QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci. It provides a platform for the data mining of abiotic stress responsive QTLs, as well as browsing and annotating associated traits, their location on a sequenced genome, mapped expressed sequence tags (ESTs) and tissue and growth stage-specific expressions on the whole genome. Information on QTLs related to abiotic stresses and their corresponding loci from a genomic perspective has not yet been integrated on an accessible, user-friendly platform. QlicRice offers client-responsive architecture to retrieve meaningful biological information-integrated and named 'Qlic Search'-embedded in a query phrase autocomplete feature, coupled with multiple search options that include trait names, genes and QTL IDs. A comprehensive physical and genetic map and vital statistics have been provided in a graphical manner for deciphering the position of QTLs on different chromosomes. A convenient and intuitive user interface have been designed to help users retrieve associations to agronomically important QTLs on abiotic stress response in rice. Database URL: http://nabg.iasri.res.in:8080/qlic-rice/

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci. It provides a platform for the data mining of abiotic stress responsive QTLs, as well as browsing and annotating associated traits, their location on a sequenced genome, mapped expressed sequence tags (ESTs) and tissue and growth stage-specific expressions on the whole genome. Information on QTLs related to abiotic stresses and their corresponding loci from a genomic perspective has not yet been integrated on an accessible, user-friendly platform. QlicRice offers client-responsive architecture to retrieve meaningful biological information—integrated and named ‘Qlic Search’—embedded in a query phrase autocomplete feature, coupled with multiple search options that include trait names, genes and QTL IDs. A comprehensive physical and genetic map and vital statistics have been provided in a graphical manner for deciphering the position of QTLs on different chromosomes. A convenient and intuitive user interface have been designed to help users retrieve associations to agronomically important QTLs on abiotic stress response in rice

Identification of Missing Carbon Fixation Enzymes as Potential Drug Targets in Mycobacterium Tuberculosis

Metabolic adaptation to the host environment has been recognized as an essential mechanism of pathogenicity and the growth of Mycobacterium tuberculosis (Mtb) in the lungs for decades. The Mtb uses CO2 as a source of carbon during the dormant or non-replicative state. However, there is a lack of biochemical knowledge of its metabolic networks. In this study, we investigated the CO2 fixation pathways (such as ko00710 and ko00720) most likely involved in the energy production and conversion of CO2 in Mtb. Extensive pathway evaluation of 23 completely sequenced strains of Mtb confirmed the existence of a complete list of genes encoding the relevant enzymes of the reductive tricarboxylic acid (rTCA) cycle. This provides the evidence that an rTCA cycle may function to fix CO2 in this bacterium. We also proposed that as CO2 is plentiful in the lungs, inhibition of CO2 fixation pathways (by targeting the relevant CO2 fixation enzymes) could be used in the expansion of new drugs against the dormant Mtb. In support of the suggested hypothesis, the CO2 fixation enzymes were confirmed as a potential drug target by analyzing a number of attributes necessary to be a good bacterial target

Factors Influencing the Rheology of Methane Foam for Gas Mobility Control in High-Temperature, Proppant-Fractured Reservoirs

Gas-enhanced oil recovery (EOR) through huff-n-puff (HnP) is an important method of recovering oil from fracture-stimulated reservoirs. HnP productivity is hampered by fracture channeling, leading to early gas breakthroughs and gas losses. To mitigate these issues, foam-generating surfactants have been developed as a method of reducing injected gas phase mobility and increasing oil recovery. This work investigates foam generation and propagation by a proprietary surfactant blend in high-temperature, high-pressure, high-permeability, and high-shear conditions that simulate the environment of a proppant-packed fracture. Bulk foam tests confirmed the aqueous stability and foaming viability of the surfactant at the proposed conditions. Through several series of floods co-injecting methane gas and the surfactant solution through a proppant pack at residual oil saturation, the effects of several injection parameters on apparent foam viscosity were investigated. The foam exhibited an exceptionally high transition foam quality (>95%) and strong shear-thinning behavior. The foam viscosity also linearly decreased with increasing pressure. Another flood series conducted in an oil-free proppant pack showed that swelling of residual oil had no effect on the apparent foam viscosity and was not the reason for the inversely linear pressure dependency. An additional flood series with nitrogen as the injection gas was completed to see if the hydrophobic attraction between the methane and surfactant tail was responsible for the observed pressure trend, but the trend persisted even with nitrogen. In a previous study, the dependence of foam viscosity on pressure was found to be much weaker with a different foaming surfactant under similar conditions. Thus, a better understanding of this important phenomenon requires additional tests with a focus on the effect of pressure on interfacial surfactant adsorption

Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis

Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis unveiled six interaction networks/crosstalks through overlapping edges between commonly dysregulated pathways of EMS and MS. The PTPN1, ERBB3, and CDH1 were observed to be the highly ranked hub genes connected with disease-related genes of both EMS and MS. Androgen receptor (AR) and nuclear factor-kB p65 (RelA) were observed to be the most enriched transcription factor in the upstream of shared down-regulated and up-regulated genes, respectively. The two disease sample sets compared through crosstalk interactions between shared pathways revealed commonly up- and down-regulated expressions of 10 immunomodulatory proteins as probable linkers between EMS and MS. This study pinpoints the number of shared genes, pathways, protein kinases, and upstream regulators that may help in the development of biomarkers for diagnosis of MS and endometriosis at the same time through improved understanding of shared molecular signatures and crosstalk

Influence of interparticle interaction on the structural, optical and magnetic properties of NiO nanoparticles

In this work, we have synthesized nickel oxide (NiO) nanoparticles using a simple wet chemical method. The synthesized nanoparticles were annealed at different temperatures ranging from 573 to 973 K. The structural, magnetic, and optical properties were characterized using X-ray diffraction (XRD), Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM), Superconducting Quantum Interference Device (SQUID), UV-VIS and Photoluminescence (PL) spectrophotometer. The optical properties depict that as NiO particles grow bigger, the intensity of the UV emission increases. The broad emission band can be attributed to the direct recombination of photogenerated charge carriers from the conduction band with the holes in the valence band. This kind of emission due to the transition of 3d8 electrons of the Ni2+ ions was also observed in the PL spectra. NiO nanoparticles exhibit antiferromagnetic behaviour with varied magnetic moment values of 3.08-5.72 ??B. The ZFC curves of all samples show cusp and sharp decrease in magnetization at temperatures in the region of 10-21 K. This is due to the surface cluster spins whose thermal fluctuations freeze in a cluster-glass-like state. The bifurcation temperature between ZFC-FC curves increases with respect to the particle size due to the exchange field which is related to the overlap of electron wave functions of two magnetic ions (Ni2+). This field acts indirectly through the neighbouring anions O2−, as Ni2+ ions are too far apart for direct exchange forces mechanism called super exchange and originates from Pauli exclusion principle and electrostatic force