Evolution of histone 2A for chromatin compaction in eukaryotes.

During eukaryotic evolution, genome size has increased disproportionately to nuclear volume, necessitating greater degrees of chromatin compaction in higher eukaryotes, which have evolved several mechanisms for genome compaction. However, it is unknown whether histones themselves have evolved to regulate chromatin compaction. Analysis of histone sequences from 160 eukaryotes revealed that the H2A N-terminus has systematically acquired arginines as genomes expanded. Insertion of arginines into their evolutionarily conserved position in H2A of a small-genome organism increased linear compaction by as much as 40%, while their absence markedly diminished compaction in cells with large genomes. This effect was recapitulated in vitro with nucleosomal arrays using unmodified histones, indicating that the H2A N-terminus directly modulates the chromatin fiber likely through intra- and inter-nucleosomal arginine-DNA contacts to enable tighter nucleosomal packing. Our findings reveal a novel evolutionary mechanism for regulation of chromatin compaction and may explain the frequent mutations of the H2A N-terminus in cancer

EXPOSING AND PROVIDING ACCESS TO INDIAN BIORESOURCE INFORMATION NETWORK (IBIN) SPECIES OCCURRENCE DATASET AS WEB SERVICE USING OGC WPS STANDARD

Species occurrence data are collected by many researchers worldwide as record of species present at a specific time at some defined place as part of biological field investigation serving as primary or secondary dataset. These datasets reside in separate silos across numerous distributed systems having different formats limiting its usage to full potential. IBIN portal provides a single window for accessing myriad spatial/non-spatial data on bioresources of the country. To promote reuse of occurrence dataset among organizations in an interoperable format including support for integration across various platforms & programming languages, it is been exposed as web service using OGC Web Processing Service (WPS) standard. WPS provides standardized interface for performing online geo-processing by exposing spatial processes, algorithms and calculations thereby enabling machine to machine communication and wider usage in various scenarios (e.g. service chaining etc.). Open source ZOO-project is used for developing the ‘Species Search’ WPS service. WPS takes inputs as either the species name or bounding box or shapefile defining the area of interest and returns queryable OGC complaint Web Map Service (WMS) as output with specie(s) occurrences represented in grid (5km x 5km) format, with each grid possessing attributes like specie(s) name, family, state, medicinal detail etc. WPS process can be invoked asynchronously, enabling proper feedback regarding status of the job submitted. JavaScript based web client for consuming this service has also been developed along with custom QGIS plugin to allow potential users to access the same in GIS software for wider reusability

DEVELOPMENT OF WEBGIS BASED REAL TIME ROAD TRAFFIC INFORMATION SYSTEM

Abstract. Rapid increase in road traffic density results into a serious problem of Traffic Congestion (TC) in cities. During peaks hours TC is very high and hence public search least congested path for their journeys in order to minimize ravel time and hence transportation cost. In this study, a new empirical model was developed to estimate congestion levels using real time road Traffic Parameters (TPs) such as vehicle density, speed, class and vehicle-to-vehicle (V2V) gap. These real time road TPs were collected using latest generation Inductive Loop Detector (ILD) technology. Further, a WebGIS based Road Traffic Information System (RTIS) for Dehradun city was developed for real time TD analyses and visualisation. This RTIS is very useful for public and user departments for planning and decision making processes. No other such system is available in India, which handles multiple traffic parameters simultaneously to provide solution of day-to-day problems. Document type: Articl

DEVELOPMENT OF WEBGIS BASED REAL TIME ROAD TRAFFIC INFORMATION SYSTEM

Rapid increase in road traffic density results into a serious problem of Traffic Congestion (TC) in cities. During peaks hours TC is very high and hence public search least congested path for their journeys in order to minimize ravel time and hence transportation cost. In this study, a new empirical model was developed to estimate congestion levels using real time road Traffic Parameters (TPs) such as vehicle density, speed, class and vehicle-to-vehicle (V2V) gap. These real time road TPs were collected using latest generation Inductive Loop Detector (ILD) technology. Further, a WebGIS based Road Traffic Information System (RTIS) for Dehradun city was developed for real time TD analyses and visualisation. This RTIS is very useful for public and user departments for planning and decision making processes. No other such system is available in India, which handles multiple traffic parameters simultaneously to provide solution of day-to-day problems

An improved parameter estimation and comparison for soft tissue constitutive models containing an exponential function

Motivated by the well-known result that stiffness of soft tissue is proportional to the stress, many of the constitutive laws for soft tissues contain an exponential function. In this work, we analyze properties of the exponential function and how it affects the estimation and comparison of elastic parameters for soft tissues. In particular, we find that as a consequence of the exponential function there are lines of high covariance in the elastic parameter space. As a result, one can have widely varying mechanical parameters defining the tissue stiffness but similar effective stress–strain responses. Drawing from elementary algebra, we propose simple changes in the norm and the parameter space, which significantly improve the convergence of parameter estimation and robustness in the presence of noise. More importantly, we demonstrate that these changes improve the conditioning of the problem and provide a more robust solution in the case of heterogeneous material by reducing the chances of getting trapped in a local minima. Based upon the new insight, we also propose a transformed parameter space which will allow for rational parameter comparison and avoid misleading conclusions regarding soft tissue mechanics

TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool.

BACKGROUND: Transmembrane proteins (TMPs) are the key components of signal transduction, cell-cell adhesion and energy and material transport into and out from the cells. For the deep understanding of these processes, structure determination of transmembrane proteins is indispensable. However, due to technical difficulties, only a few transmembrane protein structures have been determined experimentally. Large-scale genomic sequencing provides increasing amounts of sequence information on the proteins and whole proteomes of living organisms resulting in the challenge of bioinformatics; how the structural information should be gained from a sequence. RESULTS: Here, we present a novel method, TMFoldRec, for fold prediction of membrane segments in transmembrane proteins. TMFoldRec based on statistical potentials was tested on a benchmark set containing 124 TMP chains from the PDBTM database. Using a 10-fold jackknife method, the native folds were correctly identified in 77 % of the cases. This accuracy overcomes the state-of-the-art methods. In addition, a key feature of TMFoldRec algorithm is the ability to estimate the reliability of the prediction and to decide with an accuracy of 70 %, whether the obtained, lowest energy structure is the native one. CONCLUSION: These results imply that the membrane embedded parts of TMPs dictate the TM structures rather than the soluble parts. Moreover, predictions with reliability scores make in this way our algorithm applicable for proteome-wide analyses. AVAILABILITY: The program is available upon request for academic use

Rural-to-Urban Labor Migration, Household Livelihoods, and the Rural Environment in Chongqing Municipality, Southwest China

Rural migration and its relationship to the rural environment have attracted increasing research interest in recent decades. Rural migration constitutes a key component of human population movement, while rural areas contain most of the world’s natural resources such as land and forests. This study empirically evaluates a conceptual framework incorporating rural household livelihoods as an integrative mediating factor between rural migration and the rural environment in the context of rural-to-urban labor migration in Chongqing Municipality, Southwest China. The analysis draws on data collected through household surveys and key informant interviews from four villages. Results confirm the hypothesis that labor-migrant and non-labor-migrant households differ significantly in livelihood activities including agricultural production, agricultural technology use, income and consumption, and resource use and management. Implications for the subsequent environmental outcomes of rural labor out-migration and corresponding natural resource management and policy in rural origin areas are discussed