An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

<p>Abstract</p> <p>Background</p> <p>Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.</p> <p>Results</p> <p>We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server <url>http://bioinf.fbb.msu.ru/SDPfoxWeb/</url> and a stand-alone Java application available from the website.</p> <p>Conclusions</p> <p>SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.</p

Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops

Oilseed crops are one of the most important sources of vegetable oils for food and industry. Nutritional and technical properties of vegetable oil are primarily determined by its fatty acid (FA) composition. The content and composition of FAs in plants are commonly determined using gas chromatography-mass spectrometry (GS-MS) or gas chromatography-flame ionization detection (GC-FID) techniques. In the present work, we applied ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technique to FA profiling of sunflower and rapeseed seeds and compared this method with the GC-FID technique. GC-FID detected 11 FAs in sunflower and 13 FAs in rapeseed, while UPLC-MS appeared to be more sensitive, detecting about 2.5 times higher numbers of FAs in both plants. In addition to even-chain FAs, UPLC-MS was able to detect odd-chain FAs. The longest FA detected using GC-FID was an FA with 24 carbon atoms, whereas UPLC-MS could reveal the presence of longer FAs with the tails of up to 28 carbon atoms. Based on our results, we may conclude that UPLC-MS has great potential to be used for the assessment of FA profiles of oil crops

MAGIC observations of very high energy gamma-rays from HESS J1813-178

Recently, the HESS collaboration has reported the detection of gamma-ray emission above a few hundred GeV from eight new sources located close to the Galactic Plane. The source HESS J1813-178 has sparked particular interest, as subsequent radio observations imply an association with SNR G12.82-0.02. Triggered by the detection in VHE gamma-rays, a positionally coincident source has also been found in INTEGRAL and ASCA data. In this Letter we present MAGIC observations of HESS J1813-178, resulting in the detection of a differential gamma-ray flux consistent with a hard-slope power law, described as dN/(dA dt dE) = (3.3+/-0.5)*10^{-12} (E/TeV)^{-2.1+/-0.2} cm^(-2)s^(-1)TeV^(-1). We briefly discuss the observational technique used, the procedure implemented for the data analysis, and put this detection in the perspective of multifrequency observations.Comment: Accepted by ApJ Letter

Yolk sac cell atlas reveals multiorgan functions during human early development

The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds

Observation of VHE gamma-ray emission from the Active Galactic Nucleus 1ES1959+650 using the MAGIC telecope

The MAGIC Cherenkov telescope has observed very high energy (VHE) gamma-ray emission from the Active Galactic Nucleus 1ES1959+650 during six hours in September and October 2004. The observations were carried out alternated with the Crab Nebula, whose data were used as reference source for optimizing gamma/hadron separation and for flux comparison. The data analysis shows VHE gamma-ray emission of 1ES1959+650 with ~ 8 sigma significance, at a time of low activity in both optical and X-ray wavelengths. An integral flux above ~ 180 GeV of about 20% of the Crab was obtained. The light curve, sampled over 7 days, shows no significant variations. The differential energy spectrum between 180 GeV and 2 TeV can be fitted with a power law of index -2.72 +/- 0.14. The spectrum is consistent with the slightly steeper spectrum seen by HEGRA at higher energies, also during periods of low X-ray activity.Comment: 16 pages, 6 figure

Observation of Gamma Rays from the Galactic Center with the MAGIC Telescope

Recently, the Galactic Center has been reported to be a source of very high energy (VHE) gamma-rays by the VERITAS, CANGAROO and HESS experiments. The energy spectra as measured by these experiments show substantial differences. In this Letter we present MAGIC observations of the Galactic Center, resulting in the detection of a differential gamma-ray flux consistent with a steady, hard-slope power law, described as dN/(dA dt dE) = (2.9+/-0.6)*10^{-12} (E/TeV)^{-2.2+/-0.2} cm^{-2}s^{-1}TeV^{-1}. The gamma-ray source is centered at (Ra, Dec)=(17h 45m 20s, -29deg 2'. This result confirms the previous measurements by the HESS experiment and indicates a steady source of TeV gamma-rays. We briefly describe the observational technique used, the procedure implemented for the data analysis, and discuss the results in the perspective of different models proposed for the acceleration of the VHE gamma-rays.Comment: ApJL submitte

Variable Very High Energy Gamma-ray Emission from the Microquasar LS I +61 303

Microquasars are binary star systems with relativistic radio-emitting jets. They are potential sources of cosmic rays and laboratories for elucidating the physics of relativistic jets. Here we report the detection of variable gamma-ray emission above 100 gigaelectron volts from the microquasar LS I +61 303. Six orbital cycles were recorded. Several detections occur at a similar orbital phase, suggesting the emission is periodic. The strongest gamma-ray emission is not observed when the two stars are closest to one another, implying a strong orbital modulation of the emission or the absorption processes.Comment: 11 pages with 4 figure

Variable Very High Energy Gamma-ray Emission from the Microquasar LS I +61 303

Microquasars are binary star systems with relativistic radio-emitting jets. They are potential sources of cosmic rays and laboratories for elucidating the physics of relativistic jets. Here we report the detection of variable gamma-ray emission above 100 gigaelectron volts from the microquasar LS I +61 303. Six orbital cycles were recorded. Several detections occur at a similar orbital phase, suggesting the emission is periodic. The strongest gamma-ray emission is not observed when the two stars are closest to one another, implying a strong orbital modulation of the emission or the absorption processes.Comment: 11 pages with 4 figure

Observation of VHE Gamma Radiation from HESS J1834-087/W41 with the MAGIC Telescope

Recently, the HESS array has reported the detection of gamma-ray emission above a few hundred GeV from eight new sources located close to the Galactic Plane. The source HESS J1834-087 is spatially coincident with SNR G23.3-0.3 (W41). Here we present MAGIC observations of this source, resulting in the detection of a differential gamma-ray flux consistent with a power law, described as dN/(dA dt dE) = (3.7 +/- 0.6)*10^(-12) (E/TeV)^(-2.5 +/- 0.2) \ cm^(-2)s^(-1)TeV^(-1). We confirm the extended character of this flux. We briefly discuss the observational technique used, the procedure implemented for the data analysis, and put this detection in the perspective of the molecular environment found in the region of W41. We present 13CO and 12CO emission maps showing the existence of a massive molecular cloud in spatial superposition with the MAGIC detection.Comment: Accepted by ApJ Letter

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements