There's a Wooden Phallus in this Post

Thursday I was given the task of running around Lilongwe to various UNC Project facilities and taking pictures and the square footage of each. It was nice to get a tour of the spots I hadn't yet visited, but at times it felt awkward. Armed with measuring tape that maxed out at 12 ft I would make my way around the walls of clinics, 12 ft at a time, as fast as possible. In order to do this at some buildings I would pass by window after window where patients inside were being counseled for sensitive issues like STI care, or anti-retroviral therapy. I imagine seeing me pass by their window muttering something like, "642 plus 121...," made some of them uncomfortable. At any rate I was left with a bunch of pictures of where I work, and looking over them I realize I haven't really made a thorough effort to share just what I'm doing here. Allow me to remedy that...

I live in the UNC Project guest house:


Monday to Friday I head to the Derm lab (the lab set up in the dermatology clinic) around 7:30:


The typical day involves processing plasma samples and whole blood samples to determine the levels of HIV RNA and DNA in them, respectively. These samples come from a number of studies being performed here such as BAN, HPTN 052 and CHAVI (brief overviews here). We get the reagents and controls we need to do such processing in kits we import from South Africa. Spare kits are kept in the fridge in this room:


As you can see we're running low on kits. This is a frequent problem and I have come to realize my work load is dictated by a predictable cycle: we begin to run low on kits and don't know exactly when the next shipment will come in; to ensure we have something to do each day we only run one plate (9 samples, uses half the materials of one kit); the pending samples begin to pile up as we process fewer due to kit rationing; the turn around time for a sample to be processed is supposed to be one week from collection; a new shipment of kits come in and we burn through many quickly doing as many as 3 plates per day each to ensure that samples are processed before the one week time limit; we begin to run low on kits... and so on. Is that correct usage of semicolons?

When I'm done running the viral load assay I take the results over to the main lab building, Tidziwe, which means "we will find out" in Chichewa.


Coming through the front entrance you are greeted with a beautiful mural:


I then say whatsup to the lab techs in the core lab and enter my results in the lab information system (LIS) on one of the computers there:


For the first month or so I was here this was all I had to do, and I was getting pretty bored. Thankfully I have since been assigned work on other projects and I'm gearing up to be pretty busy as they all start to take off.

One study has the potential to have a great impact in reducing HIV transmission in Lilongwe. Currently patients coming in for HIV testing get a rapid test (the test produces results in only 20 minutes so patients learn of their status the same day) that determines if anti-HIV antibodies are present in the blood. Acute HIV, the stage of infection lasting roughly 1-6 weeks after contraction, in which one has the largest amount of virus in their system and are thus the most likely to transmit, typically occurs before the body produces antibodies against the virus. The viral load assays that I typically run testing for HIV RNA can catch infections during this period, but as I've mentioned the test results don't usually come back for a week. A new rapid test has become available that tests for both anti-HIV antibodies and a portion of the virus called the p24 antigen. This p24 antigen is detectable during the acute phase, and typically becomes undetectable after the acute phase ends as most become complexed with the antibodies. Thus this new rapid test can catch infected patients the antibody-only rapid test couldn't, specifically those at the stage of infection where transmission is most likely! My job is to validate this rapid test using both the HIV RNA viral load assay I have been running, and another new ultrasensitive assay that tests specifically for the p24 antigen. This is all setting the stage for a larger study that will examine the feasibility and success of catching patients in this acute phase, and what are the best methods of preventing transmission in such highly infectious individuals.

Some of the patients are coming from the STI clinic. Here's one of the clinic's counselors demonstrating proper condom application:


Another imminent study I get to work on is going to use an awesome new technique called Massively Parallel Pyrosequencing (MPP) to survey the genetic diversity of different malarial parasites present in patients eligible for a new experimental malaria vaccine developed by GlaxoSmithKline (holler, Jen) and the Bill and Melinda Gates Foundation. Because the vaccine is monovalent, it may only be effective against malarial parasites with certain genetic makeups. By mapping the genetic diversity of malarial parasites in patients before they receive the vaccine, the hope is to be able to determine which variants are the culprits in patients for whom the vaccine fails to provide protection. All I'll be doing is reading malaria smears to confirm that patients have a specific species of malarial parasite, Plasmodium falciparum (the MPP gets done back in Chapel Hill), but it'll be great to become proficient in malaria microscopy and to be part of such a sweet study.

The drug-resistant tuberculosis study I mentioned in my first post has been in bureaucratic limbo for some time, but there is a good chance it will get approved this month, and then I'll be doing more of that as well.

Hoo-ah Science! In other news, my college and senior thesis advisor, the Tuckerman, presented some of the work he and I did for my senior thesis quite elegantly with a poster at the Society for Neuroscience annual conference last week. If you feel like reading about asymmetrical eye movements in baby zebrafish, you can download the poster here.

Happy Halloween y'all. I'm stealing one of Luke's previous costume ideas and being a Cholo this year. What's gonna be your costume?