increased base pair reading from 200 to 400.

define a fungus

A fungus is a chemoorganotrophic eukaryote that lacks chlophyll and forms spores Its cell wall contains polysaccharides often chitin or cellulose, and it absorbs nutrients. Its membrane contains ergosterol as the major sterol Classification is principally based on morphology - Mushrooms - Moulds - Yeast

Where do archaea live?

A high proportion of archaea live in environments humans describe as extreme However archaea are ubiquitous: aquatic, soil, animals and food. Many of them live all over the show, they live everywhere. One way of demonstrating that is referring to low temperature enciornments. If you look at the biomass of what's in the marine environment and you add up all the whales, sponges and thing you can see, it represents less than 5% of the biomass, the rest is microbial. It's on the 10^28 (lots of cells) and many of these are archaea. If you think of marine environment as 'normal' environment, archaea are in a lot of normal environments.

What is an advantage of a monolayer cell membrane, as is found in some Archaea?

A monolayer membrane is more stable at high temperatures.

The respiratory tract has multiple systems to help protect against airborne diseases. Some of these systems include:

A mucociliary blanket to remove contaminants, secretion of lysozyme and other antimicrobial chemicals, and alveolar macrophages helps protect against airborne diseases.

What is the benefit, for a virus, to be a temperate or lysogenic virus?

A single infection event can produce millions of new viral particles instead of hundreds of viral particles.

moulds - what are they, how do they grow?

A spore lands right in the centre of the agar plate, filaments grow outwards from the spore once the spore germinates and keep creeping all the way along the plate and radiating outwards. As the fungus matures it produces spore structures. Sometimes it produces a pigment from melanin which is in the wall of those spores. Hypha - filaments, often branched, one hypha will have multiple branches Septa - barrier that forms between compartments in a hypha Can have hypha that are aseptase (no septa) one big long multinucleaic compartment. Spore structures - (bottom right) spores that grow off the hypha are called conidiophores, on top they have conidia coming out which are asexual spores they are what disperse for example in the air.

What are antibiotcs?

A substance produced by one microorganism that selectively inhibits the growth of another. We are very late to the antibiotic party. Microorganisms have been on this planet for 3.5 billio years, potentially they have been using anti-microbials against each other for billions of years. They potentially have been using anti-microbials against each other for millions of years, where there is an arms race to develop anitmcorbials and resitance ot them. Modern interpretation: a compound that kills or controls growth of microorganisms in the host Anitbiotics are selectively toxic to microorganisms and not us Exploit evolutionary divergence of Bacteria and Eukaryotes

how are viruses classified?

A universal system for classifying viruses and a unified taconomy, has been established by International committee of taxonomy of viruses. Over 100 different families of viruses. Have differnet commitees for different fmailies of viruses. Predictions about replication, pathogenesis. If you know classification of viruses you know what it does. What it's transmission is, the shape. More than 2,475 species belonging to 6 orders, 96 families, 22 subfamilies, 420 genera recognised by ICTV Out of date. With new sequencing tehcnology means finding viruses all of the time. One guy published 1500 new viruses from sequencing technology. Classificaiton: The type of nucleic acid, The presence or absence of a lipid envelope, Number of strands of nucleic acid and their phsycial construction (Ss or ds, linear, circular with breaks or segmented) Segmented - influenza is segmented. It has 8 segments means it has 8 separate RNAs *8 bits of RNA not joined together at all) makes about 10 or 11 genes. Polarity of viral genome - viral genome acts as mRNA are termed 'postivie stranded' those where a transcript is made firs are termed 'negative stranded', Replication strategy, Symmetry of nucleocapsid (helical or envelope) Most viruses don't encode proteins, we make 22000 oroteibs, most viruses make 20 unless they're big. Lot less proteins than us and much smaller genomes.

What is strange about viruses? what have we learned from them?

A virus is just a pit of RNA and DNA with a protein coat surrounding it. It can't respire or move or have a metabolic process. It can replicate and divide. It's a bit living but really classigied as a non-living thing. Bacteriophage infecting E. Coli. Gives a sense of the size of them. Bacteriophages will infect and take over the whole cell and turn it into a bacteriophage factory machine. That single bacterial cell will start to produce 4-500 bacteriophages. When one of our cells get infected with a human virus it turns our cell into a virus factory as well, but we make 50,000 viruses. The origins of molecular biology use viruses to infect bacteria. We learn a lot of things (replication, DNA as genetic material in Hershey experiment) many nobel prizes were won in 50s and 60s using bacteriophages to work out how genetics works in bacteria and in humans.

what are three mechanisms of antifungal resistance?

Antifungal resistance mechanisms Target alteration or overexpression Upregulation of mutli-drug transporters/efflux pumps Cellular stress responses that make antifungal useless

Why is ATP necessary for active transport?

ATP provides energy to transfer material against its concentration gradient.

what are the disadvantages to us of biofilms?

According to US navy: Biofilm micro-fouling can increase drag on ships by 20%. Bioufouling can casue economic damages up to 200 billion US $ per year in the US alone Medical industry biofilms are responsible for 65% of soft tissue and wound infections

What is AIDS>

Acquired immunodeficiency (AIDS) first described in 1981. HIV isolated in 1983 by French. First case in Aus in 1981 at POWH. Clinicians started seeing gay men with immuno-supressent diseases. They saw people with chronic fungal lung infections which they nly sawi n immunosuppresed people. They had rare cancers on their face. They were coming in with these oppurtunistic infections where immune system seemed to be finished and they eventually died from aids and no one could figure out what was going on. At long bay prison down the road, an inmate got stabbed with a syringe needle full of blood and there was no treatment back then, and then he died 4 years later of HIV. Was used as weapon as well.

describe the different morphologies of different viruses

Adenovirus - Causes colds and gastro. See spikes, 12 of these coming out of twelve corners and are receptor hunting. HSV-1 - is enveloped with an icosahedral virus in the middle, huge DNA virus HPV - If you get vaccinated wont get genital warts. Icocahedral but non-enveloped HBV - Unsuual - makes three types of shapes. Not icocahedral. There is small circular, large cicrular and rod. The only infectious virus is the large circles. It makes the others as decoys. Ebola - helical virus Influenza - Looks round but it is a helical virus Measles - helical virus Norovirus - naked helical virus causing gastro

What are some of the advantages of bacteriophages and antibiotics?

Advantages of bacteriophages: Very specific - affects the targetted bacterim only Change of developing secondary infections reduced No side effects Phage able to reproduce as long as host bacteria is available - therefore repeated administration is greatly reduced. Development of resistance may lead to attenuation of virulence Selection of new phages can overcome resistance and is easy Production is simple and relativey inexpensive Advantages of antibiotics: Can be used without knowing the ID of the bacteria

describe cell wall of fungal pathogens

All fungi have chitin and beta 1-3 glucan in cell wall, as structural compnents, but what you have in a lot of other fungi e.g. asperfillous spores is melanin, and a lyer of hydrophobins on outside. These are sheilded, can see why echinocandins don't get in or aren't as good. Has polysaccharide capsule on the outside for cryptococcous. Sugars in the capsule stop the drug from getting in (the one above) `

describe some properties of naked viruses

All icosahedral Environmentally stable Temperature, acid, proteases, detergents, desiccation. Norovirus can survive in a river at 0 degrees for a month and still be infective. , Usually viruses can only exist 4-6 hours at room temperature before not being infective Consequences: Easily spread, retain infectivity after drying, resistant to detergents, survive in the gut, resistant to sewage treatment, induce an immune resposne,

When describing the viral genome, which terms could be used? - ds DNA - ds RNA - ss DNA - All of the listed responses are correct.

All of the listed responses are correct.

Which compounds can serve as electron acceptors in anaerobic respiration? - ferric iron - protons - fumarate

All of them

Which of the following statements is TRUE about HIV infections? - The cDNA can integrate into the host chromosome. - T-helper cells are greatly reduced in number. - The viral nucleocapsid of the virus enters the host cell when the viral and host membranes fuse. - All of these statements are true.

All of these statements are true.

Why are microbes so ahead of us in antimicrobial resistance?

Antimicrobial resistance has been going on for millions of years We are very late to this thing Microbes have two advantages - a lot more numbers. Even in our own gastrointestinal tract, have more bacterial cells than cells in our own bodies. Genetic Diversity of those microorgnaisms is much higher than in our own genes. Sdvantage of numbers and genetic diversity, so if we have started throwing these things at them, they probably already have the solution or if not, they are good at evolving these solutions to problems. When applying accute selection pressure like an antibiotic, the pressure isreally on and then they come up with solution or will die.

What substance is used as a decolorizing agent in the Gram stain?

Ethyl alcohol

HIV genome

All retroviruses look like that This is the genome, it is reverse transcribed. The RNA is turned into DNA by reverse transcriptase (which belongs to the virus) and then that DNA is inserted into your chromosomal DNA as a provirus, ab it like lysogenic phase of a bacteriphage. It uses a very similar, if not identical, co-enzyme called integrase to get genome. Once genome is in iyour genome it can replicate, make message and make more virus. Classic elements include the long terminal repeats in pro-phage form that provides promoters etc. for gene expression. These proteins gag red vpu, all help with virulence of the virus or infectivity of the virus. The virus has 7 main proteins. It has gag, which is the structure (nuclear and matrix protein - protection prtiens of the virus, also the capsid). There is pol for polymerase, but there are three enzymes in there. There is protease to chop up larger proteins into smaller ones. There's a polymerase and there's an integrase, integrase needed to insert into chromosome. Then over here have two envelopes that are cleaved around here into two, that are cleaved by protease into two proteins, stalk and head, of the envelope glycoproteins on surface of the virus.

What is an alpha toxin?

Alpha toxin - it cleaves phosholipid head bit off of the phospholipid bilayer membrane, causing it to become usntable. The cell will lyse and pop open. Perfringens (anaerobe causing gas gangrene) secretes alpha toxins, destroying cells in local vacinity, which benefits the pathogen. Immune response then walls off that area nad it becomes an anaerobic niche for bacteria to multiply in. HBA - essentially what you are looking for. Beta heamolysis is the secretion of glycophospholipase or a pore forming toxin, and it bursts the red blood cell. Not specific for red blood cells, can affect any cell, it's just a nice convenient way to see pore forming activity.

cellular stress response of candida to echinocandin

Also has cellular stress response: This is due to fact that there are two structural components in fungal cell wall. What found was when you treat a cell with cacpofungin, it inhibits the beta-1, 3- glucan synthase so you get less of that in the wall. But when that happens, a whole bunch of transcription regulatory pathways are activated in response to cell wall stress. The end result of the stress signally pathways is an upregualtion of chitin synthesis. Although there's less green, there is a lot more brown, which restores the robustness of thecell wall. Also shown this works in reverse. If we inhibit chitin synthesis (no drug at the moment that can do this, have to do it in lab) get activation of those same cell wall stress pathways which result in upregulation of Fks expression and more beta-glucan. Cell regulates to respond to stress. To find fungal equivalent of penicilin need to find something that will target both of those at same time.

What is the effect of a dysbiotic gut microbiota on the immune system:

Altered gut environment Antibiotics, diet, hydiene, pollutants, virus? Leads to dysbiosis - decrease I peace keeping bacteria Damagef epithelial barrier, indreased bacterial adherence and penetration Pathological inflammation If someone has a severe monogenic immunodeficioncy e.g. mutation in IL 10 receptor which is inportant in reducing inflammation then can see increase in inflamation can occur in that group. There are a number of groups e.g. NO2.. That are important in regulating our immune system which have an affect.

What are aminoglycosides?

An aminoglycoside because it has amino sugars (amine groups on sugar rings) and connected by glycosidic linkages. They all are very similar but just have derivatives on the side which are slightly different. They all act by blocking protein synthesis by binding to the small subunit. The smal lsubunit has 16s ribosomal RNA but when it has proteins attached as part of the ribosome it's called the 30S subunit. Gentamycin is good at killing broad spectrum of bacteria. It good at killing gram negatives but has restricted use because it is actually toxic. It is restricted to serious infections. Common aminoglycosides are: gentamycin, kanamycin, streptomycin

What is Bioinformatics (wiki definition)

An interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics and engineering to analyse and interpret biological data.

Who was Anne Miller?

Anne Miller died in 1999 at age of 90s she lived full and fulfilling life. She contracted a streptococcul infection in 1942 and had been in hospital for multiple weeks with high temeprature and treating physicians didn't know what to do. Temeprture chart from 1942, had high temp of 106 degrees They gave her blood transfusions, she had lost a child from this infection and physicians didn't know how to treat her. Her treating Physicians were treating another patient at the time called George Fulton. He was good friends with a chap caleld Howard Florey who was working at oxford univeristy on new antibacterial to treat infections. George helped Howared to bring him and famliy over to the states. They were quite cose. George new that howard was working on these things, and asked if they could use compound he was experimenting with have a patient Anne Miller who is about to die. He wrote to them and Florrey who was at merrick dispatched a paper bag with a trooper containing 5.5g of penniciln and took it to hospital. Physicians didn't know what to do with pennicilin so they gave two injections, 5.5g divided into two and gaver her two infections over the evening. By the morning temperature had come back down, after a week she was eating again, and soon rady for full recovery.

how antibiotic resistance spreads from agriculture to us

Antibiotics going into animals - selecting for resistance and then going into the food chain. If you don't cook your chicken properly and can be infected with antimicrobial. This transfer from animal to humans and it isn't as uncommon as you think. Run-off and fertilisers from farms can get into salads uncooked vegatables Treated with antibiotics, going into hospital where everyone is getting antibiotics in confiend space, and then giong into outside world.

What is the affect of antibiotics on microbiota?

Antibiotics kill and inhibit infectious bacteria however disrupt normal microbiota leading to dysbiosis. Use of antibitics has also been associated with intra- and extra- intestinal diseaes such as CDAD, type 1 diabetes, type 2 diabets, VRE, vulvovaginitis, Excema, Atutism

antibiotics vs antifungals

Antibiotics take advantage of things that bacterial (or prokaryotic cells have that eukaryotic or human cells) do not. There are loads of characteristics that can be exploited for therapies.

Why are antibiotics often ineffective in treating food poisoning (food intoxication)?

Antibiotics target bacteria; they do not damage toxins.

What is the antimicrobial resistance era?

Antimicrobial resistance poses a catastrophic threat. If we don't act now, any one of use could go into hospital in 20 years for minor surgery and die because of an ordinary infection that can't be treated by antibiotics. And routine operations like hip replacements or organ transplants could be deadly because of the risk of infection. Only been in this game for less than a hundred years

Which type of active transport protein uses one protein to pump two different molecules? (can pick multiple) - Uniport - Antiport - Symport

Antiport and Symport

what regions of our body have a microbiota?

Any region of the human body exposed to outside world has microbial community: Hair(dry), The linings of nasal passages (nostrils - moist), Vagin, Oral cavity, Stomach, Gastrointestinal tract. Can see that similar groups are present in all areas, but the percentage will change depending on which site. Oral cavity, has quite a lot of firmicutes etc. differ slighlty but on the whole they have same groups of bacteria just present in different percentages. Never believed that there were any other organisms in stomach except for helical bactropilory. And before the discovery of helicalbactropilory they thought stomach was sterile. They thought it would be sterile because pH in stomach is ph2. helocalbactropilory can survive there because it produves an enzyme called urease that allows the pH to be increased. Can see from colouring, tend to go into different clusters. They tend to separate out, there are some similarities but can be separated on principle component analysis.

properties of viruses

Anything that passes through that 0.22 micron filter and you can inject into an animal and it causes disease isn't a bacteria and is probably a virus. 20-350nm in size. Totally dependent on living cells for replication and existence Possess only one species of nucleic acid either RNA or DNA (can be single stranded or double stranded). Have a component for attaching or docking to cells. Able to take over the host cell to propagate themselves. Small ones for humans like parvovirus, (Slapcheek rash) herpes viruses are quite big , really big viruses infect algae and we don't talk about them too much but they are called mimicviruses and they have up to a million base pairs. Most genomes in viruses are between 5000-250,000 base pairs. Parasites take over the cell to make proteins which make more viruses

What are the differences between archaea, bacteria and eukaryotes?

Archaea and bacteria don't have nuclei or orgnalele while eukaryotes do. Lipids - bacteria and archaea have esther linked lipids with a glycerol 3 phosphate backbone while archaea don't, they have this. Metabolism - on the whole archaea the environments they live in are similar to bacteria and they have similar metabolic processes. Really interestingly though if you look at gene expression aspect, e.g. RNA polymerase which is involved in transcription, structure in archaea is similar to eukaryotes. So easy to see in structure of complex . Archaeal one looks just like eukaryotic one. Many of these subunits are interchangeable. The gene expression in eukaryotes is very much like archaea. Also some unique aspects of archaea in this domain of life (always some exception) But methanogenisis as a process is production of biolgoical methane. Everhthing that is biological methane on the planet comes from archaea Those interested in medical science, not one archaea is known as a pathogen. 10^10 per gram stool sample in us. No pathogen of plants, or any animals. Not a reaosn we can identify why they shouldn't be.

summary of comparison between archaea and other domains of life

Archaea have a bacterial like life style: Metabolism energy generation and environments Archaea have eucaryal like fundamental processes: Replication, transcription, translation Archaea have their own 'unique characteristics': Methanogenesis, lack of pathogenicity

describe an archaea that provides potential evidence of first form microbial respiration

Archaea strain 121 grows at 121 degrees celcuius (autoclave). Survived 2h at 130 degrees. Anaerobic, N2 CO2 formate is electron donor and ferric oxide is electron acceptor. Discovered it has a electron transport chain baed on iron 3, reason it may have been one of the first microbial respiration cycles.

Describe the Architecture of virions

Architecture of virions regardless of host is baed on two simple themes: Spherical - normally in form icosahedron Best way of producing a shell of equivalently bonded indentical structures with ltos of the same subunit Mimumum free energy state, don't need energy to assmeble Strong structure that can enclose a maximal volume Helix - cylindrical shape (spiral staircase) Complex virus e.g. small pox An icosahedron is composed of 20 faces, each an equilateral triangle, and 12 vertices. used in modern architecture. Because of rotational symmetry is said to have 5:3:2 symmetry.

What are Firmicutes?

Are all gram positive microorganisms With yellow section (archaeobacteria) and ternericutes, they constitute half of all charachterised bacteria. Firmicutes have low G + C in their genomes Not as many GC pairs, in contrast to actinobacteria with a lot of G+C pairs Many medically and industrial important species Lactobacillus - used in dairy fermentation Some are disease causing - Staphylococcus , listeria, streptococcus, clostridium Has a few genre to generate endosphores Certain species of Bacilus and Clostridium are able to form endospores which are just iwhtin the fermicutes

Name and describe a hypothermile environment in Australia

Artesian basin - one reason to stop coal sema gas because frackign destroys water. Hypothermophiles - area of asrtesian basin is massive. What makes it unique is because its heated because its deep. Its not volcanically heated, its just heated because its deep into the Earth. This water is 100 degrees coming out. No one has ever taken a sample from deep down where the water comes from and sample the microorganisms. Quite alogisical challenge to get down there and take the saples, but untapped area in microbiology.

Microbes capable of fermentation are often used in food. What is the main function of fermentation for the microbes?

Fermentation regenerates NAD+ so that glycolysis can continue.

How does broad range of topics in bioinformatics contribute to the certainty mathematicians have over their data?

As a field has to be as broad as molecular and cell biology itself, cause it has to support all those areas. Bioinformaticians don't know about all these topics. In some cases, they know hardly anything about any of these areas. The reason for that is because it's such a big field and it's impossibel to know everhthing. The other thing is that bioinformatics is changing very quickly. Technqiues that might have been important and state of the art five years ago may now be considered obsolete. When these sort of shifts happen then these computational methods also have to keep up. In the field of bioinformatics theres often lots of sophisticated methods, and sometimes there are lots of methods and comptuational tools that need to be used, and the data might go into some method andp roduce some output, which needs to put into another computational tool, which produces another output, which needs to go into another computaitonal tool etc. Might have a string of tools lined up and they might be organised in what's called a pipeline. Stick raw data in one end. Sometimes each component is like a blackbox. It's like a blackbox where a person using the tool might not know what's happening inside. Might know a little bit about how it works, but not quite enough so that your comfortable that its doing what you think it should be going. When your at that point it makes you nervous if you can really trust the output. Even if you feel really comfortable with four of these mehtods, there may be one step/method where you're not quite sure what the tool is doing. If tha'ts the case then arguably the whole thing is a little potentially problematic. There's a bit of a problem in the field, where because it's so big, and there's lots of things to know, there may be some problems here and there where we don't really understand what's happening in analysis of data. Again all these things are changing and lots of methods get supplanted by new ones so you have to be on the ball if your in this field. Even if your not in the field and your using computers in biology, you have to convince yourslef that you're using the right tool for the right situation.

How does our microbiome naturally change over time

As we age our gut microbiota changes. Most dramatic changes occur between birth and 2-3 years, when it starts to resemble a typical adult microbiome. Over 2-3 years, infants gradually acquire a microbiome resembling that in a typical adult. Bifidobacteria - good bacteria. E. Coli can be non-disease causing Some E. Coli usually not in babies can cause severe gastrointeritis. Colstridium perfringens is a gram pos rod that forms spores We are constantly changing our microbiota according to age

what is aspergillosis?

Aspergillosis - collective name for all the infections caused by aspergillis species. Are saprophytic (grow off of decaying plant matter) and are ubiquitous (everywhere) Things that allow them to degrade plant matter, mean in the right circumstance they are also great at killing your body. Enzymes that you need to break down leaf material Caused by inhalation of conidia (Spores) Most common cause is aspegilus fumigatus, althought there are a lot of aspergillous species that can casue infections. Over 200,000 life-threatening infections. Stem cell and organ transplant patients most susceptible. We breath in hundreds of thousands of these spores a day. When they get into our lung, the innate immune cells mop them up. Generally they don't cause us problems. If macrophages aren't working well e.g. in cytic vibrosis patients, they are going to have issues. If the conidia aren't moppped up in thel ungs, they can germinate and fungus can cause disseminative disease. diseases caused by aspergillus app: Simple asthma, alergic asthma, aspergiloma (fungal ball that forms inbig mass organ usually the lungs), aspergillosis (disease caused by aspergillus species) Difficult to diagnose these, just looks like a big mass, could be anything. 30-95% mortality even with surgical intervention and antifungals

In which stage does formation of mature viruses occur? - Assembly - Biosynthesis - Release - Penetration - Attachment

Assembly

What is the lifecycle of a bacteriophage?

At first, it infects bacteria by injecting DNA into host. then bacteriophage genome circularises. Makes a decision, do I want to enter lysogenic cycle and integrate into bacterial chromosome, and sit there as a silent piece of SNA in the chromosome and carried through generation of bacteria as it goes Or it can decide for it to enter lytic cycle (caused by stress mostly, e.g. when bacteria is under stress) when it starts to make phage particles - caps and tail - replicate its genome and stuff it into phage particles, and then it lysis and releases new particles to find new hosts.

Plasmids are _________.

Autonomously replicating, circular DNA

What are some examples of chemolithotophs, including their use and their electron acceptors and donors.

Azopira oryzae - Using ferric iron as electron donor, in aerobic environment, some of these occur in really low pH (acidophiles) really important in bioremediation, particularly acid mine drainage Ralstonia - Some can use hydrogen or CO2 as carbon and energy sources donors, really basic molecules Degalococcoides mccartyi - Uses perchloroethene Really important for cleanning up global pollution This one is isolated here by researchers at uni, big problem at the ORICA botany bay site. Use these organims to bioremediate there

Very long and thin shaped cells are called _________.

Filamentous

Thermotogae and Aquificae characteristics...

hyperthermophilic, terrestrial and marine thermal springs and vents, deeply branched, closest to LUCA, many are hydrogen gas chemolithotrops

Why is the concept of prokaryote wrong?

Bacteria and archaea have separate lineages

What is Lateral Gene Transfer?

Bacteria are evolving very rapidly in environment and can adapt to very complicated environments Bacteria are able to adapt to very complicated environments In E Coli it already had machinery there just needed to express machinery in right conditions. We were looking at closed system with richard's experiments, but how do we generate a lot of dicersity in this asexually producing population. Unlike us they don't exchange genetic material every time they divide. Answer - lateral gene transfer (horizontal gene transfer) Allows bacteria to take quantum leaps in evolution Pass DNA from one to another to see if it's useful Is the Transfer of foreign genetic information between microorganisms. As two organisms become less related the rate of transfer decreases. It depends on the transfer method and properties of DNA transferred The DNA replication and machinery for reading the DNA is not going to be abslutely conserved between every bacteria, so there are some differences If you transfer it into a new host, may not be read correctly or have cofactors required

What are biofilms?

Bacteria form biofilms on surfaces. They form on medical devices, in aquatic systems, slime on toilet bowl or sink, slime on a rock, medical devices, our own infections are bacteria formed in a biofilm. Biofilm has specific processes .in the past nothing known about biofilms - just known as a slime. The biofilm process is very dynamic, it's almost like development of tissue.

enteric virus transmission

Bacteria transmission is also similar Main routes - for norovirus its through the air and vomit Contaminated water - spread virus and bacteria, sewerage gets into water system Food Person-person transmission Environmental surfaces - don't wash hands and touch door handle of toilet Tolerant to temepratire change Survives high levels of chlorine Transmission through the fecal-oral route Highly contagious

The microbiome contains all organisms that are present...

in and on the body.

What are exotoxins?

Bacterial pathogens also produce disease-specific toxins termed exotoxins Secreted toxins may act Locally, at distance sites, independent of bacterial pathogen. Where you are injected they can release toxins and cause tissue damage, can act at distance sites by getting into blood flow and nymphatic system, circulate around the body and cause disease elsewhere in the body. Can act independent of the pathogen - e.g. boctulinin toxin, can cause disease in absence of the bacteria entirely. Bacterial toxins may be: non-specific, cell-specific Non-specific toxins are often attack host cell membrane Phospholipase C (lecthinase), pore forming toxins. Clostridium perfringens is an anaerobe that causes gas gangrene Secretes alpha toxin Causes tissue damage that perpetuates infection.

What are bacteriophages?

Bacterial viruses (phage) - incredible diversity of types Estimated at over 10^31 10M per cm3 10-100 fold more than bacteria (very abundant) Obligate parasite - requires bacteria for replication (are viruses) Two live cycles Lytic (explores bacterium to release phage) Replicates within the bacterial cell, explodes the cell and releases bacteria phage particles. That's reasonably limiting if you kill all your hosts - you run out of places to replicate Lysogenic (integrates in bacterial chromosome) can be replicated with bacteria as it frows There are a number of different strategies they use, these are the general ones.

All of the following are typical gram-positive organisms found on the skin EXCEPT __________. - Propionibacterium - Staphylococcus - Bacteroides - Corynebacterium

Bacteroides

who are predators in microbial world?

Bdellovibrio - a delta proteobacteria. Small culred spiral shape It agressively crashes into a gram negatice prey bacteria Foes into preiplasmic space and rapidly repilcates and then bursts the cells Vampirococcis Legionella is predator of ameoba / macrophages Phagotrophic protists flagellates, amoeba, ciliates. Eukaryotic microorganisms - they often main feeders on bacteria When people study predation in microbial interactions see similar fluxes in lion and prey. Prey goes down, predator up, predator goes down, prey goes up. can be eukaryotes, viruses, bacteria

what is Saccharomyces cerevisiae?

Best known or called 'bakers yeast' or 'brewers yeast' - It makes bread, beer and wine Instrumental in making these thigns since ancient time It is a glucose loving fungus - it is a glucophile. It loves glucose to the extent that it will completey ignroe any other sugar if there is glucose present. It will actively supress the genes involved in the metabolism of other carbon sources if glucose is present. It challenges the dogma because it ferments glucose first and then respires it. Do you make more ATP from glycolysis or fermentation? Make way more from glycolysis. Fermentation produces alcohol which is what we take advantage of. Most organisms aren't tolerant to high amounts of alcohol. Can outcompete other microbes in similar situation Natural habitat - grapes

describe echinocandins mode of action and their effectiveness

Best on the market for treating candida infections. Only new class of fungal infeciton to come in the last 15 years. Fungicidal for candida, fungistatic for aspergillus but won't inhibit cryptoccoous. This is because of difference in the cell wals which is why it can't inhibit cryptococcouse. Inhibit the enzyme that makes one of the structural components of the cell wall, beta 1, 3 glucan synthase which in most fungi is called Fks. If you can't make one of structural components the wall is in hteory weaker and that causes death. Can only be administered by Ivbut testing some topical applications for superficial infections. Are not toxic, nothing like fungal cell wall in a human. Good candidate but haven't found right way to properly target it. Bigger difference between human cells and fungal cells - cell wall Can't kill cryptococcus and and zygomycetes. Resistance emerging.

Bacteria divide through _______.

Binary fission

what are the benefits to us of biofilms?

Biofilms important for us and maintaining water ways. Biofilms can be like microbial mats (Similar to winogradsky columns) Flocs considered type of biofilm Lots of geobiochemical cycling is occurring in biofilms. Carbon nitrogen phosphorus sulphur etc. all occurring in the processes. Can have damages in other areas as well.

What is photosynthesis?

Biological process that converts solar energy to biomass, bio-products, and biofuel. Only major natural solar energy storage mechanism on Earth Phototrophic bacteria use light as the energy source to produce ATP and reductants. Energy and reducing equivalents generated from light-induced electron transport drive diverse carbon metabolic pathways for producing cellular material. Additionally, numerous photosynthetic bacteria play essential roles in global carbon, nitrogen and sulfur cycles

The host DNA is usually degraded during which stage? - Penetration - Release - Biosynthesis - Attachment - Assembly

Biosynthesis

outline the issue with algal blooms

Bloom - particularly in summer. Can be a big problem in Aus. Some of these are toxic. Trying to regulate toxin production, to make sure its not poisoning our water ways.

what is some historical perspective of cyanobacteria?

Blue green algae is cyanobacteria. Responsible for blooms, particularly in the summer. One of the oldest known organisms Have fossil evidence of life on earth, some of the olders (3.5 billion years). Oldest rocks: 3.8 billion years old. Not necessarily the first form of life, but definitely one of the earliest dated. Likely that oxygenic photosynthesis evolved in these organisms.

What do hepatitis A and hepatitis B have in common? - Both can be prevented by a vaccine. - Both are transmitted via the fecal-oral route. - Both can result in a carrier state. - Both often result in a mild disease.

Both can be prevented by a vaccine.

What is Competition ?

Both exist at lower levels, due to sharing a limited resource. Live together, take a bit of a cut. Don't grow to best than to what they can be than if they were on their own or microbe A outcompetes B

What are some medical/cosmetic uses of botulinum toxins?

Botulinum toxin is used clinically to prevent involuntary muscle contractions. With a very small dose can prevent blepharospasm - where it causes your eyes to contract. Can have localised muscle paralysis, which stop the involuntary muscle spasms. Also used cosmetically to relax facial muscles. If injected into wrinkles, stops muscles around the wrinkles from contracting and release. So can become smoother on the forehead.

Transduction

mediated by bacteriophage

What are tenericutes?

Break some of the rules in sturcutre and function lecture Between actinobacteria and firmicutes is the tenericutes (very small phyla) They are often called the mycoplasma. They are characterised by most studied genus in the phyla called the mycoplasmas They don't have a cell wall. In structure function lecture, we said cell wall was critical to stabalise cytoplasmic membrane. Without it, osmotic pressure inside cell would burst cytoplasmic membrane. Raises the question - why don't they burst? Their membrane is special High cotent of sterols and lipoglycans. Kind of like LPS (LPS - outside membrane of gram neg bacteria, used to stabilise that membrane) Allows them to go without a cell wall Because they don't have a cell wall, are not able to be target by antibiotics which specigically target cells with cell walls. Common antibiotics like penicillin target cell wall synthesis. These are resistant to those target antibiotics.

Maraca shaped cells are called ________.

Budding & appendaged

What are proteobacteria?

By far the largest phylum of Bacteria Contains more than a third of characterised Bacteria Majority of medical industrial and agriculturally important bacteria All gram negative Morphologically and metabolically diverse Huge array of different metabolisms that they use Six major subgroups - alpha, beta, delta, epsilon, gamma, zeta. Characterised a lot of these Alpha and gamma are some of the larger clades of proteobacteria

Why is studying stromatolites important?

By studying one of these systems, stromatilistes, similar to a winogradsky column, we can really try and understand what's going on. We got organisms that exploit pretty much any energetic opportunity. And they itneract, with each other, whatever they are using, the waste product of a different organism at a different level. Sometimes organism can also move. Cyanobcateria drive it from the top.

Where do candida albicans live?

C Albicans live in our body as a commensal fungus. Don't find it in environemnt, only ever find it associated with mucous membranes really on mammals and in particular humans. For exmaple, it doesn't colonise mice. It's a commensal on us. Mycobiome studies (studies to sequence all the fungi prsent) in a place or on the body, have shown that the gastro-intestinal tract by at least 50% of humans is colonised by candida albicans. It's also found in the mouth and the vagina on mucous membranes. It has been detected through sequence on skin but it's really not a great coloniser of skin. Can get it there though. A person gets colonised at birth. In scientific sense it is veritcal transmission from mother to birth. Very little evidence that strains are passed between people in other ways. Whatever you get when you start life is candida that will remain there. It isn't transmitted to other people and even if it is it goes through and does't do anything.

Bacteria that are able to grow in humans and cause disease have likely evolved to be: - hyperthermophiles. - psychrophiles. - thermophiles. - mesophiles.

mesophiles

A microbiologist wants to study the virus particles from a urine sample, but not any bacteria that might be present. How can the bacteria be eliminated without harming the viruses?

Filter the sample with a 0.2 ïm pore filter.

What is active transport?

Can also have active transporters - these can transport solutes against the chemical gradient. For these you need energy input and that often comes from ATP or proton motive force, or even by phosphorylation of the substrate via energectic input. Because they use energy can transport solutes against chemical gradient which is important when you need trace elements to bring into the cell and have inside the cell in high concentration, but not available in very high concentrations outside of the cell.

what is antibiotic inactivation through modification?

Can also have modification of antibiotic. Instead of modifying target, there are specific enzyme resistance genes that wil modify antibiotic. This is gentamycin aminoglycodie, there are specific resistance enzymes that weill add adenylate, acetulate or phosphorylate residues on the gentomycin molecule which prevents gentamcin from binding to 16s ribosomal RNA. It's charged and has the wrong shape and doesn't fit like a lock and key to site on ribosomal RNA. Gentamycin can be inactivated by enzymes : acetylase, acetylae phosphorylase, adenylation.

what is one main way norovirus spreads?

Can be spread through vomitus Hotel restaurant with 126 patrons One patron vomited at table 52/83 surevey responders ill. 63% overall attack rate Attack rates higher at closer tables. Consistent with airborne transmission of NoV Example of airborne spread of virus

what are colonising infections?

Can replicate in your gut. They are invasive, they will invade the wall if your jerodeum or irrillium they will inflitrate the wall through the mucous. They will infiltrate and then replicate. Salmonella, shigella (dissentry), campylobacter, yersinia, escherichia coli, vibrio cholerae, vibrio parahaemolyticus, aeromonas and plesiomonas, clostridium difficile.

Catabolism is ________.

How organisms obtain energy and raw materials from nutrients.

Where were norovirus infections most documented?

Can see this is norovirus outbreaks in NSW divivded into age care, child care and hopsitals. There's the spole for sydney - what we saw last year - another big strike in gastro. If we look at bottom slide here, these are main viruses here - 6 major pandemic viruses of norovirus has caused most of outbreaks in last 20 years. This year could be a bad winter for winter casue of 164 strain we have see

Which of the following is considered an opportunistic pathogen? - Trichomoniasis vaginalis - Plasmodium vivid - Toxoplasma gondii - Candida albicans

Candida albicans

morphology and metabolism of candida albicans

Candida albicans are polymorphic yeasts. Candida bud same way saccharomyces does, but is also creates pseudohyphae which are elongated cells with constrictions in between the compartments. There are also true filaments or hypahae. There are septa in between the compartments as it forms as it gorws from their tip. We use candida alpicans as a model for polarised growth, modelling esentially how neurons grow and things like that, through polarise growht at a tip. The yeast pseudohyphae and hyphae are the classic white cells of candida albicans. They are what most have used. They propogate stably, you can inter-convert between these morphologies just by putting them in different conditions. E.g. if you want the yeast cell to turn into a hypha you stick it in serum for 37 degrees. If you want it to stay it as a yeast you grow it at 30 degrees at YPD. If you want pseudohyphae stick it in 30 degres in YPD (kind of an intermediate between those two but not really) Chlamydospores produced by candida albicans - large, spherical thick walled cell Only produced under in vitro conditions in a lab. They are used as a diagnostic to confirm a specimen has candida albicans in it. They are not sexual spores, they aren't really spores at all. Nobody has actually figured out what they really are for. You don't see them unless you make them in a lab. Don't confuse them with them being sexual spores. Chlamydospores, no one really knows what they do, there are lots of better interesting things to study, so do that. Very metabolically diverse, it will grow just as well on other carbon sources as it does on glucose. It will utilise multiple carbon sources at once, so if you have multiple sugars present it will just keep growing on all of them. It grows happily on them, it does't care.

What are the steps of the dark reaction in photosynthesis?

Carbon dioxide is coming in, we are looking at 3 CO2s comng in. 3 CO2s are used per cycle. Rubisco takes these 3 CO2s and joins them, to a 5 carbon molecule (happening 3 times). We get 6 carbons now. Along the way we need ATP and we need NADPH The enzyme that catalyses those reactions needs ATP and NADPH as its cofactor For that reaction to occur, it won't occur spontaneously, it needs the cofactor to work We have a rearrangement of the molecule, splitting into two, now we have 3 CO2s, 3 5 Carbon molecule, this becomes 3 6 carbon molecules, then we get them being split into six 3 carbon molecules, our product is clyceraldehyde 3-phosphate (3 carbon sugar), one of them comes out of the reaction, and the 5 of them are recycled around, and become the 5 carbon molecules (at the beginning) and they come around again. Each time that cycle goes around with the intermediates, three carbon dioxides come in, a G3P comes out, and the rest go around going through different configurations. When we get to the end, we can join the two G3Ps in a different process to get glucose.

Relationship between microbes and carbon cycle.

Carbon is main global cycle All the cycles are linked It's because they make up marjority of life: carbon, oxygen, nitrogen Photosynthesis removes carbon dioxide and produces oxygen Respiration produces carbon dioxide, and removes oxygen Different organisms do different parts of these cycles Autotrophs use CO2 to make organic compounds Heterotrophs use organic compounds to use CO2 ( rely on autotrophs to grow, to provide organic compounds to use and then release CO2) Carbon and oxygen cycles are closely connected Example of entire ecosystem Photosynthesis remove CO2 produce O2, respiration removes O2 produces CO2 Sediments and rocks are largest reservoirs -> why its important to not dig everything up, releasing carbon present locally CO2 and nitrogen cycles are linked.

Who was Carl Woese and what was his discovery for phylogenetics (not about archaea)

Carl Woese realised the thing in the last common ancestor that was conserved across all life which would be a great comparitive for establishing evolutionarhy relationships is the ribosome. It's a large RNA machine composed of RNA. It's required to translate sequence info DNA that gets transcribed to RNA and translated into protein. All living organisms have to have that ability. All living organisms have to have ribosomes. The cyan and grey parts here are RNA. Largely composed of RNA. The structure of ribosomes are used as supporting evidence to suggest prebiotic life before LUCA was an RNA based world. Carl ='s breakthrough realisation was actually these ribosomes are strongly evolutionary conserved. Can't accumulate many point mutations in here, structure has to be very well conserved. If you were to sequence ribosomal subunit, you should be able to compare distantly related life. This is the secondary structure here for ribosomal RNA. In bacteria it's called 16s Ribsoomal RNA In bacteria larger subunit is 23s

What provides the energy to attach a third phosphate to ADP?

Catabolic reactions

what is a primary pathogen?

Cause disease in otherwise healthy individuals Has a number of virulence factors that allow it to overcome all our defences

Most known methanogens are nonhalophilic _______.

mesophiles

cholesterol vs ergosterol

Cell membrane: Phospholipid bilayer. Cell membrane is made of ergosterol while our cell membrane is made of cholesterol. Difference is a small little bit, so a very subtle different in these two molecules. They have a polysaccharide cell wall made of two sugars chitin and beta13 glucan. Attached to that wall are highly mannosylated cell wall proteins. Attached is Manaan polymer of manose (a type of sugar)

advantages and disadvantages of targeting cell wall

Cell wall is a great way to target it, but only have one class of drugs that target it. Every time you try study the wall, you find a new way that fungal drug isn't going to work. Pennicilin in bacteria is very good, disrupts peptidoglycan, kills structural integrity, cells die. Doesn't happen with fungi. We have two strutural components of cell wall. There is chitin and beta 1,3 glucan. When you deplete one structural component you get an upregulation in the other and fungus is fine. Need to find something to target both of them.

How bacteria overcome innate immune defences

Cellular innate immunity consists of: Complement system and phagocytic cells First layer of immune system Complement system - a protein cascade within the a serum that is able to identify non-cell molecules Anything that it thinks are not part of the host will assemble a membrane attack complex on the surface. It is a big pore that inserts into the bacterial membrane and disrupts proton motive force (lets H2 back into the cell) and leak all inside into outside world and kills cell. Bacteria can defend themselves against complement system using capsules. Sialic acid is on the surface of our cells and complement recruits specific proteins to tell the complement that that's us. Sialic acid on bacteria makes compliment system think its our cells. If bacteria sialate the capsule, our compliment system will think that it's us. Nesseri meningitis and streptoccocus pneumoniae do this.

what are Chemolithotrophs?

Chemolithotrophs Use inorganic compounds as a source of energy This group of organisms includes sulfur oxidizers, nitrifying bacteria, iron oxidisers and hydrogen oxidizers. The term chemolithotrophy refers to a cell's acquisition of energy from the oxidation of inorganic compounds, also known as electron donors. Probably these ones really important in terms of closing, completing or carrying out a lot of major nutrient cycles. Microorganisms are ones that drive it all. They are doing their thign to survive, but if they won't, would get a build up of ammonia or sulfate etc.

E. Coli is which type of chemotroph?

Chemoorganotroph

What are the predominant bacterial phyla that make up our microbiome?

Classification of bacteria: Firmicutes Bacteroidetes Verrucomicrobio Proteobacteria Actinobacteria

What is norovirus?

Classified in the caliciviridae family Leading cause of acute gastroenteritis globally Positive sense, single stranded RNA virus Non-enveloped, icosahedral capsid (27nm) very small Highly infectious and transmissible 699 million infections globally, approx 2,2 million australia per year Economic costs to the world around US $60 billion The ferari of viruses, one of the most infectious viruses we know. It only takes 100-1000 viruses to infect you. When you are shedding when you're ill about tne million Infects about 700 million people each year Economic costs for the globe are around 60 billion

Give example of relationship between bacterial virulence and plasmids

Closely related to bacillus cereus When sequencing the genome of these two species they really only differ by two plasmids Bacillus anthracis has two plasmids pXO1 and pXO2. pXO1encodes the anthrax toxin and the ability to cause more disease in humans. Yersinia is an example of this Yersinia pestis is what caused the plague. Very closely related to enterocoliticia and pseudotuberculusis - cause gatrointestinal disease. Pestis has two plasmids - pPCP1 and pMT1 has a number of virulence genes including molecular syringe for injecting proteins into host cells which allows it to cause more severe disease. In these cases plasmids carry the required accessory genes for disease to make them more pathogenic

What is Botulinum toxin and how does it work?

Clostridium botulinum causes boltulism Flaccid paralysis - Muscles completely relax and can't stimulate muscles anymore 400g is enough to kill everyone on Earth - can ingest toxin and it will cause disease in the absence of the bacteria. Muscles completely relax and can't stimulate muscles anymore . It circulates in the system until it finds a neuromuscular junciton. It specficially looking for receptors on the surface of neuronal cells. It recognises those and it is endosotosed into an endosome that becomes acidified and releases a component of the toxin called a protease. It is a protease thatcleaves synaptobrevin that is a receptor on the outside of the synaptic vesicles. They cleave off the receptor of the synaptic vesicle, so those vesicles can no longer fuse with neuronal membrane and be released ot the muscle. By clipping off receptors, it prevents neuron from stimulating the muscle. Can no longer release a neurotransmitter. Flacid paralysis where your neurons are no longer able to trigger the muscles to contract.

Round shaped cells are named _________.

Cocci

what is commensalism?

Commensal - often don't know benefit of other party One organism gives something to another which benefits second organism, but neither harms or benefits first organism. Waste product of one organism can function as a substrate for another Example of waste product, one group of organisms can oxidise ammonia into nitrite. Another group can make it from nitrite to nitrate. Modification of environment to make it suitable for a second organism

List relationships with positive or neutral impact

Commensalism Mutualism Cooperation

What are functional guilds?

Community with different guild. A functional guild is a group of taxa that can carry out a similar function E.g. photosynthesis have a community at surface with a lot of light. Have a lot of different species that can carry out photosynthesis that are present. Not just one type .e.g cyanobacteria, but lots of different organisms that drive community present. As you go down, e.g. below sediment in a marine system, it's not very oxic, so have conditions where you have fermentative bacteria that seem to thrive. . In anoxic sediment: guild 1: denitrifying bacteria, guild 2: sulfate-reducing bacteria, guild 3: fermentative bacteria, guild 4: methanogens . Conditions determine type of organism present.

What is the new advancement of FMT?

Companies looked at bacteria that were producing positive effect (being donated from people's stools) and have now created pills made from different microbiota. They are freeze dried, encapsulated . Had a success rate of 87.8%, where most people prefer taking a pill.

Potential treatment for IBD

Companies want to develop product where you can now buy a product that can change your microbiota to what it should be. This is a study done by large group , they were looking to validate markers in IBD. In study had healthy controls (40), 34 patients with chrones and 33 with UC. You can see in healthy controls, UC and Crohns can see different changes occuring in bacteria content of these organisms. Did a bigger trials which contained over 2045 faecal samples.

List relationships with negative impact

Competition Amensalism Predation Parasitism

Flagella runs along ________.

Concentration gradient

What is conjugation? how is it done?

Conjugation refers to the movement of DNA on plasmids among bacterial species Specific type of movement of plasmids. Plasmids autonomosly replicate separate to chromosomes. They can be self transmisible or mobilisable The F-plasmid is self-transmisable refers to fact that F plasmid encodes all the genes to make conjugal pilus It's a hollow filament that goes from donor to recipient bacteria The f plasmid will start to replicate itself and will feed one strand through the conjugal pilus and will enter the new cell and will recirculaise and replicate so this plasmid now has a copy of the conjugal plasmid. They can also be mobilisable referring to the fact that plasmids that don't have the ability to make this pilus, but they hitch a ride. They hitch onto conjugal plasmids and are transferred through the pilus without having any of the pilus encoded on the plasmid Can have broad or narrow host range Some plasmids can replicate in number of different bacteria some can only replicate in some Broad host range can be transferred to a broad range of hosts Carry diverse functions - can be up to megabases big If you can fit it on the plasmid you can basically transfer it Really bad in hospital settings where antibiotic resistance genes are accumulating on plasmids and transferred around pathogens in the hospital.

What are gammaproteobacteria?

Contains nearly half od the species in proteobacteria Highly diverse metabolism Enterobacetiales Contains many human pathofens e.g. echesrichia, salmonella, yersinia (caused the plague), klebsiella Facultative aerobes (can switch to fermenttion) Well characterised - easy of ID Oxidase negative and catalse positive. Many can be differentiated on sugar fermentation

what is Cryptococcosis?

Cryptococcosis - infection due to any species of cryptococcous. Infection from inhalation of basidosphores (secual spores). If healthy, macrophages will mop up these spores in the lung. One of the biggest groups that get cryptococcus meningitis live in sub-sahara Africa with HIV. More than a million of these infectiosn occur every eyar. Pulmonary cryptococcosis - cryptococcus stays in your lung. Breath in the spores, get lodged in aveoli and if your immune system is suppressed can travel up into your CNS cross the blood brain barrier and cause Cryptococcal meningitis. 20-70% mortality rate even with anti-fungal intervention. Even with intervention, patient has to be on treatment for quite a while. Over 500,000 deaths in sub Saharan Africa Estimated 25.8 million people in sub-Saharan Africa who have HIV

Describe the microbial ecology toolbox

Culture dependent - bacteria, fungi, or archaea into pure culture or an enrichment. Enrichment - if you want to try isolate a bateria that can grow on ammonia, then would put ammonia in the media. Example - want to do an enrichment means you have a mixed culture, but if you add ammonia is you are hoping to enrich for organisms that can grow on it. Simple thing to do - can get a lot more diversity. Trick is going from mixed culture to pure culture - why it's more difficult. Culture independent is the more simple way. Can take a sample, extract DNA and look at entire community. Can tag it to look at who is there, or shotgun sequencing and look at metabolic potential of entire communty. Microscopy and fluorescence staining - can get down now to single cell level, while in the past you didn't. just did whole community analysis. Radioisotopic methods - can label, for example CO2 in atmosphere with 14 carbon and work out who can take that material up. Microsensors Can do a combination of approaches to characterise the community.

Unique characteristics of archaea

methanogenesis, non pathogenic, ester g-1-p, cell wall lacks muramic acid and most lack LPS, S-layer of protein or glycoprotein

Antifungal medications are often used topically. Why is this the case?

Like human cells, fungal cells are eukaryotic. To develop systemic fungal medications requires finding specific characteristics of fungal cells that can be targeted, such as the ergosterol in fungal cell membranes.

What is the structure of a phage?

DNA sits inside sheath. It sits on top of the bacteria, it will inject a bacteria with its DNA through this sheath and the bacteria phages held on to the bacteria using these tail fibres and tail pins. Tail fibres attach to specific receptors. This digs into the membrane of the bacteria (outer membrane) the DNA is injected out of there, through the sheath and into the bacteria. The capsid never enters the bacteria, its on the outside, only the DNA goes in. and then it starts to take over the bacteria cell. Can attach to LPS, pili (MS2 gets into bacteria through pili) and lipoproteins. Many structures they can use to get into cell.

diseases cause by dermatophytes

Dermatophytes: Fungus loves growing on keratin - skin, hair, nails Dermatophytes love growing on keratin Lots of different types of tinea defined by where you find that tinea E.g. Tinea capatis - on your head One type of Tinea called ringworm, it starts in centre and then radiates outwards Not a worm Require repeated long term topical application of anti fungal New treatments coming out work really well based on antimicrobial peptides, but drug companies will lose money because they work so well Ring comes from zone of inflamation from hyphae growing outweards, so get inflamation at hyphal tips. Dermatophytes grow outwards as well.

What is Pseudomembranous colitis?

Develops if you are in hospital and you have antibiotcs, what can happen is while you are in hospital you can be infected by clostrifium difficile. You are a healthy individual with healthy microbiota, you are given antibiots which reduces gut microbiota diversity, because you are in hospital the CDI are present around the hospital. You can ingest these, the spores germentate and you get a growht of CD. This causes a dysbiosis of the gut microbiota. What happens is if the CD remains you develop a pseudomembranous colitis. This is inflamation of the colon and this includes severe diarrhea, nasuea and fever, the toxins of CD can increase inflamation and ultimately lead to death. This develops if left untreated.

What is the relationship between ecosystems and habitats

Different types of environmental factors that drive certain habitats. For example, hydrothermal vent. Sometimes bacteria can thrive in habitats where no other organisms can thrive e.g. that type of system Eosystem can contain anything - plants, humans, microbes Ecosystems contain different habitats - Can have microbial habitats not suited to animals and plants. Hotsprings hydrothermal vents, intestinal tract etc. Enviornmental conditions drive microbial community structures

What are some of the disadvantages of bacteriophages and antibiotics?

Disadvantages of bacteriophages: The disease causing bacteria must be identified before therapy Disadvantages of Antibiotics: Non-specific action that targets pathogen and normal flora- this can affect microbial balance leading to secondary infections Multiple side effects: yeast infection, allergies, intestinal disorders Repeated administration is needed Antibiotic resistant bacteria remains pathogenic Development of new antibiotics takes years Production is expensive

What is the general strategy of endo-toxins?

Disrupt intercellular process Receptor binding domain binds to specific receptor on the surface of eukaryotic cell, some kind of sugar, for shiga toxin this is a lipid called GP3. these toxins bind to cell specific receptors. It is then internalised and taken into a vesicle that becomes acidified. This is an endosome. The acidification of the endosome triggers a conformational change and the toxin b sub unit inserts itself into the vesicle membrane and releases the enzymatic domain (a subunit) into the cytoplasm. Enzymatic domain disrupts the host cell processes. That can go on and inhibit a number of cell processes.

What are the advantages of using microbes to study evolution?

Distinct advantages to using micrbes to studying evolution (in contrast to plants and animals... event though plants have seeds) We can cryogenically store each generation allowing us to reserect past generations and compete them agaisnt new/current generations We can see if there has been any 'increase in fittness' Can monitor changesi n fitness by competing against eachother Can sequence genome fairly easily to monitor mutations and what's occuring in genome over time as they are becoming more or less fits Because they are quite small can set up replicates. At beginning had 12 flasks. So has 12 replicates of evolution experiment that started at same point

What is dysbiosis?

Disybiosis - An unnatural shift in the composition of our microbiota Resulsts in a reduction in the number of symbionts and/or an increase in the number of pathobionts. disease occuring. Increase in TH1 cells. They are important because they lead to inflammation, they can cause along with the orgnaism, some of the effects of being infected by organisms. TH2 and TH15 also inflamation. An increase in Treg cells. These cells regulate whats happening with inflammation in the gut.

What is an opportunistic pathogen?

Do not normally cause disease in healthy individuals Will cause disease in compromised host Break in defence e.g wound Immunocompromised. Take oppurtunity and will start to cause disease We have a number of barriers that cause these pathogens to be blocked. Once once of them is comprimised provides oppurtinity for these pathogens to cause disease.

how common are viruses?

Do you have a cold? Colesore - half of everyone in the world has the virus for this (HSV1). There are over 100 viral families. Going to pick on herpes family. HHV71 - half of 350 is 175 (coldsores) HHV2- genital coldsores about 10%. Only time you can pass it on to your partner is if you ha e aactive lesion. Once you have it, can't get rid of it. HHv3 - Glandular fever - 98% of people have had it. People get it as an asymptematic infection. About a third of people getting others are very benign other than HHV 8. CMV Antibodies to CMV in blood - as you get older more chance of getting it. The virus isn't harmful unless immunosuppressed. It can be nasty in immunocomprimised or immunosupressed patients.

How do we name organisms?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species Mnemonic - king philip came over for good soup There are more similar organisms as you go down the naming system Genus and species give binomial naming system E.g. for Escherichia coli - Escherichia is the genus and coli is the species Abbreviated to E. Coli

What are the most common viral agents for gastroenteritis?

Familiar with common putative viral agents Norovirus - Most prevelant is norovirus, rotavirus used to be most prevelant but now have vaccine for rotavirus. Rotavirus Adenovirus - many different tupes. Some can give you cold or gastro or eye infection. Astrovirus 1 Sapovirus Some picornaviruses - Kobuvirus Parvovirus - Human Bocavirus Bottom two are rare

define metagenome

Metagenome: the collection of gnomes and genes belonging to the members of microbiota

Describe the rest of archaea cell envelope

Don't tend to have a typuical cell wall structure, tend to have a variety of thigns, as a generality, they don't tend to have muramic acid, and they don't tend to have LPs , polysacharides. What they have most in common is an S layer. Not all have it but most of them do. It tends to be a single protein or a glycoprotein it forms a surface. Electron mcrograph of S layer protein This S layer came from hypothermophile. The structure is so rigid and uniform that they can use it as a means of filtration. You take S layer and produce a bunch of it, you can make filters for very defined pores for filtering material thorugh. On surface of cells, there is a crystaline latice, all this regular structure is because of the S layer that's on surface of the cells

antibiotics overuse in patients

Drivers of antibiotic resistance: extensive use Overuse in patients In the USA almost a prescription per person per year An estimated two-thirds of global antibiotic sales occur without any prescription. Studies in Indonesia, Pakistan and India show that over 70% of patients weer prescribed antibiotics. The great majority - up to 90% of injections were estimated to be unnecessary.

what are the two drugs that target ergosterol?

Drugs that target ergosterol - Polyenes - Azole

What's better - c-section or vaginal birth?

During and immediately following birth, babies are colonized by range of microorganisms. They are colonised by similar groups, but the percentages differ substantially based on the way they were born. Major sites: skin, first gets colonized, oro-nasopharynx, GIT , urogenital tract - If baby is coming through by vaginal delivery will probably take in some organisms as coming through vagina. Gut microbiome of babies born by vaginal delivery differs from that of babies born by C-section. People have put this forward initially to say that it is better to have a vaginal delivery than c-section. Overtime within first 6 weeks they will move to where they overlap.

What are some chemoorganotrophs with oxygen as electron acceptor? including their use and their electron donors.

E. Coli uses glucose Is really good for biology research - easy to replicate. Has oxygen as an elctron acceptor. Is a chemoorganotroph Pseudonomas putida: Benzene can be huge problem in environment, but these organisms really like that and cleaning up fuels and other hydrocarbon based material Methylocystis Parvus - Methane oxidizing, can get bacteria and archaea that oxidise methane. Use oxygen as electron acceptor, but use methane as electron donor Problems with methane as it increases increased global warming These kinds of organisms, although depends on their level, can regulate this way. Good way to regualte some of problems we are casuing with global temperature Aremonas Hydrophila - Acetate Important in wastewater treatment, get a lot of organisms that can degrade material in wastewater.

characteristics of common human enteric viruses

Each virus comes from different virus family. Sapovirus causes more mild gastrointeritis and is more associated with children otherwise is very similar virus to norovirus. Incubdation period for all these is quite short. Illenss is usually less than a week, it is very difficult to tell different viruses apart based on the symptoms. Can't say 'oh you're vomitting you have norovirus'.

emergence of new norovirus strain?

Each year in australia, roughly 2.2 million people become ill from norovirus infections. Some are asymptomatic but most will suffer from gastroenteritis. After 3 years, nearly 7 million people will have neen infected and have some sort ofparial immunity. (around a third of the population). A new strain pops up and herd immunity doesn't work so well agaisnt the new dog on the block. Immunity you have agaisnt sydney doesn't work on new strain. Why, many of the antibodies and T cells don't hit the target i.e. virus has become invisible to parts of the immune defence army. The strain has mutated, so have amino acid changes in the capsid, antibodies don't recognise these capsids. THEN: The new strain out competes the 3 year old virus as it has a larger susceptible population to inffect, gastro cases for that year icnreae. This is analagous to influenza, same epidimeology

history of HIV

Early 80's homosexual-related immune deficiency (not totally accurate) Blood products recepients .e.g haemophiliacs. Some heterosexual transmission, paritcularly in developing countries. Test for antibody developed in 1984, widespread implementation in 1985. Late 80s epidemic spreads to most parts of world (in particular Africa) with explosive epidemics in developing countries with few resources to combat spread. Throughout 90s number increase to become worldwide pandemic. As soon as you find the virus, want to find test so you can take out virus from organ and blood products. We were screening blood and organs, and transipients in the 80s because of the test. Once we were screening population of HIV anti-bodies, found out infection rate was 10 times higher than previously thought. This is very similar to reason for Hep C. most people who get it are asymptomatic, so don't know you had it, don't go to doctor and won't know you have it until you die of Aids 10 years later. With Hep C won't know you got it until your liver pakcs up 20 years later. Many people who don't know they have these infections because they are asymptomatic, but eventually they will show symptoms. The 90s, and perhaps early 2000s was the worst of the pandemic until we found how to deal with it using drugs.

describe 'pearls' of archaea

Euryarchaeon SM1 Sulfurous marsh water Germany, 10 degrees Pearls 0.2-3mm dia Contain 10^7 archaeal cocci surrounded by filamentous bacteria embedded in unknown polymer Image of looking down into a stream - water flowing by and this is like a macrophatography, these little pearls here , this snotty stuff in the water. There is a single kind of archaeon and single kind of bacterian. Together they grow and form structure so large you can see it with the naked eye. Group that went on to study went on to find out that these appendages actually have hooks on them. So it's a new kind of structure called hami. Can see just how many it produces just aorund, obviously quite useful for its lifestyle.

how Saccharomyces cerevisiae mates

Easy to grow and culture and smells nice Goes through full sexual lifecycle (meiosis and mitosis) Saccharomyces can exist stably as a haploid or a diploid. There are two types of haploid cells. One is a mating type 'alpha' and one is a mating type 'a'. A little bit like 'male' and 'female'. Diploid is a combination of a and alpha. As a diploid it can do mitosis, it buds. In this case have single round of DNA replication, one meiotic division just where your sister chromatids split, and then a straight clone. Can also do meiosis (sporalation) when sporalation happens, have a single round of DNA replication but then get two divisions. It's a diploid to start with so have two copies of every chromosome. When undergo DNA replication, get a sister chromatid. In first division each of those homologous pairs separate, in second division, sister chromatids separate (like in mitosis). At end of this, each of four haploid products get packaged into a single ascal sack. It's an ascomycete because it has asco-spores This is called tetrads for saccharomyces cerevisiae because there are four haploid products in single ascal sack. Because they stay together after spores are produced, they are useful for tetrad analysis to follow events that happened during recombination during meiosis. Useful tool to study those processes. If you have a haploid of opposite mating type, the spores can germinate and form a normal haploid cell, these will do mitosis as normal and bud. If you have a haploid alpha or haploid a they can mate. These two cells will come together and you can get a pheremone induced shmooing. The two cells fuse and form a diploid, and diloid goes on to do whatever it is going to do. Well defined and easy to do in lab, useful for genetic studies.

What are efflux pumps

Efflux pumps are membrane transport molecules out of the cell Resistance to Tetracycline is conferred by the TetA efflux pump. Tetracycline inhibits ribosome function andTetA reduces the cocnentraion in cytoplasm. Two types - can be non-sepcific and just pump things out of the cell. Or resistance pump for tetracylcine - tetA is a protein that specifically pumps tetracycline out of the cell. Because tetracycline needs to bind to ribosome to to have its activity, if you deplete the cytoplasmic concentration of tetracycline then cell can live happily in presence of tetracycline.

What are the two different classes of an organism based on electron source?

Electron source - organic Organism that obtains electrons from organic substrates. Primary difference between organic compounds and inorganic compounds is that organic compounds always contain carbon while most inorganic compounds do not contain carbon. Almost all organic compounds contain carbon-hydrogen bonds Note, containing carbon is not sufficient for a compound to be considered organic (e.g. cyanids) Inorganic - organism that depends upon inorganic compounds as electron donors. = lithotrophy. Electron source - organotrophs if they use something that contains carbon except for something like Cyanide. They use carbon containing molecules as their energy choice

What is the relationships between bacteriophages and virulence?

Encodes many important virulence genes Transfer genes through Generalised Transduction Bacteriophage carry toxins in important human pathogens. Why is this important for bacterial virulence or evolution? There is a number of points in the phage that allows them to carry extra genes, they can tolerate insertions of genes, often they can carry genes that can cause virulence but they can carry genes for lots of different things. Just by lysogenizing the host, they can bring virulence genes that help them cause disease Toxin is a small category, they can bring in a lot of things When bacteriophage is packaging itself ans stuffing its genome into tail sometimes it will make a mistake. It will backage part of the bacterial chromosome instead and that can be transferred into a new host in that viral particle. That occurs more frequently than expected, cause there are so many viral particles being packaged at once.

________ are intracellular bacteria that are usually localized to specialized organs within their host. - Symbiodinium - Endosymbionts - Epibionts - Arbuscules

Endosymbionts

Enteric viral symptoms

Enteric viral symptoms Vomiting (more associated with norovirus) Diarrhea Nausea Abdominal cramps Headache, muscle aches Fever (minority) Dehydration in young and elderly victims Some viruses may caus asymptomaic infections Happens in 10-15% of noroviruses cases. If O- can be ten times harder to infect vs O+.

characteristics of enteric viruses

Enteric viruses Naked viruses (no envelope) they can survive the gut. Envelopes don't survive gastrointestinal tract. Mainly all icosahedral Common in young infants and children because they aren't very hygenic. Occur in colder months were virus can survive longer in outside environments Nosocomial and day-care and aged-care facilities outbreaks reported. Emergence of new norovirus strain leads to epidemics of gastrointeritis. Norovirus a bit like influenza, new strain comes along and cuses epidemics and outbreaks, Hep E and Hep A virus share similar properties to enteric viruses e.g. transmission, structure, but cause hepatitis not gastroenteritits. Norovirus a bit like influenza, new strain comes along and cuses epidemics and outbreaks,

example of gammaproteobacteria is...

Enterobacteriales

What is the direction tRNA takes in a ribosome.

Enters at A-site, and is then transferred to the P-site

What did belinda rename the candidate phyla in antarctic soils, and what are the implications of their metabolisms?

Eremiobactereota - desert bacteria Dormibacteraeota - sleeping bacteria Cultivation of candidatus eremiobacteraeota candidatus dormibacteraeota - Through enrichment of the ability to scavende trace gases Does trace gas chemosynthesis occur in other nutrient poor or oligotrophic environemnts? What other phyla carry out this process? Does it co-occur with photosynthesis? Kakadu national park may have this process happening

Clostridium tetani is an obligate anaerobe that can cause tetanus. When it enters the human body, it can produce tetanus toxin. Considering that C. tetani is an obligate anaerobe, how can it survive and cause disease in the human body?

Especially in deep wounds, C. tetani can sometimes survive in areas with damaged tissue and poor to no blood flow.

why do we know so much more about microbiome?

Evolution of molecular technologies allows determination of entire microbial communities: This area has blossomed over the last 10-15 years. This has come about because we have the techniques to determine all the organisms e.g. in gastrointestinal flora from high tech sequencing Prior to these technologies, 200 bacterial species were recognized as co-habitants of the human body. instead of just looking at pathogens in the gut, can loko at all the microoganisms im a person gut that are a part of the microbiota. Currently restimated that over 10,000 different microbial species occupy our human microbiome. All comes down to having the technique to do it, have always known there are lots of orgnaisms there but couldn't define exactl ywhat they were.

Describe experiment done on pond water for methane

Experiment that looked at ponds which are source sof methane. This is the lognest running mesocosm experiment. Started in 2003. there are mescohosmc here. Having all thes systems here could mainpulate the nutrification (nutrients and temperaute) and could examine what occurs over long time course. Not much info on time course experiments. Indicated shallow lakes make a much larger contribution to atmospheric methan than we knew about . Links microorganisms to processes they perform and gives an idea of how long it can take to ge the data.

What is a novel approach to culturing 'non culturable' bacteria?

Extended incubation times, artificial media with limited nutrients, simulate natural environment of organism. Example: big paper came out. SAR11 a ubiquitous organism present in marine systems. Dominated all the oceans, but no one had been able to culture it. These guys did something simple - Used ariticial media. Took seawater bacteria were in to culture the bacteria. Instead of lookig for growth over 24 hours, made incubation time for a month. Made microcosm, little bit of agar in there and cells from same environment, put it back in the ocean and let it sit there in the marine sediment and let bacteria grow. Bacteria don't always grow as big colony, grow like this - microcolonies. Need to use microscope to see if you cultured something. Sometimes only 10-100 cells present in microcolony, just how it grows. Did something simple - used artificial media. Usually only recover less than 1%, they recovered up to 40% of bacteria present from extending incubation time, looking for microcolonies and simulating natural conditions. A lot of people doing that since. If you got them to this stage, you can sub sample them and domesticate them, make them switch to make them grow fast on media.

What is the I chip method of cultivation?

Extended method from 2002 paper Now have a little I chip, one cell per well in little chip, put it back in soil and let it grow. Get up to 60% of species recovered, by looking at backyard soil, were able to isolate a new species of proteobacteria that had a novel antibiotics. Need a lot of time an patience, screened over 10,000 isolates. Cultivation outside the top four easily cultured phyla is now possible. Candidate phyla OP10 and TM7 recently characterised.

Food that is heavily salted or candied does not need to be refrigerated. Why not?

Extremely concentrated solutions are very hypertonic and therefore desiccate microorganisms. As a result, there is no need for lower temperatures through refrigeration to slow growth.

What things can impact our microbiome over our life?

Factors that impact microbiome: Diet - in gestetation the maternal diet, obesityr and excess gestational weight can result in different microbiota. If at birth baby is born weeks before baby is due it usually goes into an intensive care unti. In that there are other babies so chances are the flora that develops there will develop differently than those taken to their family. Changes due to breast feeding or formula Introduction to solids Big factor that changes microbiota is antibiotics taken Hormonal changes, or obesity In adulthood - diet, pregnancy, obesity, ethinicity, host genetics, environmental chemicals and exposures.

What is faeces?

Faeces - wase or excrement from digestive tract Water, food residue, bacteria, secretions of the intestien and liver. Why is it brown? It's the breakdown of haemoglobin from the blood that is passed through the lipid, and the byproduct of it is a very dark yellow colour. Why your urine is yellow and poo is brown, it's the breadkdown of haemoglobin products. Diarrhoea - frequent passage of water bowel movements

What were the results from Richard Lenski's experiment about rate of mutation and increase in fitness?

Fairly linear relationship or mutations accumulating e.g. SNPS. Not a lot but accumulating There is an increase in fitness which isn't linear Have a very sharp increase in relative fitness (new generations become more fit very quickly) and then more steady increase as it goes along. The reason for this is for the point mutations that confer for strongest selection advantage are going to reach fixation within the population very rapidly. Those that confer a smaller fitness advantage will accumulate slowly over time Have an initial selection for the poitn mutations that can make it more fit very early on, rapid increase in fitness which outgrow everything.

ALL microorganisms that live in the human body are harmful. T or F?

False

Certain species of Bacteria have been identified to cause obesity. T or F?

False

The bacterium Escherichia coli comprises a significant fraction of the bacterial population in healthy adult humans, ranging from 10-50%. T or F?

False

True or false: Biofilms are always composed of only one species at a time.

False

True or false: In a Gram stain, the wash steps are not required if you need to perform the stain quickly due to time constraints.

False

True or false: The more bacteria you put on the glass slide, the better your results will be.

False

The incidence of HIV among hemophiliacs and transfusion recipients has remained constant since 1994. T or F?

False.

Describe mechanisms of colonisation and adherence.

Fimbriae - allow pathogenic bacteria to adhere to host cells (key virulence factor) A lot of bacterial diseases need to be able to attach to our epidelium (tissues) Bladder urethra and kidneys have a lot of urine flowing over it, lot of hydrodynamic forces. They produce a number of fimbriae. Fimbriae tip recognises specific residues on host cell surface - often polysaccharides. E. Coli is common cause of UTI They have a number of fimbriae. Type 1 recognises and Bind to D-mannose a sugar on surface of uroepithelium cells. Binds tightly and prevents it from being washed out. Can progress infection from bladder and move up to kidneys Pili play similar role - adherence and attachment, often longer and fewer expressed on cell

What are fimbriae?

Fimbriae are short hair-like extensions from the bacterial cell Can bind specific receptors (like some sugars on human cells) to attach bacteria - important for adhesion to different surfaces Often important for pathogenesis Fimbriae often have a receptor at the end of the fibre which allows it to bind to specifically to certain molecules in the environment. These fimbriae are important for adhesion to different surfaces.

What is hep C virus?

First identified in 1989. eveloped (+) ss RNA virus. Family (flaviviridae) Typically known as a blood borne virus, pased on from contaminated blood. It means its quite difficult to transmit. You need to inject needle, blood transfusion etc to get virus. Most viruses found in this family are things like Denge , japenese encefolidis virus All these viruses are carried by mosquitos, ticks or sand flies. They are arboviruses, they are insect borne viruses. Hep c is different, even though it's in the same family, it's not carried by mosquitos. It works in a similar way. If you think of the probiscous of a mosquito as an injection into the blood, then in the same way the main transmission route of Hep C is the used needle of a drug user that injects itself into the patient or the victim. All these hep viruses (A-E) are all from different virus families, but what they all have in common is they infect the liver as sole target organ. They don't affect the spleen like herpes or measles. They only cause liver disease. They all cause hepatitis with subtle differences.

What is the process of binary fission?

First step is to replicate everything in the cell Does this starting with chromosome, but also needs to replicate ribosomes, tRNA and other essential biomolecules FTsZ creates a centre in the cell and tells cell it can start to divide Helps to form division spetum It starts to form a division septum, formed by the protein FtsZ, which forms a ring around the precise centre of the cell and tells it that it can now start to divide. Membrane starts to envaginate the chromosome segregates to either side of the cell, and we get a division septum formed. This consists of a cytoplasmic membrane, and cell wall, formed down the centre of the cell. The cell is pinched off into two identical bacterial cells. Very important for cell to divide precisely in the centre, if you divide asymetricaly, one cell will have more cellular components than the other, and one will get less.

Mass producing penicillin - work of Florey

Florey was an australian working at oxford until he was at merrick . Ernst chain and howard florey were at merrick trying to work on how to mass-produce pennicilin. Felming, florey and chain awarded 1945 Nobel Prize in physiology and medicine. Demonstrated efficacy of penicillin to treat infection - patient died as too little penicillin available. Estimated to have saved 50-200 million live Thisi s about time of WW2 and contributing factor to numbers here. Many soldiers were dying of non-mortal wounds that were getting infected. In WW2 had pennicilin that could save most of the soilders. Howard florey used to be on $50 note.

The incidence of HIV/AIDS among transfusion recipients has... - decreased since the discovery of HIV. - increased since the discovery of HIV. - never been more than a few individuals per year. - remained the same since the discovery of HIV.

decreased since the discovery of HIV.

What is the definition of species for bacteria?

For sexually producing organism: They are a reproductively isolated unit. If you are in the same species you should be able to produce viable offspring. Bacteria are asexually reproducing so have a problem, this definition doesn't apply. For bacteria these are the three conditions to define a species. Reasonably arbitrary A) Share phenotypic characteristics (which you would hope for a species. Want them to have similar phenotypes. Outward characteristics) B) 70% total genome similarity C) When looking at our 16S ribosomal subunit want them to have over 97% similarity. Should have 97% same nucleotides across ribosomal RNA. Microorganisms though evolve really quickly. So just because they are in the same species doesn't mean that they are the same. Strain Escherichia coli -K12 is a commensal in warm blooded animals that is usually harmless, and even exists in us Escherichia Coli O157:H7 can kill you Same species but acquired bunch of genes that enable it to cause disease by horizontal gene transfer.

What is chlorophyll f?

Found chlorophyl f, which is an important discovery, found from stromatolites Found new chlorophyl that absorbed light in infra red range, found they could live in environments oeriginally thought we couldn't. down in the soil, or bottomw of column. Might be able to find different kinds of pigments that show they can survive in different kidns of envornments

Why care about bacterial disease?

From WHO - top ten causes of death people worldwide Orange - 3 of top ten causes is bacterial infections Lower respiratory tract infections, diarrheal disease, tuberculosis Sometimes caused by viruses Why matter to us? - data skewed by people in mature age Older age - risk of dying of heart disease and stroke The younger you get the more inclined you are to die from infectious diseases including respiratory diseases In western world - high sanitation means less lkelu to be a risk of infections, but tuberculousis and lower respiratory infection still in top ten In this age bracket, most common cause of death is road injury and self-harm

What is the importance of archaea in our understanding of biology?

From these things from archaea and just studying them, we can learn really fundamental things from biology. Evolution of life, connectiosn to viruses. That's why I do highlihgt that the work that Carl Woese did, when he discovered archaea as separate domain, really iopened biology in terms of thinking about it and seeing how life we know about today, how we got there and what sort of evolutionary past

how do we kill fungi without killing ourselves?

Fungi are eukaryotes. can only exploit, the cell wall and ergosterol. There are only 5 classes of antifungals drugs And over 200 classes of antibiotics. Good reflection of large difference of bacteria cells vs. human cells in comparison to human cells vs fungal cells. Ergosterol in cell membrane Targets synthesis of ergosteral Targets cell wall

what are GUT cells?

GUT - gastro intestinally induced transition cells. They look a bit like opaque cells in the sense they are elongated as singular cells but don't have pimples. They are also genetically distinct from opaque cells because they are a on alpha diploids. Group in san fran cisco found them when they passage candida albincans through the mouse gut, where they were induced. If you compete white cells with gut cells through the mouse gut, the gut cells will outcompete the white cells. The idea is the gut morphology is better suited for growth in gastrointestinal tract than white cells. Once gut cell comes out of the gut, it rapidly converts back to the the cell. Candida albicans has morphological plasticity, can grow in lots of different shapes and sizes. The different host cells are optimised for different host niches.

What are mechanisms of gene evolution (mutation)

Genetic diversity is introduced by replication and repair errors. Mutagenic agents (UV, oxidative stress, chemical) increase the rate of mispair or error in replication, general mutation in the genome. Basic mechanisms for gene change Point mutations (mispairing) (SNP) - Polymorphisms - substitute a single nucleotide for another Deletion of bases (strand slippage) insertion of bases (strand slippage) Duplication Inversion Can be single nucleotudes or large pieces of DNA

genetics of Saccharomyces cerevisiae

Genetics are well defined. The genome has been sequenced. Was the first eukaryote to be sequenced in 1996. really easy to manipulate, very easy to knock out genes and to tag them e,g, with fluorescent proteins to look at localisation. Know requirement for crispr cas because yeast does recombination really well. Have been doing designer deletions in saccharomyces over 25 years. Have developed systems to do genome editing in cerivisiae, it is useful in some cases e.g. to knowkc out a gnee family with 7 or 8 copies for genes that are very similar, can knock them out with crispr cas. Has it's uses.

genome of norovirus

Genome is only 1500 base pairs long, it only makes about 10 proteins. This is quite similar for many viruses. On right hand side have structural proteins on outside of the cell. 180 VP1 proteins join together to make up the capsid. Inside capsid is the RNA floating around waiting to infect. Left hand side of the genome is when virus is in the cell, these are the enzymes it uses to replicate its genome and take over the cell. We use this for study, want to inhibit the polymerase which makes more genomes of the virus. Lots of norovirus out there, 5 different genome groups Two big groups infect humans - there is a G2.4, all the pandemic viruses we see from this group.

