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Plos Biology : Nutrient-regulated Antisense and Intragenic Rnas Mo...

By: Masafumi Nishizawa

Description : The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate inorganic phosphate (Pi) metabolism for adaptation to Pi starvation. Pi starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Ph...

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Plos Biology : High-throughput in Vivo Analysis of Gene Expression...

By: John Sulston

Description : Using DNA sequences 59 to open reading frames, we have constructed green fluorescent protein (GFP) fusions and generated spatial and temporal tissue expression profiles for 1,886 specific genes in the nematode Caenorhabditis elegans. This effort encompasses about 10% of all genes identified in this organism. GFP-expressing wild-type animals were analyzed at each stage of development from embryo to adult. We have identified 59 DNA regions regulating expressi...

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Plos Biology : Invertebrate Post-segregation Distorters ; a New Em...

By: Public Library of Science (Plos)

Description : Cytoplasmic incompatibility induced by inherited intracellular bacteria of arthropods, and Medea elements found in flour beetles, are both forms of postsegregation distortion involving the killing of embryos in order to increase the ratio of progeny that inherit them. The recently described peel-zeel element of Caenorhabditis elegans also uses this mechanism: like Medea the genes responsible are in the nuclear genome but it shares a paternal mode of action ...

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Plos Biology : a New Type of Na+-driven Atp Synthase Membrane Roto...

By: Raimund Dutzler

Description : The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a trans membrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consiste...

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Plos Biology : Hyperparasitoids Use Herbivore-induced Plant Volati...

By: Stéphane Audic

Description : Plants respond to herbivory with the emission of induced plant volatiles. These volatiles may attract parasitic wasps (parasitoids) that attack the herbivores. Although in this sense the emission of volatiles has been hypothesized to be beneficial to the plant, it is still debated whether this is also the case under natural conditions because other organisms such as herbivores also respond to the emitted volatiles. One important group of organisms, the enem...

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Plos Biology : More Than Just Access ; Delivering on a Network-ena...

By: J. Marie Hardwick
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Plos Biology : Correction ; All Β Cells Contribute Equally to Isle...

By: Kristen Brennand
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Plos Biology : the Dna Methylome of Human Peripheral Blood Mononuc...

By: Wolf Reik

Description : DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian ...

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Plos Biology : Nodal Dependent Differential Localisation of Dishev...

By: Brigid Hogan

Description : The anterior visceral endoderm (AVE), a signalling centre within the simple epithelium of the visceral endoderm (VE), is required for anterior-posterior axis specification in the mouse embryo. AVE cells migrate directionally within the VE, thereby properly positioning the future anterior of the embryo and orientating the primary body axis. AVE cells consistently come to an abrupt stop at the border between the anterior epiblast and extra-embryonic ectoderm,...

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Plos Biology : an Unbiased Cell Morphology–based Screen for New, B...

By: Tom Misteli

Description : We have implemented an unbiased cell morphology–based screen to identify small-molecule modulators of cellular processes using the Cytometrix (TM) automated imaging and analysis system. This assay format provides unbiased analysis of morphological effects induced by small molecules by capturing phenotypic readouts of most known classes of pharmacological agents and has the potential to read out pathways for which little is known. Four human-cancer cell line...

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Plos Biology : Fast, Slow, or Not at All ; the Extracellular Matri...

By: Public Library of Science (Plos)
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Plos Biology : Gene-environment Interaction in Yeast Gene Expressi...

By: Erin N. Smith

Description : The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly characterize the architecture of gene–environment interactions. We examined the genetic and molecular basis of variation in gene expression betwe...

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Plos Biology : Directional Transport is Mediated by a Dynein- Depe...

By: Simon Bullock

Description : Cytoplasmic RNA localization is a key biological strategy for establishing polarity in a variety of organisms and cell types. However, the mechanisms that control directionality during asymmetric RNA transport are not yet clear. To gain insight into this crucial process, we have analyzed the molecular machinery directing polarized transport of RNA to the vegetal cortex in Xenopus oocytes. Using a novel approach to measure directionality of mRNA transport in...

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Plos Biology : Invasive Mutualists Erode Native Pollination Webs, ...

By: Marcelo A. Aizen

Description : Plant–animal mutualisms are characterized by weak or asymmetric mutual dependences between interacting species, a feature that could increase community stability. If invasive species integrate into mutualistic webs, they may alter web structure, with consequences for species persistence. However, the effect of alien mutualists on the architecture of plant–pollinator webs remains largely unexplored. We analyzed the extent of mutual dependency between interac...

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Plos Biology : Transcriptome Analysis of the Arabidopsis Megaspore...

By: Gregory P. Copenhaver

Description : Germ line specification is a crucial step in the life cycle of all organisms. For sexual plant reproduction, the megaspore mother cell (MMC) is of crucial importance : it marks the first cell of the plant ‘‘germline’’ lineage that gets committed to undergo meiosis. One of the meiotic products, the functional megaspore, subsequently gives rise to the haploid, multicellular female gametophyte that harbours the female gametes. The MMC is formed by selection an...

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Plos Biology : Comparative Sex Chromosome Genomics in Snakes ; Dif...

By: Nick H. Barton

Description : Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in ...

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Plos Biology : Draft Crystal Structure of the Vault Shell at 9-a° ...

By: Gregory A. Petsko

Description : Vaults are the largest known cytoplasmic ribonucleoprotein structures and may function in innate immunity. The vault shell self-assembles from 96 copies of major vault protein and encapsulates two other proteins and a small RNA. We crystallized rat liver vaults and several recombinant vaults, all among the largest non-icosahedral particles to have been crystallized. The best crystals thus far were formed from empty vaults built from a cysteine-tag construct...

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Plos Biology : a High Precision Survey of the Molecular Dynamics o...

By: Sandra L. Schmid

Description : Dual colour total internal reflection fluorescence microscopy is a powerful tool for decoding the molecular dynamics of clathrin-mediated endocytosis (CME). Typically, the recruitment of a fluorescent protein–tagged endocytic protein was referenced to the disappearance of spot-like clathrin-coated structure (CCS), but the precision of spot-like CCS disappearance as a marker for canonical CME remained unknown. Here we have used an imaging assay based on tota...

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Plos Biology : Compilation and Network Analyses of Cambrian Food W...

By: Jennifer A. Dunne

Description : A rich body of empirically grounded theory has developed about food webs—the networks of feeding relationships among species within habitats. However, detailed food-web data and analyses are lacking for ancient ecosystems, largely because of the low resolution of taxa coupled with uncertain and incomplete information about feeding interactions. These impediments appear insurmountable for most fossil assemblages: however, a few assemblages with excellent sof...

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Plos Biology : Nkt Cell-tcr Expression Activates Conventional T Ce...

By: Philippa Marrack

Description : Natural killer T (NKT) cell development depends on recognition of self-glycolipids via their semi-invariant Va14i-TCR. However, to what extent TCR-mediated signals determine identity and function of mature NKT cells remains incompletely understood. To address this issue, we developed a mouse strain allowing conditional Va14i-TCR expression from within the endogenous Tcra locus. We demonstrate that naïve T cells are activated upon replacement of their endoge...

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