Genome Biology | Volume 4 Issue 7

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	Volume 4 Issue 7
	Comment
	Comment A new recruit for the army of the men of death Gregory A Petsko Genome Biology 2003, 4:113 (27 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask.
	Review
	Review Taste and pheromone perception in mammals and flies Hiroaki Matsunami, Hubert Amrein Genome Biology 2003, 4:220 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the olfactory systems in Drosophila and mouse uncovers clear differences and a few surprising similarities.
	Protein family review Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression David A Mangus, Matthew C Evans, Allan Jacobson Genome Biology 2003, 4:223 (1 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The poly(A)-binding proteins (PABPs) are highly conserved polypeptides that bind to poly(A) tails of mRNAs. Although they lack catalytic activity, PABPs have several roles, including actions in regulating the length of the poly(A) tail, in regulating the export of mRNAs from the nucleus, in translation initiation and termination, in recycling of ribosomes, and in mRNA stability.
	Minireview Profiling the response of plants to herbivorous insects Kenneth L Korth Genome Biology 2003, 4:221 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent experiments with insect-damaged plants have revealed coordinated up- and down-regulation of transcripts encoding proteins with related functions, suggesting that large-scale shifts in metabolism take place.
	Minireview Genomic approaches to identifying transcriptional regulators of osteoblast differentiation Joseph P Stains, Roberto Civitelli Genome Biology 2003, 4:222 (1 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent microarray studies of mouse and human osteoblast differentiation in vitro have identified novel transcription factors that may be important in the establishment and maintenance of differentiation.
	Report
	Paper report Articles selected by Faculty of 1000: identifying cereal cell wall biosynthetic genes; unspecific knockdown by RNAi; protoemics of lipid rafts; mating-type gene in asexual fungus; genomic identification of hyperthermophiles Genome Biology 2003, 4:329 (4 June 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the identification of cereal cell wall biosynthetic genes, off-target gene regulation by RNAi, protoemics of lipid rafts, a mating-type gene in Aspergillus fumigatus and genomic identification of hyperthermophiles.
	Paper report Articles selected by Faculty of 1000: the quantification of proteins and phosphoproteins; haplotype structure in Arabidopsis; genomewide analysis of small interfering RNAs; screening newborns for inborn errors of metabolism; and profiling vaccinia virus infection of human HeLa cells Genome Biology 2003, 4:330 (18 June 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the quantification of proteins and phosphoproteins, haplotype structure in Arabidopsis, genomewide analysis of small interfering RNAs, screening newborns for inborn errors of metabolism; and profiling vaccinia virus infection of human HeLa cells.
	Meeting report Understanding the language of gene regulation Wynand Alkema, Wyeth W Wasserman Genome Biology 2003, 4:327 (18 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: genomic approaches to transcriptional regulation', Cold Spring Harbor, USA, 6-9 March 2003.
	Meeting report With the finished human genome in hand, what next? Julio Collado-Vides, Arturo Medrano-Soto, Maria Tusié-Luna Genome Biology 2003, 4:328 (27 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.
	Research news Open-access publishing finds official favor Helen Gavaghan Genome Biology 2003, 4:spotlight-20030701-01 (1 July 2003) Abstract \| Full text \| Editor’s summary The UK government backs open-access publishing while proponents move to promote it more widely
	Research news Joining the dots Cathy Holding Genome Biology 2003, 4:spotlight-20030703-01 (3 July 2003) Abstract \| Full text \| Editor’s summary Successful cloning depends on proper epigenetic reprogramming of transferred nuclei
	Research news EU Parliament vote on genetic modification Andrew Scott Genome Biology 2003, 4:spotlight-20030703-02 (3 July 2003) Abstract \| Full text \| Editor’s summary Traceability and labelling regulations may be a step towards resolving the US - EU trade dispute but true resolution is some way off
	Research news EMBO to set up research awards Pat Hagan Genome Biology 2003, 4:spotlight-20030707-01 (7 July 2003) Abstract \| Full text \| Editor’s summary Member states will be asked to fund a new initiative to stimulate research
	Research news Mixed-sex embryo controversy Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030709-01 (9 July 2003) Abstract \| Full text \| Editor’s summary Scientific skepticism and ethical criticism greet chimera research presented in Spain
	Research news Plant-to-plant horizontal gene transfer CL Bishop Genome Biology 2003, 4:spotlight-20030710-01 (10 July 2003) Abstract \| Full text \| Editor’s summary Frequent horizontal gene transfer has occurred between distantly related angiosperms
	Research news Proliferation organizes specification Cathy Holding Genome Biology 2003, 4:spotlight-20030711-01 (11 July 2003) Abstract \| Full text \| Editor’s summary Temporal colinearity of Hox gene expression is driven by cellular proliferation
	Research news Politicizing research or responsible oversight? Ted Agres Genome Biology 2003, 4:spotlight-20030714-01 (14 July 2003) Abstract \| Full text \| Editor’s summary A 'mischievous amendment' has been narrowly defeated in the US House vote on the 2004 budget
	Research news Science in conflict Eugene Russo Genome Biology 2003, 4:spotlight-20030715-01 (15 July 2003) Abstract \| Full text \| Editor’s summary Symposium explores conflicts of interest and the extent of industry influence on scientific findings
	Research news A new defense alliance Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030717-01 (17 July 2003) Abstract \| Full text \| Editor’s summary Interferons and p53 cooperate to suppress tumors and strengthen antiviral responses
	Research news Anthrax stifles dendritic cells Tudor Toma Genome Biology 2003, 4:spotlight-20030717-02 (17 July 2003) Abstract \| Full text \| Editor’s summary Anthrax lethal toxin suppress host immunity by targeting dendritic cell MAP kinases
	Research news Hox: total knockout Cathy Holding Genome Biology 2003, 4:spotlight-20030718-01 (18 July 2003) Abstract \| Full text \| Editor’s summary Removing Hox gene functional redundancy reveals fundamental roles in skeletal formation
	Research news Postcards from the edge of time Cathy Holding Genome Biology 2003, 4:spotlight-20030719-02 (18 July 2003) Abstract \| Full text \| Editor’s summary Our single-celled ancestors could interact with the environment and each other
	Research news Science communication under scrutiny Helen Gavaghan Genome Biology 2003, 4:spotlight-20030721-01 (21 July 2003) Abstract \| Full text \| Editor’s summary The peer review process is to be examined in a Royal Society consultation
	Research news 2004 US life science funding Ted Agres Genome Biology 2003, 4:spotlight-20030722-01 (22 July 2003) Abstract \| Full text \| Editor’s summary NIH, NSF and BioShield budgets are advancing briskly
	Research news XX marks the spot Cathy Holding Genome Biology 2003, 4:spotlight-20030724-01 (24 July 2003) Abstract \| Full text \| Editor’s summary Epigenetic modification of both X chromosomes in female cells marks them for X inactivation
	Research news Microbial geography Tudor Toma Genome Biology 2003, 4:spotlight-20030725-01 (25 July 2003) Abstract \| Full text \| Editor’s summary Populations of thermophilic microorganisms have diverged due to geographic isolation
	Research news William L. Russell dies Bob Calandra Genome Biology 2003, 4:spotlight-20030731-01 (31 July 2003) Abstract \| Full text \| Editor’s summary Geneticist who pioneered study of mutagenesis in mice dies at 92
	Research
	Research Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria Julien Sylvestre, Stéphane Vialette, Marisol Corral Debrinski, Claude Jacq Genome Biology 2003, 4:R44 (6 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mitochondrial biogenesis requires concerted expression of the many genes whose products make up the organelle. Combining biochemical fractionations with oligonucleotide array analyses allowed identification of interesting genes whose mRNA localization might be essential for mitochondrial biogenesis in most eukaryotic cells.
	Research Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice Chad Creighton, Rork Kuick, David E Misek, David S Rickman, Franck M Brichory, Jean-Marie Rouillard, Gilbert S Omenn, Samir Hanash Genome Biology 2003, 4:R46 (23 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The full extent to which gene expression in cancer cells is modulated by extrinsic factors remains to be determined. Global gene-expression profiles of tumors produced from two cancer cell lines transplanted subcutaneously into immunodeficient mice were determined, based on analysis of expression of human genes, and compared with expression profiles of the cell lines grown in culture.
	Research Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii Sophie Brachat, Fred S Dietrich, Sylvia Voegeli, Zhihong Zhang, Larissa Stuart, Anita Lerch, Krista Gates, Tom Gaffney, Peter Philippsen Genome Biology 2003, 4:R45 (25 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, it still benefits substantially from comparison to the completed sequence and syntenic gene map of Ashbya gossypii, an evolutionarily related fungus.
	Research Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S Lander, Michael B Eisen Genome Biology 2003, 4:R43 (26 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts groups of target genes that are specific for common patterns of gene expression.
	Research Computational identification of Drosophila microRNA genes Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin Genome Biology 2003, 4:R42 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An informatic procedure has been used to analyze the euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and display other characteristics of known miRNAs.
	Correspondence
	Correspondence EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues Neil R Smalheiser Genome Biology 2003, 4:403 (18 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A significant population of ESTs encodes chimeric transcripts containing miRNA precursor sequences as well as pieces of adjacent mRNAs in sense orientation.

	Volume 4 Issue 7
	Comment
	Comment A new recruit for the army of the men of death Gregory A Petsko Genome Biology 2003, 4:113 (27 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask.
	Review
	Review Taste and pheromone perception in mammals and flies Hiroaki Matsunami, Hubert Amrein Genome Biology 2003, 4:220 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the olfactory systems in Drosophila and mouse uncovers clear differences and a few surprising similarities.
	Protein family review Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression David A Mangus, Matthew C Evans, Allan Jacobson Genome Biology 2003, 4:223 (1 July 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The poly(A)-binding proteins (PABPs) are highly conserved polypeptides that bind to poly(A) tails of mRNAs. Although they lack catalytic activity, PABPs have several roles, including actions in regulating the length of the poly(A) tail, in regulating the export of mRNAs from the nucleus, in translation initiation and termination, in recycling of ribosomes, and in mRNA stability.
	Minireview Profiling the response of plants to herbivorous insects Kenneth L Korth Genome Biology 2003, 4:221 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent experiments with insect-damaged plants have revealed coordinated up- and down-regulation of transcripts encoding proteins with related functions, suggesting that large-scale shifts in metabolism take place.
	Minireview Genomic approaches to identifying transcriptional regulators of osteoblast differentiation Joseph P Stains, Roberto Civitelli Genome Biology 2003, 4:222 (1 July 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent microarray studies of mouse and human osteoblast differentiation in vitro have identified novel transcription factors that may be important in the establishment and maintenance of differentiation.
	Report
	Paper report Articles selected by Faculty of 1000: identifying cereal cell wall biosynthetic genes; unspecific knockdown by RNAi; protoemics of lipid rafts; mating-type gene in asexual fungus; genomic identification of hyperthermophiles Genome Biology 2003, 4:329 (4 June 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the identification of cereal cell wall biosynthetic genes, off-target gene regulation by RNAi, protoemics of lipid rafts, a mating-type gene in Aspergillus fumigatus and genomic identification of hyperthermophiles.
	Paper report Articles selected by Faculty of 1000: the quantification of proteins and phosphoproteins; haplotype structure in Arabidopsis; genomewide analysis of small interfering RNAs; screening newborns for inborn errors of metabolism; and profiling vaccinia virus infection of human HeLa cells Genome Biology 2003, 4:330 (18 June 2003) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering the quantification of proteins and phosphoproteins, haplotype structure in Arabidopsis, genomewide analysis of small interfering RNAs, screening newborns for inborn errors of metabolism; and profiling vaccinia virus infection of human HeLa cells.
	Meeting report Understanding the language of gene regulation Wynand Alkema, Wyeth W Wasserman Genome Biology 2003, 4:327 (18 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: genomic approaches to transcriptional regulation', Cold Spring Harbor, USA, 6-9 March 2003.
	Meeting report With the finished human genome in hand, what next? Julio Collado-Vides, Arturo Medrano-Soto, Maria Tusié-Luna Genome Biology 2003, 4:328 (27 June 2003) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.
	Research news Open-access publishing finds official favor Helen Gavaghan Genome Biology 2003, 4:spotlight-20030701-01 (1 July 2003) Abstract \| Full text \| Editor’s summary The UK government backs open-access publishing while proponents move to promote it more widely
	Research news Joining the dots Cathy Holding Genome Biology 2003, 4:spotlight-20030703-01 (3 July 2003) Abstract \| Full text \| Editor’s summary Successful cloning depends on proper epigenetic reprogramming of transferred nuclei
	Research news EU Parliament vote on genetic modification Andrew Scott Genome Biology 2003, 4:spotlight-20030703-02 (3 July 2003) Abstract \| Full text \| Editor’s summary Traceability and labelling regulations may be a step towards resolving the US - EU trade dispute but true resolution is some way off
	Research news EMBO to set up research awards Pat Hagan Genome Biology 2003, 4:spotlight-20030707-01 (7 July 2003) Abstract \| Full text \| Editor’s summary Member states will be asked to fund a new initiative to stimulate research
	Research news Mixed-sex embryo controversy Tabitha M Powledge Genome Biology 2003, 4:spotlight-20030709-01 (9 July 2003) Abstract \| Full text \| Editor’s summary Scientific skepticism and ethical criticism greet chimera research presented in Spain
	Research news Plant-to-plant horizontal gene transfer CL Bishop Genome Biology 2003, 4:spotlight-20030710-01 (10 July 2003) Abstract \| Full text \| Editor’s summary Frequent horizontal gene transfer has occurred between distantly related angiosperms
	Research news Proliferation organizes specification Cathy Holding Genome Biology 2003, 4:spotlight-20030711-01 (11 July 2003) Abstract \| Full text \| Editor’s summary Temporal colinearity of Hox gene expression is driven by cellular proliferation
