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Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria

Thiago M Venancio, L Aravind Journal of Biology 2009, 8:29 (15 April 2009)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Venancio and Aravind review recent studies, including one in BMC Systems Biology, that offer new ways to reconstruct transcriptional regulatory networks in previously uncharacterised prokaryotes, such as the actinobacteria.

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Genome degeneration affects both extracellular and intracellular bacterial endosymbionts

Heike Feldhaar, Roy Gross Journal of Biology 2009, 8:31 (6 April 2009)

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Feldhaar and Gross discuss a new study in BMC Biology that suggests extracellular endosymbionts, like obligate intracellular bacteria, lose essential genes and become slaves to their hosts.

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Distant metastasis: not out of reach any more

François Bertucci, Daniel Birnbaum Journal of Biology 2009, 8:28 (27 March 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Bertucci and Birnbaum review gene expression profiles published in BMC Medicine and BMC Cancer on distant cancer metastasis that predict poor outcome, but may help target anti-angiogenesis therapies.

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Pitfalls in the phylogenomic evaluation of human disease-causing mutations

Andrew OM Wilkie Journal of Biology 2009, 8:26 (24 March 2009)

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Andrew Wilkie discusses (the pitfalls of) a new phylogenomic study, published in BMC Evolutionary Biology, that has identified conserved sequences in the MSX homeobox family proteins suspected to be involved in human diseases.

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Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins

Hue Chan, Zhuqing Zhang Journal of Biology 2009, 8:27 (13 March 2009)

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Chan and Zhang, discussing a study published in BMC Structural Biology, argue that while close contacts between amino acids stabilize protein folds, long-range destablilizing interactions may be important in allowing them to evolve new functions.

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Are we training pit bulls to review our manuscripts?

Virginia Walbot Journal of Biology 2009, 8:24 (9 March 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 4 comments |  Editor’s summary

Virginia Walbot accepts some of the blame for remorselessly negative reviewers, and suggests a training program for graduate students and post docs that will deliver a fairer assessment of manuscripts.

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In ovo omnia: diversification by duplication in fish and other vertebrates

Ingo Braasch, Walter Salzburger Journal of Biology 2009, 8:25 (5 March 2009)

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Ingo Braasch and Walter Salzburger discuss an article published in BMC Evolutionary Biology that suggests how differential evolution of the duplicated vitellogenin yolk protein genes in fish allowed the development of crucial new spawning strategies.

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The light of evolution

Miranda Robertson Journal of Biology 2009, 8:10 (27 February 2009)

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Estimating rates and patterns of morphological evolution from phylogenies: lessons in limb lability from Australian Lerista lizards

John J Wiens Journal of Biology 2009, 8:19 (24 February 2009)

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Why didn't Darwin discover Mendel's laws?

Jonathan C Howard Journal of Biology 2009, 8:15 (24 February 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

In an opinion piece, Jonathan Howard suggests that Darwin failed to discover the laws of inheritance (Mendel’s laws) due to his focus on small quantitative variations as the raw material of evolution.

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Darwin and Huxley revisited: the origin of allometry

Charles F Stevens Journal of Biology 2009, 8:14 (23 February 2009)

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Charles Stevens argues that evolution respects power laws, and that explains the way that organs scale with the size of the individual- first described by Julian Huxley as "allometry".

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Mayr, mathematics and the study of evolution

James F Crow Journal of Biology 2009, 8:13 (23 February 2009)

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James Crow picks up the gauntlet thrown down by Mayr at the feet of JBS Haldane, and describes the essential contribution of mathematics to the understanding of evolution from genetic drift to molecular clocks.

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Evolutionary genomics and the reach of selection

Laurence D Hurst Journal of Biology 2009, 8:12 (23 February 2009)

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Laurence Hurst explains how evolutionary genomics, married to an understanding of molecular mechanisms, can show the impact of selection where it is not expected.

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Q&A: What did Charles Darwin prove?

Paul Harvey Journal of Biology 2009, 8:11 (23 February 2009)

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Paul Harvey argues that Darwin was an accomplished 21st-century biologist and marvels that in his extensive studies on the inheritance of variation he failed to discover Mendel’s laws.

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Contrast enhancement of stimulus intermittency in a primary olfactory network and its behavioral significance

Hong Lei, Jeffrey A Riffell, Stephanie L Gage, John G Hildebrand Journal of Biology 2009, 8:21 (20 February 2009)

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Discrete bursts of activity in the olfactory neurons of moths allow them to track drifting odors, essential for locating pheromone-releasing females.

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Representations of odor plume flux are accentuated deep within the moth brain

Thomas C Baker Journal of Biology 2009, 8:16 (20 February 2009)

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Apes, lice and prehistory

Robin A Weiss Journal of Biology 2009, 8:20 (10 February 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 2 comments |  Editor’s summary

In a special issue to celebrate the bicentennial of Darwin's birth, Robin Weiss reviews recent speculations on human prehistory based on louse phylogeny, and adds his own on the origins of pubic hair.

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Timing the first human migration into eastern Asia

Roscoe Stanyon, Marco Sazzini, Donata Luiselli Journal of Biology 2009, 8:18 (6 February 2009)

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Conserved elements within open reading frames of mammalian Hox genes

Joost M Woltering, Denis Duboule Journal of Biology 2009, 8:17 (6 February 2009)

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Joost Woltering and Denis Duboule, writing on a paper published in BMC Evolutionary Biology, discuss the increasing evidence for regulatory elements in the coding sequences of genes, and possible explanations of their specialized functions.

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What are journals for?

Miranda Robertson Journal of Biology 2009, 8:1 (27 January 2009)

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Journal of Biology launches a re-review opt-out experiment in response to widespread dissatisfaction with peer review, and publishes the first of two new regular features - a full review on the ribosome and a question-and-answer feature on systems biology.

Research article   Open Access Highly Accessed

A circuit supporting concentration-invariant odor perception in Drosophila

Kenta Asahina, Matthieu Louis, Silvia Piccinotti, Leslie B Vosshall Journal of Biology 2009, 8:9 (26 January 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology |  Editor’s summary

In Drosophila, inhibitory interneurons are progressively recruited as olfactory sensory neurons are activated at increasing odor concentrations, allowing the flies to identify distinct odors at different intensities.

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The ribosome returned

Peter B Moore Journal of Biology 2009, 8:8 (26 January 2009)

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Lateral inhibition and concentration-invariant odor perception

Susy M Kim, Jing W Wang Journal of Biology 2009, 8:4 (26 January 2009)

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'Validation' in genome-scale research

Timothy R Hughes Journal of Biology 2009, 8:3 (26 January 2009)

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Q&A: Systems biology

James E Ferrell Journal of Biology 2009, 8:2 (26 January 2009)

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Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association

Patrick Forterre, Simonetta Gribaldo, Céline Brochier-Armanet Journal of Biology 2009, 8:7 (23 January 2009)

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Sperm dumping as a defense against meiotic drive

Tom Price, Zenobia Lewis, Nina Wedell Journal of Biology 2009, 8:6 (20 January 2009)

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Limb regeneration revisited

Jessica L Whited, Clifford J Tabin Journal of Biology 2009, 8:5 (13 January 2009)

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The future of artemisinins: natural, synthetic or recombinant?

Marcel Hommel Journal of Biology 2008, 7:38 (15 December 2008)

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Neuronal remodeling on the evolutionary timescale

Ithai Rabinowitch, William Schafer Journal of Biology 2008, 7:37 (15 December 2008)

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Research article   Open Access

Bridge helix and trigger loop perturbations generate superactive RNA polymerases

Lin Tan, Simone Wiesler, Dominika Trzaska, Hannah C Carney, Robert OJ Weinzierl Journal of Biology 2008, 7:40 (2 December 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Mutations targeted to key functional areas of RNA polymerases can generate superactive enzymes that suggest how conformational changes in specialized domains of the enzyme contribute to the catalytic cycle.

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A bridge to transcription by RNA polymerase

Craig D Kaplan, Roger D Kornberg Journal of Biology 2008, 7:39 (2 December 2008)

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Obesity genes: so close and yet so far...

Daniel Pomp, Karen L Mohlke Journal of Biology 2008, 7:36 (27 November 2008)

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Globin genes on the move

Ross C Hardison Journal of Biology 2008, 7:35 (20 November 2008)

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RNA interference in nematodes and the chance that favored Sydney Brenner

Marie-Anne Félix Journal of Biology 2008, 7:34 (13 November 2008)

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Aquaglyceroporins: ancient channels for metalloids

Hiranmoy Bhattacharjee, Rita Mukhopadhyay, Saravanamuthu Thiyagarajan, Barry P Rosen Journal of Biology 2008, 7:33 (7 November 2008)

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Islands in the sky: the impact of Pleistocene climate cycles on biodiversity

Allan J Baker Journal of Biology 2008, 7:32 (3 November 2008)

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Guanylyl cyclase sees the light

John JG Tesmer Journal of Biology 2008, 7:31 (31 October 2008)

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X-chromosome inactivation: the molecular basis of silencing

Barbara Panning Journal of Biology 2008, 7:30 (27 October 2008)

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NFIX – one gene, two knockouts, multiple effects

Vladimir Pekarik, Juan Belmonte Journal of Biology 2008, 7:29 (23 October 2008)

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Immune function keeps endosymbionts under control

Stuart Reynolds, Jens Rolff Journal of Biology 2008, 7:28 (16 October 2008)

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Bridging spinal cord injuries

James W Fawcett Journal of Biology 2008, 7:25 (15 October 2008)

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Observing bacteria through the lens of social evolution

Carey D Nadell, Bonnie L Bassler, Simon A Levin Journal of Biology 2008, 7:27 (30 September 2008)

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Will he still look good with the lights on? Spectral tuning of visual pigments in fish

Julia C Jones, Helen M Gunter, Axel Meyer Journal of Biology 2008, 7:26 (25 September 2008)

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Transplanted astrocytes derived from BMP- or CNTF-treated glial-restricted precursors have opposite effects on recovery and allodynia after spinal cord injury

Jeannette E Davies, Christoph Pröschel, Ningzhe Zhang, Mark Noble, Margot Mayer-Pröschel, Stephen JA Davies Journal of Biology 2008, 7:24 (19 September 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Glial cells can promote the repair of damaged spinal cord, but experiments in rats show that while some promote functional recovery others cause abnormal growth and pain, depending on the growth factor used to cultivate them in culture.

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Appetite for reproduction: dietary restriction, aging and the mammalian gonad

Roopa L Nalam, Scott D Pletcher, Martin M Matzuk Journal of Biology 2008, 7:23 (16 September 2008)

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Evolution of virulence in malaria

Bridget Penman, Sunetra Gupta Journal of Biology 2008, 7:22 (28 August 2008)

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Music, memory and emotion

Lutz Jäncke Journal of Biology 2008, 7:21 (8 August 2008)

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Drug-therapy networks and the prediction of novel drug targets

Zoltan Spiro, Istvan A Kovacs, Peter Csermely Journal of Biology 2008, 7:20 (31 July 2008)

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Genomics technology for assessing soil pollution

Nico M van Straalen, Dick Roelofs Journal of Biology 2008, 7:19 (14 July 2008)

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