Feasibility of Late Transplanted Summer Pearl Millet for Prolonged rabi Season With Integrated Nitrogen Management Under Indian Coastal Region

Experiments were conducted in coastal South Gujarat region of India to evaluate the feasibility of late transplanted summer pearl millet under prolonged rabi season with integrated nitrogen management (INM) during 2014, 2015 and 2016. INM treatments were consisted of four combinations of biocompost and inorganic nitrogen fertilizers. Two planting methods were evaluated, namely drilling and transplanting. Premature heading in transplanted pearl millet was observed up to 8-10% population during all the three experimental years, the possible causes for this are slow nitrogen availability, weather conditions, the thickness of the seedlings, root pruning and seedling age at transplanting. Application of 100% Recommended Dose of Fertilizer (RDF) + 5 t biocompost had significantly increased growth, yield (3862 kg ha-1), benefit-cost ratio (B:C ratio) (3.52) and quality of parameters of pearl millet followed by 75% Recommended Dose of Nitrogen (RDN) + 25% RDN through biocompost. Late transplanted summer pearl millet was little feasible to grow over timely drilled pearl millet as it had reduced pearl millet grain yield by 6.07% and also reduced the net profit by 72.46 US $ ha-1. However, overall, it was feasible to grow late transplanted pearl millet and gave yield up to 3150 kg ha-1 in prolonged rabi season condition for brining summer season well in time

The BioJS article collection of open source components for biological data visualisation.

Data-driven research has gained momentum in the life sciences. Visualisation of these data is essential for quick generation of hypotheses and their translation into useful knowledge. BioJS is a new proposed standard for JavaScript-based components to visualise biological data. BioJS is an open source community project that to date provides 39 different components contributed by a global community. Here, we present the BioJS F1000Research collection series. A total of 12 components and a project status article are published in bulk. This collection does not intend to be an all-encompassing, comprehensive source of BioJS articles, but an initial set; future submissions from BioJS contributors are welcome

Effect of weed and fertilizer management on weed control and productivity of onion (Allium cepa)

An experiment was conducted to examine the effect of weed management and plant nutrition practices on weed biomass, growth parameters and bulb yield of onion (Allium cepa L.). Weed management practices included alone application of herbicides, viz. pendimethalin, oxyfluorfen and fluazipop-p-butyl, their combination with hand weeding, weed free and weedy check. The crop was fertilized with three levels viz., 75% RDF, RDF (100:50:50 NPK kg/ha) and 125% RDF. The results indicated that weed management and fertilizer levels had a significant effect on weed population dynamics and onion bulb crop. The total weed density decreased significantly with application of pendimethalin 1 kg/ha or oxyfluorfen 0.24 kg/ha + one hand weeding at 40 days after transplanting (DAT) during both the seasons of investigation. Echinochloa ssp., Trianthema portulacastrum, Digera arvensis Forsk. Physalis minima L. and Cynodon dactylon (L.) Pers. were found as major weeds in the crop. Higher onion bulb yield (38.0 t/ha) was recorded with pendimethalin 1 kg/ha + one hand weeding at 40 DAT. The increase in yield was 83.7% compared to the yield obtain in weedy check. Increasing level of fertilizer applications increased the total biomass of grassy and broad leaves weeds. Application of 125% RDF significantly improved bulb yield and increase in yield was 19.4 and 10.5% over 75% RDF and RDF respectively. On the basis of interaction, combination of pendimethalin 1 kg/ha fb 1 hand weeding at 40 DAT and 100% RDF was most productive (39.8 t/ha) and profitable (Net return 2,69,422/ha and benefit: cost ratio 7.85)

GGE biplot based assessment of yield stability, adaptability and mega-environment characterization for hybrid pigeonpea (Cajanus cajan)

GGE biplot methodology is a powerful tool to study relationship among test environments (E), genotypes (G) and genotype-by-environment interaction (GE). Present study was conducted on 10 short-duration genotypes in five test environments for two years, and 16 medium-duration genotypes in six test locations for three years in randomized complete block design with two replications. In short-maturity group three mega-environments (ME) were found—ME1 comprised of Phaltan, Patancheru and Hyderabad1; ME2 and 3 constituted Jalna and Aurangabad, respectively. In scenario of limited resources, Patancheru may be a good testing location for general adaptability of short-duration hybrids, while Aurangabad and Hyderabad1 may be right environments for testing specific adaptation of short-duration cultivars in pigeonpea. ICPH 2433 was a winning genotype in ME1 in terms of high yield and stability. In medium-maturity group, two MEs were observed. Jalna, Jalna 1, Parbhani and Hyderabad grouped together as ME1, while Patancheru and Phaltan formed the second mega-environment (ME2). Parbhani was found to be most representative of all the six test locations. Jalna (ME1) and Phaltan (ME2) produced longest environment vectors, and hence may be regarded as highly discriminating. In mediummaturity group ICPH 2673 was found to be stable and high-yielding genotype for ME

RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization

To survive diverse host environments, the human pathogen Streptococcus pneumoniae must prevent its self-produced, extremely high levels of peroxide from reacting with intracellular iron. However, the regulatory mechanism(s) by which the pneumococcus accomplishes this balance remains largely enigmatic, as this pathogen and other related streptococci lack all known redox-sensing transcription factors. Here we describe a two-component-derived response regulator, RitR, as the archetype for a novel family of redox sensors in a subset of streptococcal species. We show that RitR works to both repress iron transport and enable nasopharyngeal colonization through a mechanism that exploits a single cysteine (Cys128) redox switch located within its linker domain. Biochemical experiments and phylogenetics reveal that RitR has diverged from the canonical two-component virulence regulator CovR to instead dimerize and bind DNA only upon Cys128 oxidation in air-rich environments. Atomic structures show that Cys128 oxidation initiates a "helical unravelling" of the RitR linker region, suggesting a mechanism by which the DNA-binding domain is then released to interact with its cognate regulatory DNA. Expanded computational studies indicate this mechanism could be shared by many microbial species outside the streptococcus genus

Morphological Classification of Galaxies by Shapelet Decomposition in the Sloan Digital Sky Survey

We describe application of the `shapelet' linear decomposition of galaxy images to morphological classification using images of $\sim$ 3000 galaxies from the Sloan Digital Sky Survey. After decomposing the galaxies we perform a principal component analysis to reduce the number of dimensions of the shapelet space to nine. We find that each of these nine principal components contains unique morphological information, and give a description of each principal component's contribution to a galaxy's morphology. We find that galaxies of differing Hubble type separate cleanly in the shapelet space. We apply a Gaussian mixture model to the 9-dimensional space spanned by the principal components and use the results as a basis for classification. Using the mixture model, we separate galaxies into seven classes and give a description of each class's physical and morphological properties. We find that several of the mixture model classes correlate well with the traditional Hubble types both in their morphology and their physical parameters (e.g., color, velocity dispersions, etc.). In addition, we find an additional class of late-type morphology but with high velocity dispersions and very blue color; most of these galaxies exhibit post-starburst activity. This method provides an objective and quantitative alternative to traditional and subjective visual classification.Comment: 21 pages, 16 figures, accepted by AJ, minor changes per the referee's comment

GGE biplot based assessment of yield stability, adaptability and mega-environment characterization for hybrid pigeon pea (Cajanus cajan

ABSTRACT GGE biplot methodology is a powerful tool to study relationship among test environments (E), genotypes (G) and genotype-by-environment interaction (GE). Present study was conducted on 10 short-duration genotypes in five test environments for two years, and 16 medium-duration genotypes in six test locations for three years in randomized complete block design with two replications. In short-maturity group three mega-environments (ME) were found-ME1 comprised of Phaltan, Patancheru and Hyderabad1; ME2 and 3 constituted Jalna and Aurangabad, respectively. In scenario of limited resources, Patancheru may be a good testing location for general adaptability of short-duration hybrids, while Aurangabad and Hyderabad1 may be right environments for testing specific adaptation of short-duration cultivars in pigeonpea. ICPH 2433 was a winning genotype in ME1 in terms of high yield and stability. In medium-maturity group, two MEs were observed. Jalna, Jalna 1, Parbhani and Hyderabad grouped together as ME1, while Patancheru and Phaltan formed the second mega-environment (ME2). Parbhani was found to be most representative of all the six test locations. Jalna (ME1) and Phaltan (ME2) produced longest environment vectors, and hence may be regarded as highly discriminating. In mediummaturity group ICPH 2673 was found to be stable and high-yielding genotype for ME1

Development of ‘super-early’ pigeonpeas with good yield potential from early × early crosses

To enhance the adaptability of pigeonpea at higher latitude and altitude, a breeding program was initiated at ICRISAT involving different sources of early-maturity. A full diallel mating design involving 11 early-maturing lines were used as parents. In F2–F5 generations, selection was followed for early flowering and maturity, grain yield and 100-seed weight by pedigree method. Four brown seeded (ICPX 060064-4-6-10, ICPX 060077-6-5-14, ICPX 060064-4-6-2 and ICPX 060063-11-8-4) and one cream seeded (ICPX 060036-13-4-8) F4/F5 indeterminate super-early progenies that matured, respectively 25 and 23 days earlier than the control cultivar ICPL 88039 were recovered. ICPX 060036-13-4-8 recorded 107% and 34% grain yield advantage over the checks ICPL 86022 and ICPL 88039, respectively. These super-early lines were derived from crosses involving AL 1518-2 × ICPL 85010, AL 1621 × MN 5, AL 1518-2 × MN 8 and MN 8 × AL 1518-2. Other super-early progenies [ICPX 060016-10-8-1 (from MN 1 × AL 1518-2 cross) and ICPX 060017-12-12-20 (from MN 1 × AL 1621 cross)] with greater 100-seed weight were also recovered. Besides serving as excellent donors for earliness, these lines may be photo/thermo insensitive. These super-early pigeonpea lines may open new niches for this crop and help in intensification of farming system

Prophylactic Delivery of a Bacteriophage Cocktail in Feed Significantly Reduces Salmonella Colonization in Pigs

Nontyphoidal Salmonella spp. are a leading cause of human food poisoning and can be transmitted to humans via consuming contaminated pork. To reduce Salmonella spread to the human food chain, bacteriophage (phage) therapy could be used to reduce bacteria from animals' preslaughter. We aimed to determine if adding a two-phage cocktail to feed reduces Salmonella colonization in piglets. This first required spray drying phages to allow them to be added as a powder to feed, and phages were spray dried in different excipients to establish maximum recovery. Although laboratory phage yields were not maintained during scale up in a commercial spray dryer (titers fell from 3 × 108 to 2.4 × 106 PFU/g respectively), the phage titers were high enough to progress. Spray dried phages survived mixing and pelleting in a commercial feed mill, and sustained no further loss in titer when stored at 4°C or barn conditions over 6 months. Salmonella-challenged piglets that were prophylactically fed the phage-feed diet had significantly reduced Salmonella colonization in different gut compartments (P < 0.01). 16S rRNA gene sequencing of fecal and gut samples showed phages did not negatively impact microbial communities as they were similar between healthy control piglets and those treated with phage. Our study shows delivering dried phages via feed effectively reduces Salmonella colonization in pigs. Infections caused by Salmonella spp. cause 93.8 million cases of human food poisoning worldwide, each year of which 11.7% are due to consumption of contaminated pork products. An increasing number of swine infections are caused by multidrug-resistant (MDR) Salmonella strains, many of which have entered, and continue to enter the human food chain. Antibiotics are losing their efficacy against these MDR strains, and thus antimicrobial alternatives are needed. Phages could be developed as an alternative approach, but research is required to determine the optimal method to deliver phages to pigs and to determine if phage treatment is effective at reducing Salmonella colonization in pigs. The results presented in this study address these two aspects of phage development and show that phages delivered via feed prophylactically to pigs reduces Salmonella colonization in challenged pigs

BioJS: An open source standard for biological visualisation - its status in 2014

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs