highly conserved surface: Topics by Science.gov

Sample records for highly conserved surface

Energy conservation of the scattering from one-dimensional random rough surfaces in the high-frequency limit.

PubMed

Pinel, Nicolas; Bourlier, Christophe; Saillard, Joseph

2005-08-01

Energy conservation of the scattering from one-dimensional strongly rough dielectric surfaces is investigated using the Kirchhoff approximation with single reflection and by taking the shadowing phenomenon into account, both in reflection and transmission. In addition, because no shadowing function in transmission exists in the literature, this function is presented here in detail. The model is reduced to the high-frequency limit (or geometric optics). The energy conservation criterion is investigated versus the incidence angle, the permittivity of the lower medium, and the surface rms slope.
Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

PubMed

Blakaj, Dukagjin M; Fernandez-Fuentes, Narcis; Chen, Zigui; Hegde, Rashmi; Fiser, Andras; Burk, Robert D; Brenowitz, Michael

2009-01-01

Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed.
Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

NASA Astrophysics Data System (ADS)

Robinson, Nathaniel Paul

Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production across the CONUS domain. The main results of this work are three publicly available datasets: 1) 30 m Landsat NDVI; 2) 250 m MODIS based GPP and NPP; and 3) 30 m Landsat based GPP and NPP. My goal is that these products prove useful for the wider scientific, conservation, and land management communities as we continue to strive for better conservation and management practices.
Surface conservation laws at microscopically diffuse interfaces.

PubMed

Chu, Kevin T; Bazant, Martin Z

2007-11-01

In studies of interfaces with dynamic chemical composition, bulk and interfacial quantities are often coupled via surface conservation laws of excess surface quantities. While this approach is easily justified for microscopically sharp interfaces, its applicability in the context of microscopically diffuse interfaces is less theoretically well-established. Furthermore, surface conservation laws (and interfacial models in general) are often derived phenomenologically rather than systematically. In this article, we first provide a mathematically rigorous justification for surface conservation laws at diffuse interfaces based on an asymptotic analysis of transport processes in the boundary layer and derive general formulae for the surface and normal fluxes that appear in surface conservation laws. Next, we use nonequilibrium thermodynamics to formulate surface conservation laws in terms of chemical potentials and provide a method for systematically deriving the structure of the interfacial layer. Finally, we derive surface conservation laws for a few examples from diffusive and electrochemical transport.
Future battlegrounds for conservation under global change

PubMed Central

Lee, Tien Ming; Jetz, Walter

2008-01-01

Global biodiversity is under significant threat from the combined effects of human-induced climate and land-use change. Covering 12% of the Earth's terrestrial surface, protected areas are crucial for conserving biodiversity and supporting ecological processes beneficial to human well-being, but their selection and design are usually uninformed about future global change. Here, we quantify the exposure of the global reserve network to projected climate and land-use change according to the Millennium Ecosystem Assessment and set these threats in relation to the conservation value and capacity of biogeographic and geopolitical regions. We find that geographical patterns of past human impact on the land cover only poorly predict those of forecasted change, thus revealing the inadequacy of existing global conservation prioritization templates. Projected conservation risk, measured as regional levels of land-cover change in relation to area protected, is the greatest at high latitudes (due to climate change) and tropics/subtropics (due to land-use change). Only some high-latitude nations prone to high conservation risk are also of high conservation value, but their high relative wealth may facilitate additional conservation efforts. In contrast, most low-latitude nations tend to be of high conservation value, but they often have limited capacity for conservation which may exacerbate the global biodiversity extinction crisis. While our approach will clearly benefit from improved land-cover projections and a thorough understanding of how species range will shift under climate change, our results provide a first global quantitative demonstration of the urgent need to consider future environmental change in reserve-based conservation planning. They further highlight the pressing need for new reserves in target regions and support a much extended ‘north–south’ transfer of conservation resources that maximizes biodiversity conservation while mitigating global climate change. PMID:18302999
Quantifying solute transport processes: are chemically "conservative" tracers electrically conservative?

USGS Publications Warehouse

Singha, Kamini; Li, Li; Day-Lewis, Frederick D.; Regberg, Aaron B.

2012-01-01

The concept of a nonreactive or conservative tracer, commonly invoked in investigations of solute transport, requires additional study in the context of electrical geophysical monitoring. Tracers that are commonly considered conservative may undergo reactive processes, such as ion exchange, thus changing the aqueous composition of the system. As a result, the measured electrical conductivity may reflect not only solute transport but also reactive processes. We have evaluated the impacts of ion exchange reactions, rate-limited mass transfer, and surface conduction on quantifying tracer mass, mean arrival time, and temporal variance in laboratory-scale column experiments. Numerical examples showed that (1) ion exchange can lead to resistivity-estimated tracer mass, velocity, and dispersivity that may be inaccurate; (2) mass transfer leads to an overestimate in the mobile tracer mass and an underestimate in velocity when using electrical methods; and (3) surface conductance does not notably affect estimated moments when high-concentration tracers are used, although this phenomenon may be important at low concentrations or in sediments with high and/or spatially variable cation-exchange capacity. In all cases, colocated groundwater concentration measurements are of high importance for interpreting geophysical data with respect to the controlling transport processes of interest.
Conserved Amphipathic Helices Mediate Lipid Droplet Targeting of Perilipins 1–3*

PubMed Central

Rowe, Emily R.; Mimmack, Michael L.; Barbosa, Antonio D.; Haider, Afreen; Isaac, Iona; Ouberai, Myriam M.; Thiam, Abdou Rachid; Patel, Satish; Saudek, Vladimir; Siniossoglou, Symeon; Savage, David B.

2016-01-01

Perilipins (PLINs) play a key role in energy storage by orchestrating the activity of lipases on the surface of lipid droplets. Failure of this activity results in severe metabolic disease in humans. Unlike all other lipid droplet-associated proteins, PLINs localize almost exclusively to the phospholipid monolayer surrounding the droplet. To understand how they sense and associate with the unique topology of the droplet surface, we studied the localization of human PLINs in Saccharomyces cerevisiae, demonstrating that the targeting mechanism is highly conserved and that 11-mer repeat regions are sufficient for droplet targeting. Mutations designed to disrupt folding of this region into amphipathic helices (AHs) significantly decreased lipid droplet targeting in vivo and in vitro. Finally, we demonstrated a substantial increase in the helicity of this region in the presence of detergent micelles, which was prevented by an AH-disrupting missense mutation. We conclude that highly conserved 11-mer repeat regions of PLINs target lipid droplets by folding into AHs on the droplet surface, thus enabling PLINs to regulate the interface between the hydrophobic lipid core and its surrounding hydrophilic environment. PMID:26742848
Hybrid Eulerian and Lagrangian Simulation of Steep and Breaking Waves and Surface Fluxes in High Winds

DTIC Science & Technology

2012-09-30

Lagrangian methods for free - surface turbulence and wave simulation . In the far field, coupled wind and wave simulations are used to obtain wind...to conserve the mass precisely. When the wave breaks, the flow at the free surface may become very violent, air and water may be highly mixed...fluids free - surface flows that can be used to study the fundamental physics of wave breaking. The research will improve the understanding of air-sea
High-precision measurement of chlorine stable isotope ratios

USGS Publications Warehouse

Long, A.; Eastoe, C.J.; Kaufmann, R.S.; Martin, J.G.; Wirt, L.; Finley, J.B.

1993-01-01

We present an analysis procedure that allows stable isotopes of chlorine to be analyzed with precision sufficient for geological and hydrological studies. The total analytical precision is ?????0.09%., and the present known range of chloride in the surface and near-surface environment is 3.5???. As Cl- is essentially nonreactive in natural aquatic environments, it is a conservative tracer and its ??37Cl is also conservative. Thus, the ??37Cl parameter is valuable for quantitative evaluation of mixing of different sources of chloride in brines and aquifers. ?? 1993.
Ground-water flow and ground- and surface-water interaction at McBaine Bottoms, Columbia, Missouri--2000-02

USGS Publications Warehouse

Smith, Brenda J.

2003-01-01

McBaine Bottoms southwest of Columbia, Missouri, is the site of 4,269 acres of the Eagle Bluffs Conservation Area operated by the Missouri Department of Conservation, about 130 acres of the city of Columbia wastewater-treat-ment wetlands, and the city of Columbia munici-pal-supply well field. The city of Columbia wastewater-treatment wetlands supply treated effluent to the Eagle Bluffs Conservation Area. The presence of a sustained ground-water high underlying the Eagle Bluffs Conservation Area has indicated that ground-water flow is toward the municipal well field that supplies drinking water to the city of Columbia. The U.S. Geological Survey, in cooperation with the Missouri Department of Conservation and the city of Columbia, measured the ground-water levels in about 88 monitoring wells and the surface-water elevation at 4 sites monthly during a 27-month period to determine the ground-water flow and the ground- and surface-water interaction at McBaine Bottoms. Lateral ground-water flow was dominated by the presence of a ground-water high that was beneath the Eagle Bluffs Conservation Area and the presence of a cone of depression in the northern part of the study area. The ground-water high was present during all months of the study. Ground-water flow was radially away from the apex of the ground-water high; west and south of the high, flow was toward the Missouri River, east of the high, flow was toward Perche Creek, and north of the high, flow was toward the north toward the city of Columbia well field. The cone of depression was centered around the city of Columbia well field. Another permanent feature on the water-level maps was a ground-water high beneath treatment wetland unit 1. Although the ground-water high beneath the Eagle Bluffs Conservation Area was present throughout the study period, the configuration of the high changed depending on hydrologic conditions. Generally in the spring, the height of the ground-water high began to decrease and hydraulic gradients around the high became more shallow than in the winter months. In early summer, the high was the least pronounced. During mid-sum-mer, the high became more pronounced, and it continued to become higher, increasing until it reached its maximum height in late fall or early winter. Fluctuations in the ground-water high were partially produced by the cycle of flooding of the Eagle Bluffs Conservation Area wetland pools in the fall and subsequent drainage so crops could be planted in many of the wetland pools. The cone of depression in the northern part of the study area generally extended from the base of the ground-water high in the northern part of the Eagle Bluffs Conservation Area throughout the rest of the study area. The depth of the cone primarily was affected by the altitude of the Missouri River and the quantity of water being pumped from the alluvial aquifer by the city of Columbia well field. Ground-water flow in the alluvial aquifer in McBaine Bottoms in the late 1960?s before the development of the city of Columbia well field and the Eagle Bluffs Conservation Area was from northwest to southeast approximately parallel to the Missouri River. The ground-water high beneath the Eagle Bluffs Conservation Area and the cone of depression around the city of Columbia well field were not present in water-level maps for 1968 and 1978. The Missouri River can be a source of recharge to the alluvial aquifer. Generally the altitude of the river in the northern part of the study area was higher than the water table in the aquifer. Ground-water flow in this area was from the river into the alluvial aquifer. In the southern part of the study area adjacent to the Eagle Bluffs Conservation Area, the Missouri River was lower than the water table in the alluvial aquifer, indicating that the river was receiving water from the alluvial aquifer beneath the Eagle Bluffs Conservation Area.
Motion of gas in highly rarefied space

NASA Astrophysics Data System (ADS)

Chirkunov, Yu A.

2017-10-01

A model describing a motion of gas in a highly rarefied space received an unlucky number 13 in the list of the basic models of the motion of gas in the three-dimensional space obtained by L.V. Ovsyannikov. For a given initial pressure distribution, a special choice of mass Lagrangian variables leads to the system describing this motion for which the number of independent variables is less by one. Hence, there is a foliation of a highly rarefied gas with respect to pressure. In a strongly rarefied space for each given initial pressure distribution, all gas particles are localized on a two-dimensional surface that moves with time in this space We found some exact solutions of the obtained system that describe the processes taking place inside of the tornado. For this system we found all nontrivial conservation laws of the first order. In addition to the classical conservation laws the system has another conservation law, which generalizes the energy conservation law. With the additional condition we found another one generalized energy conservation law.
Quality assessment of the TLS data in conservation of monuments

NASA Astrophysics Data System (ADS)

Markiewicz, Jakub S.; Zawieska, Dorota

2015-06-01

Laser scanning has been recently confirming its high potential in the field of acquiring 3D data for architectural and engineering objects. The objective of this paper is to analyse the quality of the TLS data acquired for different surfaces of monumental objects, with consideration of distances and the scanning angles. Tests concerning the quality of the survey data and shapes of architectural objects, characterised by diversified curvature, structure and the uniformity of the surface, were performed. The obtained results proved that utilisation of terrestrial laser scanning techniques does not allow to achieve expected accuracy for some historical surfaces and it should be substituted by alternative, photogrammetric techniques. Therefore, the typology of constructions of historical objects is important not only for selection of the optimum technique of surveys, but also for its appropriate utilisation. The test objects were architectural details of the Main Hall of the Warsaw University of Technology. Scans were acquired using the 5006h scanner. Diversified geometry of scans was tested, and the relations between the distance and obtained accuracy were specified. In the case of numerous conservational works the precise surface reconstruction is often important, in order to specify damages. Therefore, the repeatability of obtained TLS results for selected surfaces was also tested. Different surfaces were analysed, which are composed of different materials having glittery elements and inhomogeneous structure. The obtained results and performed analyses revealed the high imperfections of the TLS technique applied for measuring surfaces of historical objects. The presented accuracy of measurements of projection of historical surfaces, obtained using the TLS technique may be applied by art conservators, museum professionals, archaeologists and other specialists, to perform wide analyses of historical heritage objects.
Prediction of Groundwater Quality Trends Resulting from Anthropogenic Changes in Southeast Florida.

PubMed

Yi, Quanghee; Stewart, Mark

2018-01-01

The effects of surface water flow system changes caused by constructing water-conservation areas and canals in southeast Florida on groundwater quality under the Atlantic Coastal Ridge was investigated with numerical modeling. Water quality data were used to delineate a zone of groundwater with low total dissolved solids (TDS) within the Biscayne aquifer under the ridge. The delineated zone has the following characteristics. Its location generally coincides with an area where the Biscayne aquifer has high transmissivities, corresponds to a high recharge area of the ridge, and underlies a part of the groundwater mound formed under the ridge prior to completion of the canals. This low TDS groundwater appears to be the result of pre-development conditions rather than seepage from the canals constructed after the 1950s. Numerical simulation results indicate that the time for low TDS groundwater under the ridge to reach equilibrium with high TDS surface water in the water-conservation areas and Everglades National Park are approximately 70 and 60 years, respectively. The high TDS groundwater would be restricted to the water-conservation areas and the park due to its slow eastward movement caused by small hydraulic gradients in Rocky Glades and its mixing with the low TDS groundwater under the high-recharge area of the ridge. The flow or physical boundary conditions such as high recharge rates or low hydraulic conductivity layers may affect how the spatial distribution of groundwater quality in an aquifer will change when a groundwater flow system reaches equilibrium with an associated surface water flow system. © 2017, National Ground Water Association.
On the formation of a conservation hotspot for juvenile North Pacific loggerhead sea turtles (Caretta caretta)

NASA Astrophysics Data System (ADS)

Wingfield, Dana K.

2009-12-01

This research examined the incorporation of highly productive regions within the marine system. I combined historical conservation literature, remotely sensed oceanography, ship based surveys, satellite tagged animals, and statistical models to explore an integrated approach to the identification of key oceanic regions that require incorporation into current marine conservation strategies. In my first chapter, I undertook a literature review of the term "hotspot", one of the most common ways by which scientists ascribe conservation prioritization in the marine and terrestrial systems. My results showed that marine literature has identified important areas of biodiversity and productivity (i.e. high primary production that results in trophic linkages and species aggregations) are in need of protection from human threats. However, current non-governmental organizations focus primarily on biodiversity, thus missing important areas of productivity for marine conservation. In my second chapter, I demonstrated how remotely sensed oceanography, ship-based surveys, and satellite tagged animals can help to identify the formation of such a "productivity hotspot". Specifically, I examined the connection between physical forcing (surface winds and vertical Ekman upwelling), sea-surface temperature, primary production (chlorophyll-a concentrations), retentive features of fronts and dynamic height, and prey abundance (red crabs) in the spatial and temporal concentration of the critically endangered North Pacific juvenile loggerhead sea turtle (Caretta caretta) within its foraging habitat off the Pacific coast of Baja California. Finally, in my third chapter, I identified habitat selection of loggerheads to better understand the species preference within suitable habitat. I sampled several environmental variables (depth, sea-surface temperature, and chlorophyll- a) within 'preferred' versus 'avoided' turtle habitat. Results from a generalized additive model showed the statistical importance of all three variables in the prediction of loggerhead presence within suitable habitat off of Baja California. I then incorporated prey distribution to fully explore the connection between a highly migratory species and its environment. These results show how knowledge of threatened and endangered species habitat use within a productivity hotspot can help to more efficiently identify and prioritize critical areas for conservation.
Protein consensus-based surface engineering (ProCoS): a computer-assisted method for directed protein evolution.

PubMed

Shivange, Amol V; Hoeffken, Hans Wolfgang; Haefner, Stefan; Schwaneberg, Ulrich

2016-12-01

Protein consensus-based surface engineering (ProCoS) is a simple and efficient method for directed protein evolution combining computational analysis and molecular biology tools to engineer protein surfaces. ProCoS is based on the hypothesis that conserved residues originated from a common ancestor and that these residues are crucial for the function of a protein, whereas highly variable regions (situated on the surface of a protein) can be targeted for surface engineering to maximize performance. ProCoS comprises four main steps: ( i ) identification of conserved and highly variable regions; ( ii ) protein sequence design by substituting residues in the highly variable regions, and gene synthesis; ( iii ) in vitro DNA recombination of synthetic genes; and ( iv ) screening for active variants. ProCoS is a simple method for surface mutagenesis in which multiple sequence alignment is used for selection of surface residues based on a structural model. To demonstrate the technique's utility for directed evolution, the surface of a phytase enzyme from Yersinia mollaretii (Ymphytase) was subjected to ProCoS. Screening just 1050 clones from ProCoS engineering-guided mutant libraries yielded an enzyme with 34 amino acid substitutions. The surface-engineered Ymphytase exhibited 3.8-fold higher pH stability (at pH 2.8 for 3 h) and retained 40% of the enzyme's specific activity (400 U/mg) compared with the wild-type Ymphytase. The pH stability might be attributed to a significantly increased (20 percentage points; from 9% to 29%) number of negatively charged amino acids on the surface of the engineered phytase.
Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea.

PubMed

Lauria, V; Gristina, M; Attrill, M J; Fiorentino, F; Garofalo, G

2015-08-14

Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world's sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.
Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea

NASA Astrophysics Data System (ADS)

Lauria, V.; Gristina, M.; Attrill, M. J.; Fiorentino, F.; Garofalo, G.

2015-08-01

Commercial fisheries have dramatically impacted elasmobranch populations worldwide. With high capture and bycatch rates, the abundance of many species is rapidly declining and around a quarter of the world’s sharks and rays are threatened with extinction. At a regional scale this negative trend has also been evidenced in the central Mediterranean Sea, where bottom-trawl fisheries have affected the biomass of certain rays (e.g. Raja clavata) and sharks (e.g. Mustelus spp.). Detailed knowledge of elasmobranch habitat requirements is essential for biodiversity conservation and fisheries management, but this is often hampered by a poor understanding of their spatial ecology. Habitat suitability models were used to investigate the habitat preference of nine elasmobranch species and their overall diversity (number of species) in relation to five environmental predictors (i.e. depth, sea surface temperature, surface salinity, slope and rugosity) in the central Mediterranean Sea. Results showed that depth, seafloor morphology and sea surface temperature were the main drivers for elasmobranch habitat suitability. Predictive distribution maps revealed different species-specific patterns of suitable habitat while high assemblage diversity was predicted in deeper offshore waters (400-800 m depth). This study helps to identify priority conservation areas and diversity hot-spots for rare and endangered elasmobranchs in the Mediterranean Sea.
Evolutionary History and Conservation Status of Cave Crayfishes Along the Cumberland Plateau

NASA Astrophysics Data System (ADS)

Buhay, J. E.; Crandall, K. A.

2005-05-01

Obligate cave-dwelling crayfish species are found only in southeastern United States, Mexico, and Cuba. Most species are considered to be endangered because of surface pollution threats to groundwater and small geographic distributions. There are currently three subterranean species of the genus Orconectes found along the Cumberland Plateau, a worldwide hotspot of cave biodiversity. The objectives of my dissertation research are to: 1) delineate species' boundaries using molecular genetic data in a phylogenetic framework, 2) examine evolutionary history of each species using Nested Clade Analysis, and 3) assess conservation status of each species using measures of effective population size and genetic diversity. This research project has uncovered a new species of cave crayfish along the border of Tennessee and Kentucky, an area previously thought to have "intergrades" between two subspecies of O. australis. It appears that Cambarus gentryi, a surface-dwelling burrowing species, is the closest living ancestor to the cave Orconectes assemblage on the Plateau. The origin appears to be Eastern Kentucky, with range expansions occuring southward down the Plateau. Although controversial, these cave species exhibit high levels of genetic diversity, especially in comparison to surface-dwellers. Conservation efforts should focus on protecting `high-traffic' areas to maintain gene flow and prevent isolation.
Rapid comparison of protein binding site surfaces with Property Encoded Shape Distributions (PESD)

PubMed Central

Das, Sourav; Kokardekar, Arshad

2009-01-01

Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity between binding sites. As postulated, the PESD method rapidly detected high levels of similarity in binding site surface characteristics even in cases where there was very low similarity at the sequence level. In a screening experiment involving each member of the PDBBind 2005 dataset as a query against the rest of the set, PESD was able to retrieve a binding site with identical E.C. (Enzyme Commission) numbers as the top match in 79.5% of cases. The ability of the method in detecting similarity in binding sites with low sequence conservations were compared with state-of-the-art binding site comparison methods. PMID:19919089
On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A.

PubMed

Fadda, Elisa; Woods, Robert J

2011-10-11

The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in previous work [ Clarke et al. J. Am. Chem. Soc. 2001 , 123 , 12238 - 12247 and Kadirvelraj et al. J. Am. Chem. Soc. 2008 , 130 , 16933 - 16942 ] for a highly conserved water molecule located in the binding site of the prototypic carbohydrate-binding protein Concanavalin A (Con A). A synthetic ligand was designed with the aim of displacing such water. While the synthetic ligand bound to Con A in an analogous manner to that of the natural ligand, crystallographic analysis demonstrated that it did not displace the conserved water. In order to quantify the affinity of this particular water for the Con A surface, we report here the calculated standard binding free energy for this water in both ligand-bound and free Con A, employing three popular water models: TIP3P, TIP4P, and TIP5P. Although each model was developed to perform well in simulations of bulk-phase water, the computed binding energies for the isolated water molecule displayed a high sensitivity to the model. Both molecular dynamics simulation and free energy results indicate that the choice of water model may greatly influence the characterization of surface water molecules as conserved (TIP5P) or not (TIP3P) in protein binding sites, an observation of considerable significance to rational drug design. Structural and theoretical aspects at the basis of the different behaviors are identified and discussed.

Optical micro-profilometry for archaeology

NASA Astrophysics Data System (ADS)

Carcagni, Pierluigi; Daffara, Claudia; Fontana, Raffaella; Gambino, Maria Chiara; Mastroianni, Maria; Mazzotta, Cinazia; Pampaloni, Enrico; Pezzati, Luca

2005-06-01

A quantitative morphological analysis of archaeological objects represents an important element for historical evaluations, artistic studies and conservation projects. At present, a variety of contact instruments for high-resolution surface survey is available on the market, but because of their invasivity they are not well received in the field of artwork conservation. On the contrary, optical testing techniques have seen a successful growth in last few years due to their effectiveness and safety. In this work we present a few examples of application of high-resolution 3D techniques for the survey of archaeological objects. Measurements were carried out by means of an optical micro-profilometer composed of a commercial conoprobe mounted on a scanning device that allows a maximum sampled area of 280×280 mm2. Measurements as well as roughness calculations were carried out on selected areas, representative of the differently degraded surface, of an ellenestic bronze statue to document the surface corrosion before restoration intervention started. Two highly-corroded ancient coins and a limestone column were surveyed to enhance the relief of inscriptions and drawings for dating purposes. High-resolution 3D survey, beyond the faithful representation of objects, makes it possible to display the surface in an image format that can be processed by means of image processing software. The application of digital filters as well as rendering techniques easies the readability of the smallest details.
Conservation of myeloid surface antigens on primate granulocytes.

PubMed

Letvin, N L; Todd, R F; Palley, L S; Schlossman, S F; Griffin, J D

1983-02-01

Monoclonal antibodies reactive with myeloid cell surface antigens were used to study evolutionary changes in granulocyte surface antigens from primate species. Certain of these granulocyte membrane antigens are conserved in phylogenetically distant species, indicating the potential functional importance of these structures. The degree of conservation of these antigens reflects the phylogenetic relationship between primate species. Furthermore, species of the same genus show similar patterns of binding to this panel of anti-human myeloid antibodies. This finding of conserved granulocyte surface antigens suggests that non-human primates may provide a model system for exploring uses of monoclonal antibodies in the treatment of human myeloid disorders.
Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.
Numerical study of drop spreading on a flat surface

NASA Astrophysics Data System (ADS)

Wang, Sheng; Desjardins, Olivier

2017-11-01

In this talk, we perform a numerical study of a droplet on a flat surface with special emphasis on capturing the spreading dynamics. The computational methodology employed is tailored for simulating large-scale two-phase flows within complex geometries. It combines a conservative level-set method to capture the liquid-gas interface, a conservative immersed boundary method to represent the solid-fluid interface, and a sub-grid curvature model at the triple-point to implicitly impose the contact angle of the liquid-gas interface. The performance of the approach is assessed in the inertial droplet spreading regime, the viscous spreading regime of high viscosity drops, and with the capillary oscillation of low viscosity droplets.
Vaccine approaches conferring cross-protection against influenza viruses

PubMed Central

Vemula, Sai V.; Sayedahmed, Ekramy E; Sambhara, Suryaprakash; Mittal, Suresh K.

2018-01-01

Introduction Annual vaccination is one of the most efficient and cost-effective strategies to prevent and control influenza epidemics. Most of currently available influenza vaccines are strong inducer of antibody responses against viral surface proteins, hemagglutinin (HA) and neuraminidase (NA), but are poor inducers of cell-mediated immune responses against conserved internal proteins. Moreover, due to the high variability of viral surface proteins because of antigenic drift or antigenic shift, many of the currently licensed vaccines confer little or no protection against drift or shift variants. Areas covered Next generation influenza vaccines that can induce humoral immune responses to receptor-binding epitopes as well as broadly neutralizing conserved epitopes, and cell-mediated immune responses against highly conserved internal proteins would be effective against variant viruses as well as a novel pandemic influenza until circulating strain-specific vaccines become available. Here we discuss vaccine approaches that have potential to provide broad spectrum protection against influenza viruses. Expert opinion Based on current progress in defining cross-protective influenza immunity, it seems that the development of a universal influenza vaccine is feasible. It would revolutionize the strategy for influenza pandemic preparedness, and significantly impact the shelf-life and protection efficacy of seasonal influenza vaccines. PMID:28925296
Water Intake by Soil, Experiments for High School Students.

ERIC Educational Resources Information Center

1969

Presented are a variety of surface run-off experiments for high school students. The experiments are analogies to basic concepts about water intake, as related to water delivery, soil properties and management, floods, and conservation measures. The materials needed to perform the experiments are easily obtainable. The experiments are followed by…
Conservative DEC Discretization of Incompressible Navier-Stokes Equations on Arbitrary Surface Simplicial Meshes

NASA Astrophysics Data System (ADS)

Mohamed, Mamdouh; Hirani, Anil; Samtaney, Ravi

2017-11-01

A conservative discretization of incompressible Navier-Stokes equations over surfaces is developed using discrete exterior calculus (DEC). The mimetic character of many of the DEC operators provides exact conservation of both mass and vorticity, in addition to superior kinetic energy conservation. The employment of signed diagonal Hodge star operators, while using the circumcentric dual defined on arbitrary meshes, is shown to produce correct solutions even when many non-Delaunay triangles pairs exist. This allows the DEC discretization to admit arbitrary surface simplicial meshes, in contrast to the previously held notion that DEC was limited only to Delaunay meshes. The discretization scheme is presented along with several numerical test cases demonstrating its numerical convergence and conservation properties. Recent developments regarding the extension to conservative higher order methods are also presented. KAUST Baseline Research Funds of R. Samtaney.
Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role.

PubMed

Khadka, Bijendra; Gupta, Radhey S

2017-08-01

Homologs of the phosphatidylinositol-4-phosphate-5-kinase (PIP5K), which controls a multitude of essential cellular functions, contain a 8 aa insert in a conserved region that is specific for the Saccharomycetaceae family of fungi. Using structures of human PIP4K proteins as templates, structural models were generated of the Saccharomyces cerevisiae and human PIP5K proteins. In the modeled S. cerevisiae PIP5K, the 8 aa insert forms a surface exposed loop, present on the same face of the protein as the activation loop of the kinase domain. Electrostatic potential analysis indicates that the residues from 8 aa conserved loop form a highly positively charged surface patch, which through electrostatic interaction with the anionic portions of phospholipid head groups, is expected to play a role in the membrane interaction of the yeast PIP5K. To unravel this prediction, molecular dynamics (MD) simulations were carried out to examine the binding interaction of PIP5K, either containing or lacking the conserved signature insert, with two different membrane lipid bilayers. The results from MD studies provide insights concerning the mechanistic of interaction of PIP5K with lipid bilayer, and support the contention that the identified 8 aa conserved insert in fungal PIP5K plays an important role in the binding of this protein with membrane surface. Proteins 2017; 85:1454-1467. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Opto-Technical Monitoring - a Standardized Methodology to Assess the Treatment of Historical Stone Surfaces

NASA Astrophysics Data System (ADS)

Rahrig, M.; Drewello, R.; Lazzeri, A.

2018-05-01

Monitoring is an essential requirement for the planning, assessment and evaluation of conservation measures. It should be based on a standardized and reproducible observation of the historical surface. For many areas and materials suitable methods for long-term monitoring already exist. But hardly any non-destructive testing methods have been used to test new materials for conservation of damaged stone surfaces. The Nano-Cathedral project, funded by the European Union's Horizon 2020 research and innovation program, is developing new materials and technologies for preserving damaged stone surfaces of built heritage. The prototypes developed are adjusted to the needs and problems of a total of six major cultural monuments in Europe. In addition to the testing of the materials under controlled laboratory conditions, the products have been applied to trial areas on the original stone surfaces. For a location-independent standardized assessment of surface changes of the entire trial areas a monitoring method based on opto-technical, non-contact and non-destructive testing methods has been developed. This method involves a three-dimensional measurement of the surface topography using Structured-Light-Scanning and the analysis of the surfaces in different light ranges using high resolution VIS photography, as well as UV-A-fluorescence photography and reflected near-field IR photography. The paper will show the workflow of this methodology, including a detailed description of the equipment used data processing and the advantages for monitoring highly valuable stone surfaces. Alongside the theoretical discussion, the results of two measuring campaigns on trial areas of the Nano-Cathedral project will be shown.
Development and Performance Evaluation of an Ozone-Contained Ice Making Machine Employing Pressurized Air Tight Containers

NASA Astrophysics Data System (ADS)

Yoshimura, Kenji; Akiyama, Tomoaki; Hirofuji, Yushi; Koyama, Shigeru

Ozone has the capability of sterilization and deodorization due to high oxidation power. It is also effective for the conservation of perishable foods and purification of water. However, ozone has a disadvantage, that is, conservation of ozone is difficult because it reacts to oxygen. Recently, ozone-contained ice is taken attention for the purpose of its conservation. The use of ozone-contained ice seems to keep food fresher when we conserve and transport perishable foods due to the effects of cooling and sterilization of ozone-contained ice. In the present study, we have developed an ozone-contained ice making machine employing pressurized air tight containers with commercially available size. And the performance evaluation of the system is also carried out. Furthermore, we investigated the sterilization effect of ozone-contained ice on conservation of fish. It was seen that ozone-contained ice is effective for sterilization of surface of fish.
New Mass-Conserving Bedrock Topography for Pine Island Glacier Impacts Simulated Decadal Rates of Mass Loss

NASA Astrophysics Data System (ADS)

Nias, I. J.; Cornford, S. L.; Payne, A. J.

2018-04-01

High-resolution ice flow modeling requires bedrock elevation and ice thickness data, consistent with one another and with modeled physics. Previous studies have shown that gridded ice thickness products that rely on standard interpolation techniques (such as Bedmap2) can be inconsistent with the conservation of mass, given observed velocity, surface elevation change, and surface mass balance, for example, near the grounding line of Pine Island Glacier, West Antarctica. Using the BISICLES ice flow model, we compare results of simulations using both Bedmap2 bedrock and thickness data, and a new interpolation method that respects mass conservation. We find that simulations using the new geometry result in higher sea level contribution than Bedmap2 and reveal decadal-scale trends in the ice stream dynamics. We test the impact of several sliding laws and find that it is at least as important to accurately represent the bedrock and initial ice thickness as the choice of sliding law.
Forecasting runoff from Pennsylvania landscapes

USDA-ARS?s Scientific Manuscript database

Identifying sites prone to surface runoff has been a cornerstone of conservation and nutrient management programs, relying upon site assessment tools that support strategic, as opposed to operational, decision making. We sought to develop simple, empirical models to represent two highly different me...
Prioritizing conservation potential of arid-land montane natural springs and associated riparian areas

USGS Publications Warehouse

Thompson, B.C.; Matusik-Rowan, P. L.; Boykin, K.G.

2002-01-01

Using inventory data and input from natural resource professionals, we developed a classification system that categorizes conservation potential for montane natural springs. This system contains 18 classes based on the presence of a riparian patch, wetland species, surface water, and evidence of human activity. We measured physical and biological components of 276 montane springs in the Oscura Mountains above 1450 m and the San Andres Mountains above 1300 m in southern New Mexico. Two of the 18 classes were not represented during the inventory, indicating the system applies to conditions beyond the montane springs in our study area. The class type observed most often (73 springs) had a riparian patch, perennial surface water, and human evidence. We assessed our system in relation to 13 other wetland and riparian classification systems regarding approach, area of applicability, intended users, validation, ease of use, and examination of system response. Our classification can be used to rapidly assess priority of conservation potential for isolated riparian sites, especially springs, in arid landscapes. We recommend (1) including this classification in conservation planning, (2) removing deleterious structures from high-priority sites, and (3) assessing efficiency and use of this classification scheme elsewhere. ?? 2002 Elsevier Science Ltd.
Study and development of 22 kW peak power fiber coupled short pulse Nd:YAG laser for cleaning applications

NASA Astrophysics Data System (ADS)

Choubey, Ambar; Vishwakarma, S. C.; Vachhani, D. M.; Singh, Ravindra; Misra, Pushkar; Jain, R. K.; Arya, R.; Upadhyaya, B. N.; Oak, S. M.

2014-11-01

Free running short pulse Nd:YAG laser of microsecond pulse duration and high peak power has a unique capability to ablate material from the surface without heat propagation into the bulk. Applications of short pulse Nd:YAG lasers include cleaning and restoration of marble, stones, and a variety of metals for conservation. A study on the development of high peak power short pulses from Nd:YAG laser along with its cleaning and conservation applications has been performed. A pulse energy of 1.25 J with 55 μs pulse duration and a maximum peak power of 22 kW has been achieved. Laser beam has an M2 value of ~28 and a pulse-to-pulse stability of ±2.5%. A lower value of M2 means a better beam quality of the laser in multimode operation. A top hat spatial profile of the laser beam was achieved at the exit end of 200 μm core diameter optical fiber, which is desirable for uniform cleaning. This laser system has been evaluated for efficient cleaning of surface contaminations on marble, zircaloy, and inconel materials for conservation with cleaning efficiency as high as 98%. Laser's cleaning quality and efficiency have been analysed by using a microscope, a scanning electron microscope (SEM), and X-ray photon spectroscopy (XPS) measurements.
Structural re-alignment in an immunologic surface region of ricin A chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less
7 CFR 1491.22 - Conservation easement deeds.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., population density, the ratio of open prime other important farmland versus impervious surfaces on the...) Impervious surfaces will not exceed 2 percent of the FRPP easement area, excluding NRCS-approved conservation practices. The State Conservationist may waive the 2 percent impervious surface limitation on a parcel-by...
7 CFR 1491.22 - Conservation easement deeds.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., population density, the ratio of open prime other important farmland versus impervious surfaces on the...) Impervious surfaces will not exceed 2 percent of the FRPP easement area, excluding NRCS-approved conservation practices. The State Conservationist may waive the 2 percent impervious surface limitation on a parcel-by...
Accumulation and persistence of chlorobiphenyls, organochlorine pesticides and faecal sterols at the Garroch Head sewage sludge disposal site, Firth of Clyde.

PubMed

Kelly, A G

1995-01-01

The sediment concentrations of organic carbon, faecal sterols, individual chlorobiphenyl congeners and organochlorine pesticides have been measured in seabed cores from the sewage sludge disposal area at Garroch Head in the Firth of Clyde. The measurements confirm the accumulative nature of the site with high levels of sedimentary faecal sterols (152 mg kg(-1) coprostanol). Levels of chlorobiphenyls, DDT compounds and dieldrin in surface sediment were elevated by factors of 12, 40 and 120, respectively, over those observed at a site remote from the effects of dumping. Total chlorobiphenyl levels of 515 microg kg(-1) Arochlor 1254 in surface sediment were comparable to levels found in other areas heavily contaminated with sewage sludge. The 20-cm depth of heavily sludge-contaminated sediment overlays a mixed sludge/basal sediment layer some 10 cm in depth. Levels of organochlorine contaminants were elevated to depths of 90 cm in the sediment, suggesting that the surface layer is a source of contaminants to the deeper sediment. Within the upper 15-20 cm sediment in the disposal area, chlorobiphenyls are conservative, the variation in their concentration with respect to depth being related to historical input. Lindane and possibly dieldrin, and hexachlorobenzene are not conservative. Faecal sterols are removed in sub-surface sediment, in contrast to conservative behaviour previously found at other sewage polluted sites.
A free energy-based surface tension force model for simulation of multiphase flows by level-set method

NASA Astrophysics Data System (ADS)

Yuan, H. Z.; Chen, Z.; Shu, C.; Wang, Y.; Niu, X. D.; Shu, S.

2017-09-01

In this paper, a free energy-based surface tension force (FESF) model is presented for accurately resolving the surface tension force in numerical simulation of multiphase flows by the level set method. By using the analytical form of order parameter along the normal direction to the interface in the phase-field method and the free energy principle, FESF model offers an explicit and analytical formulation for the surface tension force. The only variable in this formulation is the normal distance to the interface, which can be substituted by the distance function solved by the level set method. On one hand, as compared to conventional continuum surface force (CSF) model in the level set method, FESF model introduces no regularized delta function, due to which it suffers less from numerical diffusions and performs better in mass conservation. On the other hand, as compared to the phase field surface tension force (PFSF) model, the evaluation of surface tension force in FESF model is based on an analytical approach rather than numerical approximations of spatial derivatives. Therefore, better numerical stability and higher accuracy can be expected. Various numerical examples are tested to validate the robustness of the proposed FESF model. It turns out that FESF model performs better than CSF model and PFSF model in terms of accuracy, stability, convergence speed and mass conservation. It is also shown in numerical tests that FESF model can effectively simulate problems with high density/viscosity ratio, high Reynolds number and severe topological interfacial changes.
How merging droplets jump off a superhydrophobic surface: Measurements and model

NASA Astrophysics Data System (ADS)

Mouterde, Timothée; Nguyen, Thanh-Vinh; Takahashi, Hidetoshi; Clanet, Christophe; Shimoyama, Isao; Quéré, David

2017-11-01

We investigate how drops merging on a nonwettable surface jump off this surface, for both symmetric and asymmetric coalescences. For this purpose, we design and build a microelectromechanical system sensor able to quantify forces down to the micro-Newton scale at a high acquisition rate (200 kHz). Using this device, we perform direct force measurements of self-propelled droplets coupled to high-speed imaging. Experimental data show that the total momentum of the drop after coalescence mainly depends on the size of the smaller drop. Exploiting this finding, we quantitatively predict the takeoff speed of jumping drop pairs and show how to correct the usual argument based on energy conservation.

Nanoengineered Surfaces for High Flux Thin Film Evaporation

DTIC Science & Technology

2013-07-15

for a variety of heat transfer and resource conserving applications. References 1. Mudawar , I., Assessment of high-heat-flux thermal...M.B. and I. Mudawar , High-flux boiling in low-flow rate, low-pressure drop mini- channel and microchannel heat sinks. International Journal of Heat...pressure drop elements and fabricated nucleation sites. Journal of Heat Transfer, 2006. 128(4): p. 389-396. 7. Qu, W. and I. Mudawar , Measurement and
An approach to enhance the conservation-compatibility of solar energy development.

PubMed

Cameron, D Richard; Cohen, Brian S; Morrison, Scott A

2012-01-01

The rapid pace of climate change poses a major threat to biodiversity. Utility-scale renewable energy development (>1 MW capacity) is a key strategy to reduce greenhouse gas emissions, but development of those facilities also can have adverse effects on biodiversity. Here, we examine the synergy between renewable energy generation goals and those for biodiversity conservation in the 13 M ha Mojave Desert of the southwestern USA. We integrated spatial data on biodiversity conservation value, solar energy potential, and land surface slope angle (a key determinant of development feasibility) and found there to be sufficient area to meet renewable energy goals without developing on lands of relatively high conservation value. Indeed, we found nearly 200,000 ha of lower conservation value land below the most restrictive slope angle (<1%); that area could meet the state of California's current 33% renewable energy goal 1.8 times over. We found over 740,000 ha below the highest slope angle (<5%)--an area that can meet California's renewable energy goal seven times over. Our analysis also suggests that the supply of high quality habitat on private land may be insufficient to mitigate impacts from future solar projects, so enhancing public land management may need to be considered among the options to offset such impacts. Using the approach presented here, planners could reduce development impacts on areas of higher conservation value, and so reduce trade-offs between converting to a green energy economy and conserving biodiversity.
An Approach to Enhance the Conservation-Compatibility of Solar Energy Development

PubMed Central

Cameron, D. Richard; Cohen, Brian S.; Morrison, Scott A.

2012-01-01

The rapid pace of climate change poses a major threat to biodiversity. Utility-scale renewable energy development (>1 MW capacity) is a key strategy to reduce greenhouse gas emissions, but development of those facilities also can have adverse effects on biodiversity. Here, we examine the synergy between renewable energy generation goals and those for biodiversity conservation in the 13 M ha Mojave Desert of the southwestern USA. We integrated spatial data on biodiversity conservation value, solar energy potential, and land surface slope angle (a key determinant of development feasibility) and found there to be sufficient area to meet renewable energy goals without developing on lands of relatively high conservation value. Indeed, we found nearly 200,000 ha of lower conservation value land below the most restrictive slope angle (<1%); that area could meet the state of California’s current 33% renewable energy goal 1.8 times over. We found over 740,000 ha below the highest slope angle (<5%) – an area that can meet California’s renewable energy goal seven times over. Our analysis also suggests that the supply of high quality habitat on private land may be insufficient to mitigate impacts from future solar projects, so enhancing public land management may need to be considered among the options to offset such impacts. Using the approach presented here, planners could reduce development impacts on areas of higher conservation value, and so reduce trade-offs between converting to a green energy economy and conserving biodiversity. PMID:22685568
One-third of reef-building corals face elevated extinction risk from climate change and local impacts.

PubMed

Carpenter, Kent E; Abrar, Muhammad; Aeby, Greta; Aronson, Richard B; Banks, Stuart; Bruckner, Andrew; Chiriboga, Angel; Cortés, Jorge; Delbeek, J Charles; Devantier, Lyndon; Edgar, Graham J; Edwards, Alasdair J; Fenner, Douglas; Guzmán, Héctor M; Hoeksema, Bert W; Hodgson, Gregor; Johan, Ofri; Licuanan, Wilfredo Y; Livingstone, Suzanne R; Lovell, Edward R; Moore, Jennifer A; Obura, David O; Ochavillo, Domingo; Polidoro, Beth A; Precht, William F; Quibilan, Miledel C; Reboton, Clarissa; Richards, Zoe T; Rogers, Alex D; Sanciangco, Jonnell; Sheppard, Anne; Sheppard, Charles; Smith, Jennifer; Stuart, Simon; Turak, Emre; Veron, John E N; Wallace, Carden; Weil, Ernesto; Wood, Elizabeth

2008-07-25

The conservation status of 845 zooxanthellate reef-building coral species was assessed by using International Union for Conservation of Nature Red List Criteria. Of the 704 species that could be assigned conservation status, 32.8% are in categories with elevated risk of extinction. Declines in abundance are associated with bleaching and diseases driven by elevated sea surface temperatures, with extinction risk further exacerbated by local-scale anthropogenic disturbances. The proportion of corals threatened with extinction has increased dramatically in recent decades and exceeds that of most terrestrial groups. The Caribbean has the largest proportion of corals in high extinction risk categories, whereas the Coral Triangle (western Pacific) has the highest proportion of species in all categories of elevated extinction risk. Our results emphasize the widespread plight of coral reefs and the urgent need to enact conservation measures.
Selenoprotein W controls epidermal growth factor receptor surface expression, activation and degradation via receptor ubiquitination

USDA-ARS?s Scientific Manuscript database

Epidermal growth factor (EGF) receptor (EGFR) is the founding member of the ErbB family of growth factor receptors that modulate a complex network of intracellular signaling pathways controlling growth, proliferation and differentiation. Selenoprotein W (SEPW1) is a diet-regulated, highly conserved...
Multi-level, multi-scale resource selection functions and resistance surfaces for conservation planning: Pumas as a case study

PubMed Central

Vickers, T. Winston; Ernest, Holly B.; Boyce, Walter M.

2017-01-01

The importance of examining multiple hierarchical levels when modeling resource use for wildlife has been acknowledged for decades. Multi-level resource selection functions have recently been promoted as a method to synthesize resource use across nested organizational levels into a single predictive surface. Analyzing multiple scales of selection within each hierarchical level further strengthens multi-level resource selection functions. We extend this multi-level, multi-scale framework to modeling resistance for wildlife by combining multi-scale resistance surfaces from two data types, genetic and movement. Resistance estimation has typically been conducted with one of these data types, or compared between the two. However, we contend it is not an either/or issue and that resistance may be better-modeled using a combination of resistance surfaces that represent processes at different hierarchical levels. Resistance surfaces estimated from genetic data characterize temporally broad-scale dispersal and successful breeding over generations, whereas resistance surfaces estimated from movement data represent fine-scale travel and contextualized movement decisions. We used telemetry and genetic data from a long-term study on pumas (Puma concolor) in a highly developed landscape in southern California to develop a multi-level, multi-scale resource selection function and a multi-level, multi-scale resistance surface. We used these multi-level, multi-scale surfaces to identify resource use patches and resistant kernel corridors. Across levels, we found puma avoided urban, agricultural areas, and roads and preferred riparian areas and more rugged terrain. For other landscape features, selection differed among levels, as did the scales of selection for each feature. With these results, we developed a conservation plan for one of the most isolated puma populations in the U.S. Our approach captured a wide spectrum of ecological relationships for a population, resulted in effective conservation planning, and can be readily applied to other wildlife species. PMID:28609466
Multi-level, multi-scale resource selection functions and resistance surfaces for conservation planning: Pumas as a case study.

PubMed

Zeller, Katherine A; Vickers, T Winston; Ernest, Holly B; Boyce, Walter M

2017-01-01

The importance of examining multiple hierarchical levels when modeling resource use for wildlife has been acknowledged for decades. Multi-level resource selection functions have recently been promoted as a method to synthesize resource use across nested organizational levels into a single predictive surface. Analyzing multiple scales of selection within each hierarchical level further strengthens multi-level resource selection functions. We extend this multi-level, multi-scale framework to modeling resistance for wildlife by combining multi-scale resistance surfaces from two data types, genetic and movement. Resistance estimation has typically been conducted with one of these data types, or compared between the two. However, we contend it is not an either/or issue and that resistance may be better-modeled using a combination of resistance surfaces that represent processes at different hierarchical levels. Resistance surfaces estimated from genetic data characterize temporally broad-scale dispersal and successful breeding over generations, whereas resistance surfaces estimated from movement data represent fine-scale travel and contextualized movement decisions. We used telemetry and genetic data from a long-term study on pumas (Puma concolor) in a highly developed landscape in southern California to develop a multi-level, multi-scale resource selection function and a multi-level, multi-scale resistance surface. We used these multi-level, multi-scale surfaces to identify resource use patches and resistant kernel corridors. Across levels, we found puma avoided urban, agricultural areas, and roads and preferred riparian areas and more rugged terrain. For other landscape features, selection differed among levels, as did the scales of selection for each feature. With these results, we developed a conservation plan for one of the most isolated puma populations in the U.S. Our approach captured a wide spectrum of ecological relationships for a population, resulted in effective conservation planning, and can be readily applied to other wildlife species.
High-precision surface analysis of the roughness of Michelangelo's David

NASA Astrophysics Data System (ADS)

Fontana, Raffaella; Gambino, Maria Chiara; Greco, Marinella; Marras, Luciano; Materazzi, Marzia; Pampaloni, Enrico; Pezzati, Luca

2003-10-01

The knowledge of the shape of an artwork is an important element for its study and conservation. When dealing with a statue, roughness measurement is a very useful contribution to document its surface conditions, to assess either changes due to restoration intervention or surface decays due to wearing agents, and to monitor its time-evolution in terms of shape variations. In this work we present the preliminary results of the statistical analysis carried out on acquired data relative to six areas of the Michelangelo"s David marble statue, representative of differently degraded surfaces. Determination of the roughness and its relative characteristic wavelength is shown.
Geomorphological characterization of conservation agriculture

NASA Astrophysics Data System (ADS)

Tarolli, Paolo; Cecchin, Marco; Prosdocimi, Massimo; Masin, Roberta

2017-04-01

Soil water erosion is one of the major threats to soil resources throughout the world. Conventional agriculture has worsened the situation. Therefore, agriculture is facing multiple challenges: it has to produce more food to feed a growing population, and, on the other hand, safeguard natural resources adopting more sustainable production practices. In this perspective, more conservation-minded soil management practices should be taken to achieve an environmental sustainability of crop production. Indeed, conservation agriculture is considered to produce relevant environmental positive outcomes (e.g. reducing runoff and soil erosion, improving soil organic matter content and soil structure, and promoting biological activity). However, as mechanical weed control is limited or absent, in conservation agriculture, dependence on herbicides increases especially in the first years of transition from the conventional system. Consequently, also the risk of herbicide losses via runoff or adsorbed to eroded soil particles could be increased. To better analyse the complexity of soil water erosion and runoff processes in landscapes characterised by conservation agriculture, first, it is necessary to demonstrate if such different practices can significantly affect the surface morphology. Indeed, surface processes such erosion and runoff strongly depend on the shape of the surface. The questions are: are the lands treated with conservation and conventional agriculture different from each other regarding surface morphology? If so, can these differences provide a better understanding of hydrogeomorphic processes as the basis for a better and sustainable land management? To give an answer to these questions, we considered six study areas (three cultivated with no-tillage techniques, three with tillage techniques) in an experimental farm. High-resolution topography, derived from low-cost and fast photogrammetric techniques Structure-from-Motion (SfM), served as the basis to characterise the surface morphology. For each of derived Digital Elevation Model, seven morphometric indexes, such as slope, curvature, flow direction, contributing area, roughness, and connectivity was calculated. We showed then the variations of the morphology in the areas converted to the conservation agriculture, and, consequently, a possible modification of processes such as erosion and runoff. The results suggested that the agricultural surfaces interested by no-tillage practices are different from those tilled with conventional systems. The topography is rougher, with chaotic flow directions, and more concave areas, thus resulting in potential water storages, mitigating the intensity of soil erosion and runoff processes. On the other hand, the topography of traditional tillage area is more regular and smooth, with flow directions that tend to follow the same direction on the surface. These results are a novelty in the Earth Science and Agronomy: we demonstrated and quantified, from the geomorphological point of view, the potential role of conservative agriculture in mitigating, not only land degradation phenomena, but also the distribution of pollutants, and rainfall-runoff processes. References Prosdocimi, M., Tarolli, P., Cerdà, A. (2016). Mulching practice for reducing soil water erosion: A review. Earth-Science Reviews, 161, 191-203. Prosdocimi, M., Burguet, M., Di Prima, S., Sofia, G., Terol, E, Rodrigo Comino J., Cerdà, A., Tarolli, P. (2017). Rainfall simulation and Structure-from-Motion photogrammetry for the analysis of soil water erosion in Mediterranean vineyards. Science of the Total Environment, 574, 204-215. Tarolli, P., Sofia G. (2016). Human topographic signatures and derived geomorphic processes across landscapes, Geomorphology, 255, 140-161.
7 CFR 614.3 - Decisions subject to informal appeal procedures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Innovation Grants, (E) Ground and Surface Water Conservation Program, (F) Klamath Basin Program, and (G... CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE CONSERVATION OPERATIONS NRCS APPEAL PROCEDURES § 614.3... technical determinations made with respect to: (1) Conservation programs and regulatory requirements...
7 CFR 614.3 - Decisions subject to informal appeal procedures.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Innovation Grants, (E) Ground and Surface Water Conservation Program, (F) Klamath Basin Program, and (G... CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE CONSERVATION OPERATIONS NRCS APPEAL PROCEDURES § 614.3... technical determinations made with respect to: (1) Conservation programs and regulatory requirements...
Antibody Recognition of a Highly Conserved Influenza Virus Epitope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekiert, Damian C.; Bhabha, Gira; Elsliger, Marc-André

2009-05-21

Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes amore » highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.« less
Electric Double-Layer Interaction between Dissimilar Charge-Conserved Conducting Plates.

PubMed

Chan, Derek Y C

2015-09-15

Small metallic particles used in forming nanostructured to impart novel optical, catalytic, or tribo-rheological can be modeled as conducting particles with equipotential surfaces that carry a net surface charge. The value of the surface potential will vary with the separation between interacting particles, and in the absence of charge-transfer or electrochemical reactions across the particle surface, the total charge of each particle must also remain constant. These two physical conditions require the electrostatic boundary condition for metallic nanoparticles to satisfy an equipotential whole-of-particle charge conservation constraint that has not been studied previously. This constraint gives rise to a global charge conserved constant potential boundary condition that results in multibody effects in the electric double-layer interaction that are either absent or are very small in the familiar constant potential or constant charge or surface electrochemical equilibrium condition.
Energetics of oscillating lifting surfaces using integral conservation laws

NASA Technical Reports Server (NTRS)

Ahmadi, Ali R.; Widnall, Sheila E.

1987-01-01

The energetics of oscillating flexible lifting surfaces in two and three dimensions is calculated by the use of integral conservation laws in inviscid incompressible flow for general and harmonic transverse oscillations. Total thrust is calculated from the momentum theorem and energy loss rate due to vortex shedding in the wake from the principle of conservation of mechanical energy. Total power required to maintain the oscillations and hydrodynamic efficiency are also determined. In two dimensions, the results are obtained in closed form. In three dimensions, the distribution of vorticity on the lifting surface is also required as input to the calculations. Thus, unsteady lifting-surface theory must be used as well. The analysis is applicable to oscillating lifting surfaces of arbitrary planform, aspect ratio, and reduced frequency and does not require calculation of the leading-edge thrust.
Geochemistry of surface and pore water at USGS coring sites in wetlands of South Florida, 1994 and 1995

USGS Publications Warehouse

Orem, William H.; Lerch, Harry E.; Rawlik, Peter

2002-01-01

In this report, we present preliminary data on surface and pore water geochemistry from 22 sites in south Florida sampled during 1994 and 1995. These results are part of a larger study designed to evaluate the role of biogeochemical processes in sediments in the cycling of carbon, nitrogen, phosphorus, and sulfur in the south Florida ecosystem. The data are briefly discussed in regard to regional trends in the concentrations of chemical species, and general diagenetic processes in sediments. These results are part of a larger study designed to evaluate the role of biogeochemical processes in sediments in the cycling of carbon, nitrogen, phosphorus, and sulfur in the south Florida ecosystem. These elements play a crucial role in regulating organic sedimentation, nutrient dynamics, redox conditions, and the biogeochemistry of mercury in the threatened wetlands of south Florida. Pore water samples for chemical analyis were obtained using a piston corer/squeezer designed to avoid compression of the sediment and avoid oxidation and contamination of the pore water samples. Results show distinct regional trends in both surface water and pore water geochemistry. Most chemical species in surface and pore water show peak concentrations in Water Conservation Area 2A, with diminishing concentrations to the south and west into Water Conservation Area 3A, and Everglades National Park. The largest differences observed were for phosphate and sulfide, with concentrations in pore waters in Water Conservation Area 2A up to 500x higher than concentrations observed in freshwater marsh areas of Water Conservation Area 3A and Everglades National Park. Sites near the Hillsboro Canal in Water Conservation Area 2A are heavily contaminated with both phosphorus and sulfur. Pore water profiles for dissolved reactive phosphate suggest that recycling of phosphorus at these contaminated sites occurs primarily in the upper 20 cm of sediment. High levels of sulfide in pore water in Water Conservation Area 2A may inhibit mercury methylation here. At sites in Water Conservation Area 3A south of Alligator Alley, sulfide levels are much lower and sulfate reduction in the sediments here may be conducive to methyl mercury formation. Concentration versus depth profiles of biogeochemically important chemical species in pore water at most sites are smoth curves amenable to modelling using standard diagenetic equations. This should allow prediction of rates of biogeochemical processes in these sediments for incorporation in ecosystem models.
Understanding Drought and Regional Conservation Efforts on Urban Ecohydrology in Southern California

NASA Astrophysics Data System (ADS)

Hogue, T. S.

2015-12-01

Cities in the western U.S. are under increasing pressure to reduce the demand of imported water through increasing conservation efforts, altering non-native landscapes, and enhancing local water supplies. The State of California adopted emergency regulations implementing a mandatory 25% statewide reduction in potable urban water use and agricultural restrictions have also been enacted. The complexities in urban water flows and lack of granular data make understanding the impact of conservation and demand change on regional ecohydrology difficult. This presentation highlights ongoing work to better understand the coupling between humans, water and ecosystems in semi-arid urban cities, using metropolitan southern California as a case study. We evaluate historical and contemporary ecohydrologic behavior and human impacts through intensive data collection, remote sensing and high resolution modeling. The change in outdoor irrigation rates due to recent conservation measures (2008-2010) has resulted in overall decreased greenness and reduced dry season streamflow; however significant variability in conservation response is observed. Groundwater recharge, artificially supported by landscape irrigation, is also being impacted. In general, anthropogenic water fluxes (irrigation, pipe leakage, spreading grounds) are not parameterized in hydrologic and land surface models applied over urban areas. Inclusion of landscape irrigation significantly improves neighborhood scale simulations of evaporative fluxes and land surface temperatures and results in shifts in the energy partitioning. The cooling effects of irrigation on daily air temperatures has the largest influence over low intensity residential areas, with an average 2°C decrease observed in coupled model simulations (WRF-Noah-UCM). Ultimately, we strive to improve predictions of human-water interactions in semi-arid cities to better understand the effectiveness and impacts of ongoing drought and conservation efforts and guide demand strategies under future climate variability.
Resistance-surface-based wildlife conservation connectivity modeling: Summary of efforts in the United States and guide for practitioners

Treesearch

Alisa A. Wade; Kevin S. McKelvey; Michael K. Schwartz

2015-01-01

Resistance-surface-based connectivity modeling has become a widespread tool for conservation planning. The current ease with which connectivity models can be created, however, masks the numerous untested assumptions underlying both the rules that produce the resistance surface and the algorithms used to locate low-cost paths across the target landscape. Here we present...
Human hopping on damped surfaces: strategies for adjusting leg mechanics.

PubMed

Moritz, Chet T; Farley, Claire T

2003-08-22

Fast-moving legged animals bounce along the ground with spring-like legs and agilely traverse variable terrain. Previous research has shown that hopping and running humans maintain the same bouncing movement of the body's centre of mass on a range of elastic surfaces by adjusting their spring-like legs to exactly offset changes in surface stiffness. This study investigated human hopping on damped surfaces that dissipated up to 72% of the hopper's mechanical energy. On these surfaces, the legs did not act like pure springs. Leg muscles performed up to 24-fold more net work to replace the energy lost by the damped surface. However, considering the leg and surface together, the combination appeared to behave like a constant stiffness spring on all damped surfaces. By conserving the mechanics of the leg-surface combination regardless of surface damping, hoppers also conserved centre-of-mass motions. Thus, the normal bouncing movements of the centre of mass in hopping are not always a direct result of spring-like leg behaviour. Conserving the trajectory of the centre of mass by maintaining spring-like mechanics of the leg-surface combination may be an important control strategy for fast-legged locomotion on variable terrain.
Human hopping on damped surfaces: strategies for adjusting leg mechanics.

PubMed Central

Moritz, Chet T; Farley, Claire T

2003-01-01

Fast-moving legged animals bounce along the ground with spring-like legs and agilely traverse variable terrain. Previous research has shown that hopping and running humans maintain the same bouncing movement of the body's centre of mass on a range of elastic surfaces by adjusting their spring-like legs to exactly offset changes in surface stiffness. This study investigated human hopping on damped surfaces that dissipated up to 72% of the hopper's mechanical energy. On these surfaces, the legs did not act like pure springs. Leg muscles performed up to 24-fold more net work to replace the energy lost by the damped surface. However, considering the leg and surface together, the combination appeared to behave like a constant stiffness spring on all damped surfaces. By conserving the mechanics of the leg-surface combination regardless of surface damping, hoppers also conserved centre-of-mass motions. Thus, the normal bouncing movements of the centre of mass in hopping are not always a direct result of spring-like leg behaviour. Conserving the trajectory of the centre of mass by maintaining spring-like mechanics of the leg-surface combination may be an important control strategy for fast-legged locomotion on variable terrain. PMID:12965003
Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form

PubMed Central

Zheng, Heping; Mandal, Arabinda; Shumilin, Igor A.; Chordia, Mahendra D.; Panneerdoss, Subbarayalu; Herr, John C.; Minor, Wladek

2016-01-01

Sperm Lysozyme-Like Protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75Å in diameter with a 25Å central pore comprised of six monomers per helix turn repeating every 33Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally-observed SLLP1/SAS1B interaction involved in fertilization. PMID:26198801

Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.

PubMed

Zheng, H; Mandal, A; Shumilin, I A; Chordia, M D; Panneerdoss, S; Herr, J C; Minor, W

2015-07-01

Sperm lysozyme-like protein 1 (SLLP1) is one of the lysozyme-like proteins predominantly expressed in mammalian testes that lacks bacteriolytic activity, localizes in the sperm acrosome, and exhibits high affinity for an oolemmal receptor, SAS1B. The crystal structure of mouse SLLP1 (mSLLP1) was determined at 2.15 Å resolution. mSLLP1 monomer adopts a structural fold similar to that of chicken/mouse lysozymes retaining all four canonical disulfide bonds. mSLLP1 is distinct from c-lysozyme by substituting two essential catalytic residues (E35T/D52N), exhibiting different surface charge distribution, and by forming helical filaments approximately 75 Å in diameter with a 25 Å central pore comprised of six monomers per helix turn repeating every 33 Å. Cross-species alignment of all reported SLLP1 sequences revealed a set of invariant surface regions comprising a characteristic fingerprint uniquely identifying SLLP1 from other c-lysozyme family members. The fingerprint surface regions reside around the lips of the putative glycan-binding groove including three polar residues (Y33/E46/H113). A flexible salt bridge (E46-R61) was observed covering the glycan-binding groove. The conservation of these regions may be linked to their involvement in oolemmal protein binding. Interaction between SLLP1 monomer and its oolemmal receptor SAS1B was modeled using protein-protein docking algorithms, utilizing the SLLP1 fingerprint regions along with the SAS1B conserved surface regions. This computational model revealed complementarity between the conserved SLLP1/SAS1B interacting surfaces supporting the experimentally observed SLLP1/SAS1B interaction involved in fertilization. © 2015 American Society of Andrology and European Academy of Andrology.
Combining geodiversity with climate and topography to account for threatened species richness.

PubMed

Tukiainen, Helena; Bailey, Joseph J; Field, Richard; Kangas, Katja; Hjort, Jan

2017-04-01

Understanding threatened species diversity is important for long-term conservation planning. Geodiversity-the diversity of Earth surface materials, forms, and processes-may be a useful biodiversity surrogate for conservation and have conservation value itself. Geodiversity and species richness relationships have been demonstrated; establishing whether geodiversity relates to threatened species' diversity and distribution pattern is a logical next step for conservation. We used 4 geodiversity variables (rock-type and soil-type richness, geomorphological diversity, and hydrological feature diversity) and 4 climatic and topographic variables to model threatened species diversity across 31 of Finland's national parks. We also analyzed rarity-weighted richness (a measure of site complementarity) of threatened vascular plants, fungi, bryophytes, and all species combined. Our 1-km 2 resolution data set included 271 threatened species from 16 major taxa. We modeled threatened species richness (raw and rarity weighted) with boosted regression trees. Climatic variables, especially the annual temperature sum above 5 °C, dominated our models, which is consistent with the critical role of temperature in this boreal environment. Geodiversity added significant explanatory power. High geodiversity values were consistently associated with high threatened species richness across taxa. The combined effect of geodiversity variables was even more pronounced in the rarity-weighted richness analyses (except for fungi) than in those for species richness. Geodiversity measures correlated most strongly with species richness (raw and rarity weighted) of threatened vascular plants and bryophytes and were weakest for molluscs, lichens, and mammals. Although simple measures of topography improve biodiversity modeling, our results suggest that geodiversity data relating to geology, landforms, and hydrology are also worth including. This reinforces recent arguments that conserving nature's stage is an important principle in conservation. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.
Arthropod vertical stratification in temperate deciduous forests: Implications for conservation oriented management

Treesearch

Ulyshen Michael

2011-01-01

Studies on the vertical distribution patterns of arthropods in temperate deciduous forests reveal highly stratified (i.e., unevenly vertically distributed) communities. These patterns are determined by multiple factors acting simultaneously, including: (1) time (forest age, season, time of day); (2) forest structure (height, vertical foliage complexity, plant surface...
Summary of Organic Wastewater Compounds and Other Water-Quality Data in Charles County, Maryland, October 2007 through August 2008

USGS Publications Warehouse

Lorah, Michelle M.; Soeder, Daniel J.; Teunis, Jessica A.

2010-01-01

The U.S. Geological Survey, in cooperation with the government of Charles County, Maryland, and the Port Tobacco River Conservancy, Inc., conducted a water-quality reconnaissance and sampling investigation of the Port Tobacco River and Nanjemoy Creek watersheds in Charles County during October 2007 and June-August 2008. Samples were collected and analyzed for major ions, nutrients, organic wastewater compounds, and other selected constituents from 17 surface-water sites and 11 well sites (5 of which were screened in streambed sediments to obtain porewater samples). Most of the surface-water sites were relatively widely spaced throughout the Port Tobacco River and Nanjemoy Creek watersheds, although the well sites and some associated surface-water sites were concentrated in one residential community along the Port Tobacco River that has domestic septic systems. Sampling for enterococci bacteria was conducted by the Port Tobacco River Conservancy, Inc., at each site to coordinate with the sampling for chemical constituents. The purpose of the coordinated sampling was to determine correlations between historically high, in-stream bacteria counts and human wastewater inputs. Chemical data for the groundwater, porewater, and surface-water samples are presented in this report.
Discontinuous Spectral Difference Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Liu, Yen; Vinokur, Marcel

2004-01-01

A new, high-order, conservative, and efficient discontinuous spectral finite difference (SD) method for conservation laws on unstructured grids is developed. The concept of discontinuous and high-order local representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) and the Spectral Volume (SV) methods, but while these methods are based on the integrated forms of the equations, the new method is based on the differential form to attain a simpler formulation and higher efficiency. Conventional unstructured finite-difference and finite-volume methods require data reconstruction based on the least-squares formulation using neighboring point or cell data. Since each unknown employs a different stencil, one must repeat the least-squares inversion for every point or cell at each time step, or to store the inversion coefficients. In a high-order, three-dimensional computation, the former would involve impractically large CPU time, while for the latter the memory requirement becomes prohibitive. In addition, the finite-difference method does not satisfy the integral conservation in general. By contrast, the DG and SV methods employ a local, universal reconstruction of a given order of accuracy in each cell in terms of internally defined conservative unknowns. Since the solution is discontinuous across cell boundaries, a Riemann solver is necessary to evaluate boundary flux terms and maintain conservation. In the DG method, a Galerkin finite-element method is employed to update the nodal unknowns within each cell. This requires the inversion of a mass matrix, and the use of quadratures of twice the order of accuracy of the reconstruction to evaluate the surface integrals and additional volume integrals for nonlinear flux functions. In the SV method, the integral conservation law is used to update volume averages over subcells defined by a geometrically similar partition of each grid cell. As the order of accuracy increases, the partitioning for 3D requires the introduction of a large number of parameters, whose optimization to achieve convergence becomes increasingly more difficult. Also, the number of interior facets required to subdivide non-planar faces, and the additional increase in the number of quadrature points for each facet, increases the computational cost greatly.
A System of Conservative Regridding for Ice-Atmosphere Coupling in a General Circulation Model (GCM)

NASA Technical Reports Server (NTRS)

Fischer, R.; Nowicki, S.; Kelley, M.; Schmidt, G. A.

2014-01-01

The method of elevation classes, in which the ice surface model is run at multiple elevations within each grid cell, has proven to be a useful way for a low-resolution atmosphere inside a general circulation model (GCM) to produce high-resolution downscaled surface mass balance fields for use in one-way studies coupling atmospheres and ice flow models. Past uses of elevation classes have failed to conserve mass and energy because the transformation used to regrid to the atmosphere was inconsistent with the transformation used to downscale to the ice model. This would cause problems for two-way coupling. A strategy that resolves this conservation issue has been designed and is presented here. The approach identifies three grids between which data must be regridded and five transformations between those grids required by a typical coupled atmosphere-ice flow model. This paper develops a theoretical framework for the problem and shows how each of these transformations may be achieved in a consistent, conservative manner. These transformations are implemented in Glint2, a library used to couple atmosphere models with ice models. Source code and documentation are available for download. Confounding real-world issues are discussed, including the use of projections for ice modeling, how to handle dynamically changing ice geometry, and modifications required for finite element ice models.
Impact of numerical choices on water conservation in the E3SM Atmosphere Model Version 1 (EAM V1)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Kai; Rasch, Philip J.; Taylor, Mark A.

The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations for sea level rise projection. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods formore » fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model is negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in the new model results in a very thin model layer at the Earth’s surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for this model.« less
Impact of numerical choices on water conservation in the E3SM Atmosphere Model version 1 (EAMv1)

NASA Astrophysics Data System (ADS)

Zhang, Kai; Rasch, Philip J.; Taylor, Mark A.; Wan, Hui; Leung, Ruby; Ma, Po-Lun; Golaz, Jean-Christophe; Wolfe, Jon; Lin, Wuyin; Singh, Balwinder; Burrows, Susannah; Yoon, Jin-Ho; Wang, Hailong; Qian, Yun; Tang, Qi; Caldwell, Peter; Xie, Shaocheng

2018-06-01

The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model becomes negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors in early V1 versions decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in V1 results in a very thin model layer at the Earth's surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for V1.
Assessment of indicator bacteria and Aeromonas spp. in surface and nontraditional irrigation water: a conserve study

USDA-ARS?s Scientific Manuscript database

Introduction: The use of surface and nontraditional irrigation water (SNIW) (pond, tidal and non-tidal river water, reclaimed wastewater) is one way to conserve groundwater. However, SNIW may serve as reservoirs and vehicles for under-recognized enteric pathogens, spreading localized contamination d...
Edge Effects Are Important in Supporting Beetle Biodiversity in a Gravel-Bed River Floodplain

PubMed Central

Langhans, Simone D.; Tockner, Klement

2014-01-01

Understanding complex, dynamic, and diverse ecosystems is essential for developing sound management and conservation strategies. Gravel-bed river floodplains are composed of an interlinked mosaic of aquatic and terrestrial habitats hosting a diverse, specialized, and endangered fauna. Therefore, they serve as excellent models to investigate the biodiversity of multiple ecotones and related edge effects. In this study, we investigated the abundance, composition, richness, and conservation status of beetle assemblages at varying sediment depth (0, 0.1, 0.6 and 1.1 m), distance from the channel (1, 5, 20, and 60–100 m, and 5 m within the riparian forest), and time of the year (February–November) across a 200 m-wide gravel bar at the near-natural Tagliamento River (Italy), to detect edge effects in four floodplain ecotones: aquatic-terrestrial, forest-active floodplain, sediment-air, and sediment-groundwater. We used conventional pitfall traps and novel tube traps to sample beetles comparably on the sediment surface and within the unsaturated sediments. We found a total of 308 beetle species (including 87 of conservation concern) that showed multiple, significant positive edge effects across the floodplain ecotones, mainly driven by spatial heterogeneity: Total and red list beetle abundance and richness peaked on the sediment surface, at channel margins, and at the edge of the riparian forest. All ecotones possessed edge/habitat specialists. Most red list species occurred on the sediment surface, including five species previously considered extinct – yet two of these species occurred in higher densities in the unsaturated sediments. Conservation and management efforts along gravel-bed rivers must therefore promote a dynamic flow and sediment regime to create and maintain habitat heterogeneity and ecotone diversity, which support a unique and high biodiversity. PMID:25545280
Edge effects are important in supporting beetle biodiversity in a gravel-bed river floodplain.

PubMed

Langhans, Simone D; Tockner, Klement

2014-01-01

Understanding complex, dynamic, and diverse ecosystems is essential for developing sound management and conservation strategies. Gravel-bed river floodplains are composed of an interlinked mosaic of aquatic and terrestrial habitats hosting a diverse, specialized, and endangered fauna. Therefore, they serve as excellent models to investigate the biodiversity of multiple ecotones and related edge effects. In this study, we investigated the abundance, composition, richness, and conservation status of beetle assemblages at varying sediment depth (0, 0.1, 0.6 and 1.1 m), distance from the channel (1, 5, 20, and 60-100 m, and 5 m within the riparian forest), and time of the year (February-November) across a 200 m-wide gravel bar at the near-natural Tagliamento River (Italy), to detect edge effects in four floodplain ecotones: aquatic-terrestrial, forest-active floodplain, sediment-air, and sediment-groundwater. We used conventional pitfall traps and novel tube traps to sample beetles comparably on the sediment surface and within the unsaturated sediments. We found a total of 308 beetle species (including 87 of conservation concern) that showed multiple, significant positive edge effects across the floodplain ecotones, mainly driven by spatial heterogeneity: Total and red list beetle abundance and richness peaked on the sediment surface, at channel margins, and at the edge of the riparian forest. All ecotones possessed edge/habitat specialists. Most red list species occurred on the sediment surface, including five species previously considered extinct--yet two of these species occurred in higher densities in the unsaturated sediments. Conservation and management efforts along gravel-bed rivers must therefore promote a dynamic flow and sediment regime to create and maintain habitat heterogeneity and ecotone diversity, which support a unique and high biodiversity.
Patterns of amino acid conservation in human and animal immunodeficiency viruses.

PubMed

Voitenko, Olga S; Dhroso, Andi; Feldmann, Anna; Korkin, Dmitry; Kalinina, Olga V

2016-09-01

Due to their high genomic variability, RNA viruses and retroviruses present a unique opportunity for detailed study of molecular evolution. Lentiviruses, with HIV being a notable example, are one of the best studied viral groups: hundreds of thousands of sequences are available together with experimentally resolved three-dimensional structures for most viral proteins. In this work, we use these data to study specific patterns of evolution of the viral proteins, and their relationship to protein interactions and immunogenicity. We propose a method for identification of two types of surface residues clusters with abnormal conservation: extremely conserved and extremely variable clusters. We identify them on the surface of proteins from HIV and other animal immunodeficiency viruses. Both types of clusters are overrepresented on the interaction interfaces of viral proteins with other proteins, nucleic acids or low molecular-weight ligands, both in the viral particle and between the virus and its host. In the immunodeficiency viruses, the interaction interfaces are not more conserved than the corresponding proteins on an average, and we show that extremely conserved clusters coincide with protein-protein interaction hotspots, predicted as the residues with the largest energetic contribution to the interaction. Extremely variable clusters have been identified here for the first time. In the HIV-1 envelope protein gp120, they overlap with known antigenic sites. These antigenic sites also contain many residues from extremely conserved clusters, hence representing a unique interacting interface enriched both in extremely conserved and in extremely variable clusters of residues. This observation may have important implication for antiretroviral vaccine development. A Python package is available at https://bioinf.mpi-inf.mpg.de/publications/viral-ppi-pred/ voitenko@mpi-inf.mpg.de or kalinina@mpi-inf.mpg.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

PubMed Central

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-01-01

Protein–protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein–protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein–protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein–protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach. PMID:27965389
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.

PubMed

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-12-27

Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.
Marine algae are `taught' the basics of angular momentum

NASA Astrophysics Data System (ADS)

Allen, John Taylor

2017-11-01

Advanced modelling studies and high-resolution observations have shown that flows related to instability of the mesoscale ( 1-10 km scale) may provide both the fertilisation mechanism for nutrient-depleted (oligotrophic) surface waters and a subduction mechanism for the rapid export of phytoplankton biomass to the deep ocean. Here, a detailed multidisciplinary analysis of the data from an example high-resolution observational campaign is presented. The data provide direct observations of the transport of phytoplankton through baroclinic instability. Furthermore, the data confirm that this transport is constrained by the requirement to conserve angular momentum, expressed in a stratified water column as the conservation of potential vorticity. This constraint is clearly seen to produce long thin filaments of phytoplankton populations strained out along isopycnal vorticity annuli associated with mesoscale frontal instabilities.
Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.
A monotonicity preserving conservative sharp interface flow solver for high density ratio two-phase flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le Chenadec, Vincent, E-mail: vlechena@stanford.edu; Pitsch, Heinz; Institute for Combustion Technology, RWTH Aachen, Templergraben 64, 52056 Aachen

2013-09-15

This paper presents a novel approach for solving the conservative form of the incompressible two-phase Navier–Stokes equations. In order to overcome the numerical instability induced by the potentially large density ratio encountered across the interface, the proposed method includes a Volume-of-Fluid type integration of the convective momentum transport, a monotonicity preserving momentum rescaling, and a consistent and conservative Ghost Fluid projection that includes surface tension effects. The numerical dissipation inherent in the Volume-of-Fluid treatment of the convective transport is localized in the interface vicinity, enabling the use of a kinetic energy conserving discretization away from the singularity. Two- and three-dimensionalmore » tests are presented, and the solutions shown to remain accurate at arbitrary density ratios. The proposed method is then successfully used to perform the detailed simulation of a round water jet emerging in quiescent air, therefore suggesting the applicability of the proposed algorithm to the computation of realistic turbulent atomization.« less
Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076
High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

NASA Technical Reports Server (NTRS)

Potter, Christopher S.; Li, Shuang

2014-01-01

The Desert Renewable Energy Conservation Plan (DRECP), a major component of California's renewable energy planning efforts, is intended to provide effective protection and conservation of desert ecosystems, while allowing for the sensible development of renewable energy projects. This NASA mapping report was developed to support the DRECP and the Bureau of Land Management (BLM). We outline in this document remote sensing image processing methods to deliver new maps of biological soils crusts, sand dune movements, desert pavements, and sub-surface water sources across the DRECP area. We focused data processing first on the largely unmapped areas most likely to be used for energy developments, such as those within Renewable Energy Study Areas (RESA) and Solar Energy Zones (SEZs). We used imagery (multispectral and radar) mainly from the years 2009-2011.
Conservation of soil, water and nutrients in surface runoff using riparian plant species.

PubMed

Srivastava, Prabodh; Singh, Shipra

2012-01-01

Three riparian plant species viz. Cynodon dactylon (L.) Pers., Saccharum bengalensis Retz. and Parthenium hysterophorus L. were selected from the riparian zone of Kali river at Aligarh to conduct the surface runoff experiment to compare their conservation efficiencies for soil, water and nutrients (phosphorus and nitrogen). Experimental plots were prepared on artificial slopes in botanical garden and on natural slopes on study site. Selected riparian plant species showed the range of conservation values for soil and water from 47.11 to 95.22% and 44.06 to 72.50%, respectively on artificial slope and from 44.53 to 95.33% and 48.36 to 73.15%, respectively on natural slope. Conservation values for phosphorus and nitrogen ranged from 40.83 to 88.89% and 59.78 to 82.22%, respectively on artificial slope and from 50.01 to 90.16% and 68.07 to 85.62%, respectively on natural slope. It was observed that Cynodon dactylon was the most efficient riparian species in conservation of soil, water and nutrients in surface runoff.

Behavioral abnormalities in prion protein knockout mice and the potential relevance of PrPc for the cytoskeleton

USDA-ARS?s Scientific Manuscript database

The cellular prion protein (PrPC) is a highly conserved protein, which is anchored to the outer surface of the plasma membrane. Even though its physiological function has already been investigated in different cell or mouse models where PrPC expression is either up-regulated or depleted, its exact p...
A NEW GIS NITROGEN TRADING TOOL CONCEPT FOR CONSERVATION AND REDUCTION OF REACTIVE NITROGEN LOSSES TO THE ENVIRONMENT

USDA-ARS?s Scientific Manuscript database

Nitrogen inputs to agricultural systems are important for their sustainability. However, when N inputs are unnecessarily high, the excess can contribute to greater agricultural N losses that impact air, surface water and groundwater quality. It is paramount to reduce off-site transport of N by using...
Identification of an evolutionarily conserved extracellular threonine residue critical for surface expression and its potential coupling of adjacent voltage-sensing and gating domains in voltage-gated potassium channels.

PubMed

Mckeown, Lynn; Burnham, Matthew P; Hodson, Charlotte; Jones, Owen T

2008-10-31

The dynamic expression of voltage-gated potassium channels (Kvs) at the cell surface is a fundamental factor controlling membrane excitability. In exploring possible mechanisms controlling Kv surface expression, we identified a region in the extracellular linker between the first and second of the six (S1-S6) transmembrane-spanning domains of the Kv1.4 channel, which we hypothesized to be critical for its biogenesis. Using immunofluorescence microscopy, flow cytometry, patch clamp electrophysiology, and mutagenesis, we identified a single threonine residue at position 330 within the Kv1.4 S1-S2 linker that is absolutely required for cell surface expression. Mutation of Thr-330 to an alanine, aspartate, or lysine prevented surface expression. However, surface expression occurred upon co-expression of mutant and wild type Kv1.4 subunits or mutation of Thr-330 to a serine. Mutation of the corresponding residue (Thr-211) in Kv3.1 to alanine also caused intracellular retention, suggesting that the conserved threonine plays a generalized role in surface expression. In support of this idea, sequence comparisons showed conservation of the critical threonine in all Kv families and in organisms across the evolutionary spectrum. Based upon the Kv1.2 crystal structure, further mutagenesis, and the partial restoration of surface expression in an electrostatic T330K bridging mutant, we suggest that Thr-330 hydrogen bonds to equally conserved outer pore residues, which may include a glutamate at position 502 that is also critical for surface expression. We propose that Thr-330 serves to interlock the voltage-sensing and gating domains of adjacent monomers, thereby yielding a structure competent for the surface expression of functional tetramers.
7 CFR 1466.20 - Application for contracts and selecting applications.

Code of Federal Regulations, 2014 CFR

2014-01-01

... concerning soil, water and air quality; wildlife habitat; and ground and surface water conservation; (vi... include water conservation or irrigation efficiency practices, the State Conservationist will give... conservation practices; (ii) The magnitude of the expected environmental benefits resulting from the...
7 CFR 1466.20 - Application for contracts and selecting applications.

Code of Federal Regulations, 2012 CFR

2012-01-01

... concerning soil, water and air quality; wildlife habitat; and ground and surface water conservation; (vi... include water conservation or irrigation efficiency practices, the State Conservationist will give... conservation practices; (ii) The magnitude of the expected environmental benefits resulting from the...
7 CFR 1466.20 - Application for contracts and selecting applications.

Code of Federal Regulations, 2013 CFR

2013-01-01

... concerning soil, water and air quality; wildlife habitat; and ground and surface water conservation; (vi... include water conservation or irrigation efficiency practices, the State Conservationist will give... conservation practices; (ii) The magnitude of the expected environmental benefits resulting from the...
Long-term N fertilization and conservation tillage practices conserve surface but not profile SOC stocks under semi-arid irrigated corn

USDA-ARS?s Scientific Manuscript database

No tillage (NT) and N fertilization can increase surface soil organic C (SOC) stocks, but the effects deeper in the soil profile are uncertain. Subsequent tillage could counter SOC stabilized through NT practices by disrupting soil aggregation and promoting decomposition. We followed a long-term ti...
Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis

PubMed Central

Ramanathan, Arvind; Agarwal, Pratul K.

2011-01-01

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme–substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme–substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design. PMID:22087074
Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.

PubMed

Ramanathan, Arvind; Agarwal, Pratul K

2011-11-01

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function. Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 Å away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme-substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme-substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.
Options for reducing carbon dioxide emissions

NASA Astrophysics Data System (ADS)

Rosenfeld, Arthur H.; Price, Lynn

1992-03-01

Improvements in energy efficiency can significantly reduce the annual growth in greenhouse gas emissions. Such improvements occur when energy intensity is reduced; no reduction in energy services is required. Using the concept of ``cost of conserved energy'' to develop conservation supply curves similar to resource supply curves, researchers consistently find that electricity and natural gas savings of nearly 50% of current consumption are possible for U.S. buildings. Such reductions in energy consumption directly reduce emissions of greenhouse gases. To capture these savings, we must continue to develop energy-efficient technologies and strategies. This paper describes three recent energy-efficient technologies that benefitted from energy conservation research and development (R&D) funding: high-frequency ballasts, compact fluorescent lamps, and low-emissivity windows. Other advanced technologies and strategies of spectrally selective windows, superwindows, electrochromic windows, advanced insulation, low-flow showerheads, improved recessed lamp fixtures, whitening surfaces and planting urban trees, daylighting, and thermal energy storage are also discussed.
Temperature impact on the micro structure of tungsten exposed to He irradiation in LHD

NASA Astrophysics Data System (ADS)

Bernard, Elodie; Sakamoto, Ryuichi; Tokitani, Masayuki; Masuzaki, Suguru; Hayashi, Hiromi; Yamada, Hiroshi; Yoshida, Naoaki

2017-02-01

A new temperature controlled material probe was designed for the exposure of tungsten samples to helium plasma in the LHD. Samples were exposed to estimated fluences of ∼1023 m-2 and temperatures ranging from 65 to 600 °C. Transmission Electron Microscopy analysis allowed the study of the impact of He irradiation under high temperatures on tungsten micro structure for the first time in real-plasma exposure conditions. Both dislocation loops and bubbles appeared from low to medium temperatures and saw an impressive increase of size (factor 4 to 6) most probably by coalescence as the temperature reaches 600 °C, with 500 °C appearing as a threshold for bubble growth. Annealing of the samples up to 800 C highlighted the stability of the dislocation damages formed by helium irradiation at high surface temperature, as bubbles and dislocation loops seem to conserve their characteristics. Additional studies on cross-sections showed that bubbles were formed much deeper (70-100 nm) than the heavily damaged surface layer (10-20 nm), raising concern about the impact on the material mechanical properties conservation and potential additional trapping of hydrogen isotopes.
Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome

PubMed Central

Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

2013-01-01

The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the identification of novel protein targets for influenza antivirals. PMID:24282564
Managing the maintainance and conservation of the built heritage: a web-gis approach for the Richini courtyard in Milan

NASA Astrophysics Data System (ADS)

Toniolo, L.; Gulotta, D.; Bertoldi, M.; Bortolotto, S.

2012-04-01

The Richini courtyard is a masterpiece of northern Italy baroque and it is part of the complex that currently hosts the "Università degli Studi" of Milan. Its four internal façades are based on a double arcade structure with granitic columns along a rectangular plan. The architectural elements are enriched by an outstanding sculpted decoration made of Angera stone (a typical Lombard dolostone) with bas-relief panels, high-relief figures, mouldings and voussoirs. The courtyard suffers the consequences of a troubled conservation history: the Second World War bombardment caused devastating damages to both the structure and the sculpted surfaces, so that an extensive restoration was carried out during the early fifties. Moreover, a further and massive conservative intervention was required during the nineties due to the increasing degradation rate of the Angera stone subjected to severely polluted environmental conditions. The overall durability of this last intervention, as well as the long-term compatibility of the restoration materials, has been evaluated almost twenty years later, in 2011. A thorough study of representative areas of the courtyard has been conducted by a multi-disciplinary research group. The aim of the study was the evaluation of the state of conservation of the ancient and restoration materials, as well as the identification of the decay phenomena. A high-accurate 3D laser scanner survey of the courtyard has been performed as well. The results of the diagnostic activity has been summarised in the present work. The wide range of different type of data (analytical and geometrical data, historical records, photographic documentation) have been managed by the latest release of a web-GIS software specifically designed for the application in the built heritage conservation. A new data structure has been purposely designed in order to maximize the efficiency for what concerning data entry, data query and data updating. The enhanced web-GIS software has become a user-friendly platform for the collection and reference of all the results of the façades, based on high-resolution images of the sculpted surfaces. The data elaboration allowed the definition of a risk priority scheme for each different type of architectural elements. Guidelines for a long term monitoring and for a sustainable planned maintenance of the courtyard has been consequently set-up.
Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasan, Neil; Hutagalung, Alex; Novick, Peter

2010-08-13

The Golgi-associated retrograde protein (GARP) complex is a membrane-tethering complex that functions in traffic from endosomes to the trans-Golgi network. Here we present the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2.9 {angstrom}. We show that the C terminus consists of two {alpha}-helical bundles arranged in tandem, and we identify a highly conserved surface patch, which may play a role in vesicle recognition. Mutations of the surface result in defects in membrane traffic. The fold of the Vps53 C terminus is strongly reminiscent of proteins that belong to threemore » other tethering complexes - Dsl1, conserved oligomeric Golgi, and the exocyst - thought to share a common evolutionary origin. Thus, the structure of the Vps53 C terminus suggests that GARP belongs to this family of complexes.« less
The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together

PubMed Central

Pathare, Ganesh Ramnath; Nagy, István; Bohn, Stefan; Unverdorben, Pia; Hubert, Agnes; Körner, Roman; Nickell, Stephan; Lasker, Keren; Sali, Andrej; Tamura, Tomohiro; Nishioka, Taiki; Förster, Friedrich; Baumeister, Wolfgang; Bracher, Andreas

2012-01-01

Proteasomes execute the degradation of most cellular proteins. Although the 20S core particle (CP) has been studied in great detail, the structure of the 19S regulatory particle (RP), which prepares ubiquitylated substrates for degradation, has remained elusive. Here, we report the crystal structure of one of the RP subunits, Rpn6, and we describe its integration into the cryo-EM density map of the 26S holocomplex at 9.1 Å resolution. Rpn6 consists of an α-solenoid-like fold and a proteasome COP9/signalosome eIF3 (PCI) module in a right-handed suprahelical configuration. Highly conserved surface areas of Rpn6 interact with the conserved surfaces of the Pre8 (alpha2) and Rpt6 subunits from the alpha and ATPase rings, respectively. The structure suggests that Rpn6 has a pivotal role in stabilizing the otherwise weak interaction between the CP and the RP. PMID:22187461
Evolution of helical perturbations in a thin-shell model of an imploding liner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryutov, D. D.; Dorf, M. A.

A thin-shell model of the liner stability has been revisited and applied to the stability of the helical perturbations. Several stages of the implosion have been identified, starting from a long initial “latent” phase of an almost resting liner, continuing to the second stage of a rapid contraction and significant perturbation growth, and then transitioning to the third stage where perturbations become ballistic and highly non-linear. The stage of stagnation and rebound is beyond the scope of this paper. An importance of vorticity conservation during the late stages is emphasized. Nonlinear evolution of perturbations is followed up to the pointmore » of the formation of cusp structures. Effects of in-surface flows and of their enhancement due to the vorticity conservation are discussed. It is shown that the pre-machined perturbations created only on the outer surface of the liner grow much slower than one could anticipate. The limitations on the thin-shell description are discussed.« less
Preliminary Genetic Analysis Supports Cave Populations as Targets for Conservation in the Endemic Endangered Puerto Rican Boa (Boidae: Epicrates inornatus)

PubMed Central

Revell, Liam J.

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas. PMID:23691110
Preliminary genetic analysis supports cave populations as targets for conservation in the endemic endangered Puerto Rican boa (Boidae: Epicrates inornatus).

PubMed

Puente-Rolón, Alberto R; Reynolds, R Graham; Revell, Liam J

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.
Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes.

PubMed

Gibbons, John G; Rokas, Antonis

2009-03-01

Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication, and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs were evolutionarily labile, their functional associations appeared. To be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface-associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.
Satellite Estimation of Spectral Surface UV Irradiance. 2; Effect of Horizontally Homogeneous Clouds

NASA Technical Reports Server (NTRS)

Krothov, N.; Herman, J. R.; Bhartia, P. K.; Ahmad, Z.a; Fioletov, V.

1998-01-01

The local variability of UV irradiance at the Earth's surface is mostly caused by clouds in addition to the seasonal variability. Parametric representations of radiative transfer RT calculations are presented for the convenient solution of the transmission T of ultraviolet radiation through plane parallel clouds over a surface with reflectivity R(sub s). The calculations are intended for use with the Total Ozone Mapping Spectrometer (TOMS) measured radiances to obtain the calculated Lambert equivalent scene reflectivity R for scenes with and without clouds. The purpose is to extend the theoretical analysis of the estimation of UV irradiance from satellite data for a cloudy atmosphere. Results are presented for a range of cloud optical depths and solar zenith angles for the cases of clouds over a low reflectivity surface R(sub s) less than 0.1, over a snow or ice surface R(sub s) greater than 0.3, and for transmission through a non-conservative scattering cloud with single scattering albedo omega(sub 0) = 0.999. The key finding for conservative scattering is that the cloud-transmission function C(sub T), the ratio of cloudy-to clear-sky transmission, is roughly C(sub T) = 1 - R(sub c) with an error of less than 20% for nearly overhead sun and snow-free surfaces. For TOMS estimates of UV irradiance in the presence of both snow and clouds, independent information about snow albedo is needed for conservative cloud scattering. For non-conservative scattering with R(sub s) greater than 0.5 (snow) the satellite measured scene reflectance cannot be used to estimate surface irradiance. The cloud transmission function has been applied to the calculation of UV irradiance at the Earth's surface and compared with ground-based measurements.

Impacts of Soil and Water Conservation Practices on Crop Yield, Run-off, Soil Loss and Nutrient Loss in Ethiopia: Review and Synthesis.

PubMed

Adimassu, Zenebe; Langan, Simon; Johnston, Robyn; Mekuria, Wolde; Amede, Tilahun

2017-01-01

Research results published regarding the impact of soil and water conservation practices in the highland areas of Ethiopia have been inconsistent and scattered. In this paper, a detailed review and synthesis is reported that was conducted to identify the impacts of soil and water conservation practices on crop yield, surface run-off, soil loss, nutrient loss, and the economic viability, as well as to discuss the implications for an integrated approach and ecosystem services. The review and synthesis showed that most physical soil and water conservation practices such as soil bunds and stone bunds were very effective in reducing run-off, soil erosion and nutrient depletion. Despite these positive impacts on these services, the impact of physical soil and water conservation practices on crop yield was negative mainly due to the reduction of effective cultivable area by soil/stone bunds. In contrast, most agronomic soil and water conservation practices increase crop yield and reduce run-off and soil losses. This implies that integrating physical soil and water conservation practices with agronomic soil and water conservation practices are essential to increase both provisioning and regulating ecosystem services. Additionally, effective use of unutilized land (the area occupied by bunds) by planting multipurpose grasses and trees on the bunds may offset the yield lost due to a reduction in planting area. If high value grasses and trees can be grown on this land, farmers can harvest fodder for animals or fuel wood, both in scarce supply in Ethiopia. Growing of these grasses and trees can also help the stability of the bunds and reduce maintenance cost. Economic feasibility analysis also showed that, soil and water conservation practices became economically more viable if physical and agronomic soil and water conservation practices are integrated.
Impacts of Soil and Water Conservation Practices on Crop Yield, Run-off, Soil Loss and Nutrient Loss in Ethiopia: Review and Synthesis

NASA Astrophysics Data System (ADS)

Adimassu, Zenebe; Langan, Simon; Johnston, Robyn; Mekuria, Wolde; Amede, Tilahun

2017-01-01

Research results published regarding the impact of soil and water conservation practices in the highland areas of Ethiopia have been inconsistent and scattered. In this paper, a detailed review and synthesis is reported that was conducted to identify the impacts of soil and water conservation practices on crop yield, surface run-off, soil loss, nutrient loss, and the economic viability, as well as to discuss the implications for an integrated approach and ecosystem services. The review and synthesis showed that most physical soil and water conservation practices such as soil bunds and stone bunds were very effective in reducing run-off, soil erosion and nutrient depletion. Despite these positive impacts on these services, the impact of physical soil and water conservation practices on crop yield was negative mainly due to the reduction of effective cultivable area by soil/stone bunds. In contrast, most agronomic soil and water conservation practices increase crop yield and reduce run-off and soil losses. This implies that integrating physical soil and water conservation practices with agronomic soil and water conservation practices are essential to increase both provisioning and regulating ecosystem services. Additionally, effective use of unutilized land (the area occupied by bunds) by planting multipurpose grasses and trees on the bunds may offset the yield lost due to a reduction in planting area. If high value grasses and trees can be grown on this land, farmers can harvest fodder for animals or fuel wood, both in scarce supply in Ethiopia. Growing of these grasses and trees can also help the stability of the bunds and reduce maintenance cost. Economic feasibility analysis also showed that, soil and water conservation practices became economically more viable if physical and agronomic soil and water conservation practices are integrated.
Modeling and measurement of microwave emission and backscattering from bare soil surfaces

NASA Technical Reports Server (NTRS)

Saatchi, S.; Wegmuller, U.

1992-01-01

A multifrequency ground-based radiometer-scatterometer system working at frequencies between 3.0 GHz and 11.0 GHz has been used to study the effect of soil moisture and roughness on microwave emission and backscattering. The freezing and thawing effect of the soil surface and the changes of the surface roughness due to rain and erosion are reported. To analyze the combined active and passive data, a scattering model based on physical optics approximation for the low frequency and geometrical optics approximation for high frequency has been developed. The model is used to calculate the bistatic scattering coefficients from the surface. By considering the conservation of energy, the result has been integrated over a hemisphere above the surface to calculate the emissivity. The backscattering and emission model has been coupled with the observed data in order to extract soil moisture and surface roughness.
Low effect of young afforestations on bird communities inhabiting heterogeneous Mediterranean cropland

PubMed Central

Rey Benayas, José M.; Carrascal, Luis M.

2015-01-01

Afforestation programs such as the one promoted by the EU Common Agricultural Policy have spread tree plantations on former cropland. These afforestations attract generalist forest and ubiquitous species but may cause severe damage to open habitat species, especially birds of high conservation value. We investigated the effects of young (<20 yr) tree plantations dominated by pine P. halepensis on bird communities inhabiting the adjacent open farmland habitat in central Spain. We hypothesize that pine plantations located at shorter distances from open fields and with larger surface would affect species richness and conservation value of bird communities. Regression models controlling for the influence of land use types around plantations revealed positive effects of higher distance to pine plantation edge on community species richness in winter, and negative effects on an index of conservation concern (SPEC) during the breeding season. However, plantation area did not have any effect on species richness or community conservation value. Our results indicate that the effects of pine afforestation on bird communities inhabiting Mediterranean cropland are diluted by heterogeneous agricultural landscapes. PMID:26664801
A thermophilic mini-chaperonin contains a conserved polypeptide-binding surface: combined crystallographic and NMR studies of the GroEL Apical Domain with implications for substrate interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hua, Q. X. H.; Dementieva, I. S. D.; Walsh, M. A. W.

2001-02-23

A homologue of the Escherichia coli GroEL apical domain was obtained from thermophilic eubacterium Thermus thermophilus. The domains share 70 % sequence identity (101 out of 145 residues). The thermal stability of the T. thermophilus apical domain (T{sub m}>100{sup o}C as evaluated by circular dichroism) is at least 35{sup o}C greater than that of the E. coli apical domain (T{sub m}=65{sup o}C). The crystal structure of a selenomethione-substituted apical domain from T. thermophilus was determined to a resolution of 1.78 {angstrom} using multiwavelength-anomalous-diffraction phasing. The structure is similar to that of the E. coli apical domain (root-mean-square deviation 0.45 {angstrom}more » based on main-chain atoms). The thermophilic structure contains seven additional salt bridges of which four contain charge-stabilized hydrogen bonds. Only one of the additional salt bridges would face the 'Anfinsen cage' in GroEL. High temperatures were exploited to map sites of interactions between the apical domain and molten globules. NMR footprints of apical domain-protein complexes were obtained at elevated temperature using {sup 15}N-{sup 1}H correlation spectra of {sup 15}N-labeled apical domain. Footprints employing two polypeptides unrelated in sequence or structure (an insulin monomer and the SRY high-mobility-group box, each partially unfolded at 50{sup o}C) are essentially the same and consistent with the peptide-binding surface previously defined in E. coli GroEL and its apical domain-peptide complexes. An additional part of this surface comprising a short N-terminal {alpha}-helix is observed. The extended footprint rationalizes mutagenesis studies of intact GroEL in which point mutations affecting substrate binding were found outside the 'classical' peptide-binding site. Our results demonstrate structural conservation of the apical domain among GroEL homologues and conservation of an extended non-polar surface recognizing diverse polypeptides.« less
Structural conservation, variability, and immunogenicity of the T6 backbone pilin of serotype M6 Streptococcus pyogenes.

PubMed

Young, Paul G; Moreland, Nicole J; Loh, Jacelyn M; Bell, Anita; Atatoa Carr, Polly; Proft, Thomas; Baker, Edward N

2014-07-01

Group A streptococcus (GAS; Streptococcus pyogenes) is a Gram-positive human pathogen that causes a broad range of diseases ranging from acute pharyngitis to the poststreptococcal sequelae of acute rheumatic fever. GAS pili are highly diverse, long protein polymers that extend from the cell surface. They have multiple roles in infection and are promising candidates for vaccine development. This study describes the structure of the T6 backbone pilin (BP; Lancefield T-antigen) from the important M6 serotype. The structure reveals a modular arrangement of three tandem immunoglobulin-like domains, two with internal isopeptide bonds. The T6 pilin lysine, essential for polymerization, is located in a novel VAKS motif that is structurally homologous to the canonical YPKN pilin lysine in other three- and four-domain Gram-positive pilins. The T6 structure also highlights a conserved pilin core whose surface is decorated with highly variable loops and extensions. Comparison to other Gram-positive BPs shows that many of the largest variable extensions are found in conserved locations. Studies with sera from patients diagnosed with GAS-associated acute rheumatic fever showed that each of the three T6 domains, and the largest of the variable extensions (V8), are targeted by IgG during infection in vivo. Although the GAS BP show large variations in size and sequence, the modular nature of the pilus proteins revealed by the T6 structure may aid the future design of a pilus-based vaccine. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Algal subsidies enhance invertebrate prey for threatened shorebirds: A novel conservation tool on ocean beaches?

NASA Astrophysics Data System (ADS)

Schlacher, Thomas A.; Hutton, Briony M.; Gilby, Ben L.; Porch, Nicholaus; Maguire, Grainne S.; Maslo, Brooke; Connolly, Rod M.; Olds, Andrew D.; Weston, Michael A.

2017-05-01

Birds breeding on ocean beaches are threatened globally, often requiring significant investments in species conservation and habitat management. Conservation actions typically encompass spatial and temporal threat reductions and protection of eggs and broods. Still, populations decline or recover only slowly, calling for fresh approaches in beach-bird conservation. Because energetic demands are critically high during the nesting and chick rearing phases, and chick survival is particularly low, supplementing prey to breeding birds and their offspring is theoretically attractive as a means to complement more traditional conservation measures. Prey for plovers and similar species on ocean beaches consists of invertebrates (e.g. small crustaceans, insects) many of which feed on stranded masses of plant material (e.g. kelp and seagrass) and use this 'wrack' as habitat. We added wrack to the upper beach where plovers nest and their chicks forage to test whether algal subsidies promote the abundance and diversity of their invertebrate prey. Adding wrack to the upper beach significantly increased the abundance and diversity of invertebrate prey items. At wrack subsidies greater than 50% of surface cover invertebrate assemblages became highly distinct compared with those that received smaller additions of wrack. Substantial (2-4 fold) increases in the abundance amphipods and isopods that are principal prey items for plovers drove these shifts. This proof-of-concept study demonstrates the feasibility of food provisioning for birds on ocean shores. Whilst novel, it is practicable, inexpensive and does not introduce further restrictions or man-made structures. Thus, it can meaningfully add to the broader arsenal of conservation tools for threatened species that are wholly reliant on sandy beaches as breeding and foraging habitats.
Influence of surface flattening on biodiversity of terrestrial arthropods during early stages of brown coal spoil heap restoration.

PubMed

Moradi, Jabbar; Potocký, Pavel; Kočárek, Petr; Bartuška, Martin; Tajovský, Karel; Tichánek, Filip; Frouz, Jan; Tropek, Robert

2018-08-15

Heterogeneity of environmental conditions is the crucial factor supporting biodiversity in various habitats, including post-mining sites. The effects of micro-topographic heterogeneity on biodiversity and conservation potential of arthropod communities in post-industrial habitats had not been studied before now. At one of the largest European brown coal spoil heaps, we sampled eight groups of terrestrial arthropods with different life strategies (moths, spiders, ground beetles, ants, orthopteroids, centipedes, millipedes, and woodlice), in successionally young plots (5-18 y), with a heterogeneous wavy surface after heaping, and compared the communities with plots flattened by dozing. A combination of the standardized quantitative sampling, using two different methods, and a paired design of the plot selection enabled a robust analysis. Altogether, we recorded 380 species of the focal arthropods, 15 of them nationally threatened. We revealed the importance of the micro-topographic heterogeneity for the formation of the biodiversity of arthropods in their secondary refuges. The communities with higher biodiversity and conservation value were detected in the plots with heterogeneous surfaces; exceptions were ground beetles and millipedes. The surface flattening, often the first step of technical reclamation projects, thus suppress biodiversity of most terrestrial arthropods during the restoration of post-mining sites. Since the communities of both surface types differed, the proportional presence on both surfaces could be more efficient in supporting the local biodiversity. We suggest reducing the surface dozing for the cases with other concerns only, to achieve a proportional representation of both surface types. Such a combination of different restoration approaches would, thus, efficiently support high biodiversity of groups with various needs. Copyright © 2018 Elsevier Ltd. All rights reserved.
SPHRINT - Printing Drug Delivery Microspheres from Polymeric Melts.

PubMed

Shpigel, Tal; Uziel, Almog; Lewitus, Dan Y

2018-06-01

This paper describes a simple, straightforward, and rapid method for producing microspheres from molten polymers by merely printing them in an inkjet-like manner onto a superoleophobic surface (microsphere printing, hence SPHRINT). Similar to 3D printing, a polymer melt is deposited onto a surface; however, in contrast to 2D or 3D printing, the surface is not wetted (i.e. exhibiting high contact angles with liquids, above 150°, due to its low surface energy), resulting in the formation of discrete spherical microspheres. In this study, microspheres were printed using polycaprolactone and poly(lactic-co-glycolic acid) loaded with a model active pharmaceutical ingredient-ibuprofen (IBU). The formation of microspheres was captured by high-speed imaging and was found to involve several physical phenomena characterized by non-dimensional numbers, including the thinning and breakup of highly viscous, weakly elastic filaments, which are first to be described in pure polymer melts. The resulting IBU-loaded microspheres had higher sphericity, reproducible sizes and shapes, and superior drug encapsulation efficiencies with a distinctly high process yield (>95%) as compared to the conservative solvent-based methods used presently. Furthermore, the microspheres showed sustained release profiles. Copyright © 2018 Elsevier B.V. All rights reserved.
Computation of nonstationary strong shock diffraction by curved surfaces

NASA Technical Reports Server (NTRS)

Yang, J. Y.; Lombard, C. K.; Bershader, D.

1986-01-01

A two-dimensional, high resolution shock-capturing algorithm was used on a supercomputer to solve Eulerian gasdynamic equations in order to simulate nonstationary strong shock diffraction by a circular arc model in a shock tube. The hypersonic Mach shock wave was assumed to arrive at a high angle of incidence, and attention was given to the effect of varying values of the ratio of specific heats on the shock diffraction process. Details of the conservation equations of the numerical algorithm, written in curvilinear coordinates, are provided, and model output is illustrated with the results generated for a Mach shock encountering a 15 deg circular arc. The sample graphics include isopycnics, a shock surface density profile, and pressure and Mach number contours.
Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light

PubMed Central

Lichtenberg, Mads; Brodersen, Kasper E.; Kühl, Michael

2017-01-01

We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under low light conditions and amounted to 18.1% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis, and light distribution. The light acclimation index, Ek, i.e., the irradiance at the onset of saturation of photosynthesis, was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. The aim was to investigate how the physical structure and light propagation affected energy budgets and light utilization efficiencies in loosely organized vs. compact phototrophic sediment under diffuse and collimated light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments. PMID:28400749
Radiative Energy Budgets of Phototrophic Surface-Associated Microbial Communities and their Photosynthetic Efficiency Under Diffuse and Collimated Light.

PubMed

Lichtenberg, Mads; Brodersen, Kasper E; Kühl, Michael

2017-01-01

We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O 2 , temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under low light conditions and amounted to 18.1% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis, and light distribution. The light acclimation index, E k , i.e., the irradiance at the onset of saturation of photosynthesis, was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. The aim was to investigate how the physical structure and light propagation affected energy budgets and light utilization efficiencies in loosely organized vs. compact phototrophic sediment under diffuse and collimated light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments.
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

DOE PAGES

Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.; ...

2018-02-14

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

PubMed Central

2018-01-01

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed. PMID:29442996
Conclusion: From describing to prescribing--transitioning to place-based conservation [Chapter 18

Treesearch

William P. Stewart; Daniel R. Williams; Linda E. Kruger

2013-01-01

The chapters of this book describe various perspectives from the social sciences of place-based conservation. The prescriptive implications are often close to the surface and become entangled with them. This chapter highlights four overlapping approaches to the practice of place-based conservation and acknowledges the difficulty of separating descriptions from...
The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases.

PubMed

Toth, Marta; Smith, Clyde A; Antunes, Nuno T; Stewart, Nichole K; Maltz, Lauren; Vakulenko, Sergei B

2017-08-01

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) produce resistance to the last-resort carbapenem antibiotics and render these drugs ineffective for the treatment of life-threatening infections. Here, it is shown that among the clinically important CHDLs, OXA-143 produces the highest levels of resistance to carbapenems and has the highest catalytic efficiency against these substrates. Structural data demonstrate that acylated carbapenems entirely fill the active site of CHDLs, leaving no space for water molecules, including the deacylating water. Since the entrance to the active site is obstructed by the acylated antibiotic, the deacylating water molecule must take a different route for entry. It is shown that in OXA-143 the movement of a conserved hydrophobic valine residue on the surface opens a channel to the active site of the enzyme, which would not only allow the exchange of water molecules between the active site and the milieu, but would also create extra space for a water molecule to position itself in the vicinity of the scissile bond of the acyl-enzyme intermediate to perform deacylation. Structural analysis of the OXA-23 carbapenemase shows that in this enzyme movement of the conserved leucine residue, juxtaposed to the valine on the molecular surface, creates a similar channel to the active site. These data strongly suggest that all CHDLs may employ a mechanism whereupon the movement of highly conserved valine or leucine residues would allow a water molecule to access the active site to promote deacylation. It is further demonstrated that the 6α-hydroxyethyl group of the bound carbapenem plays an important role in the stabilization of this channel. The recognition of a universal deacylation mechanism for CHDLs suggests a direction for the future development of inhibitors and novel antibiotics for these enzymes of utmost clinical importance.
Developing the Cleanliness Requirements for an Organic-detection Instrument MOMA-MS

NASA Technical Reports Server (NTRS)

Perry, Radford; Canham, John; Lalime, Erin

2015-01-01

The cleanliness requirements for an organic-detection instrument, like the Mars Organic Molecule Analyzer Mass Spectrometer (MOMA-MS), on a Planetary Protection Class IVb mission can be extremely stringent. These include surface molecular and particulate, outgassing, and bioburden. The prime contractor for the European Space Agencys ExoMars 2018 project, Thales Alenia Space Italy, provided requirements based on a standard, conservative approach of defining limits which yielded levels that are unverifiable by standard cleanliness verification methods. Additionally, the conservative method for determining contamination surface area uses underestimation while conservative bioburden surface area relies on overestimation, which results in inconsistencies for the normalized reporting. This presentation will provide a survey of the challenge to define requirements that can be reasonably verified and still remain appropriate to the core science of the ExoMars mission.
Experimental investigation of the laser ablation process on wood surfaces

NASA Astrophysics Data System (ADS)

Panzner, M.; Wiedemann, G.; Henneberg, K.; Fischer, R.; Wittke, Th.; Dietsch, R.

1998-05-01

Processing of wood by conventional mechanical tools like saws or planes leaves behind a layer of squeezed wood only slightly adhering to the solid wood surface. Laser ablation of this layer could improve the durability of coatings and glued joints. For technical applications, thorough knowledge about the laser ablation process is necessary. Results of ablation experiments by excimer lasers, Nd:YAG lasers, and TEA-CO 2 lasers on surfaces of different wood types and cut orientations are shown. The process of ablation was observed by a high-speed camera system and optical spectroscopy. The influence of the experimental parameters are demonstrated by SEM images and measurement of the ablation rate depending on energy density. Thermal effects like melting and also carbonizing of cellulose were found for IR- and also UV-laser wavelengths. Damage of the wood surface after laser ablation was weaker for excimer lasers and CO 2-TEA lasers. This can be explained by the high absorption of wood in the ultraviolet and middle infrared spectral range. As an additional result, this technique provides an easy way for preparing wood surfaces with excellently conserved cellular structure.
Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.

PubMed

Wang, Lan; Ren, Shifang; Zhu, Haiyan; Zhang, Dongmei; Hao, Yuqing; Ruan, Yuanyuan; Zhou, Lei; Lee, Chiayu; Qiu, Lin; Yun, Xiaojing; Xie, Jianhui

2012-08-01

CLEC-2 was first identified by sequence similarity to C-type lectin-like molecules with immune functions and has been reported as a receptor for the platelet-aggregating snake venom toxin rhodocytin and the endogenous sialoglycoprotein podoplanin. Recent researches indicate that CLEC-2-deficient mice were lethal at the embryonic stage associated with disorganized and blood-filled lymphatic vessels and severe edema. In view of a necessary role of CLEC-2 in the individual development, it is of interest to investigate its phylogenetic homology and highly conserved functional regions. In this work, we reported that CLEC-2 from different species holds with an extraordinary conservation by sequence alignment and phylogenetic tree analysis. The functional structures including N-linked oligosaccharide sites and ligand-binding domain implement a structural and functional conservation in a variety of species. The glycosylation sites (N120 and N134) are necessary for the surface expression CLEC-2. CLEC-2 from different species possesses the binding activity of mouse podoplanin. Nevertheless, the expression of CLEC-2 is regulated with a species-specific manner. The alternative splicing of pre-mRNA, a regulatory mechanism of gene expression, and the binding sites on promoter for several key transcription factors vary between different species. Therefore, CLEC-2 shares high sequence homology and functional identity. However the transcript expression might be tightly regulated by different mechanisms in evolution.

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results, we estimate that the construction of the conservation structures in our study area in Eritrea required over 300,000 person-days of work, which underlines the huge efforts involved in soil and water conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.
The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant

PubMed Central

Slotow, Rob; Di Minin, Enrico

2016-01-01

Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana. Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant. PMID:27812404
The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant.

PubMed

Selier, Sarah-Anne Jeanetta; Slotow, Rob; Di Minin, Enrico

2016-01-01

Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana . Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant.
Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

PubMed

Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

2016-05-24

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.
The Effects of Reduced Tillage on Phosphate Transport from Agricultural Land.

DTIC Science & Technology

1981-01-01

SOLUBLE INORGANIC I’IIOSPIORUS IN RUNOFF ................................................... 12 .F.ECT OF PHOSPHATE FERTILI ZATION ON LOSSES OF AVAILABLE...an reverse side if necessary end identifY by block number) Conservation Tillage Soil Loss Phosphorus Loss Surface Runoff 20 AMThAC? fCinf--- mbb iV...tillage (primarily no till) versus conventional tillage on surface runoff , soil loss and phosphorus loss. The data show that conservation tillage
Amino Acid Residues Critical for Endoplasmic Reticulum Export and Trafficking of Platelet-activating Factor Receptor*

PubMed Central

Hirota, Nobuaki; Yasuda, Daisuke; Hashidate, Tomomi; Yamamoto, Teruyasu; Yamaguchi, Satoshi; Nagamune, Teruyuki; Nagase, Takahide; Shimizu, Takao; Nakamura, Motonao

2010-01-01

Several residues are conserved in the transmembrane domains (TMs) of G-protein coupled receptors. Here we demonstrate that a conserved proline, Pro247, in TM6 of platelet-activating factor receptor (PAFR) is required for endoplasmic reticulum (ER) export and trafficking after agonist-induced internalization. Alanine-substituted mutants of the conserved residues of PAFRs, including P247A, were retained in the ER. Because a PAFR antagonist, Y-24180, acted as a pharmacological chaperone to rescue ER retention, this retention is due to misfolding of PAFR. Methylcarbamyl (mc)-PAF, a PAFR agonist, did not increase the cell surface expression of P247A, even though another ER-retained mutant, D63A, was effectively trafficked. Signaling and accumulation of the receptors in the early endosomes were observed in the mc-PAF-treated P247A-expressing cells, suggesting that P247A was trafficked to the cell surface by mc-PAF, and thereafter disappeared from the surface due to aberrant trafficking, e.g. enhanced internalization, deficiency in recycling, and/or accelerated degradation. The aberrant trafficking was confirmed with a sortase-A-mediated method for labeling cell surface proteins. These results demonstrate that the conserved proline in TM6 is crucial for intracellular trafficking of PAFR. PMID:20007715
Hydrologic connection between ponds positively affects macrophyte alpha and gamma diversity but negatively affects beta diversity.

PubMed

Akasaka, Munemitsu; Takamura, Noriko

2012-05-01

Connections between habitat patches can positively influence the number of species in respective patches, providing a basis for preferentially conserving interconnected patches. However, from a regional perspective, it is not known whether conserving multiple sets of interconnected habitat patches would include more species (i.e., show higher gamma diversity) than conserving multiple, unconnected, solitary patches. We studied aquatic macrophytes in 15 sets of unidirectionally interconnected ponds and 19 unconnected ponds and also tested whether alpha and beta diversity, expressed as the number of species and dissimilarity in species composition, respectively, differed between connected and unconnected ponds. We found that gamma diversity was higher in connected ponds than in unconnected ponds, even after controlling for surface area. This resulted from a higher alpha diversity in connected ponds, despite lower beta diversity. These results suggest that connections between habitat patches positively influence diversity at both local and regional scales. When the total surface area available for conservation is limited, interconnected habitat patches should be preferentially conserved.
A conserved WW domain-like motif regulates invariant chain-dependent cell-surface transport of the NKG2D ligand ULBP2.

PubMed

Uhlenbrock, Franziska; van Andel, Esther; Andresen, Lars; Skov, Søren

2015-08-01

Malignant cells expressing NKG2D ligands on their cell surface can be directly sensed and killed by NKG2D-bearing lymphocytes. To ensure this immune recognition, accumulating evidence suggests that NKG2D ligands are trafficed via alternative pathways to the cell surface. We have previously shown that the NKG2D ligand ULBP2 traffics over an invariant chain (Ii)-dependent pathway to the cell surface. This study set out to elucidate how Ii regulates ULBP2 cell-surface transport: We discovered conserved tryptophan (Trp) residues in the primary protein sequence of ULBP1-6 but not in the related MICA/B. Substitution of Trp to alanine resulted in cell-surface inhibition of ULBP2 in different cancer cell lines. Moreover, the mutated ULBP2 constructs were retained and not degraded inside the cell, indicating a crucial role of this conserved Trp-motif in trafficking. Finally, overexpression of Ii increased surface expression of wt ULBP2 while Trp-mutants could not be expressed, proposing that this Trp-motif is required for an Ii-dependent cell-surface transport of ULBP2. Aberrant soluble ULBP2 is immunosuppressive. Thus, targeting a distinct protein module on the ULBP2 sequence could counteract this abnormal expression of ULBP2. Copyright © 2015 Elsevier Ltd. All rights reserved.
Ground-water levels in the alluvial aquifer in eastern Arkansas, 1988

USGS Publications Warehouse

Westerfield, P.W.; Baxter, C.R.

1990-01-01

This report, prepared by the U.S. Geological Survey in cooperation with the Arkansas Soil and Water Conservation Commission, the U.S. Soil Conservation Service, and local Conservation Districts, contains groundwater level measurements of 509 wells that tap the alluvial aquifer in the Quaternary deposits of the Mississippi Alluvial Plain. The measurements were made by district Soil Conservation Service personnel during 1988. The shallowest prepumping season water levels occurred in Ashley, Clay, Greene, Mississippi, Phillips, and Randolph Counties where water levels averaged less than 20 ft below the land surface. The deepest water levels occurred in Arkansas, Lonoke, Poinsett, and Prairie Counties where water levels of more than 100 ft below land surface were measured. Water levels in the postpumping season averaged about 4.1 ft lower than during the prepumping season. (USGS)
The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.

PubMed

Lahr, Roni M; Mack, Seshat M; Héroux, Annie; Blagden, Sarah P; Bousquet-Antonelli, Cécile; Deragon, Jean-Marc; Berman, Andrea J

2015-09-18

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

DOE PAGES

Lahr, Roni M.; Mack, Seshat M.; Heroux, Annie; ...

2015-07-22

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. Amore » putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.« less
Rapid characterisation of surface modifications and treatments using a benchtop SIMS instrument

NASA Astrophysics Data System (ADS)

McPhail, D. S.; Sokhan, M.; Rees, E. E.; Cliff, B.; Eccles, A. J.; Chater, R. J.

2004-06-01

The development of a novel benchtop SIMS instrument (Millbrook MiniSIMS) [Appl. Surf. Sci. 144 (1999) 106] has brought routine SIMS analysis to many new users, for example museum conservators. This is a result of the simple operation and the relatively low capital cost of the instrument. We report here on the continued development of the system in terms of increasing performance and functionality and its use in museum conservation based applications where a mobile instrument for high throughput, rapid SIMS analysis has proven to be of great benefit to the user. The example we describe here is the application of the MiniSIMS to the analysis of silver thread woven into a silk dress before and after laser cleaning.
Laser ablation of iron-rich black films from exposed granite surfaces

NASA Astrophysics Data System (ADS)

Delgado Rodrigues, J.; Costa, D.; Mascalchi, M.; Osticioli, I.; Siano, S.

2014-10-01

Here, we investigated the potential of laser removal of iron-rich dark films from weathered granite substrates, which represents a very difficult conservation problem because of the polymineralic nature of the stone and of its complex deterioration mechanisms. As often occurs, biotite was the most critical component because of its high optical absorption, low melting temperature, and pronounced cleavage, which required a careful control of the photothermal and photomechanical effects to optimize the selective ablation of the mentioned unwanted dark film. Different pulse durations and wavelengths Nd:YAG lasers were tested and optimal irradiation conditions were determined through thorough analytical characterisations. Besides addressing a specific conservation problem, the present work provides information of general valence in laser uncovering of encrusted granite.
Dark texture in artworks

NASA Astrophysics Data System (ADS)

Parraman, Carinna

2012-01-01

This presentation highlights issues relating to the digital capture printing of 2D and 3D artefacts and accurate colour reproduction of 3D objects. There are a range of opportunities and technologies for the scanning and printing of two-dimensional and threedimensional artefacts [1]. A successful approach of Polynomial Texture Mapping (PTM) technique, to create a Reflectance Transformation Image (RTI) [2-4] is being used for the conservation and heritage of artworks as these methods are non invasive or non destructive of fragile artefacts. This approach captures surface detail of twodimensional artworks using a multidimensional approach that by using a hemispherical dome comprising 64 lamps to create an entire surface topography. The benefits of this approach are to provide a highly detailed visualization of the surface of materials and objects.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Leitner, Peter; Heyn, Martin F.; Kernbichler, Winfried

In this paper, the impact of momentum and energy conservation of the collision operator in the kinetic description for Resonant Magnetic Perturbations (RMPs) in a tokamak is studied. The particle conserving differential collision operator of Ornstein-Uhlenbeck type is supplemented with integral parts such that energy and momentum are conserved. The application to RMP penetration in a tokamak shows that energy conservation in the electron collision operator is important for the quantitative description of plasma shielding effects at the resonant surface. On the other hand, momentum conservation in the ion collision operator does not significantly change the results.
Bio-inspired dewetted surfaces based on SiC/Si interlocked structures for enhanced-underwater stability and regenerative-drag reduction capability

PubMed Central

Lee, By Junghan; Zhang, Zhuo; Baek, Seunghyun; Kim, Sangkuk; Kim, Donghyung; Yong, Kijung

2016-01-01

Drag reduction has become a serious issue in recent years in terms of energy conservation and environmental protection. Among diverse approaches for drag reduction, superhydrophobic surfaces have been mainly researched due to their high drag reducing efficiency. However, due to limited lifetime of plastron (i.e., air pockets) on superhydrophobic surfaces in underwater, the instability of dewetted surfaces has been a sticking point for practical applications. This work presents a breakthrough in improving the underwater stability of superhydrophobic surfaces by optimizing nanoscale surface structures using SiC/Si interlocked structures. These structures have an unequaled stability of underwater superhydrophobicity and enhance drag reduction capabilities,with a lifetime of plastron over 18 days and maximum velocity reduction ratio of 56%. Furthermore, through photoelectrochemical water splitting on a hierarchical SiC/Si nanostructure surface, the limited lifetime problem of air pockets was overcome by refilling the escaping gas layer, which also provides continuous drag reduction effects. PMID:27095674
Improving Simulated Soil Moisture Fields Through Assimilation of AMSR-E Soil Moisture Retrievals with an Ensemble Kalman Filter and a Mass Conservation Constraint

NASA Technical Reports Server (NTRS)

Li, Bailing; Toll, David; Zhan, Xiwu; Cosgrove, Brian

2011-01-01

Model simulated soil moisture fields are often biased due to errors in input parameters and deficiencies in model physics. Satellite derived soil moisture estimates, if retrieved appropriately, represent the spatial mean of soil moisture in a footprint area, and can be used to reduce model bias (at locations near the surface) through data assimilation techniques. While assimilating the retrievals can reduce model bias, it can also destroy the mass balance enforced by the model governing equation because water is removed from or added to the soil by the assimilation algorithm. In addition, studies have shown that assimilation of surface observations can adversely impact soil moisture estimates in the lower soil layers due to imperfect model physics, even though the bias near the surface is decreased. In this study, an ensemble Kalman filter (EnKF) with a mass conservation updating scheme was developed to assimilate the actual value of Advanced Microwave Scanning Radiometer (AMSR-E) soil moisture retrievals to improve the mean of simulated soil moisture fields by the Noah land surface model. Assimilation results using the conventional and the mass conservation updating scheme in the Little Washita watershed of Oklahoma showed that, while both updating schemes reduced the bias in the shallow root zone, the mass conservation scheme provided better estimates in the deeper profile. The mass conservation scheme also yielded physically consistent estimates of fluxes and maintained the water budget. Impacts of model physics on the assimilation results are discussed.
Spatiotemporal dynamics of surface water networks across a global biodiversity hotspot—implications for conservation

NASA Astrophysics Data System (ADS)

Tulbure, Mirela G.; Kininmonth, Stuart; Broich, Mark

2014-11-01

The concept of habitat networks represents an important tool for landscape conservation and management at regional scales. Previous studies simulated degradation of temporally fixed networks but few quantified the change in network connectivity from disintegration of key features that undergo naturally occurring spatiotemporal dynamics. This is particularly of concern for aquatic systems, which typically show high natural spatiotemporal variability. Here we focused on the Swan Coastal Plain, a bioregion that encompasses a global biodiversity hotspot in Australia with over 1500 water bodies of high biodiversity. Using graph theory, we conducted a temporal analysis of water body connectivity over 13 years of variable climate. We derived large networks of surface water bodies using Landsat data (1999-2011). We generated an ensemble of 278 potential networks at three dispersal distances approximating the maximum dispersal distance of different water dependent organisms. We assessed network connectivity through several network topology metrics and quantified the resilience of the network topology during wet and dry phases. We identified ‘stepping stone’ water bodies across time and compared our networks with theoretical network models with known properties. Results showed a highly dynamic seasonal pattern of variability in network topology metrics. A decline in connectivity over the 13 years was noted with potential negative consequences for species with limited dispersal capacity. The networks described here resemble theoretical scale-free models, also known as ‘rich get richer’ algorithm. The ‘stepping stone’ water bodies are located in the area around the Peel-Harvey Estuary, a Ramsar listed site, and some are located in a national park. Our results describe a powerful approach that can be implemented when assessing the connectivity for a particular organism with known dispersal distance. The approach of identifying the surface water bodies that act as ‘stepping stone’ over time may help prioritize surface water bodies that are essential for maintaining regional scale connectivity.
An Unified Multiscale Framework for Planar, Surface, and Curve Skeletonization.

PubMed

Jalba, Andrei C; Sobiecki, Andre; Telea, Alexandru C

2016-01-01

Computing skeletons of 2D shapes, and medial surface and curve skeletons of 3D shapes, is a challenging task. In particular, there is no unified framework that detects all types of skeletons using a single model, and also produces a multiscale representation which allows to progressively simplify, or regularize, all skeleton types. In this paper, we present such a framework. We model skeleton detection and regularization by a conservative mass transport process from a shape's boundary to its surface skeleton, next to its curve skeleton, and finally to the shape center. The resulting density field can be thresholded to obtain a multiscale representation of progressively simplified surface, or curve, skeletons. We detail a numerical implementation of our framework which is demonstrably stable and has high computational efficiency. We demonstrate our framework on several complex 2D and 3D shapes.
Alanine substitution of conserved residues in the cytoplasmic tail of herpes simplex virus gB can enhance or abolish cell fusion activity and viral entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruel, Nancy; Zago, Anna; Spear, Patricia G.

2006-03-01

Herpes simplex virus (HSV) glycoprotein B (gB) is one of the four viral glycoproteins required for viral entry and cell fusion and is highly conserved among herpesviruses. Mutants of HSV type 2 gB were generated by substituting conserved residues in the cytoplasmic tail with alanine or by deleting 41 amino acids from the C-terminus. Some of the mutations abolished cell fusion activity and also prevented transport of gB to the cell surface, identifying residues in the gB cytoplasmic tail that are critical for intracellular transport of this glycoprotein. These mutations also prevented production of infectious virus, possibly because the mutantmore » forms of gB were not transported to the site of envelopment. Other mutations, particularly the deletion, significantly enhanced cell fusion activity. These mutations, as well as others described previously, identify regions of the gB cytoplasmic domain that modulate cell fusion activity.« less

The Prp19 WD40 Domain Contains a Conserved Protein Interaction Region Essential for its Function

PubMed Central

Vander Kooi, Craig W.; Ren, Liping; Xu, Ping; Ohi, Melanie D.; Gould, Kathleen L.; Chazin, Walter J.

