A new analysis of the WASP-3 system: no evidence for an additional companion

In this work we investigate the problem concerning the presence of additional bodies gravitationally bounded with the WASP-3 system. We present eight new transits of this planet and analyse all the photometric and radial velocity data published so far. We did not observe significant periodicities in the Fourier spectrum of the observed minus calculated (O-C) transit timing and radial velocity diagrams (the highest peak having false-alarm probabilities of 56 per cent and 31 per cent, respectively) or long-term trends. Combining all the available information, we conclude that the radial velocity and transit timing techniques exclude, at 99 per cent confidence limit, any perturber more massive than M \gtrsim 100 M_Earth with periods up to 10 times the period of the inner planet. We also investigate the possible presence of an exomoon on this system and determined that considering the scatter of the O-C transit timing residuals a coplanar exomoon would likely produce detectable transits. This hypothesis is however apparently ruled out by observations conducted by other researchers. In case the orbit of the moon is not coplanar the accuracy of our transit timing and transit duration measurements prevents any significant statement. Interestingly, on the basis of our reanalysis of SOPHIE data we noted that WASP-3 passed from a less active (log R'_hk=-4.95) to a more active (log R'_hk=-4.8) state during the 3 yr monitoring period spanned by the observations. Despite no clear spot crossing has been reported for this system, this analysis claims for a more intensive monitoring of the activity level of this star in order to understand its impact on photometric and radial velocity measurements.Comment: MNRAS accepted (14/08/2012

Extraction, integration and analysis of alternative splicing and protein structure distributed information

<p>Abstract</p> <p>Background</p> <p>Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools.</p> <p>Results</p> <p>A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches.</p> <p>Conclusion</p> <p>PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions.</p

Excitatory effect of ATP on rat area postrema neurons

ATP-induced inward currents and increases in the cytosolic Ca2+ concentration ([Ca]in) were investigated in neurons acutely dissociated from rat area postrema using whole-cell patch-clamp recordings and fura-2 microfluorometry, respectively. The ATP-induced current (IATP) and [Ca]in increases were mimicked by 2-methylthio-ATP and ATP-γS, and were inhibited by P2X receptor (P2XR) antagonists. The current–voltage relationship of the IATP exhibited a strong inward rectification, and the amplitude of the IATP was concentration-dependent. The IATP was markedly reduced in the absence of external Na+, and the addition of Ca2+ to Na+-free saline increased the IATP. ATP did not increase [Ca]in in the absence of external Ca2+, and Ca2+ channel antagonists partially inhibited the ATP-induced [Ca]in increase, indicating that ATP increases [Ca]in by Ca2+ influx through both P2XR channels and voltage-dependent Ca2+ channels. There was a negative interaction between P2XR- and nicotinic ACh receptor (nAChR)-channels, which depended on the amplitude and direction of current flow through either channel. Current occlusion was observed at Vhs between −70 and −10 mV when the IATP and ACh-induced current (IACh) were inward, but no occlusion was observed when these currents were outward at a Vh of +40 mV. The IATP was not inhibited by co-application of ACh when the IACh was markedly decreased either by removal of permeant cations, by setting Vh close to the equilibrium potential of IACh, or by the addition of d-tubocurarine or serotonin. These results suggest that the inhibitory interaction is attributable to inward current flow of cations through the activated P2XR- and nAChR-channels

Examining the orbital decay targets KELT-9 b, KELT-16 b, and WASP-4 b, and the transit-timing variations of HD 97658 b,

Context. Tidal orbital decay is suspected to occur for hot Jupiters in particular, with the only observationally confirmed case of this being WASP-12 b. By examining this effect, information on the properties of the host star can be obtained using the so-called stellar modified tidal quality factor Q′∗, which describes the efficiency with which the kinetic energy of the planet is dissipated within the star. This can provide information about the interior of the star. Aims. In this study, we aim to improve constraints on the tidal decay of the KELT-9, KELT-16, and WASP-4 systems in order to find evidence for or against the presence of tidal orbital decay. With this, we want to constrain the Q′∗ value for each star. In addition, we aim to test the existence of the transit timing variations (TTVs) in the HD 97658 system, which previously favoured a quadratic trend with increasing orbital period. Methods. Making use of newly acquired photometric observations from CHEOPS (CHaracterising ExOplanet Satellite) and TESS (Transiting Exoplanet Survey Satellite), combined with archival transit and occultation data, we use Markov chain Monte Carlo (MCMC) algorithms to fit three models to the data, namely a constant-period model, an orbital-decay model, and an apsidal-precession model. Results. We find that the KELT-9 system is best described by an apsidal-precession model for now, with an orbital decay trend at over 2 σ being a possible solution as well. A Keplerian orbit model with a constant orbital period provides the best fit to the transit timings of KELT-16 b because of the scatter and scale of their error bars. The WASP-4 system is best represented by an orbital decay model at a 5 σ significance, although apsidal precession cannot be ruled out with the present data. For HD 97658 b, using recently acquired transit observations, we find no conclusive evidence for a previously suspected strong quadratic trend in the data

Harmonizing methods for wildlife abundance estimation and pathogen detection in Europe-a questionnaire survey on three selected host-pathogen combinations

__Background:__ The need for wildlife health surveillance as part of disease control in wildlife, domestic animals and humans on the global level is widely recognized. However, the objectives, methods and intensity of existing wildlife health surveillance programs vary greatly among European countries, resulting in a patchwork of data that are difficult to merge and compare. This survey aimed at evaluating the need and potential for data harmonization in wildlife health in Europe. The specific objective was to collect information on methods currently used to estimate host abundance and pathogen prevalence. Questionnaires were designed t

Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments

High-throughput methods such as EST sequencing, microarrays and deep sequencing have identified large numbers of alternative splicing (AS) events, but studies have shown that only a subset of these may be functional. Here we report a sensitive bioinformatics approach that identifies exons with evidence of a strong RNA selection pressure ratio (RSPR) —i.e., evolutionary selection against mutations that change only the mRNA sequence while leaving the protein sequence unchanged—measured across an entire evolutionary family, which greatly amplifies its predictive power. Using the UCSC 28 vertebrate genome alignment, this approach correctly predicted half to three-quarters of AS exons that are known binding targets of the NOVA splicing regulatory factor, and predicted 345 strongly selected alternative splicing events in human, and 262 in mouse. These predictions were strongly validated by several experimental criteria of functional AS such as independent detection of the same AS event in other species, reading frame-preservation, and experimental evidence of tissue-specific regulation: 75% (15/20) of a sample of high-RSPR exons displayed tissue specific regulation in a panel of ten tissues, vs. only 20% (4/20) among a sample of low-RSPR exons. These data suggest that RSPR can identify exons with functionally important splicing regulation, and provides biologists with a dataset of over 600 such exons. We present several case studies, including both well-studied examples (GRIN1) and novel examples (EXOC7). These data also show that RSPR strongly outperforms other approaches such as standard sequence conservation (which fails to distinguish amino acid selection pressure from RNA selection pressure), or pairwise genome comparison (which lacks adequate statistical power for predicting individual exons)