Shakira Bandolin's blog

I finished out last week with a practice presentation to my lab group. It went really well, and I got some great feedback which will, hopefully, make my presentation much better. Other than that, this week will be spent finishing up my final paper and making minor changes on my powerpoint :) I cannot believe that this internship is basically over...

Last week, we ended up getting back our results from both the MS/MS, and the genetic sequencing lab.

The MS/MS gave us fairly strange results which suggested that the column in our lab may have been contaminated with proteins from a strain of bacteria 9A1 (arantimonus). This seems unlikely since great care was taken to clean the column, but to ensure reliable results, more investigation will be necessary; more samples will be run through the FPLC and the results of the MS/MS of these samples will be compared to the original results. Hopefully it turns out that the bacteria we are studying have Mn-oxidizing protiens that are similar to arantimonus, as opposed to contaminated with 9A1.

So today is Monday already! Last week was the final stretch of lab work for me and my project. The week (after our return from the labs at OHSU) was spent preparing a PCR of our samples to isolate and amplify DNA (including some colony isolates as well as three 9A1 samples). Most of the samples worked in the PCR and yielded good results, so some were chosen and the DNA was cleaned. On Friday, the cleaned DNA was concentrated down and taken to the primate center to be sequenced :)

Every week, since week 4 has been spent repeating the protein fractionation protocol for each sample, so as to separate out the proteins found in various areas of the cell (ie outer membrane, soluble proteins, inner membrane, and outer membrane washed proteins). Unfortunately, I only made it through the initial stages of protein fractionation on week 5 before I got sick. I went home on Wednesday afternoon and did not come back for the next week! It is now Wednesday of the 7th week and I am back in the lab at CMOP!

So this week was a crazy one! Monday was Day 1 of a protein fractionation protocol that Craig and I were going to follow for one of our sample. We have a total of four more samples which we will use this protocol on, so this week was our first run through; a "gain some experience" week. Everything was set up and ready to go on Monday morning, but the samples needed to be thawed out first. Craig came in earlier than normal and put out the samples, so by the time I arrived, the samples had been sitting out for about 1 hour. to be continued...

I cannot believe that it is already my third week here at CMOP. Everything is going really well; I could not have asked for a better lab to work in and people to work with. Before I tell you the riveting details of the last week, I would like to issue a correction for last weeks blog. Apparently I was incorrect in my description of how tetrazolium works in regards to cells. I had previously described it as working in the glycolysis pathway, but it seems to actually act as a substrate analogue for reductases and hydrogenases in mitochondria. It seems that by binding preferentially to these enzymes, the cell slowly exhausts itself because it uses up NADH and NADPH, thereby decreasing its reducing power.
Also, the product of this reaction is formazan, which is nasty, and may work to kill off the cells.

So it is only Tuesday and yes, I have indeed broken my first piece of glassware in the lab... It was bound to happen, but I was hoping it would be when the lab was completely empty. Instead, the loud shattering sound was enough to bring everyone out of their offices to see what equipment had been destroyed. After cleaning up the mess, I moved on with my day, glad to have gotten that out of my system once and for all.

So here goes my first blog ever! This was a whirlwind week and I cant believe that I am about to start week 2 already! Week 1 consisted of a lot of frantic running around (and flailing at times) but overall, everything was taken care of an I survived. As of right now, I am working with Dr. Craig Anderson, a New Zeland native who is really cool, and we are studying manganese oxidation by microorganisms. I have basically jumped onto a project he started and Tuesday was day one of intense research.