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Week 7 - Already?

This week I have spent the majority of my time looking for additional energy generating pathways the Warren Cave community might be utilizing for use in biosynthesis and respiration. Because the cave receives no external organic input, all must come from within. Having identified a 2:1 ratio of Rubisco to coxL gene abundance, I still need to identify additional metabolic pathways that could feed electrons into Rubisco for carbon fixation. Having already built a database of particulate methane monooxygenase (pMMO) genes in Week 2, I screened the metagenome for pmoA. Surpringly, ~780 sequences were extracted that had high sequence similarity. These sequences were assembled and generated a contig of 747 residues representing 429 sequences in the sample. A manual BLASTx search ( revealed the contig had 100% amino acid sequence identity to numerous uncultured methanotrophic bacteria from diverse environments. Although methane oxidation does not comprise a significant portion of the community metabolism, it is providing energy for some underrepresented members. 

I then screened for sulfur oxidation (sox-dependent pathway) using the genes soxA and soxB. After analysis, neither genes were detected. It appears the sox-dependent pathway is not present in the community. However, because there are sources of inorganic sulfur present within these caves, I will next look for genes involved in the sox-independent pathway of sulfur oxidation. This pathway utilizes a few different enzyme which include: reversible dissimilatory sulfite reductase (Dsr) and APS reductase. Next week I will try to locate orthologous genes encoding these enzymes and hopefully piece together the rest of this story.

This week we also had an opportunity to talk to grad students on the main campus of OHSU and learn more about the research going on in other labs. I am trying to take advantage of any opportunity I can to learn more about the graduate school application process, as I will be looking to apply to programs very soon. It was great to hear different perspectives on what to look for in a program and how to narrow down your interests (the latter is the most difficult part for me). 

It was another great week at CMOP, cannot believe I am already in week 7!