Microbio FINAL

Agrobacterium

the method of introducing genes into plants

Agrobacterium characteristics (3)

• gram negative

• lives in soil

• efficient conjugation

examples of agrobacterium delivery (4)

• herbicide resistance

• drought resistance

• change in nutritional value

• suppression of ripening genes

bioremediation

use of biological organisms to detoxify environmental pollutants

composting

arranging organic waste to promote microbial degradation

bioaugmentation

enhancing the activities of already present bacterial populations via adding commercially prepared bacterial strains with particular catabolic properties

xenobiotics

resistant to degradation

bioremediation method (3 steps)

• identify the target chemical

• select microbes (act as chemical machines) with unique enzymes to degrade the chemical

• consider the downstream effects ecologically

D. radiodurans

• radiation resistant (strong DNA repair systems)

• metabolizes toluene and mercury from radioactive sites

Ideonella sakaiensis

eats plastic

some Pseudomonas

• degrade agent orange and dioxins

genetically engineered microbes (GEMs)

Ralstonia eutropha engineered to express metallothionein on its surface, better sequesters cadmium, prevents plants from absorbing toxic metal

4 examples of bioremediation bacteria

• D. radiodurans

• ideonella sakaiensis

• some pseudomonas

• Ralstonia eutropha

study phytoremediation

plants cleaning the air ? sunflowers in chernobyl

study mycoremediation

fungus clearing up toxic waste

wastewater plants

primary- dirt removal (sludge to landfills)

secondary- removal of biological matter with oxidizing microbes

tertiary- disinfected chemically or physically (lagoon)

Methanogens

• obligate anaerobess

• oxidize decomposing organic waste in landfills

• end product is methane gas, CH4

biofuels

produced from biomass, shorter time than natural gas

renewable!

3 biofuels

methane, ethanol, methyl ester

catalysts used for biofuels (3)

sodium hydroxide, potassium hydroxide, microbes

number of bacteria living on/in us

40-100 trillion

microbiome

all the microbes in a region/body

symbiotic

separate species living close together

mutualistic

both species benefit

commensal

one species benefits, one is unharmed

parasitic

one species harms another

study microbiome analytical pipeline

skin bacteria

staphylococcus, streptococcus, propionibacteria, corynebacteria

stomach ph and bacteria

ph2, heliobacter, proteobacteria, bacteroidetes

large intestine ph and bacteria

ph 4-5, enterococci and lactobacilli

small intestine ph and bacteria

ph 7, escherichia, clostridium, bifidobacterium

microbiome is afffected by:

early life exposure, late life impact, host physiology, diet, host environment, genetics

alpha diversity

within ONE sample

beta diversity

ACROSS multiple samples

dysbiosis

microbial imbalance on or inside the body

Firmicutes associated with

fat-rich diet

symbionts

organism closely related with another organism

pathobionts

microbes that are typically opportunistic and grow in the disturbance of a healthy microbiome

know how c. diff gets bad and treatment

(c. scindens, FMT, bacteriotherapy)

know necrotizing enterocolitis steps

(bifidobacterium, etc)

benefits of bifidobacterium

stabilize gut microbiome, reduce retrovirus shedding, reduce gut permeability, increase IgA antibodies and support immune system, helps stimulate vitamin production

bifidobacterium characteristics

gram +, anaerobic gut bacteria

ferments breast milk sugars in babies

human milk oligosaccharides (HMOs) = growth promoting factors

know how microbiome affects obesity, gestational diabetes, and IBS

Prions characteristics

no nucleic acid, extremely resistant to heat, chemicals, and decomposition, infectious sporadic or genetic, come from accumulation of PrPSC (isomer of normal PrPC)

Prion long name

proteinaceus infectious particle

scrapie

poor sheep, 1939- intraoccular inoculation of sick brain material into healthy sheep took 2 years for symptoms

big outbreak due to contaminated vaccine

Kuru

papua new guinea, 25% of women, trembling and death 9-12 months after 1st symptoms. Gajdusek and Hallow figured it out. Gajdusek is a creep. discovered it was infectious

Tikvah alper

used UV on scrapie, showed it had no DNA, replicates WITHOUT nucleic acid

Stanley Prusiner

finds weight of protein in scrapie and identifies the protein

Transmissible spongiform encephalopathy

prions cause in mammals

normal function of PrP

WEIRD (study)

Alison Krauss

made imaging of prions using Cryo-EM

Amyloid plaques

misfolded, insoluble, protease resistant, fibrous protein aggregates, cause over 20 degenerative diseases

Alzheimer’s protein(s)

amyloid-beta, Tau

parkinson’s disease protein

alpha-synuclein

Amyotrophic lateral scelerosis protein

TDP-40

human prion diseases

kuru, creutzfeldt-jakob, fatal familial insommnia, gerstmann-straussler-scheinker syndrome

creutzfeldt-jakob disease

1 in a million. average 50-70 year olds, relentlessly progressive, die in 1 year, 85% of human prion diseases

causes of CJD

genetic (10%), Iatrogenic (from other brains via brain surgery, cadaver hormones) (<5%), variant CJD (kuru, eat bad meat), Sporadic or Classical CJD (85%)

know differences between CJD and vCDJ

nice table page54

Bovine spongiform encephalopathy (vCJD)

first case 1986, cannabilistic cows, 1995, people got sick

fatal familial insommnia

genetic, autosomal dominant, 40-80 families, mutation of PrP gene at codon 178, hypothalamus is targeted

gerstmann-straussler-scheinker syndrome

genetic, 56 known families (1 in 100 million people). age 35-50, survival 5 years, codon mutation 102

why are there different prion diseases?

different folded shapes, different brain locations

HIV stats

38.4 million people living with it

Influenza stats

20% of people get it each year, 1918 killed 5% of population

Cold viruses

rhinovirus, endemic coronavirus, RSV

Ebola stats

1,000 deaths 1976-2013, 10,000 deaths 2014-2015

Herpesvirus

chicken pox, cold sores, mono, shingles

Hepatitis

58 million people living with chronic HCV (bad water). 296 million with HBV

Human Papillomavirus

100 different types, 4 cause cancer. 80% of women affected by 50.

viruses infect

animals, plants, protists, fungi, prokaryotes, and other viruses

transduction

how viruses contribute to bacteria evolution

Phage therapy

viruses that kill bacteria (highly targeted)

oncolytic viruses

measles injected into cancerous tumors, attacks the tumor and get the immune system into drive

virus therapies

phage therapy, genetic therapy, oncolytic, vaccination

virus

microscopic particle that can infect the cells of an organism

virus characteristics

obligate intracellular pathogen, acellular

virus size

20-300nm 1/1000 of animal cell

bacteria size

0.5-5um

plant/animal cell size

10-100um

capsid

protein shell

virus genetic information

RNA OR DNA (inside capsid)

do viruses share a common ancestor/genome?

no, each genome is very different

viral proteins

structural and regulatory

structural proteins

make up capsids and structural components

regulatory proteins

enzymes (polymerases, helicases), transcription factors, influence host cell functions to make it a more suitable environment. some inside the capsid, some in genetic material

T-antigen is in

Polyomaviruses

T-antigen blocks

pRb and p53

pRb

tumor suppresor gene

p53

guardian of DNA integrity

pRB +T-antigen in mice

lotsa tumors

p53 + T-antigen in monkeys

no tumors (cells blow up)

retrovirus proteins

specific to each virus, have specific functions

viral morphology

helical, polyhedral, spherical, complex

helical

ebola, rabies, respiratory syncytia virus

icosahedral

polyhedral

polyhedral

20 sided, poliovirus, polyomavirus, papillomavirus, adenovirus

spherical

(kinda). coronaviruses

complex

bacteriophage, variola(pill shaped)