Two new additions to the crew. We had Dr. Jo-Ann Stanton from New Zealand bring her PDQx (pretty damn quick extraction) machine to test in the field and we had Dr. Ibrahim Mohammad from Kebbi State University in Northern Nigeria. All gathered around getting technology and science to farmers to diagnose what is killing their cassava and to ID the whitefly species in the farmer’s fields.
We have just finished our 10 days with the Tanzanian team. Our highlights were visiting Asha’s farm after 9 months- she has gone from 0 tonnes/hectare to 35-40 tonnes/hectare. See our first visit here: https://vimeo.com/233953210. She was given two varieties of cassava to grow in September 2017 – Kiroba & Mkuranga. Prior to this she and her group were growing local varieties.
Clara interviewing Asha
Asha (far left) and her group.
The yield from ONE plant.
Asha now has a new problem- she needs a market to sell her extra cassava because her family is food secure… and so are the families of the group members. This is a good problem to have and now we will work with Asha to navigate selling her excess. The power of science and technology was witnessed first hand.
The MinIT (aka the mini-supercomputer) in the lab:
Step one was to get power banks that would work in the field. We bought two laptop power banks – within regulations of the airlines because we are traveling between countries (Tanzania, Uganda and Kenya). Another key was to do a test run before we took it into the field- we did this with Clara- a PhD student from Sokoine University of Agriculture- at Mikocheni Agricultural Research Institute- our lead node in TZ. Clara is studying African Swine Fever- a DNA virus so we thought this was a good test before heading into the field to test cassava. She did a DNA extraction and we tested out the MinIT. Rich from Oxford Nanopore sent us a couple of pages of quick start guides and away we were. In addition, Chris S. gave us lots of good advice on the device and saved us a few times! We connected to it via wi-fi and on there is a MinKnow version that we used to QC the flow cell- all that was fine. When we went to start the run the software on the MinIT wasn’t giving us the option to select the kits so we immediately switched to starting the MinIT via the MinKnow software on the laptop and telling it to connect to a remote device (the MinIT connected via wi-fi). The run started and immediately the MinIT started basecalling and keeping up with reads being produced! We let that run for a day.
Clara and the first MinIT run in the wild.
The crew at MARI
MinIT in the field- Musoma, Tanzania:
Our BIG test was to sequence IN THE FIELD. So we set out to the Mara Region of Tanzania where the cassava team has been working with farmers in the region for 4 years- giving them clean planting material, training extension workers, training farmers about planting, etc. Our mission here was to 1) test their improved varieties for virus 2) test whiteflies for virus and to ID species and 3) introduce the devices to the government officials. All were accomplished- more on this soon. BUT we did it. We did a DNA extraction of 12 samples, library prep (SQK-RBK004) and data analyses all while farmers waited and we gave them immediate feedback on what to do next. EPIC day. Full of challenges. We used local blast databases installed on a laptop for both the cassava viruses and whiteflies and once we had some .fastq files we imported them into Geneious and blasted them and we were able to see what viruses were in the whiteflies and the cassava leaves. Both Jo’s device and the MinIT lived up to the hype- couldn’t have done it end to end without them. Power of diversity. Huge shout-out to the MARI team- Peter, Charles, Deo and Joseph in addition the farmers who trust us to do this.
All the devices minus the laptop we needed.
Jo’s amazing DNA extraction device that also was used to heat.
farmers waiting for results
lab under a tree
using Jo’s device to heat for the library prep.
We are now in Uganda and going to sit with Dr. Titus Alicai’s team to plan our next lab under a tree.