Cabot Institute blog

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Wednesday, 31 August 2016

Saying goodbye and reflecting on lessons from the field

Last week I said goodbye to the National Crops Resources Research Institute (NaCRRI) where I have spent the last three months learning about Cassava brown streak disease (CBSD). I’m currently in the second year of my PhD at the University of Bristol, where I’m researching how CBSD viruses cause symptoms, replicate and move inside plants.

Cassava is a staple food crop for approximately 300 million in Africa. However cassava production is seriously threatened by CBSD, which causes yellow patches (chlorosis) to form on leaves and areas of tubers to die (necrosis), rot and become inedible. CBSD outbreaks are currently impacting on the food security of millions of cassava farmers in east Africa and it appears to be spreading westward, threatening food security in many countries.

I decided that I wanted to experience the problem for myself, see the disease in the field, meet the farmers affected and understand the different solutions. I am so pleased that I decided to visit NaCRRI; a government institute, which carries out research to protect and improve production of key crops, including cassava. The focus is on involving farmers in this process so that the best possible varieties and practices are available to them. Communication between researchers and farmers is therefore vital, and it was this that I wanted to assist with.

When I arrived I was welcomed so warmly, and was immediately part of the team. The root crop team leader Dr. Titus Alicai came up with a whole series of activities to give me a real insight into CBSD. I was invited to the field sites across Uganda, where I got to see CBSD symptoms in the flesh! I assisted with the 5CP project, which is screening different cassava varieties from five East and Southern African countries for CBSD and Cassava mosaic disease (CMD) resistance across different agro-ecological zones. I helped to score plants for CBSD symptoms. The researchers thought I was bit strange, getting very excited and taking lots of photos.

Main insight: complex and dynamic CBSD situation 


The main insight I’ve gained is that the situation is both complex and dynamic. Different cassava varieties respond differently to CBSD infection, some plants show strong symptoms on the leaves and nothing in tubers, and other varieties show the opposite. Symptoms also depend on environmental conditions, which are unpredictable.

The whiteflies which carry viruses are also complex, and are expanding into new areas and responding to changing environmental conditions. There are also different viral strains found across different areas, and viral populations are also continually adapting.

Learning about solutions


It has been fascinating to learn how NaCRRI is tackling the CBSD problem through screening different varieties in the 5CP project, breeding new varieties in the NEXTGEN project, providing clean planting material and developing GM cassava.

Saying goodbye to new friends: Dr. Titus Alicai (NaCRRI root crops team leader), Phillip Abidrabo (CBSD MSc student) and Dr. Esuma Williams (cassava breeder)

And there’s the human element…


In each of these projects, communication with local farmers is crucial. I’ve had the opportunity to meet farmers directly affected, some of whom have all but given up on growing cassava. I’ve learnt a lot about how NaCRRI is constantly engaging farmers and involving them in solutions to the CBSD problem.

Challenges 


Communicating has not been easy for me, as there are over 40 local languages. I’ve really had to be adaptable and learn from those around me. For example, in the UK we like to email the person sat next to us, whereas in Uganda you really have to talk to people to hear about what’s going on. This is all part of the experience and something I’m hoping to bring back to the UK!

I’ve had some funny moments too, during harvesting the Ugandans couldn’t believe how weak I was. I couldn’t even cut one cassava open!

Real world reflections


I’m going to treasure my experiences at NaCRRI. The insights into CBSD are already helping me to plan experiments, with more real-world applications. I can now see how all the different elements of the disease (plant-virus-vector-environment-human) join up and interact, something you can’t learn from reading papers alone!

Working with the NaCRRI team has given me the desire and confidence to collaborate with an international team. I’ve formed some very strong connections with people here and hope to have discussions about CBSD with them throughout my PhD and beyond. This will help make our research more relevant to the current situation. Above all, I’ve learnt the importance of getting out of the lab to experience and learn from what is happening in the field.


Thank you!


I would like to thank: Dr. Titus Alicai for welcoming me into the NaCRRI team and providing me with so many valuable experiences; the whole of the NaCRRI team for their generosity; my supervisors: Prof. Gary Foster and Dr. Andy Bailey for supporting my trip and my funders: Biotechnology and Biosciences Research Council, the Cabot Institute (University of Bristol), the British Society for Plant Pathology and the Society for Experimental Biology for supporting my internship.

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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series:  

Paying a visit to the Plant Doctor in Uganda

Two weeks ago I organised a visit to a plant clinic in the Mukono district of central Uganda. The plant clinics are run by district local government extension staff with support from CABI’s Plantwise programme and offer a place where farmers can bring crop samples to get advice on how to prevent and cure diseases.

Why does Uganda need plant clinics?


It’s estimated that smallholder farmers loose 30 – 40% of their produce to plant health problems before harvest, which threaten food security, income and livelihoods. Ugandan farmers suffer heavily from pests and diseases, including maize stalk borer, wheat rust, banana bacterial wilt, coffee wilt and cassava viral diseases. The situation is always changing, as outbreaks of disease emerge and persist across the country.

Getting access to information is a challenge in rural settings. Often smallholder farmers have very little contact with extension workers and have no way of diagnosing diseases or finding solutions. The plant clinics provide farmers with access to current information to help make rapid, informed decisions that will save their crops. There are now over 191 plant clinics across Uganda and the aim is to have at least one plant clinic in every sub-county by 2020.

On the day…


I was picked up by Benius Tukahirwa an Agricultural Inspector from the Ministry for Agriculture Animal Industry and Fisheries (MAAIF). We drove to Mukono to meet Mukasa Lydia, who’s been a plant doctor for eight years! She has a wealth of plant health knowledge and is in touch with the local community.

When we arrived, we set up a base in the heart of the smallholder village of Nakifuma, Kimenyedde Sub-county, Mukono district. Local farmers find out about the monthly plant clinics through radio announcements and word of mouth. Before long a set of five farmers had arrived with their sickly plant samples. I was told that normally the plant clinics have around 20-50 visitors in a day. On this day the turnout was low as the rains had just started so farmers were in the field planting.
Local famers gather round to hear advice from the plant doctors

Patient 1


The first patient to be examined was a passion fruit branch with “woodiness” viral disease, which causes fruit to become misshapen, woody and inedible. The farmer was told to remove and destroy the infected plants immediately to prevent spread to other plants.

Patient 2


The second patient was a coffee plant with coffee berry disease, a fungal disease which causes coffee berries to rot, turn black and mouldy. The farmer was advised to immediately remove and destroy infected branches, and to apply copper based fungicides to the remaining plants.

Patient 3


The third patient I was very familiar with. The farmer had brought a cassava branch with Cassava brown streak viral disease, the leaves showed characteristic yellow patches and tubers were spoiled and inedible. The plant doctors advised him to get hold of some clean, virus-free planting material from a tolerant variety such as NAROCASS 1, NASE 14, NASE 19 from the government.

Plant patients: passion fruit with woodiness disease (left), coffee wilt disease (middle) and cassava brown streak disease (right)
The farmer: Kayondo Edrissa told me:

“I have been growing cassava for 20 years. I was hard hit in the 90’s by Cassava mosaic disease (CMD), which totally destroyed cassava crops and caused widespread famine. Since the release of CMD resistant varieties people had begun relying on cassava again. But now these varieties have been overcome with Cassava brown streak disease. I’m not going to plant cassava until I get hold of a variety which can resist the disease. Cassava is the real food which can keep our houses going so we really need a solution.”

After the crops were diagnosed, the plant doctors gave clear instructions for how to prevent or cure the diseases in the local language. These instructions were also sent as text messages to the farmers’ phones. Information and images of the diseases were also uploaded to the Plantwise Knowledge Bank so the government can track and respond to outbreaks. There was a challenge in getting a strong enough internet signal to upload the reports.

We then took a tour of Kayondo’s small-holding where we discovered lots of other problems, including a cassava plant with: CBSD, CMD, bacterial wilt and green mites! I was surprised at how many different plant diseases the farmers are facing. The visit helped me to recognise the importance of the clinics; they offer a meeting point for farmers to learn and communicate with each other and trained extension works about similar problems they are facing.

I would like to thank Plantwise for allowing me to visit the clinic, I had a very informative day!

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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series:  

Thursday, 18 August 2016

Taking basic research to application: Using light quality to improve herb growth

Coriander has a distinctive flavour and is popular in dishes such as curry. (Image By Deeptimanta (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons)
Coriander is the UK’s top-selling culinary herb, an industry worth £18 million a year. However, maintaining high standards of product quality is expensive and can lead to lots of plants being rejected before they make it to supermarket shelves. One of the key objectives for the potted herb industry is the production of compact plants with dark green leaves, but the plants that consumers end up with often do not conform with this ideal and can appear leggy and weak.

Plants compete for light by growing taller


Plants go to extraordinary lengths to maximise their light capture for photosynthesis. When plants grow close together however, they compete for resources and one resource that becomes limited in closely spaced plants is light due to mutual shading.

Shade has a negative impact on a plant’s health as it limits the light that a plant can use for photosynthesis. But unlike animals, which can move to new areas once space, water or food becomes limited, plants are immotile and have evolved unique strategies to compete for and maximise light capture. Chief among these is the shade avoidance syndrome. Incredibly, plants anticipate that they are at risk of being shaded even before they actually are shaded through the detection of local light quality – the depletion of red and blue light and the relative enrichment of longer wavelengths of light due to the absorption and reflection properties of vegetation. The shade avoidance syndrome is triggered in response to this change in light quality and the most dramatic changes in plant form involve the elongation of stems and the raising of leaves so as to move light capturing organs into sunlight.

Elongation does have drawbacks however – resources are diverted away from seed, chlorophyll and leaf production; there is also an increased risk of lodging (where plants fall over due to over-elongation making them unable to support their organs), which puts a limit on how densely we can plant crops before they over-compete with each other and it impacts yields.

UV-B suppresses elongation


On the other hand, plants have mechanisms in place to prevent over-elongation. These are often related to light-quality as well and one such mechanism is the sensing of UV-B wavelengths.

