I’ve been having a fantastic time living ten minutes from the beach, learning little bits of Zulu, eating as much cheap and delicious fruit as I can get my hands on, and – of course – doing lots science.
I’ve been working with Prof Thumbi Ndung’u at the KwaZulu-Natal Research Institute for TB & HIV (K-RITH) since the end of September. My part of the lab is interested in understanding how HIV affects anti-TB immunity in the lungs. My contribution to this story is going to be using a novel assay my lab in Cambridge helped to develop in order to look at the transcriptional profiles of antimicrobial genes involved in the innate immune response to TB. Because it’s science, progress comes in fits and spurts, and everything takes longer than you think it will. Naturally, I’m still optimizing and haven’t gotten to the real meat of the question just yet. For those of you with knowledge of flow cytometry, I’m working with alveolar macrophages, which are very autofluorescent due to their size and granularity. This complicates everything else in the panel, including the RNA FISH aspect as the target sequences are also conjugated to fluorophores. Hopefully I can have some real data and possibly a figure or two by the end of my time here to share with you all.
Another exciting part of my position here is that I get to spend two mornings a week at one of the large public hospitals in Durban collecting patient samples. We work with bronchoalveolar lavage fluid, which you obtain by sticking a bronchoscope down into the lobes of the lung, flushing them with half a pint of saline, and then sucking back as much liquid/cells you can. We collect samples from patients with a variety clinical indications, ranging from TB (with or without co-morbid HIV), lung and blood cancers, to sarcoidosis, lupus, and interstitial lung disease. The pulmonologists have been very welcoming and eager to teach me, and I get to assist the nurses in distributing the fluid for various clinical and research needs.
Most of all it’s been a real pleasure to get to talk with folks before and after the procedure and make connections between their medical history/clinical presentation and what I observe from their cells. For example, seeing a black pellet of cells (for the non-scientists, your cells should be white) in a tube from a person who has smoked for 30 years is just another reminder not to smoke!
Since TB is so common in SA, especially in this province, we treat all samples as potentially infectious. Accordingly, all of our work is done in a BSL3 facility to prevent the inhalation of TB-containing aerosols. This has been another transition for me coming from a HIV background where a full suit and respirator isn’t necessary, though it’s surprisingly enjoyable!
I’ve also dipped my toes into a bit of a side project, which has — unknowingly — been made possible by Professor Taylor. Another part of the lab works on mucosal associated invariant T (MAIT) cells, which participate in the innate response to bacterial infections, and express a MHC class I – related (though non-polymorphic) protein. The ligands for this receptor are still being elucidated, though there have not yet been any endogenous ligands identified. However, with the skills I learned in Professor Taylor’s Biomedicinal Chemistry course, I’ve been able to do some preliminary molecular docking studies that are giving a pretty good indication that my PI may have found the first endogenous ligand! So cheers to Professor Taylor and Wesleyan for those skills!
Thank you again for each of your contributions to make this possible for me. In particular, thank you to MB&B and African studies for the financial support, and to Professor Oliver for sticking with me when my plans were in jeopardy.