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Search Results: 1 - 10 of 8033 matches for " Jyotsna Sharma "
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Efficiency of microsatellite isolation from orchids via next generation sequencing  [PDF]
Madhav Pandey, Jyotsna Sharma
Open Journal of Genetics (OJGen) , 2012, DOI: 10.4236/ojgen.2012.24022
Abstract: Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic, co-dominant genetic markers commonly used for population genetics analyses although de novo development of species specific microsatellites is cost-and time-intensive. Orchidaceae is one of the most species-rich families of angiosperms with more than 30,000 species estimated. Despite its high species-diversity, microsatellites are available only for a few species and all were developed by only using Sanger sequencing methods. For the first time in orchids, we used 454 GS-FLX sequencing to isolate microsatellites in two species (Cypripedium kentuckiense and Pogonia ophioglossoides), and report preliminary results of the study. From 1/16th plate that was subjected to sequencing, 32,665 reads were generated, from which 15,473 fragments contained at least one SSR. We selected 20,697 SSRs representing di-, tri-, and tetra-nucleotides. While 3,674 microsatellites had flanking regions on both sides, useable primer pairs could be designed for 255 SSRs. The mean numbers of reads, SSRs, and SSR-containing reads useful for primer design estimated for other 15 orchid species using Sanger sequencing method were 166, 78 and 31, respectively. Results demonstrate that the efficiency of microsatellite isolation in orchids is substantially higher with 454 GS-FLX sequencing technique in comparison to the Sanger sequencing methods.
Disjunct Populations of a Locally Common North American Orchid Exhibit High Genetic Variation and Restricted Gene Flow  [PDF]
Madhav Pandey, Jyotsna Sharma
Open Journal of Genetics (OJGen) , 2015, DOI: 10.4236/ojgen.2015.54012
Abstract: Whether the persistence of natural plant populations is limited by genetic diversity, gene flow, or other ecological and evolutionary factors is an important question in plant population genetics. An assessment of the distribution of genetic variation within and among populations is thus useful for understanding broad-scale gene flow patterns in plants with diverse pollination syndromes. We studied Pogonia ophioglossoides (L.) Ker Gawl., which is self-compatible but a primarily outcrossing species in the Tribe Pogonieae in the family Orchidaceae. Using three self-developed, highly polymorphic nuclear microsatellite (simple sequence repeat, or SSR) markers and two chloroplast microsatellites, we assessed genetic variation in eight populations representing its natural distribution. Relatively high within-population genetic variation (mean An = 9.08, Ho = 0.44, and He = 0.71) was detected in P. ophioglossoides. Eleven different alleles and 13 unique haplotypes were detected for two cpDNA microsatellites. Genetic differentiation based on the hierarchical AMOVA showed that 21% (ФPT = 0.21, P = 0.000) and 63% (ФPT = 0.63, P = 0.000) of the nuclear and cpDNA microsatellite allelic diversity, respectively, was distributed among populations. Pairwise FST values ranged from 0.041 to 0.224 and each was statistically significant at P ≤ 0.05. The isolation by distance estimate did not show an association between genetic differentiation and geographic distance indicating that populations were diverging independently. We documented fine-scale spatial genetic structure (FSGS) up to 40 m distance in Texas. Overall, gene flow across the sampled populations of P. ophioglossoides appears restricted, and the short-distance SGS suggests localized seed dispersal in this locally common North American terrestrial orchid.
Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides
Kaushik Naveen K,Sharma Jyotsna,Sahal Dinkar
Malaria Journal , 2012, DOI: 10.1186/1475-2875-11-256
Abstract: Background A lack of vaccine and rampant drug resistance demands new anti-malarials. Methods In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. Results Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2) (X = F,ΔF) (Fm, ΔFm IC50 >100 μM)}, the lysine-branched,dimeric versions showed far greater potency {IC50 (μM) Fd 1.5 , ΔFd 1.39}. The more helical and proteolytically stable ΔFd was studied for mechanistic details. ΔFq, a K-K2 dendrimer of ΔFm and (ΔFm)2 a linear dimer of ΔFm showed IC50 (μM) of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (ΔFd), >20 (ΔFm)2 and 10 (ΔFq). FITC-ΔFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that ΔFd binds DNA. Trophozoites and schizonts incubated with ΔFd (2.5 μM) egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. Conclusion Good selectivity (>35), good resistance index (1.1) and low cytotoxicity indicate the promise of ΔFd against malaria.
Do Meio- and Macrobenthic Nematodes Differ in Community Composition and Body Weight Trends with Depth?
Jyotsna Sharma,Jeffrey Baguley,Bodil A. Bluhm,Gilbert Rowe
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014491
Abstract: Nematodes occur regularly in macrobenthic samples but are rarely identified from them and are thus considered exclusively a part of the meiobenthos. Our study compares the generic composition of nematode communities and their individual body weight trends with water depth in macrobenthic (>250/300 μm) samples from the deep Arctic (Canada Basin), Gulf of Mexico (GOM) and the Bermuda slope with meiobenthic samples (<45 μm) from GOM. The dry weight per individual (μg) of all macrobenthic nematodes combined showed an increasing trend with increasing water depth, while the dry weight per individual of the meiobenthic GOM nematodes showed a trend to decrease with increasing depth. Multivariate analyses showed that the macrobenthic nematode community in the GOM was more similar to the macrobenthic nematodes of the Canada Basin than to the GOM meiobenthic nematodes. In particular, the genera Enoploides, Crenopharynx, Micoletzkyia, Phanodermella were dominant in the macrobenthos and accounted for most of the difference. Relative abundance of non-selective deposit feeders (1B) significantly decreased with depth in macrobenthos but remained dominant in the meiobenthic community. The occurrence of a distinct assemblage of bigger nematodes of high dry weight per individual in the macrobenthos suggests the need to include nematodes in macrobenthic studies.
A Comparison of Hemoglobin Levels in Untreated and Treated Groups of HIV Patients on ART Including Zidovudine
Jitendra Singh Nigam,Jyotsna Naresh Bharti,Dinker Kumar,Ankit Sharma
Pathology Research International , 2013, DOI: 10.1155/2013/828214
Abstract: Objective. To assess the level of haemoglobin A2 in HIV patients on antiretroviral therapy (ART) including zidovudine with untreated HIV patients. Material and Methods. The study was a case control study. A total of 185 patients were included in the study; the case group included 125 HIV patients who were on antiretroviral therapy (ART) including zidovudine and 60 were in the control group who were not receiving ART. The high-performance liquid chromatography (HPLC) was done and hemoglobin A2 level was observed; value more than 3.5% was considered significant. The Hb A2 percentages of HIV patients were compared with those of control using an unpaired t-test. Results. The mean of Hb A2 in case group was 3.462% (SD 0.675) and in control group it was 2.815% (SD0.246). The higher Hb A2 value was seen in significant number of treated patients than control group ( ). Conclusion. The clinicians, pathologists, haematologists, and genetic counsellors should be aware of effects of nutritional anaemia and ART on Hb A2 to reduce the chances of misdiagnosis of β-thalassaemia especially in developing countries and for centres for antenatal screening. 1. Introduction Cooley and Lee were the first to describe the diminished rate of synthesis of one or more globin chains or its part, which consequently results in reduced rate of synthesis of the haemoglobin. Whipple and Bradford in 1936 gave the term “Thalassaemia” [1]. -thalassaemia is commonly seen in Mediterranean region, Indian subcontinent, Southeast Asia, and African ancestry [1]. For -thalassaemia, screening of populations was done either by measuring the haemoglobin A2 percentage or by red cell indices in patients with MCV or MCH below a certain cut-off point [1]. The haemoglobin A2 is 4%-5% in most cases of heterozygous or severe thalassaemia and 3.6–4.2% in heterozygous mild thalassaemia [1]. The raised Hb A2 values are seen in unstable haemoglobins, hyperthyroidism, and megaloblastic anaemia, and human-immunodeficiency-virus- (HIV-) infected patients on antiretroviral therapy, while hypochromic microcytic red cell picture is seen only in heterozygous -thalassaemia [2]. History, clinical details, and coexisting condition help to rule out the causes of increase in Hb A2, which can avoid unnecessary investigation and reduce the financial burden of institutional setting in developing countries. Awareness of the fact that there are increases in Hb A2 due to antiretroviral drugs among clinicians and pathologists should be must. Spiga et al. reported that zidovudine inhibits -globin gene expression in human
A New Approach to Software Development Fusion Process Model  [PDF]
Rupinder Kaur, Jyotsna Sengupta
Journal of Software Engineering and Applications (JSEA) , 2010, DOI: 10.4236/jsea.2010.310117
Abstract: There are several software process models that have been proposed and are based on task involved in developing and maintaining software product. The large number of software projects not meeting their expectation in terms of functionality, cost, delivery schedule and effective project management appears to be lacking. In this paper, we present a new software fusion process model, which depicts the essential phases of a software project from initiate stage until the product is retired. Fusion is component based software process model, where each component implements a problem solving model. This approach reduces the risk associated with cost and time, as these risks will be limited to a component only and ensure the overall quality of software system by considering the changing requirements of customer, risk assessment, identification, evaluation and composition of relative concerns at each phase of development process.
