Blogs

This week I spent a lot of time working with data collected on the water samples from Astoria.  After running the samples through the FlowCAM and eliminating the unwanted metrics, I performed principal component analysis (PCA), taking the first three principal components (PCs). 

 The Data Annotation Interface is as done as its going to get before presentations. I'll have a week and two days to fix it up after that's done but from now until Friday its paper writing and Powerpoint making time. As for new features there are two: the interface is now (mostly) compatible with the data explorer's POST/GET variables. There's still a bug that prevents previously made comments from showing up when you click on them but that can be fixed when I get back. I also added Internet Explorer 8 compatibility.

 This last week saw me testing out the new compounds we got - 2,4-DNT and 1,3-dinitrobenzene. I started the runs with the slowest combinations - the lowest pH and temperature. By the end of the week, neither of the compounds had shown any sign of a reaction - when I did my calibration curves on Thursday and Friday, the concentrations hadn't really changed at all. So, on Friday, I tested the 1,3-dinitrobenzene in the theoretically fastest run, the highest pH and temperature to see how it would do. And it did nothing.

One thing I can say with confidence is that conducting research demands a certain level of patience and dedication that can breed frenzy in even the most sensible people.

Once again, business as usual in the lab. I employ a special concoction of lucky-guess and brute-force methods to measure shear thinning behavior of xanthan solutions. I announce with great excitement that the capillary experiments have, for the most part, reached a conclusion. The soil column, however, continues to illude my greatest efforts to obtain any sensible data.

This week was super busy!  We've been trying to wrap up the experiment from a couple weeks ago and I've been working on my final presentation for next Friday.  Although I am sad that this adventure is almost over, I can't wait to see what doors it has helped me open for the future!

Monday:  I purified the RNA from last week.  Because we had 20 samples, it took quite some time.

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.

       This week was very different from weeks in the past. That is because Kati, my mentor, was on vacation the whole week. It was a very relaxed week, because I had the freedom to choose which experiments I wanted to run and I could do everything on my own time. Yet it was also one of my busiest weeks because I wanted to run a lot of different tests. I was also not here on Friday, due to a family wedding, and so I needed to fit everything into four days.

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).