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Week 10 - It's been fun!

My last week at CMOP has been filled with a lot of hard work, but it definitely paid off. This week I had primarily been working on my final paper, getting my presentation ready, and performing some final analysis on my data. Overall I have had a very productive summer and have really been able to answer some interesting questions with the metagenomic data I have been woking with.

Week 8 - Sulfur oxidation?

This week I have been trying to identify the potential for sulfur oxidation within the community. Because I did not find either soxA or soxB genes (Week 7), I began my research on the sox-independent pathway of sulfur oxidation. A key enzyme in this pathways is APS reductase which catalyzes the conversion of APS --> AMP + sulfite. The gene, aprA, which encodes APS reductase was used to screen the metagenome.

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.

Week 6 - Assembling genomes

This week I worked on the arduous task of whole-genome shotgun fragment assembly, or putting back together the randomly cut DNA to form contiguous sequences (genomes) representative of the most predominant members in the community. Whole-genome assembly is an important step in studying this microbial community because it allows us to answer two important questions: (1) who is present and (2) and how are they contributing to key metabolic processes like carbon and nitrogen fixation (through gene prediction and annotation).

Week 5 - Screening for Rubisco and 3-HPO bicycle

The weeks are really flying by. I am already at the halfway point! I have already progressed so far in my project and have learned so many valuable skills. I have spent the week working to quantify and characterize the phylogenetic placement of Form I Rubisco large subunit (cbbL) genes in the Warren Cave metagenome. Rubisco is the enzyme used by plants, algae and bacteria to fix atmospheric carbon dioxide into biomass via the CBB cycle (Badger and Bek 2008).

Week 4 - Phylogenies and presentations

After having identified an abundance of coxL in the Warren cave metagenome last week, I spent the first half of this week building a phylogenetic tree in order to learn more about the evolutionary radiation of the coxL gene and the relatedness of the cave samples to cultured and uncultured microbial species. In order to begin the tree-building process, I first had to align the contiguous sequences from the metagenome with the coxL IMG database and translate the nucleotide sequences to amino acids.

Week 3 - Antarctic samples are in!

This was a very short, yet productive week in the lab. The Mt. Erebus/Warren cave metagenome sequences finally arrived from Illumina sequencing Friday evening and I began my work Monday querying the samples for coxL, the gene encoding the enzyme carbon monoxide dehydrogenase (CODH), then assembling those genes for analysis.

Week 2 - Methanotrophes and NSF site visit fun

My second week at CMOP has largely been an interest-driven, rather than project-focused week. Because I am still patiently awaiting the Mt. Erebus metagenomic sequences to arrive, I have continued work on the hydrothermal vent data trying to learn more about the metabolic potential of microbes in deep-sea hydrothermal environments. I began my week searching through the literature to learn about the metabolic pathways involved in methane oxidation as well as the principal genes involved.

Week 1 - Having a BLAST

WOW! How do I even begin to summarize one full week of CMOP-interning into one blog entry!?

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