PRIVATE CLOUD INITIATIVES USING BIOINFORMATICS RESOURCES AND APPLICATIONS FACILITY (BRAF)

ABSTRACT The bioinformatics research community has a demand of enormous compute resources to run bioinformatics tools. Next generation sequencing technologies have further increased the overall demand for computational analysis. The traditional Cluster and Grid computing are having their own complexities to program and use while there is a silver-line in cloud for on-demand high-performance infrastructures with the advent of cloud computing era and its advantages. We have adopted the technology so that it can prove its mandate with more benefits to the community. We are able to bring out a private cloud using BRAF which is a high end cluster facility dedicated for bioinformatics. Open source equivalents to prominent commercially available solutions are used as the cloud middle-ware stack. In this paper we will summarize our implementation of a virtualized private cloud environment using Eucalyptus

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Not AvailableSoils of large areas of the globe are affected by deficiency or toxicity of iron (Fe), making it one of the major limitations to higher productivity of rice. Deficiency of Fe, an essential micronutrient for growth and development of rice, produces grain with low Fe-content. Consumption of low-Fe rice causes malnutrition affecting human health. Biofortification is an easy and low-cost way to enhance Fe content in rice, the staple food of more than half of the global population. Identification of relevant quantitative trait loci (QTLs) and genes controlling the stresses are needed for developing tolerant genotype(s). Fe deficiency is commonly observed in alkaline and aerobic soils, while toxicity is seen in low pH soils of lowland rice ecology. Rice plants cope up under deficiency or toxicity conditions through various morphological, physiological and differential gene expression strategies.Rice plant uses various transporter genes like OsNAS1, OsNAS2, OsIRT1, OsIRT2, OsNRAMP1, OsYSL15 and OsYSL16 under deficiency stress while OsIRT1, OsFRO2, OsVIT1, OsVIT2, OsNRAMP6, OsNAAT1, OsNAS3, OsNAC4, OsNAC5 and OsNAC6 under toxicity condition are involved for Fe homeostasis. Several QTLs including qFe3:1, qFe3:2, qFe7:1, qFe9:1, qFe9:2, qFe10:1, Fe11:1, qFe3.3 and qFe7.3 associated with grain-Fe content have been identified. Many Fe binding and transporters genes like OsZIP1, OsHMA4, OsACA2, OsZIP2, OsCNGC, OsZIP3, OsZIP5, OsZIP9, OsHma2, ABC transporter, OsNAS3, heavy metal transporter, Chy zinc finger and OsACA9 have been identified to improve grain-Fe content. Donor lines for grain-Fe content have been identified from rice germplasms showing even up to 147 μg g−1 in brown rice. Fe content in rice grain has been enhanced to many folds using ferritin genes of soybean and common bean, NAS gene and mugineic acid synthase genes (HvNAS1 and HvNAAT-A,-B or IDS3) of barley, nicotianamine transporter gene (OsYSL2) and nicotinamine synthase genes (OsNAS1, OsNAS2 and OsNAS3) through transgenic approach. The paper analyses the mechanisms of tolerance to Fe-deficiency and toxicity, identification of genes/QTLs responsible for tolerance under the stresses and helping for biofortification, assesses the stress affected symptoms, reviews the screening and summarizes the efforts for breeding programs for improving tolerance to Fe-deficiency and toxicity in rice.Not Availabl

Risk factors for Brucella spp. and Coxiella burnetii infection among small ruminants in Eastern India

Small ruminants are the main reservoirs for brucellosis and coxiellosis, two zoonotic diseases affecting livestock production, and posing a public health threat in India. Understanding disease prevalence and risk factors associated with small ruminant infection can help mitigate disease transmission. We report a cross-sectional survey in the states of Assam and Odisha in Eastern India. We interviewed 244 farmers to assess knowledge, attitude and practices relevant to brucellosis and coxiellosis infection. Serum samples from 411 goats and 21 sheep were analysed using enzyme-linked immunosorbent assay and Rose-Bengal Brucella agglutination plate test. Higher Brucella and Coxiella burnetii seroprevalence were found in Odisha (22% and 11.5%, respectively) than Assam (9.8% and 1.6%, respectively), and certain districts in Odisha were at higher risk. No association was found between seropositive animals and clinical signs, a challenge when attempting to identify seropositive animals in the herd. None of the farmers interviewed were aware of brucellosis, its aetiology, clinical form, or zoonotic risk. This study acts as a first indication of the extent of these diseases among small ruminants in these Indian states, highlighting how farming practices are associated with increased risk of infection. More research is urgently needed to mitigate zoonoses transmission in this region

From Molecular Signal Activation to Locomotion: An Integrated, Multiscale Analysis of Cell Motility on Defined Matrices

The adhesion, mechanics, and motility of eukaryotic cells are highly sensitive to the ligand density and stiffness of the extracellular matrix (ECM). This relationship bears profound implications for stem cell engineering, tumor invasion and metastasis. Yet, our quantitative understanding of how ECM biophysical properties, mechanotransductive signals, and assembly of contractile and adhesive structures collude to control these cell behaviors remains extremely limited. Here we present a novel multiscale model of cell migration on ECMs of defined biophysical properties that integrates local activation of biochemical signals with adhesion and force generation at the cell-ECM interface. We capture the mechanosensitivity of individual cellular components by dynamically coupling ECM properties to the activation of Rho and Rac GTPases in specific portions of the cell with actomyosin contractility, cell-ECM adhesion bond formation and rupture, and process extension and retraction. We show that our framework is capable of recreating key experimentally-observed features of the relationship between cell migration and ECM biophysical properties. In particular, our model predicts for the first time recently reported transitions from filopodial to “stick-slip” to gliding motility on ECMs of increasing stiffness, previously observed dependences of migration speed on ECM stiffness and ligand density, and high-resolution measurements of mechanosensitive protrusion dynamics during cell motility we newly obtained for this study. It also relates the biphasic dependence of cell migration speed on ECM stiffness to the tendency of the cell to polarize. By enabling the investigation of experimentally-inaccessible microscale relationships between mechanotransductive signaling, adhesion, and motility, our model offers new insight into how these factors interact with one another to produce complex migration patterns across a variety of ECM conditions

Mapping and pyramiding of two major genes for resistance to the brown planthopper (Nilaparvata lugens [Stål]) in the rice cultivar ADR52

The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most serious and destructive pests of rice, and can be found throughout the rice-growing areas of Asia. To date, more than 24 major BPH-resistance genes have been reported in several Oryza sativa ssp. indica cultivars and wild relatives. Here, we report the genetic basis of the high level of BPH resistance derived from an Indian rice cultivar, ADR52, which was previously identified as resistant to the whitebacked planthopper (Sogatella furcifera [Horváth]). An F2 population derived from a cross between ADR52 and a susceptible cultivar, Taichung 65 (T65), was used for quantitative trait locus (QTL) analysis. Antibiosis testing showed that multiple loci controlled the high level of BPH resistance in this F2 population. Further linkage analysis using backcross populations resulted in the identification of BPH-resistance (antibiosis) gene loci from ADR52. BPH25 co-segregated with marker S00310 on the distal end of the short arm of chromosome 6, and BPH26 co-segregated with marker RM5479 on the long arm of chromosome 12. To characterize the virulence of the most recently migrated BPH strain in Japan, preliminary near-isogenic lines (pre-NILs) and a preliminary pyramided line (pre-PYL) carrying BPH25 and BPH26 were evaluated. Although both pre-NILs were susceptible to the virulent BPH strain, the pre-PYL exhibited a high level of resistance. The pyramiding of resistance genes is therefore likely to be effective for increasing the durability of resistance against the new virulent BPH strain in Japan

Sensitivity of MRI Tumor Biomarkers to VEGFR Inhibitor Therapy in an Orthotopic Mouse Glioma Model

MRI biomarkers of tumor edema, vascular permeability, blood volume, and average vessel caliber are increasingly being employed to assess the efficacy of tumor therapies. However, the dependence of these biomarkers on a number of physiological factors can compromise their sensitivity and complicate the assessment of therapeutic efficacy. Here we examine the response of these MRI tumor biomarkers to cediranib, a potent vascular endothelial growth factor receptor (VEGFR) inhibitor, in an orthotopic mouse glioma model. A significant increase in the tumor volume and relative vessel caliber index (rVCI) and a slight decrease in the water apparent diffusion coefficient (ADC) were observed for both control and cediranib treated animals. This contrasts with a clinical study that observed a significant decrease in tumor rVCI, ADC and volume with cediranib therapy. While the lack of a difference between control and cediranib treated animals in these biomarker responses might suggest that cediranib has no therapeutic benefit, cediranib treated mice had a significantly increased survival. The increased survival benefit of cediranib treated animals is consistent with the significant decrease observed for cediranib treated animals in the relative cerebral blood volume (rCBV), relative microvascular blood volume (rMBV), transverse relaxation time (T2), blood vessel permeability (Ktrans), and extravascular-extracellular space (νe). The differential response of pre-clinical and clinical tumors to cediranib therapy, along with the lack of a positive response for some biomarkers, indicates the importance of evaluating the whole spectrum of different tumor biomarkers to properly assess the therapeutic response and identify and interpret the therapy-induced changes in the tumor physiology

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns