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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.  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
3.  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
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.  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
9.  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
10.  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
11.  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
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.  Modularity of gene-regulatory networks revealed in sea-star development 
BMC Biology  2011;9:6.
Evidence that conserved developmental gene-regulatory networks can change as a unit during deutersostome evolution emerges from a study published in BMC Biology. This shows that genes consistently expressed in anterior brain patterning in hemichordates and chordates are expressed in a similar spatial pattern in another deuterostome, an asteroid echinoderm (sea star), but in a completely different developmental context (the animal-vegetal axis). This observation has implications for hypotheses on the type of development present in the deuterostome common ancestor.
See research article: http://www.biomedcentral.com/1741-7007/8/143/abstract
doi:10.1186/1741-7007-9-6
PMCID: PMC3032766  PMID: 21281525
19.  History and phylogeny of intermediate filaments: Now in insects 
BMC Biology  2011;9:16.
Intermediate filaments include the nuclear lamins, which are universal in metazoans, and the cytoplasmic intermediate filaments, which are much more varied and form cell type-specific networks in animal cells. Until now, it has been thought that insects harbor lamins only. This view is fundamentally challenged by the discovery, reported in BMC Biology, of an intermediate filament-like cytoplasmic protein, isomin, in the hexapod Isotomurus maculatus. Here we briefly review the history of research on intermediate filaments, and discuss the implications of this latest finding in the context of what is known of their structure and functions.
See research article: http://www.biomedcentral.com/1741-7007/9/17
doi:10.1186/1741-7007-9-16
PMCID: PMC3046923  PMID: 21356127
20.  Promiscuity and preferences of metallothioneins: the cell rules 
BMC Biology  2011;9:25.
Metalloproteins are essential for many cellular functions, but it has not been clear how they distinguish between the different metals to bind the correct ones. A report in BMC Biology finds that preferences of two metallothionein isoforms for two different cations are due to inherent properties of these usually less discriminating proteins. Here these observations are discussed in the context of the cellular mechanisms that regulate metal binding to proteins.
See research article: http://www.biomedcentral.com/1741-7007/9/4
doi:10.1186/1741-7007-9-25
PMCID: PMC3084178  PMID: 21527046
21.  Sex, sex chromosomes and gene expression 
BMC Biology  2011;9:30.
The X chromosome has fewer testis-specific genes than autosomes in many species. This bias is commonly attributed to X inactivation in spermatogenesis but a recent paper in BMC Biology provides evidence against X inactivation in Drosophila and proposes that somatic tissue- and testis- but not ovary-specific genes tend not to be located on the X chromosome. Here, we discuss possible mechanisms underlying this bias, including sexual antagonism and dosage compensation.
See research article {http://www.biomedcentral.com/1741-7007/9/29}
doi:10.1186/1741-7007-9-30
PMCID: PMC3087707  PMID: 21542945
22.  DNA replication: archaeal oriGINS 
BMC Biology  2011;9:36.
GINS is an essential eukaryotic DNA replication factor that is found in a simplified form in Archaea. A new study in this issue of BMC Biology reveals the first structure of the archaeal GINS complex. The structure reveals the anticipated similarity to the previously determined eukaryotic complex but also has some intriguing differences in the relative disposition of subunit domains.
See research article: http://www.biomedcentral.com/1741-7007/9/28
doi:10.1186/1741-7007-9-36
PMCID: PMC3104950  PMID: 21627856
23.  Following autophagy step by step 
BMC Biology  2011;9:39.
Autophagy is an evolutionarily conserved lysosomal degradation route for soluble components of the cytosol and organelles. There is great interest in identifying compounds that modulate autophagy because they may have applications in the treatment of major diseases including cancer and neurodegenerative disease. Hundeshagen and colleagues describe this month in BMC Biology a screening assay based on flow cytometry that makes it possible to track distinct steps in the autophagic process and thereby identify novel modulators of autophagy.
See research article: http://www.biomedcentral.com/1741-7007/9/38
doi:10.1186/1741-7007-9-39
PMCID: PMC3107173  PMID: 21635796
24.  The bending of cell sheets - from folding to rolling 
BMC Biology  2011;9:90.
The bending of cell sheets plays a major role in multicellular embryonic morphogenesis. Recent advances are leading to a deeper understanding of how the biophysical properties and the force-producing behaviors of cells are regulated, and how these forces are integrated across cell sheets during bending. We review work that shows that the dynamic balance of apical versus basolateral cortical tension controls specific aspects of invagination of epithelial sheets, and recent evidence that tissue expansion by growth contributes to neural retinal invagination in a stem cell-derived, self-organizing system. Of special interest is the detailed analysis of the type B inversion in Volvox reported in BMC Biology by Höhn and Hallmann, as this is a system that promises to be particularly instructive in understanding morphogenesis of any monolayered spheroid system.
See research article: http://www.biomedcentral.com/1741-7007/9/89
doi:10.1186/1741-7007-9-90
PMCID: PMC3248374  PMID: 22206439
25.  Difficult phylogenetic questions: more data, maybe; better methods, certainly 
BMC Biology  2011;9:91.
Contradicting the prejudice that endosymbiosis is a rare phenomenon, Husník and co-workers show in BMC Biology that bacterial endosymbiosis has occured several times independently during insect evolution. Rigorous phylogenetic analyses, in particular using complex models of sequence evolution and an original site removal procedure, allow this conclusion to be established after eschewing inference artefacts that usually plague the positioning of highly divergent endosymbiont genomic sequences.
See research article http://www.biomedcentral.com/1741-7007/9/87
doi:10.1186/1741-7007-9-91
PMCID: PMC3248379  PMID: 22206462

Results 1-25 (675191)