Monthly Archives: January 2013
Louis Dreyfus – Weidenfeld DPhil scholarships in Food Security (crop science, biodiversity, conservation)
Last application deadline: 08 March, 2013
Outstanding students from Africa, Asia and South America are invited to apply.
Scholarships are funded by the Louis Dreyfus Foundation and cover tuition fees and living expenses for three years.
Available projects are listed below. Interested candidates should contact the relevant supervisor for more information and to discuss their application. Only applications that come forward with the prior approval of one of these supervisors will be considered. Please read through the application process details and the graduate admissions criteria. Please also see details of the graduate training programmeand training provision.
Note that successful applicants would be admitted through the Louis Dreyfus – Weidenfeld Scholarship and Leadership Programme. Only the most outstanding candidates with leadership potential are likely to be successful.
The application process is as follows:
- Initial email contact with one of the project supervisors listed below
- Selection as the preferred candidate of a project supervisor
- Formal online application. Please select Louis Dreyfus – Weidenfeld Scholarship and Leadership Programme as the source of funding and also complete the Weidenfeld Scholarships questionnaire
- Interview by Department of Plant Sciences
- Interview of selected candidates by the Weidenfeld Scholarship and Leadership Programme
* will be joining the department in 2013.
Postgraduate Research Project Details
Increasing crop plant soil-salinity tolerance via increase in root reactive oxygen species levels
Prof N Harberd
Tel: +44 (0)1865 275000
We have recently shown that the soil-salinity tolerance of Arabidopsis thaliana is dependent upon salinity-induced increases in the root levels of transcripts of the gene AtrbohF. These increases cause increase in the production of reactive oxygen species (ROS) in internal xylem-vessel bearing zones of the root, and this increased ROS in turn reduces the amount of salt in the xylem, thus reducing the amount of potentially toxic salt that is delivered to the shoot via the xylem-based transpiration stream (Jiang et al., 2012). We will now determine if the same mechanism regulates soil-salinity tolerance in two genetically tractable crop-plants: barley and oil-seed rape. First (1), we will determine if treatment of barley and oil-seed rape roots with DPI (a chemical inhibitor of ROS production) increases shoot salt sensitivity (as it does in Arabidopsis thaliana). Second (2), we will access publically available ‘TILLING’ populations of barley and oil-seed rape for plants carrying mutations in genes related to Arabidopsis AtrbohF, and determine if these mutant lines have increased salt-sensitivity. Third (3), we will specifically over-express (using cell-specific gene promoters) genes discovered in (2) in the central zone of barley/oil-seed rape roots and determine if such expression confers increased soil-salinity tolerance. Soil salinity is a major world-wide agricultural problem, one that is increasing as the world increasingly adopts irrigation methods to enhance crop yields. This project therefore addresses a major issue in the drive towards strengthened global food security.
Jiang, C., Belfield, E.J., Mithani, A., Visscher, A., Ragoussis, J., Mott, R., Smith, J.A.C and Harberd, N.P. (2012). ROS-mediated vascular homeostatic control of root-to-shoot soil Na delivery in Arabidopsis. EMBO Journal 31, 4359.
Diversity, inputs and yield in small-scale tropical agriculture
Dr L Turnbull
Tel: +41 (0)44 635 61 20
Buffering agricultural systems against climatic variation is a major challenge in attaining food security in developing countries. For example, in sub-Saharan Africa (SSA) roughly 90% of cereal production is directly dependent on rainfall and this region houses roughly 26% of the world’s malnourished population. It is therefore crucial that we identify as many potential adaptive mechanisms in such areas as possible and assess just how much vulnerability they are able to offset. In addition, effective adaptation has to begin with the lowest level in the food security pyramid: cropping systems in the farms. It has been shown in several experiments that high biodiversity can increase terrestrial productivity. This implies that biodiversity is a potential tool to buffer agricultural productivity against climatic perturbations in developing countries. We propose to use a model system composed of 50 farms in Western Kenya to establish whether in the context of declining precipitation, farms with greater biotic diversity record higher yields and greater yield stability than those with lower diversity. The project will include detailed on-site studies of diversity for both crop and non-crop plants coupled with measurements of productivity obtained on the farm and via NDVI satellite data. Using remote sensing to assess biodiversity and yields will potentially allow us to extend the analysis to examine historical patterns in this region and to construct models to understand the relationships between precipitation, diversity and yields. Finally we will use targeted and controlled interventions to quantitatively assess the relative benefits of increasing diversity in comparison with other kinds of inputs.
Transcriptomic analyses of Cassava development
Dr J Agusti
Tel: +44 (0)1865 275000
The root of cassava (Manihot esculenta Crantz) is best known for being the main source of food for ~ 500 million people in Africa, Asia and Latin America, due to its capacity of starch storage. Its ability to grow in many types of soil and to resist severe drought makes it very valuable for third world breeders. Furthermore, cassava is an outstanding energy source, as its roots contain 20-40% starch that costs 15-30% less to produce per hectare than starch from corn, making it an attractive and strategic source of renewable energy (www.fao.org). The yield of the Cassava root depends on the activity of the vascular cambium, a stem-cell niche that brings about thickening. Increased cambium activity leads to thicker roots with increased capacity of starch storage and, thus, increased yield and quality. The main goal of this project is to understand the molecular events that govern the activity of the vascular cambium of the root of cassava with the view of optimizing the yield of this crop. To achieve this goal we will first study the transcriptome remodeling of the vascular cambium at the tissue type resolution during root development. To this end cells from the vascular cambium will be harvested using laser-capture microdissection (LCM) at different developmental stages. Harvested samples will be used for genome-wide transcriptome analyses. This approach aims to identify relevant genes in the control of cambium activity of the cassava root. To prove tissue-specific expression of candidate genes we will use RNA-in situ on roots. Given that transformation techniques in cassava are well established, further functional analyses will be pursued on candidate genes proved to be specifically expressed within the cambium. This project will be the starting point of a long-term biotechnology program on cassava root based on the basic knowledge of the regulation of its vascular cambium and aimed to improve food and energy security.
Metabolic flux analysis of symbiotic nitrogen fixation
Dr NJ Kruger
Tel: +44 (0)1865 275000
Prof RG Ratcliffe
Tel: +44 (0)1865 275000
Symbiotic nitrogen fixation by legumes is an essential component of sustainable agricultural systems. As a result there is considerable interest in transferring nitrogen fixation to non-leguminous crop species, but the success of this strategy will depend on the metabolic integration of the nitrogen-fixing bacteria and the roots of the host plant. The metabolic adjustments that will be required in an engineered symbiosis, and the extent to which they can be achieved, are unclear since the metabolic crosstalk that occurs between the host and symbiont has still to be fully defined. For example, it is only relatively recently that amino acid import into the bacteroid from the host cell has been shown to be a prerequisite for the net provision of fixed nitrogen to the host cell in pea root nodules. This surprising result highlights the need for a better understanding of the processes that lead to metabolic integration.
While genetic approaches can pinpoint critical activities, they do not explain the roles of these steps, and a complete understanding of the metabolic phenotype of the bacteroid and its host cell requires methods for measuring cell-specific metabolic processes. We propose to address this problem by measuring the metabolic fluxes that are supported by the bacterial and plant cell metabolic networks in the symbiosis. To achieve this we shall apply a novel strategy for analyzing cell-specific metabolism based on stable isotope labelling of cell-specific marker proteins. This work will build on our expertise in steady-state metabolic flux analysis (MFA) and constraints-based flux balance analysis (FBA). The proposed analysis will focus on the organism-specific proteins that are expressed in bacteroids and host cells, and it will also take advantage of a new technique we have developed that uses GFP as a marker protein to interrogate the metabolic state of specific cell types following incubation with 13C-labelled substrates.
We shall apply these methods to Rhizobium leguminosarum, with the aim of understanding the changes in metabolic phenotype that occur between the free-living organism and the symbiotic state. Working with wild type and mutant strains of the bacterium, we shall deduce flux maps of primary metabolism for the bacteroid within its host, and for the host in the presence of the bacteroid, for the first time.
J. Prell, A. Bourdès, S. Kumar, E. Lodwig, A. Hosie, S. Kinghorn. J. White and P. Poole (2010) Role of symbiotic auxotrophy in the Rhizobium-legume symbioses. PLoS one 5, e13933.
S.K. Masakapalli, P. Le Lay, J.E. Huddleston, N.L. Pollock, N.J. Kruger and R.G. Ratcliffe (2010) Subcellular flux analysis of central metabolism in a heterotrophic Arabidopsis thaliana cell suspension using steady-state stable isotope labeling. Plant Physiology 152, 602-619.
T.C.R. Williams, M.G. Poolman, A.J.M. Howden, M. Schwarzländer, D.A. Fell, R.G. Ratcliffe and L.J. Sweetlove (2010) A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiology 154, 311-323.
D.J.V. Beste, B. Bonde, N. Hawkins, J.L. Ward, M.H. Beale, S. Noack, K. Nöh, N.J. Kruger, R.G. Ratcliffe and J. McFadden (2011) 13C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathogens 7, e1002091.
N.J. Kruger, S.K. Masakapalli and R.G. Ratcliffe (2012) Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems. Journal of Experimental Botany 63, 2309-2323.
This project would suit a candidate with a strong background in biochemistry, including metabolism, an interest in metabolic analysis, and an aptitude for computational methods.
Sustainable Palm Oil: Living up to the Label
Dr A Hector
Tel: +41 (0)44 635 48 04
Palm oil is one of the principle agricultural products from many countries in Asia as well as being increasingly grown in S. America and its original home, Africa. Consequently, plantations of oil palm are now one of the major land uses in Asia. While palm oil production is a central pillar of the agricultural economies of many nations it also raises many environmental issues. Balancing the economic benefits with environmental considerations is a key scientific and social challenge being tackled by initiatives like the Roundtable for Sustainable Palm Oil (RSPO). This DPhil will examine sustainable palm oil production within the context of food security. Can the environmental impacts of oil palm plantations be reduced at little or no cost to productivity? Can biodiversity within oil palm plantations can be increased and could this potentially bring benefits to crop production and ecosystem services?
Increasing nutrient uptake efficiency in rice
Prof L Dolan
Tel: +44 (0)1865 275000
Root hairs are critical for nutrient uptake in crops and for seedling establishment. We have developed transgenic lines of rice and brachypodium with longer root hairs than wild type and these plants develop higher grain yields than untransformed controls. The aim of this project will be quantify the enhancement of yield and to develop further technologies to enhance nutrient uptake by modulating root hair development.
Required skills: evidence of a high level of molecular biology practical experience is essential and some experience with rice would be desirable.
Convergent pathways to C4 photosynthesis: understanding differential photosynthetic development through comparative transcriptomic analysis of hundreds of C3 and C4 species.
Dr S Kelly
Tel: +44 (0)1865 275000
It is predicted that by 2050 global food production must increase by at least 50%. The predicted demand exceeds the predicted capacity for yield increase through traditional crop breeding techniques alone. Therefore, it will be necessary to introduce and/or manipulate the expression of genes with desirable properties in several disparate crop species. One naturally occurring enhancement to photosynthetic efficiency that has the potential to dramatically increase yields in many crop species is C4 photosynthesis. Although C4 photosynthesis involves many physiological and anatomical changes, it has evolved independently from conventional C3 photosynthesis in more than 60 different lineages of angiosperms making it one of the most abundant examples of convergent evolution in plant biology. The shear number of times the C4 system has been re-invented in nature combined with the urgent need to improve crop yields has led to significant international efforts to engineer the C4 photosynthetic pathway into C3 crops such as rice. This project aims to understand what changes in gene expression are necessary to convert a C3 plant into a C4 plant through comparative transcriptomic analyses of multiple C3 and C4 species. Specifically, the project will focus on bioinformatic approaches to provide new insight into the evolution of C4 photosynthesis and determine the extent that gene expression changes underpinning C4photosynthesis are convergent/parallel in different families of angiosperms.
Rowan F. Sage, Pascal-Antoine Christin, and Erika J. Edwards. The C4 plant lineages of planet Earth J. Exp. Bot. first published online March 16, 2011 doi:10.1093/jxb/err048
Jane A. Langdale, C4 Cycles: Past, Present, and Future Research on C4 Photosynthesis, The Plant Cell November 2011 vol. 23 no. 11 3879-3892
Udo Gowik, Andrea Bräutigam, Katrin L. Weber, Andreas P.M. Weber and Peter Westhoff Evolution of C4 Photosynthesis in the Genus Flaveria: How Many and Which Genes Does It Take to Make C4? The Plant Cell June 2011 vol. 23 no. 6 2087-2105
This project would suit a candidate with a strong background in biology or mathematics or physics, with an interest in bioinformatic analysis and an aptitude for computational methods.
The function and evolution of parasite surface proteins: A comparative multi-omic study of trypanosomatid parasites of Plants and Man
Dr S Kelly
Tel: +44 (0)1865 275000
Trypanosomatids are monophyletic group of single celled eukaryotic parasites that are spread between larger hosts by insect vectors. The majority of characterised species are pathogenic and collectively they inhabit a diverse range of hosts from coconut palms to kangaroos with several species causing globally important parasitic diseases of humans, livestock and crops. Trypanosomes are unique amongst eukaryotes as all endo and exocytosis occurs in a single specialised an invagination of the pellicular membrane called “the flagellar pocket.” Where documented in trypanosomatids, the flagellar pocket is the sole site for localisation of receptors and transporters thus rendering them invisible to the innate immune responses of the mammalian host. Given that all receptors and transporters localise to the flagellar-pocket, this leaves the majority of the cell surface available for other functions. In mammalian infective trypanosomatids it is thought that the majority of cell surface proteins are involved in evasion of immune responses. The aim of this project is to characterise the cell surface proteome of the trypanosomatid parasites of plants and determine how the parasite uses these proteins to interact with the plant host. Specifically this project will determine whether convergent mechanisms have been evolved to deal with disparate host environments and will identify those proteins which allow the parasite to evade the plant immune responses.
Chaoqun Yao, Yalan Li, John E. Donelson, and Mary E. Wilson, Proteomic examination of Leishmania chagasi plasma membrane proteins: contrast between avirulent and virulent (metacyclic) parasite forms. Proteomics Clin Appl. 2010 January; 4(1): 4–16.
J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster and Neil E Reiner, Proteomic analysis of the secretome of Leishmania donovani. Genome Biology 2008, 9:R35
Oberholzer M, Langousis G, Nguyen HT, Saada EA, Shimogawa MM, Jonsson ZO, Nguyen SM, Wohlschlegel JA, Hill KL. Independent analysis of the flagellum surface and matrix proteomes provides insight into flagellum signaling in mammalian-infectious Trypanosoma brucei. Mol Cell Proteomics. 2011 Oct;10(10):M111.010538.
This project would suit a candidate with a strong background in biology or biochemistry, with an interest in bioinformatic analysis and an aptitude for computational methods.
Increasing nitrogen use efficiency in rice
Dr L Sweetlove
Tel: +44 (0)1865 275000
Nitrogen is one of the main growth-limiting nutrients for plants. The efficiency with which plants utilise nitrogen sources in the soil depends partly on their capacity for uptake of nitrate / ammonium ions through their roots and partly on the extent to which these nitrogen sources can be assimilated and used to drive growth. This project concerns the latter. There is evidence that plants monitor their internal nitrogen status through the sensing of levels of nitrate and key amino acids and that this information is integrated into growth regulatory pathways. The aim of this project will be to identify the mechanisms used by rice plants to sense internal amino acid content and to explore the potential for manipulation of these sensing pathways for increasing nitrogen use efficiency.
We are looking for a student with a demonstrable interest in nitrogen metabolism and signalling. Evidence of high level practical experience of plant molecular biology skills is a perquisite. Some prior experience with rice would be desirable.
Original post and more information can be found on the organisation’s website at http://www.plants.ox.ac.uk/plants/students/postgraduates/Louis-Dreyfus.aspx
The Leverhulme Centre for Integrative Research on Agriculture and Health (LCIRAH) PhD Project studentship
Deadline: 2 April 2013
Public investments, agricultural strategy and malnutrition in rural South Asia
The Leverhulme Centre for Integrative Research on Agriculture and Health (LCIRAH) has been established under a generous grant from the Leverhulme Trust to build an intersectoral and interdisciplinary platform for integrating research in agriculture and health, with a focus on international development goals.
Applications are invited for a LCIRAH doctoral studentship tenable at SOAS for 3 years starting in October 2013. This studentship is run by the Centre for Development Environment and Policy (CeDEP) at SOAS.
Nature & scope of doctoral thesis
Despite strong economic growth, undernutrition prevalence continues to be alarmingly high in South Asia, with nearly half the region’s children classified as stunted. It is recognised that agriculture has a potentially critical role to play in future efforts to improve nutrition in the region. Strategic choices made by policymakers may be important in determining how effectively agriculture and other sectors can contribute to improved nutrition. For example, does agricultural investment in marginal and less-favoured areas yield better returns in terms of food security and nutrition outcomes than investment in favoured areas? What categories of government investment, particularly rural infrastructure investments (eg. roads, irrigation, cold-chains), yield the highest returns in terms of nutrition outcomes? Some research exists on the nexus between government expenditure and rural poverty outcomes (eg. Fan, Hazell and Thorat, 2009),but there is little information extending to nutrition outcomes.
This PhD research project will attempt to bridge this gap in knowledge by exploiting regional and temporal variation in government expenditures, nutrition outcomes and other variables in one of the countries in the region, and applying appropriate econometric methods to uncover key relationships. Collating and merging various pieces of secondary data (eg. district-level public expenditures, income and poverty, nutrition outcomes data, etc.) will be a key part of the project.
The lead supervisor will be Professor Bhavani Shankar, Centre for Development, Environment, and Policy (CeDEP), SOAS. For more information on this topic, please contact Prof Shankar at firstname.lastname@example.org
Value of the studentship
The studentship will cover fieldwork costs (10K for the duration of the studentship), student stipend at the Research Council UK Doctoral (London) rate (for 2012-13, this was £15,590), and UK/EU tuition fees. Applicants paying fees at the overseas rate will be required to meet the additional cost of overseas fees.
Criteria and Requirements
- Subject –This studentship is available for work on a doctoral thesis to be undertaken full time at SOAS.
- Only new applicants may apply: those already enrolled on a research degree programme at SOAS are not eligible to apply.
- Academic – Applicants must normally possess or be expected to possess a good UK Master’s degree (or a qualification deemed equivalent by the School) in a relevant discipline. This will be an inter-sectoral project, and we are looking for students with a good grounding in applied economics and relevant skills or interests in nutrition and/or agriculture, who would enjoy and be comfortable with learning and using skills across different sectors in a multi-disciplinary, multi-sectoral research group.
- Candidates will be assessed on academic merit by a Selection Panel consisting of three academic members.
- The assessment of your application will be based on the information in your studentship application. Selectors will be looking at the degree results and also at academic references, statement and other relevant information.
Studentship Application Deadline
- The LCIRAH studentship application form must be received as soon as possible but no later than 2 April 2013.
- Late or incomplete applications will not be considered
- Applicants must have also applied for admission as soon as possible but no later than the studentship application deadline (2 April) in order to be considered for this studentship. As the studentship is run through the Centre for Development, Environment, and Policy (CeDEP), which is based in the Department of Financial & Management Studies, applicants must choose‘MPhil/PhD FINANCIAL AND MANAGEMENT STUDIES’ as the programme of study in their application for admission. The application for admission must be complete and references must have been submitted.
Notifications of Results
Successful candidates will be notified by e-mail regarding the outcome of their studentship application by the end of June. If you have not heard from us by the end of June, you should assume that your studentship application was unsuccessful.
Studentship Application Procedures
The LCIRAH studentship application form and further information about the project is available for download from the download box at the top right or can be obtained from:
Telephone: +44 (0)20 7074 5094/5091
More information on application can be found on the website of the organisation at http://www.soas.ac.uk/registry/scholarships/lcirah-project-studentship.html
The Challenge: Optimum Process Designs
The oil and gas production, gas processing, petroleum refining and chemicals industries must optimize their process designs to achieve more reliable and stable operations. Optimum designs must be quickly identified with minimum risk of rework so that companies remain competitive and maximize theirbusiness performance. Process engineers are challenged with making timely business decisions while meeting the business objectives of designing and operating efficient, safe and profitable plants. The Opportunity: Linking Business Objectives and Process Design Process modeling is a powerful technology that enables decision makers and engineers to link critical business objectives to process design, thus enabling true plant lifecycle modeling.