	Research news Politicizing research or responsible oversight? Ted Agres Genome Biology 2003, 4:spotlight-20030714-01 (14 July 2003) Abstract \| Full text \| Editor’s summary A 'mischievous amendment' has been narrowly defeated in the US House vote on the 2004 budget
	Research news Science in conflict Eugene Russo Genome Biology 2003, 4:spotlight-20030715-01 (15 July 2003) Abstract \| Full text \| Editor’s summary Symposium explores conflicts of interest and the extent of industry influence on scientific findings
	Research news A new defense alliance Andrea Rinaldi Genome Biology 2003, 4:spotlight-20030717-01 (17 July 2003) Abstract \| Full text \| Editor’s summary Interferons and p53 cooperate to suppress tumors and strengthen antiviral responses
	Research news Anthrax stifles dendritic cells Tudor Toma Genome Biology 2003, 4:spotlight-20030717-02 (17 July 2003) Abstract \| Full text \| Editor’s summary Anthrax lethal toxin suppress host immunity by targeting dendritic cell MAP kinases
	Research news Hox: total knockout Cathy Holding Genome Biology 2003, 4:spotlight-20030718-01 (18 July 2003) Abstract \| Full text \| Editor’s summary Removing Hox gene functional redundancy reveals fundamental roles in skeletal formation
	Research news Postcards from the edge of time Cathy Holding Genome Biology 2003, 4:spotlight-20030719-02 (18 July 2003) Abstract \| Full text \| Editor’s summary Our single-celled ancestors could interact with the environment and each other
	Research news Science communication under scrutiny Helen Gavaghan Genome Biology 2003, 4:spotlight-20030721-01 (21 July 2003) Abstract \| Full text \| Editor’s summary The peer review process is to be examined in a Royal Society consultation
	Research news 2004 US life science funding Ted Agres Genome Biology 2003, 4:spotlight-20030722-01 (22 July 2003) Abstract \| Full text \| Editor’s summary NIH, NSF and BioShield budgets are advancing briskly
	Research news XX marks the spot Cathy Holding Genome Biology 2003, 4:spotlight-20030724-01 (24 July 2003) Abstract \| Full text \| Editor’s summary Epigenetic modification of both X chromosomes in female cells marks them for X inactivation
	Research news Microbial geography Tudor Toma Genome Biology 2003, 4:spotlight-20030725-01 (25 July 2003) Abstract \| Full text \| Editor’s summary Populations of thermophilic microorganisms have diverged due to geographic isolation
	Research news William L. Russell dies Bob Calandra Genome Biology 2003, 4:spotlight-20030731-01 (31 July 2003) Abstract \| Full text \| Editor’s summary Geneticist who pioneered study of mutagenesis in mice dies at 92
	Research
	Research Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria Julien Sylvestre, Stéphane Vialette, Marisol Corral Debrinski, Claude Jacq Genome Biology 2003, 4:R44 (6 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mitochondrial biogenesis requires concerted expression of the many genes whose products make up the organelle. Combining biochemical fractionations with oligonucleotide array analyses allowed identification of interesting genes whose mRNA localization might be essential for mitochondrial biogenesis in most eukaryotic cells.
	Research Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice Chad Creighton, Rork Kuick, David E Misek, David S Rickman, Franck M Brichory, Jean-Marie Rouillard, Gilbert S Omenn, Samir Hanash Genome Biology 2003, 4:R46 (23 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The full extent to which gene expression in cancer cells is modulated by extrinsic factors remains to be determined. Global gene-expression profiles of tumors produced from two cancer cell lines transplanted subcutaneously into immunodeficient mice were determined, based on analysis of expression of human genes, and compared with expression profiles of the cell lines grown in culture.
	Research Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii Sophie Brachat, Fred S Dietrich, Sylvia Voegeli, Zhihong Zhang, Larissa Stuart, Anita Lerch, Krista Gates, Tom Gaffney, Peter Philippsen Genome Biology 2003, 4:R45 (25 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, it still benefits substantially from comparison to the completed sequence and syntenic gene map of Ashbya gossypii, an evolutionarily related fungus.
	Research Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S Lander, Michael B Eisen Genome Biology 2003, 4:R43 (26 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts groups of target genes that are specific for common patterns of gene expression.
	Research Computational identification of Drosophila microRNA genes Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin Genome Biology 2003, 4:R42 (30 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An informatic procedure has been used to analyze the euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and display other characteristics of known miRNAs.
	Correspondence
	Correspondence EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues Neil R Smalheiser Genome Biology 2003, 4:403 (18 June 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A significant population of ESTs encodes chimeric transcripts containing miRNA precursor sequences as well as pieces of adjacent mRNAs in sense orientation.

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Volume 4 Issue 7

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