Recent freshwater Ostracoda and Bivalvia from Indo-Nepal border (Tethys Himalaya): Ecological implications

We report for the first time Recent ostracods and bivalves from Central Tethys Himalaya, collected from Changru village, which is situated in the Tinker valley of northwestern Nepal near the Indo-Nepal border. The specimens were collected from the surface sediments of a small pond, shaped by a small tributary of the glacier fed Tinker River. The ostracod species belonging to the families Ilyocyprididae, Cyprididae and Candonidae and one bivalve (Pisidium sp., Family Pisidiidae) have been identified. Psychrodromus olivaccus and Potamocypris villosa are being reported for the first time from India and Nepal. Several broken and unidentifiable gyrogonites of charophyta were also recovered. The ostracod sample, as a whole, points to a shallow freshwater lake environment influenced by slowly running carbonate rich waters under cool temperatures, low mineralization and sparse vegetation. This is in accordance with the occurrence of Pisidium, which is commonly associated with ostracods in the freshwater lakes and streams. The ostracod fauna shows affinity with the fossil and extant forms recovered from the Higher and Tethys Himalaya of NW India. This opens a new opportunity for studying ostracods in the Indian Central Himalaya - a region which otherwise has been ignored until now.

Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

Background: Candida auris is a multidrug resistant, emerging agent of fungemia in humans. Its actual global distribution remains obscure as the current commercial methods of clinical diagnosis misidentify it as C. haemulonii. Here we report the first draft genome of C. auris to explore the genomic basis of virulence and unique differences that could be employed for differential diagnosis. Results: More than 99.5 % of the C. auris genomic reads did not align to the current whole (or draft) genome sequences of Candida albicans, Candida lusitaniae, Candida glabrata and Saccharomyces cerevisiae; thereby indicating its divergence from the active Candida clade. The genome spans around 12.49 Mb with 8527 predicted genes. Functional annotation revealed that among the sequenced Candida species, it is closest to the hemiascomycete species Clavispora lusitaniae. Comparison with the well-studied species Candida albicans showed that it shares significant virulence attributes with other pathogenic Candida species such as oligopeptide transporters, mannosyl transfersases, secreted proteases and genes involved in biofilm formation. We also identified a plethora of transporters belonging to the ABC and major facilitator superfamily along with known MDR transcription factors which explained its high tolerance to antifungal drugs. Conclusions: Our study emphasizes an urgent need for accurate fungal screening methods such as PCR and electrophoretic karyotyping to ensure proper management of fungemia. Our work highlights the potential genetic mechanisms involved in virulence and pathogenicity of an important emerging human pathogen namely C. auris. Owing to its diversity at the genomic scale; we expect the genome sequence to be a useful resource to map species specific differences that will help develop accurate diagnostic markers and better drug targets.

Novel pppGpp binding site at the C-terminal region of the Rel enzyme from Mycobacterium smegmatis

Mycobacterium tuberculosis elicits the stringent response under unfavorable growth conditions, such as those encountered by the pathogen inside the host. The hallmark of this response is production of guanosine tetra-and pentaphosphates, collectively termed (p)ppGpp, which have pleiotropic effects on the bacterial physiology. As the stringent response is connected to survival under stress, it is now being targeted for developing inhibitors against bacterial persistence. The Rel enzyme in mycobacteria has two catalytic domains at its N-terminus that are involved in the synthesis and hydrolysis of (p)ppGpp, respectively. However, the function of the C-terminal region of the protein remained unknown. Here, we have identified a binding site for pppGpp in the C-terminal region of Rel. The binding affinity of pppGpp was quantified by isothermal titration calorimetry. The binding site was determined by crosslinking using the nucleotide analog azido-pppGpp, and examining the crosslink product by mass spectrometry. Additionally, mutations in the Rel protein were created to confirm the site of pppGpp binding by isothermal titration calorimetry. These mutants showed increased pppGpp synthesis and reduced hydrolytic activity. We believe that binding of pppGpp to Rel provides a feedback mechanism that allows the protein to detect and adjust the (p)ppGpp level in the cell. Our work suggests that such sites should also be considered while designing inhibitors to target the stringent response.

The X-ray photoelectron spectroscopy and high-temperature structural studies of Zn1-xNixO/NiO two-phase composites

Detailed investigation of the chemical states and local atomic environment of Ni and Zn in the two-phase composites of Zn1-xNixO/NiO was reported. The X-ray photoelectron spectra of both Ni-2p and Zn-2p revealed the existence of a doublet with spin-orbit splitting approximate to 17.9 and 23.2eV, respectively confirming the divalent oxidation state of both Ni and Zn. However, the samples fabricated under oxygen-rich conditions exhibit significant difference in the binding energy approximate to 18.75eV between the 2p3/2 and 2p1/2 states of Ni. The shift in the satellite peaks of Ni-2p with increasing the Ni composition x within the Zn1-xNixO/NiO matrix signifies the attenuation of nonlocal screening because of reduced site occupancy of two adjacent Zn ions. The temperature dependence of X-ray diffraction analysis reveals a large distortion in the axial-rhombohedral angle for oxygen-rich NiO. Conversely, no significant distortion was noticed in the NiO system present as a secondary phase within Zn1-xNixO. Nevertheless, the unit-cell volume of both wurtzite h.c.p. Zn1-xNixO and f.c.c. NiO exhibits an anomalous behavior between 150 and 300 degrees C. The origin of such unusual change in the unit-cell volume was discussed in terms of oxygen stoichiometry.

Nickel substitution induced effects on gas sensing properties of cobalt ferrite nanoparticles

Ni2+ ion induced unusual conductivity reversal and an enhancement in the gas sensing properties of ferrites based gas sensors, is reported. The Co1-xNixFe2O4 (for x = 0, 0.5 and 1) nanoparticles were synthesized by wet chemical co-precipitation method and gas sensing properties were studied as a function of composition and temperature. The structural, morphological and microstructural characterization revealed crystallite size of in the range 10-20 nm with porous morphology consisting of nano-sized grains. The Energy Dispersive X-ray (EDX) mapping confirms homogeneous distribution of Co, Ni, Fe and O elements in the ferrites. The non-stoichiometry of the inverse spinel type ferrites and the relative concentration of Ni3+/Co3+ defects were studied using X-ray photoelectron spectroscopy. It is found that the addition of Ni2+ ions into cobalt ferrite shows preferred selectivity towards CO gas at high temperature (325 degrees C) and ethanol gas at low temperature (250 degrees C), unlike undoped cobalt ferrite or undoped nickel ferrite, which show similar response for both these gases. Moreover, an unusual conductivity reversal is observed, except cobalt ferrite due to the difference in reactivity of the gases as well as characteristic non-stoichiometry of ferrites. This behavior is highly gas ambient dependent and hence can be well-exploited for selective detection of gases. (C) 2015 Elsevier B.V. All rights reserved.

Genome-wide analysis correlates Ayurveda Prakriti

The practice of Ayurveda, the traditional medicine of India, is based on the concept of three major constitutional types (Vata, Pitta and Kapha) defined as ``Prakriti''. To the best of our knowledge, no study has convincingly correlated genomic variations with the classification of Prakriti. In the present study, we performed genome-wide SNP (single nucleotide polymorphism) analysis (Affymetrix, 6.0) of 262 well-classified male individuals (after screening 3416 subjects) belonging to three Prakritis. We found 52 SNPs (p <= 1 x 10(-5)) were significantly different between Prakritis, without any confounding effect of stratification, after 10(6) permutations. Principal component analysis (PCA) of these SNPs classified 262 individuals into their respective groups (Vata, Pitta and Kapha) irrespective of their ancestry, which represent its power in categorization. We further validated our finding with 297 Indian population samples with known ancestry. Subsequently, we found that PGM1 correlates with phenotype of Pitta as described in the ancient text of Caraka Samhita, suggesting that the phenotypic classification of India's traditional medicine has a genetic basis; and its Prakriti-based practice in vogue for many centuries resonates with personalized medicine.

Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase

Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.

A novel gene THSD7A is associated with obesity

Body mass index (BMI) is a non-invasive measurement of obesity. It is commonly used for assessing adiposity and obesity-related risk prediction. Genetic differences between ethnic groups are important factors, which contribute to the variation in phenotypic effects. India inhabited by the first out-of-Africa human population and the contemporary Indian populations are admixture of two ancestral populations; ancestral north Indians (ANI) and ancestral south Indians (ASI). Although ANI are related to Europeans, ASI are not related to any group outside Indian-subcontinent. Hence, we expect novel genetic loci associated with BMI. In association analysis, we found eight genic SNPs in extreme of distribution (P <= 3.75 x 10(-5)), of which WWOX has already been reported to be associated with obesity-related traits hence excluded from further study. Interestingly, we observed rs1526538, an intronic SNP of THSD7A; a novel gene significantly associated with obesity (P = 2.88 x 10(-5), 8.922 x 10(-6) and 2.504 x 10(-9) in discovery, replication and combined stages, respectively). THSD7A is neural N-glycoprotein, which promotes angiogenesis and it is well known that angiogenesis modulates obesity, adipose metabolism and insulin sensitivity, hence our result find a correlation. This information can be used for drug target, early diagnosis of obesity and treatment.

Ancilla-assisted measurements on quantum ensembles: general protocols and applications in NMR quantum information processing

Quantum ensembles form easily accessible architectures for studying various phenomena in quantum physics, quantum information science and spectroscopy. Here we review some recent protocols for measurements in quantum ensembles by utilizing ancillary systems. We also illustrate these protocols experimentally via nuclear magnetic resonance techniques. In particular, we shall review noninvasive measurements, extracting expectation values of various operators, characterizations of quantum states and quantum processes, and finally quantum noise engineering.

