Evaluation of selected soft winter wheat lines for main ear grain weight

Received: February 28th, 2021 ; Accepted: May 8th, 2021 ; Published: May 12th, 2021 ; Correspondence: [email protected] to assess the breeding samples of soft winter wheat by weight of grain from the main ear anddetermine the indicators of adaptability were conducted at the Bila Tserkva Research and Selection Station (BTRSS) in 2011–2013. The study revealed significant differences in breeding lines in the range of variability of grain mass from the main ear and identified small, medium and significantcoefficients of variation, which indicates their excellent response to environmental conditions. It was due to genotype, year conditions and their interaction. Line 42 KS had significantly higher than the standard grain weight of the main ear (0.14 g) and the lowest value of the coefficient of variation (8.7%). According to the indicators of adaptability(GAC, σ²(GxE)gi, σ²SACi, σSACi, etc.) the lines 42 KS, 24 KS and 44 KS were distinguished. There was asignificant correlation between the weight of grain from the ear and the weight of 1,000 grains (0.603–0.674) and the direct influence of the weight of grain from the main ear on the weight of grain from the plantand grain yield (0.805–0.942). Selected lines as a result of research (2015–2020) from these populations of soft winter wheat are competitively tested in the conditions of Bila Tserkva Research and Selection Station, forming high grain yields (7.39–8.12 t ha-1 ) and will be transferred to 2021 for the State variety test for inclusion in the Register of plant varieties suitable for distribution in Ukraine

Analyzing X-Ray Pulsar Profiles: Geometry and Beam Pattern of Her X-1

We report on our analysis of a large sample of energy dependent pulse profiles of the X-ray binary pulsar Hercules X-1. We find that all data are compatible with the assumption of a slightly distorted magnetic dipole field as sole cause of the asymmetry of the observed pulse profiles. Further the analysis provides evidence that the emission from both poles is equal. We determine an angle of 20 deg between the rotation axis and the local magnetic axis. One pole has an offset of 5 deg from the antipodal position of the other pole. The beam pattern shows structures that can be interpreted as pencil- and fan-beam configurations. Since no assumptions on the polar emission are made, the results can be compared with various emission models. A comparison of results obtained from pulse profiles of different phases of the 35-day cycle indicates different attenuation of the radiation from the poles being responsible for the change of the pulse shape during the main-on state. These results also suggest the resolution of an ambiguity within a previous analysis of pulse profiles of Cen X-3, leading to a unique result for the beam pattern of this pulsar as well. The analysis of pulse profiles of the short-on state indicates that a large fraction of the radiation cannot be attributed to the direct emission from the poles. We give a consistent explanation of both the evolution of the pulse profile and the spectral changes with the 35-day cycle in terms of a warped precessing accretion disk.Comment: 24 pages, 12 figures. To appear in ApJ 529 #2, 1 Feb 200

Energetics in Condensate Star and Wormholes

It is known that the total gravitational energy in localized sources having static spherical symmetry and satisfying energy conditions is negative (attractive gravity). A natural query is how the gravitational energy behaves under circumstances where energy conditions are violated. To answer this, the known expression for the gravitational energy is suitably modified to account for situations like the ones occurring in wormhole spacetime. It is then exemplified that in many cases the modified expression yields desirable answers. The implications are discussed.Comment: 16 pages, 1 figure, references added, To appear in PR

Digital receivers for low-frequency radio telescopes UTR-2, URAN, GURT

This paper describes digital radio astronomical receivers used for decameter and meter wavelength observations. This paper describes digital radio astronomical receivers used for decameter and meter wavelength observations. Since 1998, digital receivers performing on-the-fly dynamic spectrum calculations or waveform data recording without data loss have been used at the UTR-2 radio telescope, the URAN VLBI system, and the GURT new generation radio telescope. Here we detail these receivers developed for operation in the strong interference environment that prevails in the decameter wavelength range. Data collected with these receivers allowed us to discover numerous radio astronomical objects and phenomena at low frequencies, a summary of which is also presented.Comment: 24 pages, 15 figure

Complex experiment on studying the microphysical, chemical, and optical properties of aerosol particles and estimating the contribution of atmospheric aerosol-to-earth radiation budget

The primary objective of this complex aerosol experiment was the measurement of microphysical, chemical, and optical properties of aerosol particles in the surface air layer and free atmosphere. The measurement data were used to retrieve the whole set of aerosol optical parameters, necessary for radiation calculations. Three measurement cycles were performed within the experiment during 2013: in spring, when the aerosol generation is maximal; in summer (July), when atmospheric boundary layer altitude and, hence, mixing layer altitude are maximal; and in late summer/early autumn, during the period of nucleation of secondary particles. Thus, independently obtained data on the optical, meteorological, and microphysical parameters of the atmosphere allow intercalibration and inter-complement of the data and thereby provide for qualitatively new information which explains the physical nature of the processes that form the vertical structure of the aerosol field

Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions

<p>Abstract</p> <p>Background</p> <p>In protein evolution, the mechanism of the emergence of novel protein domain is still an open question. The incremental growth of protein variable regions, which was produced by stochastic insertions, has the potential to generate large and complex sub-structures. In this study, a deterministic methodology is proposed to reconstruct phylogenies from protein structures, and to infer insertion events in protein evolution. The analysis was performed on a broad range of SCOP domain families.</p> <p>Results</p> <p>Phylogenies were reconstructed from protein 3D structural data. The phylogenetic trees were used to infer ancestral structures with a consensus method. From these ancestral reconstructions, 42.7% of the observed insertions are nested insertions, which locate in previous insert regions. The average size of inserts tends to increase with the insert rank or total number of insertions in the variable regions. We found that the structures of some nested inserts show complex or even domain-like fold patterns with helices, strands and loops. Furthermore, a basal level of structural innovation was found in inserts which displayed a significant structural similarity exclusively to themselves. The β-Lactamase/D-ala carboxypeptidase domain family is provided as an example to illustrate the inference of insertion events, and how the incremental growth of a variable region is capable to generate novel structural patterns.</p> <p>Conclusion</p> <p>Using 3D data, we proposed a method to reconstruct phylogenies. We applied the method to reconstruct the sequences of insertion events leading to the emergence of potentially novel structural elements within existing protein domains. The results suggest that structural innovation is possible via the stochastic process of insertions and rapid evolution within variable regions where inserts tend to be nested. We also demonstrate that the structure-based phylogeny enables the study of new questions relating to the evolution of protein domain and biological function.</p

Source contributions to Northern Hemisphere CO and black carbon during spring and summer 2008 from POLARCAT and START08/preHIPPO observations and MOZART-4

International audienceAnthropogenic pollution and wildfires are main producers of carbon monoxide (CO) and black carbon (BC) in the Northern Hemisphere. High concentrations of these compounds are transported into the Arctic troposphere, influencing the ecosystem in high northern latitudes and the global climate. The global chemical transport model MOZART-4 is used to quantify the seasonal evolution of the contribution of CO and BC from different source regions in spring and summer 2008 by tagging their emissions. Aircraft observations from the POLARCAT experiments, in particular NASA ARCTAS, NOAA ARCPAC, POLARCAT-France, DLR GRACE and YAK-AEROSIB, as well as the NSF START08/preHIPPO experiments during Spring-Summer 2008 are combined to quantify the representation of simulated tracer characteristics in anthropogenic and fire plumes. In general, the model reproduces CO and BC well. Based on aircraft measurements and FLEXPART back-trajectories, the altitude contribution of emissions coming from different source regions is well captured in the model. Uncertainties of the MOZART-4 model are identified by comparing the data with model results on the flight tracks and using MOPITT satellite observations. Anthropogenic emissions are underestimated by about 10% in high northern latitudes in spring, and shortcomings exist in simulating fire plumes. The remote impact of East-Siberian fire emissions is underestimated for spring, whereas the impact of Southeast Asian fire emissions to mid-latitude CO values is overestimated by the model. In summer, mid-latitude CO values agree well between model and observations, whereas summer high latitude East-Siberian fire emissions in the model are overestimated by 20% in comparison to observations in the region. On the other hand, CO concentrations are underestimated by about 30% over Alaska and Canada at altitudes above 4 km. BC values are overestimated by the model at altitudes above 4 km in summer. Based on MOZART-4, with tagged CO and BC tracers, anthropogenic emissions of Asia, Europe and the US have the largest contribution to the CO and BC in mid- and high latitudes in spring and summer. Southeast Asian, Chinese and Indian fires have a large impact on CO pollution in spring in low latitudes with a maximum between 20° and 30°, whereas Siberian fires contribute largely to the pollution in high latitudes, up to 10% in spring and up to 30% in summer. The largest contributions to BC values in high latitudes are from anthropogenic emissions (about 70%). CO and BC have larger mass loadings in April than in July, as a result of photochemistry and dynamics

A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction

An accurate potential function is essential to attack protein folding and structure prediction problems. The key to developing efficient knowledge-based potential functions is to design reference states that can appropriately counteract generic interactions. The reference states of many knowledge-based distance-dependent atomic potential functions were derived from non-interacting particles such as ideal gas, however, which ignored the inherent sequence connectivity and entropic elasticity of proteins.We developed a new pair-wise distance-dependent, atomic statistical potential function (RW), using an ideal random-walk chain as reference state, which was optimized on CASP models and then benchmarked on nine structural decoy sets. Second, we incorporated a new side-chain orientation-dependent energy term into RW (RWplus) and found that the side-chain packing orientation specificity can further improve the decoy recognition ability of the statistical potential.RW and RWplus demonstrate a significantly better ability than the best performing pair-wise distance-dependent atomic potential functions in both native and near-native model selections. It has higher energy-RMSD and energy-TM-score correlations compared with other potentials of the same type in real-life structure assembly decoys. When benchmarked with a comprehensive list of publicly available potentials, RW and RWplus shows comparable performance to the state-of-the-art scoring functions, including those combining terms from multiple resources. These data demonstrate the usefulness of random-walk chain as reference states which correctly account for sequence connectivity and entropic elasticity of proteins. It shows potential usefulness in structure recognition and protein folding simulations. The RW and RWplus potentials, as well as the newly generated I-TASSER decoys, are freely available in http://zhanglab.ccmb.med.umich.edu/RW

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

Abstract Background Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. Results In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary information for DNA and RNA-binding site prediction. The SVM classifiers achieved 77.3% sensitivity and 79.3% specificity for prediction of DNA-binding residues, and 71.6% sensitivity and 78.7% specificity for RNA-binding site prediction. Conclusions Predictions at this level of accuracy may provide useful information for modelling protein-nucleic acid interactions in systems biology studies. We have thus developed a web-based tool called BindN+ (http://bioinfo.ggc.org/bindn+/) to make the SVM classifiers accessible to the research community

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

Repeat-proteins are made up of near repetitions of 20– to 40–amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi–one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete “domain” (the stability and cooperativity of the repeating array) can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (ΔGwater) and the cooperativity of denaturation (m-value), which do not ordinarily apply for globular proteins. We show how the parameters for the “coarse-grained” description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR) repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are “poised” at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions