Sustainable Quality Fodder Production under Temperate Mountain Agriculture in Kashmir

Inadequate supply of quality feed and fodder is the primary cause of lower productivity of milch animals in India. Oats (Avena sativa L.) is an important fodder crop in J&K. Jammu and Kashmir state the fodder requirement is about 4.31 million tonnes against the available 3.26 million tonnes (Anonymous, 2008). Kashmir valley experiences a long lean period of winter, resulting in scarcity of green and quality fodder which results in drastic decrease in milk production. Therefore, to meet the need of animal products, there is a great importance of fodder cultivation to compensate fodder scarcity during lean period (Rabi crops remain dormant due to snow/ freezing temperatures). The best measure related to forage quality is animal productivity, which can be affected by nutrient intake, digestibility and utilization efficiency. Quality forage must have high intake, digestibility and efficient utilization. Physiological characteristics have significant impacts on growth and development of plants grown in production systems. Keeping the above facts in view, the present investigation was undertaken to identify the parents and their crosses for physiological and forage quality traits which are economically sustainable for forage yield and quality for sustainable consumption in hill agriculture

Fodder Yield, Nutrient Uptake and Quality of Oats (\u3cem\u3eAvena sativa\u3c/em\u3e L.) as Influenced by Different Agronomic Practices

The green fodder requirement and availability in India does not match and leaves a shortfall of about 63%. There is a little possibility of any tangible increase in fodder area due to competition from other economically competitive agricultural crops (Aulakh et al., 2012). Therefore, there is urgent need to maximize the tonnage and quality of fodder within the existing farming systems. Multicut nature of the crop ensures continuous supply of fodder. Kashmir valley possesses temperate type of climate, with snowfall and harsh conditions in the winter. Behaviour of crop under these conditions is entirely different from rest of country, which can be modified through different agronomic manipulations to derive maximum benefits. Sowing time has great impact on fodder yield. In agronomic techniques fertilizer management is the most important aspect. To improve supply of fodder over a period best cutting management needs to be evaluated. In view of these an experiment was undertaken to study the response of fodder oat to different sowing dates, fertility levels and cutting managements

Tuning the activity/stability balance of anion doped CoSxSe2−x dichalcogenides

We present a thorough assessment of the compositional dependent hydrogen evolution reaction (HER) activity and stability for Co-based mixed chalcogen, CoSxSe2−x, transition metal dichalcogenides (TMDs). In direct contrast to other reports on mixed chalcogen TMDs that have been limited to Mo and W, we observe a decrease in HER activity for any departure from the pure, single chalcogen composition, CoS2 and CoSe2. The single chalcogen TMDs are found to have nearly identical HER activity. Bulk resistivity of the pure and mixed chalcogen TMDs as well as the charge transfer resistance for the HER are found to be most optimal for CoSe2. However, CoSe2 is predicted to have an endothermic hydrogen adsorption free energy in contrast to the slightly exothermic hydrogen adsorption free energy for CoS2. This highlights the convolution of hydrogen adsorption free energy and material conductivity in determining the HER activity for even metallic conducting TMDs. Sulfur-rich Co-based TMDs with a pyrite-type crystal structure are found to quickly deactivate through loss of Co and formation of passivating reduced sulfur species at the surface while Se-rich compositions are observed to be more stable. Therefore, with an HER activity matching that of CoS2, but with a dramatic improvement in stability, CoSe2 breaks away from the traditional inverse activity – stability relationship and represents a promising non-PGM HER electrocatalyst for acidic PEM electrolyzers. © 2018 Elsevier Inc

Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.

The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein's surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of Thermococcus kodakarensis DNA polymerase.-Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis

Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of proteins found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over-represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution