Encounter complexes and dimensionality reduction in protein-protein association

An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition

Status of the AGS Polarized H- Source

Development of a polarized H/sup -/ source for the AGS polarized proton project, initially begun at Argonne National Laboratory in 1979, has been continuing at Brookhaven National Laboratory since early 1982. A description of the source is given and the status of the project is reviewed

Reefs at Risk: A Map-Based Indicator of Threats to the Worlds Coral Reefs

This report presents the first-ever detailed, map-based assessment of potential threats to coral reef ecosystems around the world. "Reefs at Risk" draws on 14 data sets (including maps of land cover, ports, settle-ments, and shipping lanes), information on 800 sites known to be degraded by people, and scientific expertise to model areas where reef degradation is predicted to occur, given existing human pressures on these areas. Results are an indicator of potential threat (risk), not a measure of actual condition. In some places, particularly where good management is practiced, reefs may be at risk but remain relatively healthy. In others, this indicator underestimates the degree to which reefs are threatened and degraded.Our results indicate that:Fifty-eight percent of the world's reefs are poten-tially threatened by human activity -- ranging from coastal development and destructive fishing practices to overexploitation of resources, marine pollution, and runoff from inland deforestation and farming.Coral reefs of Asia (Southeastern); the most species-rich on earth, are the most threatened of any region. More than 80 percent are at risk (undermedium and high potential threat), and over half are at high risk, primarily from coastal development and fishing-related pressures.Overexploitation and coastal development pose the greatest potential threat of the four risk categories considered in this study. Each, individually, affects a third of all reefs.The Pacific, which houses more reef area than any other region, is also the least threatened. About 60 percent of reefs here are at low risk.Outside of the Pacific, 70 percent of all reefs are at risk.At least 11 percent of the world's coral reefs contain high levels of reef fish biodiversity and are under high threat from human activities. These "hot spot" areas include almost all Philippine reefs, and coral communities off the coasts of Asia, the Comoros, and the Lesser Antilles in the Caribbean.Almost half a billion people -- 8 percent of the total global population -- live within 100 kilometers of a coral reef.Globally, more than 400 marine parks, sanctuaries, and reserves (marine protected areas) contain coral reefs. Most of these sites are very small -- more than 150 are under one square kilometer in size. At least 40 countries lack any marine protected areas for conserving their coral reef systems

Outcomes of Durable Mechanical Circulatory Support in Myocarditis: Analysis of the International Society for Heart and Lung Transplantation Registry for Mechanically Assisted Circulatory Support Registry

Myocarditis can be refractory to medical therapy and require durable mechanical circulatory support (MCS). The characteristics and outcomes of these patients are not known. We identified all patients with clinically-diagnosed or pathology-proven myocarditis who underwent mechanical circulatory support in the International Society for Heart and Lung Transplantation Registry for Mechanically Assisted Circulatory Support registry (2013-2016). The characteristics and outcomes of these patients were compared to those of patients with nonischemic cardiomyopathy (NICM). Out of 14,062 patients in the registry, 180 (1.2%) had myocarditis and 6,602 (46.9%) had NICM. Among patients with myocarditis, duration of heart failure was22%, 1-12 months in 22.6%, and \u3e1 year in 55.4%. Compared with NICM, patients with myocarditis were younger (45 vs. 52 years, P \u3c 0.001) and were more often implanted with Interagency Registry for Mechanically Assisted Circulatory Support profile 1 (30% vs. 15%, P \u3c 0.001). Biventricular mechanical support ( biventricular ventricular assist device [BIVAD] or total artificial heart) was implanted more frequently in myocarditis (18% vs. 6.7%, P \u3c 0.001). Overall postimplant survival was not different between myocarditis and NICM (left ventricular assist device: P = 0.27, BIVAD: P = 0.50). The proportion of myocarditis patients that have recovered by 12 months postimplant was significantly higher in myocarditis compared to that of NICM (5% vs. 1.7%, P = 0.0003). Adverse events (bleeding, infection, and neurologic dysfunction) were all lower in the myocarditis than NICM. In conclusion, although myocarditis patients who receive durable MCS are sicker preoperatively with higher needs for biventricular MCS, their overall MCS survival is noninferior to NICM. Patients who received MCS for myocarditis are more likely than NICM to have MCS explanted due to recovery, however, the absolute rates of recovery were low

Lipidomic QTL in Diversity Outbred mice identifies a novel function for α/β hydrolase domain 2 (Abhd2) as an enzyme that metabolizes phosphatidylcholine and cardiolipin.

