PDF file: Annual Report 2002/2003 - Scottish Crop Research Institute

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Environment EST Bioinformatics D. Marshall, L. Cardle & P. Shaw Amajor change to the information landscape in which we operate for most of our key crop and pathogen species has occurred over the last 2-3 years as the result of a dramatic change in the volume of available sequence information. This is true both for organisms themselves and for the key model organisms which form a major comparative genome resource. For this account we will focus on barley and potatoes. The major contribution has come from a number of large scale EST (Expressed Sequence Tag) sequencing programmes, though a small amount of BAC-scale genomic sequence is also becoming available in both species. This has generated some 370,000 barley and 132,000 potato ESTs (See dbEST current EST statistics at: http://www.ncbi.nlm.nih.gov/dbEST/dbEST_ summary.html ). These resources are leading to a dramatic change in working patterns in molecular biology and to an increasing role for bioinformatics within the institute’s research programmes. EST sequencing programmes rely on a philosophy based on a relatively ‘quick and dirty’ approach which involves single pass sequencing of ESTs from a range of cDNA libraries. This is usually 5’ sequence though individual clones may also be sequenced in the 3’ direction. Such single pass sequences then form the template for a range of subsequent molecular biology and bioinformatics activities. The first stage after the removal of low quality sequence and vector contamination is to obtain an initial indication of function through homology searches against a range of public databases using the Blast suite of programmes. The second step is to carry out sequence assembly which Figure 1 Data from 31 barley EST libraries chosen to show the relative abundance of the most highly abundant expressed endosperm sequences across a range of other tissues uses software tools such as CAP3 to assembly the EST sequence fragments into contigs and then subsequently derive consensus sequences. The high redundancy level of EST sequences from relatively highly expressed genes and the occurrence of cDNA clones truncated at the 5’ end together lead to the generation of consensus sequences which are both of surprisingly high quality and much longer than the individual single pass EST sequences. Within the Computational Biology Programme at SCRI we have built up a considerable expertise in the process of EST sequence assembly and the use of the subsequent assemblies and consensus sequences as the substrate for a whole series of downstream activities ranging from the identification of Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) genetic markers, expression analysis (based on microarrays, SAGE analysis and electronic Northerns - see Figure1) and for the identification of barley and potato orthologues of genes that have been characterised on other species especially in model organisms such as Arabidopsis. The task we face in helping develop the EST sequence resource from potato and barley as a major tool in our research is confounded by the continuing generation of new sequence information as well as the rate of change in sequence annotation, especially due to the progress of functional genomics in Arabidopsis and rice as well as more directly in barley and potatoes. To meet this challenge we have adopted two main approaches. The first of these is to develop a relatively lightweight scalable database infrastructure based on a combination of public domain software tools and applications tools, including MySQL, PostgreSQL, Perl and Apache. This has now been applied to a series of database applications both for day to day support for individual research programmes and as a central resource for internal and external interaction with SCRI data resources. Examples may be seen though the SCRI Bioinformatics web server at http://bioinf.scri.sari.ac.uk/. The second major activity has been to develop strong relationships with a number key of information providers. These include the Graingenes, Gramene and BarleyBase cereal databases in North America. A key aspect of our involvement has been to highlight the importance of data quality and data validation in comparatively map and sequence analysis and the promotion of appropriate informatics standards. 130
Environment Mathematical modelling B. Marshall Models are an intricate part of our everyday life. We use them to make decisions in the belief that taking certain actions will probably result in particular outcomes. The underlying models are simplified but effective “pictures” of reality. Likewise, models are the cornerstone of scientific method. A model is essentially a hypothesis, a statement of how something works or interacts, which is tested by its predictions. Its truth can never be proven, since it can always fail the next test. Newtonian Mechanics was believed to apply in all circumstances, but ultimately failed in conditions extreme compared to our everyday experience. Nevertheless, much of our modern world still exploits the models of classical mechanics because the predictions remain accurate in the world we live in. We use the familiar to describe the unfamiliar. We define things by their behaviour and by analogy. The electron with a fixed mass and charge, could be thought of as a minute billiard ball. These properties are exploited in the domestic TV. However, it also exhibits wave like properties. Imagine waves entering a harbour. They emerge within as circular wave fronts and with two entrances, close by, produce the familiar patterns of interference. Exactly the same patterns were seen when a single electron was “aimed” at a much smaller pair of slits. This means the electron “passed” through both slits at the same time, which seems surprising if you only think of electrons as particles. Electrons are both like particles and like waves. Aristotle was a keen observer, especially of biological systems, and emphasised the importance of considering the whole. He believed the "physical method", promoted by Democritus, failed because it tried to explain things by decomposing them into their parts and ignored the whole. Knowing that a house is built of bricks, mortar and timber tells us little about its architecture and nothing of its purpose. Similarly, reducing an animal or plant to its parts and ignoring the whole tells us nothing of its form or function. Aristotle believed that the study of nature should focus on the coordination of the parts in the whole and this is never more applicable than today. The behaviour of the system as a whole is referred to as an emergent property. It is not a property of the component parts but a consequence of the interactions between them. The Gas Laws are a classic example – the temperature, pressure and volume of a gas are related by a simple rule. Boyle discovered this rule, an emergent property, by making measurements at the scale of the system. If he had been able to break down the gas into its components, to see the molecules insitu, then he would have observed them moving in random directions, at different speeds and occasionally colliding (interacting) with each other and the walls of the container. He would have seen nothing of the large scale behaviour of gases. Only by modelling these interactions could he then possibly predict the emergent property. In ecological systems we face this challenge. It is easier to observe the individual than x10 Zoom x100 Population Extinction Stable state 2 cycle state Chaos Reproductive rate Figure 1 An electron is both like a particle and a wave. A single electron passes through both slits at the same time producing interfering waves on the far side, like waves of the sea passing through two entrances to a harbour. Figure 2 Steps to chaos. The behaviour of a population with a limited food resource can change dramatically if the reproductive rate of the individuals is altered e.g. a different species or warmer temperatures. 131
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Scottish Crop Research Institute ®
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The Scottish Crop Research Institut
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Contents Biomathematics and Statist
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Introduction upon the Commissioner
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Introduction ® Scottish Crop Resea
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Report of the Director John R. Hill
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Director’s Report tion from dismi
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Director’s Report paper A revised
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Director’s Report and the relatio
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Director’s Report Member States A
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Director’s Report US subsidies fr
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Director’s Report regions of the
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Director’s Report of silver and m
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Director’s Report tions. Obscenel
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Director’s Report participation.
