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.


NO! The flow cells were dead. Suggestions for labeling the box.

Ok, so we had ZERO pores on our two flow cells.  We suspect our flow cells were frozen in customs. Why? 1) It’s the first time they have been shipped here (so these items were not in the Kenyan customs officials database) and 2) We feel the labeling on the Nanopore box needs a bit of improvement when shipped to Kenya (and E. Africa in general). So here are our suggestions:

On the BOX:

1.     Ship separate boxes for each temperature (customs can’t open the box to separate).

2.     In large font on the box  “Store Freeze -20C” OR

3.     In large font on the box  “Store Fridge 2-8C”

4.     Highlight the temperature in the paperwork
5.     Put recipients phone number on the outside of the box

Paperwork taped ON THE BOX:

1.     Clearly state the material is not poisonous or for human consumption

2.     Clearly state it has no resale value and is for research only
We have another shipment on the way. Let’s hope we get it quickly and with new labelling.

We got the goods!

Elijah is a star!!!  He freed the box from customs. And now we are on our way. We visited Rose – a farmer here in Eldoret, Kenya  she has a small plot of cassava and we suspect it is infected  soon we will know!

The team here at University of Eldoret has kindly hosted us in their biotechnology lab for the DNA extractions.

Tomorrow we do the library prep & start the nanopore run!

Customs- the struggle is real

Our things have been stuck in customs for 2 weeks.  Elijah has driven 5 hours one way (back to Nairobi from Eldoret) and is planning a sit-in at the customs building to get our supplies.  Then he and Benson are driving another 5 hours back to Eldoret!  The shipping struggle is real. If anyone has connections, solutions, ideas about making this easier please get in touch.  We are determined to do this on Thursday with the class at University of Eldoret. Wish us luck.

Kenya prep continues!

2 weeks left before we leave.  The shipment from Nanopore is on it’s way to Prof. Ateka in Kenya.  We have ordered two of the R9.4 flow cells – to go with the 1 new Rapid Barcoding Kit RBK004. It was advised to use the 9.4 flow cells instead of the 9.5 so that is what we will do!  Also the Anders Savill has been preparing the MacMini we are taking with us to do the work and then leave at JKUAT.  The third time around things are falling into place.  It’s all very exciting.

Laura and CVAP win Gifted Citizen Prize for 2017!

Dr. Laura M Boykin has won the international Gifted Citizen Prize for 2017 in Puebla, Mexico as part of the La Cuidad de las Ideas Festival awarded November 18, 2017. Each year the Gifted Citizen Prize is given to the best social entrepreneurship project that has the ability to benefit 10 million people over the next six years. This international prize honors the passions of those that seek to develop real solutions to humanity’s most pressing issues. Those that are recognized with the Gifted Citizen Prize are celebrated for their ability to defy contemporary paradigms and generate pragmatic answers to the most urgent global needs. This year there were over 1700 applications and the top 32 were invited to Mexico to compete in the competition and Dr. Boykin came out on top and won the prize of one million pesos.

She presented the team’s latest project, The Cassava Virus Action Project, which is a network of researchers, farmers and industry people, collaborating to use a pocket DNA sequencer to improve the management of cassava viruses in east Africa. For the first time in September 2017, farmers struggling with diseased cassava crops can take immediate, positive action to save their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA analysis device.  The team now plans to expand the project; 800 million people worldwide depend on the threatened cassava crop. The project aims to reduce the risk of community crop failure and help preserve livelihoods.

The CVAP team will use the prize winnings to launch a node of the project in Kenya in early 2018 and the overall goal of the project is to scale up across the continent and touch the lives of millions of farmers in east Africa.