This workshop will focus on developing solutions that can help detect, diagnose, forecast and map plant pathologies in the field. Primarily the workshop will focus on potential diagnostic kit and remote sensing applications that can be deployed in the African agriculture industry.
To do this we are bringing together an international group of attendees from a broad spectrum of research areas ranging from Agricultural Sciences, Molecular and Systems Biology, Computing, Chemistry, Physics and Engineering. With the specialist expertise available at this workshop, we will look to identify ways in which technologies such as multidimensional spectrometry, diagnostic chemistries and next generation sequencing can be used to help characterise cryptic plant pathologies in the field.
The primary goal of the workshop will be to develop grant proposals that we can submit to a relevant funding body such as the recently launched Global Challenges Research Fund. The application focus of the workshop will have a very broad remit and the only constraints will be to ensure that identified challenges can sensibly and practically addressed in the time frame of project grants and lead to economic benefits and enhanced food security for African nations. We envisage this will help realise the development of detection and diagnostic solutions that help quantify plant stresses limiting yield and /or phenotyping of traits in crop breeding programs.
Programme
Day 1 – Developing affordable, scalable detection solutions for crop threats (16 February)
- 09.30 Arrival and coffee
- 09.50 Welcome and introduction
- 10.00 STEFAN LEUTENEGGER, Imperial College London, UK
- 10.25 STEPHEN ASTON, One Acre Fund, Rwanda
- 10.50 FIRAT GÜDER, Imperial College London, UK
- 11.15 Coffee break
- 11.35 PHIL SWARBRICK, CABI, UK
- 12.00 COLIN TURNBULL, Imperial College London, UK
- 12.25 DANNY COYNE, IITA, Kenya
- 12.50 Lunch and networking
- 13.50 TONY CASS, Imperial College London, UK
- 14.15 DOUGLAS MIANO, University of Nairobi, Nairobi
- 14.40 PAUL FRENCH, Imperial College London, UK
- 15.05 Coffee and networking
- 15.30 Introduction to Sandpit event
- 15.40 Participant introductions (1 minute pp)
- 16.10 Workshop Session 1: Identifying the challenges in developing countries
- 16.50 Wine and Nibbles (continuing discussions)
- 17.30 Check-in at De Veres Sunningdale Park Hotel (for overnight attendees)
- 18.30 Dinner at De Veres Sunningdale Park Hotel
Day 2 – Sandpit event (17 February)
- 09:00 Coffee and networking
- 09:20 Workshop Session 2: Identifying strategies / ideas to address shortlisted challenges
- 10:30 Coffee Break and discussions
- 10:50 Workshop Session 3: Technologies needed to implement strategies / ideas
- 12:00 Working Lunch
- 13:00 Workshop Session 4: Formulating proposals
- 14:00 Workshop Session 5: Pitching proposals
- 16:00 Coffee Break (proposal evaluation by judges)
- 16:30 Workshop Session 6: Judges feedback
- 17:00 Drinks & Nibbles
- 17:30 Workshop close
Talk abstracts
Autonomous Navigation and Mapping with Small Drones
Stefan Leutenegger
Department of Computing, Imperial College London, UK
Abstract
The use of drones for crop monitoring seems and interesting and viable choice, since small drones have undergone a commercial explosion in the last few years. Remote controlling them or having them in GPS-based automatic control mode far enough from terrain/structure has acheived maturity. However, many challenges remain when it comes to operation in close proximity to terrain/obstacles, people, and in GPS-denied environments. This is very much linked to the non-trivial nature of localisation and mapping under these circumstances. In this talk, some recent progress on robust and accurate vision-based localisation of drones will be presented, along with new apporaches to produce ever higher resolution and even semanitcally meaningful maps that enable autonomous navigation of drones. Ultimately, the same mapping techniques may be used in the context of monitoring crop health in real-time.
Towards delivering locally-optimised agronomy… at scale
Stephen Aston
One Acre Fund, Rwanda
Abstract
One Acre Fund (1AF) serves over 400,000 farming families across East Africa, providing financing, distribution for agricultural technologies, and training on their use. Clients roughly double their yeilds on average, but divergence in agronomic variables means that farmers receiving the same guidance and inputs can experience widely different yield outcomes.
Optimisation of basic agronomy at a more granular scale as enourmous potential to significantly increase yields. Achieving this requires transferring to farmers, detailed knowledge on local agronomic variables, including crop disease. 1AF is working to (i) develop data systems & analytical tools to convert knowledge into geospatially-differentiaed agronomic recommendations, and (ii) operationalise the delivery of management zone-specific products and services.
Low-cost sensing with paper-based devices
Firat Güder
Department of Bioengineering, Imperial College London, UK
Abstract
Paper is a ubiquitous, biodegradable, and porous material which is an ideal substrate for the fabrication of affordable sensors, primarily through printing. Unlike its conventional counterparts, paper-based microfluidic do not require pumps and other complex components, allowing construction of highly compact miniaturized devices for rapid, multiplex detection of various bioanalytes in the field. Paper can also be used for the sensing of gases. These low-cost, flexible substractes have the potential for integration in food package for monitoring spoilage, especially fresh foods such as raw meats. In this talk, I will present our latest work on paper-based sensors and how they can enable new technologies in agricultural and food sciences.
Providing information and applying scientific expertise to solve problems in agriculture and the environment
Phil Swarbrick
CABI, UK
Abstract
CABI is an international not-for-profit organization that combats threats to agriculture from pests and diseases, protects biodiversity from invasive species, improves market access for smallholder producers and provides agricultural and environmental scientific knowledge. Our global Plantwise programme helps initiate in-country plant clinics that deliver free plant health advice to farmers. Coupled with diagnostics, a comprehensive knowledge bank provides and collects information to and from the clinics). Another project ‘Pest Risk Information SErvice’ is forecasting, crowd-sourcing and ground-truthing pest prevalence in Africa. We are a member of Centre for Applied Crop Science (CHAP) through Plantwise and our Molecular and Microbial Services (which hosts over 28,000 microbial strains).
Overview of research activities at the Department of Life Sciences, Imperial College London
Colin Turnbull
Department of Life Sciences, Imperial College London, UK
Abstract
The Department of Life Sciences at Imperial College represents a very large grouping of around 100 academic research groups spanning the whole range of biological sciences from ecosystems and conservation biology through to molecular, structural, systems and synthetic biology. There is internationally recognised expertise in disciplines relevant to GCRF priorites in food production and food security. Specific foci include plant pathogens and pests, improving photosynthetic efficiency, plant stress biology and plant developmental biology. Research spans laboratory model organisms that enable rapid learning through to several major crop species. In this talk, research relevant to GCRF goals will be highlighted.
Status and prospects of pest and disease management in Africa
Danny Coyne, Lava Kumar, James Legg, George Mahuku, Leena Tripathi
International Institute of Tropical Agriculture
Abstract
IITA has established a ‘One Health Platform’ with the aim of mitigating climate-driven biorisks. Five major themes of this initiative will be: 1) Pests and diseases; 2) Soil health; 3) Improved diagnostics; 4) Sustainable Intensification; and 5) Loss estimation. We will tackle these challenges using diverse approaches that will embrace new partners and promote the use of new diagnostic tools and novel smartphone apps, whilst building on existing areas of expertise such as biocontrol. IITA works closely with partner centres in the CGIAR, but will increasingly look to broaden collaboration and build on existing strong linkages with UK research institutions.
Low Cost Biosensors: from Continuous Monitoring to Single Use Device
Tony Cass
Department of Chemistry, Imperial College London, UK
Abstract
We are developing low cost biosensors for a range of applications in human, animal and environmental health. These range from continuous monitoring of metabolites, biomarkers and drugs in patients through rapid virus detection to drinking water quality in LMICS. To achieve these aims we use a range of biorecognition molecules and signal transduction methods, primarily electrochemical. In my talk I will illustrate these ideas with 3 examples:
• Continuous glucose monitoring in diabetes using minimally invasive microneedle devices that can be mass produced at low cost and hence are disposable.
• Rapid influenza detection with lateral flow assays that combine the respective advantages of RNA aptamers and monoclonal antibodies.
• Disposable enzyme electrodes for the quantitation of arsenic in drinking water using a novel arsenite oxidase and low cost fabrication methods.
Managing emerging viruses diseases in Eastern Africa: The case of maize and cassava
Douglas Miano
University of Nairobi, Nairobi
Abstract
Farming systems in sub-Saharan Africa are characterized by mixed cropping small farm sizes and is continuous throughout the year. This type of farming results in build-up of pests and diseases and when new diseases emerge, or in the case of outbreaks, the rate of spread and yield losses can be extremely high. Such has been the case of cassava brown streak disease (CBSD) and maize lethal necrosis (MLN) in eastern and central Africa. Efforts towards identification, diagnostics and management of the two diseases and challenges encountered are discussed.
Multidimensional fluorescence imaging and spectroscopy
Paul French
Department of Physics, Imperial College London, UK
Abstract
Fluorescence provides a powerful means to provide molecular contrast and has wide applications in biological imaging. While intensity-based fluorescence imaging provides information on the spatial distribution of fluorophores, spectroscopic readouts such as fluorescence lifetime, spectrum and polarization measurements can provide functional information (e.g. about molecular interactions, photophysics and the local molecular environment of the fluorophore). We are exploring the application of technology originally developed for medically-orientated projects to agriscience. In particular, we are exploring the application of multidimensional fluorescence imaging and spectroscopy of plants with a view to study the distribution and impact of agrichemicals.
Delegates
| NAME | RESEARCH BACKGROUND |
| PROF GABRIEL AMEKA, University of Ghana | Gabriel K. Ameka, obtained his PhD in Botany from the University of Ghana where he is Professor in the Department of Plant and Environmental Biology (formerly Botany). He has varied research interests which include organismic biology, food security and climate change, and DNA Barcoding of Life. Current research is focused on food security and climate change, and so plant disease, detection and diagnostic is an important priority research area for me. |
| DR STEPHEN ASTON, One Acre Fund | Steph’s research with One Acre Fund focuses on locally optimised agronomy for smallholders in the Great Lakes region. Step began his career with IITA, working on cassava, before pursuing his PhD in soil science. Before joining One Acre Fund, Step worked for Defra, managing research on sustainable intensification. |
| PROF TIM BARRACLOUGH, Imperial College London | TBC |
| DR BOSIBORI BETT, KALRO | My research is in the area of plant biotechnology and molecular biology. Research on improving cowpea for pest resistance using genetic engineering approaches where a Bt gene encoding toxin to Maruca vitrata was identified for subsequent transformation into cowpea. I currently lead a team on distribution of clean planting material to smallholder farmers, and offer regulatory support to projects at KALRO. |
| DR TOLGA BOZKURT, Imperial College London | I work on understanding how oomycete and fungal plant pathogens modulate plant processes at the host interface. My group focuses on dissecting the molecular mechanisms underlying plant immunity and the role of plant intracellular transport system in this process. We aim to characterize the host processes required for accommodation of filamentous pathogens inside the plant cells and identify perturbations caused by the pathogens |
| MR ALEX CAMUTO, Imperial College London | TBC |
| PROF TONY CASS, Imperial College London | Tony’s research is focused on using analytical science to solve problems in animal, human and environmental health especially through creating devices that perform the analysis at point of decision. Currently his research includes microneedle sensors, penside avian influenza diagnostics, and well-side determination of arsenic(III) in drinking water. To realise these devices his research uses a combination of biomolecular engineering of proteins and nucleic acids, low cost production of electrochemical sensors and performance enhancement through the use of nanomaterials |
| DR DANNY COYNE, IITA | Danny Coyne has worked in tropical agriculture since 1989, at the rural, national and international research institute level. He has in depth experience of the important tropical food crops and cropping systems in Africa. Specialized in plant nematology, he has lately broadened into the wider field of soil health. |
| DR ROGER DAY, CABI | 35 years’ experience in research, development and capacity building in tropical agriculture, focusing on crop protection, invasive species, biosecurity, and sanitary and phytosanitary systems. >20 years based at CABI’s Regional Office in Nairobi. Interested in the processes by which research results contribute to development outcomes. |
| DR CHRIS DUNSBY, Imperial College London | Chris’ research is in the field of biomedical optics and includes the development and application of quantitative fluorescence-based sensing and imaging techniques, including fluorescence lifetime imaging (FLIM). The groups’ FLIM instrumentation has been applied to study protein-protein interactions in cells, to studies of tissue autofluorescence – including in clinical trials – and to measurements of plant autofluorescence. |
| PROF JOSHUA EDEL, Imperial College London | Prof. Joshua is currently a Professor in the Department of Chemistry from 2011 onwards. Research activities within the Edel group runs at the interface between chemistry, chemical biology, physics, and medicine in order to improve and develop new classes of sensors. Expertise includes an array of techniques and methods such as micro and nanofabrication, material processing, surface modification chemistries, semiconductor processing and characterization techniques, confocal microscopy, plasmonics, surface enhanced Raman spectroscopy, and single molecule techniques using both optical and electrical methods. |
| DR JULIE FLOOD, CABI | Dr Julie Flood is Global Director for Trade & Commodities in CABI. Her main areas of research has been vascular wilt disease of oil palm, cocoa and coffee, Ganoderma diseases of oil palm and Phytophthora diseases of cocoa and coconut.She was President of the British Society for Plant Pathology in 2016. She has over 120 publications and has edited three books. |
| PROF PAUL FRENCH, Imperial College London | Paul French’s research has evolved from ultrafast dye and solid-state laser physics to biomedical optics with a particular emphasis on FLIM for applications in molecular cell biology, drug discovery and clinical diagnosis. His current portfolio (with Chris Dunsby) includes the development and application of multidimensional flouresence imaging technology for microscopy, automatic high content analysis, endoscopy and tomography with a particular emphasis on flourescence lifetime imaging (FLIM) and open source applications to image data acquisition and analysis. |
| DR FIRAT GÜDER, Imperial College London | With a first degree in computer engineering and a PhD in materials, Dr Güder has recently moved to Imperial College from Harvard University, Department of Chemistry where he worked with Prof. Whitesides on the development of new paper-based technologies. With the vision of translating technologies from lab to field, the Güder research group currently focuses on developing new tools for use in agricultural and food sciences including new sensor platforms for monitoring plants and animals, disease diagnostics and spoilage detection. |
| DR ANDREW KIGGUNDU, NARO | Andrew Kiggundu is a senior research officer at the National Agricultural Research Organization (NARO), Uganda. He is the leader of the Biodiversity and Biotechnology Programme whose core functions are plant genetic resource conservation, biological control and development of biotechnology tools for phylogenetics, crop breeding and disease diagnostics for important crop plants in Uganda. He holds a PhD. in plant biotechnology from the University of Pretoria, South Africa. |
| DR LAVA KUMAR, IITA | Lava Kumar is the Head of the Germplasm Heath/Virologist at IITA, Ibadan, Nigeria. His R4D program is focused on finding solutions to control plant virus diseases affecting food staples, including development and application of conventional and modern diagnostics, and integration of ICT tools for disease diagnosis, surveillance and seed quality management in sub-Saharan Africa. He obtained his MSc and PhD in Virology from SV University, Tirupati, India. For the past 20 years, he has been actively involved in international AR4D in South Asia and sub-Saharan Africa. Dr Kumar is interested in multidisciplinary approaches for plant health management. |
| DR JAMES LEGG, IITA | James Legg is a principal scientist at the International Institute of Tropical Agriculture, with 25 years’ experience of working on plant viruses and their insect vectors. Most of James’ professional career has focused on strengthening understanding of cassava viruses/vectors, and using that improved understanding to develop and facilitate the promotion of control strategies. |
| DR STEFAN LEUTENEGGER, Imperial College London | Stefan Leutenegger is a Lecturer in the Dyson Robotics Lab, co-leading it with Andrew Davison. His research is centred around autonomous robot navigation: robots need dedicated sensing capabilities as well as algorithms for localisation inside a potentially unknown environment. He has received a BSc and MSc in Mechanical Engineering from ETH Zurich in 2006, 2008, respectively, and a PhD in 2014, working at the Autonomous Systems Lab of ETH Zurich on Unmanned Solar Airplanes: Design and Algorithms for Efficient and Robust Autonomous Operation. |
| DR GEORGE MAHUKU, IITA | George Mahuku, Senior Plant Pathologist, IITA, has over 20 years of research and development experience, mostly in CGIAR. His research focuses on developing management strategies for critical diseases in banana, cereals and legumes in Africa; developing pathogen diagnostic tools; monitoring and surveillance for new and emerging disease threats and implementing pre-emptive disease management strategies. He has authored more than 60 publications. |
| PROF DOUGLAS MIANO, University of Nairobi | Dr. Miano is a plant pathologist specializing in plant virology and biotechnology. His research involves identification, diagnostics, characterization and management of viruses in cassava, maize and sweet potato. He has wide experience in biosafety regulations of genetically modified crops. His interests also include pest risk assessment and disease forecasting. |
| DR JOSEPH MULEMA, CABI | Joseph has worked on a number of pathosystems involving both fungi and bacteria to understand resistance and pathogenicity. He has a particular interest in understanding the effect of climate change and changing farming systems in Africa on the evolution of pathogens and developing sustainable means of detection and management. In recent years, Jospeh has been involved in strengthening plant heath systems in Uganda and Zambia through CABI’s Plantwise Initiative. |
| PROF HENRY MUTEMBEI, Director, University of Nairobi | Prof. Henry Mutembei is the Director Wangari Maathai Institute for Peace and Environmental Studies. Prior to joining the Institute, Henry maintained a strong path of vibrant research and teaching careers with wealth of experience in leadership, mentorship and management of human resource. Henry graduated with bachelor s degree of veterinary medicine and masters in clinical studies from University of Nairobi. He is a Suma Cum Laude doctorate graduate from Giessen University, Germany. Henry has a blended experience across disciplines, published over 40 papers in refereed journals, supervised over 20 students (Msc & PhD) and established successful collaborations with local and international institutions. Henry has been the PI and spearheaded disaster management projects for the last ten years. Whenever called to duty, he brings on board proven skills that would attract project funds, mentor human resource and produce publications. |
| MR GEORGE NGUNDO, Kenya Plant Health Inspectorate Service (KEPHIS) | George is currently an inspector and the lab manager at the Plant Quarantine and Bio-security Station. He is trained in plant pathology and has experience in certification, plant variety registration, Phytosanitary inspection and plant disease diagnosis. George is interested in development and implementation of effective diagnostic protocols especially for quarantine pathogens of interest to the country. |
| ASSOC. PROF EDWARD NGUU, University of Nairobi | Heavy metal pollution impacts on omega-3 PUFA accumulation in fish due to loss of phytoplankton biodiversity in the aquatic food web. Understanding the effect of heavy metal pollution on phytoplankton diversity, richness and effect on PUFA levels in commercial fish in Lake Victoria is of importance since fish forms an important source of omega-3 for human nutrition. |
| MS ELIZABETH NOBLE, Imperial College London | I am working in the Photonics Group, Physics Department, at Imperial College London to apply fluorescence imaging techniques to investigate agrochemical uptake and distribution patterns in plants and developing a practical in-vivo imaging/measurement technique for the mapping the response to agrochemicals including herbicides. These techniques have the potential to be extended as screening tools to pick up early herbicide responses and monitor them over the course of time. |
| DR RICHARD ODUOR, Kenyatta University | Richard is a molecular Biologist whose current research focuses on using modern biotechnologies including genetic engineering to improve local staple food crops such as maize, sweetpotato, cassava and sorghum to overcome both biotic and abiotic constraints. He is the National Chair of Kenya University Biotechnology Consortium and serves as a Senior Lecturer and Head of Plant Transformation Laboratory in Kenyatta University, Nairobi, Kenya. |
| DR MARIAN DORCUS QUAIN, CSIR- Crops Research Institute | TBC |
| PROF ALESSANDRA RUSSO, Imperial College London | TBC |
| PROF VINCENT SAVOLAINEN, Imperial College London | I combine molecular phylogenetic techniques, comparative analyses, population genomics, and intensive fieldwork to help explain the origin of biodiversity and, where possible, find solutions for its preservation in a rapidly changing world. Also, with funding from the Royal Society and the South African NRF for capacity building, 197 students and members of staff received training in ecological genetics, which led to the creation of the African Centre for DNA Barcoding (ACDB) at the University of Johannesburg. |
| PROF IRENEE SOMDA, Université polytechnique de Bobo-Dioulasso | TBC |
| PROF PIETRO SPANU, Imperial College London | My main research interest are the interactions between plants and microbes with a particular focus on plant diseases. In practice, we use molecular biology and genomic tools available to understand the mechanisms pathogenic fungi use to subvert the host plant immunity and establish infection |
| DR PHIL SWARBRICK, CABI | As part of CABI’s Project Development Group, I work with scientists and senior staff to develop grant proposals for our international development projects. Prior to working at CABI, I worked as a research scientist on projects involving coconut ‘lethal yellowing’ disease, the parasitic plant Striga and powdery mildew of barley. |
| DR LEENA TRIPATHI, IITA | Leena Tripathi Principal scientist leading the plant transgenic research at the International Institute of Tropical Agriculture (IITA) based at BecA/ ILRI hub, Nairobi, Kenya. Her primary research focuses on genetic improvement of banana, cassava, enset and yam for disease and pest resistance to enhance production, which will lead the food security, income and well-being of resource-poor farmers in sub-Saharan Africa. |
| DR COLIN TURNBULL, Imperial College London | Colin Turnbull is a Reader in Molecular Plant Physiology, focussing on signals in defence and development. Current projects include improving post-harvest storage life in potato; regulation of flowering for beneficial manipulations in agricultural contexts and its role in speciation; and hte molecular basis of virulence-resistance relationships in insect-plant interactions. |
| PROF GEOFFREY TUSIIME, Makerere University | My research interest is in crop disease management with specific interest in pathogen identification, diagnosis, variability and distribution. With other research teams, I have contributed towards developing management packages for diseases of tropical perennial and annual crops. My research has mainly focused on banana, potato, beans, hot pepper and cassava. |
| DR CHRIS WILSON, Imperial College London | I am an evolutionary ecologist investigating the role of genetic diversity in parasite-host interactions, using lab and field-based empirical approaches. I work with fungal and bacterial antagonists of microscopic soil invertebrates, and have a recent interest in fungal biocontrol of plant pathogenic root-knot nematodes, especially asexual species such as Meloidogyne incognita. |
| DR OLIVER WINDRAM, Imperial College London | Oliver’s research involves generation and interpretation of large scale omics data using network modelling techniques. His research focuses on taking this novel systems biology-based data and using it to generate novel organism phenotypes through synthetic biology approaches. These phenotypes involve the generation of organisms useful for agriculture and other industries such as crop plants with enhanced defence capabilities and organisms capable of producing useful chemicals and proteins. |
| DR RUDIGER WOSCHOLSKI, Imperial College London | Dr Rudiger Woscholski’s research interests are focussed on employing chemical biology approaches to answer questions in lipid dependent signalling. In particular, lipid phosphatases and kinases are the main targets to generate suitable chemical tools that can be used to probe and quantify these targets and their regulators. Since 2006 this work involved the use of synthetic as well as physical chemistry to generate new tools and techniques, respectively, to probe and disturb cellular signalling. Since 2011, Rudiger has engaged plant scientists in academia and industry to port the achievements generated in chemical biology towards the plant sciences. |