Genome analysis of amaranths: determination of inter- and intra-species variations

Amaranths are an important group of plants and include grain, vegetable and ornamental types. Despite the economic importance of the amaranths, there is very little information available about the extent and nature of genetic diversity present in the genus Amaranthus at molecular level. We now report the randomly amplified polymorphic DNA (RAPD) profiles of different species of Amaranthus as well as different accessions of the species. These RAPD analyses have been carried out using 65 arbitrary sequence decamer primers. From the RAPD data, an UPGMA dendrogram illustrating the inter-as well as intra-species relationships has been computed. The putative hybrid origin of A.dubious from A. hybridus and A. spinosus is also ruled out by the RAPD data. The trends of species relationships amongst the amaranths determined by RAPDs is consistent with their cytogenetic and evolutionary relationships that have already been determined

Patterns in abundance and diversity of faecally dispersed parasites of tiger in Tadoba National Park, central India

BACKGROUND: Importance of parasites in ecological and evolutionary interactions is being increasingly recognized. However, ecological data on parasites of important host species is still scanty. We analyze the patterns seen in the faecal parasites of tigers in the Tadoba National Park, India, and speculate on the factors and processes shaping the parasite community and the possible implications for tiger ecology. RESULTS: The prevalence and intensities were high and the parasite community was dominated by indirect life cycle parasites. Across all genera of parasites variance scaled with the square of the mean and there was a significant positive correlation between prevalence and abundance. There was no significant association between different types of parasites. CONCLUSIONS: The 70 samples analyzed formed 14 distinct clusters. If we assume each of the clusters to represent individual tigers that were sampled repeatedly and that resident tigers are more likely to be sampled repeatedly, the presumed transient tigers had significantly greater parasite loads than the presumed resident ones

Spectral properties of entanglement witnesses

Entanglement witnesses are observables which when measured, detect entanglement in a measured composed system. It is shown what kind of relations between eigenvectors of an observable should be fulfilled, to allow an observable to be an entanglement witness. Some restrictions on the signature of entaglement witnesses, based on an algebraic-geometrical theorem will be given. The set of entanglement witnesses is linearly isomorphic to the set of maps between matrix algebras which are positive, but not completely positive. A translation of the results to the language of positive maps is also given. The properties of entanglement witnesses and positive maps express as special cases of general theorems for $k$-Schmidt witnesses and $k$-positive maps. The results are therefore presented in a general framework.Comment: published version, some proofs are more detailed, mistakes remove

Exploring entity-centric methods in the UK Government Web Archive

Being able to explore large digital collections effectively is of interest to both academics and practitioners alike. The need to go beyond the provision of keyword-driven functionality to features that support exploration and discovery is widely recognised. In addition, providers are seeking to support more diverse groups of users with varying information needs and tasks. Increasing amounts of cultural heritage are being stored in web archives that present unique challenges as a form of digital cultural heritage. This paper describes a collaboration between the University of Sheffield and the UK National Archives to investigate entity-based methods for exploring the UK Government Web Archive

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state

Continuing mortality of vultures in India associated with illegal veterinary use of diclofenac and a potential threat from nimesulide

AbstractThe collapse of South Asia's Gyps vulture populations is attributable to the veterinary use of the non-steroidal anti-inflammatory drug (NSAID) diclofenac. Vultures died after feeding on carcasses of recently-medicated animals. The governments of India, Nepal and Pakistan banned the veterinary use of diclofenac in 2006. We analysed results of 62 necropsies and 48 NSAID assays of liver and/or kidney for vultures of five species found dead in India between 2000 and 2012. Visceral gout and diclofenac were detected in vultures from nine states and three species: Gyps bengalensis, Gyps indicus and Gyps himalayensis. Visceral gout was found in every vulture carcass in which a measurable level of diclofenac was detected. Meloxicam, an NSAID of low toxicity to vultures, was found in two vultures and nimesulide in five vultures. Nimesulide at elevated tissue concentrations was associated with visceral gout in four of these cases, always without diclofenac, suggesting that nimesulide may have similar toxic effects to those of diclofenac. Residues of meloxicam on its own were never associated with visceral gout. The proportion of Gyps vultures found dead in the wild in India with measurable levels of diclofenac in their tissues showed a modest and non-significant decline since the ban on the veterinary use of diclofenac. The prevalence of visceral gout declined less, probably because some cases of visceral gout from 2008 onwards were associated with nimesulide rather than diclofenac. Veterinary use of nimesulide is a potential threat to the recovery of vulture populations.Financial support and assistance for the project from the Director, Indian Veterinary Research Institute (IVRI), the UK Government’s Darwin Initiative and the Royal Society for the Protection of Birds is gratefully acknowledged.This is the accepted manuscript. The final version is available from Cambridge University Press via http://dx.doi.org/10.1017/S003060531500037

A different approach to soil analysis: Indicative studies

Soil analysis is a tool that has been employed with the primary goal of providing recommendations for soil rectification, crop productivity and for soil health management. Time tested methods like ammonium acetate extraction and diethylene triamine penta acetic acid (DTPA) are commonly used for analysis of bioavailable nutrients. However, there are some limitations to these methods as both extraction fluids are buffered to neutral or near-neutral pH. Hence extracted nutrients represent a “potential or ideal-case” fertility status of soil instead of an “actual” field status. In the ‘Regular methods’, we are overlooking the role of pH, the master variable, in determining the availability of nutrients. Hence, in ‘Modified methods’, the extraction fluid is buffered to actual soil pH. Results obtained with over 150 random samples representing a range of pH, have indicated a difference in values between regular and modified extraction methods. The modified methods (MM) of ammonium acetate and DTPA extraction adjusted to soil pH were found to be better than regular method (RM) for estimation of calcium, magnesium with ammonium acetate and iron and manganese with DTPA in alkaline soils above pH 8.0. For a complete picture of soil health, productivity and fertility, microbiological and enzymatic analysis of soils were included in the present study. Soil solution equivalent medium (SSE) was found to be the appropriate culture medium for microbial counts. A linear relationship was found between urease activity and available nitrogen of soil

Trends in Metal Oxide Stability for Nanorods, Nanotubes, and Surfaces

The formation energies of nanostructures play an important role in determining their properties, including the catalytic activity. For the case of 15 different rutile and 8 different perovskite metal oxides, we find that the density functional theory (DFT) calculated formation energies of (2,2) nanorods, (3,3) nanotubes, and the (110) and (100) surfaces may be described semi-quantitatively by the fraction of metal--oxygen bonds broken and the bonding band centers in the bulk metal oxide

Mariculture of mussels in India

Worldwide, bivalves are recognised as a source of inexpensive protein of high nutritional value. In India bivalve resources are still exploited at a subsis tence level. The growth performance, natural abundance, adaptability to new environment, simple and inexpensive culture techniques have made mussel a candidate species for culture operations. The bivalve mussels of the genus Perna are ex tensively cultured in Thailand, Philippines and New Zealand

Getting a Head Start: Diet, Sub-Adult Growth, and Associative Learning in a Seed-Eating Passerine

Developmental stress, and individual variation in response to it, can have important fitness consequences. Here we investigated the consequences of variable dietary protein on the duration of growth and associative learning abilities of zebra finches, Taeniopygia guttata, which are obligate graminivores. The high-protein conditions that zebra finches would experience in nature when half-ripe seed is available were mimicked by the use of egg protein to supplement mature seed, which is low in protein content. Growth rates and relative body proportions of males reared either on a low-protein diet (mature seed only) or a high-protein diet (seed plus egg) were determined from body size traits (mass, head width, and tarsus) measured at three developmental stages. Birds reared on the high-protein diet were larger in all size traits at all ages, but growth rates of size traits showed no treatment effects. Relative head size of birds reared on the two diets differed from age day 95 onward, with high-diet birds having larger heads in proportion to both tarsus length and body mass. High-diet birds mastered an associative learning task in fewer bouts than those reared on the low-protein diet. In both diet treatments, amount of sub-adult head growth varied directly, and sub-adult mass change varied inversely, with performance on the learning task. Results indicate that small differences in head growth during the sub-adult period can be associated with substantial differences in adult cognitive performance. Contrary to a previous report, we found no evidence for growth compensation among birds on the low-protein diet. These results have implications for the study of vertebrate cognition, developmental stress, and growth compensation