Browsing by Subject "genome"

Now showing 1 - 9 of 9
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    1997 Delegates to the Second International Strategy Meeting on Human Genome Sequencing in Bermuda from Gert-Jan van Ommen
    (2016-08-31)
    Photographs from the February 1997 Bermuda meeting. Courtesy of Gert-Jan van Ommen.
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    2000 NHGRI e-mail request for HGP sequencing center information, and corresponding aggregate data from NHGRI, compiled by Kris Wetterstrand
    (2016-08-31)
    Email exchange in 2013 between Kathryn Maxson (Duke) and Kris Wetterstrand (NHGRI), regarding country funding and other data for the HGP sequencing centers. Also includes the email request for such information, from NHGRI to the centers, in 2000, and the aggregate data collected.
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    2011 18 August Mark Guyer-Jane Peterson interview
    (2011-08-18)
    Mark Guyer and Jane Peterson, in-person interview with Kathryn Maxson and Robert Cook-Deegan, conducted in Rockville, MD (NIH campus), 18 August 2011. Mark Guyer and Jane Peterson were grants program officers at the NIH during the HGP, and were some of the longest-standing employees in the HGP administrative structure. Both witnessed the transformation of the Office of Genome Research into the National Center for Human Genome Research and, finally, the National Human Genome Research Institute. They were close participants in the history of the Bermuda Principles within the NIH.
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    2012 09 February Jean Weissenbach interview
    (2016-08-31)
    Jean Weissenbach, telephone interview by Kathryn Maxson and Robert Cook-Deegan, conducted from Durham, NC 09 February 2012. Jean Weissenbach, a leader in French genetic mapping, directed the French national sequencing center, Généthon, during the HGP and was instrumental in helping to build agreement to the Bermuda Principles in France.
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    Cyclic Sulfones as Novel P3-Caps for Hepatitis C Virus NS3/4A (HCV NS3/4A) Protease Inhibitors: Synthesis and Evaluation of Inhibitors with Improved Potency and Pharmacokinetic Profiles
    (2010) Velázquez, Francisco; Sannigrahi, Mousumi; Bennett, Frank; Lovey, Raymond G; Arasappan, Ashok; Bogen, Stéphane; Nair, Latha; Venkatraman, Srikanth; Blackman, Melissa; Hendrata, Siska; Huang, Yuhua; Huelgas, Regina; Pinto, Patrick; Cheng, Kuo-Chi; Tong, Xiao; McPhail, Andrew T; Njoroge, F George
    HCV infection affects more than 170 million people worldwide and many of those patients will reach the end stage complications of the disease which include hepatocarcinoma and liver failure. The success rate for treatment of patients infected with genotype-1 is about 40%. Therefore, novel treatments are needed to combat the infection. The HCV NS3 protease inhibitor Boceprevir (1) was reported by our research group and efforts continue for the discovery of more potent compounds with improved pharmacokinetic profiles. A new series of HCV NS3 protease inhibitors having a cyclic sulfone P3-cap have been discovered. Compounds 43 and 44 showed K-i* values in the single-digit nM range and their cellular potency was improved by 10-fold compared to 1. The pharmacokinetic profiles of 43 and 44 in rats and monkeys were also improved to achieve higher plasma levels after oral administration.
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    Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus
    (2010) Chang, Kung-Yen; Georgianna, D Ryan; Heber, Steffen; Payne, Gary A; Muddiman, David C
    Identification of proteins from proteolytic peptides or intact proteins plays an essential role in proteomics. Researchers use search engines to match the acquired peptide sequences to the target proteins. However, search engines depend on protein databases to provide candidates for consideration. Alternative splicing (AS), the mechanism where the exon of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore protein variants, enable higher eukaryotic organisms, with only a limited number of genes, to have the requisite complexity and diversity at the proteome level. Multiple alternative isoforms from one gene often share common segments of sequences. However, many protein databases only include a limited number of isoforms to keep minimal redundancy. As a result, the database search might not identify a target protein even with high quality tandem MS data and accurate intact precursor ion mass. We computationally predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from 20 371 expressed sequence tags to investigate whether an alternative splicing protein database can assign a greater proportion of mass spectrometry data. The newly constructed AS database provided 9807 new alternatively spliced variants in addition to 12 832 previously annotated proteins. The searches of the existing tandem MS spectra data set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal genes appeared to have multiple protein isoforms. In addition to the discovery of splice variants, AS database also showed potential to improve genome annotation. In summary, the introduction of an alternative splicing database helps identify more proteins and unveils more information about a proteome.
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    Potential Influence of Staphylococcus aureus Clonal Complex 30 Genotype and Transcriptome on Hematogenous Infections.
    (Open Forum Infect Dis, 2015-09) Sharma-Kuinkel, Batu K; Mongodin, Emmanuel F; Myers, Jason R; Vore, Kelly L; Canfield, Greg S; Fraser, Claire M; Rude, Thomas H; Fowler, Vance G; Gill, Steven R
    Background.  The contemporary Staphylococcus aureus clonal complex (CC) 30 lineage is associated with complicated infections, including endocarditis and osteomyelitis. This lineage diverged from the phage-type 80/81 S aureus clone responsible for a major bacterial epidemic of the 20th century. The genome and transcriptome features that contribute to complicated infections of the CC30 lineage are unknown. Methods.  Twenty-nine clinical methicillin-resistant S aureus (MRSA) strains (8 from CC30 and 21 from other major CCs were evaluated for virulence using murine and Galleria mellonella sepsis models. Genomic features of CC30 were identified by comparative genome sequencing and RNA-Seq transcriptome analysis of the 29 strains and 31 previously sequenced S aureus genomes. Results.  The CC30 isolates displayed lower virulence in the sepsis models compared with other CCs [P < .0001]. Comparisons of orthologous proteins and transcriptome analysis identified genes (eg, nitric oxide reductase) and changes in metabolic pathways (eg, pyrimidine metabolism) that contribute to the distinct CC30 phenotype. Previously reported nonsynonymous single-nucleotide polymorphisms (SNPs) were found in accessory gene regulator C (agrC) and α-hemolysin (hla), molecules important for virulence. Additional nonsynonymous SNPs conserved across clinical CC30 isolates when compared with the first sequenced contemporary CC30 clone, MRSA-16, were identified in multiple genes, suggesting continuing evolutionary divergence in this lineage. Conclusions.  Genomic and transcriptional analyses suggest that the CC30 lineage has acquired metabolic features that contribute to persistent and complicated infections. Absence of sepsis-induced mortality in animal models may be due in part to its unique genomic profile and suggests that specific genotypes of S aureus elicit distinct types of infection types.