Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features

Background There is a need for software scripts and modules for format parsing, data manipulation, statistical analysis and annotation especially for tasks related to marker identification from sequence data and sequence diversity analysis. Results Here we present several new Perl scripts and a module for sequence data diversity analysis. To enable the use of these software with other public domain tools, we also make available PISE (Pasteur Institute Software Environment) wrappers for these Perl scripts and module. This enables the user to generate pipelines for automated analysis, since PISE is a web interface generator for bioinformatics programmes. Conclusion A new set of modules and scripts for diversity statistic calculation, format parsing and data manipulation are available with PISE wrappers that enable pipelining of these scripts with commonly used contig assembly and sequence feature prediction software, to answer specific sequence diversity related questions

Genetic diversity analysis using molecular marker in Terminalia chebula

Terminalia chebula is an important medicinal plant, extensively used in Ayurveda, Unani and Homoeopathic medicines. The present study was aimed to reveal its genetic diversity based on molecular markers from twelve T. chebula accessions. Molecular diversity was studied using RAPD markers. A total of 8 polymorphic primers produced 314 polymorphic bands and 195 monomorphic bands. Unweighted Pair Group Method with Arithmetic Mean (UPMGA) dendrogram divided the accessions into 2 major clusters. Accession IIHRTc2 and IIHRTc10 showed maximum genetic diversity with 55% similarity. This characterization based on molecular markers will help in identification of economically useful accessions for further crop improvement programme

Evaluation of Neonatal Streptozotocin Induced Diabetic Rat Model for the Development of Cataract

Type 2 diabetes (T2D) generally follows prediabetes (PD) conditions such as impaired fasting glucose (IFG) and/or impaired glucose tolerance (IGT). Although studies reported an association of IGT or IFG with cataract, the experimental basis for PD associated cataract is not known. Hence, we evaluated neonatal streptozotocin (nSTZ) induced rat model to study PD associated cataractogenesis by injecting STZ to two-day old rats. While majority (70%) of nSTZ injected pups developed IGT (nSTZ-PD) by two months but not cataract even after seven months, remaining (30%) nSTZ rats developed hyperglycemia (nSTZ-D) by two months and mature cataract by seven months. Lens biochemical analysis indicated increased oxidative stress as indicated by increased SOD activity, lipid peroxidation, and protein carbonyl levels in nSTZ-D cataractous lens. There was also increased polyol pathway as assessed by aldose reductase activity and sorbitol levels. Though nSTZ-PD animals have not shown any signs of lenticular opacity, insolubilization of proteins along with enhanced polyol pathway was observed in the lens. Further there was increased oxidative stress in lens of IGT animals. These results suggest that oxidative stress along with increased polyol pathway might play a role in IGT-associated lens abnormalities. In conclusion, nSTZ-PD rat model could aid to investigate IGT-associated lens abnormalities

Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features

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To Achieve An Optimal Tradeoff Between P2p Overlay Maintenance And Video Sharing Efficiency In Osn’s

Video sharing has been a gradually more popular application in OSNs facilitating users to share their personal videos or interesting videos they found with their friends. However OSN’s additional progress is strictly caught up by the inherent limits of the conventional client/server architecture of its video sharing system which is not only costly in terms of server storage and bandwidth but also not scalable with the high amount of users and video content in OSNs. The efforts have been dedicated to perk up the client/server architecture for video sharing with the peer-to-peer (P2P) architecture being the most promising. P2P-based video sharing has been used in on demand video streaming.The dimension reveals that mainly of the viewers of a user’s videos are the user’s close friends, most video views are driven by social relationships and the rest are driven by interests and viewers of the same video tend to live in the same location. Based on our observations we propose Social Tube a system that discover the social relationship interest resemblance and location to improve the presentation of video sharing in OSNs. Specifically an OSN has a social network (SN)-based P2P overlay construction algorithm that come together peers based on their social relationships and interests.

Erythrocyte aldose reductase activity and sorbitol levels in diabetic retinopathy

PurposeActivation of polyol pathway due to increased aldose reductase (ALR2) activity has been implicated in the development of diabetic complications including diabetic retinopathy (DR), a leading cause of blindness. However, the relationship between hyperglycemia-induced activation of polyol pathway in retina and DR is still uncertain. We investigated the relationship between ALR2 levels and human DR by measuring ALR2 activity and its product, sorbitol, in erythrocytes.MethodsWe enrolled 362 type 2 diabetic subjects (T2D) with and without DR and 66 normal subjects in this clinical case-control study. Clinical evaluation of DR in T2D patients was done by fundus examination. ALR2 activity and sorbitol levels along with glucose and glycosylated hemoglobin (HbA1C) levels in erythrocytes were determined.ResultsT2D patients with DR showed significantly higher specific activity of ALR2 as compared to T2D patients without DR. Elevated levels of sorbitol in T2D patients with DR, as compared to T2D patients without DR, corroborated the increased ALR2 activity in erythrocytes of DR patients. However, the increased ALR2 activity was not significantly associated with diabetes duration, age, and HbA1C in both the DR group and total T2D subjects.ConclusionsLevels of ALR2 activity as well as sorbitol in erythrocytes may have value as a quantitative trait to be included among other markers to establish a risk profile for development of DR

An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis...