The End of my PhD Internship in Kenya – A Reflective Look Back

Over the past 3 months, I have been based in East Africa, in Kenya as part of my PhD program under the PIPS scheme (Professional Internships for PhD Students). It was here that I was given the opportunity to work on projects related to science communication, science media production and international capacity building.

For the bulk of my internship, I was in Nairobi, Kenya. It was here that I was creating an online bioinformatic and soft skill training video series. Following this, my internship ended with the organisation and running of “AfriPlantSci19” in Kilifi, a plant science training course for early-career African researchers.

The amount I have grown and developed over the past few months has been vast. I’ve been able to build both technical and transferable soft skills, many of which will serve me well with the rest of my PhD and beyond. The internship has also really opened my eyes to the possibilities surrounding a career in science communication, science media and international capacity building. I have enjoyed all three areas more than I could have ever predicted and as such, I am so grateful to have been given such an opportunity to experience them.

My gratitude extends to the PIPS program as a whole. The idea of the internship is to give us PhD students a broader range of skills and experiences outside of the lab. This in turn will help us move in to a wider range of careers and will make us ultimately more employable once the PhD has drawn to a close. I think this is a fantastic idea and I have gained an awful lot from my internship.

I’ve gained a new insight into differenent career paths away from the lab and I have developed a wide variety of skills. Examples of technical skills included videography, animation, editing and bioinformatics . Examples of soft transferable skills included
project management, communication, leadership, creativity and problem-solving skills.

The PIPS Interns

Kenya has been an incredible country with friendly people, stunning scenery and impressive wildlife. I would strongly encourage anyone to visit in the future should the opportunity present itself, it will be an experience you will not forget.

I am now back in England ready to head back in to the lab, its back to the PhD life once again. Thank you for taking the time to read this blog. A special thanks to all those who read and supported this blog post by post during the internship itself.

Back in Norwich

My PhD internship has been summarised in an articled published by the Times Higher Education (THE). If you did enjoy reading this blog or if you would like a condensed version of my time in Nairobi, please consider reading and sharing the article available at the following link – https://www.timeshighereducation.com/opinion/my-phd-internship-preparing-me-life-beyond-degree

https://www.timeshighereducation.com/opinion/my-phd-internship-preparing-me-life-beyond-degree

This may be farewell from this KenyaPIPS blog, but you can still keep following my onward PhD journey! Please do follow my Twitter and Instagram accounts to stay up-to-date with my life in the lab and see how the science is unfolding.

Twitter – https://twitter.com/dannyJamesWard

Instagram – https://www.instagram.com/dannyjamesward/

Feel free to connect with me professionally on LinkedIn – https://www.linkedin.com/in/dannyjamesward/

To all those embarking upon internships, PhDs and PIPS of their own – I wish you the best of luck and I hope my blog will prove useful or interesting to you in some way.

And so with that, I would like to say thank you once more and goodbye from KenyaPIPS2019!

Danny Ward

AfriPlantSci19 Draws To A Close

The final few days of the AfriPlantSci summer school 2019 at Pwani University, Kilifi, Kenya were upon us.

The final sessions revolved around insect-mediated disease led by Saskia Hogenhout, assisted by Roland Wouters and James Canham. After learning a little about the theory behind the science, participants went out in to the university botanical garden and plant tunnels to search for aphids. In the lab, DNA was then extracted and analysed from the collected aphids using molecular techniques practiced in research laboratories which are interested in understanding insect-mediated diseases.

Slowly but surely, the end of AfriPlantSci19 was approaching. It wasn’t over just yet however, people who had been working on their ‘concept note’ from the first week were given the chance to present their findings and get feedback on their work and ideas. Also, we had a group writing session where everyone contributed something towards the single-figure paper we wished to publish regarding transient green fluorescent protein in Amaranth. Everyone was tasked on writing a specific portion of the paper and everyone gave feedback and made alterations to the wording itself once it had been compiled. It was great to get everyone involved with something like this where we would hopefully produce a tangible output which could go on to help fellow researchers in similar regions.

The AfriPlantSci19 summer school ended with a closing ceremony featuring the Pwani University vice-chancellor where certificates, awards and plenty of gratitude were given to the participants and course facilitators.

Overall the AfriPlantSci summer school 2019 was a roaring success. I feel strongly that both participants as well as us facilitators and organisers got a lot out of the course; we all learnt a lot. It was fantastic to meet, network and form potential future collaborations with participants, all of whom were so talented, enthusiastic and passionate about science. I am sure we will all stay in contact and many of us may be working together in the near future, which I think speaks volumes about the success of this summer school. The diverse range of skills developed, knowledge of research learned and experience in the laboratory gained will help these participants in their onward careers and I am confident that we will see many success stories in the world of plant and agricultural research from individuals who took part in the course.

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)”]

AfriPlantSci19 Week 2

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).

Amaranthus hybridus

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.  

Successful transient expression of green fluorescent protein via Agrobacteria leaf infiltration in Amaranthus hybridus

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)”]

AfriPlantSci Summer School 2019 at Pwani University, Kilifi, Kenya

We had arrived in Kilifi on the eastern coastline of Kenya. Our accommodation was a little more unorthodox that most. We were to be staying on a boathouse!

The boathouse was located by the Kilifi boatyard on the water and required dinghy service to get to and from. On board were 3 bedrooms, a kitchen living area, a bathroom and a generously sized terrace area on top.

Our new home for the next few weeks

We arrived at the boatyard, said our hellos, and then we proceeded to jump on to the dinghy that we would be frequenting so much over the next couple of weeks. The 3 of us (Hans, fellow PhD student James and I) boarded the dinghy with all our luggage along with the other curious PIPS students and off we went. The dinghy driver pulled up to the houseboat and off we went. This was certainly going to be a unique experience that’s for sure.

One of my favourite aspects about the houseboat already was the incredible views of the creek from both the roof terrace as well as all the bedrooms. The scenery was stunning. The houseboat had been anchored in the creek for several years now and as such, it had formed its own mini ecosystem. It was surrounded by interesting fish, crabs and everything else where their existence was solely around the houseboat. Our own miniature reef right on our doorstep…literally!

To then get to the shore, we were able to ring a bell on the houseboat itself or phone up the dinghy driver on shift to pick us up. We made use of this the first day to try lunch at the boatyard restaurant. Our first impressions of Kilifi and our new home were great so far.

Once we had settled in and ran a few errands, we headed toward Pwani University for the first time. We were introduced to people and promptly began helping to set-up one of the lab practicals for the AfriPlantSci Summer School 2019 that was due to start the following day. Excitement was brewing, we couldn’t wait to meet the participants.

The university campus itself was a nice location, perfect for the summer school. The campus had extensive green space filled with trees, plants, flowers and some wildlife to boot.

And so here it was, the reason we were all here. It was the first day of the AfriPlantSci Summer School 2019. This was a 2 week residential course teaching early-career scientists and PhD students from Africa all about cutting-edge plant and agricultural science, helping to build capacity for their home institutions and labs while advancing their scientific skillset.  

The day started with an “ice-breaker”, a chance to meet and chat with everyone in a fun and informal session. We stood outside where the ground represented a world map. We all firstly had to stand on our respective locations from where we had come from. From here we would then move around the globe and share our local greetings with each other and to learn a bit more about that person. The aim was to try to learn as many new greetings as you could and to find out as much as you could about everyone.

From here, the workshops began. Workshops focused on building soft transferrable skills, teaching scientific concepts and helping to develop everyone as a better scientist. These were a combination of taught components and interactive segments where the students could get stuck in with applying what they had just heard about to further build upon those skills.

The following are a selection of some of the sessions students took part in.

Rose Kigathi of Pwani University kicked off the sessions, starting with a workshop on career development. This was followed by workshops from Levi yant of Nottingham University discussing the best way to formulate research questions and a chance to work a ‘concept note’ (a piece of writing such as a grant application that could be shared with the course for feedback and improvement).

Peter Emmrich from the BecA-ILRI hub in Nairobi through a John Innes Centre alliance led a session on presentation skills. I think this gave everyone a lot of food for thought. Too often we are subjected to the standard age-old ‘academic’ presentation which features hundreds of densely filled slides which are quickly glossed over, not taking in to account in experience-level of the audience. As such, many people emulate this style which is not as engaging. Instead, we were taught the value of clean sides, explaining concepts and data in an accessible manner, speaking with purpose and really forming that connection with the audience. These are all very important to make science accessible to a wider range of scientists and non-scientists.

Throughout the course, students were tasked with giving presentations of their own and they were all excellent, it was clear that everyone had taken on board a lot of the advice given in this session.  

Connor Tansley of the University of East Anglia delivered a session later in the week which focused on critically analysing a research paper in the form of a journal club. This was a good opportunity for students to learn what makes a good journal publication, and what makes for a bad one. The quality of the data and the way that it is presented was a large feature, as these are the backbone of a research publication.

Next up, it was in to the lab. This week, we were first starting off with the fundamentals of molecular biology including some DNA and RNA work from plant tissue. Many participants had never experienced any molecular biology previously and so these lab sessions proved incredibly useful.

It was good fun to help with these lab practicals as a demonstrator and it also helped build upon my scientific understanding of certain concepts while helping to develop my science communication skills.

Led by Anne Edwards and Sian Bray of the John Innes Centre, we extracted and purified both DNA and RNA from local plant samples. From here, we were able to analyse specific genetic fragments through polymerase-chain reaction (PCR) and gel electrophoresis. These are techniques frequently used in molecular biology research to amplify specific regions of genetic information, and to then visualise and interpret that information. Such fragments could then be used for further molecular biology work such as molecular cloning and transformation, both of which the students carried out.

Later in the week, we focused on the world of plant stress research. Plants and crops are grown all around the world but that doesn’t mean things are perfect. Many crop harvests are wiped out due to diseases, droughts, flooding, soil composition and pests for example. By working with seed, soil and hydroponics, participants learnt more about research techniques used to understand more about these plant growth stresses, and how we as scientists can work to improve plant life to tolerate or resist these stresses better. This is particularly important across African nations where in many parts, food security is constantly at risk due to many of these plant stresses. Yields may be inconsistent, and many peoples’ livelihoods could be easily destroyed.

Students were tasked with treating seeds to allow for germination, analysing soil composition, acid extractions of plant tissue for ion research, and preparation of hydroponic chambers for plant growth-based research.

To accompany these lab sessions, students were taught about related current research advancements and the theory behind them from invited guest lecturers and group leaders. The invitation for these lectures was also extended beyond the course with the wider university student body and as such, these lectures generated a lot of interest. It was fantastic to see such excitement and interest for plant and molecular biology-related research across campus. We heard all about cutting-edge research from Levi Yant and Silvia Busoms.

In between these sessions, we squeeze in lunch, dinner and some tea breaks. These served as excellent opportunities for students and course facilitators to really get to know each other. As a result of these informal chances to network, many future collaborations and friendships were formed. This just goes to show the value of lunch-time in science – its not just a chance to grab food, but a chance to really connect with your fellow scientists.

After a very busy first few days, we all got some time off on the Sunday to relax by the pool and spend time getting to better know the participants. It was great to meet people from various countries, cities and towns from across Africa. You could tell from each and everyone on the course, that they really did have a passion for science, and they did want to make a difference through their work. To be given the chance to work with such enthusiastic researchers and students was a privilege and it was quite clear that we had many future leaders in our midst. 

D

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)”]

Crunch Time

This week was the big editing week and the final push. It was our final week here in Nairobi and there was still a lot to do. We needed to full edit the raw footage into two professional final pilot episodes, we still had a final few things to shoot and we needed to finish of creating technical user guides for people to use to easily carry on video production once we had gone.

After many mouse clicks, various button presses and a ‘sprinkling’ of frustration, I had created a final pilot edit for bioinformatics BLAST starring Bernice. This video taught the fundamentals of BLAST searches in bioinformatics and had interactive segments where the audience could engage with the content. There were then additional exercises for the viewers to try for themselves and get feedback by posting the answers in the comment section of the video.

A ‘sprinkling’ of frustration….

We were able to fit in our final remaining filming sessions and I was able to complete the user guide as planned. Now it was time for the big final render. The video was created in multiple parts to make the editing process more manageable. In the final file, all of these parts were combined, transitions, music and credits were added and then it was all exported into a single output file.  

Success, I have a final video! Ah, but there are about 5 annoying mistakes in it – re-render time. You can go over something a hundred times in the editing screen, but you’ll always notice something not quite right in the initial render. After a few quick fixes and a few more renders, now I have a final video!

On the Friday morning, we were planning to present our work to all of the capacity development team (known as CapDev). We were the final talk of the morning following some interesting talks from researchers associated with the department.

The first talk was on the molecular characterisation of Samonella isolates from Ethiopia. The second focused on the application of digital technology to improve market linkages in drylands. The third talk before our own discussed the spatial distribution of Anthrax in Kenya. Lastly, the session ended with us presenting a bit about who we were and the project we had been working on during our time in Nairobi. This was a nice way to start to wrap things up and share our work within the department.

The fun didn’t stop there, however. Immediately after this presentation, we were invited to MC the Friday morning coffee site-wide meeting. Hans and I took hold of the microphones and led a session focusing on review and reflection in relation to peoples work. This was a lot of fun and served as another good way to wrap up our time in Nairobi.

On the weekend, we packed up our things, headed to the SGR train station and it was off to Kilifi via Mombasa, located on the Eastern Kenyan coast.

The train itself was an experience worth talking about. Some of the views outside of the windows were incredible, especially so towards Mombasa. As we whizzed past, we could see miles and miles of savannah filled hundreds of elephants going about their business. These were the first elephants we had seen since we had been in Kenya and they were impressive.

We arrived at our destination station and continued our onward journey on to Kilifi. A new chapter in our internships was about to start.

Danny Ward

[“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)”

Key personnel/contributors linked to this project:

BecA-ILRI hub (Nairobi) – Dr. Jean-Baka Domelevo Entfellner ¦ Dr. Peter Emmrich ¦ Dr. Wellington Ekaya

John Innes Centre/UEA – JIC Graduate School Office ¦ UEA Internships and Placements team ¦ Hans Pfalzgraf ¦ Danny Ward    

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]

A Fresh Start

Another week was upon as and to start off, we thought more about the branding behind the channel we would be using to upload our online training video series. Initially a few ideas were floating around. We thought hard about a suitable name, but it was tough. Either the names were somewhat lacklustre, were too ambiguous or were already taken. Eventually, we all came to an agreement with a suitable name…and a logo and theme to go with it. We opted for “Enabling Science” which would be represented with a spinning globe icon. This name and logo helped to infer that the show was more created and will target audiences from low- and middle-income countries. This is exactly what we were after. There are few channels and videos reaching this audience-base and so it made perfect sense to help deliver engaging and useful educational content made by people from the target countries themselves.

We were very lucky to have two enthusiastic and talented people who volunteered to help present our pilot episodes. We had Mwihaki and Bernice who would present a soft-skills for scientists and a bioinformatics pilot episode respectively.

Initial filming started with Mwihaki. The pilot episode was all about predatory conferences, a common problem in science. Mwihaki described what they are and how best to spot them. We thought she did a really fantastic job; her personality really came across well on camera.

After scouting around the research institute site, we managed to find a room which had the best acoustics and sound-proofing available. It was by no means perfect however and so we had to adapt on the fly when it came to recording. The room had windows located all around the top border and so some ambient noise could disrupt a take. People chatting directly outside and aeroplanes were the big issue as these could clearly be heard on the audio track. We never let this ruined a filming session however. We either waited for the noise to pass or we let people know politely that we were filming and the issue was quickly alleviated. The luxury of a fully sound-proof professional recording studio is one which many people do not have access to, especially so here in Kenya, and so it suited the project better that we had the filming location that we did. It will allow others to more easily continue the project with minimal or no budget and it can also help serve as a ‘proof-of-concept’ that such a project is a viable undertaking for other such research institutes and organisations.

This is important as video production and science communication can often be seen as having a high barrier to entry due to cost limitations. Using freeware software, low spec laptops and standard meeting rooms on campus, I hope that we will go to show that it can be done. The biggest barrier that exists, at least for us, is acquisition of hardware. This can be expensive and hard to buy in certain areas. This is where collaborations and partnerships with other research organisations and universities who do have access to such equipment is so important. Our project simply wouldn’t have been possible without the generous donation of hardware from the “ACACIA” initiative.

Science communication is a necessary element of science and research. Without this step, science is held back, and its effects are felt less so in wider society. Fostering international and national partnerships between organisations and institutes to promote science communication really can make a difference and as such, I think it would be brilliant to see more of this. 

Alongside the video filming, we also got chatting and did a few test shoots with a few people who would be interested out in helping present and produce the final video series. It was great to see such enthusiasm for continuing the video series for once we had left and it was rewarding to help those interested in presenting and science communication get an opportunity to demonstrate and grow their skills and experience. There are many talented and passionate science communicators and researchers here in Kenya. It has been a pleasure to work with some of them during our time here.

In a couple of weeks, once our time in Nairobi will have ended, it would be off to the Kenyan coast for us. This was to help organise and run the AfriPlantSci Summer School at Pwani University – a training workshop teaching early-career scientists and PhD students from Africa all about cutting-edge plant and agriculture science. Arrangements for the coast were made, we would be heading over on the relatively new ‘SGR’ train.

After another busy week, it was time to see more of what Nairobi had to offer on the weekend.

We jumped on one of the matatu buses and headed towards the National Museum of Kenya. We were hoping to learn more about Kenya itself in the museum but unfortunately, to our surprise, it was closed for renovation. We weren’t going to make this a wasted trip however; we took the time to walk and enjoy the adjacent botanical gardens. Hans and I both really enjoyed this surprise walk through the flora and nature. Not only did it provide a good bit of shade from the strong Nairobi sun, but it was also nice to experience a bit of tranquillity in the busy city.

Following this, we took a leisurely stroll through the city streets to the Kenyatta International Conference Centre (KICC). Here we went to see the city from the top. You can pay a small entrance fee to travel to the helipad at the top of the KICC tower where you are gifted with incredible 360 degrees panoramic views of the city.  

First however, we stopped off at City Market. A re-purposed aircraft hanger that is now a market that sells a wide variety of things. We unfortunately went in the wrong entrance and ended up in the meat market section. Hans is a vegetarian and so this probably wasn’t the best way to head in!

The main hanger hall was quite impressive once we were through. Small vendors and stalls sat underneath a tall roof where they were selling their wares.

Once we left City Market and arrived at KICC, we paid our entrance fee, signed in and went through a security check. From here, I was expecting a long climb up the stairs but thankfully they had a lift that took us right up to the top in a few seconds. We walked out to the lower level, then promptly climbed a small staircase to the upper helipad level. The view was stunning. You could feel the life of the city. People were working and exploring down below with Nairobi national park and Karura forest in the distance. New skyscrapers and construction projects were being built in between. It was really something, you could see the city growing before your eyes.

The KICC helipad would be one of my strongest recommendations for newcomers into the city of Nairobi, I absolutely loved it. I could have spent all day up there.

After pulling ourselves away from the incredible scenic views, we headed to a restaurant called CJs for dinner. I had a craving for a good hamburger and CJs didn’t disappoint. This was washed down with a ‘blue lagoon’ lemonade, a bright blue freshly-made lemonade that I quite happily could have drunk several litres of. Following our feast, it was on to tonight’s entertainment. We headed to a classical music concert where one of our friends was playing. Over the course of my time in Nairobi, we certainly hadn’t been deprived of live music, all of which was excellent.

On Sunday, we embarked on a mutatu bus extravaganza to get to Oloolua forest. We took three different matatus to the forest, but we made it all in one piece. Once we had arrived, we were greeted with acres of forest to explore…and curious monkeys! We weaved in and out of trees, up and down hillsides, back and forth along trails. It was surprising to see so many different environment types and habitats in such a relatively small area in relation to the size of Kenya. This helps to explain the wide diversity of flora and fauna which we were lucky enough to see in the forest.

To reward ourselves after a day of busy adventuring, we visited Stedmak, a floating restaurant located in the neighbourhood of Karen. We were served yet more tasty food complete with plenty of chapati. A perfect end to the week I’d say.

Danny Ward

[“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)”

Key personnel/contributors linked to this project:

BecA-ILRI hub (Nairobi) – Dr. Jean-Baka Domelevo Entfellner ¦ Dr. Peter Emmrich ¦ Dr. Wellington Ekaya

John Innes Centre/UEA – JIC Graduate School Office ¦ UEA Internships and Placements team ¦ Hans Pfalzgraf ¦ Danny Ward    

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]

For the Love of Chapatis

This week was another big filming week. We had worked a lot with Mwihaki last week on a predatory conferences video. This week we would be working with Bernice filming a bioinformatic BLAST video. We were recording presenter-to-camera inside shots in front of a green-screen, and outside on-location multi-camera shots. We were so fortunate to have two individuals who came across brilliantly on camera and were easy to work with.

