Peddie EXP 2017

Week3:                 This week was really exciting since my primer finally showed up at the doorstep right when I entered the lab on Monday. The first step of processing such primer is to reconstitute it. I was really confused by the word “reconstitution” since I have never heard of such word in my entire life. This is actually a common experience since research labs often use very advanced word for very simple idea. And in this case, reconstituting a primer literally means adding water to dissolve the DNA piece that was laying at the bottom of the test tube. I “reconstitute” the primer in the fancy fume hood we got in tissue culture lab. A fume hood is basically a sterile environment that would prevent particles from entering or exiting the hood. Here, since the primer is very delicate and we would not want any contamination to it, we performed the reconstitution process with molecular biology grade water (...

T This week I have been taking the samples that I have gotten from Catalina and begun to crush them  into a powder that can be turned into pellets that are able be burned in an Elemental Analyzer and then transferred to a mass spectrometer in ord er to test for carbon/nitrogen ratios. To the right you can see my work station. In order to get my samples crushed I needed to first retrieve a labeled foil pocket that contained each sample, then I would crush each sample and place them into a tube labeled with the specific species, day, and replicate.   Later in the week I will be using the Mass Spec machine in order to look for carbon nitrogen ratios in the samples that could suggest nitrogen fixation, and not just nitrogen uptake. This is however a tricky task due to the fact that the mass spec machine is not tuned to run macro algae samples, rather it is tuned more to running filtered water samples.  The main problem is that for these small of s...

This is my first blog post in two weeks as both weeks have been shortened by the fourth of July and my grad student Joe’s mini vacation to New York City.  That said despite spending less time in the lab than previous weeks, I still managed to accomplish a great deal of work. I only worked 3 out of 5 business days during the week of the fourth of July.  After celebrating our nation’s independence over the four day weekend, I went back to work on Wednesday, picking back up where we (Kennadi and I) left off.  Using a QIAprep Spin Miniprep Kit, we isolated the DNA from the bacteria cultures that we grew in LB broth the previous week.  Additionally, this day marked the end of Khin’s (a graduate student) time in the Bouchard Laboratory.  We celebrated her many hardworking years in the lab as we welcomed a new transfer student who will be spending the next 10 weeks in the lab.  It seems like every week someone is either leaving or joining the lab giving me the ...

            While, of course, Mr. Sham's visit was the highlight of the third week here in London, the third week of EXP has been the most productive and formative so far.              The science portion of the third week had been diverse, and by that, I mean that I have had an immense amount of more work (which is great!). Besides my work in the insectory, which pertains to finding the optimal conditions of the Anopheles funestus strain described in the last blog, I have been assigned two more projects. Although the initial regulation for me in the lab required constant and strict supervision, the rules have been disbanded due to the work I have submitted already (the gene drive paper and the preliminary results of the Anopheles funestus project). The mosquitoes would only bite my feet, and I was tired of it           Th...

Hey everyone, I’m combining Weeks 2 and 3 because I did essentially the same thing for each day: Read. After learning a bit more about my project from Kayla, I came to the realization that the information from the metabolomics papers I had been researching in the spring was not entirely applicable to the work I will be doing this summer. The project that I am working on relates to drug metabolism, with it’s title being “ Compound cocktails for metabolic profiling for drug efficacy and safety assessment.” The central aim is to take advantage of molecules that are structurally similar to common drugs, by substituting them as substrates to common drug metabolism enzymes. After doing so, a comprehensive metabolic profile will be taken, then inferences can be made regarding how a patient reacts to other compounds that are structurally similar to the molecule. In doing this, one can reduce the cost and time needed to test the safety and efficacy of a drug, compared with the traditional meth...

Bowling with friends On the first day of week 3, Shawn and I changed media and did von Frey testing on the male mice. As usual, their pain threshold was higher than the female's and they were less fidgety. The following day, we sacrificed 10 more mice: 5 males and 5 females. We plated the bone marrow cells as we typically do and continued to change the media for all of the batches of cells. Shawn removing bone marrow using a syringe and tweezer The hood where we change media and plate cells  Additional image of female BMSCs plated on 6/14/17 Image taken on 6/30/17 of female BMSCs plated on 6/14/17 On the Wednesday of week 3, we made new media because we were running low. We put two antibiotics, penicillin and streptomycin, and fetal bovine serum (FBS) in the media. Though I knew why we put the antibiotics in the media, I did not know why we put FBS in. As it turns out, the FBS provides proteins that are necessa...

Note: Weeks 1, 2, and 3 all blend together, and so I decided to make a blog post for all three. Week 2 was my actual start at the lab, and Week 3 was a shorter week, due to the Fourth of July Holiday. So far, my lab experience has been extremely interesting and fun, if not a bit surprising. I came into this lab thinking I was going to be working with brown fat, as that is the main focus of the lab, so I was quite surprised when I found myself working with intestines instead. Before I came to the lab, my supervisor had found that in mice, whole body deletion of Prdm16 , which is required for brown fat development and maintenance, led to greatly reduced intestinal length, killing the mice within seven days of Prdm16  knockout.  This phenomenon had not been previously observed, and so the project I'm working on is an entirely brand new area of research. My first task was to genotype mice and find a particular mouse with Rosa26CreER,  an on-off switch that can be activate...

Week two, because I got my animal training approved and all my paperwork done, was when things really began to get interesting! Just a quick overview of the past two weeks: I dissected a mouse, helped Snow perform sacrifices and heart harvests, analyzed cardiac tissue using flow cytometry, and learned about projects that'll begin next week. I was also able to visit the Inner Harbor and Washington DC this weekend, a due recess after a busy workweek. I wrote two protocols with Snow, handled some more mice, analyzed a lot of flow cytometry data, and even got my own mini-project (in addition to helping Snow with hers)!  Things got interesting on Monday. Snow was sick, so I was shadowing Paul and watching what he was doing. One of the mice he was immunizing in the animal room suddenly died in the hood (the sterile area that people work with live mice in). Katie and I took it back to the lab to dissect it to see if we could figure out what went wrong. When we cut it open, we could see ...

Week three and four have been very eventful and promising. In the beginning of the third week, I had my mouse lab orientation, which now means that I have granted access to the mouse room by myself! Although it took longer than I expected for me to get this, I am excited that I have my own independence now to visit the mouse room. Elizabeth sent the lung samples that we collected from the dissections the previous week to the Duke CORE facility to be embedded in paraffin. It takes at least a week to get the sample back so in the mean time we have been working on the ex vivo project involving the bone marrow derived macrophages. Since Sarcoidosis is a chronic inflammatory disease and its pathogenesis is still unknown, we are only using the macrophages to see the granuloma structure under a microscope, if there are increased expression of specific genes during the disease, and how different concentrations of carbon nanotubes affect granuloma growth. Our main gene of focus that week...