Genome Biology | Volume 5 Issue 3

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	Volume 5 Issue 3
	Comment
	Comment Good chemistry Gregory A Petsko Genome Biology 2004, 5:103 (26 February 2004) Abstract \| Full text \| PDF \| Editor’s summary The subject matter in chemistry courses reflects almost nothing of the issues that chemists are interested in. It is important to formulate a set of topics - and a Medical College Admissions Test reflecting them - that would leave chemistry departments no choice but to change their teaching.
	Review
	Review Identifying transcriptional targets Nicola V Taverner, James C Smith, Fiona C Wardle Genome Biology 2004, 5:210 (27 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This article reviews how the targets of transcription factors have previously been isolated and outlines new technologies that are being developed to identify novel direct targets.
	Protein family review The caveolin proteins Terence M Williams, Michael P Lisanti Genome Biology 2004, 5:214 (1 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Caveolins are markers of caveolae, invaginations in the plasma membrane, and there are three members of the family in vertebrates. Caveolins participate in many important cellular processes, including vesicular transport, cholesterol homeostasis, signal transduction, and tumor suppression.
	Minireview Transcription-coupled mutagenesis by the DNA deaminase AID Erik D Larson, Nancy Maizels Genome Biology 2004, 5:211 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary Evidence now shows that activation-induced deaminase (AID), wich is involved in switch recombination and somatic hypermutation, travels with RNA polymerase II to deaminate actively transcribed DNA.
	Minireview Leaf senescence - not just a 'wear and tear' phenomenon Shimon Gepstein Genome Biology 2004, 5:212 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex with gene products involved in a broad spectrum of regulatory, biochemical and cellular events.
	Minireview Interactions between light and carbon signaling pathways in Arabidopsis José L Reyes, Nam-Hai Chua Genome Biology 2004, 5:213 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A new report has examined the interactions between the light and carbon signaling pathways on a genomewide scale in Arabidopsis.
	Report
	Paper report Articles selected by Faculty of 1000: human plasma proteome; C. elegans interactome; primitive Y chromosome in papaya; robot scientist; profiling preimplantation mouse embryos Genome Biology 2004, 5:316 (18 February 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a description of the human plasma proteome, the C. elegans interactome, a primitive Y chromosome in papaya, a robot scientist and the expression profiling of preimplantation mouse embryos.
	Paper report Articles selected by Faculty of 1000: culturing novel soil bacteria; profiling biofilm formation; regulatory role for miRNA:miRNA duplexes; synthesis of combinatorial libraries; phylogenetic analysis of coelomata Genome Biology 2004, 5:317 (26 February 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 culturing novel soil bacteria, profiling biofilm formation, a regulatory role for miRNA:miRNA duplexes, synthesis of combinatorial libraries and a phylogenetic analysis of coelomata.
	Meeting report Biological networks: from physical principles to biological insights Dennis Vitkup Genome Biology 2004, 5:313 (16 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Fourth Georgia Tech and UGA. International Conference on Bioinformatics 'Biological. Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.
	Meeting report Of rats and men Simon N Twigger Genome Biology 2004, 5:314 (25 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the third biannual 'Rat Genomics and Models' meeting, Cold Spring Harbor, USA, 11-14 December 2003.
	Meeting report Pathogens: the plight of plants Catherine Henderson, Susannah Lee, Sarah Gurr Genome Biology 2004, 5:315 (25 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the British Society for Plant Pathology, Presidential meeting 'Plant pathogen genomics - from, sequence to application', University of Nottingham, UK, 15-18 December 2003.
	Deposited research article Universality in large-scale structure of complete genomes Li-Ching Hsieh, Ta-Yuan Chen, Chang-Heng Chang, Wen-Lang Fan, Hoong-Chien Lee Genome Biology 2004, 5:P7 (28 January 2004) Abstract \| Full text \| PDF \| Editor’s summary Our analysis of occurrence frequencies of short oligonucleotides in all extant complete genomes suggests that ancestral genomes grew via a mechanism whose main components were neutral stochastic segmental replicative translocations and random small mutations.
	Research news Chromosome 13: unlucky for genes? Genome Biology Genome Biology 2004, 5:spotlight-20040331-02 (31 March 2004) Abstract \| Full text \| Editor’s summary Analysis of human chromosome 13 reveals a surprisingly low number of genes
	Research
	Research The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes Jonathan A Sheps, Steven Ralph, Zhongying Zhao, David L Baillie, Victor Ling Genome Biology 2004, 5:R15 (11 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary The ABC transporters in the Caenorhabditis elegans genome have been identified and characterized. Phylogenetic analysis shows a large amount of gene loss and duplication, which is unusual for such a highly conserved protein family.
	Research Long terminal repeat retrotransposons of Mus musculus Eugene M McCarthy, John F McDonald Genome Biology 2004, 5:R14 (13 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This article describes the identification of long terminal repeat retrotransposons in the mouse genome. These elements can be classified in to 21 families, of which 13 have not been described previously.
