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PhD Projects for Food Security

Dr Walter Federle, Dept. of Zoology

Physical structure and function of cuticular hydrocarbons in insects

PhD Project Description: Cuticular hydrocarbons are responsible for water proofing in the “wax layer” of insect cuticle, and play a key role in chemical communication. The water proofing function depends on the crystalline structure of long-chained cuticular hydrocarbons, and can be destroyed by superficial abrasion of the cuticle. However, body surfaces of insects are visibly covered by a liquid oil film, which may consist of shorter-chain hydrocarbons. In adhesive pads, the oily secretion contains watery droplets, which may help insects to avoid slipping, but it is still unclear whether hydrophilic droplets are also present on cuticle of other body parts. This project aims to clarify the physical structure and function of the insects’ wax layer and its liquid components. We will study the two-phasic adhesive secretion of smooth adhesive pads, in comparison with hydrocarbons from other (rigid and soft) body parts. We will use interference reflection microscopy (IRM) to determine the fluid’s secretion rate, and its wettability on different surfaces. We will use IRM to analyze the melting and phase change of hydrocarbons at different temperatures, and compare it to measurements of cuticular evaporation. The effect of abrasion on the wax layer’s structure will be investigated by cryo-SEM and staining methods. The hydrocarbons studied will be chemically analysed through collaborators. We will manipulate the two-phasic secretion of adhesive pads using de-emulgators, different substrates and temperatures, to study the effects on the forces the pads produce. The student will learn many experimental methods including light/electron microscopy, chemical analysis, force measurements, and quantifying evaporation rate.

Referees:

Dirks J-H, Clemente CJ, Federle W (2010) Insect tricks: two-phasic foot pad secretion prevents slipping. J R Soc Interface 7: 587-593.

Dirks J-H, Federle W (2011) Mechanisms of fluid production in smooth adhesive pads of insects. J R Soc Interface 8(60): 952-960.

Gibbs AG (2002) Lipid melting and cuticular permeability: new insights into an old problem. J Insect Physiol 48(4): 391-400.

Other relevant themes: Basic Bioscience Underpinning Health & World Class Underpinning Bioscience

Link: http://www2.zoo.cam.ac.uk/federle/Home.html

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Dr Walter Federle, Dept. of Zoology

Second Supervisor/Collaborator: Ian Wilson, Dept of Chemical Engineering

Trapping fluids of carnivorous pitcher plants: ecology and biomechanics

PhD Project Description: Nepenthes pitcher plants possess special leaves that can capture and digest arthropod prey. The pitchers contain a pool of digestive fluid, which in many species is viscoelastic owing to plant-derived polysaccharides in solution. The fluid’s stickiness allows the plant to immobilize and kill insects. Many interesting questions about the biomechanics, chemistry, biological function and evolution of these specialized fluids remain unanswered: Which polysaccharides make the pitcher fluids sticky? How do different chemical components affect the fluids’ rheological properties? What causes the variation in stickiness over time, and between different Nepenthes species? How does the fluid’s rheology determine insect-trapping success? How do plants cope with polysaccharide dilution by rain? How have differences in fluid properties and function evolved in the genus Nepenthes? How do specialized arthropods avoid being trapped in the pitcher fluids? The project will include laboratory and field work (in SE Asia). We will 1) characterize the chemical composition of pitcher plant polysaccharides, 2) quantify the fluid’s rheology using advanced lab-based and portable field set-ups, 3) study the effects of ionic strength, pH and temperature on fluid rheology and insect capture efficiency, 4) study how dilution by rain affects fluid properties and how pitchers control fluid levels, 5) analyze interspecific variation of fluid properties in the context of available phylogenetic information, and 6) characterize biomechanical adaptations of specialist insects to move within the plants’ sticky trapping fluids. The student will be trained in techniques including rheometry, mathematical modelling, chemical analysis of polysaccharides, high-speed motion capture, microscopy and phylogenetically-based analyses.

Referees:

Bauer U, Grafe TU, Federle W (2011) Evidence for alternative trapping strategies in two forms of the pitcher plant, Nepenthes rafflesiana. J Exp Bot 62(10): 3683-3692.

Bohn HF, Federle W (2004) Insect aquaplaning: Nepenthes pitcher plants capture prey with the peristome, a fully wettable water-lubricated anisotropic surface. Proc Natl Acad Sci USA 101(39): 14138-14143.

Gaume L, Forterre Y (2007) A viscoelastic deadly fluid in carnivorous pitcher plants. PLoS ONE 2(11): e1185.

Other relevant themes: Bioenergy and Industrial Biotechnology

Link: http://www2.zoo.cam.ac.uk/federle/Home.html http://www.ceb.cam.ac.uk/directory/ian-wilson

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Dr Julia Davies, Dept. of Plant Sciences

Phosphate deficiency signalling and responses in Arabidopsis

PhD Project Description: Phosphate is an absolute requirement for plant productivity but our reserves for fertiliser production are running out. The model plant Arabidopsis responds to deprivation by modifying its root system architecture, including root hair elongation. This implicates the regulation of cytosolic calcium, plasma membrane calcium influx channels (including mechanosensitive channels), strigolactones and purinergic (extracellular ATP) signalling. This project will test the hypothesis that under phosphate deprivation, increased production of strigolactones suppresses purinergic signalling to conserve phosphate. This may have consequences for ATP-regulated mechanical signalling and growth through soil. Additionally, it will aim to identify the (channel) genes involved in root hair elongation by a combination of forward and reverse genetics. Judicious use of mutants combined with analyses of transcriptional and growth responses will help elucidate mechanisms in this critical aspect of plant nutrition.

Referees: Nature 422: 442-446.

Other relevant themes: World Class Underpinning Bioscience

Link: www.plantsci.cam.ac.uk

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Dr Phil Howell, National Institute of Agricultural Botany

Grain cadmium levels in tetraploid and hexaploid wheat

PhD Project Description: The NIAB pre-breeding group are intercrossing tetraploid wheats (Triticum durum, T. dicoccum and T. dicoccoides) with hexaploid bread wheat (T. aestivum), as part of WISP (http://www.wheatisp.org). Grain samples of tetraploid wheat have consistently shown higher levels of the toxic heavy metal cadmium (Cd) than hexaploid wheat, and low-Cd accumulation is now a trait of major importance to durum wheat breeders. However, a significant proportion of recent UK bread wheat varieties have tetraploid parentage in their pedigrees, largely coming from T. dicoccoides, which has unknown Cd status. In addition, our WISP pre-breeding work may be inadvertently transferring high-Cd alleles from tetraploid wheat into low-Cd hexaploid wheat. Recent work has identified a locus (Cdu1) which explained 82% of the phenotypic variation in Cd accumulation in a segregating durum wheat population. Flanking markers can be used to screen a large range of tetraploid and hexaploid accessions from our WISP crossing work. Wholegrain flour samples can be prepared for ICP-MS analysis to determine Cd levels. This screening approach will allow a detailed genetic analysis of cadmium uptake in our WISP material. A diagnostic genetic marker suitable for high-throughput genotyping in wheat can be used for routine selection against high-Cd alleles in segregating WISP populations, and transferred to commercial breeding programmes as necessary. Cadmium accumulation may also be a suitable phenotype for exploring changes in gene expression following polyploidisation i.e would a hexaploid derived from a high-Cd tetraploid through re-synthesis necessarily accumulate the same Cd levels as its tetraploid progenitor? What is the role of the Cdu1 homoeologues on the A- and D-genomes?

Referees: Wiebe et al., 2010. Theor Appl Genet 121:1047-1058

Link: http://www.niab.com/pages/id/387/Dr_Phil_Howell

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Dr Emma Wallington, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Uta Paszkowski, Dept. of Plant Sciences, and in collaboration with Martin Broadley, University of Nottingham.

Improved Root Traits in Wheat

PhD Project Description: We would like to offer a PhD project to study potential improved root traits in wheat, extending published work from other species. The aim is to increase wheat root length, and thus improve water use efficiency, to improve P, N & K uptake and measure the effect on yield. UpBeat1 encodes a transcription factor which regulates the balance between cellular proliferation and differentiation in the root. In transgenic plants with reduced or abolished expression, a longer root develops (Tsukagoshi et al. 2010). OsPUP encodes a protein kinase, expression of which increases under conditions of phosphate starvation, which increases P, N & K uptake and increases yield. Highly expressing transgenic rice result in a higher dry weight, length and surface area of the rice root, plus a 60% increase in yield above normal levels in low P soils. (Gamuyao et al. 2012). We have transformed wheat with constructs to constitutively express wheat homologues of Upbeat1 and OsPUP, or to reduce expression of Upbeat (by RNAi-silencing). Initially the PhD student would genotype T1 plants to identify homozygous material for detailed phenotyping and expression analysis to determine the effect of these genes in wheat, and develop lines with both beneficial traits. Further constructs for wheat transformation could be made, to further characterise the wheat genes, express OsPUP, employ root specific promoters, or use genome engineering techniques such as TALENS or CRISPR. A non-GM approach could include assessment of diverse wheat germplasm or TILLING populations.

Referees:

1. Tsukagoshi et al. 2010 Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root. Cell 143 (4), 606-616

2. Gamuyao et al. 2012 The protein kinase Pstol1 from traditional rice confers tolerance

 

Link: http://www.niab.com/pages/id/8/Research

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Dr Matthew Milner, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Emma Wallington

Analysis of a candidate gene for increased yield in wheat when grown on low phosphate soil

PhD Project Description: OsPUP was a gene first identified from O.sativa v. Kasalath, a variety which is native to nutrient-poor soils of eastern India (Gamuyao et al. 2012). The gene encodes a protein kinase, expression of which increases under conditions of phosphate starvation. Expression of OsPUP in rice increases P, N & K uptake and increases yield when grown on soil with low levels of P. Transgenic rice expressing OsPUP resulted in a higher dry weight and a 60% increase in yield above normal levels when grown on low P soils. We have identified a homologous PUP gene in wheat and have made an over-expression construct as well as an RNAi construct which have been transformed into wheat. Seeds from these plants will need to be characterized for their ability to grow under P limited conditions. During this 10-week project a student will analyze wheat plants with altered TaPUP expression to determine the effect of altered TaPUP expression on growth and yield. It is anticipated these plants will continue to be grown after the end of the 10-week project so that seed yield data can also be obtained. Further wheat transformation constructs could also be made during this project. A PhD project would be to understand the molecular and biochemical effects of TaPUP in plants and how we can use this knowledge to help grow crops on more marginal soils. An assessment of the heterogeneity of this gene in diverse wheat germplasm, and identification of TILLING mutants, could lead to the incorporation of novel alleles for breeding wheat via a non-GM strategy, to increase yield in a major UK crop.

Referees:

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Rico Gamuyao, Joong Hyoun Chin, Juan Pariasca-Tanaka, Paolo Pesaresi, Sheryl Catausan, Cheryl Dalid, Inez Slamet-Loedin, Evelyn Mae Tecson-Mendoza, Matthias Wissuwa & Sigrid Heuer. Nature 488, 535–539 (23 August 2012) doi:10.1038/nature11346


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Dr Ian Mackay, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Dr Sarah Holdgate

Deploying next-generation biological resources and dense SNP chips for the genetic dissection of brown rust resistance in wheat

PhD Project Description: This project will deploy the NIAB 8 founder elite wheat MAGIC population and the dense 90k genotype dataset to investigate the genetic basis of brown rust resistance, a major wheat pathogen in the UK and worldwide. Brown rust is caused by the fungal pathogen Puccina recondita, and can reduce yields by up to 50%. As leaders of the UK Cereal Pathogen Virulence Survey, NIAB possesses the national brown rust isolate collection. Using the expertise and resources available, this project will undertake replicated phenotypic tests for seedling resistance to specific brown rust isolates under controlled environment conditions. Subsequently, the phenotypic data generated will be combined with the existing 90k SNP data to identify genetic components of brown rust resistance. The genomic context of these markers will be investigated using emerging wheat physical and sequence resources and comparative genomic approaches, and breeder-friendly genetic markers generated, as time permits. Previous screens for yellow rust resistance in the MAGIC population have identified highly significantly associated genetic markers, and interestingly, transgressive segregation for resistance. This workpackage forms part of a wider objective of utilising wheat MAGIC for the efficient application of genomics-assisted plant breeding for sustainable wheat production, targeting (but not limited to) disease resistance and yield components within a unified genetic mapping platform.

Link: http://www.niab.com/pages/id/74/Dr_Ian_Mackay http://www.niab.com/pages/id/411/Dr_Sarah_Holdgate

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Dr Ian Mackay, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Dr Keith Gardner

Statistical and Quantitative Genetics

PhD Project Description: Covering the application of methods from statistical, population and quantitative genetics to improve the efficiency of plant breeding, NIAB can offer projects ranging from the development of novel methods and algorithms for trait mapping to more practical lab & field based experimentation including:  Association mapping in wheat and barley  Development and application of methods for genomic selection in autogamous species.  Processes for improving the speed and efficiency of inbreeding in crop breeding.  The Multiparent Advanced Generation Intercross (MAGIC)  The design of breeding programmes

Link: http://www.niab.com/pages/id/74/Dr_Ian_Mackay

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Dr Fiona Leigh, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Prof Howard Griffiths, Plant Sciences

Capturing Photosynthetic Efficiency Traits from Tetraploid Wheat

PhD Project Description: Ancestral wheat species harbour novel genetic variation that we hope to capture in wheat improvement efforts. At NIAB we are intercrossing a range of tetraploid wheats (Triticum durum, T. dicoccum, and T. dicoccoides) with modern hexaploid bread wheat (T. aestivum), through resynthesis and direct crossing, as part of WISP, the BBSRC public-good wheat pre-breeding program (http://www.wheatisp.org). Diversity in photosynthetic and water use efficiency (WUE) traits was observed in our collection of tetraploid wheats, extending above and below the values obtained for elite bread wheats. This PhD will interrogate the tetraploid gene pool with the ambition of improving the photosynthetic capacity of bread wheat in future varieties. The research will involve: a) development of novel mapping populations from reciprocal crosses between parents which contrast for key traits b) phenotyping of these populations with gas exchange techniques to establish the heritability of photosynthesis and WUE traits c) identification of quantitative trait loci (QTL) using high density molecular markers and bioinformatic tools to begin trait dissection d) investigation of the influence of influence of the cytoplasm in the expression of photosynthesis / WUE phenotypes

Link: http://www.niab.com/pages/id/76/Fiona_Leigh_PhD http://www.plantsci.cam.ac.uk/research/howardgriffiths

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Dr Phil Howell, National Institute of Agricultural Botany

Developing genetic markers for wheat domestication traits

PhD Project Description: As part of the ‘synthetics pillar’ of WISP, (http://www.wheatisp.org), NIAB is introducing diversity from a range of wild and cultivated diploid and tetraploid species into elite hexaploid wheat varieties. Many of the lines we produce will display many undesirable “weedy” characteristics, such as shattering seed heads or adhering glumes. Shattering is caused by the homoeologous Br loci whilst tenacious glumes are controlled by the Sog and Tg loci. The most important domestication gene, the Q locus, has been cloned and appears to belong to the AP2 family of transcription factors. Genetic markers for these characters will greatly aid the selection of improved pre-breeding material and help widen the pool of diversity available to wheat breeders. Diploid, tetraploid and hexaploid materials from our WISP programme can be characterised for threshability and then screened with published markers linked to these major domestication loci, together with additional SNP-based markers developed by WISP genotyping partners. Existing segregating populations will be used to develop co-dominant markers suitable for high-throughput genotyping. This is likely to require a bio-informatics approach exploiting synteny with rice, maize and brachypodium. Once very close linkage is established, it should be possible to develop near-isogenic lines for these loci in order to better understand the underlying mechanism of each character and how they interact. As well as making the pool of non-domesticated wheat relatives more accessible to breeders, this may give some new indications on how to optimise the balance between desirable threshability and undesirable grain shedding.

Referees:

Watanabe et al., 2006. J Appl Genet 47: 93-98

Sood et al., 2009. Theor Appl Genet 119: 341-351

Simons et al., 2006. Genetics 172: 547-555

Link: http://www.niab.com/pages/id/387/Dr_Phil_Howell

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Dr Alison Bentley, National Institute of Agricultural Botany

Second Supervisor/Collaborator: Dr Ian Mackay, NIAB

The effect of Ppd on stress tolerance at germination and establishment in wheat

PhD Project Description: Ppd is a locus in cereals characterised primarily by its major effect on flowering time and height. However, it is also known to influence frost tolerance and winter kill. This project will use a set of near isogenic lines in wheat to assess if an effect of Ppd-D1 can be detected on germination and coleoptile emergence rates in laboratory tests. The tests will then be extended to impose water logging, drought and freezing tests on seeds and seedlings. The work will be extended to survey variation across parents of mapping population and representatives of adapted UK germplasm prior to initiating linkage and association mapping experiments.

Link: http://www.niab.com/pages/id/398/Dr_Alison_Bentley http://www.niab.com/pages/id/74/Dr_Ian_Mackay

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Siobhan Braybrook, The Sainsbury Laboratory

Second Supervisor/Collaborator: Sebastian Schornack (SLCU), Genome editing

Development of branching patterns in basal lineages: cell wall mechanics and dichotomous branching

PhD Project Description: Dichotomous branching is the oldest branching pattern present in extant plants. It is described as the formation of two equal sized branches from a terminal bud. This can be observed in several plants, but here we will focus on Marchantia and Selaginella: the Marchantia thallus exhibits dichotomous branching as does the Selaginella shoot. A recent study indicates that branching in Selaginella kraussiana is regulated by the phytohormones auxin and cytokinin. We are currently investigating how auxin is involved in plant cell growth, and cell wall mechanics, in Arabidopsis thaliana and algae. The aim of this project is to understand how auxin regulates cell wall mechanics during dichotomous branching in Selaginella and Marchantia. The project will include examining cell wall mechanics, characterizing cell wall composition, and tracking growth during dichotomous branching. The effect of hormone application and chemical cell wall alteration will be examined as well. Genome editing in these species of auxin and cell-wall altering genes will be performed in order to assess their impact of branching pattern. The project will be undertaken in a multi-disciplinary group including plant biologists, ecologists, biochemists, mathematicians and physicists. The group is based at The Sainsbury Laboratory, a new institute centred on understanding plant development.

Referees:

Saunders and Langdale. Conserved transport mechanisms but distinct auxin responses govern shoot patterning in Selaginella kraussiana. New Phytologist. 2013. 198(2):419-428.

Braybrook and Peaucelle. Mechano-Chemical Aspects of Organ Formation in Arabidopsis thaliana: The Relationship between Auxin and Pectin. PLoS ONE 8(3): e57813.

Other relevant themes: Bioenergy and Industrial Biotechnology & World Class Underpinning Bioscience

Link: https://braybrookgroup.wordpress.com/

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Prof Sarah Lummis, Dept. of Biochemistry

Bee and mite Cys loop receptors

PhD Project Description: Certain insecticides have recently come under scrutiny, as there is increasing evidence that some highly effective compounds (including neonicotinoids, which act at Cys loop receptors) have significant deleterious effects on beneficial insects, even at sublethal doses. In bees these effects include impaired spatial learning, which is critical for navigation, and a decrease in the numbers of queen bees. A further problem for bees is infestation with its most serious pest, Varroa destructor. This project will involve characterising bee and mite Cys-loop receptors, which are also insecticide targets, with the ultimate aim of providing information that could lead a insecticidal agent that kills mites but not bees. It will involve molecular biology (creating mutants, restriction digest, making mini and midi preps etc) and functional studies (using membrane potential sensitive dyes and electrophysiology).

Referees:

1. Price KL, Lummis SC. (2014) An atypical residue in the pore of Varroa destructor GABA-activated RDL receptors affects picrotoxin block and thymol modulation. Insect Biochem Mol Biol. ;55C:19-25.

2. Thompson, A. J., McGonigle, I., Duke, R., Johnston, G. A., and Lummis, S. C. (2012) A single amino acid determines the toxicity of Ginkgo biloba extracts. Faseb J 26, 1884-91.

Other relevant themes: World Class Underpinning Bioscience

Link: www.bioc.cam.ac.uk/people/uto/lummis

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Dr Jill Harrison, Dept. of Plant Sciences

The evolution of branching forms in the colonization of land

PhD Project Description: Branching patterns are a primary determinant of plant architecture and strongly impact on productivity by regulating light harvesting potential and resource allocation. Although branching forms have arisen by convergence across the plant tree of life, mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. The hormones auxin, cytokinin and strigolactone regulate branching, and auxin transport plays a key role in their co-ordinated action. The proposed project will characterise the branching pattern in a filamentous alga closely related to land plants: Coleochaete nitellarum. Candidate hormonal regulators of branching will be identified using hormone treatments, and a new transcriptomic resource developed in Liam Dolan’s lab in Oxford will be searched for homologues of genes involved in hormonal regulation of branching in Arabidopsis. Functional analysis will be prioritised depending on the results generated, and will be undertaken in conjunction with a computational modelling approach to aid interpretation of mutant phenotypes and guide experiments. Identifying the genetic basis of diversity in form remains a major challenge in modern biology, and branching was a key innovation in plants’ transition to land. The project will generate information relevant to understanding a basic developmental process in plants, and will identify the gene regulatory networks involved in branching in a close relative of land plants. Outputs from the project could be used to increase yields in algal biofuel crops. The project will provide training in molecular biology, imaging, bioinformatic and further computational techniques.

Referees: Domagalska and Leyser 2011. Signal integration in the control of shoot branching. Nat Rev Mol Cell Biol. 12(4):211-21. Bennett TA, Liu MM, Aoyama T, Bierfreund N, Braun M, Coudert Y, Dennis RJ, O’Connor D, White CD, Wang XY, Decker EL, Reski, R and Harrison, CJ. 2014 Two plasma membrane targeted PIN proteins regulate shoot development in a moss. Accepted for publication in Current Biology. Bennett TA, Brockington S, Rothfels C, Graham S, Stevenson D, Kutchan T, Rolf M, Thomas P,, Wong GK-S, Leyser O, Glover BJ and Harrison CJ. 2014. Paralogous radiations of PIN proteins with multiple origins of non-canonical PIN structure. Molecular Biology and Evolution (doi:molbev.msu147).

Link: http://www.plantsci.cam.ac.uk/research/jillharrison

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Sebastian Schornack, Sainsbury Laboratory (SLCU)

Characterisation of a genetic element involved in colonisation of plants by filamentous microbes

PhD Project Description: At SLCU, our research aims at identifying the genetic basis for successful plant microbe interactions. We mainly study interactions of the oomycete pathogen Phytophthora palmivora and beneficial mycorrhiza fungi with monocot (barley, wheat) and dicot (Niotiana, Medicago) plants. We have identified a number of mutants and genetic traits impacting on the plant microbe interactions. Prospective ph.D. candidates will utilise a range of methods including cloning, microscopy, genome editing, protein biochemistry and microbiology to follow up interesting leads. We also offer more bioinformatics oriented projects utilising extensive transcriptomics data on plant microbe interactions. Interested ph.D. students should get in touch to discuss details of available research projects.

Referees:

Rey et al, 2014 - New Phytologist Evangelisti et al, 2014 - New Phytologist

Wang et al, 2012, Current Biology

Other relevant themes: World Class Underpinning Bioscience

Link: www.schornacklab.net

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Dr Julian Hibberd, Dept. of Plant Sciences

Second Supervisor/Collaborator: Griffiths

PhD Project Description: Understanding the regulation of gene expression in the C4 Bundle sheath

Referees:

Williams et al eLife eLife, 2: e00961.

Brown et al . Science, 331: 1436-1439.

Link: http://hibberdlab.com

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Jim Kaufman, Dept. of Pathology

PhD Project Description: The major histocompatibility complex (MHC) is the genetic region with the most associations with disease in humans, many due to highly polymorphic class I and class II genes involved in adaptive immunity. Other genes in the MHC are involved in regulation and innate immunity, including cell-surface molecules called butyrophilins, which recently have been associated with various autoimmune diseases (Abeler-Dorner et al 2011 Trends Immunol). The closest relatives in chickens are the BG genes, which are extremely polymorphic and associated with resistance to certain viral diseases, including the economically-important Marek’s disease, caused by an oncogenic herpesvirus (Goto et al 2010 PNAS). We discovered, sequenced and ordered all 14 BG genes of a single haplotype, determined their cell/tissue distribution, and compared them to other haplotypes (Salomonsen et al, in revision for PLoS Genetics). We found that individual BG genes have very specific expression patterns, but altogether they have a wide tissue distribution. Comparison between haplotypes shows that the BG multigene family is undergoing extremely rapid expansion and contraction, leading to hybrid genes and copy number variation. We have expressed the extracellular domains of BG genes as Fc-fusion proteins, in order to produce specific monoclonal antibodies, search for ligands and use in functional assays. We will express the long cytoplasmic tails of BG genes for use in interaction assays. In doing so, we hope to discover and then examine in detail the biological roles of individual BG genes, in particular how they are involved in resistance to infectious pathogens.

Referees:

Abeler-Dorner et al. 2011. Butyrophilins: an emerging family of immune regulators.Trends Immunol 33: 34-41

Goto et al. 2009. BG1 has a major role in MHC-linked resistance to malignant lymphoma in the chicken. PNAS 106: 16740-5

Salomonsen et al. 2014. Sequence of a complete BG haplotype shows two gene lineages with specific expression patterns and dynamic expansion and contraction. PLoS Genetics, in revision

Link: http://www.path.cam.ac.uk/research/investigators/kaufman/

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Dr Uta Paszkowski, Dept. of Plant Sciences

Second Supervisor/Collaborator: Jeongmin Choi

PhD Project Description: Plants can improve their nutrients and water provision by establishing symbiosis with Arbuscular Mycorrhizal (AM) fungi, a fascinating phenomenon that still has to be fully understood and taken advantage of within more modern and integrated agricultural practices (Smith and Read 2008). All the information available to date indicates that the very early stages of this interaction are critical for its successful outcome. Plant-fungus communication begins before physical contact and a suite of mobile signals have been implicated in the process (Genre et al. 2013, Oldroyd 2013). The recent identification and initial characterization in our lab of the inhospitable (iho) rice mutant which is non responsive to the fungus in the earliest steps of the interaction, provides a unique tool for performing a highly focused comparison to gain a deeper insight in the earliest signalling events. As the identity of the IHO gene is highly consistent with its potential direct role as receptor for a fungal derived signal, the generated information will also help in following investigations aimed at the molecular identification of such signal. During the PhD project you will take a closer look at early symbiotic communication by examining plant molecular dynamics activated in response to fungal signals. On one hand you will mine transcriptome data that have recently been generated by RNAseq. These experiments will lead to the identification of molecular pathways activated upon IHO mediated fungal perception and to the characterization of molecular markers to monitor IHO signalling activation. In addition, you will lead our efforts towards a structural and evolutionary approach to defining the mechanisms of IHO signalling specificity and dynamics following fungal perception.

Referees:

Genre, A., M. Chabaud, C. Balzergue, V. Puech-Pages, M. Novero, T. Rey, J. Fournier, S. Rochange, G. Becard, P. Bonfante, and D. G. Barker. 2013. Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone. New Phytol 198:190-202.

Oldroyd, G. E. 2013. Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol 11:252-263. Smith, S. E. and D. J. Read. 2008. Mycorrhizal Symbiosis 3rd Edition. Academic Press.

Link: http://www.plantsci.cam.ac.uk/research/utapaszkowski.html

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Professor George Salmond, Dept. of Biochemistry

PhD Project Description: Food security, biotechnology, quorum sensing and flotation: antibiotics from biocontrol bacteria and plant pathogens active against other plant pathogens! We work on bioactive molecules called heterumalides. They have potent anti-oomycete activities (e.g. against Phytophthora, the potato blight pathogen) and antifungal properties. They also have anti-cancer activities. Some Gram-negative bacteria make bioactive haterumalides such as oocydin A (which is a potent anti-oomycete). We defined large gene clusters in environmental isolates of the enterobacterium, Serratia, responsible for oocydin biosynthesis and we have studied the production of the molecule using mutants (both by transposon mutagenesis and through allelic engineering), bioassays, and chemical analysis (with Dr Leeper in the Chemistry Department). Various plant pathogens can make the molecule, or analogues. We have used bioinformatics, physiological studies and gene fusion techniques to investigate regulation of biosynthesis in Serratia. This project will involve a molecular biological study of bacteria that make the bioactive molecule(s), investigating environmental and physiological signals (including Quorum Sensing) that act as regulatory inputs to production of oocydin and other bioactives. Given the impact on phytopathogens, this project has obvious “food security” importance, but is also pertinent to the “industrial biotechnology” theme because of possible translational utility, and “synthetic biology” because of the opportunities for engineering genes and gene clusters for production of new, bioactives, including in bacterial pathogens that are capable of flotation!

Referees:

1. Matilla, MA et al (2012) Bacterial gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A. Journal of Biological Chemistry, 287: 39125-39138

2. Ramsay, J., et al (2011) A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium. PNAS, USA 108, 14932-14937

3. Poulter, S., et al (2011) The Serratia LuxR-family quorum sensing regulator, CarR, activates transcription in the absence of N-acyl homoserine lactone signals. Molecular Microbiology, doi: 10.1111/j.1365-2958.2011.07634.x

Other relevant themes: Bioenergy and Industrial Biotechnology

Link: http://www.bioc.cam.ac.uk/people/uto/salmond

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Dr Ian Henderson, Dept. of Plant Sciences

Fine-mapping crossover recombination using flow cytometry and deep sequencing of fluorescent pollen’

PhD Project Description: During meiosis homologous chromosomes undergo programmed recombination that can result in reciprocal crossover. The likelihood of crossover is highly variable along the physical length of chromosomes. This project will develop a novel methodology to analyse recombination distributions at the megabase scale. The student will use fluorescent reporters of crossover that can be analysed using flow cytometry. The student will generate lines that are heterozygous for the fluorescent transgenes, collect pollen and use sorting to purify the pollen that contain crossover events in the analysed interval. This pollen will be used to generate DNA sequencing libraries. Sequencing data from these libraries will then be analysed to monitor crossover frequency, inferred from frequency of single nucleotide polymorphisms. Following methodological development this approach will be used to test the role of genetic and epigenetic factors on recombination distributions. During this project the student will acquire training in genetics, molecular biology and next generation sequencing technology.

Referees:

1. Choi, K.*, Zhao, X.*, Kelly, K.A., Venn, O., Higgins, J., Yelina, N., Hardcastle, T., Ziolkowski, P., Copenhaver, G.P., Franklin, C. McVean, G.A. and Henderson, I.R. ‘Meiotic crossover hotspots overlap with H2A.Z nucleosomes at Arabidopsis gene promoters.’ Nature Genetics (2013) 45: 1327-1336.

2. Yelina, N.E.*, Ziolkowski, P.A.*, Miller, N., Zhao, X., Kelly, K.A. Munoz, D.F. Mann, D.J., Copenhaver, G.E. and Henderson, I.R. ‘High throughput measurement of meiotic crossover frequency and interference via flow cytometry of fluorescent pollen in Arabidopsis thaliana.’ Nature Protocols (2013) 8: 2119-2134.

Link: http://www.plantsci.cam.ac.uk/research/ianhenderson

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