Back to California

I have just recently returned to California after a semester as a visiting assistant professor in the Department of Civil Engineering and Geological Sciences at the University of Notre Dame. My wife insisted that among the first things that I do, I should update my blog. I spent the semester teaching Environmental Microbiology and a laboratory class entitled Molecular Tools for Environmental Microbial Ecology. Well, now that the semester is over I can say that I quite enjoyed it, but it was a lot of work. It looks like I will be getting a position at the SETI institute for the time being, and I am looking for a full time faculty position, or more funding to help me remain at SETI/NASA. Anyway, it is good to be back. More soon.
Cheers,
Stefan

Unifrac Update

I received an email from Micah Hamady at the University of Colorado. He informed me that there is now an online version of UniFrac available, and can be found at thefollowing website:

http://bmf.colorado.edu/unifrac/index.psp

In addition, there is a manuscript available:

http://www.biomedcentral.com/1471-2105/7/371

This should be a welcome improvement from having to install and operate Unifrac from Python.

Cheers,

Stefan

FIBR Conference and New Job

I just recently returned from a conference in Bozeman, Montanta. This conference was funded by the NSF Project - Frontiers in Integrative Biological Research, and is part of an ongoing research program at the University of Montana. This research program is involved in investigating microbial communities in hot spring environments in Yellowstone to ask the question - "Do Species Matter in Microbial Communities?"(http://landresources.montana.edu/FIBR/). The conference was excellent, and one of the most intriguing pieces of information I learned was related to the genome sequences of two relatively closely related cyanobacteria of the genus Synechococcus. Two environmental isolates of this genus, recovered from different temperatures along a thermal gradient of a Yellowstone hot springs, had their full genomes sequences. Amazingly, when these genomes were assembled and compared, they were found to have very little synteny (genes or sequences occurring in the same order on chromosomes of different species), despite having ribosomal RNA gene sequences nearly 97% identical. These genomes can be found at The Institute for Genome Research (TIGR) (http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi).

Other interesting news. I will be teaching two courses at the University of Notre Dame this fall as a visiting assistant professor in the Civil Engineering and Geological Sciences Department (CEGEOS). The two courses will be Environmental Microbiology, and a laboratory course entitled Molecular Techniques for Microbial Ecology.

Return from ASM

Just got back from the ASM meeting in Orlando, FL. The meeting was good - amazing things being done with full genome comparisons, plus microarray gene expression analyses. Anyway, just a few notes here:

1) A new software package called CLC that is definately worth investigating. [http://www.clcbio.com/]

2) A product called Perfect Match® PCR Enhancer from Statagene. Here is the manual.

See an article by De Milito et al. 1995. I also found this comment in a molecular biology group:

"[Perfect match is] Tetramethyl Ammonium Chloride. It costs about $30 for 500 gms from Fisher, and stinks to high heaven.I titrated it between 10 uM (micromolar) and 1 nanomolar leaving allother conditions the same."

This is not verified information.

Cheers,
Stefan

Update

Well, good news. Another manuscript of mine has been accepted for publication in the journal Applied and Environmental Microbiology. Wooh! I just sent the galley proofs back to the editor. It really looks great. I had a very positive experience with AEM - not just because my manuscript was accepted. The peer-review was excellent - great commentary by two reviewers and by the editor as well. After acceptance, the page proofs were generated very rapidly, and I'm happy to say that the manuscript has been published. Reference:

Stefan J. Green, Ehud Inbar, Frederick C. Michel, Jr., Yitzhak Hadar, and Dror Minz. 2006. Succession of Bacterial Communities during Early Plant Development: Transition from Seed to Root and Effect of Compost Amendment. Appl. Environ. Microbiol. 72:3975-3983.


Anyway, things are moving along here at NASA. We finally received all the various bits of our real-time PCR machine from Bio-Rad. Since I still have no reagents, I haven't really been able to check out if the thing is working or not. But it looks nice! Also, a third sulfate experiment has been begun and I've gathered some microbial mat samples at the initial time point (before removal of sulfate). I'm hoping to examine microbial communities at different depths during a diurnal cycle in the mat.

The summer is shaping up to be very busy. Meeting in Orlando next month (ASM) and Vienna in August (ISME). Plus, I am co-advising a student working on microbial communities associated with ophiolites. Should be interesting research. However, my position is very much in flux as my fellowship is expiring at the end of September this year. More on the state of affairs as it becomes clear.

A publication of interest: A computer program ("TreeClimber") to analyze microbial communities via analysis of phylogenetic trees. This seems similar to UniFrac, but I haven't examined it closely. However, the documentation seems better than UniFrac. Find the article here. Find the website here.

Finally, I note that NCBI has started a "Probe" database. Should be very useful.

Cheers,
Stefan

UniFrac Analysis

Well, just a note of some interesting articles regarding new statistical techniques to analyze sequence libraries in a manner akin to analyzing DGGE profiles:

Lozupone, C. and R. Knight. 2005. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities. AEM: 71: 8228-35.

And an application of UniFrac:
Ley, R.E. et al. 2005. Obesity alters gut microbial ecology. PNAS. 102:11070-11075.

To use UniFrac, you will need to download and operate "Python" software.
You will also need to download a special "Numeric" module. Make sure you download the Numeric, not the NumPy, module.
Then you will need to download the .zip file of the unifrac program (http://bayes.colorado.edu/unifrac.zip).

The UniFrac program is not trivial to use if you haven't had any experience with Python or similar languages. I've emailed Dr. Lozupone and she has indicated that eventually a web-based UniFrac program will be available. However, not yet.

You will need phylogenetic trees in Newick tree format as the input data file for this program.