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1.  No severe and global X chromosome inactivation in meiotic male germline of Drosophila 
BMC Biology  2012;10:50.
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.
doi:10.1186/1741-7007-10-50
PMCID: PMC3391177
2.  Regeneration review reprise 
Journal of Biology  2010;9(2):15.
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.
doi:10.1186/jbiol224
PMCID: PMC2871519  PMID: 20236485
3.  Prospects for automated diagnosis of verbal autopsies 
BMC Medicine  2014;12:18.
Verbal autopsy is a method for assessing probable causes of death from lay reporting of signs, symptoms and circumstances by family members or caregivers of a deceased person. Several methods of automated diagnoses of causes of death from standardized verbal autopsy questionnaires have been developed recently (Inter-VA, Tariff, Random Forest and King-Lu). Their performances have been assessed in a series of papers in BMC Medicine. Overall, and despite high specificity, the current strategies of automated computer diagnoses lead to relatively low sensitivity and positive predictive values, even for causes which are expected to be easily assessed by interview. Some methods have even abnormally low sensitivity for selected diseases of public health importance and could probably be improved. Ways to improve the current strategies are proposed: more detailed questionnaires; using more information on disease duration; stratifying for large groups of causes of death by age, sex and main category; using clusters of signs and symptoms rather than quantitative scores or ranking; separating indeterminate causes; imputing unknown cause with appropriate methods.
Please see related articles: http://www.biomedcentral.com/1741-7015/12/5; http://www.biomedcentral.com/1741-7015/12/19; http://www.biomedcentral.com/1741-7015/12/20; http://www.biomedcentral.com/1741-7015/12/21; http://www.biomedcentral.com/1741-7015/12/22; http://www.biomedcentral.com/1741-7015/12/23.
doi:10.1186/1741-7015-12-18
PMCID: PMC3912493  PMID: 24495788
Cause of death; Verbal autopsy; Automated diagnosis; Health information system; Evaluation of health programs; Public health
4.  The water flea Daphnia - a 'new' model system for ecology and evolution? 
Journal of Biology  2010;9(2):21.
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.
doi:10.1186/jbiol212
PMCID: PMC2871515  PMID: 20478012
5.  Ethylene and the regulation of plant development 
BMC Biology  2012;10:9.
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
Commentary
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 [1]. 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. [2] 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 [3], form an important step in defining how a hormonal network regulates a key developmental process.
doi:10.1186/1741-7007-10-9
PMCID: PMC3282650  PMID: 22348804
6.  Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies 
BMC Genetics  2010;11:65.
Background
The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized.
Results
We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.
Conclusion
These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.
See commentary: http://www.biomedcentral.com/1741-7007/8/90
doi:10.1186/1471-2156-11-65
PMCID: PMC2910014  PMID: 20626846
7.  Scale-eating cichlids: from hand(ed) to mouth 
Journal of Biology  2010;9(2):11.
Two recent studies in BMC Biology and Evolution raise important questions about a textbook case of frequency-dependent selection in scale-eating cichlid fishes. They also suggest a fascinating new line of research testing the effects of handed behavior on morphological asymmetry.
See research article http://www.biomedcentral.com/1741-7007/8/8.
doi:10.1186/jbiol218
PMCID: PMC2871516  PMID: 20236497
8.  Smart biomaterials - regulating cell behavior through signaling molecules 
BMC Biology  2010;8:59.
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
doi:10.1186/1741-7007-8-59
PMCID: PMC2873335  PMID: 20529238
9.  The (r)evolution of cancer genetics 
BMC Biology  2010;8:74.
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
doi:10.1186/1741-7007-8-74
PMCID: PMC2883958  PMID: 20594288
10.  Bed bug deterrence 
BMC Biology  2010;8:117.
A recent study in BMC Biology has determined that the immature stage of the bed bug (the nymph) signals its reproductive status to adult males using pheromones and thus avoids the trauma associated with copulation in this species. The success of this nymphal strategy of deterrence is instructive. Against the background of increasing problems with bed bugs, this research raises the question whether pheromones might be used to control them.
See research article http://www.biomedcentral.com/1741-7007/8/121
doi:10.1186/1741-7007-8-117
PMCID: PMC2936290  PMID: 20828375
11.  Inferring the Tree of Life: chopping a phylogenomic problem down to size? 
BMC Biology  2011;9:59.
The combination of molecular sequence data and bioinformatics has revolutionized phylogenetic inference over the past decade, vastly increasing the scope of the evolutionary trees that we are able to infer. A recent paper in BMC Biology describing a new phylogenomic pipeline to help automate the inference of evolutionary trees from public sequence databases provides another important tool in our efforts to derive the Tree of Life.
See research article: http://www.biomedcentral.com/1741-7007/9/55
doi:10.1186/1741-7007-9-59
PMCID: PMC3176480  PMID: 21933452
12.  Genome of a songbird unveiled 
Journal of Biology  2010;9(3):19.
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/
doi:10.1186/jbiol222
PMCID: PMC2871510  PMID: 20359317
13.  Systems-biology dissection of eukaryotic cell growth 
BMC Biology  2010;8:62.
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
doi:10.1186/1741-7007-8-62
PMCID: PMC2875221  PMID: 20529234
14.  Folate status of gut microbiome affects Caenorhabditis elegans lifespan 
BMC Biology  2012;10:66.
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
doi:10.1186/1741-7007-10-66
PMCID: PMC3409036  PMID: 22849295
15.  The intriguing evolutionary dynamics of plant mitochondrial DNA 
BMC Biology  2011;9:61.
The mitochondrial genome of plants is-in every respect and for yet unclear reasons-very different from the well-studied one of animals. Thanks to next-generation sequencing technologies, Davila et al. precisely characterized the role played by recombination and DNA repair in controlling mitochondrial variations in Arabidopsis thaliana, thus opening new perspectives on the long-term evolution of this intriguing genome.
See research article: http://www.biomedcentral.com/1741-7007/9/64
The mitochondrial genome of plants is a challenge to molecular evolutionary biologists. Its content is highly dynamic: plant mitochondrial DNA (mtDNA) is large and variable in size (200 to 2,500 kb), contains many introns and repeated elements (typically 90% of the total sequence), and experiences frequent gene gain/loss/transfer/duplication, and genome rearrangements [1]. Its nucleotide substitution rate, paradoxically, is remarkably low-even lower than for nuclear DNA. These features are in sharp contrast with the highly studied mtDNA of animals, which is small-sized, structurally conserved, devoid of selfish elements, and has a very fast nucleotide substitution rate [2]. Why these two genomes behave so differently is one of the most head-scratching questions of current comparative genomics. The study by Davila et al. [3] contributes a potentially decisive argument by connecting the plant mtDNA mutation rate to yet another intriguing feature of this organellar genome-recombination.
doi:10.1186/1741-7007-9-61
PMCID: PMC3181201  PMID: 21951676
16.  Proteasome inhibition, the pursuit of new cancer therapeutics, and the adaptor molecule p130Cas 
BMC Biology  2011;9:72.
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
doi:10.1186/1741-7007-9-72
PMCID: PMC3203852  PMID: 22034840
17.  How a bird is an island 
BMC Biology  2012;10:53.
Replicate adaptive radiations occur when lineages repeatedly radiate and fill new but similar niches and converge phenotypically. While this is commonly seen in traditional island systems, it may also be present in host-parasite relationships, where hosts serve as islands. In a recent article in BMC Biology, Johnson and colleagues have produced the most extensive phylogeny of the avian lice (Ischnocera) to date, and find evidence for this pattern. This study opens the door to exploring adaptive radiations from a novel host-parasite perspective.
See research article: http://www.biomedcentral.com/1741-7007/10/52
doi:10.1186/1741-7007-10-53
PMCID: PMC3379931  PMID: 22715854
18.  TBP2 is a general transcription factor specialized for female germ cells 
Journal of Biology  2009;8(11):97.
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
doi:10.1186/jbiol196
PMCID: PMC2804282  PMID: 19951399
19.  Adaptations of proteins to cellular and subcellular pH 
Journal of Biology  2009;8(11):98.
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
doi:10.1186/jbiol199
PMCID: PMC2804283  PMID: 20017887
20.  On the scent of sexual attraction 
BMC Biology  2010;8:71.
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
doi:10.1186/1741-7007-8-71
PMCID: PMC2880966  PMID: 20504292
21.  The architecture of RNA polymerase fidelity 
BMC Biology  2010;8:85.
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
doi:10.1186/1741-7007-8-85
PMCID: PMC2889878  PMID: 20598112
22.  The hidden diversity of ribosomal peptide natural products 
BMC Biology  2010;8:83.
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
doi:10.1186/1741-7007-8-83
PMCID: PMC2890512  PMID: 20594290
23.  Scribble at the crossroads 
Journal of Biology  2009;8(12):104.
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.
doi:10.1186/jbiol190
PMCID: PMC2804276  PMID: 20053305
24.  Mapping the protistan 'rare biosphere' 
Journal of Biology  2009;8(12):105.
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
doi:10.1186/jbiol201
PMCID: PMC2804278  PMID: 20067591
25.  Regulation of lipid droplet turnover by ubiquitin ligases 
BMC Biology  2010;8:94.
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/
doi:10.1186/1741-7007-8-94
PMCID: PMC2906420  PMID: 20646264

Results 1-25 (675179)