Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies

Peripheral ameloblastoma of the gingiva

Peripheral Ameloblastoma (PA) is a benign odontogenic tumor, arising from the cell rest of Serres, reduced enamel epithelium and basal cells of the surface epithelium. Peripheral ameloblastoma is a rare odontogenic neoplasm occurring commonly in the mandibular gingiva. PA clinically resembles other peripherally occurring lesions like pyogenic granuloma, peripheral ossifying fibroma, peripheral giant cell granuloma, and squamous papilloma. The recurrence rate of PA is 16-19% which demands a straight follow up. We report a case of recurrent peripheral ameloblastoma occurring in a 72-year old male located in the mandibular lingual gingiva in relation to the 44, 45 element’s regions. The patient had a primary lesion excised from the same site 6 years before which was diagnosed as ameloblastoma

WITHDRAWN: Analysis, design and experimentation of Switched Reluctance Hub Motor

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Neutrophils-A key component of ischemia-reperfusion injury

Ischemia-reperfusion injury (IRI) is a common occurrence following myocardial infarction, transplantation, stroke, and trauma that can lead to multiple organ failure, which remains the foremost cause of death in critically ill patients. Current therapeutic strategies for IRI are mainly palliative, and there is an urgent requirement for a therapeutic that could prevent or reverse tissue damage caused by IRI. Neutrophils are the primary responders following ischemia and reperfusion and represent important components in the protracted inflammatory response and severity associated with IRI. Experimental studies demonstrate neutrophil infiltration at the site of ischemia and show that inducing neutropenia can protect organs from IRI. In this review, we highlight the mechanisms involved in neutrophil recruitment, activation, and adherence and how this contributes to disease severity in IRI. Inhibiting neutrophil mobilization, tissue recruitment, and ultimately neutrophil-associated activation of local and systemic inflammatory responses may have therapeutic potential in the amelioration of local and remote tissue damage following IRI. Copyrigh

User-Centric Design for Mathematical Web Services

A web service is a programmatically available application logic exposed over the internet and it has attracted much attention in recent years with the rapid development of e-commerce. Very few web services exist in the field of mathematics. The aim of this paper is to seamlessly provide user-centric mathematical web services to the service requester. In particular, this paper focuses on mathematical web services for prepositional logic and set theory which comes under discrete mathematics. A sophisticated user interface with virtual keyboard is created for accessing web services. Experimental results show that the web services and the created user interface are efficient and practical

Irredundant and open irredundant colorings of graphs

An irredundant( open irredundant) coloring of a graph G = (V, E) is a partition of V(G) into irredundant(open irredundant) sets. The irratic number X_ir(G) (open irratic number X_oir(G)of a graph G equals the minimum order of an irredundant (open irredundant) coloring of G. In this paper we present several results on these two parameters

Rate-induced tipping and regime shifts in a spatial ecological system

We study how a rate of environmental change affects stability and persistence of an ecological community. Using an explicit rate of change in the environmental parameters of a spatially coupled ecological system, we study the rate-dependent responses associated with extinction of a metacommunity. Our results elucidate various scenarios of rate-induced extinction (R-tipping) such as tipping through increasing amplitude of oscillations, tipping through synchronized dynamics, and tipping through tracking unstable states. Further, we show rate-dependent delayed responses away from bifurcation points, but with tracking unstable states. Our results emphasize that the rate of environmental change can reveal the unexpected extinction dynamics which may not be predicted from stable equilibrium states and bifurcation points of the system. Thus, our results illustrate the importance of rate-dependent responses to understand stability and persistence of an ecological system

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Not AvailableAvailability of transcriptome datasets for use in accelerated molecular-based breeding in Musa species is limited. Illumina Hiseq technology was employed to determine differential gene expression between the contrasting cultivars for three different stresses (Eumusae leaf spot –Mycosphaerella eumusae, root lesion nematode – Pratylenchus coffeae and moisture deficit stress) under challenged and unchallenged conditions. An average of 34.72 million of reads was assembled into *47629 contigs, and *5,466 simple sequence repeats (SSR) from each library were identified. GO annotation and KEGG pathway analysis were carried for all the transcripts and the SSR, SNPs were also detected. Based on this information, a MusatransSSRDB has been developed. Currently, the database consists of 32,800 SSRs with the unique information like putative function of the SSR-containing genes and their metabolic pathway and expression profiling under various stress conditions. This database provides information on in silico polymorphic SSRs (2830 SSRs) between the contrasting cultivars for each stress and within stress. Information on in silico polymorphic SSRs specific to differentially expressed genes under challenged condition for each stress can also be accessed. This database facilitates the retrieval of results by navigating the tabs for cultivars, stress and polymorphism. This database was developed using HTML, Java and PHP; datasets are stored in MySQL database and accessible in the public domain (http://bioinfnrcb.byethost7.com/nrcbbio/). This unique information facilitates the banana breeder to select the SSR primers based on specific objectives. MusatransSSRDBalong with other genomics databases will facilitate the genetic dissection and breeding for complex traits in banana. Thus,this database is a step forward in economizing cost, time, manpower and other resources.ICAR, NPTC–Functional Genomics

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Not AvailableLong non-coding RNAs (lncRNAs) are important regulators of gene expression in plant response to biotic and abiotic stresses. The participation of lncRNAs in plant disease resistance in bananas is largely unknown. Therefore, we attempted to identify novel lncRNAs responsive to Mycosphaerella eumusae, a causative agent of Eumusae leaf spot disease and root lesion nematode, Pratylenchus coffeae and their differential expression patterns during stress and normal conditions in respective resistant and sensitive banana genotypes. Illumina paired-end transcriptome sequencing of control and infected samples of resistant and sensitive banana cultivars was performed and the sequence reads assembled into 172434, 201256 transcriptional units (TUs) for M. eumusae and P. coffeae, respectively. The genome-wide analysis for ELSD-responsive lncRNAs led to identification of 5142 novel lncRNAs including 3031-intergenic, 1672-intragenic, and 440 antisense lncRNAs classes collectively from ELSD-resistant and sensitive cultivars. Similarly, 5615 lncRNAs comprised of 3283 intergenic, 1878-intragenic, and 454 antisense classes were identified from P. coffeae-infected resistant and sensitive banana cultivars. Most of the lncRNAs were stress specific, evenly distributed among banana chromosomes and the average length is ranging from 620 to 684 nucleotides. In addition, 1250 and 1284 lncRNAs were differentially expressed to M. eumusae and P. coffeae infections, respectively. The LncRNA–mRNA interaction-based functional role showed lncRNA-mediated downregulation of horcolin, an antifungal protein is likely responsible for ELSD sensitivity in banana cultivars. Furthermore, we identified 100 of these lncRNAs also play a role in drought stress response of banana indicating a possible crosstalk between biotic and abiotic stresses.NPTC-Functional Genomics component of the Indian Council of Agricultural Research (ICAR), India