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FOXP3 and GARP (LRRC32): the master and its minionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - February 5, 2010 Category: Biology Authors: Michael Probst-KepperJan Buer Source Type: journals

Low level of polymorphism in two putative NPR1 homologs in the Vitaceae familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - February 5, 2010 Category: Biology Authors: Karine BergeaultChristophe BertschDidier MerdinogluBernard Walter Source Type: journals

Cooperativity within proximal phosphorylation sites is revealed from large-scale proteomics dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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.Review...
Source: Biology Direct - January 26, 2010 Category: Biology Authors: Regev SchweigerMichal Linial Source Type: journals

Rate of sequence divergence under constant selectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - January 21, 2010 Category: Biology Authors: Alexey KondrashovInna PovolotskayaDmitry IvankovFyodor Kondrashov Source Type: journals

Including RNA Secondary Structures improves Accuracy and Robustness in Reconstruction of Phylogenetic TreesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - January 15, 2010 Category: Biology Authors: Alexander KellerFrank ForsterTobias MullerThomas DandekarJoerg SchultzMatthias Wolf Source Type: journals

Elastic, not plastic species: Frozen plasticity theory and the origin of adaptive evolution in sexually reproducing organismsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - January 13, 2010 Category: Biology Authors: Jaroslav Flegr Source Type: journals

Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial speciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - January 13, 2010 Category: Biology Authors: Marc BaillyValerie de Crecy-Lagard Source Type: journals

Novel eukaryotic enzymes modifying cell-surface biopolymersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biology Direct - January 7, 2010 Category: Biology Authors: Vivek AnantharamanL Aravind Source Type: journals

Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 phyl...
Source: Biology Direct - December 18, 2009 Category: Biology Authors: Natalya YutinEugene Koonin Source Type: journals

Mass action models versus the Hill model: An analysis of tetrameric human thymidine kinase 1 positive cooperativityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - December 9, 2009 Category: Biology Authors: Tomas Radivoyevitch Source Type: journals

Automated mass action model space generation and analysis methods for two-reactant combinatorially complex equilibriums: An analysis of ATP-induced ribonucleotide reductase R1 hexamerization dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - December 9, 2009 Category: Biology Authors: Tomas Radivoyevitch Source Type: journals

Depauperate genetic variability detected in the American and European bison using genomic techniquesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev (Source: Biology Direct)
Source: Biology Direct - December 8, 2009 Category: Biology Authors: Cino PertoldiMalgorzata TokarskaJan WojcikDitte DemontisVolker LoeschckeVivi GregersenDavid ColtmanGregory WilsonEttore RandiMichael HansenChristian Bendixen Source Type: journals

Human gamma/delta T cell Recognition of lipid A is predominately presented by CD1b or CD1c on dendritic cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - December 1, 2009 Category: Biology Authors: Yongchun CuiLei KangLianxian CuiWei He Source Type: journals

Evolution by leaps: gene duplication in bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - November 23, 2009 Category: Biology Authors: Margrethe SerresAlastair KerrThomas McCormackMonica Riley Source Type: journals

Exceptional error minimization in putative primordial genetic codesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Biology Direct - November 19, 2009 Category: Biology Authors: Artem NovozhilovEugene Koonin Source Type: journals

Trees and networks before and after DarwinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur. (Source: Biology Direct)
Source: Biology Direct - November 16, 2009 Category: Biology Authors: Mark Ragan Source Type: journals

Is evolution Darwinian or/and Lamarckian?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - November 11, 2009 Category: Biology Authors: Eugene KooninYuri Wolf Source Type: journals

CD44 expression positively correlates with Foxp3 expression and suppressive function of CD4+ Treg cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - October 22, 2009 Category: Biology Authors: Tie LiuLynn SoongGang LiuRolf KonigAshok Chopra Source Type: journals

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 ArchaeaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Andrei Osterman and Patrick Forterre (nominated by Purificacion Lopez-Garcia) (Source: Biology Direct)
Source: Biology Direct - October 13, 2009 Category: Biology Authors: Fabian BlombachKira MakarovaJeannette MarreroBettina SiebersEugene KooninJohn van der Oost Source Type: journals

Strong association between pseudogenization mechanisms and gene sequence lengthEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Dr. Dan Graur and Dr. Craig Nelson (nominated by Dr. J Peter Gogarten). (Source: Biology Direct)
Source: Biology Direct - October 5, 2009 Category: Biology Authors: Amit KhachanePaul Harrison Source Type: journals

Correction: Hypothesis for heritable, anti-viral immunity in crustaceans and insectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Correction to Flegel, TW: Hypothesis for heritable, anti-viral immunity in crustaceans and insects. Biology Direct 2009, 4:32. (Source: Biology Direct)
Source: Biology Direct - September 30, 2009 Category: Biology Authors: Timothy Flegel Source Type: journals

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 D...
Source: Biology Direct - September 28, 2009 Category: Biology Authors: Eugene KooninYuri Wolf Source Type: journals

Prokaryotic evolution and the tree of life are two different thingsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - September 28, 2009 Category: Biology Authors: Eric BaptesteMaureen O'MalleyRobert BeikoMarc EreshefskyJ. Peter GogartenLaura Franklin-HallFrancois-Joseph LapointeJohn DupreTal DaganYan BoucherWilliam Martin Source Type: journals

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - September 28, 2009 Category: Biology Authors: Chih-Horng KuoHoward Ochman Source Type: journals

Hypothesis for heritable, anti-viral immunity in crustaceans and insectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. Aravi...
Source: Biology Direct - September 1, 2009 Category: Biology Authors: Timothy Flegel Source Type: journals

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of lifeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - August 24, 2009 Category: Biology Authors: Ruben ValasPhilip Bourne Source Type: journals

On the need for widespread horizontal gene transfers under genome size constraintEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov. (Source: Biology Direct)
Source: Biology Direct - August 24, 2009 Category: Biology Authors: Herve IsambertRichard Stein Source Type: journals

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elementsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - August 24, 2009 Category: Biology Authors: Kira MakarovaYuri WolfJohn Van der OostEugene Koonin Source Type: journals

On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on EarthEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Biology Direct - August 23, 2009 Category: Biology Authors: Armen Mulkidjanian Source Type: journals

The Anabaenasensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domainsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by M. Madan Babu and Mark A. Ragan. (Source: Biology Direct)
Source: Biology Direct - August 13, 2009 Category: Biology Authors: Robson De SouzaLakshminarayan IyerL Aravind Source Type: journals

Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in ArchaeaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Chris P. Ponting and Eugene V. Koonin. (Source: Biology Direct)
Source: Biology Direct - July 28, 2009 Category: Biology Authors: Jan-Peter DanielsSteven KellyBill WicksteadKeith Gull Source Type: journals

Divergent evolution and purifying selection of the flaA gene sequences in AeromonasEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - July 20, 2009 Category: Biology Authors: Maribel FarfanDavid Minana-GalbisM Carmen FusteJ Gaspar Loren Source Type: journals

Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - June 25, 2009 Category: Biology Authors: Christophe BertschMonique BeuveValerian DoljaMarion WirthFrederique PelsyEtienne HerrbachOlivier Lemaire Source Type: journals

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution ratesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - June 15, 2009 Category: Biology Authors: Da-Peng WangHao-Lei WanSong ZhangJun Yu Source Type: journals

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 syst...
Source: Biology Direct - June 3, 2009 Category: Biology Authors: Kira MakarovaYuri WolfEugene Koonin Source Type: journals

Chaotic expression dynamics implies pluripotency: when theory and experiment meetEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by David Krakauer, Jeroen van Zon (nominated by Rob de Boer), and Williams S. Hlavacek. (Source: Biology Direct)
Source: Biology Direct - May 15, 2009 Category: Biology Authors: Chikara Furusawa and Kunihiko Kaneko Source Type: journals

A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Andrei Osterman and Lakshminarayan Iyer. (Source: Biology Direct)
Source: Biology Direct - April 21, 2009 Category: Biology Authors: Daniel H Haft Source Type: journals

Transcript length bias in RNA-seq data confounds systems biologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Biology Direct - April 16, 2009 Category: Biology Authors: Alicia Oshlack and Matthew J Wakefield Source Type: journals

Massive comparative genomic analysis reveals convergent evolution of specialized bacteriaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution. Reviewers: This article was reviewed by Eugene V. Koonin, Nicolas Galtier, and Jeremy Selengut. (Source: Biology Direct)
Source: Biology Direct - April 10, 2009 Category: Biology Authors: Vicky Merhej, Manuela Royer-Carenzi, Pierre Pontarotti and Didier Raoult Source Type: journals

Correction: Pitfalls of the most commonly used models of context dependent substitutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Correction to Lindsay H, Yap VB, Ying H, Huttley GA: Pitfalls of the most commonly used models of context dependent substitution. Biology Direct 2008, 3:52 (Source: Biology Direct)
Source: Biology Direct - March 18, 2009 Category: Biology Authors: Helen Lindsay, Von Bing Yap, Hua Ying and Gavin A Huttley Source Type: journals

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Evolution of eukaryotic DNA polymerases seems to have involved previously unnoticed complex events. We hypothesize that the archaeal ancestor of eukaryotes encoded three DNA polymerases, namely, two distinct B-family polymerases and a D-family polymerase all of which contributed to the evolution of the eukaryotic replication machinery. The Zn-finger might have been acquired from PolD by the B-family form that gave rise to Pol prior to or in the course of eukaryogenesis, and subsequently, was captured by the ancestor of the other B-family eukaryotic polymerases. The inactivated polymerase-exonuclease module of ...
Source: Biology Direct - March 18, 2009 Category: Biology Authors: Tahir H Tahirov, Kira S Makarova, Igor B Rogozin, Youri I Pavlov and Eugene V Koonin Source Type: journals

The origins of phagocytosis and eukaryogenesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The present findings suggest a hypothetical scenario of eukaryogenesis under which the archaeal ancestor of eukaryotes had no cell wall (like modern Thermoplasma) but had an actin-based cytoskeleton including branched actin filaments that allowed this organism to produce actin-supported membrane protrusions. These protrusions would facilitate accidental, occasional engulfment of bacteria, one of which eventually became the mitochondrion. The acquisition of the endosymbiont triggered eukaryogenesis, in particular, the emergence of the endomembrane system that eventually led to the evolution of modern-type phagoc...
Source: Biology Direct - February 26, 2009 Category: Biology Authors: Natalya Yutin, Maxim Y Wolf, Yuri I Wolf and Eugene V Koonin Source Type: journals

Issues associated with assessing nuclear localization of N-terminally unphosphorylated β-catenin with monoclonal antibody 8E7Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These findings reveal that interpretation of nuclear, signaling active β-catenin using monoclonal antibody 8E7 should be considered judiciously, and in conjunction with independent methods.ReviewersThis article was reviewed by Frank J. T. Staal (nominated by Rachel Gerstein), Jyoti M. Sen (nominated by Avinash Bhandoola) and Manabu Sugai. (Source: Biology Direct)
Source: Biology Direct - February 2, 2009 Category: Biology Authors: Meghan T Maher, Annette S Flozak, Alyssa M Hartsell, Susan Russell, Rohinee Beri, Ofra N Peled and Cara J Gottardi Source Type: journals

Pitfalls of the most commonly used models of context dependent substitutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results establish that the NF form should be used for analysis of independent-tuple context dependent processes. Although neighboring effects in general are still important, prominent influences such as the elevated CpG transversion rate previously identified using the TF form are an artifact. Our results further suggest as few as 5 parameters may account for ~85% of neighboring nucleotide influence. Reviewers: This article was reviewed by Dr Rob Knight, Dr Josh Cherry (nominated by Dr David Lipman) and Dr Stephen Altschul (nominated by Dr David Lipman). (Source: Biology Direct)
Source: Biology Direct - December 16, 2008 Category: Biology Authors: Helen Lindsay, Von Bing Yap, Hua Ying and Gavin A Huttley Source Type: journals

The evolution of domain-content in bacterial genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results establish a direct quantitative connection between the scaling of domain numbers with genome size, and the rate of addition and deletions of domains during short evolutionary time intervals. Reviewers: This article was reviewed by Eugene V. Koonin, Martijn A. Huynen, and Sergei Maslov. (Source: Biology Direct)
Source: Biology Direct - December 11, 2008 Category: Biology Authors: Nacho Molina and Erik van Nimwegen Source Type: journals

Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by L Aravind, Wing-Cheong Wong and Frank Eisenhaber. For the full reviews, please go to the Reviewers' Comments section. (Source: Biology Direct)
Source: Biology Direct - November 25, 2008 Category: Biology Authors: Dapeng Zhang, Huiling Xiong, Jufang Shan, Xuhua Xia and Vance L Trudeau Source Type: journals

On the brink between extinction and persistenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was reviewed by Mark W. Schwartz (nominated by Peter Olofsson), Josef Bryja (nominated by Aniko Szabo) and Wai-YuanTan. For the full reviews, please go to the Reviewers' Comments section. (Source: Biology Direct)
Source: Biology Direct - November 19, 2008 Category: Biology Authors: Cino Pertoldi, Lars A Bach and Volker Loeschcke Source Type: journals

Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These analyses show that editing mostly affects functionally important and evolutionarily conserved codon positions, codons and genes encoding membrane-bound proteins. In particular, abundance of RNA editing in plant organellar genomes may be associated with disproportionately large percentages of genes in these two genomes that encode membrane-bound proteins, which are rich in hydrophobic amino acids and selectively constrained. These data support a hypothesis that natural selection imposed by protein functional constraints has contributed to selective fixation of certain editing sites and maintenance of the ...
Source: Biology Direct - October 21, 2008 Category: Biology Authors: Richard W Jobson and Yin-Long Qiu Source Type: journals

Same-strand overlapping genes in bacteria: compositional determinants of phase biasEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our model explains the phase bias in same-strand overlapping genes by compositional factors without invoking selection. Therefore, it can be used as a null model of neutral evolution to test selection hypotheses concerning the evolution of overlapping genes. Reviewers This article was reviewed by Bill Martin, Itai Yanai and Mikhail Gelfand. (Source: Biology Direct)
Source: Biology Direct - August 21, 2008 Category: Biology Authors: Niv Sabath, Dan Graur and Giddy Landan Source Type: journals

Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cellEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Ribosome chimerism can provide a direct link between the selective forces for and the mechanisms of evolving nuclear transport and compartmentalisation. The detailed molecular scenario presented here provides a solution to the gradual evolution of nuclear compartmentalization from an anuclear stage. Reviewers This article was reviewed by Eugene V Koonin, Martijn Huynen, Anthony M. Poole and Patrick Forterre. (Source: Biology Direct)
Source: Biology Direct - July 24, 2008 Category: Biology Authors: Gaspar Jekely Source Type: journals