Biology Direct via MedWorm.com MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Biology Direct' source. Mon, 06 Feb 2012 14:26:00 +0100 Lateral transfer of tetrahymenol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen http://www.medworm.com/index.php?rid=5656291&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F7%2F1%2F5 Tetrahymanol functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments, and genes encoding the tetrahymanol synthesizing enzyme have been laterally transferred among several phylogenetically diverged eukaryotes. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5656291 Wed, 01 Feb 2012 05:00:00 +0100 5656291 Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? http://www.medworm.com/index.php?rid=5616914&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F7%2F1%2F4 The greater stability of key RNA bonds at acidic pH, such as link the phosphodiester backbone and between amino acids and tRNA, suggests the RNA world evolved in acidic conditions. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5616914 Fri, 20 Jan 2012 05:00:00 +0100 5616914 IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice http://www.medworm.com/index.php?rid=5603829&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F7%2F1%2F3 In MRL/lpr mice, which spontaneously develop autoimmune glomerulonephritis like that in systemic lupus erythematosus, genetic elimination of IgG3 antibody production diminishes renal pathology and extends lifespan. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5603829 Mon, 16 Jan 2012 05:00:00 +0100 5603829 On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes http://www.medworm.com/index.php?rid=5592847&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F7%2F1%2F2 New large-scale comparative genome analyses provided further evidences indicating that polymerases involved in either replication or repair pathways underlie the GC content variability in eubacteria. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5592847 Tue, 10 Jan 2012 05:00:00 +0100 5592847 Evolution before genes http://www.medworm.com/index.php?rid=5568669&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F7%2F1%2F1 Conclusions: We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.ReviewersThis article was reviewed by William Martin... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5568669 Thu, 05 Jan 2012 05:00:00 +0100 5568669 Accurate State Estimation from Uncertain Data and Models: An Application of Data Assimilation to Mathematical Models of Human Brain Tumors http://www.medworm.com/index.php?rid=5533102&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F64 State estimation schemes, employed operationally for weather forecasting, can be applied in principle to make useful short-term predictions of the growth and spread of malignant tumors in individual patient cases. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5533102 Wed, 21 Dec 2011 05:00:00 +0100 5533102 CRISPR loci reveal networks of gene exchange in archaea http://www.medworm.com/index.php?rid=5533101&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F65 Conclusions: CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense.Open peer review: This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten) (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5533101 Wed, 21 Dec 2011 05:00:00 +0100 5533101 Purine Biosynthesis in Archaea: Variations on a Theme http://www.medworm.com/index.php?rid=5512260&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F63 Conclusions: The patchy distribution of purine biosynthetic genes in archaea is consistent with a pathway that has been shaped by horizontal gene transfer, duplication, and gene loss. Our results indicate that manual curation can improve upon automated annotation for a small number of automatically-annotated proteins and can reveal a need to identify further pathway components even in well-studied pathways.Reviewers: This article was reviewed by Dr. Celine Brochier-Armanet, Dr Kira S Makarova (nominated by Dr. Eugene Koonin), and Dr. Michael Galperin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5512260 Wed, 14 Dec 2011 05:00:00 +0100 5512260 The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. http://www.medworm.com/index.php?rid=5492475&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F62 A model whereby new species arise by budding from the ancestral stock rather than by splitting into separate populations, with advantageous recessive phenotypes promoting the direct selection of reproductive barriers. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5492475 Fri, 09 Dec 2011 05:00:00 +0100 5492475 Transcription factor binding sites are highly enriched within microRNA precursor sequences http://www.medworm.com/index.php?rid=5473502&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F61 Conclusions: The transcription factor binding sites localized within small hairpin microRNA precursor sequences may possibly regulate their transcription. Transcription factors may also possibly bind directly to nascent primary microRNA gene transcripts or small hairpin microRNA precursors and regulate their processing.ReviewersThis article was reviewed by Guillaume Bourque (nominated by Jerzy Jurka), Dmitri Pervouchine (nominated by Mikhail Gelfand), and Yuriy Gusev. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5473502 Fri, 02 Dec 2011 05:00:00 +0100 5473502 On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence http://www.medworm.com/index.php?rid=5447558&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F60 Douglas Theobald, in response to recent criticisms, provides evidence to further support his claim that Darwin's hypothesis that all life on earth has a universal common ancestor has been formally confirmed by a homology independent statistic test. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5447558 Thu, 24 Nov 2011 05:00:00 +0100 5447558 Extensive intron gain in the ancestor of placental mammals http://www.medworm.com/index.php?rid=5447559&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F59 Phylogenomic analysis of domesticated genes provides evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5447559 Wed, 23 Nov 2011 05:00:00 +0100 5447559 Molecular musings in microbial ecology and evolution http://www.medworm.com/index.php?rid=5396656&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F58 This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5396656 Thu, 10 Nov 2011 05:00:00 +0100 5396656 Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins http://www.medworm.com/index.php?rid=5355226&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F57 Transmembrane helices can be either complex (possibly common ancestry) or simple (likely of convergent evolution); the latter should be excluded from similarity searches to avoid false assignments of protein homology. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5355226 Tue, 25 Oct 2011 04:00:00 +0100 5355226 Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxydase I gene http://www.medworm.com/index.php?rid=5355227&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F56 Background: Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as mitochondrial DNA (mtDNA). Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1).Presentation of the hypothesisA positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. This putative gene has been named gau for gene antisense ubiquitous in mtDNAs. The length of the deduced protein is approximately 100 amino acids. In vertebrates, several s... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5355227 Mon, 24 Oct 2011 04:00:00 +0100 5355227 The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria http://www.medworm.com/index.php?rid=5343436&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F55 Conclusions: The most plausible scenario of the origin of the mitochondrion is that ancestors of Rickettsiales and Rhizobiales merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the Rickettsiales and Rhizobiales cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for enhanced gene exchange. Therefore, the tree of life is not sufficient to explain the chimeric structure of current genomes, and the theory of a single common ancestor and a top-down tree does not reflect our current state of knowledge. Mitochondrial evolution constit... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5343436 Thu, 20 Oct 2011 04:00:00 +0100 5343436 Phylogenetic analysis reveals wide distribution of globin X http://www.medworm.com/index.php?rid=5330403&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F54 Phylogenetic analysis and comparative genomics reveal wide distribution of globin X in vertebrates and its invertebrate orthologs confirming its ancient origin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5330403 Mon, 17 Oct 2011 04:00:00 +0100 5330403 A Network-Based Approach to Classify the Three Domains of Life http://www.medworm.com/index.php?rid=5321416&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F53 Conclusions: Our results show that these particular topological network descriptors are able to capture domain-specific structural characteristics for classifying metabolic networks between the three domains of life. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5321416 Thu, 13 Oct 2011 04:00:00 +0100 5321416 Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria http://www.medworm.com/index.php?rid=5310606&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F52 This article was reviewed by Dr. Michael Galperin and Dr. Rob Knight. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5310606 Mon, 10 Oct 2011 04:00:00 +0100 5310606 Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data http://www.medworm.com/index.php?rid=5292735&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F51 Fish the ChIPs is a computational pipeline for complete ChIP-Seq data analysis of unlimited samples; it can be run on any Unix machine while providing a graphic interface for Mac. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5292735 Thu, 06 Oct 2011 04:00:00 +0100 5292735 Structural analysis of hubs in human NR-RTK network http://www.medworm.com/index.php?rid=5292737&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F49 Conclusions: Although the methods require human intervention and judgment, they can identify the interactions that could occur together or ones that are mutually exclusive. This adds a fourth dimension to interaction network that of time and can assist in obtaining concrete predictions consistent with experiments.ReviewersThis article was reviewed by Dr. Anthony Almudevar, Prof. James Faeder and Prof. Eugene Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5292737 Wed, 05 Oct 2011 04:00:00 +0100 5292737 Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome http://www.medworm.com/index.php?rid=5292736&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F50 The universality of volutin granules and presence of the vacuolar pyrophosphatase in the three superkingdoms of life reveals that the acidocalcisomes may have originated in the Last Universal Common Ancestor. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5292736 Wed, 05 Oct 2011 04:00:00 +0100 5292736 Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins http://www.medworm.com/index.php?rid=5292738&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F48 Diversification of orthologous genes provokes specific physico-chemical changes in proteins of related species, revealing particular trends required to perform their functional roles in the adaptation to niche and intra-cellular conditions. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5292738 Tue, 04 Oct 2011 04:00:00 +0100 5292738 Biased gene transfer and its implications for the concept of lineage http://www.medworm.com/index.php?rid=5257174&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F47 Evolutionary histories of three aminoacyl-tRNA synthetases show that the concept of organismal lineage in the prokaryotic world is defined by vertical inheritance and horizontal gene transfer biased towards close relatives. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5257174 Fri, 23 Sep 2011 04:00:00 +0100 5257174 A mathematical model for targeting chemicals to tissues by exploiting complex degradation http://www.medworm.com/index.php?rid=5246108&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F46 A mathematical model describing the co-diffusion of binding partners into a tissue is presented, elucidating a general method for targeting a chemical to a tissue. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5246108 Thu, 22 Sep 2011 04:00:00 +0100 5246108 A Rooted Net of Life http://www.medworm.com/index.php?rid=5246109&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F45 We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where in... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5246109 Wed, 21 Sep 2011 04:00:00 +0100 5246109 Expression levels of microRNAs are not associated with their regulatory activities http://www.medworm.com/index.php?rid=5233272&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F43 MicroRNAs (miRNAs) regulate their targets by triggering mRNA degradation or translational repression. The negative relationship between miRNAs and their targets suggests that the regulatory effect of a miRNA could be determined from the expression levels of its targets. Here, we investigated the relationship between miRNA activities determined by computational programs and miRNA expression levels by using data in which both mRNA and miRNA expression from the same samples were measured. We found that different from the intuitive expectation one might have, miRNA activity shows very weak correlation with miRNA expression, which indicates complex regulating mechanisms between miRNAs and their target genes.Reviewers: This manuscript was reviewed by an anonymous reviewer and Dr Yuriy Gusev. (So... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5233272 Mon, 19 Sep 2011 04:00:00 +0100 5233272 Families of transposable elements, population structure and the origin of species http://www.medworm.com/index.php?rid=5233271&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F44 Families of transposable elements (TEs) originate primarily by genetic drift in small populations and may fundamentally impact the origin of species and genome evolution. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5233271 Mon, 19 Sep 2011 04:00:00 +0100 5233271 Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy http://www.medworm.com/index.php?rid=5217608&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F42 Conclusions: Our results have implications for understanding pharmacodynamics of and improving activity of antiretroviral drugs. Our findings predict that drug activity can be improved through co-administration of synergistic drugs that delay the viral life cycle but are not inhibitory by themselves. Moreover, our results may easily extend to treatment of other pathogens.This article was reviewed by Dr. Ruy Ribeiro, Dr. Ha Youn Lee, Dr. Alan Perelson and Dr. Christoph Adami. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5217608 Mon, 12 Sep 2011 04:00:00 +0100 5217608 The public goods hypothesis for the evolution of life on Earth http://www.medworm.com/index.php?rid=5155483&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F41 It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another org... Biology Direct journals http://www.medworm.com/rss/comments.php?id=5155483 Mon, 22 Aug 2011 23:00:00 +0100 5155483 Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species. http://www.medworm.com/index.php?rid=5076283&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F40 Striking changes in the pI of major milk proteins reflecting adaptive evolution are not restricted to differences between species with markedly different intestinal pH compartments, suggesting other selection constraints. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5076283 Thu, 28 Jul 2011 23:00:00 +0100 5076283 Of Woods and Webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli http://www.medworm.com/index.php?rid=5048201&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F39 ${item.shortDescription} (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5048201 Tue, 19 Jul 2011 23:00:00 +0100 5048201 Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems http://www.medworm.com/index.php?rid=5026744&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F38 Conclusions: Because of the extreme diversity of CRISPR-Cas systems, in-depth sequence and structure comparison continue to reveal unexpected homologous relationship among Cas proteins. Unification of Cas protein families previously considered unrelated provides for improvement in the classification of CRISPR-Cas systems and a reconstruction of their evolution.Open peer review: This article was reviewed by Malcolm White (nominated by Purficacion Lopez-Garcia), Frank Eisenhaber and Igor Zhulin. For the full reviews, see the Reviewers' Comments section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5026744 Wed, 13 Jul 2011 23:00:00 +0100 5026744 CREST - a large and diverse superfamily of putative transmembrane hydrolases http://www.medworm.com/index.php?rid=5006237&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F37 Conclusions: Universal conservation of a set of histidine and aspartate residues across all groups in the CREST superfamily, coupled with independent discoveries of hydrolase activities in alkaline ceramidases and the Per1 family as well as results from previous mutational studies of Per1, suggests that the majority of CREST members are metal-dependent hydrolases. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=5006237 Tue, 05 Jul 2011 23:00:00 +0100 5006237 How stands the Tree of Life a century and a half after The Origin? http://www.medworm.com/index.php?rid=4991654&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F32 This article was reviewed by W. Ford Doolittle, Nicholas Galtier and Christophe Malaterre. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4991654 Wed, 29 Jun 2011 23:00:00 +0100 4991654 From the scala naturae to the symbiogenetic and dynamic tree of life http://www.medworm.com/index.php?rid=4991653&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F33 This article was reviewed by Mark Ragan, W. Ford Doolittle, and StaffanMuller-Wille. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4991653 Wed, 29 Jun 2011 23:00:00 +0100 4991653 Telling the Whole Story in a 10,000-Genome World http://www.medworm.com/index.php?rid=4991652&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F34 Conclusions: These complex relationships highlight the need for an inclusive approach to genomicdata, and current methods with minor alterations will likely scale to allow the analysisof datasets with 10,000 or more genomes. The main challenges lie in the visualizationand interpretation of genomic relationships, and the redefinition of microbialtaxonomy when subsets of genomic data are so evidently in conflict with one another,and with the "canonical" molecular taxonomy.ReviewersThe manuscript was reviewed by William Martin, W. Ford Doolittle, Joel Velascoand Eugene Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4991652 Wed, 29 Jun 2011 23:00:00 +0100 4991652 Energetics and genetics across the prokaryote-eukaryote divide http://www.medworm.com/index.php?rid=4991651&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F35 Conclusions: The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes. Reviewers: This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4991651 Wed, 29 Jun 2011 23:00:00 +0100 4991651 Early evolution without a tree of life http://www.medworm.com/index.php?rid=4991650&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F36 This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4991650 Wed, 29 Jun 2011 23:00:00 +0100 4991650 Structural Influence of gene networks on their inference: Analysis of C3NET http://www.medworm.com/index.php?rid=4959217&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F31 Conclusions: The availability of gene network inference algorithms with known inferential properties opens a new era of large-scale screening experiments that could be equally beneficial for basic biological and biomedical research with auspicious prospects. The availability of our easy to use software package c3net may contribute to the popularization of such methods.Reviewers: This article was reviewed by Lev Klebanov, Joel Bader and Yuriy Gusev. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4959217 Tue, 21 Jun 2011 23:00:00 +0100 4959217 A Computational Approach to Candidate Gene Prioritization for X-Linked Mental Retardation using Annotation-based Binary Filtering and Motif-Based Linear Discriminatory Analysis http://www.medworm.com/index.php?rid=4932043&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F30 Conclusions: The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR.Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius); Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4932043 Sun, 12 Jun 2011 23:00:00 +0100 4932043 Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns http://www.medworm.com/index.php?rid=4901132&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F29 Conclusions: The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities.Reviewers:This article was reviewed by Prof. Chris... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4901132 Thu, 02 Jun 2011 23:00:00 +0100 4901132 Interplay of recombination and selection in the genomes of Chlamydia trachomatis. http://www.medworm.com/index.php?rid=4870626&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F28 Conclusions: C. trachomatis is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole C. trachomatis genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding C. trachomatis pathogenesis.ReviewersThis article was reviewed by Dr. Jeremy Selengut, Dr. Lee S. Katz (nominated by Dr. I. King Jordan) and Dr. Arcady Mushegian. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4870626 Wed, 25 May 2011 23:00:00 +0100 4870626 ConReg-R: Extrapolative recalibration of the empirical distribution of p-values to improve false discovery rate estimates http://www.medworm.com/index.php?rid=4847187&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F27 Conclusions: ConReg-R provides an efficient way to improve the FDR estimates. It only requires the p-values from the tests and avoids permutation of the original test data. We demonstrate that the proposed method significantly improves FDR estimation on several gene expression datasets obtained from microarray and RNA-seq experiments.Reviewers: The manuscript was reviewed by Prof. Vladimir Kuznetsov, Prof. Philippe Broet, and Prof. Hongfang Liu (nominated by Prof. Yuriy Gusev). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4847187 Thu, 19 May 2011 23:00:00 +0100 4847187 A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes http://www.medworm.com/index.php?rid=4839572&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F26 Conclusion: The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches.Reviewers: This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4839572 Wed, 18 May 2011 23:00:00 +0100 4839572 MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival http://www.medworm.com/index.php?rid=4839574&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F23 Conclusions: In summary, this work has identified aberrantly expressed microRNAs associated with the diagnosis, pathogenesis and prognosis of MM, data which will prove an invaluable resource for understanding the role of microRNAs in this devastating disease.Reviewers: This article was reviewed by Prof. Neil Smalheiser, Prof. Yuriy Gusev, and an unknown reviewer. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4839574 Tue, 17 May 2011 23:00:00 +0100 4839574 Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity http://www.medworm.com/index.php?rid=4839573&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F24 This article was reviewed by Dr Arcady Mushegian, Dr Igor B Rogozin (nominated by Dr I King Jordan) and Dr Alexey S Kondrashov. For the full reviews, please go to the Reviewer's Reports section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4839573 Tue, 17 May 2011 23:00:00 +0100 4839573 Evolutionary plasticity determination by orthologous groups distribution http://www.medworm.com/index.php?rid=4839575&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F22 Conclusions: The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes.ReviewersThis article was reviewed by Prof Manyuan Long, Hiroyuki Toh, and Sebastien Halary. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4839575 Mon, 16 May 2011 23:00:00 +0100 4839575 Statistical methods for detecting periodic fragments in DNA sequence data http://www.medworm.com/index.php?rid=4762174&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F21 Conclusions: For estimating the dominant period, we find the Hybrid period estimation method empirically to be the most effective for both eroded and approximate periodicity. The blockwise bootstrap was found to be effective as a significance measure, performing particularly well in the problem of period detection in the presence of eroded periodicity. The autocorrelation method was identified as poorly suited for use with the blockwise bootstrap. Application of our methods to the genomes of two model organisms revealed a striking proportion of the yeast and mouse genomes are spanned by NPS. Despite their markedly different sizes, roughly equivalent proportions (19-21%) of the genomes lie within period-10 spans of the NPS dinucleotides fAA; TT; TAg. The biological significance of these reg... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4762174 Wed, 27 Apr 2011 23:00:00 +0100 4762174 On the relationship between the load and the variance of relative fitness http://www.medworm.com/index.php?rid=4713968&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F20 Conclusions: Although it is impossible to deduce the load from knowledge of the variance of relative fitness alone, it is possible to determine the minimal load consistent with a particular variance of relative fitness. The concept of minimal load consistent with a particular biological phenomenon may be applicable to studying several aspects of natural selection.ReviewersThe manuscript was reviewed by Sergei Maslov, Alexander Gordon, and Eugene Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4713968 Wed, 13 Apr 2011 23:00:00 +0100 4713968 The struggle for life of the genome's selfish architects http://www.medworm.com/index.php?rid=4605170&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F19 This article was reviewed by Jerzy Jurka, Jurgen Brosius and I. King Jordan. For complete reports, see the Reviewers' reports section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4605170 Thu, 17 Mar 2011 00:00:00 +0100 4605170 Functional analysis of archaeal MBF1 by complementation studies in yeast http://www.medworm.com/index.php?rid=4570010&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F18 Conclusions: The absence of MBF1-interacting activators in the archaeal domain, the presence of a Zn ribbon motif in the divergent N-terminal domain of aMBF1 and the complementation experiments using archaeal- yeast chimeric proteins presented here suggests that archaeal MBF1 is not able to functionally interact with the transcription machinery and/or Gcn4 of S. cerevisiae. Based on modeling and structural prediction it is tempting to speculate that aMBF1 might act as a single regulator or non-essential transcription factor, which directly interacts with DNA via the positive charged linker or the basal transcription machinery via its Zn ribbon motif and the HTH domain. However, also alternative functions in ribosome biosynthesis and/or functionality have been discussed and therefore furthe... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4570010 Thu, 10 Mar 2011 00:00:00 +0100 4570010 Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale http://www.medworm.com/index.php?rid=4531367&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F15 Conclusions: Our study opens a debate on validity of using many popular pathway databases to obtain transcriptional regulatory targets. We conclude that the choice of pathway databases should be informed by solid scientific evidence and rigorous empirical evaluation.Reviewers: This article was reviewed by Prof. Wing Hung Wong, Dr. Thiago Motta Venancio (nominated by Dr. L Aravind), and Prof. Geoff J McLachlan. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4531367 Mon, 28 Feb 2011 00:00:00 +0100 4531367 The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon http://www.medworm.com/index.php?rid=4531366&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F16 Conclusion: We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes.Reviewers: This article was reviewed by Patrick Forterre, Eugene Koonin, and Gaspar Jekely (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4531366 Mon, 28 Feb 2011 00:00:00 +0100 4531366 Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes http://www.medworm.com/index.php?rid=4506612&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F13 Conclusion: Our study suggests that Ka calculation, which is less biased compared to Ks and Ka/Ks, can be used as a parameter to sort genes by evolution rate and can also provide a way to categorize common protein functions and define their interaction networks, either pair-wise or in defined lineages or subgroups. Evaluating gene evolution based on Ka and Ks calculations can be done with large datasets, such as mammalian genomes.Reviewers:This article has been reviewed by Drs. Anamaria Necsulea (nominated by Nicolas Galtier), Subhajyoti De (nominated by Sarah Teichmann) and Claus O. Wilke. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4506612 Tue, 22 Feb 2011 00:00:00 +0100 4506612 On origin of genetic code and tRNA before translation http://www.medworm.com/index.php?rid=4506611&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F14 Conclusion: Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4506611 Tue, 22 Feb 2011 00:00:00 +0100 4506611 Endosymbiont or host: who drove mitochondrial and plastid evolution? http://www.medworm.com/index.php?rid=4498070&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F12 The recognition that mitochondria and plastids are derived from alphaproteobacterial and cyanobacterial endosymbionts, respectively, was one of the greatest advances in modern evolutionary biology. Researchers have yet however to provide detailed cell biological descriptions of how these once free-living prokaryotes were transformed into intracellular organelles. A key area of study in this realm is elucidating the evolution of the molecular machines that control organelle protein topogenesis. Alcock et al. (Science 2010, 327 [5966]:649-650) suggest that evolutionary innovations that established the mitochondrial protein sorting system were driven by the alphaproteobacterial endosymbiont (an "insiders' perspective"). In contrast, here we argue that evolution of mitochondrial and plastid to... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4498070 Sat, 19 Feb 2011 00:00:00 +0100 4498070 A rebuttal to the comments on the genome order index and the Z-curve http://www.medworm.com/index.php?rid=4488745&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F10 Conclusion: Elhaik et al. confuse S (a single number) with Z-curve (a series of 3D coordinates), which are distinct. To use S as a case study of Z-curve, by itself, is invalid. S and H are neither equivalent nor derivable from each other. The criticisms of Elhaik, Graur and Josic are wrong.Reviewers: This article was reviewed by Erik van Nimwegen. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4488745 Wed, 16 Feb 2011 00:00:00 +0100 4488745 Enhanced immunogenicity of pneumococcal surface adhesin A (PsaA) in mice via fusion to recombinant human B lymphocyte stimulator (BLyS) http://www.medworm.com/index.php?rid=4454634&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F9 Conclusion: This study identifies covalent attachment of BLyS as a highly effective adjuvant strategy that may yield improved vaccines. In addition, this is the first report demonstrating an unexpected role for TACI in the elicitation of antibodies by the PsaA-BLyS fusion protein.ReviewersThis article was reviewed by Jonathan Yewdell, Rachel Gerstein, and Michael Cancro (nominated by Andy Caton). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4454634 Wed, 09 Feb 2011 00:00:00 +0100 4454634 Gene gain and loss events in Rickettsia and Orientia species http://www.medworm.com/index.php?rid=4449685&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F6 Conclusions: Our phylogenetic analysis allowed us to track the gene gain and loss events occurring in bacterial genomes during their evolution from a free-living to an intracellular lifestyle. We have shown that the primary mechanism of evolution and specialization in strictly intracellular bacteria is gene loss. Despite the intracellular habitat, we found several horizontal gene transfers between Rickettsiales species and various prokaryotic, viral and eukaryotic species.Open peer review: Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4449685 Tue, 08 Feb 2011 00:00:00 +0100 4449685 The Multiple Personalities of Watson and Crick Strands http://www.medworm.com/index.php?rid=4449684&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F7 This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4449684 Tue, 08 Feb 2011 00:00:00 +0100 4449684 Consequences of cell-to-cell P-glycoprotein transfer on acquired multidrug resistance in breast cancer: a cell population dynamics model http://www.medworm.com/index.php?rid=4404878&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F5 Conclusions: We confirmed cell-to-cell transfer of functional P-gp. The transfer process depends on the gradient of P-gp expression in the donor-recipient cell interactions, as they evolve over time. Extragenetically acquired drug resistance is an additional aptitude of neoplastic cells which has implications in the diagnostic value of P-gp expression and in the design of chemotherapy regimens.ReviewersThis article was reviewed by Leonid Hanin, Anna Marciniak-Czochra and Marek Kimmel. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4404878 Wed, 26 Jan 2011 00:00:00 +0100 4404878 Issues associated with the use of phosphospecific antibodies to localise active and inactive pools of GSK-3 in cells http://www.medworm.com/index.php?rid=4393529&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F4 Conclusions: Our findings indicate that care should be taken when examining the subcellular localisation of active or inactive GSK-3 and, furthermore, suggest that the role of GSK-3 phosphorylation in some cellular processes be reassessed.Reviewers: Dr. David Kaplan, Dr. Robert Murphy and Dr. Cara Gottardi (nominated by Dr Avinash Bhandoola) (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4393529 Mon, 24 Jan 2011 00:00:00 +0100 4393529 Modeling RNA polymerase competition: the effect of sigma-subunit knockout and heat shock on gene transcription level http://www.medworm.com/index.php?rid=4381949&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F3 Conclusions: The developed model is in good agreement with virtually all relevant experimental data. The model can be applied to estimate intensities of binding of the holoenzyme and phage type RNA polymerase to their promoters using data on gene transcription levels, as well as to predict characteristics of RNA polymerases and the transcription process that are difficult to measure directly, e.g., the intensity (frequency) of holoenzyme binding to the promoter in correlation to its nucleotide composition and the type of sigma-subunit, the amount of transcription initiation aborts, etc. The model can be used to make functional predictions, e.g., heat shock response in isolated chloroplasts and changes of gene transcription levels under knockout of different sigma-subunits or RNA polymerase... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4381949 Fri, 21 Jan 2011 00:00:00 +0100 4381949 Impact of Alu repeats on the evolution of human p53 binding sites http://www.medworm.com/index.php?rid=4317813&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F2 Conclusions: The primate-specific Alu repeats play an important role in shaping the p53 regulatory network in the context of chromatin. One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu transcription, which, in turn, influences expression of the host genes.ReviewersThis paper was reviewed by Igor B. Rogozin (nominated by Pavel A. Pevzner), Sandor Pongor, and I. King Jordan. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4317813 Thu, 06 Jan 2011 00:00:00 +0100 4317813 The advantages and disadvantages of horizontal gene transfer and the emergence of the first species http://www.medworm.com/index.php?rid=4308906&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F6%2F1%2F1 Conclusions: Modern cells should therefore evolve to reduce HGT if they can, although the prevalence of independently replicating mobile elements and viruses may mean that cells cannot avoid HGT in practice. In the model, natural selection leads to gradual improvement of the replication accuracy and gradual decrease in the optimal rate of HGT. By clustering genomes based on gene content, we show that there are no separate lineages of organisms when the rate of HGT is high; however, as the rate of HGT decreases, a tree-like structure emerges with well-defined lineages. The model therefore passes through a Darwinian Threshold.Reviewers - This article was reviewed by Eugene V. Koonin, Anthony Poole and J. Peter Gogarten. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4308906 Mon, 03 Jan 2011 00:00:00 +0100 4308906 Mitochondrial pathogenic mutations are population-specific http://www.medworm.com/index.php?rid=4301937&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F68 Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.ReviewersThis article was revie... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4301937 Fri, 31 Dec 2010 00:00:00 +0100 4301937 Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers http://www.medworm.com/index.php?rid=4298290&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F67 Conclusions: We were able to elucidate some aspects of the evolution of gene regulation for three genes associated with pluripotency. Based on the expected return on investment for the community, we encourage other scientists to contribute experimental data on gene regulation (original work as well as data collected for reviews) to the UCSC system, to enable studies of the evolution of gene regulation on a large scale, and to report their findings.Reviewers:This article was reviewed by Dr. Gustavo Glusman and Dr. Juan Caballero, Institute for Systems Biology, Seattle, USA (nominated by Dr. Doron Lancet, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel), Dr. Niels Grabe, TIGA Center (BIOQUANT) and Medical Systems Biology Group, Institute of Medical Biometry a... Biology Direct journals http://www.medworm.com/rss/comments.php?id=4298290 Wed, 29 Dec 2010 00:00:00 +0100 4298290 The common ancestry of life http://www.medworm.com/index.php?rid=4178557&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F64 Conclusion: A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.Reviewers: this article was reviewed by William Martin, Ivan Iossifov (nominated by Andrey Rzhetsky) and Arcady Mushegian. For the complete reviews, see the Reviewers' Report section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4178557 Thu, 18 Nov 2010 00:00:00 +0100 4178557 How many antiviral small interfering RNAs may be encoded by the mammalian genomes? http://www.medworm.com/index.php?rid=4149694&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F62 Conclusions: This hypothesis proposes that mammalian organisms may use their own genomes as sources of thousands of putative interfering RNA motifs that can be recruited to repress intracellular pathogens like proliferating viruses.ReviewersThis article was reviewed by Eugene V. Koonin, Valerian V. Dolja and Yuri V. Shpakovski. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4149694 Mon, 08 Nov 2010 00:00:00 +0100 4149694 Modeling compositional dynamics based on GC and purine contents of protein-coding sequences http://www.medworm.com/index.php?rid=4149693&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F63 Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4149693 Mon, 08 Nov 2010 00:00:00 +0100 4149693 Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1 http://www.medworm.com/index.php?rid=4132377&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F61 Conclusions: Our results suggest that the COM1p may regulate the transcription of genes involved in various cellular processes indispensable for conidial development and appressorial penetration. These functions are likely to contribute to the effects of COM1p upon the aberrant phenotypes of M. oryzae.ReviewersThis article is reviewed by George V. Shpakovski, Karthikeyan Sivaraman (nominated by M. Madan Babu) and Lakshminarayan M. Iyer. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4132377 Tue, 02 Nov 2010 00:00:00 +0100 4132377 Riboswitches as hormone receptors: Hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana http://www.medworm.com/index.php?rid=4085507&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F60 This article was reviewed by Anthony Poole, Rob Knight, Mikhail Gelfand. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4085507 Tue, 19 Oct 2010 23:00:00 +0100 4085507 The calculation of information and organismal complexity http://www.medworm.com/index.php?rid=4059584&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F59 Conclusions: The effective information can be used as a quantitative measure of phenotypic complexity of living organisms and also as an estimate of functional fraction of genome.Reviewers: This article was reviewed by Dr. Lavanya Kannan (nominated by Dr. Arcady Mushegian), Dr. Chao Chen, and Dr. ED Rietman (nominated by Dr. Marc Vidal). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4059584 Mon, 11 Oct 2010 23:00:00 +0100 4059584 Application of computational approaches to study signalling networks of nuclear and Tyrosine kinase receptors http://www.medworm.com/index.php?rid=4055278&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F58 Conclusions: We infer that the NR-RTK interaction network is scale-free topology. We also uncovered the key receptors mediating the signal transduction between these two types of receptors. Furthermore, NR-RTK database is expected to be useful for researchers working on various aspects of the molecular basis of signal transduction by RTKs and NRs.Reviewers:This article was reviewed by Professor Paul Harrison (nominated by Dr. Mark Gerstein), Dr. Arcady Mushegian and Dr. Anthony Almudevar. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4055278 Sun, 10 Oct 2010 23:00:00 +0100 4055278 The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms http://www.medworm.com/index.php?rid=4035617&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F57 Conclusions: The close genetic resemblance to Italians accords with the historical presumption that Ashkenazi Jews started their migrations across Europe in Italy and with historical evidence that conversion to Judaism was common in ancient Rome. The reasons for the discrepancy between the biparental markers and the uniparental markers are discussed.Reviewers: This article was reviewed by Damian Labuda (nominated by Jerzy Jurka), Kateryna Makova and Qasim Ayub (nominated by Dan Graur). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=4035617 Tue, 05 Oct 2010 23:00:00 +0100 4035617 Relating underrepresented genomic DNA patterns and tiRNAs: the rule behind the observation and beyond http://www.medworm.com/index.php?rid=3992536&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F56 Conclusions: The presented results seem to support the emerging model of the RNA-driven eukaryotic gene expression control. Beyond that, the model detects spanion clusters at genetic positions where no tiRNA counterpart was considered and reported. The GO-term analysis of genes with high concentration of spanion clusters in their promoter proximal region indicates involvement in gene regulatory processes. The results of the analysis suggest that the gene regulatory potential of the small non-coding RNAs is grossly underestimated at present.ReviewersThis article was reviewed by Frank Eisenhaber, Sandor Pongor and Rotem Sorek(nominated by Doron Lancet). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3992536 Tue, 21 Sep 2010 23:00:00 +0100 3992536 Asymmetric and non-uniform evolution of recently duplicated human genes http://www.medworm.com/index.php?rid=3945994&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F54 Conclusions: The increase of negative selection pressure over time after a duplication event seems to be a major trend in the evolution of human paralogous gene families. The observed asymmetry in the evolution of paralogous genes shows that in many cases one of two gene copies remains practically unchanged, while the other accumulates functional substitutions. This supports the hypothesis that slowly evolving gene copies preserve their original functions, while fast evolving copies obtain new specificities or functions.ReviewersThis article was reviewed by Dr. Igor Rogozin (nominated by Dr. Arcady Mushegian), Dr. Fyodor Kondrashov, and Dr. Sergei Maslov. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3945994 Tue, 07 Sep 2010 23:00:00 +0100 3945994 Uniting sex and eukaryote origin in an emerging oxygenic world http://www.medworm.com/index.php?rid=3895225&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F53 Background: Theories about eukaryote origin (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. Models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. Sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories about eukaryogenesis. The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure.Presentation of the hypothesisWe propose that a local rise... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3895225 Sun, 22 Aug 2010 23:00:00 +0100 3895225 Measuring gene expression divergence: the distance to keep http://www.medworm.com/index.php?rid=3830895&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F51 Conclusions: Different trends exist in the high-dimensional numeric data, and to highlight a particular trend an appropriate distance measure needs to be chosen. The choice of the distance measure for measuring expression divergence can be dictated by the expression patterns that are of interest in a particular study.Reviewers. This article was reviewed by Mikhail Gelfand, Eugene Koonin and Subhajyoti De (nominated by Sarah Teichmann). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3830895 Thu, 05 Aug 2010 23:00:00 +0100 3830895 A kinetic model of TBP auto-regulation exhibits bistability http://www.medworm.com/index.php?rid=3826479&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F50 Conclusions: Results on the necessity of a minimum basal TBP level support the in vivo observations that TBP is maternally inherited, providing the small amount of TBP required to establish its ubiquitous expression. The model shows that the system is sensitive to variations in parameters indicating that it is vulnerable to mutations in TBP. A reduction in TBP-DNA binding constant can lead the system to a regime where the unviable state is the only steady state. Contrary to the current hypotheses, we show that under some physiological conditions the dimer is not very important in restoring the system to steady state. This model demonstrates the use of mathematical modelling to investigate system behaviour and generate hypotheses governing the dynamics of such nonlinear biological systems.R... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3826479 Wed, 04 Aug 2010 23:00:00 +0100 3826479 Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development http://www.medworm.com/index.php?rid=3822332&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F49 Conclusions: Results and observations presented in this study, allow us to conclude that during evolution, the Wnt5 gene has been duplicated in early vertebrates, and that some paralogs conserved a module within their regulatory region, functionally related to embryonic development of pancreas. Interestingly, our results allowed advancing a possible explanation on why the Wnt5 orthologs do not share the same function during pancreas development. As a final remark, we suggest that an in silico comparative analysis of regulatory regions, especially when associated to published experimental data, represents a powerful approach for explaining shift of roles among paralogs.ReviewersThis article was reviewed by Sarath Janga (nominated by Sarah Teichmann), Ran Kafri (nominated by Yitzhak Pilpel),... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3822332 Tue, 03 Aug 2010 23:00:00 +0100 3822332 Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis http://www.medworm.com/index.php?rid=3812196&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F48 Conclusions: The prevalence of these predicted biosynthetic pathways in phylogenetically distant, pathogenic or symbiotic bacteria suggests that metabolites synthesized by them might participate in interactions with the host. More generally, these findings point to a complete spectrum of recruitment of AAtRS to various non-ribosomal biosynthetic pathways, ranging from the conventional AAtRS, through closely related paralogous AAtRS dedicated to certain pathways, to highly derived versions of the class-I AAtRS catalytic domain like the CDPSs. Both the conventional AAtRS and their closely related paralogs often provide aminoacylated tRNAs for peptide ligations by MprF/Fem/MurM-type acetyltransferase fold ligases in the synthesis of peptidoglycan, N-end rule modifications of proteins, lipid a... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3812196 Sun, 01 Aug 2010 23:00:00 +0100 3812196 Some considerations for analyzing biodiversity using integrative metagenomics and gene networks http://www.medworm.com/index.php?rid=3805370&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F47 This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3805370 Thu, 29 Jul 2010 23:00:00 +0100 3805370 Opportunities and challenges for digital morphology http://www.medworm.com/index.php?rid=3729380&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F45 This article was reviewed by Marc D. Sutton (nominated by Stephan Beck), Gonzalo Giribet (nominated by Lutz Walter), and Lennart Olsson (nominated by Purificacion Lopez-Garcia). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3729380 Mon, 05 Jul 2010 23:00:00 +0100 3729380 Save the tree of life or get lost in the woods http://www.medworm.com/index.php?rid=3717906&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F44 Conclusions: The tree of life is alive, but not well. Construction of the tree of cells has been viewed as the end goal of the study of evolution, where in reality we need to consider it more of a starting point. We propose a duality where we must consider variation of genetic material in terms of networks and selection of cellular function in terms of trees. Otherwise one gets lost in the woods of neutral evolution.ReviewersThis article was reviewed by Dr. Eric Bapteste, Dr. Arcady Mushegian, and Dr. Celine Brochier. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3717906 Wed, 30 Jun 2010 23:00:00 +0100 3717906 Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains http://www.medworm.com/index.php?rid=3713521&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F43 Conclusion: Based on this relationship and the phyletic patterns of these enzymes we infer that the Thg1 protein is likely to represent an archaeo-eukaryotic branch of the same clade of proteins that gave rise to the mobile CRISPR polymerases and in bacteria spawned the GGDEF domains. Thg1 is likely to be close to the ancestral version of this family of enzymes that might have played a role in RNA repair in the last universal common ancestor.ReviewersThis article was reviewed by S. Balaji and V.V. Dolja. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3713521 Tue, 29 Jun 2010 23:00:00 +0100 3713521 Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms http://www.medworm.com/index.php?rid=3709938&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F42 This article was reviewed by John Logsdon, Arcady Mushegian, and Patrick Forterre. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3709938 Mon, 28 Jun 2010 23:00:00 +0100 3709938 An age-dependent branching process model for the analysis of CFSE-labeling experiments http://www.medworm.com/index.php?rid=3686575&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F41 Conclusions: The proposed model offers a widely applicable approach to the analysis of CFSE-labeling experiments. The model fitted very well our experimental data. It provided reasonable estimates of cell kinetics parameters as well as meaningful insights into the processes of cell division and cell death. In contrast, the competing risk branching process could not describe the kinetics of CD8+ T cells. This suggested that the decision of cell division or cell death may be made early in the cell cycle if not in preceding generations. Also, we show that analyses based on the proposed model are robust with respect to cross-sectional dependencies and to dependencies between fates of linearly filiated cells.Reviewers: This article was reviewed by Marek Kimmel, Wai-Yuan Tan and Peter Olofsson. ... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3686575 Mon, 21 Jun 2010 23:00:00 +0100 3686575 Co-lethality studied as an asset against viral drug escape: the HIV protease case http://www.medworm.com/index.php?rid=3670804&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F40 Conclusions: These three replication-critical targets, located outside of the active site, are key to our anti-escape strategy. Indeed, biological evidence shows that 2/3 of those target positions perform essential biological functions. Their mutational variations to escape antiviral medication could be lethal, thus limiting the apparition of drug-resistant strains.ReviewersThis article was reviewed by Arcady Mushegian, Shamil Sunyaev and Claus Wilke. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3670804 Wed, 16 Jun 2010 23:00:00 +0100 3670804 Undetected antisense tRNAs in mitochondrial genomes? http://www.medworm.com/index.php?rid=3665421&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F39 Conclusions: These properties correlate as if they adaptively coevolved for translational activity by some antisense tRNAs, and to avoid such activity by other antisense tRNAs. Analyses also suggest previously unsuspected particularities of aminoacylation specificity in mt tRNAs: combinations of competition between tRNAs on tRNA synthetases with competition between tRNA synthetases on tRNAs determine specificities of tRNA amino acylations. The latter analyses show that alignment methods used to detect tRNA cognates yield relatively robust results, even when they apparently fail to detect the tRNA's cognate amino acid and indicate high misacylation potential.ReviewersThis article was reviewed by Dr Juergen Brosius, Dr Anthony M Poole and Dr Andrei S Rodin (nominated by Dr Rob Knight). (Sour... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3665421 Tue, 15 Jun 2010 23:00:00 +0100 3665421 Spontaneous chiral symmetry breaking in early molecular networks http://www.medworm.com/index.php?rid=3606977&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F38 Conclusion: It follows that chiral selection may be an emergent consequence of early mutually catalytic molecular networks rather than a prerequisite for the initiation of primeval life processes. Elaborations of this model could help explain the prevalent chiral homogeneity in present-day living cells.Reviewers: This article was reviewed by Boris Rubinstein (nominated by Arcady Mushegian), Arcady Mushegian, Meir Lahav (nominated by Yitzhak Pilpel) and Sergei Maslov. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3606977 Wed, 26 May 2010 23:00:00 +0100 3606977 Genome factor and gene pleiotropy hypotheses in protein evolution http://www.medworm.com/index.php?rid=3595028&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F37 This article was reviewed by Dr Eugene Koonin, Dr Arcady Mushegian and Dr Claus Wilke (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3595028 Sun, 23 May 2010 23:00:00 +0100 3595028 GTPases and the origin of the ribosome http://www.medworm.com/index.php?rid=3584911&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F36 Conclusion: The evolution of translational GTPases of both the Archaea and Bacteria point to the evolution of the ribosome. The elongation factors, EFTu/EF1, began as a Ras-like GTPase bringing the activated minihelix tRNA to the Large Subunit Unit. The initiation factors and elongation factor would then have evolved from the EFTu/EF1 as the small subunit was added to the evolving ribosome. The SRP has an SRP54 GTPase and a specific RNA fold in its RNA component similar to the PTC. We consider the SRP to be a remnant of an ancient form of an LSU bound to a membrane.Reviewers: This article was reviewed by George Fox, Leonid Mirny and Chris Sander. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3584911 Wed, 19 May 2010 23:00:00 +0100 3584911 Selection for the compactness of highly expressed genes in Gallus gallus http://www.medworm.com/index.php?rid=3563283&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F35 Conclusion: Natural selection appears to favor the compactness of highly expressed genes in chicken genome. This observation can be explained by the selection of economy model.Reviewers: This article was reviewed by Dr. Gavin Huttley, Dr. Liran Carmel (nominated by Dr. Eugene V. Koonin) and Dr. Araxi Urrutia (nominated by Dr. Laurence D. Hurst). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3563283 Thu, 13 May 2010 23:00:00 +0100 3563283 Modularity and anti-modularity in networks with arbitrary degree distribution http://www.medworm.com/index.php?rid=3541901&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F32 Conclusions: Growing networks with specified characters (degree distribution and modularity) provides the opportunity to create surrogates for biological and technological networks, and to test hypotheses about the processes that gave rise to them. We find that many celebrated network properties may be a consequence of the way in which these networks grew, rather than a necessary consequence of how they work or function. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3541901 Wed, 05 May 2010 23:00:00 +0100 3541901 Disruption of a Quorum Sensing mechanism triggers tumorigenesis: a simple discrete model corroborated by experiments in mammary cancer stem cells http://www.medworm.com/index.php?rid=3486233&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F20 Conclusions: This study suggests that stem cell immortalization may be triggered by reduced intercellularcommunication, rather than exclusively result from somatic evolution, and implies that stem cell proliferationcan be attenuated by signal manipulation, or enhanced by cytotoxics targeted to differentiated cells. In vivoverification and identification of the QS mediating molecules will pave the way to a higher level control of stemcell proliferation in cancer and in tissue engineering.Reviewers: This article was reviewed by Glenn Webb and Marek Kimmel (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486233 Mon, 19 Apr 2010 23:00:00 +0100 3486233 Selection in spatial stochastic models of cancer: Migration as a key modulator of fitness http://www.medworm.com/index.php?rid=3486232&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F21 Conclusions: These models can help explain the many examples in the biological literature, where genes involved in a cell's migratory and invasive machinery are also associated with increased cellular fitness, even though there is no known direct effect of these genes on the cellular reproduction. The models can also help to explain how chemotherapy may provide a selection mechanism for highly invasive phenotypes.Reviewers: This article was reviewed by Mark Kimmel and Glenn Webb. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486232 Mon, 19 Apr 2010 23:00:00 +0100 3486232 Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity http://www.medworm.com/index.php?rid=3486231&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F22 Conclusions: Model simulations demonstrate that repeated episodes of transient systemic acidosis will interrupt critical evolutionary steps in the later stages of carcinogenesis resulting in substantial delay in the evolution to the invasive phenotype. Our results suggest transient systemic acidosis may mediate the observed reduction in cancer risk associated with increased physical activity.Reviewers: This article was reviewed by Natalia Komarova (nominated by Marek Kimmel), Heiko Enderling(nominated by Marek Kimmel), Mark Little (nominated by Marek Kimmel) and Yang Kuang. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486231 Mon, 19 Apr 2010 23:00:00 +0100 3486231 Tumor morphological evolution: directed migration and gain and loss of the self-metastatic phenotype http://www.medworm.com/index.php?rid=3486230&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F23 Conclusions: We show that invasive clustering can derive from basic kinetic assumptions often neglected in more complex models. While higher-order mechanisms, e.g. directed migration upon chemotactic stimuli, may result in clustering growth morphologies, exclusive attributions of this phenotype to this or other structured microenvironments would be inappropriate, in light of our finding these features are observable in a homogeneous environment. Furthermore, directed migration will result in loss of the invasive phenotype as the tumor approaches the attractor source.Reviewers: This article was reviewed by Mark Little and Glen Webb. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486230 Mon, 19 Apr 2010 23:00:00 +0100 3486230 The evolutionary impact of androgen levels on prostate cancer in a multi-scale mathematical model http://www.medworm.com/index.php?rid=3486229&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F24 Conclusions: The model represents a useful initial framework for understanding the role of androgens in prostate cancer etiology, and it suggests that low androgen levels can increase selection for phenotypes resistant to hormonal therapy that may also be more aggressive. Moreover, clinical treatment with 5alpha-reductase inhibitors such as finasteride may increase the incidence of therapy resistant cancers.Reviewers: This article was reviewed by Ariosto S. Silva (nominated by Marek Kimmel) and Marek Kimmel. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486229 Mon, 19 Apr 2010 23:00:00 +0100 3486229 A theoretical quantitative model for evolution of cancer chemotherapy resistance http://www.medworm.com/index.php?rid=3486228&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F25 Conclusions: These results suggest that the maximum potential of a combined therapy may depend on how each of the drugs modifies the evolutionary landscape and that a rational use of these properties may prevent or at least delay relapse.Reviewers: This article was reviewed by Dr Marek Kimmel and Dr Mark Little. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486228 Mon, 19 Apr 2010 23:00:00 +0100 3486228 A new stochastic and state space model of human colon cancer incorporating multiple pathways http://www.medworm.com/index.php?rid=3486227&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F26 Conclusions: Our results indicate that the model not only provides a logical avenue to incorporate biological information but also fits the data much better than other models including the 4-stage single pathway model. This model not only would provide more insights into human colon cancer but also would provide useful guidance for its prevention and control and for prediction of future cancer cases.Reviewers: This article was reviewed by M.P. Little,and M. Kimmel (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486227 Mon, 19 Apr 2010 23:00:00 +0100 3486227 Oscillatory dynamics in a model of vascular tumour growth - implications for chemotherapy http://www.medworm.com/index.php?rid=3486226&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F27 Conclusions: We have developed a mathematical model of vascular tumour growth formulated as a system of partial differential equations (PDEs). Employing a combination of numerical and analytical techniques, we demonstrate how the spatio-temporal dynamics of the untreated tumour may influence its response to chemotherapy.Reviewers: This manuscript was reviewed by Professor Zvia Agur and Professor Marek Kimmel. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486226 Mon, 19 Apr 2010 23:00:00 +0100 3486226 A mathematical model of bone remodeling dynamics for normal bone cell populations and myeloma bone disease http://www.medworm.com/index.php?rid=3486225&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F28 Conclusions: The curent model accurately reflects myeloma bone disease and illustrates how treatment approaches may be investigated using such computational approaches.Reviewers: This article was reviewed by Ariosto Silva and Mark P. Little (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486225 Mon, 19 Apr 2010 23:00:00 +0100 3486225 Evolution and cancer: a mathematical biology approach http://www.medworm.com/index.php?rid=3486224&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F29 This thematic series is concerned with various ways Evolution is intertwined with cancer. A group of cancer researchers and mathematical modelers, with an interest in the subject, was invited to contribute papers on topics ranging from carcinogenesis through progression of cancer through therapy. The resulting collection of ten papers is briefly introduced below. Publication of the series was planned to coincide with Darwin's Year, 2009, however various obstacles delayed publication.Mathematical modeling of processes related to cancer evolution has come of age. What used to be a mathematical metaphor or speculation, has become progressively more infused with genetic and biological details and is reconcilable with epidemiology of a given cancer. The seminal biological discoveries, which lea... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3486224 Mon, 19 Apr 2010 23:00:00 +0100 3486224 The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain http://www.medworm.com/index.php?rid=3459732&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F17 This article was reviewed by Zvi Kelman (nominated by Michael Galperin) and Kira Makarova. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3459732 Sun, 11 Apr 2010 23:00:00 +0100 3459732 The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA? http://www.medworm.com/index.php?rid=3453086&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F16 This article was reviewed by Eugene Koonin, Rob Knight and Berthold Kastner (nominated by Laura Landweber). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3453086 Thu, 08 Apr 2010 23:00:00 +0100 3453086 The evolution and functional repertoire of translation proteins following the origin of life http://www.medworm.com/index.php?rid=3448181&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F15 Conclusions: We propose that this early robust translation system evolved by virtue of a positive feedback cycle in which the system was able to create increasingly complex proteins to further enhance its own function.ReviewersThis article was reviewed by Janet Siefert, George Fox, and Antonio Lazcano (nominated by Laura Landweber) (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3448181 Wed, 07 Apr 2010 23:00:00 +0100 3448181 OST-HTH: a novel predicted RNA-binding domain http://www.medworm.com/index.php?rid=3385100&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F13 Conclusions: Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized domain (DUF88). We present evidence that it is an RNAse belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains and might be recruited to degrade certain RNAs.ReviewersThis article was reviewed by Sandor Pongor... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3385100 Fri, 19 Mar 2010 00:00:00 +0100 3385100 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve http://www.medworm.com/index.php?rid=3279415&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F10 Conclusion: The "genome order index" S does not represent a constraint on nucleotide composition. Moreover, S can be easily computed from the Gini-Simpson index and be directly derived from entropy and is redundant. Overall, the Z-curve and S are over-complicated measures to GC content and Shannon H index, respectively.Reviewers:This article was reviewed by Claus Wilke, Joel Bader, Marek Kimmel and Uladzislau Hryshkevich( nominated by Itai Yanai). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3279415 Wed, 17 Feb 2010 00:00:00 +0100 3279415 Proteome changes of Caenorhabditis elegans upon a Staphylococcus aureus infection http://www.medworm.com/index.php?rid=3279414&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F11 Conclusions: Exploring four time-points discloses a dynamic insight of the reaction against a gram-positive infection at the level of the whole organism. The remarkable upregulation after 8h and 24h of many enzymes involved in the citric acid cycle might illustrate the cost of fighting off an infection. Intriguing is the downregulation of chaperone molecules, which are presumed to serve a protective role. A comparison with a similar experiment in which C. elegans was infected with the gram-negative Aeromonas hydrophila reveals that merely 9% of the identified spots, some of which even exhibiting an opposite regulation, are present in both studies. Hence, our findings emphasise the complexity and pathogen-specificity of the worm's immune response and form a firm basis for future functional ... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3279414 Wed, 17 Feb 2010 00:00:00 +0100 3279414 FOXP3 and GARP (LRRC32): the master and its minion http://www.medworm.com/index.php?rid=3243136&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F8 The transcription factor FOXP3 is essential for the development and function of CD4+CD25hiFOXP3+ regulatory T (Treg) cells, but also expressed in activated human helper T cells without acquisition of a regulatory phenotype. This comment focuses on glycoprotein-A repetitions predominant (GARP or LRRC32) recently identified as specific marker of activated human Treg cells, which may provide the missing link toward a better molecular definition of the regulatory phenotype.Reviewers: Dr Jim Di Danto, Dr Benedita Rocha and Dr Werner Solbach. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3243136 Fri, 05 Feb 2010 00:00:00 +0100 3243136 Low level of polymorphism in two putative NPR1 homologs in the Vitaceae family http://www.medworm.com/index.php?rid=3243135&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F9 Conclusion: Our study shows that NPR1.1 and NPR1.2 are highly conserved among different accessions in the Vitaceae family. VvNPR1.1 and VvNPR1.2 are phylogenetically closer to the group of positive or negative SAR regulators respectively. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3243135 Fri, 05 Feb 2010 00:00:00 +0100 3243135 Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics data http://www.medworm.com/index.php?rid=3207822&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F6 Conclusions: We present evidence supporting the notion that clusters of pS/pT but generally not pY should be considered as the elementary building blocks in phosphorylation regulation. Indeed, closely positioned sites tend to be activated by the same kinase, a signal that overrides the tendency of a protein to be activated by a single or only few kinases. Within these clusters, coordination and positional dependency is evident. We postulate that cellular regulation takes advantage of such design. Specifically, phosphosite clusters may increase the robustness of the effectiveness of phosphorylation-dependent response.Reviewers: Reviewed by Joel Bader, Frank Eisenhaber, Emmanuel Levy (nominated by Sarah Teichmann). For the full reviews, please go to the Reviewers' comments section. (Source: ... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3207822 Tue, 26 Jan 2010 00:00:00 +0100 3207822 Rate of sequence divergence under constant selection http://www.medworm.com/index.php?rid=3193107&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F5 Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.ReviewersThis article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3193107 Thu, 21 Jan 2010 00:00:00 +0100 3193107 Including RNA Secondary Structures improves Accuracy and Robustness in Reconstruction of Phylogenetic Trees http://www.medworm.com/index.php?rid=3175225&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F4 Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion.Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3175225 Fri, 15 Jan 2010 00:00:00 +0100 3175225 Elastic, not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organisms http://www.medworm.com/index.php?rid=3166537&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F2 Conclusion: Frozen plasticity theory, which includes the Darwinian model of evolution as a special case - the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories.Reviewers: This article was reviewed by Rob Knight, Fyodor Kondrashov and Massimo Di Giulio (nominated by David H. Ardell). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3166537 Wed, 13 Jan 2010 00:00:00 +0100 3166537 Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species http://www.medworm.com/index.php?rid=3166536&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F3 This article was reviewed by Celine Brochier-Armanet, Igor B. Zhulin and Mikhail Gelfand. For the full reviews, please go to the Reviewers' reports section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3166536 Wed, 13 Jan 2010 00:00:00 +0100 3166536 Novel eukaryotic enzymes modifying cell-surface biopolymers http://www.medworm.com/index.php?rid=3152844&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F5%2F1%2F1 Conclusions: We posit that the combined action of the acyltransferase and esterase domain plays an important role in controlling the acylation levels of glycans and thereby regulates their physico-chemical properties such as hygroscopicity, resistance to enzymatic hydrolysis and physical strength. We present evidence that the action of these novel enzymes on glycans might play an important role in host-pathogen interaction of plants, fungi and metazoans. We present evidence that in plants (e.g. PMR5 and ESK1) the regulation of carbohydrate acylation by these acylesterases might also play an important role in regulation of transpiration and stress resistance. We also identify a subfamily of these esterases in metazoans (e.g. C7orf58), which are fused to an ATP-grasp amino acid ligase domain... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3152844 Thu, 07 Jan 2010 00:00:00 +0100 3152844 Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity http://www.medworm.com/index.php?rid=3104503&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F51 Conclusions: Examination of phyletic patterns and phylogenetic analysis of DNA ligases of the NCLDV suggest that the common ancestor of the extant NCLDV encoded an NAD-dependent ligase that most likely was acquired from a bacteriophage at the early stages of evolution of eukaryotes. By contrast, ATP-dependent ligases from different prokaryotic and eukaryotic sources displaced the ancestral NAD-dependent ligase at different stages of subsequent evolution. These findings emphasize complex routes of viral evolution that become apparent through detailed phylogenomic analysis but not necessarily in reconstructions based on phyletic patterns of genes.Reviewers: This article was reviewed by: Patrick Forterre, George V. Shpakovski, and Igor B. Zhulin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3104503 Fri, 18 Dec 2009 00:00:00 +0100 3104503 Mass action models versus the Hill model: An analysis of tetrameric human thymidine kinase 1 positive cooperativity http://www.medworm.com/index.php?rid=3070536&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F49 Conclusions: The TK1 model presented supports both K and k positive cooperativity. Three-parameter mass action models can and should replace the 3-parameter Hill model.ReviewersThis article was reviewed by Philip Hahnfeldt, Fangping Mu (nominated by William Hlavacek) and Rainer Sachs. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3070536 Wed, 09 Dec 2009 00:00:00 +0100 3070536 Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: An analysis of ATP-induced ribonucleotide reductase R1 hexamerization data http://www.medworm.com/index.php?rid=3070535&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F50 Conclusions: The analysis presented suggests that three a-sites may not be occupied by ATP in R1 hexamers under the conditions of the data analyzed. If a-sites fill before h-sites, this implies that the dataset analyzed can be explained without the existence of an h-site.ReviewersThis article was reviewed by Ossama Kashlan (nominated by Philip Hahnfeldt), Bin Hu (nominated by William Hlavacek) and Rainer Sachs. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3070535 Wed, 09 Dec 2009 00:00:00 +0100 3070535 Depauperate genetic variability detected in the American and European bison using genomic techniques http://www.medworm.com/index.php?rid=3066414&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F48 This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3066414 Tue, 08 Dec 2009 00:00:00 +0100 3066414 Human gamma/delta T cell Recognition of lipid A is predominately presented by CD1b or CD1c on dendritic cells http://www.medworm.com/index.php?rid=3043937&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F47 Conclusions: Taken together, we found a novel mechanism that human gamma/delta T cells recognize LA in a CD1b- or CD1c-restricted manner in first response against Gram- bacteria, while the interaction between TLR4 on gamma/delta T cells and LA might strengthen the subsequent response of gamma/delta T cells.Reviewers: This article was reviewed by Dr.Youwen He (nominated by Dr.Laurence C Eisenlohr),Dr.Hao Shen,Dr.Michael Lenardo and Dr. Pushpa Pandiyan. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3043937 Tue, 01 Dec 2009 00:00:00 +0100 3043937 Evolution by leaps: gene duplication in bacteria http://www.medworm.com/index.php?rid=3022439&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F46 Conclusions: Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.REVIEWERS This article was reviewed by Drs. Iyer Aravind, Arcady Mushegian, and Pierre Pontarotti. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=3022439 Mon, 23 Nov 2009 00:00:00 +0100 3022439 Exceptional error minimization in putative primordial genetic codes http://www.medworm.com/index.php?rid=3007441&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F44 Conclusions: The results of the computational experiments with putative primordial genetic codes that contained only two meaningful letters in all codons and encoded 10 to 16 amino acids indicate that such codes are likely to have been nearly optimal with respect to the minimization of translation errors. This near-optimality could be the outcome of extensive early selection during the co-evolution of the code with the primordial, error-prone translation system, or a result of a unique, accidental event. Under this hypothesis, the subsequent expansion of the code resulted in a decrease of the error minimization level that became sustainable owing to the evolution of a high-fidelity translation system.Reviewers: This article was reviewed by Paul Higgs (nominated by Arcady Mushegian), Rob Kn... Biology Direct journals http://www.medworm.com/rss/comments.php?id=3007441 Thu, 19 Nov 2009 00:00:00 +0100 3007441 Trees and networks before and after Darwin http://www.medworm.com/index.php?rid=2995264&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F43 This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2995264 Mon, 16 Nov 2009 00:00:00 +0100 2995264 Is evolution Darwinian or/and Lamarckian? http://www.medworm.com/index.php?rid=2984339&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F42 Conclusions: Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment.Reviewers: this article was reviewed by Juergen Brosius, Valerian Dolja, and Martijn Huynen. For complete reports, see the Reviewers' reports section. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2984339 Wed, 11 Nov 2009 00:00:00 +0100 2984339 CD44 expression positively correlates with Foxp3 expression and suppressive function of CD4+ Treg cells http://www.medworm.com/index.php?rid=2922984&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F40 Conclusions: This study indicates the presence of two novel phenotypes of Treg cells in the thymus, the functional relevance of CD44 in defining Treg cell subsets, and the role of both IL-10 and Foxp3 in modulating the function of Treg cells. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2922984 Thu, 22 Oct 2009 23:00:00 +0100 2922984 Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea http://www.medworm.com/index.php?rid=2893816&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F39 This article was reviewed by Andrei Osterman and Patrick Forterre (nominated by Purificacion Lopez-Garcia) (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2893816 Tue, 13 Oct 2009 23:00:00 +0100 2893816 Strong association between pseudogenization mechanisms and gene sequence length http://www.medworm.com/index.php?rid=2865132&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F38 This article was reviewed by Dr. Dan Graur and Dr. Craig Nelson (nominated by Dr. J Peter Gogarten). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2865132 Mon, 05 Oct 2009 23:00:00 +0100 2865132 Correction: Hypothesis for heritable, anti-viral immunity in crustaceans and insects http://www.medworm.com/index.php?rid=2850849&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F36 Correction to Flegel, TW: Hypothesis for heritable, anti-viral immunity in crustaceans and insects. Biology Direct 2009, 4:32. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2850849 Wed, 30 Sep 2009 23:00:00 +0100 2850849 The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum http://www.medworm.com/index.php?rid=2842003&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F33 Conclusions: A logical analysis of the units and processes of biological evolution suggests thatthe natural fundamental unit of evolution is a FUE, that is, a genetic element with an independent evolutionary history. Evolution of a FUE on the macro scale is naturally represented by a tree. Only the full compendium of trees for individual FUEs (the FOL) is an adequate depiction of the evolution of life. Coherent evolution of FUEs over extended evolutionary intervals is a crucial aspect of the history of life but a "species" or "organismal" tree is not a fundamental concept.Reviewers: This articles was reviewed by Valerian Dolja, W. Ford Doolittle, Nicholas Galtier, and William Martin (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2842003 Mon, 28 Sep 2009 23:00:00 +0100 2842003 Prokaryotic evolution and the tree of life are two different things http://www.medworm.com/index.php?rid=2842002&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F34 Conclusions: Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.ReviewersThis article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2842002 Mon, 28 Sep 2009 23:00:00 +0100 2842002 Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria http://www.medworm.com/index.php?rid=2842001&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F35 Conclusions: Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution.ReviewersThis article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2842001 Mon, 28 Sep 2009 23:00:00 +0100 2842001 Hypothesis for heritable, anti-viral immunity in crustaceans and insects http://www.medworm.com/index.php?rid=2757064&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F32 Conclusions: This hypothesis for immunity based on an imRNA generation mechanism fits with the general principle of invertebrate immunity based on a non-host, "pattern recognition" process. If proven correct, understanding the process would allow directed preparation of vaccines for selection of crustacean and insect lines applicable in commercial production species (e.g., shrimp and bees) or in control of insect-borne diseases. Arising from a natural host mechanism, the resulting animals would not be artificially, genetically modified (GMO).ReviewersThis article was reviewed by Akria Shibuya, Eugene V. Koonin and L. Aravind. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2757064 Tue, 01 Sep 2009 23:00:00 +0100 2757064 Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life http://www.medworm.com/index.php?rid=2733562&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F30 Conclusions: We conclude that there is no contradiction between the polarization datasets. The combination of these datasets excludes the root from every possible position except near the Chloroflexi.ReviewersThis article was reviewed by Greg Fournier (nominated by J. Peter Gogarten), Purificacion Lopez-Garcia, and Eugene Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2733562 Mon, 24 Aug 2009 23:00:00 +0100 2733562 On the need for widespread horizontal gene transfers under genome size constraint http://www.medworm.com/index.php?rid=2729518&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F28 This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2729518 Mon, 24 Aug 2009 23:00:00 +0100 2729518 Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements http://www.medworm.com/index.php?rid=2729517&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F29 Conclusions: The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements implies a functional analogy with the prokaryotic CASS and a direct evolutionary connection with eukaryotic RNAi. The predictions of the hypothesis including both the activities of pAgos and those of the associated endonucleases are readily amenable to experimental tests.ReviewersThis article was reviewed by Daniel Haft, Martijn Huynen, and Chris Ponting. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2729517 Mon, 24 Aug 2009 23:00:00 +0100 2729517 On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth http://www.medworm.com/index.php?rid=2818984&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F26 Conclusion: The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms.ReviewersThis paper was reviewed by Arcady Mushegian, Simon Silver (nominated by Arcady Mushegian), Antoine Danchin (nominated by Eugene Koonin) and Dieter Braun (nominated by Sergey Maslov). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2818984 Sun, 23 Aug 2009 23:00:00 +0100 2818984 The Anabaenasensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains http://www.medworm.com/index.php?rid=2774317&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F25 This article was reviewed by M. Madan Babu and Mark A. Ragan. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2774317 Thu, 13 Aug 2009 23:00:00 +0100 2774317 Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea http://www.medworm.com/index.php?rid=2653192&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F24 This article was reviewed by Chris P. Ponting and Eugene V. Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2653192 Tue, 28 Jul 2009 23:00:00 +0100 2653192 Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas http://www.medworm.com/index.php?rid=2625323&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F23 Conclusions: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection.ReviewersThis article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2625323 Mon, 20 Jul 2009 23:00:00 +0100 2625323 Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance http://www.medworm.com/index.php?rid=2521835&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F21 Conclusion: The pararetroviral sequences in plant genomes may be maintained due to the benefits of virus resistance to this class of viruses conferred by their presence. Such resistance could be particularly significant for the woody plants that must withstand years- to centuries-long virus assault. Experimental research into the RNA interference pathways involving the integrated pararetroviral inserts is required to test this hypothesis.ReviewersThis article was reviewed by Arcady R. Mushegian, I. King Jordan, and Eugene V. Koonin. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2521835 Thu, 25 Jun 2009 23:00:00 +0100 2521835 Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates http://www.medworm.com/index.php?rid=2503893&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F20 Conclusions: Our results indicate that unequal substitution rates among different sites have variable influences on omega under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure omega.ReviewersThis paper was reviewed by Kateryna Makova, David A. Liberles (nominated by David H Ardell), Zhaolei Zhang (nominated by Mark Gerstein), and Shamil Sunyaev. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2503893 Mon, 15 Jun 2009 23:00:00 +0100 2503893 Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes http://www.medworm.com/index.php?rid=2455984&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F19 Conclusions: The defining properties of the TAS, namely, the typically small size of the toxin and antitoxin genes, fast evolution, and extensive horizontal mobility, make the task of comprehensive identification of these systems particularly challenging. However, these same properties can be exploited to develop context-based computational approaches which, combined with exhaustive analysis of subtle sequence similarities were employed in this work to substantially expand the current collection of TAS by predicting both previously unnoticed, derived versions of known toxins and antitoxins, and putative novel TAS-like systems. In a broader context, the TAS belong to the resistome domain of the prokaryotic mobilome which includes partially selfish, addictive gene cassettes involved in vario... Biology Direct journals http://www.medworm.com/rss/comments.php?id=2455984 Wed, 03 Jun 2009 04:00:00 +0100 2455984 Chaotic expression dynamics implies pluripotency: when theory and experiment meet http://www.medworm.com/index.php?rid=2413141&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F17 This article was reviewed by David Krakauer, Jeroen van Zon (nominated by Rob de Boer), and Williams S. Hlavacek. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2413141 Fri, 15 May 2009 04:00:00 +0100 2413141 A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs http://www.medworm.com/index.php?rid=2353061&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F15 This article was reviewed by Andrei Osterman and Lakshminarayan Iyer. (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2353061 Tue, 21 Apr 2009 04:00:00 +0100 2353061 Transcript length bias in RNA-seq data confounds systems biology http://www.medworm.com/index.php?rid=2340023&cid=s_34015_62_f&fid=34015&url=http%3A%2F%2Fwww.biology-direct.com%2Fcontent%2F4%2F1%2F14 Conclusions: Transcript length bias for calling differentially expressed genes is a general feature of current protocols for RNA-seq technology. This has implications for the ranking of differentially expressed genes, and in particular may introduce bias in gene set testing for pathway analysis and other multi-gene systems biology analyses. Reviewers: This article was reviewed by Rohan Williams (nominated by Gavin Huttley), Nicole Cloonan (nominated by Mark Ragan) and James Bullard (nominated by Sandrine Dudoit). (Source: Biology Direct) Biology Direct journals http://www.medworm.com/rss/comments.php?id=2340023 Thu, 16 Apr 2009 04:00:00 +0100 2340023