DNA History, Genetics Microbiome

disadvantages of phage therapy

- safety: the original phage administered might be safe to use on a human body but who is to know what this phage will evolve into (Antibiotics are currently a safer method because they do not evolve and their effects are predictable_

Avery, MacLeod, McCarty

-1940: Known that DNA, RNA, and proteins are major constituents of living cells -Prepared cell extracts from type IIIS cells containing each of these macromolecules -Cell extracts were treated with different enzymes

stats for fecal transplant

-46 out of 49 patients got better within a week of the treatment. -four (or 8%) experienced a recurrence of their infection during the follow-up period while 25-30% for antibiotics, -Four patients in the study died, including three whose C. diff infection had been successfully treated with the transplant. (cancer)

Phoebus Levene

-Discovered ribose sugar in 1909 and dexoyribose in 1929 -nucleic acids were a repeating tetramer Model suggested that nucleic acid a uniform, simple structure - no variety possible tetranucleotide model

Friedrich Miescher (1869)

-Isolated "nuclein" from cell nuclei - believed to be phosphorus-rich protein (actually DNA with associated proteins) - First to identify/isolate DNA -Used pus from band aids, Studied salmon sperm Isolated nuclein from cell nuclei and came upon a substance that has phosphorus [first to identify/isolate DNA)

Bacteria resistance to antibiotics

-evolve a new version of a trait that will escape targeting by a specific drug (altering of ribosomes/DNA to not posess charactersitic of antiobitoc attack) -Biochemical pathways can be adapted to create products that either destroy or inactivate the drug when it enters the cell. -cells can prevent lethal level of drugs by blocking entry or efflux pumps (proteins that shuttle the drug out of the cell before it can do any real damage) -if drug inhibits a pathway bacteria evolved an alternative pathway that is unaffected by the antibiotic, allowing them to survive and grow unhindered.

Acenobacter Baumannii

-opportunistic pathogen -fifth most common pathogen implicated in nosocomial (hospital acquired) infections worldwide -create biolfilms (sticky films of polysaccharides secreted by the bacteria that surround them and act as a physical barrier to disinfectants and antibiotics.) can survive on dry surfaces -extremely adept at rapidly acquiring antibiotic resistance making treatment harder -Many of these multi-drug resistant strains of A. baumannii are resistant to an entire category of antibiotics, known as beta-lactam antibiotics -pick up any surrounding DNA in the environment, allowing them to gain antibiotic resistance coding genes extremely quickly. This trait evolved due to long-term coexistence in the soil with other microbes that naturally produced their own antibiotics, leading to natural selection favoring strains of A. baumannii that could quickly pick up antibiotic resistance coding genes from their surroundings!

advantage of phage therapy

-phages can evolve right along with the bacteria. If the bacteria evolve resistances to phages, the phages will evolve to overcome that resistance. -specificity of phages also allows them to only target the "bad" bacteria. Barring unforeseen events, the phages will not kill any of the useful or "good" bacteria that are in our bodies (antibiotics kill all bacteria)

Griffith Conclusion

1. Something from the dead type IIIS was transforming type IIR into type IIIS 2. The substance that allowed this to happen was termed the Transforming Principle 3. The transforming principle was the genetic material

T2 bacteriophage life cycle

1. phage binds to host cell 2. phage injects DNA into host 3. Phage DNA directs synthesis of viral component 4. Phage components assembles 5. Host cell lyses and new phage released LYTIC

What do all bacteria have

16s ribosomal DNA

Mendel 1866

A "factor" is passed on from parent to offspring, therefore inherited did not know what factor was discovered basic principles of genetics by conducting experiments on pea plants Laws of heredity & distinction between dominant and recessive traits

bacteriophage

A virus that infects bacteria

Avery critique

DNA extracts Avery used contained trace quantities of protein that might produce the transforming effect.

immune study

mice injected with clostridium wanted to investigate whether Clostridium could not only stimulate the production of regulatory T cells but also whether or not this stimulation affected the autoimmune response of Clostridium inoculated mice with clostridium injection, t cell higher both groups given 2% DSS to stimulate colitis, disease score higher for mice without clostridium (more severe) mice with clostridium lower antibodies to ovalbumin (allergen) clostridium educates t cells

information

necessary to make an entire organism

Avery, MacLeod, McCarty conclusion

DNA is the transforming principle

lytic cycle

newly assembled phages then lyse the cell, causing the cellular contents to spill out along with all the newly synthesized phages into the surroundings, where they can go and infect neighboring cells

ecological succession

occurs when the intestinal microbiome starts to develop. Succession is the process of colonizing a "blank slate" environment like those of infants

multi-drug resistant (MDR) Acinetobacter

overusing common antibiotics like tetracycline, humans drastically increase selection for antibiotic resistant bacteria, and accelerate their growth and spread. ess developed Asian and Middle Eastern countries such as Iran, Taiwan, and India show higher rates of these nosocomial infections

transmission

passed from parent to offspring

Acne

pathogenic Propionibacterium acnes fills and blocks sebaceous glands p. acnes normally found on skin and unharmful (commensal) amount of p. acnes in acne/nonacne people same but strains differ forms biofilms within pores

Beta-lactam antibiotics

penicillin and ampicillin, which function by blocking cell wall synthesis in bacteria, causing them to burst when they try to divide. "beta lactam" ring in their chemical structures

Thomas Hunt Morgan (1910)

Discovered that genes are on chromosomes, and some are sex linked fruit fly experiment

Barbara McClintock 1944

Discovered the ability of genes to change positions on the chromosome transposons (jumping genes) mosaic colors of maize

Golgi apparatus

Eukaryotes

Rosalind Franklin 1952

Franklin produced the best data to date that led to the discovery of the shape of DNA using X-rays crystallography shows phsophates must be on outside diameter of DNA helix is constant used water to get B form DNA

Chargaff 1950

Given that DNA was essentially composed of four bases it was unclear how it could produce the almost infinitely different effects produced by genes. 20 a.a. > 4 nt The amount of A roughly equals the amount of T, and the amount of C roughly equals the amount of G (A = T and G = C). different species have different amount of nucleotides used paper chromatography

diet and microbiome

Immune microbiome lives in the stomach and coexists with the digestive system. Therefore with healthier dietary choices we can allow this immune microbiome to thrive and therefore with the aid of vitamins and probiotics our bodies are protected from foreign invaders.

m. smithii and bacterodetes

It obtains hydrogen from Bacteroidetes, which produces hydrogen as an end product of metabolism. M. smithii removes the excess hydrogen from Bacteroidetes' environment. This hydrogen removal promotes the population of Bacteroidetes in the gut to increase which leads to an increase in hydrogen production.

Bacteriodetes

Major flora of the human colon provides the human gut with vitamins and nutrients, while the human gut provides nutrients (in the form of food that we consume) and a place to live for both Bacteroidetes and M. smithii. mutualistic

Darwin 1859

Proposed theory of evolution occurring by process of natural selection Published Origin of Species - argued that living things best suited to their environment are more likely to survive, reproduce, pass on their characteristics to future generations

Frederick Griffith

S. pneumoniae comes in two strains: A. Smooth (S) Rough ( R )

experiment for phage therapy

Scientists have isolated a phage that specifically targets and kills P. aeruginosa. first treatment, mice were infected with P. aeruginosa. (very low survival) In the second treatment, mice were treated with phage. (full survival (no bacteria to track) Finally in the third treatment, they infected mice with P. aeruginosa first and then administered the phage (full survival showing phage therapy works)

rough strain

Unable to secrete a capsule Produce colonies with a rough appearance nonvirulent

Hershey and Chase

Used radioactive material to label DNA and protein; infected bacteria passed on DNA; helped prove that DNA is genetic material not proteins

Watson and Crick 1953

Watson and Crick saw the image without Franklin's permission and using nothing but paper cutouts and paperclips built a model determines how A and T, G and , formed base pairs (hydrogen bonds) critiqued pauling model for phosphates on inside, bases outside, and triple helix brought up idea for dna replication

oily skin bacteria

actinobacteria (corynebacterium, propionibacterium, micrococcineae) stapholococcae (some) protobacteria bacteriodetes

George Gamow 1953

aimed to decipher genetic code (made the club) Proposed 3 nucleotide base = 1 amino acid DNA has code for protein syntehsis; attempted RNA tie club

virus

an infectious particle made of protein surrounding genetic information in the form of DNA or RNA depend upon a host for survival and reproduction, as they cannot replicate on their own.

M. smithii

anaerobic (not requiring oxygen) microbe that uses hydrogen and produces methane. Hydrogen helps M. smithii break down the complex sugars we consume and turns them into short chain fatty acids (SCFAs), which we can then use as a source of energy (extra calories). mutualistic

Cell membrane

both

Cytoplasm

both

DNA

both

Ribosomes

both

cell wall w/ celullose

both (plant)

variation

capable of changes to account for the known phenotypic variation in each species

Antiobiotics

chemicals that inhibit the growth of or kill other microorganisms target an aspect of bacterial physiology not present in humans

ribotyping

classification or identification of bacteria based on rRNA genes

Acne experiment

colonies of bacteria were allowed to grow and form biofilms for a 24-hour period before antimicrobials were added. 2% salicylic acid most effective 30 mM azelaic acid least effective

Pseudomonas aeruginosa

common bacterium that under certain circumstances can cause infections that can be fatal. tested in mice

Bacteriophage T2

composed of DNA and protein 32P labeled DNA specifically (found in pellet) 35S labeled protein specifically (found in supernatant) radioactively-labeled phages were used to infect non-radioactive Escherichia coli cells DNA is injected into the bacterial cytoplasm during infection This is the expected result if DNA is the genetic material lytic

replication

copied In order to be passed from parent to offspring

DNA building blocks

deoxynucleotides

Maurice Wilkins

determines DNA is crystalline

genome sequencing

determining the nucleotide base sequence of the entire genome of an organism helped discovered the specific species of microbes that inhabit the skin. Scientists can now take a sample of microbes from the skin, isolate the ribosomal RNA, amplify it to make millions of copies, and then use computer aided technology to sequence the different types of ribosomal RNA present. This information helps scientists identify the wide variety of specific microbes present on the skin. each area of the skin has a different environment (i.e. oily, moist, dry, or other), which promotes the growth of certain types of microbes over others.

Frederick Sanger 1977

developed rapid DNA sequencing techniques First to order the amino acids and obtain protein sequence ( won NP) Deduced that if proteins were ordered molecules, then DNA that makes them order as well idenity free amino acid in insulin started with RNA thne DNA dideoxy method

RNA

eukaryote

central vacuole

eukaryote (plant only)

ER

eukaryotes

Microtublues

eukaryotes

Mitochondria

eukaryotes

Nucleolus

eukaryotes

Smooth ER

eukaryotes

centrioles

eukaryotes (animal)

Lysosomes

eukaryotes (kind of plant, def animal)

chloroplast

eukaryotes (plant)

nucleus

eukaryotic

dry skin bacteria

firmicutes proteabacteria stapholococcae almost all most diverse area: palm, forearm, buttocks

bacteriophage cycle

first attach to a bacterial cell and inject all of its genetic information, or genome, into the bacterial cell. The virus will "hijack" the cell's replication and transcription machinery in order to replicate and transcribe its own genome. blueprint to synthesize the necessary pieces to produce and assemble more phages inside the bacterium.

Marshall Nirenberg 1965

first person to sequence the bases in each codon with Heinrich Matthaei 1961 - Added synthetic mRNA made of uracils to test tube containing materials for protein synthesis → showed UUU codon specifies phenylalanine.

Sir Archibald Edward Garrod 1908

first to associate Mendel's theories with a human disease enetic disorder attributed to "inborn errors of metabolism" - certain diseases were results of errors in missing steps of body's chemical pathways Found that alkaptonuria, albinism, cystinuria, and pentosuria were autosomal recessive traits

Acenobacter

genus of 27 different species of bacteria that can thrive in a wide variety of habitats from moist soil to dry surfaces in a hospital room to human skin. typically rod shaped, and are classified as Gram Negative (they have a thin layer of peptidoglycan between their inner and outer cell membranes). Many species are resilient (ex: some can grow on benzene, an organic component of crude oil that is highly carcinogenic to humans. some are pathogenic some arent (found in skin and mucous)

biofilms

groups of microorganisms that collectively adhere to each other and attach to a surface. protected by an extracellular matrix that can withstand harsher conditions and facilitate microbial communication. improved ability to be resistant to antibiotics

skin

home to a wide variety of microbes including bacteria, archaea, fungi, viruses and mites. Before advanced genome sequencing technology, scientists took samples of different areas of the skin and cultured these in the laboratory. However, certain bacteria, such as staphylococci, will outgrow other types of microbes and scientists could not observe the other types of microbes living on the skin because staphylococci grew exceedingly better than the other microbes on the culture plates.

Oswald Avery 1944

identified DNA as transforming principle

Requirements necessary for genetic material

information transmission replication variation

vacuole

(eukaryote)

Stapholococcus epidermis

present in overwhelmingly great quantities on the skin of healthy people. S. epidermidis, then, must somehow out-compete other bacteria for space and resources, providing a protective "shield" from potentially harmful microbes. brings up question of commensal or mutual?

flagella

proakryote

Beta-lactam resistance

produce enzymes called beta-lactamases that destroy these rings and disable the drug before it can do a lethal level of damage, allowing the bacteria to continue infecting patients treated with these beta-lactam antibiotics. beta-lactamases can only be produced if the bacterium possesses a gene in its DNA that codes for the information necessary to produce these beta-lactamase enzymes and can exist on plasmids

plasmid

prokaryote

nucleoid

prokaryote (DNA bundle)

Carl Erich Correns

rediscovered Mende;'s work and reported results of hybridization similar to Mendel's findings Also worked with pea plants & published paper that redefined law of segregation and independent assortment

regulatory t cells

responsible for identifying which cells of the human body are "self" and "foreign", and are also in charge of regulating when the immune system should "turn off" after an invading pathogen has been eliminated. prevent autoimmune diseases that have become increasingly prevalent in industrialized societies, such as allergies, asthma, and psoriasis.

RNA building blocks

ribonucleotides

strains

same species but slight DNA differences

Eugenics Movement/Francis Galton (1880-1900s)

science of hereditary + good breeding Humans can improve by removing undesirable traits using selective breeding so that only people with the best genes could replace + improve species = scientific racism

phage theraphy

scientists have isolated lytic phages that can specifically target certain bacteria and kill them.

smooth strain

secretes a polysaccharide capsule Protects bacterium from the immune system of animals Produce smooth colonies on solid media virulent

moist skin bacteria

stapholococcae corynebacterium bacteriodetes proteabacteria micrococcineae

obtaining plasmids

taken up from the environment swapped between bacteria, allowing pathogens to build resistance by mixing and matching genes with completely different species of bacteria.

weight study

tested subjects based on content of breath normal: 20 ppm H 3ppm M hydrogen: >20ppm H, <3 ppm M methane: <20ppm H, >3ppm M hydrogen+methane: >20ppm H, >3ppm M methane and hydrogen together in high levels found in overweight people

lysogenic cycle

the viral genome integrates into the bacterial genome. This viral genome is now a part of the bacterial genome and so when the bacteria divide the viral genome also divides and all the bacterial progeny also have the virus. This will continue until other signals are given to the virus that will make it go into the lytic cycle.

Pauling and Corey

thought DNA was a triple helix

factors that impact infant microbiome

type of birth formula feeding antimicrobials

Ribotype

unique genomic fingerprint containing the 16S ribosomal DNA sequence

crystal violet stain

used to determine the amount of bacteria present easily visible under a microscope.