Issue 10: Winter 2007/8

Advances shows an interesting balance between not only ground-breaking science from JIC and TSL published in high impact journals, but also a number of interesting and useful papers on tools and breeding resources. Andy Maule’s front page discovery would not have been possible with short term grants and was dependent on taking adventurous approaches in proteomics only possible within an institute environment. We also highlight new funding – both in the form of substantial grants to support fundamental science, and smaller but none the less vital awards to support science into practice.

There are several breakthroughs en route to applications through exploitation of intellectual property. Many of these applications are ‘early-stage’, with some time to go before a successful outcome can be reported, and we are pleased that one of our earliest spin-out companies, Novacta Biosystems Ltd, the anti-infective therapeutics company established with PBL, has won a £3.2M award from Wellcome Innovations. Novacta will use the award to progress development of a drug which, it is hoped, will help combat hospital-based Clostridium difficile (Cdiff) infections. On a slightly different note, our newest spin-out, Procarta Biosytems Ltd, with science to combat antibiotic-resistant “superbugs”, received front page attention in The Financial Times recently, highlighting the potential economic impact as well as a societal benefit of this breakthrough.

Plans are well in hand for the celebration of the 100th anniversary of the founding of what is now the John Innes Centre. By the late spring of this year we will launch new webpages to describe our outstanding contribution to a century of genetics, and the conferences, alumni events and memorabilia planned for September 2009-July 2010. I look forward to sharing our ideas with you.

Chris Lamb
Director, John Innes Centre

Cells with something to say

The roadway between cells

For any multicellular organism to work, it is essential that one cell can talk to another. JIC scientists, working with collaborators in France, have taken the first step in defining the structure of communication channels between plant cells.

A team led by Andy Maule has identified a class of proteins new to plant biology. These proteins affect cell-to-cell communication and their discovery could make it possible to regulate the flow of molecules between cells. Communication between plant cells is essential for plant defence, growth and development. For example, the mobile protein that initiates flowering has to move between cells from the leaves to the plant apex to transmit its message.

In animals, cells can communicate by establishing physical contact and forming a pore in the cell membrane known as a gap junction. Molecules can pass through the junction without ever entering the external environment. Plants are more rigid and such direct communication is blocked by the plant cell wall.

Plant cells manage to transport molecules and messages across the cell wall by creating a roadway between cells. These roadways are called plasmodesmata. They are not simply a hole, but plant biologists have been unable to describe them much further. The JIC team has proved that their newly identified proteins are located exclusively in plasmodesmata, and could be used to regulate what moves from one cell to another.

Reference: Specific targeting of a plasmodesmal protein affecting cell-to-cell communication. Thomas, C. L. et al. (2008) PLOS Biology 6(1) e7 doi:10.1371/journal.pbio.0060007 http://dx.doi.org/10.1371/journal.pbio.0060007

Funding: BBSRC Core Strategic Grant, CNRS and Université Louis Pasteur, Strasbourg, and a John Innes Foundation PhD Studentship

Collaboration: Institut de Biologie Moléculaire des Plantes du CNRS and Université Louis Pasteur (Strasbourg)

How SIZE matters

The beauty of nature is partly due to the uniformity of leaf and flower size in individual plants, and JIC and Sainsbury Laboratory scientists led by JIC’s Michael Lenhard have discovered how plants arrive at these aesthetic proportions. Cells at the margins of leaves and petals play a particularly important role in setting their size by secreting a mobile growth signal.

The cells at the margins seem to secrete a mobile growth signal that keeps the cells throughout the leaf dividing. The more of this signal that is produced, the larger the leaves and flowers get. Surprisingly, this signal seems to be distinct from the classical and well-studied plant hormones that are known to influence growth and development.

As the signal only seems to come in from the margins, Lenhard suggests it gets diluted as the leaf or petal grows. Once the concentration falls below a certain threshold, the cells in the leaf or petal stop dividing. Strikingly, animals seem to use the same principle of dilution for measuring size, for example in the wings of a fly, although the molecules used are very different. Efforts are under way to use this discovery to increase leaf growth in biofuel crops for the generation of sustainable energy and to boost the yield of fruits and seeds.

Reference: Control of plant organ size by KLUH/CYP78A5-dependent intercellular signalling. Anastasiou et al. (2007) Developmental Cell 13 843–856
http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580707003796

Funding: Deutsche Forschungsgemeinschaft and a BBSRC David Phillips Fellowship

Collaboration: Christian Fleck and colleagues at the Physics Department, University of Freiburg, Germany

Autonomous Pathways

The switch from vegetative growth to flowering is regulated by environmental cues, which align flowering to when conditions are most favourable for successful reproduction. Flowering is accelerated by prolonged cold (winter), a process known as vernalization, and central to this is the FLC gene encoding a repressor of flowering.

Previous work in Caroline Dean’s laboratory had shown vernalization induces changes at FLC chromatin that prevent the gene being re-expressed when plants return to warm conditions.

Recent work from her laboratory, published in Molecular Cell, has now shown that another pathway (known as the autonomous floral pathway) regulating FLC also affects chromatin structure. An RNA-binding protein FCA was shown to require a protein that demethylates histones (FLD) in order to repress FLC expression. This work opens up analysis of how RNA metabolism induces chromatin changes, a question relevant to gene silencing mechanisms across the plant and animal kingdoms.

Individual seedlings imaged by bright field camera and FLC::LUC signal of the same seedlings taken by CCD camera Genotype of the seedlings is shown at the bottom

In collaboration with Sainsbury Laboratory scientists led by David Baulcombe, her team has also recently reported in Science that this autonomous pathway, thought for many years to specifically regulate flowering time, has widespread roles in the silencing of the Arabidopsis genome. They propose that the autonomous pathway regulates chromatin silencing of single or low copy number genes and has distinct outcomes at specific genes through differential interaction with the machinery regulating small RNA-mediated DNA methylation.

Reference: The Arabidopsis RNA binding protein FCA requires a lysine specific demethylase 1 homologue to downregulate FLC. Liu, F. et al. (2007) Molecular Cell 28 398-407
http://www.molecule.org/content/article/abstract?uid=PIIS1097276507007009

Funding: BBSRC Core Strategic Grant, grants from BBSRC and the Natural Environment Research Council, an EU Marie Curie training grant, an EMBO Long-Term Fellowship and the Polish Ministry of Science & Higher Education

Reference: Widespread role for the flowering time regulators FCA and FPA in RNA mediated chromatin silencing. Bäurle, I., Smith, L., Baulcombe, D. C. & Dean, C. (2007) Science 318 (5847) 109-112
http://www.sciencemag.org/cgi/content/abstract/318/5847/109

Funding: BBSRC Core Strategic Grant, grants from NERC, Gatsby Charitable Foundation, EU training Network and an EMBO Long-Term Fellowship

Bacteria shed light on an important group of human proteins

Collaboration between researchers in Switzerland, the UK and France has led to the solution of the first crystal structure of a member of the Rhesus protein family and thereby shed new light on a group of proteins of great importance in human transfusion medicine. The UK team was led by Mike Merrick.

Ammonium is a fundamental source of nitrogen for almost all living cells but in excess it can also potentially be toxic. Bacteria, fungi and plants take up ammonium using proteins, called Ammonium Transport (Amt) proteins, which span the membranes of cells. Animals use a related family of proteins, known as the Rhesus (Rh) proteins to move ammonium across cell membranes. In humans the Rh proteins are also responsible for the Rhesus negative blood type found in 15% of the human population.

Work on the mode of action of the Amt proteins has been pioneered by studies at JIC. In collaboration with researchers at the Paul Sherrer Institute in Switzerland and France’s Université Paris Descartes and Institut Jacques Monod, Merrick’s group have now taken advantage of the fact that a Rhesus protein has been found to be made by a bacterium, Nitrosomonas europaea. They have determined at very high resolution (1.3 Å), the first X-ray crystal structure of a Rhesus protein. This offers important insights into how these proteins facilitate the movement of ammonium across cell membranes. It also gives new information about the likely structure of these clinically important proteins in humans. For instance, this research strongly suggests that the equivalent human proteins are likely to be trimers and not tetramers as previously proposed.

Reference: The 1.3-Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. Lupo, D. et al. (2007). Proceedings of the National Academy of Sciences 104 (49) 19303-19308
http://www.pnas.org/cgi/content/abstract/104/49/19303

Funding: Swiss National Science Foundation within the framework of the National Centre of Competence in Research in Structural Biology, and BBSRC Core Strategic Grant

Collaboration: Paul Sherrer Institut: http://www.psi.ch/,
Université Paris Descartes: http://www.univ-paris5.fr/ ,
L’Institut Jacques-Monod: http://www.ijm.fr

View of the Rh50 trimeric protein - by establishing the structure of the Rh protein we have a much better understanding of how it works. The three identical Rh50 subunits are shown in different shades of blue and the relative position of the cell membrane is indicated by horizontal lines (National Academy of Sciences 2007).

Understanding maturity could mean new varieties

Judith Irwin

Purple sprouting broccoli is an increasingly popular fresh vegetable. The current UK market is about £4M, but extending the season outside the current 3 month period could grow the market to a potential £20M. A Defra funded Feasibility HortLINK project involving JIC’s Judith Irwin and Elsoms Seeds aims to identify if there is sufficient allelic variation in the genes controlling vernalization to provide breeding tools to control the heading date of broccoli.

The information will inform the extent to which further research will facilitate breeding of new varieties, which would help growers to better match crop production to consumer demand whilst improving quality and reducing waste. The knowledge gained should also be applicable to other Brassica vegetables, and help inform breeding in other over-wintered crops.

PA2 mutation may have feed value

Work funded by Defra, and a multinational EU project, co-ordinated from the John Innes Centre, has led to the potential for improved animal feed made from peas, and shed light on how important processes in the development of plants may be regulated. Pea albumin 2 (PA2) is a seed protein that is poorly digested by piglets and chickens (and has been identified as a potential allergen in humans). Reducing the amount of PA2 in peas would therefore be of benefit in producing improved animal feeds. Claire Domoney and colleagues screened a sub-set of the John Innes pea collection, which consists of over 3,500 cultivated and wild pea varieties, to find peas naturally lacking in PA2. Despite missing the genes needed to make PA2, seeds from these plants have a higher than normal nitrogen content. Therefore, the mutation may have added value for feed crop improvement, as well as providing a tool for the study of variation in nitrogen storage.

They found that plants lacking PA2 had reduced amounts of the polyamines, spermidine and spermine, in mature seeds. The reduction was linked with lower activities of two enzymes responsible for polyamine accumulation. Polyamines are involved in a wide range of biological processes, including growth, stress responses and metabolism. The interesting link between the PA2 protein and the regulation of polyamine metabolism will be a subject for future study. Further work is underway to explore the changes in gene expression linked to a loss of PA2, as well as to establish the benefits of the mutation for feed and food uses.

Reference: Combined metabolomic and genetic approaches reveal a link between the polyamine pathway and albumin 2 in developing pea seeds. Vigeolas, H. et al. (2007) Plant Physiology 146 74-82
http://www.plantphysiol.org/cgi/content/abstract/146/1/74

Funding: EU FP6 FOOD-CT-2004- 506223 Grain Legumes Integrated Project, and DEFRA (projects AR0105 and AR0711)

Estimating the gene contents of closely related organisms

Genome sequencing projects have now uncovered the DNA blueprints of hundreds of organisms. However, the extraordinary breadth of the tree of life means that when studying a group of closely related organisms, we are only likely to see at most one whose genome has been sequenced. Comparative Genome Hybridisation (CGH) microarray experiments have been developed to partially overcome this problem, assessing the similarities and differences between the gene sets of one sequenced organism and several closely related but unsequenced organisms.

As part of a long-term collaboration between Jo Dicks’ Group in Computational and Systems Biology, and Ian Robert’s Group in the National Collection of Yeast Cultures (NCYC) at the Institute of Food Research, two PhD students have been developing new computational methods to visualise and analyse the results of CGH microarray experiments. The result of this collaboration is MPP, a new software tool which can read in a series of experimental results, and pass it through an analytical pipeline. The pipeline, a mixture of public and bespoke algorithms, normalises the data, estimates the gene content of each unsequenced organism, calculates a measure of distance between each pair of gene contents and outputs a tree or network structure representing the relationships between them. MPP has been used to analyse a diverse range of organisms such as yeast, E. coli and Campylobacter jejuni. The MPP pipeline has also been adapted to analyse the results of Tagged Microarray Marker (TAM) experiments. TAM microarrays have been used to characterise around 3,000 accessions within the JIC Pisum collection for 76 RBIP markers. The resulting MPP analysis has uncovered a fascinating network of relationships between the pea accessions.

Software: The MPP software was written in Java and implements the R statistical environment. It is freely available and can be downloaded at http://cbr.jic.ac.uk/dicks/software/mpp/index.html

Reference: MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets. Davey, R., Savva, G., Dicks, J. & Roberts, I.N. (2007) Bioinformatics 23 (8) 1023-1025
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/8/1023

Funding: BBSRC and John Innes Foundation PhD studentship and BBSRC Core Strategic Grant

Brachypodium - workhorse for research on grasses

Grasses provide a substantial source of global nutrition and have significant potential as sources of biomass for renewable bioenergy and biofuels. Unlike many cereals and forage grasses their close relative and wild grass Brachypodium distachyon has the advantage of a small genome. A genome sequencing project sponsored by the BBSRC and the US Department of Energy Joint Genome Institute has reached a milestone, with significant sequence coverage for most of the genome.

The sequence assemblies are available to users at www.brachypodium.org and annotated features can be browsed at www.modelcrop.org; when complete the high quality genome sequence of Brachypodium will allow development of this plant as a workhorse for food and bioenergy crop research. Ready transformation and the capacity for large scale functional genomics has also set the stage for new research activities in temperate grasses. In particular, these resources should enable UK scientists to contribute to developing grasses as bioenergy crops.

To promote the use of Brachypodium as a model for UK plant scientists, a satellite workshop to the 2007 Garnet meeting was held at JIC, organised by Mary Byrne and John Snape bringing together approximately 50 delegates, including scientists from France, Germany and the USA.

Contacts: Mike Bevan – genomics, John Snape – genetics, Mary Byrne – mutagenesis and Philippe Vain - transformation and functional genomics

Website: www.modelcrop.org

 

WHEAT ROUNDUP

Yellow rust - breaking the Boom & Bust cycle

Among the many fungal pathogens that infect wheat, yellow rust is a serious disease in temperate and maritime regions of the world. In the UK and Northern Europe yellow rust is an annual disease and without the necessary control measures would produce devastating epidemic year after year. Many sources of yellow rust resistance deployed in wheat cultivars have proven short lived. Within a short period from release of a new yellow rust resistant cultivar, resistance has become ineffective, new pathogenic isolates of the pathogen having evolved within the pathogen population. Strategies of resistance breeding are required to overcome this short term Boom and Bust cycle of resistance gene deployment. One such strategy is to stack effective resistance genes with different modes of action within the same wheat genotype. This can only be achieved with the use of molecular tools that independently identify each resistance source.

During the last few years, these molecular tools have been developed at JIC for two sources of wheat yellow rust resistance, Yr5 and Yr10. Both Yr5 and Yr10 remain effective against yellow rust in the UK and Europe and therefore represent potentially useful sources of resistance. As part of an EU Framework 6 Integrated Programme – BioExploit these molecular tools are being used to stack Yr5 and Yr10 in the development of new wheat cultivars by the breeding company, Bioplante-Florimond Desprez, France.

Reference: STS markers for the wheat yellow rust resistance gene Yr5 suggest a NBS-LRR-type resistance gene cluster. Smith, P. H. et al. (2007) Genome 50 259-265
http://www.ingentaconnect.com/content/nrc/gen/2007/00000050/00000003/art00001

Funding: BBSRC Core Strategic Grant, Department of the Environment, Food & Rural Affairs & the EU

Collaboration: Bioplante-Florimond Desprez and the Scottish Crops Research Institute

Gene x environmental interactions

Over the last 30 years, wheat has shown an average of 1% per year yield gain. To date most selection for improved yield has been based on empirical selection of observed phenotypes rather than for specific, desirable alleles. Traditionally we think of yield as a trait determined by many genes of small effect acting together, but this is an untested hypothesis, and John Snape and colleagues have set out to test whether there are particular quantitative trait loci (QTL) with large effects. Separate analyses of populations grown over 3 seasons in England, Scotland, France and Germany revealed QTL for yield performance showing both general and stable effects, and the results are starting to give us a ‘physiological handle’ on which traits are exhibiting significant variation that can be manipulated by breeders either over environments or in specific environments.

Reference: Dissecting gene x environmental effects on wheat yields via QTL and physiological analysis. Snape, J. W. et al. (2007) Euphytica 154 401-408
http://www.ingentaconnect.com/content/klu/euph/2007/00000154/00000003/00009208

Funding: Syngenta/JIC Alliance, Defra competitive grant

Collaboration: Syngenta, Nickerson-Advanta, University of Nottingham

Drought resistance

Because of our unpredictable rainfall, droughts cannot be predicted in the UK and the most valuable traits for drought resistance will be those for which there is no yield penalty in the absence of drought. Research involving John Snape and colleagues at JIC has identified one trait showing a strong and clear correlation with maintenance of yield under drought, which is green leaf area persistence. A screen for leaf persistence including marker-assisted selection will have value in future breeding programmes in the UK and world-wide.

Reference: Identifying physiological traits associated with improved drought resistance in winter wheat. Foulkes, M. J. et al. (2007) Field Crops Research 103 (1) 11-24
http://dx.doi.org/10.1016/j.fcr.2007.04.007

Funding: DEFRA

Collaboration: University of Nottingham and the Agricultural Development and Advisory Service, Boxworth

Adaptive winter wheat

Conventional UK wheat crops are monocultures of individual varieties selected for production under high inputs; yield and quality shortfalls result under low input, particularly organic, conditions. Taken together with predictions for increased climate variation and rising input prices, varieties with more internal genetic variability would help buffer environmental variation. In a DEFRA-funded JIC-Organic Research Centre (ORC) collaboration the concept of ‘evolutionary breeding’ using composite cross populations (CCPs) is being tested.

In a new Sustainable Arable LINK project coordinated by the ORC, John Snape and colleagues will provide genetic inputs into work to evaluate the performance of CCPs, determine their processing capability and transfer the CCPs to farmers to facilitate commercial evaluation of potential. JIC’s role will be to use molecular markers to monitor the genetic evolution of CCPs to region, management and year. One of the interesting outcomes should be a massive increase in diversity within the crop which allows control of pests and weeds which should help to significantly reduce agrochemical and physical inputs.

Novel marker systems receive funding boost

Lesley Boyd has been successful in a bid for funding to look at genetic diversity and develop molecular markers for novel sources of resistance to the diseases of yellow rust and stem rust in African wheat genotypes. Her research is in collaboration with colleagues at the University of the Free State, South Africa and the National Agricultural Research Centres in Kenya. The outputs from their 4 year programme will feed into the Global Rust Initiative - www.globalrust.org, which was set up after the appearance of the new, virulent stem rust isolate Ug99 in East Africa in 1999.

The funding comes from the Department for International Development (DFID) and BBSRC’s new joint funding scheme for research on sustainable agriculture for international development.

Translating breakthroughs into application

Inspiralis to search for cancer drugs and antibiotics

Inspiralis, a new company based at the Norwich Bio-Incubator at JIC,will help pharmaceutical companies and academics to screen for new and better cancer drugs and antibiotics. The company has grown out of JIC researchers' world-leading expertise in a group of enzymes called DNA topoisomerases.

How do these enzymes work? Strands of DNA need to be kept compact, as they can be many times the length of the cells they inhabit. They therefore supercoil like a telephone cord, or form knots or chains. However, during important cellular processes like replication, DNA needs to be detangled. Topoisomerase enzymes cut one or both strands of DNA allowing them to untwist and then reform them into the DNA double helix. Without DNA topoisomerases, DNA becomes tangled, cells cannot replicate or repair themselves and they die.

Some key anti-cancer drugs and powerful antibiotics, such as one to treat anthrax, act by inhibiting topoisomerases. In cancer, cells rapidly divide and the excess cells can form a tumour. Topoisomerase inhibitors block this uncontrolled cell division. They are an important target for new drug development, and a new way to screen for inhibitors has been patented so that millions of compounds can be screened in an analysis rather than hundreds.

A high-throughput assay announced in 2006 is a huge advance on the standard gel-based screening method. The technology can now be accessed as a service or as a kit. Inspiralis also sells topoisomerase enzymes themselves as well as associated products and can test potential new drugs against topoisomerases as well as help discover brand new inhibitors as a first step to developing brand new drugs.

For more information: www.inspiralis.com

"Fresh green" compounds

Richard Hughes and JIC Emeritus Rod Casey have developed a novel way of preparing and storing a group of enzymes, CYP74s, that are important to plant health and of interest to the food industry. CYP74s are members of a large family of enzymes called cytochrome P450s which are ubiquitous and essential to life as they can metabolise a plethora of naturally-occurring compounds. One example of a CYP74 enzyme is hydroperoxide lyase (HPL), which catalyses the formation of volatile oxylipins, aldehydes which help to contribute to the aroma of many plant fruits and flowers and so affect the way that plants smell or taste. HPL activity is responsible for the smell of freshly mown grass (in essence a response to mechanical damage) or the “fresh green” odour of fruits and vegetables.

Hughes and Casey have developed new reliable protocols to obtain milligram, potentially gram, quantities of purified recombinant CYP74 enzymes. Patent-protected procedures have been developed for the stabilisation of purified enzymes in a dried, detergent-free state. The enzyme preparations have a greatly improved shelf-life, without loss of activity. The new disruptive technology is predicted to outperform current procedures using available sources of CYP74 enzymes and may also permit the development of other, as yet unexplored, applications where the production of “fresh green” compounds using “green chemistry” has value. Potential applications may also include their use as aromatics for the home or as natural food flavourings; essentially, any situation where the rapid replacement on demand of an unpleasant smell with a natural “fresh green” odour would have benefit.

The patented technology is being commercialised by PBL and is currently being evaluated by a major flavour & fragrances company. Interested parties can access the technology under an Evaluation Licence with samples of stabilised enzyme ready and available for assessment. The researchers hope the future will see more diverse applications for CYP74 enzymes in the food, chemical and other industries.

 

Breakthrough for diagnostics

Cowpea Mosaic Virus (Image courtesy of Prof J E Johnson at The Scripps Research Institute, La Jolla, USA)

Researchers at JIC, in collaboration with the Institute of Animal Health, have developed a method of engineering synthetic sequence elements into a genomic fragment of the Cowpea Mosaic Virus (CPMV). The CPMV particles are highly resistant to degradation, even over periods of many months in contact with biological fluids, and therefore make an ideal protective environment for the RNA.

The virus particles make ideal controls for molecular screening, as they can be added to a fresh sample prior to any processing and control for errors at all stages of the testing protocol. This is invaluable when screening for notifiable diseases, for instance, where a false-negative result can have serious implications for infection control.

The technology is currently being evaluated by the Veterinary Laboratories Agency, and attracting interest from commercial testing and reagent manufacturing companies.

For more information, contact Martin Stocks - martin@pbltechnology.com

Genomics collaboration agreement

The John Innes Centre has completed an agreement with Cogenics™, a division of Clinical Data, Inc. Under the terms of the agreement, Cogenics will provide the John Innes Centre (JIC) with gene expression and other genomics services in a solutions-oriented approach. JIC and Cogenics announced the first result of their collaboration – a custom Brassica gene expression microarray, at the Plant and Animal Genome Conference in San Diego, California, on January 12, 2008. The microarray was developed in conjunction with the J. Craig Venter Institute, and allows researchers to interrogate 91,854 transcribed sequences across multiple Brassica species.

Ian Bancroft, Crop Genetics Project Leader and Head of the JIC Genome Laboratory comments that having access to high quality, cost-effective technologies is a high priority for JIC; the partnership provides exciting opportunities to bring more advanced genomics technologies for plant and microbial research into the reach of the wider science community.

SPE patent granted

PBL’s European patent for Stationary Phase Expression (SPE) technology, developed by Keith Chater and colleagues at JIC has now been granted. The technology allows for the tightly controlled expression of heterologous genes in Streptomyces species without the need for chemical inducers to be added to fermentations; relying upon the triggering of a genetic cascade as cells enter stationary phase.

In collaboration with the JIC, PBL have also developed a suite of proprietary Streptomyces expression vectors (StrepX™). These highly effective vectors have been specifically designed to be free of third-party IPR thereby streamlining their transfer from the laboratory into commercial production systems.

Annual non-exclusive commercial R&D licences are available for both the SPE system and the StrepX™ vectors at an introductory rate valid until 1 March 2008. For more information, please contact Andrew Lee - andrew@pbltechnology.com

'Open minded' cells

Silvia Costa has returned to the JIC as a project leader to analyse the genetic basis of cell fate switch, using the Arabidopsis root epidermis as a model system and funded by a Royal Society University Research Fellowship. Silvia gained her PhD in Liam Dolan’s lab, analysing Arabidopsis root epidermal patterning, before moving to Peter Shaw’s group and has also spent time doing postdoctoral work at the University of Dundee

Cells in the epidermis of Arabidopsis roots can become hair cells or non-hair cells. The two types of cells divide to form alternating files that run down the length of the root. This pattern is established very early on, and is maintained throughout the plant’s life. This differentiation process is controlled by the cell’s position and the new cell’s fate is not determined by the parental cell. In work published in Nature in 2006, Silvia Costa and Peter Shaw showed that determining the cell’s fate involves chromatin (the complex between the DNA molecule and associated proteins such as histones that are used to package up the DNA in the cell). Importantly, they also showed that the chromatin state is not inherited from parent cells, but it can be reset within one cell cycle, depending on the positional cues. This allows changes to occur rapidly, and shows that the plant cells are constantly assessing their surroundings and can perform rapid cell fate switching when required.

Writing in the journal Trends in Cell Biology, they have reviewed how cells can change fate in animals and plants. This ability seems much more restricted in animals than in plants. When a stem cell differentiates, it acquires a pattern of gene expression specific to the cell type it has become. When a differentiated animal cell divides, it passes on this pattern of gene expression to its daughter cells. This ‘cellular memory’ depends on the inheritance of the chromatin structure, rather than the DNA sequence, and is known as epigenetics. Understanding how cellular memory works may explain why plants are much more able to change their fate than animal cells.

Plants however, do use cellular memory. The switch to flowering is a key point in the life cycle of many plants, as it marks the start of the plant’s reproductive phase. Investigations in Caroline Dean’s group have shown that vernalization, a prolonged period of cold some plants require to trigger flowering, brings about changes in gene expression and chromatin structure. These changes are then passed on epigenetically, using cellular memory mechanisms.

NORWICH SYSTEMS BIOLOGY EXPERTS IN SHARE OF £26M

The Biotechnology and Biological Sciences Research Council has announced almost £26M of new funding for systems biology research to tackle significant questions in biology. The sum includes £3.38M over 5 years to JIC and University of East Anglia scientists Enrico Coen and Andrew Bangham, to investigate how shapes in biology are formed.

Biological organisms, like other complex systems such as the internet or the economy, are made up of parallel processes operating at many different scales. The key link between these scales is growth. Through growth, changes at the molecular level lead to cell division and eventually the production of whole tissues and organisms. The scientists will study leaf growth, shapes and patterns at four scales at the same time and they expect to discover links that would not reveal themselves if they studied each scale in isolation. Using a combination of genetic analysis, image processing and computer modeling, Coen and Bangham will be able to study the effects of genes on growing leaf cells in 3D. Live 3D tracking of growth is a huge leap from studying one gene and its function at a time.

Systems biology is a revolution in the way bioscientists think and work. It brings together researchers across different disciplines, combining theory, computer modelling and experiments. Over the last three years the UK Research Councils have invested around £100M in making the UK a world leader in this area. Systems biology will make the outputs of bioscience research more useful and easier to apply in the real world, as well as advancing our understanding of biological processes.

http://www.bbsrc.ac.uk/media/releases/2007/071127_systems_biology.html

New plant handbook is the perfect place to look up a query

The sheer amount of information that is accumulating about plant science, and the difficulty of grasping it all, understanding it and evaluating it, has been addressed in a new Handbook of Plant Science edited by JIC Emeritus, Keith Roberts. The stunning cover images, obtained using optical projection tomography, are by Karen Lee from Enrico Coen’s group.

This is the first spin-off work from Wiley’s enormous on-line Encyclopedia of Life Sciences, for which Keith acts as the Plant Section editor. All of the plant-related articles in this work have been sorted into coherent sections, gaps identified and new articles commissioned, with over 250 peer-reviewed articles by world experts in each subject, includng thirteen JIC authors. The various sections of the work find an echo in many of the key research areas at JIC, and include Cell Biology, Growth and Development, Molecular Genetics, Biotechnology, Evolution, Primary and Secondary Metabolism, Plants and their Environment and Plants and other Organisms.

Keith and Karen (holding the volumes) with the JIC editorial advisory board

CUE EAST - Bridging the gap

The public will soon be able to play a more interactive role in the important work of higher education institutions, thanks to a new £9.2M initiative - Beacons for Public Engagement.

UEA and partners, as CUE East (Community University Engagement East) will establish a one-stop shop for the public, located in ‘The Forum’ in Norwich alongside the UK’s most successful regional library and the BBC’s regional offices and studios. Their twenty two external partners include JIC, IFR and the Teacher Scientist Network, who will play a vital role in their delivery programme and critical thinking.

Their overall theme will be sustainable living, with a priority target audience of pupils, teachers and parents.

Championing sustainability and the environment

Kate Thodey

At two recent ‘Friends of JIC’ events, sellout audiences had a chance to find out if gardening could help offset their carbon emissions and how to farm for food, fuel and the environment. New Zealand-born PhD student Kate Thodey was one of the speakers at the gardening event. She had calculated how much garden she would need to offset the amount of carbon dioxide she generates, taking into account issues such as flights home to New Zealand. She explained how although gardening can help, we must also look to technological advances in plant science to provide solutions to reduce the amount of carbon in the atmosphere.

A 200 strong audience heard Peter Kendall, President, National Farmers Union, argue his position on “Science for 21st Century Agriculture - how to farm for food, fuel and the environment” at the 5th Annual Lecture. Despite the set backs and hardships endured this year, Kendall, a Bedfordshire arable farmer, argued the case of farmers as custodians of the countryside and the importance of embracing new technology to enable them to farm greener, yet supply the needs of an increasing population with decreasing hectareages available for premium production. In the discussion which followed, he defended buying locally produced food, criticised the lack of joined up thinking in Government funding of science, and expressed concerns about the lack of accessibility for farmers and growers in the UK to GM technology.

JIF Contribution to life at JIC

JIF - Funded Rotation PhD student Alex Graf comments “the rotation PhD programme really changed my scientific interests – before I saw myself more as a developmental biologist or plant pathologist but with my project in Alison Smith’s lab I entered the world of starch metabolism. Alison gave me almost complete freedom in designing my project. I was very interested in how Arabidopsis thaliana is able to degrade its starch in a linear way over the night period; the project links ‘two worlds’ – the circadian clock and metabolism.”

A new website has been developed to describe the work of the John Innes Foundation. JIF Trustees play an active part in the management of the JIC and have the right to appoint three members of its Governing Council.

JIF is the major sponsor of the Rotation PhD Programme, having provided support for sixteen students during the five years since this programme was initiated. With enhanced levels of stipend and student support, this attracts some excellent applicants and its multidisciplinary training programme is proving to be a great success with both students and supervisors.

Other important activities supported by the JIF grant include the JIC Student Voice Committee which organises a wide range of activities for students, including an annual Student Science Meeting and the invitation of student seminar speakers. The trustees also support educational programmes such as the Nuffield scholarship programme, whereby A-level students from local schools spend four weeks working in the laboratory with a JIC scientist. The Foundation and the Trustees will also be actively involved with JI 100 Celebrations.

www.johninnesfoundation.org.uk