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Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell–cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development.
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Session opened with Erick Denamur talking about insertion and deletion hotspots of E.coli. He also talked about the coliscope consortium which is "a sequencing project for the understanding of commensalism and virulence emergence in the Escherichia coli/Shigella species". Then the mic was handed to Carmen Buchrieser who highlighted the importance of Legionella which made the Queen run back to the palace. The following talk was from Tim Stinear who mentioned how poking finger(s) into fish can lead to Mycobacterium marinum (which along with M.ulcerans, is closest to M.tuberculosis giving positive mantoux test) infection! He also mentioned about Gene Spaghetti a cool tool for "visualizing base and amino acid usage in a genome", COG's 3-way genome blast approach and synteny map generation. 
Image via WikipediaThen came Marrion karrasch who talked about ERA-NET PathoGenoMics, Interferon interference (?), invasive propeties of C.albican (with liver capsule invasion as an example) and RNAi for possible therapeutic approach (?). Again thanks to Swati for the better notes below:
Population phylogenomics of the E.coli species
Erick Denamur, medical faculty Xavier Bichat, Paris
- Phylogeny of complete genome within species.
- Majority of E.coli strain can be assigned to one of 4 main phylogenetic groups (A, B1, B2 and D).
- These 4 phylogenetic groups differ in their phenotypic and genotypic characteristics.
- Gene conversion doesn’t affect the tree topology.
- E.coli ancestor is close to K-12
Comparative Genomics of Legionella pneumophila and Legionells longbeachae, ttwo human pathogens that coevolved with protozoa.
Carmen Buchrieser, Pasteur Institute, Paris
- Organisms- Legionella pneumophila and Legionella longbeachae.
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I joined the session when Fiona Brinkman was saying that hyperthermophilic bacterias have higher number of cytoplasmic protein. Later came Alexei Savchenko who was speaking that pathogens manipulate the host signalling for their benefit (e.g. uibiquitination). He also mentioned that Toronto centre has target of getting 60 high quality pdb structure per year and also look at these for catalytic activity using enzymatic assay. For more on this session, I took the nice notes from Swati which are pasted below:
The tubercle bacilli: Molecular determinants of pathogenicity and attenuation.
Generating protein interaction map for pathogens using yeast two hybrid.
Russel L. Finley, Wayne State University, Detroit, USA
- Organism- Campylobacter jejuni
Insights into the evolution of pathogens using improved bioinformatics approaches.
Fiona Brinkman, Simon Fraser University, Canada
- Computational methods for the predication of protein subcellular localization, predication of genomic island and identification of orthologous.
- Signature tagged mutagenesis data
- Analysed 100 pathogens and nonpathogens.
- Increase in Genome size = Increase in networks
- Certain offensive virulence factor associated with
Genomewide structural and biochemical annotation of uncharacterized proteins from pathogenic bacteria.
Alexei Savchenko, University of Toronto, Canada
- Selected uncharacterized proteins from pathogenic bacteria.
- The main focus of this study was to annotate effectors proteins from Shigella flexneri cause shigellosis in humans.
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Session opened with talk from Jean Weissenbach
who talked about mining metagenomes with focus on di-codon frequency and GC content, followed by a talk from Victor de Lorenzo and George Weinstock
who mentioned that error rates are pretty low for 454 data compared to Solexa and looking at the price decrease from 2 runs for 20K/genome to 2K/genome with 500b reads, 454 is going in a good direction :)
For more, check out the previous post ( http://computationalbiologynews.blogspot.com/2008/04/conference-genomes-2008-10-th-april-s5.html ) for notes from Anders.
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I was present in Tracy Palmer's talk who works on The Tat protein export pathway
and Mariagrazia Pizza who works in the area of vaccine discovery , more specifically Serogroup B Meningococcus . Later Athanasios Typas came and talked about GIANT coli system for determining genetic interactions (12X12 plate with pixel marked borders followed by inplate normalization and central substraction, the image thus obtained can be compared across similar experiments).
Image via Wikipedia
Environmental (meta)genomics
(either using alignment or PCA analysis of nucleotide freq.)
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