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RA5a: Structure,environment and staffing policy

Introduction
We aim to conduct internationally-competitive research across a broad spectrum of experimental plant and microbial sciences, encompassing all levels from molecular biology to ecology. We are largely located in a single, extensively-refurbished building which facilitates interactions. We also benefit from our own library (with an impressive selection of relevant periodicals and 20,000 books), a Herbarium (with nearly I million sheets including 50,000 type specimens and all of Darwin’s specimens from the Beagle) and the Botanic Garden (with a living collection of over 1000 trees and 10,000 other plants). We have 18 University-funded technicians who contribute directly to research and currently we train around 50 postgraduate research students.

Developments since 1996
We have successfully implemented all of the plans outlined in the 1996 RAE submission. The appointment of Professor Roger Leigh to the Chair of Botany in March 1998, following the untimely death of Professor Tom ap Rees in October 1996, was accompanied by an acceleration and expansion of the Department’s staff recruitment and building refurbishment programmes. Seven new academic appointments have been made since 1996: Professor John Parker (1996; Director of Botanic Garden and Professor of Plant Cytogenetics), Dr Julia Davies (1997; University Lecturer), Professor Roger Leigh, Dr Jim Haseloff (1999; University Lecturer), Dr Beverley Glover (1999; University Lecturer), Dr Julian Hibberd (1999; University Lecturer), and Professor Howard Griffiths (2000; to newly established Chair of Plant Ecology). Jim Haseloff and Julian Hibberd are presently on leave-of-absence from their University Lectureships while on prestigious externally-funded Fellowships which they hold in the Department. Several new independent Research Fellows joined us: Charles Brearley (1997; BBSRC Advanced Fellow; moved to a Lectureship at UEA, 2001), Ruth Mould (1997; Royal Society University Research Fellow), Alex Webb (1999; Royal Society University Research Fellow) and Kate Maxwell (transferred from Newcastle, 2000; Royal Society University Research Fellow). These various appointments have resulted in a considerable expansion of research activity in molecular and cell biology as well as a welcome strengthening of organismal and ecological research. The Department’s paleobotanists both left in 1998, Keith Bennett to a Chair in Uppsala and Kathy Willis to a Lectureship at the University of Oxford. A decision was taken to discontinue this area in order further to focus research. Three members of the Department, were promoted to Personal Chairs: John Gray (1996), Christopher Gilligan (1999) and Peter Grubb (2000). The following retired: Peter Sell (1996), Enid MacRobbie (1999) and Patrick Echlin (1999). Enid MacRobbie remains research active and will take up a Leverhulme Emeritus Fellowship in 2001. She became a Foreign Associate of the US National Academy of Sciences in 1999.

The University-funded refurbishment of our main building cost approximately £2 million and our research activities have benefited from the creation of three new laboratories, the upgrading of three existing ones, replacement of glasshouses, new autoclave and glassware-washing facilities, an IT suite in the Library, and the extension of the lift to the basement (opening the opportunity for the future development of this area). In 1996/97, the Cory Laboratory at the Botanic Garden was upgraded to molecular standards to accommodate John Parker’s research. In 2000, the University undertook an institutional review of the Herbarium which recognised its unique value to future research in Cambridge and recommended that it should eventually move to the Botanic Garden as part of a new major centre for plant systematics and evolution.

The total value of grants won each year has increased since 1996 with £2.26 million awarded in 2000. During the period 1996-2000, we were awarded 72 grants with a total value of £7.91 million, with most coming from Research Councils (69%), charities (15%) and industry (14%). Thirty grants were less than £50k, 38 were £50k-250k and 4 were more than £250k. Successful applications to the JREI (supported by Biogemma UK, Advanced Technologies Cambridge, Provac Services Ltd, and Mineral Solutions Ltd) allowed us to purchase a confocal microscope, a Typhoon phospho- and fluoro-imaging system, and a mass spectrometer. Other purchases have given us world-class facilities for cell physiological studies including equipment for sampling and analysing the contents of individual cells, a combined patch clamping and quantitative calcium imaging facility, and a luminometer with a photon counting camera to measure aequorin and luciferase. The purchase of new mass spectrometers for Howard Griffiths has given us outstanding facilities for using stable isotopes in physiological research. Although our research grant expenditure continues to rise, the information set out in RA4 for the first 5 months of the present financial year underestimates our expenditure by an estimated £67k. This is due to the introduction of a new accounts system on 1 August 2000 which delayed significantly the payment of invoices and the backlog was not cleared until early 2001.

Seventy one PhDs and 12 research-based MPhils have been awarded to our postgraduate students since 1996. Half of our studentships come from Research Councils, 15% from charities, and 15% from UK Central Government or industry (excluding CASE support).

Strategic Planning and Management
Each individual is expected to develop, fund and supervise their own internationally-competitive research programme but the Department supports them through its administrative and other activities. Strategic developments are considered by the Department’s Strategic Planning Group which also acts as the Resources Committee. It identifies future infrastructural and other needs and decides how they should be funded. All important decisions are discussed at termly staff meetings before implementation. Periodic meetings of all group leaders (most recently in December 2000) discuss research strategy, future research opportunities and other research-related issues which are then fed into the above process. The Departmental Administrator and his staff are responsible for all administrative, financial and personnel matters. Technical management is provided by the Chief Technician. The research training of graduates is overseen by a Graduate Education Committee which is responsible for recruitment, monitoring progress, and ensuring early submission of theses. This Committee liaises closely with the new Graduate School in Biological, Medical and Veterinary Sciences which provides information for potential applicants, encourages dissemination of best practice, and coordinates generic training courses.

Support for Research
All new academic staff receive a "start-up“ allowance of approximately £17k from the University and the Department provides additional funds. We provide each staff member with their own laboratory and, because we are well-provided with University-funded technicians, their own research technician. Independent research fellows (IRFs) are also provided with their own research space although some share laboratories with colleagues when this brings clear scientific advantages. They are also given some start-up funds, if needed. Teaching commitments for staff are minimised in the first few years after appointment to give them time to establish their research. We use our annual subvention from the University to provide consumable support to groups (based on postgraduate numbers) and to purchase new equipment through a bidding process open to all academic staff and IRFs. We also use our research bequest, the Brooks Fund, to support strategic research developments and have committed over £400k since 1998. All staff are encouraged to take their entitlement of sabbatical leave in order to learn new techniques or explore new research directions. Since 1996, the following have had sabbaticals or were freed from teaching and administration through Fellowship awards: Christopher Gilligan (1998/99), Keith Johnstone (1998/99), David Hanke (1998/99), John Gray (1999/2000), Edmund Tanner (1999/2000), Julian Hibberd (2000/04), Jim Haseloff (1999/04), Mark Tester (2000/01) and David Briggs (2001). John Carr and Alison Smith will be taking sabbaticals in 2001/02. Postgraduate studentships are awarded to students on merit and they then select a project from those on offer. Second- and third-year postgraduates can apply competitively for a Frank Smart Studentship in Botany which provides them with a bursary to spend on research-associated activities, while those in hardship can apply to the Tom ap Rees Fund for financial support. All academic staff and IRFs participate in the University’s staff appraisal system which provides them with an opportunity to discuss their research achievements and plans. The Department organises a Research Day at which all groups present aspects of their work, and during Term has weekly seminars given by external speakers. Most groups organise weekly meetings to discuss research progress, often jointly with others.

Research Organisation and Achievements
Since 1998 our research has been organised into four themes that will be the focus of future activities and growth. Groups from within the Department contribute to a number of inter-Departmental initiatives including the Multi-Imaging Centre, the Cambridge Centre for Molecular Recognition, and The King’s College Research Centre Project on Spatially-Extended Dynamics. We had productive collaborations (resulting in a paper, grant or studentship) with 68 individuals in 27 universities, 20 research institutes and 3 companies. Approximately half of these were with scientists outside the UK. The accounts below highlight our main achievements. Publications are referred to by staff name and publication number in RA2


Plant and Organelle Development (Haseloff, Glover, Gray, Mould): This area has been substantially strengthened, with the appointments of Jim Haseloff and Beverley Glover giving us considerable expertise in molecular genetic approaches to plant development. Jim Haseloff has made major technological advances for studies in plant development and cell biology. His GFP gene constructs optimised for expression in plants (Haseloff 4) have been disseminated widely (over 1000 samples distributed) and used extensively worldwide. His Arabidopsis enhancer trap lines with cell-specific expression of GFP are a major resource and over 300 have been distributed since May 2000. They have been used in his laboratory to provide insight into the organisation and development of cells in the Arabidopsis root (Haseloff 3). Beverley Glover has gained important understanding of mechanisms of epidermal cell differentiation and has shown how manipulation of expression levels of a Myb transcription factor can lead to dramatic changes in cell shape, including ectopic trichome formation (Glover 4). Her demonstration that epidermal cell shape in petals affects the probability of successful pollination by bumble bees (Glover 3) was highlighted in News and Views articles in Nature, New Scientist and national daily newspapers, and led to an invitation to speak at the International Botanical Congress in 1999. John Gray was responsible for the map-based cloning of a major gene (TTG1) controlling trichome initiation and anthocyanin biosynthesis in Arabidopsis (Gray 4). The identification of the gene product as a WD40-repeat protein is having a major influence on mechanistic studies of trichome initiation. In studies of chloroplast biogenesis, he identified plastid translation as an important prerequisite for expression of nuclear genes encoding photosynthesis components (Gray 3). With Julian Hibberd, he introduced a method for the microinjection of DNA into individual chloroplasts in living cells (Hibberd 1) and this has had an important impact on studies of macromolecular movement between chloroplasts. Ruth Mould has made major progress in identifying the mechanisms targeting of chloroplast-encoded proteins to the thylakoid membrane. She demonstrated the involvement of SecA in cytochrome f insertion into the membrane (Mould 4), and showed the interaction of thylakoid-targeting sequences of several proteins with the chloroplast signal recognition particle (Mould 3).

Transport, Signalling and Metabolism (Leigh, Tester, Davies, Webb, MacRobbie, Brearley, Lakin-Thomas, Hanke, Smith): The Department has long been recognised as a centre of excellence for studies of ion transport, intracellular signalling, and metabolism in plants. Research in this area has become increasingly focussed on cell-based events in relation to the functioning of whole plants. Roger Leigh provided the first fully quantitative insights into the regulation of K+ concentrations in the vacuole and cytosol in response to K-deficiency (Leigh 4) and, using covalent inhibitors, confirmed the identity of the substrate of the vacuolar proton-pumping pyrophosphatase, resolving a long-running debate (Leigh 3). Mark Tester has used Jim Haseloff’s GAL4-GFP enhancer trap lines of Arabidopsis to make the first comparison of Ca2+ currents in different cell types in roots (Tester 1) and to express a transgene in selected root cells (Tester 3), opening up the opportunity of investigating the functions of individual root cells in more detail. Julia Davies made the first measurements of plasma membrane ion channels in the human pathogenic fungus Candida albicans (Davies 3) and her demonstration of a novel calcium channel in the plasma membrane of root hairs and fungal hyphae has provided important insight into tip growth in these cells (Davies 1). Alex Webb initiated investigations into the role of calcium in circadian regulation of stomatal movements, building on his earlier work which showed that TOC1 is involved in the circadian control of stomatal movements (Webb 2) and that the pathways by which ABA, CO2 and Ca2+ close stomata converge (Webb 3, 4). Enid MacRobbie’s demonstration that ABA-induced release of vacuolar K+ in stomatal guard cells is triggered by an increase in cytosolic Ca2+, involving both influx from the outside and release from internal stores, has provided important insight into the regulation of salt export from the vacuole (MacRobbie 1). She and Charles Brearley made the major discovery that inositol hexakisphosphate acts as a second messenger in guard cells and has a more potent effect on inward rectifying potassium channels than inositol 1,4,5-trisphosphate (MacRobbie 2). Pat Lakin-Thomas’s work with lipid-deficient mutants of Neurospora crassa has made fundamental contribtions to the control of circadian rhythmicity by implicating diacylglycerol in this process (Lakin-Thomas 3), while her demonstration that strains with 'clock’ mutations are rhythmic when lipid-deficient has fundamental implications for the clock mechanism (Lakin-Thomas 2). David Hanke has made important contributions to the understanding of inositol metabolism and function by determining the complete biosynthetic and degradative pathways for inositol hexakisphosphate (phytic acid), in collaboration with Charles Brearley (Hanke 3, 4). Alison Smith has made important progress on the pathway of haem synthesis, establishing its subcellular location and the targeting of the enzymes (Smith 3, 4). With Chris Abell (Chemistry) she elaborated the entire pathway of pantothenate biosynthesis in plants and microorganisms, including isolation of genes, and overexpression, purification and crystallisation of the enzymes (the latter with Tom Blundell, Biochemistry). The structure of one of the enzymes was solved in a transition state giving important mechanistic information (Smith 2).

Photosynthesis and Physiological Ecology (Hibberd, Maxwell, Griffiths, Grubb, Parker): This area has been strengthened by recruitment during the assessment period providing an important future opportunity for understanding photosynthesis in the context of whole plant physiology, ecology and evolutionary biology. Julian Hibberd developed a method to microinject chloroplasts in whole plants (Hibberd 1) and showed that GFP can be used as a reporter for chloroplast gene expression (Hibberd 3). He demonstrated that photosynthesis in the parasitic plant Cuscuta reflexa occurs only in cells surrounding the vasculature (Hibberd 4) and is protected by a novel xanthophyll cycle (Hibberd 2). Kate Maxwell has discovered that long-lived leaves of the epiphytic bromeliad, Guzmania monostachia, acclimate to high light with a programmed reduction in cell and chloroplast constituents (Maxwell 1) and that diurnal changes in Rubisco activity in CAM plants are quite distinct from those in C3 plants (Maxwell 2). These studies have involved collaboration with Howard Griffiths who has used his expertise with stable isotopes to establish that distinct "C4“ signals are associated with changing carboxylation patterns in CAM plants (Griffiths 2) and to explain the basis of carbon isotope discrimination during photorespiration (Griffiths 1). Peter Grubb has made a seminal contribution to theoretical and practical understanding of how competition for resources varies during the course of plant and community development (Grubb 2). He has determined how far sensitivity of seedlings to competition for nutrients and water reflects the trade-off between ability to persist in the understorey and capacity to respond rapidly to gap creation in the forest canopy (Grubb 1, 4). John Parker has initiated a new research programme since moving to Cambridge, using molecular markers to understand genetic variation in natural plant populations. He has exploited the unique collection of Juniperus communis in the Botanic Garden to show that the British populations of this tree have diverse origins (Parker 1).

Pathology and Epidemiology (Gilligan, Carr, Johnstone, Ashby): Studies of plant pathogens have been a long-standing focus in the Department and the present emphasis is on quantitative and molecular understanding of the processes underlying infection, resistance and spread. Christopher Gilligan uses an innovative combination of experimentation and mathematical modelling to investigate the dynamics of host-pathogen interactions in heterogeneous environments and has successfully derived a coherent theoretical framework to analyse and predict the spread of beneficial and harmful microorganisms. The generic usefulness of this approach has been demonstrated through its successful application to Dutch elm disease (Gilligan 2), bubonic plague (Gilligan 1), and paleoecological invasions (Gilligan 3). John Carr has made the important discovery of a novel defensive signalling pathway that confers resistance to viruses by preventing their replication and movement (Carr 2-4). Keith Johnstone has identified a novel RecA-dependent mechanism of phenotypic switching of pathogenicity in the mushroom pathogen, Pseudomonas tolaasii (Johnstone 2, 3) and has identified a key role for extracellular cutinase in pathogenicity in the brassica light leaf spot pathogen, Pyrenopeziza brassicae (Johnstone 1). Alison Ashby was the first to clone and characterise the mating type locus of P. brassicae (Ashby 3) and has developed PCR-based techniques to detect the two mating type idiomorphs of the fungus on oilseed rape (Ashby 2).


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Copyright 2002 - HEFCE, SHEFC, ELWa, DEL

Last updated 17 October 2003

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