We and others have previously shown that genetic association can be used to make causal connections between gene loci and small molecules measured by mass spectrometry in the bloodstream and in tissues. We identified a locus on mouse chromosome 7 where several phospholipids in liver showed strong genetic association to distinct gene loci. In this study, we integrated gene expression data with genetic association data to identify a single gene at the chromosome 7 locus as the driver of the phospholipid phenotypes. The gene encodes α/β-hydrolase domain 2 (Abhd2), one of 23 members of the ABHD gene family. We validated this observation by measuring lipids in a mouse with a whole-body deletion of Abhd2. The Abhd2KO mice had a significant increase in liver levels of phosphatidylcholine and phosphatidylethanolamine. Unexpectedly, we also found a decrease in two key mitochondrial lipids, cardiolipin and phosphatidylglycerol, in male Abhd2KO mice. These data suggest that Abhd2 plays a role in the synthesis, turnover, or remodeling of liver phospholipids

Mitigation of Urban Runoff Impacts on Atlanta Streams

Proceedings of the 1999 Georgia Water Resources Conference, March 30 and 31, Athens, Georgia.An interdisciplinary scientific panel was convened to assess the condition of Atlanta's streams and to identify those watershed management actions with the greatest potential to improve water quality and riparian and stream habitat in the Atlanta region. Broad recommendations included a description of elements to incorporate into a watershed management program for Atlanta, and specific suggestions for demonstration projects in four small, headwater watersheds. The four chosen demonstration sub-watersheds collectively reflect the gradient of impervious cover and stream quality present in Atlanta, and individually represent conditions comm.only observed throughout the area. Therefore, the general recommendations for these demonstration areas should be broadly applicable to the rest of the region.Sponsored and Organized by: U.S. Geological Survey, Georgia Department of Natural Resources, The University of Georgia, Georgia State University, Georgia Institute of TechnologyThis book was published by the Institute of Ecology, The University of Georgia, Athens, Georgia 30602-2202 with partial funding provided by the U.S. Department of Interior, geological Survey, through the Georgia Water Research Insttitute as authorized by the Water Research Institutes Authorization Act of 1990 (P.L. 101-397). The views and statements advanced in this publication are solely those of the authors and do not represent official views or policies of the University of Georgia or the U.S. Geological Survey or the conference sponsors

INFLUENCES OF WATERSHED URBANIZATION AND INSTREAM HABITAT ON MACROINVERTEBRATES IN COLD WATER STREAMS 1

We analyzed data from riffle and snag habitats for 39 small cold water streams with different levels of watershed urbanization in Wisconsin and Minnesota to evaluate the influences of urban land use and instream habitat on macroinvertebrate communities. Multivariate analysis indicated that stream temperature and amount of urban land use in the watersheds were the most influential factors determining macroinvertebrate assemblages. The amount of watershed urbanization was nonlinearly and negatively correlated with percentages of Ephemeroptera-Plecoptera-Trichoptera (EPT) abundance, EPT taxa, filterers, and scrapers and positively correlated with Hilsenhoff biotic index. High quality macroinvertebrate index values were possible if effective imperviousness was less than 7 percent of the watershed area. Beyond this level of imperviousness, index values tended to be consistently poor. Land uses in the riparian area were equal or more influential relative to land use elsewhere in the watershed, although riparian area consisted of only a small portion of the entire watershed area. Our study implies that it is extremely important to restrict watershed impervious land use and protect stream riparian areas for reducing human degradation on stream quality in low level urbanizing watersheds. Stream temperature may be one of the major factors through which human activities degrade cold-water streams, and management efforts that can maintain a natural thermal regime will help preserve stream quality.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72139/1/j.1752-1688.2003.tb03701.x.pd