The major business benefits of process modeling using UniSim Design Suite include:
- Utilizing ‘what-if’ scenarios and sensitivity analyses to identify the optimal design based on operating and business targets
- Ensuring that process equipment is properly specified to deliver desired product throughput and specifications
- Evaluating the effect of feed changes, upsets and equipment downtime on process safety, reliability and profitability
- Monitoring equipment performance against expectations
- Improving plant control, operability and safety using dynamic simulation models of planned and existing plants
The Solution: UniSim Design Suite
UniSim Design Suite provides an intuitive and interactive process modeling solution that enables engineers to create steady-state and dynamic models for plant and control design, performance monitoring, troubleshooting, operational improvement, business planning and asset management.
UniSim Design Suite helps process industries improve productivity and profitability throughout the plant lifecycle. The powerful simulation and analysis tools, real-time applications and the integrated approach to engineering solutions provided by UniSim Design Suite enables companies to improve designs, optimize production and enhance decision-making. These models may be leveraged into advanced training and optimization solutions provided by the UniSim Operations and UniSim Optimization suites.
More information about UniSim Design Suite!
- All expenses-paid trip to the Honeywell Users’ Group Conference in your region.
- The supervisor of the winning student(s) will be offered a Honeywell UniSim Design Training Course at one of Honeywell’s training centers and paid attendance to 2013 Honeywell Users Group in your region.
- Network with top management in your region.
- Read more about last year’s winner in EMEA.
Notice of intent to compete:
Notice of intent to compete:
Notice of intent to compete:
More details and original post can be found on the website of the competition at http://unisim.studentcompetitions.com/
15 Feb 2013
The MasterCard Foundation funds citizens and residents of Sub-Saharan Africa for graduate studies at Michigan State University, USA. The fields of study at MSU include agriculture and natural resources; veterinary medicine; natural sciences; and many others.
Among other criteria, applicants should be able to demonstrate:
- Prior completion of a Bachelors Degree from an African University, with academic achievements suggesting continued academic success as a graduate student;
- Strong commitment to a professional path in line with an area of study that can positively impact Africa.
The university posts instructions and the scholarship application form. Completed applications must be sent to the appropriate university department before 15 February 2013.
20 Mar 2013
The U.S. Agency for International Development in India (USAID-Delhi) invites applications for the India-Africa Agricultural Innovation Bridge Program. The program will make grants to transfer proven Indian agriculture innovations to Liberia, Kenya, and Malawi.
Eligibility for grants extends to Indian nonprofit organizations, as well as to Indian business organizations willing to forego profits. Universities and research organizations in India are among the eligible groups.
The program will accept concept papers on a quarterly basis with deadlines of 20 March 2013; 20 June 2013: 20 September 2013; and 30 December 2013.
USAID provides more details about the program, application guidelines and contact information.
31 Mar 2013
The Aga Khan Foundation supports programs in rural development, broadly defined, in a number of developing countries. It provides scholarships and loans for postgraduate studies to outstanding students from the developing world, with priority for masters studies.
The Foundation also considers applications for PhD programs, and for travel and study awards for PhD students doing their research in developing countries on topics judged to be of interest to the Aga Khan Development Network.
The Foundation invites applications from Bangladesh, India, Pakistan, Afghanistan, Tajikistan, Kyrgystan, Syria, Egypt, Kenya, Tanzania, Uganda, Mozambique, Madagascar, France, Portugal, UK, USA, and Canada. Preference is given to students under 30 years of age.
The Foundation assists students with tuition fees and living expenses only. The cost of travel is not included in AKF scholarships. Applicants are requested to make every effort to obtain funding from other sources as well, so that the amount requested from the Foundation can be reduced to a minimum. Preference is given to those who have been able to secure some funding from alternative sources.
Half of the scholarship amount is considered as a loan, which must be reimbursed with an annual service charge of 5%.
Students may obtain application forms from AKF offices or Aga Khan Education Services / Boards in their countries of current residence. The application deadline is 31 March 2013, although it may be earlier in certain countries.