Investigations of aerosol black carbon from a semi-urban site in the Indo-Gangetic Plain region

Long-term (2009-2012) data from ground-based measurements of aerosol black carbon (BC) from a semi-urban site, Pantnagar (29.0 degrees N, 79.5 degrees E, 231 m amsl), in the Indo-Gangetic Plain (IGP) near the Himalayan foothills are analyzed to study the regional characterization. Large variations are seen in BC at both diurnal and seasonal scales, associated with the mesoscale and synoptic meteorological processes, and local/regional anthropogenic activities. BC diurnal variations show two peaks (morning and evening) arising from the combined effects of the atmospheric boundary layer (ABL) dynamics and local emissions. The diurnal amplitudes as well as the rates of diurnal evolution are the highest in winter season, followed by autumn, and the lowest in summer-monsoon. BC exhibits nearly an inverse relation with mixing layer depth in all seasons; being strongest in winter (R-2 = 0.89) and weakest (R-2 = 0.33) in monsoon (July-August). Unlike BC, co-located aerosol optical depths (AOD) and aerosol absorption are highest in spring over IGP, probably due to the presence of higher abundances of aerosols (including dust) above the ABL (in the free troposphere). AOD (500 nm) showed annual peak (>0.6) in May-June, dominated by coarse mode, while fine mode aerosols dominated in late autumn and early winter. Aerosols profiles from CALIPSO show highest values close to the surface in winter/autumn, similar to the feature seen in surface BC, whereas at altitudes > 2 km, the extinction is maximum in spring/summer. WRF-Chem model is used to simulate BC temporal variations and then compared with observed BC. The model captures most of the important features of the diurnal and seasonal variations but significantly underestimated the observed BC levels, suggesting improvements in diurnal and seasonal varying BC emissions apart from the boundary layer processes. (C) 2015 Elsevier Ltd. All rights reserved.

DNA methylation analysis of phenotype specific stratified Indian population

Background: DNA methylation and its perturbations are an established attribute to a wide spectrum of phenotypic variations and disease conditions. Indian traditional system practices personalized medicine through indigenous concept of distinctly descriptive physiological, psychological and anatomical features known as prakriti. Here we attempted to establish DNA methylation differences in these three prakriti phenotypes. Methods: Following structured and objective measurement of 3416 subjects, whole blood DNA of 147 healthy male individuals belonging to defined prakriti (Vata, Pitta and Kapha) between the age group of 20-30years were subjected to methylated DNA immunoprecipitation (MeDIP) and microarray analysis. After data analysis, prakriti specific signatures were validated through bisulfite DNA sequencing. Results: Differentially methylated regions in CpG islands and shores were significantly enriched in promoters/UTRs and gene body regions. Phenotypes characterized by higher metabolism (Pitta prakriti) in individuals showed distinct promoter (34) and gene body methylation (204), followed by Vata prakriti which correlates to motion showed DNA methylation in 52 promoters and 139 CpG islands and finally individuals with structural attributes (Kapha prakriti) with 23 and 19 promoters and CpG islands respectively. Bisulfite DNA sequencing of prakriti specific multiple CpG sites in promoters and 5'-UTR such as; LHX1 (Vata prakriti), SOX11 (Pitta prakriti) and CDH22 (Kapha prakriti) were validated. Kapha prakriti specific CDH22 5'-UTR CpG methylation was also found to be associated with higher body mass index (BMI). Conclusion: Differential DNA methylation signatures in three distinct prakriti phenotypes demonstrate the epigenetic basis of Indian traditional human classification which may have relevance to personalized medicine.

Localized Charge Carrier Transport Properties of Zn1-x Ni (x) O/NiO Two-Phase Composites

We report the localized charge carrier transport of two-phase composite Zn1-x Ni (x) O/NiO (0 a parts per thousand currency sign x a parts per thousand currency sign 1) using the temperature dependence of ac-resistivity rho (ac)(T) across the N,el temperature T (N) (= 523 K) of nickel oxide. Our results provide strong evidence to the variable range hopping of charge carriers between the localized states through a mechanism involving spin-dependent activation energies. The temperature variation of carrier hopping energy epsilon (h)(T) and nearest-neighbor exchange-coupling parameter J (ij)(T) evaluated from the small poleron model exhibits a well-defined anomaly across T (N). For all the composite systems, the average exchange-coupling parameter (J (ij))(AVG) nearly equals to 70 meV which is slightly greater than the 60-meV exciton binding energy of pure zinc oxide. The magnitudes of epsilon (h) (similar to 0.17 eV) and J (ij) (similar to 11 meV) of pure NiO synthesized under oxygen-rich conditions are consistent with the previously reported theoretical estimation based on Green's function analysis. A systematic correlation between the oxygen stoichiometry and, epsilon (h)(T) and J (ij)(T) is discussed.

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue96 in the Plasmodial Enzyme

Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residuephenylalanineat this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms.