The Waiting And Mating Game: Condition Dependent Mate Sampling In Female Gray Treefrogs (Hyla Versicolor)

Strong sexual selection by receivers can lead to the evolution of elaborate courtship behaviors in signalers. However the process by which receivers sample signalers and execute mate choice under complex signaling conditions—and thus the realized strength of sexual section—is poorly understood. Moreover, receivers can vary in condition, which can further influence mate sampling strategies. Using wild female frogs we tested two hypotheses at the intersection of these important problems: that some of the individual variation in mate sampling is explained by (1) the reproductive urgency hypothesis, which predicts that receivers in a more urgent reproductive state will sample mates less and/or (2) the reproductive investment hypothesis, which predicts that receivers that have invested less in the current reproductive effort will sample mates less. Eastern gray treefrogs, Hyla versicolor, were collected in amplexus and repeatedly tested for phonotaxis behavior using a dynamic playback assay. To evaluate if hormonal mechanisms explained variation in the mate sampling, three steroid hormones, estradiol, progesterone, and corticosterone, were collected using a noninvasive water-borne hormone assay, validated for this species in the present study. Finally, we measured clutch size (investment) and the duration of time required for each female to oviposit after being reunited with their male mate (urgency). We found repeatability in many of the behaviors, including mate sampling. We found that females with higher concentrations estradiol and corticosterone made quicker choices, and that females with higher progesterone sampled mates more. We also found that female frogs in a more urgent reproductive state had lower concentrations of progesterone and estradiol, thereby providing the first evidence of a relationship between gonadal hormones and reproductive urgency. Collectively we found some support for the reproductive urgency but not the investment hypothesis. Thus, even though a female frog\u27s reproductive readiness is a highly transient life history stage, fine scale variation in her reproductive timeline could mitigate the strength of directional selection

SOPHIE velocimetry of Kepler transit candidates XVI. Tomographic measurement of the low obliquity of KOI-12b, a warm Jupiter transiting a fast rotator

We present the detection and characterization of the transiting warm Jupiter KOI-12b, first identified with Kepler with an orbital period of 17.86 days. We combine the analysis of Kepler photometry with Doppler spectroscopy and line-profile tomography of time-series spectra obtained with the SOPHIE spectrograph to establish its planetary nature and derive its properties. To derive reliable estimates for the uncertainties on the tomographic model parameters, we devised an empirical method to calculate statistically independent error bars on the time-series spectra. KOI-12b has a radius of 1.43$\pm$0.13$R_\mathrm{Jup}$ and a 3$\sigma$ upper mass limit of 10$M_\mathrm{Jup}$. It orbits a fast-rotating star ($v$sin$i_{\star}$ = 60.0$\pm$0.9 km s$^{-1}$) with mass and radius of 1.45$\pm$0.09 $M_\mathrm{Sun}$ and 1.63$\pm$0.15 $R_\mathrm{Sun}$, located at 426$\pm$40 pc from the Earth. Doppler tomography allowed a higher precision on the obliquity to be reached by comparison with the analysis of the Rossiter-McLaughlin radial velocity anomaly, and we found that KOI-12b lies on a prograde, slightly misaligned orbit with a low sky-projected obliquity $\lambda$ = 12.6$\stackrel{+3.0}{_{-2.9}}^\circ$. The properties of this planetary system, with a 11.4 magnitude host-star, make of KOI-12b a precious target for future atmospheric characterization.Comment: 19 pages, 10 figure

Гендерний аспект вивчення жаргонної лексики

В статье определяется понятие "общий жаргон", обосновывается актуальность гендерного подхода к изучению жаргонизмов. На материале выборок из словарей, художественной литературы, по результатам проведенного автором психолингвистического эксперимента осуществляется семантический анализ, определяются способы образования жаргонизмов на обозначение женщин в украинском языке.У статті визначається поняття "загальний жаргон", обґрунтовується актуальность ґендерного підходу до вивчення жаргонізмів. На матеріалі вибірок зі словників, художньої літератури, за результатами проведеного автором психолінгвістичного експерименту здійснюється семантичний аналіз, визначаються способи утворення жаргонізмів на позначення жінок в українській мові.The author of the article defines the concept "general jargon", bases actuality of gender aspect of jargon words investigation. Using dictionaries, literature and the results of psycho-linguistic experiment, the author analyses semantic and formation ways of jargon words for designation of women in Ukrainian

Derivation via Hamilton's principle of a new shallow-water model using a color function for the macroscopic description of partial wetting phenomena

This paper presents a new shallow-water type model suitable for the simulation of partially wetting liquid films without the need for very fine resolution of the contact line phenomena, which is particularly suitable for industrial applications. This model is based on the introduction of a color function, propagated at the averaged velocity of the bulk flow, and equal to one where there is a liquid film and zero in the dry zone, which implies a non zero gradient only at the interface. This approach has the advantage of easily locating the interface, allowing to model macroscopically the forces acting at the contact line, which is essential for the simulation of partial wetting phenomena. The formal derivation of this model is based on the principle of least action known as Hamilton's principle. Here this principle is applied in a full Eulerian form to derive the complete system of equations with the color function. This method proves to be particularly suitable for this type of development and as an illustration it is also applied to recover another model proposed by Lallement et al. [39, 73]. Finally, both models are compared from a theoretical point of view and the advantages of the new color function based model are discussed

Protein S-nitrosylation: specificity and identification strategies in plants

The role of nitric oxide (NO) as a major regulator of plant physiological functions has become increasingly evident. To further improve our understanding of its role, within the last few years plant biologists have begun to embrace the exciting opportunity of investigating protein S-nitrosylation, a major reversible NO-dependent post-translational modification (PTM) targeting specific Cys residues and widely studied in animals. Thanks to the development of dedicated proteomic approaches, in particular the use of the Biotin Switch Technique (BST) combined with mass spectrometry, hundreds of plant protein candidates for S-nitrosylation have been identified. Functional studies focused on specific proteins provided preliminary comprehensive views of how this PTM impacts the structure and function of proteins and, more generally, of how NO might regulate biological plant processes. The aim of this review is to detail the basic principle of protein S-nitrosylation, to provide information on the biochemical and structural features of the S-nitrosylation sites and to describe the proteomic strategies adopted to investigate this PTM in plants. Limits of the current approaches and tomorrow's challenges are also discussed

Molecular study of organic residues in an exceptional collection of potteries from Deir el-Médineh (XVIIIth dynasty, Egypt).

Communication oraleInternational audienceWithin this study of molecular archaeology, an exceptional set of Egyptian organic remains stored in containers from Deir el-Médineh (XVIIIth dynasty), and put at disposal by the Department of Egyptian Antiquities of the Louvre Museum has been analyzed

Colib'read on galaxy : a tools suite dedicated to biological information extraction from raw NGS reads

Background: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Findings: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. Conclusions: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.Peer reviewe

A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions

One of the routine clinical treatments to eliminate ischemic stroke thrombi is injecting a biochemical product into the patient’s bloodstream, which breaks down the thrombi’s fibrin fibers: intravenous or intravascular thrombolysis. However, this procedure is not without risk for the patient; the worst circumstances can cause a brain hemorrhage or embolism that can be fatal. Improvement in patient management drastically reduced these risks, and patients who benefited from thrombolysis soon after the onset of the stroke have a significantly better 3-month prognosis, but treatment success is highly variable. The causes of this variability remain unclear, and it is likely that some fundamental aspects still require thorough investigations. For that reason, we conducted in vitro flow-driven fibrinolysis experiments to study pure fibrin thrombi breakdown in controlled conditions and observed that the lysis front evolved non-linearly in time. To understand these results, we developed an analytical 1D lysis model in which the thrombus is considered a porous medium. The lytic cascade is reduced to a second-order reaction involving fibrin and a surrogate pro-fibrinolytic agent. The model was able to reproduce the observed lysis evolution under the assumptions of constant fluid velocity and lysis occurring only at the front. For adding complexity, such as clot heterogeneity or complex flow conditions, we propose a 3-dimensional mesoscopic numerical model of blood flow and fibrinolysis, which validates the analytical model’s results. Such a numerical model could help us better understand the spatial evolution of the thrombi breakdown, extract the most relevant physiological parameters to lysis efficiency, and possibly explain the failure of the clinical treatment. These findings suggest that even though real-world fibrinolysis is a complex biological process, a simplified model can recover the main features of lysis evolution.</p

A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

<p>Abstract</p> <p>Background</p> <p>Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to accurately estimate alignment scores and statistical significance with sequences sharing marked compositional biases.</p> <p>Results</p> <p>We present a general and simple methodology to build matrices that are especially fitted to the compositional bias of proteins. Our approach is inspired from the one used to build the BLOSUM matrices and is based on learning substitution and amino acid frequencies on real sequences with the corresponding compositional bias. We applied it to the large scale comparison of Mollicute AT-rich genomes. The new matrix, MOLLI60, was used to predict pairwise orthology relationships, as well as homolog families among 24 Mollicute genomes. We show that this new matrix enables to better discriminate between true and false orthologs and improves the clustering of homologous proteins, with respect to the use of the classical matrix BLOSUM62.</p> <p>Conclusions</p> <p>We show in this paper that well-fitted matrices can improve the predictions of orthologous and homologous relationships among proteins with a similar compositional bias. With the ever-increasing number of sequenced genomes, our approach could prove valuable in numerous comparative studies focusing on atypical genomes.</p

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation