Genome Biology | Volume 2 Issue 9

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	Volume 2 Issue 9
	Comment
	Comment Hell is a karaoke cruise Gregory A Petsko Genome Biology 2001, 2:comment1011-comment1011.1 (31 August 2001) Full text \| PDF \| PubMed \| Editor’s summary What would constitute a definition of hell for a scientist in the post-genomics era?
	Review
	Review The nuclear pore complex Stephen A Adam Genome Biology 2001, 2:reviews0007-reviews0007.6 (31 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of components of the complex by proteomics and genomics have provided new insights.
	Protein family review The PITP family of phosphatidylinositol transfer proteins Justin Hsuan, Shamshad Cockcroft Genome Biology 2001, 2:reviews3011-reviews3011.8 (31 August 2001) Full text \| PDF \| PubMed \| Editor’s summary The PITP family of single and multi-domain proteins play vital, but as yet only partially characterized, roles in several higher eukaryotic cell functions that are regulated by phosphoinositide signaling pathways.
	Minireview Being in the right location at the right time Rainer Pepperkok, Jeremy C Simpson, Stefan Wiemann Genome Biology 2001, 2:reviews1024-reviews1024.4 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function of each of these genes and to deciphering functional networks. This article highlights current approaches aimed at achieving this goal.
	Minireview New clues to the puzzle of mammalian sex determination Josephine Bowles, Peter Koopman Genome Biology 2001, 2:reviews1025-reviews1025.4 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary WT1 and SOX9 are transcription factors with critical roles in mammalian sex determination and gonadal development. Recent studies in vivo clarify the roles of two alternative splice isoforms of WT1, and demonstrate that SOX9 can induce male sex determination.
	Minireview The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis Andrew J Furley Genome Biology 2001, 2:reviews1026-reviews1026.5 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A key problem in using genetics to dissect the wiring of the mammalian brain lies in discovering which of the billions of neural connections have been disrupted by a particular mutation. A novel gene-trap approach targets the genes involved in brain wiring and labels the axons of neurons expressing those genes, enabling the effects of mutations to be observed directly.
	Report
	Web report Little weed: Arabidopsis genomic and related data Penny Webb Genome Biology 2001, 2:reports2010 (29 August 2001) Abstract \| Full text
	Web report BINDing molecules John C Rockett Genome Biology 2001, 2:reports2011 (29 August 2001) Abstract \| Full text
	Paper report Opioid receptors Maria Östergård Genome Biology 2001, 2:reports0028 (17 August 2001) Abstract \| Full text \| Editor’s summary Mouse μ-opioid receptor carboxy-terminal splice variants have been shown to differ in their responses to agonists.
	Paper report Haploid female mites S Subramanian Genome Biology 2001, 2:reports0029 (17 August 2001) Abstract \| Full text \| Editor’s summary Brevipalpus phoenicis, the false spider mite, has been shown to exist only in the haploid state.
	Paper report Yeast fitness and protein evolution Reiner Veitia Genome Biology 2001, 2:reports0030 (17 August 2001) Abstract \| Full text \| Editor’s summary The impact on fitness of homozygous deletions in yeast has been shown to correlate with the rate of protein evolution assessed as the evolutionary distance between yeast and Caenorhabditis elegans.
	Paper report You are what you eat S Subramanian Genome Biology 2001, 2:reports0031 (30 August 2001) Abstract \| Full text
	Meeting report Genomic and proteomic techniques applied to reproductive biology John C Rockett Genome Biology 2001, 2:reports4020-reports4020.3 (24 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Frontiers in Reproduction Symposium 2001 'Reproductive genetics, genomics and proteomics: advances in genetic, molecular and bioinformatics techniques', Cambridge, USA, 30 June to 1 July, 2001.
	Meeting report The miracle of microarray data analysis Yuk Fai Leung, Dennis Shun Chiu Lam, Chi Pui Pang Genome Biology 2001, 2:reports4021-reports4021.2 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the tenth Annual Bioinformatics and Genome Research meeting of the Cambridge Healthtech Institute's Beyond Genome 2001 series, San Francisco, USA, 17-19 June 2001.
