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Recent "genomes" articles

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Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
Jesus Salazar-Gonzalez et al.
The Journal of Experimental Medicine, (01 Jun 2009)
Identification of full-length transmitted HIV-1 genomes could be instrumental in HIV-1 pathogenesis, microbicide, and vaccine research by enabling the direct analysis of those viruses actually responsible for productive clinical infection. We show in 12 acutely infected subjects (9 clade B and 3 clade C) that complete HIV-1 genomes of transmitted/founder viruses can be inferred by single genome amplification and sequencing of plasma virion RNA. This allowed for the molecular cloning and biological analysis of transmitted/founder viruses and a comprehensive genome-wide assessment of the genetic imprint left on the evolving virus quasispecies by a composite of host selection pressures. Transmitted viruses encoded intact canonical genes (gag-pol-vif-vpr-tat-rev-vpu-env-nef) and replicated efficiently in primary human CD4+ T lymphocytes but much less so in monocyte-derived macrophages. Transmitted viruses were CD4 and CCR5 tropic and demonstrated concealment of coreceptor binding surfaces of the envelope bridging sheet and variable loop 3. 2 mo after infection, transmitted/founder viruses in three subjects were nearly completely replaced by viruses differing at two to five highly selected genomic loci; by 12–20 mo, viruses exhibited concentrated mutations at 17–34 discrete locations. These findings reveal viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses.
 
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Geraldine Butler et al.
Nature, published online 24 May 2009
Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/alpha2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.
 
The E23K Variant of KCNJ11 and the Risk for Severe Sulfonylurea-induced Hypoglycemia in Patients with Type 2 Diabetes.
A Holstein et al.
Hormone and metabolic research. Hormon- und Stoffwechselforschung. Hormones et metabolisme, (12 Feb 2009)
 
CpG islands in vertebrate genomes.
M Gardiner-Garden and M Frommer
Journal of molecular biology 196 (2), 261-82 (20 Jul 1987)
Posted by JBDamask to cpg genomes genomics on Sun Mar 29 2009 at 17:39 UTC | info | related
 
QSRA - a quality-value guided de novo short read assembler
Douglas W Bryant, Weng-Keen Wong, and Todd C Mockler
BMC Bioinformatics 10 (1), 69 (24 Feb 2009)
 
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