Monday, June 24, 2013

BacterioFiles Special Edition - ASM2013 General Meeting Day 4

Presenting my poster
Here's my summary of the fourth and final day of ASM2013, with a special surprise guest appearance at the end!

Session 1: Synthetic Genomics to Create a Minimal Bacterial Cell and Some Other Neat Stuff
Presented by John I. Glass
He talked about the cell with the synthetic genome (full episode 13), and about how important it is to determine what is the minimal amount of genome a cell needs to grow--knowing that, you can start there and build almost anything you want.
He also talked about a new method of producing new flu strains for vaccine production using synthetic nucleic acids, which could greatly shorten the time it takes to get a new vaccine going to counter a pandemic.

Session 2: C. difficile vs. the Microbiota: The Enemy of My Enemy is My Friend
Presented by Shonna McBride
When a probiotic (Lactococcus lactis) was grown with C. difficile, the latter was killed.

Session 3: An Intriguing Bacterial Symbiont in the Nucleus of Amoebae
Presented by Frederik Schulz
Interactions between amoebae and bacteria are interesting and also relevant to our health, considering the similarities between amoebae and cells of our immune system. This interaction is particularly interesting: bacteria living inside the nucleus.

Download Episode (5.5 MB, 6 minutes)

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Monday, June 17, 2013

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

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)!

Download Episode (4.3 MB, 4.6 minutes)

Post questions or comments here or email to Thanks for listening!

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Saturday, June 8, 2013

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.

Download Episode (7.36 MB, 8 minutes)

Post questions or comments here or email to Thanks for listening!

Subscribe at iTunes, check out the show at TwitterMicrobeWorld, or Facebook