Genome Biology | Volume 3 Issue 8

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	Volume 3 Issue 8
	Comment
	Comment Summer reading Gregory A Petsko Genome Biology 2002, 3:comment1011-comment1011.2 (29 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 23rd-most frequently ordered book on the sales list at Amazon.com is a hardcover book that's 1197 pages long: A New Kind of Science by Stephen Wolfram.
	Opinion Is mass spectrometry ready for proteome-wide protein expression analysis? Juri Rappsilber, Matthias Mann Genome Biology 2002, 3:comment2008-comment2008.5 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent advances in mass spectrometry will soon allow routine analysis of protein expression levels. How close are we to true quantitative proteomics?
	Review
	Protein family review Toll-like receptors: a family of pattern-recognition receptors in mammals Myriam A Armant, Matthew J Fenton Genome Biology 2002, 3:reviews3011-reviews3011.6 (29 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Toll-like receptors are a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products, including bacterial cell-wall components, and that can elicit pathogen-specific cellular immune responses. Toll-like receptors share characteristic features with the interleukin-1 and interleukin-18 cytokine receptors and these receptor classes activate similar signal-transduction pathways.
	Minireview Transcriptome analysis of the retina Anand Swaroop, Donald J Zack Genome Biology 2002, 3:reviews1022-reviews1022.4 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual transduction and the availability of mutants.
	Minireview Can mammalian cloning combined with embryonic stem cell technologies be used to treat human diseases? Anna-Katerina Hadjantonakis, Virginia E Papaioannou Genome Biology 2002, 3:reviews1023-reviews1023.6 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cloning can be used to obtain genetically matched embryo-derived stem cells, which could potentially be used in the treatment of patients.
	Minireview Iron stress in plants Erin L Connolly, Mary Guerinot Genome Biology 2002, 3:reviews1024-reviews1024.4 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Plants, therefore, respond to both iron deficiency and iron excess by inducing expression of different gene sets.
	Minireview Anticipatory evolution and DNA shuffling Jamie M Bacher, Brian D Reiss, Andrew D Ellington Genome Biology 2002, 3:reviews1021-reviews1021.4 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mix of theoretical and applied research has provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions.
	Report
	Paper report Tissue-specific circadian cycles Jeffrey T Ehmsen Genome Biology 2002, 3:reports0046 (31 July 2002) Abstract \| Full text \| Editor’s summary Examination of cyclic gene expression in the suprachiasmatic nuclei (SCN) and liver suggests tissue-specific circadian cycles corresponding to organ-specific physiological functions
	Paper report Primate mitochondrial evolution Diane P Genereux Genome Biology 2002, 3:reports0040 (1 August 2002) Abstract \| Full text \| Editor’s summary Disparity between primate phylogenetic trees that are based on mitochondrial versus nuclear DNA is likely to be due to differences between lineages in nucleotide substitution bias in the mitochondrial genomes
	Paper report Methanogenic archaeon sequenced Wim D'Haeze Genome Biology 2002, 3:reports0041 (1 August 2002) Abstract \| Full text \| Editor’s summary Determination of the complete genome sequence of the methanogen Methanosarcina acetivorans reveals unusual metabolic versatility
	Paper report Clostridium virulence cysteine protease Wim D'Haeze Genome Biology 2002, 3:reports0042 (1 August 2002) Abstract \| Full text \| Editor’s summary Clostridium perfringens secretes a cysteine protease in a VirR/VirS-dependent manner
	Paper report Galactose metabolism in Trypanosoma brucei Wim D'Haeze Genome Biology 2002, 3:reports0043 (1 August 2002) Abstract \| Full text \| Editor’s summary The study of galactose metabolism in Trypanosoma brucei reveals possible new drug targets
	Paper report Doubling up the genome Jeffrey T Ehmsen Genome Biology 2002, 3:reports0045 (1 August 2002) Abstract \| Full text \| Editor’s summary The distribution of orthologous genes within the major histocompatibility complex paralogous regions of amphioxus and humans supports the idea of genome-wide duplication events in vertebrate evolution
	Paper report Genome of antibiotic-producing Streptomyces revealed Jean-Nicolas Volff Genome Biology 2002, 3:reports0044 (2 August 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the antibiotic-producing bacterium Streptomyces coelicolor should aid the genetic engineering of new anti-bacterial compounds
	Meeting report Comparative biology and genomics join forces to decipher the diversity of life Nicole King Genome Biology 2002, 3:reports4023-reports4023.3 (15 July 2002) Abstract \| Full text \| PDF \| PubMed
	Meeting report Comparative genomics comes of age Leonard Lipovich Genome Biology 2002, 3:reports4024-reports4024.2 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2002 annual Cold Spring Harbor Laboratory meeting on Genome Sequencing and Biology, Cold Spring Harbor, NY, USA, 7-11 May 2002.
	Meeting report The many layers of immunity Sascha Martens Genome Biology 2002, 3:reports4025-reports4025.3 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cologne Spring Meeting 'Immunity', Cologne, Germany, 13-15 March 2002.
	Meeting report Back to basics Susan Hardin Genome Biology 2002, 3:reports4026-reports4026.2 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the annual Association of Biomolecular Resource Facilities (ABRF) meeting, Austin, Texas, 9-12 March 2002.
	Meeting report Integromics: challenges in data integration TV Venkatesh, Harry B Harlow Genome Biology 2002, 3:reports4027-reports4027.3 (17 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on Barnett International's 4th annual Bioinformatics and Data Integration conference, Philadelphia, USA, 7-8 March 2002.
	Deposited research article Preferred codons and amino acid couples in hyperthermophiles Sávio de Farias, Maria Bonato Genome Biology 2002, 3:preprint0006-preprint0006.18 (19 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The preferential usage of certain couples of amino acids and codons in thermal adaptation was investigated, by comparative proteome analysis, using 28 complete genomes. The results suggested that the Glu+Lys/Gln+His ratio may provide a useful mark for distinguishing hyperthermophilic, thermophilic and mesophilic prokaryotes
	Research news Runt repression Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020801-01 (1 August 2002) Abstract \| Full text \| Editor’s summary A genetic screen in flies demonstrates a distinction between the establishment and maintenance of transcriptional repression.
	Research news Genotype and violence Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020802-01 (2 August 2002) Abstract \| Full text \| Editor’s summary A functional polymorphism correlates with the development of antisocial behaviour in maltreated children.
	Research news Tsix tricks Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020805-01 (5 August 2002) Abstract \| Full text \| Editor’s summary Deleting both copies of the Tsix gene results in random inactivation of the X chromosome and causes a reduction in female births.
	Research news Mouse map Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020806-01 (6 August 2002) Abstract \| Full text \| Editor’s summary A new physical map should help navigation of the mouse genome.
	Research news Cellular genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020807-01 (7 August 2002) Abstract \| Full text \| Editor’s summary Fluorescence probe microscopy allows the monitoring of several genes simultaneously in single cells.
	Research news Silencing in mice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020808-01 (8 August 2002) Abstract \| Full text \| Editor’s summary Researchers describe an efficient protocol for RNA interference silencing in postnatal mice.
	Research news Balanced amplification Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020809-01 (9 August 2002) Abstract \| Full text \| Editor’s summary A new method allows simultaneous amplification of two complex genomes without introducing bias.
	Research news Human variation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020812-01 (12 August 2002) Abstract \| Full text \| Editor’s summary A genome-wide study provides evidence for recombination 'hot spots' in the human genome that influence genetic variation.
	Research news Survival signals Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020813-01 (13 August 2002) Abstract \| Full text \| Editor’s summary Signalling via the JNK pathway regulates both cell survival and oncogenic transformation.
	Research news Small-molecule microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020814-01 (14 August 2002) Abstract \| Full text \| Editor’s summary Microarrays with small molecules can be used for activity-based profiling of protein function.
