EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

<p>Abstract</p> <p>Background</p> <p>Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSat<it>db </it>(<b>Eu</b>karyotic <b>MicroSat</b>ellite <b><it>d</it></b>ata<b><it>b</it></b>ase) <url>http://ipu.ac.in/usbt/EuMicroSatdb.htm</url> is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes.</p> <p>Description</p> <p>A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP). The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided.</p> <p>Conclusion</p> <p>The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.</p

PCR-based Methods for Identification and Detection of Phytophthora infestans in Infected Leaves of Tomato

Every year there is a huge amount of loss of tomato crop due to infection of late blight caused by P. infestans. To minimise this loss, it is important to visualise disease infection, so as the control measures can be taken up rapidly. The aim of this study was to develop a schematic protocol in order to examine the disease outbreak. P. infestans were isolated and identified based on morphological characteristics, serological and species-specific PCR assays. Ten samples were processed and examined morphologically and serologically (dipstick). However, on molecular examination only three isolates were confirmed as P. infestans. Four sets of PCR primers i.e., AE-7, O-8, INF, ITS 3 and ITS 4 were validated for accurate detection of P. infestans infection. All the sets of primers gave positive result by giving amplicons of expected size

MicroRNAs: potential targets for developing stress-tolerant crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20–24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties

Biofuels for Defence Use: Past, Present And Future

Defence sector desires to attain energy self-sufficiency and security. In recent years, emergence of biofuel as an alternative source has raised the hopes of Defence. Ethanol and bio-diesel are currently being used as blends in different parts of the world. While, bio-diesel is mostly being blended in 2-20% in different parts of the world, ethanol blending has reached upto 85%. Owing to the sustainability reasons, the choice of feedstock for ethanol production is gradually changing from corn to lignocelluloses biomass. Jatropha curcas, is still the choice feedstockfor bio-diesel in most third world countries. This institute has put in rigrous efforts to identify high yielding varieties of Jatropha, improving its yield, standardizing trans-esterification to obtain high quality bio-diesel and its trials and testing in various vehicles and equipment. Second generation biofuels using biomass such as farm and forest wastes as feedstocks are promising in terms of their overall sustainability and volume produced. They can be used as drop in fuels. However, time is required to utilize their potential fully. Algae, the third generation biofuel feedstock still needs extensive R&amp;D to make it economically sustainable. Whatever, the technology used, defence forces will accept any biofuel, which should be available constantly and priced below the existing petroleum fuels. The scope of producing by-products and finding a lucarative market for these products can ensure that prices ofbiofuels remain lower than the petroleum fuel

Cardiac surgery: What the future holds?

Cardiac surgery has been scrutinized and challenged as no other specialty has. That has brought new ideas and structural frameworks but has also brought uncertainty and scepticism

Identification of Abiotic Stress Responsive Genes from Indian High Altitude Lepidium latifolium L. (Short Communication)

Abiotic stresses are major environmental factors that periodically account for significant loss in crop productivity. In order to improve the abiotic stress tolerance in vegetable crops through transgenic approaches, authors isolated and cloned six up-regulated, LlaDREB1b (JN214345), LlaGPAT (JN398166), LlaNAC (FJ423495), LlaCIPK (FJ423496), LlaPR5 (GQ853409) and LlaIPK (FJ487575) and two down-regulated LlaRan (JN214347) and LlaDRT (JN214346) abiotic stress responsive genes from Indian high altitude Lepidium latifolium L. plant that that may be used for abiotic stress-tolerance engineering upon functional validation.Defence Science Journal, 2012, 62(5), pp.315-318, DOI:http://dx.doi.org/10.14429/dsj.62.149

Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome

Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome

Phenotypic detection and molecular characterization of beta-lactamase genes among Citrobacter species in a tertiary care hospital

Objective: To examine the distribution, emergence, and spread of genes encoding beta-lactamase resistance in Citrobacter species isolated from hospitalized patients in a tertiary care hospital. Methods: A prospective study was conducted in a 1000-bed tertiary care center in Pune, India from October 2010 to October 2013. A total of 221 Citrobacter spp. isolates were recovered from clinical specimens from different patients (one isolate per patient) admitted to the surgical ward, medical ward and medical and surgical Intensive Care Units. Polymerase chain reaction (PCR) assays and sequencing were used to determine the presence of beta-lactamase encoding genes. Conjugation experiments were performed to determine their transferability. Isolate relatedness were determined by repetitive element based-PCR, enterobacterial repetitive intergenic consensus-PCR and randomly amplified polymorphic DNA. Results: Among 221 tested isolates of Citrobacter spp. recovered from various clinical specimens, 179 (80.9%) isolates showed minimum inhibitory concentration (MIC) >4 μg/ml against meropenem and imipenem. One hundred and forty-five isolates with increased MICs value against carbapenems were further processed for molecular characterization of beta-lactamase genes. Susceptibility profiling of the isolates indicated that 100% retained susceptibility to colistin. Conjugation experiments indicated that blaNDM-1was transferable via a plasmid. Conclusion: The ease of NDM-1 plasmid transmissibility may help their dissemination among the Citrobacter species as well as to others in Enterobacteriaceae. Early detection, antimicrobial stewardship and adequate infection control measures will help in limiting the spread of these organisms