BIOLOGY 346 Microbes and society
Ebola virus: Family name
Filoviridae
Antoni van Leeuwenhoek (1684)
First describe the presence of bacteria in pepper-‐water soltions (and other natural substances). Also described eggs on the wheat grains with his microscope. Opposed the theory of spontaneous generation
Robert Koch
First scientist to prove a specific bacterium causes a specific disease (1890). Develop methodology to develop pure cultures of bacteria. Worked with B. anthracis, M. tuberculosis (all on the open counter) -‐ never contracted disease.
Inactivated Vaccine organism
Made from microbes (viruses, bacteria, other) that have been killed through many physical or chemical processes. These organisms cannot cause disease. -less strong immune response compared to live vaccines -excellent stability profile
PROKARYOTIC CELL: cytoplasmic membrane
Made of phospholipids and proteins. Determines what moves into the cell and out of the cell. Also performs the same function as the mitochondria and chloroplasts found in eukaryotic cells
What are vaccines?
-an agent that provides active acquired immunity to a particular disease -one of the most significant advances in medical science -Contains: suspending fluid (water, saline, fluid containing protein), preservativees and stabalizers, antigen: agent that resembles part of the disease-causing microbe -adjuvants or enhancers
Triclosan
-antibacterial agent that has multiple targets: cytoplasmic membrane at high concentration and bacteriostatic at low concentration -was found in hospital scrubs in the 70s, but has expanded to commercial use: soap, shampoo, deoderant, toothpaste, mouth wash -it is lipophili, thus passes through our skin -found in the urine of approx. 75% of individuals tested (2517 total)
what is genetic engineering?
-any changes in genetic makeup that result from the direct manipulation of DNA using various technical methods: -genetically modified plants -genetically modified animals
Phases of clinical trials: Phase lll
-assess effectiveness in comparisson to 'gold standard' -only 18% of phase ll studies make it to phase lll -randomized and controlled -large pateint groups: 300-3000+
denal plaque
-bacterial biofilm: -bacteria (60-70%), salivary polymers, bacterial extracellular products -300-500 cells thick -bacterial metabolites are responsible for dental diseases
Small intestine microbial composition: GIT
-proximal small intestine relatively sparse -distal small intestine several diff. species (includes some coliforms e.g. E Coli.)- coliforms used as a bacterial indicator of water quality
foods stored under a controlled atmosphere
-put food into storage chamber, draw in a vaccum to remove the air, replace air with CO2 or N2 (basically reduce the amount of O2 present) -Co2 storage has been used to extend the shelf life of apples
for what reasons would bacteria NOT grow
-there was no bacteria in the place that was swabbed -wrong medium was used for the bacteria- maybe AGAR was not suitable for this particular bacteria -the bacteria is potentially not developing quickly enough
How do infections arise?
-through skin contact or skin injury -inhalation of aerosols containing microbes -ingestion of contaminated water or food -insect bites (e.g. ticks or mosquitos) -sexual contact -injection
How TB settles in lungs
-uptake of pathogen into macrophages, - replication within macrophages, -killing of macrophages, -re-uptake by further macrophages -trigerring of inflammation -formation of tubercles comprising of tightly packed macrophages -enclosure of infected macrophages by collagen -death of infected cells in centre of tubercle -rupture of tubercle and reactivation of infection (often in patiens with supressed immune system)
How many people in world pop. are infected with mycobacterium tuberculosis?
1/3 5-10% infected develop disease -TB causes one fourth of all HIV related deaths -480000 people developed multi drug resistant TB in 2013
how many pathogenic bacteria that affect humans?
1000
bacteria in GIT how much bacteria compared to rest of body?
10x more bacteria in our GIT than cells in our entire bodies 0metabolic activity roughly equivalent to that of an organ
Examples of epidemics/ pandemics in human history: black death
1346-1350, over 25 million deaths
History of vaccination
1803- royal Jennerian institue founded 1870s- voilent opposition to vaccination 1880s- a vaccine against rabies- Louis Pastuer 1890s- Emile Von Behring discovers basis of Diptheria and tetanus vaccines- showed that animals injected with small amounts of the tetanus toxin become immune to the disease 1920s- vaccines became widely avaliable for diphtheria, whooping cought, tetanus 1955: polio vaccination begins 1956: WHO fights to erradicate small pox, 1980 smallpox erradicated from the world 2008-Cervical cancer, human papiloma virus
The first pure cultures of bacteria first obtained and grown in the ___
1850s (19th cent)
Golden age of microbiology
1876-1902. Human pathogenic bacteria were discovered during this peroid
around what time did microbiology really get going?
1880
strange mosiac disease in tobacco in netherlands (1879): Adolf Mayer
1882: enzyme like contagium 1886: Infectious agent is bacterial but that the infectious forms have not yet been isolated.
charles chamberland
1884: invented a filter with pores smaller than bacteria
life attenuated vaccine
Derived from disease causing pathogens (virus, bacteria) that have weakened under lab conditions PROS: excellent immune response CONS: attenuated pathogens can revert to original and cause disease, less safe
semi conservative replication
During DNA replication, each strand is a template for the synthesis of a new strand. The term semi-‐conservative replication means that in the new DNA molecule there is one old and one new strand. DNA molecules are asymmetrical
where did viruses come from? cellular origin hypothesis
Evolved from bits of DNA or RNA that escaped from genes of a larger organism. The escaped DNA could have come from plasmids or transporons (molecules of DNA that replicate and move around to different positions within the genes of the cell)
organism classification based on the types of sources they use for carbon and energy: heterotroph
use organic molecules for carbon and energy some heterotrophs need N P and S to be in organic form too other heterotrophs can use N P S inorganic
EUKARYOTIC CELLS: Lysosomes
used for cellualr digestion- they would take a very large molecule and break into smaller molecules
Nitrites as food preservation
used for meat to keep a bright red color-has been found to be a carrcinogen precursor
ethylene and propylene oxide food preservation
used for spices, dired fruit and nuts -known mutagens
food preservation with sodium proponate (used in bread) and sodium benzonate (fruit, pickles, margarine)
used for years, no evidence of harm to humans
Dimitri Ivanosky (1892)
used the filter with small pores to study tobacco mosaic virus -crushed leaf extracts from infected tobacco plants remain infectious after filtration. thought it was a toxin produced by bacteria
virus host cell interaction
absorbiton and attachment to a suceptible host -virus and host cell must have complimentary structures to be able to interact - chance event, recognition/ specificty -host cell has a "virus receptor" a normal cell structure that the virus exploits as a binding site -virus has an antireceptor a virus structure that binds to the host cell a host cell is suceptible if it has the right virus recpetor
what happens if respiratory tract becomes damaged?
can be damaged by bronchitis or viral pneumonia -can become susceptible to secondary infections by pathogens descending from the nasopharynx
currently circulating influenza strains are identified by...?
WHO global influenza surveillance and response system, partnership of national influenza centres around world
Golden rice and Vitamin A deficiencies
WHO summary tables and maps describe global problem of Vitamin A defieciency VAD affects people in 120 countries -190 million children and 19 million pregnant women -millions of cases of Xeropthalmia (drying of eyes) -causes 500,000 cases of irreversible blindness -causes 1-2 milllion deaths anually
PROKARYOTIC CELL: cytoplasm
Water filled compartment where the cell does most of its chemical reactions. Filled with building blocks of cellular molecules
PROKARYOTIC CELL: Cell wall
Water moves freely across the membrane. So much water moves in that the cell membrane could rupture -‐ the cell wall adds mechanical strength to the cytoplasmic membrane
ATP explained
X + Y--> bonding two things requires energy X - Y --> releases energy when bonds are broken
Of the five classes if microbes, which two are related closest to humans?
Yeasts and fungi
5 Classes of microbes
Yeasts, Bacteria, Viruses, Fungi, Archea
Does the cell usually die after bacterial infection?
Yes (too much DNA or protein)
Ebola virus: five subtypes
Zaire ebola virus, sudan ebola virus, Tair forest ebola virus, bundibugyo ebola virus, reston ebola virus
what is agar?
a carbohydrate
viruses have to grow in___
a cell (attacks the cell and makes 100s or 1000s of virus copies per cell)
PROKARYOTIC CELL: somethings that may be on the outside of the cell... capsule
a layer to protect the cell from drying out- some capsule material is used in food industry (Xanthan gum)
permissible
can support replication of the virus
microbial products take many forms such as:
carbohydrates (future of microbiology is to figure out the function of these molecules)
Listeria- food born pathogen
causes gastrointestinal illnesses -can be transferred from soil and fed to cattle from cattle the bacteria find their way into meat and milk -from there, consumption of contaminated meat or milk leads to human illness -listeria is a type of microbe that is well adapted to growing at cooler temperatures (e.g. it will grow in food that is being properly stored in the refridgerator)
Mycobacterium tuberculosis
causing agent of TB -no clear classification into gram pos/neg =protective cell was with high content of waxy lipid - capable of intracellular growth -main target lungs, but can also spread to various other organs -airborne transmission
naked
cell lyses, all progyny is relased at once, cell is dead
Antibiotic targets
cell wall, DNA/RNA sythesis, folate synthesis, cell membrane, protein synthesis
ACNE!
cells lining the hair follicle shed too quickly and clump together which plugs the follicle opening -prevents sebum from escaping -sebum and cell debris causes P. acnes to grow quickly -bacterial metabolites cause inflammation -when the bulky material is too much, then contents spill to nearby tissues causing acne -if plugged follicle stays beneath skin (closed) it is called a white head -if the plugged follicle reaches the surface and opens up it is called a black head the colour is a result of melanin oxidation, not debris/dirt
symptoms of ebola: systemic
a) flu like symptoms, such as fever and chills b) hemorrhagic manifestaions (internal bleeding, present in less than 50% of affected patients)
symptoms of ebola: neurologic
a) headache b) confusion c) coma
symptoms of ebola: gastrointestinal
a) lack of appetite b)nausea c) vomiting d) abdominal pain e) Diarrhea
Koch
develop principles to determine if bacteria is pathogenic on not
influenza virus structure
diameter- 80-120 nm -envelopped ss rna virus -hemagglutinin HA for binding and host cell entry -Neuraminidase for host cell exit but also entry/ mucus degredation -11 proteins
Pasteur
did alot of work on Tuberculosis- great white plague.
Each strand of DNA in the double helix is oriented in the opposite ____
direction (the DNA strands are said to be anti parallel
Emil von behring and shibasaburo Kitaso
discovered that serum of animals immune to diptheria or tetanus contain specific antitoxic activity -antibodies- serum therapy
1976: Edward Jenner
discovers vaccination, discovered it in its modern form, proved to the scientific community that it worked -cowpox= milder, smallpox=deadly
Lazzaro Spallanzani (1767)
discredited Needham- said that the heating of his bottle didnt kill everything inside
Tetanus
disease caused by neurotoxin produced by Clostridium tetani. Cells of this microbe remain localized at the site of infection; only the toxin moves to central nervous system -obligate anerobe (no 02), endospore forming -tightening of the jaw and neck muscles, -- called lockjaw -Other early symptoms include sweating, grouchiness, drooling, back spasms, potential for heartbeat irregularities, fluctuations in blood pressure -patients die bc they cannot properly exhale- unrelentring contraction of the diaphragem results in last inhalation -any break in the skin can alow clostidium tetani to enter e.g. splinters, shaving nicks, puntcutres, serious cuts -muscle contractions can be so severe they break bones -treatment: thurough cleaning of wounds to remove endospores, immediate passive immunotherapy directed at neurotoxin (neutralizes toxin before it can attach to neruons), administration of antimicrobials like penacillin, active immunizaion -once nuerotoxin binds to neuron, treatment limited to supportive care
Three reservoirs of infectious disease: What is it called when disease is spread from animal to human?
disease that is spread naturally from thier usual animal host to humans is called zoonotic disease
endogenous disease
diseases that are caused by the normal flora
Bacillus Subtilis
divides by cell division- can form spores, almost indestructive
How does e coli grow?
divides by cell division- does not form spores. When it runs out of nutrition it is stagnant
Non pathogens
do not cause disease
effectiveness defined
does the vaccine help people? -usually assessed retrospectively
define efficacy
does the vaccine or drug work?
different toxins/cell types you may come accross with food poisoning
enterotoxin-acts on intestinal cells -leading to diarrhea neurotoxin- acts on motor neurons- leading to paralysis or muscle contraction cytotoxin-kills the cells
suviving in the environment: Enveloped vs naked
enveloped viruses are less stable than naked
What do microbes help clean up
environmental disasters (such as oil spills, they degrade it with enzymes)
metabolic reactions are:
enzyme mediated reactions, some do happen spontaneously however
Percy Schmeiser Vs. Monsanto court case
farmer from sask. who grows canola. He maintained his own seed stocks instead of buying seed from monsanto. His crop became contaminated with pollen from nearby GM crops -Monsanto tested a patch of his crop by dumping round up on it -monsanto sued Schmiester and had his crops removed
where to TB drugs target?
inhibits cell wall synthesis (Isoniazoid and Ethanbutol), exact target unclear, disrupts plasma membrane and energy metabolism (pyraznlamide), Rifampin inhibits RNA synthesis
Membrane associated protein (VP24)
inhibits interferon signalling. Promotes virus assembly and budding.
How do antibiotics work? bacteriostatic
inhibits/ stops growth
Immediately following a break in the skin, phagocytes engulf bacteria within the wound. This is an example of an _____ immune response which is _____ against a pathogen
innate, nonspecific
Term variolation refers to:
innoculation of scab material into small skin wounds
lysogenic cycle
integrates genome into host and stays there
Salmonella pathogensis
intracellular (mostly in SCV) -microvilli effacement -actin involved in host cell invasion -Type 3 Secretion system : two
infection
invasion of body by pathogen that overcomes the body's external defences, multiplies and becomes established in the body (short or long term). An infection may result in disease
Ernest William Goodpasture
invented methods for growing viruses in chicken emryos and fertilized chicken eggs --> enabled development of vaccines against a variety of viruses
Immunization: passive immunity
involves the transfer of preformed antibodies
Anything fermented means ______ were at work
microbes
organic molecules are produced by:
microbes
Are all soaps created equally? bar soap
microbes can grow on the bar and spread from one individual to another -should not be used in public places -microbe growth is more pronounced on soap that stays wet or sits in water
American centre for disease control reports indicate that antibiotic resistance is responsible for...
more than two million illnesses -23000 deaths
tissue trophism
microbial preference for certain tissues for growth -host provides specific nutrition, growth factors, and/or growth conditions for bacterial growth -suitable gases, pH, temperature
resident microbiota
microbial species that are life long residents, but are not found everywhere in the body (e.g. blood, brain)
prions
misfolded proteins that infect cells and guide in misfolding more proteins e.g. mad cow disease
There is evidence to suggest that at one time chloroplasts and mitochondrion were actually prokaryotic cells that were engulfed by a primitive eukayotic cell and then they co evolved together and became dependent on eachother. What is the evidence?
mitochondiron and chloroplasts have their own DNA. This DNA is different that was in the nucleus.
tissue adherance
most bacteria colonize specific tissues and/or sites because they can stick (adhere) to the eukaryotic cells at that tissue -bacterial surface molecules (Called ligands or adhesins) interact with receptors on the host cell
Examples of epidemics/ pandemics in human history: swine flu
over 14000 deaths, 2009
Examples of epidemics/ pandemics in human history:AIDS
over 30 million deaths, 1981 to present
food preservation and chemicals
over 3000 different chemicals that can be added to food -the additives are generally regarded as safe -some are used to enhance/ preserve texture, color, freshness and falvor -some are used to inhinit microbial growth and extend shelf life -the efficacy of chemical preservations depends primarily on the concentration of the preservation, the consumption of the food, and the type of organisms to be inhibited -still data being collected on whether chemical additives are safe or not
Examples of epidemics/ pandemics in human history: spanish flu
over 75 million dead. 1918-1920
Examples of epidemics/ pandemics in human history:Haiti cholera outbreak
over 8500 deaths 2010-present
GURT
overturns traditional agriculture of over a billion farmers -instead of saving seeds for the next years crop, forced to buy seeds anually from biotech companies so its not good for farmers in developing nations -terminator plants still produce pollen
Martinus Bejernick:
repeated experiments and got convinced that the filtered solution contained a new form of infectious agent 0infection is not due to microbe but to a non corpuscular (non cellular) entity contagium vivim fluidium -he though viruses were liquid in nature -coined term virus
innate immunity summarized
primitive and broad -fast (hours) -short duration -no memory
probiotics and prebiotics
probiotics: good bacteria that exploit microbial antagonism to compete with pathogenic species -may produce substances that are toxic to pathogenic strains -prebiotics: food for the good bacteria -encourage growth of good bacteria- indicated for intestinal health
Ebola virus: matrix protein VP40
promotes structural integrity, virus assembly and budding
Minor nucleoprotein VP30
promotes transcription initiation
PROKARYOTIC CELL: ribosomes
protein manufacturers for the cell- they recieve orders from DNA by they way of an intermediate called mRNA -They translate the information on mRNA to make protein. -They assemble proteins from amino acids. There are 20 different amino acids that are used to make proteins. The instructions of what order and how many amino acids are needed is provided in the mRNA (messenger RNA)
what was collip's contribution to insulin?
purified the insulin, so that it was suitable to give to humans, also decided the dosage
what are clinical trials?
purpose: to determine the safety, efficacy, and effectiveness of new treatments -vaccines, drugs, medical devices etc -ethical approval must be granted in the country where the approval is being saught- evaluates the risk/benefit ratio -carried out in several phases
HIV is not a virus from outerspace:
study with sunspot numbers and HIV pandemic-- correlation not causation
RNA bases
sugar is ribose bases are: adenine, guanine, uracil, cytosine
theory of spontaneous generation: John Needham 1748
suggested that microbes arise spontaneously in mutton gravy. Needham had boiled the gravy and sealed the containers with cork, but yet microbes appeared -‐ his experiments were faulty. the heating of the bottle did not kill all of the microbes that were living there
epithelial layers:
surface of cells that make up skin and all structures within body that is in contact with the environment
Three reservoirs of infectious disease: human carrier
symptomatic (showing symptoms of a disease) vs. asymptomatic carrier
Genotype
the order of or sequence of the AGCT's in the genome, more of a qualitative term
why do fermentation if it doesnt produce that much ATP?
the production of lactic acid build up--> not getting enough O2. Fermentation then used to create energy
w to avoid getting infected # 7
travel safely
chemicals that serve as nutrients can be divided into two groups: major bioelements
"CHONPS" Carbon (C), Hydrogen (H), oxygen (O), nirtogen (N), phophorous (P), sulfur (S)
Ignaz Semmelweis (1847)
"Savior of mothers"-discovered that the incidence of childbed fever could be drastically cut by the use of hand disinfection in maternity wards Some doctors were offended at the suggestion that they should wash their hands. Practice became accepted later after his death and Pasteur confirmed the germ theory.
theory of spontaneous generation: Jan Baptista van Helmont (early 1600s)
"observed" that rats originate from wheat bran and old rags. A 17th century mouse recipe: •1 pair sweaty underwear •several husks of wheat Place sweaty underwear and wheat husks in an open-‐mouthed jar -‐ let sit for 21 days - Accepted by common people -‐ based on their observations of slime that produced toads, and meat that generated worm-‐like maggots
estimated economic cost associated with antimicrobial resistance in 2050 and amount of people that will have died..
$$ 100 trillion 10 million dead
Modes of transmission (infectious disease): 3) vector transmission
(animals that transmit disease from one host to another) a) biological vector (transmits and serves as a host) b) Mechanical vector (transmits but not required as a host)
Are all soaps created equally? plain soap
(not antibacterial) -recommended for home/ business use -easy to find and cheap
salt and acidity for food preservation
(salt + vinegar) -for other foods, sucrose would be added in place of the salt -smoking and drying have been used in combination with salt for the preservation of fish and meat
900AD Chinese and variolation
(vaccination_ Chinese first to discover and use primitive forms of vaccination called variolation -the procedure was most commonly carried out by inserting/ rubbing powdered smallpox scabs or fluid from pustules into superficial scratches in the skin -worked for some peole, b/c superficial cuts were not deep and body could fight it off
different terminator systems (GURT)
- GURTs aka trait technology -inserts modifying gene such that genes governing good growth, germination, and other desirable characteristics can be activated only when the plant is sprayed with a propreitary chemical -the seed compant would produce the plant, treat it with the chemical and allow it to produce viable seeds which it sells to gorwers -the seeds produced by the plant would be sterile unless the grower was also able to purchase the chemical
EPEC/ EHEC
-EPEC uses a syringe like type 3 secretion system (T3SS) to inject effector proteins into the host cell -type 3 secreted effectors manipulate host cell function. Among many other things they manipulate actin structure (actin= component of cells skeleton) This leads to a protrusion termed pedestal on which hte extracellular bacterium resides -EPEC does not eneter the cell. Its attachment to the host cell surface leads to an effacment of the microvilli sturcture (hair like membrane protrusions of the intestine) at the side of adhesion
Beta Carotene
- a precursor to vitamin A is normally acquired in the diet by the consumption of green vegetable. Beta carotine is then converted to retinal and subsequently into Vitamin A in the gut -rice is a staple food for many of the people living in countries where vitamin A difieicieny is a problem -the production of genetic modified rice "golden rice" that contains beta carotene is thought to be a less expensive solution than vitamin A supplementation programs or increased farming to produce green vegetables
refridgeration slows the growth of most microbes
-BUT it can also select for the growth of some that are well-adapted to growing at temperatures of 2-6 degrees C -freezing halts the growth of most microbes but they often survive and will resume growth once the food is thawed
Anti-resistance drugs: beta lactamase inhibitors
-Beta lactam antibiotics target cell wall synthesis -beta lactamases hydrolze the beta lacatam ring -combining beta lactamse inhibitors with beta lactam antibiotics can increase the efficacy and spectrum of these antibiotics
Metabolism and building up
-DNA replication -RNA -Proteins (enzymes) these things determine the cell and guide other reactions
Helicobacter Pylori and a scientists dedication: Drs. Warren and Marshall
-Dr. Warren identified a new bacteria (H. pylori) in stomach biopsies -Patient interviews suggested similar symptoms - inflammation in the stomach -endoscopies on 100 patients- people with ulcers had H. pylori more often than those without -People hesitant to believe bacteria could live in the stomach -Have to prove that the bacteria are harmful or harmless--> kochs postulates!
Microbes as food
-Food you eat is seldom sterile- preserved, fresh, or prepared. -microbes can cause food spoilage, or food borne illness -microbes are also essential in the production of specific food products (yogurt, cheese) -microbes are believed to confer certain health benefits when taken in tablet form or as part of foods (eg yogurt) -these are the probitoics and they are though to augment perhaps replace the microbiota of the gut
Normal flora: repiratory tract
-Nostrils heavily colonized -S. epidermis, S. aureus (20% of pop.) -nasopharynx is colonized -pharynx (throat) -streptococci -sometimes pathogens colonize the pharynx- kept in check by non pathogenic species -sinuses are sterile
Why is TB rate so high among miners in South Africa?
-Silica dust increases risk of pulmoary TB (particularly gold miners) -living and working conditions (mine shafts are crowded and poorly ventilated and so are hostels with many other people) -prostitution is common in the areas where the miners settle by their work- high rates of transmission of HIV which has been attributed to subsequent increases in TB. It increases the likelihood that a person infected with TB will progress to active disease, shortens survival time among co-infected individuals and increases likelihood of atypical TB manifestations that are difficult to diagnose -smoking and alcohol -increae of drug resistant TB -poor medical infrastructure at the mine and rural areas -no vaccination -migration patterns: infects community memers- collapse of apartheid system enhanced workers migration- TB levels raised
Thimerosal
-Thimerosal acts as preservative -does not alter potency of the vaccine -contains ethyl mercury -methyl mercury (bad mercury) is found in tuna and other foods -Thimerosal claimed to have caused autism--- nope! -WHO concluded no evidence of toxicity and no reason to switch to more expensive forms -CDC asked manufacturers to remove thimersol from vaccins as a precautionary measure -since autism diagnosis is one the rise, some parents saw it as indication that it caused autism -autism cases continue to rise despite removal
Microbial Composition in GIT: Large intestine
-bacterial composition similar to that found in feces (up to 60% dry fecal weight is bacteria) -coliforms more predominant -predominant species are anaerobic: Methanogens may be present, only direct association with archea as normal flora
Host directed therapies: toll like receptor agonists
-bavterial components (e.g. LPS) bind to TLR on immune cells causing them to be activated -Using TLR agonists (molecules that bind to TLR receptors) cause immune cell activation and the generation of cytokines involved in clearing the infection
Phases of clinical trials: Phase ll
-begins to examine efficacy -conducted in larger numbers 100-300 -may be randomized controlled trials -ongoing safety investigation -great chance of failure here
HElicobacter pylori and MArshall's reaction
-bloating, decreased appetite, bad breath, vomiting clear liquid every morning, endoscopy (severe gastirtis, immune cell infiltration, damaged epithelium) -treated with antibiotics
cultivation of viruses in lab: embryonated eggs
-can innoculate membrane that best supports specific virus
THE BAD.. role of microbiota in lrg. intestine
-certain species (e.g. bacteroides) produce carcinogenic metabolites -antibiotic induced diarrheal disease -some speculate alterations to gut flora and . or reduced immune tolerance contribute to IBD
Extravasation
-changes in the blood vessel wall that makes it sticky and leaky. This allows more fluids and proteins like complement to enter the tissue -recruitment of more pagocytic cells- neutrophils and monocytes- to engulf and kill the pathogen. The changes in the blood vessel allow these cells to leave the blood and enter the tissue- extravasation
antigenic shift
-changes in viral genome due to re-assortment of RNA segments deriving from 2 virus strains infecting the same host cell -less frequent than antigenic drift -leads to new strain that no one has immunity to and has pandemic potential
why do lactobacilli bacteria take over vagina in reproductive years?
-circulating estrogens cause the production of glycogen -lactobacilli metablozies glycogen to lactic acid, which lowers vaginal pH -low pH (approx. <4.5) inhibits growth of other bacteria and yeast -another downside to having to take antibiotics! -unclear whether the microbial composition changes through out menstrual cycle -excessive vaginal cleansing also alters microbial composition, which has a similar effect to antibiotic therapy -lactobacilli also produce hydrogen peroxide and bacteriocins (antibacterial peptide) -increase in hydrogen peroxide producing lactobacilli in pregnant women -sexual intercourse changes lactobacilli concentration -also increases the e coli conectration -other factors seem to contribute to microbial compostion e.g. race, type of birth control
Normal flora: Urogenital tract
-colonized during birth -urine and urogenital tract normally sterile- flushed regularly -vagina and distal 1cm of urethra are colonized -distal urethra consists predominantly of skin bacteria - may also contain enteric bacteria
clinical significance of repiratory tract microbiota: Chronic obtrusive pulmonary disease (COPD)
-common in smokers -difference in mircrobial composition betweenCOPD patients and healthy controls
inactivated- subunit vaccine
-containing only antigenic parts of the pathogen -these parts are necessary to illicit an immune reponse -less strong immune system response, excellent stability profile Disadvantage: Proteins, if denatured may bind to different antibodies than the protein of the pathogen -some bacteria have polysaccharide (sugar) capsule that helps the organism evade human defence systems especially in infants and young children -polysaccharide vaccines create a repsonse against the molecules in the pathogens capsule. E.g. meningitis -against the molecules in the pathogens capsule, polysaccharide conjugated into carrier protein -proteins are best to make immune response
what are the concerns with golden rice?
-contamination of other farmers feilds -loss of markets for farmers as their product may not meet exportation requirements -loss of diversity of other crops
HIV structure
-diameter: 120 nm -envelopped ssRNA virus - key proteins: gp120 (attachment to host cell), gp41 (fusion with host cell), reverse transcriptase (generation of DNA from RNA, very error prone), integrase (integration of viral genome into host genome), protease (virus assmbly after budding from host cell)
simple virus replication
-dissassembly, uses host cells replication, reassembly
What type of proteins are necessary on enveloped virus to attach to host cell?
-envelope glycoprotiens (proteins modified with carbohydrates) -encoed by the virus are embeded in the membrane these glycoproteins are required for attachment to the host cell
Phases of clinical trials: Pahse 0
-exploratory first in human trial -small pop. of 10-15 -pharmacokinetic study -dose too low for effect (therefore does not provide safety or efficacy data)
steps to an infection
-exposure to pathogen, (contact to skin, or inhalation through lungs, injection into tissue, ingestion), adhere to cell surface, invasion through epithelium, colonization and growth, meanwhile spreading to other sites, production of virulence factors, tissue damage and disease
Anatomical and physiological barriers
-eye: blinking, tears, lysozyme (capable of destroying the cell walls of certain bacteria and thereby acting as a mild antiseptic) -skin: structural barrier, sweat sebum, lactic acid, propionic acid, lysozyme, normal flora -urogenital tract: Lavaging action of urine, acidity of urine, lysozyme, vaginal lactic acid (normal flora) -respiratory tract: coughing, sneezing, mucus, cillary action, phagocytes, lysozyme -GI tract: stomach acidity, normal flora, peristalsis, antimicrobial compounds
solutions to TB in southern africa
-face masks- wear it in mine and to reduce exposure -improve living conditions: better/ less crowded housing -encourage housing that allows families to live close to mines -better mining practices- change strategies, like how much dust is produced -HIV prevention (e.g. condoms) -keep patients son their treatment (e.g. take antibiotics for one year) -keep medical records
Solutions to TB in South Africa
-face masks-> wear it in the mine and to reduce exposure -improve living conditions- better/ less crowded housing -encourage housing that allows families to live close to mines -better mining practices- change strategies like how much dust is produced -HIV prevention (e.g. condoms) -education -keep patients on their treatment (e.g. antibiotics for one year) -must introduce medical records
Thalidomide
-first marketed in 1957 -was used to treat morning sickness in pregnant women -5000-7000 infants born with limb malformation in Germany alone -40% survival
why would food be fermented?
-food preservation- the waste products of the bacteria (e.g. and acid/ acohol) inhibit further growth of microbes in the food -Improve digestability of the food - breakdown of fibrous macromolecules, tenderizes the product (e.g. some vegetables, meat) -add nutrients and flavours- microbial metabolism generates vitamins (e.g. B12) and produces metabolites that flavour the food
susceptibility and permissiveness
-for virus to be successful, must encounter cell that is susceptible and permissive
political economic benefits:
-generate heat for building -generate methane to use for heating or generation of electricity -reduction of heat in thhe water would be advantageous before discharging it (after treat,ment) into a body of water -if there is less heat in the sewage there is less corrosion of the pipes carrying it
injection of recipient with preformed antibodies- when would this happen?
-if you are not up to date on your tetanus immunization and get a puncture wound, you're given an injection of horse anti-serum to tetanus toxin or human gamma globulin -given to individuals exposed to diptheria, hepatitis, measles, rabies -snake bites -spider bites
Vitmain A defieicney results in
-imapired growth and increased morbidity to common childhood illnesses in children -eye damage (leading to night blindness, then complete blindness) -damage to mucous membran tracts (increased susceptability to respiratory g.i. ppathogens) -impaired immunity and blood cell development
Why do GE crops?
-improve nutritional quality of food -reduces use of pesticides/ herbicides in the growing process -improve production yeilds at lower costs
extracellular state of virus
-inert particle (protein, nucleic acid, maybe lipid)
peridontal disease
-infections of the supporting structures of the tooth -gingivitis is the most common kind (inflammation of gum tissue) -diseases confined to the gums do not lead to tooth loss but other more serious diseases can (periodontitis) -mechanisms of tissue destruction are not clearly defined
Acute inflammation characteristically involves:
-influx of neutrophils-- most abundant of immune cells in blood
what surfaces does the epithelial layer consist of?
-intact skin, dry, high salt, catonic peptides -mucous and ciliated cells in respiratory tract -mucous and peristalsis in gastrointestinal tract -stomach acid, lysozyme in saliva and tears
Immunization: Active
-involves long term protection (memory) -natural infection -vaccination
Vaginal flora in prenant vs. non pregnant women
-its different! -bacteria found in newborn meconium (A dark green fecal material that accumulates in the fetal intestines and is discharged at or near the time of birth) -composition different from vaginal flora prompted investigators to look at the placenta
differences between spoilage microbes and pathogens
-microbes can help make food better, spoil food, or be the cause of food borne illness -pathogens are those that have specific mechanisms that enable them to colonize in the hosts digestive gut -pathogens would have some mechanism to survie passesage through the stomach and collonize in the small or large intestine -pathogens may have the ability to produce a toxin that causes damage to the host
when does human colonization occur-after how long? How does the normal flora change as the baby grows?
-microbiota and normal flora typically established within 48 hours -organisms that constitute the normal flora are dynamic and are altered with changes in: Diet, infection by pathogens, drug therapy, puberty, tooth eruption
Source of antibotics: actinomycetes
-produce tetracyclines, aminoglycosides, macrolides, and other clinically useful antibiotics that aren't beta- lactams -branched bacteria -reproduce by spore formation -responsible for wet soil smell
Maggot therapy
-military surgeons noted that wounded soldiers bearing infested wounds had beteer outcomes than those who did not -routinely used in the 30's prior to the discovery of antibiotics and improved surgical techniques -first modern studies were performed in 1989- successful for the treatment of chronic pressure ulcers, diabetic foot ulcers, post traumatic wounds etc -in 2004 the FDA granted permission to market maggots for use in patients
Helicobacter pylori
-more than 50% of pop. is colonized ->80% are asymptomatic -10-20% risk of developing peptic ulcers -1-2% risk of developing stomach cancer -survives in the stomach by burrowing into the mucus lining where it adheres to epitherlial cells
oral diseases
-most common and economically important condition resulting from microbiome/ human interaction (dental carries, aka cavities) -includes: dental carries, gingivitis, peridontal disease, abscesses and severe infections upon invasion
Host directed therapies: immunomodulatory peptides
-multifacted peptides with many biological properties -upregulated immune response required to clear infection -downregulated potentially harmfull inflammation
How do bacteria become resistant? to antibiotics?
-mutation in the target of the antibiotic (e.g. altered binding site) -expression of efflux pumps -decreased permeability (e.g. mutate proteins that allow for antibiotic passage into the cell) -expression of enzymes that degrade the antibiotic
Antibiotic resistance
-noted shortly after discovery of penacillin -about 70% of bacteria causing infections in hospitals are resistant to at least one antibiotic used to treat patients -some organisms are resistant to all approved drugs
What are virsuses?
-obligate intracellular parasites- replicate only inside the living cells of other organisms -They do not fall under any domain. The term acytota or Aphanobionta is occassionaly used to describe viral domain -Viruses are highly specific: specific to cells/ species -Structure: some naked, envelopped or complex capsids -Viral genetic material: ssDNA, dsDNA, ds RNA, ssRNA -viral replication strategies: where the genome is replicated or replication cycle (lytic, persistent, latent)
what does microbial antagonism do for the host?
-occupy space so that pathogens cannot -outcompete pathogens for nutrients -producing inhibitory substances (e.g. substances with antibiotic effects) -lower the pH so that pathogens cannot grow
where is golden rice being grown?
-only production facilities in greenhouses and a few feilds in the phillipines -internation rice research institute initiated multilocation feild trials in August 2013 only to have some of the feilds vandalized -crop yeilds were lower than expected (lower than what farmers would have achieved with their regular seed) but the beta carotene levels were good -a few countries have expressed interest in growing the crop to reduce the problems with Vitamin A defieiceny in their peoples
Stomach microbes
-pH of 1-3 when the stomach is empty -inhospitable for most bacteria- exceptions include acid-tolerant lactobacilli (and others) -helicobacter pylori
what was known at the time about diabetes and insulin:
-pancreas of deceased diabetic patients showed damage -thought that damage might have been caused by digestive juices produced by the pancreas
Phases of clinical trials: preclinical trial proof of concept
-performed before testing in humans -exact studies performed may differ -pharmacodynamics: what the drug does to the body -pharmacokenetics: what the body does to the drug ADME: absrobtion, distribution, metabolism, elimation, toxicity -performed in tissue culture/ lab animals
Why is antibiotic resistance on the rise?
-physician misue/ abuse- 80 million perscriptions filled in 1998 -patient misuse/ abuse stopping medication when you 'feel better' and sharing medications -use in livestock as a growth enhancer- accounts for 60% of antibiotic use
Phases of clinical trials: phase lV
-postmarketing surveillance -may be required by regulatory agencies -can be used to test for drug interactions -can be used to examine specific populations not evaluated in clinical trials (pregnant women)
Bacillus Anthrax summarized
-potentially fatal, mostly herbivorous mammals, some other mammals and birds, can spread to humans (mainly prob. for farmers) -Koch's work on anthrax resulted in first proof of bacterium that caused disease -humans acquire disease directly/indirectly from infected animals, occupational exposure to infected/ contaminated animal products--> controlling livestock is key -generally regarded as non contagious, records of person-to-person cases exist but are rare -gram pos, endospore forming, aeoribic/sometimes not, secretes anthrax toxin-->kills human cells and triggers adema (swelling due to fluid accumulation) -can cause problems with GIT, repriatory tract, cutaneous (skin), injection -Gastrointestinal symptoms in humans= rare -Cutaneous= Bacillus anthracis shed by infected animals enters would, produces black, swollen skin nodule called an aschar -Inhalational anthrax= Most severe, often fatal. Inhalation of endospores that germinate and secrete anthrax toxin. Initial stages are like the flu (e.g. malaise, muscle pains, sore throat, mild fever), after several days symptoms progress to severe coughing, vomiting, fainting, confusion, shock and death -First anthrax vaccine developed by Pasteur in 1881--> farmers must use this and bury and burn the bodies of dead animals who had anthrax -Vaccine available to famrers, healthcare workers, military , researchers -treated w antimicrobial drugs e.g. penacillin -biological terror agents--> 2001 terrorists spread it through US postal system and 5 died
Source of antibotics: pencillium and Cephalosporium
-produce beta-lactam antibiotics -fungi found in soil -largely reproduce by spore formation
Source of antibotics: bacillus species
-produce polypeptide antibiotics -form endospores -live in the soils
Helicobacter Pylori and a scientists dedication
-there is no animal model- not sucseptible to infection SO Dr. Barry MArshall infected himself with it
Minkowski and mering (1889) demonstrated that:
-removal of the pancreas would result in the development of diabetes -surgical ligation of the duct that delivered digestive juices to the intestine impaired digestion, but not the development of diabetes Resulted in the conclusion that the pancreas has two functions: -production of digestive juices to be delivered to the intestine -production of a substance involved in the regulation of blood glucose
what surfaces are covered in bacteria? Respiratory, urogenital and GIT
-repiratory tract (nostrils, nasopharynx, pharynx) -urogenital tract (anterior urethra, vagina) -gastrointestinal tract (esophogus, stomach, sm intestine, large intestine)
intracellular state of virus
-replicating nucleic acids (gene expression, viral proteins)
Fecal transplants
-restores colonic microflora -few studies done on C diff infections- show fecal microbiota transplantation as an effective treatment, study in 2013 showed better results than vancomycin (antibiotic) alone -used experimental to treat colitis, constipation, irritable bowel syndrome
Human Immunodefiecieny Virus (HIV): Everything about the virus
-retrovirus family -two types: HIV 1 and HIV 2 (differences in genome and geogrpahical distribution) -cause of acquired immune deficiency syndrome (AIDS) -among others, it infects CD4 presenting immine cells such as helper T cells, monocytes, marcophages, and dendritic cells -latent infection (integration of viral genome into host genome) -scientists believe that the chimp version of the immunodificiency virus called SIV most likely was transmitted to humans and mutated into HIV when humans hunted these chimps for meet and came into contact with their infected blood (time estimate between 1884 to 1924)
What is golden rice?
-rice plants naturally produce beta carotene in the leaf structure, but this is not the edible part of the plant (the endoderm) -the golden rice plant has been modified to have the endoderm produce beta carotene by the introduction of two genes needed for beta carotene- one frim the dafodil plant and the other from a bacterium (Erwinia Uredovora) -As a result, rice appears golden in color
Roundup Ready Soybeans
-roundup is a herbicide -Its active ingredient is a chemical called glyphosate -Glyphosate inhibits an enzyme at a common branch point in the amino acid biosynthesis pathway for 3 amino acids -This particular pathways is found only in plants and microbes -Argobacterium tumefaciens is a common soil bacterium that has a mutation in the gene encoding the enzyem -it is tolerant to glyophosate -if round uo is consumed by humans it may upset the microbiota of the gut -when conventional plants are treated with glyphosate the plants cannot produce all the amino acids needed for growth and survival
Pasteur and his swan neck flasks
-shape of the flask was an important part of the experiment -The life force in the air can enter flask -‐ flask is not sealed. The bend in the flask's neck traps microbes -There's nothing wrong with the broth in the flask- it will support the growth of microbes if microbes are added to it. -The theory of spontaneous generation has been disproved
why are TB rates so high among miners in africa?
-silica dust inc. risk of pulmonary TB (particulalry gold miners) -living and working conditions- mine shafts are crowded and poorly ventilated and so are the hostels they share with many other people -prostitution- high rates of transmission of HIV- been attributed to subsequent inc. in TB. HIV inc likelihood that a person infected with TB will progress to active disease, shortens survival time among coinfected individuals and inc. likelihood of atypical TB manifestations (difficualt to diagnose) -smoking, drinking -inc. of drug reistant TB -poor medical infrastructure and mines and in rural areas -no vaccination -migration patterns: infects community members- collapse of apartheid system enhanced worker migration - TB levels raised
environment for mouth normal flora
-skin (gums, soft tissues, -teeth -environment: moist, epithelia debris, lots of nutrients, antimicrobial compounds (lysosome, lactoperoxidase, antimicrobial peptides)
Host defence against infection
-skin, mucociliary clearance, antimicrobial compounds e.g. lysozyme (antimicrobial compound found in numerous secretions that attacks peptidogylcan), antimicrobial peptides, immune system (innate and adaptive immunity)
Phases of clinical trials: Phase l Clinical trial
-small group: 20-100 healthy volunteers -assesses safety, tolerability, pharmacokinetics, and pharmacodynamics -pateints recieve excellent care from full time staff -involve drug does ranging (escalation studies)- dtermines does to use in subsequent studies
skin colonization
-superficial layers (epidermis) -hair follicles (vellus hair- peach body fuzz), all body hair, facial hair -environment = dry, high salt concentration, low pH (fatty acids, lactic acids) -antimicrobial peptides
what does a virus need to be successful?
-susceptible and permissive host cell -reproduce and package entire viral genome -package functional enzymes involved in replication of genome -be able to remain intact in the environment to infect new host cell -must have multiple structures to interact with the host cell in case some get damaged
nutritional benefits of microbes to the host
-sysnthesis of vitamins (e.g. vitamin K and B12) -metabolize steroids into molecules that can be absorbed by the host -break down food into digestible components
adaptive responses
-takes several days (7-10) -highly specific, memory, improves -two types of responses: antibody mediated and cell mediated -the cells that are involved are already present in the body, but they need to be activated, they need to proliferate and they need to differentiate into effectors and memory cells. There are also changes in gene expression
Phage therapy
-use of bateriophages to treat bacterial infection is not new -first done in 1917 0broadly used in soviet Union, USA, europe -USA and Europe developed phage products in the 1930s until the discovery of antibiotics -host range is exxtremely specific- do not harm the host or normal flora -sequencing of genome is essential as toxins may also be encoded -pahse l and ll clinical trials are underway
Salmonella
-uses its first T3SS to inject effector proteins into host cell -initial type 3 secreted effectors manipulate host cell functions. Among many other things they manipulate actin structure which leads to engulfment and finally uptake of the bacterium -once inside host, Salmonella remains within a salmonella containing vacuole (SCV) and uses its second T3SS to create a protective environment for the pathogen
Entry of virus
-virus genome and replicative enzymes enter host cell -different strategies for different viruses, but one species of virus always uses same strategy -after binding to cells virus receptor: only the genome enter cell, virus enters cell in endosome, genome is released into cytoplasm, virus envelope fuses to cell membrane, releasing genome into cytoplasm
virus replication cycle:
-virus host cell interaction- binding occurs -virus fusion and entry (uncoating) -synthesis of viral mRNA -synthesis of viral proteins -replication of viral genome -assembly of the virus from parts -release from host cell
Wendell stanley
-viruses are partciles -crystallized TMV in 1935, won nobel prize -nobel winning research soon to be shown incorrect, the crystals of the mosaic virus he isolated were pure protein, and assembled by autocatalysis
what do we do for microbes?
-we are their envrionment and provide: moisture, nutrients, warmth, suitable pH -we are essentially giant incubators for these bacteria
HIV Replication cycle
1) Binding, 2) fusion and entry, 3) Uncoating and reverse transcription trafficking 4) Nuclear entry 5) integration 6) transcription 7) translation 8) assembly 9) budding 10) maturation
LIMITATIONS OF KOCHS POSTULATES
1) Corresponding with number one. Microorganisms of the normal flora/ orignal, under specific circumstances, can cause disease in others. Microorganisms would then be found on healthy and sick individuals (EX: ear infections- caused by bacteria present on the skin) 2) corresponds with number two. Some microorganisms can't be grwon as pure culture- we might not have suitable growth media (we dont know what they eat), some microorganisms must exist in partnership with another microorganism. Virsuses cant be cultivated as pure cultures, cells must always be present. 3) corresponds with number three. Some microorganisms cause disease in one species but not in another. Salmonella is pathogenic to humans but not to turtles or chickens
three levels of defence against infection
1) anatomical and physiological barriers 2) innate repsonses 3) adaptive responses
three general steps of HIV host cell entry
1) attachment 2) co receptor engagement 3) fusion (See video on connect for detailed description)
Portals of exit (infectious disease)
1) bodily secretions 2) bodily excretions
ebola vaccines
1) cAd3-ZEBOV 2)rVSV-ZEBOV 3) 3rd vaccine candidate in phase 1 trials in UK further vaccine candidates in development a and b started clinical trials in Sept. 2014 and are about to wnter phase 2 and 3 in a number of african countries
Characteristics of immune system
1) capability to discriminate between self and foreign components 2) specificity 3) memory
sewage treatment steps:
1) collection from houses/ businesses 2) removal of things that should not have enetered the system (bottles, diapers) 3) the rest of the sewage is pumped into a settling tank- in the settling tank the solids (sludge) settle out because of gravity. The sludge is removed to an 'anerobic digester' in a primary treatment plant, the water may be disenfected before being discharged -in a secondary treatment plant, the water is altered to encourage microbes to metabolize the organic molecules 4) in the anerobic digester, the microbes are allowed to metabloize the organic molecules that are present -heterotrophic microbes consume the organic molecules -lithotrophic microbes consume the waste products of the heterotrophs in doing so they generate methane gas 5) after the digestion, the sludge can be heated then used as fertilizer or it can be burned to generate heat (to make steam to generate electricity)
HAART- highly effective antiretroviral therapy
1) combination of more than three antiretroviral agents 2) six classes of antiretroviral agents: a) chemokine receptor antagonists b) fusion inhibitors c)nucleoside reverse transcriptase inhibitors c) fusion inhibitors d) nonnucleoside revers transcriptase inhibitors e) integrase inhibitors f) protease inhibitors
the periods of a cell
1) growth, 2) degredation, 3) repair
Main reasons for increasing antimicrobial resistance
1) improper use by physicians and patients 2) use in agriculture (for animals and plants) 3) Use in industrial and household chemicals
five steps in ebola virus disease
1) infection of immune cells (such as dendritic cells, macrophages)- first line in host defence 2) inhibition of interferon signaling- the host antiviral response 3) induction of inflammation, which leads to increased damage of blood vessel lining 4) systemic dissemination via lymphatic system and blood 5) Dysregulation of coagulation and blood pressure via infection of liver and adrenal gland cells
reasons for devastating dimesions of spanish flu:
1) influenza virus from 1918 was a highly virulent pathogen, which triggered severe disease 2) similarity to avian strain might explain dissemination 3) virus seemed to have appeared first time in humans 4)three influenza waves within short period of time 5) no threapudic drugs and vaccinations avaliable 6) crowding e.g. military camps
Ebola life cycle
1) initial attachment via GP 2)uptake via macropinocytosis (engulfs virus) 3) trafficking in endosomal compartment 4) a) GP processing/ priming by proteases Cathepsin L and Cathepsin B b)pH- dependent fusion with endosomal membrane c) release of nucleoplasmid into host cytoplasm 5) replication 6) transcription (monocistronic mRNA's_ 7) Translation 8) GP processing in endoplasmic reticulum 9) GP processing in Golgi and secretion to plasma membrane 10) Viral assembly and budding 11) secretion of sGP
Researchers taking advantage of getting foreign DNA into plant cells (4 steps)
1) isolate the plasmid from Argobacterium Tumefaciens 2) introduce the plasmid back into Argobacterium tumefaciens 3) apply bacteria to injured site of plant, or dip flower plant into solution of bacteria (Want DNA to be incrooporated into gamete of plant) 4) Give bacteria time to move its plasmid DNA into the plant cell and be inserted into the plant's DNA
problems of HAART
1) long term use might lead to side effects, such as heart disease, liver toxicity ot osteroperosis 2) infection not cleared
Portals of entry into the body (infectious disease)
1) mucous membranes 2) Placenta 3) Parenteral route (other than digestive canal)
what factors make the ebola outbreak 2014 such a health catastophe?
1) poor medical infrastructure 2) ease of transmission 3) misdiagnosis 4) burial practices 5) poor boarder control 6) fast incubation time 7) globalization and travel 8) population density 9) Global panic/ media 10) late response timing 11) no perfect treatment 12) issue with quarentine 13) hunting culture- multiple species infected 14) transmission among healthcare workers 15) problem of isolation
ebola medicines
1) pre-existing antivirals such as favipiravir, brincidofivir 2) specifically developed for Ebola, such as ZMapp, siRNA
Possible solutions for increasing antimicrobial resistance
1) prevention via vaccines 2) proper use of antibiotics (e.g. no antibiotics in agriculture) 3) discovery of novel antibiotics 4) reactivation of "old" antibiotics by targeting bacterial resistance mechanisms
guidelines for preventing seasonal influenza at workplace
1) promtoe influenza vaccination among workers 2) encourage proper hand washing and respiratory hygiene practices 3) educate workers on influenza signs and symptoms. stay home when sick
Common diagnostics of ebola
1) reverse transcriptase polymerase chain reaction (RT-PCR) assay: high sensitivity, but require infrastructure and trained staff 2) Antigen detection test- easier use, less sensitive
Problems with most current antimicrobial strategies
1) target also "Good bacteria" 2) high selective pressure promotes development of antimicrobial resistance Solutions? -pathogen specific targeting (e.g. via bacteriophage) and or low slective pressure (e.g. targeting virulence factors such as secretion systems)
Koch's postulates/ principles
1) the suspected pathogenic organism should be present in all cases of the disease and absent from healthy animals 2) the suspected organism should be grown in a pure culture 3) cells from a pure culture of the suspected organism should cause disease in a healthy animal 4) the organism should be reisolated and shown to be the same as the original
Bacteria acquire antimicrobial resistance via exchange of genetic information by:
1) transformation (bacteria pick up DNA and its encorporated into their genome) 2) transduction (bacterial virus encorporated into genome) 3) Conjugation (DNA transfer- like a plasmid)
the developement of effective vaccine for HIV encounters some challenges such as
1) tremendous global diversity and mutational capacity (estimated that diversity of HIV sequences present at any one time in a patient is greater than diversity of flu virsuses worldwide per year) 2) latent infection, which is difficult to target 3) no examples of spontaneous immune mediated clearance indicative of natural immunity, ie types of immune response induced by vaccine are not well understood 4) ethical and medical restrictions since HIV is pathogen in only humans
chemicals that serve as nutrients can be divided into two groups: minor bioelements
Calcium (Ca), magensuim (Mg), iron (Fe), zinc (Z)
Using the polymerase chain reaction: review
1.For PCR we need a pair of primers that flank the sequence to be amplified and are complementary to opposite strands. They point towards each other. 2.We need to know DNA sequence to get the right primers
PCR amplication
1. Thermostable DNA polymerase. Isolate from hyperthermophiles 2.Lots of nucleotides. 3.A tiny amount of template with the region to be amplified. 4. Lots of the two primers needed for amplification. 5.Use the thermocycler to cycle through the temperatures: 1. 1 min at 95 C 2. 30 sec at 60 C 3. 1 min at 72 C 4. Go to 95 C again (1) After 30 cycles stop (see slides for visual description)
Robert Hooke First description of cells (1665)
1.All organisms* are composed of fundamental units called cells. 2.All organisms are unicellular or multicellular 3.All cells are fundamentally alike with regard to their structure and metabolism 4.Cells arise only from previously existing cells ("life begets life")
size of viruses
20-400 nm
History of vaccinations: Smallpox
429 BC Greek Historian, Thucydides, notices that people who survive smallpox in Athens did not become reinfected with the disease
Specific antibodies are readily detectable in serum following primary contact with antigen after:
5-7 days
Ebola virus: how many genes?
7, humans have 20,000!
Post midterm
:)
SEE SLIDES FOR CARBON, SULFUR AND NITROGEN CYCLES
:)
SEE SLIDES MARCH 16th for digestion process
:)
see slides for ebola genome
:)
Eukaryote
A cell that contains a nucleus and membrane bound organelles
Eukaryote
A cell that contains a nucleus and membrane bound organelles- structurally complex and larger than eukaryote ex) plants, yeasts, molds, fungi, animals
codon
A codon is the 3-‐base sequence in the mRNA that codes for an amino acid
DNA bonds and structure
A molecule of DNA is formed by millions of nucleotides joined together in a long chain. In a cell, DNA is found as a double-‐ stranded molecule, whereas RNA is found as a single-‐stranded molecule. DNA us a polymer of nucleotides. Hydorgen bonds join DNA together- one hydrogen bond is very weak but there are hundreds or thousand on DNA
homeostasis
A tendency to maintain a balanced or constant internal state; the regulation of any aspect of body chemistry. Interactions within cells and between cells
Prokaryote
A unicellular organism that lacks a nucleus and membrane bound organelles--> most plentiful and can be aerobic/ anaerobic (no oxygen needed)
Adaptive immunity that is naturally acquired
ACTIVE- antigens enter the body naturally, body induces antibodies and specialized lymphocytes PASSIVE- antibodies pass from mother to fetus via placenta or to infant via the mothers milk
Adaptive immunity that is artificially acquired
ACTIVE: antigens are introduced in vaccines; body produces antibodies and specialized lymphocytes PASSIVE: preformed antibodies in immune serum are introduced by injection
Lysozyme:
Abundant in tears, saliva, and mucous AND splits peptidoglycan (makes up cell wall)
Bases pairing
Adenine and Thymine (IN RNA use uracil instead of thymine) Guanine and cytosine
Metabolism
All cellular life needs nutrients some serve as the raw materials to make the cells building blocks -others serve as sources of energy that could be used for a variety of purposes: movement, assembling building blocks into cellular structures, the synthesis of the building blocks from the nutirent, moving nutrients into cells so they can be use to build cell molecules
Genome
All of the DNA that a cell possesses--> quantitative terms.
what type of cell molecules do these major bioelements end up in?
Amino acids- All but P Nucleic acids- All but S Fatty acids, lipids, C, H,O Phospholipids that make of cell membranes- all (lipids, phsophate group, amino acid)
Joseph Lister 1865
An early application of the germ theory was Joseph Listers use of carbolic acid as an antiseptic in the treatment of surgical wounds Death rate from infection dropped drastically
metabolism has two distinct divisions:
Anabolism: a cell uses ATP to contstcut complex molecules and perform other functions such as creating cellular structure catabolism: cell breaks down complex molecules to yeild ATP
Antibiotics
Antibiotic: anti (against) biotic (life) -in 1897 ernest Duchesne submitted his thesis in which he noted that certain fungi kill bacteria -indepndently discovered that a product of his fungi could cure guniea pigs from typhoid -Alexander flemming is credited with discovery of penacillin (1929)
Archea
Any of the unicellular microorganisms that is genetically distinct from bacteria and eukaryotes, and often inhabiting extreme environmental conditions.Can survive extreme hot and cold temperatures
Eukaryote
Anything with a relationship to humans --> Any of the single-celled or multicellular organisms whose cell contains a distinct, membrane-bound nucleus.
around the time of 1880 what were people arguing around disease?
At this time, people were beginning to argue that disease was a transmittable agent. Others disbelieved -disease was considered a punishment for sin. Infectious disease was thought of in strange ways -caused by vapours or miasmas. When people came to believe that diseases were caused by germs, it made for a more logical and practical treatment of disease
Fungal disease examples
Athletes foot. Difficult to treat bc Fungi is a Eukaryote (too closely related to humans- can negatively impact humans)
Name all antigen presenting cells
B cell, macrophage, dendritic cell
____ are responsible for the production of antibody against free pathogens and soluble products from pathogens while _____ destroy pathogen and virally infected cells and abnormal cells
B cells, cytotoxic T cells
Humoral immunity is mediated by antibodies from ____ and is involved in the elimination of ____ pathogens. Cell mediated immunity is mediated by ____ and is involved in the elimination of _____ pathogens.
B lymphocytes, extracellular, T lymphocytes, intracellular
Bt and Bt- corn
Bacillus Thuringiensis kurstaki (Btk) is a soil bacterium that prodces insecticidal toxins -Bt is comercially available insceticide- it is a solution of live bacteria mixed with a chemical mix that can be sprayed onto trees -the bacterium produce a protein called the cry toxin -the cry toxin binds to a specific protein in the insects midgut and it is activated by the enzymes and pH of the insects mid gut -it then produced a pore in the insects intestine, bacteria from the gut enter the insects blood and the insect dies of septicemia
Gettng a microbe to produce human insulin
Bacteria do not have the genetic information to make human insulin. However, we can add the gene to bacteria so that they can make insulin. 1.Restriction endonucleases (restriction enzymes) 2.Joining DNA together 3.Plasmids 4.Inserting DNA into plasmid structures (to make recombinant plasmids) 5.Introducing recombinant plasmids into bacterial
What can happen if food isnt cooked properly?
Bacterial infections like salmonella from eggs, dairy, undercooked meet, -Shigella contaminated H20, poor hand wahsing -listeria deli meat, soft chesse Viral infections like norovirus, hep A PArasites like Trichinella spiralis (undercooked meat or wild game) Chemicals like shellfish, wild mushrooms, pesticides
primary mode of action of select antibiotics
Beta-lactams: inhibit cell wall (peptidogylcan synthesis) -tetracyclin: inhibit translation -Aminoglycosides: inhibit translation -Macrolides: inhibit translation -Polymoxin: damages cytoplasmic membrane -Quinolones: inhibit DNA replication -Trimethoprim: inhibit folic acid metabolism Rifamycins: inhibit transcription
Bacterial Disease examples
Botulism, Campylobacter, staphylococcus, Escherichia Coli (normally good but is infective), salmonella
Kelp- marine algae
Brown algae. -Main source of MSG, source of alginate (thickner for ice cream, salad dressing, paint), source of carragreenen (pies, toothpaste)
Elemental cycles
C N S cycle between inorganic and organic forms this i because in any environment there are organisms with different metabolisms these organisms can be microbes only or microbes and plants/ animals key point: one organisms waste is another organisms nutrient
CODIS
CODIS: COmbined DNA Index System. 13 genes selected to test. Use by various law enforcement agencies (e.g.,FBI, RCMP, Interpol). Contains DNA profiles from crime scenes and known individuals (convicted offenders).
what are viruses NOT?
Cells- they cant synthesize their own ATP, amino acids, nucleotides
CDC and BCCDC
Centre for disease control- tell you where not to travel
Antibiotic induced diarrheal disease- c diff and pseudo membranous colitis
Clostridium difficle: growth controlled by other species in the gut, antibiotic therapy pertubrs the balance and C. diff can grow out. Causes diarrhea to pseudomembranous colitis -pseudomembranous colitis is characterized by- diarrhea, abdominal pain, blood or pus in stool -can be deadly if not treated -can be a nosocomial infection
Ebola virus: Polymerase cofactor VP35
Cofactor in RNA polymerase transcription and replication complex.
How do you know that something is living? Hallmarks of life
Compartmentalization and metabolism - Cells take up nutrients from the environment, transform them, and release wastes into the environment. The cell is thus an open system. Reproduction (growth)- chemicals from the environment are turned into new cells under the genetic direction of preexisting cells Differentiation- Some cells can form new cell structures such as a spore, usually as a part of a cellular life cycle Communication- cells communicate or interact by means of chemicals that are released or taken up Movement- Some cells are capable of self propulsion Evolution- Cells contain genes and evolve to display new biological properties. Phylogenetic trees show the evolutionary relationship between cells
Why do we not have vaccines against all infectious agents?
Consider this: over 5 million individuals die from HIV every year- why no vaccine? Were working on it! More money has been spent trying to develop HIV vaccine than any other vaccine in history -has been the focus of research for over two decades -very complex virus -mutates easily (function of RT) therefore diffficult to do speedily -takes YEARS to do the research indluding clinical testing
DNA amplification: the net effect
Copies = T (2)^N T= number of templates at start, N = number of cycles, 2 because both strands are copied. 30 cycles is relatively easy to do: 2^30 =1,073,741,824 In theory, 1 original template should result in over 1 billion copies
Dom Perignon (1678)
Credited with discovering (accidentally) champagne. Wine was fermented in a barrel, but fermentation went dormantwiththe cold weather of winter. It resumed in the spring, and the yeast begin a second fermentation. Additional yeast and sugars are added (to produce the bubbles)
Head of virus contains
DNA
DNA bases
DNA sugar is deoxyribose bases are: adenine, guanine, cytosine, thymine
DNA analysis in identification of people
DNA is 99.7% identical between any two people. ONLY 0.3% variation: but this is enough to identify individuals (exception: identical twins). The scientists use PCR to amplify the DNA at several specific regions within the human genome. With these regions are small repeated sequences within the DNA called short tandem repeats (STRs) STRs are a class of variations in DNA sequence that are found at specific sites in specific genes. The STRs are two or more nucleotides that are repeated, and the repeated sequences are directly adjacent to each other. Repeats are present in variable numbers in individuals, and the number of repeats distinguishes one person from another. The different regions are amplified and analyzed to determine how many STRs are present in each region, and this data is used to create a DNA profile or fingerprint. The DNA sequence flanking each of regions containing the STRs is the same in all humans. This is what we would design the primer sets to bind the region of the DNA that flanks the STRs. The primers are then used to amplify (multiply) the region of the DNA that contains the STRs and the size of the PCR product is measured. We will obtain two sizes from this person for the STRs at this specific gene
What makes PCR possible?
DNA polymerase from Thermus aquaticus. It was isolated from a hot spring in Yellowstone National Park in 1969. It is a thermophilic bacterium that thrives at 70C! Its DNA polymerase can tolerate the 95C temperatures needed to separate the two DNA strands. The DNA polymerase has been called Taq polymerase.
Central dogma of cells and the addition
DNA--> RNA--> Protein + organic molecules (EX penacilin- one of the most important discoveries in terms of infectious disease)
DNA vaccine and Recombinant Vaccine
DNA: Identify and culture organism, sequence DNA, identify immunogenic peptide motifs, Identify DNA sequences which code for immunogenic peptides, construct plasmid vector, purify plasmid DNA, Administer DNA vaccine, test efficacy TRACYS EXAMPLE A DNA vaccine would only have the DNA - no other physical (protein) part of the virus would be present. It would not be the entire virus genome - only the part of the gene that codes for a protein on the outer structure of the virus. The idea is that the host cell would take up the DNA and then make the virus protein so that the host would make an immune response. . Recombinant vaccine: Combine a plasmid and influenza gene to create vaccine. A recombinant vaccine involves constructing or modifying a pathogen. You might take a gene from a nasty bug and insert into something that "less nasty". For example, a gene from the Ebola virus might be inserted into the common cold virus. You would then have a common cold virus particle with the extra DNA and when the modified cold virus was being replicated in the host cell, it would make the Ebola protein as well as its own. The Ebola proteins are part of the particle and the host would make antibodies to Ebola
What were microbes first associated with?
Disease (BUT they do alot of good as well)
Prokaryote
Do not have a membrane bound nucleus - simpler morphologically ex) bacteria and archea
Vitamin A supplementation
Done in some countries but not all, some have them for pre-school aged children only -a few of the Vitamin A supplementation programs involve the administeration of two high doses of Vitamin A per year (the liver can store 80-90% of the body's vitamin A and release it into circulation when needed) -Uicef and other non-gov. organizations would prefer to see more frequent low does supplements available
SEE SLIDES FOR MOVIE
EPEC AND EHEC
pathogens of the eye
EXAMPLES: Neisseria gonorrhoeae and Chlamydia trachomatis -thought t attach to conjuntival epithelium -problem for newborns -if untreated: Conreal ulceration--> perforation -blindness -secondary infections -pneumonia (10-20%)
HIV replication cycle
Fusion, uncoating, reverse transcription, integration into host DNA, transcription, RNA export, translation, assembly, release, maturation
Binomial bacteria name examples
Escherichia (family) Coli (class) Staphylococcus (family) aureus/ epidermis (class)
3 domains of life:
Eukaryote, Prokaryote (bacteria), and Archea (like bacteria)
envelope glycoprotein (GP)
Facillitates cellular entry, decreases endothelial barrier function and impairs host immune repsonse
structure of bacteria (example with gram positive)
Flagella, pili, Capsule, cell wall, plasma membrane, cytoplasm, ribosomes, plasmid, nucleoid with circular DNA
Viral disease examples
Flu, cold, smallpox, AIDS, measels, mumps. Difficult to treat. Grows in cells of the host.
Genetic use restriction technology (GURT)
GE foods have been promoted by the manufacturers as the solution to world hunger -GURT is a method for restricting the use of genetically modified crops by rendering the second generation seeds sterile -it is considered a type of containment strategy for the foreign genes -different terminator systems have been developed
where do antiretroviral drugs target HIV in replication cycle?
Fusion inhibitors, entry inhibitors, NRTI (nuceloside reverse transcription inhibitors), integration inhibitors, protease inhibitors (maturation)
Where do microbiota have the greatest effect on the host?
GIT -produce vitamins, (biotin, vitamins B and K) -produce hormones -metabolize bile acids and steroids -help digest starch, fiber, oligosaccharides, and sugars that our bodies failed to digest -protect host from infection by pathogens -stimulate immune system development (e.g. Peyers Patches)- responsible for immune surveillance in the gut -may influence oral tolerance -May protect against IBD (inflammatory bowel disease)- prevent inflammation, probiotics seem to help control IBD
exception of size of virsues
Giant mimivirus 600-800nm
Banting and Best's experiment with insulin
History -‐ Discovery of insulin Banting and Bests experiment Removal of the dog pancreas would result in diabetes. Treatment with an extract made from the pancreas would manage the dogs diabetes. Early work -‐ pancreas donor was pretreated to cause the part that produce digestive juices to degenerate. Later work -‐ recognized the pretreatment was not necessary
Development of penacillin as medical agent is also attributed to...
Howard Florey (conducted clinical trials) Ernst Chain (helped Florey discover chemical composition and mechanism of action) Norman Heatley (discovered how to prepare penicillin in large quantities; was the only one who didnt recieve nobel prize)
Structure of insulin
Human insulin is very similar in structure to bovine and porcine insulin, which is why the animal insulins could be used in the treatment of diabetes in human patients Concerns using animal insulin? It is foreign to the body, might be recognized as intrusive. The animals insulin could carry disease pertinent to the animal- ex mad cow
How to identify a pathogen: Robert Koch's Principles
If you find it in sick and healthy people, it is probably not a pathogen. If you find it in only sick people it is probably a pathogen. 1) INFECTIOUS ORGANISM FOUND ONLY IN SICK PEOPLE. 2) GIVE THE PATHOGEN TO ANIMALS AND IT MAKES THEM SICK--> you isolate the pathogen from the sick rat to confirm the organism is the cause of sickness
How do you get bacteria to make human insulin?
If you know the amino acid sequence of a protein, you can reverse engineer the gene. Since the mature form of insulin as an A and B chain, an easy way to do this is to make a plasmid with the gene to make A, and another plasmid with the gene to make B. Purify both the A chain and the B chain protein. Do a lifle chemistry to join them together
Edward Jenner 1796
In 1796, (before the germ theory), Edward Jenner did the first clinical trial of vaccination -people had been doing some form of vaccination before Jenner but Jenner did the first public demonstration. He demonstrated that if you vaccinated someone with cowpox (a minor skin disease for humans) that they would protected against smallpox (a more severe disease)
A summary of the flow of genetic information in a cell
Information is stored in the triplet codes (codons) of DNA nucleotides. •This information is transcribed into 3 types of RNA. •mRNA carries the information to assemble a polypeptide. •In the nucleus, introns are removed and the remaining exons spliced together to make a functional mRNA strand. •tRNA molecules attach to specific amino acids -rRNA and proteins form ribosomes • mRNA attaches to a ribosome and the message is decoded when the anticodon of a tRNA is bonded to a mRNA codon •Subsequent amino acids are attached to the growing peptide chain until a stop codon is reached and the chain is terminated
Watson and Crick
James Watson and Francis Crick worked out the three-‐dimensional structure of DNA, based on work by Rosalind Franklin
Acetobactor
MAKES VINEGAR. produces carbohydrate and grows in very little oxtgen
which immune cells is responsible for the quickest release of histamine that causes the red itchy welts associated with allergies?
Mast cells
where did viruses come from? Coevolution hypothesis
May have evolved from complex molecules of protein and nucleic acid at the same time cells first appeared on earth and would have been dependent on cellular life for billions of years
what is one of the most important elements in a cell?
Mg ++
HABER PROCESS INDTURIAL PRODUCTION of N based fertilizers N2- NH3
N2 gas and H2 gas are pumped into a tank and pressurized to 200 atmopheres, exposed to an iron catalyst and heated to 450C N2 reacts with H2 to form NH3 NH3 recovered from a gaseous state when it cools and liquifies
are there many bacteria on the eye?
NO! -small numbers of bacteria -kept wet by secretions from the lachrymal glands (blinking is a mechanical force that washes away microbes that cannot attach) -lacrymal secretions contain batericidal substances e.g. lysozyme- damages bacterial cell walls causing cell death
Hansens disease (leprosy)
Named after Hansen who discoeverd its bacterial cause -Mycrobacterium Laprae= non spore forming, gram positive, unusal cell wall with waxy lipid which is responisble for slow growth rate (hours to several days), protection from lysis once it is taken up by immune cells via phagocytosis, growth within phagocytes, resistance to gram staining, detergents many common antimicrobial drugs and desisccation -never been able to grow in lab -found in armadillo -strong cell mediated immune response patients are able to kills cells infected with the bacterium resulting in non progressive from of disease called "tuberculoid leprosy"- regions of skin that have lost sensation as a result of nerve damage are characteristic of this form of leprosy -patients with weak cell mediated immune response develop "lepromatous leprosy" where the bacterium multiplies in skin, mucous membranes, and nerve cells, gradually destorying tissue and leading to progressive loss of fcail features, fingers, and toes and other body stuctures -signs and symptoms slow, incubation may take years -Death by leprosy is rare and usually results from infection of leprous lesions by other pathogens -only known bacterial pathogen of peripheral nerves, lives in cooler places in body (30 C) -baterium may live unnoticed in host for up to 30 Y and then be recognized by host cells, immune response attacks infected cells and destroys nerves and other tissues in the process -person to person contact transmission, inhalation of respiratory droplets, also may occur through breaks in the skin -therapy consists of administering multiple drugs, typically minimum of 2 year treatment and can be lifelong for some
Can viruses grow in petri plates?
No, they need to infect cells
define epidemic
Occurs in greater frequency than usual for an area or population
where did viruses come from? regressive hypothesis
Once small cells that parasited larger cells. Over time, genes not required by their parasitism got lost.
DNA Extraction and Quantitation-STR
Only very small amounts of DNA are needed with STR analysis- use PCR to amplify the DNA. Use a pair of primers specific for each of the 13 loci
clinical significance of repiratory tract microbiota: cystic fibrosis
P. aeuruginosa, S. aureus, Burkholderia cepacia often isolated from CF lung -Inflammation and thickened mucus: hiding spot for opportunistic pathogens
PCR
PCR stands for polymerase chain reaction. Is it a neat tool to amplify (multiply) DNA in vitro (in a test tube) -it acts like a molecular photocopier. PCR is ideal when you want to copy relatively small segmements of DNA
the first production of live but non-virulent forms of chicken cholera bacillus was achieved by:
Pasteur
Louis Pasteur (1859)
Pasteur finally thought out the experiment to disprove the theory of spontaneous generation, once and for all
Making recombinant DNA (rDNA) and Paul Berg
Paul Berg was the first two join DNA from two difference sources together. DNA from SV40 (a tumour virus that infects monkeys) was joined with DNA from a bacteriophage. DNA ligase was used to stitch the two pieces together.
EUKARYOTIC CELLS: cell wall
Plant and algae cells are examples that do have cell walls .Provides mechanical strength to the cytoplasmic membrane.
Among vaccine preventable diseases, which one kills the most people from this list?
Pneumonia, meningitis, flu, hep A FLU!!
Transcription
Process of converting DNA to RNA, the DNA is copied by enzymes in the cell
Pathogens: Extracellular
Produce toxins outside the cell. EX) Staphylococcus,
What do you need to have in sufficient supply for bacteria to grow?
Protein (chemically supplies amino acids) metal ions (ex. FE) vitamins sugar need to have chemical interactions between a community
EUKARYOTIC CELLS:Chloroplasts
Responsible for photosynthesis the conversion of CO2 from the air into sugar using light energy. Found in plant and algae
Restriction endonucleases
Restriction Endonucleases (RE) are enzymes that recognize specific sequences in the DNA (a specific order and number of A, C, G and Ts) and cut into the DNA. REs are found in bacterial cells and archaeal cells and may represent a primitive immune system a gainst infection with bacterial viruses. Herbert Boyer had discovered one in E. coli Called it EcoR1
Rhizobium legume
Rhyzoibium bacteria live within root nodules of specifc legume plants (eg soybean) the leafy part of the plant does the photosynthesis and produces sugars some of the sugar (organic C) is used to feed the root cells and the bacteria living within the nodules of the root the rhizobium fixes the N2 into NH3 and incorporates NH3 into the amino acid glutamine the Rhizobium uses the glutamine for itself and provides some for the root cells and leaf cells of plant after harvestig crop, farmers plow rest of plant into soil, the plant decays and NH4 is released into the soil
theory of spontaneous generation: Fransesco Redi (1668)
Set up a series of tests -‐ covered some jars of meat with fine gauze or paper (test cases) to prevent the entry of flies, compared results to jars of meat left exposed (control). Hypothesis: covered meat should not produce maggots. One piece was left in the open air, resulting in maggots. Another jar was covered with fine gauze to prevent flies from entering the jar. No maggots develop on the meat Although Redi's experiment should have put the notion of spontaneous generation to rest, reports of wee animalcules became widespread during the 1700s
1993 Nobel Prize in Chemistry
Shared by Michael Smith (UBC professor) and Kary Mullis (PCR inventor)
which of the following does not protect body surfaces?
Skin, mucus, gastric acid, salivary amylase, gut microflora -salivary amylase! doesn't have lysozyme, only breaks down starch
Spallanzanis experiment
Spallanzani boiled broth's for longer periods of time, sealed some flasks by melting the glass, left others open -After 2 days, the open flasks were teaming with microbes, sealed flasks were sterile. This initiated a heated argument between Needham and Spallanzani over sterilization (boiled broth in closed vs opencontainers) as a way of refuting spontaneous generation Needham claimed that Spallanzanis over-‐extensive boiling used to sterilize the containers had killed the vital force or life force. Needham argued that bacteria could not spontaneously generate in the sealed containers because the life force could not get in. In open containers, the life force could be replenished. In the minimally-‐boiled flasks, he felt the boiling was not severe enough to destroy the life force, so bacteria were still able to develop
what factors influence microbial composition? GIT
Specific location in GIT -varies along the tract and across the tract (bacteria that have adhesin stick to side of tract) -Microbes in the stomach wouldnt be the same as microbes in the large intestine -Age- diversity greater in adults than children -Diet- prevotella associated with carbs bacteroides associated with animal proteins and saturated fats -Antibitoic use
What is a secondary lymphoid organ?
Spleen
How to get Plasmids to enter bacterial cell Stanly Cohen
Stanley Cohens work focused on plasmids. Cohen's had developed a method to get bacteria to take up the plasmid DNA. Cells are incubated with DNA in a calcium chloride solution on ice. A heat-‐shock results in DNA crossing the membrane.
what targets do we have left for antibiotics?
Target must be: essential protein, drugs must be taken up without excessive efflux, must lead to bactericidal or at least bacteriostatic effect, possible targets: ribosome, RNA polymerase, cell wall synthesis -Adjuvants- dont need to work on their own, but rather make it possible for the antibiotic that functions at that target to work--- these are called antiresistance drugs
conjunctiva colonization
eye
EUKARYOTIC CELLS:Endoplasmic reticulum (ER) and Golgi
The cells protein trafficking system -‐ directs newly made protein to the correct location in the cell- feeds into the golgi which helps transport proteins outside cell
microbiome
The complete genetic content of all the microorganisms that typically inhabit a particular environment, especially a site on or in the body, such as the skin or the nose
when did the theory of spontaneous generation continue to and why??
The controversy over spontaneous generation continued into the mid-‐1800s because many felt that air was necessary for life, and Spallanzanis experiment excluded air
theory of spontaneous generation: Aristotle
The idea that life forms arose spontaneously from non-‐living matter. Aristotle wrote that: •flies, worms, etc., arise from decaying matter, •frogs arise from flooded fields.His observations laid the basis for the doctrine of spontaneous generation
Use electrophoresis to monitor the size of the PCR products
The number of STRs in 13 different genes are analyzed. Electrophoresis separates DNA based on size. Small pieces move faster than large pieces. We can get an idea of how many repeats are in each gene that was analyzed
EUKARYOTIC CELLS: Mitochondrion
The power-‐house of the cell. Takes the energy obtained from nutrients and converts to a form of energy that the cell can use. Takes energy obtained from nutrients and converts to a form of energy that the cell can use (ATP)
DNA sequencing
The sequence of bases in DNA forms the Genetic Code. The different amino acids and the order in which they are joined up determines the sort of protein being produced. A group of three bases (a triplet) specifies which particular amino acid should be used in when building the protein. This is a small, imaginary protein molecule showing how a sequence of 5 different amino acids could determine the shape and iden-ty of the protein Each triplet codes for a specific amino acid The amino acids are joined together in the correct sequence to make part of a protein The proteins build the cell structures. The DNA controls which enzymes are made and the enzymes determine what reac-ons take place. The structures and reac-ons in the cell determine what sort of a cell it is and what its func-on is. So DNA exerts its control through the enzymes. A sequence of triplets in the DNA molecule may code for a complete protein. Such a sequence forms a gene. There may be a thousand or more bases in one gene DNA carries informa-on that can be used to construct the proteins which form structures and regulate the body's activities
Three things microbiology was trying to uncover during the time of 1880
The spontaneous genera<on of life (life from inanimate objects).* Infectious disease (transmissible forms).* Philosopher's Stone (substance that was said to be able to turn base metals, such as lead, into gold)
Boyer and Cohen collaboration (Genetic engineering)
Their product worked out the basics of recombinant DNA -They demonstrated that a piece of foreign DNA can be introduced into bacteria, and it can be expressed by the bacteria (i.e. transcribe the DNA and translate the mRNA)
Boyer and Cohen collaboration
Their projects worked out the basics of recombinant DNA. They demonstrated that a piece of foreign DNA can be introduced into bacteria, and it can be expressed by the bacteria (i.e., transcribe the DNA and translate the mRNA)
triplet codes
There are 64 (4X4X4) possible triplet codes, but only 20 amino acids. As seen in the table, more than 1 triplet may code for the same amino acid. This is no problem, as long as no triplet can code for more than one amino acid. Note that several codons can also act as start (AUG) or stop (UAA) signals
Different types of RNA
There are three types of RNA produced in the cell mRNA, tRNA, rRNA Messenger RNA (mRNA) is a copy of the DNA that codes for a polypeptide. rRNA forms part of the ribosome, the protein factories of the cell. tRNA brings the amino acid to the ribosome that the mRNA coded for
EUKARYOTIC CELLS: ribosomes
They translate the information on mRNA to make protein. The assemble proteins from amino acids- ribsomes bigger than those found in prokayotes
Microbiolgy and its history-when did things begin to happen?
Things really started to happen around the 19th century
DNA is...
This chemical substance is present in all cells in all living organisms. DNA controls all the chemical changes which take place in cells. The kind of cell which is formed, (muscle, blood, nerve etc) is controlled by DNA. The kind of organism which is produced (bacterium, giraffe, human etc) is controlled by DNA
PROKARYOTIC CELL: nucleoid
This is the region of the cell where the DNA is concentrated. DNA is the genetic blue-‐print of the cell. DNA is transcribed (copied) by RNA polymerase to make mRNA.
PCR
To do PCR, you need the DNA that you want to make copies of (i.e., your template) all you need is a single copy, - Primers - these are short DNA molecules that are used to set the boundaries of the regions of DNA you want copied, -nucleotides- the building blocks of DNA, -DNA polymerase - this particular one is very special. The DNA polymerase is called Taq polymerase and it was isolated from a bacterium called Thermus aquaticus
What was the first virus to be discovered?
Tobacco mosaic virus
where can normal flora cause an infection/ disease?
UTI (e coli) -ear infections (skin bacteria) -can cause infections if the balance changes e.g. yeast infections following antibiotic therapy (referred to as secondary infection) -can promote disease like dental carries -can also cause unpleasant effects: intestinal gas, body odor, morning breath, acne
what are the advantages of round up ready crop that is planted with no till method?
Use less water, dont lose top soil (because tilling causes the production of dust), dont have to till, saves time, monet plants arent competing with weeds, get better yeild
Viral coat
Viruses have a coat of viral proteins and a tail that peirces the cell
How do cells make ATP? there are two modes- respiration (see fermentation later)
a process where the electrons are removed from a nutrient molecule being used as an energy source moved through an electron transport chain tranferred to different nutrient molecule being used as an electron acceptor once the molecule that is used as the energy source gives up the electron, it is waste to the cell once the other nutrient molecule that is used as the electron accpetor accepts the electron, it is waste to the cell EX) there are some microbes that use H2 as an energy source (the way you might use water) the microbes might use O2 as the electron receptor--> waste would be water. The electrons from H2 are transferred to the electron transport chain which releases packets of energy that the cell can turn into ATP The energy released is the used by a membrane bound ATPase to make ATP for bacteria and acrchea this happens at the cell membrane' for eukayotes- this happens at the mitochondrion
Modes of transmission (infectious disease): 2) vehicle transmission
a) Airborne (aerosol that travels >1m) b) Waterborne c) Foodborne
symptoms of ebola: repiratory
a) chest pain b) cough
symptoms of ebola: vascular
a) conjunctival injestion (bloodshot eyes) b) drop in blood pressure c) edema
Modes of transmission (infectious disease): 1) contact transmission
a) direct contact transmission b) Indirect contact transmission (e.g. via needles, toothbrushes) c) Droplet transmission (travel <1m)
above group concrete corrosion
acid producing bacteria that use N-containing molecules as an energy source two main culprits- use NH4 and NO2 as energy sources they use CO2 from the air they can get N in the form of NO3 and S in the form of SO4 from the burning of fossil fuels and P in the form of PO4 from soil dust -H20 from the environment would provide the H -NH4 from the burning of gasoline in catalyst equipped engines or the decomposition of anumal urine and feces provide the energy for the first group of bacteria -the microbes that use NH4 as an energy source then produce NO 2 as a waste product -the other microbes use NO2 as an energy source it produces NO3 as a waste product -there metabolism generates acid as a waste product then the dissolves the binding agents in cement
below ground concrete corrosion
acid producing bacteria that use S-containing molecules as an energy source -sewage contains a lot of organic matter and heterotrophs and lithotrophic microbes some of the heterotrophic bacterua produce H2s (hydrogen sulfide gas) when they breakdown some of the organic molecules in the sewage -H2S is a volatile gas and would enter into the airspace of the pipe -lithotrophic microbes growing on the concrete surface use H2S as an energy souce (they use CO2 as a C source) -the product of their metabolism is sulfuric acid H2SO4 which dissolves the cement in the concrete in the pipe
aside from cycling CNS into forms that plants could assimilate to make biomass, when have metabolic activities of microbes led to environmental damage?
acidic mine run off, microbial mining production of N-based fertilizers aquariums
food preservation and canning foods with different microbial populations
acidity, fat content, water content, of the food is important -spike food with a known number of specific heat reisitant spore -determine how much time is needed to reduce the number of spores by 10% then multiple this number by 12 (safety margin)
Two Branches of immune system: Adaptive
acts within days of infection -involves special cells- lymphocytes that need to proliferate and differentiate into effector cells -requires events of the innate responses to activate adaptive responses
Two Branches of immune system: Innate
acts within minutes to hours of infection -involves preformed proteins, resident cells and cells recruited to infection site
why do microbiota not induce immune response?
actually they do! -normal flora appears to be important in training immune system to respond to pathogens -think of the normal flora as a sparring partner for the human immune system -important for the development of certain lymphatic tissues (e.g. peyers pathes in GIT) -your body creates antibodies in response to normal flora and antibody concentration are lower than those that exist for pathogenic bacteria -cross react to certain pathogens, thereby preventing infection/ invasion
what are the two types of immunity?
adaptive and innate
Hosts and transmission: assumed natural reservoir
african fruit bats
What do vaccines contain (detailed)
aluminum or salt: adjuvant -adjuvant is a compound added to vaccines to trigger a rapid and more potent immune response, reduces the amount of antigen needed -antibiotics (select vaccines) -egg protein (influenza and yellow fever vaccines - prepared using chicken eggs. -formaldehyde: inactivated bacterial products in toxoid vaccines (when inactive bacterial toxin is used to generate immunity) and virus particles--> ten times less in a vaccine than in a baby naturally -MSG (some vaccines): acts as stabalizer -Thimerosal: used in multidose vaccines to prevent contamination
normal flora: vagina
after birth, the vagina is colonized by several bacterial species, including E Coli and tohers -during reproductive years Lactobacilli take over
Use of chemotheraputic agents to kill bacteria: antiseptic
agent used on surface tissues that kills microbes but should not be toxic to human tissues
Use of chemotheraputic agents to kill bacteria: disinfectants
agents used on inanimate objects to kill microbes. These agents are also toxic to human tissues
Use of chemotheraputic agents to kill bacteria: antibiotics
agents used to kill bacteria. Should not be toxic to human tissue
life in the absense of light
all ecosystmes pocess primary producers organisms that sysnthesize organic molecules from CO2 -in ecosystems that are exposed to sunlight the primary producers are the phototrophic orgganisms (plants and some type of bacteria) -then someone discovered deepsea thermal vents in 1977 and a whole ecosystem that thrived in the absense of light
hematopoietic cell differentiation
all the cells come from bone marrow from the stem cell- e.g. RBC, neutrophil, basopihil. plasma cell. antibodies
PROKARYOTIC CELL: somethings that may be on the outside of the cell... pili
allows transfer of genetic material
order of defence levels
anatomical and physiological barriers----> pathogen breeches---> innate response----> pathogen overwhelms or evades---> adaptive responses
Pre-small/ secreted glycoprotein (sGP)
anti-inflammatory activity
where would you expect to find most bacteria on humans?
arm pit, groin, between toes, between fingers, umbilical stump, aroudn nostrils
food spoilage begining with harvest
as soon as substance is harvested, chemical changes begin to occur in the food -some changes are desriable (e.g. tenderizing of meat) but some are undesirable (putrefaction) and render the food unfit for consumption -some changes occur within the product itself (limited breakdown of proteins by enzymes in cellls of the meat, conversion of sugar into starch in plants) -some changes result by chemical reactions with the environment (e.g. oxidization of lipids leading to rancid odours) -some changes occur as a result of microbial action- microbes on the surface of the food begin to consume it
mutualistic relationships
associations in which both the host and bacteria derive benefit
pathogenic relationship
associations in which the mircrobial organisms cause disease
parasitic relationships
associations in which the normal flora live at expense of their host
commensal relationship
associations in which there is no apparent benefit or harm
health problems related to fermentation
auto brewary sydrome or gut fermentation syndrome -people experience drunkeness even if they havent drinken alcohol- they have yeasts in the microbiota of the intestine that ferments carbs they have consumed in a meal -the yeats produce alcohol which is absorbed into their blood stream -they would get drunk from eating pasta!
sensitivity vs resistance
bacteria that respond (stop growing or die) in the presence of antibiotics are sensitive to it -bacteria that continute to grow in presence of antibiotic are antibiotic resistant -disk diffusion assay is a simple way to determine whether a culture is sensitive or resistant to the antibiotic of interest
Esophogus microbes
bacteria that were in saliva and food
in humans what is the normal flora composed of?
bacteria, also fungi and few protists
what are the major causes of food spoliage?
bacteria, yeasts, and moulds -they produce various enzymes that decompose constiuents of food -moulds are the major cause of spoilage of foods with reduced water acitivty e.g. dry cereal and cereal product -bacteria spoil foods with relatively high water activity such as milk and milk products
cholera
bacterial disease
Why are clinical trials necessary?
because not testing a drug clinically could have dire consequences
Influenza virus- family and three types of viruses
belongs to family Orthomyxovirus -three types of influenza viruses: a) humans, other mammals, birds, major cause of pandemics) b) humans, horses, seals c) humans, pigs, dogs -cause of seasonal epidemics and occasional pandemics
benefits to host and normal flora in the mouth
benefits to microbe: given nutrients, given habitat benefits to host: vitamin synthesis, microbial antagonism, contribute to immunity (low levels of secretory antibodies)
least similarity between people: bacteria composition
between fingers, toes, armpits, umbilical stump
PROKARYOTIC CELL: periplasm
between the membrane and the cell wall- it has proteins which help to transport nutrients into the cell
metabloism defined
bichecmical modificiation of chemical compounds in cells
plant cells are the ___ cells
biggest
adjuvants directed against biofilms
biofilms: microbial communities consisting of extracellular polymeric substances (e.g. proteins, DNA) that protect bacteria from antibiotic penetration -no antibiofilm agents on the market -most clinical infections have some level of biofilm involvement -if you can destroy the biofilm you can increase the effectiveness of the antibiotic -certain cationic peptides, including human LL-37, prevent biofilm formation -select synthetic peptides are capable of causing biofilm dissolution -some of thes peptides also work synergistically with certain antibiotics
transmission of ebola
blood or body fluid (inlc. but not limited to urine, saliva, sweat, feces, vomitus, breast milk, semen, and exposure to contaminated objects like needles and syringes)
where do hematopoietic cells come from?
bone marrow
T cells are made in the _____ and complete their differentiation in the _____
bone marrow, thymus
what do lambs and trees have in common?
both used as contraceptives (condoms) -latex is obtained from tree leaves and used for condoms -lamb skin is used as contraception but doesn't prevent spread of STD's
lytic cycle
bursting, virus enters cell, makes more virus, lyses
how to bacteria grow?
by dividing into two identical cells- binary fission (A type of asexual reproduction common among prokaryotes wherein a cell divides giving rise to two cells, each having the potential to grow to the size of the original cell.) One cell turns into two.. two into four.. etc
anitgenic drift
changes in viral genome due to mutations occuring during replication -possible evasion of host immune response -main reason for seasonal flus
is influenza more common in adults or children?
children-20-30% of cases compared to adults- 5-10%
food born disease- divided into food poisoning and food infection
classified as food poisoning -estimated 76 million gastrointestinal ilnesses each year in the USA -most are unreported -many intestinal pathogens can be present in food without any indications that the food is spoiled Where do they come from? water, fertilizer, processing contamination, poor food prep, people handling food
lions gate treatment facility
collects wastewater from north van, and district of west van (147,000 people) discharges 318,000 m3/ day of treated sewage into burrard inlet -it is being upgraded to become secondary treatment faciltiy
WHEN IS THE GIT COLONIZED?
colonized at first feeding -breast feeding - bifidobacteria (90%), human milk contains bifidobacteria growth factor -prevents infections by pathogenic bacteria -formula feeding: bifodobacteria not dominant
Lichen
combination of fungus and algae and bacteria. It can be poisonous but it purifies the air and reduces pollution. If lichens are growing in a certain area, it means the air is pretty clean
ATP is
energy currency
how did mining disaster at Britania beach happen
combination of spontanrous chemical reactions and bacterial metabolism triggered when the rocks were exposed to air the bacteria wanted to grow- it could use iron as an energy source ironically this same process can be used in the mining indusrty to increase yeilds of materials recovered 25% of copper in NA used microbial mining
capsomere
component of capsid, basic subunit of capsid in capsomere(can be proteins in diff. arrangements)
Normal flora: Conjuntiva- what is it?
conjunctiva: The mucous membrane that lines the inner surface of the eyelid and the exposed surface of the eyeball-covers eye including iris -function: helps lubricate the eye by producing mucus and tears -prevents microbe entry into the eye
viroids
consists solely of single stranded, circular RNA w/o protein coats, mostly plant pathogens
mast cells main functions
contain granules rich in histamine, responsible for allergies
ebola blood and blood products
convalescent whole blood/ plasma from Ebola recovered patients
Production of N based fertilizers N2- NH3 biological
converted by an enzyme called nitrogenase some bacteria have this enzyme and do the reaction at normal temperatures and pressures N based fertilizers are expensive and cause problems if the are washed into streams/ rivers but some farmers are able to take advantage of its benefits
Translation
converts message of RNA and produces proteins
Brittania beach
copper mine operated from 1905 to 1974 5 open ppits excavated to mine the ore worst source of heavy metal pollution in NA problem related to metabolic activities of bacteria that used iron as an energy source their metabolism produced acid before water was treated, 12 million litres containing 650 kg of metals and contaminants flowed into the Howe Sound/ Pacific ocean daily Fish and other aquatic life killed
concrete corrosion
corrosion is the process of destroying or damaging metal, stone or other meterials slowly by chemical action -the metabolic of certain microorganisms can cause or promote corrosion of both metals and non metals (concrete, stone) -concrete is a mixture of gravel or other crushed rocks, sand, water, cement, and other additives like accelorators -the waste product of the microbial community is often an acid that dissolves the binding agent in the cement
Edward Jenner vaccinated against smallpox using:
cowpox
1796: Edward Jenner
cowpox vaccination for small pox, rub cowpox into wound to vaccinate
Sections of DNA can be _____
cut out ( EX G paired with T)
dental carries:
demineralization (destruction of enamel) -due to lactic acid produced by bacteria in plaque - created as a byproduct of sugar and carbohydrate fermentation -S.mutans produces more acid and is more acid tolerant than most others species of Streptococci -after enamel is weakened other species can come in and contribute to tooth decay
biofilm and human disease- why do we care?
dental cavities, catheter (A hollow flexible tube for insertion into a body cavity, duct, or vessel to allow the passage of fluids or distend a passageway)
DNA stands for
deoxyribose nucleic acid
composition of normal flora-what microbe is found almost everywhere?
depends on the site -some species are found at most/all sites (e.g. staph epidermidis) while others are more specialized e.g. staph mutans in the oral cavity -may change over time as envrionment changes
symbiosis
describes the relationships between the microbiota and the body (or any two species living together) -can be mutualistic, parasitic, commensalism
how do cells make ATP? fermetation
doesnt involve ETC- molecules like molecular O2 are not needed. Instead enzymes in the cytoplasm catalyze the addition of PO4 to ADP -fermentation produces organic molecules as waste products- alot of potneital energy is still trapped in the waste product -system produces only a small amount of ATP
w to avoid getting infected # 6
dont share personal hygiene products or other personal items
macrophages and neutrophils main functions
eat bacteria (phagocytosis) release messenger molecules (backup)
How do antibiotics work? broad spectrum
effective on gram pos and gram neg bacteria
antiresistance drugs: pump inhibitors
efflux pumps: proteins that expel antibiotics before they are able to reach their target -efflux pump expression is a big problem for Gram negative bacteria due to the slow rate of uptake through semi-permeable outer membrane -can lead to drug resistance -pump inhibitors inhibit efflux pump thus the inhibitor must target the correct pump in the bacteria of interest -pump inhibitors may be chemical compounds or natural products
Antibiotic resistance
efflux, immunity and bypass, target modification, inactivating enzymes
Ebola virus: nucleoprotein (NP)
encapsidation of genome (necessary for encapsulated RNA)
opportunistic infections
endogenous bacterial diseases in which the organism causes disease at a time of weakness or let down in the host e.g. pneumonia following cold e.g. flesh eating disease
define pandemic
epidemic that occurs simutaneously on more than one continent
cell replication
everything in the cell must be duplicated including DNA (old strands of DNA used as templates and DNA polymerase attaches appropriate nucleotides that produces identical DNA molecules in the end)
Ebola virus: structure
filamentous, enveloped, ssRNA virus
Aquarium hobbyists
fish eat and excrete waste in a closed environment fish waste is very high in NH3 or NH4 it can be toxic to the gills of the fish causing them to become inflamed and bleed --> fish struggles to breathe
food infection results when...
food is ingested with sufficient numbers of viable pathogens to cause illness in the host -it is very common -the bacteria grow in the host and then start to produce the toxins -onset of diarrhea may take 8-48 hours. may take a few days to resolve
food poisoning is the result of:
food that is ingested with preformed bacterial toxins -the bacteria that produced the toxins do not have to grow in the host, and may not even be alive in the food when it is consumed -onset of diease within a few hours (resolves pretty quickly)
Three reservoirs of infectious disease: nonliving reserviors
food, water,soil
herd immunity
form of immunity that occurs when the vaccination of a significant portion of a population provides a measure of protection for indiciduals who have not developed immunity
dendritic cells
form the bridge between innate and adaptive immune responses -captuure antigen and present it to T and B clles -Help T and B cells -phagocytosis -brain of immune system
Elie Metchnikoff
found that microorganisms could be engulfed and digested by phagocytotic cells called macrophages
how do cells make ATP? repsiration
in respiration, the electron transport chain and a different molecule like O2 is needed All the potential energy can be converted to ATP for ex) an organic molecule like glucose can be catabolized completely to CO2 resulting in the production of as much as 36038 molecules of ATP
food placed near a gamma ray source
gamma irradiation is a method that kills bacteria by the hydroxyl radicals from water -this damages the DNA of the bacteria -Radiation does measured in Grays (Gy) -dental and chest x rays < 1 mGy -the amount needed to kill 90% of growing microbes is about 0.5 kGy -the amount needed to kill 90% of endospores is 3kGy (because of less water0 -effectiveness varies with food product: takes a higher does to kill bacteria in frozen food -The food does not become radioactive
Roundup ready soybean process
gene from Argobacterium tumefaciens that codes for glyphosate tolerant enzyme is added to the genome of the soybean -this makes the soybean plant now tolerant to glyphosate -the promise of this technology was that it would increase crop yeilds 0the idea was that by planting a roundup ready crop, then treat the feilds with roundup to kill the undersired weeds -both roundup ready crops and roundup are sold by the same company -the company soybean was generated so that is could be planted with a no till methos
what type of relationship would you expect to have between the bacteria and the host?
generally non pathogenic -mutualistic relationship e.g. staphylococci and proprionbacteria produce fatty acidss that inhibit fungal growth -can be parasitic e.g. if propirnibacteirum acnes becomes trapped in hair follicle it may grow quickly cuasing inflammation and acne -Staph aureus can be found on face and hands of nasal carriers -may autoinoculate, may infect others or spread it to food
microbial composition may be influenced by:
genetics, health status, age, sex, stress, nutrion
What are genetically modified organisms?
