WEEK 9 AND 10
LAST ONE GOOD ONE
THE WEEK
Hello hello hello!
I am so sorry for the delayed report for Week 9, everybody. Things have gotten quite busy in the last two weeks. I have finally had data that does not rely on hands-on lab work, so I have been working later at home for the first time this summer. So when I sat down to write the report on Week 9, it was almost the end of Week 10! So I will give you the summarized version of both weeks in this Stack. I apologize for depriving my loyal readers of their weekly fix.
Way back on Monday of last week, we began by running another DNA extraction. We found 24 samples among our 135 positives that had both large sample volume as well as a high value for the ELISA. This would give us the best chance of getting good results. We ran the DNA extraction in the morning, then ran the first round PCR in the afternoon. We added some more samples to the PCR run that we had extracted successfully earlier. On Tuesday we had our weekly lab meeting, then ran the second round PCR afterwards. In the afternoon we tested how the PCR went by running a gel. We got 14 samples with bands, so those were what we could sequence.
If we remember back to earlier in the summer, we were waiting on a shipment of new ELISA plates, which were delayed. Well they finally came! Just in time for me to not need any more plates. Well we decided to run one more confirmatory test. For the samples that initially tested positive, we tested them again. 54 tests initially tested positive then tested negative the second time. We ran all those samples one more time to confirm their serology. And we used the new plates to ensure that it was an accurate result. So we ran the 54 tests and found 4 positives! They were low positives, so it makes sense that they tested negative, but we felt good about the final result. In the afternoon, we purified the PCR results to prepare for sequencing the next day.
On Thursday, we ran the Sanger sequencing! Very exciting. There was a person that specialized in this so she showed us how it works. There was a big machine that ran the procedure. Afterwards we ran another DNA extraction. Someone else in the lab needed 6 samples extracted so we added 18 more samples of our own to get the maximum of 24 samples. In the afternoon I did something new! I had been messaging with an Emergency Medicine physician at Princess Marina hospital, and I was invited to a staff meeting to listen in on their morbidity and mortality monthly presentation. It was really interesting to hear about the statistics of their number of deaths and the types of illnesses/injuries they treat the most. There was discussion about specific cases and protocol that needs to be implemented among the physicians. There were issues brought up that were very similar to issues faced at Beth Israel Emergency Department, like wait times, but also a lot of differences. Supply availability and difficulty getting consults from other departments were major problems brought up.
On Friday I learned how to edit and analyze the sequences we found. We were successfully able to sequence 7 of the 14 samples (a pretty good ratio). I learned how to edit out the dirty data, then combine the forward and reverse sequences. From there you input the files into a different software, then can edit it more, eliminating the errors. After that you can plug the sequences into HBV databases, which tells you the known mutations and the genotype! Very cool and a lot to study from the sequences we got!
THE WEEKEND
This brings me to the last weekend in Gaborone! It is so crazy how fast time flies. On Friday afternoon we went to the gym then came back, showered, then headed to a nice restaurant in the new Fields Mall.
I got some yummy pasta and we split a nutella crepe. Afterwards we went to the movies to watch Twister, which was really fun! At first I went into the theater they said and I sat down and watched the opening scene of Inside Out 2. I remembered that there are no previews here and realized I was in the wrong theater. I went out to look, and realized that we were in fact in the right theater and they were playing the wrong movie – that’s never happened to me before! We both really enjoyed Twister, although it was very American and thus there were only 2 other people in the theater with us.
On Saturday we went to an art gallery in the late morning. It was a 40 minute walk or so to an area that I hadn’t been to before. The gallery was quite nice! It was small but had some beautiful paintings, sculptures, and prints. It was also a studio so we got to see some art in the works and even an artist painting right there. I almost bought a print, but there were no more copies in the colors I liked. We thought there was a cafe there, and when I asked the guy working said it was closed, I thought that meant it would open in 20 minutes or something, but it turns out I totally misunderstood, and the cafe was closed permanently for construction! Haha.
From there we went to a different cafe/restaurant that had a very nice outdoor patio seating area. We got cappuccinos and ordered spring rolls, which was unexpected but we were really excited to have something different. 30 minutes later our waiter came out and told us that they were out, womp womp (and also clearly hadn’t started on our food). Classic!
So Sara has been playing field hockey with a team here, and they were hosting some sort of event nearby that Sara wanted to stop by, so we walked there after lunch. We went to the location that was sent, through a neighborhood that we hadn’t been before. There were a ton of people out on the street and walking around and we got soooo many looks and greetings, I highly doubt any white people are ever walking around there. And we couldn’t find the field! It was very odd, we were at the location sent. We just gave up and headed home. We stopped by Main Mall right by our apartment and browsed the markets there, finally buying some items (no spoilers). Also this day was the first day all summer that my stomach was quite upset. I had avoided it for two months and it got me in the last weekend :/ it was quite unfortunate and I really felt off.
Anyhooooo, Sunday we decided to hike Kgale Hill for the last time. The weather was sunny but very hazy, which may have kept people away because it was a lot less busy! We passed some people going up, but there was no one at the top when we got there. It was a nice jaunt as always, then we headed to Sanita’s Tea Garden for the last time as well. It is so pretty there! We split some sandwiches and enjoyed seeing the monkeys. And that was pretty much it for the weekend! I kept reading Long Walk to Freedom and enjoyed the nice weather.
THE WEEK (pt 2)
And that brings us back to Monday! LAST WEEK how time has flown. On Monday I shadowed the EM physician on her shift in the Accident & Emergency Department. I went on morning rounds with her, in which the overnight residents gave report on all the patients in the department. Some general takeaways: there was a definite lack of resources (as compared to the US), with some high acuity patients in chairs instead of beds. There also seemed to be less teamwork with different types of healthcare workers — I did not see much interaction between the doctors and nurses. The most intense/interesting/painful thing I saw was a man with a stab wound in the abdomen. The resident was going to stitch it up, but the attending said not to, because the wound had breached the fascia (and showed me). Anyway, I could only stay for 2 hours, since I still had a full day of work at the lab.
Back in my natural habitat, we did PCR for the 18 samples that we had extracted last week. It was pretty straightforward, not anything new. Then on Tuesday I practiced my final presentation during our lab meeting. I have been working on slides that summarize the background and research, and practiced for my Thursday presentation. It went well, but I realized I could really improve my slides after someone else in the lab presented before me with superb slides. After the meeting, we ran a gel to see how the PCR went…. And the gel was SO GOOD. The best I had seen all summer, we amplified 16 out of 23 samples! WOW. We were all really excited about it.
Afterwards we began purifying the PCR extracts for sequencing the next day. On Wednesday we ran sequencing in the morning, then did the manual editing in the afternoon. Out of the 16 samples we attempted to sequence, 11 of them worked! That was a really good result, and it left me with a lot more data to present the next day.
The next day was the big presentation! I had about an hour to prep, then I went down to get the projector ready. It turns out that they got some food as refreshments afterwards, which I didn’t know was happening, but was so sweet! There were maybe 25 people that came, both from my lab and other labs, and Sara. It was really nice to see all the people come watch. The presentation went really, really well! I spent a while going over the background, the rationale for the study, the methods, and the results we have gotten so far.
I then answered questions for a while, then thanked everyone so much for coming as well as all of the kindness and generosity everyone had shown all summer. Then I was surprised with a farewell gift 😭😭😭😭I was so moved, it was incredibly kind! I got an awesome crewneck sweatshirt with the outline of Africa and Botswana, as well as a notebook, pen, and card signed by the whole lab. Everyone was so, so kind and really liked the presentation, it was truly a fabulous way to wrap up the research for the summer. We then had some snacks and returned to the office. I did a little work, and then in the afternoon had a meeting with Dr. Simani (the PI), Bonolo (my supervisor), and Chanana (my lab-mate) to talk about research continuation after I leave. I plan on continuing this research as a thesis, and everything is set for that! More data will be collected and I’ll write a potential manuscript draft. Win-win for all involved.
Then that night, we watched history! The men’s 200m olympic race had Botswana athlete Letsile Tebogo, alongside Noah Lyles and Kenny Something (idk). Lyles was favored to win. We turned it on and watched with suspense….. As TEBOGO BROUGHT HOME THE GOLDDDDDDDD!!!!! RAHHHHHH!!!! We were yelling and jumping up and down. It was AMAZING!!! That was the first gold medal EVER for Botswana, and the first time anyone from Africa won gold in that race! It was so cool I was so proud of him!
Anyway, I show up for work the next day (LAST DAY) and that is all anyone is talking about. The guy next to me pulls up interviews and videos of the race, then Chanana shows me that the PRESIDENT of Botswana issued a national half day of work in honor of Tebogo’s achievement. WHAT?!?!?! I didn’t know you could do that?!?!? Loveeeeeee. The energy was electric, everyone was so excited! I went to meet with the lab’s expert in Biostatistics, and he explained some of the computational analysis and helped me download some needed software. There was some problem with the download, so I was so grateful that he could help me through it! Literally so kind. While that was happening, I went back to the office to give everyone my parting gift, which was a big box of Ferrier Rocher chocolates and some permanent markers for everyone to use (they’re always needed and in short supply in the lab). It went over really well and everyone enjoyed them! I also gave Bonolo and Sims each a thank you card and chocolate. After I finished up, Bonolo and I took some pictures (cute!) as well as a couple of me in the lab (LinkedIn anyone?), before I headed out!
Walking out of the hospital complex was a surreal feeling, I can’t believe it’s all over. I have had such an amazing experience, and I plan to send another Stack with more overall reflections. As a treat I went to the cafe by my apartment and had half of a ginormous sandwich. That leads me to right here and now, typing this Stack in the outdoor lawn of my apartment. I need to pack everything up before leaving for Kruger tomorrow, so I should probably go do that now.
This feels like an end of an era, but don’t worry, I will make sure to write a Stack for my trip to Kruger National Park and Cape Town, as well as a full reflection of the summer and everything I have learned.
Thank you all for reading, and I am so sorry for keeping you waiting!
I will see you all (not everyone, obviously) soon!
XOXO,
Emily in Botswana