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  • Oxford University Press  (29)
  • The Oceanography Society  (14)
  • 2015-2019  (43)
  • 1
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 14–17, doi:10.5670/oceanog.2016.34.
    Description: The Bay of Bengal has a surprisingly large influence on the world. It nurtures the South Asian summer monsoon, a tremendous ocean-atmosphere-land phenomenon that delivers freshwater to more than a third of the human population on this planet. During summer, southwesterly winds gather moisture from the ocean and carry it deep inland over the Indian subcontinent, bringing welcome rains to a parched land. During winter, the winds reverse to northeasterly, and the ocean circulation responds by dispersing the terrestrial freshwater runoff concentrated in the northern part of the bay. This freshwater impacts the ocean’s structure, circulation, and biogeochemistry in numerous ways and, through modification of sea surface temperature, feeds back to influence air-sea fluxes. Because the atmosphere obtains its moisture and heat for convection from the ocean, the interplay between ocean and atmosphere is crucial for the development and sustenance of the monsoon.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 50–61, doi:10.5670/oceanog.2016.38.
    Description: Upper-ocean turbulent heat fluxes in the Bay of Bengal and the Arctic Ocean drive regional monsoons and sea ice melt, respectively, important issues of societal interest. In both cases, accurate prediction of these heat transports depends on proper representation of the small-scale structure of vertical stratification, which in turn is created by a host of complex submesoscale processes. Though half a world apart and having dramatically different temperatures, there are surprising similarities between the two: both have (1) very fresh surface layers that are largely decoupled from the ocean below by a sharp halocline barrier, (2) evidence of interleaving lateral and vertical gradients that set upper-ocean stratification, and (3) vertical turbulent heat fluxes within the upper ocean that respond sensitively to these structures. However, there are clear differences in each ocean’s horizontal scales of variability, suggesting that despite similar background states, the sharpening and evolution of mesoscale gradients at convergence zones plays out quite differently. Here, we conduct a qualitative and statistical comparison of these two seas, with the goal of bringing to light fundamental underlying dynamics that will hopefully improve the accuracy of forecast models in both parts of the world.
    Description: We gratefully acknowledge support from the Office of Naval Research, the National Science Foundation, and the Ocean Mixing and Monsoon (OMM) program of the Monsoon Mission of India.
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 134–145, doi:10.5670/oceanog.2016.46.
    Description: The structure and variability of upper-ocean properties in the Bay of Bengal (BoB) modulate air-sea interactions, which profoundly influence the pattern and intensity of monsoonal precipitation across the Indian subcontinent. In turn, the bay receives a massive amount of freshwater through river input at its boundaries and from heavy local rainfall, leading to a salinity-stratified surface ocean and shallow mixed layers. Small-scale oceanographic processes that drive variability in near-surface BoB waters complicate the tight coupling between ocean and atmosphere implicit in this seasonal feedback. Unraveling these ocean dynamics and their impact on air-sea interactions is critical to improving the forecasting of intraseasonal variability in the southwest monsoon. To that end, we deployed a wave-powered, rapidly profiling system capable of measuring the structure and variability of the upper 100 m of the BoB. The evolution of upper-ocean structure along the trajectory of the instrument’s roughly two-week drift, along with direct estimates of vertical fluxes of salt and heat, permit assessment of the contributions of various phenomena to temporal and spatial variability in the surface mixed layer depth. Further, these observations suggest that the particular “barrier-layer” stratification found in the BoB may decrease the influence of the wind on mixing processes in the interior, thus isolating the upper ocean from the interior below, and tightening its coupling to the atmosphere above.
    Description: This work was accomplished with Office of Naval Research support under the umbrella of the Air-Sea Interactions Regional Initiative (ASIRI). AJL was specifically supported by ONR Grant N00014-13-1-0489.
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 82–91, doi:10.5670/oceanog.2016.41.
    Description: The upper 200 m of the two northern Indian Ocean embayments, the Bay of Bengal (BoB) and the Arabian Sea (AS), differ sharply in their salinity stratification, as the Asian monsoon injects massive amounts of freshwater into the BoB while removing freshwater via evaporation from the AS. The ocean circulation transfers salt from the AS to the BoB and exports freshwater from the BoB to mitigate the salinity difference and reach a quasi-steady state, albeit with strong seasonality. An energetic field of mesoscale features and an intrathermocline eddy was observed within the BoB during the R/V Revelle November and December 2013 Air-Sea Interactions Regional Initiative cruises, marking the early northeast monsoon phase. Mesoscale features, which display a surprisingly large thermohaline range within their confines, obscure the regional surface water and thermohaline stratification patterns, as observed by satellite and Argo profilers. Ocean processes blend the fresh and salty features along and across density surfaces, influencing sea surface temperature and air-sea flux. Comparing the Revelle observations to the Argo data reveals a general westward migration of mesoscale features across the BoB.
    Description: Support for Bay of Bengal research is provided by the Office of Naval Research. ALG award number N00014-14-10065. AM and MF award number N00014-13-10451 and for MF a WHOI summer student fellowship. ES award number N00014-14-10236.
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 242–253, doi:10.5670/oceanog.2016.56.
    Description: Because the monsoon strongly affects India, there is a clear need for indigenous expertise in advancing the science that underlies monsoon prediction. The safety of marine transport in the tropics relies on accurate atmospheric and ocean environment predictions on weekly and longer time scales in the Indian Ocean. This need to better forecast the monsoon motivates the United States to advance basic research and support training of early career US scientists in tropical oceanography. Earlier Indian field campaigns and modeling studies indicated that an improved understanding of the interactions between the upper ocean and the atmosphere in the Bay of Bengal at finer spatial and temporal scales could lead to improved intraseasonal monsoon forecasts. The joint US Air-Sea Interactions Regional Initiative (ASIRI) and the Indian Ocean Mixing and Monsoon (OMM) program studied these interactions, resulting in scientific advances described by articles in this special issue of Oceanography. In addition to these scientific advances, and while also developing long-lasting collaborations and building indigenous Indian capability, a key component of these programs is training early career scientists from India and the United States. Training has been focusing on fine-scale and mixing studies of the upper ocean, air-sea interactions, and marine mammal research. Advanced methods in instrumentation, autonomous robotic platforms, experimental design, data analysis, and modeling have been emphasized. Students and scientists from India and the United States at all levels have been participating in joint cruises on Indian and US research vessels and in training participants in modern tools and methods at summer schools, at focused research workshops, and during research visits. Such activities are building new indigenous capability in India, training a new cadre of US scientists well versed in monsoon air-sea interaction, and forging strong links between Indian and US oceanographic institutions.
    Description: We are grateful for the support of the administration of NARA
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-26
    Description: Author Posting. © The Oceanography Society, 2016. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 29, no. 2 (2016): 72–81, doi:10.5670/oceanog.2016.40.
    Description: The strong salinity stratification in the upper 50–80 m of the Bay of Bengal affects the response of the upper ocean to surface heat fluxes. Using observations from November to December 2013, we examine the effect of surface cooling on the temperature structure of the ocean in a one-dimensional framework. The presence of freshwater adds gravitational stability to the density stratification and prevents convective overturning, even when the surface becomes cooler than the subsurface. This stable salinity stratification traps heat within subsurface layers. The ocean’s reluctance to release the heat trapped within these subsurface warm layers can contribute to delayed rise in surface temperature and heat loss from the ocean as winter progresses. Understanding the dispersal of freshwater throughout the bay can help scientists assess its potential for generating the anomalous temperature response. We use the Aquarius along-track surface salinity and satellite-derived surface velocities to trace the evolution and modification of salinity in the Lagrangian frame of water parcels as they move through the bay with the mesoscale circulation. This advective tracking of surface salinities provides a Lagrangian interpolation of the monthly salinity fields in 2013 and shows the evolution of the freshwater distribution. The along-trajectory rate of salinification of water as it leaves the northern bay is estimated and interpreted to result from mixing processes that are likely related to the host of submesoscale signatures observed during our field campaigns.