In our small studio set-up, we would record multiple takes of lines standing in-front of a green screen for some shots and outside on-location for others. These ultimately would be edited and spliced together later in post-production

One of us would read a line aloud, then the presenter would repeat that line on camera. We did initially have a laptop which acted as a makeshift teleprompter, but we found this didn’t work as well. Unless the text is directly over the lens as with a traditional glass mirror teleprompter, the angle of the eyes looking towards the laptop is just too obvious and looks unprofessional. We tried to rectify this by having the presenters read the line off the laptop placed to the side, then say this line to the camera. What we all found is that, under the pressure of filming, this is near impossible to do consistently. Reading a sentence is one thing but trying to remember and then say that sentence perfectly in just a few seconds was just too tough. Reading aloud the lines however led to far better results and as such, we’d recommend this method to anyone trying a similar presenter-to-camera segment without a traditional teleprompter (which are usually quite expensive).

We were filming in front of a green-screen which is exactly that, a screen or sheet which is bright green. This allows the green colour to be removed and replaced through a technology known as chromakey in post-production. This green could then become a picture of video behind the presenter. In our case, the green would be replaced with a background image that we had made for the video series. The green-screen needs to be evenly and well lit with stage lights and must be relatively crease-free to allow for optimal chromakeying. Our lights were battery power LED lights and our green screen seemed to have more creases than we thought was possible, but we made it work. We used the LED lights at full power in combination with the ceiling lights and natural ambient light from the windows to allow for a better lit green screen and we tried to remove as many creases from the sheet as we could by ironing, rolling and hanging. The end result was by no means perfect, but it gave us a professional-level chromakey removal which we were happy with considering the limitations. The background was clear, and the presenter stood out well with minimal spill-over, distortion, noise or artefacts. 

During the filming process, we met with a person called David. He had previous experience with filming and video production and so he was able to offer us several useful tips and tricks. This is another thing we would recommend for others trying to produce a video series like ours. Getting the advice and possible mentorship from someone who has previous experience can really make a big difference with the final output. This helps to highlight the importance of building networks and establishing collaborations and partnerships; you never know who might be able to help.

Once we had all the multiple-takes of footage we needed, it was off to the editing suite (a.k.a. our laptops). This would be our challenge for next week, our final week in nairobi.

Now for a slight change of pace. I see this as an ample opportunity to share just how great the lunches have been. A surprising interlude for you I am sure, but such a simple thing can make a day so much better. We’ve been able to sample a wide variety of traditional Kenyan cuisine everyday at lunchtime, freshly prepared.

Some examples of my regular lunchtime feasts – bean casseroles, grilled chicken, beef stews, goat, fish, ugali (a maize/cornmeal-based white, starchy set porridge/dumpling – its quite hard to describe), mixed vegetables and greens.  

My favourite food? This award has to go to chapatis. These are flaky, buttery, dry yet oily unleavened pancake-like breads. They reminded me of a naan bread, crossed with a pancake, crossed with a tortilla, crossed with a croissant. I have never had anything like this before but wow, were they tasty! You can get something similar back in the UK from Indian restaurants, roti or paratha, but they aren’t quite the same. To get the real deal, you have to head out to Kenya.

It’s also very difficult to make yourself. There is a real art to it. It requires a good technique with several waiting periods. For many who make it, it will have the wrong texture entirely. The art of chapati-making is not to be under-estimated.

Overall, chapatis are great and you should definitely try it, should the opportunity arise!

With that, it is time to draw this blog post to a close. Thank you for taking the time to stop by and give this a read!

Danny Ward

[“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)”

Key personnel/contributors linked to this project:

BecA-ILRI hub (Nairobi) – Dr. Jean-Baka Domelevo Entfellner ¦ Dr. Peter Emmrich ¦ Dr. Wellington Ekaya

John Innes Centre/UEA – JIC Graduate School Office ¦ UEA Internships and Placements team ¦ Hans Pfalzgraf ¦ Danny Ward    

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]