The DOE Joint Genome Institute is an integrated high-throughput sequencing facility which provides high-quality genomic sequences to the scientific community. Currently there are approximately 300 microbial genomes in the JGI production genomics facility (PGF) pipeline in Walnut Creek and to date, 160 have been completely finished. The PGF microbial finishing group is involved in improving the microbial genomic sequences that come directly out of production. The finishing team is responsible for solving misassemblies, closing gaps, improving low-quality areas in the DNA assemblies and submitting high-quality data to the annotation group which in turn submit the sequence to the public domain. The finishing pipeline at PGF starts with resolving DNA repeats using an automated pipeline developed at JGI/PGF. Low quality and gap regions in the assemblies are resolved by directed reactions mainly using primers designed by applying Autofinishing functionality of Consed and other software developed in-house. Finally, manual checks are performed to ensure a minimum consensus phred quality of 30 or above, error rate is less than 1 base per 50,000 bp and 2 times coverage throughout the DNA sequence assemblies. The strategies for solving repeats, misassemblies and difficult to finish regions will be further discussed in detail in this poster.

The Bacillus cereus group consists of gram-positive, spore-forming bacteria with an impact on human activities due to their pathogenic properties. The most famous pathogens of animals and insects, B. anthracis and B. thuringiensis, carry their toxins in large plasmids. However, the bacteria of this group are also involved in mild food poisoning, causing rather noxious, although not fatal, vomiting or diarrhea. The emetic group strains appear to represent a very narrow phylogenetic group, and the corresponding toxin is encoded by a plasmid (Ehling-Schulz et al., 2005). Contrary to that, the characterized diarrheic toxins (Nhe, Hbl and CytK) are always present in the chromosome. To provide the comprehensive genomic characterization of the group, in addition to the genomes already sequenced, we selected three different strains for complete sequencing. The work is being done as a collaboration of INRA (France), Joint Genome Institute (Walnut Creek, USA) and CNS Genoscope (Evry, France). One of the strains, NVH398-91, is now completely sequenced. It was isolated from a severe food poisoning case in France (Lund et al, 2000). Surprisingly, the strain contains a gene for only one of known diarrheic toxins ? Cyt K, which was shown to be synthesized in elevated amounts and to be particularly effective (Brillard and Lereclus, 2004; Fagerlund et al., 2004). The strain is rather different from other representatives of the B. cereus group and has a compact chromosome of 4.1 Mb, compared to 5.2-5.4 Mb genomes of other sequenced strains. This strain can also be regarded as the first bacterium of the group in which a highly effective toxin is chromosome-encoded. Divergence of the strain from other and its phenotypic particularities inspires to consider it as a representative of a new species, for which we propose a name Bacillus cytotoxis. However, only one such strain was described for the moment. The second strain being sequenced, Bwe KBAB4, isolated from forest soil, is a typical representative of recently recognized species - B. weihenstephanensis (Lechner et al., 1998; Sorokin et al., 2006). It contains a total of 5.6 Mb of genetic material, which includes genes to encode Nhe and Hbl, but lacks genes for CytK and HlyII. Although closely related strains are frequently reported to be food contaminants, they are in almost all cases not poisonous. However, the presence of Nhe and Hbl encoding genes suggests that such strains can also become toxic. Finally, the third strain, B. cereus F0837/76, can be regarded as one of typical strains that can cause a severe diarrheic food poisoning. It synthesizes at least two characteristic toxins, Nhe and Hbl, in elevated amounts and was isolated from a contaminated surgical wound in a hospital (Turnbull et al, 1979; Beecher and MacMillan, 1990; Lund and Granum, 1997). Genomically the strain appeared to be very closely related to B. anthracis and this is probably the closest to it B. cereus strain known. It does not however contain the relevant pathogenic plasmids.

The DOE Joint Genome Institute is an integrated high-throughput sequencing facility which provides high-quality genomic sequences to the scientific community. Currently there are approximately 300 microbial genomes in the JGI production genomics facility (PGF) pipeline in Walnut Creek and to date, 160 have been completely finished. The PGF microbial finishing group is involved in improving the microbial genomic sequences that come directly out of production. The finishing team is responsible for solving misassemblies, closing gaps, improving low-quality areas in the DNA assemblies and submitting high-quality data to the annotation group which in turn submit the sequence to the public domain. The finishing pipeline at PGF starts with resolving DNA repeats using an automated pipeline developed at JGI/PGF. Low quality and gap regions in the assemblies are resolved by directed reactions mainly using primers designed by applying Autofinishing functionality of Consed and other software developed in-house. Finally, manual checks are performed to ensure a minimum consensus phred quality of 30 or above, error rate is less than 1 base per 50,000bp and 2 times coverage throughout the DNA sequence assemblies. The strategies for solving repeats, misassemblies and difficult to finish regions will be further discussed in detail in this poster.

The complete genome of a model obligate methylotroph, M. flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol- and methylamine dehydrogenases, the tetrahydromethanopterin-linked formaldehyde oxidation pathway, the assimilatory and dissimilatory branches of the ribulose monophosphate cycle, and a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or non-identical) copy. The obligate dependence on single carbon compounds is likely due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alphaketoglutarate-, malate- or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared, in terms of methylotrophy functions, to the previously sequenced genomes of three methylotrophs: Methylobacterium extorquens (Alphaproteobacterium, 7 Mbp), Methylibium petroleophilum (Betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (Gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, methylotrophy functions in M. flagellatus are more similar to the ones in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleophilum, providing the first genomic evidence of polyphyletic origin of methylotrophy in Betaproteobacteria.

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

We present a collection of signatures for physics beyond the standard model that need to be explored at the LHC. The signatures are organized according to the experimental objects that appear in the final state, and in particular the number of high pT leptons. Our report, which includes brief experimental and theoretical reviews as well as original results, summarizes the activities of the "New Physics'' working group for the "Physics at TeV Colliders" workshop (Les Houches, France, 11-29 June, 2007).