Lab Snob

Kenya Medical Research Institute (KEMRI)

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People warned me about the lab facilities in Kenya. Everyone expressed some variation of  “You know it’s not the same as in the US, right?” And every time I looked at them like they were crazy, but not because I was surprised. I am not some naive, sheltered PhD student who thinks everyone gets an LSR-II and precast gels. Nor am I a lab snob- at least I try not to be. I have worked in low budget labs, low access labs, unsanitary labs, you name it. I have also worked in a lab abroad before so I’m not exactly a noob. Whatever my situation was, I made it work.

So you don’t think I’m full of shit, here’s a brief example. A few summers ago I worked in a lab in China- a land of duality with old and new co-existing everywhere you look. The lab was no different. We had a NanoDrop but were still developing Western Blots on film in a dark room (which smelled like a rotting vivarium fyi). It was a weird place to do science. At one point, the air conditioning broke in the main lab room and, because of nonsense bureaucracy, it didn’t get fixed for a couple of weeks. Beijing in the summer is easily 90 degrees Fahrenheit and humid. If I wore my gloves for more than 20 minutes, sweat would start to pool in the fingertips causing my fingers to prune. Super cute, I know. We had to do all our experiments on ice just in case. But we did it and we got beautiful data for the grad student we were assisting! Long story short, science doesn’t care about your comfort.

So when people warned me about Kenya, I looked at them like they were crazy because duh. Literally duh. Of course it’s not the same. I would never expect to have the same luxuries that I have at Emory, but it’s not like that would ever deter me from the experience. Regardless, I heeded the warning and steeled myself up for terrible lab conditions. Now that I have spent three weeks here I can safely say that everyone is a Big. Fat. Baby. The TB lab at KEMRI is SO NICE. Now maybe my opinion is biased because I was expecting a shit hole, but really the facilities are pretty awesome.

Like this is the avenue you drive down to get to the lab (after driving through two guard posts mind you). Not a bad place to spend 3 weeks.

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My first day in the lab, I got three separate tours. Everyone wanted to make sure I could orient myself and show me what kinds of projects they had going on at the site. Each one of my tour guides kept saying things like “I know it’s not much” and “It’s not like at Yerkes/Emory/The US.” And I was just staring at them blankly because in a lot of ways it is EXACTLY like the US. They have all the standard immunology stuff- hoods, incubators, centrifuges, autoclave, ELISA readers. There were even a few crazy, high tech pieces of equipment that I did not recognize. I really didn’t understand everybody’s sheepishness.

IMG_5792 (1)I later discovered that the building the TB lab is in is in fact one of the nicer ones on campus. On day two I shadowed one of the scientists doing helminth diagnostics. We went to a Neglected Tropical Disease (NTD) room in another building and it was pretty dated. But then again, so are the methods used to diagnose NTDs so I wasn’t that surprised. The only things you need for helminth diagnostics are stains, slides and a simple light microscope. Plus NTD diagnostics usually involve poo so who wants to waste a fancy clean room on that. The point is that it doesn’t really matter how nice the facility is as long as you can do your work. Does the campus here have all the hoity-toity cores that we have at Emory? No, of course not. I’m not even sure there is a vivarium. But for standard immunology and microbiology assays, they are pretty set.

I feel like it is important to disseminate this information so that other scientists think to partner with KEMRI or even come here to do their own work. I certainly didn’t have a good grasp on the lab facilities prior to working here and I cannot be the only one. Plus back home people have this misconception that if a lab isn’t state of the art, that the science conducted is sub-par. But fancy equipment isn’t as important as good scientific questions and experimental design. Eight color flow cytometry can answer A LOT of questions if you design your panel well and have the right samples. And boy does KEMRI have all the right samples for scientists like me.

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As stated in my last post, it is beyond weird that we just take these samples and run back to the US to study them. Why do we do that? Or I guess the better question is why don’t we study them here? Why not conduct science in a place where the results actually matter? Why not bridge the gap between the patient population and the bench work? I fully admit that I’m being a huge hypocrite in saying this because in fact I could not do my 13-color flow assay here, but there are a lot of things I CAN do for my project. During this trip I ran 18 ELISA plates to quantify antibodies against the worm I study. There was a moment when I was prepping plasma for a plate and a new sample came in from a study participant pertinent to my assay. The lab techs aliquoted off some plasma for me right then and there and continued on with their day. Easy as that. No freezing. No waiting for enough samples to batch in a shipment. Furthermore, while the results of this assay will be a blip in a paper when I graduate, they matter tremendously to the scientists and community here. I briefly presented my results regarding discordant diagnostic results during seminar last week and it stirred up quite a discussion between the various teams here.

I get that there are challenges in conducting certain experiments here, especially since there are issues with the supply chain and government corruption (more on that later). I concede that not everything can be done on site, but there is always a happy medium. My boss has done a great job at finding that medium. While she has a majority of samples shipped back to the states, she leaves what she can here in Kisumu for the Kenyan scientists to conduct their own experiments. She makes a point to leave at least two vials of cells from every participant here, even if there are only two to begin with. She also works with the students here to help them develop and execute masters and PhD thesis projects. This way some of the work and expertise always stays local.

This is so important because it builds capacity at places like KEMRI. By physically basing science here, it empowers local scientists here to take agency over their work. It trains these scientists in new techniques which can then be passed on to the next generation further building the scientific community. Increasing capacity in turn entices more people to base their studies here, bringing in money, supplies and expertise from around the world. And so the cycle repeats.

We shouldn’t treat KEMRI like it’s a post office. It’s not. It’s a fully functional scientific campus. And more importantly it is full of people ready and willing to work towards the same goal we (presumably) all have- to improve human health and eradicate nonsense like TB.

Science Smuggler

By now, you’ve probably heard about my traumatizing customs experience attempting to smuggle a bag full of lab supplies into Kenya. Of course I wasn’t actually smuggling anything since I had paperwork to back me up, but it definitely felt sketchy. Considering the appearance of some of the things I was carrying, I think my unsettled feeling was justified. Someone could have thought I was in Kenya to start a meth lab or be a bioterrorist. Of course they could have also thought I was doing medical work, but my paranoid mind couldn’t come up with any benevolent explanations for this suitcase at the time.

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Upon deeper inspection it is obvious that I am not in fact trying to start a meth lab. Hopefully one would be able to deduce that I am in Kenya to do some sort of biological lab work. Quite a lot of lab work judging by the size of my suitcase.

On the surface this suitcase might seem excessive. Did I really have to bring all of that? I guess not, but when you travel to a collaborating lab, it’s very common to bring the supplies you will be utilizing with you. (I once knew a guy who flew with seedlings in his luggage to a collaborating lab abroad so that they could study a particular genetic mutation.) This is especially true if you are going to a lab that is more resource scarce than the lab you are coming from. They are being kind enough to provide you space and guidance for your work, the least you can do is not use their shit. Furthermore, if this is a lab that you regularly benefit from, you want there to be a mutually beneficial relationship, not a parasitic one. Since literally every sample I use in Atlanta is prepped and shipped from this lab, Cheryl and I wanted to make sure that not only was I bringing what I needed, but that I was also considering their needs. I am already a big enough resource suck by taking samples that require their time and reagents. I don’t want to also be the douche who shows up, uses all their supplies and then bounces. That’s an egocentric way of doing science and not at all in the spirit of international collaboration. 

So I brought a ton of stuff. And while I do provide a full list below, you do not need to read it. Most of it is just science jargon to any non-immunologists out there anyways. Of course if you want to know about them, I have *briefly* explained the purpose and use of every item at the very bottom of this post. But really, the important part is the big picture. There are three trends in the kinds of items I brought that together make an important point about global health and international science.

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  • Long brown box- 25 ELISA plates.
  • Larger plastic bags- 500 loose plastic flow tubes.
  • Square white styrofoam box-
    • 2 bottles fixation reagent
    • 2 bottles fixation diluent
    • 2 bottles perm-wash
    • 4 bottles ELISA coating buffer
    • 4 bottles ELISA diluent
    • 4 bottles serum/plasma diluent
    • 4 bottles TMB
  • Plastic tubes with blue lids and orange label- Leucosep tubes
  • Black lab notebooks
  • Red sharpies
  • Brown boxes- two packages of CPT tubes
  • Other white styrofoam box-
    • 1 set of Schisto antibody standards
    • 3 Schisto antibody positive controls
    • 3 Schisto antibody negative controls
    • 7 vials SEA
    • 2 antibody detection antibodies
    • 8 IP-10 ELISA standards
    • 4 vials IP-10 capture antibody
    • 4 vials IP-10 detection antibody
    • 4 vials avidin-HRP
    • BFA
    • Monensin
    • 9 different flow antibodies
    • 3 vials zombie dye
    • DNase
    • 2 bottles of comp beads
    • 1 bottle of calibration beads
    • 60 TB peptide pools
    • 2 sets of HIV peptide pools (clade A and clade D)
    • 1 set of CMV peptide pools
    • 1 set of SEB aliquots
    • DMSO
  • Clear bottle- I liter 10x PBS
  • 3 white diagonal rectangles- stacks of 5 reagent reservoirs
  • 20 additional ELISA plates
  • Blue box- xs gloves
  • two small plastic bags- sarstedt tubes
  • White tubes with orange lids- nonfat dry milk
  • clear tubes with blue lids- SEA coating buffer
  • Small bottle with purple liquid- 100 mL Trypan Blue
  • orange circle- label tape

So here I go up on my soapbox. The three things I/we should realize when looking at this list are:

1. Most of us need to seriously check our lab supply privilege.

Many of the items I brought with me we completely take for granted in the states. Things like label tape and sharpies aren’t a given in other places. I knew I would be traveling with supplies so I wasn’t at all surprised I was bringing these things. It was more that I never realize how much of a difference these kinds of things make in my day to day lab work. By day three of this trip, I had fully realized how deep my love of sharpies truly is.

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I also brought supplies that in the states we consider to be unnecessary and annoying, like the lab notebook Cheryl had me bring for the grad student I am working with- Jeremiah. How many times have I bitched about having to write in my lab notebook? Probably every day. Students of my generation mostly think they are outdated. I record everything electronically. Why would I need a physical book? I am perpetually like 10 experiments behind in it because of my attitude. In contrast, Jeremiah was so stoked to receive the lab notebook. He was so nervous to even fill out the first page (in case he screwed it up) that he had me write his name and the project title for him. It’s not like he hadn’t been taking notes on his experiments, because he had been. I just realized that, to him, this was an important step in his scientific career. Having a legit lab notebook empowered him.

2. Regardless of finances, access to lab supplies is not universal.

On the flip side, some of the items I was carrying are absolutely critical reagents to the work being done in Kisumu. CPT tubes and Leucosep tubes are used literally every day. And since they have to be available when a study participant is available, it’s not like you can pause and wait for a backorder. The day before I left, I found a bag of Leucosep tubes at my desk in Atlanta. Apparently Jeremiah had sent Cheryl a WhatsApp message saying they were running low and asked if I could bring some. I had space and was prepared to bring as much as two checked bags would fit so it was not a big deal, but what if I wasn’t? Would they have run out? When would they have been able to order them again? How long would getting them shipped take? These are all questions I can’t answer, but if a four-day trek in my luggage is the quickest way to get them… it makes me wonder. It’s not like this was a budgeting restriction. These are considered staples in the lab here. You can’t NOT have them. So what was the deal? After talking with a few people about trying to get a supplier with sodium heparin tubes and receiving expired QFT tubes, it makes me think that perhaps getting proper lab supplies is just more difficult here, regardless of cost. In contrast, I can order something and 9 times out of 10 it comes in two days. As such, I have now come to expect immediate delivery of my supplies. I am sure many others do as well. How many of us have thrown a little baby hissy fit when an item we *want* is backordered. I definitely have.

But most importantly…

3. Holy shit, these diseases are real.

TB + Parasite DistributionMost of the items in the larger styrofoam box were vials containing frozen bits and pieces of pathogens- HIV, CMV, TB, Schisto. Of these, HIV is probably the only one widely discussed in the United States. Only pregnant women care about CMV. Most people think we cured TB decades ago. No one even knows what Schisto is. Since I work on these bugs at Emory, I have a much different perspective. I think about TB every day. I think about neglected tropical diseases (NTDs) every day. I use these exact same reagents on samples every day. But even so, something clicked in my head when I was packing them…

The reason I have to pack these particular reagents in the first place is because in Kenya, TB is an actual issue. The reason my project even exists and that I have this opportunity is because in Kenya, Schisto is an actual issue.

Maybe that makes me sound naive, because like duh that is how biology works. But I’m telling you, it’s different. Intellectually I knew these facts, but at home in the states you can shelter yourself from what that really means. When you are sitting in the hood pooling HIV Clade D peptides to stick in an ice chest in your luggage to take to Kenya, you can’t. There is no buffering your feelings then. You realize just how smug you were thinking you were worldly. Silly girl.

Which brings me to my point.

Doesn’t it suck that the places that suffer most from a particular disease don’t have the supplies they need to solve problems that only they can truly understand?

Isn’t it illogical that those of us working in more “prestigious” universities around the world are the ones with access to all the supplies and equipment we could possibly need to solve scientific problems that we will never know first hand?

Yea. It’s fucking weird.

But such is the way the world works. There is a serious disconnect between the science and the people it impacts. Because of this, there is a lot of criticism towards international collaborations such as the one I receive samples from. When I talk about my project I get a fair amount of backlash from people who feel like I’m just snatching samples from Africa without giving anything back. Up to now, these critics have pretty much been right, but I hope to change that over the course of this trip and beyond. Smuggling a big ass bag of supplies through customs was just the first step in doing so.

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Appendix

Techniques Explanation

  • ELISA (#1-11) – an ELISA is an assay to detect specific proteins by having them bind to a different protein on plates. Then you add a color changing chemical which binds to the combination. The color is used to visualize and quantify the amount of protein of interest.
  • Flow cytometry (#12-21) – a technique used to determine what proteins are on/in each cell in a population of cells by using fluorescent labels and lasers

Reagents Explanation

  1. ELISA Plates – special plates that bind the first protein in the assay which serves to “capture” your protein of interest. They have 96 reservoirs for 96 separate samples.
  2. Reagent reservoirs – allow you to pick transfer liquids of interest easily to ELISA plates
  3. Coating buffer (ELISA and SEA) – liquid that allows the first protein to stick really well to the plate
  4. SEA and IP-10 capture antibody – the proteins that start the ELISA
  5. Diluent – liquid to dilute your samples in so you can use a small amount but not fuck up the samples
  6. “Standards” (ELISA and schisto) – samples with known concentrations of your protein of interest so you can compare your experimental samples back to get an actual number value
  7. “Controls”  – samples with known reactivity so you can make sure your assay is working. A positive should turn color and a negative should not.
  8. “Detection” antibody (antibody or IP-10)- binds to the protein of interest which has been “captured”
  9. Avidin-HRP – helps with the color change by binding to the “detection” antibody
  10. TMB – the chemical that binds to your combo and changes color
  11. Nonfat milk – disrupts non-specific interactions so you only “capture” the protein you want
  12. Flow tubes – your samples have to go in here because they fit on the machine that reads the assay
  13. Fixation reagent/fixation diluent/perm-wash – These three are used to poke holes in cells and then stabilize the punctured cells so you can look for proteins inside the cells.
  14. BFA/Monensin – keep proteins inside the cell
  15. Zombie dye – lights up inside dead cells during flow cytometry
  16. Flow antibodies – these have fluorescent labels and bind specifically to proteins of interest
  17. Comp beads – allow you to do magic with lasers (seriously I barely know how this works)
  18. Calibration beads – calibrate the machine you will be using
  19. DNase – so your cells don’t clump together and screw up your results
  20. “Peptide pools” – bits and pieces of the pathogen that are used to stimulate immunology samples. They are entirely harmless.
  21. SEB – a “superantigen” that binds to T cells and activates them
  22. DMSO – some gnarley chemical used to dissolve shit
  23. Leucosep tubes – tubes used to separate red blood cells, white blood cells and serum
  24. CPT tubes – tubes used to collect blood from study participants
  25. 10x PBS – concentrated buffer that everyone and their mom uses in biological science
  26. sarstedt tubes – small tubes to do small biological reactions in