    Description: This work was supported by the Office of Naval Research (grant N000141310451).
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2016-06-21
    Description: Persistent hepatitis C virus (HCV) infection leads to chronic hepatitis C (CHC), which often progresses to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). The molecular mechanisms that establish CHC and cause its subsequent development into LC and HCC are poorly understood. We have identified a cytoplasmic double-stranded RNA binding protein, Stau1, which is crucial for HCV replication. In this study, Stau1 specifically interacted with the variable-stem-loop region in the 3' NTR and domain IIId of the HCV-IRES in the 5' NTR, and promoted HCV replication and translation. Stau1 coimmunoprecipitates HCV NS5B and a cell factor, protein kinase R (PKR), which is critical for interferon-induced cellular antiviral and antiproliferative responses. Like Stau1, PKR displayed binding specificity to domain IIId of HCV-IRES. Stau1 binds to PKR and strongly inhibits PKR-autophosphorylation. We demonstrated that the transport of HCV RNA on the polysomes is Stau1-dependent, being mainly localized in the monosome fractions when Stau1 is downregulated and exclusively localized in the polysomes when Stau1 is overexpressed. Our findings suggest that HCV may appropriate Stau1 to its advantage to prevent PKR-mediated inhibition of eIF2α, which is required for the synthesis of HCV proteins for translocation of viral RNA genome to the polysomes for efficient translation and replication.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2015-07-12
    Description: We propose a novel mechanism of gene regulation in Mycobacterium tuberculosis where the protein Rv1222 inhibits transcription by anchoring RNA polymerase (RNAP) onto DNA. In contrast to our existing knowledge that transcriptional repressors function either by binding to DNA at specific sequences or by binding to RNAP, we show that Rv1222-mediated transcription inhibition requires simultaneous binding of the protein to both RNAP and DNA. We demonstrate that the positively charged C-terminus tail of Rv1222 is responsible for anchoring RNAP on DNA, hence the protein slows down the movement of RNAP along the DNA during transcription elongation. The interaction between Rv1222 and DNA is electrostatic, thus the protein could inhibit transcription from any gene. As Rv1222 slows down the RNA synthesis, upon expression of the protein in Mycobacterium smegmatis or Escherichia coli , the growth rate of the bacteria is severely impaired. The protein does not possess any significant affinity for DNA polymerase, thus, is unable to inhibit DNA synthesis. The proposed mechanism by which Rv1222 inhibits transcription reveals a new repertoire of prokaryotic gene regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2016-02-20
    Description: Somatic mosaicism refers to the existence of somatic mutations in a fraction of somatic cells in a single biological sample. Its importance has mainly been discussed in theory although experimental work has started to emerge linking somatic mosaicism to disease diagnosis. Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA from healthy donors as well as DNA from tumor samples, we present an ultra-fast computational pipeline, LocHap that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an LH exhibits more than two genotypes, we call it a local haplotype variant (LHV). The presence of LHVs is considered evidence of somatic mosaicism because a genetically homogeneous cell population will not harbor LHVs. Applying LocHap to whole-genome and whole-exome sequence data in DNA from normal blood and tumor samples, we find wide-spread LHVs across the genome. Importantly, we find more LHVs in tumor samples than in normal samples, and more in older adults than in younger ones. We confirm the existence of LHVs and somatic mosaicism by validation studies in normal blood samples. LocHap is publicly available at http://www.compgenome.org/lochap .
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2016-02-27
    Description: : Riboswitches are non-coding RNA located in the 5' untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity. Availability and implementation: Riboswitch Scanner can be freely accessed on the web at http://service.iiserkol.ac.in/~riboscan/ . Contact: mukherjee.sumit89@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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