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Volume 2 Issue 1
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Comment |
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The buckyball effect
Gregory A Petsko Genome Biology 2001, 2:comment1001-comment1001.2 (10 January 2001)
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Editor’s summary
What happens to old scientific areas of investigation when a new one, such as genomics, comes along? Science pays a heavy price for the constant shifting of mobs of researchers towards the latest fad. |
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Review |
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The nitrilase superfamily: classification, structure and function
Helen C Pace, Charles Brenner Genome Biology 2001, 2:reviews0001-reviews0001.9 (15 January 2001)
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Editor’s summary
The nitrilase superfamily consists of thiol enzymes involved in natural product biosynthesis and post-translational modification in plants, animals, fungi and certain prokaryotes. On the basis of sequence similarity and the presence of additional domains, the superfamily can be classified into 13 branches, nine of which have known or deduced specificity for specific nitrile- or amide-hydrolysis or amide-condensation reactions. Genetic and biochemical analysis of the family members and their associated domains assists in predicting the localization, specificity and cell biology of hundreds of uncharacterized protein sequences.
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The ring-type polymerase sliding clamp family
Irina Bruck, Mike O'Donnell Genome Biology 2001, 2:reviews3001-reviews3001.3 (9 January 2001)
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Editor’s summary
Ring-type polymerases consist of a DNA polymerase, a ring-shaped sliding clamp protein and a clamp-loading complex. Sliding clamp proteins are found in all organisms and slide along DNA and tethers the polymerase to the DNA, enabling rapid and processive DNA replication. |
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Replicative DNA polymerases
M Mar Albà Genome Biology 2001, 2:reviews3002-reviews3002.4 (12 January 2001)
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Replicative DNA polymerases are essential for genomic DNA replication in all organisms. Though there is little sequence similarity between the three known types, types A and B are structurally similar and all three types have a conserved role. |
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Unraveling regulatory networks in plant defense using microarrays
Owen Rowland, Jonathan DG Jones Genome Biology 2001, 2:reviews1001-reviews1001.3 (3 January 2001)
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Editor’s summary
DNA microarrays are being used to comprehensively examine gene expression networks during the plant defense response that is triggered when a plant encounters a pathogen or an elicitor molecule. In addition to identifying new genes induced during defense, these studies are providing new insights into the complex pathways governing defense gene regulation. |
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Leaving the meristem behind: regulation of KNOX genes
M Kathryn Barton Genome Biology 2001, 2:reviews1002-reviews1002.3 (9 January 2001)
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Editor’s summary
The mechanism by which the plant reserves some cells as pluripotent stem cells while partitioning others into differentiated leaf tissue is fundamental to plant development. New work in Arabidopsis elucidates the genetic circuitry that distinguishes meristem from leaf.
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Arabidopsis genome sequence as a tool for functional genomics in tomato
Kirankumar S Mysore, Robert P Tuori, Gregory B Martin Genome Biology 2001, 2:reviews1003-reviews1003.4 (12 January 2001)
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Editor’s summary
Tomato is a well-established model organism for studying many biological processes including resistance and susceptibility to pathogens and the development and ripening of fleshy fruits. The availability of the complete Arabidopsis genome sequence will expedite map-based cloning in tomato on the basis of chromosomal synteny between the two species, and will facilitate the functional analysis of tomato genes.
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Polymorphism in regulatory gene sequences
N A Mitchison Genome Biology 2000, 2:comment2001-comment2001.6 (20 December 2000)
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Editor’s summary
The extensive polymorphism revealed in non-coding gene-regulatory sequences, particularly in the immune system, suggests that this type of genetic variation is functionally and evolutionarily far more important than has been suspected, and provides a lead to new therapeutic strategies. |
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Report |
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The desktop genome
Colin Semple Genome Biology 2000, 2:reports2001 (22 December 2000)
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Editor’s summary
The Ensembl software automatically produces and archives annotation of the draft human genome sequence.
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Microarray analysis of plant defenses
Thomas Eulgem Genome Biology 2000, 2:reports0001 (22 December 2000)
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Editor’s summary
Three major defense signaling molecules have been shown to trigger partly overlapping gene expression profiles in Arabidopsis.
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Signaling in plants
Tony Fordham-Skelton, Keith Lindsey Genome Biology 2000, 2:reports4001-reports4001.3 (20 December 2000)
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Editor’s summary
A report on the 52nd Harden Conference on 'Signaling in Plants', Wye College, Kent, UK, 18-22 September 2000.
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Shocking phosphorylation of histones
Jonathan Weitzman Genome Biology 2001, 2:spotlight-20010104-01 (4 January 2001)
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Editor’s summary
Immunocytochemistry experiments show that histone phosphorylation, rather than acetylation, is important for transcription during the heat shock response in Drosophila. |
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Loopy expression
William Wells Genome Biology 2001, 2:spotlight-20010104-02 (4 January 2001)
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Telomere looping allows transcriptional activators to work at a distance in yeast. |
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Cycling surprises
William Wells Genome Biology 2001, 2:spotlight-20010104-03 (4 January 2001)
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Editor’s summary
Array analysis of dividing cells indicates that diverse processes are driven by the cell cycle. |
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SNPs by SPR
William Wells Genome Biology 2001, 2:spotlight-20010108-01 (8 January 2001)
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Editor’s summary
SNPs can be identified rapidly using a mismatch-specific ligand and surface plasmon resonance. |
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Evolution caught in the act
William Wells Genome Biology 2001, 2:spotlight-20010108-02 (8 January 2001)
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Editor’s summary
Reduced polymorphism around a fly gene indicates that selection for the gene is ongoing. |
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FANCY metabolomics
William Wells Genome Biology 2001, 2:spotlight-20010109-01 (9 January 2001)
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Editor’s summary
When mutation of a gene causes no obvious phenotype, metabolite profiling can still give clues to gene function. |
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Rapid SNP scanning
William Wells Genome Biology 2001, 2:spotlight-20010112-03 (12 January 2001)
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Editor’s summary
Mass spectrometry and pooled DNA samples allow for rapid genotyping of SNPs. |
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How melanomas avoid apoptosis
William Wells Genome Biology 2001, 2:spotlight-20010112-02 (12 January 2001)
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Editor’s summary
Although metastatic melanomas retain an intact p53, they lose the p53 effector Apaf-1 through deletion and methylation. |
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How to get hot
William Wells Genome Biology 2001, 2:spotlight-20010112-01 (12 January 2001)
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The same duplication event arises in multiple lines of bacteria as they adapt to heat. |
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How things get complicated
William Wells Genome Biology 2001, 2:spotlight-20010116-02 (16 January 2001)
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Pre-biotic evolution was able to occur in a reasonable time because complexity and stability evolve rapidly and inevitably. |
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Matrix modulation in monocytes
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010116-01 (16 January 2001)
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The interaction of monocytes with the extracellular matrix modifies gene expression. |
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Gastric interactions
William Wells Genome Biology 2001, 2:spotlight-20010117-01 (17 January 2001)
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Editor’s summary
Random genomic fragments have been used to build the first prokaryotic protein-protein interaction map. |
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Gene profiles in developing worms
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010117-02 (17 January 2001)
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Editor’s summary
Genome-wide microarray analysis identifies genes regulated during development and sex determination in Caenorhabditis elegans. |
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Isolating the cow genome
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010118-02 (18 January 2001)
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Editor’s summary
Microsatellite analysis reveals the genetic homozygosity of an isolated herd of wild white cattle. |
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Loss of imprinting in colorectal cancer
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010118-01 (18 January 2001)
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Editor’s summary
Biallelic methylation causes 'loss of imprinting' (LOI) in colorectal cancer. |
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Tales of PU
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010119-01 (19 January 2001)
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Analysis of orthologs of the PU.1 transcription factor in cartilaginous fish provide insights into the evolution of the mammalian immune system. |
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Nucleosome remodelling takes its Toll
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010119-02 (19 January 2001)
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Toll-like receptors induce nucleosome remodelling events at the interleukin 12 promoter, linking chromatin regulation to the inflammatory response. |
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Taming horses
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010124-01 (24 January 2001)
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Editor’s summary
Analysis of mitochondrial DNA from domesticated horses gives clues about the relationship between men and horses throughout history. |
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Killer genome
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010125-02 (25 January 2001)
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Comparing bacterial genome sequences identifies over a thousand genes that turn E. coli into a killer bug. |
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Mother nurture
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010125-01 (25 January 2001)
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A gene implicated in maternal nurturing behavior in mice is also imprinted in humans. |
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Sir silencing
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010126-02 (26 January 2001)
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Extrachromosomal rings containing the mating-type HMR locus demonstrate that silencing can occur in the absence of DNA replication. |
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Weapons lab to develop Celera's new supercomputer
Robert Walgate Genome Biology 2001, 2:spotlight-20010126-01 (26 January 2001)
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The computer to solve all biology - that's what's in Craig Venter's mind. Sandia, the US nuclear weapons lab, will make the first step towards his dream, along with Celera and Compaq. |
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Transcriptional targets
Jonathan B Weitzman Genome Biology 2001, 2:spotlight-20010130-01 (30 January 2001)
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Immunoaffinity-microarray experiments identify hundreds of target genes for transcriptional regulators. |
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Research |
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Expression profiles during honeybee caste determination
Jay D Evans, Diana E Wheeler Genome Biology 2000, 2:research0001-research0001.6 (20 December 2000)
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Editor’s summary
Depending on their larval environment, female honeybees develop into either queens or workers. Gene-expression profiling during caste determination has been used to present the first genomic view of development in a social insect. Many of the differently expressed genes identified have been tied to metabolic rates and cellular responses to hormones, consistent with known physiological differences between queen and worker bees. |
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Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans
Ravi S Kamath, Maruxa Martinez-Campos, Peder Zipperlen, Andrew G Fraser, Julie Ahringer Genome Biology 2000, 2:research0002-research0002.10 (20 December 2000)
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Editor’s summary
RNAi can be achieved by feeding worms Escherichia coli expressing dousble-stranded RNA corresponding to a specific gene. An optimized feeding method is presented that results in phenotypes at least as strong as those produced by direct injection of RNA for embryonic lethal genes, and stronger for genes with post-embryonic phenotypes. |
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Supervised harvesting of expression trees
Trevor Hastie, Robert Tibshirani, David Botstein, Patrick Brown Genome Biology 2001, 2:research0003-research0003.12 (10 January 2001)
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Editor’s summary
A new method for supervised learning from gene expression data, 'tree harvesting', is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worthy of further investigation. The method is illustrated on data from a lymphoma study, and on a dataset containing samples from eight different cancers. It identified some potentially interesting gene clusters. |
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Correspondence |
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Functional genomics does not have to be limited to a few select organisms
Douglas L Crawford Genome Biology 2001, 2:interactions1001-interactions1001.2 (12 January 2001)
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Editor’s summary
A response to Whither genomics by Andrew W Murray, Genome Biology 2000, 1:comment003.1-003.6
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Genome sequences and great expectations
Ioannis Iliopoulos, Sophia Tsoka, Miguel A Andrade, Paul Janssen, Benjamin Audit, Anna Tramontano, Alfonso Valencia, Christophe Leroy, Chris Sander, Christos A Ouzounis Genome Biology 2000, 2:interactions0001-interactions0001.3 (29 December 2000)
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