http://jbiol.com/ The most accessed research articles published by Journal of Biology 2010-02-24T00:00:00Z Good early training of graduate students and postdocs is needed to prevent them turning into future generations of manuscript-savaging reviewers. How can we intercalate typical papers into our training? http://jbiol.com/content/8/3/24 Journal of Biology 2009, null:24 2009-03-09T00:00:00Z doi:10.1186/jbiol125 With or without lipstick 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. /content/figures/jbiol125-toc.gif Journal of Biology 1475-4924 ${item.volume} 24 2009-03-09T00:00:00Z XML 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. http://jbiol.com/content/8/1/1 Journal of Biology 2009, null:1 2009-01-27T00:00:00Z doi:10.1186/jbiol111 Ending the peer review 'nightmare' 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. /content/figures/jbiol111-toc.gif Journal of Biology 1475-4924 ${item.volume} 1 2009-01-27T00:00:00Z XML Background: Secondary-ion mass spectrometry (SIMS) is an important tool for investigating isotopic composition in the chemical and materials sciences, but its use in biology has been limited by technical considerations. Multi-isotope imaging mass spectrometry (MIMS), which combines a new generation of SIMS instrument with sophisticated ion optics, labeling with stable isotopes, and quantitative image-analysis software, was developed to study biological materials. Results: The new instrument allows the production of mass images of high lateral resolution (down to 33 nm), as well as the counting or imaging of several isotopes simultaneously. As MIMS can distinguish between ions of very similar mass, such as 12C15N- and 13C14N-, it enables the precise and reproducible measurement of isotope ratios, and thus of the levels of enrichment in specific isotopic labels, within volumes of less than a cubic micrometer. The sensitivity of MIMS is at least 1,000 times that of 14C autoradiography. The depth resolution can be smaller than 1 nm because only a few atomic layers are needed to create an atomic mass image. We illustrate the use of MIMS to image unlabeled mammalian cultured cells and tissue sections; to analyze fatty-acid transport in adipocyte lipid droplets using 13C-oleic acid; to examine nitrogen fixation in bacteria using 15N gaseous nitrogen; to measure levels of protein renewal in the cochlea and in post-ischemic kidney cells using 15N-leucine; to study DNA and RNA co-distribution and uridine incorporation in the nucleolus using 15N-uridine and 81Br of bromodeoxyuridine or 14C-thymidine; to reveal domains in cultured endothelial cells using the native isotopes 12C, 16O, 14N and 31P; and to track a few 15N-labeled donor spleen cells in the lymph nodes of the host mouse. Conclusion: MIMS makes it possible for the first time to both image and quantify molecules labeled with stable or radioactive isotopes within subcellular compartments. http://jbiol.com/content/5/6/20 Claude Lechene Francois Hillion Gregory McMahon Douglas Benson Alan Kleinfeld J. Patrick Kampf Daniel Distel Yvette Luyten Joseph Bonventre Dirk Hentschel Kwon Moo Park Susumu Ito Martin Schwartz Gilles Benichou Georges Slodzian Journal of Biology 2006, null:20 2006-10-05T00:00:00Z doi:10.1186/jbiol42 Multi-isotope imaging in biology For the first time it is possible to image and quantify at nanometer resolution biological samples labeled with stable isotopes, using multi-isotope imaging mass spectrometry, applicable to all fields of biomedical research. /content/figures/jbiol42-toc.gif Journal of Biology 1475-4924 ${item.volume} 20 2006-10-05T00:00:00Z XML None of the advantages of traditional scientific journals need be sacrificed in order to provide free online access to scientific journal articles. Objections that open access to scientific journal literature requires the sacrifice of peer-review, revenue, copyright protection, or other strengths of traditional journals, are based on misunderstandings. http://jbiol.com/content/1/1/3 Peter Suber Journal of Biology 2002, null:3 2002-06-18T00:00:00Z doi:10.1186/1475-4924-1-3 /content/figures/1475-4924-1-3-toc.gif Journal of Biology 1475-4924 ${item.volume} 3 2002-06-18T00:00:00Z XML A phylogeographic analysis of gene sequences important in determining body size in dogs, recently published in BMC Biology, traces the appearance of small body size to the Neolithic Middle East. This finding strengthens the association of this event with the development of sedentary societies, and perhaps even has implications for the inception of human social inequality.See research article http://www.biomedcentral.com/1741-7007/8/16/ http://jbiol.com/content/9/2/10 Journal of Biology 2010, null:10 2010-02-24T00:00:00Z doi:10.1186/jbiol226 Levantine taming of the wolves Commenting on a phylogeographic analysis in BMC Biology that supports a Middle Eastern origin of small dogs, Driscoll and Macdonald speculate on the implications of wolf domestication and size reduction occurring at a time of transition between hunter-gatherer and sedentary societies. /content/figures/jbiol226-toc.gif Journal of Biology 1475-4924 ${item.volume} 10 2010-02-24T00:00:00Z XML Because emotions enhance memory processes and music evokes strong emotions, music could be involved in forming memories, either about pieces of music or about episodes and information associated with particular music. A recent study in BMC Neuroscience has given new insights into the role of emotion in musical memory. http://jbiol.com/content/7/6/21 Journal of Biology 2008, null:21 2008-08-08T00:00:00Z doi:10.1186/jbiol82 /content/figures/jbiol82-toc.gif Journal of Biology 1475-4924 ${item.volume} 21 2008-08-08T00:00:00Z XML Background: Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results: Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion: This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell. http://jbiol.com/content/6/2/4 Juan Castrillo Leo Zeef David Hoyle Nianshu Zhang Andrew Hayes David Gardner Michael Cornell June Petty Luke Hakes Leanne Wardleworth Bharat Rash Marie Brown Warwick Dunn David Broadhurst Kerry O'Donoghue Svenja Hester Tom Dunkley Sarah Hart Neil Swainston Peter Li Simon Gaskell Norman Paton Kathryn Lilley Douglas Kell Stephen Oliver Journal of Biology 2007, null:4 2007-04-30T00:00:00Z doi:10.1186/jbiol54 Systems biology of cell growth The first comprehensive systems biology study on growth rate control in yeast integrates information from the transcriptome, proteome and metabolome to reveal how cell growth underlies key cellular and development processes. /content/figures/jbiol54-toc.gif Journal of Biology 1475-4924 ${item.volume} 4 2007-04-30T00:00:00Z XML Although most epidemic human infectious diseases are caused by recently introduced pathogens, cospeciation of parasite and host is commonplace for endemic infections. Occasional host infidelity, however, provides the endemic parasite with an opportunity to survive the potential extinction of its host. Such infidelity may account for the survival of certain types of human lice, and it is currently exemplified by viruses such as HIV. http://jbiol.com/content/8/2/20 Journal of Biology 2009, null:20 2009-02-10T00:00:00Z doi:10.1186/jbiol114 On the origin of pubic lice 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. /content/figures/jbiol114-toc.gif Journal of Biology 1475-4924 ${item.volume} 20 2009-02-10T00:00:00Z XML Background: Chemotherapy in cancer patients can be associated with serious short- and long-term adverse neurological effects, such as leukoencephalopathy and cognitive impairment, even when therapy is delivered systemically. The underlying cellular basis for these adverse effects is poorly understood. Results: We found that three mainstream chemotherapeutic agents – carmustine (BCNU), cisplatin, and cytosine arabinoside (cytarabine), representing two DNA cross-linking agents and an antimetabolite, respectively – applied at clinically relevant exposure levels to cultured cells are more toxic for the progenitor cells of the CNS and for nondividing oligodendrocytes than they are for multiple cancer cell lines. Enhancement of cell death and suppression of cell division were seen in vitro and in vivo. When administered systemically in mice, these chemotherapeutic agents were associated with increased cell death and decreased cell division in the subventricular zone, in the dentate gyrus of the hippocampus and in the corpus callosum of the CNS. In some cases, cell division was reduced, and cell death increased, for weeks after drug administration ended. Conclusion: Identifying neural populations at risk during any cancer treatment is of great importance in developing means of reducing neurotoxicity and preserving quality of life in long-term survivors. Thus, as well as providing possible explanations for the adverse neurological effects of systemic chemotherapy, the strong correlations between our in vitro and in vivo analyses indicate that the same approaches we used to identify the reported toxicities can also provide rapid in vitro screens for analyzing new therapies and discovering means of achieving selective protection or targeted killing. http://jbiol.com/content/5/7/22 Joerg Dietrich Ruolan Han Miranda Yang Margot Mayer-Proschel Mark Noble Journal of Biology 2006, null:22 2006-11-30T00:00:00Z doi:10.1186/jbiol50 Chemotherapy affects neural cells Chemotherapeutic agents are more toxic to cells of the central nervous system than to cancer cells when administered to mice and cultured cells, providing an explanation for adverse neurological effects of systemic chemotherapy. /content/figures/jbiol50-toc.gif Journal of Biology 1475-4924 ${item.volume} 22 2006-11-30T00:00:00Z XML Parasites are accomplished evaders of host immunity. Their evasion strategies have shaped every facet of the immune system, driving diversity within gene families and immune gene polymorphisms within populations. New studies published recently in BMC Biology and Journal of Experimental Medicine document parasite-associated immunosuppression in natural populations and suggest that host genetic variants favoring resistance to parasites may be detrimental in the absence of infection. http://jbiol.com/content/8/7/62 Journal of Biology 2009, null:62 2009-08-05T00:00:00Z doi:10.1186/jbiol166 Parasites and immunosuppression Rick Maizels discusses a recent paper in BMC Biology on wild mammals that lend support to the hygiene hypothesis, and explains why genetic variants that reduce parasite-induced immunosuppression are associated with an increase in allergic reactions. /content/figures/jbiol166-toc.gif Journal of Biology 1475-4924 ${item.volume} 62 2009-08-05T00:00:00Z XML