What are the HCV genotypes and their prevalence world wide

Genotype 1 is most common followed by genotype 3 Genotype 3 is most important in Aus. There are a lot of genotype 3 infections, but not as many drugs for it. Genotype 3 is significant genotype, in india is responsible for around 70% of infections, in Australia is about 35%, increasing to 40% of infections, brazil 35% percent, in UK (scottland in particular) can be 50%. Most other places will be dominated with genotype 1. 80% genotype 1a in the states, 80% genotype 1b in China. Genotype 3 is 33% in Aus which is a lot larger than other developing countries.

Compatible solutes counteract the tendency of a cell to become...

dehydrated in high ionic strength environments.

What is the negatives of using gentamycin?

Gentamycin treatment can lead to: nephrotoxicity (kidney damage), ototoxicity (hearing loss) Damage to hair folicles in the ear. It can cause hearing loss. There is a genetic predisposition for hearing loss. Genetic predisposition for ototoxicity have a mitochondrial mutation from 1555A to G, 50% of aminoglycoside ototoxicity. From phylogeny lectures - if we plot mitochondrial 16 S ribosome RNA phylogenically it's quite close to a proteobacteria. Mitochondrial have evolutionary very similar (more similar ribosomes) to a bacteria ribosome than to us. This means that mitochondrial ribsosome loooks more like bacterial ribosome tha than our own. Gentamycin is probably blockin ribosomesi n mitochondrian causing cell death cause you can't make energy in those cells - it's inhibiting mitochondrial function.

What was the experiment ferrari did on the candidate phyla in the antarctic soil, and what was the result?

Got 23 draft genomes including 2 novel phyla,looking at metabolism of the phyla, as well as actinobacteria, chloraflexia and an archaea as well Found they all have high affinity hydrogenases. Enzymes allow bacteria to pull low levels of hydrogen in the atmosphere out of the atmosphere and use it to produce energy. Do it to produce enough energy to survive dormacy. Well characterised in aerobic cel around the world, what had not been characterised was that they had carbon monoxide dehydrogenases as well. Bacteria use it as a carbon source to grow. Really weird RuBisco (protein in plants to conduct photosytnehsis) new type that allows them to carry out carbon fixaiton throgh energy that isp roduced through consuming hydrogen. Had hypothesis - set up microcosms, put in hydrogen in atmosphere, and found bacteria where consuming hydrogen. Did 14-C labelling, to see in presence of hydrogen if the communities were fixing hydrogen. Confirmed carbon fixation in presence of H2. new primary production strategy discovered. Might be global process - in areas of aridity

What are cable bacteria?

Got microorganism that links together filaments that expands over centimetres, going from anaerobic zone to oxic zone above. Get suflide oxidation deep within Then pushing electrons up and getting electric current, virtually as a battery , into the upper layers And oxygen is an electron donor Can't happen in one zone on it's own, needs both.

What is the purpose of using Gram's iodine during the Gram staining procedure?

Gram's iodine is a killing agent, binds to crystal violet (forming an insoluble complex), and serves as a mordant(increasing the cells' affinity for the stain).

how are biofilms related to predation?

Grazes are protozoa, amaeobas etc. predators of bacteria. Biofilms protect bacteria from these grazing predators Top surface down - dots are bacteria Before grazing was added (predators) they are in early stages of colonisation, no pressure to form a biofilm. Add the protozoa bacteria and start to see them aggregating - forming these micro colonies (one of first stages of biofilm forming) grey shading is EPS Grazers are driving biofilm formation. They can't eat the biofilm (penetrate it) can only eat individuals.

what are hypothermophiles?

Grow at 80 degrees or higher. Can find them in submarine vents, artificially heated places Environments: Hot springs, mud pots, sulfataras, volcanically heated soil, submarine vents, artesian basin, power plants, drilling platforms Many anaerobes but some aerobes Many chemotrophs and acidophiles Sulphur compounds H2SO4 Some parophiles and radiotolerent In deep sea because of the impact on the cells, DNA breaks down. A side product is they are quite resitant to radiation.

how do pathogens damage our cells?

Growth of bacteria inside the cell can damage the cells, many of them produce toxins as well, specifically meant to damage our cells. Idea is if it can damage our cells, it can release all the nutrients into the extracellular space, and has access to more nutrients. Can use toxins to create nice niche for itself. Leukocidins can kill immune cells Often these toxins can be responsible for the signs and symptoms of a particular disease. Painting from 1800s - tetnus is a disease where main symptoms are from a toxin. It causes involuntary muscle contractions. Initial sign is a locked jaw, but as it develops more and you become more rigid, the back muscle starts to spasm and lock up.

Describe the Phylogenic Tree

How we express the microbial diversity Keep coming back to this tree There is three kingdoms - bacteria, archaea and eukaryotes Microbes are found across entiritiy of each kingdom Archaea and bacteria - unicellular microbes, eukarya also have unicellular microbes - fungi yeasts etc. How we structure and understand relationships between 1 trillion microbes - what we look into today 8.7 million species.

What is the function of our gut microbiota?

Gut microbes rely on complex carbohyrdates ( dietry fiber) to complete their functions in the gut They digest reistant complex polysaccharides that we ingest in plant materials e.g. fruits, vegetables, legumes and whole grains. Digestion of these foods by the gut microbiota leads to the releae of compounds (metabolites) into our gut that are taken up into the bloodstream. These metabolites help to maintain the balance of our immune system and whether we store or burn calories.

What is the Epidemiology of HCV

HCV Epidemiology Around 2% of world population are infected with HCV (135 million people) Six times more than HIV, only 30 million cases of HIV in entire world. These are estimates by WHO. Injection rug use acocunts for majority of transmission (in Aus about 80%) In Aus, at the peak of the epidemic new there were 10,000 infections per year. Gone down now to 4-5000, going down further because of cures we have. Most common reason for liver transplant (around 50%). Kills 476,000 per year (liver failure or HCC (liver cancer)) There are 7 genotypes of virus (1 to 7) Each genotype is quite diverse. They vary up to the nucleotide level. One genotype is 35% different to another. Can consider each genotype being a different virus

HIV route of transmission

HIV routes of transmission Sexual transmission (over 80%) Blood or blood products e.g. transfusion, IDU Vertical transmission Can happen 25% chance giving HIV to baby on delivery, whether cezerian or natural birth. (including breastfeeding) Occupational exposure to blood (needlestick injuries)

Harvard demonstration

Had massive Petri dish. First section had no antibiocs which ecoli could grow on. Second section and just over the amount e.coli can survive. Then amount of antibiotics increased ten fold each section until centre has 1000 times more antibiotic than e.coli can naturally withstand. Bacteria can move in this plate. Each population has a mutation to withstand the next level of antibiotics until u have bacteria growing in the 1000 x plate within 11 days through accumulative mutations

What is a viral envelope? describe them

Half of viruses have an envelope and the other half don't. Some virions acquire an envelope during maturation through a process termed budding . This process of budding is when the virus leaves the cell, it steals a little bit of the plasma membrane. The virus likes to steal a bit of the cellular membrane because if it puts a coat around itself, it's less likely to be recognised by the immune system. It is a host component, the virus didn't make it, the cell made it. The virus steals it from cell. Proteins in the envelope are viral encoded. Two main types: glycoproteins that form the projections known as spikes (Keys to open receptor doors, so HIV has GP41 and GP120 (mushroom) ) Matrix protein - layer on inside envelope It helps stabilise envelope and keep it in a nice structural position. Is a scaffold for the nevelope.

What are halophiles?

Halophiles live in salty environments. Types of colours you get on saltans/ ponds where halophiles grow. Can literally grow in crystaline salt. Some of the crystaline salt has seemd to have preserved halophiles form hundreds if not thousands of years old . You can't recognise them under microscope because they can be literally any shape.

Describe the relationship between analysis of data and the choice of computational technology.

Happens a lot in microbial genetics and bioinformatics, partly because that's an approach which is available. When scientists generate data, they analyse data according to methods which are there. When other people do it, say 'oh ill do that too'. Fine cause those mthods are good, other times where you wonder, is there more to the data I have in front of me, than what I get out of simple application I get out of a standard method. E.g. with data set showm before, can draw a tree and infer what evolutionary history must have been, behind these 14 isolates. But it doesn't tell us very much. If you think about the original table of SNPS, and the sort of changes that we saw, the tree doesn't tell us very much about how to interpet those data. Doesn't tell us much about what it means that there are some changes that are indels (insertions and deletions) vs SNPs. Doesn't tell us why some of the SNPS are in intergenic sequences and some are inside protein coding sequnces. Don't know what that means or if there's any significance. What does it mean if there are two cases when the protein is altered? The codon is altered and that leads to change in protein sequence. We don't know how to interpret this. When we see data like this, think there is a bit more to explore there, may be nothing to get out of it, but asm ore and more data come out, we will be faced with a situation where methods from 2 decades ago may tell us only so much and we have to think about new computational models and methods which will help explain these kinds of data.

morphology of HCV

Hard to get a good picture of this virus because even when you purify it from the blood, it associates with lipid dropplets. It's an envelope virus, it's about 60nm in size. It's icosahedral capsid lipid envelope and that's what it looks like by EM. I

HIV virion structure

Has two identical genomes in there, two single stranded RNA molecules about 10,000 base pairs long in the middle here. This is a capside (althought it doesn't look like one) it's a 20 sided shape squashed into the shape of a cone. On the outside, there is an envelope derrived from CD4 positive cell. Have a matrix protein here that stabilises the envelope then we got these GP41 stalk and GP120 which is the glycoprotein on the surface of the virus that is looking for CD4 receptor on the cells. If it finds the CD4 receptor (all immune cells have this receptor) then it can go into the immune cell and take over. In the middle here, virus also carries polymerase so itcan do the replicaiton, replicate genome when it gets insidethe cell.

How do bacteria secrete the toxins?

Have developed specific secretion systems that allow them to deliver toxins straight into the host cell. They produce 4 secretion systems, that act like a molecular syringe. Type 4, 3, 6, and 7 can inject proteins directly into the host cell. On right hand side - inner and outer membrane, the type 3 secretion system treverses the inner and outer membraes. There is a needle fillament (EspA) that treversed between two scells and then a pore, EspBD (pathogenic E. Coli) forms a pore in the host cytoplasm and then conencts to the host. It is available to deliver a cocktail of proteins directly into the host cell and take ocntrol of host cell processes. Salmonella and E. Coli can deliver up to 40 different proteins or toxins into the cell and remodel all sorts of process in the cell for benefit of the pathogen.

Which of these microorganisms is MOST likely to be found in the human gut? - Helicobacter pylori - Streptococcus mutano - Streptococcus sobrinus - Roseobacter denitrificans

Helicobacter pylori

Gene loss in bacteria

deletion bias

Describe and explain injection of nucleic acid in lytic cycle

Hershey and Chase Experiments - 1952 Phage DNA carries genetic information into the cells. All of this protein structural stuff never gets into the cell. Only the Dna does. This famous hershey chase experiment done in 1952, basically proved that DNA are not protein, it's the genetic material of life. Labeled protein with S35 and DNA with P32, and only DNA labelled P32 was passed down to subsequent generations. S35 couldn't see after first infection. Phage has pins and legs to help it attach the bacteria, and then get injection, tail contraction penetration pushes the injection into the bacteria and then DNA goes down. DNA then needs to do something.

Explain how your diet can affect future generations

High fibre diet has diverse microbiota, continued through all 3 generations Look at low fibre diets - have reduced diversity. If that mouse transfers to hight fibre diet get some recovery If the low fibre diet mouse has a progeny the second generation will have further redued diversity and in this case there will be less recovery than some recovery group. In the third group with most reduced diversity there is even less recivery If you have a diet and you feed your children low fat fibre diet then gut microbiota diversity will decrease. In early stages can recover, but as generaitons go on, the ability to recover is less. Diet can reduce future generaitons.

Endospores are _______.

Highly resilient, dormant cells.

Describe and explain Adsorption

Highly specific: Each phage tends to like its own species of bacteria Interaction between tail and cell surface receptors (can be lipoproteins or LPS) Host range mutation may occur in phages - If a phage has a mutation, it can on rare occasion can switch the species barrier. It might mutate, say before it couldn't get into one bacteria, but because it has mutated it will have a slightly different tail pin and then it can get into a different species of bacteria. Host range can increase through mutation under certain circumstances. E Coli vs phages When it bursts open will get about 200 phages coming out. Bacteria aren't very big only about a micron. Our cells are about 20-40 microns, so how many viruses coing out of our cells? Way ore then 200, sometimes 25-50 thousand coming out of a human cell.

factors that spread HCV disease

Host factors that can speed disease progesison: Chronic hepatitis - liver becomes vibrotic, fibrerous and that fibrotic leads to cirrhosis and then get hepatocellular carcinoma developing from that. Once the liver is cirrhotic it doesn't functio nas well as it should do. These are the host factors and host genetics. If you have I11 29 ( correct polymorphism) then do better with treatment than if you have other one. Few genetic variabels that affect how well you do when treated. Pathogen : if there are a high number of viruses per ml (a high viral load) then if that's high then you do badly, if you are co-infected with HIV then you can do badly because the immune system, although it can't get rid of the virus it can dampen and reduce amount of virus in the body. How complex and diverse is the population of viruses in the body. In hep C and HIV the sequences of those viruses are not all the same, each virus varies from 1-2% than the next virus. That creates diversity in the population, and diversity enables selection. Diversity allows virus to adapt and escape drug pressures and immune pressures. That's why it's so difficult to get rid of these. Hep C mutates more than HIV but they both mutate a lot. That's how it enables them to do chroic infections. The immune system can't attack because they change too quickly.

How are viruses different from cells?

How are viruses different from cells?

List and describe some factors in microbial ecology, when looking at how a community assembles

How communities assemble - important for destroying a habitat, not just trees and big things Interaction of community with environment: Do this for specific environment, when looking at soil, need to think about not just what microbes are there, but also abiotic processes there e.g. carbon present, moisture, temeprature. Bioticp rocesses - what other orgnaisms are in that enivonrment? Bacteria there? How do htye interact Wide distribution of microorganisms: Microbes are widely distributed, like larger animals, environment selects for what organisms survive. At microbial ecology, look at processes that drive communities and how they are formed. Many theories about how communities assemble, some people think environment doesn't select for organisms, some think it does. Belinda thinks it's a bit of both, about what organisms are first present in the enviornment, and factors that also dribe who can survive. The microbial ecology toolbox: Toolbox has changed, used to just have assays and culturing. Now have culture independent methods e.g. genomics, metabolomics etc. Look at sophisticated technologies ot understand how microbial diversity exists. Microbial activity: Not only what types of organisms are there, but also microbial activity. In the past, would see whole community in sample ,and do a biochemical assay. But now know, within a sample ,different organisms are doing different things. Have ways of looking at specific parts or processes to understand what different organisms can do in that whole community.

Describe today's bacterial tree of life

How diverse microbes are, how little we know about them. Bacteria we don't know much about- termed microbial dark matter. Like matter outside the Earth. Surveys, most of the data as to why this is the tree of life is by doing 16 S or 18 S studies. Do PCR targeting that gene, do 1600 base pairs of that gene, and carry out phylogeny, to work out what kind of organisms are present. Don't know about functions, just have DNA which suggests you might have a certain type of organism.How these studies have evolved. Indicates a lot of life out there which we don't know what they do. These are just estimates. These molecular surveys suggest for this tree of life there are 100 phyla known for bacteria alone. The region here of different phyla was discovered 2 years ago. If there's a red dot on the arm, means we don't have an isolate on whole phyla to characterise. Know nothing about what organism can look like and what it can do. More and more doing metagenomics, where pull out draft genomes and get bit of an idea what they do. Still don't know what they look like, haven't gotten them in a pure culture. Candidate division - unless you get a culture, and isolate it, you can't name something. More and more now trying to name divisions based on genomic data. Moving more to this approach. Big discrepancy at the moment. Some people believe need to be able to culture, some people believe can use a draft genome to characterise a species. Or are in the middle - use genomes to try and get a culture. Now becoming acceptable to name a species from draft genome. Can use info from draft genomes to work out how to culture the bacteria

Describe the human GUT microbiota

Human gut microbiome: Seen really interesting results in relaiton to disease Home to a diverse and complex microbial community of bacteria. Essential for human development, immunity and nutrition. Bacteria living in and on human body are not invaders but are beneficial to their host. An individual's microbiome may influence their future health. If we look at human gut, it starts with stomach (very few organisms there) then increasing number in judgunen, small intestine there's more, until large intesting and colon there are heaps. There are up to ten to the 14 organisms in our colon.

What is a possible advantage of having a relatively high proportion of hydrophobic amino acids in proteins?

Hydrophobic amino acids within a protein tend to be located inside the protein while hydrophilic proteins tend to be located on the outside. Proteins fold this way because it is more energetically favorable than having more of the hydrophobic amino acids in contact with the watery cytoplasm. A protein with a substantial proportion of hydrophobic amino acids is less likely to unfold at high temperatures.

Hyperthermophiles have proteins that are stable at very high temperatures. What is different about these proteins that allows them to keep their function at temperatures above 80 degrees C?

Hyperthermophilic proteins are folded differently.

What is IBD, how does it develop?

IBD develops at the intersection of: genetic predisposition (Usually have single nucleotide polymorphisms in a number of their genes that control immune system), dysbiosis of gut microbiota, environmental influences. (sleep, medicaiton, diet etc. ) None of the risk factors alone are sufficient for development of IBD Complex interactions between each factor occurs, leading to the development of IBD. IBD includes ulcerative colitis and crohn's disease, and these are life long diseases. People who have these diseases have very difficult lives because they have reccurent episodes of diahhrea of 8-10 stools a day. Treatment for that is not great.

How to combat resistance mechanisms

If antibiotics are being cleaved we can actually odify some of the antibiotic so that it is resistance to Beta-lactamases. There are oxacillin and methicilin that is attached to it, that prevents it from being cleaved by beta-lactamase and can no longer fit in beta-lactamases anymore. Methicilin and oxacilin are reistant to a numbero f beta-lactamases. Emergence of beta-lactamases that are able to cleave these substrates as well. It's a backwards and forwards antimicrobial war, between killing activity and resistance. Another way to prevent this cleavage activity, are inhibitors. Peple have deisnged inhibitors of beta-lactamases. (copy from slide the examples) They can specifically block beta-lactamases which saves antibiotic. These inhibitors don't have any anti-bacterial activity themselves. But they rpevent degredation. Augmentin = ampicilin + culvanic acid. Ampcilin is usually affected by these beta-lactmases but with culvanic acid is effective in killing bacterial cell. A surprising amount of staphylococul infections occuring in clinical setting are resistant to methicilin now. So we are back at square one using last line antibiotics that are fairly toxic.

what is gene loss? why is it important? what is muller's ratchet?

If having all this transfer of DNA all around would think genomes of bacteria are huge Would have contingency of absolutely every scenario We have a very narrow window when it comes to bacteria genome There is a deletional bias to bacterial genomes There is more deletion events occuring than insertion events It all comes down to selective pressure on the genes There are genes of neutral selective pressure, there is random mutation in the genome, if there is no selection pressure to maintain that gene it will just accumulate mmutations. It's because they are reproducing asexually, there is limited oppurtunity to get rid of that mutation once they acquire it. In bacteria it's a clonal lineage from parent to daughter. In neutrally selective genes they accumulate it and never get rid of it. Can get rid of it in recombination - refers to horizontal gene transfer. That's limited, and can be decreased if they are genetically isolated. E.g. if they become intracellular there is limited oppurtunities to get material from other bacteria. Exaserbated with smaller population size, because there is less chance for horizontal gene transfer and easier for point mutations to reach fixation in that population Collectively neutral genes can accumulate deletions and can be lost from the populaiton exaserbated by mutation rate, if that's increased, decreased recombination rate, and decreased population size. These three interacting with eachother is called muller's ratchet. Obviously if a bacteria changes environment it now decides it's intracellular and some genes are holding it back, they will be under negative selection and rapidly lost from population as it will be outgrown by those that require mutations. Refers to it as the cheshire cat effect. As the chesire cat disapeared it was just the teeth left. Only those things under positive selection are maintained in the genome and the rest are lost over evolutionary time .

what is the relationship between hyperthermophiles and LUCA?

If we actually come back to some aspects of real biology and our trees here again, here is a tree with three domains and the lines here that I've colured in red are at the base of the tree, and all of these are hypothermophiles (live at high temperature) This is the reasoning that's being used. It's not proof- its an idea based on this information Hypothermophiles at the base of the tree have these short branches, the ideas is then perhaps they haven't changed very much since life first evolved, hence the notion that life may have evolved in high temperature environments. That's the inferences that come from looking at the three and that hypothermophiles form their branches Hypothermophiles may therefore be more similar to LUCA (last universal common ancestory) than other life forms. (base of the tree)

What are the different types of flagella?

If we have a single one extending from one cell then it's polar, a number extending from the cell its peritrichous, or a number extending from one pole is lophotrichous

What are thermotogae and Aquificae

If we look at phylogenetic tree are the ones branching closest to LUCA Are very deeply branching They are specially because all hyperhtermophilic, growth at over 80 degrees celcius. In terrestrial and marine springs/vents They contain a bunch of archaeal genes (around 20%) Similar to archaea at bottom of tree These genes are acquired by horizontal gene transfer. They are interesting because they are all hydrogen chemolithotrophs. Like thermophilic archaea at bottom of that kingdom are also. Suggests that perhaps primitive organisms closer to LUCA were also hydrogen chemolititrophs and early life was using hydrogen as an electron donor

how does diet influence gut microbiota?

If we think back to traditional populations, what these populations have or eating are microbiota accesible carbodydratees. This shows to increase microbiota diversity and metabolic output. This is seen to protect from western diaseases. When you eat green vegetables, they go to colon, in the colon they produce metabolites - the most important is short chain fatty acids, these get into the circulation and have effects in ut and other areas of the body. Industrialised populations, there is a decrease in the amount of people taking in accessible carbohydrates. This leads to a reduction in microbiota diversity and metabolic output, this leads to development of diseases we are seeing a lot more in western society.

What are some mechanisms bacteria use as resistance against phages?

If you are using bacteria to make yoghurt or cheese, worst thing you can get in factory is a phge Once bacteria gets in, it kills all good bacteria This has plagued bacteria for years and year so started engineering phage resistance into bacteria. Blocking of phage DNA injection Abortive infection systems - interfering with phage DNA replication, DNA transcription, phage development, and morphogenesis - stopping phage assembling into virion The evolutionary arms race between bacteria and their phages has been well documented by dairy microbiologists. Geneticaly engineered phage resistance: Per-phage encoded resistance Iby the bacteria) say phage needs pili to get into bacteria, get rid of pili. Antisense RNA (Crispa/cas): Bacteria can colelct a bit of phage DNA to use against phages. This lead to development of Crispa Cas system for DNA editing. Bacteria colelcts sequence data from a phage and can use it to attack the phage.

What archaea can you find in hydrothermal vents?

If you go down to a hydrothermal vent and see the kind of things that live there - these are microbes living down there (methangon) Look at life being supported in a hydrothermal vent Look at size of the muscles! They are massive Theres a lot of life down there, all of that life only are there because of the microbes. The fluorescent organism here (is called (see slife below) This is what it eats, this is what it needs for growth. If you look at what it requires, it requires these sorts of things (minerals, non-organic compounds) As a nitrogen and carbon source - it can use inorganic nitrogen, it uses CO2 and hydrogen for both carbon and energy. It doesn't requrie organic matter for growth at all but it produces organic matter itself. So you can see how something that can utilise inorganic material can ultimately produce organic matter. That's what it is itself, the beginning of the food web that feeds all the creatures that are down there, therefore it seems failry resounable to think that maybe these thigns are more similar to things that could have started life on the planet. Doesn't need oxygen, light or organic carbon but yet it produces life.

How do you make a phylogenetic tree with big data?

If you have more species, or really a lot of differences and a lot of thigns to deal with, it would help to have a computer to calculate all the things. The likelihood calculations get incredibly complicate, not conceptually, just computationally fiddley as you increase the number of species (taxa). Can apply this method to much bigger data-set, which is done in this study here which looked at a whole lot of different bacteria looking at genomic data. They used maximum likelihood method to make tree for a huge number of species. Thisi s what they get. They have colour coded all the major groups of bacteria, and we can see how they are related to each other. Can also see how the tree is intuitive in the sense that it groups together all the bacteria that taxonomists have grouped together cause they think they belong in the same group. The tree is consistence with a grouping that taxonamists do. Of course sometiems there will be an inconcistency and the gentically obtained tree will be corect and taxonomists will be wrong . Good thing about making trees is it helps to find evolutionary histoyr, and therefore also to classify things. This particular tree was made using maximum likelihood mehtod, there are other methods based on different statistical or computational arguments. They are all very similar but subtly different. If you are a careful scientist you will think carefully about differences in method and will think of method that is appropriate to question and data you have.

What is a plague? how does it form?

If you plate out bacteria, there will be a lawn of bacteria (Which is a whole lot of bacteria) If you infect them with a bacteriophage, what you will see are these clear areas called plaques. We do this stuff wth animal viruses as well except infecting cells rather than bacteria. And this is where phages have infected cells with bacteria, and have created a small zone of clearing known as a plaque. You can use these plaques to count how many pahges. One plaque = one phage. Plaque formaiton is very important. It's the only way to see bacteriophage except for if you have an electron microscope.

how do pigments work?

Illustrate how pigments work Z scheme of oxygenic photosynthesis Light absorbed in two photosystems These absorb at different wavelengths of light In photosystem 2 - light is absorbed in reaction centre and this excited electrons, and these are pushed down ETC. similar to chemotrophs Because u have electrons moving from this photosystem, you cant have oxidation and reduction, you need to have electrons being replenished. There is electrons from water that replenish the photosystem More light being absorbed in photosystem 1, get ATP and reducing power being produced. They can generate ATP but can use CO2 as carbon source, fed into calvin cycel. Have reducing power from light reactions in Z scheme. (go over this slide)

explain and describe steps of transcription and translation process. how does bacteriophage transcript and translate genetic information?

Immediately the early genes (like in herpes viruses) the pacteriphage doesn't just make all its gene products all in one go. It has three ways, early midle and late. Say it made the late genes first before it has replicated its DNA, it means its made a lysis protein that has killed bacteria before it has even replicated. So can't have all genes made in one go. Have to do sequential gene expression. Human viruses work similarly to this way. Immediate early and delayed early genes - shut off cellular macromolecule synthesis of bacteria, tell bacteria to stop making their own proteins. The get replicaiton of phage DNA Middle Genes - transcribed throughout infection DNA replication and recombination - Then get integrase and those enzymes needed in lysogenic phase, that will get phage DNA into chromosome of bacteria Late genes - capsid protein and enzymes for lysing the cells. Each capsid has at least 180 proteins (maybe 240 if a big phage) that's a lot of proteins, so need to make a lot of capsids at the end and package DNA up into the capsid, then lysing enzyme and out the DNA goes. All viruses are parasites- what they really paristise is the ribosomal machinery of the cell. Viruses can't make own protein, so need cel lto make proteins. They hijack ribosomes- they tell the cell to stop making own proteins to make the viral proteins and most abundant are strctural ones, T4 is main component of the head. The capsid protein is main protein of capsid head

What was the impact of FMT on gut microbiota diversity in UC patients?

Impact of FMT: Once they had been on FMT for 4 and 8 weeks, the nmber of operation taxonomal units (number of bacteria) had increased. This was based on final follow up. In those who were on placebo, they didn't differ much from the beginning as those who were on base line. The individual donors for FMT had higher diversity than the patients before the FMT. When looked at donor batches there were individual donors and mixture of donors, can see ther ethe number of OTUS were inceased highly.

Describe the scales of terrestrial microbial diversity

Important to notice, normally bigger animals (looking at macro scale) levels where looking at landscape, is equal to looking in the bacterial world with soil, is one gram. 1 g of soil - entire communities, different habitats present Looking at ecology with soil, the measures are a lot smaller alpha diversity - diversity within a local habitat, local diversity - 1g diversity Beta diversity - diversity across habitats, changes of species composition along a gradient of habitats. Gama diversity - diversity over a region comprising many different habitats. Depending on question, different targets of scale

What is HIV

Important virus, devestating in the 80s, people were dropping dead and no one knew why. There has been a backlash from rest of the world saying we need to sort our shit out. The rate of HTLV-1 in Aboriginal Australians is ridiculously high, in UK only get 20,000 caes in whole population. Australia is beginning to provide funding to investigate this infection more. This virus can cause adult T-Cell leukemia if you have it for long enough. And it can cause otherthings like lung diseae, but don't know much about it. It is a human retro-virus like HIV. Not as nasty about HIV though.

Why have cases of gastroenteritis improved in recent years?

In 2004, the estimated incidence of diarrheal disease was over 4.6 billion cases worldwide. Why has number gone down to 1.8 billion more recently? Better salinity facilities, better sewerage. Increased sanitations, improved living standards. Most of world cities do't have proper sewerage system. Most people in the world have open sewers. This leads to food contamination. Worst thing for food is human sewerage. Human swewerage carries a million noroviruses per litre.

Drugs to treat HCV

In 2012 there were four drugs, Phase 2 clinical trial cuts 200 million Phase 3 clinical trial costs 800 million Different drug targets - protease, NS5A which is invovled in hep C replication, polymerase. 2 types of polymerase inhibiotrs 1 is nucelocide analogues that mimic a base pair, they get encorporated into RNA and then change terminate so that RNA can't extend anymore. Then have non-nucleocide inhibitors that bind to actual polymerase protein and stop it from working. Go back couple of years, 11 or 12 drugs approved, pretty much one from each class. Anenine, nuclocide analogue, NS5 inibitors which are very potent, protease inhibitors, Can begin to combine them, combine two or three drugs which stops virus from becoming resistant to these drugs, and increaes the cure rate and now we can cure Hep C patients in 8-12 weeks (instead of 48 weeks) with over 96% cure rate even in difficult patients. This year alone have cured over 5000 patients in australia. Estimated that by 2028 nearly everyone in Australia will be cured from Hep C. this is cure, not supression. Eventually when they come off patent, they will become much cheaper and most people in the world will be cured of Hep C.

first case of antimicrobial resistance in medicine

In 2013, Brian Pool suffered a brain haemorrhage and was operated on in a Vietnamese hospital. He was evacuated to Wellington Hospital where he was shown to have a strain of Klebsiella pneumoniae Wellington Hospital clinical microbiologist Mark Jones stated: 'nothing would touch it. Absolutely nothing. It's the first one that we've ever seen that is resistant to every single antibiotic known.' The emergence of resistant bacteria is really threatening us to a time beforehand where common infectiosn would cause life-threatening illenss.

Halobacteria tend to have fewer hydrophobic amino acids in their proteins than other bacteria. Why?

In a highly saline environment, hydrophobic proteins have an increased likelihood of precipitating out of solution.

Some Archaea live in remarkably saline environments. What is the challenge of living in a highly saline environment?

In a highly saline environment, most cells desiccate. Extreme halophiles have specialized adaptations to prevent desiccation.

Part complete Antibiotic resistance is a major concern as microbes can rapidly develop resistance when antibiotics are not used appropriately. How does this occur?

In any population of microbes, some individuals may have resistance genes. When exposed to an antibiotic, there is selection for the microbes that have these genes.

what are the steps of the lytic cycle?

Infection of most phages, every phage pretty much has a lytic cycle but some phages have lytic and lysogenic. Lytic cycle is easy with 5 stages: 1. Adsorption - Attaches itself to surface of bacteria 2. Injection of genomic nucleic acid, down sheath of bacteria. 3. transcription and translation 4. replication of DNA 5. Maturation and Release: The phage structure comes together, packages together the DNA and then releases (usually by lysis) of the phage into the environment to infect more bacteria.

What is the electron source for chemolithotrophs?

Inorganic substances.

How do biofilms form?

In any substratum, the bacteria from the plankton, from surrounding water, will be attracted by chemical cues, to that surface. They will undergo a reverisble attachment first. Some will decide to leave, some will stay. Then they will forman irreversible attachment process, and start to produce an extraceullar extracellular polymetric matrix. This is the sticky stuff that binds them together and protects them from environment around them. The matrix allows different nturients to come in and out in decisive matter. Allows chemical communication between them to occur, oxygen exchange etc. they start to form microcolonies and structures which aren't just plain flat surfaces. This is important for water transfer throughout this. Get sloughing and dispersal.

Describe example of diversity giving rise to microbial relationships - hydrothermal vent

In hydrothermal community is completely dark 1km into the ocean. There are very limited nutrients coming down, no photosynthesis. In blackwater vents, get a wealth of diversity. Have tube worms, spider crap, giant clams, microbial mats living there. Have hydrogen sulphide coming up as black smokers. Where is the energy coming from to fuel larger organisms? It's coming from chemosynthesis - chemoautotrophic oxidation of reduced sulphur. Microbes that have metabolic diversity to use hydrogen sulphide compounds coming from the vent, they oxidise and get energy from this, living as microbial mats on the surface, or live symbiotically with giant tube worms. These hydrogen suflide-oxidising bacteria form the base of this ecosystem's food chain. The tube worm has haemoglobin on outside, is getting oxygen, carbon dioxide and hydrogen sulfur from surrounding water, and takes it into the body of the tube worm. Isnide body of tubeworm is community of microorganisms living inside the tubeworm symbiotically. These symbiotic microbes convert hydrogen sulfide and oxygen and generate energy from that. They use the energy to drive, something similar to photosynthesis, from the CO2 from the water, they convert it into glucose. They use hydrogen sulphide and oxygen instead of water and light. The main drivers of diversity in hydrothermal vents.

Reheating food to a temperature sufficient to kill bacteria is helpful in making food safer. However, is there a way that one can get food poisoning from food despite its having been heated in this way?

In some cases, toxins may be heat-stable above temperatures that kill bacteria.

What are the main sources of methane production globally?

In terms of methane production, most is biological, some geological processes which oroduce methane. Most of it, or bit big part of it comes from ruminant animals. Methane is a very bad green house gasm it is very potent but has a very short half like. Ruminant animals belch out huge amounts of methane, and we have contributed to huge maount of profuction to the environment .kangaroos don't produce methanogens so if you're a meat eater, better off eating kangaroo.

Describe resources and conditions that affect microbial communities

In terms of soil or any other natural environment, human environment as well, resource availability is huge driver of what organisms can live in a kind of system. Table with different types of resources nad conditions as well that can govern what types of organisms might thrive. E.g. carbon in a system. Bacteria that are oligatrophic and doesn't like a lot of nutrients. If you have a high level of carbon, won't survive in that environment. Have nitrogen, macro nutrients, micronutrients, oxygen. Have anaerobes, aerobic organisms. Have conditions e.g. temperature. Try to grow Antarctic organisms at 37 degrees, where most f the human microorganisms grow to, won't survive in that culture. Can use temperature to select for organisms. Same thing goes for moisture, ph. Have extreme bacteria that survive in extreme temperatures or pH, which survive in extremities. Have oxygen, light as well (photosynthesis) etc. whole array of factors which contribute to types of communities present.

What energy source do archaea typically have at higher temperatures

In terms of the process to generate energy, the phototrophs (there are some thermophilic phototrophs) Chemoorganotrophs can go to 73 degrees. Chemolithotrophs are winners, that don't need organic material, and they can grow at highest temperatures. E.g. methanopyrus and pyroductiium. These are the ones isolated, but experients that have gone down with submarine and use tobotic arm to stick glass slide in the hydrothermal vent and have seen colonisation growth on glass slide at 140 degrees. Indicates they could possibly isolated and grown at that temperture. These are his cookers (guru on hypothermophiles) Made out of titanium First ones made from stainless steel but because of pressure, tmeperature and acid they dell apart so needed titanium to withstand.

What light zone are we living in?

In the goldilocks zone, the temperature is just right so you can get liquid water on the surface If too far away - freezes If too hot - all the water is gone Light or sun at this distance is why you are getting light

describe focus study on FMT treatment for UC.

In this sutdy, people with UC were blindly put into a placebo group or those getting FMT. The parients were given double blind FMT . On the first time they got their infusion through a colonoscope. And then for 8 weeks had doiuble blind therapy 5 times per week. These were enemas put into the rectum, and the end point of the study was 8 weeks, and then followed up with patients at 16 weeks. Looked to see if they had clinical remission or if they ha an endoscopic response or remission. For those who had been on placaebo put them onto FMT - cause saw that there was an effect of FMT, so had to give those who were on placebo the chance to try it and that went for a further 8 weeks and they were followed up to week 24. Primary composition at week 8: Steroid free clinical remission + endoscopic remission or response Clinical remission: total Mayo score of less than 2 with sub-scores of less than one for each of rectal bleeding, stool frequency and endoscopic appearance. Endoscopic remission or response Greater than one point reduction form baseline in the endoscopy score: 27% went into remission and 8% from placebo.

Mutation rates are similar in Bacteria and Archaea, yet certain stressful conditions mutation rates increase. Why is the mutation rate not constant and close to zero all of the time?

Increased mutation rates can be advantageous in rapidly changing environments because some random mutations may be useful for survival.

The Gram stain is an example of a __________ stain, because the process uses two contrasting stains to separate bacteria into groups based on cell wall composition.

differential

how do pathogens overcome adaptive immune response?

Intracellular bacterial are protected from circulating antibodies. Staphyloccocus produce protein A. this is on the surface of staphylococcus, it binds the antibody at the bottom part (Fc), a conservative part that the phagocytic cells would usually be binding to. It presents it in wrong orientation back to the phagocytic cell, and so now it can't be recognised, it's not recognised as being bound to that antibody Some bacterial pathogens have come up in a unique way to change the antigens bound by antibodies. They change their appearance - termed antigenic variation, change immuno-dominant surface proteins. We have developed antibodies against specific proteins on the surface of the cell

describe salmonella

Is gram negative bacilli with flagella that helps it to move around. It's a motile bacteria, highly adaptable to different environments. Contaminated foods (milk and meat, especially poultry) serotyping is important and can be done using a bacteriophage. Enteric fever or typhoig fever often acquired overseas. Individuals can become carriers.

Bacteria will become part of a biofilm because __________.

It allows them to remain in a favorable niche.

Amphotericin B is an antifungal medication. What might its mechanism of action be? - It prevents synthesis of peptidoglycan cell walls - It binds to ergosterol. - It binds to phospholipids in fungal membranes. - It binds to ribosomes.

It binds to ergosterol.

What is gentamycin's mechanism of action?

It binds where the tRNA is being read in the A-site. The ribosome has three sites - A , P and E. the T-RNA moves from a to P then ejected. At the P-site is where the amino acid is crosslinked to peptide chain. Gentamycin binds to small subunit and blocks the progression of this t-RNA from A site into the P site where it can be cross-linked to growing peptide chain. If you can't fo that, can't synthesize ribsoome, can't synthesize anymore protein. Can't make more protein can't grow can't do anything. It is bacteriocidal because it blocks protien synthesis. It can also intefre with binding of tRNA reading as well, binding at around same site. If you bind near third (wobble) base of the tRNA, it actually prevents it from accurately reading tRNA and if you can't read the mRNA get wrong proteins which can be lethal as well.

target alteration and overexpression in candida against Echinocandin

It inhibits enzyme that makes one of the sugars in the wall. 2 main ways cells become resistant, again through target alteration or over-expression, but also through cellular stress response. In terms of target alteration, see in clinic when we sequence the echinocandin resistant strains from patients, we see mutations in Fks which is the target or what Echinocandin binds to. Mutations generally occur in a couple of hot spots in this protein. Three hot spots we now see. These hot spots are in DNA sequence where mutations happen often. If you map where these hot spots are the topology of the Fks or glucan synthase enzyme, it's a huge nezyme, multiple transmembrane domains (huge membrane protein) all hotspots for resistance come from bits of the protein that are predicted to be sitting outside the cell, outside the membrane. This is where drug will come and bind to Fks and inhibit its funciton. See how the mutations result in alteration of protein which means drug can no longer bind.

What does the minimum inhibitory concentration (MIC) of a chemical tell you?

It tells you the smallest concentration of the chemical that is needed to inhibit the growth of a specific microorganism.

Why is a special polymerase, such as Taq polymerase, used for PCR?

It works at relatively high temperatures.

What are some 'flavours' of pathogenic E. Coli?

It's a commensal found in warm blooded mamals Number of different pathotypes of E. Coli Can cause urinary infections, neonatal meiningitis Diarrheagnic E. Goli The way it has acquired this abiity to casue this disease is through acquisiton of mobile genetic elements in horizontal transfer. Urophatogenic ecoli has acquried a number of adhesions that have allowed it to stick to the urinary tract Dihareogenic e coli has acquired a molecular syringe to inject proteins and toxins into cells Enteroinvasive e coli also has molecular syringe and sugar toxin Shiga toxigenic e. coli has molecular syringe and sugar toxin

What is the theory of panspermia and how is it related to archaea? what is some research done on extra-terrestrial biology?

It's also really stimulated the astrobiology community. Theory of Panspermia. Think about evidence to support this idea. It's the idea of - we don't know how life evolved on earth, maybe it evolved somewhere else, hitched a ride on a meteorite and then landed in our oceans and started to form life here on the planet. Learning about extremes have expanded the horizon of where extra-terrestrial life may be. Study from 2018 - picture of the moon (Enceladus) what they did was they took methanogenic archaea (paritcular species) and they utilised conditions for growth in the laboratory that was similar on this moon, and they were able to demonstrate that it could grow on it. It was actually some real experimental data that took an organism here on earth and tried to utilise conditions from an extra-terrestrial world and said 'well is there even a possibility that it could grow?' and what they showed was yes it could. So you never know, the methane that you see coming from Mars and these other extra-terrestrial locations could be produced by archaea/microorganisms similar to what we have here on Earth.

Carl Woese

discovered archaea, disproved prokaryote terminolgy

What is phiX174

It's very small phage no tail, icocahedral. It's genome is very small - only 5000 base pairs. Phi X174 one of the most simplest viruses. Has enough nucleic acid to code 3-5 gene products while the more complex phages may code over 100 gene produces. The phage phiX174 was the first organism to have its entire nucleotide sequence determined, a feat that was accomplished by Frederick Sanger and colleagues in 1977.

what are Mechanisms of resistance

Key points - such an acute selection with antibiotic resistance if it will kill the cell, it's not a fitness advantage it's all or none. Strong selective pressure in environments when using antibiotics. More worryingly - there are resistance determinants specific genes that will activated that can confer antibiotic resistance which are presnet on mobile genetic elemtns (like plasmids) So you can have outbreaks of antibiotics resistance plasmids transferring through multiple populations within a hospital setting conferring antibiotic resistance to anything willing to take it up. Some mechanisms of antibiotic resistance: reduced permeability, efflux pumps, target modification, antibiotic inactivation by modification, antibiotic inactivation by cleavage.

Mechanisms of production of disease:

Kill the cell, particularly if naked virus, or cell kills itself through apoptosis, or white blood cell (CTL) will come along viral proteins will be displayed by that cell on the surface, CTL will recognise that it's a viral protein and will go and kill that cell. Inteference with function of essential cells - hepatitis, myocarditis Body's response to deal with cell damage e.g. mucus production Local effects of immune response (rashes) Systemic effects of the immune response - fever Triggering auto-immune response (post infectious encephalomyelitis) A lot of diseases, particularly hep virus, the liver is destroyed by immune system killing virus infected cells rather than virus killing infected cells. The virsu can cause host to attack itself If you get infection in heart, gut or liver can get disease because organ doesn't function as well as it did before

history of HCV

Knew in the 70s that there were viruses out there like hep A and hep B that caused an infectious hepititis. There was also a third one out there, that we knew was there but didn't know what it was. People would go into hospitals, have some type of transfusion or something and pick up virus from contaminated blood or operating equipment, and they would test for hep A and B and were negtive in both but we knew they had hepatitis. Was finally discovered in 1989, and was an elegant use of modern molecular virology, using our friend the bacteriophage

how to diagnose bacterial gastro-infections

Lab analysis: Micsocopy: You can see blood (white cells and red cells) in the faeces of the bacterial gastro from colonising organisms. They invade gut lining and then cause bleeding. In lab look for blood in the faeces. Food particles, fat globules, cysts ova and parasites. Used to culture for bacterial pathogens, but don't do it anymore. Because what do you do if you find salmonella? Can't do much.

Proteobacteria

Largest Phylum of bacteria. Morphologically and metabolically diverse

What is asgard? what's its relationship to eukarya?

Latest one published this month. Here is all this radiation with bacteria, then branch heading off to archaea and then here is eukarya branching off close to Asgard archaea. Latest inference from information now. The ones that they are most closely related to are asgard archaea which were only discovered in 2015 - 2017. very new stuff. One of fundamental differences between archaea and bacterial and eukaryotes is the lipids. Archaea have ether lipids with glycerol 1 phosphte backbones. This is very fundamental - can't swap between the two. This has always been what we have thought and expected. This paper came out in 2017 and they talk about the lipid divide. The lipid membrane is one of the most characteristic traits distinguishing three domains of life. This lipid divide has taised questions. If eukaryotes have thought ot be evolved from archaea - it would require a very radical change in membrane composition. How does this work? Lokiarchaeotia - asgard archea close to eukaryote branch. In lockiarchaeaota found there is no gene to synthesise the glycerol 1 phosphate backbone. In fact their genetic capacity to make a glycerol 3 backbone. This indicates that the lochearchaeota may reflect the archaea to eukaryotic membrane transition stage. Recent discovery based on the fact that these other archaea have been identified.

Are lichen a mutual or parasitic relationship?

Lichens - photobiont (algae or cyanobacteria) and fungi. Fungi forming the structure - protect algae from environmental stress. form hyphae that algae are entangled in. Algae forming pigments and are primary producers that provide fungi with carbohydrates. When interaction falls apart - no longer lichens forming Pollution can break down that interaction Most people thought it was mutualistic But in some cases - what real benefit is algae getting than the fungus? Algae can grow by itself and does much better in lab conditions - is it really being 'protected' Maybe fungi is controlling dampening the ability of algae to grow. Maybe this is some case of controlled paratism or fungal infection that algae is dealing with Can't always box things, we are looking at snapshot in evolutionary time, very dynamic in biology. Boxes aren't always correct.

why is light so important?

Life is dependent on light One of the reason we get life on earth is distance we are from the sun

What are the steps of the light reaction in photosynthesis?

Light comes in and directly or indirectly excites electrons. Those excited electrons, in a high energy state, will be transferred from one molecule to another and they are going to go to lower energy states, the electrons are becoming more and more comfortable. some of that energy that's released as the electron comes down back to ground state from high energy state, is used to create a proton gradient across the membrane, where there are hydrogen ions coming in from outside the membrane (in the stroma) to inside the membrane inside the thylakoid. (building a hydrogen ion (or proton) concentration gradient across the membrane). This concentration gradient can fuel the production of ATP from ADP by ATP synthase. Those hydrogen ions want to go back out, they want to go down the concentration gradient and as they go back out through the ATP synthase, it essentially turns that motor that can jam the phosphate group onto ADP to create ATP. It is used pretty much the exact same way a motor is used with electricity. The other thing that is responsible for this concentration gradient is the P680 pigment or version of chlorophyll. Once the exctied electron in the PS2 gets donated, it needs to be replaced. The thing that is doing the donating, that gets excited and donates that electron, is the P680, p standing for pigment and 680 standing for nanometers (the wavelength of light it absorbs best). When excited it becomes P680* and when it has donated its electron it becomes P680+. P680+ is a very strong oxidising agent, one of the strongest, if not the strongest oxidising agent. This means it likes to grab electrons from other things. The thing that it can grab electrons from is actually water. It is such a strong oxidising agent that it can oxidise the oxygen in water. The water then falls apart because of this oxidation, so you are left with oxygen molecules and hydrogen ions. These hydrogen ions ALSO contribute to the proton gradient. The second part of the reaction is that these electrons make their way to photosystem one, where there is P700 (pigment that absorbs 700 nanometer wavelengths best) Again, light can directly or indirectly excite its electron, and as that electron moves down lower energy levels, it can be used to fuel the reduction of NADP+ to NADPH. The P700 then wants its electron back, which it gets essentially form the P680 where the electron has been moving down the energy levels from photosystem 2 all the way to photosystem 1.

Gammaproteobacteria are metabolically...

diverse

biogeochemical diversity in soil aggregate

Like the winogradsky column, a soil aggregate is compised of microbes with diverse lifestyles. There are facultative aerobes, anaerobic orgnaisms, depending on what part of the particle they colonise and live in. important indicator - if understanding what process is happening, which part of the process are you trying to target.

The 3 parts of LPS are ____________.

Lipid A, core, and variable O-specific

What anchors the peptidoglycan to the membrane in Gram-positve cell walls?

Lipoteichoic acids

what is aspergillus spp.

Live in soil and break down plant material. They are very good at it, get a lot of nutrient recycling from gunfi in the soil. Dispersal is via conidia which are asexual spores, it also lives in compost in particularly. Aspergillus fumigatas is a good fungus to have on compost heap. Something to remember about compost heap is temerpature in compost heap fluctuates a lot. One of things about aspergillus fumigatas is it is temperatuer tolerant. Will grow at many different temperatures. The wall of aspergillus condidia - get nice pigments because of mellanin in the spore/conidia walls. The mellanin is thought to protect cells from UV damage in the sun. these guys come with their own suscreen. To be able to degrade the complex materials in the soil, there is a lot of secreted enxymes that the fungi produce. Lots of extracellular hydrolasesthat break down complex sugars to assimilate nutrients.

What organ is most affected by hepatitis B virus?

Liver

Pili are ________.

Long extensions from the cell.

describe typical soil phylogenetic diversity

Look at typical microbial diversity present in soil sample - Extract total microbial community DNA from 0.25 of a gram. - Do next generation sequencing, get data on total population in terms of who is there. - In soil, bacterial community is dominated by proteobacteria e.g. pseudomonas, acidobacteria. There are segments that are comprised of the phyla. - For acidobacteria (phyla quite well known but onl handful of isolates cultured). Therefore lots of numbers but not names. Is a group within the phyla, but no one has cultured them. - Overall, usually dominated by uncultured microbe, as well as bactrodites, acidobacteria, proteobacteria and actinobacteria as well.

What is experimental evolution?

Looking back through time (paleontology) (ancestrol organisms - not good for microorganisms, not many fossilised microorganisms. Except for stromatilites. Don't have much good structural informaiton Comparing extant species (e.g. 16S rRNA trees Experimental evolution (plant and animal breeding..and microbes) Examples of this with plants, and animal breeding. With a lot of agriculture props, we are the selective pressure, we have put pressure on them for particular traits and have evolved them over time to be more desirable crops for us. For animal breedings - good example is dogs and we have selected for particular traits we want and evovled them over time For microbes we can definitely use this, they have short gneeration time, ideally suited for studying evolution within our ligetime.

________ in saliva cleaves glycosidic linkages in peptidoglycan present in bacterial cell walls, weakening the wall and causing cell lysis. - Mucus - Lysozyme - Lipid A - Fibrin

Lysozyme

What is M13?

M13: Circular ss DNA filamentous. No lysogenic cycle. Worm like phage

What is soil?

Made up of 40% inorganic matter. Depending on mixture of sand clay silt makes up beginnings of what is soil. That then drives what properties of that soil is. Proportions of groups determine soil texture. With lots of sand, water flows through easily Lot of clay, more humic if have water flow over, will just sit there. This drives kinds of communiteis that can be present Made up 5% organic matter, and 50% air and water. Get entirely different communities that livei n that area (rhizopheres)

what makes up candida cell wall?

Made up of proteins an sugars, but different proteins and sugars to bacteria nad arranged differently. In brown and green have two structural components, chitin in brown and beta-1, 3-glucan in green. They are two structural sugars, they are like the wooden frame of a house, they are the scaffold. Have a whole bunch of cell wall proteins (blue globular things) which are highly monoselated (purple things sticking out from that). They are attached through beta 1, 6-glucan linkages. They get attached to structural components, cell wall proteins get attached to structrual components, and the cell wall proteins themselves have eben more sugars on them. Once proteins are made and they pass through the ER and golgi they are glycocelated. In this case the glycocelation that occurs is through edition of manose, multiple manose residues makes a manon. So these are mannosylated cell wall proteins. Not all fungal cell walls are exactly like this. They all have a structural component and all have cell wall proteins (generally mannosylated) but they are all arranged differently. They can also have additional sugars or different sugars or extra layers like a capsule.

upregulation of multi-drug transporters in candida agaisnt azoles

Major mechanism of azole resistance is the upregulation of efflux pumps. You get activation of membrane asociated efflux pumps that pump drug straight out. 2 efflux pumps in candida, these are ATP binding cassete or ABC superfamily of efflux pumps (Cdr1 or Cdr2) and Mdr1. similar to bacteria, same mechanism similar names. Can get over expresison of the efflux pump itself, the protein that makes the pump, get mutations in the transcription factors that regulate the expression of those efflux pumps. Also mean upregulation of the product. Not just mutations in the thing itself, it can be mutaitons in the activators (regulatory network) involved in expression of these things.

What are some genetic and enzymic properties of methanogens?

Methanogens Produce weird co-enzymes. Cause them to autofluoresce. Easy to see under microscope. G+C content very broad. Very big range (26-62%) , quite phylogentically distinct, very diverse. Can you tell what they look like under microscope? To see if it's a methanogen Have all sorts of weird shape, so no. shape doesn't tell you! Might even think they are bacterium ,but they aren't.

clinical features of Hep C virus?

Malaise, lethargy, anorexia, nausea, liver enlargement may cause upper righ quadrant pain of torso. This leads to the icteric phase or yellpw stage. Jaundice phase (icteric) - billuria (dark urine, bile pigments in the urine), pale stools and jaundice. Break down product of heamoglobin. It will release the yellow substance into the blood, which give you the jaundice colour, clay coloured stool, very dark urine and yellowing eyes. Some babies are born with hepatitis but then it disappears very quickly, but is nothing to do with virus, is just baby catching up with birth.

What factor has delayed the development of laboratory-based genetic systems in Archaea?

Many archaea grow in extreme or unusual conditions that make the use of agar and traditional mutant screening techniques problematic.

how we limit nutrients from pathogens

Many growth limiting nutrients are sequested within the host. Normal flora of the body competes for nutrients within many exposed niches (restricts growth) Skin, gastrointestinal, mouth Iron is tightly sequestered in the body We restrict iron Bacteria require for a number of their enxymes, particularly a number of enzymes in the respiratory complex such as metalo-enzymes that have iron centre and need iron to function. We have sequestered it so that iron is limited and they can't replicate We secrete lactoferrin in mucosal surfaces that binds to iron very tightly Secrete transferrin in our serum to prevent it being bioavailable to pathogens. Iron is required by bacteria for many metalloproteins - respiratory chain complexes

What is endotoxin? what are the effects?

Many of our immune responses particularly in innate system, target conserved structures in bacterial cell e.g. peptidoglycan, some flagella proteins, and particularly on gram negative cells the LPS. If innate response sees these molecules knows it's a bacterial infection. LPS is able to stimulate an innate immune response. This purple region (O-specidic polysaccharide) is highly variable, but lipid A is highly conserved. Our innate immune response has recognised lipid A as a conserve signal that there's bacteria about. If it's in the wrong spot - swill trigger immune response. In small doses, endotoxin produces a basal level immune response, Problem really becomes (imagine we are colonised by trillions of flora) so we allready have some stimulation from gram negative bacteria that are colonising us. Problem comes when you have bacterial infection - the lipid A trigger can become quite strong at this stage. Get what's termed a gram negative toxic shock You induce a very strong immune repsonse, and the worst is DIC. The immune response is meant to destroy bacterial cells, but if it gets over stimulated it can destroy our cells in our local vacinity. It can destroy capillaries and damage capillary linings for our cell and destruction, can see bleeding on skin surface. Gram negatives can cause gram negative toxic shock which can lead to DIC.

What are the major agents of gastroenteritis in Australia?

Many of these agents are carried in food. Common scneario for developed countries, but n developing countries we see a larger proportion of agents for gastro being bacteria. Viruses are much more sturdy than bacteria. Good sanitation will control bacteria, but less so for viruses. Big 45% is norovirus, done by EIA enzyme Rotavirus - gone down a lot (around 30%?)

What are the different types of exotoxins?

Many severe disease symptoms are caused by the release of cell-specfific exotoxins Highly variable but often have A-B organisation A sub unit is a toxic enzyme (that disrupt host cell functioning) B sub-unit is for receptor binding and trafficking of exotoxin. Receptor domain that binds to specific receptor on the cell surface. Is also responsible for trafficking. These toxins will circulate in our system until they find the right host cell and then will bind to specific receptor motif usually a sugar on the outside of our cell and be taken into the cell and start to cause chaos. Three major families: AB (diptheria toxin), 2AB (anthrax toxin), AB5 (shiga toxin)

Recent pandemic variant of norovirus

March 2012 found sydney 2012 strain that started emerging and causing outbreaks in Aus and NZ. If you zoom out at tree on left hand side,the strain casuing all the outbreaks before was New Orleans virus from 2010 and 2012. we started seeing this strain in march and in november 2012, started causing global pandemic of gastrointeritis. There is a dominant strain here, at end of 2012, the Sydney 2012 strain began to replace New Orleans strain. These are institutional oubtreaks in NSW If you see NZ and Aus data together, the NO strain that dominated for three years suddenly replaced by Sydney 2012. It dominated for 2012, 2013, and 2014, and expected it to be replaced, but didn't get replaced. In 2015 it was going down, prevelance going downm, 2016 it is going down even further. There are six major strains, the one that dominates in 2018 out of all of those is the P16 sydney. It's a recombinant strain, it's left handside coems from genotype 16 and right hand side is still sydney. It's hald sydney and half something else. Interestng finding.

Transmission of Hep C Virus

Member of flaviviridae (which include yellow fever virus, Dengue fever virus, West Nile virus) Route of infection - parenteral is most prevelant, unlike other flaviviruses HCV is not transmitted by athropod vectors. High rates in IDVU, haemophiliacs, recipients of unscreened blood transfusions. (before 1990) in Australia 82% of transmission is Intravenous drug use. If you go to a prison where there is a lot of drug use prevelant, 1/3 of the prisoners have had hep C. 1/3 have never had it and the remaining third have had it and still do. 1/3 of 30,000 people in NSW prison system have it. Not only heroine addicts it's metamephatine adicts who inject up to 5 times a day in each finger. Sexual and mother-to-baby transmission does occur but is uncommon 1.5% among long term partners. Unprotected sex - If you want to transmit virus sexually, blood needs to be involved. It is unlike hep B which can be sexually transmitted. Hep B is prevalent in Africa as well as HIV. People get confused by that.

Bacterial cytoplasm is contained by ___________.

Membrane and cell wall

Describe how microbes dominate and drive ecosystem processes.

Microbes dominate and drive ecosystem processes. Microbes are the most abundant lifeform on the planet. They thrive in every habitat imaginable. Understanding of their phylogenetic and funcitonal diversity is frowing. Over 10^30 cells and over 10^9 species predicted. They perform key functions that are critical for life to exist. Most importantly they drive global geochemical cycles: carbon, nitrogen, sulphur. Perti dish in the lab, have seen bacteria grown in it with nothing in it, just plastic.

What are pigments and their use in photosynthesis?

Microbes that have particular pigments that can trap light energy, can harvest directly from photons Increasing excitation and electrons moved down electron transport chain. Chlorophyl is main pigment, but range of different organisms that have different coloured pigments which associate with caputring a particular wavelength of light. Light attenuates through water/soil so get different wavelengths that go deeper. At top, plants and chlorophyl, but infrared goes quite deep and microorganisms can use this with their pigments. Pigments important with giving phototrophic organisms an advantage in their environment They are basically using light energy to reduce a high potential electron acceptor Usually are going down a chemioosmotic gradient in the cell

Which of the following statements is FALSE? - Microbial cells carry out their life processes of growth independently. - Microbial cells exist as single cells. - Microbial cells exclude the type of cells found in plants and animals. - Microbial cells include both bacteria and viruses.

Microbial cells include both bacteria and viruses.

Explain quorum sensing using aliivibrio fischeri

Microbial genetics - how can that organism control when it is prducing and not producing luminesence (is costly) It does it by knowing it's own cell density. Can imagine bringing it into the lab. The AHL - is a molecule that is diffusible in and out of the cell membrane of the bacterium. The bacterium produces this at low density in small amounts. When the density increases, either in amount, or because it's jam packed in the light organ, there's more of the AHL around, and with more of the communication small molecule you get luminescence (lighting up). Coding for LuxR protein - p is promoter lux box is part of the promoting region in operon. The lux I and rest of the genes are coding for phenotype (luminescence). Lux R produces the protein Lux R which is a transcriptional regulator. Lux I produces signal molecule. This Lux R regulator binds to the Lux box but only does that in presence of AHL (OHHL is one type of AHL). At high cell density, the AHL can bind to the Lux R protein and starts transcription of the luminescence as well as the Lux I and the Lux R. these are bacterial auto-induces, they induce the synthesis of themselves. Bacteria benefits because it's in a protected environment, and its population gets regenerated every night. Lots of interactions similar to this in other bacteria. Not just for luminescence. Nearly all of them involve phenotype expression that involve a quorum for expression - pathogenesis, positive symbiosis, motility, biofilm formation, antibiotics etc.

Describe example of strong evolutionary relationship between organisms - aphid and buchnera

Microbial interaction in aphids Aphids have a special relationships with bacteria that belong to buchnera Their relationship is so close that they can basically become endosymbionts. The main diet of aphids is sap. They are many agriculture pests. Sap is not very nutritious. It's missing many essential amino acids. Aphids get that from other source. They have teamed up with bacteria that produce all the other amino acids for them. That relationship has become so close over evolutionary time, that those bacteria are no longer able to live on their own, and the aphid can no longer lives by itself. This is a mutualistic relationship. It's become that tight, that the aphid, Blue is nucleic acid of the aphid, the green is the nucleic acid of the bacteria. The green is all basically tied up together, indicating green with red dot in there, are the bacteria site.s these are specialised cells that aphid now has that are jam packed with aphid bacteria. Red dot is nucleus green on outside. These are farms of amino acids for aphid. Similar in concept intracellular pathogens of humans. The buchnera and avid have co-evolved over evolutionary time. Characteristics are similar to obligate intracellular pathogen.

define microbiome

Microbiome: the entire habitat including microorganisms, their genomes and their environmental (metabolic/physiological) outputs living inside and on the body

Define microbiota

Microbiotia: the collection of microorganisms present in a defined environment e.g. microbiota of the skin, is a defined areas of the skin. This area has blossomed over the last 10-15 years because of metagenomes.

What are some applications of bacteriophages?

Model system of molecular biology (many nobel prizes have been won using the phage Cloning and expression, Phage display systems, Phage typing (typing salmonella - classic example), Phage therapy: phages as natural, self-replicating antibiotics. People ditched working with phages when anti-biotics came out. Conventional bacteriophage therapy: In early days bacteriophage therapy was used by making bacteriophage preperation and are effective agaisnt P. aeruginosa, E. Coli S. aureus, Streptococcus and Proteus. The first reviwed report of the therapeutic efficacy of PahgoBioDerm (cocktail of lytic bacterophages) was bublished. 107 patients with ulcers - failed to resposne to conventiona ltherapy (comin in diabetics with skin ulcer from bacteria) With PhagoBioDerm - Ulcers healed completely in 67 (70%). Was basically a bandage with a little bit of medication with phages in it. Nasty legion on this guys back, put phage bioderm over the top and thenits cleared out after couple of weeks. This is a staphoryious skin infection. It lives all over our skin but some people get infected by it. It's still used today to treat skin lesions. Antimicrobial wound dressing biodegradable polymeric film (artificial skin) containing bacteriophages.

what is non-typhoid salmonella

Most common form of salmonellosis Incubation period 6-48 hours (needs to replicate in gut before getting sick) Nausea, vomiting and diarrhoea Symptoms may last for 2 to 7 days In some circumstances it can go on for longer Salmonella infection in old people can be very serious. Nearly always an old person will die from it in an outbreak.

LPS is important to maintain ____________.

Outer membrane strength

what is candidiasis?

Most common serious fungal pathogen of humans. It lives in your GI tract (50% of humans) part of your microbiota, very metabolically diverse. Does a lot of good things in your gut. Main two ways It is kept in check in healthy individuals, one is competition of bacteria in microbiota that occupy that site. E.g. oral and vaginal thrush occur from overgrowth after antibitoics. Another thing that keeps fungus in check really well is your natural immune system. Macrophages, phagocytes nad neutrophyls are good at recognising fungal pathogens, engulfing them and dealing with them. Can inject 10^8 candida cells into the blood stream of a mouse and the neutrophils would have mopped that up in three seconds. Important to note - it's candida from your GI tract. Groups at risk include: major immunosuppression e.g. cancer, AIDS, transplants etc, When it is systemic infections - escapes from your gut, travels through your blood, disseminates into your organs and forms lesions there and most often leads to death even with treatment. 46-75% mortality rate depending on where in the world, even with with antifungal treatment.

What idea underpins many of these relationship?

Most interactions highlight the fact that micorbes are so metabolically diverse. Because they are so diverse, they give many different kinds of benefits to organisms. nitrogen and supply organic nitrogen to plants, we wouldn't be here. Guts of ruminate animals, they are designed to digest wood products that we can't do. The enzymes in microbes to ferment allows organisms to digest grass, and evolve the organs they have. Leaf cutting ants that farm fungus. Wouldn't be able to exist if fungus couldn't metabolise material into something they can eat.

How HIV progresses to AIDS

Most of us will have 1,000 CD4 T cells per microlitre of blood. The T cells are very important because they will kill infected cells, they are part of our immune system. When you get infected, with or without symptoms, first thing is virus will kill T cells ad goes below 500. then the immune system starts to kick in, you get IGM antibogies after ten days, the n IGG after a month. The CTL white blood cells system or cytotoxic T lymphosites will kick in around 2 weeks, then fight the virus and get a recovery in CD4 levels because of immune system fighting the virus, and immune system will go back up to 6/700 but never to 1000. the virus is now sieated itself as a provirus in all the CD4+ cells hiding in your genome (because it's a retrovirus) and eventually over ten years or so, the CD4 count will fall (it will fall below 250, then you are in symptomatic phase because you will start getting opportunistic infections. You're immune system is very week at this stage. One of the main tests for HIV infective people is to work out what CD4 count is, there is handheld devices now that can work out CD4 counts. Symptomatic phase can lead to AIDS, where you can die from lots of different things, opportunistic infections. Declining memory T-Cells also means that your B-cell function (T-Cells need to help B-Cells) isn't very good, and you can develop parasite infections, intracellular bacteria, fungi, viruses. Down the bottom is rarer infections. Get these opportunistic infctiosn and then eventually, you can try treat these infections but you're immune system will be too far gone so you will eventually die.

natural history of HCV

Most people who get it never know they got it. It is very silent. Only 25% of people are symptomatic. Symptoms are fever, nausea, liver enlargement etc. If lucky, 30% of people infected will be cleared and will be fine. They can be infected again with this virus (doesn't give you much immunity). We have looked at people in the prisons, some who keep injecting drugs, one guy who they have been follwing for 8 years, and has had hep C four times, cured himself got it again, cured again, got it again without any drugs. Something special about this guy because he can keep clearing hep C whereas most people can't and go down chronic road. Virus continues to replicate in your liver all of your life. The immune damage as well, leads to liver damage and after 20 -30 years start getting vibrosis and seirosis and leading to N stage liver disease .about 20% of people with hepatitis will go down this road and need some serious intervention. If they drink, are obese, HIV positive, old and are male will make the diseae worse. Before about 5 years ago, had inteferon (natural cytochion we produce in body against virus and bacteria) and riboviron (nucleoside analogue) together they were used in combination, and had to use it for a year. If you were lucky 50% of people would be cured, but half of the people would have terrible side effectives (both drugs equally have terrible side effects) wouldn't be able to work, would get lumps developed on body, auto-immune problems when on these drugs, and you come off them and will find you aren't even cured when you have been on these drugs for a year and just as bad as you were if not worse before you started. A lot of people did't take these drugs because of this. Was a huge issue up to 5 years ago.

phage morphology and genomes

Most phages are double stranded and look like this. Over 95% of all phages have head tail configuration. This is icosahedral head and has a sheath here which is a helical structure. These are main families shown here Most of these phages have a 40, 50, 100 thousand base pairs of DNA which means they can make about 100-200 proteins. That's a lot more than human viruses. That's a lot more proteins than most viruses that would infect us would make apart from herpes which makes about 150-200. Can get every congifugration - double stranded Rna, Dna, circular. Lots of configurations of genomes similarly to human viruses.

What is the term used for the filamentous body found in many fungal species?

Mycelium

What is myoviridae (What is T4 and T7?)?

Myoviridae P2, T2 and T4 are most famous family of phages. Can get single stranded phage DNA which are very small. linear ds DNA, icosahedral, lysogenic cycle. These are the head-tail phages they can have a lysogenic cycle

What provides electrons to make a proton gradient across the membrane in cellular respiration (oxidative phosphorylation)?

NADH and FADH2

What are some common mechanisms by which bacteria are able to survive antibiotic exposure?

Resistant bacteria may modify the antibiotic or pump the antibiotic out of the cell.

Tenericutes and antiobiotics...

Resistant to antibiotics that target the cell wall

candida polyene resistance mechanisms

Name of polyene - Amphiteracin B It works by hugging ergosteral, disrupting membrane and resulting in lysis. Top row is those three mechanisms in ays antifungal happens. Underneath are examples of different fungi. If figure is dimmed, it means not a particularly big resistance mechanism for this drug. Polyene resistance is generally attributed to loss-of-function mutations in ergosteral biosynthesis genes. What this means Is that mutations in the genes in the Erg 11 genes, any of the ergosteral biosynthesis genes, mutations in them means end product is not so much ergosteral anymore. If the end product is less ergosteral like, the polyene can't hug it anymore. Lower affinity for drug, means resistance.

describe nanoarchaeum equitans

Nanoarchaeum aquitans Very small form of archaea which is red (the red dots here) they attach to a green host (large host) called ignicoccus. Image of ignicoccus cell. Here is the lipid membrane and here is the outer membrane - quite unusual for archaea. Has a large peroplasmic space. Here are the baby nanoarcheaum growing. Genomes of these sequenced - the genomes of the baby nanoarchaeum have the smallest genome of anything sequenced, smaller than that of viruses. Genome size is less than hald a mega base It doesn't have genes for:: Copy it out It can't even make lipds It is clearly an obligate parasite-symbiont, it grows and requries a host. Discovery is areally intresting one. Turns out these nanosized archaea seem to be/are the ones that are like lokiarchaeota, ones near the base of the tree near the asgard archaea. Have interesting implicaitons for having a small genome - what does that mean about how things evollved? They are self adjuvanting vaccine delivery vehicles made from archaeal lipids. Meaning they stimulate the immune system and deliver the antigen. Why? No idea. They work! Someone tested it and found they work really well. Canadian groups have got lots of patents on these things. Making money off archaea being able to deliver vaccines.

Flagella are complex _______.

Nanomachines

new antibiotics researched

New antibiotics in late phase development. Mainly is small start-up companies doing it. (creating new antibiotics)

How do candida albicans mate?

New growth morphologies are being discovered in efforts to better understand commensalism of candida albicans Candida doesn't do meiosis so only is diploid, no haploid forms. Makes it harder tow work with in lab and manipulate genetically Has been shown to mate, except happens really really inefficiently When it mates the two diploid cells fuse together to form a tetraploid. As they divide it randomly chucks out chromosomes until it goes back to beng diploid. Proces of mating involves opaque cells which are elongated cells with pimples on them (don't know what pimples do). They tend to be thought of as the mating competent form say that loosley, because even though opaque cells are a million times more competent at mating than white cells, they are still pretty incompetent. They tend to be better colonisers of the skin than white cells. This is where it is thought for mating to occur, but not very good colonisers of skin. The conversion from white to opaque cells is a reversible epigenetic switch. To mate you need opposite mating cells. (a on a or a on alpha)

How microbes can tell us about nitrogen cycle

Nitrogen cycle complicated Last couple of years - thoght we new everything about nitrogen cycle Found commamox, nitrogen spira that can carry out two of the processes in nitrogen cycle. A missing link recently discovered. Basically - uncovering new strategies for life in terms of microbial world.

describe a naked virus.

No envelope = naked virus. Naked viruses are much more stronger and tougher than envelope ones. What's stronger - lipid membrane or protein shell? Lipids are susceptible to desiccation, drying any organic solvent will destroy lipids traight away. And once you have destroyed the envelope, there's no key left because the key is in that envelope, and there is no viral glycoprotein in the envelope, so even those the virus may still be protecting the RNA, it won't be able to infect anything. So envelope viruses are week. They like to be transmitted through moisture, naked viruses are not. All gastro causing viruses have protein shells and are naked viruses, because they can survive the low pH gut. Envelope viruses cannot. Main 6 gastro causing viruses are all naked.

Why resistance is catching up with us

No new classes of antibiotic to market since 1980s. Pharmeceutical industries have lost interst in discovering antimicrobials. Since 1984 - no new antibiotic class discovered. Why antimicrobial resistance is catching up with us arriers to development of new antibiotics: Scientific barriers - high rate of re-discovery (Keep finding same anitbiotics) Economic: Patient cured - short treatment cd. Chronic disease (Big problem that patient is cured, if you are a pharmeceutical company you ideally want to be developing drugs that you need to take for the rest of your life. ) Eventual resistance - drug will become obsolete Comaparatively small market - narrow approval for specific disease. Other diseases are making the billions of dollars, so antibitiocs aren't the most attractive to make. Semi-synthetic. Teflaro made 50 million in first two years, which isn't much when you look at how much the cost to make it is. Regulatory: Estimated $100-300M from bench to beside

list and explain non-colonising bacterial infections

Non colonisers (do not grow or divide in gut, they don't make gut your home they just go through) These guys make a toxin (staphylococcus aureus, clostridium perfingens (spores), bacillus cereus (spores)) It's not the bug making you sick, it's the toxin that it makes. The bug doesn't need ot replicate in your gut. If everyone gets sick within 6 hours of eating a particular food - know it's one of these things. Norovirus incubation is 36 hours. This is a toxin producing morgnaisms with short incubatin period. Get diahhroea and vomitting caused as a toxin. Spores are tougher than bacteria When food is cooked, may not be cooked properly. It will kill bacteria but won't kill toughest spores. Have spores remaining in food. You take out food and heat it up to 60 degrees. If you leave that food to higher than 4 and less than 60 degress, those spores were sporelate in your gut and produce a toxin. Reheated food allows bacteria to multiply, replicate and then you have lots of bacteria in the food. Then you eat the food and get sick

What are top 5 food-borne illnesses in the US?

Norovirus - Top pathogen associated with food-borne illeness follower by salmonella, then clostridium perfringes, campylobacter, staph aureus Story not nuch different for australia.

how is norovirus detected?

Norovirus detection Reverse transcriptase polymerase chain reaction (RT-PCR) of stool Sequencing for genotype and strain ID Enzyme immunosorbant assays (EIA) Old: firect and immune Em of stool samples. Viruses associated with old people home outbreaks, aged care vacilities, child care facility outbreaks, cruise ships and hostpials.

describe exposure to pathogen, and how it varies for pathogens.

Not all pathogens have the same virulence Some require very small numbers of cells to cause disease termed: infectious dose, lethal dose. Infectious dose - The number of cells required to cause infection in half the population Lethal dose - the number of cells required to cause death in half the population Highly virulent streptococcus pneumoniae LD50 = 10-200 cells to kill half of the infected population Common foodbourne pathogen salmonella enterica str. Typhimurium LD50=1000-10000 cells Many cells killed by stomach acids/host defences Very few of them even make it to that point Therefore need much more lethal dose.

Give an example of gene reduction in a non-pathogenic organism, and how this came about.

Not only pathogens - genome reduction can be driven by any environmental sepcialisation Non pathogenic has same gene as pathogen except ten percent has pseudogenes 0 many of which are virulence genes. Streptococcus thermophilus - Theory is we had 10,000 years ago on Mongolian steeps, there was that people were fermenting milk and were spitting into the milk to inoculate it with streptococci to ferment the milk. Over time people realised that they didn't have to spit in it every time and they could take a little bit of the fermented milk and inoculate it with the next culture and so over ten thousand years people were inoculating that milk and passaging that streococcus salivirus into a new niche where it just has to live on milk and not live on us anymore. Overtime has accumulated pseudo genes and genome is being reduced as it is becoming adapted to new specialised niche we have put it into.

Give a brief history about taxonomy

Not something that is new It's somehting we inately do as people - we give things names. It's part of the human condition Wasn't till 400 BC when Aristotle started to reallyh try systemize our naming conventions. Trying to classify organisms on what he thought were conserved characteristics. E.g. does it have blood, does it live in water He came up with binomial naming system (which we use today) He used a system of two names, first the group that we clasify the organism in and the second name refers to how it differs from that group. Andrea Cesalpino was first one to characterise organisms on structural similarities Wasn't til 1735 that Carl Linnaeus really started to tease out the heriarchichal naming system we use today Systema nature - used heriarchal system where we use kingdoms, classes, order, genre and species which we still use today

What is Shiga-toxigenic EAEC 2011

Novel pathogenic E. Coli are still emerging 4000 cases of infection 908 cases of haemolytic uremic syndrome (Shiga toxin) damage to kidney 50 deaths Got hybrid pathogen that swept through germany in 2011 These processes still happening today

How can archaea grow in a nuclear water core?

Nucleur core - water core of nuclear reactir have to add biocides to prevent microbial growth. Bacterium, but archaea that can do something similar. If you hit 9D R ) with radiation and you study its DNA its actually not resistant, the DNA breaks down, but you leave it there and it puts the DNA back together and it goes on to start growing if you take the radiation away from it. It's got remarkable proteins that are able to resist the radiation. If you think ecologically or evolutionary, what's the selection pressure for radiation resistance? This is a trick question - not a straight forward answer. Can you imagine an environment that would select for being able to grow in water core of nuclear reactor? Not really. Interesting thing in regards to selection pressures and thinking about what that can mean for microbial growth. When you look at DB which you naturally find in the desert in dry environments, in dry environments you have low water activity, when a cell dehydrates, the DNA breaks down. So the selection pressure is dehydration, and that's given deinococcus the ability to put its DNA back togther, when it gets water it rehydrates and puts DNA back together. It turns out that ability also enables it to survive radiation, that's why it can grow in the water core of a nuclear reactor.

Endospores are triggered by ________.

Nutrient limitation

How has the increase in data been conveyed in journals etc.? what are the problems associated with it?

Often get pictures like this (on the left) in review articles, which often describe the states of things in the field, in this case we are talking about bacterial genomics. This chart shows the growth in the numebr of whole ngeome sequences we have. Back in 1995-2004, there were only a few bacterial species that were entirely sequenced, that was because it was so difficult, even getting one genome was a big deal. As you can see, this pick ups and then from around 2008/2009 things explode and we get a huge spike, and this only takes us up to 2014, so don't even know what numbers are like in 2018, but those bars must be super high. Sort of comments you get in these sorts of papers describing these kinds of studies are like this, 'most biologists are drowning in their own data' or from NCBI 'explosive growth' and 'deluge' There's a lot of information, and the biologists are a bit desperate, cause they need to know what to do with all this information. Once again there is a sentiment that there is a huge amount of data, and we need to deal with it, and we need computers and we need good computational methods to be able to do thigns with the data. Not just annalysing, but also storing, organising and retrieving. Just getting databses right is a big deal.

What is the problem with culturing bacteria?

One of issues in environmental microbiology, is that although there are 10^9 species, we have only cultured and characterised 10, 000. Typically when you are trying to culture from soil, normally get species cultured from these four groups (below) Readily cultured from any environment How to tap into ones don't know much about? Use shotgun sequencing. Not just 16 SU sequencing. Now get entire fragments of DNA and put puzzle together to figure out not only what community looks like but potential functions they carry out. Do process to do sequencing, get idea of what microbes do, and then culture them. Most of them recalcitrant - a lot of soil bacteria live in environment with low nutrients. If you put these organisms on high nutrient plates, they wont survive. This is because media can be toxic to organism. A lot of bacteria don't form a big colony on a plate. When you can see a big colony on a plate, there is 10^6 on a plate. A lot of bacteria don't grow like that. We also don't know what nutrients they need, or what they do. How do we know nutrients on plate are the right ones? Cell signalling needed to tell bacteria to grow. Sometimes need co-cultures, because one bacteria might need product prodcued by another to grow. Big discrepancy, big area fro last 2 decades now. This was developed over a century ago. Need new ways, need to change way we think about culturing.

why is there so much azole resistance?

One of reasons for high ammount of azole resistance is because azole is a widely used drug in agricilture to protect crops from fungal pathogens. Particularly aspergillus and crypto, in the environemnt on plants etc. any of those kinds of fungi, if they are already resistant to azole in environemnt when we ge them, they will be azole resistant.

What is the importance of stromatilites in understanding evolution?

One of their claims to fame, is that where these cyqanobacteria (fossil ones) have been found are in what we call the rock record, and stromatilistes are what we are finding here. These are complex communities which are dated back 3.7 billion years. Seeing as the easrth was formed 4.5 billion years, can see how early these complex systems evolved. Imporant for understadning evolution of life on earth. Seawater is hypersaline which excludes a lot of eukaryotic life (one of the reasons we think they can happoy form there) also been thought that ancietn seawater was hypersaline. Can use these as modern analogues to understand the past a little bit better.

What are stromatolites?

One organism, which is an example of that is stromatolites. Very similar to winogradsky column, at a small level, probably a couple of centimeters, can see some of the layers/pigment coloured layers forming here. These form naturally, normally in coastal areas, yet a really steep gradient of nutrients. Could be anything from oxygen to CO2 to sulfur and nitrogen compounds. Similar to a winogradsky columnm organisms will position themselves at a mm zoone where its useful for them and they can really efficiently recycle nutrients. If you took a m squared of one of these ,more efficient than a m squared of a rainforest. These can stretch for km. these microbial mats which are like precursors for stromatolites (hard rock like structure oalmost like concrete) are really complex microbial communities which interact iwht natural environment to trap sediment and precipitate minerals to make these structures and are really functionally diverse. Stromatilites are rock like structures which are a metre an a half tall or so, If you take a cross section through one of them can actually start to see the microorganisms, particularly cyanobacteria that hang out at the top. Can see some of the microfossils you see, and some of the fossil stromatolites you can start to identify specfiic microorganisms in there. Different locations in the world they are found. One of the best ones, which we are lucky in Aus is in shark bay. These are km reefs of the stromatilites.

Describe temperature range of methanogenic archaea

One thing interesting about methanogens, especially if interested in thermal adaptation,s is a group of organisms, individuals span a broader tempertature range than an other type or organism, can grow like methanogenium frgidum (frige cold) - 2 degrees while methanopyrus kandleri can grow up to 122 degrees. Enormous range. No other type of orgnaism that can do that. Very good models for examining thermal adaptation. most thermally diverse group of organisms we know.

What are Methanogens

Only lige forms known to produce methane Strict anaerobes Methanogenesis: Anaerobic respiration, energy generation pathway Unqiue coenzumes (not cytochromes, quinones) Trace elements: Ni Fe Co Means of generating energy producing methane Funky enzumes Utilise three different types of substrates - lithotrophic substrates, carbon dioxide and hydrogen. Also formate, can use carbon monozide. Methylamines, methanol, acetate.

What is the electron source for chemoorganotrophs?

Organic substances

What is Adaptive Radiation?

Organisms diversify from a common ancestor. Often driven by environmental change. Radiate out as they become more specialised for their environment. Eventually become new speices Need some diversity between individuals which can be propogated I(mainly through selection pressure - environment change, which starts to select for particluar individuals which are most fit Therefore requires selection pressure (environmental change) and genetic diversity Random background mutation occuring within the genome wso through rangom fluctuation there are some alleles or mutants that can come to dominate within a population. Termed genetic drift. More common in small populations. In large populations these sort of effects get dilluted down. The probability of a single allele rising to fixation is quite narrow. Bujt in small population genetic drift can be a determining facotr. Also important where you have population bottlenecks. A population gets reduced in size and expands again. These point mutaitons that aren't necessarily positively or nagatively selected can randomly become fixated in population. Can lead to specification This pplies to whole organisms - bacteria in new environment,m with particualr spelective advanteges Genes - when looking at horizontal gene transfer, a particular gene can be selected in an environment and tranferred between microorganisms.

What are chemotrophs?

Organisms that obtain energy by oxidation of electron donors in their environment.

What is chemoorganotrophy

Organisms that oxidise of one or more of a variety of organic compound acting as electron donors

what are some chemoorganotrophs which use other elements as electron acceptors?

Other electron acceptors Organisms adapt to huge range of environments where they can use different electron donors and acceptors Can use acetate as electron donor and have heaps of other options for electron acceptor. good for bioremediation. Microbes live in very competitive world, so if they can utilise something, another orgnaism cant' or be somewhere that's toxic for one organism where htye can survive, they will get an advantage eventually

What were the results from Richard Lenski's experiment about mutations that E. Coli gained in 20-30 years?

Over 20K generations E. coli was selected for incremental increases in fittness. 30K generations - E. Coli evovles ability to east citrate (Vitamin C) as a carbon source. The defined media he was using used glucose as a carbon source, but also included citrate. initially the biomass spiked within these cultures. They thought it was a contamination. Strains in the increase biomass was actually the E. Coli strain. Went back and sequence d the genome of this E. Coli which was one of the 12 replicates which was now able to grow to much higher biomass. The reason why E Coli can't use citrate as a carbon source is because it can't import it into the cell under aerobic conditions. It's because the citrate transporter is under control of the promoter which is repressed inthe presence of oxygen. When they sequenced their new organism of their evovled strain there had been a gene duplication occur. This transporter gene had copy and pasted itself infront of the promoter (mk) So that it is expressed under aerobic conditions. So it duplicated itself, and put it under the control of a promoter which was now expressed in aeroic conditions so it couldn ow make citrate transported under aerobic conditions and take citrate into the cell. If cultured even further it became better and better at growing under these conditions. When sequencing these organisms they had duplicated it over and over again, so that there was higher expression of the citrate transporter So now it could grow much better with an extra carbon source in addition to glucose.

What is adaptive immunity?

Overcoming adaptive immunity Adaptive immunity is a highly specific immune response developed against a foreign antigen (s) Takes a whlie to develop (5-7 days) It's antigen specific and has an immunologic memory. Antigen-specific antibodies are raised agains the pathogen to increase killing. Direct complement-mediated killing, direct macrophages, neutrophils and other immune cells to kill bacterial cell. It is both cellular adhumeral (involves cells) but also involves antibodies We have a constant domain which is the way our immune cells will recognise this antibody and kill whatever is attached to it. Antibodies can direct the compliment system - why it's termed compliment system, it is killing what is compliment bound to it It can also direct phagocytic cells like macrophages and neutrophils - anything the antibody is bound to. Whenever you have an antibody against a particular pathogen's antigen presented on a particular pathoge, you can readily start to kill it.

How has society evolution changed our gut microbiota?

Overtime a number of factors have led to a decrease in diversity of the gut microbiota in industrialized societies. We would have been taking in mictobiota that stimulated our guts and lead to production of short chain fatty acid. As we move through time get to agrigulture. Then move through to industrial food production, processes and sanitized food can all lead to different outcomes. What we want to see is a high carb diet, to do that even if you haven't been eating these complex carbs you can change your microbiotia by eating the right foods. Western population has different microbiota to malawians and amerindians because in their diet they are taking in these complex carbohydrates. The number of phylotypes present in the amerindians arenearly 1600, and get less and less according to population. Only 1200 in US.

Who does gastroenteritis mainly kill and where?

Overwhelming amount of people who die from it are under 5 mainly in developing countries because of weaker immune systems and less facilities. Major way we can do something about this is vaccines, vaccinate against pathogens that cause gastrointeritis. Was a rotrovirus vaccinethat came out in 2006in Australia, no vaccine for noro-virus. Vaccine for roto-virus reduced prevelance of virus by 70%.

What is chemical energy?

Oxidation of chemical compounds to obtain energy.

Use Phage P1 as an example to explain transduction

P1 is a phage famous for transduction - used to map E. Coli genome. Transduction is the transfer of bacterial DNA from one bacteria to another, usually same species, because phages are species specfici but phage is the vector that does the job of using a bit of DNA from one E. Coli into another E. coli. About 1/10,000 of the P1 phage particules carry chromosomal DNA - on the end of the phage DNA from E. Coli. From the E. coli. They have own DNA (94, 000 base pairs) plus a little bit maybe 10,000 or 5,000 from the E. Coli it has just infected. It can do this because it has terminal redundancy on either end of its genome. It's linear in the virion but in the cell it circularises for replication Say you insert DNA from E. Coli into the genome, the phage will still function because it has the genes for function on this end, so it has 15kb of DNA which is duplicated which means it can capture E. Coli DNA in the other bit. Termed terminal redundancy. Importance of this is that DNA can be inserted into it without infecting the phage. The phage can still functin and carry out its lifecycle. The foreign DNA can be moved around from bacteria to bacteria. Some cells will gain a gene from the other E. Coli. So recipient cells have encorporated donor DNA and thorugh recombination will push it into their chromosome and have gained a piece of DNA from original E. Coli. The phage was thing that did the job of mocing it from one E. Coli to another. The phage components - this phage here is infecting the recepient bacteria by inserting through recombination a little bit of DNA from a bug into transuced bacteria to gain function from new gene.

What was published about DPANN and what does it say about eukaryotes?

Paper from a few weeks ago published in Cell. From same group, update from paper just shown. They have added new lineages to the group called DPANN. One of the things they conclude - the phyolgenetic analyses results in placement of eukaryotes as a branch within archaea. This notion is continuing, what ill talk about in terms of characteristics of archaea, you will see the connections between archaea and eukaryotes. They share similarities with bacteria, but also share characteristics with eukaryotes.

The field of study that can reveal how genes function, reveal how organisms interact with the environment, and show evolutionary relationships is __________.

comparative genomics

experimental evolution

compare and monitor changes in fitness

Why are bacteria becoming resistant - agriculture

Part of problem is over-use Cactus farms in US - cattle are bread elsewhere. They come into cactus farms , fed on a corn diet and they are fattened up and then after a few weeks are sent off. If you have this many animals tucked in together, all stressed out, they are all really susceptible to infection. This would spread like wild-fire, they are all really close to each other. This is a problem. What they do, is they give these cattle every day antibiotics. They ahev to give it them, otherwise they start losing cattle to disease. This is perfect if you are a resistant bacteria this is heaven, there are no other bacteria that can gorw here except for resistant ones. We are selectng in all of these cows anti-microbial resistance and then we are putting it into the food chain. Turns out, if we compare human usage vs agriculture usage, 64 million metric tons fed to agridulture every year.

What is oxygenic photosynthesis?

Particularly with plants, using water as electron donor Resulting in release of oxygen. Includes modern plants, algae, and some bacteria (e.g. cyanobacteria) Produces glucose molecules, and oxygen If it wasn't for photosynthetic organisms we wouldn't have oxygenatic atmosphere and us as we know it Cyanobacteria can harvest at high light intensities, e.g. surface of water body cyanobacteria gain a competitive advantage

What is the general pathogenic process?

Pathogenic process is highly varied and depends on pathogen Many strategies to overcome host defences In general: Exposure Adherence/colonisation (and invade out tissues to grow and replicate) Multiple, overcome host immune defences, tissue damage (once replicating or secrete toxins) and then start to see symptoms Transmit to new host

In which stage is the viral DNA introduced into the cell? - Penetration - Release - Biosynthesis - Attachment - Assembly

Penetration

Why doesn't penicillin work on GNB?

Pennicilin is really good on gram positives, but rubbish at inhibiting gram negatives. Gram negatives have peptidoglycan cell walls aswell, pennicilin can bind just as well to penicilin bindin proteins in gram negatives, the problem is that the outer membrane is really good at preventing the uptake of these sorts of chemcials into the cel. It can't get past the membrane even in significant quantities. The outer membrane provides permeability barrier to many abtibiotics nad pennicilin can't get in. Pennicilin can glie through peptidolycan and can work fine on GPB.

The cross-linked peptides and sugar chains of the cell wall are called __________.

Peptidoglycan

What is the relationship between gut microbiota and UC and Crohns

Person may inherit 'gut' bacteria that cause Crohn's disease and Elcerative colitis Mutations in the human genome may cause shifts in the gut bacteria of patients with inflammatory bowel disease. A human subjects' DNA is linked to the bacteria in their intestines. Patients with IBD have lower bacterial biodiversity and high opportunistic bacteria. Patients with UC have a dysbiotic microbiota In patients with UC: higher proportion of Actinobacteria and Proteobacteria Lower proportion of Bacteroidetes in patients with ulcerative colitis as compared with their healthy siblings Relative abundance of predominant bacterial phyla in caecal samples of patients with UC vs. healthy controls

What are phagocytic cells? how do they work?

Phagocytic cels remove foreign antigens by engulfing and destroying Include: neutrophils, macrophages, dendritic cell. They recognise conserved bacterial motifs. Patrol tissues and serum, and engulf things they notice as foreign. The innate and adaptive immune systems are highly linked, they don't act independently. If one is activated, will activate others. Engulfed and taken into a designated vesicle determined a phagolysosome where it is destroyed by phagocytic cell. Target enzymes that will produce reactive oxygen species and reactive nitrogen species e.g. superoxide Will fill the compartment with reactive species and degrade the bacteria in the phagolysosome. Effective killing machine.

What is Phi 6?

Phi 6 - this is a bacteriphage but it is thought that some of the human viruses actually came originally, it's the ancestor of some human viruses. A few of these around, but not that common.

What is substrate-level phosphorylation?

Phosphate group is transferred directly from from substrate to ADP (to make ATP).

What bioenergetic process CANNOT occur in hyperthermophiles?

Photosynthesis

What are two types of photosynthesis?

Photosynthesis is Not only related to where they are found but also the end product producing oxygen

What are the barriers to infection?

Physical barriers: Skin, lysozymes - Enzyme in secretive fluids e.g. tears and degrades peptidoglycan (present in cell wall of bacteria) and lyses the cell. Cilary escelator - In mucus there are hair like fibres beating mucus up respiratory tract. Bacteria get stuck in the mucous and moved up the cilary escalator and pushed out of the body. Normal flora: Trilions of microorganisms that colonise our intestines, skin, mouth compete with pathogens and deplete nutrients in that environment. They physically occupy those niches, and produce bacteriocin which is a toxin that kills other bacteria Nutritional barriers Iron limitation - iron required for bacteria to live. We sequest the iron to limit it from microorganisms for growth. Innate immunity: Complement system, Phagocytic cells Adaptive immune response: Antibodies (that target specific bacteria antigens to eliminate from body) Bacterial pathogens must overcome these defences to cause an infection Virulence factors allow pathogens to overcome these barriers and cause disease.

Cell Wall

consists of alternating crosslinked peptides and sugar chains (N-acetylglucosamine and N-acetylemuramic acid) to form peptidoglycan. Lattice-like sheets wrap around cell to give structural rigidity and characteristic shape.

Describe how experimental data looks today, and in the most recent years?

Picture on the left on data. Is a phylogenetic tree based on information they found. Can see that there is variation across different isolates. Table of all different isolates. Points in the genome where differences were observed, can see what most of the sequence look like, and sometimes there's a difference. A bunch of these have these genes and these positions for example. Sometimes the changes lead to changes in some protein coding gene and could lead to a change in amino acid sequence. Can look for differences which alter protein. A newer paper - 90 whole genome sequences. Wait a few months and you get an even bigger paper, with even more amounts of data. On left is a picture from that article. So they did various things, one of them was apply non-metric multidimensional scaling. This is a fancy sophisticated computational technique which can be applied to large data sets. Don't need to know exactly what this is. If you become a progessional scientist, may find yourself faced with a very large data set and think 'what should I do with this' and you end up using some sophisticated tool, which might be quite complex and hard to understand, just enough to apply it and look at some results. This is the nature of modern microbiology. The data-sets are big and the methods used to analyse them can be quite sophisticated. In this case the point is to summarise a large data set that is multi-dimensional. On right is an even newer paper with 815 whole genome sequences from this year. The field moves very quickly, there's a slow start and then suddenly all these isolates of bacteria are being sequenced.

Which of the following antibiotics are properly matched with their target of action? - tetracycline-50S ribosomal subunit - aminoglycoside-50S ribosomal subunit - Platensimycin-lipid biosynthesis - macrolide-30S ribosomal subunit

Platensimycin-lipid biosynthesis

Of the following, which is the MOST common AIDS-associated opportunistic disease? - histoplasmosis - cryptosporidiosis - Pneumocystis carinii pneumonia - cryptococcosis

Pneumocystis carinii pneumonia

Environment of microorganisms in Vestfold Hills

Polar desert soils are underexplored. Not many macro-organisms, no human interactions Pretty much rock soil Pretty much no moisture or carbon Extremely arid Most of the years it's frozen, water will melt and then flow away Also arid Moisture is 4.4% Nutrient poor (0.17% carbon). Frozen majority of the year. No vascular plants. Little human/animal impact. Soils have up to 50% Low in carbon, nitrogen etc. The Vestfold Hills: Hyperarid: Its down to 0.42% moisture and severely nutrient limited (0.09% carbon) No vascular plants and large animal life Microbial diversity and functioning unknown. Who lives here and how do they survive? Shotgun sequencing to find types of bacteria that live there.

describe polyenes mode of action and their effectiveness

Polyenes are quite effective - they work agaisnt the big three major fungal pathogens. They are fungicidal, they kill it dead, rather than being fungistatic where they just inhibit growth. Interacts with only really ergosteral and not cholesterol. Amphotericin B gives ergosteral a hug and stops it from forming the double membrane. forms Pores in the membrane that are leaky and kills the cell causing them to burst. Can't work on zygomycetes and dermatophytes. It is Nephrotoxic - liver toxicity. Liver toxicity, because binding infinity from polyene to ergosterol wants to hug ergosterol only 10x more than cholesterol, so is toxic to us, particularly in the kidneys. but best you got. Only thing bad about them is you have to administer intravenously instead of oral tablets., they will be in hospital anyway because people who get invasive infectins are sick and in hospital already. It's pretty toxic. Resistance is known but uncommon

examples of drugs in each class:

Polyenes: Amphotericin B Azoles: Fluconazole Posaconazole Voriconazole echinocandins: Micafungin Caspofungin

What features would be required in a system to compare all life? Which is more important? (rank them) Present in all life Group morpholigically similar organisms together Group biochemically similar organsims Able to compare DISTANTLY related organisms Able to compare CLOSELY related organisms

Present in all life - #1 (important that we are comparing/observing is conserved in all life across all organisms if we are comparing) Morphological - not as important. Used to use it. Have convergent evolution where organisms look similar but at DNA sequence level are distantly related Biochemical - was used before we had ability to sequence organisms. Similar to morphological. Able to compare distantly related organisms #2 - want to be looking at something conserved enough that we are able to compare across a large evolutionary distances. E.g. compare bacteria to ourselves. Want to be able to differentiate closely related organisms (ideally) but there's a bit of a trade off there.

How can Pseudomembranous colitis be treated?

Previously to treat the disease was to give the drug an antibiotic called vanctomysm. Weird that misbalance of gut microbiota was due to antibiotcs and then giving antibiotcs again, and the abiility to recover using this method was quite low. Give antibiotcs, then give it again. In last ten years have seen advent of faecal micorbiota transplantation. Get healty donors which are screened to make sure they aren't carrying infectious disease, then use the faecal material to transfer into a person who has pseudomembranous colitis. This has shown to revolutionise the treatment. In fact, fro mstudies looking at changes in microbiota, they have now been able to do transplants wth specific bacteria present in it. In the faecal microbiota, transplant stools taken from healthy donor are used to replace patients microbiota in the colon. Extract pereperations vary, cant' be same person giving micorbiota every time. Usually is groups of people donating their faeces. The faecal microbiota transplantaion can be given in different ways can be given using endoscope down ino dmall intestine, or up from the rectum to large intestine. Have to wash out bad bacteria and put in the new bacteria. What has been shown with this disease is that FMT transplantaion has achieved over a 90% success rates.

describe the RNA virus replication cycle

Protection with genome in the middle, this finds the receptor, gets into the cell, the protein uncodes leaving the RNA. RNA needs to replicate, usually carry a viral polymerase and makes lots of copies of the genome. The RNA needs to be translated to make all the viral proteins, then capsid proteins and genome comes together and then assemble. Even though viruses are made of 240 proteins, they will assemble into an icosahedron in the cell. They package up RNA and then exit and when it leaves the cell picks up a bit of the plasma membrane.

___________ drives protons across the membrane through ATP synthase's proton channel.

Proton motive force.

what's a medical example of biofilms?

Pseudomonas aerigonsa - model organism for biofilms in lungs, and forms complications in cystic fibrosis patients. The EPS makes it so difficult to treat with antibiotics. They can't penetrate into the biofilm. Any other toxins or compounds can't break through. They are protected from shear stress (physical force) UV radiation and resistant to predators. Major predators of bacteria: Viruses, Protozoa & Bacteria

What is another life form discovered to produce methane?

Published march this year Pathway for biological methane production Bacteria iron-only nitrogenase Amount of methane they produce is small, but it's enough to allow a methylatrophic bacterium to grow. Pretty interesting. They speculate in this paper that the methane production contributes to interactions in the community so that these guys can have some sort of cyntrophic interaction.

What are cyanobacteria?

Range of different morphologies Unicellular or colonial. Can be free living or symbionts with coral or sponges as well. First organisms to have 2 photosystems PS1 and PS2 More efficient in terms of getting energy Pigments chl, a, d (and f!) phycobiliproteins Phycoerythin Phycocyanin * blue green colour Sometimes called blue-green algae. Really adaptable and have survived in nearly every type of environment. From the hot pools in yellow stone national park, to really dry valleys in antartica. Another one of interest is the stromatolites in different settings, particularly in australia.

What are Archaea?

Really important person who put archaea on the map, and made a huge impact in biology. Try think about ecology and evolution. If you are trying to learn a biochemical pathway and think 'why I have to remember this thing' when looking at phsysiology what matters is environment where it lives and evolutionary process that selected for it. If you think about that, allows you to ask why. If it does something then why does it do something. Need to think about the environmental setting. Very controversial (3.8 billion years ago) Carl woese - he's the man Demonstrated that prokaryote is a very educaitonally unsoud term to use, doesn't reflect how life evolved on the planet

HIV life cycle

Red arrows show three of six ways of drug targets. We now have integrase inhibitors to stop integrae from working. Virus finds CD4 receptor shown in yellow with its gp120 (glycoprotein 120) gets into the cell, gets its RNA out, usses its reverse transcription to turn RNA to Dna, the DNAgoes to the nucleaus. The integrase integrates it into the chromosome of CD4 positive cell, and then it can make message and more virus. Once it make message it can make all the proteins it needs for replicaiton and structure. They will assemble, transcription, assmebly of virus inside the cell and reelase by budding (no lysis). As the virus moves out of the cell, it will steal abit of the plasma membrane to use as an envelope, and coat its cell. The glycoproteins are already embedded in the membrane. It picks up its glycoproteins as it leaves.

describe Reduced permeability

Reduced entry of antibiotic into cell Outer and inner membranes of GNB prevent uptake of many antibiotics Vacomycin tolerant S. aureus (VISA) produves thicker cell walls. Penniciln can't get into GNB because of outer membrane - creates permeability barrier to prevent pennicilin coming back in. true of GPB as well. This is S. aureus - turns out that it can become tolerant to vancomycin by creating thicker cell walls. Vancomycin has to get into this division septum in order to be active. Having complex physiological changes allowing it to have thick cell wall make it more tolerable to vancomycin by reducing permeabilty among other things.

Describe some properties of enveloped viruses:

Released by budding mainly and cell lysis Environmentally sensitive: acid, detergent, desiccation (drying) and heat. Modify host cell membrane during replication - screw up cell membranes. Can get giant multi-nucleated cells. They will fuse multiple cell membranes together. Viral capsid, the viral proteins have already been made in cell and embedded in the virus. All viruses don't bother picking up proteins until they pick up envelope on exit of the cell. The virus is leaving, wrapping tiself with membrane and picking up its red glycoproteins. Consequences: Must remain in moist environments Like to be spread by respiratory droplets, sexual activity and blood to blood direct transmisiosn. Don't like being out of tbody too long. Can't survive in the GIT Doesn't always kill the cell to disseminate Protection from host immune system - disguised as a cell

What is mutualism?

Required interaction for two parties where both benefit. Can be macro and micro or micro and micro etc. - Aphids and buchnera - Corals and zooxanthellae - Lichens?

What is the restriction modification system that bacteria use against phages?

Restriciton modification system: Every bacteria has an enzyme that chops up DNA Each bacteria has its own restriction enzyme. That restriction enzyme doesn't cut its own dna because it methalates its own DNA which stops restrictio nenzume fro mworking. But when phage comes in its restriction enzyme will cut every 4000 base pairs and will chop up that phage DNA into quite a few different bits. The resitriction modeification system came from phages, the bacteria protects its own DNA by methylating but chops up any invading DNA using that enzyme.

Ribosomes are in which type of organism?

Ribosomes are in ALL organisms.

Who is Richard Lenski?

Richard Lenski is famous for long time evolution experiemnt which he set up 20-30 years ago. E.coli replicates about every 20min, so can get in a lot of generations and a lot of selective pressure over the course of his lifetime and can watch E Coli evolve over time. They have a culture of E. Coli (comensal organism) Has enoculated it using in thise case defined media, where he knows all the constituents in that media - all chemically defined Every day he subcultures them into a new flask of media. This has been going on for the last 20-30 years Have been evolving e coli in this. Important to note that E. Coli doesn't belong in laboratory. It's a commensal that colonises warm blooded mammals and also livesi nthe environemnt .happy living in equatic systems, in soil, and has a very diverse lifestyle. This is very restricted for it, it's a small niche and not used to growin in it.

What is richness and abundance? what's the difference?

Richness - how man species present in envirnment Abundance - one species dominate E.g. cyanobacterial bloom typically in a lake without this event happen, would have complex community. There would be high richness, with even abundamce (same/similar abundance of species). If you have an event, sometimes happens with a bloom, might have a lot of nutrients come into the system. Might have one or two species thrive and overtake. This is what happens during a bloom. What happens in microscope - one or two species which dominate. In that case have a low richness, and a high abundance of one or two. Means community is uneven. This is pertubation. If you have some sort of human impact on some sort of environment ,see a huge shift in community dynamics (what belinda is trying to study)

Rod shaped cells are called ________.

Rod

what are Neisseria meningitidis (meningitis) and neisseria gonorrhoeae (gonorrhea) and how do they hide fro adaptive immune system?

STD - colonies surfaces of urigenital stract. Major addhesion is Opa - it is an an adhesion on the ouside of the cell, and it is immunodominant. We readily develop antibodies against Opa which is a problem for this pathogen. It's living on the outisde of the cell and has to adapt to that immunoresponse. Bow tie is the Opa cell and it will adhere to the cells it will develop antibody against that. We can target it now and can start to clear the gonorrhoueae. Through antigenic variation the Neisseria can change the protein, so it can still adhere to tissues but now looks different so antibodies are no longer effective to it. It takes 5-7 days to develop antibodies, and every time there is a new 'disguise' we need to develop a new Opa antibody. Throuh antigenic variation it can persist in the face of the immune response.

Ways salmonella enterica severol typhi can overcome immune system.

Salmonella enterica seroval typhi causes typhoid fever - Get a rash then infectious bleed. Salmonella typhi invades epothelial cells and macrophages as well, it induces it's uptake into epolthelial cells - it makes the membrane ruffle around it and then it's engulfed b y the cell. When inside the cell it has virulence factors that allow it to prevent phagolysosome formation. This destructive vesicle doused with reactive oxygen and nitrogen species is actually blocked. It blocks the recruitment of nzumes to that vesicle Now its in a vesicle termred the salmonella vacuole It can replicate readily inside the cell, it has available al the nutrients and it's hidden away from the immune system Virulence factor is type 3 secretion system - way for the bactria to modify host cell process and block processes in side the cell Relpicates within host cell in specialised compartment termed the salmonella conaining vacuoe.

Describe example of salmonella and gene reduction

Salmonella is a really good example of this Salmonella has diverged from E. Coli from lateral gene transfer 100 million years ago S typhi is the second top cause of gastrointestinal disease in humans - common food poisining agent Has a broad host range, can effect a number of different animals There is a number of host-adapted salmonella species. For cattle we have salmonella dublin and for us we have salmonella typhi. Typhi causes severe systemic infection called typhoid fever. It is spread from human to human - host adapted and only infects us. If you compare the genome of salmonella typhi and typhimurium which has a very broad lifestyle we see that

foods most at risk for contamination

Shellfish (oyters, clams, muscles) Cooking process itself kills bacteria most of the time, except sporolating bacteria. Ready to eat foods that require handlng but no subsequent cooking Salads, peeled fruits, deli-sandwhiches, finger foods, Hors d'oeuvres Dips, communal foods - Pick bread roll up with your hand or your tongs Tongs have been touched by a thousand people who have their bread roll, five of those probably didn't wash their hands. You know you washed your hands

Frimbria are __________.

Short, hairlike extensions from the cell.

How is a phylogenetic tree constructed - give example of three speices?

Say we have these three species (on left) and want to know how they are related to each other. There are three possibilities. Want to use a mathematical model of what describes the evolutionary history of what we might call an evolutionary model. And compute the likely hood of each of the three scenarios. This s the basis of the maximum likelihood method for phylogenetic reconstruction, one method, many others. For each given tree, want to know what the probability is with observing the genetic states which you see. So when you align the seuqnces and see those differences, want to know what the probability is of observing that configuration of genetic states which you see, under some evolutionary model. You write down the probability that you get seuqneces that you see if tyou have this tree structure. One of these has the highest probability. That tree is the maximum likelihood tree. It's the one thaty ou pick because it's the one that is best abel to explain the genetic data you see. Want ot pick the explanation that gives you the highest probabilty of your observed information. The computer program will calculate all these probabilites, look at these different trees and pick one that it thinks is the highest probability

What are alphaproteobacteria?

Second largest class of proteobacteria Mostly obligate and facultative aerobes Many oligotrophic - low nutrient environments (good at growing in low nutrient environments) Includes rhizobales Named after polyphetic rhizobia. Many of them involved in nitrogen fixation Can grown in low nitrogen soils and fix nitrogen from the atmosphere. Are often associated with the roots of plants where they are able to fix nitrogen grom the atmosphere and supply nitrates and nitirtes which the plant needs to grow, directly to the plant. They can grow in specialised compartments in the roots called root nodules. The rickettsiales - intracellular parasites.

Describe some of the information you can get from sequencing E. Coli genome

Sequences get assembled into a big long thing for each genome. Here is an example of the E. Coli genome assembled from lots of little fragments. If we get the bioinformatics right we can draw a pic like this which depicts the whole genome and tries to show some features in the genome. This picture shows thingsl ike, where is the origin and the terminus, and it shows other features like where are there sime genes, maybe some of these are important from a microbiological point of view. That's four and something million base pairs. There's a lot of information just sitting there. What happens when we sequence a lot of individuals, a lot of isolates from the same species. Here is an example of what we might find.

Diagnostics of HCV

Serology (not useful in acute phase) Enzyme immunoassay (EIA) - looks for antibodies to virus (testing can be done after 3 months) Takes 3 months for antibodies to appear properly. Some patients take a year to sero-convert means get infected but antibodies don't appear for a year later. Quantitative RT-PCR is used to determine how much virus is in the blood and we can use that to find out how well the therapy is working. If you start iwht 10^6 viruses per ml of blood, then give you treatment for 2 weeks, and measure you again and it's gone down to 10^2, then have gotten rid of most of the viruses in your body and can monitor how well drug is working. Nucleic acid monitoring, quantitiative PCR or RT-PCR.

What are the diagnostics for enteric gastroenteritis?

Serology: Can use antibody tests to diagnose. Usual test for example measles is they look for anitbody in blood for measel viruses. For gastro - They look for viruses in the poo using antibodies A faecal sample os required to look for viral antigen by EIA or RT-PCR/PCR (em no longer used). EIAs detect viral capsid proteins which are present in huge numbers (10^8 viruses per g faeces for most enteric viruses) EIA's exist commercially for Norovirus, Rotavirus, adenovirus, and astrovirus but not for sapovirus. Molecular Methods: In recent years - most common system now is molecular tests. Used to use look for one virus for one test and now have multiplex PCRs. Hospital next door lok for six different viruses that cause gastro with one multiplex PCR test. Nucleic acid testing PCR based or RTPCR based is most common method now for looking for these viruses. If you find it, what are you going to do? No real treatment - Going to be on fluids anyways, going to take oral rehydration salts, because losing those salts, want to put glucose and minerals back into your body. Not much you can do, except does tlel you it isn't a bacteria and not to use antibiotics.

describe helical structure

Several RNA viruses undergo self asembly as a cylindrical nucleocapsid (hollow tube). More varied in their structure, can look circular and rod shaped. This is tobacomosaic virus. First one photographed with electron microscope. If you hear term nuecleocapsid in future it always means helical virus. This is because the proteins wind up with nucleic acid in the spiral like white picture. Have nucleic acid na and viral protein cp and is like a spiral staircase being made. On outside there is the protein,m on inside is nucleic acid. Protein protects the nucleic acid. Ebola would look like this. Generally helical viruses are RNA viruses and they have a matrix protein to stabilise the envelope and they are all enveloped . Enveloped viruses - can roughly figure out its transmission route (likes repspiratory and sexual transmission) not It has matrix protein, know it's RNA, know its helical, know it's enveloped. The RNA forms a spiral, each capsima consists of single protein, and all animal viruses with helical symmetry have an envelope and matrix proteins. Icosahedral is a little bit more common. Icosahedral may or may not be enveloped, all helical viruses are unless they are plant, because plants don't have plasma membranes they have cell walls.

What is the most fatal symptom of gastroenteritis?

Severe dehydration - Can't absorb fluids taking in, these kids are severely dehydrated. If you are dehydrated, it will fall back to normal position.

classification of fungal kingdom (spores)

Sexual spores are a result of the process of sporulation, which is essentially the process of miosis followed by spore formation. Basidiomycota - Basidiospore - conidium Asomycota - Ascospore - conidium Zygomycota - Zygospore - sporanggiospore Have very different structures Look very very different Can have an ascomycete but can't sporolate/produce sexual spores e.g. candida albicans Process of meiosis followed by spore formation, meisosis in the same way we produced eggs and sperm (haploid gametes produces) There are obvious differences between the spores. There are always exceptions Fungi can produce asexual spores, which is done to survive hard times, done by mitosis and then spore formation These are generally called conidia or singular conidium.

After performing a Gram stain, gram-negative cells appear __________, while gram-positive cells appear __________.

pink or red; purple

Why is the word prokaryote controversial?

Should we be talking about three fomains? Fundamental to our understanding of how life evolved. Archaea and bacteria are separate lineages, it has big flow on effect on how we interpret and evaluate what we see. Shouldn't use the word prokayote as it teaches the wrong idea of evolution . In this article written when he died, his work goes back to 1977 when he sequenced ribosomal RNA. Based on getting these sequences he discovered there were these three lineages that exist. Up until that point we did not have that molecular information. He goes on to talk about the eukaryote prokaryote problem. These three domain classifications are still widely accepted. But still somewhat controversial.

history of antiretroviral use

Since 1993 (high point) incidence of AIDS has been reduced by 4-fold. We got drugs, not as good as Hep C drugs because they never get rid of virus. If you stop taking drugs, virus comes back. But If you take the drugs, can reduce viral level to almost zero. First drug Zidovudine (AZT) -1987 Treatment of late stage AIDS patients increased their survival for several months They found this as a nucleocide analogue. It did work in patients for a few months but not for very long. In 1994 was used for use in preventing mother to child 25% chance of baby getting HIV was reduced to 6%,by giving the mother a dose of this drug before giving briht. The problem of using single drug on the virus: resisance to AZT quickly emerged - viral loads increased and progression to AIDS resumed. Viruses mutate very quickly, the base pair mutation required to overcome the drug, will happen very qucikly sooner or later. That's why drugs only last few months. Need combinational treatments all with different mechanisms used together. HIV antiretrovirals: Another major breakthrough because started combination therapy. Vented protease inhibitors, integrase inhibitors, sentry inhibitors. Combination Usually 3-4 different drugs in combination Reducing viral load to undetectable levels, slows the development of resistance Stop CD4 decline - extedning time to AIDS Decreasing transmission of HIV including vertical transmission

How do deletions and insertions happen with single bases?

Single bases - common method is slip stranding , if we have homopolymer repeats (repeats of particular nucleotides or motifs of nucleotides we can get puckering. One nucleotide will bulge out will still maintain base pairing because it is a homopolymer repeat. If that happens on template strand as we sunthesise our new strand of DNA it will get a deletion. The new strand is not copying this T so you get a deletion in the new strand which is propagated in daughter cell. Can conversely get an insertion, where the newly synthesised strand bulges. This does happen, and can get an insertion in the daughter cell. Can also have duplicaitons and inversions Our particular genes can be duplicated and inverted

What factors have been shown to lead to changes in the gut microbiota?

Single nucelotide polymorphisms (mutations in NOD2, IL23R, ATGI6L nd IGRM), lifestyle (diet and stress), early colonization (birth in hospitals, altered exposure to microbes), medical practices (vaccines, antibiotics, hygiene) Antibiotics change microbiota considerably. Depends on antibiotic used. If it's narrow spectrum then particular gorup (grma pos) wil be effective. If it's broad spectrum and can effect both gram and negative antibiotics, will see changes in both groups. This can lead to dysbiosis

How does recombination occur with phage and bacteria?

Site specific recombination system. This is the attachment phage, Attachment P and attachment B for bacteria. This is usually a conserved sequence in the E. coli that the phage recognises. These two join up, so we get cutting (restriction bit) and then lygation and production of the prophase. Its restriction enzyme and integrae.

Positive vs Negative RNA

Small pox is complex viruses. Other than small box, you are icosahedral if you are DNA virus. Can be enveloped like herpes virus or hep B or can be naked. If the viral genome is an negative sense it means it has to reverse compliment that into messenger RNA to get it translated. It's the opposite strand, has to be reverse complimented then can be translated. It's called a negative sense virus. Hep C and HIV are posiive sense cvirus. This means their genome is in the right setting to be translated directly. Genome can be genome or mRNA directly. If it's an RNA virus, don't have to go from DNA to RNA. Positive sense RNA virus can be directly translated with no replicaiton which means it doesn't need a polymerase. Negative viruses need polymerase on board, and reatro viruses do, positive sense viruses don't need polymerase in virion.

Relationship between soil bacteria and global processes

Soil microbes are critical to global processes. As we can't culture the majority of species metagenomics is being increasingly used to uncover new microbial metabolisms proving new understanding of key processes, especially for soil bacteria.

Missing piece in CO2 microbial fixation

Soil organisms, microbes fix carbon as well. Major stratefy usually photosynthesis (plants and microbes). Cyanobacteria use light as an energy source to fix carbon Then have other types of autotrophs that use chemicals; inorgaic molecules to provide energy to fix carbon Phototrophy vs chemotorphy Autotrophs - fix carbon Heterotrophs - eat it Thought two forms to carry out this process - through light or inorganic material But some environments - there was no evidence for photosynthesis happening and not high amounts of inorganic chemicals. Nutrient poor arid soils. Trying to find out how they are surviving.

What are the physiological and pathological roles of gut microbial metabolites?

Soluble dietary fibers Fructans, pectinm inulin, xylans, and resistant starch are activey fermented by commensal microbiota in the colon Produciton of short chain fatty acids: acetate, prupionate and butyrate have beneficial effects on intestinal epithelium and the gut immune system (anti-inflammatory) A high fat diet and inflammation - dysbiosis and an altered metabolic produle in the intestinal lumen, implicated in systemic and gatrointestinal disorders.

How to laterally transfer DNA?

Some bacteria are determined naturally competent and are able to take up DNA from the environment As bacteria grow or populations they are lysing and are releasing DNA into the environment. Some bacteria can scavenge that DNA and stick it into the cell and into their chromosomes and see if it helps them in some way Transformation - transfer of naked DNA between bacteria Transduction - gene trasnfer mediated by bacterial viruses called bacteriophage Viruses can move DNA between bacterial species Conjugation - movement of DNA among plasmids

The human oral flora consists of... - monoculture biofilms on tooth surfaces. - a small group of phylogenetically related aerobic microorganisms. - diverse aerobic and anaerobic microorganisms. - the same phyla that are found in the human gut.

diverse aerobic and anaerobic microorganisms.

what is antibiotic inactivation through cleavage?

Some enzymes will cleave the antibiotic. Best example is for the beta-lactamases that pennicilin was a member of. Beta-lactamases confer resistance by cleaving lactam ring required for activity. Once this ring is borken, the antibiotics are no longer active, and can no longer bind to pennicilin binding proteins and no longer has activity.

What are some organisms who have relationships with methanogens?

Some methanogens on a protozoa. Have cyntrophic relaitonship with orgnaism, they live togther. Deep in ocena there are methan hydrates, because of pressure and temperature you get this gel like material (methane hydratE). If you can see on this yellow hydrate there are these worms liiving there. These worms we think eat methanogens. One group publisehd in 2012 was first attempt to get a polycete (a little worm) and found out they can actually get it to grow by eating archaea. First experiment showing they can be a food source.

How do pathogens overcome phagocytes?

Some pathogens are able to prevent digestion by phagocytic cells. Inhibit recruitment of neutrophils - Inactivation of complement through capsule or proteases Processes are highly inter-linked If you prevent activation of compliment, with capsule will prevent to some degree the recruitment of phagocytic cells on the site Once compliment is activated, it releases signals to the phagocytes to attract them in and tell them to engulf the bacteria. Kill phagocytic cells - streptococcus Production of toxins termed leukocidins that kill neutrophils and macrophages Escape injection by phagocytic cells Prevent recoginition by phagocytic cells: Capsule - Prevents phagocytic cell from getting a good purchase on the bacteria and engulfing it and destroying it. Some capsules can slip away from phagocytic cell Protein A binds antibodies at the wrong end. Perevents phagocytic cell from getting a good purchase on the bacteria and engulfing it and destroying it. Some capsules can slip away from phagocytic cell. Some bacterial pathogens are able to live inside host cells Nutrient rich niche - All nutrients not previously available will now be there, and can grow and replicate using the nutrients needed in the host cell cytoplasm. Hidden from immune system.

A small farm pond containing many species of microorganisms (bacteria, cyanobacteria, algae, and protozoa) was perturbed when runoff from a manure pile entered the pond. The added nutrients soon turned the water green due to a bloom of cyanobacteria. How did this affect the microbial community in the pond?

Species richness decreased and species abundance increased.

Wavy shaped cells are called ________.

Spirillium

What are bacteria phyla?

Started using 16S ribosomal rna to classify diversity of microorganisms people were identifying At the time people were using biochemical tests to characterise microorganisms and work out which oens are most closely related to eahcohter. Went to different labs and found cultures of microorganisms and sequencing the ribosomal RNA from those cultured orgnaisms By 1987 he was able to classify all the microoganisms he was sequencing into 11 phyla Today, 40-50 years later we have 29 phyla We are also able to sequence DNA directly from environmental samples. We know there are at least 70 other phyla which we haven't been able to culture in the laboratory and characterise in a laboratory. The conditions sing in laboratory are not permissive to get those microorganisms A huge amount of 'dark' microbial matter which we haven't been able to culture Probably have about 100 phyla Those with proper names have been characterised in the laboratory, isolated and determined what biochemical and phenotypic characteristics are Systemic names (letters and numbers) haven't been cultured. But we know they exist because we see there RNA when sequencing environmental samples.

What are the clinical symptoms of gastroenteritis?

Study done 10 years ago - orovirus outbreak in nursing home Symptoms lasted median of 2 days, range 0-3 days Common clinical manifestations: vomiting, diarrhoea and nausea The courier who had norovirus walked into ward where sick people were kept and vomitted on the floor. And this lead to norovirus outbreak where 70 people got sick. Asked the people what the main symptoms they had are. Some people get vomiting and no diarrhoea some people get just one.

In 2003, the majority of AIDS deaths occurred in...

Sub-Saharan Africa.

What would happen to an obligate aerobe if cytochrome oxidase were affected by an inhibitor?

The electron transport chain would stop functioning properly and the organism might die from lack of ATP.

Epidemiological studies of AIDS in Africa have confirmed that ________ transmission of the virus is the norm in that region.

heterosexual

diseases caused by Candida Albicans (superficial)

Superficial - on surface of you, not invasice. Although not pleasant, will never kill you. Candida often called thrush lots of different kinds of thrush. Oral thrush often get it in the mouths of AIDS patients and babies. Get it in babies because they don't have have well developed immune system or microbiota to compete with candida at that site. When immune supressed can have overgrowth. Generally only happens because it is an overgrowth of a pre-existing fungus. Happens due to a lack of competition with bacteria that also occupy that space. Not an infection per say, it is an overgrowth of fungus that is already there because the other microorganisms in the microbiota are depleted Also can get nappy rash, caused by candida species. Women often get thrush of the vagina when they are on antibiotics, because there is a depletion of bacteria (When on the antibiotics) and there is an overgrowth of candida in that area. Once you stop source of antibiotics, the bacteria will come back and the candia will be out-competed and go back to a normal level. Superficial, transient, unpleasent, never kill you. Quite rare: Candida Intertrigo - in between your fingers on the skin Can also get thrush on the nails

what is chornic mucocutaneous?

Superficial fungal infection caused by candida, chornic mucocutaneous candida. This man has an auto-immune disease caleld APECED - this is an unusual combined immune and endocrine dysfunction. The candida infection won't kill him but outlook is not great.

seriousness of invasive fungal infections

Superficial infections can be unpleasant and affect 25% of world population. They are unpleasent but won't kill you. There are plenty that will kill you. Opportunistic invasive fungal infections - very serious and will kill you Red is top 5 causative agents of systemic fungal diseases. More people die from invasive fungal diseases than from tuberculosis or malaria 2 million life-threatening infections per year world wide (from just these 5) Mortality 20-95% depending on which one it is (this is with anti-fingal intervention)

what are different types of fungal infections? list some in each category

Superficial infections: Diseases caused by the dermatophytes, Ringworm and athelte's foot are all under tinea. Diseases caused by candida spp: thrush in: mouth, vagina, penis, nails and skin. Invasive systemic infections: Candidiasis Aspergillosis Cryptococcosis Mucormycosis Pneumocystis Superficial infections caused mainly by dermatophytes and candida species Demadophytes are spoken about pretty much all of the time, so read a text book if want to know more. Superficial infections affect 25% of world's population

Flagella allow the cell to ______.

Swim (running and tumbling)

what is target modification?

Target modification: Modification of the bacterial target can prevent antibiotic binding conferring resistance. Point mutations at target site, biochemical modification e.g. methulation. Many of these antibiotics have very specific targets .e.g cell wall synthesis or protein synthesis (ribosomes) If you accumulate mutations in these targets, you can change their binding affinity to a particular anitbiotic. It may come at fitness cost, but because antibiotics are going to kill everyone else, doesn't matter if you're 50% less fit, because you are still alive. Can accumulate point mutations which is probably what we saw in large petri dish from harvard med. Can also have biochemical modification such as methylation of phorsphoylation of a particular target that will prevent antibiotic from binding to its active site.

What did the lecturer do in his study? what was the method?

Team looking at how these organisms interact with each other, particularly their adaptive responses, cycling of nutrients and looking for novel microorganisms, that help us understand how these ecosystem could have survived for so long through the history of life on earth. (look at stromatolites as a winogradsky column - but also interaction with light is different at different columns) An example of power of next generation sequencing. Can look at these systems at a mm level and we can sequence all the DNA at everhy mm and can identify which organisms are there. Can start to get a really good handle on who is wehre and that can give us inference on how they are interacting

What binds the layers of petidoglycan in Gram-positive cell walls?

Teichoic acids

how were viruses discovered?

That's how they were discovered. They can pass through a 0.22 microm filter. Bacteria can't pass through that cause they are about 1-2 micron in size. How they were discovered is we took a disease (say we had a diseased rabbit( we took the diseased material, took it through one of these filters knowing that bacteria can't pass through these filters, and we took what came through the other end of the filter and injected a new rabbit. If that rabbit got a disease. If the rabbit got the disease then it was caused by something different to a bacteria, something smaller than a bacteria. And that;s how we knew without seeing viruses (until 1950s) that they were there.

Describe soil as a habitat for soil microorganisms

That's soil at landscape/site level. Soil often analysed at 1 g level. Many biogeochemical processes occur at scales relevent to this unit e.g. gas diffusion and water movement create microsites and gradients. Half the volume is void space (pores) connected by totuous pathways with a range of pore neck sizes. Relationships between interconnecting pathways, channesl and pores provides the microhabitat space (niche) for soil microbes. When lookin at diversity in soil, 1. Soil habitat - where little communities can grow, can be analysed at aggregate level. In soil get little grains, is a whole community per grain. 2. Different types of particles - big sand, small clay, organisms secreting EPS forming different structures in that aggregate. Aggregates are potential niches or habitats for one of more species of soil microorganisms. Can have pores, oxic, anoxic areas, areas of organic matter. Different communities in soil particle. Different niches drive community structure

Which of the following is NOT true of human gut microbes? - They produce and excrete amino acids. - They are involved in the "maturing" of the gastrointestinal tract. - The population size is low, but diversity is high. - They help catabolize polysaccharides.

The population size is low, but diversity is high.

Describe example of strong cooperative relationship between organisms (bobtail squid and aliivibrio fischeri)

The Hawaiian bobtail squid. Researchers are interested in how it has this light organ, which is jam packed with a bacter called aliivibrio fischeri. It is famous because it luminesces at high cell densities. In sea water at 100 cells per ml and will spend all its energy glowing but no one will see it. When it's in the light organ, can reach high cell density (10^10-10^11 cells/ml) can luminesce together to help symbiosis. Benefit to squid - it's predation protection. Other organisms use light organs to square predators away. It deposits the vibrio in the sand, it hides in the it in the sand. At night it comes back for a new innoculum of this bacteria into its light organ and at night at maximum capacity, full healthy and luminescence. This lasts the night. It confuses predators as to where it is - it shadows. It's a tight interaction that it has.

If you fixed a sample from a week old culture of E.coli on a glass slide and stained it, what would your results look like?

The bacteria may not be uniform in color after the staining procedure due to dead cells and cellular debris.

What other organisms can you get in microbiome, other than bacteria?

The bacterial composition is represented by the six most commonly detected phyla: actinobacteria, bacteriodetes, cyanobacteria, firmicutes, fusobacteria and proteobacteria. Fundal compositiong: the most prominent genera are: aspergillus, candida, malassezia, cladosporium and saccharomyces. viral composition: pacteriophages or eukaryotic viruses.

What occurs during viral uncoating? - The viral proteins are synthesized. - The viral envelope is released. - The nucleic acid breaks apart, allowing for translation. - The capsid breaks apart, releasing the viral genome.

The capsid breaks apart, releasing the viral genome.

Anabolic reactions are driven by _______.

The cleaving of the third phosphate of ATP.

What is in our microbiome?

The collection of microorganisms (bacteria, fungi and viruses) that inhabit specific regions on and within our body. Can look at it as a 'mini-ecosystem' The human microbiome is composed of a range of different microbial communities that compose a range of different microorganisms. That relates really to enviornment. E,g, skin is a really dry environemnt, and temeprature is a little lower, so microorganisms that are there are different on our skin vs those in our gut or in our throat inside our body where we have normal flora.

From sequencing and analysis, what information can you find about genomes of a whole species, and comparing individuals.

The core genome is a set of genes shared by all the genomes of the same species. As you add more and more complete genomes, the number of genes that are shared (proton coding genes) stabilises. At first there is a little drop, because you discover there are some genomes that don't have this gene and that gene, but as you add more and more genome, you find they all share this number of genes. But then you also find, but then you also find other genes that can be found in some genomes but not in others. So they are the non-core genes. So the number of those increases a lot. As you add more and more genomes, you get more and more of those genes which are not shared by all the genomes. This picture shows us that this number seems to keep growing, we get more nad more genes which we see in some isolates but not others. We see all sorts of other features in genomes, where the genes are, what sort of orientations they are in, if they do similar things if they are close together? We find some genomes undergoing decay, there are lots of genes, reminents of genes that are no long er funcitoning as genes (pseudo genes). We also know proportion of genome which is protein coding (87%) but it varies depending on species you are looking at.

Which of the following is NOT true for both hepatitis B and hepatitis C infection? - The disease is prevented by vaccination. - Diagnosis can be achieved through testing the blood for antibodies. - The infection is transmitted through blood and body fluids. - The virus can cause a chronic disease.

The disease is prevented by vaccination. (There is a vaccine for Hep B)

What was the drug used to cure Anne Miller?

The experimental drug was penicillin. A 'miracle' compound the effects of which were discovered by Alexander Fleming and eventually purified by Howard Florey and Ernst Boris Chain. The 5.5 g was hald the world's supply at the time. It was really difficult to purify this antimicrobial and they put half merricks supply into anne miller. They collected her urine to retrieve 70% of the antibiotic back. Since then, penicillin is estimated to have saved the lives of between 50-200 million people. In the following 60 years of Mrs Miller's life we have witnessed an amazing window of partial relief form many bacterial scourges that have haunted our species and those of many animals we share the planet with.

How diverse can things live? name some extreme environments archaea can live in.

The fact that you can find archaea in particular living in these human extreme environments (depends on what we call extreme) proliferated in journals Can ask the question - how diverse and extreme What do you need to get that temperature? Need high pressure. What is used for producing high presure and high temperature used for sterliisation Grows in an autoclave (122 degrees celcius)- big pressure cooker Where do u find such high pressure - deep in the ocean hyrothermal vents. Under the pressure water, get to such high temeprature without it boiling If you are in bottom of mariana trench - like two elephants standing on a ten cent piece. These organisms often require that pressure to grow. Take them to the surface and they explore. World record omes from area in japan near volcano in soil called pycrophilus. It likes 0.7 (optimal pH) and 60 degrees. That's like grabbing battery from your car and heating it up to 60 degrees and that's what it likes growing in At least to about -20. as logn as you can maintain liquid water you can see growht. How do you matinain liquid water at -20? Pressure? Salt!! One lake in antartica gets to -20 and doesn't freexe because it's hyper saline Coldest known e vironment to support life Colouration you see from saltants is due to growth of halophiles, and sometimes algae. They grow in saturated salt Origin energy. Isolated an organsims (baceria( that can grow benzene for breakfast which is top ten carcinogen in the world.

Why base phylogenetics off the SSU rRNA gene?

The fantastic thing about small unit ribosomal RNA is that it's present in all living organisms but also provides sufficient conserved sequences and variable sequences that we can start to compare closely and distantly related organisms. For the most part very conserved, can't have point mutations without preventing the ribsoomes to make protein, which is fatal to the cell. Does have nine regions that we designate 1-9 that arem ore variable that the rest. This occurs on outside of organisms and less selective pressure - can change a little bit Can compare using conserved parts and can look at more variable regions and get higher rate of mutations and start to look at more closely related organisms and compare them and qork out how close they are. SSU rRNA provides sufficient sequence information (variable and invariant regions) to permit statistically significant comparisons between homologues. Large databases now. Have been sequencing for quite some time. Huge databases. Can compare new ribosomal Rna sequence and work out exactly what your sequence is most similar to.

How does diet effect gut microbiota?

The food we consume feeds not only us, but also a vast and diverse community of micrbiota within our gastrointestinal tract. Mounting in vitro and in vivo evidence suggests that DIET selects for the gut microbiota composition and that several health promoting and deleterious effects of fiet are mediated by the gut microbiota.

what is the relationship between gut microbiota and IBS?

The gut microbiota modulates the pathophysiological mechanisms underlying IBS Gastrointestinal motility Sensation Immune activation Intestinal Barrier Function Gut brain axis Gut microbiota composition on IBS is affected by a number of underlying risk factors: Host genetics, stress, diet, antibiotics usage and early childhood experiences

what diseases do gut microbiota play important role in?

The gut microbiota play an important tole in Pseudomembranous colitis Inflammatory bowel disease Crohn's disease Ulcerative colitis Irritable bowel syndrome Coeliac disease Colorectal cancer

What is lysogeny?

The indefinite persistence of the phage DNA in the host cells, without phage production Temeperate phages: can produce the phenomenon of lysogeny which means it higes in DNA of E.Coli Prophages: the integrated non-infectious form of phages (this is the result of lysogeny) replicates when bug replicates and is a very clever way to hide.

Use lambda as an example to explain gene suppression in lysogenic cycle

The life cycle of lmbda phages is controlled by cl and Cro proteins. The lambda phage will remain in the lysogenic state if cl proteins predominate - when nutrients are low C1is stable and leads to lysogenic cycle (these are bad conditions) Cl repressor turns off phage transcriptor Integrase catalyzes integration of lambda DNA into bacterial chromosome via short sites of homology (site-specific recombination) - prophage The phage will transform to the lytic cycle if cro proteins predominate. Lets say food suddenly comes up, the phage now wants to come out. And knows if it comes out now ther will be lots of bacteria around. When nutrients are high, more proteases are in the cell and leads to breakdown of repressor cl-leading to lytic cycle. Allowing for more Cro, which leads to lytic cycle.

What are lokiarchaeot

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. In terms of where eukaryotes come from, us plants etc. where that branch point is, what they are related to is contentious, we actually still don't know. But we can infer and that's what comes from these sorts of analysies. What they get on to say is that they discover this group called lokiarchaeota They discovered that they think that eukaryotes literally branched off from archaea. Which is interesting The lokiarchaeota bit where they came from is a hydrothermal vent. This one isn't super hot, so could be where life potentially coud have evolved. The term lokiarchoeota come from the norse god of fire and trickery, Used because of confusion of origin of eukaryotes Provides information of where eukaryotes could have come form, and reflects its uncertainty Come into biology and think everything is known. Even some fundamental stuff is not really well known

Haloarchaea adaptation to high salt...

high intracellular salt, entire cellular medium has adapted

What is the source of our microbiome?

The source of microbiome: Majority of our microbiota comes from other humans Newborn babies encouter microbes for the first time during birth when they are coated with microbes from their mother's birth canal. In general have bacteria on their skin that reflects organisms present in the vagine Babies born by cesarean section fist encounter microbes from the mother's skim amd frpm other individuals who touch the baby .

How is anaerobic respiration different from aerobic respiration?

The terminal electron acceptor in anaerobic respiration is not oxygen.

How do we classify archaea?

The three domains are the Archaea, Bacteria and Eucarya Domain is highest level of taxanomic division. Another term floating around is sort of kingdom, and it's called super-phylum. There's always new terminoogy, and its always important to learn how people are using so you understand what the meaning is. At least four archaeal kingdoms have been proposed. Many isolates in euryarchaeota and crenarchaetoa - things we can grow in the lab. We can grow them, manipulate them. We can learn more easily about them because we can manipulate them. The other one, we have no isolates here, we only know about them from sequences of samples. Paper in nature 2013 - shows this explosion of discovery of microbial dark matter (sexy way of discovering things we don't know). If you go to archaea, theres a whole bunch of other ones here. Now put them into two categoreis. Tack and dpann. In a couple of years found out so much more

What would be the fate of a lytic bacteriophage if the host cell died prior to the assembly stage?

The virus would not be able to infect new hosts.

Which of the following is a similarity between Archaea and Eukarya? - Their cell membranes are the same. - Their DNA is complexed with histones. - They have identical RNA polymerases. - They both have peptidoglycan.

Their DNA is complexed with histones.

What is pyrrolysine?

There are 20 amino acids. In fact theres not - there's 22. pyrrolysine is 22nd o be disocveded. 21st one is (selinosistine ) not all organisms have these. Pyrrolysine was discored in 2002 Science paper. Can see pyrolysine compared to lysine and there is a complete system for tRNA, there is synthatase, its charge, added on. It can be encorporate. Not all organisms have it. In 2004 running some protein gels, a pand at 62kDa, did mass spectromety to determine identity of protein was and matched with tehese reading frames. Pyrrikysine gets encoroprated in UAG which is a stop codon.

What are some extra-terrestrial uses for microorganisms? what are the two different approaches?

There are missions to send out vehicles to eplore. One side of the coin is, get prepulsion laboratory wants to make sure that if they use special facilities IVC facilities, to make a spacecraft that has less than 3 spores per spacecraft. Don't want to contaminate environment it's going to. They found this oeganism on titanium surface of the space craft. By using huge amounts of gama rays and ultravoilet, it killed everything else off and made a nice place for this bacterium to grow. Never seen before, new lineage. Microbes will find a way, interesting to think about how they can react. Terraforming - wanting to use methanogens from Antarctica as the base (If they can use CO2 and hydrogen) then they can grow then they can produce organic matter which can then feed on to produce organic matter and change the environent to a planet we can live on.

where is Saccharomyces cerevisiae found?

There has been a lot of work done on wild yeast by winemakers. You can make wine without adding any yeast. There is sometimes enough wild yeast on the grapes so that it will do it itself. Have been doing seuqncing genomes of wild yeast to see what's different to production yeast. Advantage of wild yeast - lots of different flavours can be produced, good for making boutique wines. Disadvantage - can't get consistent flavours from batch to batch

Why is there such a difference between the flora in the duodenum and that in the ileum?

There is a large pH difference between these regions of the small intestine.

What was growing in polar desert soils?

Two types of phyla: phyla we know nothing about were thriving. Diversity different to typical soils. Candidate phyla dominated windmill island soils. Up to 24% WPS-2 and 17% AD3 (novel phyla) antinobacteria dominate Vestfold hills. Very little phototrophic species. Really weird - not happening anywhere else on Earth High abundance of these two candidate divisions that dominated is rare. Published a paper in nature describing what bacteria do They are renaming them These organisms were thriving, what they found was through bioinformatics can pull out draft genomes from shotgun sequencing. Teamed up with group in queensland that made first draft sequence to find out why they dominate polar desert soils.

What do we do, when we are analysing large amounts of mutations? not just SNPS?

There will also be some variants which are not single nucleotide differences, they will be someitmes bigger changes like insertion or deletion (or three-4 bases) could be incersions and rearrangements. All of this info is telling us some osrt of informaiton, about the history of genomes we are looking at. This is the result of a huge amount of sequencing. Most sites were not vairable. Seems redundant to do a massive amount of sequencing to find out that millions of sites are not variable at all across these isolates. That is still telling us information, cause we didn't know tha they weren't variable before the seuqncing. Can boil it down to tiny little table. Can tell us where differences are and which genes are effected by mutation, and what consequences are. Pic on left of evolutionary history slide, is a phylogenetic tree. This shows us the evolutionary history of the isolates in question (what we call taxa). Want to know how these different taxa are related to each other. This tells us that these three are very closely related to each other (in fact identical) and these are also similar to each other and quite different from these ones. Tree shows us exactly what the hisotyr would have been. How do we use the information to generate evolutionary histoyr.

If the biochemical oxygen demand (BOD) of a lake is very high, how will that affect the aquatic life in the lake?

There will be less oxygen available for the aquatic life due to the microbial activity.

Where are mitochondria and chloroplasts on phylogenetic tree? Why are they there?

These are bacteria...or are they? Wedged within the kingdom of bacteria are mitochondria and choloroplasts. Reason is that we believe that these organelles were actually bacteria that became endosymbionts of eukaryotic cells very early on in the branching of phylogenetic tree Reason we think that - is that they actually have their own genomes. If we sequence those genomes, they have 16s ribosomal Rna like a bacteria. Because they have 16s ribosomal RNA we can add them to the phylogenetic tree. Chloroplasts cluster very closely to cyanobacteria and they are photosynthetic bacteria that are thought to involve in generating photogenic atmosphere easlry on Mitochondria are energy making part of cell, and cluster closely to alphaproteobacteria. These included Wolbachia which are intracellular parasites. So dieas is that these organelles were in fact at one stage bacteria that became endodsymbionts of the eukaryotic cell which gave up some of their functions.

Highly alkaline environments, like those in which haloalkaliphiles are found, are best described by which of the following statements? - These environments contain relatively low concentrations of hydrogen ions. - Without knowing the specific molecules present it is impossible to know if they are electron acceptors or electron donors. - These environments contain equal concentrations of hydrogen and hydroxide ions. - These environments contain relatively high concentrations of hydrogen ions.

These environments contain relatively low concentrations of hydrogen ions.

How is it possible for haloarchaea to survive in environments such as the Great Salt Lake without lysis?

They accumulate compatible solutes to prevent water loss.

How are viruses parasites? why are they? what do they parisitise?

They are parasites, they parasatise the cell for translational machinery. No virus can make proteins, no cirus can do translation. They can do transcription, but fant do protein making. The main thing they parasitise is the protein machinery from the cell. They steal it, shut down what ribosome was making for the cell, and force it to make the viral protein. Some viruses also will parasitise replication process of the cell. E.g. parvo virus needs human polymerase to replicate its own genome. Lots of viruses have replicatory machinery, smaller viruses don't.

What are the properties of viruses?

They can pass through a 0.22 microm filter. They are parasites There is one species of nucleic acid (DNA or RNA) and it can have many types of configurations. We just have linear double strandard DNA. They gcan have single stranded, circulaer, RNA, segmented RNA, all sorts of configurations of RNA. All viruses have a component. They have to be abel to get into the cell. They have a component of the surface of the virus that enables them to find a cellular receptor and then get inside the cell. E.g. HIV attacks immune cells and what it looks for in the properties of that cell is the CD4 receptor on the top of immune cells. Most cells have this receptor so HIV can affect them. It uses their GP41 and 120 glycoproteins to bind with the receptor to get inside. They need a key to unlock the door of the cell. They take over the cell, the cell ends up dying or kills itself through apoptosis and the virus comes out.

How do antibiotics work?

They exploit differences so that they can particularly target fundamental prcesses in the bacterial cell. Bacteria have peptidoglycan that is required to resist turgor pressure in cell, cytoplasmic membrane has no mechanism of doing that. Pennicilin inhibits cell wall synthesis. If you interupt cell will lyse. DNA gyrasce is important for DNA unwinding A lot of them target protein synthesis Can specifically target bacterial ribosomes with compounds Some now target lipid biosynthesis as well.

semi-synthetic penicillin

They had a look at penniclin and deicded the problem was the side chain. Started to make modifications so they put in a amine group or carboxyl group and they could then give it to a gram negative bacteria and it was able to be aken thorugh gram negative porins. These are pores in the outer membrane that allow solutes to come in and out of outer membrane. By changing the charge on very hydrophobic ring they could make it more soluble and to go intothe porins and get access to pennicilin binding proteins. They invented ampicillin and carbenicillin. These are active a gainst gram negatives, as they are sem-synthetic derrivatives that can go through gram neg porins. This is how we get from first generation to third fourht fifth etc. generation antibiotcs. By incrementally improving them by changing chemical structure to give them better properties. This isn't exclusive to pennicilin, is done for all antibiotics, they are all derrivitives of classes. That's how we have classes with lots of different antibiotics in them. They are all semi-synthetic or natural derivitives of the same one.

The virus repressor protein... - controls the prophage's lytic genes but not the incoming genomes of the same virus. - has different actions in different situations. - does not control the prophage's lytic genes but does control the incoming genomes of the same virus. - controls both the lytic genes on the prophage and prevents an incoming virus of the same type.

controls both the lytic genes on the prophage and prevents an incoming virus of the same type.

Give an example of how a research group analysed data for transmission of a bacteria

They set up a simulation like this and they said suppose there is some mutation process as you get transmission of this organism, and then we can count how many SNPS accumulated since the original strain. That's what the colour scale is. The more blue dots, the more mutations have accumulated. We can show where the transmission events occurred as well. Again we can combine these two different processes. The transmission of the bacterium, along with its mutation. It's kind of a virtual population. We can use that to see what we expect. What sort of variation would we expect? Having that understanding is going to help us analyse real data. Another example by sae group (on the left) this time saying what if we have some number of hosts, and there is some kind of structure among those hosts, some of those interact with others but not everyone interacts with everybody. So if you set up some kind of contact network structure, then that imposes constraints on how the bacterium can spread in a population. If you superimpose some sort of genetic and evolutionary process, you can come up with a computer simulation of a sort of variation you can see in nature and compare that with a real data set to make some inferences.

describe azoles mode of action and their effectiveness

They target the enzyme that is involved in the biosynthesis of ergosteral, not the ergosteral itself. They are quite good against candida species and cryptococcus species but don't work against aspergillous species. They are a lot less toxic than polyenes. In early 80s that's when HIV epidemic hit in westenr world. Clinicians were seeing a lot of oppurtunistic pathogens, particulalry oral thrush. Good indication that smeone is immunosupressed. Can take some of them orally. Inhibit Erg 11 - in biosynthesis of ergosterol, in any biosynthetic pthway, you have a substrate which is acted on by an enzyme which turns it into a product which is a substrate for next reaction for biosynthetic pathway and so on until you reach final product. Erg 11 sits early on in the pathway and when you don't have Erg 11 have a build up in substrate for this enzyme which eventually when it builds up enough can be acted on by Erg 3 which is a toxix sterol in the membrane which causes membrane stress, that's how this inhibits growth. They are fungistatic, not fungicidal. Resistance is a huge problem. Have to be careful with what other treatments you are giving a patient when you are giving azoles because there a lot of non-helpful interactions between the drug. Can't work on aspergillus and zygomycetes

Are Gram-positive cell walls thick or thin?

Thick, many layers of peptidoglycan

Are Gram-negative cell walls thick or thin?

Thin, and surrounded by a 2nd membrane

discovery of Hep C

This chimp was infected with hep c from patient that had hep C. now chimp is infected. Not able to do these experiments now, cause not ethically good idea. Hep C genome is in this chimp. We go to cDNA library of all the RNA from chimpanzee. Not just chimp's genes but every infecting viral gene as well would be part of that library. This library was made in lamda GT10. It is a temperate virus with a lytic and lysogenic cycle. So if the insert goes in (Echo1 fragment with 20,000 base pairs) all the RNA in the chimp was chopped up into these fragments and were inserted into lamda, and if the insert went in, you got a lytic cycle and if it didn't you got a lysogenic cycle. It's a cloning method. Then plate out plaques. Each one of the plaques has a different bit of RNA in it from the chimp, and one of them in it will have RNA virus in it. Screen millions of these plaques looking for the viral genome. To screen it, use antibodies form serum from patient that they knew had the disease (hep C). When you screen library with human serum, one of the clones lit up, so it reacted to the serum from the patient with hep C infection, then they sequence the clone and find nearly whole virus genome in one go. Lead immediately to tests to detect hep C and then next thing happened, took all contaminated blood out of the system, no transfussions therefore happened with blood that had hep C. Lead to diagnosis and then later on, treatment and cure to hep C.

What is the timeline in our understanding of archaea?

This graph shows the increase in knowledge over time, increase in data associated with archaea, and this was published in 2011, and it has contineud up and up. Hardly any understanding before 1990, and exponentially as increased, esepcially between 2000-2010.

What is LUCA? why is LUCA important in phylogenetic system?

This is a phylogenetic tree of life. It's a different representation as a circle like it more, it shows the bacteria form the vast majority of species on earth. Realistically should be much much bigger In the centre is LUCA - last universal common ancestor When thinking about features we can use to compare between all of this life on outside of the circle we will be thinking of features present in the last universal common ancestor.

How did HIV develop?

This is from colleague Eddie Hoades who works at Sydney uni he is a famous RNA virologist. Found out that somewhere between 1890-1920, these are small monkeys and they all have these simeon viruses (related immuno-defficiancy viruses) the chimpanzee eats these small monkeys for breakfast. It goes hunting them and eating them. It hunted a few, and hunting and eating them created a recombinant virus, which was half one virus and half the other. It got into the chimpanzee, it's a hybrid virus, and because it was a hybrid virus it was able to infect humans and transmit from human to human. It was basically a big mutation that created a hybrid virus that was transmitted from people eating bush meat, and if you are hunting the monkey and monkey scratches you you can get their viruses. Was a recombination of two viruses that created HIV.

What study did lecturer do and what did they find?

This is the coldest environment on the planet known to support life. Bucketing water to sample water and filter it away to study samples. Took samples down though water column. Water is brought back and filtered through samples - sequential filtration from here onto here onto here etc. capture the biomass so then we can do metagenomics (environmental genomics) Instead of looking at individual orgnaism try to understand whole community. Lake in winter, water gets to minus 20 and air -40, and still doesn't freeze cause it's so salty. Get promiscuous haloarchaea in there. Each outside bar represents a genome, 1,2,3 &4. four different organisms and shows they are exchanging DNA. Between distinct genrea. According to theory of spiece this shouldn't occur. But they do! Exchange massive pieces of DNA with each other, hasn't been seen before.

progression of liver disease with Hep C

This is the liver, what happens if we leave hepititis virus in ther elong enough, it will go down this progression route. Out of 5 hep viruses, only B, C and D cause chornic hepititis which can be life long - they are the nasty ones. The enteric hepititis is A and E that is passed through contaminated food and you only get sick for about a month or so and then you get better, virus is eliminated, and liver gets better.

What is the soil substrate membrane system

This is the method developed in ferrari lab Work with soil instead of marine system This is a tissue culture insert - use in tissue culture experiments to grow human cells Instead of using it traditionally, put in some soil, wet it with some water, make a little mud slurry, then put a membrane (some of same bacteria on top) put it on top of membrane, incubate it for a week, get up to 60% of bacteria growing (60X improvement over an agar plate) It's a mixed community ,get it from a mixed culture to a pure culture. Soil is the media, porous membrane allows the nutrients from the soil to pass up to feed bacteria growing.

Describe the cell membrane of archaea and why they are different to other domains of life.

This shows structurally they are very similar, mechanistically very similar, but chemically they are very different. If you do a comparison of these types of lipids (streochemistry), fundamental different in how you form a lipid. What that means is because you can't exchange between one form and the other, you imagine way back in evolution in your prebiotic soup, all these things floating around and you now want to develop a cell, something that becomes inherited through vertical inheritance in evolution. You have to capture it (encapsulate it) you can do something with it, undergo cell division, produce prodgeny, and now you get individual speciation and all these things. The fundamental aspect of going from soup to cell is encapsulating it. If you have to form a lipid membrane around the thing, because chemistry is different, suggests that once the lineage that lead to archaea was formed, it couldn't change, it basically had to remain in that form because the chemistry is so distinct. While bacteria nad eukaryotes had a different beginning point. This simple aspect in distinction between the lipids can have ramifications that suggest to us the distinctiveness of evolutionary process that lead to them being around today.

What is the function of frimbria?

To bind bacteria

What is the function of the structural elements of a virus?

To package and protect the viral genome

What were old definitions of successful cultivation

Traditional cultivation was developed over a century ago. Turbidity and colony development meant successful cultivation (approx 24 hrs). Most bacteria only grow as microcolonies (invisible to the naked eye). Novel approaches to culturing are thus required. If it formed a colony you could see - was measure of success Most don't grow to that stage In past missing what is culturable.

What is the function of ribosomes?

Translate RNA into proteins

What are some examples of 'good' viruses?

Virus causes a bit of a disease but makes tulip more beautiful. These tulips were selling for about 40,000 pounds in holand a few hundred years ago because of the markings on them. Didn't know what the cause was back then. On the side of volcano there is a symbiotic relationship with this plant and a fungus. As the heat increases only this plant can grow which is infected with both virus and fungus, because virus helps it tolerate the heat. In the mucosal lining of our lungs, there are hiding and sitting bacteriophages. They attack bacteria, so if we have pathogenic bacteria in our lungs, they will attack the bacteria and kill them for us. In our gut we have heaps of bacteria. Those bacteria help us digest the food, keep our guts funcitoning in a good way. If we disrupt the microbiome e.g. with antibiotics we get gastro and are susceptible to other infections, because we don't have those bacteria to fight bacteria off. The bacteria do good things and so do viruses.

how many archaea that live in cold environments can we cultivate? What information can we get from them?