	Deposited research article Assembling and gap filling of unordered genome sequences through gene checking Amit K Maiti, Patrice Bouvagnet Genome Biology 2001, 2:preprint0008-preprint0008.11 (7 August 2001) Abstract \| Full text \| PDF \| Editor’s summary The first draft of human genome is complete but a considerable number of gaps remain to be filled. A simple method is described by which a large number of BACs could be arranged. Gaps could subsequently be traced and filled by further hybridizations and sequencing.
	Research news Transplastomic tomatoes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010903-01 (3 September 2001) Abstract \| Full text \| Editor’s summary Plastid genome engineering has created transgenic tomatoes, paving the way for the development of appetizing edible vaccines.
	Research news High-throughput SIN-ning Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010904-02 (4 September 2001) Abstract \| Full text \| Editor’s summary A new expression cloning method based on SIN replicon particles from the Sindbis alphavirus promises high-throughput mammalian expression cloning.
	Research news Dendritic cell function Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010905-01 (5 September 2001) Abstract \| Full text \| Editor’s summary Microarray analysis of dendritic cells identifies interleukin-2 as a key cytokine in the priming of naive T cells.
	Research news Mitochondrial inheritance Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010906-01 (6 September 2001) Abstract \| Full text \| Editor’s summary Examining co-inheritance of mitochondrial and female-specific nuclear DNA supports the hypothesis of clonal inheritance.
	Research news Loss of p16Ink4a Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010907-01 (7 September 2001) Abstract \| Full text \| Editor’s summary Knockout mice clearly establish p16Ink4a as a tumour suppressor.
	Research news Spanish flu Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010910-01 (10 September 2001) Abstract \| Full text \| Editor’s summary Analysis of the hemagglutinin gene of the 1918 Spanish influenza virus suggests that a recombination event created the deadly strain.
	Research news Metastatic medulloblastoma Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010911-01 (11 September 2001) Abstract \| Full text \| Editor’s summary Expression profiling identifies a set of genes associated with metastatic medulloblastomas.
	Research news Aging liver Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010912-01 (12 September 2001) Abstract \| Full text \| Editor’s summary Microarray analysis of gene expression in mouse livers identifies genes involved in the aging process.
	Research news Classifying carcinomas Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010913-01 (13 September 2001) Abstract \| Full text \| Editor’s summary Breast carcinomas can be classified into different subclasses using microarray profiling.
	Research news p53 in worms Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010914-01 (14 September 2001) Abstract \| Full text \| Editor’s summary A p53-like protein is involved in the stress response and apoptosis in nematode worms.
	Research news Predictable Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010917-01 (17 September 2001) Abstract \| Full text \| Editor’s summary Gene expression patterns can predict the chemosensitivity of cancer cell lines.
	Research news New era for the European Bioinformatics Institute Susan Aldridge Genome Biology 2001, 2:spotlight-20010919-01 (19 September 2001) Abstract \| Full text \| Editor’s summary Janet Thornton takes over as head of the EBI and outlines her vision of the development of the field of bioinformatics.
	Research news Genomic mountains Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010919-02 (19 September 2001) Abstract \| Full text \| Editor’s summary Three-dimensional maps of microarray data help in navigating the nematode genome.
	Research news Agrin therapy Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010920-01 (20 September 2001) Abstract \| Full text \| Editor’s summary Gene therapy with a mini-agrin transgene rescues muscular dystrophy in mice lacking a functional lama2 gene.
	Research news Antisense in Staphylococcus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010921-01 (21 September 2001) Abstract \| Full text \| Editor’s summary Comprehensive genomic analysis of a human pathogen has been achieved by combining regulated expression and antisense technology.
	Research news Cod origins Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010924-01 (24 September 2001) Abstract \| Full text \| Editor’s summary Microsatellite marker analysis can identify the population of origin of individual cod in the Atlantic Ocean.
	Research news Red squirrels in Britain Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010925-01 (25 September 2001) Abstract \| Full text \| Editor’s summary Human forestation programmes had a dramatic affect on the genetic structure of British squirrel populations.
	Research news Modifying DiGeorge Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010926-02 (26 September 2001) Abstract \| Full text \| Editor’s summary Analysis of a mouse model for DiGeorge syndrome suggests that genetic modifiers affect the disease phenotype.
	Research news Minos in mammals Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010926-01 (26 September 2001) Abstract \| Full text \| Editor’s summary Transgenic mice show that the Minos mobile genetic element from Drosophila can transpose in mammalian tissues.
	Research news Viral discovery Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010927-01 (27 September 2001) Abstract \| Full text \| Editor’s summary A simple new technique can isolate novel virus genomes from contaminated plasma samples.
	Research news Intronic sequences Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010928-01 (28 September 2001) Abstract \| Full text \| Editor’s summary Analysis of intronic sequences from five eukaryote genomes provides insights into information required for intron recognition by the splicing machinery.
	Research
	Research A functional update of the Escherichia coli K-12 genome Margrethe H Serres, Shuba Gopal, Laila A Nahum, Ping Liang, Terry Gaasterland, Monica Riley Genome Biology 2001, 2:research0035-research0035.7 (20 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Escherichia coli K-12 has been reannotated, with the aid of new biological characterization and as the functions of sequence-similar proteins has become available. The coding sequences are represented by modules (protein elements of at least 100 amino acids). Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli.
	Research On the species of origin: diagnosing the source of symbiotic transcripts Peter T Hraber, Jennifer W Weller Genome Biology 2001, 2:research0037-research0037.14 (23 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Symbiotic interactions range from pathogenic to mutualistic, and many of the underlying molecular mechanisms remain to be discovered. Given a sequence expressed in an interaction between two symbionts, the challenge is to determine from which organism the transcript originated. Previous investigations into GC content and comparative similarity searching provide solutions, but a comparative lexical analysis, which uses a likelihood-ratio test of hexamer counts, is more powerful. Microbial transcripts comprised 75% of a Phytophthora sojae-infected soybean library, contrasted with 15% or less in root tissue libraries of Medicago truncatula from axenic, P. medicaginis-infected, mycorrhizal, and rhizobacterial treatments. Mycorrhizal libraries contained about 23% microbial transcripts; an axenic plant library contained a similar proportion of putative microbial transcripts. Many of the transcripts isolated from mixed cultures were of unknown function, suggesting specificity to symbiotic metabolism.
	Research Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda2 protein Janusz M Bujnicki, Leszek Rychlewski Genome Biology 2001, 2:research0038-research0038.6 (23 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The reovirus λ2 protein catalyzes mRNA capping, as well as transfer of a methyl group from S-adenosyl-L-methionine to the N7 atom of the added guanosyl moiety and subsequently to the ribose 2'-O atom of the first template-encoded nucleotide. The structure of the human reovirus core has been previously solved, revealing a series of domains that include two putative methyltransferase (MTase) domains. It has been suggested that the m⁷G (cap O) and the 2'-O-ribose (cap 1) MTase activities may be exerted by the MTase 1 and the MTase 2 domains, respectively. Now it is clear that the reovirus MTase 1 domain shares a putative active site with the structurally characterized 2'-O-ribose Mtases, whereas the MTase 2 domain is similar to glycine N-Mtase; so, it is proposed that the previously suggested functional assignments of the MTase 1 and MTase 2 domains should be swapped.
	Research Abundant protein domains occur in proportion to proteome size Joel A Malek Genome Biology 2001, 2:research0039-research0039.5 (24 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Average occurrences of conserved domains have been calculated in each of five eukaryote genomes using two databases of conserved domains. Ratios between two genomes of genes containing a conserved domain, on average, reflected the ratio of the predicted total number of genes in the two genomes.
	Research Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions Anton J Enright, Christos A Ouzounis Genome Biology 2001, 2:research0034-research0034.7 (28 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Detection of gene fusion events across genomes can be used for predicting functional associations of proteins. An exhaustive search for gene fusion events within 24 available completely sequenced genomes was carried out, and 7,224 single-domain proteins that are components of gene fusions in other genomes were detected. The number of predicted functional associations is 39,730 for all genomes; 9% of genes in a given genome appear to code for single-domain, component proteins predicted to be functionally associated.
	Research Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins Kira S Makarova, Vladimir A Ponomarev, Eugene V Koonin Genome Biology 2001, 2:research0033-research0033.14 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Bacterial genomes were searched for duplications of ribosomal proteins. Of the four ribosomal proteins for which paralogs were detected in several genomes, three come in two distinct versions. One form contains a metal-binding Zn-ribbon while in the second, the metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions. Lineage-specific gene loss and horizontal gene transfer therefore seem to make major contributions to the evolution of bacterial ribosomal proteins.
	Research A rapid method to map mutations in Drosophila Sophie G Martin, Krista C Dobi, Daniel St Johnston Genome Biology 2001, 2:research0036-research0036.12 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Drosophila it is now possible to screen for mutant phenotypes in virtually any cell by performing clonal screens using the flp/FRT system. The rate-limiting step in mutant analysis is often identification of the mutated gene. A single-nucleotide polymorphism map for chromosome arm 3R has been developed which contains 73 polymorphisms between the standard FRT chromosome and the mapping chromosome. Using this, mutants can be mapped to a 400 kb interval in a single meiotic mapping cross, and discovery of further SNPs in the region of interest allows the mutation to be mapped to a region of about 50 kb.
	Research Molecular archeology of an SP100 splice variant revisited: dating the retrotranscription and Alu insertion events Eric J Devor Genome Biology 2001, 2:research0040-research0040.6 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary PCR amplification of the 3' end of the nuclear protein encoding gene SP100 using genomic DNAs from human and New World and Old World monkey species, followed by sequencing of the amplicons, has made dating the HMG1L3 and Alu insertion events possible. The HMG1L3 retrotransposition into the SP100 locus occurred after divergence of New World and Old World monkey lineages, some 35-40 million years ago. An upstream Alu sequence was inserted in the last SP100-HMG intron after divergence of the Old World monkey and ape lineages. Sequencing of the Alu in five Old World monkey species places this event at around 19 million years ago.

	Volume 2 Issue 9
	Comment
	Comment Hell is a karaoke cruise Gregory A Petsko Genome Biology 2001, 2:comment1011-comment1011.1 (31 August 2001) Full text \| PDF \| PubMed \| Editor’s summary What would constitute a definition of hell for a scientist in the post-genomics era?
	Review
	Review The nuclear pore complex Stephen A Adam Genome Biology 2001, 2:reviews0007-reviews0007.6 (31 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of components of the complex by proteomics and genomics have provided new insights.
	Protein family review The PITP family of phosphatidylinositol transfer proteins Justin Hsuan, Shamshad Cockcroft Genome Biology 2001, 2:reviews3011-reviews3011.8 (31 August 2001) Full text \| PDF \| PubMed \| Editor’s summary The PITP family of single and multi-domain proteins play vital, but as yet only partially characterized, roles in several higher eukaryotic cell functions that are regulated by phosphoinositide signaling pathways.
	Minireview Being in the right location at the right time Rainer Pepperkok, Jeremy C Simpson, Stefan Wiemann Genome Biology 2001, 2:reviews1024-reviews1024.4 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function of each of these genes and to deciphering functional networks. This article highlights current approaches aimed at achieving this goal.
	Minireview New clues to the puzzle of mammalian sex determination Josephine Bowles, Peter Koopman Genome Biology 2001, 2:reviews1025-reviews1025.4 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary WT1 and SOX9 are transcription factors with critical roles in mammalian sex determination and gonadal development. Recent studies in vivo clarify the roles of two alternative splice isoforms of WT1, and demonstrate that SOX9 can induce male sex determination.
	Minireview The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis Andrew J Furley Genome Biology 2001, 2:reviews1026-reviews1026.5 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A key problem in using genetics to dissect the wiring of the mammalian brain lies in discovering which of the billions of neural connections have been disrupted by a particular mutation. A novel gene-trap approach targets the genes involved in brain wiring and labels the axons of neurons expressing those genes, enabling the effects of mutations to be observed directly.
	Report
	Web report Little weed: Arabidopsis genomic and related data Penny Webb Genome Biology 2001, 2:reports2010 (29 August 2001) Abstract \| Full text
	Web report BINDing molecules John C Rockett Genome Biology 2001, 2:reports2011 (29 August 2001) Abstract \| Full text
	Paper report Opioid receptors Maria Östergård Genome Biology 2001, 2:reports0028 (17 August 2001) Abstract \| Full text \| Editor’s summary Mouse μ-opioid receptor carboxy-terminal splice variants have been shown to differ in their responses to agonists.
	Paper report Haploid female mites S Subramanian Genome Biology 2001, 2:reports0029 (17 August 2001) Abstract \| Full text \| Editor’s summary Brevipalpus phoenicis, the false spider mite, has been shown to exist only in the haploid state.
	Paper report Yeast fitness and protein evolution Reiner Veitia Genome Biology 2001, 2:reports0030 (17 August 2001) Abstract \| Full text \| Editor’s summary The impact on fitness of homozygous deletions in yeast has been shown to correlate with the rate of protein evolution assessed as the evolutionary distance between yeast and Caenorhabditis elegans.
	Paper report You are what you eat S Subramanian Genome Biology 2001, 2:reports0031 (30 August 2001) Abstract \| Full text
	Meeting report Genomic and proteomic techniques applied to reproductive biology John C Rockett Genome Biology 2001, 2:reports4020-reports4020.3 (24 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Frontiers in Reproduction Symposium 2001 'Reproductive genetics, genomics and proteomics: advances in genetic, molecular and bioinformatics techniques', Cambridge, USA, 30 June to 1 July, 2001.
	Meeting report The miracle of microarray data analysis Yuk Fai Leung, Dennis Shun Chiu Lam, Chi Pui Pang Genome Biology 2001, 2:reports4021-reports4021.2 (29 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the tenth Annual Bioinformatics and Genome Research meeting of the Cambridge Healthtech Institute's Beyond Genome 2001 series, San Francisco, USA, 17-19 June 2001.
	Deposited research article Assembling and gap filling of unordered genome sequences through gene checking Amit K Maiti, Patrice Bouvagnet Genome Biology 2001, 2:preprint0008-preprint0008.11 (7 August 2001) Abstract \| Full text \| PDF \| Editor’s summary The first draft of human genome is complete but a considerable number of gaps remain to be filled. A simple method is described by which a large number of BACs could be arranged. Gaps could subsequently be traced and filled by further hybridizations and sequencing.
	Research news Transplastomic tomatoes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010903-01 (3 September 2001) Abstract \| Full text \| Editor’s summary Plastid genome engineering has created transgenic tomatoes, paving the way for the development of appetizing edible vaccines.
	Research news High-throughput SIN-ning Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010904-02 (4 September 2001) Abstract \| Full text \| Editor’s summary A new expression cloning method based on SIN replicon particles from the Sindbis alphavirus promises high-throughput mammalian expression cloning.
	Research news Dendritic cell function Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010905-01 (5 September 2001) Abstract \| Full text \| Editor’s summary Microarray analysis of dendritic cells identifies interleukin-2 as a key cytokine in the priming of naive T cells.
	Research news Mitochondrial inheritance Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010906-01 (6 September 2001) Abstract \| Full text \| Editor’s summary Examining co-inheritance of mitochondrial and female-specific nuclear DNA supports the hypothesis of clonal inheritance.
	Research news Loss of p16Ink4a Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010907-01 (7 September 2001) Abstract \| Full text \| Editor’s summary Knockout mice clearly establish p16Ink4a as a tumour suppressor.
	Research news Spanish flu Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010910-01 (10 September 2001) Abstract \| Full text \| Editor’s summary Analysis of the hemagglutinin gene of the 1918 Spanish influenza virus suggests that a recombination event created the deadly strain.
	Research news Metastatic medulloblastoma Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010911-01 (11 September 2001) Abstract \| Full text \| Editor’s summary Expression profiling identifies a set of genes associated with metastatic medulloblastomas.
	Research news Aging liver Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010912-01 (12 September 2001) Abstract \| Full text \| Editor’s summary Microarray analysis of gene expression in mouse livers identifies genes involved in the aging process.
	Research news Classifying carcinomas Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010913-01 (13 September 2001) Abstract \| Full text \| Editor’s summary Breast carcinomas can be classified into different subclasses using microarray profiling.
	Research news p53 in worms Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010914-01 (14 September 2001) Abstract \| Full text \| Editor’s summary A p53-like protein is involved in the stress response and apoptosis in nematode worms.
	Research news Predictable Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010917-01 (17 September 2001) Abstract \| Full text \| Editor’s summary Gene expression patterns can predict the chemosensitivity of cancer cell lines.
	Research news New era for the European Bioinformatics Institute Susan Aldridge Genome Biology 2001, 2:spotlight-20010919-01 (19 September 2001) Abstract \| Full text \| Editor’s summary Janet Thornton takes over as head of the EBI and outlines her vision of the development of the field of bioinformatics.
	Research news Genomic mountains Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010919-02 (19 September 2001) Abstract \| Full text \| Editor’s summary Three-dimensional maps of microarray data help in navigating the nematode genome.
	Research news Agrin therapy Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010920-01 (20 September 2001) Abstract \| Full text \| Editor’s summary Gene therapy with a mini-agrin transgene rescues muscular dystrophy in mice lacking a functional lama2 gene.
	Research news Antisense in Staphylococcus Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010921-01 (21 September 2001) Abstract \| Full text \| Editor’s summary Comprehensive genomic analysis of a human pathogen has been achieved by combining regulated expression and antisense technology.
	Research news Cod origins Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010924-01 (24 September 2001) Abstract \| Full text \| Editor’s summary Microsatellite marker analysis can identify the population of origin of individual cod in the Atlantic Ocean.
	Research news Red squirrels in Britain Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010925-01 (25 September 2001) Abstract \| Full text \| Editor’s summary Human forestation programmes had a dramatic affect on the genetic structure of British squirrel populations.
	Research news Modifying DiGeorge Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010926-02 (26 September 2001) Abstract \| Full text \| Editor’s summary Analysis of a mouse model for DiGeorge syndrome suggests that genetic modifiers affect the disease phenotype.
	Research news Minos in mammals Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010926-01 (26 September 2001) Abstract \| Full text \| Editor’s summary Transgenic mice show that the Minos mobile genetic element from Drosophila can transpose in mammalian tissues.
	Research news Viral discovery Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010927-01 (27 September 2001) Abstract \| Full text \| Editor’s summary A simple new technique can isolate novel virus genomes from contaminated plasma samples.
	Research news Intronic sequences Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010928-01 (28 September 2001) Abstract \| Full text \| Editor’s summary Analysis of intronic sequences from five eukaryote genomes provides insights into information required for intron recognition by the splicing machinery.
	Research
	Research A functional update of the Escherichia coli K-12 genome Margrethe H Serres, Shuba Gopal, Laila A Nahum, Ping Liang, Terry Gaasterland, Monica Riley Genome Biology 2001, 2:research0035-research0035.7 (20 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Escherichia coli K-12 has been reannotated, with the aid of new biological characterization and as the functions of sequence-similar proteins has become available. The coding sequences are represented by modules (protein elements of at least 100 amino acids). Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli.
	Research On the species of origin: diagnosing the source of symbiotic transcripts Peter T Hraber, Jennifer W Weller Genome Biology 2001, 2:research0037-research0037.14 (23 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Symbiotic interactions range from pathogenic to mutualistic, and many of the underlying molecular mechanisms remain to be discovered. Given a sequence expressed in an interaction between two symbionts, the challenge is to determine from which organism the transcript originated. Previous investigations into GC content and comparative similarity searching provide solutions, but a comparative lexical analysis, which uses a likelihood-ratio test of hexamer counts, is more powerful. Microbial transcripts comprised 75% of a Phytophthora sojae-infected soybean library, contrasted with 15% or less in root tissue libraries of Medicago truncatula from axenic, P. medicaginis-infected, mycorrhizal, and rhizobacterial treatments. Mycorrhizal libraries contained about 23% microbial transcripts; an axenic plant library contained a similar proportion of putative microbial transcripts. Many of the transcripts isolated from mixed cultures were of unknown function, suggesting specificity to symbiotic metabolism.
	Research Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda2 protein Janusz M Bujnicki, Leszek Rychlewski Genome Biology 2001, 2:research0038-research0038.6 (23 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The reovirus λ2 protein catalyzes mRNA capping, as well as transfer of a methyl group from S-adenosyl-L-methionine to the N7 atom of the added guanosyl moiety and subsequently to the ribose 2'-O atom of the first template-encoded nucleotide. The structure of the human reovirus core has been previously solved, revealing a series of domains that include two putative methyltransferase (MTase) domains. It has been suggested that the m⁷G (cap O) and the 2'-O-ribose (cap 1) MTase activities may be exerted by the MTase 1 and the MTase 2 domains, respectively. Now it is clear that the reovirus MTase 1 domain shares a putative active site with the structurally characterized 2'-O-ribose Mtases, whereas the MTase 2 domain is similar to glycine N-Mtase; so, it is proposed that the previously suggested functional assignments of the MTase 1 and MTase 2 domains should be swapped.
	Research Abundant protein domains occur in proportion to proteome size Joel A Malek Genome Biology 2001, 2:research0039-research0039.5 (24 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Average occurrences of conserved domains have been calculated in each of five eukaryote genomes using two databases of conserved domains. Ratios between two genomes of genes containing a conserved domain, on average, reflected the ratio of the predicted total number of genes in the two genomes.
	Research Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions Anton J Enright, Christos A Ouzounis Genome Biology 2001, 2:research0034-research0034.7 (28 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Detection of gene fusion events across genomes can be used for predicting functional associations of proteins. An exhaustive search for gene fusion events within 24 available completely sequenced genomes was carried out, and 7,224 single-domain proteins that are components of gene fusions in other genomes were detected. The number of predicted functional associations is 39,730 for all genomes; 9% of genes in a given genome appear to code for single-domain, component proteins predicted to be functionally associated.
	Research Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins Kira S Makarova, Vladimir A Ponomarev, Eugene V Koonin Genome Biology 2001, 2:research0033-research0033.14 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Bacterial genomes were searched for duplications of ribosomal proteins. Of the four ribosomal proteins for which paralogs were detected in several genomes, three come in two distinct versions. One form contains a metal-binding Zn-ribbon while in the second, the metal-chelating residues are completely or partially replaced. Typically, genomes containing paralogous genes for these ribosomal proteins encode both versions. Lineage-specific gene loss and horizontal gene transfer therefore seem to make major contributions to the evolution of bacterial ribosomal proteins.
	Research A rapid method to map mutations in Drosophila Sophie G Martin, Krista C Dobi, Daniel St Johnston Genome Biology 2001, 2:research0036-research0036.12 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In Drosophila it is now possible to screen for mutant phenotypes in virtually any cell by performing clonal screens using the flp/FRT system. The rate-limiting step in mutant analysis is often identification of the mutated gene. A single-nucleotide polymorphism map for chromosome arm 3R has been developed which contains 73 polymorphisms between the standard FRT chromosome and the mapping chromosome. Using this, mutants can be mapped to a 400 kb interval in a single meiotic mapping cross, and discovery of further SNPs in the region of interest allows the mutation to be mapped to a region of about 50 kb.
	Research Molecular archeology of an SP100 splice variant revisited: dating the retrotranscription and Alu insertion events Eric J Devor Genome Biology 2001, 2:research0040-research0040.6 (30 August 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary PCR amplification of the 3' end of the nuclear protein encoding gene SP100 using genomic DNAs from human and New World and Old World monkey species, followed by sequencing of the amplicons, has made dating the HMG1L3 and Alu insertion events possible. The HMG1L3 retrotransposition into the SP100 locus occurred after divergence of New World and Old World monkey lineages, some 35-40 million years ago. An upstream Alu sequence was inserted in the last SP100-HMG intron after divergence of the Old World monkey and ape lineages. Sequencing of the Alu in five Old World monkey species places this event at around 19 million years ago.

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