BacterioFiles Special Edition - ASM2013 General Meeting Day 3

Here's my summary of the third day of ASM2013, wherein I met with neat people and ideas.

Session 1: Microbe-Microbe Interactions - Cell Contact-Dependent Outer Membrane Exchange in Myxobacteria
Presented by Dan Wall
Myxobacteria are super cool, a fascinating example of complex cooperative behavior in relatively simple single-celled organisms. They swarm around eating other bacteria until they get low on food, at which point they gather together to form reproductive structures called fruiting bodies to spread to new environments.
As part of the mechanism they use to coordinate their activity and distinguish between friends and foes, they seem to exchange components of their outer membrane, but only with closely-related strains.

Poster: 1485 - Understanding the Syntrophic Metabolism of a Bacterial Co-culture for Hydrogen Production
(Combination of Clostridium cellulolyticum and Rhodopseudomonas palustris to convert cellulosic plant material into hydrogen)
Y. Jiao, A. Navid, B. Stewart, J. McKinlay, M. Thelen, J. Pett-Ridge

Poster: 1702 - Non-Photosynthetic, Deep-Branching Cyanobacteria of the Human Gut and Subsurface Permit Inference of the Cyanobacterial Ancestor
S.C. Di Rienzi, I. Sharon, K.C. Wrighton, O. Koren, L.A. Hug, B.C. Thomas, J.K. Goodrich, J.T. Bell, T.D. Spector, J.F. Banfield, R.E. Ley

This Week in Microbiology 56: Live at ASM in Denver

They started out talking about scientific misconduct with Ferric Fang, then with Andrew Camilli about the virus with a CRISPR system (listen at about 1 hour 2 min in to hear my question!), and also with Suzanne Fleiszig and Michelle Swanson about a gruesome-sounding eye infection and defenses against intracellular bacteria. You should give it a listen (or watch)!

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BacterioFiles Special Edition - ASM2013 General Meeting Day 2

Here's my summary of the second day of ASM2013, an exciting day full of science.

Session 1: Pumping at the Microbial Well
Section 1: Advanced Plant to Advanced Fuel
Presented by Jay D. Keasling,
In order to produce long-chain carbon compounds for diesel and jet fuels, it is possible to engineer bacteria like E. coli to produce them the way they produce long fatty acids for their membranes, but in a better form for extraction. Also, plants produce many terpene compounds for defense, such as bisabolene, that can also be good for fuel, and bacteria can be engineered to produce these too, but it can be tricky due to these compounds' toxicity.
Paper on good efflux pumps for biofuel production: Dunlop et al, 2011, Mol. Sys. Biol. 7:487 doi: 10.1038/msb.2011.21

Section 2: Is There a Path to Cellulosic Biofuels?
Presented by Thomas W. Jeffries
His main point was that the use of fossil fuels should be a transitional state between the pre-industrial era and a sustainable system of renewable energy. Fossil fuels should be an investment in the future, not something we should build our whole infrastructure around. They are going to run out someday, after all.

Poster: 280 - Comparisons of CRISPR Content Between Saliva and Skin: Viral Exposures May Not Be Body Site Specific
R. Robles-Sikisaka, M. Naidu, M. Ly, J. Saizman, S.R. Abeles, T. Boehm, D.T. Pride

Session 2: Uncovering the Function of Unknown Proteins
Section 1: Evolution and the Proteome: Insights into Protein Function from Deeply Conserved Gene Modules
Presented by Edward Marcotte
How should one go about figuring out the function of unknown proteins? Possibly by comparing homologs in other, even distantly related organisms. Even homologous genes in yeast and humans can have similar functions. And of the ~500 essential proteins in yeast that have human homologues, 60% of them can be replaced with the human version and the yeast will still be viable.

Section 2: Small Proteins Can No Longer Be Ignored
Presented by Gisela Storz
Her group has discovered some bacterial proteins smaller than 50 amino acids long, that seem to be related to metal metabolism.


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BacterioFiles Special Edition - ASM2013 General Meeting Day 1

I went to the General Meeting of the American Society for Microbiology, in Denver, Colorado, and I wanted to share some of the fascinating science that I experienced. So here's my summary of the first day!

Section 1: I missed it because Denver is confusing and it took me so long to find parking. Apparently it was interesting, though, discussing how a certain bacterium, Caulobacter crescentus, divides into two daughter cells, one that holds onto a surface and the other that swims away.

Section 2: The Killers, the Cures, and the Limits of Life: Frontiers of Science in the Unseen World
Presented by Nathan D. Wolfe
I missed some of this section, but what I heard was interesting, about how endogenous retroviruses may have made mammalian development possible, and how significant portions of the microbial world may still be unknown.

Section 3: Engineering by Evolution
Presented by Frances Arnold
This was quite interesting. As an engineer, Dr. Arnold is interested in making cells and their enzymes do stuff, so she works on improving their abilities. There is tremendous diversity of amino acid sequences (i.e. proteins) in nature, but it represents only a small amount of the possible combinations of amino acids. Most such combinations are useless as enzymes, but a few are even more effective than anything (yet found) in nature. Dr. Arnold discussed how to find these combinations.
Here is the paper published about the heat-stable cellulases that I discussed: Wu and Arnold, 2013, Biotechnol. Bioeng. 110:1874 doi: 10.1002/bit.24864.


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BacterioFiles Micro Edition 124 - Chlamydomonas Constructs Coming Coal

This episode: Green algae's hydrogen production is analyzed and improved!


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Transcript

Show notes:
News item/Journal Paper

Other interesting stories:

**Scientists take protein from flesh-eating bacteria and make useful adhesive
**Fungus from horse gut could be good for breaking down plant material for biofuels
**Dogs are an important influence on our microbiota
**Bacterial fossils could contain evidence of an ancient supernova
**E. coli modified to produce imitation petroleum

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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This show features music from Mevio's podsafe Music Alley.

BacterioFiles Micro Edition 123 - Proteobacteria Protonate Poison

This episode: Soil microbe has a good enzyme for degrading cyanide pollution!


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Transcript

Show notes:
Journal Paper

Other interesting stories:

**Company developing virus to treat cancer
**Prions help fungi regulate their multicellularity
**History and status of phage therapy
**Protists from termite gut named after elder gods
**Screening many chemicals, scientists found some that increase algal oil production

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

This show features music from Mevio's podsafe Music Alley.

BacterioFiles Micro Edition 122 - Coliforms Consume Caffeine Compulsively

This episode: Scientists engineer E. coli to be addicted to caffeine!


Download Episode (4.3 MB, 4.75 minutes)
Transcript

Show notes:
News Item 1/News Item 2/Journal Paper

Other interesting stories:

**Figuring out how microbes survive in salty freezing lakes
**Bacterial wires conduct electricity because of certain amino acids
**Making cyanobacteria produce butanol biofuel
**Byproduct of algal biofuel production could be made into biodegradable plastic
**Phage therapy looking more promising

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

This show features music from Mevio's podsafe Music Alley.

BacterioFiles Micro Edition 121 - Horizontal Hacks Help Harsh Habitation

This episode: Alga adapts to hot, toxic environments by copying prokaryote genes!


Download Episode (3.4 MB, 3.75 minutes)
Transcript

Show notes:
News Item 1/News Item 2/Journal Paper

Other interesting stories:

**Same species of bacteria that causes acne might also protect against it
**Bacteria in sourdough bread inhibit mold growth
**Navy develops device to treat wastewater and produce electricity simultaneously
**Marine bacteria could make useful new antibiotics
**Fungi seem to protect plant foliage from leaf-cutter ants

Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

Subscribe at iTunes, check out the show at Twitter, MicrobeWorld, or Facebook

This show features music from Mevio's podsafe Music Alley.