Engineered Pathways for Correct Disulfide Bond Oxidation

Correct formation of disulfide bonds is critical for protein folding. We find that cells lacking protein disulfide isomerases (PDIs) can use alternative mechanisms for correct disulfide bond formation. By linking correct disulfide bond formation to antibiotic resistance, we selected mutants that catalyze correct disulfide formation in the absence of DsbC, Escherichia coli's PDI. Most of our mutants massively overproduce the disulfide oxidase DsbA and change its redox status. They enhance DsbA's ability to directly form the correct disulfides by increasing the level of mixed disulfides between DsbA and substrate proteins. One mutant operates via a different mechanism; it contains mutations in DsbB and CpxR that alter the redox environment of the periplasm and increases the level of the chaperone/protease DegP, allowing DsbA to gain disulfide isomerase ability in vivo. Thus, given the proper expression level, redox status, and chaperone assistance, the oxidase DsbA can readily function in vivo to catalyze the folding of proteins with complex disulfide bond connectivities. Our selection reveals versatile strategies for correct disulfide formation in vivo. Remarkably, our evolution of new pathways for correct disulfide bond formation in E. coli mimics eukaryotic PDI, a highly abundant partially reduced protein with chaperone activity. Antioxid. Redox Signal. 14, 2399-2412.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90429/1/ars-2E2010-2E3782.pd

Firm Level Competitiveness of Small and Medium Enterprises (SMEs): Analytical Framework Based on Pillars of Competitiveness Model

The research on competitiveness has been increasing in popularity amongst scholars, there is a lack of studies focusing on the firm level competitiveness of Small and Medium Enterprises (SME). The objective of this paper is to develop a framework model, which can be used to analyze the competitiveness of the SME at the firm level. In this paper, we propose a framework of six pillars of competitiveness, which constitute the physical and human resources, innovation, networking, management processes as well as customers (demand conditions) and competitors (supply conditions). The methodology is unique in the sense that it incorporates the unique analytical framework called the bottlenecks over the pillars of competitiveness, which calculate the individual level competitiveness points for each SME and competition points that can collate significantly with the selected measures of competitiveness. This comprehensive framework needs to be tested empirically with the data in future research

A viral strategy for targeting and manipulating interneurons across vertebrate species

A fundamental impediment to understanding the brain is the availability of inexpensive and robust methods for targeting and manipulating specific neuronal populations. The need to overcome this barrier is pressing because there are considerable anatomical, physiological, cognitive and behavioral differences between mice and higher mammalian species in which it is difficult to specifically target and manipulate genetically defined functional cell types. In particular, it is unclear the degree to which insights from mouse models can shed light on the neural mechanisms that mediate cognitive functions in higher species, including humans. Here we describe a novel recombinant adeno-associated virus that restricts gene expression to GABAergic interneurons within the telencephalon. We demonstrate that the viral expression is specific and robust, allowing for morphological visualization, activity monitoring and functional manipulation of interneurons in both mice and non-genetically tractable species, thus opening the possibility to study GABAergic function in virtually any vertebrate species.National Institutes of Health (U.S.) (Grant MH071679)National Institutes of Health (U.S.) (Grant NS08297)National Institutes of Health (U.S.) (Grant NS074972)National Institutes of Health (U.S.) (Grant MH095147)National Institutes of Health (U.S.) (Grant MH066912)National Institutes of Health (U.S.) (Grant EY022577)National Institutes of Health (U.S.) (Grant MH063912

Functional Topography and Development of Inhibitory Reticulothalamic Barreloid Projections

The thalamic reticular nucleus (TRN) is the main source of inhibition to the somatosensory thalamus (ventrobasal nucleus, VB) in mice. However, the functional topography and development of these projections with respect to the VB barreloids has been largely unexplored. In this respect, to assist in the study of these projections, we have utilized a vesicular gamma-aminobutryic acid (GABA) transporter (VGAT)-Venus transgenic mouse line to develop a brain slice preparation that enables the rapid identification of inhibitory neurons and projections. We demonstrate the utility of our in vitro brain slice preparation for physiologically mapping inhibitory reticulothalamic (RT) topography, using laser-scanning photostimulation via glutamate uncaging. Furthermore, we utilized this slice preparation to compare the development of excitatory and inhibitory projections to VB. We found that excitatory projections to the barreloids, created by ascending projections from the brain stem, develop by postnatal day 2–3 (P2–P3). By contrast, inhibitory projections to the barreloids lag ~5 days behind excitatory projections to the barreloids, developing by P7–P8. We probed this lag in inhibitory projection development through early postnatal whisker lesions. We found that in whisker-lesioned animals, the development of inhibitory projections to the barreloids closed by P4, in register with that of the excitatory projections to the barreloids. Our findings demonstrate both developmental and topographic organizational features of the RT projection to the VB barreloids, whose mechanisms can now be further examined utilizing the VGAT-Venus mouse slice preparation that we have characterized.SVM CORP (Grant LAV 3487

An unstructured-grid, finite-volume sea ice model : development, validation, and application

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 116 (2011): C00D04, doi:10.1029/2010JC006688.A sea ice model was developed by converting the Community Ice Code (CICE) into an unstructured-grid, finite-volume version (named UG-CICE). The governing equations were discretized with flux forms over control volumes in the computational domain configured with nonoverlapped triangular meshes in the horizontal and solved using a second-order accurate finite-volume solver. Implementing UG-CICE into the Arctic Ocean finite-volume community ocean model provides a new unstructured-grid, MPI-parallelized model system to resolve the ice-ocean interaction dynamics that frequently occur over complex irregular coastal geometries and steep bottom slopes. UG-CICE was first validated for three benchmark test problems to ensure its capability of repeating the ice dynamics features found in CICE and then for sea ice simulation in the Arctic Ocean under climatologic forcing conditions. The model-data comparison results demonstrate that UG-CICE is robust enough to simulate the seasonal variability of the sea ice concentration, ice coverage, and ice drifting in the Arctic Ocean and adjacent coastal regions.This work was supported by the NSF Arctic Program for projects with grant numbers of ARC0712903, ARC0732084, and ARC0804029. The Arctic Ocean Model Intercomparison Project (AOMIP) has provided an important guidance for model improvements and ocean studies under coordinated experiments activities. We would like to thank AOMIP PI Proshutinsky for his valuable suggestions and comments on the ice dynamics. His contribution is supported by ARC0800400 and ARC0712848. The development of FVCOM was supported by the Massachusetts Marine Fisheries Institute NOAA grants DOC/NOAA/ NA04NMF4720332 and DOC/NOAA/NA05NMF4721131; the NSF Ocean Science Program for projects of OCE‐0234545, OCE‐0227679, OCE‐ 0606928, OCE‐0712903, OCE‐0726851, and OCE‐0814505; MIT Sea Grant funds (2006‐RC‐103 and 2010‐R/RC‐116); and NOAA NERACOOS Program for the UMASS team. G. Gao was also supported by the Chinese NSF Arctic Ocean grant under contract 40476007. C. Chen’s contribution was also supported by Shanghai Ocean University International Cooperation Program (A‐2302‐10‐0003), the Program of Science and Technology Commission of Shanghai Municipality (09320503700), the Leading Academic Discipline Project of Shanghai Municipal Education Commission (J50702), and Zhi jiang Scholar and 111 project funds of the State Key Laboratory for Estuarine and Coastal Research, East China Normal University (ECNU)

Effectiveness of End-of-Life Strategies to Improve Health Outcomes and Reduce Disparities in Rural Appalachia: An analytic codebook

Appalachia is one of the most medically underserved areas in the nation. The region has provider shortages and limited healthcare infrastructure. Children and adolescents in this area are in poor health and do not receive the needed quality care. Implementation of section 2302 of the 2010 Patient Protection and Affordable Care Act (ACA) enabled children enrolled in Medicaid/Children\u27s Health Insurance Program with a terminal illness to use hospice care while continuing treatment for their terminal illness. In addition to being more comprehensive than standard hospice care, this relatively new type of care is more culturally congruent with the end-of-life values of rural Appalachian families, who often view standard hospice as hastening death. The overall goal of this project was to investigate access to pediatric concurrent hospice care in Appalachia. Our central hypothesis was that concurrent care reduces rural/urban disparities in access to hospice care. Data from the Centers for Medicare and Medicaid Services (CMS) used in this project was used and included 1,788 children who resided in the Appalachian region– from January 1, 2011, to December 31, 2013. Observations with missing birth dates, death dates, and participants older than 21 years were removed from the final sample. Geographic Information Systems (GIS) databases were created to map the boundaries of the Appalachian region, hospice locations, and driving times to them

Seasonal and interannual variability of the Arctic sea ice : a comparison between AO-FVCOM and observations

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016): 8320–8350, doi:10.1002/2016JC011841.A high-resolution (up to 2 km), unstructured-grid, fully ice-sea coupled Arctic Ocean Finite-Volume Community Ocean Model (AO-FVCOM) was used to simulate the sea ice in the Arctic over the period 1978–2014. The spatial-varying horizontal model resolution was designed to better resolve both topographic and baroclinic dynamics scales over the Arctic slope and narrow straits. The model-simulated sea ice was in good agreement with available observed sea ice extent, concentration, drift velocity and thickness, not only in seasonal and interannual variability but also in spatial distribution. Compared with six other Arctic Ocean models (ECCO2, GSFC, INMOM, ORCA, NAME, and UW), the AO-FVCOM-simulated ice thickness showed a higher mean correlation coefficient of ∼0.63 and a smaller residual with observations. Model-produced ice drift speed and direction errors varied with wind speed: the speed and direction errors increased and decreased as the wind speed increased, respectively. Efforts were made to examine the influences of parameterizations of air-ice external and ice-water interfacial stresses on the model-produced bias. The ice drift direction was more sensitive to air-ice drag coefficients and turning angles than the ice drift speed. Increasing or decreasing either 10% in water-ice drag coefficient or 10° in water-ice turning angle did not show a significant influence on the ice drift velocity simulation results although the sea ice drift speed was more sensitive to these two parameters than the sea ice drift direction. Using the COARE 4.0-derived parameterization of air-water drag coefficient for wind stress did not significantly influence the ice drift velocity simulation.This work was supported by NSF grants OCE-1203393 for the UMASSD team and PLR-1203643 for R. C. Beardsley.2017-05-2

Functional Topography and Development of Inhibitory Reticulothalamic Barreloid Projections

The thalamic reticular nucleus (TRN) is the main source of inhibition to the somatosensory thalamus (ventrobasal nucleus, VB) in mice. However, the functional topography and development of these projections with respect to the VB barreloids has been largely unexplored. In this respect, to assist in the study of these projections, we have utilized a vesicular gamma-aminobutryic acid (GABA) transporter (VGAT)-Venus transgenic mouse line to develop a brain slice preparation that enables the rapid identification of inhibitory neurons and projections. We demonstrate the utility of our in vitro brain slice preparation for physiologically mapping inhibitory reticulothalamic (RT) topography, using laser-scanning photostimulation via glutamate uncaging. Furthermore, we utilized this slice preparation to compare the development of excitatory and inhibitory projections to VB. We found that excitatory projections to the barreloids, created by ascending projections from the brain stem, develop by postnatal day 2–3 (P2–P3). By contrast, inhibitory projections to the barreloids lag ~5 days behind excitatory projections to the barreloids, developing by P7–P8. We probed this lag in inhibitory projection development through early postnatal whisker lesions. We found that in whisker-lesioned animals, the development of inhibitory projections to the barreloids closed by P4, in register with that of the excitatory projections to the barreloids. Our findings demonstrate both developmental and topographic organizational features of the RT projection to the VB barreloids, whose mechanisms can now be further examined utilizing the VGAT-Venus mouse slice preparation that we have characterized

A new high-resolution unstructured grid finite volume Arctic Ocean model (AO-FVCOM) : an application for tidal studies

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C08017, doi:10.1029/2008JC004941.A spherical coordinate version of the unstructured grid 3-D FVCOM (finite volume coastal ocean model) has been applied to the Arctic Ocean to simulate tides with a horizontal resolution ranging from 1 km in the near-coastal areas to 15 km in the deep ocean. By accurately resolving the irregular coastlines and bathymetry in the Arctic Ocean coastal regions, this model reproduces the diurnal (K1 and O1) and semidiurnal (M2 and S2) tidal wave dynamics and captures the complex tidal structure along the coast, particularly in the narrow straits of the Canadian Archipelago. The simulated tidal parameters (harmonic constituents of sea surface elevation and currents) agree well with the available observational data. High-resolution meshes over the continental shelf and slope capture the detailed spatial structure of topographic trapped shelf waves, which are quite energetic along the Greenland, Siberia, and Spitsbergen continental slope and shelf break areas. Water stratification influences the vertical distribution of tidal currents but not the water transport and thus tidal elevation. The comparison with previous finite difference models suggests that horizontal resolution and geometric fitting are two prerequisites to simulate realistically the tidal energy flux in the Arctic Ocean, particularly in the Canadian Archipelago.This research was supported by the NSF Office of Polar Programs through grants OPP ARC-0712903, ARC- 0732084, and ARC-0804029 for C. Chen, G. Gao, and G. Cowles; OPP ARC-0804010 and ARC-0712848 for A. Proshutinsky; OPP ANT-0523223, ARC0712848, NOAA Cooperative Agreement NA17RJ1223 (409) and the WHOI Smith Chair for R. C. Beardsley. J. Qi was supported by the SMAST fishery program under NOAA grants NA04NMF4720332 and NA05NMF4721131. The spherical coordinate version of FVCOM was developed with initial funds from NSF grants OCE-0606928 and OCE- 0726851. Gao was also supported by the Chinese NSF Arctic Ocean grant under contract 40476007

Studies of the Canadian Arctic Archipelago water transport and its relationship to basin-local forcings : results from AO-FVCOM

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016): 4392–4415, doi:10.1002/2016JC011634.A high-resolution (up to 2 km), unstructured-grid, fully coupled Arctic sea ice-ocean Finite-Volume Community Ocean Model (AO-FVCOM) was employed to simulate the flow and transport through the Canadian Arctic Archipelago (CAA) over the period 1978–2013. The model-simulated CAA outflow flux was in reasonable agreement with the flux estimated based on measurements across Davis Strait, Nares Strait, Lancaster Sound, and Jones Sounds. The model was capable of reproducing the observed interannual variability in Davis Strait and Lancaster Sound. The simulated CAA outflow transport was highly correlated with the along-strait and cross-strait sea surface height (SSH) difference. Compared with the wind forcing, the sea level pressure (SLP) played a dominant role in establishing the SSH difference and the correlation of the CAA outflow with the cross-strait SSH difference can be explained by a simple geostrophic balance. The change in the simulated CAA outflow transport through Davis Strait showed a negative correlation with the net flux through Fram Strait. This correlation was related to the variation of the spatial distribution and intensity of the slope current over the Beaufort Sea and Greenland shelves. The different basin-scale surface forcings can increase the model uncertainty in the CAA outflow flux up to 15%. The daily adjustment of the model elevation to the satellite-derived SSH in the North Atlantic region outside Fram Strait could produce a larger North Atlantic inflow through west Svalbard and weaken the outflow from the Arctic Ocean through east Greenland.NSF Grant Numbers: OCE-1203393, PLR-1203643; National Natural Science Foundation of China Grant Number: 41276197; Shanghai Pujiang Program Grant Number: 12PJ1404100; Shanghai Shuguang Program2016-12-2