Issue 11: Spring 2008

Zoologist William Bateson lay the foundation for genetics and the "green revolution" more than 100 years ago. He found there are many cases where there are large jumps in characteristics with no smoothly evolving evolutionary steps between, and in 1905 he coined a new word for the study of inheritance and variation: Genetics. Bateson was the first Director of the John Innes Horticultural Institution, founded at Merton in 1910. This centenary will be marked at JIC by a year of celebrations beginning with a launch conference in September 2009 [more »].

A flavour of the important outcomes from our century of science appear in a report on our economic and social impact by external consultants, DTZ. The report, published in April, is available on the JIC website; DTZ's impact analysis suggests that the sum total of operating impact and final market impact, covering work from antibiotic resistance to wheat improvement, is around £405M per annum in the UK alone. We will be developing this information further as part of our centenary web-pages. In 2010 we plan events focussing on the ground-breaking work of JIC's leading young scientists. One of these, Giles Oldroyd, was one of over 9000 scientists who submitted applications for funding to the first call for 'Starting Independent Investigators' by the European Research Council - the success rate was only 1 in 30, and his £1.3M award will support major new research on mycorrhizal associations [more »].

Having publicly launched the Earth & Life Systems Alliance recently, we are now promoting exciting new collaborations between UEA and JIC researchers. A total of seven projects have been funded already and a second internal funding call is planned this year.

Finally, I would like to congratulate Caroline Dean on her election to the National Academy of Sciences - one of the highest honours given to a scientist or engineer in the USA, and Mervyn Bibb on his election to a Fellowship of the American Academy of Microbiology. These Fellowships recognise 'excellence, originality and creativity', essential attributes of the outstanding scientists at JIC.

Chris Lamb
Director, John Innes Centre

Science Accolades

Caroline Dean and Chris Lamb have received prestigious honours recognising their internationally important contributions to science. In April Caroline Dean OBE FRS was elected a member of the National Academy of Sciences for her excellence in original scientific research. She is one of 5 UK scientists elected to receive one of the highest honours given to a scientist or engineer in the USA.

In May, Chris Lamb was elected a Fellow of the Royal Society, the UK's national academy of science, in recognition of his scientific achievements in fundamental research and in leading scientific progress. The Fellowship of the Royal Society is composed of 1300 of the most distinguished scientists from the UK, Ireland and the Commonwealth. "This honour is a great thrill but also further recognition of the strength of plant and microbial science at the John Innes Centre" said Professor Lamb.

ELSA launches

The UK’s House of Commons in London saw a gathering of Members of Parliament, policy-makers and senior members of the national research community for the formal launch of ELSA, the Earth and Life Systems Alliance. A collaborative initiative between JIC and the University of East Anglia, ELSA is focussed on pulling together life, earth and social sciences to tackle the issues of a changing environment.

Professor Bob Watson speaking at the ELSA launch

Presentations at the Earth and Life Systems Alliance launch event by high level scientists confirmed the need for collaborative efforts to tackle environmental change. Professor Bob Watson, Chief Scientific Adviser to the Department for the Environment, Food and Rural Affairs, explained the global challenges facing the planet, from the food / fuel land use debate to the cultivation of hostile environments and availability of water. He pointed out how well placed ELSA is to help address some of these issues. Professor Chris Rapley, Director of the Science Museum focused on the value of collaboration and how ELSA’s multi-disciplinary approach can help unravel some of the massive challenges facing the human race. As former Director of the British Antarctic Survey, he brought a fresh perspective on the global challenges associated with environmental change, as well as the socioeconomic impact of climate change.

The three “pillars” of ELSA were outlined in more detail by Alliance representatives. Caroline Dean (JIC) gave the overview of the Biodiversity and Adaptation pillar, while Kerry Turner (UEA Environmental. Sciences) described the activities within the Agricultural Transitions pillar, and David Richardson (UEA Biological Sciences) explained the background and future of the Elemental Cycles pillar.

Website: www.elsa.ac.uk

Plant gene clusters for natural products

JIC scientists have found that plants may ‘cluster’ the genes needed to make defence chemicals. Their findings may provide a way to discover new natural plant products of use as drugs, herbicides or crop protectants. Using a gene cluster that makes an antifungal compound in oats as a template, they uncovered a previously unknown gene cluster making a related compound in a very different species, and now want to extend the search to other plants.

Anne Osbourn and colleagues previously found that the genes needed to make an antifungal compound in oats, called avenacin, were next to each other in the genome. One of a group of chemicals known as triterpenes, avenacin is produced exclusively by oats and protects the roots against a wide spectrum of fungal diseases. Gene clusters are common in bacteria and fungi but extremely rare in plants. Maize has a gene cluster for a defencerelated compound, and another possible cluster has been reported in rice.

Could other plant gene clusters exist, and how do they arise? To investigate this, the researchers used the ‘signature’ of the avenacin genes to scan the genome of the model plant Arabidopsis. Publishing in the journal Science, they have identified a gene cluster for a new pathway that makes and modifies a triterpene called thalianol, which has not been found in plants before. The thalianol gene cluster consists of four genes next to each other in the Arabidopsis genome. The first gene, responsible for making thalianol, is from the same family as the gene for the first step of the avenacin pathway in oats. The next three genes in the thalianol cluster are responsible for making sequential modifications to thalianol. Having successfully discovered one gene cluster, the researchers now plan to look for other gene clusters that may produce novel natural products of value for crop protection or as medicines, and investigate how and why these clusters evolve.

Although the oat, maize, rice and this new Arabidopsis gene cluster make related products, they have been assembled independently of each other as a result of relatively recent evolutionary events.

This suggests that plant species are able to show remarkable plasticity in their genomes to assemble the clusters. Understanding the evolutionary driving forces behind their assembly will give insights into why some plant product pathways are maintained in these clusters whilst others are not, and this may have implications for our understanding of plant metabolism. Clustering genes together lets plants easily inherit an entire pathway.

The thalianol gene cluster is one of the most conserved areas of the genome, suggesting that this beneficial combination of genes has recently and rapidly spread throughout the population. Breaking up a gene cluster can have severe consequences. When the avenacin pathway is blocked, then unfinished intermediates accumulate that can have a toxic effect on the roots, making them deformed and ineffective. Intermediates which affect plant growth also accumulate when the thalianol synthesis pathway is blocked. If these intermediates accumulate in parts of the plant where the thalianol pathway is usually not present then they cause severe stunting of growth. Co-author Ben Field comments that this suggests that gene clusters, as well as keeping beneficial combinations of genes together, may prevent toxic side-effects by strictly controlling where and when the pathway is switched on.

Reference: Metabolic diversification – Independent assembly of operon-like gene clusters in different plants. Field, B. & Osbourn, A. (2008) Science 320 (5875) 543-547
http://www.sciencemag.org/cgi/content/abstract/320/5875/543

Funding: BBSRC Core Strategic Grant

Signalling changes in the cell wall

Cell wall materials represent the major carbohydrate component in most plants. Understanding how plant cell wall composition is controlled is highly relevant because of the potential for converting cell wall material to biofuels and chemical feedstocks. A major research objective in this area is to alter cell wall composition in biomass crops such as rapidly growing willow, poplar and perennial grasses. Recent research has identified genes encoding enzymes involved in synthesising different cell wall components, but many other aspects of cell wall function and organisation are not well understood.

Mike Bevan’s group in collaboration with Norwich Research Park colleagues have recently described several mutants in genes encoding enzymes synthesising sugars destined for incorporation into cell wall polysaccharides. The mutants exhibit strong sugardependent growth and developmental phenotypes in the dark, and elevated starch levels. These phenotypes require a well characterised protein involved in regulating sugar, hormone and light responses. They also showed that changes in cell wall structure and composition are most likely responsible for the observed phenotypes.

With new funding from BBSRC gained through ‘Responsive Mode’ Mathilde Seguela, who has recently joined Mike Bevan’s group from Montpellier, will define other components of this pathway using genetic screens and establish links with known sugar-response pathways.

The outcomes of this research will establish, possibly for the first time, that plant cell wall composition and levels are regulated in response to carbohydrate availability. This knowledge will provide an understanding of how resources are allocated to cell wall synthesis and may also help design crops that allocate more resources to cell wall biomass.

Reference: Cell wall composition changes caused by hsr8/mur4 mutations activate PRL1- dependant sugar responses in Arabidopsis thaliana. Li, Y. et al. (2007) The Plant Cell 19 2500-2515
http://www.plantcell.org/cgi/reprint/19/8/2500.pdf

Funding: BBSRC grant and BBSRC Core Strategic Grant

Collaboration: Institute of Food Research, UK and University of East Anglia, UK

Wheat Pairing

Conventional breeding in wheat can be hampered due to the nature of the genome. Hexaploid bread wheat contains 3 related genomes, each with 7 pairs of chromosomes (unlike most organisms which are diploid, with two sets of homologous chromosomes, one from each parent).

The different sets of chromosomes are kept under control by a gene locus called Ph1. Each chromosome will only pair with the homologous chromosome from its own genome, and not those from the other genomes. This essentially means that wheat acts like a diploid plant. Ph1 prevents non-homologous chromosomes from pairing, and stabilises the genome. Importantly for plant breeders, Ph1 prevents the chromosomes of wheat from pairing with those of different related species, making it very difficult to introduce new genes or traits by crossing. Breeders have used mutants lacking Ph1 to overcome this, but the resultant hybrids are unstable, because Ph1 is required to stabilise the whole genome.

Graham Moore and Peter Shaw, working with former JIC Visiting Scientist Michael Wanous from South Dakota, and colleagues in Spain and Australia, have shown recently that pairing requires remodelling of the chromatin (the structure of the chromosomal DNA and its associated proteins). Ph1 ‘senses’ whether two chromosomes are identical, and if so it synchronises the remodelling of their chromatin. If the chromosomes are not homologous pairs, chromatin remodelling is not synchronised and this prevents them from pairing effectively.

Further work is now looking at temporarily turning off the Ph1 locus to allow non-homologous chromosomes to pair. This would facilitate the breeding-in of beneficial traits such as drought tolerance and disease resistance from wild relatives. In subsequent generations, Ph1 is turned back on, so only homologous chromosomes pair, and the genome stability is restored.

Reference: Effective chromosome pairing requires chromatin remodeling at the onset of meiosis. Colas, I. et al. (2008) Proceedings of the National Academy of Sciences 105 (16) 6075- 6080
http://www.pnas.org/cgi/content/abstract/105/16/6075

Funding: BBSRC Core Strategic Grant, Marie Curie Fellowship from the Early Stage Training Program, National Institutes of Health Grant from the National Center for Research Resources IDeA Network of Biomedical Research Excellence Program

Collaboration: Instituto de Agricultura Sostenible, Alameda del Obispo Spain, Scientific and Industrial Research Organisation, Canberrra and Biology Department, Augustana College, SD USA

How roots find a route

Liam Dolan’s group have discovered how roots find their way past obstacles to grow through soil. Their work, with Japanese collaborators, also explains how germinating seedlings penetrate the soil without pushing themselves out as they burrow. The key is in the fuzzy coat of hairs on the roots of plants. Root hairs explore the soil in much the same way as a person would feel their way in the dark. If they come across an obstacle, they feel their way around until they can continue growing in an opening. In the meantime, the plant is held in place as the hairs grip the soil. This ability is governed by a self-reinforcing cycle. A protein at the tip of root hairs called RHD2 produces free radicals that stimulate the uptake of calcium from the soil. Calcium then stimulates the activity of RHD2, producing more free radicals and further uptake of calcium. When an obstacle blocks the hair’s path, the cycle is broken and growth starts in another location and direction.

This remarkable system gives plants the flexibility to explore a complex environment and to colonise even the most unpromising soils, and also explains how seedlings are able to grow so quickly once they have established.

In nutrient poor soils such as in parts of Australia and sub- Saharan Africa, plants have adapted by producing more root hairs. A better understanding of this adaptation will allow the development of crops able to grow in inhospitable environments.

Reference: Local positive feedback regulation determines cell shape in root hair cells. Takeda, S. et al. (2008) Science 319 (5867) 1241 - 1244
http://www.sciencemag.org/cgi/content/abstract/319/5867/1241

Funding: BBSRC Core Strategic Grant and BBSRC Grant BBS/B/04498, a Marie Curie International Incoming Fellowship, the John Innes Foundation and support from the Japanese Ministry of Education, Culture, Sports, Science and Technology Collaboration

Collaboration: Tokyo University of Science, Chiba, Japan

 

Spotlight on Diseases

Plants and their pathogens and parasites have evolved together for millions of years. Disease can result in rots, water-soaked lesions, blights, wilts, powdery or downy mildews, or rust lesions on the plant.

Effectors

- the key to understanding pathogenicity

TSL’s Cyril Zipfel and Sophien Kamoun have recently been funded by BBSRC to continue their ground-breaking work on bacterial pathogen-associated molecular patterns (PAMP)-triggered immunity in plants, and the molecular mechanisms that enable oomycete pathogens, such as Phytophthora infestans (late potato blight) to successfully infect plants, and the plant processes that are perturbed by this pathogen.

Volker Lipka, who joined TSL recently from the Dept. of Plant-Microbe Interactions at the Max-Planck-Institut für Züchtungsforschung, Köln, has just coauthored a paper published in Nature ‘Letters’ on pre-invasive resistance pathways against powdery mildew. He continues this area of work at TSL. Reference: Co-option of a default secretory pathway for plant immune responses. Kwon, C. et al. (2008) Nature 451 835-840 http://www.nature.com/nature/journal/ v451/n7180/abs/nature06545.html#abs

Downy mildew (Hyaloperonospora parasitica) is a pathogen of more than 140 species in the family Crucifereae as well as the plant model organism, Arabidopsis thaliana. H. parasitica and other downy mildews are classified as oomycetes, and are biotrophic, extracting nutrients only from living host tissue. Plants have evolved the capacity to recognise molecules made by the pathogens, known as “Pathogen-associated molecular patterns (PAMPs)” which trigger a defence response. In response pathogens make so-called effector molecules, which shut down the defence response elicited by PAMPs. Bacterial PAMPs and effectors are becoming well characterised, but those from fungi and oomycetes are mostly unknown.

The H. parasitica-Arabidopsis system is being developed as a model to explore the mechanisms by which biotrophic pathogens manipulate their hosts. At The Sainsbury Laboratory (TSL), PhD students Kee Hoon Sohn (Korea University), Rita Lei (Cambridge), and Adnane Nemri (ENSAT, France ) have been working with Jonathan Jones, using the H. parasitica-Arabidopsis system to investigate functions of the effector proteins that H parasitica secretes to promote disease susceptibility by contributing to pathogen virulence inside host cells. Plants have evolved mechanisms to circumvent these effectors by recognising them as cues to activate defence. Resistance (R) genes encode proteins that act as receptors for such effectors. To overcome an R gene, a pathogen must cease to produce or alter the molecule the R protein detects; pathogens thus need a suite of effectors so that if one is resisted and must be discarded, others can substitute. Effector molecules recognised by R genes are said to be encoded by Avirulence genes (Avr genes), so-called because if they are functional, the pathogen will be avirulent on plants carrying the corresponding R gene.

Deciphering the biochemical activities of effectors to understand how pathogens successfully colonise and reproduce on their host plants is a key target of research at TSL.

Reference: The downy mildew effector proteins ATR1 and ATR13 promote disease susceptibility in Arabidopsis thaliana (2007) Sohn, K. H. et al. The Plant Cell 19 (12) 4077-4090
http://www.plantcell.org/cgi/content/abstract/19/12/4077

Funding: Gatsby Charitable Foundation

In JIC's Dept of Disease & Stress Biology, Paul Nicholson heads a group investigating facultative pathogens involved in disease complexes of the stem-base and heads of cereals.

Eyespot markers

CASE-funded PhD student Chris Burt is working on eyespot, supervised by Paul Nicholson. Chris studied for an MSc in plant breeding at JIC, sponsored by the Chadacre Agricultural Trust, and then spent 4 years working for Floranova including periods in Costa Rica and California before returning to JIC. Chris spoke at a meeting recently on ‘Tomorrows People, Enhancing Education and Research in Agriculture’ organised by Chadacre Agricultural Trust, where he described how the charity had supported his MSc studies.

Eyespot (caused by Oculimacula yallundae and O. acuformis) is a necrotrophic fungal disease of wheat, which occurs on the stem bases of infected plants. It is one of the most important diseases of the stem base in temperate regions. The infestation weakens the straw and yield losses mainly occur as a result of lodging before the wheat can be harvested.

Up until now, there have been no useful molecular markers for one of the major eyespot seedling resistance genes, Pch2 originally derived from the variety Cappelle Desprez.

Nicholson’s group used genomics resources to identify simple sequence repeat (SSR) and gene-based markers closely linked to Pch1 (the most potent resistance, which derives from a wild grass species). His group went on to develop a series of PCRbased markers to facilitate selection of these two eyespot resistance genes. This advance will enable breeders to test their breeding material for these two important genes using a single technology.

Reference: The development of PCR-based markers for the selection of eyespot resistance genes Pch1 and Pch2 . Chapman, N. H. et al. (2008) Theoretical & Applied Genetics online prior to print
http://www.ncbi.nlm.nih.gov/pubmed/
18483719?dopt=Abstract

Funding: Nickerson (UK)Ltd, UK Home-Grown Cereals Authority and BBSRC via BBSRC-CASE awards.

Head blight susceptibility

- the dwarfing link

Fusarium head blight (FHB) is an important disease of wheat worldwide and is of particular concern because the fungi produce trichothecene mycotoxins, such as deoxynivalenol, which are harmful to human and animal consumers. Resistance to FHB is horizontal and non-species and non-strain specific, and the development of FHB-resistant cultivars is generally accepted as the most cost-effective and environmentally benign way to minimise the infection.

The JIC group used a mapping population from a cross between the most resistant UK winter wheat cultivar Spark and the FHB susceptible cultivar, Rialto to identify quantitative trait loci associated with resistance. This has allowed them to show that the Rht2 semi-dwarfing allele that predominates among UK wheat varieties is linked to susceptiblity to FHB. The resistance of Spark, it transpires, may be due to the presence of a wild-type (tall) allele at the Rht-D1 locus rather than the semi-dwarfing allele.

It also appears from their most recent work that the two semi-dwarfing alleles used thoughout the world (Rht1 and Rht2) differ in their association with susceptibility to FHB. The long-term aim is to provide information to breeders to enhance FHB resistance in their varieties and to identify candidate FHB resistance genes for exploitation by scientists and plant breeders.

Reference: Susceptibility to Fusarium head blight is associated with the Rht-D1b semi-dwarfing allele in wheat. Srinivasachary et al. (2008) Theoretical & Applied Genetics 116 (8) 1145-1153

Funding: UK Home-Grown Cereals Authority and Defra-LINK Collaboration: Nickersons Seeds (UK) Ltd, Elsoms Seeds Ltd, Advanta Seeds (UK) Ltd and RAGT (UK) Ltd.

REVIEWING SCIENCE

Breeding for tolerance to stresses

JIC’s Germplasm and Field Trials Manager Steve Reader has contributed to a major review of breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity which cause large and widespread yield reductions in cereal crops. Drought will increase in importance with climate change, the area of irrigated land that is salinised continues to rise, and the cost of inorganic N is increasing. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the authors examine the complex mechanisms of tolerance.

Reference: Breeding for abiotic stresses for sustainable agriculture. Witcombe, J. R. et al. (2008) Philosophical Transactions of the Royal Society B - Theme Issue ‘Sustainable Agriculture II’ compiled by Pollock, C. et al. 363 (1492) 703-716

Collaboration: CAZS Natural Resources, University of Wales, Bangor and the Institute of Grassland and Environmental Research, Aberystwyth

Pharma-Planta

Significant advances over the last few years have seen plant-made pharmaceuticals (PMPs) move from the exploratory research phase towards clinical trials. These emerging products are set to challenge the complex and overlapping regulations that currently govern GM plants and ‘conventional’ pharmaceutical production. JIC’s Penny Sparrow is lead author of a recent article discussing the development of robust risk-assessment and riskmanagement practices for PMPs, working with EU regulatory authorities to ensure appropriate regulatory oversight.

Reference: Pharma-Planta: road testing the developing regulatory guidelines for plant-made pharmaceuticals. Sparrow, P. A. C. et al. (2007) Transgenic Research 16(2) 147-161
http://www.ingentaconnect.com/content/klu/trag/2007/00000016/00000002/00009074

Funding: Pharma-Planta (www.pharma-planta.org) is an EU funded academic research consortium Collaboration: Universities of York & London

 

RevGenUK launches

Agriculture has relied for millennia on plant variation to improve its crops. We can now generate variation in a species at will using reverse genetics.

Reverse genetics involves making a change to a specific gene, seeing what effect this has, and so working out the gene’s normal function. JIC is at the forefront of reverse genetics through collaborative work between Trevor Wang and Giles Oldroyd, with the establishment of TILLING and de-TILLING technologies in model legumes, and Lars Østergaard’s research on Brassica rapa, a model brassica closely related to Arabidopsis, and so useful for translating knowledge learnt in this model plant. BBSRC has now provided funding of £1M over 4 years to support the development of this science into a single-stop, self-sustaining biological and bioinformatics resource for the wider plant scientific community, providing an integrated reverse genetics platform for model plants.

The technology to detect the mutations has been adapted by JIC scientists to work on highthroughput sequencers to greatly increase efficiency. A researcher interested in a particular gene will be able to apply to RevGenUK at the Centre’s Genome Laboratory to get seeds of plants in which their favouritegene has an altered function.

RevGenUK launched on May 15th with a research meeting in Norwich.

Contact trevor.wang@jic.ac.uk for further details.

Website: Revgenuk.jic.ac.uk

 

BBSRC’s CoSyst funding encourages new collaborations in systematics that could lead to novel Responsive Mode proposals to BBSRC or NERC

Tendril-less genes

JIC is the leading centre in the UK for pea genetics, and the recent discovery by Noel Ellis’s Group of the identity of the Tendril-less gene in pea provides the opportunity for studying the origin of this novel structure and the molecular basis of variant forms in several crop species; pea, lentil, faba bean and chickpea.

CoSyst support will allow a new link to colleagues with expertise in legume systematics and evolution at the Royal Botanic Garden, Edinburgh.

How do wild plants respond to climate change?

Global climate change is already altering the timing of important developmental and behavioural events in plants. Phil Wigge is studying how plants sense and respond to changes in ambient temperature. CoSyst support will enable him to work with David Roberts from Kew Gardens on the highly co-evolved pollination systems in orchids, which could be particularly susceptible to disruption. Having molecular markers and assays for analysing the effects of climate change on wild plants would be a ‘first’.

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Flowering time

- an important adaptive character

Barley and wheat, in common with many plants, use day length and temperature as cues from the environment to regulate the timing of flowering during the year. Flowering time is an important adaptive character with major impacts on yield and quality because it affects the efficiency with which the optimal growing conditions in a given environment can be exploited. Studies by the University of East Anglia, Climate Research Unit predict hotter and drier summers in the UK. This should favour earlier flowering winter wheat varieties because this has been the adaptive solution to similar conditions that exist now in central and Southern Europe. Photoperiod-1 (Ppd-1) is the key gene that provides this adaptation in wheat.

New BBSRC Responsive Mode funding will allow David Laurie’s group to study the Ppd gene in detail to understand how variation at the DNA sequence level creates variation that impacts upon plant development in ways that affect productivity. Their preliminary work on wheat Ppd has provided a “first generation” of diagnostic markers which have been successfully tested by the British Wheat Breeders Group, other companies, and by the international wheat breeding centre (CIMMYT) in Mexico. Longer term goals of the work are to advance the understanding of flowering to a level that enables plant breeders in the UK and elsewhere to predict which genotypes will be suited to particular farming environments.

In parallel and also funded by BBSRC and HGCA under the Crop Science Initiative, the National Institute for Agricultural Botany is establishing a pre-breeding programme that will provide a delivery mechanism to exploit the lead established by the Laurie group on Ppd, allowing novel traits to flow from publicly funded research to exploitation in commercial breeding.

MODELLING

Growth and gene regulation

Systems biology aims to predict the behaviour of complex biological systems by quantitative modelling of the interactions between the relevant components. With support from a Franco-British national funding agencies initiative, Robert Sablowski will coordinate a JIC/UEA/ENS Lyon/CNRS Grenoble/ INRIA Montpellier team to advance understanding of how networks of genes control organ growth. The team will produce quantitative models of how regulatory genes co-ordinate the cell behaviour that produces the macroscopic shape of floral organs.

An Optical Projection Tomography image of Antirrhinum with the reconstruction based on Zernike moments. Although the reconstruction suffers from a number of shortcomings and inaccuracies, this is an excellent starting point on which to base future developments

3-dimensional object processing

Theoretician Richard Morris’s recent work has been to develop a mathematical framework for modelling and comparing 3D shapes accurately and efficiently. BBSRC ‘Tools and Resources’ funding will enable him to extend his work from macromolecules and binding pockets, to make a significant contribution to the development of computational modelling in the form of software for the analysis of plant images.

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Plant molecular pharming opportunity

Kay Denyer and colleagues have received ‘follow-on’ funding from BBSRC to enable them to research a commercially-viable expression system for valuable proteins in plants. They have discovered a novel starch-targeting sequence by which proteins are targeted to granules. The proteins retain their activity when embedded in the starch granules and have increased heat-stability. The starch containing the proteins can be easily purified, stored dry, and has exceptional shelf-life. The project is being undertaken in collaboration with PBL Technology and EnaGen LLC of Ames, Iowa.

Triticeae Genome

Mike Bevan is a partner in an EU-funded Integrating project funded under Framework 7, a major contribution to a series of coordinated international projects that aim to construct physical maps of the barley and wheat genomes. The outcomes of the project will support efficient breeding of new varieties for European agriculture.

Tapping into Thai resources

Many of the drugs used in medicine today are derived from microbial natural products, and include antiinfectives, anti-tumour agents, immunosuppressants and cholesterol lowering agents. Thailand boasts a wealth of microbial diversity, yet many of these organisms have proven refractory to culture under laboratory conditions.

Funded by the British Council, JIC’s Mervyn Bibb and Kasetsart University’s Arinthip Thamchaipenet will now use metagenomic approaches to identify novel natural products with potential pharmaceutical application. The aim of their two year project is to combine the microbial expertise of the Thai group and their access to untapped biological resources with the molecular expertise at JIC to unleash some of this thus far unexplored microbial and chemical diversity.

In addition to screening rare actinomycetes (the bacteria that produce about two thirds of all know antibiotics) isolated from pristine Thai environments, a culture-independent approach will be taken to identify to novel biosynthetic pathways from metagenomic libraries derived from both soil and marine environments. Given the increasing prevalence of multiply antibiotic resistant pathogens, the team will be paying particular attention to any novel compounds with anti-microbial activity.

VOICES OF YOUNG SCIENCE

Circadian clocks

PhD students at JIC and TSL hold an annual meeting with presenters selected based on voting for posters displayed at the in-house Annual Science Meeting (ASM). It is an opportunity for young scientists to present their work to a sympathetic audience and they also decide who will be nominated as the student speaker at the next ASM – a great honour.

Congratulations go to Alex Graf (also see Advances 10) who was voted the winner on the day for his talk ‘A question of time? Starch turnover in Arabidopisis thaliana and the circadian clock’.

Showcase for young scientists

JIC PhD student Amy Strange, accompanied by Judith Irwin, spoke on ‘About blooming time: a plant’s response to changing climate’ at a Showcase for Young Scientists event at the Royal Institution in April.

Many plants need a long period of cold before they are able to flower but average winter temperatures have been rising over the past 25 years, and soon our changing climate may result in temperatures that are no longer cold enough for plants to perceive as winter. One consequence of this may be that plants fail to flower at the correct time.

Arabidopsis thaliana (thale cress) grows throughout the northern hemisphere from the equator to the Arctic circle, surviving in a huge range of climates. Amy is contributing to research to understand how this plant species has adapted to very different winter conditions, adjusting its flowering response to the length of the winter. This information may then be used to help plant breeders select crops suited to our changing climate.

“Giving a talk in the Faraday lecture theatre at the RI was a fantastic experience. There was a diverse audience and some really interesting questions were asked after the talk. It was a thoroughly enjoyable evening.”

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DEFRA updated

Lord Jeff Rooker, Minister of State at the Department for the Environment, Food & Rural Affairs toured JIC recently, to meet scientists including James Brown, Associate Head of the Dept. of Disease & Stress Biology.

Evidence Ltd report on TSL

The results of a bibliometric analysis on the 406 publications in 96 journals produced by The Sainsbury Laboratory in 1997- 2006 show that almost one-third (32.1%) of papers published by TSL are highly-cited (cited more than 4 times the relevant world average). About 5% of total UK papers normally pass this hurdle.

TSL scientists have published more than 50 papers (12.5%) in the three elite, multidisciplinary journals Nature, Science and Proceedings of the National Academy of Sciences USA.

The impact of TSL research in all research fields has been consistently high throughout the 10-year period covered by the report.

Access the full report via www.tsl.ac.uk

Visit to CIMMYT Mexico

To promote cooperation between JIC and the International Centre for Wheat and Maize Improvement (CIMMYT), John Snape and Simon Griffiths visited their main trials site in Ciudad Obregon, north-west Mexico, and headquarters at El Batan, near Mexico City recently. A number of collaborative initiatives on wheat were activated by the visit, including work on yield potential, nitrogen use efficiency, molecular markers and alien gene transfers.

CIMMYT is the global centre for wheat genetics, genomics, physiology, pathology and wheat breeding aimed for the benefit of the Developing World. It has an enormous wealth of expertise and germplasm which could be used by the UK wheat research and breeding communities to advance studies on sustainable agriculture

Brush Strokes

Eva is an artist.
She paints chromosomes.

The gene for love, coloured red
lies close to the telomere
on chromosome five
next to envy
green as cat’s eyes.

Hope is polygenic,
scattered through the genome
like gold dust.

JI100 celebrations

In 2010 it will be 100 years since the John Innes Horticultural Institution was founded at Merton, near London. The centenary will be marked by a year of celebrations beginning with a launch conference in September 2009. This will reflect on the various areas of human interest that have been informed by a genetics approach, and where these areas are now. There will be a retrospective exhibiton on the work of John Innes scientists from the early days to the time of the creation of the Centre at Norwich, highlighting their outstanding contribution to genetics, plant science and microbiology, and their importance to the advance of horticulture, agriculture, biotechnology and medicine.

Other celebratory plans include an Alumni weekend, special ‘Friends of JIC’ events, themed exhibitions and concerts. The centenary year will close in July 2010 with events in London and Norwich focussing on the ground-breaking work of JIC’s leading young scientists, and will look forward to the next 100 years of excellence in biological research.

For further information please contact Sarah Wilmot, Outreach Curator - sarah.wilmot@jic.ac.uk