Classical Ultra-Violet research on plants has focused on the damaging effects that this shorter wavelength, higher energy light can have on DNA, or cell structure through production of reactive oxygen species. These UV-B wavelengths are beyond our visible range, but plants have specific photoreceptors that can detect UV-B and trigger a signaling cascade that will lead to the accumulation of sun screening compounds as well as architectural changes. Indeed, it is now clear that the plant responses to UV-B are not only a reaction to UV-B damage, but also a specific response to the sensing of UV-B (read more on this on the UV4Plants society website).

A finding that emerged from our laboratory in Bristol was that the elongation that plants exhibited in crowded conditions could be suppressed with the addition of UV-B to their light conditions (Hayes et al., 2014). UV-B is a component of direct sunlight, so an interpretation of this adaptation is that plants use UV-B as a signal that they are in direct sunlight and hence no longer need to elongate to escape shade.

Applying our research to the glasshouse


Armed with this new knowledge of plant responses to light, we are collaborating with a major potted herb grower to improve their product quality. A problem with glasshouse grown coriander in the winter months is that they grow long and spindly. Often these herbs are planted densely with around 60 seedlings per pot - conditions that are conducive to shade avoidance. Short days and cloud cover during winter further contribute to over-elongation. To compound this, many materials used in glasshouse construction such as glass or clear acrylic filter out UV-B radiation. Thus, plants growing in these conditions are no longer receiving the UV-B brake on elongation that they would be if they were growing outdoors. If we restore this brake by using artificial UV-B light sources then we could solve this problem. We’ve started trialing UV-B treatments this summer and early results look promising. However, we need to wait until winter to collect our most informative data as in summer, with bright and long days, coriander plants grow far more compact than in winter.
Both pots were planted at the same density, the coriander on the left were grown in normal conditions while the coriander on the right were supplemented with UV-B radiation.
Hayes S, Velanis CN, Jenkins GI, Franklin KA. UV-B detected by the UVR8 photoreceptor antagonises auxin signalling and plant shade avoidance. Proc Natl Acad U.S.A. 2014. 111(32):11894-9

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This blog is written by Cabot Institute member Donald Fraser who is a PhD student in the Department of Life Sciences at the University of Bristol, he is studying plant responses to light and the circadian clock.
Donald Fraser



'Back in buzziness'

Awareness of the plight of bees and other insect pollinators, both across the UK and globally, has grown in recent years. One of the main contributing factors is habitat loss and the decline in flowers that provide nectar and pollen, which are vital resources for pollinators. This was highlighted by research conducted by Mathilde Baude and colleagues from the University of Bristol, which featured on the cover of the journal Nature this February (Baude et al., 2016).
Image courtesy of Nature.
Facilitated by generous support from the Alumni Foundation and a Grow For It Award grant, a group of students at the University of Bristol initiated a project to address this issue. Using recycled scaffolding planks from the Bristol Wood Recycling Project, they constructed two raised beds to be sown with a highly diverse mixture of native wildflowers.
Raised beds created at the University of Bristol behind the Biomedical Sciences building using recycled scaffolding planks and native wildflowers.
Get Bristol Buzzing assisted in selecting the seed mix, which is made up of annuals and perennials of thirty-seven species (including some rare species). When complete, the planters will create over 30 m2 of rich urban pollinator habitat.

In June 2016, student volunteers prepared one of the planters with topsoil and recycled construction material from the local area. The meadow, which occupies a previously open concrete space behind the Biomedical Sciences building, is in now in bloom and buzzing with bees.
Next year, a group of student volunteers will prepare the remaining bed, ready for the summer. There are also plans to organise other events and workshops to continue to raise awareness amongst students, while sharing information on practical ways in which individuals can contribute to creating more pollinator habitat. Student volunteers will also be responsible for the ongoing maintenance of the beds.

The diverse meadows not only create habitat for pollinators and other insects, but also provide food for seed-eating birds and shelter for small animals. As well as promoting biodiversity within the campus, the meadows are sure to contribute positively to the wellbeing of staff, students and members of the public who use this space.
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This blog is written by Harry Wells, from the Bristol Hub, a student-led group offering practical volunteering, skilled placements, project incubation and events to help you shape a better world.

Olympic opening ceremony leaves some feeling green

For the first time in South America, the ‘greatest show on earth’ opened with a Brazilian bang last Saturday. The ceremony was a colourful celebration of the diversity of Brazilian culture complete with 50m long animated microbes, Amazonian dancers and pop-up favelas. As the BBC’s Andrew Cotter (slightly awkwardly) remarked ‘Beijing was grandiose, London was smart. This is going to be cool’.

Somewhat to my surprise, intertwined with the samba and sparkles the ceremony carried a strong environmental message, showing the world that the diving pool isn’t the only thing with a hint of green in Rio. It was apparent that the organisers planned to tackle the environmental concerns around the most recent Olympics head-on by brazenly exhibiting Brazil’s environmental conscientiousness rather than its negligence. As the ceremony unfolded, this seemed to sit a little uncomfortably against the backdrop of the polluted waters of Gunanabara Bay, which reportedly have resulted in several competitors contracting illnesses.
This is an easy thing to bash from the comfort of our keyboards and credit should be given where it is due. The Brazilians have done something that no country has done before. They had the world’s spotlights on them and instead of producing a nothing but a stream of outlandish pyrotechnics and expensive set design, they took the opportunity to speak directly to the globe about one of the biggest challenges facing humankind. Whatever the motive, this must be a good thing, surely? They screened a film about the causes and effects of sea-level rise and coupled it with stunning footage of the amazon in all its natural beauty. They also gave each competitor a seed which will be planted to form a forest as a legacy of the Rio Olympics.
A Flor e a Nausea by Carlos Drummond de Andrade 
“A flower has sprouted in the street
Buses, streetcars, steel stream of traffic: steer clear!
A flower, still pale, has fooled the police,
it’s breaking through the asphalt.
Let’s have complete silence, halt all business,
I swear that a flower has been born
Its colour is uncertain.
It’s not showing its petals.
Its name isn’t in the books.
It’s ugly. But it really is a flower.
I sit down on the ground of the nation’s capital at five in the afternoon
and fondle with my fingers this precarious form.
It’s ugly. But it’s a flower. It broke through the asphalt, tedium, disgust, and hatred.”
Amongst this, they interwove the poem ‘A Flor e a Nausea’ (Flower and Nausea) by Carlos Drummond de Andrade, which was read by our own Dame Judy Dench. The Portuguese and English recitals rolled into each other as the poem was read out. Married with film of the streets of Rio it expressed both the fragility and resilience of nature amongst the polluted artificial environment. The decision to end on a poetic note was a good one in my opinion, providing a more uplifting conclusion to the climate change-chunk of the proceedings. I came away feeling hopeful that the world might have taken heed and we may see some good come out of it.

This feeling of excitement didn’t last long. Looking through the twitter reaction to the ceremony I can’t help but feel a little frustrated. The most animated response were reserved for Brazilian model Gisele Bundchen’s (albeit impressive) catwalk across the stage and the muscled Tongan flag bearer who was so oiled it would put Dominos pizza to shame. The message of global unity in the fight to prevent irrevocable environmental devastation paled into insignificance against his shiny torso. It seemed that people, in the UK Twittersphere at least, are a little bored of hearing the climate change rhetoric.

Perhaps even more frustrating was the media reaction from some outlets…  I suppose we should be happy at the use of the word ‘lectures’ rather than ‘lies’. Small victories.

In other coverage, the green-theme was simply ignored. The BBC write up lacked even one mention of the words ‘climate’ or ‘environment’: clearly the 11,5000-strong forest being built as the legacy of the games was totally irrelevant compared to Pele’s kidney troubles and the presence of Russians in the stadium.

Still, there are lessons to be learnt everywhere and maybe this wasn’t the best location for this message to be broadcast.  Perhaps the irony of Brazil’s environmental damage and the hypocrisy surrounding a lot of what the games entail was too much for some to bear:


For others, the focus on climate was seen as ‘green-washing’ technique to try and mask the social inequality that is reported across Brazil. Coupled with political turbulence and accusations of corruption, many believe the Olympics games are bad news for the country full stop.

Whatever the answer is, I believe that this was a positive step forward in global climate change acceptance. On a stage that is meant to celebrate some of the greatest achievements of humankind we were brave enough to highlight our failures. With the closing ceremony around the corner, let’s hope it doesn’t get forgotten amongst the excitement of scandals, medals and world records.

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This blog is written by Cabot Institute member Keri McNamara, a PhD student in the School of Earth Sciences at the University of Bristol.
Keri McNamara


Tuesday, 16 August 2016

Breeding cassava for the next generation

Last week I helped to harvest and score cassava tubers a breeding trial at the National Crops Resources Research Institute (NaCRRI). The trial is part of the NEXTGEN Cassava project which applies genetic techniques to conventional breeding and aims to produce new varieties with Cassava brown streak disease (CBSD) and Cassava mosaic disease (CMD) resistance.

Why cassava and what’s the CBSD problem?


Approximately 300 million people rely on cassava as a staple food crop in Africa. It is resilient to seasonal drought, can be grown on poor soils and harvested when needed. However cassava production is seriously threatened by CBSD, which can reduce the quality of tubers by 100% and is currently threatening the food security of millions of people.
Cassava brown streak symptoms on tubers

Crossing cassava from around the world


Cassava varieties show a huge variation in traits including disease resistance. The NEXTGEN Cassava project has crossed 100 parent plants from Latin America with high quality African plants to produce new improved varieties, with higher levels of CBSD and CMD resistance. Crossing involves rubbing the pollen from one parent variety on to the female flower part (pistil) of the second parent variety to produce seeds.

Cassava flowers used to cross different varieties

Cutting back on time


The process is not easy. The complex heritability of traits in cassava means that many plants have to be screened to identify plants with the best traits. To cut down on this time, researchers from Cornell University sequenced the DNA from 2,100 seedlings and selected plants containing sequences linked to desirable traits.

Screening for resistance


These plants were transferred to field site in Namulonge, where there is a high level of CBSD, making it easier to spot resistant plants. After 12 months the tubers were dug up and cut into sections. Each root was scored for the severity of CBSD. Plants which  show no disease symptoms have now been selected for the next stage of breeding. Eventually varieties will be tested for their performance at sites across Uganda and given to farmers for their feedback.

We harvested and scored tubers for Cassava brown streak symptoms. I then tagged disease free plants for selection!

Time to harvest!


Alfred Ozimati is managing the breeding  programme
I helped to score and tag plants, it was hard work! I was impressed by the stamina of the workers who harvested from 8 am until 3 pm without a rest. I was struck by the mammoth task of breeding cassava for so many traits and by the programme manager Alfred Ozimati’s determination to get the work done as quickly as possible. Alfred is currently a  PhD student at Cornell University; he kindly offered to answer these questions:

What are the challenges of conventional breeding and how does sequencing help to address these?


Typical conventional breeding cycle of cassava is 8-10 years before parents are selected for crossing. The sequencing information allows a breeder to select parents early at the seedling stage, allowing more crossing cycles over time than conventional cassava breeding. With sequencing, the process of releasing varieties with improved CBSD and CMD resistance should take about 5 years.

What are your long term hopes for the project and the future of cassava breeding?


We hope to use genomic selection routinely, to address any other challenges cassava as a crop of second importance to Uganda will face. And also to take the technology to other East African, cassava breeding programs to faster address their major breeding constraints.


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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series:  

Tuesday, 9 August 2016

Talking sweet potatoes at the Source of the Nile

Last month I was invited to the Source of the Nile agricultural trade show in Jinja, Uganda. The show brings together all aspects of agriculture: from crops to chickens, cows and tractors. The event attracts over 120,000 visitors each year and runs for seven days.

I was needed on a National Crops Resources Research Institute (NaCRRI) stand where Agnes Alajo (a PhD student and breeder) was selling improved sweet potato varieties, which are resistant to pests and diseases with higher levels of pro-vitamin A.

It is estimated that around 35% of children and 55% of child-bearing mothers in rural Uganda suffer from vitamin A deficiency, which is associated with preventable child blindness and mortality. The orange-fleshed NAROSPOT varieties developed by NaCRRI are enriched with pro-vitamin A and it’s hoped their adoption will help improve the deficiency problem.

The stand also had an impressive array of biscuits, cakes and even juice made from processing sweet potato. Agriculture is very important in Uganda; it accounts for around 24% of GDP and 43% of the working population are subsistence farmers (2013). Processing sweet potatoes to produce flour can be economically viable and provides farmers with an opportunity to add value to their crop, boost income and reduce poverty.
The range of products made through processing sweet potato
I had to hurriedly absorb information about sweet potato, as very soon hoards of excited school children arrived. The main challenge was that not everyone can speak English and my UK accent was quite difficult for them to understand. I had to speak clearly and slowly to get my message across. Often teachers had to repeat what I had said in their local language. There are over 40 local languages in Uganda, so even Ugandans can find it difficult to communicate!
Agnes explains the importance of pro-vitamin A rich sweet potatoes to school students
Agnes explains the importance of pro-vitamin A rich sweet potatoes to school students
There was a lot of interest from young people who want to pursue agricultural careers and are attracted to opportunities for commercialization. Most people were very intrigued about the cakes, and couldn’t believe that they were made using sweet potato flour. Unfortunately, we couldn’t give out samples to taste until the end of the week, which caused a lot of pleading and disappointment!
Walking around the show I discovered giant cassava tubers, a “speaking head” and impressive looking cabbages. I later  saw the source of the Nile itself!
I had a great time walking around. There was plenty of entertainment and I also got to see where the Nile flows from Lake Victoria!
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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series:  

Get connected, stay connected

So after a couple months of experiencing the life of being a science policy advisor at the Royal Society, on my RCUK policy internship, I thought it was time to update you on what I’ve thinking about as I come to the end of my internship.

Getting the right people involved…


An essential start to policy advice is to gain a grounding in the areas you are working in, without this, advice would be uninformed, unrepresentative and simply wasting time. So in huge areas such as climate science, the environment and energy, how do you find the right research, how do you find the right people to talk to?

Imagine a stadium full of people at the start of a football match. You need to walk in and find out who is thinking what. Where do you start?

Literature streams


If every one of those people is a research article, it will be impossible to look at all of them. Start with groups and target particular areas that may be relevant, beginning with more general reading but deepen as time allows. None of this should be new to anybody, but it is important to realise that there will be literature you will not be able to find, those people not on the stands in the stadium, but in the tunnels surrounding it. For this reason, and that peoples’ views and research perspectives change with time, like a crowd throughout the game, it is worth following literature streams as much as possible.

Consultations


Consultations can take a variety of forms (email, online survey, postal, formal interview, informal meeting), and the form needs to match the type or group of people you are trying to consult. Don’t try to consult rural areas if rural broadband is problematic for example. But consultations can be so useful for getting current information on research areas and other pieces of work that might be on-going or planned for the future. Often, many of us can be guilty of staying within our known networks, contacts and work areas, but by consulting widely and being aware of those silos is important to get a better understanding of how interconnected problems fit together.

Image credit: Wikimania2009 Beatrice Murch [CC BY 2.0 (http://creativecommons.org/licenses/by/2.0) or CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

Trends


Amongst all of this, it is always worth taking time out of intense research to think about trends. The timing of policy advice is essential and trends make up a significant part of seeing where opportunities are. It is almost impossible to gain all information one needs from quantitative consultations.

Invaluable information can be gained from formal and informal interviews, good relationship building with the right mix of people, and an open and aware mindset.

It is interesting that often having the ‘right connections’ is seen as an unscientific, unrepresentative and privileged stance. Yet it may be that we sometimes forget how important maintaining and building relationships are in postgraduate research. Post PhD, maintaining good relationships and building positive working environments are key factors for developing your own research projects, or for the wider work place in any and every field. So… take some time to think about who you are talking to, and who you should perhaps talk with next to develop ideas or make new links.

During the last month or so I have been exposed to many of these challenges at the Royal Society. I have found It surprising how many links there are to my own world under the canopy of a PhD and I am looking forward to taking some of those thoughts back with me. Tell you more next time…

(Views in this blog post are my own and do not represent those of the Royal Society.)
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This blog is by Cabot Institute member Henry Webber, PhD student in the Department of Archaeology and Anthropology, studying the interactions between precision agriculture and archaeology.  
Henry Webber

Other blogs in this series:

Friday, 29 July 2016

Using GM to fight cassava brown streak disease

Last week I helped plant a new confined field trial for genetically modified (GM) cassava in western Uganda. The aim is to find how well the plants resist Cassava brown streak disease (CBSD).

Before planting, the National Crops Resources Research Institute (NaCRRI) held discussions with people from the local government and farmers’ groups. It’s vital to engage the local community so that people are correctly informed and on-board with the project. There were certainly some very strange myths to debunk!

Henry Wagaba (Head of Biosciences at NaCRRI) explained the huge losses caused by CBSD, which spoils tubers and can wipe out entire fields. CBSD is now the most devastating crop disease in Uganda and there are no resistant varieties currently available.

To fight the disease, NaCRRI researchers have developed GM cassava plants, which show high levels of resistance to CBSD at sites in southern and central Uganda. This trial will test how the plants perform in the growing conditions in western Uganda. Work will also be carried out to cross the GM plants wither farmer varieties to improve their growing and taste qualities.
I enjoyed getting stuck in and planting my first GM cassava!
GM crops are a contentious topic in Uganda. The passing of a National Biotechnology and Biosafety law has stalled in Parliament for over three years due to disagreements. Currently GM technology is used for research on banana, cassava, maize, potato, rice and sweet potato. However these are not approved for human consumption.

In nearby countries Kenya and Sudan, GM food products have been approved and many of these food products are imported into Uganda without regulation. It’s hoped the law will be passed soon to enable Ugandan farmers to reap the benefits of GM crops and protect against any potential risks.
Before the trial, I went on a safari in the Queen Elizabeth National Park, where I saw elephants, hippos and even lions!
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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
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Monday, 25 July 2016

In defence of wasps: why squashing them comes with a sting in the tale


Image credit: Trounce
They are one of the most unwelcome signs of summer. Buzzing through beer gardens, attacking innocent picnics, wasps arrive ominously with a sting in their tails. Universally disliked, they are swatted, trapped and cursed. But would a wasp-free world really be a better place?

Despite their poor public image, wasps are incredibly important for the world’s economy and ecosystems. Without them, the planet would be pest-ridden to biblical proportions, with much reduced biodiversity. They are a natural asset of a world dominated by humans, providing us with free services that contribute to our economy, society and ecology.

Wasps, as we know, turn up everywhere. More than 110,000 species have been identified, and it is estimated there are still another 100,000 waiting to be discovered. One recent study described 186 new wasp species in one small corner of Costa Rican rainforest alone. In contrast there are only around 5,400 species of mammals, and 14,000 recorded species of ant.

This huge and diverse assemblage belongs to the order Hymenoptera and is divided into two groups, the Parasitica and the Aculeata. Almost 80,000 species of wasps belong to the Parasitica group, which lay their eggs in or on their prey or plants using elongated tubular organs called ovipositors. The remaining 33,000 species are Aculeates, most of which are predators, and the ones whose ovipositors have been modified through evolution to form a sting.

Both parasitic and predatory wasps have a massive impact on the abundance of arthropods, the largest phylum in the animal kingdom, which includes spiders, mites, insects, and centipedes. They are right at the top of the invertebrate food chain. Through the regulation of both carnivorous and plant-feeding arthropod populations, wasps protect lower invertebrate species and plants. This regulation of populations is arguably their most important role, both ecologically and economically.

Although the majority of wasps lead solitary lives, it is the 1,000 or so species of social wasps which make the biggest impression on insect populations. Social wasp queens share their nests with thousands of offspring workers, who raise upwards of 10,000 sibling larvae during the colony cycle. This means a single nest provides a whopping bang for buck in terms of ecosystem services, killing vast numbers of spiders, millipedes and crop-devouring insects.
Pest control. shutterstock
Many social wasps are generalist predators too, which means they control populations of a wide range of species, but rarely wipe any single species out. This makes them an extremely useful, minimising the need for toxic pesticides, but unlikely to threaten prey biodiversity. It is not yet possible to accurately quantify their huge economic value in this regard, but their diet of agricultural pests such as caterpillars, aphids and whiteflies makes a massive contribution to global food security.

Wasps also play a crucial role in ecosystems as specialist pollinators. The relationship between figs and fig wasps is arguably the most interdependent pollination symbiosis known to man. Without one another, neither the fig nor fig wasp can complete their life-cycle – a textbook example of co-evolution which is estimated to have been ongoing for at least 60m years. Figs are keystone species in tropical regions worldwide – their fruit supports the diets of at least 1,274 mammals and birds. The extinction of fig wasps would therefore be catastrophic in tropical ecosystems.


The birds and the bees … and the wasp


Almost 100 species of orchids are solely reliant on the action of wasps for pollination. The plants mimic the appearance and chemical profile of female wasps, tricking males into attempting to mate with them, so that as the male wasps attempt to copulate with the flower they are loaded with pollen which is then transferred to the next male-seducing orchid. Without the wasp, these orchids would be extinct.
Working wasp. Shutterstock
Wasps also function as generalist pollinators, inadvertently transferring pollen between flowers they visit for nectar collection. One type even provide their larvae with pollen instead of insect prey. These “pollen-wasps” are considered to perform the same ecological roles as bees, pollinating a diverse array of plants. Unfortunately, while bees are credited with contributing at least €100 billion a year to the global economy through their acts of pollination, the works of wasps in the same sector is often ignored.

Even the wasps' sting could have a positive impact on the human population. Medical researchers are exploring the potential use of biologically active molecules found within wasp venom for cancer therapy. A chemical found in the venom of the tropical social wasp Polybia paulista, has been shown to selectively destroy various types of cancerous cells.

Since they protect our crops, make ecosystems thrive, sustain fruit and flowers, and might help us fight disease, perhaps we should appreciate the wonderful work of wasps before we next swipe at them with a rolled up newspaper. They may be a nuisance on a sunny afternoon - but a world without wasps would be an ecological and economic disaster.

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This blog is written by Cabot Institute member, Seirian Sumner, a Senior Lecturer in Behavioural Biology, University of Bristol and Ryan Brock, MRes candidate, University of Bristol.  This article was originally published on The Conversation. Read the original article.
Seirian Sumner

Why we need a new science of safety

It is often said that our approach to health and safety has gone mad. But the truth is that it needs to go scientific. Managing risk is ultimately linked to questions of engineering and economics. Can something be made safer? How much will that safety cost? Is it worth that cost?

Decisions under uncertainty can be explained using utility, a concept introduced by Swiss mathematician Daniel Bernoulli 300 years ago, to measure the amount of reward received by an individual. But the element of risk will still be there. And where there is risk, there is risk aversion.
Risk aversion itself is a complex phenomenon, as illustrated by psychologist John W. Atkinson’s 1950s experiment, in which five-year-old children played a game of throwing wooden hoops around pegs, with rewards based on successful throws and the varying distances the children chose to stand from the pegs.

The risk-confident stood a challenging but realistic distance away, but the risk averse children fell into two camps. Either they stood so close to the peg that success was almost guaranteed or, more perplexingly, positioned themselves so far away that failure was almost certain. Thus some risk averse children were choosing to increase, not decrease, their chance of failure.

So clearly high aversion to risk can induce some strange effects. These might be unsafe in the real world, as testified by author Robert Kelsey, who said that during his time as a City trader, “bad fear” in the financial world led to either “paralysis… or nonsensical leaps”. Utility theory predicts a similar effect, akin to panic, in a large organisation if the decision maker’s aversion to risk gets too high. At some point it is not possible to distinguish the benefits of implementing a protection system from those of doing nothing at all.

So when it comes to human lives, how much money should we spend on making them safe? Some people prefer not to think about the question, but those responsible for industrial safety or health services do not have that luxury. They have to ask themselves the question: what benefit is conferred when a safety measure “saves” a person’s life?

The answer is that the saved person is simply left to pursue their life as normal, so the actual benefit is the restoration of that person’s future existence. Since we cannot know how long any particular person is going to live, we do the next best thing and use measured historical averages, as published annually by the Office of National Statistics. The gain in life expectancy that the safety measure brings about can be weighed against the cost of that safety measure using the Judgement value, which mediates the balance using risk-aversion.

The Judgement (J) value is the ratio of the actual expenditure to the maximum reasonable expenditure. A J-value of two suggests that twice as much is being spent as is reasonably justified, while a J-value of 0.5 implies that safety spend could be doubled and still be acceptable. It is a ratio that throws some past safety decisions into sharp relief.

For example, a few years ago energy firm BNFL authorised a nuclear clean-up plant with a J-value of over 100, while at roughly the same time the medical quango NICE was asked to review the economic case for three breast cancer drugs found to have J-values of less than 0.05.
Risky business. shutterstock
The Government of the time seemed happy to sanction spending on a plant that might just prevent a cancer, but wanted to think long and hard about helping many women actually suffering from the disease. A new and objective science of safety is clearly needed to provide the level playing field that has so far proved elusive.


Putting a price on life


Current safety methods are based on the “value of a prevented fatality” or VPF. It is the maximum amount of money considered reasonable to pay for a safety measure that will reduce by one the expected number of preventable premature deaths in a large population. In 2010, that value was calculated at £1.65m.

This figure simplistically applies equally to a 20-year-old and a 90-year-old, and is in widespread use in the road, rail, nuclear and chemical industries. Some (myself included) argue that the method used to reach this figure is fundamentally flawed.

