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Identification of SNPs in Goats (Capra hircus) using RNA-Seq Analysis
Upasna Sharma,Priyanka Banerjee,Jyoti Joshi,Ramesh Kumar vijh
International Journal of Animal and Veterinary Advances , 2012,
Abstract: Single Nucleotide Polymorphisms (SNPs) have become the marker of choice for genome-wide association studies. In order to provide the best genome coverage for the analysis of performance and production traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves be causative SNPs for traits. The main objective of our work was to identify large numbers of gene-associated SNPs using high-throughput next generation sequencing. Transcriptome sequencing was conducted on 2 tissues viz. liver and kidney for 5 breeds of goat (Kanniadu, Osmanabadi, Black Bengal, Changthangi and Sirohi) using Illumina next generation sequencing technology. Approximately 46.4 million reads for Black Bengal, 61.9 from Kanniadu, 58.2 from Changthangi, 47.3 from Osmanabadi, 73.2 from Sirohi were obtained by sequencing gene transcripts derived from kidney while 37, 27.2, 19.4, 56.9 and 80.7 million reads were obtained by gene transcripts derived from liver. The analysis of total number of SNPs in liver and kidney revealed that out of a total of 68597 SNPs in liver, the total number of transversions was 21300 and the number of transitions was 47297. A total of 1574 SNPs of liver were complex. Similarly for kidney the total number of 72047 SNPs were categorised into 22774 transversions and 49273 transitions. The total number of complex SNPs in kidney was 1597. The number of transitions is more than double the number of transversions in both the tissues. Further analysis of transversion revealed a preponderance of cytosine and guanine change compared to other nucleotides. 12863 and 11319 transversions out of 21300 and 22774 transversions respectively for liver and kidney revealed this bias. When multiple individuals with different genetic backgrounds were used, RNA-Seq was very effective for the identification of SNPs. The SNPs identified in this report provides a much needed resource for genetic studies in goat and shall contribute to the development of a highdensity SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for genome association studies and whole genome-based selection in goats.
Ubiquitous Expression of Genes in tissues of Goat (Capra hircus) Using RNA-seq
Upasna Sharma,Priyanka Banerjee,Jyoti Joshi,Ramesh Kumar vijh
International Journal of Animal and Veterinary Advances , 2012,
Abstract: Since very little information is available on goat transcriptome (only few sequenced genes and ESTs are available in the database), our main aim was to analyze the goat transcriptome for identification of ubiquitous genes through RNA-Seq approach, expression of genes across tissues and analyse the functional pathways which these highly expressed genes follow. RNA-Seq analysis was carried out on 10 tissues of Osmanabadi goats. The data was 2x76 base pair paired end reads generated using Illumina Genome Analyser GAIIx. More than 40 million reads per tissue were generated. The data was mapped using CLC Genomics Workbench on Ensembl cattle (Btau_4.0) genes version 62 downloaded from BioMart. The mapping statistics was discerned for each of the mapped gene for all the 10 tissues. There was a great deal of homology between the genes of cattle and goats and this was expected as both are ruminants and phylogenetically close to one another. The expression profile for genes of each of the 10 tissues was calculated in terms of RPKM values. The differential expression of genes among the different tissues was carried out using 3 algorithms. The genes common among the 3 algorithms were associated with GO IDs and the functional annotation was carried out by estimating the GO term occurrences using CateGOrizer web server. The study revealed that more than 75% genes are ubiquitously expressed (expressed in all tissues) with very limited number of tissue specific genes based on expression values (expressed in only one tissue). These genes are mostly related with the specific functions performed by various tissues.
Population Differentiation in Dromedarian Camel: A Comparative Study of Camel Inhabiting Extremes of Geographical Distribution
Priyanka Banerjee,Jyoti Joshi,Upasna Sharma,Ramesh Kumar Vijh
International Journal of Animal and Veterinary Advances , 2012,
Abstract: The camel has not been subject to selective pressures and is not differentiated. The present study was undertaken to evaluate differentiation of camels inhabiting the extreme geographical habitats for the species. In this paper we compared the camel populations of India and Southern region of Africa to adjudge the differentiation between the two populations. Utilizing 12 microsatellite loci it has been demonstrated that the populations i.e., of India and South Africa are very well differentiated. The camel population of India shows differentiation among themselves owing to selection pressure and breeding for specific economic traits/parameters like carting, baggage, riding etc. The differentiation among the two camel populations was 23% while that of among population, within the two groups was 11%. A small group of Bactrian camel exhibited closeness to hill camels. Based on the published literature and in the present study it is evident that there is a general trend of increased population differentiation from South region of Africa to Indian subcontinent with India having highly differentiated populations.
Genetic Discontinuities and Sub structuring in buffaloes of Indo Gangetic Plains
Upasna Sharma,Priyanka Banerjee,Jyoti Joshi,Ramesh Kumar vijh
International Journal of Animal and Veterinary Advances , 2012,
Abstract: The Indo-Gangetic plains of India are fertile basin and have more than 23% buffaloes of India. Bhadawari is the only one recognised breed of buffalo in the basin. The population structure of this vast buffalo population was not known. In this present study, we generated data on 11 microsatellite markers on 625 buffaloes from Indo- Gangetic plains. We utilised landscape genetic tools combining molecular genetic data and spatial coordinates to decipher the genetic structure. We utilised wombling analysis and Bayesian clustering using Markov models. We also utilised Monmonier’s maximal difference algorithm for the identification of genetic barriers and tested their significance using 16 different genetic distances. The Womble analysis revealed three statistically significant barriers. The genetic bandwidth mapping revealed that buffaloes of Tarai area and Bhadawari buffaloes to have distinctive population structure. The buffaloes of Mau, Balia and Ghazipur also had a distinctive genetic structure. Most of the buffaloes of Central region of Indo-Gangetic plains were found to be heterogeneous. The variation in allele frequency in buffalo population in Indo Gangetic plains occurred at multiple scales. A sharp change in allele frequency in Eastern and Western Uttar Pradesh buffaloes was observed and detectable by all the techniques utilised and the buffalo population could be substructured into 5 clusters.
Identification of Key Contributory Factors Responsible for Vascular Dysfunction in Idiopathic Recurrent Spontaneous Miscarriage
Priyanka Banerjee, Sanghamitra Ghosh, Mainak Dutta, Elavarasan Subramani, Jaydeep Khalpada, Sourav RoyChoudhury, Baidyanath Chakravarty, Koel Chaudhury
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080940
Abstract: Poor endometrial perfusion during implantation window is reported to be one of the possible causes of idiopathic recurrent spontaneous miscarriage (IRSM). We have tested the hypothesis that certain angiogenic and vasoactive factors are associated with vascular dysfunction during implantation window in IRSM and, therefore, could play a contributory role in making the endometrium unreceptive in these women. This is a prospective case-controlled study carried out on 66 women with IRSM and age and BMI matched 50 fertile women serving as controls. Endometrial expression of pro-inflammatory (IL-1β, TNF-α, IFN-γ, TGF-β1), anti-inflammatory (IL-4, -10), angiogenesis-associated cytokines (IL-2, -6, -8), angiogenic and vasoactive factors including prostaglandin E2 (PGE2), vascular endothelial growth factor (VEGF), endothelial nitric oxide synthase (eNOS), nitric oxide (NO) and adrenomedullin (ADM) were measured during implantation window by ELISA. Subendometrial blood flow (SEBF) was assessed by color Doppler ultrasonography. Multivariate analysis was used to identify the significant factor(s) responsible for vascular dysfunction in IRSM women during window of implantation and further correlated with vascular dysfunction. Endometrial expression of pro-inflammatory cytokines and PGE2 were up-regulated and anti-inflammatory and angiogenesis-associated cytokines down-regulated in IRSM women as compared with controls. Further, the angiogenic and vasoactive factors including VEGF, eNOS, NO and ADM were found to be down-regulated and SEBF grossly affected in these women. Multivariate analysis identified IL-10, followed by VEGF and eNOS as the major factors contributing towards vascular dysfunction in IRSM women. Moreover, these factors strongly correlated with blood flow impairment. This study provides an understanding that IL-10, VEGF and eNOS are the principal key components having a contributory role in endometrial vascular dysfunction in women with IRSM. Down-regulation of these factors is also associated with impaired endometrial perfusion which possibly makes the endometrium unreceptive that may eventually cause early pregnancy loss.
Modified Shuffled Frog Leaping Algorithm for Solving Economic Load Dispatch Problem  [PDF]
Priyanka Roy, A. Chakrabarti
Energy and Power Engineering (EPE) , 2011, DOI: 10.4236/epe.2011.34068
Abstract: In the recent restructured power system scenario and complex market strategy, operation at absolute minimum cost is no longer the only criterion for dispatching electric power. The economic load dispatch (ELD) problem which accounts for minimization of both generation cost and power loss is itself a multiple conflicting objective function problem. In this paper, a modified shuffled frog-leaping algorithm (MSFLA), which is an improved version of memetic algorithm, is proposed for solving the ELD problem. It is a relatively new evolutionary method where local search is applied during the evolutionary cycle. The idea of memetic algorithm comes from memes, which unlike genes can adapt themselves. The performance of MSFLA has been shown more efficient than traditional evolutionary algorithms for such type of ELD problem. The application and validity of the proposed algorithm are demonstrated for IEEE 30 bus test system as well as a practical power network of 203 bus 264 lines 23 machines system.
Optimum Probability Distribution for Minimum Redundancy of Source Coding  [PDF]
Om Parkash, Priyanka Kakkar
Applied Mathematics (AM) , 2014, DOI: 10.4236/am.2014.51011

In the present communication, we have obtained the optimum probability distribution with which the messages should be delivered so that the average redundancy of the source is minimized. Here, we have taken the case of various generalized mean codeword lengths. Moreover, the upper bound to these codeword lengths has been found for the case of Huffman encoding.

An Algorithm to Generate Probabilities with Specified Entropy  [PDF]
Om Parkash, Priyanka Kakkar
Applied Mathematics (AM) , 2015, DOI: 10.4236/am.2015.612174
Abstract: The present communication offers a method to determine an unknown discrete probability distribution with specified Tsallis entropy close to uniform distribution. The relative error of the distribution obtained has been compared with the distribution obtained with the help of mathematica software. The applications of the proposed algorithm with respect to Tsallis source coding, Huffman coding and cross entropy optimization principles have been provided.
Predicting Multiple-Borrowing Default among Microfinance Clients  [PDF]
Kanish Debnath, Priyanka Roy
Theoretical Economics Letters (TEL) , 2018, DOI: 10.4236/tel.2018.810116
Abstract: In order to control over-indebtedness that often leads to capacity failure, the Reserve Bank of India recently issued directives for Micro Finance Institutions to restrict multiple loans to borrowers. These institutions are also required to regularly share their current borrowers’ loan records with a Credit Information Company. We argue here that ex-post loan record verification is inefficient and inadequate considering the socio-economic and informational asymmetries in micro-credit markets. Instead, we reason, household characteristics can predict multiple-borrowing behaviour. Our empirical analysis shows that this is true to some extent. We dwell on policy implications and ways to improve our model.
Optimization of conditions for in vitro seed germination and shoot multiplication of Aconitum heterophyllum Wall
Priyanka SOLANKI,Priyanka SIWACH
International Journal of Medicinal and Aromatic Plants , 2012,
Abstract: Aconitum heterophyllum is a critically endangered medicinal plant species of Indian Himalayas. Micropropagation of this plant is considered important for its ex-situ conservation as well as to generate large scale planting material for commercial supply. During the present study, seeds were taken as starting material. Seeds of A. heterophyllum are associated with a dormancy period and so optimization of conditions was needed for in vitro germination. Mechanical scarification of seeds by rubbing between hands (to crack the seed coat randomly) reduced the microbial contamination and was also found essential for germination, as seeds with no mechanical treatment could not germinate. Further, germination could be observed only on cotton moistened with distilled water; MS medium was found inhibitory for in vitro seeds germination. The soaking of seeds at low temperature (4oC) for 72 hours, before culturing, enhanced the germination frequency to 95.83%. Amongst various parts of seedling used for in vitro shoot induction, shoot organogenesis was obtained only from plumule tip and that too on MS media with 0.5ml/l BAP.
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