African Bushmeat Expedition

What an adventure it has been to carry out our Bushmeat Identification Workshop here at Mweka. Late last night, our pivotal piece of equipment, the thermocycler, stopped working, showing us an unusual error message that seemed to be related to the power source. After converting power, moving from outlet to outlet, and using a stable generator, still no luck for the thermocycler. We sent many emails, but there was not much to do. Thus, it is time for plan B. We decided to go old fashion, and do PCR as best as we could; we decided to do PCR by hand.

PCR works by using temperature and a chemical mixture of the necessary components to carry out artificial DNA replication. It brings the DNA up to 95C to denature the double helix, then to 50C to allow the primers to anneal, and 72C to allow the polymerase to extend. This meant we would need to simulate these temperatures on the dot to be able to successfully perform this final step at Mweka.

The next morning, Dr. Vavra began by teaching the class about PCR and gel electrophoresis. We set up a heat block, a cooking hot plate, and an old poorly sealed drying oven at each temperature and with one thermometer and various water baths, we were ready to attempt 35 cycles of 1:00 minute each.

In the process of obtaining the equipment we would need for our Plan B PCR, the IT director for Mweka, Simon, mentioned the possibility of utilizing the services of a local hospital. After some talk Dr. Vavra, Simon, and the lab director, Emanuel, headed down through the surrounding coffee plantations to the Kilimanjaro Christian Clinic and Hospital. The trip involved a series of discussions with hospital officials in an attempt to bring the PCR reactions down to the research division. A partially blinded man named Panga (short sword) showed the visitors an immaculate clean room for medical genetics. The thermocycler was brand new. However, after a long discussion with a lab supervisor it was determined that running the bushmeat class samples may contaminate the diagnostic thermocycler. The whole lab section was dedicated to HIV detection. It was quite depressing in a sense to see such a large section of the hospital devoted to HIV. Evidently, the number of cases continue to rise in Tanzania. It was suggested that the biotech research lab next door could also help. After a short visit it was determined that a letter from Mweka would be needed for the offsite supervisor to give approval. A very bright and helpful molecular biology Ph.D. from Dar Es Salaam, Theonest Ndyetabura showed Dr. Vavra a room with several thermocyclers that were the same as the lab at High Tech High. Hopefully, with approval one of them can be used by the class tomorrow.

In the meantime, the rest of the expedition team broke into rotations in order to interview, carry out our Plan B PCR, and assess the needs of our workshop members to move forward with conservation in East Africa.

A third of the group began with our Plan B PCR, setting up ten samples to cycle through our hotplate setup. In a chain of passing samples, the six workshop participants transferred samples from 95C to 50C to 72C as quickly as time could allow. No better way to understand PCR than to transfer ten small tubes from the denaturing step to the annealing to the extension. 35 cycles plus the time in between, the total PCR took nearly four hours to complete. Each time a new group would come in from the rotation, our workshop members had to keep the one minute cycles going between the three heated machines. We had some difficulties with temperature spikes and drops, but somehow, we managed to pull off our four hour procedure with the help of our lab participants.

Another rotation was to meet with Bryndan and talk about their thoughts on the workshop and the process of bushmeat identification. Each of the groups had very similar thoughts, but many interesting and different stories. All of the groups were curious as to what we would be planning next once the workshop was over. It was hard to answer at first, but with some conversations on what they thought should be next, some ideas were created to keep the momentum of the African Bushmeat Expedition going. Every individual also had amazing and intense stories of their personal experiences dealing with bushmeat. Some were very focused on the law and policy aspect, while others were more interested in the forensic and biology part. But regardless of their point of view, everybody agreed that this need for identification was a very important and were willing to work hard to keep this program in place.

During the rotations, we also pulled out a couple individuals to interview more in depth and hear their personal stories about wildlife conservation and their reaction to the workshop. Through these interviews, we heard some amazing stories about the bushmeat crisis in East Africa. Some of the workshop participants came from families that ate bushmeat for cultural and subsistence purposes when they were young. Others had adventurous stories of near-death encounters with buffalo and leopards in the field. These 30 to 40 minute interviews were able to cover much about conservation practices in East Africa. In addition to discussions of each individual’s work in the bushmeat trade, we were able to hear reactions from the workshop we had been hosting for the last few days. Many were excited by the new techniques they had come to learn. Others were surprised by what it took to identify a sample via DNA. Yet each of the participants prompted the question, “but what is next? How do we put this into practice?” The interviews gave insights which were both illuminating and invaluable to our research of the value of conservation in East Africa.

Something worth noting is the laboratory where we are carrying out our DNA workshop. The lab is a seemingly archaic museum, filled with some of the most amazing specimen in glass jars on shelves, all Tanzanian animals, many which have been stored for years. With trophy heads covering the empty bench tops, we have discovered jars filled with elephant ovaries, fetal blue monkeys, spitting cobras, and black mambas. These jars are filled with the specimen that researchers in the western-world write muilti-thousand dollar grants to collect. Yet here, they are commodities similar to how our biotechnology equipments are commodities to us. Today, the lab manager dissected a spitting cobra that was found in Tarangire National Park to preserve in formalin for future examples in class. At home, we marvel at the laboratory we were fortunate to use at High Tech High, I can only imagine what it would be like to learn about anatomy and ecology with the specimens present in the lab.

Yet by the end of the day, we were all anxious to know: did our crazy Plan B work to amplify our bushmeat samples? We ran an agarose gel which is the method to view whether or not there is DNA present after PCR and anxiously loaded the ten samples which we had labored over for the past four hours. Doing molecular biology is tricky because there are so many parameters which must be at the optimal condition in order to replicate DNA. After twenty minutes of running the gel, we viewed with Life Technologie’s Safe Imager to see any results. Rows 1 through ten showed no result yet 11 (our bushmeat sample control) showed a feint sign of DNA at the right size region. Could it be that our crazy plan B actually worked? It was very difficult to tell, and we are unable to determine whether or not we received a sample from the old-fashioned PCR. Still, it made us hopeful that a working piece of equipment could show some amazing results. Worn out by the end of the day, we closed down the lab and began to discuss what our last day at Mweka would be like.

Perhaps tomorrow, we will be able to partner with the hospital in Moshi and run our samples one more time to bring back to the states. Perhaps another gel at a different parameter will tell us whether or not we actually saw banding from our bushmeat sample. We are hopeful and we are optimistic yet all we can do now is rest and see what tomorrow will bring. We will be sad to leave and sad to end our workshop, but this experience has been one we will not soon forget.

(Brittney saw three more birds today. Our count is now 154.)

(We were able to send our pictures from the last couple of days, so please be sure to check previous posts for our photos.)