In the modern industrial world, however, we are all exposed to dangers at work and at home, on the move and at rest. We need to feel safe, and this comes at a cost. The problems and confusions associated with current methods reinforce the urgent need to develop a new science of safety. Not to do so would be too much of a risk.

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The ConversationThis blog is written by Cabot Institute member Philip Thomas, Professor of Risk Management, University of Bristol.  This article was originally published on The Conversation. Read the original article.
Philip Thomas

Wednesday, 13 July 2016

Taking a trip to the cassava field!

At the end of last week I was lucky enough to be invited on a trip to the field. I didn’t really know what to expect but was very excited to find out!

The purpose of the trip was to collect data for the 5CP project to find out how different varieties of cassava respond to Cassava brown streak disease (CBSD) and Cassava mosaic disease (CMD) in different areas.

We set off at 5.30am in the morning; the first stop was Lake Victoria to catch a ferry to the Sesse Islands. The team consisted of me, the driver (Bosco), research assistant (Gerald Adiga) and research technician (Joseph). Along the road, we saw several accidents, sadly a far too common occurrence in Uganda…

Due to delays, the ferry was rammed, and by the time we arrived it was almost the evening. We raced to the agricultural school with the field trial. Here the team have planted blocks of 25 clean cassava varieties from five African countries and our job was to score them for disease symptoms. CBSD and CMD are not very common on the Sesse Islands, and so most of the plants were healthy.
An agricultural student digs up a healthy cassava plant.
After a night of drinking Guinness in a corner shop we headed out, again at 5.30am! This time we headed to the city of Mbarara in the western region. The drive was really beautiful, passing Lake Mburo National Park and mountains covered with matoke.

Whilst scoring the cassava plants here we noticed a super abundance of whiteflies, which carry CBSD viruses. The weather had been particularly dry, allowing the whiteflies to breed like crazy. Fortunately, CBSD is also uncommon in this area and very few plants were diseased.
Super abundance of whiteflies on cassava which carry CBSD viruses.
The data from the 5CP project will help farmers to decide which cassava varieties offer the most protection against CBSD and CMD in their local areas; helping to protect them from the devastating yield losses caused by these diseases.

Fun stuff


On the way back we passed the equator line, and I got the chance to take some touristy photos. This week I also saw the Ndere dance troupe, who showcase the different dance and music styles from all over Uganda and other neighbouring countries. It was a lot of fun, some dances bared a weird resemblance to morris dancing and marching brass bands!
Crossing the equator!
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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series:  

Friday, 8 July 2016

Clean cassava to solve brown streak problem?

Since arriving in Uganda, I’ve been learning a lot about the affects of Cassava brown streak disease (CBSD), which is devastating cassava production and threatening food security. The disease is spread by the whitefly insect, which picks up the virus from an infected plant and carries it to neighbouring healthy plants.

Cassava plants are grown by planting stem cuttings in the ground, which go on to become new plants. If farmers use cuttings from infected plants, the new plants will also become infected. This is a big problem, as infected cuttings can be transported to new areas, spreading CBSD across large distances.

What can be done?



Tolerance


Huge efforts are being put into a number of different solutions. These include breeding new cassava varieties, which are tolerant to CBSD. This is a very long and challenging process, as cassava plants also need to be resistant to Cassava mosaic disease (CMD) and have yield/taste properties which farmers and consumers prefer.

The National Crops Resources Research Institute (NaCRRI) has recently developed a new variety: NAROCASS1, which is tolerant to CBSD and resistant to CMD. This is now being used in areas where CBSD is particularly common and severe. Unfortunately, even tolerant cassava varieties can contain CBSD viruses and so it’s vital that farmers have access to clean cuttings.
Cassava variety NAROCASS1 with CBSD tolerance and CMD resistance.


Clean seed system (CSS)


The cassava CSS project in Uganda is run by NaCRRI and involves picking the very youngest tip of the cassava plant to produce embryonic tissue, which develops into a new plant. These plants are then checked to see whether the CBSD virus is present before being taken to nurseries where they are carefully multiplied and eventually used for clean planting material for farmers. As you can imagine, this process takes a long time and is much more expensive than taking cuttings from a mature cassava plant. However it means that farmers can benefit from quality assurance that the cuttings they buy are virus free and stand the best chance of remaining healthy.
A clean cassava plantlet produced through tissue culture.
The cassava CSS project has been running as a pilot for three years. It will be very interesting to hear how this project goes, as it’s likely to be a major solution to the CBSD problem.

Reviewing progress


Last week I had helped take minutes for the annual CSS review at NaCRRI, which involved lots of manic typing and concentration! As part of the review I got to visit a field where an entrepreneur is growing clean cassava plants. The plants certainly looked healthy, with no CBSD and CMD symptoms at all. With so much to think about, we still found time to have a cocktail party to let of some steam!

Clean cassava seed entrepreneur David Mpanga explains how he uses record keeping to track of outgoings and income.
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This blog has been written by University of Bristol Cabot Institute member Katie Tomlinson from the School of Biological Sciences.  Katie's area of research is to generate and exploit an improved understanding of cassava brown streak disease (CBSD) to ensure sustainable cassava production in Africa.  This blog has been reposted with kind permission from Katie's blog Cassava Virus

Katie Tomlinson
More from this blog series: