Genome Biology | Volume 2 Issue 3

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	Volume 2 Issue 3
	Comment
	Comment Size doesn't matter Gregory A Petsko Genome Biology 2001, 2:comment1003-comment1003.2 (28 February 2001) Full text \| PDF \| PubMed \| Editor’s summary The first 'official' count of the number of genes in the human genome is in, and the total is smaller than almost anyone had imagined. How could we have evolved as such complex beings with such a minimalist genome?
	Review
	Review Nuclear dynamics: where genes are and how they got there Jason R Swedlow, Angus I Lamond Genome Biology 2001, 2:reviews0002-reviews0002.7 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA is highly organized spatially, both within domains of chromatin along each chromosome and within the nucleus as a whole. Recent studies suggest that chromatin localization can affect transcriptional and replicational activity. The similarity between the movements of chromatin nuclear bodies suggests a common mechanism that regulates nuclear dynamics.
	Protein family review Fibroblast growth factors David M Ornitz, Nobuyuki Itoh Genome Biology 2001, 2:reviews3005-reviews3005.12 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fibroblast growth factors (FGFs) are a large family of peptide growth factors that require heparan sulfate to activate their tyrosine kinase receptors. They have diverse roles in development, regulating proliferation, migration and differentiation. In adult animals, FGFs are important for homeostasis and tissue repair.
	Minireview Watching the hands of the Arabidopsis biological clock Seth J Davis, Andrew J Millar Genome Biology 2001, 2:reviews1008-reviews1008.4 (5 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oligonucleotide and cDNA microarrays have been used to analyse the mRNA levels of 8,000 genes in Arabidopsis thaliana throughout the day/night cycle. Genes involved in signal transduction and in various metabolic pathways were found to be coordinately regulated by circadian rhythms and/or by light.
	Minireview Fungal virulence studies come of age Frank C Odds, Neil AR Gow, Alistair JP Brown Genome Biology 2001, 2:reviews1009-reviews1009.4 (5 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sophisticated molecular biological research has revealed many virulence attributes in at least four pathogenic fungi, but the future study of fungal virulence requires investigators to distinguish between molecules that directly interact with the host, molecules that regulate these, and molecules that are always required for fungal growth and survival, independent of the host.
	Minireview Rhesus factors and ammonium: a function in efflux? Uwe Ludewig, Nico von Wirén, Doris Rentsch, Wolf B Frommer Genome Biology 2001, 2:reviews1010-reviews1010.5 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters.
	Minireview Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence Andrew H Paterson, Tien-hung Lan, Richard Amasino, Thomas C Osborn, Carlos Quiros Genome Biology 2001, 2:reviews1011-reviews1011.4 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Those studying the genus Brassica will be among the early beneficiaries of the now-completed Arabidopsis sequence. The remarkable morphological diversity of Brassica species and their relatives offers valuable opportunities to advance our knowledge of plant growth and development, and our understanding of rapid phenotypic evolution.
	Opinion Twin peaks: the draft human genome sequence Colin AM Semple, Kathryn L Evans, David J Porteous Genome Biology 2001, 2:comment2003-comment2003.5 (1 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Once thought to be impossible or a waste of resources, the initial high-volume stages of sequencing the human genome have been completed.
	Report
	Paper report RNAi in mammals Edupalli Subbaiah Venkata Genome Biology 2001, 2:reports0007 (28 February 2001) Abstract \| Full text \| Editor’s summary A method for double-stranded RNA interference of gene expression in mammalian cells.
	Paper report Studying cell division by RNAi Joe Hao Genome Biology 2001, 2:reports0008 (28 February 2001) Abstract \| Full text \| Editor’s summary A large-scale RNA interference screen has proved an efficient and powerful reverse genetic approach for identifying genes involved in cell division in Caenorhabditis elegans.
	Meeting report Beyond a 'skeleton': understanding cellular functions of the cytoskeleton Coumaran Egile, Terry Lechler, Rong Li Genome Biology 2001, 2:reports4005-reports4005.3 (6 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the cytoskeleton sessions of the 40^th Annual Meeting of the American Society for Cell Biology, San Francisco, 9-13 December 2000.
	Meeting report Genomics meets informatics Katsumi Isono Genome Biology 2001, 2:reports4006-reports4006.3 (6 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the 11th Workshop on Genome Informatics, the annual meeting on genome informatics and related subjects supported by the Genome Informatics Society of Japan, Tokyo, Japan, 18-19 December, 2000.
	Meeting report Rhizobium goes genomic Xavier Perret, William J Broughton Genome Biology 2001, 2:reports4007-reports4007.3 (9 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report from the Rhizobium Functional Genomics Workshop, Sevilla, Spain, 15-16 September 2000.
	Deposited research article A draft annotation and overview of the human genome Fred A Wright, William J Lemon, Wei D Zhao, Russell Sears, Degen Zhuo, Jian-Ping Wang, Hee-Yung Yang, Troy Baer, Don Stredney, Joe Spitzner, Al Stutz, Ralf Krahe, Bo Yuan Genome Biology 2001, 2:preprint0001-preprint0001.39 (16 February 2001) Abstract \| Full text \| PDF \| Editor’s summary The recent draft assembly of the human genome is sufficiently accurate to provide useful annotation. A functionally annotated human gene index is reported, placed directly on the genome, based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. The genome is estimated to contain 65,000-75,000 transcriptional units, with exonic sequences comprising 4%.
	Deposited research article Improving SAGE di-tag processing Jacques Colinge, Georg Feger Genome Biology 2001, 2:preprint0002-preprint0002.10 (22 February 2001) Abstract \| Full text \| PDF \| Editor’s summary A method for improved processing of SAGE sequences is presented that allows one extra base to be obtained for reasonably abundant tags and includes a statistical test for controlling the relevance of extra base predictions. The improved SAGE sequence processing reduces the uncertainty in SAGE tag to gene mapping and can be applied to any SAGE library.
	Research news Plants cope better without telomerase Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010302-01 (2 March 2001) Abstract \| Full text \| Editor’s summary Arabidopsis mutants lacking telomerase can survive up to ten generations.
	Research news Gene discovery by stringent annotation Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010305-01 (5 March 2001) Abstract \| Full text \| Editor’s summary Careful annotation methodology uncovers over 1,000 novel genes in the Drosophila genome.
	Research news Role of the ATM protein in neurogenesis Kenneth Lee Genome Biology 2001, 2:spotlight-20010306-02 (6 March 2001) Abstract \| Full text \| Editor’s summary The ATM protein essential in DNA repair and cell-cycle regulation is also implicated in neurogenesis in the adult hippocampus.
	Research news Two populations of memory T cells Kenneth Lee Genome Biology 2001, 2:spotlight-20010306-01 (6 March 2001) Abstract \| Full text \| Editor’s summary Tracking CD4+ T cells injected into mice suggests that there are two discrete populations of memory T cells.
	Research news Uniparental disomy in ES cells Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010307-01 (7 March 2001) Abstract \| Full text \| Editor’s summary Selection with the drug G418 can be used to drive chromosome-specific loss of heterozygosity in targeted embryonic stem cells.
	Research news Chemokines may be used in metastasis Kenneth Lee Genome Biology 2001, 2:spotlight-20010308-02 (8 March 2001) Abstract \| Full text \| Editor’s summary Chemokines and their receptors help guide tumour cells to their targets.
	Research news Clues to how prions cross the species barrier Kenneth Lee Genome Biology 2001, 2:spotlight-20010308-03 (8 March 2001) Abstract \| Full text \| Editor’s summary A hybrid prion, created by fusing together prions from two distantly related yeast species, can adopt two distinct shapes and infect both yeast species.
	Research news BAG-1 can predict survival from breast cancer Tudor Toma Genome Biology 2001, 2:spotlight-20010308-01 (8 March 2001) Abstract \| Full text \| Editor’s summary There is preliminary evidence that women with malignant breast tumours that contain high levels of the protein BAG-1 have a longer survival time.
	Research news Making sense of antisense Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010308-04 (8 March 2001) Abstract \| Full text \| Editor’s summary A strategy combining antisense RNA and promoter interference technology allows for genome-wide screening of gene function in Candida albicans.
	Research news Hyper-IgM syndrome dissected Tudor Toma Genome Biology 2001, 2:spotlight-20010309-01 (9 March 2001) Abstract \| Full text \| Editor’s summary Mutations in the gene encoding NEMO that prevent the normal functioning of NF-?B, can explain the hyper-IgM syndrome associated with ectodermal dysplasia.
	Research news Wiring up Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010309-03 (9 March 2001) Abstract \| Full text \| Editor’s summary A gene-trap screen identifies molecules that regulate axon guidance and wiring patterns in the mammalian brain.
	Research news Mouse Mecp2 knockouts and Rett syndrome Kenneth Lee Genome Biology 2001, 2:spotlight-20010309-02 (9 March 2001) Abstract \| Full text \| Editor’s summary Mice lacking the transcriptional repressor Mecp2 have symptoms resembling the neurological disorder Rett syndrome.
	Research news Musical twins Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010312-01 (12 March 2001) Abstract \| Full text \| Editor’s summary A study of monozygotic and dizygotic twins indicates that there is a strong genetic contribution to musical pitch perception.
	Research news Pasteur's genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010313-02 (13 March 2001) Abstract \| Full text \| Editor’s summary The genome sequence of Pasteurella multocida gives insights into the evolution and virulence mechanisms of the multispecies pathogen.
	Research news Protein folding Kenneth Lee Genome Biology 2001, 2:spotlight-20010313-01 (13 March 2001) Abstract \| Full text \| Editor’s summary Under specific conditions globular proteins can assume a structure resembling amyloid and prion aggregates.
	Research news Caretakers and gatekeepers Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010314-01 (14 March 2001) Abstract \| Full text \| Editor’s summary Knockout mouse experiments reveal complex genetic interactions between the ATM protein kinase and non-homologous end-joining factors.
	Research news Budding interactome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010315-01 (15 March 2001) Abstract \| Full text \| Editor’s summary A high-throughput screen has defined over 4500 connections that build up an extensive interaction map of budding yeast proteins.
	Research news How plants cope with the damaging effects of UV radiation Kenneth Lee Genome Biology 2001, 2:spotlight-20010316-03 (16 March 2001) Abstract \| Full text \| Editor’s summary The identification of an Arabidopsis mutant that is hypersensitive to UV radiation provides an insight into how plants cope with genotoxic stress.
	Research news Fungal sexual cycle Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010316-04 (16 March 2001) Abstract \| Full text \| Editor’s summary Comparative genomic analysis has identified genes implicated in meiosis, recombination and pheromone responses in the fungus Candida albicans.
	Research news A virulence marker for Enterococcus faecium Tudor Toma Genome Biology 2001, 2:spotlight-20010316-01 (16 March 2001) Abstract \| Full text \| Editor’s summary A variant of the esp virulence gene could provide a way to prevent the spread of vancomycin-resistant Enterococcus faecium - a common cause of US hospital infections - in Europe.
	Research news Structure of a biological propeller Kenneth Lee Genome Biology 2001, 2:spotlight-20010316-02 (16 March 2001) Abstract \| Full text \| Editor’s summary The crystal structure of flagellin - the protein found in the bacterial flagellar motor - explains how bacteria can switch between 'running' and 'tumbling' motions.
	Research news Histone codes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010319-01 (19 March 2001) Abstract \| Full text \| Editor’s summary Sequential histone modifications regulate heterochromatin assembly in fission yeast.
	Research news H. pylori strain differences influence host responses Tudor Toma Genome Biology 2001, 2:spotlight-20010320-01 (20 March 2001) Abstract \| Full text \| Editor’s summary Differences in the ability of Helicobacter pylori strains to induce epithelial cell responses related to inflammation are dependent on the presence of an intact cag pathogenicity island.
	Research news On display Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010320-02 (20 March 2001) Abstract \| Full text \| Editor’s summary An in vitro selection technique based on 'mRNA display' can select peptide aptamers with high affinity for specific protein targets.
	Research news Juicy transgenics Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010321-01 (21 March 2001) Abstract \| Full text \| Editor’s summary Transgenic citrus plants expressing flower-initiation genes from Arabidopsis have a reduced juvenile phase and flower early.
	Research news N-myc targets Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010322-01 (22 March 2001) Abstract \| Full text \| Editor’s summary Analysis of neuroblastoma cell lines identifies many target genes of the N-myc transcription factor that are involved in ribosome biogenesis.
	Research news Chromosome instability in colon cancer Kenneth Lee Genome Biology 2001, 2:spotlight-20010323-03 (23 March 2001) Abstract \| Full text \| Editor’s summary Colon cancer is often associated with mutations in the APC gene and with defects in chromosome segregation. Two studies now show that microtubules need APC for proper attachment when they pull chromosomes apart.
	Research news Heterochromatin interactions Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010323-04 (23 March 2001) Abstract \| Full text \| Editor’s summary Characterization of the Drosophila homolog of the human AF10 gene, which is associated with a translocation in leukemia, defines a role in heterochromatin function.
	Research news Two genotypes increase risk of heart attack Tudor Toma Genome Biology 2001, 2:spotlight-20010323-01 (23 March 2001) Abstract \| Full text \| Editor’s summary Two genotypes, angiotensin converting enzyme ACE-DD and angiotensin II type 1 receptor AT1 R-CC, interact to increase the risk of ischaemic events.
	Research news An emerging pattern Kenneth Lee Genome Biology 2001, 2:spotlight-20010323-02 (23 March 2001) Abstract \| Full text \| Editor’s summary Three studies shed new light on how members of the bone morphogenetic protein family are regulated during embryonic development.
	Research news Water bug genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010327-03 (27 March 2001) Abstract \| Full text \| Editor’s summary The sequence of the Caulobacter crescentus genome reveals how this proteobacterium adapts to survive in nutrient-poor aquatic and marine environments.
	Research news Overexpression CDC screen Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010328-01 (28 March 2001) Abstract \| Full text \| Editor’s summary An overexpression screen has identified novel yeast genes that control cell-cycle progression.
	Research news Spider's web Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010330-01 (30 March 2001) Abstract \| Full text \| Editor’s summary Comparative analysis of spider fibroin proteins reveals the importance of conserved repeated-sequence motifs.
	Research news Dying without mitochondrial gene expression Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010330-02 (30 March 2001) Abstract \| Full text \| Editor’s summary Loss of mitochondrial DNA expression and of respiratory chain function leads to increased apoptosis in embryonic and cardiac tissues.
	Research
	Research The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases L Aravind, Eugene V Koonin Genome Biology 2001, 2:research0007-research0007.8 (19 February 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence-profile analysis shows that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. This allows the prediction of catalytic activity for a wide range of biochemically uncharacterized proteins from eukaryotes and bacteria.
	Research Survey of transcripts in the adult Drosophila brain Karen L Posey, Leslie B Jones, Rosalinda Cerda, Monica Bajaj, Thao Huynh, Paul E Hardin, Susan H Hardin Genome Biology 2001, 2:research0008-research0008.16 (21 February 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a unique Drosophila cDNA library, constructed exclusively from adult brains, suggests that the number of genes may be underestimated in this organism. This work complements the Drosophila genome project by providing information that facilitates more complete annotation of the genomic sequence. The library should be a useful resource that will help in determining how basic brain functions operate at the molecular level.
	Research The cohesin complex: sequence homologies, interaction networks and shared motifs Susan Jones, John Sgouros Genome Biology 2001, 2:research0009-research0009.12 (6 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Searches of protein sequence databases reveal new homologs of cohesin proteins, in five families, including an ancestral family with sequences from the Archaea and Eubacteria. A cohesion interaction network has been constructed.

	Volume 2 Issue 3
	Comment
	Comment Size doesn't matter Gregory A Petsko Genome Biology 2001, 2:comment1003-comment1003.2 (28 February 2001) Full text \| PDF \| PubMed \| Editor’s summary The first 'official' count of the number of genes in the human genome is in, and the total is smaller than almost anyone had imagined. How could we have evolved as such complex beings with such a minimalist genome?
	Review
	Review Nuclear dynamics: where genes are and how they got there Jason R Swedlow, Angus I Lamond Genome Biology 2001, 2:reviews0002-reviews0002.7 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA is highly organized spatially, both within domains of chromatin along each chromosome and within the nucleus as a whole. Recent studies suggest that chromatin localization can affect transcriptional and replicational activity. The similarity between the movements of chromatin nuclear bodies suggests a common mechanism that regulates nuclear dynamics.
	Protein family review Fibroblast growth factors David M Ornitz, Nobuyuki Itoh Genome Biology 2001, 2:reviews3005-reviews3005.12 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Fibroblast growth factors (FGFs) are a large family of peptide growth factors that require heparan sulfate to activate their tyrosine kinase receptors. They have diverse roles in development, regulating proliferation, migration and differentiation. In adult animals, FGFs are important for homeostasis and tissue repair.
	Minireview Watching the hands of the Arabidopsis biological clock Seth J Davis, Andrew J Millar Genome Biology 2001, 2:reviews1008-reviews1008.4 (5 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Oligonucleotide and cDNA microarrays have been used to analyse the mRNA levels of 8,000 genes in Arabidopsis thaliana throughout the day/night cycle. Genes involved in signal transduction and in various metabolic pathways were found to be coordinately regulated by circadian rhythms and/or by light.
	Minireview Fungal virulence studies come of age Frank C Odds, Neil AR Gow, Alistair JP Brown Genome Biology 2001, 2:reviews1009-reviews1009.4 (5 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sophisticated molecular biological research has revealed many virulence attributes in at least four pathogenic fungi, but the future study of fungal virulence requires investigators to distinguish between molecules that directly interact with the host, molecules that regulate these, and molecules that are always required for fungal growth and survival, independent of the host.
	Minireview Rhesus factors and ammonium: a function in efflux? Uwe Ludewig, Nico von Wirén, Doris Rentsch, Wolf B Frommer Genome Biology 2001, 2:reviews1010-reviews1010.5 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters.
	Minireview Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence Andrew H Paterson, Tien-hung Lan, Richard Amasino, Thomas C Osborn, Carlos Quiros Genome Biology 2001, 2:reviews1011-reviews1011.4 (9 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Those studying the genus Brassica will be among the early beneficiaries of the now-completed Arabidopsis sequence. The remarkable morphological diversity of Brassica species and their relatives offers valuable opportunities to advance our knowledge of plant growth and development, and our understanding of rapid phenotypic evolution.
	Opinion Twin peaks: the draft human genome sequence Colin AM Semple, Kathryn L Evans, David J Porteous Genome Biology 2001, 2:comment2003-comment2003.5 (1 March 2001) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Once thought to be impossible or a waste of resources, the initial high-volume stages of sequencing the human genome have been completed.
	Report
	Paper report RNAi in mammals Edupalli Subbaiah Venkata Genome Biology 2001, 2:reports0007 (28 February 2001) Abstract \| Full text \| Editor’s summary A method for double-stranded RNA interference of gene expression in mammalian cells.
	Paper report Studying cell division by RNAi Joe Hao Genome Biology 2001, 2:reports0008 (28 February 2001) Abstract \| Full text \| Editor’s summary A large-scale RNA interference screen has proved an efficient and powerful reverse genetic approach for identifying genes involved in cell division in Caenorhabditis elegans.
	Meeting report Beyond a 'skeleton': understanding cellular functions of the cytoskeleton Coumaran Egile, Terry Lechler, Rong Li Genome Biology 2001, 2:reports4005-reports4005.3 (6 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the cytoskeleton sessions of the 40^th Annual Meeting of the American Society for Cell Biology, San Francisco, 9-13 December 2000.
	Meeting report Genomics meets informatics Katsumi Isono Genome Biology 2001, 2:reports4006-reports4006.3 (6 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report on the 11th Workshop on Genome Informatics, the annual meeting on genome informatics and related subjects supported by the Genome Informatics Society of Japan, Tokyo, Japan, 18-19 December, 2000.
	Meeting report Rhizobium goes genomic Xavier Perret, William J Broughton Genome Biology 2001, 2:reports4007-reports4007.3 (9 March 2001) Abstract \| Full text \| PDF \| Editor’s summary A report from the Rhizobium Functional Genomics Workshop, Sevilla, Spain, 15-16 September 2000.
	Deposited research article A draft annotation and overview of the human genome Fred A Wright, William J Lemon, Wei D Zhao, Russell Sears, Degen Zhuo, Jian-Ping Wang, Hee-Yung Yang, Troy Baer, Don Stredney, Joe Spitzner, Al Stutz, Ralf Krahe, Bo Yuan Genome Biology 2001, 2:preprint0001-preprint0001.39 (16 February 2001) Abstract \| Full text \| PDF \| Editor’s summary The recent draft assembly of the human genome is sufficiently accurate to provide useful annotation. A functionally annotated human gene index is reported, placed directly on the genome, based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. The genome is estimated to contain 65,000-75,000 transcriptional units, with exonic sequences comprising 4%.
	Deposited research article Improving SAGE di-tag processing Jacques Colinge, Georg Feger Genome Biology 2001, 2:preprint0002-preprint0002.10 (22 February 2001) Abstract \| Full text \| PDF \| Editor’s summary A method for improved processing of SAGE sequences is presented that allows one extra base to be obtained for reasonably abundant tags and includes a statistical test for controlling the relevance of extra base predictions. The improved SAGE sequence processing reduces the uncertainty in SAGE tag to gene mapping and can be applied to any SAGE library.
	Research news Plants cope better without telomerase Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010302-01 (2 March 2001) Abstract \| Full text \| Editor’s summary Arabidopsis mutants lacking telomerase can survive up to ten generations.
	Research news Gene discovery by stringent annotation Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010305-01 (5 March 2001) Abstract \| Full text \| Editor’s summary Careful annotation methodology uncovers over 1,000 novel genes in the Drosophila genome.
	Research news Role of the ATM protein in neurogenesis Kenneth Lee Genome Biology 2001, 2:spotlight-20010306-02 (6 March 2001) Abstract \| Full text \| Editor’s summary The ATM protein essential in DNA repair and cell-cycle regulation is also implicated in neurogenesis in the adult hippocampus.
	Research news Two populations of memory T cells Kenneth Lee Genome Biology 2001, 2:spotlight-20010306-01 (6 March 2001) Abstract \| Full text \| Editor’s summary Tracking CD4+ T cells injected into mice suggests that there are two discrete populations of memory T cells.
	Research news Uniparental disomy in ES cells Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010307-01 (7 March 2001) Abstract \| Full text \| Editor’s summary Selection with the drug G418 can be used to drive chromosome-specific loss of heterozygosity in targeted embryonic stem cells.
	Research news Chemokines may be used in metastasis Kenneth Lee Genome Biology 2001, 2:spotlight-20010308-02 (8 March 2001) Abstract \| Full text \| Editor’s summary Chemokines and their receptors help guide tumour cells to their targets.
	Research news Clues to how prions cross the species barrier Kenneth Lee Genome Biology 2001, 2:spotlight-20010308-03 (8 March 2001) Abstract \| Full text \| Editor’s summary A hybrid prion, created by fusing together prions from two distantly related yeast species, can adopt two distinct shapes and infect both yeast species.
	Research news BAG-1 can predict survival from breast cancer Tudor Toma Genome Biology 2001, 2:spotlight-20010308-01 (8 March 2001) Abstract \| Full text \| Editor’s summary There is preliminary evidence that women with malignant breast tumours that contain high levels of the protein BAG-1 have a longer survival time.
	Research news Making sense of antisense Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010308-04 (8 March 2001) Abstract \| Full text \| Editor’s summary A strategy combining antisense RNA and promoter interference technology allows for genome-wide screening of gene function in Candida albicans.
	Research news Hyper-IgM syndrome dissected Tudor Toma Genome Biology 2001, 2:spotlight-20010309-01 (9 March 2001) Abstract \| Full text \| Editor’s summary Mutations in the gene encoding NEMO that prevent the normal functioning of NF-?B, can explain the hyper-IgM syndrome associated with ectodermal dysplasia.
	Research news Wiring up Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010309-03 (9 March 2001) Abstract \| Full text \| Editor’s summary A gene-trap screen identifies molecules that regulate axon guidance and wiring patterns in the mammalian brain.
	Research news Mouse Mecp2 knockouts and Rett syndrome Kenneth Lee Genome Biology 2001, 2:spotlight-20010309-02 (9 March 2001) Abstract \| Full text \| Editor’s summary Mice lacking the transcriptional repressor Mecp2 have symptoms resembling the neurological disorder Rett syndrome.
	Research news Musical twins Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010312-01 (12 March 2001) Abstract \| Full text \| Editor’s summary A study of monozygotic and dizygotic twins indicates that there is a strong genetic contribution to musical pitch perception.
	Research news Pasteur's genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010313-02 (13 March 2001) Abstract \| Full text \| Editor’s summary The genome sequence of Pasteurella multocida gives insights into the evolution and virulence mechanisms of the multispecies pathogen.
	Research news Protein folding Kenneth Lee Genome Biology 2001, 2:spotlight-20010313-01 (13 March 2001) Abstract \| Full text \| Editor’s summary Under specific conditions globular proteins can assume a structure resembling amyloid and prion aggregates.
	Research news Caretakers and gatekeepers Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010314-01 (14 March 2001) Abstract \| Full text \| Editor’s summary Knockout mouse experiments reveal complex genetic interactions between the ATM protein kinase and non-homologous end-joining factors.
	Research news Budding interactome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010315-01 (15 March 2001) Abstract \| Full text \| Editor’s summary A high-throughput screen has defined over 4500 connections that build up an extensive interaction map of budding yeast proteins.
	Research news How plants cope with the damaging effects of UV radiation Kenneth Lee Genome Biology 2001, 2:spotlight-20010316-03 (16 March 2001) Abstract \| Full text \| Editor’s summary The identification of an Arabidopsis mutant that is hypersensitive to UV radiation provides an insight into how plants cope with genotoxic stress.
	Research news Fungal sexual cycle Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010316-04 (16 March 2001) Abstract \| Full text \| Editor’s summary Comparative genomic analysis has identified genes implicated in meiosis, recombination and pheromone responses in the fungus Candida albicans.
	Research news A virulence marker for Enterococcus faecium Tudor Toma Genome Biology 2001, 2:spotlight-20010316-01 (16 March 2001) Abstract \| Full text \| Editor’s summary A variant of the esp virulence gene could provide a way to prevent the spread of vancomycin-resistant Enterococcus faecium - a common cause of US hospital infections - in Europe.
	Research news Structure of a biological propeller Kenneth Lee Genome Biology 2001, 2:spotlight-20010316-02 (16 March 2001) Abstract \| Full text \| Editor’s summary The crystal structure of flagellin - the protein found in the bacterial flagellar motor - explains how bacteria can switch between 'running' and 'tumbling' motions.
	Research news Histone codes Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010319-01 (19 March 2001) Abstract \| Full text \| Editor’s summary Sequential histone modifications regulate heterochromatin assembly in fission yeast.
	Research news H. pylori strain differences influence host responses Tudor Toma Genome Biology 2001, 2:spotlight-20010320-01 (20 March 2001) Abstract \| Full text \| Editor’s summary Differences in the ability of Helicobacter pylori strains to induce epithelial cell responses related to inflammation are dependent on the presence of an intact cag pathogenicity island.
	Research news On display Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010320-02 (20 March 2001) Abstract \| Full text \| Editor’s summary An in vitro selection technique based on 'mRNA display' can select peptide aptamers with high affinity for specific protein targets.
	Research news Juicy transgenics Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010321-01 (21 March 2001) Abstract \| Full text \| Editor’s summary Transgenic citrus plants expressing flower-initiation genes from Arabidopsis have a reduced juvenile phase and flower early.
	Research news N-myc targets Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010322-01 (22 March 2001) Abstract \| Full text \| Editor’s summary Analysis of neuroblastoma cell lines identifies many target genes of the N-myc transcription factor that are involved in ribosome biogenesis.
	Research news Chromosome instability in colon cancer Kenneth Lee Genome Biology 2001, 2:spotlight-20010323-03 (23 March 2001) Abstract \| Full text \| Editor’s summary Colon cancer is often associated with mutations in the APC gene and with defects in chromosome segregation. Two studies now show that microtubules need APC for proper attachment when they pull chromosomes apart.
	Research news Heterochromatin interactions Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010323-04 (23 March 2001) Abstract \| Full text \| Editor’s summary Characterization of the Drosophila homolog of the human AF10 gene, which is associated with a translocation in leukemia, defines a role in heterochromatin function.
	Research news Two genotypes increase risk of heart attack Tudor Toma Genome Biology 2001, 2:spotlight-20010323-01 (23 March 2001) Abstract \| Full text \| Editor’s summary Two genotypes, angiotensin converting enzyme ACE-DD and angiotensin II type 1 receptor AT1 R-CC, interact to increase the risk of ischaemic events.
	Research news An emerging pattern Kenneth Lee Genome Biology 2001, 2:spotlight-20010323-02 (23 March 2001) Abstract \| Full text \| Editor’s summary Three studies shed new light on how members of the bone morphogenetic protein family are regulated during embryonic development.
	Research news Water bug genome Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010327-03 (27 March 2001) Abstract \| Full text \| Editor’s summary The sequence of the Caulobacter crescentus genome reveals how this proteobacterium adapts to survive in nutrient-poor aquatic and marine environments.
	Research news Overexpression CDC screen Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010328-01 (28 March 2001) Abstract \| Full text \| Editor’s summary An overexpression screen has identified novel yeast genes that control cell-cycle progression.
	Research news Spider's web Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010330-01 (30 March 2001) Abstract \| Full text \| Editor’s summary Comparative analysis of spider fibroin proteins reveals the importance of conserved repeated-sequence motifs.
	Research news Dying without mitochondrial gene expression Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010330-02 (30 March 2001) Abstract \| Full text \| Editor’s summary Loss of mitochondrial DNA expression and of respiratory chain function leads to increased apoptosis in embryonic and cardiac tissues.
	Research
	Research The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases L Aravind, Eugene V Koonin Genome Biology 2001, 2:research0007-research0007.8 (19 February 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence-profile analysis shows that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. This allows the prediction of catalytic activity for a wide range of biochemically uncharacterized proteins from eukaryotes and bacteria.
	Research Survey of transcripts in the adult Drosophila brain Karen L Posey, Leslie B Jones, Rosalinda Cerda, Monica Bajaj, Thao Huynh, Paul E Hardin, Susan H Hardin Genome Biology 2001, 2:research0008-research0008.16 (21 February 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a unique Drosophila cDNA library, constructed exclusively from adult brains, suggests that the number of genes may be underestimated in this organism. This work complements the Drosophila genome project by providing information that facilitates more complete annotation of the genomic sequence. The library should be a useful resource that will help in determining how basic brain functions operate at the molecular level.
	Research The cohesin complex: sequence homologies, interaction networks and shared motifs Susan Jones, John Sgouros Genome Biology 2001, 2:research0009-research0009.12 (6 March 2001) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Searches of protein sequence databases reveal new homologs of cohesin proteins, in five families, including an ancestral family with sequences from the Archaea and Eubacteria. A cohesion interaction network has been constructed.

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