Tree from 2006 - shows archaeal tree and all blue lines are representitives of organisms from cold envornments. Ones with starts are only branches of ones we have isolates od - what we can study in the lab. Kust to make point we know what is out there and very few to study. Studying in the lab - illustration of what you can learn. This is an organism I studied from antartica. Can grow well at 4 degrees in the fridge, 23 degrees beginning to get hot for it. In electromicrograph can see cells lock very different to each other. Tells you by having done this work in the lab, something ischanging. Now want to understand what the change is all about, very simple concept but what you can do in the lab. Over time you can build up a picture and understand what is happening in the organism. Develop hypotheses - say I think it's doing this, it's important for it to adapt. This is what most work does. If you have an oppurtunity to do at least two get your head into, think about doing field work. Think about what occurs in the environment. Advantage of this - you can test hypothesis made in the lab and can make new discoveries. Point is you can really begin to lern about real things - microbial processes biogeochemical cycles - the tings that really matter Then develop better hypothesis you can then test in the lab. You can conncect the two, do lab work abd field work and remain informed, feel connected to environment.

Bacteria make up about one-third the weight of fecal matter. T or F?

True

True or false: Archaea have a unique form of conjugation involving cytoplasmic bridges for bidirectional transfer of DNA.

True

True or false: Archaeal histones assist in maintaining the DNA in a double-stranded form at very high temperatures in species of Euryarchaeota.

True

True or false: Biofilm formation and dispersal are regulated processes

True

True or false: Biofilms form on virtually all submerged surfaces in nature

True

True or false: Biofilms protect organisms from antibiotics

True

True or false: Chemolithotrophs that obtain electrons from donors such as sulfide use the same electron transport chains to obtain energy as chemoorganotrophs.

True

True or false: Despite GC pairs having an additional hydrogen bond than AT pairs, hyperthermophilic Archaea generally have a lower GC ratio in their genomes when compared to other heat-sensitive prokaryotes.

True

True or false: In general, lipids in archaeal cytoplasmic membranes lack true fatty acids.

True

True or false: Organisms cultured in a solid medium must be diluted by placing one or two loopfuls of water on the center of the slide in which the cells will be emulsified.

True

True or false: The Gram stain differentiates between bacteria based on the thickness of their peptidoglycan layer.

True

Vaginal acidity in the adult female is due to acid production by Lactobacillus acidophilus. T or F?

True

research areas in Lenardon group

Trying to understand how cell wall works so we have a better understanding of how we can inhibit fungus in doing that. Researching how cell divides. If you block cell division, kill fungus dead. Antifungals aren't specific for their target. Antibodies are very specific. How candida colonizes the cut and how it competes with microbiota there. If we can modulate candida in the cut, can prevent these systemic infections.

What are the main biochemical tests we can do on bacteria?

Two tests mainly used are oxidase test and catalase test. Oxidase is looking for specific respiratory chain enxyme. (cytochrome C). The reagent specifically reacts with cytochrome C. These organisms can carry out aerobic respiration but have wrong type of cytochrome C, so are osidase negative. Catalse positive. It's common for aerobic organisms. It's an enzyme that breaks fown hygrogen peroxide into water. Hydrogen peroxide is generated as an offshoot of aerobic respiration. Have to have this enzyme to detoxify it. Because we have been looking at them for a long time so have biochemical tests. We can differentiate between two top clades. The top clase with Salmonella and Aschericha are mixed acid fermentation positive. The bottom is butanediol fermentatio npositive. More traditional test to classify microorganisms before we could seuqence their DNA.

Which of the following would be useful for treating Candida? - a fusion inhibitor - an azole - a macrolide - a nucleoside reverse transcriptase inhibitor

an azole

Compared to Eukaryotes, Bacteria and Archaea have ________ surface-to-volume ratios, causing ________ nutrient exchange and growth rates.

higher; higher

What are the two ways a bacteriophage can replicate?

Two ways to replicate: Way that you already know is caleld lytic cycle. Phage gets in, replicates itself up to 100/200 phages. Lyses open bacteria and then gets out . Viral genes fully expressed. Virulent phage (lytic phage) MS2 is lytic it has a lytic enyme to break open E.coli Lysogenic cycle Phage DNA inserted into the host (like HIV) chromosome sometimes at a specific site- prophage. Site specific recombination system is something that can cut DNA and then insert and ligate it. It is a like a ligase and restriction enzyme rolled up into one thing. Looks for certain sequence patterns. Once DNA is inserted into the host, it becomes part of host E. Coli/bacterial chromosome, and replicates when bacteria replicates. So if bacteria divides 2,4,8 you get 2,4,8 prophages. Once phage is inside chromosome - its caleld a prophage. Is very similar to how HIV works, it even uses a similar enzyme called integrase for part of that job. Most of phage functions are switched off. Temperate phage - Once it is integrated it just sits there - Good trick for bacteriophage. If it can't be bothered killing all the bacteria, it can just take a holidays and insert itself into chromosome and sit there for a few months.

describe example of Typhoid and Gene reduction

Typhi is a recent pathoden, 30-40 thousand years old. Host Specialised, and when it became specialised a number of these genes were under neutral selection. Host specialisation has rendered many genes unnecessary. Were able to accumulate mutations and if we look in genome approx 4.5% of genes are now pseudogenes See these genes accumulating in typhimirium as it becomes specialised, sugesting recent niche adaptation. In the next 10,000 years will see these genes being deleted.

What are Planctomycetes?

Unrelated bacteria - planctomycete They are a bit unique. We define the prokaryote as a cell that lacks a nuclear membrane. Turns out that some do - planctomycetes They are gram negative. Their cell wall doesn't contain peptidoglycan. Instead they have an S-layer. More akin to what we see in Archaea. They don't have peptidoglycan so are also resistant to penicilins and cephalosporins. Have internal membrane bound compartments This genus Gemmata has a nucleiod enclosed in nuclear membrane In summary - the planctomycetes and mycoplasmas are breaking some of the rules for bacteria classification. Exemplifies that there is incredible structural diversity amongst bacteria.

A computer program recognizes an ORF by looking for ribosomal binding sites, start codons, and stop codons with an appropriate number of nucleotides between each element. What is a drawback of this approach?

Unusual, but legitimate genes and non-coding RNA may be missed.

What are photoheterotrophs?

Use light for energy but CANNOT use CO2 as sole carbon source. Examples include purple sulfur bacteria, heliobacteria, some archaea Reaction centres are either bacteriochlorophyl-based (bacteria) or rhodopsin (primarily archaea) Bacteriochlorophylls wider range of wavelengths Rhodopsins function as light-driven proton pumps Carbon requirements come from fatty acids, alcohols, carbohydrates. Can adapt to range of different environments in comparison to photoautotrophs

how does the food get comtaminated?

Used to grow that food is contaminated with some osrt of sewerage, if it's animal sewerage for feriliser has to be left for three months before using. If not can get salmonella and other bacteria on the crops you are fertilising. Have oyster bed in hawksburry and farmer comes with bulldoser, breaks sewerage pipe, the sewerage runs down into the hawksbury river, the shelfish are filter feedsers that concentrate pathogen. They filter that water contaminated with virus and bacteria, they become contaminated themselces, when you eat them you get sick. This is early on in food chain. Salmonella outbreak in victoria - they were using dirty contaminated water to wash lettuce, and fourty people and a few deaths in old people as well, got sicj from food poisoning. Third one is caterer - someone who is preparing your food might have gastrointeritis, goesto toilet, doesn't wash hands properly and then makes your chicken sandwhich. You eat sandwich, eat viruses and then get sick. U.S. Asking all food handlers to now get vaccinated for Hep A. Some food handlers, leave raw meet over night on the site, forgetting to put it on the fridge, there may be a few bacteria on it, but by the next day there are millions of bacteria on it. And by the next day think 'oh it's going to be alright, was pretty cold lastn ight' and the nmake chicken sandwhich with it anyway and then you easly get sick with salmonella. Last two ways are poor food practives that shouldn't happen. This one down here - there were several outbreaks in canberra in a single food outlet. Everyone whoever went to that food outler got sick. Found out that one of the caterers was chiopping up raw meet on chopping board and then putting salad onto same board and then chopping up the salad, the raw meet could contain bacteria and then you contaminate salad and get sick.

Anabolism is the process of ________.

Using energy and raw materials to build macromolecules and cellular structures.

treatment of viral gastroenteritis

Usually get better in 2-3-4 days. Disease is self-limiting. Rotavirus in young children can leadto life-threatening dehydration. There is a poor girl who has very bad immune system who has had a chronic norovirus infection for four years. Have to intervene - want to really hydrate , treat that dehydration (go on a drip or oral rehydration) Aims of intervention: Prevention and treatment of dehydration, prevention of severe nutritional compromise Rehydration achieved using balanced glucose-alt oral rehydraiton solutions

importance and use of Saccharomyces cerevisiae in the lab

Versatility of sacharomyces cerevisiae is that it is a Eukaryote, and it shares same complex internal structure as us and plants and animals. We study eukaryotic cell biology in this model. Has been instrumental in defining key processes we know a lot about now. Highlighted by number of nobel prize winners who have used yeast as their microorganism.

The cytoplasmic proteins of Halobacterium are...

highly acidic.

Viruses role in history

Virus comes from the latin word poison. they are useful and have shaped history. In two decades HIV has killed 25 million people. Viruses killed more people in 1900s than two world wars. More than 50% of the four indigenous tribes that inhabited the Sydney region lost ther lives as a direct result of viral infections introduced by tge Europeans. Aztecs were wiped out by smallpox mumps and measles More than half of aboriginal people in four tribes in Sydney died from 1850 to 2000, from viral infections largely smallpox and measles. If you introduce deadly viruses into naïve populations they can casue devestation. In american civil war when red indians were helping the Brittish, the brittish gave them blankets ladened with small pox and gave them to the tribe and they wiped out the tribe so they could't help americans. This is early example of biological warfare.

What is the size of viruses?

Viruses are around twenty times smaller than a bacteria on average. Can get big viruses like small pox Biggest virus is about 350nm and smallest oen is about 25nm. Usually viruses are around 20-80nm in size (about 20 times smaller than bacteria) Proteins are around 2nm. A lot of viruses iether have 60, 180, 240 or 720 proteins that make that cell (count in 60s). (there's hundreds, thousands if a huge virus) usually viruses have around 240 proteins to make up their icosahedron. Proteins are about 2nm, working down small molecules then atoms are about 0.1nm.

What is a virion?

Viruses have a certain shape, a lot of them are icosahedral (20 sided) and if not, they look like a ebola and are helical. There are two main shapes. A virion is a phase of the cirus lofecycle outside of the cell looking for a new host, inert carriers of the genome. Assembled inside cells, from virus-specified components: they do not GROW and do not form by DIVISION. For division of bacteria, its 2,4, 8, 16 et.c For a virus it's 1, 50,000. different kind of replication They can produce many. If they get into a million cells, 50,000 times a million is a lot of viruses. They are regarded as extracellular phase Virion is like a spacecraft waiting to land on a planet and invade. Best was to sneeze is away from hand.

What are viruses?

Viruses infect all living things. We eat and breather billions of virions regularly. We carry viral genoems as part of our own genetic material. If you weigh the mass of viruses, because they are so small, it doesn't make up a big portion of the biomass Pi-Chart. In abundance, they are by far the most numerace thing on the planet. If you drink a ml of seawater you are drinking about 10^6, 10^7 bacteriophages. Every animal has a whole unique set of viruses. 1% of our genome is old retroviruses.

What is a virus?

Viruses may be defined as a cellular organism whose genomes cosist of nucleic acid, and which replicate inside host cells using host metabolic machinery to form a pool of components which assmeple into particles called virions, which serve to protect the genome and to transfer it to other cells. Viruses - they have two stages of their life. One - outside the cell where they are encapsidated by a hard protein shell. They float around waiting for then ext host to infect. They like to be madei n large numbers (billions) When you have gastro, in one ml of feaces, you have 10^8 viruses in one mil with a bad infection. You need lots of viruses so they can find right place to grow, so the more viruses the more chance they have at finding a new host. This is outside the cell they are called virions. When it enters the cell it takes off protein coat, and its sole job is to replicate. It wants to produce lots of genomes, lots of proteins, and rebuild thousands of viruses. Iften for this reason, viruses have teo parts of their genome. E..g hep C on the left hand side of the genome is the structural proteins ot portect RNA of the virus and on right hand side are non structural proteins used inside the cell to replicate the RNA genomes. Common rule - inside the cell nonstructural proteins and enzymes e.g. polymerases to reconstruct the genomes outside the cell structural proteins

What is the Volter experiment?

Volter experiment. Have a funnel, huge boom (burning occuring) go out into a pond where methanogenesis is occuring. Stick this funnel down inot water and put cap on the top, let all the methane come up, capture inside funnel and then light it. Illustrates how much methane is there. It really is a major gas form.

how pathogens overcome nutrient barriers

War between humans and bacterial pathogens has happened for long time. New development in weapons either way. Once we new development on one side, there is a new development on the other and bacteria fiht back. Way bacteria can steal back iron is with a molecule called siderphore. It is designed to scavange iron from us Has an essential domain with three arms coming out the side. It acts like a claw you get in the arcade. These three arms out the side with benzene rings is they fold down and coordinate the iron. They will snatch off iron from lactotransferrin or other molecules htat contain iron, (has high affinity for iron) and then will resolubalise it. Bacterial pathogens have receptors for these siderphores (this is just one example ,there are a number produce by bacterial pathogens) and they can specigically take in the iron load and siderophore back into the cell

what are some biotech applications of cyanobacteria?

We can use cyanobacteria for nutrient suplements These are rich Research going into potential novel energies, ethanol and hydrogen production utilised by cyanobacteria Production of toxins, aren't great. Some of these toxins, if they are slightly different are useful in antibiotics and anticancer compounds. Research going into modifying pathwars of these organisms so we can produce better drugs.

What is Amensalism?

counter of comensalism. Rather than benefiting, microbe A will have a negative impact on B. classic example - antibiotics. Sometimes targeting another predator, or just biproduct of antibiotic is it is toxic.

How does penicillin work?

We have cell wall up here, penicilin targets cel wall synthesis. Have repeating chains of N-acetole glucosamine, and N-acetole muramic acid that are linked by amino acid side chains. In gram positivethese are gross linked to each other by short pepticlycine bridge. The protein that does that is the penicilin-binding protein (name because found by the fact that it binds to penniciln) it is transpeptidase. It carries out transpeptidation - it cross links amino acid chains together and stabilises the wall. Have to have it or strands fly away from each other. What penicillin does, is it has this four membered rin here - the active part called the beta lactam. This sits into the penniclin active sites that interacts with it and then inactivates it. It binds to it and then inactivates PBP. When it does that, it can no longer cross link newly synthesisized peptidoglycan. If cell is growin and needs more cell wall it can't do that .so cell lyses cause it doesn't have peptidoglcan to make cell wall.

What is and isn't on our phylogenetic tree? what organisms can we compare and how?

We have phylogenetic tree which expresses the difference in all the microbial phyla to each other based on 16s ribosomal RNA. Eukaryotes have 18S ribosomal RNA but conserved enough so that we can comapre the two. Viruses are missing from tree because they do not have ribosomes. They are obligate paraistes. Can't replicate without a host cell. They have their own classification. They are not alive.

How do phylogenetic trees represent evolutionary relationships/distance?

We need to be able to align the sequences. Why we need conserved parts of 16S RNA. When we compare two sequences (align them) Can see these two nucleotides are different between our seeuqnces one and two. Can express that is a distance matrix. Can express the differences between 1 and 2 (2 nucelotides) and put them in matrix Then have graphical repsrentation (phylogentic tree where we can express those distances graphically) Distance between three and two is 1, 2, 3, 4. so the phylogenetic tree represents how closely related each organism is related to eachother. Branches are relatedness.

What are some adaptations which allow archaea to survive at such high temperatures

Wha'ts strongest base pairing - G+C (it has 3 hydrogen bonds) What would you predict, if you're a hypothermophile you would want high C+G. Then ask the organisms what they have - acidianis can grpw at 95 degrees but has 31% GC. Named DNA with 30-40% G+C melts apart at 90 degrees. Not the answer...Proteins are very thermostable. Some of the proteins you can take them out and autoclave them and they are just fine and happy. Proteins have evolved very strong structures. If you are wanting to study protein structures - first thign they will do is find one equivalent in hypothermiphile becaue they are easy to work with. Good for doing structural biology work. Some of them produce funky intracellular molecuels, stabilise proteins Soeme of them over express speficie proteins - idea of how to think about it, simple things been found.

What does salty really mean?

What foes salty nmean Relative to marine ocean - these environments have Great salt lake 10 x sodium 10 x chlorine Dead Sea Minerals present are quite different, calcium is high, bromine is high, is not exactly the same so organisms you see there could be different (generally the case) Typical Soda Lake Sodium is high, magnesium low andcalcium is low, very alkaline and hydrocarbonate is high. Means that salt doesn't mean the same thing in each enviornment.

How do halophile archaea adapt to high salt environments?

What is problem of being in high salt - dehydration! It sucks the water out. If you think about it - you can either put up a barrier or let salt in. Letting salt in is not a great strategy - but actually what archaea do. Have evolved entire intracellular machinery to be able to live in high salt If medium is up to 3 molar sodium chloride, can have intracellular concentrations of 5 molar potassium and 3 molar chloride. All enxymes, everyhting in there, has adapted to working in high salt. On the whole, bacteria living in high salt enviornments tend to exclude salt (in general) Different evolutionary strategy - but both successful. Some of them produce gas vesicles which allow them to move up and down the water column Why would they want to do that? One reason is they tend to utilise duneilela which is an algae. Primary producer which uses light energy and grows on the surface. One of its pbipoducts is glycerol which is a sugar. Haloarchaea like to go up so that they can feed on it. Allows them to go up and down water column without moving or using cheotaxis, using gas vesicle. At surface get more light, and haloarchaea can use light to generate energy. Another reason to go up when they want to and maybe get away from it when they have had a bit too much UV (damages DNA).

What were the results of the lecturer's study?

What is really cool in one of the studies, we found some organisms that don't normally survive well with oxygen, we found near the surface. So they may have some sort of novel adaptive mechanism there. Showing you if you go down to stromatilite or mat, get different wavelengths of light, particulalry at the surface that concentrate, and then different organisms can use these different wave lengths. What is interesting in the stromatilites is different wavelengths of life, the photons are trapped so that there is a microorganism sediment here, the photons are trapped and then there is a concentrate near the surface, so increased the rate of photosynthesis and lead to more productive community. Photons bounced back and forth so instead of escaping they would be trapped in there. It was suggestive of a mechanism that benefited the whole system. Some examples of some data you can get back from studying these systems. Can look for analysing all the differrnet kind of pugments that we have there. The common ones - chlorophyl with cyanobacteria, bacteriochlorophul with anogenic synthesizers. What's relaly cool is when you can find novel pigments that might be absorbing different wavenelgths e.g. cholorophyl f. by looking at these organisms and their communities in details, might be abel to pick out different pigments which icrease our understanding of photosynthesis in general.

Chloroplast closely related to...

cyanobacteria

Lactobacillus function...

dairy fermentation

Pyrodictium

hollow fibre cannulae that appear unique to archaea

what is the relationship between genome reduction and pathogenesis?

What we are really thinking about is environmental change and who this precipitates changes in the genome Initial stages are accumultion of these point mutations in neutral or negatively selected gnees which lead eventurally to stop codons introduced into the genes Many bacteria that have adopted a pathogenic lifestyle (host restriction) show evidence of genome reduction Mycobacterium leprae (leprosy) Salmonella Typhi (Typhoid fever) Bordetella pertussis (whooping cough) and many more All adotped pathogenic lifestyle where they infect humans and are transmitted between humans so they start to lose the genes that would allow them to persist in the environment or colonise other hosts. Termed - pseudogenes There can be no selective pressure on that gene anymore because its not producing a protein. Unless its non coding RNA This leads to gene loss

What is the extreme misconception?

What's normal to you, is different to what's different to a whole range of microorganisms. Need to think of how they adapt based on what's normal to them. What it means to be adapted to the cold So many grants and applications submitied not using right approach to think about how microorganism has adapted to its environment. Think about what's normal in the context of a microbe. In terms of defining stress as a human and wha't happiness, for a microbe may take a little bit of thinking but is what we need to do. First thing we need to think about is what is the natural enviornmental conditions. Right framgework for thinking about adaptations. Adopt the microbcentric view. This is something - when you think about normal - about 80% of the Earth's biosphere exists below 5 degrees. We are used to ambient temperature but most of it is the deep ocean. Polar environment, seasionaly cold enviornments, 80% of life is in these cold environemnts, below 5 degrees. Technically more 'normal' than what we experience. Archaea are found here. List of locations in aquatic and terrestrial environments of where you can find them.

What are superphyla? how did they affect classification of archaea?

When new data came around 2013 onwards, meant these Euryarchaeota and Chrenarchaeota which were referred to as kingdoms, then were split into a bunch of others and these other groups called TAK and DPANN were examples of thigns called super phyla. These ones now appear to be phyla instead of kingdoms. This term superphyla has been used, meaning it is grouping these thigns together and things like chrenarchaeota are now subsumed within this. In terms of branch point for eukaryotes that's what is wshown over here. In esence it's shifting this branch point here. So instead of eukaryotes coming from somewhere out here they are actually now being shifted up well within the archaea themselves. Making a n even closer relationship between archaea having evolved and eukaryotes evolving from the archaea.

Explain how genes of phage are suppressed in lysogenic stage

When phage enters chromosome, it only makes a few proteins. Maybe 2 or 3, not many. Very limited transcription. This is a control pannel. Main mechanism is repression of phage genome usually in bad times. If bacteria is struggling for food for example, it will go into lysogenic stage and hide away. Its struggling and phage doesn't want to struggle. Makes proteins that will stop any transcription of left and right area of the genome. Most phage genes except for repressive genes are shut off. Repressed phage genome - repression is specific. If you have prophage in your genome can't have infection of another phage. Makes few proteins in lysogenic stage, usually just to repress genome.

What is taxonomy?

When talking about classifying microorganisms, most commonly talking about taxonomy The science of defining groups of biological organisms on the basis of shared characteristics and giving name to those groups (binning) Essentially taxonomy refers to binning these - we are clustering them, often on morphological characteristics - how they look Clustering htem into gorups and giving those gorups names to get a handle on what they are

What is Phylogeny and Phylogenetics?

When talking about relationships and how organisms are related to eachother, we are talking about phylogeny The study of evolutionary relationships among groups of organisms (i.e. family trees) Traditionally before the advent of DNA sequencing that is done today, it was mainly done by morphological characteristics. How an organisms looks, how it looks, and its structures as well Today we have gone a step further, we now know it's DNA sequence that underpins the morphological differences so we can now compare the DNA sequences to establish evolutionary relationships between organism When we do that we call it Phylogenetics Phylogenetics is phylogeny based on analysis of sequences of DNA

what is the role of cyanobacteria in evolution?

When the earth formed, 4.5 billion years ago, thought cyanobacteria evolved back here. Took a while for oxygen to build up in atmosphere (1-2 billion years). Evolution of photosynthetic pathway, that lead to evolution of oxygen, then evolution of oxygen using microorganism (respiration etc.) lead to explosion of life, and then eventually us. In modern day we all think of the contribution of plants and rainforest to oxygen in atmosphere, they are important, but reality is most of primary production comes from cyanobacteria. In world's ocean there are different cyanobacteria, and these organisms are mostly involved in producing carbon and producing oxygen. If you get rid of all these organisms in the ocean, would be far worse than getting rid of plants. Endosymbiosis - cyanobacteria may have been the origin of chloroplasts. Started with cyanobacteria engulfed by membrane that lead to chloroplasts we see in plants.

How is a phylogenetic tree (with bootstrap values) constructed?

When this tree was constructed ,some of these so called kingdoms like korearchaeyota were collapsed into this one. The details don't matter too much. Something to point out about this tree though is that this statisticlly supported archaeal tree collapsing with branches with a certainty of <60%. Boot strap values - when you make a tree, these branches that occur, you can assign an umber to them and that represents a percentage and that's a certainty value. When you run a tree program, it will spit out a tree for you, and then it will run again and it will spit out another one. They won't be identical, it depedns on data and algorythm. What this says, is all these branches here, have a 76% occurance with that data set. This one has 100%, this one here has 60. they give you a certainty value, this is important to know, if a tree doesn't have boot-strap values don't trust it. You need to know what's the validity of that tree. With this particular one we set a cut off value of 60%. If it isn't a value of at least 60% then I'm going to collapse it to the next highest node until I at least have a minimum of minimum 60% certainty. (generic thing to be good to know about)

Widespread antimicrobial drug resistance is usually passed by... - heterologous gene expression. - gene splicing. - reverse transcription. - horizontal gene transfer.

horizontal gene transfer.

How does one find SNPS from sequencing?

When you do some sequencing you end up with a whole lot of sequence fragments (raw reads, bits of DNA sequenced which you get back from the machine, maybe even millions.) what you want to do with these is find out where they are from. And so what we need is a reference genome. A genome we already know, which has been assembled, we know all those features and where everything belongs. SNPS - point mutations. It is handy if it is close to the sequences you are analyzing, and then we want to line up all the raw reads. They overlap and exactly what we want, we want them to overlap, cause it gives us information, and there is software which helps with this lining up. When we do this, then you have to imagine there is more sequences of this, there would be heaps and heaps. You want to have so many sequences, that each side in the genome is covered many times by the sequencing procedure. What we will find is occasionally there will be a site that look a bit different (red signs) you want the same difference to appear many times in many reads. Why do we want to have lots of reads covering each side? When we are looking for differences, we might see and A here instead of a T, but if we see it once then is it a snip? It might not be, it might be a sequencing error. The reason we have to sequence many times is we want to make sure that if we see variation it's real variation, it's not just a difference that comes out of the machine as an error. If we do this enough, should be able to detect those. We can identify these single nucleotide polymorphisms, and we can look across the genome which is covered many times by these sequence fragments, and we can figure out where these differences are.

how is Saccharomyces cerevisiae transmitted?

Where is yeast over the winter when there is no grapes on vines? How does it spread about during the environemnt? This was only discovered recently. There is an insect vector that carries saccharomyces cerevisiae around. The insect vectors tend to be a European hornet or European paper wasp. This was the vector through people studying microbiome of these wasps. The queens of these two wasps caried them over the winter and transmit them to all their prodgeny and their progeny go and reinfect the grapes iwith them in the summer. The intestien of the paper wasp is a good place for saccharomyces cerevisiae to sporolate. Has to have certain cues for saccharaomyces to sporolate, happens inside the wasp. Haploid spores are formed tht can mate with each other that can produce diploid cells. Purpose of sporalation (meiosis) - you have recombination and generate gentic diversity. Idea is if you have diverse mutants or variants, some of them have a selective advantage in a different environment.

what is anoxygenic photosynthesis?

Where oxygen isn't involved, anaerobic organisms, can't survive in oxygen They don't produce oxygen Use something instead of water as electron source e.g. Hydrogen sulphide. Different type of pigment, e.g. purple Hanging out in low light areas, so need deeper wavelengths. Can absorb wavelengths of light further down, so they can live down there, where something like cyanobacteria couldn't. Using light to produce energy (same principle) Just different type of chlorophyll Electron donor other than water Electrons moving down the chain, getting flow of electorns, getting ATP and reducing power produced

what makes apsergillus good at infection humans?

Where you find aspergillous species - breaking down soil material and very good at it. To do that, they are producing enzymes. All these secreted enzymes they produce are not only good at breaking down plant material, but also lung tissues. They can also grow at 37 degrees (temeprature tolerant due to it's compost habitat). Melanin is being proposed that it can form a shield outside the conidia that can mask it from innate immune system. Evolved in soil with these characteristics that these fungi have that make them good sachrophytes alsohappen to make them good at invading body through the lungs.

What does metagenomics study?

Which microorganisms there are What functional capacities What biogeochemical processes What community structure/interactions What evolutionary path What future given ecosystem change

What is the future of microbial evolution studies?

Whole genome sequencing technologies Rapidly sequence pathogens (in a matter of hours) Analyse sequence for: Strain origins - can take outbreak strains and sequence them in a matter of days Antibiotic resitance genes Toxins Virulence genes Greater resolution of pathogen outbreaks Analyse microbial evolution in real itme.

discovery of clinical antibiotic classes

Whole thing kicked off in 1928 with discovery of pennicilin. From then til 1984 have disocevered over 30 classes of antibiotics that we can use. When plotting resistance emerging in clinical setting - see emergence of resistance after we start using them clinically. As soon as we use them clinically we see emergence of antibiotic resistance.

what is a winogradsky column?

Winogradsky column - cyanobacteria are a component, lead me to idea of particular natural enviornment which is relaly cool. To see some of real world research done at the moment on this area. Winogradsky column developed by winogradsky. In a column where you can have sedient and water and leave it over time, you can have almost all of the metabolisms you can think of occuring in this relatively small space. All of these different coloured pigments are these differnet kinds of chlorophyls, bacteriachlorophyls, pigments that are absorbing light naturally. The ones up here are more the chollorophyl ones. As you go down these are the anoxygenic photosynthesizers. Position themselves in gradient depending on best place for them to get something useful could be oxygen or some biproduct to keep themselves happy. Cyanobacteria hanging up at the top where they can get wavelengths of light very useful for them, oxygenic photosynthesis. Moving a little bit further down get anoxygenic photosynthesizers using different wavelengths of light, going even further down to a nother type of photosynthesizer, purpke photosynthetic bacteria and green photosynthetic bacteria, all of these are using different wavelengths of light. On top of that also got all of the heterotrophs, going evne further down not relying on light, fermentative organisms, sulfate reducers, so using different inorganic compounds, all of these organisms are positioning themselves, and they are interacting with eachother. If you were to put a plate along there, then these wouldn't be able to survive. They need to interact with their environment and with eachother. The end product of one reaction is useful as a starting point for another. An organism will position itself where its not toxic. If hydrogen sulfide was toxic for them, then they will position themselves in this column where they can survive there.

What is Wolbachia? why is it so interesting?

Wolbachia - really interesting. It's part of Rickettsiales. It's found in 70% of insect cells Specifically a parasite in insect cells Wolbachia is interesting cause it convert the insects from male to female. It has a wide range of strategies but generally will convert a male insect into a female insect. It makes sure there is a lot of females produced in the next generation. Does this through really cool techniques. It produces cytoplasmic incompatibility. It gets into the eggs and prevents an infected insect from mating with a non infected insect in generating viable eggs. They will still generate eggs but will be non-fertile. Will generate a fertile egg if they are both infected with Wolbachia. University of Queensland - looking at this Another group realised that mosquitos infected with Wolbachia were unable to transmit Dengue which is a virus that infects humans. Causes cytoplasmic incompatibilty - Way of ensuring wolbachia is over-represented in next generation Over time wolbachia spreads through a population Because it prevents Dengue, so realisedi f they took wolbachia infected mosquitos up to queensland , and released them the wolbachia would spread through population and eventually in this region where dengue is endemic, over time mosquito population woul become dengue resitant Program is called eliminatedengue

Rickettsiales example...

Wolbachia, mosquito parasite, causes reproductive defects, controlled dengue fever

What is gastroenteritis

Worldwide, 2 billion cases of acute gastroenteritis and 1.9 million deaths occur each year in children under age of 5. One of leading causes of disease and deth by infectious disease. Many of thesep athogens can be past by other ways, food transmission way is most common way. Most of the childhood deaths are in developing countries. Kids are malnourished, aren't eating well. Then get gastro bug and then dying usually from dehydratin. Over 1 billion dolars in societal costs in USA . Norovirus costs globe alone 60 billion dollars a year. Usually from health care costs or people not going to work. Vomiting, diarrhoea, fever (low grade) malaise 3 aetiological agents: parasites, bacteria and viruses.

what makes cryptoccous good at infection humans?

Yeast cells with a polysaccharide capsule and melanin where there is evidence that they form an immuno shield around the outside of the fungus spores. They are anti-phagocytic. Proteases they produce are good at degrading lung tissue which allows dissemination from lungs to other body parts. Urease - unusual thing about cryptococcus, it can survive inside a macrophage. One of the reasons why is it because it has really good scavenging mechanisms particulalry for nitrogen. Urease helps with nitrogen scavenging.

what are Cryptococcus spp?

Yeast cells with a polysaccharide capsule. Cryptococcus is more round that sacharymyces cerivisiae. Found in soils contaminated with bird poo. Mostly pigeons and around eucalyptus trees. Around the outside of yeast cell, it produces a heap of sugars aht forms a capsule. Similar to capsules for bacteria. There will be melanin produced by cryptococcus that protects form UV and heat and cold. Enzymes produced by cryptococcus in same way that they recycle nutirnets in the envornment. Lot of proteases invovledin nutrient acquisition. Have an enzyme called urease which breaks down nitorgen (involvedi n nitrogen scavenging) to grow you need nitrogen, oxygen carbon and water.

What is parasitism?

Yersinia, legionella, rickettsia, chlamydia, salmonella. Parasitism - lives within instead of eating

Which of the following would be most likely in an organism that thrives at a very high temperature, as opposed to in an organism that thrives at low temperatures? - a cell membrane lacking peptidoglycan - a cell membrane with a high proportion of saturated fatty acids - a cell membrane without phosphate groups - a cell membrane lacking fatty acids

a cell membrane with a high proportion of saturated fatty acids

what is an infectious disease?

a disease caused by the spread of a microorganism Human - human Animal - human (zoonoses) Environment to human e.g. contaminated water

An open reading frame (ORF) encodes for:

a polypeptide

Azole medications inhibit the production of ergosterols. Which infection would they be most effective against? - a tapeworm - a bacterial infection - a ringworm infection of the scalp - malaria

a ringworm infection of the scalp

Why are bacteria becoming resistant?

agricultural use (spreads from agriculture to humans) overprescription extensive use

Pan genome

all genes you can find across genomes in a species

Proteobacteria are...

all gram negative

A prophage replicates... - along with its host while the lytic genes are expressed. - independently of its host while the lytic genes are expressed. - along with its host while the lytic genes are not expressed. - independently of its host while the lytic genes are not expressed.

along with its host while the lytic genes are not expressed.

6 major subgroups of proteobacteria

alpha, beta, delta, epsilon, gamma, zeta

Rhizobales belong to...

alphaproteobacteria

Rickettsiales belong to...

alphaproteobacteria

What do MOST halobacteria use for carbon substrates?

amino and organic acids

Linking an ORF with a specific function is an example of gene...

annotation.

Mitochondria closely related to...

aplhaproteobacteria

ALL viral particles... - contain an envelope to prevent its degradation outside of a host. - are smaller than bacterial cells. - exhibit cell lysis under a particular condition. - are metabolically inert.

are metabolically inert.

Organisms that colonize skin __________. - are always aerobes - are mostly gram-positive bacteria - do not include eukaryotes - are never pathogenic

are mostly gram-positive bacteria

no. of archaeal kingdoms...

at least 4

For bacteriophages and animal viruses ________ is the step in the viral life cycle that determines host cell or tissue specificity.

attachment

We sometimes are able to generate antibodies (immune system proteins) that bind to and cover up some of the proteins on the outermost portion of a virus while it is in the bloodstream. This renders the virus unable to reproduce. Which step of viral replication are antibodies directly preventing? - uncaring - assembly - synthesis - attachment

attachment

target mutation and overexpression in candida as azole resistance

azoles inhibit Erg 11. Azole resistance emerges through multiple mechanisms (all three are a problem). Can get lots of target lateration or over-expression. In terms of alteration of the target, we see particulalry in the clinic from azole resistant isoaltes that we have sequenced is we see mutations in erg11 itself. That's the enzyme to which the azole binds. If you have mutation which affects bdingin of the drug, it doesn't inhibit it anymore. We see over-expression of Erg-11. in this case, have some mechanisms that make there be a lot more erg-11 present, so much that no matter how much azole you throw at it, there isn't enough to inhibit all the enzymes. There are lots of different types of mutations that can cause Erg 11 to be upregulated. UPC2 - is the transcriptional activator of Erg 11 gene. UPC2 binds to Erg 11 gene to activate its expresison. We see mutations in UPC2 which means it constituently activates Erg 11. see other weird chromosomal arrangements which means wee see more copies of Erg 11. more ocpies, more expresison, less inhibition then resistance.

Archaeal characteristics

bacteria like lifestyle (metabolism, energy generation, environment), eucarya like fundamental processes (replication, transcription, translation), methanogenesis, non pathogenic

The term "phage" is generally reserved for the viruses that infect...

bacteria.

Generalised Transduction

bacteriophage packages part of bacterial chromosome as a mistake

The process by which two prokaryotic cells arise from one is known as...

binary fission

The science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences for comparative purposes is known as...

bioinformatics.

What is a pathogen?

biological agent that causes disease

What is cooperation?

both organisms benefit, but it isn't obligatory Usually to do with metabolic processes (syntrophy) Many interactions in winogradsky Not obligatory

Phylogenetic trees for bacteria are constructed how?

by analyzing molecular similarities and then using computer algorithms or optimality criteria to construct phylogenetic trees showing hypothesized evolutionary relationships

what are some unique characteristics of archaea:

can be almost any shape Can be motile - chemotaxis They use these appendages to be able to swim, a lot have appendages, some mnot just involved in swimming but also attachement in an arramge of things. One has appendages looped back onto its surface. Hypothermophile produces mesh with cells presence within it at high temperature Produce structures called cannulae (not discovered in anything else yet) Not clear exactly what their function is

What components make up the structure of a virion?

capsid and genome

A chemoorganotroph and a chemolithotroph in the same environment would NOT compete for: - carbon. - phosphorous. - oxygen. - nitrogen.

carbon

A chemoorganotroph and a photoautotroph in the same environment would NOT compete for: (can pick multiple) - nitrogen - carbon - oxygen

carbon and oxygen

Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its...

carbon source.

A person who tests positive for the human immunodeficiency virus but shows no symptoms of AIDS would be termed a __________.

carrier

The only organisms that perform photosynthesis are ones that produce some form of

chlorophyll or bacteriochlorophyll.

archaeal kingdoms and isolates ()

eucaryarchaeota (many), crenarchaeota (many), korarchaeota (none), nanoarchaeota (2)

A change in allele frequencies in a set of organisms over time is called __________.

evolution

If ΔG0' is negative, the reaction is...

exergonic and energy will be released.

Lactobacillus belong to...

firmicutes

Listeria belong to...

firmicutes

Staphylococcus belong to...

firmicutes

Streptococcus belong to...

firmicutes

Rhizobales function...

fix nitrogen gas to root nodules

The factor that MOST affects the thermostability of a protein is its:

folding pattern.

Illness that results from ingestion of pathogen-contaminated food is __________.

food infection

Horizontal gene transfer in Archaea...

frequently occurs in nature and has been used to perform genetic studies in the laboratory as well.

Biggest proteobacteria subgroup is...

gammaproteobacteria

Enterobacteriales belong to...

gammaproteobacteria

Extremely halophilic Archaea often form ________ in order to access ________.

gas vesicles; oxygen

Core genome

genes shared by all genomes in a species

The genome sequence of an organism can provide information about the organism's __________.

genes, function, and evolutionary history

Arrange the following genetic components in the correct order. - genome - metabolite - transcriptome - proteome

genome, transcriptome, proteome, metabolome

Which of the following are NOT substrates for methanogens? - carbon dioxide, carbon monoxide, and formate - acetate and pyruvate - glucose and sucrose - methanol, methylamine, and methylmercaptan

glucose and sucrose

The T4 phage protects its DNA from host restriction endonuclease by...

glucosylating cytosine bases in the T4 genome to prevent DNA cleavage.

Planctomycetes characteristics...

gram negative, nuclear membrane, cell walls lack peptidoglycan

Features of Firmicutes

gram positive, low G and C genomes, some can form endospores

Tenericutes characteristics...

gram positive, without a cell wall

Predict which type of organism would be more difficult to treat with antibiotics and why.

gram-negative organisms -- extra layer of LPS

Staphylococcus aureus is a common foodborne disease, because it...

grows on many foods, is present in some humans that work in food processing, and produces several heat-stable enterotoxins

How do buildings show the change in scientific processes?

in the field of microbiology and other fields, there is so much data it is difficult to analhyse wihtout computer s and sophisticated methods. The building is the E26 building, this is the third floor, Rating Lam is in this corner office and has a nice view of randwick, so for some reason they but the microbiologists in the nice building with lots of natural light, but students and post-docs sit in here, and do experiments in the lab, and produce lots of data, including genomic data and lots of biological data. But they don't spend all their time there, they do their work and they go to office area and sit down and spend a lot of time looking at what they see, using computers, sending big computational jobs to big computer clusters to get them analysed. Lots of work done in office space. In old dats, biology buildings from 20 years ago and older, most of the building would be lab and there would be a couple of office buildings off to the side. People would be spending lots of their time in labs, and then go off to little corner to work on their little computers. Things have changed quite a lot.

When water activity is low, an organism must...

increase its internal solute concentration.

Viral replication is (dependent/independent)...

independent of the host cell's DNA but dependent on the host cell's enzymes and metabolism.

The discovery of antibiotics and other important chemicals led to the field of...

industrial microbiology.

Rickettsiales function...

intracellular parasites

Viral replication occurs... - intracellularly. - either intracellularly or extracellularly, depending on the virus involved. - both intracellularly and extracellularly. - extracellularly.

intracellularly.

Which of the following is NOT a function of the human gut micro biome? - production of essential amino acids and vitamins - maturation of the gastrointestinal tract - iron and trace metal absorption - production of volatile fatty acids from polysaccharides

iron and trace metal absorption

Toxic shock syndrome __________.

is life-threatening because of the superantigen toxin produced

HCV genome and protease cleavage

it is 9.6 kb. Only has 10 genes. Farily typical for positive-sense RNA virus. Many of human viruses divide genomes into two bits. In this case, left hand side is structural part of the virus. This makes the capsid, called the core protein. The capsid is covered by an envelope from the host cell, and then has two envelope glycoproteins that are heavily glycocelated. They sit in envelope and they are receptor hunting, they look for receptor of hepanisite to get virus into the liver. On the other end we have the IRES , internal ribosome entry site, this means virus can be translated, viral genome itself acts as a message, and the whole genome can be translated in the cytoplasm of infected cell using this. It doesn't need to go to the nucleus, has own mechanism. The right hand side has all enzymes involved in replicating this ss RNA. This polymerase at end copies RNA into RNA. It replicates the RNA and if you inhibit that you can stop the virus growing. One of the new drug targets use drugs agaisnt that polymerase. Not sure what NS5B really does but it helps with replicaiton. NS3 is a protese which means its aprotein which cuts up other proteins and it cleaves where triangles are shown. Get 1 big 3000 amino acid protein and then it gets cleaved up into ten smaller proteins by NS3 protease, apart from this juction which is cleared by NS2 - another protease. Many of these proteins have other dunctions e.g. they might dampen the immune system. NS3 is alos an RNA helicase. It has ATPase activity. LHS of genome is structural part for outside protecting the genome, is the capsid looking for blood to get into to ingect, and RHS is replication off the actual RNA.

The most heavily colonized human organ by bacteria is the ________, containing 1011-1012 bacterial cells per g.

large intestine

What is lambda?

linear ss DNA, icosahedral, lysogenic cycle Used in many molecular biology experiments. Used to make gene libraries in the 90s of bacteria and other things. Hepititis C was discovered from a gene library using bacteriophage lamda in 1987ish

Archaea that do not have cell walls must have specialized cell membranes. The membrane structure of these organisms includes __________.

lipoglycan and glycoproteins only

If a bacterium carrying a plasmid that confers resistance to ampicillin is placed into medium without ampicillin, it may...

lose the plasmid because there is no selection for ampicillin resistance.

Based on comparative studies of agricultural soils or polluted soils compared with undisturbed soils, disturbance of soil microbial communities tends to lead to __________.

lower prokaryotic diversity

Staphyloccocus aureus is an important cause of food poisoning. There are several genes associated with S. aureus that encode exotoxins associated with food poisoning. SEA is a S. aureus exotoxin encoded by a viral gene. What sort of life cycle must the phage have? - budding - lytic - cytocidal infections - lysogenic

lysogenic

Virions infecting some bacteria possess the enzyme ________ that makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter.

lysozyme

bacteriophage life cycles

lytic, lysogenic

There are ... uncultivated archaea

many

Features of Enterobacteriales

many human pathogens, facultative aerobes, oxidase negative, catalase positive, differentiable on sugar fermentation.

Method used by bionformatics for phylogenetic reproduction

maximum likelihood tree

Enteric bacteria such as Salmonella spp., Shigella spp., and Escherichia spp. most often contaminate and spoil...

meat

Once equilibrium is reached, - molecules move, but there is no net movement in a particular direction. - passive transport starts over to create a concentration gradient. - molecules no longer move. - the membrane permits all molecules to freely move across the membrane.

molecules move, but there is no net movement in a particular direction

what are bacterial virulence factors?

molecules produced by bacterial pathogens that contribute to their ability to cause disease. Overcoming our natural defences as barriers to pathogens.

ALL fungal infections can broadly be termed...

mycoses.

One example of an electron acceptor that can be used in anaerobic respiration is: - FMN. - nitrate. - water. - NADH.

nitrate.

The MOST common source of individual foodborne botulism outbreaks are due to consumption of...

nonacid, home-canned vegetables.

The collective term for the organisms living on or in the human body is...

normal microbial flora.

Archaea and Bacteria are unified as prokaryotes in lacking ________ which Eukarya contain, such as golgi.

nuclei and membrane-enclosed organelles

Changes in the human microbiome have been associated with __________. - obesity - esophageal cancer - arthritis - type 1 diabetes

obesity

Alphaproteobacteria are mostly...

obligate and facultative aerobes

Many alphaproteobacteria can grow in...

ogliotrophic environments

Hyperthermophile characteristics...

optimum growth temperate above 80 degrees, many chemotrophs and acidophiles sulfur compounds.

Adaptive radiation

organisms diversify from common ancestor

Organisms able to live in environments with high sugar concentrations are...

osmophiles.

A halotolerant facultative anaerobic bacterium would grow BEST in a ________ environment.

oxygenated non-saline

Give example using TB of how researchers analysed data

pair of figures from a recent study, where the investigators wanted to udnestand SNPS in TB. The SNPS you can see on the right, and you can arrange the isolates in a particular way so thaty ou have some sort of evolutionary history (like a phylogeny) which shows how everything is related to each other. Don't just want the phylogen tree, want to know what this tells us about transmission of the disease. So the bottom pic shows us a couple of possible roots of transmission. They are tryign to reconstruct what the patterns of transmission must have been among the people that the bacteria was collected from. These are trasnmission networkds.they are using genetic info alogn with computational models, to try and make a statistical analysis of a likely scenario for the pattern of transmission. This relies on fairly complex computational models .they have to itnergrate not just he epidemiology but the genetics as well. Have to put them together in statistical framework. How do we know that those previous methods work? Hard to know but one thing to do is simulate an outbreak and simulate the process of mutaiton that must occur in the bacteria as an outbreak is occurring. There is transmision of the disease, of the bacteria, the bacteria are dividing and as they divide they occasionaly have mutation, and as we sample the bacteria, we see the mutation and identify those SNPS. If we can simualte that process using a computer program, then we know what goes inot the program. We can set the parameters, we can make mutation rate high or low, and then we can compare that to what the methods think is going on.

Hepatitis B and C are transmitted via the ________ route.

parenteral

The ability to cause disease is __________. - colonisation - infection - pathogenicity - virulence

pathogenicity

Both lysozyme and penicillin disrupt the bacterial cell wall peptidoglycan, leading to cell lysis. However, their mechanisms of action are different, resulting in the fact that __________.

penicillin kills only growing cells

While gram-positive cells have a thick layer of __________ in their cell walls, gram-negative cells have a thin layer, surrounded by an additional lipopolysaccharide layer.

peptidoglycan

Upper temperature limits (low to high)

phototrophy, chemoorganotrophy, chemolithotrophy

what are yeasts? how do they replicate?

prefer a unicellular life. Start with a single round mother cell. A bud emerges from the mother cell. Once it's grown a bit in a polarised manner, it then undergoes a period of isotrophic growth where new material is deposited around the bud rather than just at the tip of the bud. It increases in size until it's roughly the same size as the mother. Undergoes mitosis, then after at this stage that nuclear division is completed, undergo cytokinesis where a septum forms between the mother and the bud. The septum is a complete barrier between the two compartments. In the case of budding, the mother and the bud actually separate. When you form long hyphae the compartments don't separate in yeast the two cells do. It is a form of asexual reproduction, the bud is essentially exactly the same as the mother, the bud then goes on to be a mother. When the cells split, you get both a birth scar (first time bud comes off) and a bud scar, every time it buds another cell. Have DNA replication during the S phase, and mitosis during the M phase where chromatids split and separate to each end.

what are the two types of pathogens?

primary and opportunistic

Following antibiotic therapy, patients are often administered ________ to facilitate recolonizaton of normal flora.

probiotics

Weight gain and obesity may be partly caused by certain gut microbial communities that...

produce more volatile fatty acids by fermentation.

Which of the following are NOT found in the gastrointestinal tract of healthy humans? - protists - Clostridium - Bacteroides - Escherichia coli

protists

A key concept in evolution is that all mutations are...

random

Which of the following emergence factors has contributed to the HIV/AIDS epidemic? - exotic pet and meat trade - increasing travel to endemic areas - rapid pathogen adaptation and change - climate change

rapid pathogen adaptation and change

The principle behind salt or sugar preservation is to...

reduce water activity

Enveloped viruses have a layer of lipids surrounding their capsid. This envelope is made mostly of host cell membrane. In which step does the virus acquire this envelope? - synthesis - attachment - assembly - release

release

mechanisms of gene evolution

replication and repair errors, mutagenic agents

Some antibiotics inhibit protein synthesis by disruption of translation through interactions with the _______.

ribosome

Which of the following antibiotics inhibits RNA synthesis? - azithromycin - erythromycin - rifampin - penicillin

rifampin

Foods most at risk for gastro bacterial infection?

same as viruses

One microenvironment of the skin is an area where glands produce an oily substance called...

sebum

An antimicrobial compound that targets a pathway or structure that is present in a pathogen but not in the host exhibits __________.

selective toxicity

Incubation period of viral diseases

short incubation period Viruses tend to get in, give you a week of nastiness and then get out. Tend to be respiratory and gastroviruses Incubation period means time to exposure til time to illness. Arboviruses are viruses carried by insects e.g. dangue or mosquito carried viruses. Medium incubation time: Whole body systemic illnesses, doesn't attack one organ like gut or lungs or respiratory tract or skin. Attacks whole body, incubation periods are logner. These viruses can replicate in many organ types. Usually it's about two weeks to replicate itself up before seeing symptoms. E.g. rash, fever, muscle aches, nausea, headaches etc. Long incubation - weeks or months, all hep viruses, infectious mononucleosis, rabies. Very long incubation - years Subacuate sclerosing panencephalitis (complication with measles) Creutzfeldt-Jakob disease

Normal flora in the duodenum are... - dominated by aerobic organisms. - tolerant to high salinity. - similar to the microflora in the stomach. - tolerant to alkaline environments.

similar to the microflora in the stomach.

Nanoarchaeum characteristics...

smallest genome, lacks most processes, requires host

Microbial diversity in an ecosystem can be expressed as the number of different species present, which is termed __________.

species richness

A mechanism for penicillin resistance in bacteria is... - confirmation change of the antibiotic. - splitting the β-lactam ring of the antibiotic. - phosphorylation of the antibiotic. - acetylation of the antibiotic.

splitting the β-lactam ring of the antibiotic.

Compared with pure cultures grown in the lab, microbes in nature usually experience a wider range of environmental conditions, more variation in conditions over time, and more contact with other organisms. Therefore, the same organism in nature will __________.

typically grow slower than in pure culture

What is MS2?

ssRNA icosahedral, released by lysis. Single stranded Rna genome - liviviridae MS2 Used as a control in molecular biology assays or final diagnostic assays. We can count it, plate it out, can use it as a control. It is used to test things like hepofilters in airlines. The air-con system in a plane goes through a hepofilter that keeps all viruses out. To check that filter is working using MS2. it's a small virus (only 25 nm) almost smallest virus you can get, icosahedral, 180 proteins make up the shell of MS2. that MS2 phage goes into clefciella or E. Coli through the pilus. It uses pilus to enter the bacteria. This phage only has 4 genes, a very small genome. This protein helps package RNA into the icocahedron of the phage. Capsid protein has 180 of those to form together to form the capsid. The RNA dependent RNA polymerase which replicates the RNA genome with help of a couple of E. Coli proteins. Lysis protein - after the infection the phage needs to get out of the bacteria so it can infect more, so it has a lysis protein that will break open bacteria to release the phage. This phage gets into the E. Coli by attaching and using the pili. Can see MS2 guys holding onto pili (in the photo) this is how the phage uses the F-pili to get inside. They have some sort of attraction or bonding that gets the phage onto the pili and it will get phage into that cell.

How can Tenericutes survive without a cell wall?

sterols and lipogycans stabilise cytoplasmic membrane

The ________ produce over 500 characterized antibiotics. - pseudomonads - streptomycetes - Bacteroidetes - mycobacteria

streptomycetes

Methanogen characteristics...

strict anaerobes, use methane in anaerobic energy generation pathway, unique coenzymes that autofluoresce, most thermally diverse group of organisms

Which forms of oxygen are generally toxic to living organisms?

superoxide, hydrogen peroxide, and hydroxyl radicals are all toxic

The MOST serious types of fungal infections are... - mycotoxic infections. - subcutaneous infections. - systemic mycoses. - superficial mycoses.

systemic mycoses.

Which of the following is a mechanism of ahminoglycosides? - prevention of peptidoglycan cross linking - inhibition of DNA replication - inhibition of cell wall biosynthesis - targeting the 30S ribosomal subunit

targeting the 30S ribosomal subunit

The presence of which of the components listed below would allow you to distinguish between a gram-positive or gram-negative cell wall? - teichoic acids -- gram-positive - N-acetylglucosamine - gram-negative - teiochic acids -- gram-negative - N-acetylmuramic acid - gram-positive

teichoic acids -- gram-positive

what is pathogenicity or virulence

the ability of a pathogen to cause disease

All of the following areas of the human body should be microbially sterile EXCEPT __________.

the respiratory tract

The rhizosphere is __________.

the soil immediately surrounding the root of a plant

Hyperthermophile adaptation to high salt...

thermostable and rigid proteins

Gram-positive

thick peptidoglycan cell wall anchored to cytoplasmic membrane. Techoic acid holds layers together and lipotechoic acid anchors.

Gram-negative

thin peptidoglycan cell wall surrounded by outer membrane decorated with LPS-> lipid A, core, O-specific polysaccharide

Among the recommendations from the Centers for Disease Control and Prevention to limit the development of antibiotic resistance are __________.

to treat with the oldest, effective antimicrobial

how do we hunt for new viruses?

tool Sample, then virla RNA extraciton, reverse transcriptase, PCR, Gel Electrophoresis, Sanger Sequencing and Phylogenetic analysis. Trying to see why there are sudden increases in outbreaks, hunting for new viruses that may have emerged

lateral gene transfer

transfer of foreign genetic material between microorganisms

Conjugation

transfer of plasmids between bacteria via conjugation pilus

Transformation

transferring naked DNA between bacteria

mechanisms of lateral gene transfer

transformation, transduction, conjugation

Planctomycetes cell walls... and consequences

use s-layer like archaea, resistant to antibiotics that target cell wall

A higher number of methanogenic Archaea are found in the guts of mice and humans who are obese. It is thought that the methanogens help to foster obesity by__________.

using H2, thus allowing further fermentation of substrates

Cultivatable isolates of archaea are..

very low

The following compounds are all produced by intestinal microflora EXCEPT... - flatus. - vitamin B12. - vitamin K. - vitamin C.

vitamin C.

The change in Gibbs free energy for a particular reaction is MOST useful in determining...

whether there will be a requirement or production of energy.

The first antibiotic to be characterized was a... - β-lactam. - cephalosporin. - macrolide. - quinolone.

β-lactam.

What has occurred when organisms share a trait that was NOT inherited from a common ancestor?

convergent evolution

Which of the following is/are characteristic of ALL cellular organisms? - evolution - motility - communication - communication, evolution, and motility

Evolution

What are the three kingdoms of life? Name any facts you know about these kingdoms

3 different clades/kingdoms of life Bacteria, Archaea and Eukarya 1 trillion species of Bacteria and Archaea (1012) 8.7 million species including many microbes (yeasts, fungi, algae, protozoa) Unicellular microorganisms - bacteria and archaea (unicellular microorganisms)

How does bacteria know where centre of the cell is?

FtsZ ring formation is important for placement of division septim. The formation of the ring is inhibited by MinCD and MinCD is inhibited by ME. MInCD wants to prevent FtsZ from forming. It wants to polymerize so it starts polymerizing. MinE depolymerizes minC. A ring of minE depolumerizes MinCd. minCD starts polymerizing and is chased by MinE which will depolymerize it. You get an oscilation along the cell. The polymerized MCF will

Which of the following organisms is gram-negative? - Bacillus cereus - Staphylococcus aureus - Escherichia coli - None of the above

Escherichia coli

What is the fastest organism on the planet?

Make bacteria some of the fastest living organisms on the planet, if you measure distance traveled relative to body length Undisputed winner - methanocaldococcus (500 body lengths per second)

What is the structure of a gram positive cell envelope? What are the functions of some of these elements?

Gram Positive Arrangement Gram positive membrane, thick cell wall, held together by insertion of these techoic acids. Techoic acids have phospho and glycerol they attach to the end acid called muramic acid. The sugars (NAG AND NAM) it's cross linking to the muramic acid of those sugars, cross linking the different strands of sugars together, and by crosslinking the acids together, it gives the peptidoglycan sheets more structural integrity. They insert into the peptidoglycan layer, cross link into the sheets and give them more ridgity. They can also have a lipid tail, and these are called lipoteichoic acid, by anchoring the lipid moiety into lipid membrane it attaches cell wall to cytoplasmic membrane. Techoic acids a or lipotechoic acids cross link

How are endospores formed?

Cell grows happily, it decides not enough nutrients around for more growth, or it's very hot, or lots of UV damage. Decides to form a spore. It divides asymmetrically to form pre-spore and puts a copy of it's chromosomes, ribosomes, tRNA that it's gonna need when it reanimates into its pre-spore. It then buds off inside the cell and starts to acquire the atributes of a spore. It has a cytoplasmic membrane and a cell wall, but it requires a cortex, a protein layer that protects the spore. It acquires the dicolinic acid now, it will also get a spore coat. Once it's matured, the vegetative cell will lyse and will release the spore into the environment which is stable for years (in the soil, hospital setting evern) will persist and which conditions get better, finds its nutrients, more habitable, it will germinate and will go back into a vegetative cycle and can grow happily again.

What is the cell wall? What is its purpose?

Cell membrane is a lipid bilayer. The lipids themselves aren't covalently linked to eachother so it's a semi-fluid membrane. Not good at resisting pressure. With all the transport of sollutes into the cell, there are 2 atms of osmotic pressure inside the cell - same amount of pressure in a car tyre The cytoplasmic membrane is ill-suited to containing that type of pressure. The cell needs a rigid support around the cytoplasmic membrane to stabilise it and does that with the cell wall Cell wall provides ridgidity and shape It's composed of cross linked peptides and sugars, and they are termed peptidoglycan.

Which of the following describes the correct cellular morphology and Gram reaction for Staphylococcus aureus? - Clusters of gram-negative cocci - Clusters of gram-positive cocci - Clusters of gram-negative bacilli - Clusters of gram-negative bacilli

Clusters of gram-positive cocci

What is peptidoglycan? What is its composition?

Consists of strings of sugars, alternated with NAM and NAG. They're in strings, the strings are crosslinked together by short peptide (amino acid) chains. We have peptides here - alenine, glucose, dyaminopalemic acid and alenine again. The side chains are linked at the Dap and the Alenine. Takes these strings, cross links them together and forms these sheets of peptidoglycan that wrap around the cell. This is the confirmation of gram negative cell. Different tyep of cell wall is in gram pos. different side chain - alenine, glucose, lysine and alanine and cross linked with a pentotine of glycyne. We have sugar chains cross linked with short peptides to make sheets of peptidoglycan to wrap around the cell and give it structural rigidity and stop the cell from bursting.

What are the key differences between a gram pos and gram neg cell

Gram pos and gram neg cell wall First type is gram pos - has a thick peptidoglycan cell wall (cytoplasmic membrane, thick peptidoglycam cell wall anchored to chytoplasmic membrane) Alternative arrangement is gram neg - cytopasmic membrane, thing peptidoglycan cell wall, on the outside of that there is a second membrane (lipid bilayer, but situated on the outside of the cell wall and anchored to the cell wall using the lipid proteins) Thin cell wall, surrounded by an outer membrane

Which of the following statements is INCORRECT regarding the Gram staining procedure? - Gram staining separates cells based on the composition of their cell walls. - The primary stain, crystal violet, is able to stain all bacterial cells. - The decolorizing agent is designed to remove the primary stain from only gram-negative cells. - Gram-negative cells carry a net negative charge in their cell walls; gram-positive cells carry a net positive charge.

Gram-negative cells carry a net negative charge in their cell walls; gram-positive cells carry a net positive charge.

Which of the following describes the correct cellular morphology and Gram reaction for Bacillus cereus? - Gram-negative rods - Gram-positive cocci - Gram-negative cocci - Gram-positive rods

Gram-positive rods

Give an example of fimbriae in pathogenesis and their importance

Escherichia Coli - A urinal tract has a lot of urine flowing over it, the bacteria needs to stick tightly to the tissues to prevent it from being washed out. A lot of urigenital pathogens produce these fimbriae to allow it to stick to the tissues in the urinal tract and prevent them from being washed out so they can persist in the urinary tract

True or false: With respect to nitrogen utilization, relatively few bacteria can use NH3 whereas many more can make use of N2.

False

What are flagella?

Flagella allow bacteria to swim through aqueous and viscous environments. Twitching motility is relatively slow Flagella are complex nanomachines - Kind of like propellors for bacterial cell Flagella are pillical filaments that extend from the cell.

How do bacteria move with a flagella? What is chemotaxis?

Flagella don't just mediate random movement in aqueous environment, bacteria can navigate it's way towards chemical attractants and away from chemical repelants. Does this using chemotaxis. Bacteria is capable of doing two types of motility - 1. running mode (all flagella pointing in same direction and propelling bacteria towards something) 2. tumbling motility where flagella are asynchronous and essentially making the bacteria turn on the spot. So they can move in a straight line or turn on the spot. The cell will switch between the two motilities when it is in an aqueous environment. It will run and then it will tumble. What it can do is it will sense that it is moving up or down a chemical gradient. If it is moving towards a chemical attractant it will start to favour this running mode of motion, if it is moving away from the repellent it will favour tumbling mode of motion. It tumbles to find correct direction again. Bacteria moves towards attractant by sensing the chemical, concentraion of chemical, and modulating its motility in response to that. It's termed chemotaxis.

Which statement shows which adaptations are necessary for hyperthermophilic proteins to stay functional at temperatures above 80°C? - Hyperthermophiles have increased ionic bonds to stabilize the proteins. - Hyperthermophiles have decreased ionic bonds to stabilize the proteins. - Hyperthermophiles synthesize proteins with completely unique amino acid sequences to stabilize the proteins. - Hyperthermophiles have highly hydrophilic interiors to stabilize the proteins.

Hyperthermophiles have increased ionic bonds to stabilize the proteins.

How does membrane impermeability to charged molecules assist in metabolic processes such as oxidative phosphorylation?

Impermeabel to charged protons Incredibly Important for energy conservation. E.g. respiratory chain Series of complexes that allows the cell to transports protons out of the cell and create an electrical difference between the two sides of the cytoplamic membrane. Outside has higher concentration of protons, inside has lower concentration. This cytoplasmic membrane is impermeabel to protons as they are quite charged, so it excludes these protons from coming back into the cell. cell allows them back in, in a regulated fashion, using the movement of protons to synthesize things like ATP or motility using protons coming back into the cell with the chemical gradient to turn flagella. Impermeably to protons important for respiration. H+ can't go inside the cell, needs to through a protein to get into cell - which is what powers ATP manufacture

What is the cytoplasmic membrane? what is its structure?

Lipidbylayer that encases the cell and cytoplasm Composed of phospholipids - composed of phospholipids

What are the functions of the phospholipid bilayer cytoplasmic membrane?

Membrane is a permeability barrier Large or charged molecules can't cross bilayer Core is hydrophobic - if very charged you can't migrate through that hydrophobic environment It prevents molecules from getting into the cell. It allows cell to control whats getting into the cell Allows cell to control what's getting out. It prevents leakage of molecules from the inside of the cell into the outside environment. Delimits what's inside the cell and what's out Phospholipid bilayer won't let molecules across but cells need some larger charged molecules to come in a regulated fashion The cell produces transport proteins (embedded in phospholipid membrane). Charged molecules can't go through the membrane Prevents leakage of solutes from inside the cells

how do flagella work?

Motor complex embedded in the cytoplasmic membrane. Peptidoglycan cell wall, and an outer membrane. Gram pos can also have flagella. Have a hook that puts a kink into the drive shaft here, and then the long helical filament which is a flagella. In essence this flagella is using the proton motive force. The cytoplasmic membrane is important for maintaining the proton motive force. Flagella is using proton motive force 1000 protons = motor turns once

What is passive and facilitated diffusion?

Passive diffusion - carbon dioxide, oxygen relatively small and uncharged so they can migrate across the membrane just by diffusion (no energy required) Proteins can form a channel that allow small molecules to pass into the cell Can gate passage of solutes into the cell Passive transport (transporting with the chemical gradient) High concentration on the outside - allowing it to come into the cell where there is a lower concentration (along chemical gradient) no energy required.Some of the transporters will recognise binding of the solute and they will be open to the outside when they bind their solute they change confirmation and will be open to the inside. In such a way they can allow the solute to go inside the cell.

What are Capsules? What can it do? what are the implications?

Not all cells can be stained, some cells have on the outside, they secrete extra polysacharides which we term capsules. Cells below are being stained by india ink and there is a big halo round the cells (the india ink) which is being repelled by the cells. This is because the cells are secreting a capsule, which can be a polysacharide layer or a protein layer and tend to exclude compounds from getting at the cell. If you streak them out on a petry dish, they will be very mucoid. They get this glosy look on a plate, which means that they are making a capsule. The capsule is important from protecting the cell from desicaiton, can prevent water loss, important for ivading the immune response. The capsule can actually, because it is composed of sugars, can mimic the sugars of our own cells, and trick our compliment systems that the bacterial cell is in fact part of us. Important for cloaking some pathogenic microorganisms Because it is charged (charged sugars) it can help facilitate ionic interactions with solid surfaces.

What is the genetic material in a bacterial cell?

Nucleus but no nucelar membrane Have a Nucleoid free within the cytoplasm Bacteria have circular chromosomes Small pieces of DNA - (plasmids) encode accessory functions To translate all that info into proteins we have ribosomes

Why is it recommended that Gram staining be performed on young bacterial cultures (not older than 24 hours)?

Over time, gram-positive cells lose their ability to retain the crystal violet stain after decolorization.

What are Pili?

Pili also mediate interactions with local environment but are much longer than fimbriae Diversity of functions include: Attatchment to solid surfaces, Conjugal transfer of DNA between bacteria. Can also be used for twitching motility. This is (myxococcus xanthus) which hunts other bacteria, hunts along solid surfaces by extedning a pili that attaches to the surface and then retracts the pili like a grappling hook. In such a way it moves slowly along a solid surface. Twitching motility is mediated by pili as well. Pili are important for bacteria interacting with surfaces around them. Mediating contact with another cell Can mediate attachment to other bacteria. There is a conjugal pilus, a hollow fibre, and the donor bacteria is transfering DNA through the pilus to recepient bacteria here. Important for horizontal gene transfer

What are plasmids?

Plasmids are autonomously replicating circular pieces of DNA separate from the chromosome and can be very small, or very large, and distinguished from the chromosome by the fact that chromosomes that chromosomes code for all of the essentially pathways. Chromosomes will encode ribosomes, tRNA and essential metabolic functions, while plasmids encode accessory functions, can't encode essential functions. Important for transfer, from cell to cell using a pillus. This F plasmid will synthesise a pilis (filament) from one cell to another and can transfer the DNA from one cell to another. From host to recipient. Important for transfering traits encoded on the plasmid. Can encode just about any trait on the plasmid. The more common ones are virulence and antibiotic resistance (traits can be transferred from one to another). Vertical gene transfer - mother to daughter. Horizontal gene transfer is between two unrelated cells (conjugation, transfer of plasmid from one cell to another)

Which of the following would not move freely across the cytoplasmic membrane? - Dissolved oxygen - Dissolved carbon dioxide - Small alcohols - Positively charged hydrogen ions

Positively charged hydrogen ions

describe the genetic information of bacteria

This term 'prokaryote' is controversial in microbiology at them oment but still widely used. Refers to bacteria and archaea specifically refers to the fact that both these kingdoms don't have a nuclear membrane contrasting to eukaryotes that do. Their chromosomes or nucleoids are free within the cytoplasm. The chromosomes are usually circular. They are densely packed. If you were to gently lys the cell, you would see the chromosome is super coiled and is densley packed with DNA binding proteins. Can see loops and coils from supercoiling of DNA and packaging of different DNA binding proteins (don't have histones) need to package very tightly because a 4 million base pair chromosome (expect in E. Coli) is about 1.6mm long then you measure it end to end. E. Coli is about 1-4 microns, so you have an a thousand fold longer chromosome to fit into this cell.

If you forget to add the decolorizing agent when performing a Gram stain, what color will the gram-negative cells be?

Purple

Some organisms are capable of using aerobic respiration or anaerobic respiration but use aerobic respiration preferentially. Why do they use aerobic respiration when possible?

Respiration with oxygen as a terminal electron acceptor generates more energy than respiration with other terminal electron acceptors.

What are ribosomes?

Ribosomes translate RNA sequence into protein sequence. Present in ALL organisms. highly evolutionary conserved. Though slightly different in three kingdoms. Over ecolutionary time have diverged slightly. Predominantly composed of RNA, some proteins associated with it, the major catalytic centre in the ribosome that links together the amino acids is actually RNA based. Obviously cell needs a lot of these, have a lot of mRNA to be turned into a lot of proteins, so cell typically has about 10,000 copies of its ribosomes around the cell. has small and large subunit. Cartoon of crystal structure, cyan here is 16S rRNA, small subunit is mainly composed or RNA. The gray large subunit is in grey, mainly composed of 23S RNA. Can see in purple proteins associated with ribosomes, and a tRNA at the back. Can use differences in ribosomal sequences (different amongst organisms slightly) to identify our organism. Our bacterial ribosomes are sufficiently different to our ribosomes - good thing, cause a lot of our antibiotics we use target the ribosome. Can selectively target bacterial ribosomes without inhibiting our cell's ribosomes.

What are endospores?

Some cells don't divide symetrically. Some divide asymetrically to form an endospore. Done by some of the firmicutes. Dividing asymmetrically to form an endospore which is a highly resistant dormant form of the cell Endospores can sit in the environment for years under harsh conditions and persist, and when conditions get better they can re-animate and become normal cells again. Highly resistant to: disenfectants, UV, Heat, Dessication. Impotant role in pathogenesis of human pathogens Clostridium difficle and Bacillius anthracis Vegitative cell growing happily, encounters nutrient limitations (some sort of harsh conditions) decides not a good place to grow, so forms a spore (highly refractive spore) at one end of the cell. These endospores are able to presist in the environment, they are different from normal cell because they can't grow (they can regerminate but they can't divide) they have a copy of all the biomolecules in the cell (chromosomes, tRNA, ribosomes etc.) but they have 10% dipicolonic acid. This dehydrates the spore and stabilizes the DNA (more resistant to UV and damage/dessication by heat) Different to spores formed by fungi.

Which type of active transport protein moves two molecules into the cell at the same time? - Uniport - Antiport - Symport

Symport

What is a limiting factor for bacterial growth?

Synthesis of these ribosomes is complicated and expensive for the cell The ability to make enough ribosomes is the rate limiting step for bacteria as they grow under nutrient rich conditions. Being able to make enough ribosomes is what stops bacteria replicating even faster than they do.

Explain the phospholipid bilayer structure

We have a lipid tail - a hydrocarbon (hydrophobic) lipid tails are joined together by glycyrol phosphate. The phosphate has a neg charge on it The phosphate head group is reasonably hydrophylic (wants to be in aqueous environment) Two molecules prefer different enviornments (one hydrophobic, one hydrophilic) Most stable arrangement for phospholipid is for all the tails to come together to form a hydrophobic environment in the middle. Phosphate head groups face aqueous environments Most stable arrangement is spontaneously forms arrangement of lipid bilayer

What are the different components of LPS and why are they important?

The LPS is really important. It's composed of three components. It starts with a lipid A core. This is highly conserved across gram neg bacteria. They will all have something resembling this lipid A moedity at the bottom. This sits in the outer membrane and anchors the LPS into the membrane. It's so conserved that our bodies use it as a signal that we have bacteria where we don't want them. Bacterial cells will shed some of this LPS when they infect us. Our immune systems have become tuned to recognising this molecule and it stimulates a strong immune response which is responsible for some of the symptoms of gastrointestinal disease and septic shock from some microorganisms. This molecule is termed endotoxin. Second component is core polysacharide that attaches the lipid A moeity to o-specific polysacharide. This is the outer membrane (lipid A) this is dangling in the outside wordl. It consists of sugar motifs repeated a number of times. This O-specific polysacharide is highly variable so can have different sugar motifs here and can repeat it different numbers of time. Cause it's coating the cell, the different lengths of sugar motifs and different arrangements, make it immunologically distinct to our immune system. This o-specific polysaccharide is important for the cell.

After placing bacteria on the slide, either with a drop of water or just from a drop of a broth culture, you are directed to let it air dry before heat fixing. What would happen to the bacteria on the slide if you heat fixed it before the slide had dried?

The boiling action of the water would damage the bacteria and result in no bacteria being present for staining.

Why is no energy required in passive transport?

The concentration gradient drives the movement.

Why is it important that crystal violet be a contrasting color to safranin?

The contrast allows you to differentiate between gram-negative and gram-positive cells by observing the color of the organism.

Microbial species have a core genome and a pan genome. What is the difference between the two?

The core genome is a set of genes shared by all members of a species, while the pan genome includes the core genes as well as genes that are not shared by all members.

What is the most critical step in the Gram staining procedure?

The decolorization step

What are the different bacterial shapes? What determines these shapes

The peptidoglycan layer is modelled by interaction with proteins Bacterial species have characteristic shapes determined by shape of the cell wall Cocci - round Rod - rod shaped Spirillium - slightly wavey rod Spiroquete - very very wavey Budding and appendaged Filamentous

What is the biological function of endospores?

They enable organisms to endure extremes of temperature, drying, and nutrient depletion.

What is binary fission?

They way that bacteria replicate is termed binary fission. It refers to the ability of a cell to replicate everything in the cell and then split down the centre to form two identical daughte cells (different to miosis and mitosis) have no nucleus

What is the structure of a gram neg cell envelope? what are the functions of some of those elements?

Thiner peptidoglycan cell wall Surrounded by second lipid bilayer termed the outermembrane. Outer membrane is anchored onto the cell wall with these braun lipoproteins, and it's decorated on the outside with lipopolysacharides. Lipopolysacharides are important to maintaining structural integrity of semi-fluid bilayer on outside of the cell. The LPS is really important. It's composed of three components. It starts with a lipid A core.

What are transport proteins?

Transport proteins have a hydrophobic region that inserts into the lipid bilayer and on the outside it will be reasonably hydrophilic Transport proteins can be divided into a few different classes depending on how they transport molecules into the cell

If you forgot to add the counterstain to the mixed culture sample at the end of the staining procedure, gram-negative cells would appear __________ and gram-positive cells would appear __________.

colourless; purple

Which transport protein employs transporters that move molecules only in one direction? (can pick multiple) - Uniport - Antiport - Symport

Uniport and Symport

Which statement illustrates the chemical basis for the predominant type of fatty acids in the plasma membrane of a psychrophile? - Saturated fats have straight side chains that prevent tight packing as temperatures drop. - Saturated fats have kinked side chains that prevent tight packing as temperatures drop. - Unsaturated fats have kinked side chains that prevent tight packing as temperatures drop. - Unsaturated fats have straight side chains that prevent tight packing as temperatures drop.

Unsaturated fats have kinked side chains that prevent tight packing as temperatures drop.

A fellow student is unsure why their gram-negative Escherichia coli is dark blue. Upon examining the Gram stain kit, you notice it didn't have alcohol. What caused the bacteria to be blue instead of pink?

Without the alcohol destaining step, the bacterial cell wall and cell membrane were not altered, which prevented the Gram's iodine and crystal violet from being rinsed away.

If there are bacterial clumps visible in a drop of water on a glass slide, will this affect the staining of the bacteria?

Yes, the clumps of bacterial cells may retain the stains and lead to incorrect data being collected.

As long as you handle the slide gently during staining and use minimal water when rinsing, do you still have to heat fix?

Yes, unless fixed on the glass slide, the bacterial smear will wash away during the staining procedure.

For a carbon source, chemoorganotrophs generally use compounds such as: - nitrate and nitrite. - bicarbonate and carbon dioxide. - acetate, bicarbonate, and nitrate. - acetate, succinate, and glucose.

acetate, succinate, and glucose.

The main functions of the bacterial cell wall include all but the following __________. - limiting cell size - actively transporting solutes against the concentration gradient - resisting cell lysis due to osmotic forces - conferring a specific shape to the cell

actively transporting solutes against the concentration gradient

Which metabolic strategy does NOT invoke the proton motive force for energy conservation? - aerobic catabolism - photoautrophy - chemoorganotrophy - anaerobic

anaerobic

The time between inoculation and the beginning of growth is usually called the...

lag phase

The metabolic diversity of photosynthetic bacteria stems from different...

light-harvesting complexes, electron donors, and organic compounds they produce.