extremophiles and synthetic microbes

extremophile definition and characteristics

extremophile: microbes that are capable of living in extreme physical, chemical, or geochemical environments

acidophile - pH < 3

alkaliphile - pH > 10

halophile - approx. 1 M salt

hyperthermophile - > 80 degrees C

thermophile - 60-80 degrees C

psychrophile - <15 degrees C

piezophile - high pressure, approx. 40 MPa

endolithic - grows inside rocks

radioresistant - tolerance to high doses of radiation

metallotolerant - tolerance to high levels of heavy metals

toxitolerant - high concentrations of toxic agents

xerophiles - low water availability

why are they important to study?

1) psychrophiles do well in the cold and most of the biosphere is cold environment, understanding how their enzymes work may have significant biotech applications

2) radioresistant have the ability to repair DNA, ability to digest complex plant polymers may have applications in biofuel production and green chemistries, ability to use radiation

3) thermophiles - advancing biotech-related fields that are centered around extreme temperatures

4) halophiles - develop salt-tolerant crops, biodegrading/bioremediating hazardous compounds

why does the study of extremophiles tie in with NASA mission aims

xerophiles can be used to develop tech that detects life below soil on Mars because the microbes live in extremely dry, arid places

what is the eXtreme Microbiome Project?

XMP, sequencing extremophiles to characterize/discover/develop new pipelines and protocols for extremophiles and novel organisms

what’s unique about the symbiotic relationship of panic grass? what organisms are involved?

the panic grass has a fungus that lives with it which has a virus living inside it, giving both organisms thermal resistance. unique because it is a symbiotic relationship involving three organisms

panic grass

curvularia protetuberata

CThTV

deep-sea vent symbiotic organisms and bacteria

yeti crab grows garden of bacteria on appendage

mussels and giant clams have bacteria in gills

riftia tube worms

pompeii worms secrete mucus to feed bacteria and eats it again

bacterial, viral, fungal, and protozoal symbiotes

bacterial: streptomycetes + european beewolf, squid + vibrio fisheri

viral: cotton bollworms + densovirus, tomatoes + tomato spotted wilt virus, rosy apple aphids + densovirus

fungal: lichen + cyanobacteria and algae, plants and glomeromycota

protozoal: zooxanthellae and coral/jellyfish/slugs, lower termites + flagellates, cows + ciliates

examples of conditional mutualisms and symbiogenesis

1) humans and hepatitis g —> slows HIV replication

2) mice and gamma-herpes —> increases resistance to plague and listeria, activity against pathogens and tumors

osmotprotectant

proteins that increase osmolarity inside, mimics salt

mutualism, commensalism, and parasitism

both organisms benefitting, one benefitting/one is unharmed, one benefitting/the other being harmed

endosymbiosis

one symbiont lives within the body of the other

Angel’s Glow

soil nematodes + luminescens —> kills and attracts insects, Battle of Shiloh where soldiers were wounded and nematodes lived in the wounds leading to the wounds healing faster

conditional mutualism

an organism may not have a benefit until the conditions change and they are more resistant —> benefits come out in certain conditions

Symbiogenesis

endosymbiont becomes a part of the larger organisms

1) mitochondria/cyanobacteria becoming a part of the eukaryotic cells

2) HERVs

HERVs

human endogenous retrovirus

viruses that when entering an egg/sperm cell can pass on viral traits becoming hereditary traits for organisms

Syncytin

a protein involved with placenta development

why do bacteria make restriction enzymes and how do we utilize them?

bacteria don’t want invading viruses to come in so they have enzymes that cut off unfamiliar sequences

endonucleases: restriction enzymes that cut DNA at palindrome sequences

what are plasmids? what are their 4 elements?

circular DNA

it needs ori (allows replication), selectable marker (select presence of plasmid), MCS(location it can be inserted to), and a promoter (expression of cloned sequences)

examples of genetically modifying microbes with a plasmid

insulin —> from pancreas of cattle/pigs now have plasmids of human insulin gene to form insulin identical to human insulin

GM-CSF —> human gene inserted into plasmid, transform into GM-CSF to increase white blood cells

a. tumefaciens —> soil bacteria that contained Ti but T-DNA inserted

what are the advantages of integrating microbial DNA into genomes of higher species? what are examples?

bt-resistant cotton

round up ready soybeans

gives them enhanced resistance to pathogens, improved environmental adaptability, or the production of specific molecules

why might one want to extensively alter microbial genome? give example of synthetic biology

trying to bring a whole mechanism into an organism —> artemisinin used to give organisms traits they normally would not have, artemisinin put into yeast so anti-malarial treatment can be produced, nonprofit

what are examples of kill switches/biocontaminant strategies?

safeguards to prevent gm bacteria from escaping into the wider environment

ex. deadman, passcode, crispr system

CRISPR/Cas, how did scientists exploit CRISPR/Cas?

serves as genetic memory of infection/acts as bacterial immune system

exploited as efficient and precise genome editing tool

Model organisms, why do we use model organisms?

experiment on organisms that can give findings to humans because we do not want to use humans for experiments

no ethical concerns, reproduce and grow rapidly, survival in variable conditions, harmless

ex. e.coli

what are the goals of national microbiome initiative

1) supporting interdisciplinary research

2) developing platform technologies

3) expanding microbiome workforce

microbiota gut brain axis

signaling between enteric nervous system in gut
& brain

how does the gut microbiota influence the brain? can the diet influence this signalling?

affects by:

1. secretion of neurotransmitters ... GABA,
serotonin, tryptophan, dopamine
2. generating neuroactive compounds ...
butyrate can reduce anxiety, depression
3. activation of the vagus nerve
4. interaction with immune system ... influence mood & behavior

how did scientists determine gut microbiota is important in depression?

significantly lower amounts of Bifidobacterium, Prevotella, Lactobacillus spp.

• gut microbiota from patients with depression
  were transferred to rats without gut microbiota ...
  rats now displayed behavioral and physiological
  symptoms associated with depression

• activation of kynurenine pathway also seen with rats
  ... pathway has been linked to depression

• supplement the diet with probiotics with
  Lactobacillus species ... symptoms of
  depression decreased

how could bacteria be used as vehicles to deliver drugs to tumors

bacteria will accumulate at tumor cites —> slowing tumor growth, bacteria can have anti-tumor toxin and deliver toxin

circuit would secrete quorum sensor, trigger lysis, and deliver toxin to cancer cells

why is polio being investigated as a tool to treat glioblastoma

uses polio to make virus that is unable to grow in brain tissue —> immune system kills themed

how has forensic microbiology been used to trace bio-attacks or disease?

studying ebola in 2014 —> seeing how it changed as it when to different places

thanatomicrobiomics

microbes in death—> how do they move in bodies when they die

why do we think microbes will be important for space travel? what are some issues?

to prepare us to go to Mars

neurotransmitters

chemical messengers that transmit signals between nerve cells and other target cells, such as muscles and glands

oncolytic viruses

HSV viruses where genes are inserted