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:

  1. Initial email contact with one of the project supervisors listed below
  2. Selection as the preferred candidate of a project supervisor
  3. Formal online application. Please select Louis Dreyfus – Weidenfeld Scholarship and Leadership Programme as the source of funding and also complete the Weidenfeld Scholarships questionnaire
  4. Interview by Department of Plant Sciences
  5. Interview of selected candidates by the Weidenfeld Scholarship and Leadership Programme
Dr J Agusti Transcriptomic analysis of cassava development
Dr D Boshier Genetic conservation of trees in agroecosystems
Prof L Dolan Increasing nutrient uptake efficiency in rice
Prof N Harberd Increasing crop plant soil-salinity tolerance via increase in root reactive oxygen species levels
Dr A Hector* Sustainable palm oil: living up to the label
Dr S Kelly Convergent pathways to C4 photosynthesis: understanding differential photosynthetic development through comparative transcriptomic analysis of hundreds of C3 and C4 species.
Dr S Kelly The function and evolution of parasite surface proteins: A comparative multi-omic study of trypanosomatid parasites of Plants and Man
Dr GM Preston The effect of N fertilisation on plant disease resistance
Prof RG Ratcliffe &Dr NJ Kruger Metabolic flux analysis of symbiotic nitrogen fixation
Prof JAC Smith Drought-tolerant bioenergy crops for marginal lands
Dr L Sweetlove Increasing nitrogen use efficiency in rice
Dr L Turnbull* Diversity, inputs and yield in small-scale tropical agriculture (now closed for new applications)

* 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

email: nicholas.harberd@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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.

Recent Publications

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

email: lindsay.turnbull@ieu.uzh.ch
Tel: +41 (0)44 635 61 20

Project Description

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

email: javier.agusti@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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

email: nick.kruger@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Prof RG Ratcliffe

email: george.ratcliffe@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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.

Recent Publications

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.

Student profile

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

email: andrew.hector@uzh.ch
Tel: +41 (0)44 635 48 04

Project Description

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

email: liam.dolan@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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

email: steven.kelly@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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.

Recent Publications

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

Student profile

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

email: steven.kelly@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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.

Recent Publications

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.

Student profile

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

email: lee.sweetlove@plants.ox.ac.uk
Tel: +44 (0)1865 275000

Project Description

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.

Student profile

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

Posted on January 30, 2013, in Job Opportunities, Research grants, fellowship and scholarships, Youth and Agriculture. Bookmark the permalink. Leave a comment.

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