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Director’s Report heads of state
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Director’s Report Philippines (2.
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Director’s Report Food Aid Famine
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Director’s Report adoption of unh
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Director’s Report economy propose
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Director’s Report (herbicides, in
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Director’s Report by a combinatio
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Director’s Report mended a study
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Director’s Report notes, bulletin
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Director’s Report research instit
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Director’s Report Ireland. Also i
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Director’s Report tats, most nota
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Director’s Report shares of total
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Director’s Report tonnes in 1999.
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Director’s Report Relative Import
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Director’s Report cheap food-stuf
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Director’s Report culturally-rela
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Director’s Report on large parts
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Director’s Report minimum input s
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Director’s Report organic farming
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Viruses - evolving organisms ? Viru
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Viruses - evolving organisms ? CLCu
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Viruses - evolving organisms ? a) b
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Barley Crop Development formation o
Page 79 and 80: Barley Crop Development Year Total
Page 81 and 82: Barley Crop Development on a year t
Page 83 and 84: GM herbicide-tolerant crops Some pe
Page 85 and 86: GM herbicide-tolerant crops and som
Page 87 and 88: GM herbicide-tolerant crops mitted
Page 89 and 90: GM herbicide-tolerant crops 12 Squi
Page 91 and 92: Mechanisms & Processes Peronospora
Page 93 and 94: Mechanisms & Processes Proteomic an
Page 95 and 96: Mechanisms & Processes High-through
Page 97 and 98: Mechanisms & Processes Studying pla
Page 99 and 100: Mechanisms & Processes Phytoene pea
Page 101 and 102: Mechanisms & Processes New discover
Page 103 and 104: Mechanisms & Processes in these cel
Page 105 and 106: Mechanisms & Processes d). This dat
Page 107 and 108: Genes to Products ic enzymes (use o
Page 109 and 110: Genes to Products Carotenogenesis i
Page 111 and 112: Genes to Products accumulation in s
Page 113 and 114: Genes to Products Retrotransposons
Page 115 and 116: SH43 SL03 SH44 SH12 B20 SL22 B47 B0
Page 117 and 118: Management of genes and organisms i
Page 119 and 120: Environment Functional diversity in
Page 121 and 122: Environment Plant root biomechanics
Page 123 and 124: Environment Microbial and microfaun
Page 125 and 126: Environment The role and importance
Page 127 and 128: Environment duced from barley mixtu
Page 129: Environment IOBC GMO Guidelines Pro
Page 133 and 134: Biomathematics and Statistics Scotl
Page 135 and 136: Research services Analytical facili
Page 137 and 138: Research services Division of Finan
Page 139 and 140: Research services Information Techn
Page 141 and 142: Research services Estate, Glasshous
Page 143 and 144: Research services Engineering and M
Page 145 and 146: Research services MRS will: strengt
Page 147 and 148: Research services Health and Safety
Page 149 and 150: Publications Blok, V.C. 2002. Progr
Page 151 and 152: Publications Phenotype/genotype ass
Page 153 and 154: Publications for virus-transmitting
Page 155 and 156: Publications Muckenschnabel, I., Go
Page 157 and 158: Publications rich grassland. Procee
Page 159 and 160: Publications Woodford, J.A.T., Fent
Page 161 and 162: Statement of health & safety policy
Page 163 and 164: The Governing Body The Governing Bo
Page 165 and 166: The Governing Body development and
Page 167 and 168: Staff Theme 2 - Genes to Products T
Page 169 and 170: Staff Division of Finance and Admin
Page 171 and 172: Staff Resignations Name Unit Band M
Page 173 and 174: Staff Editorial Duties Name Positio
Page 175 and 176: Staff Name Position Committee or Or
Page 177 and 178: SCRI Research Programme 2002-2003 S
Page 179 and 180: Research Projects SCR/587/02 SCR/58
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Meteorological Records D. Petrie &
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List of Abbreviations AAB ACRE ADAS
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