The nematode Caenorhabditis elegans is a favorite model for the study of aging. A wealth of genetic and genomic studies show that metabolic regulation is a hallmark of life-span modulation. A recent study in BMC Biology identifying metabolic signatures for longevity suggests that amino-acid pools may be important in longevity.
See research article http://www.biomedcentral.com/1741-7007/8/14.
In a paper in BMC Biology Virk et al. show that Caenorhabditis elegans lifespan is extended in response to a diet of folate-deficient Escherichia coli. The deficiencies in folate biosynthesis were due to an aroD mutation, or treatment of E. coli with sulfa drugs, which are mimics of the folate precursor para-aminobenzoic acid. This study suggests that pharmacological manipulation of the gut microbiome folate status may be a viable approach to slow animal aging, and raises questions about folate supplementation.
See research article http://www.http://www.biomedcentral.com/1741-7007/10/67
Daphnia pulex is the first crustacean to have its genome sequenced. Availability of the genome sequence will have implications for research in aquatic ecology and evolution in particular, as addressed by a series of papers published recently in BMC Evolutionary Biology and BMC Genomics.
See research articles http://www.biomedcentral.com/1471-2148/9/78, http://www.biomedcentral.com/1471-2164/10/527, http://www.biomedcentral.com/1471-2148/9/79, http://www.biomedcentral.com/1471-2164/10/175, http://www.biomedcentral.com/1471-2164/10/172, http://www.biomedcentral.com/1471-2164/10/169, http://www.biomedcentral.com/1471-2164/10/170 and http://www.biomedcentral.com/1471-2148/9/243.
There have been notable advances in the scientific understanding of regeneration within the past year alone, including two recently published in BMC Biology. Increasingly, progress in the regeneration field is being inspired by comparisons with stem cell biology and enabled by newly developed techniques that allow simultaneous examination of thousands of genes and proteins.
See research articles http://www.biomedcentral.com/1741-7007/7/83 and http://www.biomedcentral.com/1741-7007/8/5.
An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena.
See research articles http://www.biomedcentral.com/1471-2164/9/131, http://www.biomedcentral.com/1471-2164/11/220/, http://www.biomedcentral.com/1471-2202/11/46/ and http://www.biomedcentral.com/1741-7007/8/28/
The nematode Caenorhabditis elegans is a major model organism in laboratory biology. Very little is known, however, about its ecology, including where it proliferates. In the past, C. elegans was mainly isolated from human-made compost heaps, where it was overwhelmingly found in the non-feeding dauer diapause stage.
C. elegans and C. briggsae were found in large, proliferating populations in rotting plant material (fruits and stems) in several locations in mainland France. Both species were found to co-occur in samples isolated from a given plant species. Population counts spanned a range from one to more than 10,000 Caenorhabditis individuals on a single fruit or stem. Some populations with an intermediate census size (10 to 1,000) contained no dauer larvae at all, whereas larger populations always included some larvae in the pre-dauer or dauer stages. We report on associated micro-organisms, including pathogens. We systematically sampled a spatio-temporally structured set of rotting apples in an apple orchard in Orsay over four years. C. elegans and C. briggsae were abundantly found every year, but their temporal distributions did not coincide. C. briggsae was found alone in summer, whereas both species co-occurred in early fall and C. elegans was found alone in late fall. Competition experiments in the laboratory at different temperatures show that C. briggsae out-competes C. elegans at high temperatures, whereas C. elegans out-competes C. briggsae at lower temperatures.
C. elegans and C. briggsae proliferate in the same rotting vegetal substrates. In contrast to previous surveys of populations in compost heaps, we found fully proliferating populations with no dauer larvae. The temporal sharing of the habitat by the two species coincides with their temperature preference in the laboratory, with C. briggsae populations growing faster than C. elegans at higher temperatures, and vice at lower temperatures.
Often considered an 'aging' hormone due to its role in accelerating such developmental processes as ripening, senescence, and abscission, the plant hormone ethylene also regulates many aspects of growth and development throughout the life cycle of the plant. Multiple mechanisms have been identified by which transcriptional output from the ethylene signaling pathway can be tailored to meet the needs of particular developmental pathways. Of special interest is the report by Lumba et al. in BMC Biology on how vegetative transitions are regulated through the effect of the transcription factor FUSCA3 on ethylene-controlled gene expression, providing an elegant example of how hormonal control can be integrated into a developmental pathway.
See research article http://www.biomedcentral.com/1741-7007/10/8
One of the amazing qualities of plants is their phenotypic plasticity. Consider, for example, how a pine tree will grow to a towering hundreds of feet in height in Yosemite Valley, but to only a gnarled few feet in height up near the timberline. This diversity of form, though originating from the same genotype, points to the degree to which plant growth and development can be modulated. Much of this control is mediated by a small group of plant hormones that include auxin, cytokinin, gibberellin, abscisic acid, brassinosteroid, jasmonic acid, and ethylene . These are often considered 'classical' plant hormones because they were discovered decades ago; indeed, the presence of some was inferred over a century ago. Their early discovery is no doubt due in part to their general function throughout the life cycle of the plant. More recently, and in the remarkably short period of time since the advent of Arabidopsis as a genetic model, key elements in the primary signaling pathways of these plant hormones have been uncovered. The important question is no longer simply how are these hormones perceived, but how are the hormonal signals integrated into the control of particular developmental pathways? In pursuing such a question, Lumba et al.  have now uncovered a role for the plant hormone ethylene in regulating the conversion of juvenile to adult leaves. These new data, in combination with prior research implicating the plant hormones abscisic acid and gibberellin in this transition , form an important step in defining how a hormonal network regulates a key developmental process.
In the ubiquitin-proteasome system, a subset of ubiquitylated proteins requires the AAA+ ATPase p97 (also known as VCP or Cdc48) for extraction from membranes or protein complexes before delivery to the proteasome for degradation. Diverse ubiquitin adapters are known to link p97 to its client proteins, but two recent papers on the adapter protein UBXD7, including one by Bandau et al. in BMC Biology, suggest that rather than simply linking p97 to ubiquitylated proteins, this adapter may be essential to coordinate ubiquitylation and p97-mediated extraction of the proteasome substrate. These findings add to growing indications of richly diverse roles of adapters in p97-mediated signaling functions.
See research article: http://www.biomedcentral.com/1741-7007/10/36
The Hedgehog (Hh) signaling pathway differentially utilizes the primary cilium in mammals and fruit flies. Recent work, including a study in BMC Biology, demonstrates that Hh signals through the cilium in zebrafish, clarifying the evolution of Hh signal transduction.
See research article: http://www.biomedcentral.com/1741-7007/8/65
This article is a response to Klütsch and Crapon de Caprona
See correspondence article http://www.biomedcentral.com/1741-7007/8/119 and our original research article http://www.biomedcentral.com/1741-7007/8/16.
This article is a response to Wang and Luo.
See correspondence article http://www.biomedcentral.com/1741-7007/10/30/ [WEBCITE] and the original research article http://www.biomedcentral.com/1741-7007/9/24 [WEBCITE].
This article is a response to Wang and Luo.
See correspondence article http://www.biomedcentral.com/1741-7007/10/30 and the original research article http://www.biomedcentral.com/1741-7007/9/24.
This article is a response to Vibranovski et al.
See correspondence article http://www.biomedcentral.com/1741-7007/10/49 and the original research article http://www.biomedcentral.com/1741-7007/9/29
We have previously reported a high propensity of testis-expressed X-linked genes to activation in meiotic cells, a similarity in global gene expression between the X chromosome and autosomes in meiotic germline, and under-representation of various types of tissue-specific genes on the X chromosome. Based on our findings and a critical review of the current literature, we believe that there is no global and severe silencing of the X chromosome in the meiotic male germline of Drosophila. The term 'meiotic sex chromosome inactivation' (MSCI) therefore seems misleading when used to describe the minor underexpression of the X chromosome in the testis of Drosophila, because this term erroneously implies a profound and widespread silencing of the X-linked genes, by analogy to the well-studied MSCI system in mammals, and therefore distracts from identification and analysis of the real mechanisms that orchestrate gene expression and evolution in this species.
A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth.
See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68
Current interest in proteasome inhibitors for cancer therapy has stimulated considerable research efforts to identify the molecular pathway to their cytotoxicity with a view to identifying the mechanisms of sensitivity and resistance as well as informing the development of new drugs. Zhao and Vuori describe this month in BMC Biology experiments indicating a novel role of the adaptor protein p130Cas in sensitivity to apoptosis induced not only by proteasome inhibitors but also by the unrelated drug doxorubicin.
See research article: http:// http://www.biomedcentral.com/1741-7007/9/73
Important advances in the field of tissue engineering are arising from increased interest in novel biomaterial designs with bioactive components that directly influence cell behavior. Following the recent work of Mitchell and co-workers published in BMC Biology, we review how spatial and temporal control of signaling molecules in a matrix material regulates cellular responses for tissue-specific applications.
See research article http://www.biomedcentral.com/1741-7007/8/57
The complexity of the core promoter transcription machinery has emerged as an additional level of transcription regulation that is used during vertebrate development. Recent studies, including one published in BMC Biology, provide mechanistic insights into how the TATA binding protein (TBP) and its vertebrate-specific paralog TBP2 (TRF3) switch function during the transition from the oocyte to the embryo.
See research article http://www.biomedcentral.com/1741-7007/7/45
Bioinformatics-based searches for correlations between subcellular localization and pI or charge distribution of proteins have failed to detect meaningful correlations. Recent work published in BMC Biology finds that a physicochemical metric of charge distribution correlates better with subcellular pH than does pI.
See research article http://www.biomedcentral.com/1741-7007/7/69
A study in the current issue of BMC Biology has identified a mouse major urinary protein as a pheromone that attracts female mice to male urine marks and induces a learned attraction to the volatile urinary odor of the producer. See research article http://www.biomedcentral.com/1741-7007/8/75
The identification of an increasing number of cancer genes is opening up unexpected scenarios in cancer genetics. When analyzed for their systemic properties, these genes show a general fragility towards perturbation. A recent paper published in BMC Biology shows how the founder domains of known cancer genes emerged at two macroevolutionary transitions - the advent of the first cell and the transition to metazoan multicellularity.
See research article http://www.biomedcentral.com/1741-7007/8/66
The basis for transcriptional fidelity by RNA polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. A study just published in BMC Biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates.
See research article http://www.biomedcentral.com/1741-7007/8/54
A recent report in BMC Biology on the discovery and analysis of biosynthetic genes for ribosomal peptide natural products confirms that these pathways are much more common and diverse than previously suspected, contributing substantially to the chemical arsenal employed by bacteria.
See research article http://www.biomedcentral.com/1741-7007/8/70
Although proteins involved in determining apical-basal cell polarity have been directly linked to tumorigenesis, their precise roles in this process remain unclear. A recent report in BMC Biology clarifies the signaling pathways that control cell polarity, proliferation and apoptosis downstream of the tumor suppressor and apical-basal polarity determinant Scribble.
See research article http://www.biomedcentral.com/1741-7007/7/62.
The use of cultivation-independent approaches to map microbial diversity, including recent work published in BMC Biology, has now shown that protists, like bacteria/archaea, are much more diverse than had been realized. Uncovering eukaryotic diversity may now be limited not by access to samples or cost but rather by the availability of full-length reference sequence data.
See research article http://www.biomedcentral.com/1741-7007/7/72
Mutation of the protein spartin is a cause of one form of spastic paraplegia. Spartin interacts with ubiquitin ligases of the Nedd4 family, and a recent report in BMC Biology now shows that it acts as an adaptor to recruit and activate the ubiquitin ligase AIP4 onto lipid droplets, leading to the ubiquitination and degradation of droplet-associated proteins. A deficiency of spartin apparently causes lipid droplets to accumulate.
See research article: http://www.biomedcentral.com/1741-7007/8/72/