Late quaternary time series of Arabian Sea productivity: Global and regional signals

Modern annual floral and faunal production in the northwest Arabian Sea derives primarily from upwelling induced by strong southwest winds during June, July, and August. Indian Ocean summer monsoon winds are, in turn, driven by differential heating between the Asian continent and the Indian ocean to the south. This differential heating produces a strong pressure gradient resulting in southwest monsoon winds and both coastal and divergent upwelling off the Arabian Peninsula. Over geologic time scales (10(exp 4) to 10(exp 6) years), monsoon wind strength is sensitive to changes in boundary conditions which influence this pressure gradient. Important boundary conditions include the seasonal distribution of solar radiation, global ice volume, Indian Ocean sea surface temperature, and the elevation and albedo of the Asian continent. To the extent that these factors influence monsoon wind strength, they also influence upwelling and productivity. In addition, however, productivity associated with upwelling can be decoupled from the strength of the summer monsoon winds via ocean mechanisms which serve to inhibit or enhance the nutrient supply in the intermediate waters of the Indian Ocean, the source for upwelled waters in the Arabian Sea. To differentiate productivity associated with wind-induced upwelling from that associated with other components of the system such as nutrient sequestering in glacial-age deep waters, we employ a strategy which monitors independent components of the oceanic and atmospheric subsystems. Using sediment records from the Owen Ridge, northwest Arabian Sea, we monitor the strength of upwelling and productivity using two independent indicators, percent G. bulloides and opal accumulation. We monitor the strength of southwest monsoon winds by measuring the grain-size of lithogenic dust particles blown into the Arabian Sea from the surrounding deserts of the Somali and Arabian Peninsulas. Our current hypothesis is that the variability associated with the 41 kyr power in the G. bulloides and opal accumulation records derive from nutrient availability in the intermediate waters which are upwelled via monsoon winds. This hypothesis is testable by comparison with Cd records of intermediate and deep waters of the Atlantic and Indian Ocean

Physical Property and Chemical Characteristics of Surface Sediment Grab Samples from Narragansett Bay and the Providence and Seekonk Rivers

This document contains data tables, maps, plots, and documentation on Brown University’s Narragansett Bay Sediment Project compiled by David W. Murray, Brown University, for the New England Interstate Water Pollution Control Commission with support from the U.S. Environmental Protection Agency. The data were compiled and analyzed as part of a New England pilot project exploring the development of a biological condition gradient applicable to estuarine systems

Inequalities in Global Trade: A Cross-Country Comparison of Trade Network Position, Economic Wealth, Pollution and Mortality

In this paper we investigate how structural patterns of international trade give rise to emissions inequalities across countries, and how such inequality in turn impact countries’ mortality rates. We employ Multi-regional Input-Output analysis to distinguish between sulfurdioxide (SO2) emissions produced within a country’s boarders (production-based emissions) and emissions triggered by consumption in other countries (consumption-based emissions). We use social network analysis to capture countries’ level of integration within the global trade network. We then apply the Prais-Winsten panel estimation technique to a panel data set across 172 countries over 20 years (1990–2010) to estimate the relationships between countries’ level of integration and SO2 emissions, and the impact of trade integration and SO2 emission on mortality rates. Our findings suggest a positive, (log-) linear relationship between a country’s level of integration and both kinds of emissions. In addition, although more integrated countries are mainly responsible for both forms of emissions, our findings indicate that they also tend to experience lower mortality rates. Our approach offers a unique combination of social network analysis with multiregional input-output analysis, which better operationalizes intuitive concepts about global trade and trade structure

Leg 68: Introduction, Explanatory Notes, and Conventions

The sixty-eighth cruise of Glomar Challenger was devoted to using the newly developed Hydraulic Piston Corer (HPC) to recover undisturbed, continuous sequences of unlithified sediment. We returned to the vicinities of two rotary-drilled sites (83 and 154). The stratigraphy of these sites indicated that uninterrupted sections of late Neogene and Quaternary sediment should exist at these locations. The ship left Curacao, Dutch Antilles, on 13 August 1979, cored for 11 days at Site 502, and transited from the Caribbean through the Panama Canal. Site 503, in the eastern equatorial Pacific, was cored for seven days, and we then finally transited to Salinas, Ecuador. The results of this cruise (reported in this volume) include preliminary descriptions, based primarily on shipboard observations and analyses, of the material recovered (site chapters) and additional studies performed ashore after the cruise, either by scientists who participated in the cruise or by other invited investigators. The main purpose of this volume is to present not an exhaustive study of the sediment recovered but rather a description, as detailed as possible, of the material recovered on Leg 68 accompanied by interpretations and conclusions that remain preliminary

Collidoscope: An Improved Tool for Computing Collisional Cross Sections with the Trajectory Method

Ion Mobility-Mass Spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, unfolded, and/or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a “trajectory method” (TM) based CCS calculator, named “Collidoscope”, which utilizes parallel processing and optimized trajectory sampling, and implements both He and N2 as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared to those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are typically within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using x-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions

Lipid Head Group Adduction to Soluble Proteins Follows Gas-Phase Basicity Predictions: Dissociation Barriers and Charge Abstraction

Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related gas- subjected to extensive CID can in principle be affected by numerous factors related gas- subjected to extensive CID can in principle be affected by numerous factors related gas-subjected to extensive CID can in principle be affected by numerous factors related gas- subjected to extensive CID can in principle be affected by numerous factors related gas- subjected to extensive CID can in principle be affected by numerous factors related gas- subjected to extensive CID can in principle be affected by numerous factors related gas- phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation

Increasing Collisional Activation of Protein Complexes Using Smaller Aperture Source Sampling Cones on a Synapt Q-IM-TOF Instrument with a Stepwave Source

Quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometers have revolutionized investigation of native biomolecular complexes. High pressures in the sources of these instruments aid transmission of protein complexes through damping of kinetic energy by collisional cooling. Since adducts are removed through collisional heating (declustering), excessive collisional cooling can prevent removal of non-specific adducts from protein ions, leading to inaccurate mass measurements, broad mass spectral peaks, and obfuscation of ligand binding. We show that reducing the source pressure using smaller aperture source sampling cones (SC) in a Waters Synapt G2-Si instrument increases protein ion heating by decreasing collisional cooling, providing a simple way to enhance removal of adducted salts from soluble proteins (GroEL 14-mer) and detergents from a transmembrane protein complex (heptameric Staphylococcus aureus α-hemolysin, αHL). These experiments are supported by ion heating and cooling simulations which demonstrate reduced collisional cooling at lower source pressures. Using these easily-swapped sample cones of different apertures is a facile approach to reproducibly extend the range of activation in Synapt-type instruments

Biomarkers for Dementia, Fatigue, and Depression in Parkinson's Disease

Parkinson's disease is a common multisystem neurodegenerative disorder characterized by typical motor and non-motor symptoms. There is an urgent need for biomarkers for assessment of disease severity, complications and prognosis. In addition, biomarkers reporting the underlying pathophysiology assist in understanding the disease and developing neuroprotective therapies. Ultimately, biomarkers could be used to develop a more efficient personalized approach for clinical trials and treatment strategies. With the goal to improve quality of life in Parkinson's disease it is essential to understand and objectively monitor non-motor symptoms. This narrative review provides an overview of recent developments of biomarkers (biofluid samples and imaging) for three common neuropsychological syndromes in Parkinson's disease: dementia, fatigue, and depression

Reaction to Endoplasmic Reticulum Stress via ATF6 in Amyotrophic Lateral Sclerosis Deteriorates With Aging

Amyotrophic lateral sclerosis (ALS) is a multisystemic neurodegenerative disorder. Given that peripheral blood mononuclear cells (PBMCs) serve as a “window to the central nervous system” we aimed to answer whether endoplasmic reticulum (ER) stress in ALS-PBMCs is related to disease aggressiveness. We studied ER stress in the PBMCs of 49 patients with ALS and 31 age- and sex-matched healthy controls. The expression of a main ER stress marker, activating transcription factor 6 (ATF6), was significantly higher in ALS compared to controls, but did not correlate with age, disease severity, disease duration and disease progression rate. When ATF6 expression levels were plotted against relative D50 (rD50)-derived disease phases derived from the D50 ALS model, two distinct clusters of patients were observed: cluster 1, with progressively increasing ATF6 expression levels and cluster 2, which demonstrated stable ATF6 expression over the disease course. Individuals in the two clusters did not significantly differ in terms of ALS Functional Rating Scale-Revised (ALSFRS-R), disease aggressiveness, disease duration and subtype. However, patients with the increasing ATF6 level were significantly younger, indicating that aging processes might be related to ER stress in ALS. Our data suggest that the reaction to ER stress during disease course may be compromised in older patients with ALS

Role of Symbiotic Auxotrophy in the Rhizobium-Legume Symbioses

Symbiotic auxotrophy occurs in both determinate pea and indeterminate bean nodules demonstrating its importance for bacteroid formation and nodule function in legumes with different developmental programmes. However, only small quantities of branched chain amino acids are needed and symbiotic auxotrophy did not occur in the Sinorhizobium meliloti-alfalfa symbiosis under the conditions measured. The contrasting symbiotic phenotypes of aap bra mutants inoculated on different legumes probably reflects altered timing of amino acid availability, development of symbiotic auxotrophy and nodule developmental programmes