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.
Mama Maina and Mutunga watching on as we sequence.
Brenda collecting a leaf for us to test
Tree lab and Mama Maina
Brenda loading the flow cell as Mama Maina watches.
Everything we need to sequence in the field
Yes! Mama Maina and team
Elija, Me, Brend and Jo
Packing up tree lab
The team getting read the day before
everything we need for tree lab
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.
Uganda: Round 2 taking the tree lab to the farmer. This time we followed up with our farmer Naomi- turns out she has moved back to her village up north BUT her cassava fields were in good hands as her sister Olivia was looking after them and the harvest was massive. One farmer at a time we will transform the food security space.
We arrived at the lab to find no power or internet – for the entire week- so it gave us the chance to test the infield diagnostic equipment with the Ugandan team! All went well. We set-up another tree lab to help farmer Sarah and her beautiful family including her daughter Sandra. They enjoyed watching the DNA extraction, library prep, sequencing followed by some quick bioinformatics. Happy to report Jo’s DNA extraction machine coupled with the minION and the MinIT make the perfect mobile lab. On the spot diagnostics. Proud. Very proud. We are now in Kenya and will do it all over again here. Pictures are worth a thousand words- see below for the magical moments in Uganda.
The A- team.
Phillip and Geoffrey
Jo and Jacinta taking plugs for the DNA extraction
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
The yield from ONE plant.
Asha (far left) and her group.
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.
We are so excited to have in our possession the very first MinIT! Big shout out to the Oxford Nanopore team for working so hard to get this to us before we head out next Tuesday. Super excited to use it in the farmers’s field to tell them what viruses and vectors are causing such huge yield loss. Stay tuned y’all.
We are gearing up for a 3 country expedition. Super excited to have Dr. Jo-Ann Stanton from University of Otago, New Zealand joining us to try out her amazing point of care devices in the field! Jo and Laura met this past March when Laura visited Genetics Otago– many thanks to Julia Horsfield and Amarni Thomas for the connection!
Dr. Jo-Ann Stanton
Laura and Jo meeting in New Zealand
Our plan is to follow-up with Asha, our farmer in Tanzania who is featured here. Her improved cassava has been in the field for 9 months and we celebrate her harvest with her and the village. True impact! We have many exciting things planned for Uganda and Kenya. In addition, we are planning to do more rapid barcoding of infected material and also more capacity building throughout. We are also awaiting a very special package from Oxford Nanopore that will make our in-field data analyses much much easier! Stay tuned for updates.