First Results from MFOSC-P : Low Resolution Optical Spectroscopy of a Sample of M dwarfs within 100 parsecs

Mt. Abu Faint Object Spectrograph and Camera (MFOSC-P) is an in-house developed instrument for Physical Research Laboratory (PRL) 1.2m telescope at Mt. Abu India, commissioned in February 2019. Here we present the first science results derived from the low resolution spectroscopy program of a sample of M Dwarfs carried out during the commissioning run of MFOSC-P between February-June 2019. M dwarfs carry great significance for exoplanets searches in habitable zone and are among the promising candidates for the observatory's several ongoing observational campaigns. Determination of their accurate atmospheric properties and fundamental parameters is essential to constrain both their atmospheric and evolutionary models. In this study, we provide a low resolution (R$\sim$500) spectroscopic catalogue of 80 bright M dwarfs (J$<$10) and classify them using their optical spectra. We have also performed the spectral synthesis and $\chi^2$ minimisation techniques to determine their fundamental parameters viz. effective temperature and surface gravity by comparing the observed spectra with the most recent BT-Settl synthetic spectra. Spectral type of M dwarfs in our sample ranges from M0 to M5. The derived effective temperature and surface gravity are ranging from 4000 K to 3000 K and 4.5 to 5.5 dex, respectively. In most of the cases, the derived spectral types are in good agreement with previously assigned photometric classification.Comment: Accepted for Publication in MNRA

Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the ‘T’ allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT’s best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios

Amyloid Formation by the Pro-Inflammatory S100A8/A9 Proteins in the Ageing Prostate

BACKGROUND: The conversion of soluble peptides and proteins into polymeric amyloid structures is a hallmark of many age-related degenerative disorders, including Alzheimer's disease, type II diabetes and a variety of systemic amyloidoses. We report here that amyloid formation is linked to another major age-related phenomenon--prostate tissue remodelling in middle-aged and elderly men. METHODOLOGY/PRINCIPAL FINDINGS: By using multidisciplinary analysis of corpora amylacea inclusions in prostate glands of patients diagnosed with prostate cancer we have revealed that their major components are the amyloid forms of S100A8 and S100A9 proteins associated with numerous inflammatory conditions and types of cancer. In prostate protease rich environment the amyloids are stabilized by dystrophic calcification and lateral thickening. We have demonstrated that material closely resembling CA can be produced from S100A8/A9 in vitro under native and acidic conditions and shows the characters of amyloids. This process is facilitated by calcium or zinc, both of which are abundant in ex vivo inclusions. These observations were supported by computational analysis of the S100A8/A9 calcium-dependent aggregation propensity profiles. We found DNA and proteins from Escherichia coli in CA bodies, suggesting that their formation is likely to be associated with bacterial infection. CA inclusions were also accompanied by the activation of macrophages and by an increase in the concentration of S100A8/A9 in the surrounding tissues, indicating inflammatory reactions. CONCLUSIONS/SIGNIFICANCE: These findings, taken together, suggest a link between bacterial infection, inflammation and amyloid deposition of pro-inflammatory proteins S100A8/A9 in the prostate gland, such that a self-perpetuating cycle can be triggered and may increase the risk of malignancy in the ageing prostate. The results provide strong support for the prediction that the generic ability of polypeptide chains to convert into amyloids could lead to their involvement in an increasing number of otherwise apparently unrelated diseases, particularly those associated with ageing.Original Publication:Kiran Yanamandra, Oleg Alexeyev, Vladimir Zamotin, Vaibhav Srivastava, Andrei Shchukarev, Ann-Christin Brorsson, Gian Gaetano Tartaglia, Thomas Vogl, Rakez Kayed, Gunnar Wingsle, Jan Olsson, Christopher M Dobson, Anders Bergh, Fredrik Elgh and Ludmilla A Morozova-Roche, Amyloid formation by the pro-inflammatory S100A8/A9 proteins in the ageing prostate., 2009, PloS one, (4), 5, e5562.http://dx.doi.org/10.1371/journal.pone.000556

Serum Proteome Changes in Dengue Virus-Infected Patients from a Dengue-Endemic Area of India: Towards New Molecular Targets?

The global burden of dengue continues to worsen, specifically in tropical and subtropical countries, and has evolved as a major public health problem. We investigated the changes in serum proteome in dengue fever (DF) patients from a dengue-endemic area of India to obtain mechanistic insights about the disease pathogenesis, the host immune response, and identification of potential serum protein biomarkers of this infectious disease. In this study, serum samples from DF patients, healthy subjects, and patients with falciparum malaria (an infectious disease control) were investigated by 2D-DIGE in combination with MALDI-TOF/TOF MS. The findings were validated with Western blotting. Functional clustering of the identified proteins was performed using PANTHER and DAVID tools. Compared to the healthy controls, we found significant changes in the expression levels of 48 protein spots corresponding to 18 unique proteins (7 downregulated and 11 upregulated) in DF patients (p < 0.05). Among these differentially-expressed proteins, 11 candidates exhibited different trends in dengue fever compared to falciparum malaria. Importantly, our results suggest that dengue virus infection leads to alterations in expression levels of multiple serum proteins involved in diverse and vital physiological pathways, including acute phase response signaling, complement cascades, hemostasis, and blood coagulation. For the first time we report here that the serum levels of hemopexin, haptoglobin, serum amyloid P, and kininogen precursor, are altered in DF. This study informs the pathogenesis and host immune response to dengue virus infection, as well as the current search for new diagnostic and molecular drug targets

APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools

Published: 30 December 2014BACKGROUND: Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets. In order to facilitate and increase the speed of data analysis, there is a need for an integrated platform that would allow a comprehensive profiling of thousands of peptides and proteins in a single process through the simultaneous exploitation of multiple complementary algorithms. RESULTS: We have established a new proteomics pipeline designated as APP that fulfills these objectives using a complete series of tools freely available from open sources. APP automates the processing of proteomics tasks such as peptide identification, validation and quantitation from LC-MS/MS data and allows easy integration of many separate proteomics tools. Distributed processing is at the core of APP, allowing the processing of very large datasets using any combination of Windows/Linux physical or virtual computing resources. CONCLUSIONS: APP provides distributed computing nodes that are simple to set up, greatly relieving the need for separate IT competence when handling large datasets. The modular nature of APP allows complex workflows to be managed and distributed, speeding up throughput and setup. Additionally, APP logs execution information on all executed tasks and generated results, simplifying information management and validation.Erik K Malm, Vaibhav Srivastava, Gustav Sundqvist and Vincent Bulon

Embedding Instruments &amp; Modules into an IEEE1451-FPGA-based Weblab Infrastructure

Adopting standard-based weblab infrastructures can be an added value for spreading their influence and acceptance in education. This paper suggests a solution based on the IEEE1451.0 Std. and FPGA technology for creating reconfigurable weblab infrastructures using Instruments and Modules (I&amp;Ms) described through standard Hardware Description Language (HDL) files. It describes a methodology for creating and binding I&amp;Ms into an IEEE1451-module embedded in a FPGA-based board able to be remotely controlled/accessed using IEEE1451-HTTP commands. At the end, an example of a step-motor controller module bond to that IEEE1451-module is described

Plants and endophytes interaction: a “secret wedlock” for sustainable biosynthesis of pharmaceutically important secondary metabolites

Abstract Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future

Serum profiling of leptospirosis patients to investigate proteomic alterations

Leptospirosis is a zoonotic infectious disease of tropical, subtropical and temperate zones, which is caused by the pathogenic spirochetes of genus Leptospira. Although this zoonosis is generally not considered as fatal, the pathogen can eventually cause severe infection with septic shock, multi-organ failure and lethal pulmonary hemorrhages leading to mortality. In this study, we have performed a proteomic analysis of serum samples from leptospirosis patients (n=6), febrile controls (falciparum malaria) (n=8) and healthy subjects (n=18) to obtain an insight about disease pathogenesis and host immune responses in leptospiral infections. 2DE and 2D-DIGE analysis in combination with MALDI-TOF/TOF MS revealed differential expression of 22 serum proteins in leptospirosis patients compared to the healthy controls. Among the identified differentially expressed proteins, 8 candidates exhibited different trends compared to the febrile controls. Functional analysis suggested the involvement of differentially expressed proteins in vital physiological pathways, including acute phase response, complement and coagulation cascades and hemostasis. This is the first report of analysis of human serum proteome alterations in leptospirosis patients, which revealed several differentially expressed proteins, including alpha-1-antitrypsin, vitronectin, ceruloplasmin, G-protein signaling regulator, apolipoprotein A-IV, which have not been reported in context of leptospirosis previously. This study will enhance our understanding about leptospirosis pathogenesis and provide a glimpse of host immunological responses. Additionally, a few differentially expressed proteins identified in this study may further be investigated as diagnostic or prognostic serum biomarkers for leptospirosis. This article is part of a Special Issue entitled: Integrated omics. (C) 2012 Elsevier B.V. All rights reserved

Development of Nb-1%Zr-0.1%C alloy as structural components for high temperature reactors

The Nb-1Zr-0.1C (wt.%) alloy is being considered for structural components in the proposed Compact High-Temperature-Reactors (HTR). The present work reports on the development of 30-50 kg ingots of the alloy in correct composition as well as technology for forming the material in various shapes. The work deals with the deformation behavior of as-cast material at different temperatures and strain rates, recrystallization behavior at different temperature and time and evolution of microstructures at different processing conditions (as-cast, deformed and recrystallized). The as-cast Nb alloys were deformed up to 35% at different temperatures. The deformation results showed that the flow stress of the as-cast Nb alloy increases with increasing temperature from 800 degrees C to 1000 degrees C. Beyond 1200 degrees C, substantial decrease in the strength of the alloy was noticed. To determine the optimum recrystallization temperature and time for the alloy, several heat treatments were conducted by systematically varying temperature and time. It was found that the deformed Nb alloy could be recrystallized by annealing at 1300 C for 3 h. The microstructures of the as-cast, deformed and recrystallized samples of Nb-1%Zr-0.1%C alloy were systematically characterized by optical, electron back scattered diffraction (EBSD) and transmission electron microscopy techniques. The Nb-1Zr-0.1C alloy showed significant differences in the microstructure after different thermo-mechanical treatments. Microstructures of the Nb alloy showed two phases: the matrix (bcc) phase and the carbide phase. Electron Microscopy and energy dispersive spectroscopic analyses revealed that the carbide precipitation undergoes various phase transformations. The as-cast structure of Nb alloy had hexagonal Nb2C precipitates in the Nb matrix and after extrusion, the deformed microstructure had two types of carbide precipitates: needle and rectangular morphology precipitates. The needle shape precipitates were of (Nb, Zr)2C with orthorhombic structure and rectangular shape precipitates were of (Nb, Zr)(3)C-2 with hexagonal structure. After annealing, the recrystallized microstructures showed equilibrium structure i.e. (Nb, Zr)C precipitates (fcc structure) in the Nb matrix. (C) 2012 Elsevier B.V. All rights reserved