Selection on the wing in Heliconius butterflies

<p>Asbtract</p> <p>To what extent population structure favours the establishment of new phenotypes within a species remains a fundamental question in evolutionary studies. By reducing gene flow, habitat fragmentation is a major factor shaping the genetic structuring of populations, favouring isolation of small populations in which drift may rapidly change frequencies of new variants. When these variants provide advantages to individuals, the combined effect of selection and drift can lead to rapid shifts in phenotypes. In a study published in <it>BMC Genetics</it>, Albuquerque de Moura <it>et al. </it>asked whether such a general pattern of population structure can be observed in <it>Heliconius </it>species, which could have strong implication in the evolution of colour pattern diversification in these butterflies. In this commentary we discuss the potential roles of these three processes (drift, selection and dispersal) on the evolution of <it>Heliconius </it>wing patterns in regard to the findings of a common fine-scale population structure within the co-mimetic species <it>H. melpomene </it>and <it>H. erato</it>. Indeed, a general pattern of population subdivision in the history of these two species may have provoked the major phenotypical shifts observed in their wing colour patterns. The suggestion that coupled environmental pressures (counter-selection of dispersal and selection on co-evolved traits) could be responsible for identical genetic differentiation profiles in <it>H. erato </it>and <it>H. melpomene </it>clearly merits further investigations using both detailed population genetic (including landscape genetic) and ecological studies.</p

NGAL, biomarker of acute kidney injury

peer reviewedLe diagnostic precoce de l’insufissance renale aigue (IRA) est necessaire et devrait se faire au stade de lesion renale avant meme la degradation du debit de filtration glomerulaire. Plusieurs biomarqueurs d’atteinte renale aigue sont actuellement a l’etude. Parmi ceux-ci, le Neutrophil Gelatinase Associated Lipocalin (NGAL) semble l’un des plus prometteurs et fait l’objet de nombreuses publications. La performance diagnostique de NGAL, dose dans le plasma ou les urines, pour le depistage de l’IRA depend de nombreux facteurs. Bien que les donnees experimentales recentes soient en faveur de l’utilisation preferentielle du dosage urinaire de NGAL, les donnees cliniques issues de nombreuses etudes ne permettent pas de trancher formellement sur la superiorite du dosage urinaire par rapport au dosage plasmatique pour le depistage des atteintes renales aigues. Il n’en reste pas moins que sur le plan analytique, les techniques de dosage du NGAL urinaire sont actuellement plus fiables que celles du dosage plasmatique. La performance diagnostique de NGAL dans un contexte d’IRA est maximale en chirurgie cardiaque pediatrique. Les resultats, chez l’adulte en postoperatoire de chirurgie cardiaque et dans d’autres situations (reanimation, urgences, transplantation), sont moins convaincants. Par ailleurs, il n’est actuellement pas possible d’extrapoler des etudes cliniques une valeur seuil discriminante unique de NGAL, aussi bien dans les urines que dans le plasma. D’autres etudes sont necessaires pour valider definitivement NGAL comme biomarqueur de l’atteinte renale aigue et en preciser les conditions d’utilisation en pratique clinique

lpEdit: an editor to facilitate reproducible analysis via literate programming

ArticleCopyright 2013 Adam J Richards et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited .There is evidence to suggest that a surprising proportion of published experiments in science are difficult if not impossible to reproduce. The concepts of data sharing, leaving an audit trail and extensive documentation are fundamental to reproducible research, whether it is in the laboratory or as part of an analysis. In this work, we introduce a tool for documentation that aims to make analyses more reproducible in the general scientific community. The application, lpEdit, is a cross-platform editor, written with PyQt4, that enables a broad range of scientists to carry out the analytic component of their work in a reproducible manner—through the use of literate programming. Literate programming mixes code and prose to produce a final report that reads like an article or book. lpEdit targets researchers getting started with statistics or programming, so the hurdles associated with setting up a proper pipeline are kept to a minimum and the learning burden is reduced through the use of templates and documentation. The documentation for lpEdit is centered around learning by example, and accordingly we use several increasingly involved examples to demonstrate the software’s capabilities. We first consider applications of lpEdit to process analyses mixing R and Python code with the LATEX documentation system. Finally, we illustrate the use of lpEdit to conduct a reproducible functional analysis of high-throughput sequencing data, using the transcriptome of the butterfly species Pieris brassica

Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour

Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales, mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae, known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity

miRkwood: a tool for the reliable identification of microRNAs in plant genomes

International audienceBackground: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions. Conclusion: miRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool

Transgenerational plasticity of dispersal‐related traits in a ciliate: genotype‐dependency and fitness consequences

Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. Here, we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. Our results show that morphological and movement traits associated with dispersal are plastic, and that these modifications are inherited over at least 35 generations. The fitness costs and benefits associated with these plastic changes are also transmitted to further generations. We highlight that the genotype modulates the expression and reversibility of transgenerational plasticity of dispersal-related traits and its fitness outcomes. Our study thus suggests that genotype-dependent TGP could play an important role in eco-evolutionary dynamics as dispersal determines gene flow and the long-term persistence of natural populations