The second week of AfriPlantSci 2019 at Pwani University, Kilifi, Kenya was upon us. It was another jam-packed week filled with a wide range of workshops, lectures, laboratory practical sessions and group events.
This week started with multiple workshops on scientist soft skills as well as a gender in research session from AWARD (African Women in Agriculture Research and Development). The AWARD session was led by Monica Kapiriri. This got participants thinking about the importance of gender and how to best account for this factor when conducting research. Isabel Diez Santos from the John Innes Centre complemented this talk later in the week with a talk on gender inequality in science. Together, these two sessions have better armed participants at understanding the importance of gender in science and research, and how it can affect the data collected.
The scientist soft skills sessions led by Brande Wulff and Cristobal Uauy (both from the John Innes Centre) ran through the early part of the week. These covered a wide range of areas. A selection of which included skills relating to presentations, writing, and career applications and interviews.
Brande Wulff and Cristobal Uauy would also both go on to speak about the exciting research coming out from their labs as part of the guest speaker lecture series.
As the week moved on, we ventured in to the world of CRISPR (a gene editing technique) and transgenic plants with Wendy Harwood from the John Innes Centre, assisted by Connor Tansley of the University of East Anglia.
Students learnt the underlying theory behind such molecular technology, and then got to apply this knowledge at the lab bench and at the computer.
Students received hands-on practice with creating stable transgenic crops. This is an important area in current agricultural and plant research which aim to better understand and improve crops.
Two main methods were explored. The first was transformation of barley using Agrobacterium (using a specialised bacterial strain to change specific parts of the Barley’s genetic information). The second was transient expression of a green-fluorescent protein from jellyfish in a plant leaf. These are both useful techniques which are important for understanding the genomes of plants and crops, and the molecular detail associated with the individual gene systems. This understanding is then applied to help improve crops and plants to give farmers more options should the improvement be successful. Examples include crops which are more tolerant to drought, floods and more resistant to diseases. In nations and areas where food security and crop yields are often low (particularly in low and middle-income countries), these advancements can have a large impact on quality and length of life.
The transient expression of green-fluorescent protein in a plant leaf was originally supposed to be in a species known as Nicotiana benthamiana. This is often considered one of the standard plants for such work, especially so in Europe, North America and Asia. Despite our best efforts however, we could not get N. benthamiana to grow in such humid conditions here on the Kenyan coast. This is an issue many people have faced before and will continue to face in similar humid regions. As such, this greatly limits the accessibility to such research techniques in humid areas where humidity control often isn’t feasible.
So that we could still do the protocol, we thought we would try a different plant. We opted for Amaranth, a plant that is plentiful here in Kenya. We didn’t know if this plant species would work as successful transient expression in Amaranth has never been shown before (to the best of our knowledge).
To our surprise, white Amaranth (Amaranthus hybridus) seemed to work! Students, working together had been able to successfully express green fluorescent protein in Amaranth – a world first, we think. Naturally, we were ecstatic to see this result as this could open up this technique to humid low and middle-income countries where humidity control often is not implemented.
We did have to repeat this to verify with appropriate controls and to get nicer images, but the results were promising. Based on the results, we decided that is would be a good idea to publish this finding as a single figure paper where the students themselves would help write the manuscript should the data hold up. It seemed like younger, thinner Amaranth leaves expressed green fluorescent protein well while larger leaves or leaves of a purple Amaranth species did not.
Now it was into the computer lab. Participants were taught how to design sgRNA (guide RNA) constructs used in CRISPR targeting, implemented via golden gate cloning. For this, a specialist freeware software (Benchling) was used which everyone would be able to use and access after the course had finish.
Towards the middle of the week, one evening at sunset, we all got the chance to go on a dhow boat trip. This is a traditional sailboat used on the east coast of Kenya which came about due to influences from Arabia and India in the past. We sailed through the Kilifi creek enjoying the nature and the stunning sunset. This was a memorable experience; I certainly had never been on anything like this before. To see kites roosting in the trees, fish swimming underneath all complemented with incredible colours from the sunset was really something.
Towards the end of the week, it was time for my and Hans’ own session. We delivered an evening workshop on DIY ‘hackster’ technology and Biomakers. This is a rising movement of using low-budget modular electronics and microcomputers to build solutions to problems, usually applied to research problems. Such technology and innovation are perfect for many low and middle-income countries where access to expensive commercially produced equivalents either doesn’t exist or is not economically or logistically feasible. This brings the power to the researchers, who can custom-build equipment, tools or solutions to problems themselves.
This was an interactive session where we first introduced the concepts and theory to people, and then gave them the opportunity to get thinking themselves. We had a discussion session where participants would come up with real-world problems that, if they could solve, would make a difference to their research or their community. All the ideas where absolutely excellent, we were really impressed with the thought-processes going on.
Following this, it was then time to start designing a solution. We started by thinking about all the considerations and factors needed which would then lead into a short plan for how to turn it in to a reality.
This session wasn’t just a learning exercise, students did have the chance to take what they had done in the session further. Here we gave people details of the Norwich Biomakers and OpenPlant. These are groups of people with varying areas of expertise who could take these ideas, working with the students, to turn these projects in to reality by using funding available for exactly this purpose.
Overall, the response from this session was incredible and it was a lot of fun to deliver. You could really see the excitement in people’s eyes when they realised how revolutionary these tools can be and how they could directly impact their own research and their own communities.
The end portion of the week, students got to learn more about the world of bioinformatics. Diane Saunders and Burkgard Steurnagel of the John Innes Centre led sessions on applying Linux command line for field pathogenomics (using computer code to better understand and treat crop and plant diseases). Despite the steep learning curve typically associated with coding and command line, the participants really got the hang of things quickly. Soon, they were moving around the Linux command line interface, handling data and then processing that data to produce graphs and figures. Everyone did incredibly well and picked things up rapidly, especially given that there was virtually zero coding or Linux experience from the participants prior to the course. Bioinformatic analyses and computational handling of data is growing ever more important as technology advances and datasets grow bigger. The skills learnt from these workshops can either be used directly to process students’ own datasets or they can be used to learn other related aspects of bioinformatics and coding.
The end of this week ended with an excursion to the coastal town of Watamu via Malindi. We all got the chance to do a bit of shopping to buy some souvenirs before we headed to the crab shack for lunch.
Following this, we explored Gedi ruins, a historic site where we learned more about the building which once occupied the site as well as local Swahili culture associated with it. This was an enjoyable day and was a nice way to get to know the participants further.
Danny Ward
[Key personnel/contributors linked to this project:
Pwani University (Kilifi) – Dr. Santie de Villiers ¦ Dr. Rose Kigathi
John Innes Centre/UEA – Dr. Tilly Eldridge, Chris Darby, Angela Payne, Dr. Jodi Lilley, Matt Heaton, JIC Graduate School Office ¦ UEA Internships and Placements team ¦Hans Pfalzgraf ¦ Danny Ward
BecA-ILRI hub (Nairobi) – Dr. Jean-Baka Domelevo Entfellner ¦ Dr. Peter Emmrich ¦ Dr. Wellington Ekaya
We would like to extend our gratitude to all those listed, along with all others, who contributed and supported towards this project in various capacities – this wouldn’t have been possible without your help
“This work was supported by the Norwich Research Park Doctoral Training Partnership (NRPDTP), by the Biotechnology and Biological Sciences Research Council of the United Kingdom (BBSRC) through the BBSRC-STARS grant with reference BB/R020272/1 awarded for the ABCF Bioinformatics Community of Practice, and by the BecA-ILRI Hub through the Africa Biosciences Challenge Fund (ABCF) program. The ABCF program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida)”]
Kenya PIPS 2019 