Tuesday, December 10, 2013

New Domain Name

In case you hadn't noticed, the show's website is now bacteriofiles.com. Thanks to listener Andrew Billo for his donation!

Wednesday, October 2, 2013

What I've been doing in my lab

...for those who are curious.

I took this picture a while ago so I don't remember exactly what was growing, but it definitely included some strain of a soil bacterium.

The point of the complicated setup is to be able to keep these bacteria in a co
nstant state of healthy proliferation; that is, about every 5-10 hours (depending on the strain), every cell in the tank in the center will have divided into two new cells, effectively doubling the population.

This is called exponential growth, because when this takes place in a flask of a given amount of broth, nothing added or removed, the size of the population doubles every 5-10 hours, so the number of cells in the population, if you start with 2, is 2 to the nth power, where n is the number of 5-to-10-hour periods
 (depending on the strain) that have passed. So after 5-10 hours, there will be 4 cells, then after 10-15 hours, 8 cells, then 16, then 32, then 64, and it goes up exponentially.

However, this is not the case in this picture, because rather than having a given amount of broth, there's a bottle of fresh broth outside the frame up above, and new broth is being added to tank where the bacteria are growing, so their food is being constantly replenished at a certain rate. At the same time, the volume in the tank is being kept constant by removing excess material, including the cells in it, thus reducing the size of the population. So the size of the population of bacteria effectively remains constant over time.

The point of this is to study the behavior of the bacteria. There are some good reasons to maintain a population of bacteria this way; for one thing, you can repeatedly make changes to the broth you're feeding them, or other environmental factors, to see how the behavior changes, without having to repeatedly clean out and sterilize the tank, add fresh medium, and inoculate it again.

In my case, what I'm currently doing, is trying to figure out how much hydrogen gas my bacteria produce when I feed them a certain amount of sugar. As long as they have everything else that they need, it should be the case that the more sugar I give them, the more hydrogen they produce, and I'm trying to quantify the relationship between those two factors.

In order to do that, I make a tank of broth with a known amount of sugar, feed it to the bacteria until the population size stabilizes, and measure the amount of hydrogen they produce with that white box to the left. I'm also measuring the size of the population using other methods. Then, I increase the concentration of sugar in the broth, keeping everything else the same, let the population stabilize, and measure the new values of hydrogen and population size. Once I've done this a few times, I can make a graph of hydrogen produced per gram of sugar added or something.

The other cool thing about the setup in this picture is that it allows me to control many environmental factors and take measurements in real time: the unit on the right is a unit that controls and takes measurements, and it can measure the amount of oxygen in the tank, the pH, the temperature, and how much broth is left in the tank, and it uploads these values to a computer on the other side of the bench. It feeds in air (for oxygen) at a certain rate, controls the stirring (to help the oxygen dissolve), and pumps water through a jacket around the tank to control the temperature. There are also sensors on the other side that measure the concentrations of certain gases that come out of the tank, and the computer records those too. So it's a lot of control and information.

That's about it for this kind of experiment. In case I've kept your attention this long and you're interested in more, I started a new blog here to help myself review papers for my own research, so feel free to check it out.

Monday, September 30, 2013

Sunday, September 8, 2013

BacterioFiles Micro Edition 134 - Duodenum Dweller Degrades Digoxin

This episode: Bacteria in the gut can affect dosaging of medications!

Download Episode (7.1 MB, 7.75 minutes)

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

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

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

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

Saturday, August 31, 2013

BacterioFiles Micro Edition 133 - Microbe Manacles Metal, Muzzles Microbe

This episode: A strain of E. coli helps reduce severity of Salmonella infection by competing with it for iron in the gut!

Download Episode (7.6 MB, 8.3 minutes)

Show notes:
News item/Journal Paper

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

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

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

Monday, August 19, 2013

Tuesday, August 13, 2013

Crowd-funding: Help Support Research into Using Bacteria to Clean Up the Environment

I've been interested in crowd-funding science for a while. Science is one of the best investments a society can make, so why not let society invest in it directly? There are many research proposals people have made on different crowdfunding websites, but here is one that is relevant to the interests of this show:

Directing the Evolution of Bacteria to Clean Up Toxic Waste

This research team is using directed evolution to develop strains of Pseudomonas aeruginosa that can chelate and remove heavy metal contaminants from the environment. They're trying to raise money directly from the public to support their research. If you want to participate in this project, at least indirectly, you can donate and/or spread the word!

From the site: "Heavy metal pollution is more common than most people realize and it causes serious environmental and health problems. Our research aims to clean up this toxic waste using organisms modified by a process called directed evolution."

Click the link for more information. For science!

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)

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

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

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 bacteriofiles@gmail.com. Thanks for listening!

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

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 bacteriofiles@gmail.com. Thanks for listening!

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

Saturday, May 25, 2013

BacterioFiles Special Edition - ASM2013 General Meeting Day 1

Building on the 16th St mall in Denver
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.

Download Episode (6.45 MB, 7 minutes)

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

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