ALBERT

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.

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.

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.

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.

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

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).

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.

Description: A thin layer of fresh water from summer monsoon rain and river runoff in the Bay of Bengal (BoB) has profound influence on air-sea interaction across the south Asian region, but the mechanisms that sustain the low-salinity layer are as yet unknown. Using the first long time series of high-frequency observations from a mooring in the north BoB and satellite salinity data, we show that fresh water from major rivers is transported by large-scale flow and eddies, and shallow salinity stratification persists from summer through winter. The moored observations show frequent 0.2-1.2 psu salinity jumps with time scales of 10 minutes to days, due to O(1-10) km sub-mesoscale salinity fronts moving past the mooring. In winter, satellite sea surface temperature shows 10 km-wide filaments of cool water, in line with moored data. Rapid salinity and temperature changes at the mooring are highly coherent, suggesting slumping of salinity-dominated fronts. Based on these observations, we propose that sub-mesoscale fronts may be one of the important drivers for the persistent fresh layer in the north BoB.

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.

Description: Oncostatin-M (OSM) is a patho-physiologically important pleiotropic, multifunctional cytokine. OSM mRNA sequence analysis revealed that its 3'UTR contains three highly conserved GC-rich cis -elements (GCREs) whose role in mRNA stability is unidentified. In the present study, the functional role of the proximal GC-rich region of osm 3'-UTR (GCRE-1) in post-transcriptional regulation of osm expression in U937 cells was assessed by transfecting construct containing GCRE-1 at 3' end of a fairly stable reporter gene followed by analysis of the expression of the reporter. GCRE-1 showed mRNA destabilizing activity however, upon PMA treatment the reporter message containing GCRE-1 was stabilized. This stabilization is owing to a time dependent progressive binding of trans -factors (atleast five proteins) to GCRE-1 post PMA treatment. Nucleolin was identified as one of the proteins in the RNP complex of GCRE-1 with PMA treated U937 cytosolic extracts by oligo-dT affinity chromatography of poly-adenylated GCRE-1. Immuno-blot revealed time dependent enhancement of nucleolin in the cytoplasm which in turn directly binds GCRE-1. RNA co-immunoprecipitation confirmed the GCRE-1-nucleolin interaction in-vivo . To elucidate the functional role of nucleolin in stabilization of osm mRNA, nucleolin was overexpressed in U937 cells and found to stabilize the intrinsic osm mRNA, where co-transfection with the reporter containing GCRE-1 confirms the role of GCRE-1 in stabilization of the reporter mRNA. Thus in conclusion, the results asserted that PMA treatment in U937 cells leads to cytoplasmic translocation of nucleolin that directly binds GCRE-1, one of the major GC-rich instability elements, thereby stabilizing the osm mRNA. This article is protected by copyright. All rights reserved