Cosine Modulated Non-Uniform Filter Banks  [PDF]
Jyotsna Ogale, Samrat Ashok
Journal of Signal and Information Processing (JSIP) , 2011, DOI: 10.4236/jsip.2011.23024
Abstract: Traditional designs for non-uniform filter bank (NUFB) are usually complex; involve complicated nonlinear optimization with a large number of parameters and lack of linear phase ([LP) property. In this paper, we describe a simple design method for multirate near perfect reconstruction (NPR) cosine modulated filter banks with non-uniform frequency spacing and linear phase property that involves optimization of only single parameter. It is derived from the uniform cosine modulated filter bank (CMFB) by merging some relevant band pass filters. The design procedure and the structure of the uniform CMFB are mostly preserved in the non-uniform implementation. Compared to other design methods our method provides very good design and converges very rapidly but the method is applicable, only if the upper band edge frequency of each non-uniform filter is an integral multiple of the bandwidth of the corresponding band. The design examples are presented to show the superiority of the proposed method over existing one.
Analysis of Fusion Process Model—Case Study  [PDF]
Rupinder Kaur, Jyotsna Sengupta
Journal of Software Engineering and Applications (JSEA) , 2012, DOI: 10.4236/jsea.2012.53019
Abstract: Fusion Process Model is a software process model to enhance the software development process. Fusion process model have five fundamental phases and one fusion process controller to control and co-ordinate the overall development process. Fusion Process Model uses 3C-Model to generalize the process of solving the problem in each phase. 3C-Model, which helps in implementing component based development approach and provides firmer control over the software development process. Because of the component driven approach, the risk associated with cost and time is limited to component only and ensure the overall quality of software system, reduce the development cost and time by considering the changing requirements of customer, risk assessment, identification, evaluation and composition of relative concerns at each phase of development process. We have implemented Fusion Process Model to the design of a real world information system and evaluated this implementation with the initial project estimation.
Assessment of Longitudinal Gradients in Nematode Communities in the Deep Northern Gulf of Mexico and Concordance with Benthic Taxa
Jyotsna Sharma,Jeffrey G. Baguley,Paul A. Montagna,Gilbert T. Rowe
International Journal of Oceanography , 2012, DOI: 10.1155/2012/903018
Abstract: Meiobenthic nematode assemblages were examined at 16 stations along two transects on the eastern and western boundaries of the deep northern Gulf of Mexico (dNGOM) at depths of 212–3000 m. The highest abundance (297 individuals 10 cm−2) and number of genera (71) occurred at stations near the Mississippi River delta. Number of genera decreased with increasing depth, and showed differences in community composition between the east and west regions. The dominant family, Comesomatidae, was represented by Sabatieria that was present at most shallow stations but absent at greater water depths. A significant difference in nematode feeding morphology was observed between depth groups but not between the two transects at different longitudes. Patterns of nematode community structure are congruent with harpacticoid copepods. Overall, the higher abundance and diversity of nematodes in the north-central Gulf of Mexico is consistent with findings of other benthic taxa and reflects organic material loading from the Mississippi River driving deep sea communities in the Gulf. The east-west gradient in composition of nematode communities suggests that nematode assemblages have well-defined distribution patterns similar to other meiobenthic taxa in the GOM but they are not aligned in the bathymetric zones observed in macrofauna, megafauna and demersal fishes.
Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill
Holly M. Bik, Kenneth M. Halanych, Jyotsna Sharma, W. Kelley Thomas
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038550
Abstract: Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.
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