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SGM Meeting Abstracts: University of Warwick, 3-6 April 2006 Microbiologysociety for general 158th Meeting 3–6 April 2006 University of Warwick Abstracts For up-to-date details: www.sgm.ac.uk Sponsors The Society for General Microbiology would like to acknowledge the support of the following organizations and companies: Ambion Europe Ltd Roche Diagnostics Systems Brand GmBH & CO KG Sanofi Pasteur MSD GC Technology Ltd Sanofi Pasteur France GeneVac Ltd Johnson & Johnson Medical Merck Sharp & Dohme Ltd Technical Service Consultants Ltd Miltenyi Biotec Ltd Wisepress Online Bookshop Ltd New England Biolabs (UK) Ltd Yakult UK Ltd Design: Ian Atherton Front cover: The Baptistry window at Coventry Cathedral. Ian Britton, Freefoto.com © Society for General Microbiology 2006 Prokaryotic diversity: mechanisms and significance Plenary session 3 Surface anchored molecules: sticky fingers Cells & Cell Surfaces Group session 6 Viral central nervous system infections Offered papers Contents Clinical Virology Group session 8 What does an undergraduate microbiologist need to know? Education & Training Group session 10 Environmental genomics: metagenomics workshop – metagenomics principles, practice and progress Environmental Microbiology Group / NERC Environmental Genomics joint session 12 Cells as factories Fermentation & Bioprocessing Group session 16 Intestinal microbiota and health Food & Beverages Group session 18 Vaccines Microbial Infection Group / Clinical Microbiology Group joint session 22 Cyclic-di-GMP and the physiological control of intracellular signalling networks in diverse bacteria Physiology, Biochemistry and Molecular Genetics Group session 26 Eukaryotic evolution Systematics & Evolution Group session 29 Virus interactions with subcellular structures Virus persistence and latency Virus Group sessions 31 Marjory Stephenson Prize Lecture Sir John Skehel (MRC National Institute for Medical Research, London) Invasion by influenza viruses 37 Fleming Lecture Dr Frank Sargent (University of East Anglia) Constructing the wonders of the bacterial world: biosynthesis of complex enzymes 37 Posters 38 Authors 79 Late Abstracts 83 Please note: Abstracts are printed as received from the authors and are not subjected to editing. Plenary session Prokaryotic diversity: mechanisms and significance Microbial diversity in the era of genomics phylogenetic signatures to function. This is serving to identify the Plenary roles of even highly oxygen-sensitive species in processes including Rita R. Colwell the fermentation of dietary substrates, the formation of short chain University of Maryland College Park and Johns Hopkins University fatty acids, and interactions with host tissues, that have a major Bloomberg School of Public Health, USA influence upon human health. The little studied low % G+C Gram- In this era of genomics, the perspective of microbial ecologists positive Firmicute bacteria, for example, have been shown to include has been expanded, and the panorama that the world of microbial the major butyrate-producing bacteria of the human intestine. diversity comprises is only beginning to be known. In the decade Metabolic interactions and competition between these and other ahead there will be revealed a grand tapestry of life, reflecting the members of the gut community, with respect to dietary carbohydrate richness and abundance of the microbial world. With this new substrates that escape digestion in the small intestine, is central to knowledge, there will be a powerful reinforcement of the complexity of understanding the effects of diet upon gut health. life on this planet: life that is not only complicated but also integrated, and both genetically and functionally interwoven. The sustainability of The evolution of phenotypic diversity our planet rests unmistakably and irrevocably on the vast and intricate Hubertus J.E. Beaumont, Stefanie M. Gehrig, Rees Kassen, Christopher microbial diversity that we should come to appreciate and, hopefully, G. Knight, Jacob G. Malone, Andrew J. Spiers & Paul B. Rainey understand. University of Auckland, New Zealand and University of Oxford The diversity of life posses a myriad of problems for biologists; Patterns in biodiversity: are prokaryotes really different? foremost among these are the causes of phenotypic diversity. Concepts B. Bohannan that stem from Darwin’s theory of evolution by natural selection have University of Stanford, USA produced an ecological theory of diversification, but a corresponding genetic theory remains under developed. Necessary for progress is an Abstract not received understanding of how genotype, phenotype and fitness are connected through evolutionary time: in short, what is necessary is a genetical Archaeal diversity theory of evolutionary development. One of the most profound E. Koonin phenotypic innovations is the kind that promotes cooperation among individual biological units (e.g. genes, cells, organisms) in order to National Centre for Biotechnology Information, Bethesda, USA create higher-level units (e.g. chromosomes, multicellular organisms, Comparative-genomic analysis of Clustered Regularly Interspaced societies). During my talk I will focus on the evolutionary transition Short Palindrome Repeats (CRISPR) and the CRISPR-associated (cas) from single cells to simple groups. During this transition the unit of genes, which are widely represented in prokaryotic genomes, leads to selection shifts from individual cells to groups of cooperating cells. the hypothesis that the CRISPR-Cas system (CASS) is a mechanism Such a transition occurs readily in experimental populations of of defense against invading phages and plasmids that functions Pseudomonas fluorescens propagated in a spatially heterogeneous analogously to the eukaryotic RNA interference (RNAi) systems. environment and thus is amenable to empirical analysis. Cooperation is Specific functional analogies are drawn between several components mediated by simple mutations at different genetic loci that decrease the of CASS and proteins involved in eukaryotic RNAi, including the activity of negative regulatory elements that control the activity of double-stranded RNA-specific helicase-nuclease (dicer), the diguanylate cyclases (GGDEF domain proteins). The net effect of these endonuclease cleaving target mRNAs (slicer), and the RNA-dependent mutations is the over-production of an adhesive polymer. The adhesive RNA polymerase. However, none of the CASS components is polymer causes the interests of individuals to align with those of the orthologous to its apparent eukaryotic functional counterpart. It is group. Consistent with predictions from theory cooperation is costly to proposed that unique inserts of CRISPR function as prokaryotic small individuals, but beneficial to the group. Defecting genotypes evolve in interfering RNAs (psiRNA), by base-pairing with the target mRNAs and populations founded by the cooperating type and are more fit in the promoting their degradation or translation shutdown. Specific presence of this type than in their absence. In the short term defectors hypothetical schemes are developed for the functioning of the sabotage the viability of the group; nevertheless, these findings show predicted prokaryotic RNA interference system and for the formation that evolutionary transitions are readily achievable, provide insights of new CRISPR units with unique inserts. into the genetic and selective conditions, and facilitate experimental analysis of the evolution of individuality. The significance of prokaryote diversity in the human gastrointestinal tract Minimal genomes required for life Harry J. Flint Rosario Gil, Vicente Pérez-Brocal, Amparo Latorre & Andrés Moya Rowett Research Institut, Aberdeen Universitat de València, Spain The human large intestine represents one of the most densely The minimal cell field is partly anchored in solid experimental facts, colonized microbial ecosystems. While recent culture-independent and partly still belongs to the sphere of theoretical research. Projects analyses indicate that a majority of the diverse micro-organisms found designed to scan entire microbial genomes for essential genes have in the human intestine are not represented by known cultured species, revealed a remarkably compact and conserved, but not universal, set of culturability appears high relative to most non-gut communities. genes whose functions are necessary for survival or reproduction. A Research that combines cultural microbiology, molecular ecology, minimal cell cannot be sharply defined, since different essential genomics and metabolite tracking is starting to relate molecular functions can be defined depending on the environmental conditions. 3 Nevertheless, it is possible to try to delineate which functions should Chlamydia pneumoniae is a human respiratory pathogen that causes be performed in any modern living-cell, and list the genes that would acute respiratory diseases. C. pneumoniae has also been associated with be necessary to maintain such functions, although numerous atherosclerosis, a disease of chronic inflammation and the leading alternative minimal genomes can be conceived to fulfill such functions cause of morbidity and mortality in the western world. This association even for the same set of conditions. has been based on several lines of evidence including: 1) Remarkably, the different approaches used to define a minimal genome seroepidemiological studies demonstrating an increased risk of converge on the conclusion that genes dealing with RNA biosynthesis coronary heart disease and myocardial infarction in patients
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