More sequencing for farmers in Tanzania

February 2019 we had a informal training session at Dr. Ndunguru’s new research facility TARI-Selian in Arusha, Tanzania. This trip we ran our first Oxford Nanopore plant and vector diagnostic clinic! We had scientists in the region bring infected plant samples and insects they were interested in sequencing including wheat, barley, maize, beans, fall army worm, whiteflies and more. We used a the Qiagen DNeasy plant kit for extractions this time [shout-out to Dr. Monica Kehoe for the help] as we are waiting for the PDQeX to be available and Chelex for the insects. We had success but it is up to those researchers to tell their stories so we shall leave it at that. The data analyses was much harder because we had so many hosts and also we had no idea what we would find so we partnered with Associate Professor Lachlan Coin and his team who have developed a cool new cloud solution. Charles Kayuki was an excellent training and did a great job with instructions in Kiswahili! See below.

We also had the great fortune of having a meeting with Honorable Christophe Bazivamo who is the Deputy Secretary General of Product Services for the East African Community. He and the team were very impressed with the project and invited us to Kampala, Uganda to present our work to the East African Community regional consultations on the draft EAC SPS regulations and SOPS validation meeting in Kampala, Uganda on 26-28th Feb, 2019.  Dr. Sseruwagi and Dr. Laura Boykin attended the meeting and presented the work for the team. Everyone was very receptive.  Further engagement is ongoing.

And finally, we had the great honor to be featured in three news items below:

PNAS 

Cray

KENET

Some pictures from the training in Arusha, Tanzania:

Mama Maina | Kenya | MinIT on battery

We did it! Three Tree labs in three countries (Tanzania, Uganda and Kenya) in three weeks.  In Kenya we went to visit Mama Maina and Mutunga’s farms near Thika, Kenya. In September 2017, we visited their farms and detected CMD viruses in both so we wanted to check the health of their plants with another rapid barcoding kit run. Our goal on this run was to decrease our time to results.  In Tanzania in Uganda it took us 4 hours from sample collection to results, this time we got the time down to 3 hours with great team work. Brenda Muga and Elijah Ateka were crucial in executing the Tree lab for Mama Maina and Mutunga. Interestingly, we found all the plants we tested were healthy- with no virus!  This is great news and will allow both farmers to sell their cassava sticks to others with no fear of spreading the virus.

We are now actively working on the crucial list of things we used to share with everyone and also analyzing all the results to present in a manuscript. Thank you to everyone who followed along- we are now ready to scale up our efforts.  We are always looking for partners who are willing to work for farmers. Thank you to Sam & Tom Industrys for shipping us a magnetic rack. Big shout out to the Nanopore team and Jo’s Zygem team who helped remotely.  Also a big thank you to Monica Kehoe and Anders Savill who helped from Australia.

MinIT on the battery:

Each Tree lab we started the run on the battery pack: found here.  To find it we searched “laptop power bank”.  The key for the power bank is to make sure it has not only USB inputs but also a power port and cable (see picture below with yellow circle around the cord you need). It ran on average 4.5 hours set on 16.5V.  Once the battery ran out we ran it from main power in a hotel room overnight if the hotel had no power (sometimes that was the case) we had a second power bank.  A better solution provided by Clive Brown at Nanopore is to have a input splitter so you don’t have to restart the device when the battery runs out.  The biggest challenge was trying to carry the battery, MinIT and the MinION in the car- typically we used a cardboard box-but not too small because once the MinION overheated because we put it in a cooler box.

MinIT and airport security- a few times the airport security people wanted to know what it was- we made sure to have a battery in the carry-on to power it up.  We explained it was used for diagnostics of sick plants AND had photos of us using it in the field so they could easily see the use.

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