Genome Biology | Volume 2 Issue 10

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	Volume 2 Issue 10
	Comment
	Comment September 11, 01 Gregory A Petsko Genome Biology 2001, 2:comment1012-comment1012.2 (26 September 2001) Full text \| PDF \| PubMed \| Editor’s summary The events of September 11 should put to rest the notion that our behavior is completely, or even largely, determined by our genes.
	Review
	Minireview The olfactory receptor family album Chiquito Crasto, Michael S Singer, Gordon M Shepherd Genome Biology 2001, 2:reviews1027-reviews1027.4 (14 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the human genome draft sequences has revealed a more complete portrait of the olfactory receptor gene repertoire in humans than was available previously. The new information provides a basis for deeper analysis of the functions of the receptors, and promises new insights into the evolutionary history of the family.
	Minireview Functional genomics and metal metabolism David J Eide Genome Biology 2001, 2:reviews1028-reviews1028.3 (14 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Metal ions are essential nutrients, yet they can also be toxic if they over-accumulate. Homeostatic mechanisms and detoxification systems therefore precisely control their intracellular levels and distribution. The tools of functional genomics are rapidly accelerating understanding in this field, particularly in the yeast Saccharomyces cerevisiae.
	Minireview An amphibian with ambition: a new role for Xenopus in the 21st century Caroline W Beck, Jonathan MW Slack Genome Biology 2001, 2:reviews1029-reviews1029.5 (19 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Much of our knowledge about the mechanisms of vertebrate early development comes from studies using Xenopus laevis. The recent development of a remarkably efficient method for generating transgenic embryos is now allowing study of late development and organogenesis in Xenopus embryos. Possibilities are also emerging for genomic studies using the closely related diploid frog Xenopus tropicalis.
	Report
	Web report Finding mutations in your favorite gene Steven G Gray Genome Biology 2001, 2:reports2012 (14 September 2001) Abstract \| Full text \| Editor’s summary The Universal Mutation Database (UMD) was developed to allow researchers interested in particular human disease genes to query gene-specific databases for mutational information in a dynamic and interactive fashion.
	Web report More mouse SNPs Steven G Gray Genome Biology 2001, 2:reports2013 (14 September 2001) Abstract \| Full text
	Web report Collecting splice variants Steven G Gray Genome Biology 2001, 2:reports2014 (14 September 2001) Abstract \| Full text
	Paper report Arrays of DNA-binding sites John C Rockett Genome Biology 2001, 2:reports0032 (12 September 2001) Abstract \| Full text
	Paper report Human chromosome 19 homologies. S Subramanian Genome Biology 2001, 2:reports0033 (12 September 2001) Abstract \| Full text \| Editor’s summary Gene sequence conservation and lineage-specific evolution are revealed by analysis of homologous sequences in human and mouse.
	Paper report Homologous recombination in animal mitochondria James Cotton Genome Biology 2001, 2:reports0034 (12 September 2001) Abstract \| Full text
	Paper report Proteome chips and protein function Reiner Veitia Genome Biology 2001, 2:reports0035 (19 September 2001) Abstract \| Full text
	Paper report Malarial origins S Subramanian Genome Biology 2001, 2:reports0036 (19 September 2001) Abstract \| Full text \| Editor’s summary All members of the species Plasmodium falciparum seem to have been derived from a single recent ancestor.
	Paper report ABC proteins in Arabidopsis Harish Chandran Genome Biology 2001, 2:reports0037 (19 September 2001) Abstract \| Full text \| Editor’s summary A complete inventory of putative ATP-binding cassette proteins has been assembled from the Arabidopsis genomic sequence.
	Paper report Characterizing resistance to the pesticide Bt toxin. S Subramanian Genome Biology 2001, 2:reports0038 (19 September 2001) Abstract \| Full text \| Editor’s summary Cloning and characterization of the Bacillus thuringiensis toxin-resistance gene bre-5 from Caenorhabditis elegans has revealed it is a glycosyltransferase.
	Meeting report A wormer's eye view Andrew G Fraser Genome Biology 2001, 2:reports4022-reports4022.3 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the thirteenth international Caenorhabditis elegans meeting, University of California, Los Angeles, USA, 22-26 June 2001.
	Meeting report The nucleosome: from wallflower to Queen of the Ball Fabien Cubizolles, Susan M Gasser Genome Biology 2001, 2:reports4023-reports4023.4 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB meeting on Chromatin and Transcription, Snowmass, USA, 7-12 July 2001.
	Meeting report Unraveling immunology Zoltan T Fehervari Genome Biology 2001, 2:reports4024-reports4024.4 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th International Congress of Immunology, Stockholm, Sweden, 22-27 July 2001.
	Meeting report Ubiquitin junction, what's your function? Traci A Lee, Mike Tyers Genome Biology 2001, 2:reports4025-reports4025.3 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Ubiquitin and Intracellular Protein Degradation FASEB summer conference, Saxtons River, USA, 23-28 June 2001.
	Tutorial Having a BLAST with bioinformatics (and avoiding BLASTphemy) Alexander Pertsemlidis, John W Fondon Genome Biology 2001, 2:reviews2002-reviews2002.10 (27 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the implementation developed at the National Center for Biotechnology Information.
	Research news Muscle profiles Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011001-01 (1 October 2001) Abstract \| Full text \| Editor’s summary Extraocular muscle expresses hundreds of genes that distinguish it from other muscle classes.
	Research news Telomerase mutations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011002-01 (2 October 2001) Abstract \| Full text \| Editor’s summary Mutations in telomerase RNA have been found in patients with inherited dyskeratosis congenita.
	Research news Topo II & pol II Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011003-01 (3 October 2001) Abstract \| Full text \| Editor’s summary DNA topoisomerase IIα plays a critical role during transcription by RNA polymerase II.
	Research news Plague genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011004-01 (4 October 2001) Abstract \| Full text \| Editor’s summary The genome sequence of the plague-causing bacterium Yersinia pestis reveals insights into the evolution of virulent pathogens.
	Research news Watch your language! Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011005-01 (5 October 2001) Abstract \| Full text \| Editor’s summary Mutation of a forhead/winged-helix protein leads to severe speech and language disorder.
	Research news The nitroproteome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011008-01 (8 October 2001) Abstract \| Full text \| Editor’s summary Proteomics has identified over 40 proteins nitrated during inflammatory challenge.
	Research news The Nobel Prize for Physiology or Medicine 2001 David Bruce Genome Biology 2001, 2:spotlight-20011008-02 (8 October 2001) Abstract \| Full text \| Editor’s summary Leland Hartwell, Tim Hunt and Sir Paul Nurse awarded the 2001 Nobel Prize for Physiology or Medicine for their discoveries of key regulators of the cell-cycle.
	Research news Chromosome replication Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011009-01 (9 October 2001) Abstract \| Full text \| Editor’s summary A microarray approach has defined hundreds of chromosome replication origins across the yeast genome.
	Research news Apoliprotein locus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011010-01 (10 October 2001) Abstract \| Full text \| Editor’s summary Comparison of mouse and human genomic sequences reveals an unidentified apolipoprotein-like gene.
	Research news 700,000 ORESTES Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011011-01 (11 October 2001) Abstract \| Full text \| Editor’s summary A Brazilian project has added thousands of open reading frame expressed sequence tags (ORESTES) to efforts to define the complete human transcriptome.
	Research news Chromatin at centromeres Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011012-01 (12 October 2001) Abstract \| Full text \| Editor’s summary A novel separation technique shows that chromatin fibres from the centromere are more compact.
	Research news Lymphocyte signaling Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011015-02 (15 October 2001) Abstract \| Full text \| Editor’s summary An efficient gene transfer method allows dissection of signalling pathways in primary T lymphocytes.
	Research news Size matters Tudor Toma Genome Biology 2001, 2:spotlight-20011015-01 (15 October 2001) Abstract \| Full text \| Editor’s summary The shortest telomere, not average telomere length, is critical for cell viability and chromosome stability.
	Research news Phosphatase in metastasis Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011016-01 (16 October 2001) Abstract \| Full text \| Editor’s summary Serial analysis of gene expression (SAGE) identifies a tyrosine phosphatase associated with liver metastasis in colorectal cancer.
	Research news Controlling the cell cycle clock Susan Aldridge Genome Biology 2001, 2:spotlight-20011017-01 (17 October 2001) Abstract \| Full text \| Editor’s summary Using a novel DNA extraction method, the proteins that control the cell cycle regulatory proteins have been identified.
	Research news All about abo Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011017-02 (17 October 2001) Abstract \| Full text \| Editor’s summary The product of the abnormal oocyte (abo) gene is a chromosomal protein that regulates histone gene expression.
	Research news Wild olives Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011018-01 (18 October 2001) Abstract \| Full text \| Editor’s summary Genetic analysis of samples from Mediterranean forests provides evidence for the persistence of ancient wild olive forms.
	Research news Fly immunity Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011019-01 (19 October 2001) Abstract \| Full text \| Editor’s summary Microarray analysis identifies hundreds of novel genes involved in the innate immune response in Drosophila.
	Research news Ultraviolet sensitivity Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011022-01 (22 October 2001) Abstract \| Full text \| Editor’s summary A genome-wide screen in budding yeast identifies genes involved in the response to ultraviolet radiation.
	Research news The future's bright, the future's online Helen Gavaghan Genome Biology 2001, 2:spotlight-20011023-02 (23 October 2001) Abstract \| Full text \| Editor’s summary The resignation of an entire editorial board over journal access adds further impetus to the online publishing revolution.
	Research news Studying disease associations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011023-03 (23 October 2001) Abstract \| Full text \| Editor’s summary Estimates of genetic disease associations vary greatly between multiple studies and should be evaluated with caution.
	Research news Lucky Luke Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011024-01 (24 October 2001) Abstract \| Full text \| Editor’s summary Analysis of ancient DNA from a tomb in Padua explores the geographical origins of the body believed to belong to the evangelist Luke.
	Research news Sequencing Salmonella Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011025-01 (25 October 2001) Abstract \| Full text \| Editor’s summary The sequencing of two Salmonella genomes provides insights into the virulence of bacterial strains that cause typhoid fever and gastroenteritis.
	Research news Lining-up Listeria genomes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011026-01 (26 October 2001) Abstract \| Full text \| Editor’s summary Comparison of two Listeria genomes identifies islets of genes associated with bacterial virulence.
	Research news Switching on genes with GeneSwitch Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011029-01 (29 October 2001) Abstract \| Full text \| Editor’s summary GeneSwitch is a GAL4-based system that allows expression of a transgene to be induced in a temporal and spatial manner in Drosophila.
	Research news Fugu genome rough draft completed Tudor Toma Genome Biology 2001, 2:spotlight-20011030-02 (30 October 2001) Abstract \| Full text \| Editor’s summary The completion of the sequencing of the puffer fish genome will help analysis of the human genome.
	Research news Dendritic defence Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011030-01 (30 October 2001) Abstract \| Full text \| Editor’s summary Analysis of expression profiles following infection of dendritic cells identifies gene responses specific to bacterial, viral or fungal pathogens.
	Research news Large libraries Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011031-01 (31 October 2001) Abstract \| Full text \| Editor’s summary Libraries containing as many as nine trillion different peptide sequences can be used to select numerous high-affinity RNA-binding peptides.
	Research
	Research Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol Lloyd T Lam, Oxana K Pickeral, Amy C Peng, Andreas Rosenwald, Elaine M Hurt, Jena M Giltnane, Lauren M Averett, Hong Zhao, R Eric Davis, Mohan Sathyamoorthy, Larry M Wahl, Eric D Harris, Judy A Mikovits, Anne P Monks, Melinda G Hollingshead, Edward A Sausville, Louis M Staudt Genome Biology 2001, 2:research0041-research0041.11 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Flavopiridol, currently in cancer clinical trials, inhibits cyclin-dependent kinases (CDKs) but its mechanism of action has not been elucidated. Using DNA microarrays, it was found that flavopiridol inhibited gene expression broadly, unlike two other CDK inhibitors. The gene expression profile of flavopiridol closely resembled profiles of transcription inhibitors, and use of flavopiridol showed that different classes of genes had distinct mRNA turnover rates: genes encoding apoptosis regulators frequently had very short half-lives, as did several genes encoding key cell-cycle regulators.
	Research Characterization of alternatively spliced products and tissue-specific isoforms of USP28 and USP25 Rebeca Valero, Mònica Bayés, M Francisca Sánchez-Font, Olga González-Angulo, Roser Gonzàlez-Duarte, Gemma Marfany Genome Biology 2001, 2:research0043-research0043.10 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The ubiquitin-specific proteases (UBP) are a group of enzymes whose predicted function is to reverse the ubiquitinating reaction. Human USP25, a specific-ubiquitin protease gene at 21q11.2, has recently been chracterized. Database searches at the DNA and protein levels, and cDNA library screenings led to the identification of a new UBP member in the human genome, USP28, at 11q23. This gene showed preferential expression in heart and muscle. USP25 overexpression in Down syndrome fetal brains was shown by PCR. This overexpression supports the gene-dosage effects suggested for other UBP members related to aneuploidy syndromes.
	Research The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria Nico C Gey van Pittius, Junaid Gamieldien, Winston Hide, Gordon D Brown, Roland J Siezen, Albert D Beyers Genome Biology 2001, 2:research0044-research0044.18 (19 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Mycobacterium tuberculosis H37Rv has five copies of a cluster of genes known as the ESAT-6 loci. Finished and unfinished genome sequencing data of 98 available microbial genomes has been analyzed for the presence of orthologs of the loci. The multiple duplicates found in the genome of M. tuberculosis H37Rv are also conserved in the genomes of other mycobacteria. Phylogenetic analyses of the resulting sequences have demonstrated that the gene cluster known as region 4 is ancestral; it is also the only region for which an ortholog could be found in the genomes of Corynebacterium diphtheriae and Streptomyces coelicolor
	Research Analysis of strain and regional variation in gene expression in mouse brain Paul Pavlidis, William S Noble Genome Biology 2001, 2:research0042-research0042.15 (27 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A previously published set of gene expression microarray data from six brain regions in two mouse strains found 24 genes showing expression differences between the strains and about 240 genes with regional differences in expression. That analysis relied on 'fold change' and 'absent/present' criteria to select genes. To determine whether statistical methods would give a more sensitive analysis, feature selection and analysis of variance methods were used. At least 63 genes showing strain variation and approximately 600 genes showing regional variation were identified. Comparison of these results to the previous studies show that a high sensitivity was achieved.

	Volume 2 Issue 10
	Comment
	Comment September 11, 01 Gregory A Petsko Genome Biology 2001, 2:comment1012-comment1012.2 (26 September 2001) Full text \| PDF \| PubMed \| Editor’s summary The events of September 11 should put to rest the notion that our behavior is completely, or even largely, determined by our genes.
	Review
	Minireview The olfactory receptor family album Chiquito Crasto, Michael S Singer, Gordon M Shepherd Genome Biology 2001, 2:reviews1027-reviews1027.4 (14 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the human genome draft sequences has revealed a more complete portrait of the olfactory receptor gene repertoire in humans than was available previously. The new information provides a basis for deeper analysis of the functions of the receptors, and promises new insights into the evolutionary history of the family.
	Minireview Functional genomics and metal metabolism David J Eide Genome Biology 2001, 2:reviews1028-reviews1028.3 (14 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Metal ions are essential nutrients, yet they can also be toxic if they over-accumulate. Homeostatic mechanisms and detoxification systems therefore precisely control their intracellular levels and distribution. The tools of functional genomics are rapidly accelerating understanding in this field, particularly in the yeast Saccharomyces cerevisiae.
	Minireview An amphibian with ambition: a new role for Xenopus in the 21st century Caroline W Beck, Jonathan MW Slack Genome Biology 2001, 2:reviews1029-reviews1029.5 (19 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Much of our knowledge about the mechanisms of vertebrate early development comes from studies using Xenopus laevis. The recent development of a remarkably efficient method for generating transgenic embryos is now allowing study of late development and organogenesis in Xenopus embryos. Possibilities are also emerging for genomic studies using the closely related diploid frog Xenopus tropicalis.
	Report
	Web report Finding mutations in your favorite gene Steven G Gray Genome Biology 2001, 2:reports2012 (14 September 2001) Abstract \| Full text \| Editor’s summary The Universal Mutation Database (UMD) was developed to allow researchers interested in particular human disease genes to query gene-specific databases for mutational information in a dynamic and interactive fashion.
	Web report More mouse SNPs Steven G Gray Genome Biology 2001, 2:reports2013 (14 September 2001) Abstract \| Full text
	Web report Collecting splice variants Steven G Gray Genome Biology 2001, 2:reports2014 (14 September 2001) Abstract \| Full text
	Paper report Arrays of DNA-binding sites John C Rockett Genome Biology 2001, 2:reports0032 (12 September 2001) Abstract \| Full text
	Paper report Human chromosome 19 homologies. S Subramanian Genome Biology 2001, 2:reports0033 (12 September 2001) Abstract \| Full text \| Editor’s summary Gene sequence conservation and lineage-specific evolution are revealed by analysis of homologous sequences in human and mouse.
	Paper report Homologous recombination in animal mitochondria James Cotton Genome Biology 2001, 2:reports0034 (12 September 2001) Abstract \| Full text
	Paper report Proteome chips and protein function Reiner Veitia Genome Biology 2001, 2:reports0035 (19 September 2001) Abstract \| Full text
	Paper report Malarial origins S Subramanian Genome Biology 2001, 2:reports0036 (19 September 2001) Abstract \| Full text \| Editor’s summary All members of the species Plasmodium falciparum seem to have been derived from a single recent ancestor.
	Paper report ABC proteins in Arabidopsis Harish Chandran Genome Biology 2001, 2:reports0037 (19 September 2001) Abstract \| Full text \| Editor’s summary A complete inventory of putative ATP-binding cassette proteins has been assembled from the Arabidopsis genomic sequence.
	Paper report Characterizing resistance to the pesticide Bt toxin. S Subramanian Genome Biology 2001, 2:reports0038 (19 September 2001) Abstract \| Full text \| Editor’s summary Cloning and characterization of the Bacillus thuringiensis toxin-resistance gene bre-5 from Caenorhabditis elegans has revealed it is a glycosyltransferase.
	Meeting report A wormer's eye view Andrew G Fraser Genome Biology 2001, 2:reports4022-reports4022.3 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the thirteenth international Caenorhabditis elegans meeting, University of California, Los Angeles, USA, 22-26 June 2001.
	Meeting report The nucleosome: from wallflower to Queen of the Ball Fabien Cubizolles, Susan M Gasser Genome Biology 2001, 2:reports4023-reports4023.4 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB meeting on Chromatin and Transcription, Snowmass, USA, 7-12 July 2001.
	Meeting report Unraveling immunology Zoltan T Fehervari Genome Biology 2001, 2:reports4024-reports4024.4 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th International Congress of Immunology, Stockholm, Sweden, 22-27 July 2001.
	Meeting report Ubiquitin junction, what's your function? Traci A Lee, Mike Tyers Genome Biology 2001, 2:reports4025-reports4025.3 (26 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Ubiquitin and Intracellular Protein Degradation FASEB summer conference, Saxtons River, USA, 23-28 June 2001.
	Tutorial Having a BLAST with bioinformatics (and avoiding BLASTphemy) Alexander Pertsemlidis, John W Fondon Genome Biology 2001, 2:reviews2002-reviews2002.10 (27 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the implementation developed at the National Center for Biotechnology Information.
	Research news Muscle profiles Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011001-01 (1 October 2001) Abstract \| Full text \| Editor’s summary Extraocular muscle expresses hundreds of genes that distinguish it from other muscle classes.
	Research news Telomerase mutations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011002-01 (2 October 2001) Abstract \| Full text \| Editor’s summary Mutations in telomerase RNA have been found in patients with inherited dyskeratosis congenita.
	Research news Topo II & pol II Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011003-01 (3 October 2001) Abstract \| Full text \| Editor’s summary DNA topoisomerase IIα plays a critical role during transcription by RNA polymerase II.
	Research news Plague genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011004-01 (4 October 2001) Abstract \| Full text \| Editor’s summary The genome sequence of the plague-causing bacterium Yersinia pestis reveals insights into the evolution of virulent pathogens.
	Research news Watch your language! Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011005-01 (5 October 2001) Abstract \| Full text \| Editor’s summary Mutation of a forhead/winged-helix protein leads to severe speech and language disorder.
	Research news The nitroproteome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011008-01 (8 October 2001) Abstract \| Full text \| Editor’s summary Proteomics has identified over 40 proteins nitrated during inflammatory challenge.
	Research news The Nobel Prize for Physiology or Medicine 2001 David Bruce Genome Biology 2001, 2:spotlight-20011008-02 (8 October 2001) Abstract \| Full text \| Editor’s summary Leland Hartwell, Tim Hunt and Sir Paul Nurse awarded the 2001 Nobel Prize for Physiology or Medicine for their discoveries of key regulators of the cell-cycle.
	Research news Chromosome replication Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011009-01 (9 October 2001) Abstract \| Full text \| Editor’s summary A microarray approach has defined hundreds of chromosome replication origins across the yeast genome.
	Research news Apoliprotein locus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011010-01 (10 October 2001) Abstract \| Full text \| Editor’s summary Comparison of mouse and human genomic sequences reveals an unidentified apolipoprotein-like gene.
	Research news 700,000 ORESTES Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011011-01 (11 October 2001) Abstract \| Full text \| Editor’s summary A Brazilian project has added thousands of open reading frame expressed sequence tags (ORESTES) to efforts to define the complete human transcriptome.
	Research news Chromatin at centromeres Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011012-01 (12 October 2001) Abstract \| Full text \| Editor’s summary A novel separation technique shows that chromatin fibres from the centromere are more compact.
	Research news Lymphocyte signaling Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011015-02 (15 October 2001) Abstract \| Full text \| Editor’s summary An efficient gene transfer method allows dissection of signalling pathways in primary T lymphocytes.
	Research news Size matters Tudor Toma Genome Biology 2001, 2:spotlight-20011015-01 (15 October 2001) Abstract \| Full text \| Editor’s summary The shortest telomere, not average telomere length, is critical for cell viability and chromosome stability.
	Research news Phosphatase in metastasis Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011016-01 (16 October 2001) Abstract \| Full text \| Editor’s summary Serial analysis of gene expression (SAGE) identifies a tyrosine phosphatase associated with liver metastasis in colorectal cancer.
	Research news Controlling the cell cycle clock Susan Aldridge Genome Biology 2001, 2:spotlight-20011017-01 (17 October 2001) Abstract \| Full text \| Editor’s summary Using a novel DNA extraction method, the proteins that control the cell cycle regulatory proteins have been identified.
	Research news All about abo Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011017-02 (17 October 2001) Abstract \| Full text \| Editor’s summary The product of the abnormal oocyte (abo) gene is a chromosomal protein that regulates histone gene expression.
	Research news Wild olives Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011018-01 (18 October 2001) Abstract \| Full text \| Editor’s summary Genetic analysis of samples from Mediterranean forests provides evidence for the persistence of ancient wild olive forms.
	Research news Fly immunity Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011019-01 (19 October 2001) Abstract \| Full text \| Editor’s summary Microarray analysis identifies hundreds of novel genes involved in the innate immune response in Drosophila.
	Research news Ultraviolet sensitivity Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011022-01 (22 October 2001) Abstract \| Full text \| Editor’s summary A genome-wide screen in budding yeast identifies genes involved in the response to ultraviolet radiation.
	Research news The future's bright, the future's online Helen Gavaghan Genome Biology 2001, 2:spotlight-20011023-02 (23 October 2001) Abstract \| Full text \| Editor’s summary The resignation of an entire editorial board over journal access adds further impetus to the online publishing revolution.
	Research news Studying disease associations Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011023-03 (23 October 2001) Abstract \| Full text \| Editor’s summary Estimates of genetic disease associations vary greatly between multiple studies and should be evaluated with caution.
	Research news Lucky Luke Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011024-01 (24 October 2001) Abstract \| Full text \| Editor’s summary Analysis of ancient DNA from a tomb in Padua explores the geographical origins of the body believed to belong to the evangelist Luke.
	Research news Sequencing Salmonella Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011025-01 (25 October 2001) Abstract \| Full text \| Editor’s summary The sequencing of two Salmonella genomes provides insights into the virulence of bacterial strains that cause typhoid fever and gastroenteritis.
	Research news Lining-up Listeria genomes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011026-01 (26 October 2001) Abstract \| Full text \| Editor’s summary Comparison of two Listeria genomes identifies islets of genes associated with bacterial virulence.
	Research news Switching on genes with GeneSwitch Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011029-01 (29 October 2001) Abstract \| Full text \| Editor’s summary GeneSwitch is a GAL4-based system that allows expression of a transgene to be induced in a temporal and spatial manner in Drosophila.
	Research news Fugu genome rough draft completed Tudor Toma Genome Biology 2001, 2:spotlight-20011030-02 (30 October 2001) Abstract \| Full text \| Editor’s summary The completion of the sequencing of the puffer fish genome will help analysis of the human genome.
	Research news Dendritic defence Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011030-01 (30 October 2001) Abstract \| Full text \| Editor’s summary Analysis of expression profiles following infection of dendritic cells identifies gene responses specific to bacterial, viral or fungal pathogens.
	Research news Large libraries Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20011031-01 (31 October 2001) Abstract \| Full text \| Editor’s summary Libraries containing as many as nine trillion different peptide sequences can be used to select numerous high-affinity RNA-binding peptides.
	Research
	Research Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol Lloyd T Lam, Oxana K Pickeral, Amy C Peng, Andreas Rosenwald, Elaine M Hurt, Jena M Giltnane, Lauren M Averett, Hong Zhao, R Eric Davis, Mohan Sathyamoorthy, Larry M Wahl, Eric D Harris, Judy A Mikovits, Anne P Monks, Melinda G Hollingshead, Edward A Sausville, Louis M Staudt Genome Biology 2001, 2:research0041-research0041.11 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Flavopiridol, currently in cancer clinical trials, inhibits cyclin-dependent kinases (CDKs) but its mechanism of action has not been elucidated. Using DNA microarrays, it was found that flavopiridol inhibited gene expression broadly, unlike two other CDK inhibitors. The gene expression profile of flavopiridol closely resembled profiles of transcription inhibitors, and use of flavopiridol showed that different classes of genes had distinct mRNA turnover rates: genes encoding apoptosis regulators frequently had very short half-lives, as did several genes encoding key cell-cycle regulators.
	Research Characterization of alternatively spliced products and tissue-specific isoforms of USP28 and USP25 Rebeca Valero, Mònica Bayés, M Francisca Sánchez-Font, Olga González-Angulo, Roser Gonzàlez-Duarte, Gemma Marfany Genome Biology 2001, 2:research0043-research0043.10 (13 September 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The ubiquitin-specific proteases (UBP) are a group of enzymes whose predicted function is to reverse the ubiquitinating reaction. Human USP25, a specific-ubiquitin protease gene at 21q11.2, has recently been chracterized. Database searches at the DNA and protein levels, and cDNA library screenings led to the identification of a new UBP member in the human genome, USP28, at 11q23. This gene showed preferential expression in heart and muscle. USP25 overexpression in Down syndrome fetal brains was shown by PCR. This overexpression supports the gene-dosage effects suggested for other UBP members related to aneuploidy syndromes.
	Research The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria Nico C Gey van Pittius, Junaid Gamieldien, Winston Hide, Gordon D Brown, Roland J Siezen, Albert D Beyers Genome Biology 2001, 2:research0044-research0044.18 (19 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Mycobacterium tuberculosis H37Rv has five copies of a cluster of genes known as the ESAT-6 loci. Finished and unfinished genome sequencing data of 98 available microbial genomes has been analyzed for the presence of orthologs of the loci. The multiple duplicates found in the genome of M. tuberculosis H37Rv are also conserved in the genomes of other mycobacteria. Phylogenetic analyses of the resulting sequences have demonstrated that the gene cluster known as region 4 is ancestral; it is also the only region for which an ortholog could be found in the genomes of Corynebacterium diphtheriae and Streptomyces coelicolor
	Research Analysis of strain and regional variation in gene expression in mouse brain Paul Pavlidis, William S Noble Genome Biology 2001, 2:research0042-research0042.15 (27 September 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary A previously published set of gene expression microarray data from six brain regions in two mouse strains found 24 genes showing expression differences between the strains and about 240 genes with regional differences in expression. That analysis relied on 'fold change' and 'absent/present' criteria to select genes. To determine whether statistical methods would give a more sensitive analysis, feature selection and analysis of variance methods were used. At least 63 genes showing strain variation and approximately 600 genes showing regional variation were identified. Comparison of these results to the previous studies show that a high sensitivity was achieved.

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Volume 2 Issue 10

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