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  • 1
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    Radio variability from corotating interaction regions threading Wolf–Rayet winds (2020)
    Oxford University Press
    Details
    Publication Date: 2020-07-10
    Description: The structured winds of single massive stars can be classified into two broad groups: stochastic structure and organized structure. While the former is typically identified with clumping, the latter is typically associated with rotational modulations, particularly the paradigm of corotating interaction regions (CIRs). While CIRs have been explored extensively in the ultraviolet band, and moderately in the X-ray and optical, here we evaluate radio variability from CIR structures assuming free–free opacity in a dense wind. Our goal is to conduct a broad parameter study to assess the observational feasibility, and to this end, we adopt a phenomenological model for a CIR that threads an otherwise spherical wind. We find that under reasonable assumptions, it is possible to obtain radio variability at the 10 per cent level. The detailed structure of the folded light curve depends not only on the curvature of the CIR, the density contrast of the CIR relative to the wind, and viewing inclination, but also on wavelength. Comparing light curves at different wavelengths, we find that the amplitude can change, that there can be phase shifts in the waveform, and the entire waveform itself can change. These characterstics could be exploited to detect the presence of CIRs in dense, hot winds.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 2
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    Synthetic biosensors for precise gene control and real-time monitoring of metabolites (2015)
    Oxford University Press
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    Publication Date: 2015-08-29
    Description: Characterization and standardization of inducible transcriptional regulators has transformed how scientists approach biology by allowing precise and tunable control of gene expression. Despite their utility, only a handful of well-characterized regulators exist, limiting the complexity of engineered biological systems. We apply a characterization pipeline to four genetically encoded sensors that respond to acrylate, glucarate, erythromycin and naringenin. We evaluate how the concentration of the inducing chemical relates to protein expression, how the extent of induction affects protein expression kinetics, and how the activation behavior of single cells relates to ensemble measurements. We show that activation of each sensor is orthogonal to the other sensors, and to other common inducible systems. We demonstrate independent control of three fluorescent proteins in a single cell, chemically defining eight unique transcriptional states. To demonstrate biosensor utility in metabolic engineering, we apply the glucarate biosensor to monitor product formation in a heterologous glucarate biosynthesis pathway and identify superior enzyme variants. Doubling the number of well-characterized inducible systems makes more complex synthetic biological circuits accessible. Characterizing sensors that transduce the intracellular concentration of valuable metabolites into fluorescent readouts enables high-throughput screening of biological catalysts and alleviates the primary bottleneck of the metabolic engineering design-build-test cycle.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Comparative Analysis of Sea Surface Temperature Pattern in the Eastern and Western Gulfs of Arabian Sea and the Red Sea in Recent Past Using Satellite Data (2013)
    Hindawi
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    Publication Date: 2013-09-12
    Description: With unprecedented rate of development in the countries surrounding the gulfs of the Arabian Sea, there has been a rapid warming of these gulfs. In this regard, using Advanced Very High Resolution Radiometer (AVHRR) data from 1985 to 2009, a climatological study of Sea Surface Temperature (SST) and its inter annual variability in the Persian Gulf (PG), Gulf of Oman (GO), Gulf of Aden (GA), Gulf of Kutch (KTCH), Gulf of Khambhat (KMBT), and Red Sea (RS) was carried out using the normalized SST anomaly index. KTCH, KMBT, and GA pursued the typical Arabian Sea basin bimodal SST pattern, whereas PG, GO, and RS followed unimodal SST curve. In the western gulfs and RS, from 1985 to 1991-1992, cooling was observed followed by rapid warming phase from 1993 onwards, whereas in the eastern gulfs, the phase of sharp rise of SST was observed from 1995 onwards. Strong influence of the El Niño and La Niña and the Indian Ocean Dipole on interannual variability of SST of gulfs was observed. Annual and seasonal increase of SST was lower in the eastern gulfs than the western gulfs. RS showed the highest annual increase of normalized SST anomaly (+0.64/decade) followed by PG (+0.4/decade).
    Print ISSN: 1687-9406
    Electronic ISSN: 1687-9414
    Topics: Geosciences
    Published by Hindawi
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  • 4
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    Accidental Release of Chlorine from a Storage Facility and an On-Site Emergency Mock Drill: A Case Study (2015)
    Hindawi
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    Publication Date: 2015-06-12
    Description: In the current industrial scenario there is a serious need for formulating strategies to handle hazardous substances in the safest way. Manufacture, storage, and use of hazardous substances pose a serious risk to industry, people, and the environment. Accidental release of toxic chemicals can lead to emergencies. An emergency response plan (ERP) is inevitable to minimize the adverse effects of such releases. The on-site emergency plan is an integral component of any process safety and risk management system. This paper deals with an on-site emergency response plan for a chlorine manufacturing industry. It was developed on the basis of a previous study on chlorine release and a full scale mock drill has been conducted for testing the plan. Results indicated that properly trained personnel can effectively handle each level of incidents occurring in the process plant. As an extensive guideline to the district level government authorities for off-site emergency planning, risk zone has also been estimated with reference to a chlorine exposure threshold of 3 ppm.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
    Published by Hindawi
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  • 5
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    The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-28
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks (2015)
    Oxford University Press
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    Publication Date: 2015-10-08
    Description: Motivation: Synthetic lethal sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. Previous approaches to identify synthetic lethal genes in genome-scale metabolic networks have built on the framework of flux balance analysis (FBA), extending it either to exhaustively analyze all possible combinations of genes or formulate the problem as a bi-level mixed integer linear programming (MILP) problem. We here propose an algorithm, Fast-SL, which surmounts the computational complexity of previous approaches by iteratively reducing the search space for synthetic lethals, resulting in a substantial reduction in running time, even for higher order synthetic lethals. Results: We performed synthetic reaction and gene lethality analysis, using Fast-SL, for genome-scale metabolic networks of Escherichia coli , Salmonella enterica Typhimurium and Mycobacterium tuberculosis. Fast-SL also rigorously identifies synthetic lethal gene deletions, uncovering synthetic lethal triplets that were not reported previously. We confirm that the triple lethal gene sets obtained for the three organisms have a precise match with the results obtained through exhaustive enumeration of lethals performed on a computer cluster. We also parallelized our algorithm, enabling the identification of synthetic lethal gene quadruplets for all three organisms in under 6 h. Overall, Fast-SL enables an efficient enumeration of higher order synthetic lethals in metabolic networks, which may help uncover previously unknown genetic interactions and combinatorial drug targets. Availability and implementation: The MATLAB implementation of the algorithm, compatible with COBRA toolbox v2.0, is available at https://github.com/RamanLab/FastSL Contact: kraman@iitm.ac.in Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Critical assessment of genome-scale metabolic networks: the need for a unified standard (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-20
    Description: Genome-scale metabolic networks have been reconstructed for several organisms. These metabolic networks provide detailed information about the metabolism inside the cells, coupled with the genomic, proteomic and thermodynamic information. These networks are widely simulated using ‘constraint-based’ modelling techniques and find applications ranging from strain improvement for metabolic engineering to prediction of drug targets in pathogenic organisms. Components of these metabolic networks are represented in multiple file formats and also using different markup languages, with varying levels of annotations; this leads to inconsistencies and increases the complexities in comparing and analysing reconstructions on multiple platforms. In this work, we critically examine nearly 100 published genome-scale metabolic networks and their corresponding constraint-based models and discuss various issues with respect to model quality. One of the major concerns is the lack of annotations using standard identifiers that can uniquely describe several components such as metabolites, genes, proteins and reactions. We also find that many models do not have complete information regarding constraints on reactions fluxes and objective functions for carrying out simulations. Overall, our analysis highlights the need for a widely acceptable standard for representing constraint-based models. A rigorous standard can help in streamlining the process of reconstruction and improve the quality of reconstructed metabolic models.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 8
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    Image and Video Encryption based on Dual Space-Filling Curves (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-31
    Description: In this paper, a new encryption scheme with three different modes of operations is proposed based on dual space-filling curves (SFSs) and a fractional wavelet transform (FrWT). This scheme is initially proposed for images and then extended to videos. The core idea behind the proposed schemes is to decompose an image/video first by the FrWT followed by the shuffling of each sub-band coefficients by means of a dual SFC. At last, an inverse FrWT is performed to get the encrypted image/video. A reliable decryption process is also proposed to construct the original image from the encrypted image. The experimental results, security and comparative analysis demonstrate the efficiency and robustness of the proposed scheme. Further, this paper also proposes an efficient implementation of an FrWT based on chaotic maps.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 9
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    UDP-N-acetyl-{alpha}-D-galactosamine:polypeptide N-acetylgalactosaminyltransferases: Completion of the family tree (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-26
    Description: The formation of mucin-type O -glycans is initiated by an evolutionarily conserved family of enzymes, the UDP- N -acetyl-α- d -galactosamine:polypeptide N -acetylgalactosaminyltransferases (GalNAc-Ts). The human genome encodes 20 transferases; 17 of which have been characterized functionally. The complexity of the GalNAc-T family reflects the differential patterns of expression among the individual enzyme isoforms and the unique substrate specificities which are required to form the dense arrays of glycans that are essential for mucin function. We report the expression patterns and enzymatic activity of the remaining three members of the family and the further characterization of a recently reported isoform, GalNAc-T17. One isoform, GalNAcT-16 that is most homologous to GalNAc-T14, is widely expressed (abundantly in the heart) and has robust polypeptide transferase activity. The second isoform GalNAc-T18, most similar to GalNAc-T8, -T9 and -T19, completes a discrete subfamily of GalNAc-Ts. It is widely expressed and has low, albeit detectable, activity. The final isoform, GalNAc-T20, is most homologous to GalNAc-T11 but lacks a lectin domain and has no detectable transferase activity with the panel of substrates tested. We have also identified and characterized enzymatically active splice variants of GalNAc-T13 that differ in the sequence of their lectin domain. The variants differ in their affinities for glycopeptide substrates. Our findings provide a comprehensive view of the complexities of mucin-type O -glycan formation and provide insight into the underlying mechanisms employed to heavily decorate mucins and mucin-like domains with carbohydrate.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Nitrogen Uptake in the Northeastern Arabian Sea during Winter Cooling (2011)
    Hindawi
    Details
    Publication Date: 2011-03-01
    Description: The uptake of dissolved inorganic nitrogen by phytoplankton is an important aspect of the nitrogen cycle of oceans. Here, we present nitrate (NO3-) and ammonium (NH4+) uptake rates in the northeastern Arabian Sea using 15N tracer technique. In this relatively underexplored region, productivity is high during winter due to supply of nutrients by convective mixing caused by the cooling of the surface by the northeast monsoon winds. Studies done during different months (January and late February-early March) of the northeast monsoon 2003 revealed a fivefold increase in the average euphotic zone integrated NO3- uptake from January (2.3 mmolN m−2d−1) to late February-early March (12.7 mmolN m−2d−1). The f-ratio during January appeared to be affected by the winter cooling effect and increased by more than 50% from the southernmost station to the northern open ocean stations, indicating hydrographic and meteorological control. Estimates of NO3- residence time suggested that NO3- entrained in the water column during January contributed to the development of blooms during late February-early March.
    Print ISSN: 1687-9406
    Electronic ISSN: 1687-9414
    Topics: Geosciences
    Published by Hindawi
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