Thats all folks!
Hello all,
My time in Uganda is quickly coming to an end. Tuesday I leave for Tanzania for a week and a half and then back to the good ‘ol USA-----it has been a while (lets hope the British Airways strike ends by then). Given that, yesterday was the last day that it was worth collecting samples, and even though it would have been nice to go out with a bang, there were no patients. Again, good for the kids; I can always take solace in the fact that if I’m not busy, well the kids are healthy and that is good.
Although I haven’t blogged in a while, it has been an eventful (as always) last week or so. Labwise, I got the –80 freezer up and running----it involved plugging it in for the most part. It has maintained between –83 and –78 for the past 5 days, so I think it is working great (even despite the periodic power outages). The liquid N2 transfer vessel arrived, which was the last item on the list of things that were shipped from the US. Thus, everything that was on our list, 3-gas incubator, biosafety cabinet, refrigerated centrifuge, -80 freezer, millipore water purifier, pH meter, pipet aids, liquid N2 storage tank and transfer vessel, are here and fully operational.
I spent most of this week just culturing, writing up protocols, and demonstrating and then observing Sam and Moses culture. I think some practice and mistakes, and then they will be proficient in culturing parasites. On that note, Sam doesn’t believe that they can afford to purchase the N2 gas when I leave, and thus he is thinking about finding some candle jars. This is not my domain, but despite the problems with the Oxy-gas people (see below, again), I think results are much better with the controlled incubator----that’s for the bosses to decide. Certainly, long-term, we should setup our own N2 generation system.
The only setback this week was, once again, the N2 gas. I called ahead of time to have two good tanks reserved (one shouldn’t have to fill two tanks at a time, that is why there is a backup, but the backup leaked three quarters before I realized it was leaking and needed some thread tape). Moving on, I called on Monday to have tanks delivered on Wednesday. I called again Tuesday to remind them---but oh no, now they can’t deliver on Wednesday because Wednesday was just deemed a national holiday to remember the 8 Ugandans that died along with Dr. John Garang, vice-president of Sudan, in an apparent helicopter crash (or hijacking or shot down by a missile or sabotage, all depending on which paper you read and who you believe). Anyways, so I asked for two tanks to be delivered early Thursday morning. Well, after waiting until noon, I called Oxy-gas and asked where the delivery was, they said the delivery truck had broken down, “can you come pick them up?” So I call Nuhu, one of the drivers here, and went over to pickup the tanks (again a 3hr ordeal). Bring them back and set them up-----great, they are at 9% O2. Better than the 14% before, but still not what we need. Anyways, it seems the 9% O2 hasn’t killed the parasites, and the two tanks lasted until today so all is well.
The other excitement this week was finding out that the Uganda customs police confiscated the jacket that my parents sent me to climb Mt. Kilimanjaro. They said it looks like a potential UPDF (the Ugandan Army) jacket. I guess it is likely green, but that, I’m sure, is the only possible resemblance. When I called the customs agent, he said, “well, if you come down here, maybe we can work something out.” Ahhh, yes the old hold it ransom trick. I already paid 80% import tax on the value of the shipment, and so I decided I will not go down there, especially when down there, involves a 45minute drive to Entebbe. After, I hung up the phone and stormed out to take a walk to calm down, Vicky (an intern here for the summer) kindly called the man back and figured out a plan where I can pick up the jacket before I leave the country-----thus the jacket never enters the country, I don’t pay more tax (officially) and I get my jacket. She is so kind!
I guess other than that, everything has gone well. The preliminary results of the culturing are as follows. We had 8 of 9 falciparum samples mature to schizont stage parasites, which is certainly a better percentage than expected. We encountered 1 episode of vivax malaria and 1 episode of malariae malaria (it was fun viewing the differences in the microscope, yes I’m bringing back the slides). Neither of these samples grew in culture. We were able to culture 3 new strains to the point of freezing them down, and one of those strains we froze down 2 times. Thus we have 4 different samples to attempt restarts from in SF. In fifteen days, we collected 11 out of 17 possible non-asymptomatic samples. We missed 6, one because we were too far away to come and get the sample, and 5 because the doctors periodically forgot to inform us---although, they were pretty good about this (4 of these were on this last Sunday when they just thought I wasn’t working). The one sad note is that one of these missed samples had a parasite density of 558,000, which is almost triple that of any other parasite density that we collected. When patients have a parasite density of 500,000 or above, the doctors immediately put them on Quinine. With this high density, I likely could have frozen the sample down immediately and retained some for culturing as well, too bad. Moving on, thus, out of 9 falciparum samples we were able to culture 3 isolates well (to the point of freezing down, ie >9% rings in 0.5ml RBCs). That is 33%, which I think is good. I think this percentage would have certainly increased if we didn’t have such fluctuations in controlling the %O2. Also, we started culturing just when the number of malaria cases decreased fairly dramatically---into the dry season. When we arrived, they were seeing 20 patients a week for malaria. As you can see we observed only 17 during the 15 day period we were up and culturing.
I have samples of every day, for every culture to genotype when I get back to SF. It will be interesting to see whether, and if so, how the genotype changes during adaptation to in vitro culture. Do we start with a multiple infection and select for one strain, etc?
As for the samples, I am trying to arrange shipment in our new dry-shipper to San Francisco, instead of bringing them with me on the plane. I have a contact, Jimmy at World Couriers that hopefully will take care of everything on Monday (this is who Walter Reed uses). They allow net-30 billing in the US, so I thankfully won’t have to front the money here, or figure out how to get it. I’ve put Joe and Felix as the people to contact about billing.
Given the above, I certainly think we have accomplished our goals, which is great given the numerous obstacles that one ends up facing here. The lab is a lab, with benches and air conditioning and operating equipment. And, although we did not isolate as many samples as we would have liked, we certainly have demonstrated proof of concept. More importantly, it has been a wonderful, yes trying at times, but wonderful experience nonetheless. I certainly have gained a lot from learning how things get done in the non-western world. I probably still haven’t learned enough patience, but I think I’m making progress, albeit slowly. I certainly think there are wonderful opportunities for further research here in Uganda, and now we have the facilities. It is just a matter of sitting down and figuring out what are the most feasible and interesting questions.
I would like to thank the higher-ups, both Joe and Phil for providing the support for this little endeavor---brain support and financial support. Also, Sam and Moses for helping us setup the lab, and teaching me some new microscopy tricks. As well as everyone else here and in SF, working on the MU-UCSF Malaria Research Collaboration, particularly Kenneth and Catherine for being so helpful with everything, especially all the shipping issues.
Again, I leave Tuesday, the 16th, for Tanzania and I’ll be back in SF on August 30. In Tanzania, I’m setup to climb Mt. Kilimanjaro and then I’m likely to head to Zanzibar, but these plans are flexible. I am leaving again on September 2 to visit my family in WI---so I truly won’t be back working in the lab until the second week in September or so.
Jenny, Terry, and Dustin got back from their Ugandan safari all intact and healthy Thursday afternoon. They have some wonderful stories and pictures. They headed out today to go rafting on the Nile, and then they fly back on Monday. I assume they’ll be back in SF on Tuesday, SF time.
With that, I sign off, and leave this blog up to the next crew of Derisilab people that head to Uganda (although I may update the blog about my travels in Tanzania, depends on internet access).
See you all soon,
Adios,
Nate
My time in Uganda is quickly coming to an end. Tuesday I leave for Tanzania for a week and a half and then back to the good ‘ol USA-----it has been a while (lets hope the British Airways strike ends by then). Given that, yesterday was the last day that it was worth collecting samples, and even though it would have been nice to go out with a bang, there were no patients. Again, good for the kids; I can always take solace in the fact that if I’m not busy, well the kids are healthy and that is good.
Although I haven’t blogged in a while, it has been an eventful (as always) last week or so. Labwise, I got the –80 freezer up and running----it involved plugging it in for the most part. It has maintained between –83 and –78 for the past 5 days, so I think it is working great (even despite the periodic power outages). The liquid N2 transfer vessel arrived, which was the last item on the list of things that were shipped from the US. Thus, everything that was on our list, 3-gas incubator, biosafety cabinet, refrigerated centrifuge, -80 freezer, millipore water purifier, pH meter, pipet aids, liquid N2 storage tank and transfer vessel, are here and fully operational.
I spent most of this week just culturing, writing up protocols, and demonstrating and then observing Sam and Moses culture. I think some practice and mistakes, and then they will be proficient in culturing parasites. On that note, Sam doesn’t believe that they can afford to purchase the N2 gas when I leave, and thus he is thinking about finding some candle jars. This is not my domain, but despite the problems with the Oxy-gas people (see below, again), I think results are much better with the controlled incubator----that’s for the bosses to decide. Certainly, long-term, we should setup our own N2 generation system.
The only setback this week was, once again, the N2 gas. I called ahead of time to have two good tanks reserved (one shouldn’t have to fill two tanks at a time, that is why there is a backup, but the backup leaked three quarters before I realized it was leaking and needed some thread tape). Moving on, I called on Monday to have tanks delivered on Wednesday. I called again Tuesday to remind them---but oh no, now they can’t deliver on Wednesday because Wednesday was just deemed a national holiday to remember the 8 Ugandans that died along with Dr. John Garang, vice-president of Sudan, in an apparent helicopter crash (or hijacking or shot down by a missile or sabotage, all depending on which paper you read and who you believe). Anyways, so I asked for two tanks to be delivered early Thursday morning. Well, after waiting until noon, I called Oxy-gas and asked where the delivery was, they said the delivery truck had broken down, “can you come pick them up?” So I call Nuhu, one of the drivers here, and went over to pickup the tanks (again a 3hr ordeal). Bring them back and set them up-----great, they are at 9% O2. Better than the 14% before, but still not what we need. Anyways, it seems the 9% O2 hasn’t killed the parasites, and the two tanks lasted until today so all is well.
The other excitement this week was finding out that the Uganda customs police confiscated the jacket that my parents sent me to climb Mt. Kilimanjaro. They said it looks like a potential UPDF (the Ugandan Army) jacket. I guess it is likely green, but that, I’m sure, is the only possible resemblance. When I called the customs agent, he said, “well, if you come down here, maybe we can work something out.” Ahhh, yes the old hold it ransom trick. I already paid 80% import tax on the value of the shipment, and so I decided I will not go down there, especially when down there, involves a 45minute drive to Entebbe. After, I hung up the phone and stormed out to take a walk to calm down, Vicky (an intern here for the summer) kindly called the man back and figured out a plan where I can pick up the jacket before I leave the country-----thus the jacket never enters the country, I don’t pay more tax (officially) and I get my jacket. She is so kind!
I guess other than that, everything has gone well. The preliminary results of the culturing are as follows. We had 8 of 9 falciparum samples mature to schizont stage parasites, which is certainly a better percentage than expected. We encountered 1 episode of vivax malaria and 1 episode of malariae malaria (it was fun viewing the differences in the microscope, yes I’m bringing back the slides). Neither of these samples grew in culture. We were able to culture 3 new strains to the point of freezing them down, and one of those strains we froze down 2 times. Thus we have 4 different samples to attempt restarts from in SF. In fifteen days, we collected 11 out of 17 possible non-asymptomatic samples. We missed 6, one because we were too far away to come and get the sample, and 5 because the doctors periodically forgot to inform us---although, they were pretty good about this (4 of these were on this last Sunday when they just thought I wasn’t working). The one sad note is that one of these missed samples had a parasite density of 558,000, which is almost triple that of any other parasite density that we collected. When patients have a parasite density of 500,000 or above, the doctors immediately put them on Quinine. With this high density, I likely could have frozen the sample down immediately and retained some for culturing as well, too bad. Moving on, thus, out of 9 falciparum samples we were able to culture 3 isolates well (to the point of freezing down, ie >9% rings in 0.5ml RBCs). That is 33%, which I think is good. I think this percentage would have certainly increased if we didn’t have such fluctuations in controlling the %O2. Also, we started culturing just when the number of malaria cases decreased fairly dramatically---into the dry season. When we arrived, they were seeing 20 patients a week for malaria. As you can see we observed only 17 during the 15 day period we were up and culturing.
I have samples of every day, for every culture to genotype when I get back to SF. It will be interesting to see whether, and if so, how the genotype changes during adaptation to in vitro culture. Do we start with a multiple infection and select for one strain, etc?
As for the samples, I am trying to arrange shipment in our new dry-shipper to San Francisco, instead of bringing them with me on the plane. I have a contact, Jimmy at World Couriers that hopefully will take care of everything on Monday (this is who Walter Reed uses). They allow net-30 billing in the US, so I thankfully won’t have to front the money here, or figure out how to get it. I’ve put Joe and Felix as the people to contact about billing.
Given the above, I certainly think we have accomplished our goals, which is great given the numerous obstacles that one ends up facing here. The lab is a lab, with benches and air conditioning and operating equipment. And, although we did not isolate as many samples as we would have liked, we certainly have demonstrated proof of concept. More importantly, it has been a wonderful, yes trying at times, but wonderful experience nonetheless. I certainly have gained a lot from learning how things get done in the non-western world. I probably still haven’t learned enough patience, but I think I’m making progress, albeit slowly. I certainly think there are wonderful opportunities for further research here in Uganda, and now we have the facilities. It is just a matter of sitting down and figuring out what are the most feasible and interesting questions.
I would like to thank the higher-ups, both Joe and Phil for providing the support for this little endeavor---brain support and financial support. Also, Sam and Moses for helping us setup the lab, and teaching me some new microscopy tricks. As well as everyone else here and in SF, working on the MU-UCSF Malaria Research Collaboration, particularly Kenneth and Catherine for being so helpful with everything, especially all the shipping issues.
Again, I leave Tuesday, the 16th, for Tanzania and I’ll be back in SF on August 30. In Tanzania, I’m setup to climb Mt. Kilimanjaro and then I’m likely to head to Zanzibar, but these plans are flexible. I am leaving again on September 2 to visit my family in WI---so I truly won’t be back working in the lab until the second week in September or so.
Jenny, Terry, and Dustin got back from their Ugandan safari all intact and healthy Thursday afternoon. They have some wonderful stories and pictures. They headed out today to go rafting on the Nile, and then they fly back on Monday. I assume they’ll be back in SF on Tuesday, SF time.
With that, I sign off, and leave this blog up to the next crew of Derisilab people that head to Uganda (although I may update the blog about my travels in Tanzania, depends on internet access).
See you all soon,
Adios,
Nate
posted by DeRisilab in Uganda at 9:49 AM
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