	Research news Molecular evolution of language Michaela Torkar Genome Biology 2002, 3:spotlight-20020815-01 (15 August 2002) Abstract \| Full text \| Editor’s summary A gene involved in speech and language has been positively selected in recent human evolution.
	Research news Venter in new venture Jim Kling Genome Biology 2002, 3:spotlight-20020816-01 (16 August 2002) Abstract \| Full text \| Editor’s summary A new facility should grow The Institute for Genomic Research's sequencing capacity and lower costs.
	Research news RNA effective against brain cancer Tudor P Toma Genome Biology 2002, 3:spotlight-20020819-01 (19 August 2002) Abstract \| Full text \| Editor’s summary Activated double-stranded RNA-dependent protein kinase can inhibit glioblastoma growth.
	Research news Distinct Ras requirements Tudor P Toma Genome Biology 2002, 3:spotlight-20020820-01 (20 August 2002) Abstract \| Full text \| Editor’s summary Ras oncogenesis differs between human and mouse cells.
	Research news New, tacky oncogenes Tudor P Toma Genome Biology 2002, 3:spotlight-20020821-01 (21 August 2002) Abstract \| Full text \| Editor’s summary Nr-CAM, a neuronal cell adhesion molecule, plays a role in melanoma and colon cancer.
	Research news Small RNAs in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020822-01 (22 August 2002) Abstract \| Full text \| Editor’s summary Small RNAs isolated from fission yeast map to centromeric repeats and may be involved in epigenetic regulation.
	Research news Gene therapy monkey business Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020823-01 (23 August 2002) Abstract \| Full text \| Editor’s summary New adeno-associated viruses isolated from monkeys may provide safe vectors for gene therapy.
	Research news Laying down the jaw Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020827-01 (27 August 2002) Abstract \| Full text \| Editor’s summary Analysis of knockout mice highlights the role of murine Dlx genes in the development of the vertebrate jaw.
	Research news HIV favors active genes Tudor P Toma Genome Biology 2002, 3:spotlight-20020828-01 (28 August 2002) Abstract \| Full text \| Editor’s summary HIV-1 chooses active genes and local hotspots for integration in the human genome.
	Research news Transgene switch Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020828-02 (28 August 2002) Abstract \| Full text \| Editor’s summary A new system for regulating transgene expression using macrolide antibiotics promises multigene regulation in vivo.
	Research news BRCA1 enhances repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020829-01 (29 August 2002) Abstract \| Full text \| Editor’s summary The BRCA1 protein specifically enhances the global genomic repair pathway and induces the expression of DNA-repair genes.
	Research news RAF, RAS and mismatch repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020830-01 (30 August 2002) Abstract \| Full text \| Editor’s summary Colorectal tumors have mutations in either BRAF or KRAS genes but never both.
	Research news The telomerase shuttle Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020830-02 (30 August 2002) Abstract \| Full text \| Editor’s summary Experiments with a fluorescent fusion protein demonstrate shuttling of telomerase in and out of the nucleolus.
	Research
	Research Expression profiling of Drosophila imaginal discs Ansgar Klebes, Brian Biehs, Francisco Cifuentes, Thomas B Kornberg Genome Biology 2002, 3:research0038-research0038.16 (24 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of linear RNA amplification and DNA microarray hybridization has allowed the determination of expression profiles of individual imaginal discs and larval tissues and the identification of genes expressed in tissue-specific patterns.
	Research The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities L Aravind, Lakshminarayan M Iyer Genome Biology 2002, 3:research0039-research0039.7 (24 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using computational sequence-profile analysis methods, a previously uncharacterized, predicted α-helical domain of about 85 residues was identified in chromosomal proteins such as Swi3p, Rsc8p, Moira and several other uncharacterized proteins. This module, termed the SWIRM domain, is predicted to mediate specific protein-protein interactions in the assembly of chromatin-protein complexes.
	Research The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties Nicholas M Luscombe, Jiang Qian, Zhaolei Zhang, Ted Johnson, Mark Gerstein Genome Biology 2002, 3:research0040-research0040.7 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. The genomic occurrence of generalized parts follows a well-known mathematical framework called the power law, with a few parts occurring many times and most occurring only a few times. Cases of power-law behavior, were found, for example in the occurrence of pseudogenes and in levels of gene expression.
	Research Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling Karl F Hoffmann, David A Johnston, David W Dunne Genome Biology 2002, 3:research0041-research0041.12 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using cDNA microarray technology 12 new female-associated and 4 new male-associated gene transcripts were identified in mature adult Schistosoma mansoni parasites.
	Research Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays Charles Decraene, Bernard Brugg, Merle Ruberg, Eric Eveno, Christiane Matingou, Fariza Tahi, Jean Mariani, Charles Auffray, Geneviève Pietu Genome Biology 2002, 3:research0042-research0042.22 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A cell-culture model was used to establish a profile of gene expression during the effector phase of ceramide-mediated cell death. Of the 239 genes that met the criteria for differential hybridization, 10 correspond to genes previously involved in C₂-ceramide or TNF-α signaling pathways and 20 in neuronal disorders, oncogenesis or more broadly in the regulation of proliferation.
	Software BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data Lao H Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson Genome Biology 2002, 3:software0003-software0003.6 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.
	Correspondence
	Correspondence The DNA-binding region of RAG 1 is not a homeodomain Sharmila Banerjee-Basu, Andreas D Baxevanis Genome Biology 2002, 3:interactions1004-interactions1004.4 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional annotation is used to catalog information that would be of value in experimental design and analysis but annotations in public databases are often incorrect. Here, one such case is discussed.

	Volume 3 Issue 8
	Comment
	Comment Summer reading Gregory A Petsko Genome Biology 2002, 3:comment1011-comment1011.2 (29 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 23rd-most frequently ordered book on the sales list at Amazon.com is a hardcover book that's 1197 pages long: A New Kind of Science by Stephen Wolfram.
	Opinion Is mass spectrometry ready for proteome-wide protein expression analysis? Juri Rappsilber, Matthias Mann Genome Biology 2002, 3:comment2008-comment2008.5 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent advances in mass spectrometry will soon allow routine analysis of protein expression levels. How close are we to true quantitative proteomics?
	Review
	Protein family review Toll-like receptors: a family of pattern-recognition receptors in mammals Myriam A Armant, Matthew J Fenton Genome Biology 2002, 3:reviews3011-reviews3011.6 (29 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Toll-like receptors are a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products, including bacterial cell-wall components, and that can elicit pathogen-specific cellular immune responses. Toll-like receptors share characteristic features with the interleukin-1 and interleukin-18 cytokine receptors and these receptor classes activate similar signal-transduction pathways.
	Minireview Transcriptome analysis of the retina Anand Swaroop, Donald J Zack Genome Biology 2002, 3:reviews1022-reviews1022.4 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual transduction and the availability of mutants.
	Minireview Can mammalian cloning combined with embryonic stem cell technologies be used to treat human diseases? Anna-Katerina Hadjantonakis, Virginia E Papaioannou Genome Biology 2002, 3:reviews1023-reviews1023.6 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cloning can be used to obtain genetically matched embryo-derived stem cells, which could potentially be used in the treatment of patients.
	Minireview Iron stress in plants Erin L Connolly, Mary Guerinot Genome Biology 2002, 3:reviews1024-reviews1024.4 (30 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Plants, therefore, respond to both iron deficiency and iron excess by inducing expression of different gene sets.
	Minireview Anticipatory evolution and DNA shuffling Jamie M Bacher, Brian D Reiss, Andrew D Ellington Genome Biology 2002, 3:reviews1021-reviews1021.4 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A mix of theoretical and applied research has provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions.
	Report
	Paper report Tissue-specific circadian cycles Jeffrey T Ehmsen Genome Biology 2002, 3:reports0046 (31 July 2002) Abstract \| Full text \| Editor’s summary Examination of cyclic gene expression in the suprachiasmatic nuclei (SCN) and liver suggests tissue-specific circadian cycles corresponding to organ-specific physiological functions
	Paper report Primate mitochondrial evolution Diane P Genereux Genome Biology 2002, 3:reports0040 (1 August 2002) Abstract \| Full text \| Editor’s summary Disparity between primate phylogenetic trees that are based on mitochondrial versus nuclear DNA is likely to be due to differences between lineages in nucleotide substitution bias in the mitochondrial genomes
	Paper report Methanogenic archaeon sequenced Wim D'Haeze Genome Biology 2002, 3:reports0041 (1 August 2002) Abstract \| Full text \| Editor’s summary Determination of the complete genome sequence of the methanogen Methanosarcina acetivorans reveals unusual metabolic versatility
	Paper report Clostridium virulence cysteine protease Wim D'Haeze Genome Biology 2002, 3:reports0042 (1 August 2002) Abstract \| Full text \| Editor’s summary Clostridium perfringens secretes a cysteine protease in a VirR/VirS-dependent manner
	Paper report Galactose metabolism in Trypanosoma brucei Wim D'Haeze Genome Biology 2002, 3:reports0043 (1 August 2002) Abstract \| Full text \| Editor’s summary The study of galactose metabolism in Trypanosoma brucei reveals possible new drug targets
	Paper report Doubling up the genome Jeffrey T Ehmsen Genome Biology 2002, 3:reports0045 (1 August 2002) Abstract \| Full text \| Editor’s summary The distribution of orthologous genes within the major histocompatibility complex paralogous regions of amphioxus and humans supports the idea of genome-wide duplication events in vertebrate evolution
	Paper report Genome of antibiotic-producing Streptomyces revealed Jean-Nicolas Volff Genome Biology 2002, 3:reports0044 (2 August 2002) Abstract \| Full text \| Editor’s summary The complete genome sequence of the antibiotic-producing bacterium Streptomyces coelicolor should aid the genetic engineering of new anti-bacterial compounds
	Meeting report Comparative biology and genomics join forces to decipher the diversity of life Nicole King Genome Biology 2002, 3:reports4023-reports4023.3 (15 July 2002) Abstract \| Full text \| PDF \| PubMed
	Meeting report Comparative genomics comes of age Leonard Lipovich Genome Biology 2002, 3:reports4024-reports4024.2 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2002 annual Cold Spring Harbor Laboratory meeting on Genome Sequencing and Biology, Cold Spring Harbor, NY, USA, 7-11 May 2002.
	Meeting report The many layers of immunity Sascha Martens Genome Biology 2002, 3:reports4025-reports4025.3 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cologne Spring Meeting 'Immunity', Cologne, Germany, 13-15 March 2002.
	Meeting report Back to basics Susan Hardin Genome Biology 2002, 3:reports4026-reports4026.2 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the annual Association of Biomolecular Resource Facilities (ABRF) meeting, Austin, Texas, 9-12 March 2002.
	Meeting report Integromics: challenges in data integration TV Venkatesh, Harry B Harlow Genome Biology 2002, 3:reports4027-reports4027.3 (17 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on Barnett International's 4th annual Bioinformatics and Data Integration conference, Philadelphia, USA, 7-8 March 2002.
	Deposited research article Preferred codons and amino acid couples in hyperthermophiles Sávio de Farias, Maria Bonato Genome Biology 2002, 3:preprint0006-preprint0006.18 (19 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The preferential usage of certain couples of amino acids and codons in thermal adaptation was investigated, by comparative proteome analysis, using 28 complete genomes. The results suggested that the Glu+Lys/Gln+His ratio may provide a useful mark for distinguishing hyperthermophilic, thermophilic and mesophilic prokaryotes
	Research news Runt repression Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020801-01 (1 August 2002) Abstract \| Full text \| Editor’s summary A genetic screen in flies demonstrates a distinction between the establishment and maintenance of transcriptional repression.
	Research news Genotype and violence Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020802-01 (2 August 2002) Abstract \| Full text \| Editor’s summary A functional polymorphism correlates with the development of antisocial behaviour in maltreated children.
	Research news Tsix tricks Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020805-01 (5 August 2002) Abstract \| Full text \| Editor’s summary Deleting both copies of the Tsix gene results in random inactivation of the X chromosome and causes a reduction in female births.
	Research news Mouse map Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020806-01 (6 August 2002) Abstract \| Full text \| Editor’s summary A new physical map should help navigation of the mouse genome.
	Research news Cellular genomics Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020807-01 (7 August 2002) Abstract \| Full text \| Editor’s summary Fluorescence probe microscopy allows the monitoring of several genes simultaneously in single cells.
	Research news Silencing in mice Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020808-01 (8 August 2002) Abstract \| Full text \| Editor’s summary Researchers describe an efficient protocol for RNA interference silencing in postnatal mice.
	Research news Balanced amplification Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020809-01 (9 August 2002) Abstract \| Full text \| Editor’s summary A new method allows simultaneous amplification of two complex genomes without introducing bias.
	Research news Human variation Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020812-01 (12 August 2002) Abstract \| Full text \| Editor’s summary A genome-wide study provides evidence for recombination 'hot spots' in the human genome that influence genetic variation.
	Research news Survival signals Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020813-01 (13 August 2002) Abstract \| Full text \| Editor’s summary Signalling via the JNK pathway regulates both cell survival and oncogenic transformation.
	Research news Small-molecule microarrays Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020814-01 (14 August 2002) Abstract \| Full text \| Editor’s summary Microarrays with small molecules can be used for activity-based profiling of protein function.
	Research news Molecular evolution of language Michaela Torkar Genome Biology 2002, 3:spotlight-20020815-01 (15 August 2002) Abstract \| Full text \| Editor’s summary A gene involved in speech and language has been positively selected in recent human evolution.
	Research news Venter in new venture Jim Kling Genome Biology 2002, 3:spotlight-20020816-01 (16 August 2002) Abstract \| Full text \| Editor’s summary A new facility should grow The Institute for Genomic Research's sequencing capacity and lower costs.
	Research news RNA effective against brain cancer Tudor P Toma Genome Biology 2002, 3:spotlight-20020819-01 (19 August 2002) Abstract \| Full text \| Editor’s summary Activated double-stranded RNA-dependent protein kinase can inhibit glioblastoma growth.
	Research news Distinct Ras requirements Tudor P Toma Genome Biology 2002, 3:spotlight-20020820-01 (20 August 2002) Abstract \| Full text \| Editor’s summary Ras oncogenesis differs between human and mouse cells.
	Research news New, tacky oncogenes Tudor P Toma Genome Biology 2002, 3:spotlight-20020821-01 (21 August 2002) Abstract \| Full text \| Editor’s summary Nr-CAM, a neuronal cell adhesion molecule, plays a role in melanoma and colon cancer.
	Research news Small RNAs in yeast Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020822-01 (22 August 2002) Abstract \| Full text \| Editor’s summary Small RNAs isolated from fission yeast map to centromeric repeats and may be involved in epigenetic regulation.
	Research news Gene therapy monkey business Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020823-01 (23 August 2002) Abstract \| Full text \| Editor’s summary New adeno-associated viruses isolated from monkeys may provide safe vectors for gene therapy.
	Research news Laying down the jaw Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020827-01 (27 August 2002) Abstract \| Full text \| Editor’s summary Analysis of knockout mice highlights the role of murine Dlx genes in the development of the vertebrate jaw.
	Research news HIV favors active genes Tudor P Toma Genome Biology 2002, 3:spotlight-20020828-01 (28 August 2002) Abstract \| Full text \| Editor’s summary HIV-1 chooses active genes and local hotspots for integration in the human genome.
	Research news Transgene switch Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020828-02 (28 August 2002) Abstract \| Full text \| Editor’s summary A new system for regulating transgene expression using macrolide antibiotics promises multigene regulation in vivo.
	Research news BRCA1 enhances repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020829-01 (29 August 2002) Abstract \| Full text \| Editor’s summary The BRCA1 protein specifically enhances the global genomic repair pathway and induces the expression of DNA-repair genes.
	Research news RAF, RAS and mismatch repair Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020830-01 (30 August 2002) Abstract \| Full text \| Editor’s summary Colorectal tumors have mutations in either BRAF or KRAS genes but never both.
	Research news The telomerase shuttle Jonathan B Weitzman Genome Biology 2002, 3:spotlight-20020830-02 (30 August 2002) Abstract \| Full text \| Editor’s summary Experiments with a fluorescent fusion protein demonstrate shuttling of telomerase in and out of the nucleolus.
	Research
	Research Expression profiling of Drosophila imaginal discs Ansgar Klebes, Brian Biehs, Francisco Cifuentes, Thomas B Kornberg Genome Biology 2002, 3:research0038-research0038.16 (24 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A combination of linear RNA amplification and DNA microarray hybridization has allowed the determination of expression profiles of individual imaginal discs and larval tissues and the identification of genes expressed in tissue-specific patterns.
	Research The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities L Aravind, Lakshminarayan M Iyer Genome Biology 2002, 3:research0039-research0039.7 (24 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using computational sequence-profile analysis methods, a previously uncharacterized, predicted α-helical domain of about 85 residues was identified in chromosomal proteins such as Swi3p, Rsc8p, Moira and several other uncharacterized proteins. This module, termed the SWIRM domain, is predicted to mediate specific protein-protein interactions in the assembly of chromatin-protein complexes.
	Research The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties Nicholas M Luscombe, Jiang Qian, Zhaolei Zhang, Ted Johnson, Mark Gerstein Genome Biology 2002, 3:research0040-research0040.7 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The sequencing of genomes provides us with an inventory of the 'molecular parts' in nature, such as protein families and folds, and their functions in living organisms. The genomic occurrence of generalized parts follows a well-known mathematical framework called the power law, with a few parts occurring many times and most occurring only a few times. Cases of power-law behavior, were found, for example in the occurrence of pseudogenes and in levels of gene expression.
	Research Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling Karl F Hoffmann, David A Johnston, David W Dunne Genome Biology 2002, 3:research0041-research0041.12 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using cDNA microarray technology 12 new female-associated and 4 new male-associated gene transcripts were identified in mature adult Schistosoma mansoni parasites.
	Research Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays Charles Decraene, Bernard Brugg, Merle Ruberg, Eric Eveno, Christiane Matingou, Fariza Tahi, Jean Mariani, Charles Auffray, Geneviève Pietu Genome Biology 2002, 3:research0042-research0042.22 (31 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A cell-culture model was used to establish a profile of gene expression during the effector phase of ceramide-mediated cell death. Of the 239 genes that met the criteria for differential hybridization, 10 correspond to genes previously involved in C₂-ceramide or TNF-α signaling pathways and 20 in neuronal disorders, oncogenesis or more broadly in the regulation of proliferation.
	Software BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data Lao H Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson Genome Biology 2002, 3:software0003-software0003.6 (15 July 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.
	Correspondence
	Correspondence The DNA-binding region of RAG 1 is not a homeodomain Sharmila Banerjee-Basu, Andreas D Baxevanis Genome Biology 2002, 3:interactions1004-interactions1004.4 (25 July 2002) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Functional annotation is used to catalog information that would be of value in experimental design and analysis but annotations in public databases are often incorrect. Here, one such case is discussed.

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Volume 3 Issue 8

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Review

Report

Research

Correspondence