Uganda | MinIT | Sarah | Power

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.

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Naomi’s cassava- 9 months later. IMPACT.

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.

Asha/MinIT- the mini supercomputer/Lab under a tree

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.

Asha:

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.

 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.

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.

We are now in Uganda and going to sit with Dr. Titus Alicai’s team to plan our next lab under a tree.

Yasss! The MinIT has arrived- DATA, DATA, DATA.

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.

Tanzania, Uganda and Kenya- Round 4

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!

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.

Update from Njombe, Tanzania!

Report from Dr Ndunguru in Njombe, Tanzania : 107 farmers turn out to harvest the cassava variety Mkombozi which does well at low temp (16-18C) and is resistant to the CMD in the area. Massive yields and farmers are so happy. Impactful science

The first time nanopore has been used to sequence plant viruses!

A big day for the team! Our preprint is now available- Real time portable genome sequencing for global food security

‘For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers crops in sub-Saharan Africa.’

Bleeding edge technology- East African scientists leading the charge to help farmers.

Updates from the CVAP team!

  • Our TZ node won a prize at the World Government Summit Awards in Dubai UAE for applying Nanopore sequencing for smallholder farmers – Congrats. The team was on Tanzanian morning TV.
  • We successfully trained scientists at University in Eldoret and JKUAT on bioinformatics and running the MINion. Many thanks for the Crawford Fund for supporting the work and also the 69 people who donated to our crowdfunding page!  Please see Professor Elizabeth Njenga and Dr. Jayne Binot describing the course and what it means to the team in Kenya [sorry about the wind, I’m not a video pro]

  • And we are excited to be invited to give a talk at the London Calling Meeting in May! We will see you all there!Screen Shot 2018-03-27 at 12.45.18 PM
  • Special videos to our crowdfunding supporters: (we promised we would shout their names form the mountain in Kenya) .

Kenya- WE HAVE DATA!

A very challenging two weeks but we did it, we made it. We have data for 12 cassava plants – some showing symptoms and some were not.

Dr. Naomi Bissem’s tweet says it all:

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Details: We learned A LOT on this trip.  Shipping was a challenge.  We discovered FedEx froze our flow cells- and this is no joke.  It ruined all the flow cells but luckily Nanopore sent us  new flow cells (as per the suggestions below) via DHL.  We learned that that little gray pad on the flow cell is super important for temperature control (thank you twitter for helping real-time). We learned that the priming of the flow cell is important and if your library isn’t going in the spot-on port to add more priming mix to the flow cell to get things moving.  We learned that power is not a given.  We should have had a battery back up on the machine we were using.  We also learned once (actually 3 times) when the power goes off you can quickly start the machine running and it keeps sequencing.

 

The team: I also learned the team from University of Eldoret has some serious tenacity. They boarded a bus Thursday night upon hearing we received the shipment- drove 6 hours- and we began preparing the library Friday morning, started the run (3 times with the power cuts) and then got back on the bus and drove back to Eldoret. In addition, Charles Kayuki, from Mikocheni Agricultural Research Institute (MARI)  joined us for the second week at JKUAT – he was a valuable resource as he has completed runs on his own in Tanzania. Anders Savill in Australia was on-call and dealing with us at all hours- thank you Anders. Plus Angelica and Zoe from Nanopore were amazing at facilitating so many things on that end. Finally, the JKUAT team lead by Professor Ateka- was invaluable, fierce, dedicated and downright amazing. Elijah Ateka, Brenda Muga, Sam Maura, and Benson – Asante Sana for relentless fight to get this test done.

 

The farmers: Rose, from Eldoret had CMD symptomatic plants.  We tested her plants and Prof. Ateka provided her the virus resistant cassava. The team from Eldoret took the cuttings to her and she is on her way.  We also visited two other farms, Mama Maina and Mr. Lungo Mutunga’s farm in Thika, Kenya. We are awaiting the results of the run and will advise them later this week.

 

Prison Visit: While we waited for the flow cells to arrive we visited Langata Women Maximun Security Prison to conduct a cassava pest and disease training for inmates and farm managers.  We feel very strongly empowering all farmers is at the core of our movement. This was a very special day and the team plans to go back and plant virus-free cassava with the inmates on the prison farm.  Outreach matters.

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