genome has been altered by genetic engineering- the insertion, deletion, or mutation of genes within and organism -humans have modified genomes of crops/ animals for thousands of years (since 12000 BC) by selective breeding -that is, identifying organisms that have a desired trait and using them to produce the next generation
how to avoid getting infected # 2
get vaccinated
Robert Koch
infectious diseases are caused by microorganisms
Bacteriophage
infects bacteria
Salmonella enterica
gram negative -diarrheagenic (food and waterborne) -strains can be human specific or have broad host range -tens of millions of human cases occuring worldwide every year
enteropathogenic E coli and enterohemorrhagic E coli
gram negative -diarrheagenic strains (food and waterborne) -EHEC causes severe diarrhea which can progress to a fatal renal failure -EPEC causes potentially fatal infantile diarrhea (esp. in developing countries) -Main difference: EHEC harbours Shiga-like toxin and has broad hoast range -EPEC does not harbour SHiga-like toxin and has limited host range (mainly human)
antiresistance drugs: outer membrane permeabilizers
gram negative organisms are intrinsically resistant to many antibiotics due to poor penetration through the outer membrane -outer membrane contains porins -pores made by porins are quite small and restrict passage of large hydrophilic molecules -lipopolysaccharide (LPS) restricts passage of hydrophobic molecules -LPS is stabalized by cross bridging of divalen cations -> restricts the passage of hydrophobic molecules -disrupting the divalent cations increases permeability to hydophobic and hydrophilic substances -many molecules are capable of displacing divalent cations (process called self promoted uptake)- polymyxins, cationic antimicrobial peptides, aminoglycosides, chelators -also increases permeability of other compounds, including antibiotics -have not made it to the market to date
difference between gram positive and gram negative
gram positive: thick outer layer of peptidoglycan, turn violet coloir gram negative: have outer membrane surrounding peptidoglycan layer, they turn a different colour, pink
biofilm formation
group of microbes that stick to each other and to a surface. Commonly embedded in a extracellular polymeric substance (protein, polysaccharides, and DNA) -protects the baceria (e.g. antibiotics)
Ebola virus: causes what in primates?
haemorrhagic fever
T helper cells
help B cells and cytotoxic T cells
adaptive summarized
highly specific T and B cell receptors -slow (days or weeks) -long duration -memory
Hosts and transmission: accidental hosts of ebola
humans, chimps, monkey, gorillas, forest antelopes, porcupines
Virus
infects plants, humans
common cause of death by ebola
hypovolemic (diminished volume of circulating blood) shock, multi-organ failure
Herbert Boyer (Genetic engineering)
identified Restriction Endonuleases (RE) enzymes that recognize specific sequences in the DNA (a specific order and number of A, C,G,T) and cut into DNA
Pasteur
identified pathogen and was able to grow it seperately from patient -also worked with rabies -inovled in making first vaccine for TB (not successful)
Innate response
immediate- already present, acts within hours -proteins and cells: Complement- a set of blood proteins, can promote phagocytosis of the bacteria by macrophages, can lead to cytotoxic reaction that kill bacteria, resident macrophages in the tissue that engulf and kill bacteria -it is nonspecific: innate componenets recognize common structures found on pathogens -takes care of 95% of pathogens
Ebola virus: host cells
immune cells (e.g. macrophages and dendritic cells) epithelial cells, fibroblasts, heptocytes, adrenal cortical cells, several types of epithelial cells
fermentation and food
important in the production of certain foods, and for food preservation -bread, cheese, wine, beer, pickles, sausage, saurkraut, yogurt, vinegar, coffee, chocolate, soy sauce, spirits
old method of sewage treatment
in many cities raw sewage was discharged into rivers which then flowed into bodies of water -together with the industrial pollutionm there was an unbelievable stench associated with the rivers -many elaborate tunnels were constructed to cover the rivers that carried the sewage -however the raw seage was still being discharged into other bodies of water
cultivation of viruses in lab: cell culture
in transformed cell lines. 1) A tissue is treated with enzymes to separate the cells 2) Cells are suspended in culture medium 3) Normal cells or primary cells grow in a monolayer across the glass or plastic container. Transformed cells or continuous cell cultures do not grow in a monolayer. -viral growth can cause cytopathic effect in cell cultures -problem: possible contamination
when are humans sterile?
in utero- colonization happens on surface tissues during and shortly after birth (breast feeding, different people touching the baby)
gastrointestinal tract
includes the oral cavity all the way to the anus -function: to digest ad absorb nutrients
nosocomial infection
infection acquired in the hospital that is a complication of the primary reason for being in the hospital
Pasteurization
is a short term treatment with heat to reduce the overall number of bacteria in a product and to kill all pathogens -it is not a sterilization of the product -temperatures and time are slected to kill the bacteria without damaging the food value and texture -Milk is often pasteurized by heating at 63C for 30 minutes, then rapid cooling to 4 C
Archea
look and act like bacteria but have different properties -DNA analysis -discovery in 1970s
what might be concerns of growing bt corn?
it is safe for humans, animals, fish, birds, and envrionment. BUT it kills monarch butterflies! Bt produces pollen, monarchs use pollen as food substance--> died off
How do antibiotics work? bactericidal
kills the bacteria
cytotoxic T cells
kills virus infected cells and cancerous cells
The Stages of microbiology
l----microbiology-----1950 (Watson and Crick establish DNA structure)----microbial genetics------molecular biology (strucutres and functions of cells)---- ribosomes considered molecular machines---l---second period-----Recombinant DNA in 1970s (manipulate DNA and move it into different cells----l----third period---Genome sequencing (prediction based on sequence of DNA bases)---- fourth period--- Next generation sequencing (led to concept of microbe based life)
clinical significance of repiratory tract microbiota: asthma
larger numbers of Proteobacteria is asthmatic children
bacteria define the limitis of ____ (in terms of...)
life (In terms of pressure, temperature, humidity, dryness, shortage of oxygen)
types of vaccines: Classical
life attenuated, inactivated (organism, toxin, subunit)
bacteria found where:
life exists (E.g. Not in volcanoes)
How do antibiotics work? inhibiting beacterial processes
like/... -peptidoglycan snythesis, DNA replication, transcription, translation, floic acid metabolism
genome of virus may be:
linear or circular may be one peice of nucleic acid or several peices -occasionally have enzymes within their capsids that are essential for replication of their genome
2 types of bacteria important for healthy fish tank: Nitrobacteria species
lithotrophic Use No2 as a nutient and produce NO3 as a waste product NO3 is not toxic to the fish but is one reason why the tank water has to be changed NO3 can be used as a nutrient by any plant that is in the tank (plant would also us NH4 ) as a nutrient but it cant keep up with all that fish produce.
Effects of triclosam?
liver tumor promoter, could be toxic
Pathogens: Intracellular
lives inside a cell. EX) E. Coli, Salmonella
EPEC/ EHEC pathogenesis
localization: extracellular (on pedestal) Microvilli effacement: Yes (typical attaching and effacing A/E lesions) Actin involved in: pedestall formation Type 3 secretion system (T3SS): one
Annacis island
located in the south arm of the fraser river -wastewater is collected from van, brunaby, new est, port moody, port coquitlam, coquitlam, pitt meadows, maple ridge, south urrey, white rock, city of langley, township of langley, delta (about 1000000 people) -discharges 497,000 m3/ day of treated raw sewage back into fraser river -secondary treatment facility
PROKARYOTIC CELL: somethings that may be on the outside of the cell... Flagella
long protein structure- may have one or many- involved in cell movement
PROKARYOTIC CELL: chromosome
made of DNA, deoxyribonucleic acid: has all of the genitic information the cell needs on how to be a cell- it is a single chromosome and in a circular shape -sometimes there are also plasmids which are also made of DNA and circular- they can contain genetic information that gives the cell a real advantage under some circumstances
B cells
main function is to produce antibodies (humoral immunity) -act as antigen presenting cell -antibody response -B cells produce antibody (a protein that is secreted into body fluids like the blood) These responses are effective against extracellular pathogens
v-GURTS aka variety technology
makes seeds sterile, via insertion of a gene that codes for protein A that stops the manufacture of different protein B needed for germination, so if the plant goes to seedm the seeds cannot be sown -the seed company produces the plant. The A and B genes are expressed A is a toxin but it is neutralized by B. The plant produces seeds that can germinate -for commercialization the seeds are treated so that the B protein cannot be made. The A protein is made and renders the seed unable to germinate
It was originally thought that there weren't ___ bacteria
many
food borne pathogens emerge from the environment and from agriculture
many cases of disease outbreaks linked to the use of contaminated water for irigating crops -salmonella outbreak in 2008 -outbreak of salmonella infections traced back to consumption of peanut products -foods likely to be the source of the outbreak were identified and was traced back to peanuts processed by a single factory in Georgia -factory had tested its products-reported positive for salmonella contaimination but they were not disgarded
saccharoyces "brewers yeast" or "bakers yeast"
many different species -in brewing beer, certain strains are used for making ales, different ones used for making lager -can work with some types of bacteria to make kambucha (fermented sweetened tea), kefir (fermented milk drink), and ginger beer (both alcohol and non-alcohol)
Three Conversions of N
most of the nitrogen found in our air is N2 (makes up 78% of our air) in order for N to enter the food chain it must be converted into a form that plants can use conversion of N2 into NH3 or NO3 is called nitrogen fixation n2---> NO3 lightning discharge in mosit air n2--> NH3 biologically by some type of bacteria annd archea N2--> NH3 industrially
Mushrooms
mushrooms are fruiting bodies of fungi -They are a flavourful source of protein -less than one percent of the mushroom species are toxic to humans -truffles are a type of underground mushroom that have odorant molecules that encourage animals to dig them up (the truffles intent is to help disperse the spores) -there are many types of mushrooms that are farmed and marketed worldwide
which relationship best describes association btwn. the normal flora and host
mutualistic
which cell is most abundant in circulation?
neutophil
dynamic microbiota composition of mouth, from newborn to tooth eruption
newborn: soft tissues, moist, streptococcus salicarius is dominant (<98%) teething: tooth eruption causes nonepithelial surface -colonization by S. mutans and S. sangis -creation of gingival crevice generates environment for anaerobes
Lymph system
no blood, collects fluid and moves it around the body -things in the blood move into the lymph system and into the lymph nodes -circulation of lymph is slow and immune response happens in lymph nodes
Main differences between Viruses and bacteria: Virus
no cell, no plasma membrane but may have an envelope, genome is DNA or RNA ss or ds, smaller number of genes, no independent transcription and translation, require host cell, avergae 20-400 nm, no treatment with antibiotics
new antiobiotics
no new broad spectrum antibiotics and few narrow spectrum antibiotics have appeared in last 40 years
do bacteria exist on their own in nature?
no they exist in bacterial communities
Do virsuses align with koch's populates?
no- you cannot isolate them in a pure culture- have to be mixed with bacteria
is the microbiota essential for life?
no. -germ free animals exist and are developed for many model systems BUT germ free animals do have sevral problems: development of cardiovascular system and digestive system, underdeveloped immune system, vitamin supplements are essential -however, germ free animals have excellent teeth
Human/ microbe relationships- health disease and normal flora. What is the normal flora?
normal flora (indigenous microbiota) is the mixture of organisms that are found at any anatomical site on the body -found in all animals -normal flora do not usually cause disease in healthy individuals
most similarity between people : bacterial composition
nostril, nares, and on the back
Are all soaps created equally? antibacterial
not usually needed at home -no more effective than ordinary soap in killing microbes -requires 2 minutes to actually kill bacteria
Before discovery of insulin in 1921 what was the prognosis for patients? Who won the nobel peace prize for discovering insulin?
not very good- often died after a few years -the only treatment option was a strict diet to try to control blood sugar levels -Macleod won nobel peace prize for creation of insulin, but banting, best and collip should have been included
2,293,900
number of deaths caused by HIV, diarrhoea, measles, malaria, and acute respiratory infections among children agres <5yrs.
What is the growth of bacteria determined by?
nutrition/ presence of nutrients
define endemic
occurs continually (at moderately regular levels) at a relatively stable incidence within a given population or geographical area
define sporadic
occurs in only a few scattered cases within an area or population
Fecal transplantion
one transplantation may be sufficient to treat C diff infections -can be used to treat ulcerative colitis, but several transplantations are needed -Pocedure: Identify a donor, prepare specimen (200-300g), administration through enema, colonoscopy, or nasogastric tube -US now has public stool bank
How do antibiotics work? narrow spectrum
only effective against one type of bacteria
molecules that serve as nutrients can be classified as:
organic: these molecules contain at least one carbon hydrogen bond inorganic: these molecules do not contain any carbon hydrogen bonds
more bacteria on earth than any other...
organism
what is the difference between pathogens and non pathogens?
pathogens have more DNA (Genes) than non pathogens
possible explanation why flu is seasonal?
peak flu season month: FEB. 1) viral evolution leading to evasion of immune response 2) seasonal changes in host health (light exposure, diet) 3) seasonal changes in social/ behavioural patttern (e.g. crowding) 4) cold and dry conditions favor virus transmission 5) air travel could lead to almost simultaneous appearance of influenza hemisphere wide
Name the process a cell such as a neutrophil or marcophage uses to ingest its prey
phagocytosis
Marcrophage:
phagocytosis and bacteriocidal mechanisms, antigen presenting
Match the following innate immune system cell types with their function: Neutrophils
phagocytosis and bacteriocidal mechanisms, not antigen presenting
Each nucleotide is made up of a:
phosphate, sugar, base
passive immunization
pre-synthesized elements of the immune system are transferred to a person so that the body does not need to produce these elements themselves
How to avoid getting infected #4
prepare food safely- keep surfaces clean when cooking -cook meat to proper temp
Sewage treatment
problem with sewage disposal in water: wash up on shorelines -potenital contamination of drinking water with pathogens -eutrophication ( a precess whereby a body of water recieves an excess amount of nutrients, allowing the growth of microorganisms that could result in oxygen depletion in the water -sewage is very rich with organic matter that can be metabolized heterotrophic microorganisms. The waste products of the heterotrophic microorganisms are then used as nutrients by lithotrophic microorganisms
metabolism
process of body taking in food and changing that food to produce energy to generate new tissue etc. for cellular replication -combination of breaking things down (to produce energy) and building things up which requires energy -MUST be life sustaining
Original verison of golden rice
produced beta carotene but the quantity in a typical serving was low -there was some concern about the stability of the beta carotene when the rice was stored or cooked -Improved strains of golden rice now produce more beta carotene such that a person can get their daily dose with a single serving
symptoms of ebola: skin
rash
types of vaccines: Synthetic
recombinant vaccine, DNA vaccine
EUKARYOTIC CELLS: cytoplasmic membrane
regulates what goes in and out of the cell Made of phospholipids, cholesterol and proteins.
why wouldnt penalcillin be approved today?
reigorous nature of todays clinical trials
how can you prove that microbes might be producing acid to corrode concrete?
researchers isolated bacteria that use N-containing compounds for energy from corroded concrete -inoculated sterile conrete with these bacteria -concrete corroded -found nitric acid produced by N-oxidizers amounted to 14 mL concentrated nitric acid (65%) per concrete block (.5 m squared) a year' accounts for loss of 3% concrete a year
Innate response at best
resolve the problem and at worst limit the spread and initiate the adaptive responses
RNA stands for
ribonucleic acid
susceptible
right lock and key: receptor and anti receptor
what is one of the most common ways of preserving food?
salt. Also one of the oldest methods -used for perserving herbs, vegetables -salt works to preserve food by drawing out the food product -the salt also draws water out of any bacteria and fungus present in the food
Pasteur and wine :)
saved french wine industry in 1857 The theory was that wine was made by a chemical breakdown of grape juice to alcohol Pasteur observed yeast in wine, and that soured wine contain populations of barely visible bacteria Pasteur proposed that yeast was involved in the fermentation of wine, and the bacteria caused it to spoil -Boiled grape juice, add back the yeast, and fermentation proceeds normally -‐ if all bacteria were removed, the wine did not go sour
Nori- seaweed collected as food
seaweed= marine algae -nori= type of algae that has large multicellular fronds -Nori is grown initially as seeds in stater cultures, then distributed on nets in protected coastal areas -after growth, it is collected and blended into pulp -Nori pulp then formed into sheets and dried in oven -after drying nori is toasted and packaged -used for wrapping rice, vegetables, fish to make sushi
what dtermines where bacterical species are present on skin?
sebacious (hair covered areas), moist areas (umbilical stump), dry areas
Bt endotoxin
selected because it is highly effective at controlling lipidothera larvae (catepillars) -the protein is very selective, generally not harming insects in other orders (such as beetles, flies etc) -the gene for the toxin has been introduced into the plant itself -what makes this attractive to growers is that the plant produces its own insecticides, the growers dont have to purchase handle or add additional pesticides to their crops -Advantages? Save man power, time, energy, costs, shipping costs
average treatment time for TB
several months to a few years
van sewage collection
sewage collected from households, transported through several lines to treatment facilities on anacis island or north shore -there are sevral advantages to this strategy -metabolic activites of of the heterotrophic and lithotrophic microbes produce alot of heat in sewage -heat can be caputred to heat 500-700 high rise condos -70% of the heat needed for condos in olympic village is captured from the city's sewer lines -in metro van, seage collected from household is transported through several lines to the treatment facilities on anacis island or north shore -another advatage is the metabolic activities of the microbes in sewage generate methane--> if the methane is captured it can be used to generate electricity -the amount of electricity generated could be enough to run the treatment facility -burning the methane to co2 is also less damaging than releaseing methane directly into the enviro
microbes are:
single celled organisms
reservoir:
site where pathogens are maintained as a source of infection
How do you test for TB?
skin test- if you have it your skin will swell up in a bump, doesn't tell whether its active or not -chest x ray- reveales tubercles
is there a large or small number of bacteria that cause disease?
small
Virus definition
small infectious agent that contains genetic information (nucleic acid) surrounded by protein coat -genetic info can be DNa/RNa never both -some viruses contain external structures (e.g. spikes) and an enveloppe of phospholipids
bacteria cells are the ___ cells
smallest
What disease has been eradicated worldwide?
smallpox
why do some viruses contain own replicative enzymes?
some species of virus replicate their genomes in the cytoplasm of the cell- cant use cellular polyerases -cell enzymes read only DNA as a template
Getting foreign DNA into plant cells
some types of soil bacteria can transfer DNA to some types of plant cells -Agrobacterium tumefaciens enters a plant through a wound site, and inserts a segment of its own DNA into the plant's genome -The inserted genes cause tumorous growth called a "gall" -the tumour is instructed to make compounds that the bacteria can feed on -These genes that are transferred to the plant are located on the plasmid -This is a parasidic relationship
Chikunga
south american viral disease
what is NOT a major feature of the adaptive immune system?
speed
1700s: variolation
spreads around the world, eventually spread to Turkey and arrived in England in early 18th century
life cycle of e coli
starts at initial pahse, then exponential, then stationary (not increasing anymore due to lack of nutrition)
How to avoid getting infected # 3
stay home! - fever, diahrrea, vomiting
PROKARYOTIC CELL: inclusions
store nutrients for the cell or vacuoles for buoancy
Normal flora may cause serious diseases in immunocompromized individuals examples:
streptococcus pyogenes -staphlococcus aureus
what do proteins do in the cell?
structural- in cell wall, membrane, ribosomes catalytic- "enzymes" make chemical reactions occur faster inside the cell transport- to bring stuff in and out of cell sensory/ signalling- sense chemicals in the environment, they communicate it in the cell movement- movement of the cell towards a desirable compound or away from an undesirable compound
Immune system defined
system of biological sturctures, cells and processes witin an organism that protects us against disease
what happens in a typical secondary treatment facility?
take advantage of bacteria to remove organic molecules -remove the bacteria before returning the water to a river
Aquaporin
takes excess water out of animal cells without the cell wall
Frank Bruni and New York times piece
talked about ebola break out- disease can dissappear bc people have developed antibodies -there was also a measles outbreak at disneyland, bc people in that area refused to take the vaccine -"herd immunity" dont have to vaccinate 100% of the population, just 80 - 90 percent and the disaese will not propogate
oral colonization
teeth, gums and other soft tissues
exposure to bacteria in soil may cause which disease?
tetanus
translation
the RNA message is used to assemble amino acids into a protein chain. tRNA is involed in translation and its function is to attach to a specific amino acid and bring that amino acidsto the site where polypeptides are being constructed. One end of the molecule attached to a specific amino acid. The other end has an exposed sequenceof 3-‐bases. These are called the anticodon. The anticodons of the tRNAs each have a complimentary codon in the mRNA. For example the codon AUG would be the compliment of the anticodon UAC The third type of RNA is ribosomal RNA ( rRNA).Ribosomes are the decoding units of the cell. Each ribosome consists of two subunits, and is an assemblage of rRNA and proteins. Ribosomes have binding sites for both tRNA and mRNA molecule. An mRNA molecule aVaches to a ribosome. As the ribosome moves along the mRNA, 3-‐base codons are exposed one at a time. A tRNA with an an-codon that is complimentary to the codon of the mRNA temporarily bonds with the mRNA. The ribosome positions the molecules so that this bonding occurs. As the ribosome continues its journey along the mRNA additional tRNAs bring their amino acids to the site of peptide synthesis. As new amino acids are brought to the ribosome, the growing peptide chain is attached to the new amino acid by a peptide bond. Elongation of the chain continues until a stop codon is encountered. At that point the peptide chain is released from the tRNA. A single mRNA can be read repeatedly to make many copies of a polypep-de. Once a tRNA gives up its amino acid it can return to the cytoplasm and attach to another of its specified amino acid
How do non-pathogens become pathogens?
the adition of extra DNA (plasmids)
Food spoilage- what is the result of food spoilable? Microbiologically speaking
the change in appearance, odour, or taste of a food product that makes it unpredictable -it may still be safe to eat (mircobiology speaking) -food spoilage is the result of the metabolism of heterotrophic bacteria or molds
Weaning - introduction of solid foods
the colonization of GIT is dynamic -introuction of solid food produces change -new bacteria include: Enterics, Bacteroides, enterococci, clostridia
ATP is:
the energy currency of the cell
Phenotype
the expression of the genotype. Something that you can observe
Paul Berg (Genetic engineering)
the first to join DNA from two different sources together
Getting DNA into plant cells (different from foreign DNA)
the gene gun is a tool designed to introduce DNA into plant cells -it uses particles of gold coated with the recombinant DNA placed into a shell casing -usually the target of the gene is a plant's callus-undifferentiated cells of the plant- growing in gel suspension -after discharge, the callus and gel are largely disrupted, but not all of the cells in the callus are disrupted -Some of the cells will take up a gold particle, and the DNA may eventually be integrated into one of the chromosomes of the plant cell
Naked virus
the genome is enclosed only by a protein shell called the capsid or nucleocapsid -capsid is made up of multiple copies of protein subunits called capsomeres -made from only one type of protein or several different proteins -If the viral nucleic acid is enclosed by single layer of protein, the layer is called a capsid or nucelocapsid -if the nucleic acid is enclosed by more than one layer of protein, the second shell is called the capsid and the layer directly surrounding the nucleic acid is the nucleocapsid
active immunization
the immune system creates antibodies and other defences against the microbe or microbial components -active immunization can be natural or artificial -Natural active immunization occurs when a person comes into contact with a microbe naturally. -artifical immunization occurs when the pretreated microbes or parts of it are injected into the person before they are able to take it naturally- vaccine
transcription
the information in the DNA is copied to make an RNA message -When the two DNA strands of a gene separate, one of the strands is transcribed into an RNA molecule with the aid of the enzyme RNA polymerase. The RNA strand elongates until it reaches a termination signal (a sequence of bases in the DNA strand). At this time the RNA molecule is released from the DNA, allowing the DNA strands to reattach -In transcription, the DNA helix unzips (a little bit). RNA nucleotides line up along one strand of DNA, following the base-‐pairing rules. The single-‐stranded messenger RNA peels away as a single strand and DNA strands rejoin
How do corn borers cause disease in corn?
the larvae tunnel into the corn stalks -this disrupts the flow of water and nutrient to the ear of the plant -the ears can develop poorly the stalks can break and ears drop to the ground -the stalks can get infected with a fungus that causes the stalk to rot -The corn borers carry fungal spores intto the plant -the corn borers feeding on the kernels or tuneling into the stalk provide the entry point for the fungus -some fungus produce toxins that are lethal to livestock (horses, pigs) -some may be human carcinogens
Why wouldn't bacteria grow on a petri plate?
the medium (agar) did not work for that microbe-not sufficient growing conditions
DNA is ___
the most improtant molecule in genetic determination
Wastewater management
the ojective of sewage treatment is to produce a disposable effluent without causing harm to the surrounding environment -before wastewater treatment facilities, sewage would be collected in cesspits before being discharged into a river or stream -cesspits were introduced in europe as a temporary holding site of human waste -these were typically cleaned at night so not to disturb the public -hazardous work- the various fermentations that occired often produced dangerous gasses that would asphyziate the cesspit cleaners
Bioremediation
the process of changing a harmful substance (either to humans or the envrionment) into something that is less harmful or not harmful at all -the metabolic abilities of microbes can help achieve this -ex) oil spill -high pressure water systems can help disperse the oil and break it up into small droplets -bacteria are added to the oil droplets. Fertilizer is added to provide N and P to ensure that the bacter has all of the biolelemtns that it needs to grow -the bacteria break down the hydrocarbons in the oil to lipids or CO2
deep sea thermal vents
they are formed when the gigantic plates that form the earths crust move apart creating cracks and crevices in the ocean floor seawater seeps into these openings and is heated by the magma as the water is heated it rises and seeks a patj nack out into the ocean through an opening in the sea floor -the seawater contains dissolved H2S carbonates and other chemicals -Chimneys top some hydothermal vents -black smokers are the hottest if the vents -they spew mostly iron and sulfide which combine to form iron monosulfide -it was discovered that this site is ambundant with life -tubeworms and huge clams are the most distincitve inhabitants of the Pacific Ocean vent sites while eyeless shripm are found only at vents in the atlantic ocean -these giant tube worms grow up to eight feet ling and as adults they have no mouth and no digestive tract -these worms are heterotrophs, they depend on a symbiotic relationship with that bacteria that live inside them -the bacteria convert the chemicals from the hydrothermal vents into organic molecules that provide food for them -the bright red plume contains large accounts of a special hemoglobin -this is a specialized organ used for exchanging compounds such as oxygen carbon dioxidem and hydrogen sulfide with the sea water
mouse cells and polio example:
they are permissive to polio virus but not susceptible- observed by microinjecting polio into mouse cells
systems of repair
they are used in the cells -DNA replication and protein assembly make mistakes. -mistakes can be made due to: temperature changes, UV radiation, X radiation, heat shock -these mistakes can be corrected by repair systems in ALL CELL TYPES
Bt insecticides
toxic against a small range of insects (generally they are related species) -Bt insecticides can be formulated to provide protection against lepidoptera (moths/ butterflies) and coleoptera (beetles)
Transcription
transcribing DNA to make mRNA
RNA directed RNA polymerase L (L)
transcription and replication
some viruses carry extra enzymes because:
they will do reverse transcriptase (to convert their RNA--> DNA so they can replicate in cells)
different metabolic pathways lead to different kinds of spoilage
this depends on: -the nurtient content of the food itself (e.g. what type of sugars are present, the protein and fat content) -what type of microbial species are likely to be present -environmental conditions such as temperature -the "right" mixture of microbes and envrionmental conditions may lead to a fermentation and the generation of a desirable product ** Bad microbes may come from the slaughterhouse (steak) Milk may be skin bacteria from the udders -veggies- soil, waterm farm workers, fertilizers
high pressure processing (Canning)
this treatment sterilizes food -temperature is raised to >100 C using elevated steam pressure (121 C) -used for foods that can withstand such a treatment without significant loss of palatability like canned fruits, veggies -can be difficult to predict how long the food should be heated for
Rich Lenski
took e coli cultures and grew them continuously. Put them in new cultures and they went through 60,000 generations. New e coli had mutated from orniginal. There is an evolutionary force that is acting on this. There are always "chance" changes that happen to culures under unchanging conditions
when does passive immunity happen?
transfer of maternal antibodies across the placenta -transfer of maternal antibodies via colostrum and breast milk -injecting the recipient with preformed antibodies
Translation
translation of the mRNA on a ribosome to make a protein
spirulina (microbe)
type of cyanobacterium that has high food value -phototrophic organsim that can be grown in fresh water, it typically grows as long fillaments of cells -it can grow in ponds, collected, dried, and packaged as a dark green powder with flour-like consistency -many nutritional supplement drinks contain spirulina as one of their main ingredients -often used as food additive b/c its rich in protein, vitamin B12 and minerals -food industry classifies as single cell protein -some types of yeast/ algae can also be developed as single cell protein for food
Discovery of viruses: Louis Pasteur
unable to find causative agent for rabies, pathogen too small to be detectable with microscope
transient microbiota
unable to remain in the body for long periods of time -microbial antagonism (one microorganism inhibts the growth of/ kills another microorganism) -elimination by immune system -physical or chemical changes that discourage growth
fungi, yeats, and bacteria are all....
unicellular
Main differences between Viruses and bacteria: bacteria
unicellular, plasma membrane, DNA double stranded, independent transcription and translation, avergae >1000 nm, treatment with antibiotics
Ebola virus: mortality rate
up to 90 %
If you cant grow bacteria what can you do?
use genome sequencing
organism classification based on the types of sources they use for carbon and energy: lithotroph
use inorganic carbon molecules for carbon and other inorganic compounds for energy use inorganic forms of NPS "lithoautotroph"
organism classification based on the types of sources they use for carbon and energy: photo troph
use inorganic carbon molecules for carbon and sunlight for energy use inorganic forms of NPS organisms that use inorganic carbon molecules are sometimes called autotrophs Combined: photoautotroph
Xanthan gym
used to generate some elasticity of dough when making gluten-free baked goods -also found in food products as an additive (e.g. sald dressings) -Xanthan gum is prepared from the polysaccharide secreted by the bacterium, Xanthomonas campestris in to culture media. -the polysaccrhide is collected, dried, and milled to generate a powder
fermentation and industry
used to make: acetone, butanol, lipase added to laundry detergent, rennet used to make cheese -the generation of the methane gas in sewage treatment plants is possible because one tupe of heterotroph produced H2 as a waste product during fermentation (which was used as an energy source by the archea that produced the methane)
2 types of bacteria important for healthy fish tank: Nitrococcus
uses NH4 as energy source lithotrophic bacteria--> use CO2 that the fish produces as well use N as a nutrient and produce NO2 (nitrite) as a waste the problem in that NO2 is even more toxic to fish than NH4
Are all soaps created equally? Liquid
usually recommended, easy touse
Virus takes over bacterial reproduction system
vDNA is converted into RNA, makes viral proteins, reform to create complete virus
Louis Pasteur
vaccine against cholera in chickens, rabies
innactivated- Toxoid vaccine
vaccine made from toxins produced by certain bacteria Toxoid- protein based toxin is rendered harmless, and used as the antigen in the vaccine to illicit immunity -not highly immunogenic -excellent stability profile
influenza vaccine: Trivalent
vaccine target the 3 representative virus types in circulation (two subtypes of influenza A and one B)
influenza vaccine: quadrivalent
vaccines target the 4 most representative virus types in circulation (two subtypes of influenza A and two B)
steps of bacterial cell infection
viral DNA injected into bacterium, makes RNA, Mrna makes proteins producing the virus uses cell to reproduce virus, the cell will then lyse and produce 100s or 1000s of virus
prophage
viral DNA integrated into genetic material
ebola
viral disease
chikungunya
viral disease, transmission by mosquitos -in the Americas, 2013-2015, over one million cases (183 deaths) No where near as much media coverage
lower repiratory tract
virtually free of microbes bc of mucociliary system- mucus produced by goblet cells -nasal mucus also contains lysozyme
evnevloped
virus buds from the membrane and acquires envelope without killing cell immediately and virus replication occurs for prolonged periods of time
cultivation of viruses in lab: plaque method
virus, bacteria, agar mix. Plated and incubated -after replication the virus lyses the bacteria, forming plaques or clear zones
How to avoid getting infected: hand washing
wash for at least 20 seconds -use soap
Where does vancouver's dirty waste water go?
waste water treatment plant- relies on microbes to clean up the water
dehydration/ freeze drying and food preservation
water is removed from the food by heat (dehydration) or by freezing under a vaccum (freeze drying) -the methods are good for some vegetables and pastas but it may result in the loss of some nutritional content -dehydrated food-fruit, beef jerky -freeze dried- space food, microwave options, camping food, instant coffee
How to avoid getting infected # 5
wear a condrom-
EUKARYOTIC CELLS: nucleus
well defined area of the cell- the genetic material, DNA is seperated from the rest of the cytoplasm by a nuclear membrane. Inside the nucleus are chromosomes that are linear and covered with proteins- the number of linear peices depends on the species of eukaryotic cells
food spoilage and classification of perishable, semi perishable, and non perishable
what makes them different? -moisture content- related to water activity -water activity is the measure of the availability of water for metabolic processes -non-perishable foods have low water quality -perishable and semi-perishable foods have higher water activity- so these must be stored to minimize microbial growth -dry foods considered stable (pasta, beans) -semi perishable example: flowers
sulfur dioxide, sulfites and food preservation
wine,dried fruits and vegetables- some people have sensitivity
only way to eliminate infectious disease?
with vaccine. bc it protects people so they cant get the infection. -could have happened with poli- a few places wont give the vaccine for political/ religious reasons -only a few samples of smallpox around the world OR Eliminate source of disease EX) mosquitos and malaria
Stanley Cohen (Genetic engineering)
worked out a way to get bacteria to take up plasmids and recombinant plasmids
Did pasteurs work on wine shock the community?
yes! No one new that microbes could be agents of change (analogous to factories where chemical changes occur) -‐ and that bacteria appeared to make the wine sick Before Pasteurs discovery, physicians had thought that bacteria was an effect of disease (they appeared during illness) -‐ now Pasteurs work suggested they are the cause of disease
is there bacteria in placenta?
yes! even though it was considered sterile -placenta microbiota differed from women who had full term pregancies and those who experienced preterm labour or UTI in early pregnancy
Innate and adaptive branches of immune system- do they work together?
yes, to maximize protection against pathogenic organisms
where do you get your major and minor bioelements?
you get them from food- you couldnt live on a diet of just water and vitamins bc your body couldnt properly absorb the nutrients (need fat to do so)
Ebola virus: type of disease
zoonotic