	Research Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation Lorenzo F Sempere, Sarah Freemantle, Ian Pitha-Rowe, Eric Moss, Ethan Dmitrovsky, Victor Ambros Genome Biology 2004, 5:R13 (16 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Northern blot analysis of 119 previously reported microRNAs in adult organs from mouse and human identified a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons, implicating these microRNAs in mammalian neuronal development or function
	Research Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier, Patrick Forterre, Simonetta Gribaldo Genome Biology 2004, 5:R17 (26 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri.
	Research Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues Paula Casati, Virginia Walbot Genome Biology 2004, 5:R16 (1 March 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling the transcriptional response of maize tissues to UV-B irradiation suggests that a signal is transmitted from irradiated to shielded tissue. The transcriptional response occurs rapidly, even in shielded tissue.
	Method Visualization of the phylogenetic content of five genomes using dekapentagonal maps Olga Zhaxybayeva, Lutz Hamel, Jason Raymond, J Gogarten Genome Biology 2004, 5:R20 (16 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes.
	Method FlyGEM, a full transcriptome array platform for the Drosophila community Rick Johnston, Bruce Wang, Rachel Nuttall, Michael Doctolero, Pamela Edwards, Jining Lü, Marina Vainer, Huibin Yue, Xinhao Wang, James Minor, Cathy Chan, Alex Lash, Thomas Goralski, Michael Parisi, Brian Oliver, Scott Eastman Genome Biology 2004, 5:R19 (26 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary An array, FlyGEM, has been constructed based on amplification of exons from Drosophila genomic DNA. The array gene list has been extensively annotated and linked to other databases.
	Method Exploratory differential gene expression analysis in microarray experiments with no or limited replication Alexander V Loguinov, I Saira Mian, Chris D Vulpe Genome Biology 2004, 5:R18 (1 March 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An exploratory, data-oriented approach is described for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α-outliers and outlier regions, using simultaneous tolerance intervals relative to the line of equivalence.
	Software MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins Sebastian Maurer-Stroh, Masaki Gouda, Maria Novatchkova, Alexander Schleiffer, Georg Schneider, Fernanda L Sirota, Michael Wildpaner, Nobuhiro Hayashi, Frank Eisenhaber Genome Biology 2004, 5:R21 (13 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MYRbase is a database of glycine myristoylation in eukaryotes. This study shows that the functional spectrum of myristoylated proteins has been underestimated and five membrane-attachment factors that occur frequently with myristoylation have been classified.

	Volume 5 Issue 3
	Comment
	Comment Good chemistry Gregory A Petsko Genome Biology 2004, 5:103 (26 February 2004) Abstract \| Full text \| PDF \| Editor’s summary The subject matter in chemistry courses reflects almost nothing of the issues that chemists are interested in. It is important to formulate a set of topics - and a Medical College Admissions Test reflecting them - that would leave chemistry departments no choice but to change their teaching.
	Review
	Review Identifying transcriptional targets Nicola V Taverner, James C Smith, Fiona C Wardle Genome Biology 2004, 5:210 (27 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This article reviews how the targets of transcription factors have previously been isolated and outlines new technologies that are being developed to identify novel direct targets.
	Protein family review The caveolin proteins Terence M Williams, Michael P Lisanti Genome Biology 2004, 5:214 (1 March 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Caveolins are markers of caveolae, invaginations in the plasma membrane, and there are three members of the family in vertebrates. Caveolins participate in many important cellular processes, including vesicular transport, cholesterol homeostasis, signal transduction, and tumor suppression.
	Minireview Transcription-coupled mutagenesis by the DNA deaminase AID Erik D Larson, Nancy Maizels Genome Biology 2004, 5:211 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary Evidence now shows that activation-induced deaminase (AID), wich is involved in switch recombination and somatic hypermutation, travels with RNA polymerase II to deaminate actively transcribed DNA.
	Minireview Leaf senescence - not just a 'wear and tear' phenomenon Shimon Gepstein Genome Biology 2004, 5:212 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A recent, genome-wide study shows that the transcriptional program underlying leaf senescence is active and complex with gene products involved in a broad spectrum of regulatory, biochemical and cellular events.
	Minireview Interactions between light and carbon signaling pathways in Arabidopsis José L Reyes, Nam-Hai Chua Genome Biology 2004, 5:213 (27 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A new report has examined the interactions between the light and carbon signaling pathways on a genomewide scale in Arabidopsis.
	Report
	Paper report Articles selected by Faculty of 1000: human plasma proteome; C. elegans interactome; primitive Y chromosome in papaya; robot scientist; profiling preimplantation mouse embryos Genome Biology 2004, 5:316 (18 February 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering a description of the human plasma proteome, the C. elegans interactome, a primitive Y chromosome in papaya, a robot scientist and the expression profiling of preimplantation mouse embryos.
	Paper report Articles selected by Faculty of 1000: culturing novel soil bacteria; profiling biofilm formation; regulatory role for miRNA:miRNA duplexes; synthesis of combinatorial libraries; phylogenetic analysis of coelomata Genome Biology 2004, 5:317 (26 February 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 culturing novel soil bacteria, profiling biofilm formation, a regulatory role for miRNA:miRNA duplexes, synthesis of combinatorial libraries and a phylogenetic analysis of coelomata.
	Meeting report Biological networks: from physical principles to biological insights Dennis Vitkup Genome Biology 2004, 5:313 (16 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the Fourth Georgia Tech and UGA. International Conference on Bioinformatics 'Biological. Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.
	Meeting report Of rats and men Simon N Twigger Genome Biology 2004, 5:314 (25 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the third biannual 'Rat Genomics and Models' meeting, Cold Spring Harbor, USA, 11-14 December 2003.
	Meeting report Pathogens: the plight of plants Catherine Henderson, Susannah Lee, Sarah Gurr Genome Biology 2004, 5:315 (25 February 2004) Abstract \| Full text \| PDF \| Editor’s summary A report on the British Society for Plant Pathology, Presidential meeting 'Plant pathogen genomics - from, sequence to application', University of Nottingham, UK, 15-18 December 2003.
	Deposited research article Universality in large-scale structure of complete genomes Li-Ching Hsieh, Ta-Yuan Chen, Chang-Heng Chang, Wen-Lang Fan, Hoong-Chien Lee Genome Biology 2004, 5:P7 (28 January 2004) Abstract \| Full text \| PDF \| Editor’s summary Our analysis of occurrence frequencies of short oligonucleotides in all extant complete genomes suggests that ancestral genomes grew via a mechanism whose main components were neutral stochastic segmental replicative translocations and random small mutations.
	Research news Chromosome 13: unlucky for genes? Genome Biology Genome Biology 2004, 5:spotlight-20040331-02 (31 March 2004) Abstract \| Full text \| Editor’s summary Analysis of human chromosome 13 reveals a surprisingly low number of genes
	Research
	Research The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes Jonathan A Sheps, Steven Ralph, Zhongying Zhao, David L Baillie, Victor Ling Genome Biology 2004, 5:R15 (11 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary The ABC transporters in the Caenorhabditis elegans genome have been identified and characterized. Phylogenetic analysis shows a large amount of gene loss and duplication, which is unusual for such a highly conserved protein family.
	Research Long terminal repeat retrotransposons of Mus musculus Eugene M McCarthy, John F McDonald Genome Biology 2004, 5:R14 (13 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This article describes the identification of long terminal repeat retrotransposons in the mouse genome. These elements can be classified in to 21 families, of which 13 have not been described previously.
	Research Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation Lorenzo F Sempere, Sarah Freemantle, Ian Pitha-Rowe, Eric Moss, Ethan Dmitrovsky, Victor Ambros Genome Biology 2004, 5:R13 (16 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary Northern blot analysis of 119 previously reported microRNAs in adult organs from mouse and human identified a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons, implicating these microRNAs in mammalian neuronal development or function
	Research Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier, Patrick Forterre, Simonetta Gribaldo Genome Biology 2004, 5:R17 (26 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri.
	Research Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues Paula Casati, Virginia Walbot Genome Biology 2004, 5:R16 (1 March 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Profiling the transcriptional response of maize tissues to UV-B irradiation suggests that a signal is transmitted from irradiated to shielded tissue. The transcriptional response occurs rapidly, even in shielded tissue.
	Method Visualization of the phylogenetic content of five genomes using dekapentagonal maps Olga Zhaxybayeva, Lutz Hamel, Jason Raymond, J Gogarten Genome Biology 2004, 5:R20 (16 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes.
	Method FlyGEM, a full transcriptome array platform for the Drosophila community Rick Johnston, Bruce Wang, Rachel Nuttall, Michael Doctolero, Pamela Edwards, Jining Lü, Marina Vainer, Huibin Yue, Xinhao Wang, James Minor, Cathy Chan, Alex Lash, Thomas Goralski, Michael Parisi, Brian Oliver, Scott Eastman Genome Biology 2004, 5:R19 (26 February 2004) Abstract \| Full text \| PDF \| Cited on BioMed Central \| Editor’s summary An array, FlyGEM, has been constructed based on amplification of exons from Drosophila genomic DNA. The array gene list has been extensively annotated and linked to other databases.
	Method Exploratory differential gene expression analysis in microarray experiments with no or limited replication Alexander V Loguinov, I Saira Mian, Chris D Vulpe Genome Biology 2004, 5:R18 (1 March 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An exploratory, data-oriented approach is described for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α-outliers and outlier regions, using simultaneous tolerance intervals relative to the line of equivalence.
	Software MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins Sebastian Maurer-Stroh, Masaki Gouda, Maria Novatchkova, Alexander Schleiffer, Georg Schneider, Fernanda L Sirota, Michael Wildpaner, Nobuhiro Hayashi, Frank Eisenhaber Genome Biology 2004, 5:R21 (13 February 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MYRbase is a database of glycine myristoylation in eukaryotes. This study shows that the functional spectrum of myristoylated proteins has been underestimated and five membrane-attachment factors that occur frequently with myristoylation have been classified.

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Volume 5 Issue 3

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