2010-01-01

Summary Prp19 is a member of the WD40-repeat family of E3 ubiquitin ligases and a conserved eukaryotic RNA splicing factor essential for activation and stabilization of the spliceosome. To understand the role of the WD40 repeat domain of Prp19 we have determined its structure using X-ray crystallography. The domain has a distorted seven bladed WD40 architecture with significant asymmetry due to irregular packing of blades one and seven into the core of the WD40 domain. Structure-based mutagenesis identified a highly conserved surface centered around blade five that is required for the physical interaction between Prp19 and Cwc2, another essential splicing factor. This region is found to be required for Prp19 function and yeast viability. Experiments in vitro and in vivo demonstrate that two molecules of Cwc2 bind to the Prp19 tetramer. These coupled structural and functional studies provide a model for the functional architecture of Prp19. PMID:20462492
Optical coherence tomography for non-invasive examination and conservation of cultural heritage objects

NASA Astrophysics Data System (ADS)

Zaki, Farzana; Hou, Isabella; Huang, Qiongdan; Cooper, Denver; Patel, Divya; Liu, Xuan; Yang, Yi

2017-02-01

Optical coherence tomography (OCT) has great potential for the examination of oil paintings, particularly for celebrated masterpieces by great artists in history. We developed an OCT system for large field of view (FOV), high definition (HD) imaging of oil paintings. To achieve large FOV, we translated the sample using a pair of high-precision linear motors and performed sequential volumetric imaging on adjacent, non-overlapping regions. Through 3D OCT imaging, the surface terrain and subsurface microarchitecture of the paintings have been characterized and visualized.
A boundary element method for Stokes flows with interfaces

NASA Astrophysics Data System (ADS)

Alinovi, Edoardo; Bottaro, Alessandro

2018-03-01

The boundary element method is a widely used and powerful technique to numerically describe multiphase flows with interfaces, satisfying Stokes' approximation. However, low viscosity ratios between immiscible fluids in contact at an interface and large surface tensions may lead to consistency issues as far as mass conservation is concerned. A simple and effective approach is described to ensure mass conservation at all viscosity ratios and capillary numbers within a standard boundary element framework. Benchmark cases are initially considered demonstrating the efficacy of the proposed technique in satisfying mass conservation, comparing with approaches and other solutions present in the literature. The methodology developed is finally applied to the problem of slippage over superhydrophobic surfaces.
Guiding automated left ventricular chamber segmentation in cardiac imaging using the concept of conserved myocardial volume.

PubMed

Garson, Christopher D; Li, Bing; Acton, Scott T; Hossack, John A

2008-06-01

The active surface technique using gradient vector flow allows semi-automated segmentation of ventricular borders. The accuracy of the algorithm depends on the optimal selection of several key parameters. We investigated the use of conservation of myocardial volume for quantitative assessment of each of these parameters using synthetic and in vivo data. We predicted that for a given set of model parameters, strong conservation of volume would correlate with accurate segmentation. The metric was most useful when applied to the gradient vector field weighting and temporal step-size parameters, but less effective in guiding an optimal choice of the active surface tension and rigidity parameters.
Control-surface hinge-moment calculations for a high-aspect-ratio supercritical wing

NASA Technical Reports Server (NTRS)

Perry, B., III

1978-01-01

The hinge moments, at selected flight conditions, resulting from deflecting two trailing edge control surfaces (one inboard and one midspan) on a high aspect ratio, swept, fuel conservative wing with a supercritical airfoil are estimated. Hinge moment results obtained from procedures which employ a recently developed transonic analysis are given. In this procedure a three dimensional inviscid transonic aerodynamics computer program is combined with a two dimensional turbulent boundary layer program in order to obtain an interacted solution. These results indicate that trends of the estimated hinge moment as a function of deflection angle are similar to those from experimental hinge moment measurements made on wind tunnel models with swept supercritical wings tested at similar values of free stream Mach number and angle of attack.
Control-surface hinge-moment calculations for a high-aspect-ratio supercritical wing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perry, B.I.

1978-09-01

The hinge moments, at selected flight conditions, resulting from deflecting two trailing edge control surfaces (one inboard and one midspan) on a high aspect ratio, swept, fuel conservative wing with a supercritical airfoil are estimated. Hinge moment results obtained from procedures which employ a recently developed transonic analysis are given. In this procedure a three dimensional inviscid transonic aerodynamics computer program is combined with a two dimensional turbulent boundary layer program in order to obtain an interacted solution. These results indicate that trends of the estimated hinge moment as a function of deflection angle are similar to those from experimentalmore » hinge moment measurements made on wind tunnel models with swept supercritical wings tested at similar values of free stream Mach number and angle of attack.« less
An Asymptotic and Stochastic Theory for the Effects of Surface Gravity Waves on Currents and Infragravity Waves

NASA Astrophysics Data System (ADS)

McWilliams, J. C.; Lane, E.; Melville, K.; Restrepo, J.; Sullivan, P.

2004-12-01

Oceanic surface gravity waves are approximately irrotational, weakly nonlinear, and conservative, and they have a much shorter time scale than oceanic currents and longer waves (e.g., infragravity waves) --- except where the primary surface waves break. This provides a framework for an asymptotic theory, based on separation of time (and space) scales, of wave-averaged effects associated with the conservative primary wave dynamics combined with a stochastic representation of the momentum transfer and induced mixing associated with non-conservative wave breaking. Such a theory requires only modest information about the primary wave field from measurements or operational model forecasts and thus avoids the enormous burden of calculating the waves on their intrinsically small space and time scales. For the conservative effects, the result is a vortex force associated with the primary wave's Stokes drift; a wave-averaged Bernoulli head and sea-level set-up; and an incremental material advection by the Stokes drift. This can be compared to the "radiation stress" formalism of Longuet-Higgins, Stewart, and Hasselmann; it is shown to be a preferable representation since the radiation stress is trivial at its apparent leading order. For the non-conservative breaking effects, a population of stochastic impulses is added to the current and infragravity momentum equations with distribution functions taken from measurements. In offshore wind-wave equilibria, these impulses replace the conventional surface wind stress and cause significant differences in the surface boundary layer currents and entrainment rate, particularly when acting in combination with the conservative vortex force. In the surf zone, where breaking associated with shoaling removes nearly all of the primary wave momentum and energy, the stochastic forcing plays an analogous role as the widely used nearshore radiation stress parameterizations. This talk describes the theoretical framework and presents some preliminary solutions using it. McWilliams, J.C., J.M. Restrepo, & E.M. Lane, 2004: An asymptotic theory for the interaction of waves and currents in coastal waters. J. Fluid Mech. 511, 135-178. Sullivan, P.P., J.C. McWilliams, & W.K. Melville, 2004: The oceanic boundary layer driven by wave breaking with stochastic variability. J. Fluid Mech. 507, 143-174.
Soil conservation applications with C-band SAR

NASA Technical Reports Server (NTRS)

Brisco, B.; Brown, R. J.; Naunheimer, J.; Bedard, D.

1992-01-01

Soil conservation programs are becoming more important as the growing human population exerts greater pressure on this non-renewable resource. Indeed, soil degradation affects approximately 10 percent of Canada's agricultural land with an estimated loss of 6,000 hectares of topsoil annually from Ontario farmland alone. Soil loss not only affects agricultural productivity but also decreases water quality and can lead to siltation problems. Thus, there is a growing demand for soil conservation programs and a need to develop an effective monitoring system. Topography and soil type information can easily be handled within a geographic information system (GIS). Information about vegetative cover type and surface roughness, which both experience considerable temporal change, can be obtained from remote sensing techniques. For further development of the technology to produce an operational soil conservation monitoring system, an experiment was conducted in Oxford County, Ontario which investigated the separability of fall surface cover type using C-band Synthetic Aperture Radar (SAR) data.
State of Arts of Monumental Stones Diagnosis and Monitoring

NASA Astrophysics Data System (ADS)

Tiano, P.; Riminesi, C.

2017-08-01

The conservation and maintenance of a monumental stone building is a complex aim where different disciplines are involved. First step is concerning the determination of the state of conservation of stone material present, than determine its modification on time, as such and after conservation treatments applied on: cleaning, protecting, strengthening. In order to fulfill such objectives suitable parameters must be selected and the most appropriate diagnostic techniques for their quantitative evaluation operated. In this context, the determination of the surface water absorption, moisture content, colour variation and mechanical properties are important parameters for the control, and the monitoring over time, of the state of conservation of the monumental stone surfaces. These parameters are strongly related not only to the stone characteristics but also to the evaluation of products's performance: efficiency and durability. Their rate of variation, determined in monitoring campaigns, is fundamental for elaborate by properly predictive model a schedule maintenance protocol.
High-order flux correction/finite difference schemes for strand grids

NASA Astrophysics Data System (ADS)

Katz, Aaron; Work, Dalon

2015-02-01

A novel high-order method combining unstructured flux correction along body surfaces and high-order finite differences normal to surfaces is formulated for unsteady viscous flows on strand grids. The flux correction algorithm is applied in each unstructured layer of the strand grid, and the layers are then coupled together via a source term containing derivatives in the strand direction. Strand-direction derivatives are approximated to high-order via summation-by-parts operators for first derivatives and second derivatives with variable coefficients. We show how this procedure allows for the proper truncation error canceling properties required for the flux correction scheme. The resulting scheme possesses third-order design accuracy, but often exhibits fourth-order accuracy when higher-order derivatives are employed in the strand direction, especially for highly viscous flows. We prove discrete conservation for the new scheme and time stability in the absence of the flux correction terms. Results in two dimensions are presented that demonstrate improvements in accuracy with minimal computational and algorithmic overhead over traditional second-order algorithms.
Phosphorus Fate and Transport across Fields and Catchments: Addressing the Paradoxical Dilemma

NASA Astrophysics Data System (ADS)

Sharpley, Andrew; Jarvie, Helen; Johnson, Laura; Smith, Doug

2017-04-01

Awareness and scrutiny of agriculture's role in contributing phosphorus (P) to surface water impairment has increased due to recent high profile harmful algal bloom outbreaks. In addition, an inability to meet target P-load reductions in large catchments in the USA, such as Chesapeake Bay, Lake Erie, and Mississippi River, has brought into question the effectiveness of current and future conservation strategies designed to mitigate such loads. This has led many to question the efficacy of these measures and to call for stricter land and P-management strategies and the recognition of several paradoxes related to the management of agricultural P. "The Finite Resource and Environmental Abundance Paradox" While P is a finite resource, with an expected life of 300 years using modern mining technologies, less than 20% of mined fertilizer P reaches the food products consumed, only 10% of the P in human wastes is recycled back onto agricultural land, yet P deficits occur across 30% of global cropland. "The Blue - Green Paradox" An increasingly affluent population is becoming more demanding of cheap, reliable food sources and wanting inexpensive clean, safe water for many essential and recreational uses. We now face many challenges in balancing competing demands for protecting and restoring water quality and aquatic ecology, with sustainable and efficient agricultural production. After the low hanging fruit of remedial measures are adopted, remaining conservation practices become increasingly less cost-beneficial and raises the old conundrum of "who benefits and who pays?" "The Conservation Legacy P Paradox" Many conservation practices have been implemented to retain (e.g., no-tillage, cover crops, contour plowing, ridge tillage) and trap P (e.g., buffer strips, riparian zones, wetlands) on the landscape rather than enter waterways. Yet, the capacity of those practices to retain is finite and there are more and more examples of conservation practices transitioning from P sinks to P sources. In this presentation, we examine the drivers of legacy P at the watershed scale, specifically in relation to the physical cascades and biogeochemical spirals of P along the continuum from soils to rivers and lakes, and via surface and subsurface flow pathways. Close examination of long-term P flux, weather patterns, and land management identified several natural and managed drivers that have inadvertently accelerated the accumulation of P at the soil surface and flux of P via subsurface drainage. This indicates a paradoxical conundrum where well-intended conservation measures may have cumulative impacts, which have converged with changing weather patterns and catchment hydrology to increase P fluxes. In seeking solutions, we must better quantify P sinks and sources as they are transported through catchments, to develop realistic expectations for adoption of conservation strategies and timescales for aquatic ecosystem recovery.
Lack of tyrosine 320 impairs spontaneous endocytosis and enhances release of HLA-B27 molecules.

PubMed

Santos, Susana G; Antoniou, Antony N; Sampaio, Paula; Powis, Simon J; Arosa, Fernando A

2006-03-01

Several lines of evidence suggest that endocytosis of MHC class I molecules requires conserved motifs within the cytoplasmic domain. In this study, we show, in the C58 rat thymoma cell line transfected with HLA-B27 molecules, that replacement of the highly conserved tyrosine (Tyr320) in the cytoplasmic domain of HLA-B27 does not hamper cell surface expression of beta2-microglobulin H chain heterodimers or formation of misfolded molecules. However, Tyr320 replacement markedly impairs spontaneous endocytosis of HLA-B27. Although wild-type molecules are mostly internalized via endosomal compartments, Tyr320-mutated molecules remain at the plasma membrane in which partial colocalization with endogenous transferrin receptors can be observed, also impairing their endocytosis. Finally, we show that Tyr320 substitution enhances release of cleaved forms of HLA-B27 from the cell surface. These studies show for the first time that Tyr320 is most likely part of a cytoplasmic sorting motif involved in spontaneous endocytosis and shedding of MHC class I molecules.
Why do lab-scale experiments ever resemble geological scale patterning?

NASA Astrophysics Data System (ADS)

Ferdowsi, Behrooz; Jones, Brandon C.; Stein, Jeremy L.; Shinbrot, Troy

2017-11-01

The Earth and other planets are abundant with curious and poorly understood surface patterns. Examples include sand dunes, periodic and aperiodic ridges and valleys, and networks of river and submarine channels. We make the minimalist proposition that the dominant mechanism governing these varied patterns is mass conservation: notwithstanding detailed particulars, the universal rule is mass conservation and there are only a finite number of surface patterns that can result from this process. To test this minimalist proposition, we perform experiments in a vertically vibrated bed of fine grains, and we show that every one of a wide variety of patterns seen in the laboratory is also seen in recorded geomorphologies. We explore a range of experimental driving frequencies and amplitudes, and we complement these experimental results with a non-local cellular automata model that reproduces the surface patterns seen using a minimalist approach that allows a free surface to deform subject to mass conservation and simple known forces such as gravity. These results suggest a common cause for the effectiveness of lab-scale models for geological scale patterning that otherwise ought to have no reasonable correspondence.
Positive selection in octopus haemocyanin indicates functional links to temperature adaptation.

PubMed

Oellermann, Michael; Strugnell, Jan M; Lieb, Bernhard; Mark, Felix C

2015-07-05

Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.
Conservative mutation Met8 --> Leu affects the folding process and structural stability of squash trypsin inhibitor CMTI-I.

PubMed Central

Zhukov, I.; Jaroszewski, L.; Bierzyński, A.

2000-01-01

Protein molecules can accommodate a large number of mutations without noticeable effects on their stability and folding kinetics. On the other hand, some mutations can have quite strong effects on protein conformational properties. Such mutations either destabilize secondary structures, e.g., alpha-helices, are incompatible with close packing of protein hydrophobic cores, or lead to disruption of some specific interactions such as disulfide cross links, salt bridges, hydrogen bonds, or aromatic-aromatic contacts. The Met8 --> Leu mutation in CMTI-I results in significant destabilization of the protein structure. This effect could hardly be expected since the mutation is highly conservative, and the side chain of residue 8 is situated on the protein surface. We show that the protein destabilization is caused by rearrangement of a hydrophobic cluster formed by side chains of residues 8, Ile6, and Leu17 that leads to partial breaking of a hydrogen bond formed by the amide group of Leu17 with water and to a reduction of a hydrophobic surface buried within the cluster. The mutation perturbs also the protein folding. In aerobic conditions the reduced wild-type protein folds effectively into its native structure, whereas more then 75% of the mutant molecules are trapped in various misfolded species. The main conclusion of this work is that conservative mutations of hydrophobic residues can destabilize a protein structure even if these residues are situated on the protein surface and partially accessible to water. Structural rearrangement of small hydrophobic clusters formed by such residues can lead to local changes in protein hydration, and consequently, can affect considerably protein stability and folding process. PMID:10716179
DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Arvind; Agarwal, Pratul K

Proteins are intrinsically flexible molecules. The role of internal motions in a protein's designated function is widely debated. The role of protein structure in enzyme catalysis is well established, and conservation of structural features provides vital clues to their role in function. Recently, it has been proposed that the protein function may involve multiple conformations: the observed deviations are not random thermodynamic fluctuations; rather, flexibility may be closely linked to protein function, including enzyme catalysis. We hypothesize that the argument of conservation of important structural features can also be extended to identification of protein flexibility in interconnection with enzyme function.more » Three classes of enzymes (prolyl-peptidyl isomerase, oxidoreductase, and nuclease) that catalyze diverse chemical reactions have been examined using detailed computational modeling. For each class, the identification and characterization of the internal protein motions coupled to the chemical step in enzyme mechanisms in multiple species show identical enzyme conformational fluctuations. In addition to the active-site residues, motions of protein surface loop regions (>10 away) are observed to be identical across species, and networks of conserved interactions/residues connect these highly flexible surface regions to the active-site residues that make direct contact with substrates. More interestingly, examination of reaction-coupled motions in non-homologous enzyme systems (with no structural or sequence similarity) that catalyze the same biochemical reaction shows motions that induce remarkably similar changes in the enzyme substrate interactions during catalysis. The results indicate that the reaction-coupled flexibility is a conserved aspect of the enzyme molecular architecture. Protein motions in distal areas of homologous and non-homologous enzyme systems mediate similar changes in the active-site enzyme substrate interactions, thereby impacting the mechanism of catalyzed chemistry. These results have implications for understanding the mechanism of allostery, and for protein engineering and drug design.« less
The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.

PubMed

Jinek, Martin; Eulalio, Ana; Lingel, Andreas; Helms, Sigrun; Conti, Elena; Izaurralde, Elisa

2008-10-01

The removal of the 5' cap structure by the DCP1-DCP2 decapping complex irreversibly commits eukaryotic mRNAs to degradation. In human cells, the interaction between DCP1 and DCP2 is bridged by the Ge-1 protein. Ge-1 contains an N-terminal WD40-repeat domain connected by a low-complexity region to a conserved C-terminal domain. It was reported that the C-terminal domain interacts with DCP2 and mediates Ge-1 oligomerization and P-body localization. To understand the molecular basis for these functions, we determined the three-dimensional crystal structure of the most conserved region of the Drosophila melanogaster Ge-1 C-terminal domain. The region adopts an all alpha-helical fold related to ARM- and HEAT-repeat proteins. Using structure-based mutants we identified an invariant surface residue affecting P-body localization. The conservation of critical surface and structural residues suggests that the C-terminal region adopts a similar fold with conserved functions in all members of the Ge-1 protein family.
Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ecale Zhou, C L; Zemla, A T; Roe, D

2005-01-29

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set ofmore » ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.« less
Centaur: A Mobile Dexterous Humanoid for Surface Operations

NASA Technical Reports Server (NTRS)

Rehnmark, Fredrik; Ambrose, Robert O.; Goza, S. Michael; Junkin, Lucien; Neuhaus, Peter D.; Pratt, Jerry E.

2005-01-01

Future human and robotic planetary expeditions could benefit greatly from expanded Extra-Vehicular Activity (EVA) capabilities supporting a broad range of multiple, concurrent surface operations. Risky, expensive and complex, conventional EVAs are restricted in both duration and scope by consumables and available manpower, creating a resource management problem. A mobile, highly dexterous Extra-Vehicular Robotic (EVR) system called Centaur is proposed to cost-effectively augment human astronauts on surface excursions. The Centaur design combines a highly capable wheeled mobility platform with an anthropomorphic upper body mounted on a three degree-of-freedom waist. Able to use many ordinary handheld tools, the robot could conserve EVA hours by relieving humans of many routine inspection and maintenance chores and assisting them in more complex tasks, such as repairing other robots. As an astronaut surrogate, Centaur could take risks unacceptable to humans, respond more quickly to EVA emergencies and work much longer shifts. Though originally conceived as a system for planetary surface exploration, the Centaur concept could easily be adapted for terrestrial military applications such as de-Gig, surveillance and other hazardous duties.
Present status of liquid metal research for a fusion reactor

NASA Astrophysics Data System (ADS)

Tabarés, Francisco L.

2016-01-01

Although the use of solid materials as targets of divertor plasmas in magnetic fusion research is accepted as the standard solution for the very challenging issue of power and particle handling in a fusion reactor, a generalized feeling that the present options chosen for ITER will not represent the best choice for a reactor is growing up. The problems found for tungsten, the present selection for the divertor target of ITER, in laboratory tests and in hot plasma fusion devices suggest so. Even in the absence of the strong neutron irradiation expected in a reactor, issues like surface melting, droplet ejection, surface cracking, dust generation, etc., call for alternative solutions in a long pulse, high efficient fusion energy-producing continuous machine. Fortunately enough, decades of research on plasma facing materials based on liquid metals (LMs) have produced a wealth of appealing ideas that could find practical application in the route to the realization of a commercial fusion power plant. The options presently available, although in a different degree of maturity, range from full coverage of the inner wall of the device with liquid metals, so that power and particle exhaust together with neutron shielding could be provided, to more conservative combinations of liquid metal films and conventional solid targets basically representing a sort of high performance, evaporative coating for the alleviation of the surface degradation issues found so far. In this work, an updated review of worldwide activities on LM research is presented, together with some open issues still remaining and some proposals based on simple physical considerations leading to the optimization of the most conservative alternatives.

Lanthanide-labeled clay: A new method for tracing sediment transport in Karst

USGS Publications Warehouse

Mahler, B.J.; Bennett, P.C.; Zimmerman, M.

1998-01-01

Mobile sediment is a fundamental yet poorly characterized aspect of mass transport through karst aquifers. Here the development and field testing of an extremely sensitive particle tracer that may be used to characterize sediment transport in karst aquifers is described. The tracer consists of micron-size montmorillonite particles homoionized to the lanthanide form; after injection and retrieval from a ground water system, the lanthanide ions are chemically stripped from the clay and quantified by high performance liquid chromatography. The tracer meets the following desired criteria: low detection limit; a number of differentiable signatures; inexpensive production and quantification using standard methods; no environmental risks; and hydrodynamic properties similar to the in situ sediment it is designed to trace. The tracer was tested in laboratory batch experiments and field tested in both surface water and ground water systems. In surface water, arrival times of the tracer were similar to those of a conservative water tracer, although a significant amount of material was lost due to settling. Two tracer tests were undertaken in a karst aquifer under different flow conditions. Under normal flow conditions, the time of arrival and peak concentration of the tracer were similar to or preceded that of a conservative water tracer. Under low flow conditions, the particle tracer was not detected, suggesting that in low flow the sediment settles out of suspension and goes into storage.Mobile sediment is a fundamental yet poorly characterized aspect of mass transport through karst aquifers. Here the development and field testing of an extremely sensitive particle tracer that may be used to characterize sediment transport in karst aquifers is described. The tracer consists of micron-size montmorillonite particles homoionized to the lanthanide form; after injection and retrieval from a ground water system, the lanthanide ions are chemically stripped from the clay and quantified by high performance liquid chromatography. The tracer meets the following desired criteria: low detection limit; a number of differentiable signatures; inexpensive production and quantification using standard methods; no environmental risks; and hydrodynamic properties similar to the in situ sediment it is designed to trace. The tracer was tested in laboratory batch experiments and field tested in both surface water and ground water systems. In surface water, arrival times of the tracer were similar to those of a conservative water tracer, although a significant amount of material was lost due to settling. Two tracer tests were undertaken in a karst aquifer under different flow conditions. Under normal flow conditions, the time of arrival and peak concentration of the tracer were similar to or preceded that of a conservative water tracer. Under low flow conditions, the particle tracer was not detected, suggesting that in low flow the sediment settles out of suspension and goes into storage.
Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua) - Conserved synteny between fish monolobal and tetrapod bilobal transferrin loci

PubMed Central

2011-01-01

Background The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. Results The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. Conclusions The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in trans-Atlantic cod populations. PMID:21612617
Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua)--conserved synteny between fish monolobal and tetrapod bilobal transferrin loci.

PubMed

Andersen, Øivind; De Rosa, Maria Cristina; Pirolli, Davide; Tooming-Klunderud, Ave; Petersen, Petra E; André, Carl

2011-05-25

The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in trans-Atlantic cod populations.
A new approach of the surface temperature measurement for a preventive conservation of the work of arts

NASA Astrophysics Data System (ADS)

Di Tuccio, Maria Concetta; De Grandi, Sandro; Vivarelli, Arianna; Becherini, Francesca; Pockelé, Luc; Bernardi, Adriana

2015-04-01

To conserve the work of arts (paintings, sculptures, etc..) in a preventive mode, a careful monitoring of the environment around these artifacts, as well as of their surface temperature, is necessary. The latter is the only physical variable which can be measured in a non-invasive way, following directly the thermal conditions and variations of the work of arts due to the dynamics of the microclimate. Considering that the works of art are often untouchable, an automated and accurate remote sensing could be very useful to prevent dangerous processes of deterioration. For these reasons a new sensor has been developed by a spin-off of the ISAC - CNR. This sensor allows to check in real-time the surface temperature changes of the artifacts both over time and at different predefined points. This automated sensor is a radiometer sensible to wavelengths ranging from 7,5 µm to 13,4 µm. A system rotating over three dimension "pan and tilt" allows to make multiple measures on a grid of points previously defined on the surface of the work of arts. The accuracy, obtained by means of a carefull calibration process, is  0,5 °C, more precise than the usual remote sensing (thermal camera and commercial radiometers), characterized by an accuracy value of  2°C. In order to obtain accurate measures of the surface temperature for a real body, the correct emissivity values need to be integrated in the calculation. Hence, an easy to use management software has been developed allowing to set the emissivity value in each point of the grid. For rejoinable points of the surface, the exact emissivity value could be determined comparing the measurements recorded by the new infrared sensor with the ones obtained by a very sensitive sensor (0,02 - 0,03)°C manually placed on the surface for a short time. In case of work of arts placed at great distance from the sersor, the emissivity values must be determined previously. The emissivity depends on a lot of variables and one of them is the surface roughness. Since the artifacts are often charaterized by a high surface roughness, such dependence has been studied in order to obtain accurate temperature measurements. The results obtained indicate an increase of the emissivity with increasing surface roughness. In conclusion, this study has allowed to develop a reliable, accurate and automatic control system, as well as a low cost sensor that, unlike the thermal camera, can also be used by less experienced operators. Besides, in order to support the museums managers in the preventive conservation of the artifacts, an alarm system is automatically activated when dangerously large thermal variations on the surface are detected.
Development of chitosan-coated gold nanoflowers as SERS-active probes

NASA Astrophysics Data System (ADS)

Xu, Dan; Gu, Jiangjiang; Wang, Weina; Yu, Xuehai; Xi, Kai; Jia, Xudong

2010-09-01

Surface-enhanced Raman scattering (SERS) has been intensely researched for many years as a potential technique for highly sensitive detection. This work, through the reduction of HAuCl4 with pyrrole in aqueous solutions, investigated a facile one-pot synthesis of flower-like Au nanoparticles with rough surfaces. The formation process of the Au nanoflowers (AuNFs) was carefully studied, and a spontaneous assembly mechanism was proposed based on the time-course experimental results. The key synthesis strategy was to use pyrrole as a weak particle stabilizing and reducing agent to confine crystal growth in the limited ligand protection region. The nanometer-scale surface roughness of AuNFs provided several hot spots on a single particle, which significantly increased SERS enhancement. Good biocompatible stable Raman-active probes were synthesized by coating AuNFs with chitosan. The conservation of the SERS effects in living cells suggested that the chitosan-capped AuNFs could be suitable for highly sensitive detection and have potential for targeting of tumors in vivo.
78 FR 20503 - Energy Conservation Program: Availability of the Interim Technical Support Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

... Conservation Program: Availability of the Interim Technical Support Document for High-Intensity Discharge Lamps... high-intensity discharge (HID) lamps energy conservation standards in the Federal Register. This... interim analysis for high- intensity discharge lamps energy conservation standards. The notice provided...
Dust-associated microbiomes from dryland wheat fields differ with tillage practice and biosolids application

NASA Astrophysics Data System (ADS)

Schlatter, Daniel C.; Schillinger, William F.; Bary, Andy I.; Sharratt, Brenton; Paulitz, Timothy C.

2018-07-01

Wind erosion is a significant threat to the productivity and sustainability of agricultural soils. In the dryland winter wheat (Triticum aestivum L.)-fallow region of Inland Pacific Northwest of the USA (PNW), farmers increasingly use conservation tillage practices to control wind erosion. In addition, some farmers in this dry region apply municipal biosolids to soils as fertilizer and a source of stable organic matter. The impacts of soil management practices on emissions of dust microbiota to the atmosphere are understudied. We used high-throughput DNA sequencing to examine the impacts of conservation tillage and biosolids amendments on the transport of dust-associated fungal and bacterial communities during simulated high-wind events over two years at Lind, WA. The fungal and bacterial communities contained in windblown dust differed significantly with tillage (conservation vs. conventional) and fertilizer (synthetic vs. biosolids) treatments. However, the richness and diversity of fungal and bacterial communities of dust did not vary significantly with tillage or fertilizer treatments. Taxa enriched in dust from fields under conservation tillage represented many plant-associated taxa that likely grow on residue left on the soil surface, whereas taxa that were more abundant with conventional tillage were those that likely grow on buried plant residue. Dust from biosolids-amended fields harbored greater abundances of taxa that likely feed on introduced carbon. Most human-associated taxa that may pose a health risk were not present in dust after biosolids amendment, although members of Clostridiaceae were enriched with this treatment. Results show that tillage and fertilizer management practices impact the composition of bioaerosols emitted during high-wind events and have potential implications for plant and human health.
Identification and expression analysis of zebrafish glypicans during embryonic development.

PubMed

Gupta, Mansi; Brand, Michael

2013-01-01

Heparan sulfate Proteoglycans (HSPG) are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG's, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish glypicans like Gpc1a, Gpc3, Gpc4, Gpc6a and Gpc6b show conserved synteny with their mammalian cognate genes. Many glypicans are expressed during the gastrulation stage, but their expression becomes more tissue specific and defined during somitogenesis stages, particularly in the developing central nervous system. Existence of multiple glypican orthologs in fish with diverse expression pattern suggests highly specialized and/or redundant function of these genes during embryonic development.
Surface-exposed and antigenically conserved determinants of outer membrane proteins of Branhamella catarrhalis.

PubMed Central

Murphy, T F; Bartos, L C

1989-01-01

The outer membrane proteins (OMPs) of Branhamella catarrhalis were studied in an effort to identify surface-exposed determinants that are conserved among strains of the bacterium. Aliquots of polyclonal antiserum were absorbed individually by strains of B. catarrhalis. The absorbed antisera were tested in comparison with unabsorbed antiserum in an immunoblot assay against OMPs of the homologous strain. The absence of a band recognized by antibodies in the absorbed antiserum compared with the unabsorbed antiserum indicated that surface-exposed determinants of the absorbing strain cross-reacted with determinants on the homologous strain. Two antisera were absorbed individually by 20 strains of B. catarrhalis, and the absorbed sera were studied in this way in immunoblot assays. OMP E (molecular weight, ca. 56,000) expresses surface-exposed determinants that are shared among 17 of the 20 strains studied. Antibodies to OMP G (molecular weight, 28,000) were absorbed from both antisera by 14 of the 20 strains. These studies demonstrate that OMP E and OMP G express determinants that are exposed on the surface of the intact bacterium. Furthermore, these determinants are antigenically conserved among a majority of strains of B. catarrhalis. On the basis of these observations, OMPs E and G should be considered when bacterial antigens are evaluated as potential vaccine candidates. Images PMID:2476393
Non-conservation of global charges in the Brane Universe and baryogenesis

NASA Astrophysics Data System (ADS)

Dvali, Gia; Gabadadze, Gregory

1999-08-01

We argue that global charges, such as baryon or lepton number, are not conserved in theories with the Standard Model fields localized on the brane which propagates in higher-dimensional space-time. The global-charge non-conservation is due to quantum fluctuations of the brane surface. These fluctuations create ``baby branes'' that can capture some global charges and carry them away into the bulk of higher-dimensional space. Such processes are exponentially suppressed at low-energies, but can be significant at high enough temperatures or energies. These effects can lead to a new, intrinsically high-dimensional mechanism of baryogenesis. Baryon asymmetry might be produced due either to ``evaporation'' into the baby branes, or creation of the baryon number excess in collisions of two Brane Universes. As an example we discuss a possible cosmological scenario within the recently proposed ``Brane Inflation'' framework. Inflation is driven by displaced branes which slowly fall on top of each other. When the branes collide inflation stops and the Brane Universe reheats. During this non-equilibrium collision baryon number can be transported from one brane to another one. This results in the baryon number excess in our Universe which exactly equals to the hidden ``baryon number'' deficit in the other Brane Universe. © 1999
Nutrient elements in large Chinese estuaries

NASA Astrophysics Data System (ADS)

Zhang, Jing

1996-07-01

Based on comprehensive observations since 1983, this study summarizes major features of nutrient elements (nitrogen, phosphorus and silicon) in large Chinese river/estuary systems. Elevated nutrient element levels were observed in Chinese rivers, when compared to large and less disturbed aquatic systems (e.g. the Amazon, Zaire and Orinoco). Data from this study are similar to those obtained from the polluted and/or eutrophic rivers in Europe and North America (e.g. the Rhóne and Loire). Nutrient elements may have either conservative or active distributions, or both, in the mixing zone, depending on the element and the estuary. For example, non-conservative behaviors were observed in the upper estuary, where nutrient elements may be remobilized due to the strong desorption and variations of the fresh water end-member, but conservative distributions were found afterwards in the lower estuary. Outside the riverine effluent plumes, nutrient elements may be depleted in surface waters relative to elevated bioproduction, whereas the regeneration with respect to decomposition of organic material and/or nitrification/denitrification offshore, may sustain high levels of nutrient elements in near-bottom waters. Laboratory experiment data generally compares well with field observations. The high fluxes and area] yields of nutrient elements from large Chinese rivers, indicate the extensive use of chemical fertilizers and domestic waste drainage over watersheds in China.
Coupling of conservative and dissipative forces in frequency-modulation atomic force microscopy

NASA Astrophysics Data System (ADS)

Sader, John E.; Jarvis, Suzanne P.

2006-11-01

Frequency modulation atomic force microscopy (FM-AFM) utilizes the principle of self-excitation to ensure the cantilever probe vibrates at its resonant frequency, regardless of the tip-sample interaction. Practically, this is achieved by fixing the phase difference between tip deflection and driving force at precisely 90° . This, in turn, decouples the frequency shift and excitation amplitude signals, enabling quantitative interpretation in terms of conservative and dissipative tip-sample interaction forces. In this article, we theoretically investigate the effect of phase detuning in the self-excitation mechanism on the coupling between conservative and dissipative forces in FM-AFM. We find that this coupling depends only on the relative difference in the drive and resonant frequencies far from the surface, and is thus very weakly dependent on the actual phase error particularly for high quality factors. This establishes that FM-AFM is highly robust with respect to phase detuning, and enables quantitative interpretation of the measured frequency shift and excitation amplitude, even while operating away from the resonant frequency with the use of appropriate replacements in the existing formalism. We also examine the calibration of phase shifts in FM-AFM measurements and demonstrate that the commonly used approach of minimizing the excitation amplitude can lead to significant phase detuning, particularly in liquid environments.
Identification of a conserved B-cell epitope on the GapC protein of Streptococcus dysgalactiae.

PubMed

Zhang, Limeng; Zhou, Xue; Fan, Ziyao; Tang, Wei; Chen, Liang; Dai, Jian; Wei, Yuhua; Zhang, Jianxin; Yang, Xuan; Yang, Xijing; Liu, Daolong; Yu, Liquan; Zhang, Hua; Wu, Zhijun; Yu, Yongzhong; Sun, Hunan; Cui, Yudong

2015-01-01

Streptococcus dysgalactiae (S. dysgalactia) GapC is a highly conserved surface dehydrogenase among the streptococcus spp., which is responsible for inducing protective antibody immune responses in animals. However, the B-cell epitope of S. dysgalactia GapC have not been well characterized. In this study, a monoclonal antibody 1F2 (mAb1F2) against S. dysgalactiae GapC was generated by the hybridoma technique and used to screen a phage-displayed 12-mer random peptide library (Ph.D.-12) for mapping the linear B-cell epitope. The mAb1F2 recognized phages displaying peptides with the consensus motif TRINDLT. Amino acid sequence of the motif exactly matched (30)TRINDLT(36) of the S. dysgalactia GapC. Subsequently, site-directed mutagenic analysis further demonstrated that residues R31, I32, N33, D34 and L35 formed the core of (30)TRINDLT(36), and this core motif was the minimal determinant of the B-cell epitope recognized by the mAb1F2. The epitope (30)TRINDLT(36) showed high homology among different streptococcus species. Overall, our findings characterized a conserved B-cell epitope, which will be useful for the further study of epitope-based vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.
Seasonality of major redox constituents in a shallow subterranean estuary

NASA Astrophysics Data System (ADS)

O'Connor, Alison E.; Krask, Julie L.; Canuel, Elizabeth A.; Beck, Aaron J.

2018-03-01

The subterranean estuary (STE), the subsurface mixing zone of outflowing fresh groundwater and infiltrating seawater, is an area of extensive geochemical reactions that determine the composition of groundwater that flows into coastal environments. This study examined the porewater composition of a shallow STE (<5 m depth) in Gloucester Point, VA (USA) over two years to determine seasonal variations in dissolved organic carbon (DOC) and the reduced metabolites Fe, Mn, and sulfide. An additional aim of this study was to investigate the relative importance of salinity gradients (which have great geochemical influence in surface estuaries) versus redox gradients on STE geochemistry. Two freshwater endmembers were identified, between which redox potential and composition varied with depth-a shallow freshwater endmember was oxidizing and high in DOC, whereas a deep freshwater endmember was reducing, lower in DOC, and high in sulfide. Results showed that dissolved Fe, Mn, and sulfide varied along a redox gradient distinct from the salinity gradient, and that three-endmember mixing was required to quantify non-conservative chemical addition/removal in the STE. In addition to salinity, humic carbon was used as a quasi-conservative tracer to quantify mixing according to a three-endmember model. The vertical distributions of DOC and reduced metabolites remained approximately constant over time, but concentrations varied with season. Dissolved organic carbon concentrations were greatest in the summer, and shallow meteoric groundwater supplied the majority of DOC to the STE. In summer, there was additional evidence for shallow non-conservative addition of DOC. Dissolved Fe and Mn were highest in a subsurface plume through the middle of the STE (100-140 cm below sediment surface at the high tide line) which was characterized by higher concentrations and greater non-conservative addition in the winter. In contrast, sulfide was higher in summer at depths within the Fe and Mn plume (100-140 cm). We attribute the contrasting seasonal patterns of dissolved Fe, Mn, and sulfide to differences in microbial response to temperature changes and organic matter availability, and to competition at the ferrous-sulfidic transition zone between dissimilatory metal reduction and sulfate reduction, leading to sulfate/sulfur reducing bacteria (SRB) being more active in summer and metal reducers being more active in winter. Throughout the STE, seasonal temperature and DOC variations determined the spatial distribution and geochemical cycling of Fe, Mn, and sulfur.
Fine sediment sources in conservation effects assessment project watersheds

USDA-ARS?s Scientific Manuscript database

Two naturally occurring radionuclides, 7Be and 210Pbxs , were used as tracers to discriminate eroded surface soils from channel-derived sediments in the fine suspended sediment loads of eight Conservation Effects Assessment Project (CEAP) benchmark watersheds. Precipitation, source soils, and suspe...
Aerodynamic performance of high turning core turbine vanes in a two dimensional cascade

NASA Technical Reports Server (NTRS)

Schwab, J. R.

1982-01-01

Experimental and theoretical aerodynamic performance data are presented for four uncooled high turning core turbine vanes with exit angles of 74.9, 75.0, 77.5, and 79.6 degrees in a two dimensional cascade. Data for a more conservative 67.0 degree vane are included for comparison. Correction of the experimental aftermix kinetic energy losses to a common 0.100 centimeter trailing edge thickness yields a linear trend of increased loss from 0.020 to 0.025 as the vane exit angle increases from 67.0 to 79.6 degrees. The theoretical losses show a similar trend. The experimental and theoretical vane surface velocity distributions generally agree within approximately five percent, although the suction surface theoretical velocities are generally higher than the experimental velocities as the vane exit angle increases.
Modeling the Impact of Soil and Water Conservation on Surface and Ground Water Based on the SCS and Visual Modflow

PubMed Central

Wang, Hong; Gao, Jian-en; Zhang, Shao-long; Zhang, Meng-jie; Li, Xing-hua

2013-01-01

Soil and water conservation measures can impact hydrological cycle, but quantitative analysis of this impact is still difficult in a watershed scale. To assess the effect quantitatively, a three-dimensional finite-difference groundwater flow model (MODFLOW) with a surface runoff model–the Soil Conservation Service (SCS) were calibrated and applied based on the artificial rainfall experiments. Then, three soil and water conservation scenarios were simulated on the sand-box model to assess the effect of bare slope changing to grass land and straw mulching on water volume, hydraulic head, runoff process of groundwater and surface water. Under the 120 mm rainfall, 60 mm/h rainfall intensity, 5 m2 area, 3° slope conditions, the comparative results indicated that the trend was decrease in surface runoff and increase in subsurface runoff coincided with the land-use converted from bare slope to grass land and straw mulching. The simulated mean surface runoff modulus was 3.64×10−2 m3/m2/h in the bare slope scenario, while the observed values were 1.54×10−2 m3/m2/h and 0.12×10−2 m3/m2/h in the lawn and straw mulching scenarios respectively. Compared to the bare slope, the benefits of surface water reduction were 57.8% and 92.4% correspondingly. At the end of simulation period (T = 396 min), the simulated mean groundwater runoff modulus was 2.82×10−2 m3/m2/h in the bare slope scenario, while the observed volumes were 3.46×10−2 m3/m2/h and 4.91×10−2 m3/m2/h in the lawn and straw mulching scenarios respectively. So the benefits of groundwater increase were 22.7% and 60.4% correspondingly. It was concluded that the soil and water conservation played an important role in weakening the surface runoff and strengthening the underground runoff. Meanwhile the quantitative analysis using a modeling approach could provide a thought for the study in a watershed scale to help decision-makers manage water resources. PMID:24244427
High beta plasma operation in a toroidal plasma producing device

DOEpatents

Clarke, John F.

1978-01-01

A high beta plasma is produced in a plasma producing device of toroidal configuration by ohmic heating and auxiliary heating. The plasma pressure is continuously monitored and used in a control system to program the current in the poloidal field windings. Throughout the heating process, magnetic flux is conserved inside the plasma and the distortion of the flux surfaces drives a current in the plasma. As a consequence, the total current increases and the poloidal field windings are driven with an equal and opposing increasing current. The spatial distribution of the current in the poloidal field windings is determined by the plasma pressure. Plasma equilibrium is maintained thereby, and high temperature, high beta operation results.
The National Landscape Conservation System: A model for long term conservation of significant landscapes

Treesearch

Dave Harmon; Jeff Jarvis

2011-01-01

The Bureau of Land Management administers over 256 million surface acres, more than any other U.S. public agency, the vast majority of which is in the western half of the United States. A land protection system was initiated in 1970 with the creation of the King Range National Conservation Area. In 1976, the Federal Land Policy and Management Act (http://www.blm.gov/...
Extractable Bacterial Surface Proteins in Probiotic–Host Interaction

PubMed Central

do Carmo, Fillipe L. R.; Rabah, Houem; De Oliveira Carvalho, Rodrigo D.; Gaucher, Floriane; Cordeiro, Barbara F.; da Silva, Sara H.; Le Loir, Yves; Azevedo, Vasco; Jan, Gwénaël

2018-01-01

Some Gram-positive bacteria, including probiotic ones, are covered with an external proteinaceous layer called a surface-layer. Described as a paracrystalline layer and formed by the self-assembly of a surface-layer-protein (Slp), this optional structure is peculiar. The surface layer per se is conserved and encountered in many prokaryotes. However, the sequence of the corresponding Slp protein is highly variable among bacterial species, or even among strains of the same species. Other proteins, including surface layer associated proteins (SLAPs), and other non-covalently surface-bound proteins may also be extracted with this surface structure. They can be involved a various functions. In probiotic Gram-positives, they were shown by different authors and experimental approaches to play a role in key interactions with the host. Depending on the species, and sometime on the strain, they can be involved in stress tolerance, in survival within the host digestive tract, in adhesion to host cells or mucus, or in the modulation of intestinal inflammation. Future trends include the valorization of their properties in the formation of nanoparticles, coating and encapsulation, and in the development of new vaccines. PMID:29670603

Optical measurements of paintings and the creation of an artwork database for authenticity

PubMed Central

Hwang, Seonhee; Song, Hyerin; Cho, Soon-Woo; Kim, Chang Eun; Kim, Chang-Seok; Kim, Kyujung

2017-01-01

Paintings have high cultural and commercial value, so that needs to be preserved. Many techniques have been attempted to analyze properties of paintings, including X-ray analysis and optical coherence tomography (OCT) methods, and enable conservation of paintings from forgeries. In this paper, we suggest a simple and accurate optical analysis system to protect them from counterfeit which is comprised of fiber optics reflectance spectroscopy (FORS) and line laser-based topographic analysis. The system is designed to fully cover the whole area of paintings regardless of its size for the accurate analysis. For additional assessments, a line laser-based high resolved OCT was utilized. Some forgeries were created by the experts from the three different styles of genuine paintings for the experiments. After measuring surface properties of paintings, we could observe the results from the genuine works and the forgeries have the distinctive characteristics. The forgeries could be distinguished maximally 76.5% with obtained RGB spectra by FORS and 100% by topographic analysis. Through the several executions, the reliability of the system was confirmed. We could verify that the measurement system is worthwhile for the conservation of the valuable paintings. To store the surface information of the paintings in micron scale, we created a numerical database. Consequently, we secured the databases of three different famous Korean paintings for accurate authenticity. PMID:28151981
Optical measurements of paintings and the creation of an artwork database for authenticity.

PubMed

Hwang, Seonhee; Song, Hyerin; Cho, Soon-Woo; Kim, Chang Eun; Kim, Chang-Seok; Kim, Kyujung

2017-01-01

Paintings have high cultural and commercial value, so that needs to be preserved. Many techniques have been attempted to analyze properties of paintings, including X-ray analysis and optical coherence tomography (OCT) methods, and enable conservation of paintings from forgeries. In this paper, we suggest a simple and accurate optical analysis system to protect them from counterfeit which is comprised of fiber optics reflectance spectroscopy (FORS) and line laser-based topographic analysis. The system is designed to fully cover the whole area of paintings regardless of its size for the accurate analysis. For additional assessments, a line laser-based high resolved OCT was utilized. Some forgeries were created by the experts from the three different styles of genuine paintings for the experiments. After measuring surface properties of paintings, we could observe the results from the genuine works and the forgeries have the distinctive characteristics. The forgeries could be distinguished maximally 76.5% with obtained RGB spectra by FORS and 100% by topographic analysis. Through the several executions, the reliability of the system was confirmed. We could verify that the measurement system is worthwhile for the conservation of the valuable paintings. To store the surface information of the paintings in micron scale, we created a numerical database. Consequently, we secured the databases of three different famous Korean paintings for accurate authenticity.
Identification of Group B Streptococcal Sip Protein, Which Elicits Cross-Protective Immunity

PubMed Central

Brodeur, Bernard R.; Boyer, Martine; Charlebois, Isabelle; Hamel, Josée; Couture, France; Rioux, Clément R.; Martin, Denis

2000-01-01

A protein of group B streptococci (GBS), named Sip for surface immunogenic protein, which is distinct from previously described surface proteins, was identified after immunological screening of a genomic library. Immunoblots using a Sip-specific monoclonal antibody indicated that a protein band with an approximate molecular mass of 53 kDa which did not vary in size was present in every GBS strain tested. Representatives of all nine GBS serotypes were included in the panel of strains. Cloning and sequencing of the sip gene revealed an open reading frame of 1,305 nucleotides coding for a polypeptide of 434 amino acid residues, with a calculated pI of 6.84 and molecular mass of 45.5 kDa. Comparison of the nucleotide sequences from six different strains confirmed with 98% identity that the sip gene is highly conserved among GBS isolates. N-terminal amino acid sequencing also indicated the presence of a 25-amino-acid signal peptide which is cleaved in the mature protein. More importantly, immunization with the recombinant Sip protein efficiently protected CD-1 mice against deadly challenges with six GBS strains of serotypes Ia/c, Ib, II/R, III, V, and VI. The data presented in this study suggest that this highly conserved protein induces cross-protective immunity against GBS infections and emphasize its potential as a universal vaccine candidate. PMID:10992461
PPCPs in Jiulong River estuary (China): Spatiotemporal distributions, fate, and their use as chemical markers of wastewater.

PubMed

Sun, Qian; Li, Yan; Li, Mingyue; Ashfaq, Muhammad; Lv, Min; Wang, Hongjie; Hu, Anyi; Yu, Chang-Ping

2016-05-01

The occurrence and fate of 50 pharmaceuticals and personal care products (PPCPs) were investigated in the surface water of Jiulong River estuary in the southeast of China in spring, wet season, summer, autumn and winter. Results demonstrated a wide distribution of PPCPs in Jiulong River estuary, where 34 PPCPs were detected at least once and 5 PPCPs were detected in all the samples, including caffeine, diclofenac, metoprolol, methyl paraben, and propyl paraben. Spatial and seasonal variations were observed. Special emphasis was placed on the PPCP fate in the estuary. Most PPCPs showed a non-conservative behavior in the estuary, while the non-steroidal anti-inflammatory drugs and bisphenol A showed a pseudo-conservative behavior. The non-conservative and pseudo-conservative behavior was attributed to the combination of the seawater dilution, the introduction of PPCPs via the sewage water, and the physical, chemical, or biological removal processes. Furthermore, PPCP concentrations showed drastic variations in the turbidity maximum zones. To our best knowledge, this is the first work to indicate the pseudo-conservative behavior of PPCPs in the estuary, and to show the drastic variations of PPCPs in the turbidity maximum zone. In addition, the ratio of labile to conservative PPCPs was calculated to track the source of untreated sewage contamination. Results showed a significantly higher ratio compared to the average value in WWTP effluents, indicating the ubiquitous discharge of untreated domestic wastewater in Jiulong River estuary. In addition, the high ratio of bisphenol A to conservative PPCPs implied the potential input of untreated industrial wastewater in Jiulong River estuary. Copyright © 2016 Elsevier Ltd. All rights reserved.
Evaluating Microbial Purification during Soil Treatment of Wastewater with Multicomponent Tracer and Surrogate Tests

USGS Publications Warehouse

Van Cuyk, S.; Siegrist, R.L.; Lowe, K.; Harvey, R.W.

2004-01-01

Soil treatment of wastewater has the potential to achieve high purification efficiency, yet the understanding and predictability of purification with respect to removal of viruses and other pathogens is limited. Research has been completed to quantify the removal of virus and bacteria through the use of microbial surrogates and conservative tracers during controlled experiments with three-dimensional pilot-scale soil treatment systems in the laboratory and during the testing of full-scale systems under field conditions. The surrogates and tracers employed included two viruses (MS-2 and PRID-1 bacteriophages), one bacterium (ice-nucleating active Pseudomonas), and one conservative tracer (bromide ion). Efforts have also been made to determine the relationship between viruses and fecal coliform bacteria in soil samples below the wastewater infiltrative surface, and the correlation between Escherichia coil concentrations measured in percolating soil solution as compared with those estimated from analyses of soil solids. The results suggest episodic breakthrough of virus and bacteria during soil treatment of wastewater and a 2 to 3 log (99-99.9%) removal of virus and near complete removal of fecal coliform bacteria during unsaturated flow through 60 to 90 cm of sandy medium. Results also suggest that the fate of fecal coliform bacteria may be indicative of that of viruses in soil media near the infiltrative surface receiving wastewater effluent. Concentrations of fecal coliform in percolating soil solution may be conservatively estimated from analysis of extracted soil solids.
The dark side of the ring: role of the DNA sliding surface of PCNA.

PubMed

De March, Matteo; De Biasio, Alfredo

2017-12-01

The proliferating cell nuclear antigen (PCNA) sliding clamp lies at the heart of the accurate duplication of eukaryotic genomes. While the outer surface of the PCNA ring interacts with polymerases and other factors, the role of the inner wall facing the DNA is elusive. Recent evidence shows that conserved basic residues in the PCNA central channel create a specific surface that recognizes the DNA backbone and enables the clamp to slide by rotationally tracking the DNA helix. The sliding surface can be modulated (i) through lysine acetylation, which triggers PCNA degradation during nucleotide excision repair (NER) and stimulates repair by homologous recombination (HR) or (ii) through binding of the protein factor p15 PAF , which turns off DNA lesion bypass. Thus, the inner surface of PCNA is unexpectedly highly regulated to control resistance to DNA damage. From a structural viewpoint, we reflect on these findings that open a new perspective on PCNA function and offer opportunities to develop tools to manipulate the DNA damage response in cancer treatment.
Fluid-structure interaction of turbulent boundary layer over a compliant surface

NASA Astrophysics Data System (ADS)

Anantharamu, Sreevatsa; Mahesh, Krishnan

2016-11-01

Turbulent flows induce unsteady loads on surfaces in contact with them, which affect material stresses, surface vibrations and far-field acoustics. We are developing a numerical methodology to study the coupled interaction of a turbulent boundary layer with the underlying surface. The surface is modeled as a linear elastic solid, while the fluid follows the spatially filtered incompressible Navier-Stokes equations. An incompressible Large Eddy Simulation finite volume flow approach based on the algorithm of Mahesh et al. is used in the fluid domain. The discrete kinetic energy conserving property of the method ensures robustness at high Reynolds number. The linear elastic model in the solid domain is integrated in space using finite element method and in time using the Newmark time integration method. The fluid and solid domain solvers are coupled using both weak and strong coupling methods. Details of the algorithm, validation, and relevant results will be presented. This work is supported by NSWCCD, ONR.
1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.
[Identification of marine and coastal biodiversity conservation priorities in Costa Rica].

PubMed

Alvarado, Juan José; Herrera, Bernal; Corrales, Lenin; Asch, Jenny; Paaby, Pía

2011-06-01

Costa Rica is recognized as one of the most diverse countries in species and ecosystems, in their terrestrial realm as well as in the marine. Besides this relevance, the country presents a delay on conservation and management of marine and coastal biodiversity, with respect to terrestrial. For 2006, the marine protected surface was 5,208.8 km2, with 331.5 km of coastline, in 20 protected areas. The country has made progress on the conservation priority sites identification for terrestrial and freshwater biodiversity, with few efforts on marine planning. This research presents the analysis and results of the gap identification process, for marine and coastal biodiversity conservation in the protected areas system of Costa Rica. The analysis was built with the spatial information available on the presence and distribution of coastal and marine biodiversity, the establishment of the conservation goals and a threat analysis over the ecological integrity of this biodiversity. The selection of high-priority sites was carried out using spatial optimization techniques and the superposition over the current shape of marine protected areas, in order to identify representation gaps. A total of 19,076 km2 of conservation gaps were indentified, with 1,323 km2 in the Caribbean and 17,753 km2 in the Pacific. Recommendations are aimed at planning and strengthening the marine protected areas system, using the gaps identified as a framework. It is expected that the results of this study would be the scientific base needed for planning and sustainable use of marine biodiversity in the country.
SPH non-Newtonian Model for Ice Sheet and Ice Shelf Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Pan, Wenxiao; Monaghan, Joseph J.

2012-07-07

We propose a new three-dimensional smoothed particle hydrodynamics (SPH) non-Newtonian model to study coupled ice sheet and ice shelf dynamics. Most existing ice sheet numerical models use a grid-based Eulerian approach, and are usually restricted to shallow ice sheet and ice shelf approximations of the momentum conservation equation. SPH, a fully Lagrangian particle method, solves the full momentum conservation equation. SPH method also allows modeling of free-surface flows, large material deformation, and material fragmentation without employing complex front-tracking schemes, and does not require re-meshing. As a result, SPH codes are highly scalable. Numerical accuracy of the proposed SPH model ismore » first verified by simulating a plane shear flow with a free surface and the propagation of a blob of ice along a horizontal surface. Next, the SPH model is used to investigate the grounding line dynamics of ice sheet/shelf. The steady position of the grounding line, obtained from our SPH simulations, is in good agreement with laboratory observations for a wide range of bedrock slopes, ice-to-fluid density ratios, and flux. We examine the effect of non-Newtonian behavior of ice on the grounding line dynamics. The non-Newtonian constitutive model is based on Glen's law for a creeping flow of a polycrystalline ice. Finally, we investigate the effect of a bedrock geometry on a steady-state position of the grounding line.« less
Consideration of magnetically-induced and conservative electric fields within a loaded gradient coil.

PubMed

Mao, Weihua; Chronik, Blaine A; Feldman, Rebecca E; Smith, Michael B; Collins, Christopher M

2006-06-01

We present a method to calculate the electric (E)-fields within and surrounding a human body in a gradient coil, including E-fields induced by the changing magnetic fields and "conservative" E-fields originating with the scalar electrical potential in the coil windings. In agreement with previous numerical calculations, it is shown that magnetically-induced E-fields within the human body show no real concentration near the surface of the body, where nerve stimulation most often occurs. Both the magnetically-induced and conservative E-fields are shown to be considerably stronger just outside the human body than inside it, and under some circumstances the conservative E-fields just outside the body can be much larger than the magnetically-induced E-fields there. The order of gradient winding and the presence of conductive RF shield can greatly affect the conservative E-field distribution in these cases. Though the E-fields against the outer surface of the body are not commonly considered, understanding gradient E-fields may be important for reasons other than peripheral nerve stimulation (PNS), such as potential interaction with electrical equipment. Copyright 2006 Wiley-Liss, Inc.
Water conservation and hydrological transitions in cities in the United States

NASA Astrophysics Data System (ADS)

Hornberger, George M.; Hess, David J.; Gilligan, Jonathan

2015-06-01

Cities across the world have had to diversify and expand their water supply systems in response to demand growth, groundwater depletion and pollution, and instability and inadequacy of regional surface freshwater sources. In the U.S., these problems plague not only the arid Western cities but increasingly also cities in the Eastern portions of the country. Although cities continue to seek out new sources of water via Promethean projects of long-distance supply systems, desalinization plants, and the recharge of aquifers with surface water, they also pursue water conservation because of its low cost and other benefits. We examine water conservation as a complex sociotechnical system comprising interactions of political, sociodemographic, economic, and hydroclimatological factors. We provide quantitative data on the factors that affect more and less advanced transitions in water conservation regimes, and we show that water stress and other hydrological data can only partially predict the transition. We also provide qualitative case studies to identify institutional and political barriers to more advanced water conservation regimes. This interdisciplinary, mixed methods approach typifies the need for knowledge that informs hydrologists about how their research may or may not be adopted by decision-makers.
Influence of Agricultural Practice on Surface Temperature

NASA Astrophysics Data System (ADS)

Czajkowski, K.; Ault, T.; Hayase, R.; Benko, T.

2006-12-01

Changes in land uses/covers can have a significant effect on the temperature of the Earth's surface. Agricultural fields exhibit a significant change in land cover within a single year and from year to year as different crops are planted. These changes in agricultural practices including tillage practice and crop type influence the energy budget as reflected in differences in surface temperature. In this project, Landsat 5 and 7 imagery were used to investigate the influence of crop type and tillage practice on surface temperature in Iowa and NW Ohio. In particular, the three crop rotation of corn, soybeans and wheat, as well as no-till, conservation tillage and tradition tillage methods, were investigated. Crop type and conservation tillage practices were identified using supervised classification. Student surface temperature observations from the GLOBE program were used to correct for the effects of the atmosphere for some of the satellite thermal observations. Students took surface temperature observations in field sites near there schools using hand- held infrared thermometers.
Conference Proceedings on Validation of Computational Fluid Dynamics. Volume 1. Symposium Papers and Round Table Discussion Held in Lisbon, Portugal on 2-5 May 1988

DTIC Science & Technology

1988-05-01

the representation of the shock, the non -conservative difference scheme in the original method being replaced by a ’ quasi - conservative’ operator 3...domain. In order to simulate the experimentally observed pressure distribution at the exit a formulation of the non -reflecting pressure condition Is used...and Experimental Aero- dynamics: Wing Surface Generator Code, Control Surface and Boundary Conditions". DFVLR IB 221-87 A 01, 1987. [11] Kordulla, W.(ed
Hijacking Complement Regulatory Proteins for Bacterial Immune Evasion.

PubMed

Hovingh, Elise S; van den Broek, Bryan; Jongerius, Ilse

2016-01-01

The human complement system plays an important role in the defense against invading pathogens, inflammation and homeostasis. Invading microbes, such as bacteria, directly activate the complement system resulting in the formation of chemoattractants and in effective labeling of the bacteria for phagocytosis. In addition, formation of the membrane attack complex is responsible for direct killing of Gram-negative bacteria. In turn, bacteria have evolved several ways to evade complement activation on their surface in order to be able to colonize and invade the human host. One important mechanism of bacterial escape is attraction of complement regulatory proteins to the microbial surface. These molecules are present in the human body for tight regulation of the complement system to prevent damage to host self-surfaces. Therefore, recruitment of complement regulatory proteins to the bacterial surface results in decreased complement activation on the microbial surface which favors bacterial survival. This review will discuss recent advances in understanding the binding of complement regulatory proteins to the bacterial surface at the molecular level. This includes, new insights that have become available concerning specific conserved motives on complement regulatory proteins that are favorable for microbial binding. Finally, complement evasion molecules are of high importance for vaccine development due to their dominant role in bacterial survival, high immunogenicity and homology as well as their presence on the bacterial surface. Here, the use of complement evasion molecules for vaccine development will be discussed.
Hijacking Complement Regulatory Proteins for Bacterial Immune Evasion

PubMed Central

Hovingh, Elise S.; van den Broek, Bryan; Jongerius, Ilse

2016-01-01

The human complement system plays an important role in the defense against invading pathogens, inflammation and homeostasis. Invading microbes, such as bacteria, directly activate the complement system resulting in the formation of chemoattractants and in effective labeling of the bacteria for phagocytosis. In addition, formation of the membrane attack complex is responsible for direct killing of Gram-negative bacteria. In turn, bacteria have evolved several ways to evade complement activation on their surface in order to be able to colonize and invade the human host. One important mechanism of bacterial escape is attraction of complement regulatory proteins to the microbial surface. These molecules are present in the human body for tight regulation of the complement system to prevent damage to host self-surfaces. Therefore, recruitment of complement regulatory proteins to the bacterial surface results in decreased complement activation on the microbial surface which favors bacterial survival. This review will discuss recent advances in understanding the binding of complement regulatory proteins to the bacterial surface at the molecular level. This includes, new insights that have become available concerning specific conserved motives on complement regulatory proteins that are favorable for microbial binding. Finally, complement evasion molecules are of high importance for vaccine development due to their dominant role in bacterial survival, high immunogenicity and homology as well as their presence on the bacterial surface. Here, the use of complement evasion molecules for vaccine development will be discussed. PMID:28066340
Neutral line chaos and phase space structure

NASA Technical Reports Server (NTRS)

Burkhart, Grant R.; Speiser, Theodore W.; Martin, Richard F., Jr.; Dusenbery, Paul B.

1991-01-01

Phase space structure and chaos near a neutral line are studied with numerical surface-of-section (SOS) techniques and analytic methods. Results are presented for a linear neutral line model with zero crosstail electric field. It was found that particle motion can be divided into three regimes dependening on the value of the conserved canonical momentum, Py, and the conserved Hamiltonian, h. The phase space structure, using Poincare SOS plots, is highly sensitive to bn = Bn/B0 variations, but not to h variations. It is verified that the slow motion preserves the action, Jz, as evaluated by Sonnerup (1971), when the period of the fast motion is smaller than the time scale of the slow motion. Results show that the phase space structure and particle chaos depend sensitively upon Py and bn, but are independent of h.
Identifying potential recommendation domains for conservation agriculture in Ethiopia, Kenya, and Malawi.

PubMed

Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

2015-02-01

Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km(2)) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5% of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21% of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.
Identifying Potential Recommendation Domains for Conservation Agriculture in Ethiopia, Kenya, and Malawi

NASA Astrophysics Data System (ADS)

Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

2015-02-01

Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km2) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5 % of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21 % of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.
Responses of predatory invertebrates to seeding density and plant species richness in experimental tallgrass prairie restorations

USGS Publications Warehouse

Nemec, Kristine T.; Allen, Craig R.; Danielson, Stephen D.; Helzer, Christopher J.

2014-01-01

In recent decades, agricultural producers and non-governmental organizations have restored thousands of hectares of former cropland in the central United States with native grasses and forbs. However, the ability of these grassland restorations to attract predatory invertebrates has not been well documented, even though predators provide an important ecosystem service to agricultural producers by naturally regulating herbivores. This study assessed the effects of plant richness and seeding density on the richness and abundance of surface-dwelling (ants, ground beetles, and spiders) and aboveground (ladybird beetles) predatory invertebrates. In the spring of 2006, twenty-four 55 m × 55 m-plots were planted to six replicates in each of four treatments: high richness (97 species typically planted by The Nature Conservancy), at low and high seeding densities, and low richness (15 species representing a typical Natural Resources Conservation Service Conservation Reserve Program mix, CP25), at low and high seeding densities. Ants, ground beetles, and spiders were sampled using pitfall traps and ladybird beetles were sampled using sweep netting in 2007–2009. The abundance of ants, ground beetles, and spiders showed no response to seed mix richness or seeding density but there was a significant positive effect of richness on ladybird beetle abundance. Seeding density had a significant positive effect on ground beetle and spider species richness and Shannon–Weaver diversity. These results may be related to differences in the plant species composition and relative amount of grass basal cover among the treatments rather than richness.

Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody.

PubMed

Cho, Ki Joon; Schepens, Bert; Seok, Jong Hyeon; Kim, Sella; Roose, Kenny; Lee, Ji-Hye; Gallardo, Rodrigo; Van Hamme, Evelien; Schymkowitz, Joost; Rousseau, Frederic; Fiers, Walter; Saelens, Xavier; Kim, Kyung Hyun

2015-04-01

The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Global direct pressures on biodiversity by large-scale metal mining: Spatial distribution and implications for conservation.

PubMed

Murguía, Diego I; Bringezu, Stefan; Schaldach, Rüdiger

2016-09-15

Biodiversity loss is widely recognized as a serious global environmental change process. While large-scale metal mining activities do not belong to the top drivers of such change, these operations exert or may intensify pressures on biodiversity by adversely changing habitats, directly and indirectly, at local and regional scales. So far, analyses of global spatial dynamics of mining and its burden on biodiversity focused on the overlap between mines and protected areas or areas of high value for conservation. However, it is less clear how operating metal mines are globally exerting pressure on zones of different biodiversity richness; a similar gap exists for unmined but known mineral deposits. By using vascular plants' diversity as a proxy to quantify overall biodiversity, this study provides a first examination of the global spatial distribution of mines and deposits for five key metals across different biodiversity zones. The results indicate that mines and deposits are not randomly distributed, but concentrated within intermediate and high diversity zones, especially bauxite and silver. In contrast, iron, gold, and copper mines and deposits are closer to a more proportional distribution while showing a high concentration in the intermediate biodiversity zone. Considering the five metals together, 63% and 61% of available mines and deposits, respectively, are located in intermediate diversity zones, comprising 52% of the global land terrestrial surface. 23% of mines and 20% of ore deposits are located in areas of high plant diversity, covering 17% of the land. 13% of mines and 19% of deposits are in areas of low plant diversity, comprising 31% of the land surface. Thus, there seems to be potential for opening new mines in areas of low biodiversity in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.
B cell recognition of the conserved HIV-1 co-receptor binding site is altered by endogenous primate CD4.

PubMed

Forsell, Mattias N E; Dey, Barna; Mörner, Andreas; Svehla, Krisha; O'dell, Sijy; Högerkorp, Carl-Magnus; Voss, Gerald; Thorstensson, Rigmor; Shaw, George M; Mascola, John R; Karlsson Hedestam, Gunilla B; Wyatt, Richard T

2008-10-03

The surface HIV-1 exterior envelope glycoprotein, gp120, binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process. The binding site is comprised of a highly conserved region on the gp120 core, as well as elements of the third variable region (V3). Antibodies against the co-receptor binding site are abundantly elicited during natural infection of humans, but the mechanism of elicitation has remained undefined. In this study, we investigate the requirements for elicitation of co-receptor binding site antibodies by inoculating rabbits, monkeys and human-CD4 transgenic (huCD4) rabbits with envelope glycoprotein (Env) trimers possessing high affinity for primate CD4. A cross-species comparison of the antibody responses showed that similar HIV-1 neutralization breadth was elicited by Env trimers in monkeys relative to wild-type (WT) rabbits. In contrast, antibodies against the co-receptor site on gp120 were elicited only in monkeys and huCD4 rabbits, but not in the WT rabbits. This was supported by the detection of high-titer co-receptor antibodies in all sera from a set derived from human volunteers inoculated with recombinant gp120. These findings strongly suggest that complexes between Env and (high-affinity) primate CD4 formed in vivo are responsible for the elicitation of the co-receptor-site-directed antibodies. They also imply that the naïve B cell receptor repertoire does not recognize the gp120 co-receptor site in the absence of CD4 and illustrate that conformational stabilization, imparted by primary receptor interaction, can alter the immunogenicity of a type 1 viral membrane protein.
Computational unsteady aerodynamics for lifting surfaces

NASA Technical Reports Server (NTRS)

Edwards, John W.

1988-01-01

Two dimensional problems are solved using numerical techniques. Navier-Stokes equations are studied both in the vorticity-stream function formulation which appears to be the optimal choice for two dimensional problems, using a storage approach, and in the velocity pressure formulation which minimizes the number of unknowns in three dimensional problems. Analysis shows that compact centered conservative second order schemes for the vorticity equation are the most robust for high Reynolds number flows. Serious difficulties remain in the choice of turbulent models, to keep reasonable CPU efficiency.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Lorente-Crespo, M.; Mateo-Segura, C., E-mail: C.Mateo-Segura@hw.ac.uk

Nanoantennas enhance the conversion between highly localized electromagnetic fields and far-field radiation. Here, we investigate the response of a nano-patch partially reflective surface backed with a silver mirror to an optical source embedded at the centre of the structure. Using full wave simulations, we demonstrate a two orders of magnitude increased directivity compared to the isotropic radiator, 50% power confinement to a 13.8° width beam and a ±16 nm bandwidth. Our antenna does not rely on plasmonic phenomena thus reducing non-radiative losses and conserving source coherence.
Modeling of technical soil-erosion control measures and its impact on soil erosion off-site effects within urban areas

NASA Astrophysics Data System (ADS)

Dostal, Tomas; Devaty, Jan

2013-04-01

The paper presents results of surface runoff, soil erosion and sediment transport modeling using Erosion 3D software - physically based mathematical simulation model, event oriented, fully distributed. Various methods to simulate technical soil-erosion conservation measures were tested, using alternative digital elevation models of different precision and resolution. Ditches and baulks were simulated by three different approaches, (i) by change of the land-cover parameters to increase infiltration and decrease flow velocity, (ii) by change of the land-cover parameters to completely infiltrate the surface runoff and (iii) by adjusting the height of the digital elevation model by "burning in" the channels of the ditches. Results show advantages and disadvantages of each approach and conclude suitable methods for combinations of particular digital elevation model and purpose of the simulations. Further on a set of simulations was carried out to model situations before and after technical soil-erosion conservation measures application within a small catchment of 4 km2. These simulations were focused on quantitative and qualitative assessment of technical soil-erosion control measures impact on soil erosion off-site effects within urban areas located downstream of intensively used agricultural fields. The scenarios were built upon a raster digital elevation model with spatial resolution of 3 meters derived from LiDAR 5G vector point elevation data. Use of this high-resolution elevation model allowed simulating the technical soil-erosion control measures by direct terrain elevation adjustment. Also the structures within the settlements were emulated by direct change in the elevation of the terrain model. The buildings were lifted up to simulate complicated flow behavior of the surface runoff within urban areas, using approach of Arévalo (Arévalo, 2011) but focusing on the use of commonly available data without extensive detailed editing. Application of the technical soil-erosion control measures induced strong change in overall amount of eroded/deposited material as well as spatial erosion/deposition patterns within the settlement areas. Validation of modeled scenarios and effects on measured data was not possible as no real runoff event was recorded in the target area so the conclusions were made by comparing the different modeled scenarios. Advantages and disadvantages of used approach to simulate technical soil-erosion conservation measures are evaluated and discussed as well as the impact of use of high-resolution elevation data on the intensity and spatial distribution of soil erosion and deposition. Model approved ability to show detailed distribution of damages over target urban area, which is very sensitive for off-site effects of surface runoff, soil erosion and sediment transport and also high sensitivity to input data, especially to DEM, which affects surface runoff pattern and therefore intensity of harmful effects. Acknowledgement: This paper has been supported by projects: Ministry of the interior of the CR VG 20122015092, and project NAZV QI91C008 TPEO.
Low-stringency selection of TEM1 for BLIP shows interface plasticity and selection for faster binders

PubMed Central

Cohen-Khait, Ruth; Schreiber, Gideon

2016-01-01

Protein–protein interactions occur via well-defined interfaces on the protein surface. Whereas the location of homologous interfaces is conserved, their composition varies, suggesting that multiple solutions may support high-affinity binding. In this study, we examined the plasticity of the interface of TEM1 β-lactamase with its protein inhibitor BLIP by low-stringency selection of a random TEM1 library using yeast surface display. Our results show that most interfacial residues could be mutated without a loss in binding affinity, protein stability, or enzymatic activity, suggesting plasticity in the interface composition supporting high-affinity binding. Interestingly, many of the selected mutations promoted faster association. Further selection for faster binders was achieved by drastically decreasing the library–ligand incubation time to 30 s. Preequilibrium selection as suggested here is a novel methodology for specifically selecting faster-associating protein complexes. PMID:27956635
Surface temperatures in New York City: Geospatial data enables the accurate prediction of radiative heat transfer.

PubMed

Ghandehari, Masoud; Emig, Thorsten; Aghamohamadnia, Milad

2018-02-02

Despite decades of research seeking to derive the urban energy budget, the dynamics of thermal exchange in the densely constructed environment is not yet well understood. Using New York City as a study site, we present a novel hybrid experimental-computational approach for a better understanding of the radiative heat transfer in complex urban environments. The aim of this work is to contribute to the calculation of the urban energy budget, particularly the stored energy. We will focus our attention on surface thermal radiation. Improved understanding of urban thermodynamics incorporating the interaction of various bodies, particularly in high rise cities, will have implications on energy conservation at the building scale, and for human health and comfort at the urban scale. The platform presented is based on longwave hyperspectral imaging of nearly 100 blocks of Manhattan, in addition to a geospatial radiosity model that describes the collective radiative heat exchange between multiple buildings. Despite assumptions in surface emissivity and thermal conductivity of buildings walls, the close comparison of temperatures derived from measurements and computations is promising. Results imply that the presented geospatial thermodynamic model of urban structures can enable accurate and high resolution analysis of instantaneous urban surface temperatures.
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.

PubMed

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-10-01

Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

PubMed Central

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-01-01

Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains. PMID:18828911
Rhenium in seawater - Confirmation of generally conservative behavior

NASA Technical Reports Server (NTRS)

Anbar, A. D.; Creaser, R. A.; Papanastassiou, D. A.; Wasserburg, G. J.

1992-01-01

A depth profile of the concentration of Re was measured in the Pacific Ocean using a technique developed for the clean chemical separation and the precise measurement of Re by isotope dilution and negative thermal ionization mass spectrometry (ID-NTIMS). We obtain a narrow range for Re from 7.20 +/- 0.03 to 7.38 +/- 0.03 ng/kg for depths between 45 m and 4700 m. This demonstrates that Re is relatively well mixed throughout the water column and confirms the theoretical prediction that the behavior of Re in the oceans is conservative. When examined in detail, both salinity and the concentration of Re increase by approximately 1.5 percent between 400 and 4700 m, a correlation consistent with conservative behavior. However, Re appears to be depleted relative to salinity by 1.0-1.5 percent at 100 m, and enriched by approximately 4 percent at the surface. These observations suggest a minor level of Re scavenging in near surface waters, and an input of Re to the ocean surface. This work demonstrates the utility of geochemical investigations of certain trace elements not previously been amenable to detailed study.
Thermobaricity, cabbeling, and water-mass conversion

NASA Astrophysics Data System (ADS)

McDougall, Trevor J.

1987-05-01

The efficient mixing of heat and salt along neutral surfaces (by mesoscale eddies) is shown to lead to vertical advection through these neutral surfaces. This is due to the nonlinearities of the equation of state of seawater through terms like ∂2ρ/∂θ∂p (thermobaric effect) and ∂2ρ/∂ θ2 (cabbeling). Cabbeling always causes a sinking or downwelling of fluid through neutral surfaces, whereas thermobaricity can lead to a vertical velocity (relative to neutral surfaces) of either sign. In this paper it is shown that for reasonable values of the lateral scalar diffusivity (especially below a depth of 1000 m), these two processes cause vertical velocities of the order of 10-7 m s-1 through neutral surfaces (usually downward!) and cause water-mass conversion of a magnitude equal to that caused by a vertical diffusivity of 10-4 m2 s-1 (often equivalent to a negative diffusivity). Both thermobaricity and cabbeling can occur in the presence of any nonzero amount of small-scale turbulence and so will not be detected by microstructure measurements. The conservation equations for tracers are considered in a nonorthogonal coordinate frame that moves with neutral surfaces in the ocean. Since only mixing processes cause advection across neutral surfaces, it is useful to regard this vertical advection as a symptom of various mixing processes rather than as a separate physical process. It is possible to derive conservative equations for scalars that do not contain the vertical advective term explicity. In these conservation equations, the terms that represent mixing processes are substantially altered. It is argued that this form of the conservation equations is the most appropriate when considering water-mass transformation, and some examples are given of its application in the North Atlantic. It is shown that the variation of the vertical diffusivity with height does not cause water-mass transformation. Also, salt fingering is often 3-4 times more effective at changing the potential temperature of a water mass than would be implied by simply calculating the vertical derivative of the fingering heat flux.
Ground-Water Flow, 2004-07, and Water Quality, 1992-2007, in McBaine Bottoms, Columbia, Missouri

USGS Publications Warehouse

Smith, Brenda Joyce; Richards, Joseph M.

2008-01-01

The U.S. Geological Survey, in cooperation with the city of Columbia, Missouri, and the Missouri Department of Conservation, collected ground-water quality data, surface-water quality data, and water-level data in McBaine Bottoms, southwest of Columbia. McBaine Bottoms, adjacent to the Missouri River, is the location of the municipal-supply well field for the city of Columbia, the city of Columbia wastewater-treatment wetlands, and the Missouri Department of Conservation Eagle Bluffs Conservation Area. This report describes the ground-water flow and water quality of McBaine Bottoms and provides information to better understand the interaction between treated effluent from the wetlands used on the Eagle Bluffs Conservation Area and the water in the alluvial aquifer that is pumped from the city of Columbia municipal-supply well field. Changes in major chemical constituent concentrations have been detected at several sampling sites between pre- and post-effluent application data. Analysis of post-effluent data indicates substantial changes in calcium, potassium, sodium, chloride, and sulfate concentrations in ground water. These changes became apparent shortly after the beginning of the operation of the wastewater-treatment wetland in 1994 and the formation of the Eagle Bluffs Conservation Area, which uses the treated effluent as a water source for the management of migratory water fowl. The changes have continued throughout the 15 years of sample collection. The concentrations of these major chemical constituents are on the mixing continuum between pre-effluent ground water as one end member and the treated wastewater effluent as the other end member. For monitoring wells that had changes in major chemical constituent concentrations, the relative percentage of treated effluent in the ground water, assuming chloride is conservative, ranged from 6 to 88 percent. Twenty-two monitoring wells throughout McBaine Bottoms have been affected by effluent based on chloride concentrations larger than 40 milligrams per liter. The chloride concentration of ground water in the alluvial aquifer reflects several sources, including precipitation, water from the Missouri River, water in the aquifer, and the treated effluent. Chloride concentrations from precipitation, the Missouri River, and water in the alluvial aquifer were less than 40 milligrams per liter. These monitoring wells affected by effluent are located in two general areas - adjacent to treatment wetland unit 1 and near the ground-water high on and north of the Eagle Bluffs Conservation Area. The probable source of the large chloride concentrations in well samples adjacent to treatment wetland unit 1 is leakage from the unit. The source for the large chloride concentrations in the other monitoring well samples is the effluent mixed with ground water and Missouri River water that is used to fill pools on the Eagle Bluffs Conservation Area. One monitoring well had a single sample with a chloride concentration larger than 40 milligrams per liter. That sample may have been affected by the use of road salt because of the presence of ice and snow immediately before the sample was collected. Lateral ground-water flow was dominated by the presence of a persistent ground-water high beneath the Eagle Bluffs Conservation Area and the presence of a cone of depression centered around the city of Columbia well field in the northern part of the study area. Ground-water flow was radially away from the apex of the ground-water high; west and south of the high, flow was toward the Missouri River, east of the high, flow was toward Perche Creek, and north of the high, flow was to the north toward the cone of depression around the city of Columbia well field. Another permanent feature on the water-level maps was a ground-water high beneath treatment wetland unit 1. Although the ground-water high was present throughout the study period, the subsurface expression of the high changed depending on hydrolo
Readings in Wildlife and Fish Conservation, High School Conservation Curriculum Project.

ERIC Educational Resources Information Center

Ensminger, Jack

This publication is a tentative edition of readings on Wildlife and Fish Conservation in Louisiana, and as such it forms part of one of the four units of study designed for an experimental high school course, the "High School Conservation Curriculum Project." The other three units are concerned with Forest Conervation, Soil and Water…
Surface-atmosphere decoupling limits accumulation at Summit, Greenland.

PubMed

Berkelhammer, Max; Noone, David C; Steen-Larsen, Hans Christian; Bailey, Adriana; Cox, Christopher J; O'Neill, Michael S; Schneider, David; Steffen, Konrad; White, James W C

2016-04-01

Despite rapid melting in the coastal regions of the Greenland Ice Sheet, a significant area (~40%) of the ice sheet rarely experiences surface melting. In these regions, the controls on annual accumulation are poorly constrained owing to surface conditions (for example, surface clouds, blowing snow, and surface inversions), which render moisture flux estimates from myriad approaches (that is, eddy covariance, remote sensing, and direct observations) highly uncertain. Accumulation is partially determined by the temperature dependence of saturation vapor pressure, which influences the maximum humidity of air parcels reaching the ice sheet interior. However, independent proxies for surface temperature and accumulation from ice cores show that the response of accumulation to temperature is variable and not generally consistent with a purely thermodynamic control. Using three years of stable water vapor isotope profiles from a high altitude site on the Greenland Ice Sheet, we show that as the boundary layer becomes increasingly stable, a decoupling between the ice sheet and atmosphere occurs. The limited interaction between the ice sheet surface and free tropospheric air reduces the capacity for surface condensation to achieve the rate set by the humidity of the air parcels reaching interior Greenland. The isolation of the surface also acts to recycle sublimated moisture by recondensing it onto fog particles, which returns the moisture back to the surface through gravitational settling. The observations highlight a unique mechanism by which ice sheet mass is conserved, which has implications for understanding both past and future changes in accumulation rate and the isotopic signal in ice cores from Greenland.
Surface-atmosphere decoupling limits accumulation at Summit, Greenland

PubMed Central

Berkelhammer, Max; Noone, David C.; Steen-Larsen, Hans Christian; Bailey, Adriana; Cox, Christopher J.; O’Neill, Michael S.; Schneider, David; Steffen, Konrad; White, James W. C.

2016-01-01

Despite rapid melting in the coastal regions of the Greenland Ice Sheet, a significant area (~40%) of the ice sheet rarely experiences surface melting. In these regions, the controls on annual accumulation are poorly constrained owing to surface conditions (for example, surface clouds, blowing snow, and surface inversions), which render moisture flux estimates from myriad approaches (that is, eddy covariance, remote sensing, and direct observations) highly uncertain. Accumulation is partially determined by the temperature dependence of saturation vapor pressure, which influences the maximum humidity of air parcels reaching the ice sheet interior. However, independent proxies for surface temperature and accumulation from ice cores show that the response of accumulation to temperature is variable and not generally consistent with a purely thermodynamic control. Using three years of stable water vapor isotope profiles from a high altitude site on the Greenland Ice Sheet, we show that as the boundary layer becomes increasingly stable, a decoupling between the ice sheet and atmosphere occurs. The limited interaction between the ice sheet surface and free tropospheric air reduces the capacity for surface condensation to achieve the rate set by the humidity of the air parcels reaching interior Greenland. The isolation of the surface also acts to recycle sublimated moisture by recondensing it onto fog particles, which returns the moisture back to the surface through gravitational settling. The observations highlight a unique mechanism by which ice sheet mass is conserved, which has implications for understanding both past and future changes in accumulation rate and the isotopic signal in ice cores from Greenland. PMID:27386509
Axial magnetic field and toroidally streaming fast ions in the dense plasma focus are natural consequences of conservation laws in the curved axisymmetric geometry of the current sheath. II. Towards a first principles theory

NASA Astrophysics Data System (ADS)

Auluck, S. K. H.

2017-11-01

This paper continues earlier discussion [S. K. H. Auluck, Phys. Plasmas 21, 102515 (2014)] concerning the formulation of conservation laws of mass, momentum, and energy in a local curvilinear coordinate system in the dense plasma focus. This formulation makes use of the revised Gratton-Vargas snowplow model [S. K. H. Auluck, Phys. Plasmas 20, 112501 (2013)], which provides an analytically defined imaginary surface in three dimensions which resembles the experimentally determined shape of the plasma. Unit vectors along the local tangent to this surface, along the azimuth, and along the local normal define a right-handed orthogonal local curvilinear coordinate system. The simplifying assumption that physical quantities have significant variation only along the normal enables writing laws of conservation of mass, momentum, and energy in the form of effectively one-dimensional hyperbolic conservation law equations using expressions for various differential operators derived for this coordinate system. This formulation demonstrates the highly non-trivial result that the axial magnetic field and toroidally streaming fast ions, experimentally observed by multiple prestigious laboratories, are natural consequences of conservation of mass, momentum, and energy in the curved geometry of the dense plasma focus current sheath. The present paper continues the discussion in the context of a 3-region shock structure similar to the one experimentally observed: an unperturbed region followed by a hydrodynamic shock containing some current followed by a magnetic piston. Rankine-Hugoniot conditions are derived, and expressions are obtained for the specific volumes and pressures using the mass-flux between the hydrodynamic shock and the magnetic piston and current fraction in the hydrodynamic shock as unknown parameters. For the special case of a magnetic piston that remains continuously in contact with the fluid being pushed, the theory gives closed form algebraic results for the fraction of current flowing in the hydrodynamic shock, specific volume, pressure, and fluid velocity of the hydrodynamic shock region, the tangential, normal, and azimuthal components of velocity in the magnetized plasma, the density of the magnetized plasma, the normal and tangential components of the magnetic field, and the tangential, normal, and azimuthal components of the electric field. This explains the occurrence of azimuthally streaming high energy deuterons experimentally observed by Frascati and Stuttgart. The expression derived for the azimuthal component of vector potential can serve as the basis for a proposed experimental test of the theory.
Vaccination against Neisseria meningitidis using three variants of the lipoprotein GNA1870.

PubMed

Masignani, Vega; Comanducci, Maurizio; Giuliani, Marzia Monica; Bambini, Stefania; Adu-Bobie, Jeannette; Arico, Beatrice; Brunelli, Brunella; Pieri, Alessandro; Santini, Laura; Savino, Silvana; Serruto, Davide; Litt, David; Kroll, Simon; Welsch, Jo Anne; Granoff, Dan M; Rappuoli, Rino; Pizza, Mariagrazia

2003-03-17

Sepsis and meningitis caused by serogroup B meningococcus are devastating diseases of infants and young adults, which cannot yet be prevented by vaccination. By genome mining, we discovered GNA1870, a new surface-exposed lipoprotein of Neisseria meningitidis that induces high levels of bactericidal antibodies. The antigen is expressed by all strains of N. meningitidis tested. Sequencing of the gene in 71 strains representative of the genetic and geographic diversity of the N. meningitidis population, showed that the protein can be divided into three variants. Conservation within each variant ranges between 91.6 to 100%, while between the variants the conservation can be as low as 62.8%. The level of expression varies between strains, which can be classified as high, intermediate, and low expressors. Antibodies against a recombinant form of the protein elicit complement-mediated killing of the strains that carry the same variant and induce passive protection in the infant rat model. Bactericidal titers are highest against those strains expressing high yields of the protein; however, even the very low expressors are efficiently killed. The novel antigen is a top candidate for the development of a new vaccine against meningococcus.
A comparison of three approaches for simulating fine-scale surface winds in support of wildland fire management. Part II. An exploratory study of the effect of simulated winds on fire growth simulations

Treesearch

Jason M. Forthofer; Bret W. Butler; Charles W. McHugh; Mark A. Finney; Larry S. Bradshaw; Richard D. Stratton; Kyle S. Shannon; Natalie S. Wagenbrenner

2014-01-01

The effect of fine-resolution wind simulations on fire growth simulations is explored. The wind models are (1) a wind field consisting of constant speed and direction applied everywhere over the area of interest; (2) a tool based on the solution of the conservation of mass only (termed mass-conserving model) and (3) a tool based on a solution of conservation of mass...
18 CFR 8.1 - Publication of license conditions relating to recreation.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., reservoir water surface elevations, minimum water releases or rates of change of water releases and such... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Publication of license conditions relating to recreation. 8.1 Section 8.1 Conservation of Power and Water Resources FEDERAL ENERGY...

77 FR 35377 - Dolores Water Conservancy District; Notice of Completing Preliminary Permit Application Accepted...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-13

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Project No. 14328-000] Dolores Water... Comments and Motions To Intervene On May 10, 2012, Dolores Water Conservancy District, Colorado, filed an... (RCC) or embankment dam, with a total storage capacity of 8,000 acre-feet and a water surface area of...
Differential sequence diversity at merozoite surface protein-1 locus of Plasmodium knowlesi from humans and macaques in Thailand.

PubMed

Putaporntip, Chaturong; Thongaree, Siriporn; Jongwutiwes, Somchai

2013-08-01

To determine the genetic diversity and potential transmission routes of Plasmodium knowlesi, we analyzed the complete nucleotide sequence of the gene encoding the merozoite surface protein-1 of this simian malaria (Pkmsp-1), an asexual blood-stage vaccine candidate, from naturally infected humans and macaques in Thailand. Analysis of Pkmsp-1 sequences from humans (n=12) and monkeys (n=12) reveals five conserved and four variable domains. Most nucleotide substitutions in conserved domains were dimorphic whereas three of four variable domains contained complex repeats with extensive sequence and size variation. Besides purifying selection in conserved domains, evidence of intragenic recombination scattering across Pkmsp-1 was detected. The number of haplotypes, haplotype diversity, nucleotide diversity and recombination sites of human-derived sequences exceeded that of monkey-derived sequences. Phylogenetic networks based on concatenated conserved sequences of Pkmsp-1 displayed a character pattern that could have arisen from sampling process or the presence of two independent routes of P. knowlesi transmission, i.e. from macaques to human and from human to humans in Thailand. Copyright © 2013 Elsevier B.V. All rights reserved.
Mixing behavior of chromophoric dissolved organic matter in the Pearl River Estuary in spring

NASA Astrophysics Data System (ADS)

Lei, Xia; Pan, Jiayi; Devlin, Adam T.

2018-02-01

Mixing behavior of chromophoric dissolved organic matter (CDOM) in the Pearl River Estuary (PRE) and relevant hydrodynamic parameters such as horizontal transport and vertical mixing are identified and discussed based on a set of sampling data obtained during a cruise in May 2014. Using a theoretical conservative mixing model, the surface CDOM in the PRE in spring is classified into two groups by the CDOM absorption-spectral slope relationship (a(300) vs S(275-295)): First, terrigenous CDOM under a non-conservative mixing condition, and removal processes such as photobleaching are suggested to happen; second, marine CDOM behaves conservatively during mixing. The mixing of CDOM at the bottom is shown to be conservative. Controlled by the two-layer gravitational circulation in the PRE, the northern and western estuary shows higher CDOM absorption and lower spectral slope than the southern and eastern estuary, and the surface CDOM presents higher absorption and lower spectral slope than the bottom. Horizontal transport is hypothesized to be the dominant hydrodynamic mechanism affecting CDOM variation and mixing behavior in the PRE, while the vertical mixing has less influence.
The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook.

PubMed

Stanger, Frédéric V; de Beer, Tjaart A P; Dranow, David M; Schirmer, Tilman; Phan, Isabelle; Dehio, Christoph

2017-01-03

The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Bartonella effector proteins (Beps) during protein transfer into host cells infected by pathogenic Bartonella species. Furthermore, BID domains of Beps have often evolved secondary effector functions within host cells. Here, we provide crystal structures for three representative BID domains and describe a novel conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. The conserved hydrophobic core provides a rigid scaffold to a surface that, despite a few conserved exposed residues and similarities in charge distribution, displays significant variability. We propose that the genuine function of BID domains as T4S signal may primarily depend on their rigid structure, while the plasticity of their surface may facilitate adaptation to secondary effector functions. Copyright © 2016 Elsevier Ltd. All rights reserved.
Fabrication of TEOS/PDMS/F127 hybrid coating materials for conservation of historic stone sculptures

NASA Astrophysics Data System (ADS)

Liu, Yurong; Liu, Jia

2016-08-01

The present work was aimed to develop a new kind of stone conservation materials (TEOS/PDMS/F127 hybrid coating) by a facile sol-gel method for the protection of decayed sandstones of Chongqing Dazu stone sculptures in China. The hydrophobic property, surface morphology, water vapor permeability, ultraviolet aging resistance and mechanical properties were measured to evaluate the effectiveness of TEOS/PDMS/F127 hybrid coating as a stone conservation material. The results showed that the addition of hydroxyl-terminated polydimethylsiloxane (PDMS-OH) contributed to improve the hydrophobic properties and incorporation of PEO-PPO-PEO (F127) surfactant resulted in the formation of superficial protrusions with micro- and nanoscopic structures and overall alteration of surface morphology and roughness, thus preventing the coating materials from cracking. After treatment with TEOS/PDMS/F127 hybrid coating materials, the ultraviolet aging resistance and mechanical properties of stone were also improved without the obvious effects on the breathability and color of the stone, indicating promising applications of TEOS/PDMS/F127 hybrid coating materials for conservation of historic stone sculptures.
A convergent series expansion for hyperbolic systems of conservation laws

NASA Technical Reports Server (NTRS)

Harabetian, E.

1985-01-01

The discontinuities piecewise analytic initial value problem for a wide class of conservation laws is considered which includes the full three-dimensional Euler equations. The initial interaction at an arbitrary curved surface is resolved in time by a convergent series. Among other features the solution exhibits shock, contact, and expansion waves as well as sound waves propagating on characteristic surfaces. The expansion waves correspond to he one-dimensional rarefactions but have a more complicated structure. The sound waves are generated in place of zero strength shocks, and they are caused by mismatches in derivatives.
Structural and Functional Studies Indicate That the EPEC Effector, EspG, Directly Binds p21-Activated Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Germane, Katherine L.; Spiller, Benjamin W.

2011-09-20

Bacterial pathogens secrete effectors into their hosts that subvert host defenses and redirect host processes. EspG is a type three secretion effector with a disputed function that is found in enteropathogenic Escherichia coli. Here we show that EspG is structurally similar to VirA, a Shigella virulence factor; EspG has a large, conserved pocket on its surface; EspG binds directly to the amino-terminal inhibitory domain of human p21-activated kinase (PAK); and mutations to conserved residues in the surface pocket disrupt the interaction with PAK.
Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

PubMed Central

Madaoui, Hocine; Guerois, Raphaël

2008-01-01

Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein–protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein–protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. PMID:18511568
Atlantic Leatherback Migratory Paths and Temporary Residence Areas

PubMed Central

López-Mendilaharsu, Milagros; Miller, Philip; Domingo, Andrés; Evans, Daniel; Kelle, Laurent; Plot, Virginie; Prosdocimi, Laura; Verhage, Sebastian; Gaspar, Philippe; Georges, Jean-Yves

2010-01-01

Background Sea turtles are long-distance migrants with considerable behavioural plasticity in terms of migratory patterns, habitat use and foraging sites within and among populations. However, for the most widely migrating turtle, the leatherback turtle Dermochelys coriacea, studies combining data from individuals of different populations are uncommon. Such studies are however critical to better understand intra- and inter-population variability and take it into account in the implementation of conservation strategies of this critically endangered species. Here, we investigated the movements and diving behaviour of 16 Atlantic leatherback turtles from three different nesting sites and one foraging site during their post-breeding migration to assess the potential determinants of intra- and inter-population variability in migratory patterns. Methodology/Principal Findings Using satellite-derived behavioural and oceanographic data, we show that turtles used Temporary Residence Areas (TRAs) distributed all around the Atlantic Ocean: 9 in the neritic domain and 13 in the oceanic domain. These TRAs did not share a common oceanographic determinant but on the contrary were associated with mesoscale surface oceanographic features of different types (i.e., altimetric features and/or surface chlorophyll a concentration). Conversely, turtles exhibited relatively similar horizontal and vertical behaviours when in TRAs (i.e., slow swimming velocity/sinuous path/shallow dives) suggesting foraging activity in these productive regions. Migratory paths and TRAs distribution showed interesting similarities with the trajectories of passive satellite-tracked drifters, suggesting that the general dispersion pattern of adults from the nesting sites may reflect the extent of passive dispersion initially experienced by hatchlings. Conclusions/Significance Intra- and inter-population behavioural variability may therefore be linked with initial hatchling drift scenarios and be highly influenced by environmental conditions. This high degree of behavioural plasticity in Atlantic leatherback turtles makes species-targeted conservation strategies challenging and stresses the need for a larger dataset (>100 individuals) for providing general recommendations in terms of conservation. PMID:21085472
Predicting drought propagation within peat layers using a three dimensionally explicit voxel based model

NASA Astrophysics Data System (ADS)

Condro, A. A.; Pawitan, H.; Risdiyanto, I.

2018-05-01

Peatlands are very vulnerable to widespread fires during dry seasons, due to availability of aboveground fuel biomass on the surface and belowground fuel biomass on the sub-surface. Hence, understanding drought propagation occurring within peat layers is crucial with regards to disaster mitigation activities on peatlands. Using a three dimensionally explicit voxel-based model of peatland hydrology, this study predicted drought propagation time lags into sub-surface peat layers after drought events occurrence on the surface of about 1 month during La-Nina and 2.5 months during El-Nino. The study was carried out on a high-conservation-value area of oil palm plantation in West Kalimantan. Validity of the model was evaluated and its applicability for disaster mitigation was discussed. The animations of simulated voxels are available at: goo.gl/HDRMYN (El-Nino 2015 episode) and goo.gl/g1sXPl (La-Nina 2016 episode). The model is available at: goo.gl/RiuMQz.
A modeling study of methane hydrate decomposition in contact with the external surface of zeolites.

PubMed

Smirnov, Konstantin S

2017-08-30

The behavior of methane hydrate (MH) enclosed between the (010) surfaces of the silicalite-1 zeolite was studied by means of molecular dynamics simulations at temperatures of 150 and 250 K. Calculations reveal that the interaction with the hydrophilic surface OH groups destabilizes the clathrate structure of hydrate. While MH mostly conserves the structure in the simulation at the low temperature, thermal motion at the high temperature breaks the fragilized cages of H-bonded water molecules, thus leading to the release of methane. The dissociation proceeds in a layer-by-layer manner starting from the outer parts of the MH slab until complete hydrate decomposition. The released CH 4 molecules are absorbed by the microporous solid, whereas water is retained at the surfaces of hydrophobic silicalite and forms a meniscus in the interlayer space. Methane uptake reaches 70% of the silicalite sorption capacity. The energy necessary for the endothermic MH dissociation is supplied by the exothermic methane absorption by the zeolite.
Wild-type and 'a' epitope variants in chronic hepatitis B virus carriers positive for hepatitis B surface antigen and antibody.

PubMed

Mesenas, Steven J; Chow, Wan C; Zhao, Yi; Lim, Gek K; Oon, Chong J; Ng, Han S

2002-02-01

This study aims to examine the genomic variants of the 'a' epitope in chronic hepatitis B virus (HBV) carriers positive for both hepatitis B surface antigen (HBsAg) and antibody to HBsAg (anti-HBs). Eighteen HBV carriers were studied. Hepatitis B virus (HBV) DNA was extracted and the 'a' epitope region was amplified and sequenced. Eighteen Chinese asymptomatic HBV carriers were studied. There were 13 patients who were positive for both HBsAg and anti-HBs. Of these, one patient had only wild-type HBV, three had a viral mixture, and five had only 'a' epitope variant HBV. Of the three patients with a viral mixture, all had variants in the less conserved region (123-137). Of the five patients with pure HBsAg mutants, three had variants in the less conserved region while two had variants in the highly conserved region. In this study with a limited number of patients, the serum alanine aminotransferase (ALT) levels were higher in patients with wild-type HBV, compared with those with either 'a' epitope variants or a viral mixture consisting of wild type and variants. Eight of the nine (89%) patients positive for both HBsAg and anti-HBs harbored an 'a' epitope variant. The lower ALT levels seen in patients who had either pure 'a' epitope variant or a mixture of wild type and mutants suggest that a closer monitoring of these 'a' epitope variants should be required, as patients carrying these infectious viral strains may remain asymptomatic.
Genome-wide detection of conservative site-specific recombination in bacteria

PubMed Central

Mathias Garrett, Elizabeth; Camilli, Andrew

2018-01-01

The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria. One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to as conservative site-specific recombination. This phenomenon is known to occur in several bacterial lineages, however it remains notoriously difficult to identify due to the lack of conserved features. Here, we report an easy-to-implement method based on high-throughput paired-end sequencing for genome-wide detection of conservative site-specific recombination on a single-nucleotide level. We demonstrate the effectiveness of the method by successfully detecting several novel inversion sites in an epidemic isolate of the enteric pathogen Clostridium difficile. Using an experimental approach, we validate the inversion potential of all detected sites in C. difficile and quantify their prevalence during exponential and stationary growth in vitro. In addition, we demonstrate that the master recombinase RecV is responsible for the inversion of some but not all invertible sites. Using a fluorescent gene-reporter system, we show that at least one gene from a two-component system located next to an invertible site is expressed in an on-off mode reminiscent of phase variation. We further demonstrate the applicability of our method by mining 209 publicly available sequencing datasets and show that conservative site-specific recombination is common in the bacterial realm but appears to be absent in some lineages. Finally, we show that the gene content associated with the inversion sites is diverse and goes beyond traditionally described surface components. Overall, our method provides a robust platform for detection of conservative site-specific recombination in bacteria and opens a new avenue for global exploration of this important phenomenon. PMID:29621238
Characterization of the Role of a Highly Conserved Sequence in ATP Binding Cassette Transporter G (ABCG) Family in ABCG1 Stability, Oligomerization, and Trafficking

PubMed Central

2013-01-01

ATP-binding cassette transporter G1 (ABCG1) mediates cholesterol and oxysterol efflux onto lipidated lipoproteins and plays an important role in macrophage reverse cholesterol transport. Here, we identified a highly conserved sequence present in the five ABCG transporter family members. The conserved sequence is located between the nucleotide binding domain and the transmembrane domain and contains five amino acid residues from Asn at position 316 to Phe at position 320 in ABCG1 (NPADF). We found that cells expressing mutant ABCG1, in which Asn316, Pro317, Asp319, and Phe320 in the conserved sequence were replaced with Ala simultaneously, showed impaired cholesterol efflux activity compared with wild type ABCG1-expressing cells. A more detailed mutagenesis study revealed that mutation of Asn316 or Phe 320 to Ala significantly reduced cellular cholesterol and 7-ketocholesterol efflux conferred by ABCG1, whereas replacement of Pro317 or Asp319 with Ala had no detectable effect. To confirm the important role of Asn316 and Phe320, we mutated Asn316 to Asp (N316D) and Gln (N316Q), and Phe320 to Ile (F320I) and Tyr (F320Y). The mutant F320Y showed the same phenotype as wild type ABCG1. However, the efflux of cholesterol and 7-ketocholesterol was reduced in cells expressing ABCG1 mutant N316D, N316Q, or F320I compared with wild type ABCG1. Further, mutations N316Q and F320I impaired ABCG1 trafficking while having no marked effect on the stability and oligomerization of ABCG1. The mutant N316Q and F320I could not be transported to the cell surface efficiently. Instead, the mutant proteins were mainly localized intracellularly. Thus, these findings indicate that the two highly conserved amino acid residues, Asn and Phe, play an important role in ABCG1-dependent export of cellular cholesterol, mainly through the regulation of ABCG1 trafficking. PMID:24320932
Model-based estimators of density and connectivity to inform conservation of spatially structured populations

USGS Publications Warehouse

Morin, Dana J.; Fuller, Angela K.; Royle, J. Andrew; Sutherland, Chris

2017-01-01

Conservation and management of spatially structured populations is challenging because solutions must consider where individuals are located, but also differential individual space use as a result of landscape heterogeneity. A recent extension of spatial capture–recapture (SCR) models, the ecological distance model, uses spatial encounter histories of individuals (e.g., a record of where individuals are detected across space, often sequenced over multiple sampling occasions), to estimate the relationship between space use and characteristics of a landscape, allowing simultaneous estimation of both local densities of individuals across space and connectivity at the scale of individual movement. We developed two model-based estimators derived from the SCR ecological distance model to quantify connectivity over a continuous surface: (1) potential connectivity—a metric of the connectivity of areas based on resistance to individual movement; and (2) density-weighted connectivity (DWC)—potential connectivity weighted by estimated density. Estimates of potential connectivity and DWC can provide spatial representations of areas that are most important for the conservation of threatened species, or management of abundant populations (i.e., areas with high density and landscape connectivity), and thus generate predictions that have great potential to inform conservation and management actions. We used a simulation study with a stationary trap design across a range of landscape resistance scenarios to evaluate how well our model estimates resistance, potential connectivity, and DWC. Correlation between true and estimated potential connectivity was high, and there was positive correlation and high spatial accuracy between estimated DWC and true DWC. We applied our approach to data collected from a population of black bears in New York, and found that forested areas represented low levels of resistance for black bears. We demonstrate that formal inference about measures of landscape connectivity can be achieved from standard methods of studying animal populations which yield individual encounter history data such as camera trapping. Resulting biological parameters including resistance, potential connectivity, and DWC estimate the spatial distribution and connectivity of the population within a statistical framework, and we outline applications to many possible conservation and management problems.
High-order central ENO finite-volume scheme for hyperbolic conservation laws on three-dimensional cubed-sphere grids

NASA Astrophysics Data System (ADS)

Ivan, L.; De Sterck, H.; Susanto, A.; Groth, C. P. T.

2015-02-01

A fourth-order accurate finite-volume scheme for hyperbolic conservation laws on three-dimensional (3D) cubed-sphere grids is described. The approach is based on a central essentially non-oscillatory (CENO) finite-volume method that was recently introduced for two-dimensional compressible flows and is extended to 3D geometries with structured hexahedral grids. Cubed-sphere grids feature hexahedral cells with nonplanar cell surfaces, which are handled with high-order accuracy using trilinear geometry representations in the proposed approach. Varying stencil sizes and slope discontinuities in grid lines occur at the boundaries and corners of the six sectors of the cubed-sphere grid where the grid topology is unstructured, and these difficulties are handled naturally with high-order accuracy by the multidimensional least-squares based 3D CENO reconstruction with overdetermined stencils. A rotation-based mechanism is introduced to automatically select appropriate smaller stencils at degenerate block boundaries, where fewer ghost cells are available and the grid topology changes, requiring stencils to be modified. Combining these building blocks results in a finite-volume discretization for conservation laws on 3D cubed-sphere grids that is uniformly high-order accurate in all three grid directions. While solution-adaptivity is natural in the multi-block setting of our code, high-order accurate adaptive refinement on cubed-sphere grids is not pursued in this paper. The 3D CENO scheme is an accurate and robust solution method for hyperbolic conservation laws on general hexahedral grids that is attractive because it is inherently multidimensional by employing a K-exact overdetermined reconstruction scheme, and it avoids the complexity of considering multiple non-central stencil configurations that characterizes traditional ENO schemes. Extensive numerical tests demonstrate fourth-order convergence for stationary and time-dependent Euler and magnetohydrodynamic flows on cubed-sphere grids, and robustness against spurious oscillations at 3D shocks. Performance tests illustrate efficiency gains that can be potentially achieved using fourth-order schemes as compared to second-order methods for the same error level. Applications on extended cubed-sphere grids incorporating a seventh root block that discretizes the interior of the inner sphere demonstrate the versatility of the spatial discretization method.
Supernova brightening from chameleon-photon mixing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burrage, C.

2008-02-15

Measurements of standard candles and measurements of standard rulers give an inconsistent picture of the history of the universe. This discrepancy can be explained if photon number is not conserved as computations of the luminosity distance must be modified. I show that photon number is not conserved when photons mix with chameleons in the presence of a magnetic field. The strong magnetic fields in a supernova mean that the probability of a photon converting into a chameleon in the interior of the supernova is high, this results in a large flux of chameleons at the surface of the supernova. Chameleonsmore » and photons also mix as a result of the intergalactic magnetic field. These two effects combined cause the image of the supernova to be brightened resulting in a model which fits both observations of standard candles and observations of standard rulers.« less
Melicope stonei, section Pelea (Rutaceae), a new species from Kaua‘i, Hawaiian Islands: with notes on its distribution, ecology, conservation status, and phylogenetic placement

PubMed Central

Wood, Kenneth R.; Appelhans, Marc S.; Wagner, Warren L.

2017-01-01

Abstract Melicope stonei K.R. Wood, Appelhans & W.L. Wagner (section Pelea, Rutaceae), a new endemic tree species from Kaua‘i, Hawaiian Islands, is described and illustrated with notes on its distribution, ecology, conservation status, and phylogenetic placement. The new species differs from its Hawaiian congeners by its unique combination of distinct carpels and ramiflorous inflorescences arising on stems below the leaves; plants monoecious; leaf blades (5–)8–30 × (4–)6–11 cm, with abaxial surface densely tomentose, especially along midribs; and very long petioles of up to 9 cm. Since its discovery in 1988, 94 individuals have been documented and are confined to a 1.5 km2 region of unique high canopy mesic forest. Melicope stonei represents a new Critically Endangered (CR) single island endemic species on Kaua‘i. PMID:29033653
Seabird diversity hotspot linked to ocean productivity in the Canary Current Large Marine Ecosystem

PubMed Central

Attrill, Martin J.; Becker, Peter H.; Egevang, Carsten; Furness, Robert W.; Grémillet, David; Kopp, Matthias; Lescroël, Amélie; Matthiopoulos, Jason; Peter, Hans-Ulrich; Phillips, Richard A.

2016-01-01

Upwelling regions are highly productive habitats targeted by wide-ranging marine predators and industrial fisheries. In this study, we track the migratory movements of eight seabird species from across the Atlantic; quantify overlap with the Canary Current Large Marine Ecosystem (CCLME) and determine the habitat characteristics that drive this association. Our results indicate the CCLME is a biodiversity hotspot for migratory seabirds; all tracked species and more than 70% of individuals used this upwelling region. Relative species richness peaked in areas where sea surface temperature averaged between 15 and 20°C, and correlated positively with chlorophyll a, revealing the optimum conditions driving bottom-up trophic effects for seabirds. Marine vertebrates are not confined by international boundaries, making conservation challenging. However, by linking diversity to ocean productivity, our research reveals the significance of the CCLME for seabird populations from across the Atlantic, making it a priority for conservation action. PMID:27531154
Melicope stonei, section Pelea (Rutaceae), a new species from Kaua'i, Hawaiian Islands: with notes on its distribution, ecology, conservation status, and phylogenetic placement.

PubMed

Wood, Kenneth R; Appelhans, Marc S; Wagner, Warren L

2017-01-01

Melicope stonei K.R. Wood, Appelhans & W.L. Wagner (section Pelea, Rutaceae), a new endemic tree species from Kaua'i, Hawaiian Islands, is described and illustrated with notes on its distribution, ecology, conservation status, and phylogenetic placement. The new species differs from its Hawaiian congeners by its unique combination of distinct carpels and ramiflorous inflorescences arising on stems below the leaves; plants monoecious; leaf blades (5-)8-30 × (4-)6-11 cm, with abaxial surface densely tomentose, especially along midribs; and very long petioles of up to 9 cm. Since its discovery in 1988, 94 individuals have been documented and are confined to a 1.5 km 2 region of unique high canopy mesic forest. Melicope stonei represents a new Critically Endangered (CR) single island endemic species on Kaua'i.

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family

PubMed Central

Sinha, Sangita; Rappu, Pekka; Lange, S. C.; Mäntsälä, Pekka; Zalkin, Howard; Smith, Janet L.

1999-01-01

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-Å crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins. PMID:10557275
Seabird diversity hotspot linked to ocean productivity in the Canary Current Large Marine Ecosystem.

PubMed

Grecian, W James; Witt, Matthew J; Attrill, Martin J; Bearhop, Stuart; Becker, Peter H; Egevang, Carsten; Furness, Robert W; Godley, Brendan J; González-Solís, Jacob; Grémillet, David; Kopp, Matthias; Lescroël, Amélie; Matthiopoulos, Jason; Patrick, Samantha C; Peter, Hans-Ulrich; Phillips, Richard A; Stenhouse, Iain J; Votier, Stephen C

2016-08-01

Upwelling regions are highly productive habitats targeted by wide-ranging marine predators and industrial fisheries. In this study, we track the migratory movements of eight seabird species from across the Atlantic; quantify overlap with the Canary Current Large Marine Ecosystem (CCLME) and determine the habitat characteristics that drive this association. Our results indicate the CCLME is a biodiversity hotspot for migratory seabirds; all tracked species and more than 70% of individuals used this upwelling region. Relative species richness peaked in areas where sea surface temperature averaged between 15 and 20°C, and correlated positively with chlorophyll a, revealing the optimum conditions driving bottom-up trophic effects for seabirds. Marine vertebrates are not confined by international boundaries, making conservation challenging. However, by linking diversity to ocean productivity, our research reveals the significance of the CCLME for seabird populations from across the Atlantic, making it a priority for conservation action. © 2016 The Authors.
Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation

NASA Astrophysics Data System (ADS)

Venter, Oscar; Sanderson, Eric W.; Magrach, Ainhoa; Allan, James R.; Beher, Jutta; Jones, Kendall R.; Possingham, Hugh P.; Laurance, William F.; Wood, Peter; Fekete, Balázs M.; Levy, Marc A.; Watson, James E. M.

2016-08-01

Human pressures on the environment are changing spatially and temporally, with profound implications for the planet's biodiversity and human economies. Here we use recently available data on infrastructure, land cover and human access into natural areas to construct a globally standardized measure of the cumulative human footprint on the terrestrial environment at 1 km2 resolution from 1993 to 2009. We note that while the human population has increased by 23% and the world economy has grown 153%, the human footprint has increased by just 9%. Still, 75% the planet's land surface is experiencing measurable human pressures. Moreover, pressures are perversely intense, widespread and rapidly intensifying in places with high biodiversity. Encouragingly, we discover decreases in environmental pressures in the wealthiest countries and those with strong control of corruption. Clearly the human footprint on Earth is changing, yet there are still opportunities for conservation gains.
Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation

PubMed Central

Venter, Oscar; Sanderson, Eric W.; Magrach, Ainhoa; Allan, James R.; Beher, Jutta; Jones, Kendall R.; Possingham, Hugh P.; Laurance, William F.; Wood, Peter; Fekete, Balázs M.; Levy, Marc A.; Watson, James E. M.

2016-01-01

Human pressures on the environment are changing spatially and temporally, with profound implications for the planet's biodiversity and human economies. Here we use recently available data on infrastructure, land cover and human access into natural areas to construct a globally standardized measure of the cumulative human footprint on the terrestrial environment at 1 km2 resolution from 1993 to 2009. We note that while the human population has increased by 23% and the world economy has grown 153%, the human footprint has increased by just 9%. Still, 75% the planet's land surface is experiencing measurable human pressures. Moreover, pressures are perversely intense, widespread and rapidly intensifying in places with high biodiversity. Encouragingly, we discover decreases in environmental pressures in the wealthiest countries and those with strong control of corruption. Clearly the human footprint on Earth is changing, yet there are still opportunities for conservation gains. PMID:27552116
The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD

NASA Astrophysics Data System (ADS)

Calmettes, Charles; Ing, Christopher; Buckwalter, Carolyn M.; El Bakkouri, Majida; Chieh-Lin Lai, Christine; Pogoutse, Anastassia; Gray-Owen, Scott D.; Pomès, Régis; Moraes, Trevor F.

2015-08-01

Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops.
Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.

PubMed

Mizutani, Kenji; Machida, Yoshitaka; Unzai, Satoru; Park, Sam-Yong; Tame, Jeremy R H

2004-04-20

The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.
Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies.

PubMed

Jones, Harrison G; Ritschel, Tina; Pascual, Gabriel; Brakenhoff, Just P J; Keogh, Elissa; Furmanova-Hollenstein, Polina; Lanckacker, Ellen; Wadia, Jehangir S; Gilman, Morgan S A; Williamson, R Anthony; Roymans, Dirk; van 't Wout, Angélique B; Langedijk, Johannes P; McLellan, Jason S

2018-03-01

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV.
Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies

PubMed Central

Jones, Harrison G.; Brakenhoff, Just P. J.; Furmanova-Hollenstein, Polina; Wadia, Jehangir S.; Gilman, Morgan S. A.; Roymans, Dirk

2018-01-01

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV. PMID:29509814
A study of the effectiveness of particulate cleaning protocols on intentionally contaminated niobium surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reece, Charles E.; Ciancio, Elizabeth J.; Keyes, Katharine A.

2009-11-01

Particulate contamination on the surface of SRF cavities limits their performance via the enhanced generation of field-emitted electrons. Considerable efforts are expended to actively clean and avoid such contamination on niobium surfaces. The protocols in active use have been developed via feedback from cavity testing. This approach has the risk of over-conservatively ratcheting an ever increasing complexity of methods tied to particular circumstances. A complementary and perhaps helpful approach is to quantitatively assess the effectiveness of candidate methods at removing intentional representative particulate contamination. Toward this end, we developed a standardized contamination protocol using water suspensions of Nb{sub 2}O{sub 5}more » and SS 316 powders applied to BCP’d surfaces of standardized niobium samples yielding particle densities of order 200 particles/mm{sup 2}. From these starting conditions, controlled application of high pressure water rinse, ultrasonic cleaning, or CO{sub 2} snow jet cleaning was applied and the resulting surfaces examined via SEM/scanning EDS with particle recognition software. Results of initial parametric variations of each will be reported.« less
The application of electrical conductivity as a tracer for hydrograph separation in urban catchments

USGS Publications Warehouse

Pellerin, B.A.; Wollheim, W.M.; Feng, X.; Vororsmarty, C.J.

2008-01-01

Two-component hydrograph separation was performed on 19 low-to-moderate intensity rainfall events in a 4.1-km2 urban watershed to infer the relative and absolute contribution of surface runoff (e.g. new water) to stormflow generation between 2001 and 2003. The electrical conductivity (EC) of water was used as a continuous and inexpensive tracer, with order of magnitude differences in precipitation (12-46 ??S/cm) and pre-event streamwater EC values (520-1297 ??S/cm). While new water accounted for most of the increased discharge during storms (61-117%), the contribution of new water to total discharge during events was typically lower (18-78%) and negatively correlated with antecedent stream discharge (r2 = 0??55, p < 0??01). The amount of new water was positively correlated with total rainfall (r2 = 0??77), but hydrograph separation results suggest that less than half (9-46%) of the total rainfall on impervious surfaces is rapidly routed to the stream channel as new water. Comparison of hydrograph separation results using non-conservative tracers (EC and Si) and a conservative isotopic tracer (??D) for two events showed similar results and highlighted the potential application of EC as an inexpensive, high frequency tracer for hydrograph separation studies in urban catchments. The use of a simple tracer-based approach may help hydrologists and watershed managers to better understand impervious surface runoff, stormflow generation and non-point-source pollutant loading to urban streams. Copyright ?? 2007 John Wiley & Sons, Ltd.
Alaska at the Crossroads of Migration: Space Based Ornithology

NASA Technical Reports Server (NTRS)

Deppe, Jill; Wessels, Konrad; Smith, James A.

2007-01-01

Understanding bird migration on a global scale is one of the most compelling and challenging problems of modern biology with major implications for human health and conservation biology. Revolutionary advances in remote sensing now provide us with near real-time measurements of atmospheric and land surface conditions at high spatial resolution over entire continents. We use spatially-explicit, individual based bird migration models driven by numerical weather prediction models of atmospheric conditions, dynamic habitat suitability maps derived from remotely sensed land surface conditions, biophysiological models, and biological field data to simulate migration routes, timing, energy budgets, and survival of individual birds and populations. Long-distance migratory birds travel annually between breeding grounds in Alaska and wintering grounds in Latin Amierica. Approximately 25% of these species are potential vectors of Avian Influenza. Alaska is at the crossroads of Asian and New World migratory flyways and is likely to be a point of introduction of Asian H5N1 AI into the western hemisphere. If/when an infected bird is detected, a pressing question will be where was this bird several days ago, and where is it likely to go after it was released from the survey site? Answers to such questions will increase effectiveness of AI surveillance and mitigation measures. From a conservation perspective, Alaska's diverse landscape provides breeding sites for many migrants, and climatic and land surface changes along migratory flyways in the western hemisphere may reduce bird survival and physical condition upon arrival at Alaskan breeding territories, success and migrant populations.
Improving Water Quality With Conservation Buffers

NASA Astrophysics Data System (ADS)

Lowrance, R.; Dabney, S.; Schultz, R.

2003-12-01

Conservation buffer technologies are new approaches that need wider application. In-field buffer practices work best when used in combination with other buffer types and other conservation practices. Vegetative barriers may be used in combination with edge-of-field buffers to protect and improve their function and longevity by dispersing runoff and encouraging sediment deposition upslope of the buffer. It's important to understand how buffers can be managed to help reduce nutrient transport potential for high loading of nutrients from manure land application sites, A restored riparian wetland buffer retained or removed at least 59 percent of the nitrogen and 66 percent of the phosphorus that entered from an adjacent manure land application site. The Bear Creek National Restoration Demonstration Watershed project in Iowa has been the site of riparian forest buffers and filter strips creation; constructed wetlands to capture tile flow; stream-bank bioengineering; in-stream structures; and controlling livestock grazing. We need field studies that test various widths of buffers of different plant community compositions for their efficacy in trapping surface runoff, reducing nonpoint source pollutants in subsurface waters, and enhancing the aquatic ecosystem. Research is needed to evaluate the impact of different riparian grazing strategies on channel morphology, water quality, and the fate of livestock-associated pathogens and antibiotics. Integrating riparian buffers and other conservation buffers into these models is a key objective in future model development.
Conservation genetics of high elevation five-needle white pines

Treesearch

Andrew D. Bower; Sierra C. McLane; Andrew Eckert; Stacy Jorgensen; Anna Schoettle; Sally Aitken

2011-01-01

Conservation genetics examines the biophysical factors influencing genetic processes and uses that information to conserve and maintain the evolutionary potential of species and populations. Here we review published and unpublished literature on the conservation genetics of seven North American high-elevation five-needle pines. Although these species are widely...
A (2+1)-dimensional Korteweg-de Vries type equation in water waves: Lie symmetry analysis; multiple exp-function method; conservation laws

NASA Astrophysics Data System (ADS)

Adem, Abdullahi Rashid

2016-05-01

We consider a (2+1)-dimensional Korteweg-de Vries type equation which models the shallow-water waves, surface and internal waves. In the analysis, we use the Lie symmetry method and the multiple exp-function method. Furthermore, conservation laws are computed using the multiplier method.
Economic impacts on irrigated agriculture of water conservation programs in drought

NASA Astrophysics Data System (ADS)

Ward, Frank A.

2014-01-01

This study analyzes vulnerability, impacts, and adaptability by irrigation to drought.It accounts for economic incentives affecting choices on irrigation technology, crop mix, and water sources.When surface water supplies fall, farmers increase pumping, even when pumping raises production costs.Conservation program subsidies raise the value of food production but can increase crop water depletions.
Literature review of giant gartersnake (Thamnophis gigas) biology and conservation

USGS Publications Warehouse

Halstead, Brian J.; Wylie, Glenn D.; Casazza, Michael L.

2015-08-03

This report reviews the available literature on giant gartersnakes (Thamnophis gigas) to compile existing information on this species and identify knowledge gaps that, if addressed, would help to inform conservation efforts for giant gartersnakes. Giant gartersnakes comprise a species of semi-aquatic snake precinctive to wetlands in the Central Valley of California. The diversion of surface water and conversion of wetlands to agricultural and other land uses resulted in the loss of more than 90 percent of natural giant gartersnake habitats. Because of this habitat loss, giant gartersnakes are now listed by the United States and California Endangered Species Acts as Threatened. Most extant populations occur in the rice-growing regions of the Sacramento Valley, which comprises the northern portion of the giant gartersnake’s former range. The huge demand for water in California for agriculture, industry, recreation, and other human consumption, combined with periodic severe drought, places remaining giant gartersnake habitats at increased risk of degradation and loss. This literature review summarizes the available information on giant gartersnake distribution, habitat relations, behavior, demography, and other aspects of its biology relevant to conservation. This information is then compiled into a graphical conceptual model that indicates the importance of different aspects of giant gartersnake biology for maintaining positive population growth, and identifies those areas for which important information relevant for conservation is lacking. Directing research efforts toward these aspects of giant gartersnake ecology will likely result in improvements to conserving this unique species while meeting the high demands for water in California.
A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melcher, Karsten; Ng, Ley-Moy; Zhou, X Edward

2010-01-12

Abscisic acid (ABA) is a ubiquitous hormone that regulates plant growth, development and responses to environmental stresses. Its action is mediated by the PYR/PYL/RCAR family of START proteins, but it remains unclear how these receptors bind ABA and, in turn, how hormone binding leads to inhibition of the downstream type 2C protein phosphatase (PP2C) effectors. Here we report crystal structures of apo and ABA-bound receptors as well as a ternary PYL2-ABA-PP2C complex. The apo receptors contain an open ligand-binding pocket flanked by a gate that closes in response to ABA by way of conformational changes in two highly conserved β-loopsmore » that serve as a gate and latch. Moreover, ABA-induced closure of the gate creates a surface that enables the receptor to dock into and competitively inhibit the PP2C active site. A conserved tryptophan in the PP2C inserts directly between the gate and latch, which functions to further lock the receptor in a closed conformation. Together, our results identify a conserved gate-latch-lock mechanism underlying ABA signalling.« less
The Evolutionary Pattern of Glycosylation Sites in Influenza Virus (H5N1) Hemagglutinin and Neuraminidase

PubMed Central

Chen, Wentian; Zhong, Yaogang; Qin, Yannan; Sun, Shisheng; Li, Zheng

2012-01-01

Two glycoproteins, hemagglutinin (HA) and neuraminidase (NA), on the surface of influenza viruses play crucial roles in transfaunation, membrane fusion and the release of progeny virions. To explore the distribution of N-glycosylation sites (glycosites) in these two glycoproteins, we collected and aligned the amino acid sequences of all the HA and NA subtypes. Two glycosites were located at HA0 cleavage sites and fusion peptides and were strikingly conserved in all HA subtypes, while the remaining glycosites were unique to their subtypes. Two to four conserved glycosites were found in the stalk domain of NA, but these are affected by the deletion of specific stalk domain sequences. Another highly conserved glycosite appeared at the top center of tetrameric global domain, while the others glycosites were distributed around the global domain. Here we present a detailed investigation of the distribution and the evolutionary pattern of the glycosites in the envelope glycoproteins of IVs, and further focus on the H5N1 virus and conclude that the glycosites in H5N1 have become more complicated in HA and less influential in NA in the last five years. PMID:23133677
The human footprint in Mexico: physical geography and historical legacies.

PubMed

González-Abraham, Charlotte; Ezcurra, Exequiel; Garcillán, Pedro P; Ortega-Rubio, Alfredo; Kolb, Melanie; Bezaury Creel, Juan E

2015-01-01

Using publicly available data on land use and transportation corridors we calculated the human footprint index for the whole of Mexico to identify large-scale spatial patterns in the anthropogenic transformation of the land surface. We developed a map of the human footprint for the whole country and identified the ecological regions that have most transformed by human action. Additionally, we analyzed the extent to which (a) physical geography, expressed spatially in the form of biomes and ecoregions, compared to (b) historical geography, expressed as the spatial distribution of past human settlements, have driven the patterns of human modification of the land. Overall Mexico still has 56% of its land surface with low impact from human activities, but these areas are not evenly distributed. The lowest values are on the arid north and northwest, and the tropical southeast, while the highest values run along the coast of the Gulf of Mexico and from there inland along an east-to-west corridor that follows the Mexican transversal volcanic ranges and the associated upland plateau. The distribution of low- and high footprint areas within ecoregions forms a complex mosaic: the generally well-conserved Mexican deserts have some highly transformed agro-industrial areas, while many well-conserved, low footprint areas still persist in the highly-transformed ecoregions of central Mexico. We conclude that the spatial spread of the human footprint in Mexico is both the result of the limitations imposed by physical geography to human development at the biome level, and, within different biomes, of a complex history of past civilizations and technologies, including the 20th Century demographic explosion but also the spatial pattern of ancient settlements that were occupied by the Spanish Colony.
The Human Footprint in Mexico: Physical Geography and Historical Legacies

PubMed Central

Ortega-Rubio, Alfredo; Kolb, Melanie; Bezaury Creel, Juan E.

2015-01-01

Using publicly available data on land use and transportation corridors we calculated the human footprint index for the whole of Mexico to identify large-scale spatial patterns in the anthropogenic transformation of the land surface. We developed a map of the human footprint for the whole country and identified the ecological regions that have most transformed by human action. Additionally, we analyzed the extent to which (a) physical geography, expressed spatially in the form of biomes and ecoregions, compared to (b) historical geography, expressed as the spatial distribution of past human settlements, have driven the patterns of human modification of the land. Overall Mexico still has 56% of its land surface with low impact from human activities, but these areas are not evenly distributed. The lowest values are on the arid north and northwest, and the tropical southeast, while the highest values run along the coast of the Gulf of Mexico and from there inland along an east-to-west corridor that follows the Mexican transversal volcanic ranges and the associated upland plateau. The distribution of low- and high footprint areas within ecoregions forms a complex mosaic: the generally well-conserved Mexican deserts have some highly transformed agro-industrial areas, while many well-conserved, low footprint areas still persist in the highly-transformed ecoregions of central Mexico. We conclude that the spatial spread of the human footprint in Mexico is both the result of the limitations imposed by physical geography to human development at the biome level, and, within different biomes, of a complex history of past civilizations and technologies, including the 20th Century demographic explosion but also the spatial pattern of ancient settlements that were occupied by the Spanish Colony. PMID:25803839

A quasi-3D wire approach to model pulmonary airflow in human airways.

PubMed

Kannan, Ravishekar; Chen, Z J; Singh, Narender; Przekwas, Andrzej; Delvadia, Renishkumar; Tian, Geng; Walenga, Ross

2017-07-01

The models used for modeling the airflow in the human airways are either 0-dimensional compartmental or full 3-dimensional (3D) computational fluid dynamics (CFD) models. In the former, airways are treated as compartments, and the computations are performed with several assumptions, thereby generating a low-fidelity solution. The CFD method displays extremely high fidelity since the solution is obtained by solving the conservation equations in a physiologically consistent geometry. However, CFD models (1) require millions of degrees of freedom to accurately describe the geometry and to reduce the discretization errors, (2) have convergence problems, and (3) require several days to simulate a few breathing cycles. In this paper, we present a novel, fast-running, and robust quasi-3D wire model for modeling the airflow in the human lung airway. The wire mesh is obtained by contracting the high-fidelity lung airway surface mesh to a system of connected wires, with well-defined radii. The conservation equations are then solved in each wire. These wire meshes have around O(1000) degrees of freedom and hence are 3000 to 25 000 times faster than their CFD counterparts. The 3D spatial nature is also preserved since these wires are contracted out of the actual lung STL surface. The pressure readings between the 2 approaches showed minor difference (maximum error = 15%). In general, this formulation is fast and robust, allows geometric changes, and delivers high-fidelity solutions. Hence, this approach has great potential for more complicated problems including modeling of constricted/diseased lung sections and for calibrating the lung flow resistances through parameter inversion. Copyright © 2016 John Wiley & Sons, Ltd.
Bidirectional Reflectance of a Macroscopically Flat, High-Albedo Particulate Surface: An Efficient Radiative Transfer Solution and Applications to Regoliths

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Zakharova, Nadia T.

1999-01-01

Many remote sensing applications rely on accurate knowledge of the bidirectional reflection function (BRF) of surfaces composed of discrete, randomly positioned scattering particles. Theoretical computations of BRFs for plane-parallel particulate layers are usually reduced to solving the radiative transfer equation (RTE) using one of existing exact or approximate techniques. Since semi-empirical approximate approaches are notorious for their low accuracy, violation of the energy conservation law, and ability to produce unphysical results, the use of numerically exact solutions of RTE has gained justified popularity. For example, the computation of BRFs for macroscopically flat particulate surfaces in many geophysical publications is based on the adding-doubling (AD) and discrete ordinate (DO) methods. A further saving of computer resources can be achieved by using a more efficient technique to solve the plane-parallel RTE than the AD and DO methods. Since many natural particulate surfaces can be well represented by the model of an optically semi-infinite, homogeneous scattering layer, one can find the BRF directly by solving the Ambartsumian's nonlinear integral equation using a simple iterative technique. In this way, the computation of the internal radiation field is avoided and the computer code becomes highly efficient and very accurate and compact. Furthermore, the BRF thus obtained fully obeys the fundamental physical laws of energy conservation and reciprocity. In this paper, we discuss numerical aspects and the computer implementation of this technique, examine the applicability of the Henyey-Greenstein phase function and the sigma-Eddington approximation in BRF and flux calculations, and describe sample applications demonstrating the potential effect of particle shape on the bidirectional reflectance of flat regolith surfaces. Although the effects of packing density and coherent backscattering are currently neglected, they can also be incorporated. The FORTRAN implementation of the technique is available on the World Wide Web, and can be applied to a wide range of remote sensing problems. BRF computations for undulated (macroscopically rough) surfaces are more complicated and often rely on time consuming Monte Carlo procedures. This approach is especially inefficient for optically thick, weakly absorbing media (e.g., snow and desert surfaces at visible wavelengths since a photon may undergo many internal scattering events before it exists the medium or is absorbed. However, undulated surfaces can often be represented as collections of locally flat tilted facets characterized by the BRF found from the traditional plane parallel RTE. In this way the MOnte Carlo procedure could be used only to evaluate the effects of surface shadowing and multiple surface reflections, thereby bypassing the time-consuming ray tracing inside the medium and providing a great savings of CPU time.
Rainfall simulation experiments to study sediment redistribution using rare earth element oxides as tracers under conventional and conservation agricultural practices

NASA Astrophysics Data System (ADS)

Tóth, Adrienn; Jakab, Gergely; Sipos, Péter; Karlik, Máté; Madarász, Balázs; Zacháry, Dóra; Szabó, Judit; Szalai, Zoltán

2017-04-01

Rare earth elements (REE) have very favourable characteristics for being ideal sediment tracers as they are characterised by strong binding to soil particles, low mobility, low background concentration in soils, environmental benignity, high analytical sensitivity and they can be detected relatively easily and inexpensively in soils. The group of REEs consist of 16 elements with similar chemical properties, but at the same time, they are clearly distinguishable enabling multiple tracking of sediment deriving from different parts of the studied area, as well as mapping redistribution processes by appropriate designing of subareas marked by different REEs. In this study, rainfall simulation experiments were carried out to compare the loss and redistribution of soil sediments in two plots under conventional and conservation agricultural practices. Five different rainfall intensities (up to 80 mm/h) were applied to both plots. Sources and pathways of sediments within the two plots were studied using REE-oxides as tracers. Approximately 1,000 mg/kg of Er2O3, Ho2O3 and Sm2O3 (calculated to the upper 1 cm of the soil) were dispersed to the soil surface with banded distribution; each transversal band covered the third of the surface are of the plots. Concentration of the REE-oxides in the sediment leaving the plots, and that of the surface soil before and after the experiment were analysed by X-Ray fluorescence spectrometry. Significant sediment losses were found for both plots after the experiments, with slightly different characteristics between the conventional and conservation ones. Highest difference in loss of added REEs was found in the upper third of the plots with 81 ± 19% in the conventional and 71 ± 21% in the conservation ones. These values have been equalized downwards with almost complete losses in the lower third of the plots (99 ± 2% and 97 ± 4%, respectively). Only very small part of the removed sediment has been accumulated in the lower parts of the plots, they rather mostly leaved the study area. These accumulation zones showed patchy distribution and could be characterized by slightly higher REE concentrations in the conservation plot. Also, large variances in the REE amounts removed from the study plots were found during the experiment with slight differences between the two plots. Thanks to the use of the REE tracers, information was received not only on the sediment amounts leaving the area due to the individual rainfall events but also on the source of them within the plot. Our data also suggest that differences between the conventional and conservation plots can be observed even in the short term. The authors are grateful to the support of the National Research, Development and Innovation Office (OTKA PD 112729). A. Tóth also thanks for the support of the János Bolyai Research Scholarship of the Hungarian Academy of Sciences.
RNA polymerase II conserved protein domains as platforms for protein-protein interactions

PubMed Central

García-López, M Carmen

2011-01-01

RNA polymerase II establishes many protein-protein interactions with transcriptional regulators to coordinate gene expression, but little is known about protein domains involved in the contact with them. We use a new approach to look for conserved regions of the RNA pol II of S. cerevisiae located at the surface of the structure of the complex, hypothesizing that they might be involved in the interaction with transcriptional regulators. We defined five different conserved domains and demonstrate that all of them make contact with transcriptional regulators. PMID:21922063
Computing 3-D steady supersonic flow via a new Lagrangian approach

NASA Technical Reports Server (NTRS)

Loh, C. Y.; Liou, M.-S.

1993-01-01

The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.
Diversity of the P2 protein among nontypeable Haemophilus influenzae isolates.

PubMed Central

Bell, J; Grass, S; Jeanteur, D; Munson, R S

1994-01-01

The genes for outer membrane protein P2 of four nontypeable Haemophilus influenzae strains were cloned and sequenced. The derived amino acid sequences were compared with the outer membrane protein P2 sequence from H. influenzae type b MinnA and the sequences of P2 from three additional nontypeable H. influenzae strains. The sequences were 76 to 94% identical. The sequences had regions with considerable variability separated by regions which were highly conserved. The variable regions mapped to putative surface-exposed loops of the protein. PMID:8188390
In silico identification of functional regions in proteins.

PubMed

Nimrod, Guy; Glaser, Fabian; Steinberg, David; Ben-Tal, Nir; Pupko, Tal

2005-06-01

In silico prediction of functional regions on protein surfaces, i.e. sites of interaction with DNA, ligands, substrates and other proteins, is of utmost importance in various applications in the emerging fields of proteomics and structural genomics. When a sufficient number of homologs is found, powerful prediction schemes can be based on the observation that evolutionarily conserved regions are often functionally important, typically, only the principal functionally important region of the protein is detected, while secondary functional regions with weaker conservation signals are overlooked. Moreover, it is challenging to unambiguously identify the boundaries of the functional regions. We present a new methodology, called PatchFinder, that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1) Assignment of conservation scores to each amino acid position on the protein surface. (2) Assignment of a score to each putative patch, based on its likelihood to be functionally important. The patch of maximum likelihood is considered to be the main functionally important region, and the search is continued for non-overlapping patches of secondary importance. We examined the accuracy of the method using the IGPS enzyme, the SH2 domain and a benchmark set of 112 proteins. These examples demonstrated that PatchFinder is capable of identifying both the main and secondary functional patches. The PatchFinder program is available at: http://ashtoret.tau.ac.il/~nimrodg/
Multiplexed Molecular Imaging of Fresh Tissue Surfaces Enabled by Convection-Enhanced Topical Staining with SERS-Coded Nanoparticles.

PubMed

Wang, Yu W; Doerksen, Josh D; Kang, Soyoung; Walsh, Daniel; Yang, Qian; Hong, Daniel; Liu, Jonathan T C

2016-10-01

There is a need for intraoperative imaging technologies to guide breast-conserving surgeries and to reduce the high rates of re-excision for patients in which residual tumor is found at the surgical margins during postoperative pathology analyses. Feasibility studies have shown that utilizing topically applied surface-enhanced Raman scattering (SERS) nanoparticles (NPs), in conjunction with the ratiometric imaging of targeted versus untargeted NPs, enables the rapid visualization of multiple cell-surface biomarkers of cancer that are overexpressed at the surfaces of freshly excised breast tissues. In order to reliably and rapidly perform multiplexed Raman-encoded molecular imaging of large numbers of biomarkers (with five or more NP flavors), an enhanced staining method has been developed in which tissue surfaces are cyclically dipped into an NP-staining solution and subjected to high-frequency mechanical vibration. This dipping and mechanical vibration (DMV) method promotes the convection of the SERS NPs at fresh tissue surfaces, which accelerates their binding to their respective biomarker targets. By utilizing a custom-developed device for automated DMV staining, this study demonstrates the ability to simultaneously image four cell-surface biomarkers of cancer at the surfaces of fresh human breast tissues with a mixture of five flavors of SERS NPs (four targeted and one untargeted control) topically applied for 5 min and imaged at a spatial resolution of 0.5 mm and a raster-scanned imaging rate of >5 cm 2 min -1 . © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Point Cloud Analysis for Conservation and Enhancement of Modernist Architecture

NASA Astrophysics Data System (ADS)

Balzani, M.; Maietti, F.; Mugayar Kühl, B.

2017-02-01

Documentation of cultural assets through improved acquisition processes for advanced 3D modelling is one of the main challenges to be faced in order to address, through digital representation, advanced analysis on shape, appearance and conservation condition of cultural heritage. 3D modelling can originate new avenues in the way tangible cultural heritage is studied, visualized, curated, displayed and monitored, improving key features such as analysis and visualization of material degradation and state of conservation. An applied research focused on the analysis of surface specifications and material properties by means of 3D laser scanner survey has been developed within the project of Digital Preservation of FAUUSP building, Faculdade de Arquitetura e Urbanismo da Universidade de São Paulo, Brazil. The integrated 3D survey has been performed by the DIAPReM Center of the Department of Architecture of the University of Ferrara in cooperation with the FAUUSP. The 3D survey has allowed the realization of a point cloud model of the external surfaces, as the basis to investigate in detail the formal characteristics, geometric textures and surface features. The digital geometric model was also the basis for processing the intensity values acquired by laser scanning instrument; this method of analysis was an essential integration to the macroscopic investigations in order to manage additional information related to surface characteristics displayable on the point cloud.
Biodegradation of artificial monolayers applied to water storages to reduce evaporative loss.

PubMed

Pittaway, P; Herzig, M; Stuckey, N; Larsen, K

2015-01-01

Repeat applications of an artificial monolayer to the interfacial boundary layer of large agricultural water storages during periods of high evaporative demand remains the most commercially feasible water conservation strategy. However, the interfacial boundary layer (or microlayer) is ecologically distinct from subsurface water, and repeat monolayer applications may adversely affect microlayer processes. In this study, the natural cleansing mechanisms operating within the microlayer were investigated to compare the biodegradability of two fatty alcohol (C16OH and C18OH) and one glycol ether (C18E1) monolayer compound. The C16OH and C18OH compounds were more susceptible to microbial degradation, but the C18E1 compound was most susceptible to indirect photodegradation. On clean water the surface pressure and evaporation reduction achieved with a compressed C18E1 monolayer was superior to the C18OH monolayer, but on brown water the surface pressure dropped rapidly. These results suggest artificial monolayers are readily degraded by the synergy between photo and microbial degradation. The residence time of C18OH and C18E1 monolayers on clear water is sufficient for cost-effective water conservation. However, the susceptibility of C18E1 to photodegradation indicates the application of this monolayer to brown water may not be cost-effective.
G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

PubMed Central

2016-01-01

Abstract Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G‐LoSA. G‐LoSA aligns protein local structures in a sequence order independent way and provides a GA‐score, a chemical feature‐based and size‐independent structure similarity score. Our benchmark validation shows the robust performance of G‐LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure‐centric comparative biology studies. In particular, G‐LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G‐LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer‐aided drug design. We hope that G‐LoSA can be a useful computational method for exploring interesting biological problems through large‐scale comparison of protein local structures and facilitating drug discovery research and development. G‐LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336
G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

PubMed

Lee, Hui Sun; Im, Wonpil

2016-04-01

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.
Summary of the Georgia Agricultural Water Conservation and Metering Program and evaluation of methods used to collect and analyze irrigation data in the middle and lower Chattahoochee and Flint River basins, 2004-2010

USGS Publications Warehouse

Torak, Lynn J.; Painter, Jaime A.

2011-01-01

Since receiving jurisdiction from the State Legislature in June 2003 to implement the Georgia Agricultural Water Conservation and Metering Program, the Georgia Soil and Water Conservation Commission (Commission) by year-end 2010 installed more than 10,000 annually read water meters and nearly 200 daily reporting, satellite-transmitted, telemetry sites on irrigation systems located primarily in southern Georgia. More than 3,000 annually reported meters and 50 telemetry sites were installed during 2010 alone. The Commission monitored rates and volumes of agricultural irrigation supplied by groundwater, surface-water, and well-to-pond sources to inform water managers on the patterns and amounts of such water use and to determine effective and efficient resource utilization. Summary analyses of 4 complete years of irrigation data collected from annually read water meters in the middle and lower Chattahoochee and Flint River basins during 2007-2010 indicated that groundwater-supplied fields received slightly more irrigation depth per acre than surface-water-supplied fields. Year 2007 yielded the largest disparity between irrigation depth supplied by groundwater and surface-water sources as farmers responded to severe-to-exceptional drought conditions with increased irrigation. Groundwater sources (wells and well-to-pond systems) outnumbered surface-water sources by a factor of five; each groundwater source applied a third more irrigation volume than surface water; and, total irrigation volume from groundwater exceeded that of surface water by a factor of 6.7. Metered irrigation volume indicated a pattern of low-to-high water use from northwest to southeast that could point to relations between agricultural water use, water-resource potential and availability, soil type, and crop patterns. Normalizing metered irrigation-volume data by factoring out irrigated acres allowed irrigation water use to be expressed as an irrigation depth and nearly eliminated the disparity between volumes of applied irrigation derived from groundwater and surface water. Analysis of per-acre irrigation depths provided a commonality for comparing irrigation practices across the entire range of field sizes in southern Georgia and indicated underreporting of irrigated acres for some systems. Well-to-pond systems supplied irrigation at depths similar to groundwater and can be combined with groundwater irrigation data for subsequent analyses. Average irrigation depths during 2010 indicated an increase from average irrigation depths during 2008 and 2009, most likely the result of relatively dry conditions during 2010 compared to conditions in 2008 and 2009. Geostatistical models facilitated estimation of irrigation water use for unmetered systems and demonstrated usefulness in redesigning the telemetry network. Geospatial analysis evaluated the ability of the telemetry network to represent annually reported water-meter data and presented an objective, unbiased method for revising the network.
Influence of Agricultural Operations on Dust Emission During the 1930a Dust Bowl, Baca County, CO, USA.

NASA Astrophysics Data System (ADS)

Hodges, A. T.; Bolles, K.; Forman, S. L.

2017-12-01

The drought that struck the U.S. Great Plains during the 1930s was one of the most intensedroughts in the region in the last millennium, spurring a major environmental and public healthcrisis. A prominent explanation for the cause of the "dust bowl" centers on the expansion ofagriculture and poor land management practices leading to widespread soil erosion. Thisprevalent hypothesis largely excludes the impacts of naturally occurring land surface processesthat contribute to eolian erosion and dust emissivity, particularly during periods of drought. Priorwork generally focuses on economic and sociological factors in agricultural decision-making forindividual fields or farms.This study utilizes early aerial photography collected by the Soil Conservation Service in 1936 ofBaca County, Colorado, to identify and quantify spatial relationships between geomorphicprocesses and anthropogenic activities impacting dust emission. From the holdings at theNational Archives, 25 photos covering 125 km2 scanned at 1200dpi are combined into acontinuous mosaic, and geo-referenced at RMSE 78.6 m2 . Detailed land cover analyses areundertaken in ArcGIS to classify uncultivated and cultivated surfaces; cultivated surfaces arefurther divided by surface agricultural operations in relation to erosion and dust emission (e.g.listing, contour furrows, terraces, circuitous plowing, listing, eolian transport, and fallow fieldswith and without vegetation). The classified surface is overlaid with National ResourceConservation Service surveys and Soil Conservation Service reconnaissance surveys of land useand erosion carried out in 1936 to infer to potential emissivity of a given cultivated surface. Inthis way, it becomes possible to evaluate human influence on dust emission in one of theworst-struck counties of the Dust Bowl and potentially identify other causative factors to thissignificant period in American history.
In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap)

PubMed Central

Wang, Aibing; Zhang, Lijie; Khayat, Reza

2016-01-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis. PMID:27902320
In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap).

PubMed

Wang, Naidong; Zhan, Yang; Wang, Aibing; Zhang, Lijie; Khayat, Reza; Yang, Yi

2016-12-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis.
High-resolution pattern of mangrove species distribution is controlled by surface elevation

NASA Astrophysics Data System (ADS)

Leong, Rick C.; Friess, Daniel A.; Crase, Beth; Lee, Wei Kit; Webb, Edward L.

2018-03-01

Mangrove vegetation species respond to multiple environmental gradients, and an enhanced understanding of how mangrove species are distributed across these gradients will facilitate conservation and management. Many environmental gradients correlate with tidal inundation; however small-scale inundation patterns resulting from microtopographical changes are difficult to capture empirically. In contrast, surface elevation is often a suitable, measurable and cost-effective proxy for inundation. This study investigated the relationships between species distribution and surface elevation in a mangrove forest in northwest Singapore. Through high-resolution land surveying, we developed a digital elevation model (DEM) and conducted a comprehensive survey of 4380 trees with a stem diameter ≥ 5 cm. A total of 15 species were encountered, and elevation envelopes were generated for 12. Species envelopes were distributed along an elevation continuum, with most species overlapping within the continuum. Spatial autocorrelation (SAC) was present for nine of the 15 species, and when taken into account, species ordering was modified across the elevation continuum. The presence of SAC strongly reinforces the need for research to control for SAC: classical spatial description of mangrove species distribution should be revised to account for ecological factors. This study suggests that (1) surface elevation applies strong controls on species distribution and (2) most mangroves at our study site have similar physiological tolerances.
L1-Based Approximations of PDEs and Applications

DTIC Science & Technology

2012-09-05

the analysis of the Navier-Stokes equations. The early versions of artificial vis- cosities being overly dissipative, the interest for these technique ...Guermond, and B. Popov. Stability analysis of explicit en- tropy viscosity methods for non-linear scalar conservation equations. Math. Comp., 2012... methods for solv- ing mathematical models of nonlinear phenomena such as nonlinear conservation laws, surface/image/data reconstruction problems
Watershed scale impacts of buffers and upland conservation practices on agrochemical delivery to streams

Treesearch

T.G. Franti; D.E. Eisenhauer; M.C. McCullough; L.M. Stahr; Mike G. Dosskey; D.D. Snow; R.F. Spalding; A.L. Boldt

2004-01-01

Conservation buffers are designed to reduce sediment and agrichemical runoff to surface water. Much is known about plot and field scale effectiveness of buffers; but little is known about their - watershed scale impact. Our objective was to estimate the watershed scale impact of grass buffers by comparing sediment and agrichemical losses from two adjacent 141 - 165...
77 FR 11785 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-28

... Conservation Program: Public Meeting and Availability of the Framework Document for High-Intensity Discharge...) is initiating the rulemaking and data collection process to consider establishing energy conservation... Policy and Conservation Act (EPCA) (42 U.S.C. 6291, et seq.; EPCA or ``the Act'') sets forth a variety of...

Mapping Vegetation Community Types in a Highly-Disturbed Landscape: Integrating Hiearchical Object-Based Image Analysis with Digital Surface Models

NASA Astrophysics Data System (ADS)

Snavely, Rachel A.

Focusing on the semi-arid and highly disturbed landscape of San Clemente Island, California, this research tests the effectiveness of incorporating a hierarchal object-based image analysis (OBIA) approach with high-spatial resolution imagery and light detection and range (LiDAR) derived canopy height surfaces for mapping vegetation communities. The study is part of a large-scale research effort conducted by researchers at San Diego State University's (SDSU) Center for Earth Systems Analysis Research (CESAR) and Soil Ecology and Restoration Group (SERG), to develop an updated vegetation community map which will support both conservation and management decisions on Naval Auxiliary Landing Field (NALF) San Clemente Island. Trimble's eCognition Developer software was used to develop and generate vegetation community maps for two study sites, with and without vegetation height data as input. Overall and class-specific accuracies were calculated and compared across the two classifications. The highest overall accuracy (approximately 80%) was observed with the classification integrating airborne visible and near infrared imagery having very high spatial resolution with a LiDAR derived canopy height model. Accuracies for individual vegetation classes differed between both classification methods, but were highest when incorporating the LiDAR digital surface data. The addition of a canopy height model, however, yielded little difference in classification accuracies for areas of very dense shrub cover. Overall, the results show the utility of the OBIA approach for mapping vegetation with high spatial resolution imagery, and emphasizes the advantage of both multi-scale analysis and digital surface data for accuracy characterizing highly disturbed landscapes. The integrated imagery and digital canopy height model approach presented both advantages and limitations, which have to be considered prior to its operational use in mapping vegetation communities.
Tillage impact on herbicide loss by surface runoff and lateral subsurface flow

USDA-ARS?s Scientific Manuscript database

There is worldwide interest in conservation tillage practices because they can reduce surface runoff, agrichemical, and sediment loss from farm fields. Since these practices typically increase infiltration, their use may increase subsurface transport of water-soluble contaminants. Thus, to assess lo...
The effect of heat acclimation on sweat microminerals: Artifact of surface contamination

USDA-ARS?s Scientific Manuscript database

Heat acclimation (HA) reportedly conveys conservation in sweat micromineral concentrations when sampled from arm sweat, but time course is unknown. The observation that comprehensive cleaning of the skin surface negates sweat micromineral reductions during prolonged sweating raises the question of w...
An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karpowich, Nathan K.; Song, Jinmei; Wang, Da-Neng

2016-06-13

ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein–substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface inmore » which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.« less
EBS7 is a plant-specific component of a highly conserved endoplasmic reticulum-associated degradation system in Arabidopsis

PubMed Central

Liu, Yidan; Zhang, Congcong; Wang, Dinghe; Su, Wei; Liu, Linchuan; Wang, Muyang; Li, Jianming

2015-01-01

Endoplasmic reticulum (ER)-associated degradation (ERAD) is an essential part of an ER-localized protein quality-control system for eliminating terminally misfolded proteins. Recent studies have demonstrated that the ERAD machinery is conserved among yeast, animals, and plants; however, it remains unknown if the plant ERAD system involves plant-specific components. Here we report that the Arabidopsis ethyl methanesulfonate-mutagenized brassinosteroid-insensitive 1 suppressor 7 (EBS7) gene encodes an ER membrane-localized ERAD component that is highly conserved in land plants. Loss-of-function ebs7 mutations prevent ERAD of brassinosteroid insensitive 1-9 (bri1-9) and bri1-5, two ER-retained mutant variants of the cell-surface receptor for brassinosteroids (BRs). As a result, the two mutant receptors accumulate in the ER and consequently leak to the plasma membrane, resulting in the restoration of BR sensitivity and phenotypic suppression of the bri1-9 and bri1-5 mutants. EBS7 accumulates under ER stress, and its mutations lead to hypersensitivity to ER and salt stresses. EBS7 interacts with the ER membrane-anchored ubiquitin ligase Arabidopsis thaliana HMG-CoA reductase degradation 1a (AtHrd1a), one of the central components of the Arabidopsis ERAD machinery, and an ebs7 mutation destabilizes AtHrd1a to reduce polyubiquitination of bri1-9. Taken together, our results uncover a plant-specific component of a plant ERAD pathway and also suggest its likely biochemical function. PMID:26371323
DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

PubMed

Kearney, Bradley M; Johnson, Christian W; Roberts, Daniel M; Swartz, Paul; Mattos, Carla

2014-02-06

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. Copyright © 2013 Elsevier Ltd. All rights reserved.
To what extent does urbanisation affect fragmented grassland functioning?

PubMed

van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

2015-03-15

Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban grassland fragments, as well as to determine the potential for the use of LFA in decision-making involving the conservation of grassland fragments. The results indicated that the occurrence, size and characteristics of vegetated patches, and especially the presence of litter abundances, were the main factors determining differences in the LFA indices. Furthermore, mowing resulted in the overall fine-scale biophysical indices being higher for some of the urban grassland fragments. This implied that it is not necessarily the influence of urbanisation entailing high or low resource conserving patchiness and patch quality, but rather the management practices associated with urban and exurban areas. Therefore, from a conservation point of view, the grassland fragments in the City of Potchefstroom are just as conservable (on a biophysical function level involving soil processes) than the more "natural" exurban grassland fragments. Copyright © 2014 Elsevier Ltd. All rights reserved.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Liscio, A.; CNISM and Dipartimento di Fisica, Universita di Roma Tre, Via Vasca Navale 84, 00146 Roma; Ruocco, A.

This paper deals with the mechanism of grazing incidence (e,2e) events from surfaces. Two different approaches are considered. In both cases, elastic scattering with the crystal lattice assists the inelastic collision; these two steps are coupled either coherently or incoherently. Experimental evidence is given that the 'coherent' approach reproduces better the cross section dependence on momentum transfer in the specific case of asymmetric kinematics at moderate electron energies. This model has allowed us to map out the band dispersion of the outermost valence states of highly oriented pyrolytic graphite and to measure the momentum distribution of {pi}-electron states without invokingmore » the contribution of reciprocal lattice vectors in the momentum conservation. Agreement between theory and experiment is satisfactory, though the presence of events where crystal momentum is reconstructed cannot be ruled out. These results, obtained with a significant reduction of the experiment duration by an implemented apparatus, show that reflection (e,2e) can be used to build up a momentum spectroscopy with high surface sensitivity.« less
Biomimetics: lessons from nature--an overview.

PubMed

Bhushan, Bharat

2009-04-28

Nature has developed materials, objects and processes that function from the macroscale to the nanoscale. These have gone through evolution over 3.8 Gyr. The emerging field of biomimetics allows one to mimic biology or nature to develop nanomaterials, nanodevices and processes. Properties of biological materials and surfaces result from a complex interplay between surface morphology and physical and chemical properties. Hierarchical structures with dimensions of features ranging from the macroscale to the nanoscale are extremely common in nature to provide properties of interest. Molecular-scale devices, superhydrophobicity, self-cleaning, drag reduction in fluid flow, energy conversion and conservation, high adhesion, reversible adhesion, aerodynamic lift, materials and fibres with high mechanical strength, biological self-assembly, antireflection, structural coloration, thermal insulation, self-healing and sensory-aid mechanisms are some of the examples found in nature that are of commercial interest. This paper provides a broad overview of the various objects and processes of interest found in nature and applications under development or available in the marketplace.
Surface-enhanced Raman spectroscopy studies of yellow organic dyestuffs and lake pigments in oil paint.

PubMed

Mayhew, Hannah E; Fabian, David M; Svoboda, Shelley A; Wustholz, Kristin L

2013-08-21

Identifying natural, organic dyes and pigments is important for the conservation, preservation, and historical interpretation of works of art. Although previous SERS studies have demonstrated high sensitivity and selectivity for red lake pigments using various pretreatment conditions, corresponding investigations of yellow lake pigments and paints are relatively sparse. Here, surface-enhanced Raman scattering (SERS) spectroscopy is used to identify a variety of yellow organic dyestuffs and lake pigments in oil paint. High-quality SERS spectra of yellow dyestuffs (i.e., turmeric, old fustic, Buckthorn berries) and corresponding paints could be obtained with or without sample pretreatment using microliter quantities of HCl and methanol at room temperature. However, the SERS spectra of yellow lake pigments (i.e., Stil de Grain, Reseda lake) and their corresponding oil paints were only observed upon sample pretreatment. Ultimately, we demonstrate a reliable sample treatment protocol for SERS-based identification of turmeric, old fustic, Buckthorn berries, Stil de Grain, and Reseda lake as well as for microscopic samples of the corresponding oil paints.
High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation

PubMed Central

Anandapadamanaban, Madhanagopal; Andresen, Cecilia; Helander, Sara; Ohyama, Yoshifumi; Siponen, Marina I.; Lundström, Patrik; Kokubo, Tetsuro; Ikura, Mitsuhiko; Moche, Martin; Sunnerhagen, Maria

2016-01-01

The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 when bound to yeast TBP, together with mutational data. The yTAF1-TAND1, which in itself acts as a transcriptional activator, binds into the DNA-binding TBP concave surface by presenting similar anchor residues to TBP as E. coli Mot1 but from a distinct structural scaffold. Furthermore, we show how yTAF1-TAND2 employs an aromatic and acidic anchoring pattern to bind a conserved yTBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides compelling insight into the competitive multiprotein TBP interplay critical to transcriptional regulation. PMID:23851461
High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.

PubMed

Anandapadamanaban, Madhanagopal; Andresen, Cecilia; Helander, Sara; Ohyama, Yoshifumi; Siponen, Marina I; Lundström, Patrik; Kokubo, Tetsuro; Ikura, Mitsuhiko; Moche, Martin; Sunnerhagen, Maria

2013-08-01

The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.
Evaporation of LOX under supercritical and subcritical conditions

NASA Technical Reports Server (NTRS)

Yang, A. S.; Hsieh, W. H.; Kuo, K. K.; Brown, J. J.

1993-01-01

The evaporation of LOX under supercritical and subcritical conditions was studied experimentally and theoretically. In experiments, the evaporation rate and surface temperature were measured for LOX strand vaporizing in helium environments at pressures ranging from 5 to 68 atmospheres. Gas sampling and chromatography analysis were also employed to profile the gas composition above the LOX surface for the purpose of model validation. A comprehensive theoretical model was formulated and solved numerically to simulate the evaporation process of LOX at high pressures. The model was based on the conservation equations of mass, momentum, energy, and species concentrations for a multicomponent system, with consideration of gravitational body force, solubility of ambient gases in liquid, and variable thermophysical properties. Good agreement between predictions and measured oxygen mole fraction profiles was obtained. The effect of pressure on the distribution of the Lewis number, as well as the effect of variable diffusion coefficient, were further examined to elucidate the high-pressure transport behavior exhibited in the LOX vaporization process.
Hydrostratigraphy of Tree Island Cores from Water Conservation Area 3

USGS Publications Warehouse

McNeill, Donald F.; Cunningham, Kevin J.

2003-01-01

Cores and borehole-geophysical logs collected on and around two tree islands in Water Conservation Area 3 have been examined to develop a stratigraphic framework for these ecosystems. Especially important is the potential for the exchange of ground water and surface water within these features. The hydrostratigraphic results from this study document the lithologic nature of the foundation of the tree islands, the distribution of porous intervals, the potential for paleotopographic influence on their formation, and the importance of low-permeability, subaerial-exposure horizons on the vertical exchange of ground water and surface water. Figure 1. Location of Tree Islands 3AS3 and 3BS1. [larger image] Results from this hydrostratigraphic study indicate that subtle differences occur in lithofacies and topography between the on-island and off-island subsurface geologic records. Specifics are described herein. Firstly, at both tree-island sites, the top of the limestone bedrock is slightly elevated beneath the head of the tree islands relative to the off-island core sites and the tail of the tree islands, which suggests that bedrock 'highs' acted as 'seeds' for the development of the tree islands of this study and possibly many others. Secondly, examination of the recovered core and the caliper logs tentatively suggest that the elevated limestone beneath the tree islands may have a preferentially more porous framework relative to limestone beneath the adjacent areas, possibly providing a ground-water-to-surface-water connection that sustains the tree island system. Finally, because the elevation of the top of the limestone bedrock at the head of Tree Island 3AS3 is slightly higher than the surrounding upper surface of the peat, and because the wetland peats have a lower hydraulic conductivity than the limestone bedrock (Miami Limestone and Fort Thompson Formation), it is possible that there is a head difference between surface water of the wetlands and the ground water in underlying limestone bedrock.
Stressed Watersheds in a Rainfall-Rich Region

NASA Astrophysics Data System (ADS)

Kastrinos, J. R.; Miles, O.; Pickering, N. B.

2016-12-01

Southern New England has ample rainfall and, in some years, snowmelt, to sustain reservoirs and aquifers that are used primarily for municipal water supplies and secondarily for industrial and agricultural needs. Despite the humid climate, however, many watersheds are considered stressed, particularly during the summer and early fall growing-season months due to the combined effect of evapotranspiration and increased demand for lawn irrigation and other seasonal, warm-weather uses. While per capita consumption is frequently the focus of water-conservation efforts, most high-stress areas are in population centers where concentrated demand exceeds recharge (to aquifers) or runoff (to surface water supplies) within the region's small watersheds (commonly 200 mi2 or less). The parameter depletion intensity, described by Konikow (2015) in a review of groundwater-depletion trends across the United States, is used to compare seasonal stress and changes in stress level in several watersheds in Massachusetts. Areas of stress follow patterns of high depletion intensity during the summer months when demand is high. This seasonal stress is exacerbated by inter-basin transfer of water or wastewater from a watershed. Examples will be presented of projects where streamflow impacts have been offset using tools including well optimization, water conservation, storm water recharge, and reductions of infiltration/inflow to utilities, pursuant to the state's Sustainable Water Management Initiative.
Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components

PubMed Central

Baumstummler, A; Lehmann, D; Janjic, N; Ochsner, UA

2014-01-01

Slow off-rate modified aptamer (SOMAmer) reagents were generated to several Staphylococcus aureus cell surface-associated proteins via SELEX with multiple modified DNA libraries using purified recombinant or native proteins. High-affinity binding agents with sub-nanomolar Kd's were obtained for staphylococcal protein A (SpA), clumping factors (ClfA, ClfB), fibronectin-binding proteins (FnbA, FnbB) and iron-regulated surface determinants (Isd). Further screening revealed several SOMAmers that specifically bound to Staph. aureus cells from all strains that were tested, but not to other staphylococci or other bacteria. SpA and ClfA SOMAmers proved useful for the selective capture and enrichment of Staph. aureus cells, as shown by culture and PCR, leading to improved limits of detection and efficient removal of PCR inhibitors. Detection of Staph. aureus cells was enhanced by several orders of magnitude when the bacterial cell surface was coated with SOMAmers followed by qPCR of the SOMAmers. Furthermore, fluorescence-labelled SpA SOMAmers demonstrated their utility as direct detection agents in flow cytometry. Significance and Impact of the Study Monitoring for microbial contamination of food, water, nonsterile products or the environment is typically based on culture, PCR or antibodies. Aptamers that bind with high specificity and affinity to well-conserved cell surface epitopes represent a promising novel type of reagents to detect bacterial cells without the need for culture or cell lysis, including for the capture and enrichment of bacteria present at low cell densities and for the direct detection via qPCR or fluorescent staining. PMID:24935714
Crystal structure at 2.8Å of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP-protein interactor (HIPPI)

PubMed Central

Niu, Qian; Ybe, Joel A.

2008-01-01

Summary Huntington’s disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of htt permits HIP-protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits Procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain (DED). Our 2.8 Å crystal structure of the HIP1 371-481 sub-fragment that includes F432 and K474 important for HIPPI binding is not a DED, but is a partially opened coiled-coil. The HIP1 371-481 model reveals a basic surface we hypothesize is suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R from different organisms, but are not conserved in the yeast homolog of HIP1, sla2p. We have modeled ∼85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (PDB code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a “U” shaped HIP1 molecule. PMID:18155047
Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koenigsberg, Andrea L.; Heldwein, Ekaterina E.; Sandri-Goldin, Rozanne M.

Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here,more » we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37. IMPORTANCEThe ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires detailed navigational charts in the form of their three-dimensional structures. Here, we determined the crystal structure of the N-terminal half of a conserved tegument protein, UL37, from HSV-1. This structure, along with our previously reported structure of the UL37 homolog from PRV, provides a much needed 3-dimensional template for the dissection of both conserved and virus-specific functions of UL37 in intracellular capsid trafficking.« less
50 CFR 660.716 - Surface hook-and-line fishery. [Reserved

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Surface hook-and-line fishery. [Reserved] 660.716 Section 660.716 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES...
50 CFR 660.716 - Surface hook-and-line fishery. [Reserved

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Surface hook-and-line fishery. [Reserved] 660.716 Section 660.716 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES...

Soil management and conservation: Irrigation: Methods

USDA-ARS?s Scientific Manuscript database

Irrigation applies water to soil to improve crop production. The three main methods of irrigation are surface, sprinkler and micro. Surface irrigation is used on 85% of the irrigated land in the world. It generally requires lower capital investment because the soil conveys water within the field, ra...
Molecular characterization of calreticulin from Anopheles stephensi midgut cells and functional assay of the recombinant calreticulin with Plasmodium berghei ookinetes.

PubMed

Borhani Dizaji, Nahid; Basseri, Hamid Reza; Naddaf, Saied Reza; Heidari, Mansour

2014-10-25

Transmission blocking vaccines (TBVs) that target the antigens on the midgut epithelium of Anopheles mosquitoes are among the promising tools for the elimination of the malaria parasite. Characterization and analysis of effective antigens is the first step to design TBVs. Calreticulin (CRT), a lectin-like protein, from Anopheles albimanus midgut, has shown antigenic features, suggesting a promising and novel TBV target. CRT is a highly conserved protein with similar features in vertebrates and invertebrates including anopheline. We cloned the full-length crt gene from malaria vector, Anopheles stephensi (AsCrt) and explored the interaction of recombinant AsCrt protein, expressed in a prokaryotic system (pGEX-6p-1), with surface proteins of Plasmodium berghei ookinetes by immunofluorescence assay. The cellular localization of AsCrt was determined using the baculovirus expression system. Sequence analysis of the whole cDNA of AsCrt revealed that AsCrt contains an ORF of 1221 bp. The amino acid sequence of AsCrt protein obtained in this study showed 64% homology with similar protein in human. The AsCrt shares the most common features of CRTs from other species. This gene encodes a 406 amino-acid protein with a molecular mass of 46 kDa, which contains a predicted 16 amino-acid signal peptides, conserved cysteine residues, a proline-rich region, and highly acidic C-terminal domain with endoplasmic reticulum retrieval sequence HDEL. The production of GST-AsCrt recombinant protein was confirmed by Western blot analysis using an antibody against the GST protein. The FITC-labeled GST-AsCrt exhibited a significant interaction with P. berghei ookinete surface proteins. Purified recombinant GST-AsCrt, labeled with FITC, displayed specific binding to the surface of P. berghei ookinetes in comparison with control. Moreover, the expression of AsCrt in baculovirus expression system indicated that AsCrt was localized on the surface of Sf9 cells. Our results suggest that AsCrt could be utilized as a potential target for future studies in TBV area for malaria control. Copyright © 2014 Elsevier B.V. All rights reserved.
Experimental and numerical study of spatter formation and composition change in fiber laser welding of aluminum alloy

NASA Astrophysics Data System (ADS)

Wu, Dongsheng; Hua, Xueming; Ye, Youxiong; Huang, Lijin; Li, Fang; Huang, Ye

2018-05-01

A laser welding experiment with glass is conducted to directly observe the keyhole behavior and spatter formation in fiber laser welding of aluminum alloy. A 3D model is developed to investigate the spatter formation and composition change. An additional conservation equation is introduced to describe the Mg element distribution, and the Mg element loss due to evaporation is also considered. Based on numerical and experimental results, it is found that the keyhole geometry in laser welding of aluminum alloy is different from that in laser welding of steel. There are three required steps for spatter formation around the keyhole. The high momentum of the molten metal, the high recoil pressure and vapor shear stress, and the low surface tension around the keyhole contribute to the easy formation of spatter. The in-homogeneous distribution of Mg element in the weld can be attributable to the continuous evaporation of Mg element at the top surface of keyhole rear, the upward flow of low Mg element region from the bottom of the keyhole to the top surface of keyhole rear along the fusion line, the collapse of the keyhole, and the ejection of spatters.
Hydrogeology and simulation of the effects of reclaimed-water application in west Orange and southeast Lake counties, Florida

USGS Publications Warehouse

O'Reilly, Andrew M.

1998-01-01

Wastewater reclamation and reuse has become increasingly popular as water agencies search for alternative water-supply and wastewater-disposal options. Several governmental agencies in central Florida currently use the land-based application of reclaimed water (wastewater that has been treated beyond secondary treatment) as a management alternative to surface-water disposal of wastewater. Water Conserv II, a water reuse project developed jointly by Orange County and the City of Orlando, began operation in December 1986. In 1995, the Water Conserv II facility distributed approximately 28 Mgal/d of reclaimed water for discharge to rapid-infiltration basins (RIBs) and for use as agricultural irrigation. The Reedy Creek Improvement District (RCID) began operation of RIBs in September 1990, and in 1995 these RIBs received approximately 6.7 Mgal/d of reclaimed water. Analyses of existing data and data collected during the course of this study were combined with ground-water flow modeling and particle-tracking analyses to develop a process-oriented evaluation of the regional effects of reclaimed water applied by Water Conserv II and the RCID RIBs on the hydrology of west Orange and southeast Lake Counties. The ground-water flow system beneath the study area is a multi-aquifer system that consists of a thick sequence of highly permeable carbonate rocks overlain by unconsolidated sediments. The hydrogeologic units are the unconfined surficial aquifer system, the intermediate confining unit, and the confined Floridan aquifer system, which consists of two major permeable zones, the Upper and Lower Floridan aquifers, separated by the less permeable middle semiconfining unit. Flow in the surficial aquifer system is dominated regionally by diffuse downward leakage to the Floridan aquifer system and is affected locally by lateral flow systems produced by streams, lakes, and spatial variations in recharge. Ground water generally flows laterally through the Upper Floridan aquifer aquifer to the north and east. Many of the lakes in the study area are landlocked because the mantled karst environment precludes a well developed network of surface-water drainage. The USGS three-dimensional ground-water flow model MODFLOW was used to simulate ground-water flow in the surficial and Floridan aquifer systems. A steady-state calibration to average 1995 conditions was performed by using a parameter estimation program to vary values of surficial aquifer system hydraulic conductivity, intermediate confining unit leakance, and Upper Floridan aquifer transmissivity. The calibrated model generally produced simulated water levels in close agreement with measured water levels and was used to simulate the hydrologic effects of reclaimed-water application under current (1995) and proposed future conditions. In 1995, increases of up to about 40 ft in the water table and less than 5 ft in the Upper Floridan aquifer potentiometric surface had occurred as a result of reclaimed-water application. The largest increases were under RIB sites. An average traveltime of 10 years at Water Conserv II and 7 years at the RCID RIBs was required for reclaimed water to move from the water table to the top of the Upper Floridan aquifer. Approximately 67 percent of the reclaimed water applied at the RCID RIB site recharged the Floridan aquifer system, whereas 33 percent discharged from the surficial aquifer system to surface-water features; 99 percent of the reclaimed water applied at Water Conserv II recharged the Floridan aquifer system, whereas only 1 percent discharged from the surficial aquifer system to surface-water features. The majority of reclaimed water applied at both facilities probably will ultimately discharge from the Floridan aquifer system outside the model boundaries. Proposed future conditions were assumed to consist of an additional 11.7 Mgal/d of reclaimed water distributed by the Water Conserv II and RCID facilities. Increases of up to about 20 ft in the water
Discrete exterior calculus discretization of incompressible Navier-Stokes equations over surface simplicial meshes

NASA Astrophysics Data System (ADS)

Mohamed, Mamdouh S.; Hirani, Anil N.; Samtaney, Ravi

2016-05-01

A conservative discretization of incompressible Navier-Stokes equations is developed based on discrete exterior calculus (DEC). A distinguishing feature of our method is the use of an algebraic discretization of the interior product operator and a combinatorial discretization of the wedge product. The governing equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. The discretization is then carried out by substituting with the corresponding discrete operators based on the DEC framework. Numerical experiments for flows over surfaces reveal a second order accuracy for the developed scheme when using structured-triangular meshes, and first order accuracy for otherwise unstructured meshes. By construction, the method is conservative in that both mass and vorticity are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step.
The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold

PubMed Central

Kamajaya, Aron; Kaiser, Jens; Lee, Jonas; Reid, Michelle; Rees, Douglas C.

2014-01-01

Summary Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a novel beta sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in Dehydrated Hereditary Stomatocytosis (DHS) patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. PMID:25242456
The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

PubMed

Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

2014-10-07

Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.
Ammonia volatilization from surface-applied poultry litter under conservation tillage management practices.

PubMed

Sharpe, R R; Schomberg, H H; Harper, L A; Endale, D M; Jenkins, M B; Franzluebbers, A J

2004-01-01

Land application of poultry litter can provide essential plant nutrients for crop production, but ammonia (NH(3)) volatilization from the litter can be detrimental to the environment. A multiseason study was conducted to quantify NH(3) volatilization rates from surface-applied poultry litter under no-till and paraplowed conservation tillage managements. Litter was applied to supply 90 to 140 kg N ha(-1). Evaluation of NH(3) volatilization was determined using gas concentrations and the flux-gradient gas transport technique using the momentum balance transport coefficient. Ammonia fluxes ranged from 3.3 to 24% of the total N applied during the winter and summer, respectively. Ammonia volatilization was rapid immediately after litter application and stopped within 7 to 8 d. Precipitation of 17 mm essentially halted volatilization, probably by transporting litter N into the soil matrix. Application of poultry to conservation-tilled cropland immediately before rainfall events would reduce N losses to the atmosphere but could also increase NO(3) leaching and runoff to streams and rivers.
Conservative Management of Dens Evaginatus: Report of Two Unusual Cases

PubMed Central

Vijaykumar, S; Tenny, J; Ravi, GR

2010-01-01

ABSTRACT Dens evaginatus (DE) is a rare developmental anomaly characterized by presence of an extra cusp arising from occlusal or lingual surfaces. Isolated occurrence or concomitant presence of DE with other dental anomalies has been reported. DE commonly affects permanent teeth and is rarely seen in primary dentition. Treatment may be conservative or radical. This article presents two unusual cases of concomitant occurrence of a supernumerary tooth and DE affecting maxillary deciduous lateral incisor and conservative management of DE occurring concurrently with a possible Oehler’s type I invagination in maxillary permanent lateral incisor. PMID:27507925
How bacteria hack the matrix and dodge the bullets of immunity.

PubMed

Paulsson, Magnus; Riesbeck, Kristian

2018-06-30

Haemophilus influenzae , Moraxella catarrhalis and Pseudomonas aeruginosa are common Gram-negative pathogens associated with an array of pulmonary diseases. All three species have multiple adhesins in their outer membrane, i.e. surface structures that confer the ability to bind to surrounding cells, proteins or tissues. This mini-review focuses on proteins with high affinity for the components of the extracellular matrix such as collagen, laminin, fibronectin and vitronectin. Adhesins are not structurally related and may be lipoproteins, transmembrane porins or large protruding trimeric auto-transporters. They enable bacteria to avoid being cleared together with mucus by attaching to patches of exposed extracellular matrix, or indirectly adhering to epithelial cells using matrix proteins as bridging molecules. As more adhesins are being unravelled, it is apparent that bacterial adhesion is a highly conserved mechanism, and that most adhesins target the same regions on the proteins of the extracellular matrix. The surface exposed adhesins are prime targets for new vaccines and the interactions between proteins are often possible to inhibit with interfering molecules, e.g heparin. In conclusion, this highly interesting research field of microbiology has unravelled host-pathogen interactions with high therapeutic potential. Copyright ©ERS 2018.
The Promise of Using Energy Tracking Data to Promote Home-School Connections and Youth Agency in Climate Action

NASA Astrophysics Data System (ADS)

Walsh, E.; Jenkins, D.; Cordero, E.

2015-12-01

Formal classroom learning experiences that support energy conservation behaviors outside the classroom necessarily must bridge students' home and school lives, as knowledge and practice learned in the classroom is implemented outside of school. To this end, we study the impact of the Green Ninja Energy Tracker curriculum, which uses students' home energy data in the classroom to promote engagement in climate change and conservation behaviors. Data is drawn from class observations, a focus group, and pre- and post- surveys of a pilot implementation of this curriculum in a diverse 12th-grade Earth Science classroom at an alternative school. We investigate what factors contributed to student engagement in learning about and participating in energy conservation behaviors. We found that students were engaged by the immediacy of tracking their energy use in near-real time, and were motivated by the economic benefits experienced as a direct result of changing their behaviors. In addition, students reported discussing and problem-solving energy use with their families, and surfaced considerations that informed which energy behaviors were implemented and why. Students also reported high levels of personal agency in taking action on climate change, but were pessimistic about the likelihood of society as a whole taking action. We suggest that this pilot demonstrates that potential power of connecting students' home and school lives through energy tracker software as a catalyst for developing scientific expertise and engagement, and supporting energy conservation behaviors.
50 CFR 660.399 - EFH Conservation Areas off the Coast of California.

Code of Federal Regulations, 2010 CFR

2010-10-01

.... The boundary of the Harris Point EFH Conservation Area is defined by the mean high water line and... commercial and recreational take of living marine resources is allowed, exists between the mean high water... Scorpion EFH Conservation Area is defined by the mean high water line and a straight line connecting all of...
50 CFR 660.79 - EFH Conservation Areas off the Coast of California.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... The boundary of the Harris Point EFH Conservation Area is defined by the mean high water line and... commercial and recreational take of living marine resources is allowed, exists between the mean high water... Scorpion EFH Conservation Area is defined by the mean high water line and a straight line connecting all of...
A Novel Staphylococcus aureus Vaccine: Iron Surface Determinant B Induces Rapid Antibody Responses in Rhesus Macaques and Specific Increased Survival in a Murine S. aureus Sepsis Model

PubMed Central

Kuklin, Nelly A.; Clark, Desmond J.; Secore, Susan; Cook, James; Cope, Leslie D.; McNeely, Tessie; Noble, Liliane; Brown, Martha J.; Zorman, Julie K.; Wang, Xin Min; Pancari, Gregory; Fan, Hongxia; Isett, Kevin; Burgess, Bruce; Bryan, Janine; Brownlow, Michelle; George, Hugh; Meinz, Maria; Liddell, Mary E.; Kelly, Rosemarie; Schultz, Loren; Montgomery, Donna; Onishi, Janet; Losada, Maria; Martin, Melissa; Ebert, Timothy; Tan, Charles Y.; Schofield, Timothy L.; Nagy, Eszter; Meineke, Andreas; Joyce, Joseph G.; Kurtz, Myra B.; Caulfield, Michael J.; Jansen, Kathrin U.; McClements, William; Anderson, Annaliesa S.

2006-01-01

Staphylococcus aureus is a major cause of nosocomial infections worldwide, and the rate of resistance to clinically relevant antibiotics, such as methicillin, is increasing; furthermore, there has been an increase in the number of methicillin-resistant S. aureus community-acquired infections. Effective treatment and prevention strategies are urgently needed. We investigated the potential of the S. aureus surface protein iron surface determinant B (IsdB) as a prophylactic vaccine against S. aureus infection. IsdB is an iron-sequestering protein that is conserved in diverse S. aureus clinical isolates, both methicillin resistant and methicillin sensitive, and it is expressed on the surface of all isolates tested. The vaccine was highly immunogenic in mice when it was formulated with amorphous aluminum hydroxyphosphate sulfate adjuvant, and the resulting antibody responses were associated with reproducible and significant protection in animal models of infection. The specificity of the protective immune responses in mice was demonstrated by using an S. aureus strain deficient for IsdB and HarA, a protein with a high level of identity to IsdB. We also demonstrated that IsdB is highly immunogenic in rhesus macaques, inducing a more-than-fivefold increase in antibody titers after a single immunization. Based on the data presented here, IsdB has excellent prospects for use as a vaccine against S. aureus disease in humans. PMID:16552052
A novel Staphylococcus aureus vaccine: iron surface determinant B induces rapid antibody responses in rhesus macaques and specific increased survival in a murine S. aureus sepsis model.

PubMed

Kuklin, Nelly A; Clark, Desmond J; Secore, Susan; Cook, James; Cope, Leslie D; McNeely, Tessie; Noble, Liliane; Brown, Martha J; Zorman, Julie K; Wang, Xin Min; Pancari, Gregory; Fan, Hongxia; Isett, Kevin; Burgess, Bruce; Bryan, Janine; Brownlow, Michelle; George, Hugh; Meinz, Maria; Liddell, Mary E; Kelly, Rosemarie; Schultz, Loren; Montgomery, Donna; Onishi, Janet; Losada, Maria; Martin, Melissa; Ebert, Timothy; Tan, Charles Y; Schofield, Timothy L; Nagy, Eszter; Meineke, Andreas; Joyce, Joseph G; Kurtz, Myra B; Caulfield, Michael J; Jansen, Kathrin U; McClements, William; Anderson, Annaliesa S

2006-04-01

Staphylococcus aureus is a major cause of nosocomial infections worldwide, and the rate of resistance to clinically relevant antibiotics, such as methicillin, is increasing; furthermore, there has been an increase in the number of methicillin-resistant S. aureus community-acquired infections. Effective treatment and prevention strategies are urgently needed. We investigated the potential of the S. aureus surface protein iron surface determinant B (IsdB) as a prophylactic vaccine against S. aureus infection. IsdB is an iron-sequestering protein that is conserved in diverse S. aureus clinical isolates, both methicillin resistant and methicillin sensitive, and it is expressed on the surface of all isolates tested. The vaccine was highly immunogenic in mice when it was formulated with amorphous aluminum hydroxyphosphate sulfate adjuvant, and the resulting antibody responses were associated with reproducible and significant protection in animal models of infection. The specificity of the protective immune responses in mice was demonstrated by using an S. aureus strain deficient for IsdB and HarA, a protein with a high level of identity to IsdB. We also demonstrated that IsdB is highly immunogenic in rhesus macaques, inducing a more-than-fivefold increase in antibody titers after a single immunization. Based on the data presented here, IsdB has excellent prospects for use as a vaccine against S. aureus disease in humans.
Glycosylation at Asn91 of H1N1 haemagglutinin affects binding to glycan receptors

PubMed Central

Jayaraman, Akila; Koh, Xiaoying; Li, Jing; Raman, Rahul; Viswanathan, Karthik; Shriver, Zachary; Sasisekharan, Ram

2012-01-01

The glycoprotein HA (haemagglutinin) on the surface of influenza A virus plays a central role in recognition and binding to specific host cell-surface glycan receptors and in fusion of viral membrane to the host nuclear membrane during viral replication. Given the abundance of HA on the viral surface, this protein is also the primary target for host innate and adaptive immune responses. Although addition of glycosylation sites on HA are a part of viral evolution to evade the host immune responses, there are specific glycosylation sites that are conserved during most of the evolution of the virus. In the present study, it was demonstrated that one such conserved glycosylation site at Asn91 in H1N1 HA critically governs the glycan receptor-binding specificity and hence would potentially impinge on the host adaptation of the virus. PMID:22642577
Glycosylation at Asn91 of H1N1 haemagglutinin affects binding to glycan receptors.

PubMed

Jayaraman, Akila; Koh, Xiaoying; Li, Jing; Raman, Rahul; Viswanathan, Karthik; Shriver, Zachary; Sasisekharan, Ram

2012-06-15

The glycoprotein HA (haemagglutinin) on the surface of influenza A virus plays a central role in recognition and binding to specific host cell-surface glycan receptors and in fusion of viral membrane to the host nuclear membrane during viral replication. Given the abundance of HA on the viral surface, this protein is also the primary target for host innate and adaptive immune responses. Although addition of glycosylation sites on HA are a part of viral evolution to evade the host immune responses, there are specific glycosylation sites that are conserved during most of the evolution of the virus. In the present study, it was demonstrated that one such conserved glycosylation site at Asn(91) in H1N1 HA critically governs the glycan receptor-binding specificity and hence would potentially impinge on the host adaptation of the virus.
Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions

PubMed Central

Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

2014-01-01

Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador's biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation. PMID:25360277
Colloid and materials science for the conservation of cultural heritage: cleaning, consolidation, and deacidification.

PubMed

Baglioni, Piero; Chelazzi, David; Giorgi, Rodorico; Poggi, Giovanna

2013-04-30

Serendipity and experiment have been a frequent approach for the development of materials and methodologies used for a long time for either cleaning or consolidation of works of art. Recently, new perspectives have been opened by the application of materials science, colloid science, and interface science frameworks to conservation, generating a breakthrough in the development of innovative tools for the conservation and preservation of cultural heritage. This Article is an overview of the most recent contributions of colloid and materials science to the art conservation field, mainly focusing on the use of amphiphile-based fluids, gels, and alkaline earth metal hydroxide nanoparticles dispersions for the cleaning of pictorial surfaces, the consolidation of artistic substrates, and the deacidification of paper, canvas, and wood. Future possible directions for solving several conservation issues that still need to be faced are also highlighted.
Optimization-based limiters for the spectral element method

NASA Astrophysics Data System (ADS)

Guba, Oksana; Taylor, Mark; St-Cyr, Amik

2014-06-01

We introduce a new family of optimization based limiters for the h-p spectral element method. The native spectral element advection operator is oscillatory, but due to its mimetic properties it is locally conservative and has a monotone property with respect to element averages. We exploit this property to construct locally conservative quasimonotone and sign-preserving limiters. The quasimonotone limiter prevents all overshoots and undershoots at the element level, but is not strictly non-oscillatory. It also maintains quasimonotonicity even with the addition of a dissipation term such as viscosity or hyperviscosity. The limiters are based on a least-squares formulation with equality and inequality constraints and are local to each element. We evaluate the new limiters using a deformational flow test case for advection on the surface of the sphere. We focus on mesh refinement for moderate (p=3) and high order (p=6) elements. As expected, the spectral element method obtains its formal order of accuracy for smooth problems without limiters. For advection of fields with cusps and discontinuities, the high order convergence is lost, but in all cases, p=6 outperforms p=3 for the same degrees of freedom.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashgarian, M; Guilderson, T P

We utilize monthly {sup 14}C data derived from coral archives in conjunction with ocean circulation models to address two questions: (1) how does the shallow circulation of the tropical Pacific vary on seasonal to decadal time scales and (2) which dynamic processes determine the mean vertical structure of the equatorial Pacific thermocline. Our results directly impact the understanding of global climate events such as the El Nino-Southern Oscillation (ENSO). To study changes in ocean circulation and water mass distribution involved in the genesis and evolution of ENSO and decadal climate variability, it is necessary to have records of climate variablesmore » several decades in length. Continuous instrumental records are limited because technology for continuous monitoring of ocean currents (e.g. satellites and moored arrays) has only recently been available, and ships of opportunity archives such as COADS contain large spatial and temporal biases. In addition, temperature and salinity in surface waters are not conservative and thus can not be independently relied upon to trace water masses, reducing the utility of historical observations. Radiocarbon in sea water is a quasi-conservative water mass tracer and is incorporated into coral skeletal material, thus coral {sup 14}C records can be used to reconstruct changes in shallow circulation that would be difficult to characterize using instrumental data. High resolution {Delta}{sup 14}C timeseries such as ours, provide a powerful constraint on the rate of surface ocean mixing and hold great promise to augment one time oceanographic surveys. {Delta}{sup 14}C timeseries such as these, not only provide fundamental information about the shallow circulation of the Pacific, but can also be directly used as a benchmark for the next generation of high resolution ocean models used in prognosticating climate. The measurement of {Delta}{sup 14}C in biological archives such as tree rings and coral growth bands is a direct record of the invasion of fossil fuel CO{sub 2} and bomb {sup 14}C into the atmosphere and surface oceans. Therefore the {Delta}{sup 14}C data that are produced in this study can be used to validate the ocean uptake of fossil fuel CO2 in coupled ocean-atmosphere models. This study takes advantage of the quasi-conservative nature of {sup 14}C as a water mass tracer by using {Delta}{sup 14}C time series in corals to identify changes in the shallow circulation of the Pacific. Although the data itself provides fundamental information on surface water mass movement the true strength is a combined approach which is greater than the individual parts; the data helps uncover deficiencies in ocean circulation models and the model results place long {Delta}{sup 14}C time series in a dynamic framework which helps to identify those locations where additional observations are most needed.« less
76 FR 21857 - Endangered and Threatened Species; Take of Anadromous Fish

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-19

... permit to conduct research for scientific purposes from the United Water Conservation District (United... altered channel with a dynamic groundwater and surface water interchange, and (2) evaluate the effects of increased water temperature during surface flow loss and how this affects migration rates of smolts and the...
Assessing conservation opportunity on private land: socio-economic, behavioral, and spatial dimensions.

PubMed

Raymond, Christopher M; Brown, Gregory

2011-10-01

This study presents a method for assessing conservation opportunity on private land based on landholders' socio-economic, behavioral, and farm characteristics. These characteristics include age, gender, education, level of off-farm income, farm size, proportion of remnant native vegetation on-farm, and ecological value of native vegetation on-farm. A sample of landholders who own greater than 2 ha of land in the South Australian Murray-Darling Basin region were sent a mail-based survey about their values and preferences for environmental management (N = 659, 52% response). Cross-tabulations and ANOVA statistical analysis techniques were used to compare the socio-economic attributes across three landholder classes: disengaged, moderately engaged, and highly engaged in native vegetation planting. Results indicate that highly engaged landholders were more likely to be female, formally educated, hobby farmers who managed small parcels of land and have high off-farm incomes, whereas disengaged landholders held significantly stronger farming connections (more farming experience, family have lived on the farm for more generations). Spatial analysis revealed area-specific differences in conservation opportunity and conservation priority. In some areas, properties of high ecological value were managed by highly engaged landholders, but nearby properties of high value were managed by moderately engaged or disengaged landholders. Environmental managers therefore cannot assume areas of high conservation priority will be areas of high conservation opportunity. At the regional scale, the potential for revegetation seems most promising within the moderately engaged landholder group considering the vast amount of land managed by this group in areas of high ecological value, particularly within the less represented Mallee and Coorong and Rangelands sub-regions. We suggest that incentive schemes which purchase conservation need to be targeted at disengaged landholders; mentoring schemes led by commercial farmers highly engaged in native vegetation planting should be directed at moderately engaged landholders, and; awards programs which acknowledge conservation successes should be targeted at highly engaged landholders. Copyright © 2011 Elsevier Ltd. All rights reserved.
Delayed charge recovery discrimination of passivated surface alpha events in P-type point-contact detectors

NASA Astrophysics Data System (ADS)

Gruszko, J.; Majorana Collaboration

2017-09-01

The Majorana Demonstrator searches for neutrinoless double-beta decay of 76Ge using arrays of high-purity germanium detectors. If observed, this process would demonstrate that lepton number is not a conserved quantity in nature, with implications for grand-unification and for explaining the predominance of matter over antimatter in the universe. A problematic background in such large granular detector arrays is posed by alpha particles. In the Majorana Demonstrator, events have been observed that are consistent with energy-degraded alphas originating on the passivated surface, leading to a potential background contribution in the region-of-interest for neutrinoless double-beta decay. However, it is also observed that when energy deposition occurs very close to the passivated surface, charges drift through the bulk onto that surface, and then drift along it with greatly reduced mobility. This leads to both a reduced prompt signal and a measurable change in slope of the tail of a recorded pulse. In this contribution we discuss the characteristics of these events and the development of a filter that can identify the occurrence of this delayed charge recovery, allowing for the efficient rejection of passivated surface alpha events in analysis.
Documentation for emergency condition mapping of Decorated historic surfaces at the Caid Residence, the Kasbah of Taourirt (Ouarzazate, Morocco)

NASA Astrophysics Data System (ADS)

Percy, K.; Ouimet, C.; Ward, S.; Santana Quintero, M.; Cancino, C.; Wong, L.; Marcus, B.; Whittaker, S.; Boussalh, M.

2015-08-01

As it is broadly understood, recording serves as a basis for the diagnosis, treatment and preservation of historic places and contributes to record our built cultural heritage for posterity. This work is not a stand-alone practice but a part of the overall conservation process of cultural heritage at imminent risk of irreversible damage. Recording of heritage places should be directly related to the needs, skills and the technology that are available to the end users that are responsible for the management and care of these sites. They should be selected in a way that the future managers of these sites can also access and use the data collected. This paper explains an innovative heritage recording approach applied by the Getty Conservation Institute (GCI) and Carleton Immersive Media Studio (CIMS) in the documentation of historic decorated surfaces at the Caïd Residence, located at Tighermt (Kasbah) Taourirt in Ouarzazate, Morocco; as part of a collaborative project between the GCI and the Centre de Conservation et Réhabilitation du Patrimoine Architectural des Zones Atlasiques et Sub-Atlasiques (CERKAS) to rehabilitate the entire architectural ensemble. The selected recording techniques were used for the rapid mapping of conditions of the decorated surfaces at the Caïd Residence using international standards. The resulting work is being used by GCI staff, consultants and CERKAS team to conduct emergency stabilization and protection measures for these important decorated surfaces.
The conservative behavior of dissolved organic carbon in surface waters of the southern Chukchi Sea, Arctic Ocean, during early summer

PubMed Central

Tanaka, Kazuki; Takesue, Nobuyuki; Nishioka, Jun; Kondo, Yoshiko; Ooki, Atsushi; Kuma, Kenshi; Hirawake, Toru; Yamashita, Youhei

2016-01-01

The spatial distribution of dissolved organic carbon (DOC) concentrations and the optical properties of dissolved organic matter (DOM) determined by ultraviolet-visible absorbance and fluorescence spectroscopy were measured in surface waters of the southern Chukchi Sea, western Arctic Ocean, during the early summer of 2013. Neither the DOC concentration nor the optical parameters of the DOM correlated with salinity. Principal component analysis using the DOM optical parameters clearly separated the DOM sources. A significant linear relationship was evident between the DOC and the principal component score for specific water masses, indicating that a high DOC level was related to a terrigenous source, whereas a low DOC level was related to a marine source. Relationships between the DOC and the principal component scores of the surface waters of the southern Chukchi Sea implied that the major factor controlling the distribution of DOC concentrations was the mixing of plural water masses rather than local production and degradation. PMID:27658444
Governance factors in the identification of global conservation priorities for mammals

PubMed Central

Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

2011-01-01

Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development. PMID:21844045
Global priorities for conservation across multiple dimensions of mammalian diversity

PubMed Central

Graham, Catherine H.; Costa, Gabriel C.; Hedges, S. Blair; Penone, Caterina; Radeloff, Volker C.; Rondinini, Carlo; Davidson, Ana D.

2017-01-01

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity—taxonomic, phylogenetic, and traits—and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts. PMID:28674013
Global priorities for conservation across multiple dimensions of mammalian diversity.

PubMed

Brum, Fernanda T; Graham, Catherine H; Costa, Gabriel C; Hedges, S Blair; Penone, Caterina; Radeloff, Volker C; Rondinini, Carlo; Loyola, Rafael; Davidson, Ana D

2017-07-18

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to ( i ) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and ( ii ) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts.
Governance factors in the identification of global conservation priorities for mammals.

PubMed

Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

2011-09-27

Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development.
Crystal Structure of VC0702 at 2.0 angstrom: A Conserved Hypothetical Protein from Vibrio Cholerae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ni, Shuisong; Forouhar, Farhad; Bussiere, Dirksen E.

2006-06-01

VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a putative three-gene operon containing the MbaA gene, which is involved in regulating formation of the extracellular matrix of biofilms in Vibrio cholerae. The VC0702 crystal structure has been determined at 2.0? and refined to Rwork=22.8% and Rfree=26.3%. VC0702 crystallized in an orthorhombic crystal lattice in the C2221 space group with dimensions of a=66.61 ?, b=88.118 ?, and c=118.35 ? with a homodimer in the asymmetric unit. VC0702 belongs to the Pfam DUF84 and COG1986 family of proteins. Sequence conservation within the DUF84 and COG1986 families wasmore » used to identify a conserved patch of surface residues that define a cleft and potential substrate-binding site in VC0702. The three-dimensional structure of VC0702 is similar to that of Mj0226 from Methanococcus janeshii, which has been identified as a novel NTPase. The NTP-binding site in Mj0226 is similarly located in comparison to the conserved patch of surface residues in VC0702. Furthermore, the NTP binds to MJ0226 in a cleft and deep cavity, features that are present in the VC0702 structure as well, suggesting that VC0702 may have a biochemical function involving NTP binding that is associated with a cellular function of regulating biofilm formation in Vibrio cholerae.« less
When galectins recognize glycans: from biochemistry to physiology and back again.

PubMed

Di Lella, Santiago; Sundblad, Victoria; Cerliani, Juan P; Guardia, Carlos M; Estrin, Dario A; Vasta, Gerardo R; Rabinovich, Gabriel A

2011-09-20

In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings. © 2011 American Chemical Society
Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta Propeller Domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

M Collins; W Hendrickson

2011-12-31

Folding and trafficking of low-density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, are mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD {beta} propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation, and X-ray crystallography were used to define a conserved core composed of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold withmore » two distinct {beta} sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of nonspecific hydrophobic interactions that may play a role in the chaperone activity of the Boca/Mesd family.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The U.S. Department of Energy Weldon Spring Site Remedial Action Project (chemical plant site), is a former uranium processing facility located in eastern Missouri on the property of the former U.S. Army Weldon Spring Ordnance Works. Surface water, soil, sludge, sediment, and groundwater within the chemical plant site contain chemical and radioactive contaminants. The Agency for Toxic Substances and Disease Registry (ATSDR) reviewed on-site chemical exposure information and site conditions. ATSDR also prepared several Health Consultations on chemical and radioactive contaminants in areas on and off the DOE chemical plant site. ATSDR also reviewed on-site and off-site radiological exposure informationmore » and conditions. The exposure scenarios ATSDR evaluated include: trespassers swimming in quarry or raffinate pits; reservists performing field activities in the training area; anglers fishing, hunters haunting, and hikers hiking in the conservation areas; residents drinking from off-site private wells; staff and students attending the Francis Howell High School; and consumers of crops (e.g., corn) grown in conservation areas.« less
Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site.

PubMed

McNamara, Christopher J; Perry, Thomas D; Bearce, Kristen A; Hernandez-Duque, Guillermo; Mitchell, Ralph

2006-01-01

Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous nature of limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering.
The origin of two-dimensional electron gases at oxide interfaces: insights from theory.

PubMed

Bristowe, N C; Ghosez, Philippe; Littlewood, P B; Artacho, Emilio

2014-04-09

The response of oxide thin films to polar discontinuities at interfaces and surfaces has generated enormous activity due to the variety of interesting effects that it gives rise to. A case in point is the discovery of the electron gas at the interface between LaAlO3 and SrTiO3, which has since been shown to be quasi-two-dimensional, switchable, magnetic and/or superconducting. Despite these findings, the origin of the two-dimensional electron gas is highly debated and several possible mechanisms remain. Here we review the main proposed mechanisms and attempt to model expected effects in a quantitative way with the ambition of better constraining what effects can/cannot explain the observed phenomenology. We do it in the framework of a phenomenological model constructed to provide an understanding of the electronic and/or redox screening of the chemical charge in oxide heterostructures. We also discuss the effect of intermixing, both conserving and not conserving the total stoichiometry.
Origin of Two-Dimensional Electron Gases at Oxide Interfaces: Insights from Theory

DOE PAGES

Bristowe, N. C.; Ghosez, Philippe; Littlewood, Peter B.; ...

2014-03-18

The response of oxide thin films to polar discontinuities at interfaces and surfaces has generated enormous activity due to the variety of interesting effects that it gives rise to. A case in point is the discovery of the electron gas at the interface between LaAlO3 and SrTiO3, which has since been shown to be quasitwodimensional, switchable, magnetic and/or superconducting. Despite these findings, the origin of the twodimensional electron gas is highly debated and several possible mechanisms remain. Here we review the main proposed mechanisms and attempt to model expected effects in a quantitative way with the ambition of better constrainingmore » what effects can/cannot explain the observed phenomenology. We do it in the framework of a phenomenological model constructed to provide an understanding of the electronic and/or redox screening of the chemical charge in oxide heterostructures. We also discuss the effect of intermixing, both conserving and not conserving the total stoichiometry« less
Extrapolating effects of conservation tillage on yield, soil moisture and dry spell mitigation using simulation modelling

NASA Astrophysics Data System (ADS)

Mkoga, Z. J.; Tumbo, S. D.; Kihupi, N.; Semoka, J.

There is big effort to disseminate conservation tillage practices in Tanzania. Despite wide spread field demonstrations there has been some field experiments meant to assess and verify suitability of the tillage options in local areas. Much of the experiments are short lived and thus long term effects of the tillage options are unknown. Experiments to study long term effects of the tillage options are lacking because they are expensive and cannot be easily managed. Crop simulation models have the ability to use long term weather data and the local soil parameters to assess long term effects of the tillage practices. The Agricultural Production Systems Simulator (APSIM) crop simulation model; was used to simulate long term production series of soil moisture and grain yield based on the soil and weather conditions in Mkoji sub-catchment of the great Ruaha river basin in Tanzania. A 24 year simulated maize yield series based on conventional tillage with ox-plough, without surface crop residues (CT) treatment was compared with similar yield series based on conservation tillage (ox-ripping, with surface crop residues (RR)). Results showed that predicted yield averages were significantly higher in conservation tillage than in conventional tillage ( P < 0.001). Long term analysis, using APSIM simulation model, showed that average soil moisture in the conservation tillage was significantly higher ( P < 0.05) (about 0.29 mm/mm) than in conventional tillage (0.22 mm/mm) treatment during the seasons which received rainfall between 468 and 770 mm. Similarly the conservation tillage treatment recorded significantly higher yields (4.4 t/ha) ( P < 0.01) than the conventional tillage (3.6 t/ha) treatment in the same range of seasonal rainfall. On the other hand there was no significant difference in soil moisture for the seasons which received rainfall above 770 mm. In these seasons grain yield in conservation tillage treatment was significantly lower (3.1 kg/ha) than in the conventional tillage treatment (4.8 kg/ha) ( P < 0.05). Results also indicated a probability of 0.5 of getting higher yield in conservation than in conventional tillage practice. The conservation tillage treatment had the ability to even-out the acute and long intra-seasonal dry spells. For example a 36-days agricultural dry spell which occurred between 85th and 130th day after planting in the 1989/1990 season (in the CT treatment) was mitigated to zero days in the RR treatment by maintaining soil moisture above the critical point. Critical soil moisture for maize was measured at 0.55 of maximum soil moisture that can be depleted crop (0.55 D). It is concluded that conservation tillage practice where ripping and surface crop residues is used is much more effective in mitigating dry spells and increase productivity in a seasonal rainfall range of between 460 and 770 mm. It is recommended that farmers in the area adopt that type of conservation tillage because rainfall was in this range (460-770 mm) in 12 out of the past 24 years, indicating possibility of yield losses once in every 2 years.
Network Simulation solution of free convective flow from a vertical cone with combined effect of non- uniform surface heat flux and heat generation or absorption

NASA Astrophysics Data System (ADS)

Immanuel, Y.; Pullepu, Bapuji; Sambath, P.

2018-04-01

A two dimensional mathematical model is formulated for the transitive laminar free convective, incompressible viscous fluid flow over vertical cone with variable surface heat flux combined with the effects of heat generation and absorption is considered . using a powerful computational method based on thermoelectric analogy called Network Simulation Method (NSM0, the solutions of governing nondimensionl coupled, unsteady and nonlinear partial differential conservation equations of the flow that are obtained. The numerical technique is always stable and convergent which establish high efficiency and accuracy by employing network simulator computer code Pspice. The effects of velocity and temperature profiles have been analyzed for various factors, namely Prandtl number Pr, heat flux power law exponent n and heat generation/absorption parameter Δ are analyzed graphically.
Development of an oligonucleotide probe for Aureobasidium pullulans based on the small-subunit rRNA gene.

PubMed Central

Li, S; Cullen, D; Hjort, M; Spear, R; Andrews, J H

1996-01-01

Aureobasidium pullulans, a cosmopolitan yeast-like fungus, colonizes leaf surfaces and has potential as a biocontrol agent of pathogens. To assess the feasibility of rRNA as a target for A. pullulans-specific oligonucleotide probes, we compared the nucleotide sequences of the small-subunit rRNA (18S) genes of 12 geographically diverse A. pullulans strains. Extreme sequence conservation was observed. The consensus A. pullulans sequence was compared with other fungal sequences to identify potential probes. A 21-mer probe which hybridized to the 12 A. pullulans strains but not to 98 other fungi, including 82 isolates from the phylloplane, was identified. A 17-mer highly specific for Cladosporium herbarum was also identified. These probes have potential in monitoring and quantifying fungi in leaf surface and other microbial communities. PMID:8633850

The light-harvesting antenna of Chlorobium tepidum: interactions between the FMO protein and the major chlorosome protein CsmA studied by surface plasmon resonance.

PubMed

Pedersen, Marie Østergaard; Borch, Jonas; Højrup, Peter; Cox, Raymond P; Miller, Mette

2006-09-01

Green sulfur bacteria possess two external light-harvesting antenna systems, the chlorosome and the FMO protein, which participate in a sequential energy transfer to the reaction centers embedded in the cytoplasmic membrane. However, little is known about the physical interaction between these two antenna systems. We have studied the interaction between the major chlorosome protein, CsmA, and the FMO protein in Chlorobium tepidum using surface plasmon resonance (SPR). Our results show an interaction between the FMO protein and an immobilized synthetic peptide corresponding to 17 amino acids at the C terminal of CsmA. This interaction is dependent on the presence of a motif comprising six amino acids that are highly conserved in all the currently available CsmA protein sequences.
Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

USGS Publications Warehouse

Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

2014-01-01

The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina (displaying low genetic divergence and greater than average levels of genetic diversity) . Our results show the utility o f genetic data sets for identifying cross - species patterns of genetic diversity and divergence (i.e., evolutionary hotspots) in aquatic and terrestrial environments for use in conservation design and delivery across the southeastern United States.
Analysis of the osseointegrative force of a hyperhydrophilic and nanostructured surface refinement for TPS surfaces in a gap healing model with the Göttingen minipig.

PubMed

Seidling, Roland; Lehmann, Lars J; Lingner, Manuel; Mauermann, Eckhard; Obertacke, Udo; Schwarz, Markus L R

2016-10-17

A lot of advantages can result in a high wettability as well as a nanostructure at a titanium surface on bone implants. Thus, the aim of this study was to evaluate the osseointegrative potential of a titan plasma-sprayed (TPS) surface refinement by acid-etching with chromosulfuric acid. This results in a hyperhydrophilic surface with a nanostructure and an extreme high wetting rate. In total, 72 dumbbell shape titan implants were inserted in the spongy bone of the femora of 18 Göttingen minipigs in a conservative gap model. Thirty-six titan implants were coated with a standard TPS surface and 36 with the hyperhydrophilic chromosulfuric acid (CSA) surface. After a healing period of 4, 8, and 12 weeks, the animals were killed. The chronological healing process was histomorphometrically analyzed. The de novo bone formation, represented by the bone area (BA), is increased by approximately 1.5 times after 12 weeks with little additional benefit by use of the CSA surface. The bone-to-implant contact (BIC), which represents osseoconductive forces, shows results with a highly increased osteoid production in the CSA implants beginning at 8 and 12 weeks compared to TPS. This culminates in a 17-fold increase in BIC after a healing period of 12 weeks. After 4 weeks, significantly more osteoid was seen in the gap as de novo formation in the CSA group (p = 0.0062). Osteoid was also found more frequently after 12 weeks at the CSA-treated surface (p = 0.0355). The site of implantation, intertrochanteric or intercondylar, may influence on the de novo bone formation in the gap. There is a benefit by the CSA surface treatment of the TPS layer for osseointegration over an observation time up to 12 weeks. Significant differences were able to be shown in two direct comparisons between the CSA and the TPS surface for osteoid formation in the gap model. Further trials may reveal the benefit of the CSA treatment of the TPS layer involving mechanical tests if possible.
Fabricating Superhydrophobic and Superoleophobic Surfaces with Multiscale Roughness Using Airbrush and Electrospray

NASA Astrophysics Data System (ADS)

AL-Milaji, Karam N.

Examples of superhydrophobic surfaces found in nature such as self-cleaning property of lotus leaf and walking on water ability of water strider have led to an extensive investigation in this area over the past few decades. When a water droplet rests on a textured surface, it may either form a liquid-solid-vapor composite interface by which the liquid droplet partially sits on air pockets or it may wet the surface in which the water replaces the trapped air depending on the surface roughness and the surface chemistry. Super water repellent surfaces have numerous applications in our daily life such as drag reduction, anti-icing, anti-fogging, energy conservation, noise reduction, and self-cleaning. In fact, the same concept could be applied in designing and producing surfaces that repel organic contaminations (e.g. low surface tension liquids). However, superoleophobic surfaces are more challenging to fabricate than superhydrophobic surfaces since the combination of multiscale roughness with re-entrant or overhang structure and surface chemistry must be provided. In this study, simple, cost-effective and potentially scalable techniques, i.e., airbrush and electrospray, were employed for the sake of making superhydrophobic and superoleophobic coatings with random and patterned multiscale surface roughness. Different types of silicon dioxide were utilized in this work to in order to study and to characterize the effect of surface morphology and surface roughness on surface wettability. The experimental findings indicated that super liquid repellent surfaces with high apparent contact angles and extremely low sliding angles were successfully fabricated by combining re-entrant structure, multiscale surface roughness, and low surface energy obtained from chemically treating the fabricated surfaces. In addition to that, the experimental observations regarding producing textured surfaces in mask-assisted electrospray were further validated by simulating the actual working conditions and geometries using COMSOL Multiphysics.
SCISEAL: A CFD code for analysis of fluid dynamic forces in seals

NASA Technical Reports Server (NTRS)

Athavale, Mahesh; Przekwas, Andrzej

1994-01-01

A viewgraph presentation is made of the objectives, capabilities, and test results of the computer code SCISEAL. Currently, the seal code has: a finite volume, pressure-based integration scheme; colocated variables with strong conservation approach; high-order spatial differencing, up to third-order; up to second-order temporal differencing; a comprehensive set of boundary conditions; a variety of turbulence models and surface roughness treatment; moving grid formulation for arbitrary rotor whirl; rotor dynamic coefficients calculated by the circular whirl and numerical shaker methods; and small perturbation capabilities to handle centered and eccentric seals.
Evaluation of advanced lift concepts and potential fuel conservation for short-haul aircraft

NASA Technical Reports Server (NTRS)

Sweet, H. S.; Renshaw, J. H.; Bowden, M. K.

1975-01-01

The effect of different field lengths, cruise requirements, noise level, and engine cycle characteristics on minimizing fuel consumption and minimizing operating cost at high fuel prices were evaluated for some advanced short-haul aircraft. The conceptual aircraft were designed for 148 passengers using the upper surface-internally blown jet flap, the augmentor wing, and the mechanical flap lift systems. Advanced conceptual STOL engines were evaluated as well as a near-term turbofan and turboprop engine. Emphasis was given to designs meeting noise levels equivalent to 95-100 EPNdB at 152 m (500 ft) sideline.
Contribution of TyrB26 to the Function and Stability of Insulin

PubMed Central

Pandyarajan, Vijay; Phillips, Nelson B.; Rege, Nischay; Lawrence, Michael C.; Whittaker, Jonathan; Weiss, Michael A.

2016-01-01

Crystallographic studies of insulin bound to receptor domains have defined the primary hormone-receptor interface. We investigated the role of TyrB26, a conserved aromatic residue at this interface. To probe the evolutionary basis for such conservation, we constructed 18 variants at B26. Surprisingly, non-aromatic polar or charged side chains (such as Glu, Ser, or ornithine (Orn)) conferred high activity, whereas the weakest-binding analogs contained Val, Ile, and Leu substitutions. Modeling of variant complexes suggested that the B26 side chains pack within a shallow depression at the solvent-exposed periphery of the interface. This interface would disfavor large aliphatic side chains. The analogs with highest activity exhibited reduced thermodynamic stability and heightened susceptibility to fibrillation. Perturbed self-assembly was also demonstrated in studies of the charged variants (Orn and Glu); indeed, the GluB26 analog exhibited aberrant aggregation in either the presence or absence of zinc ions. Thus, although TyrB26 is part of insulin's receptor-binding surface, our results suggest that its conservation has been enjoined by the aromatic ring's contributions to native stability and self-assembly. We envisage that such classical structural relationships reflect the implicit threat of toxic misfolding (rather than hormonal function at the receptor level) as a general evolutionary determinant of extant protein sequences. PMID:27129279
Ocean forecasting in terrain-following coordinates: Formulation and skill assessment of the Regional Ocean Modeling System

USGS Publications Warehouse

Haidvogel, D.B.; Arango, H.; Budgell, W.P.; Cornuelle, B.D.; Curchitser, E.; Di, Lorenzo E.; Fennel, K.; Geyer, W.R.; Hermann, A.J.; Lanerolle, L.; Levin, J.; McWilliams, J.C.; Miller, A.J.; Moore, A.M.; Powell, T.M.; Shchepetkin, A.F.; Sherwood, C.R.; Signell, R.P.; Warner, J.C.; Wilkin, J.

2008-01-01

Systematic improvements in algorithmic design of regional ocean circulation models have led to significant enhancement in simulation ability across a wide range of space/time scales and marine system types. As an example, we briefly review the Regional Ocean Modeling System, a member of a general class of three-dimensional, free-surface, terrain-following numerical models. Noteworthy characteristics of the ROMS computational kernel include: consistent temporal averaging of the barotropic mode to guarantee both exact conservation and constancy preservation properties for tracers; redefined barotropic pressure-gradient terms to account for local variations in the density field; vertical interpolation performed using conservative parabolic splines; and higher-order, quasi-monotone advection algorithms. Examples of quantitative skill assessment are shown for a tidally driven estuary, an ice-covered high-latitude sea, a wind- and buoyancy-forced continental shelf, and a mid-latitude ocean basin. The combination of moderate-order spatial approximations, enhanced conservation properties, and quasi-monotone advection produces both more robust and accurate, and less diffusive, solutions than those produced in earlier terrain-following ocean models. Together with advanced methods of data assimilation and novel observing system technologies, these capabilities constitute the necessary ingredients for multi-purpose regional ocean prediction systems.
Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

PubMed Central

Champer, Jackson; Ito, James I.; Clemons, Karl V.; Stevens, David A.; Kalkum, Markus

2016-01-01

We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy). Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4), Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here. PMID:26878023
Phosphorus fractionation and distribution in sediments from wetlands and canals of a water conservation area in the Florida Everglades

Treesearch

Qingren Wang; Yuncong Li; Ying Ouyang

2011-01-01

Phosphorus (P) fractionation and distribution in sediments are of great concern in the Florida Everglades ecosystem because potential eutrophication of surface waters usually results from P external loading and stability. Intact core sediment samples were collected to a depth of 35 cm from wetlands and canals across Water Conservation Area 3 (WCAâ3) of the Florida...
Towards and FVE-FAC Method for Determining Thermocapillary Effects on Weld Pool Shape

NASA Technical Reports Server (NTRS)

Canright, David; Henson, Van Emden

1996-01-01

Several practical materials processes, e.g., welding, float-zone purification, and Czochralski crystal growth, involve a pool of molten metal with a free surface, with strong temperature gradients along the surface. In some cases, the resulting thermocapillary flow is vigorous enough to convect heat toward the edges of the pool, increasing the driving force in a sort of positive feedback. In this work we examine this mechanism and its effect on the solid-liquid interface through a model problem: a half space of pure substance with concentrated axisymmetric surface heating, where surface tension is strong enough to keep the liquid free surface flat. The numerical method proposed for this problem utilizes a finite volume element (FVE) discretization in cylindrical coordinates. Because of the axisymmetric nature of the model problem, the control volumes used are torroidal prisms, formed by taking a polygonal cross-section in the (r, z) plane and sweeping it completely around the z-axis. Conservation of energy (in the solid), and conservation of energy, momentum, and mass (in the liquid) are enforced globally by integrating these quantities and enforcing conservation over each control volume. Judicious application of the Divergence Theorem and Stokes' Theorem, combined with a Crank-Nicolson time-stepping scheme leads to an implicit algebraic system to be solved at each time step. It is known that near the boundary of the pool, that is, near the solid-liquid interface, the full conduction-convection solution will require extremely fine length scales to resolve the physical behavior of the system. Furthermore, this boundary moves as a function of time. Accordingly, we develop the foundation of an adaptive refinement scheme based on the principles of Fast Adaptive Composite Grid methods (FAC). Implementation of the method and numerical results will appear in a later report.
A New Formulation of Time Domain Boundary Integral Equation for Acoustic Wave Scattering in the Presence of a Uniform Mean Flow

NASA Technical Reports Server (NTRS)

Hu, Fang; Pizzo, Michelle E.; Nark, Douglas M.

2017-01-01

It has been well-known that under the assumption of a constant uniform mean flow, the acoustic wave propagation equation can be formulated as a boundary integral equation, in both the time domain and the frequency domain. Compared with solving partial differential equations, numerical methods based on the boundary integral equation have the advantage of a reduced spatial dimension and, hence, requiring only a surface mesh. However, the constant uniform mean flow assumption, while convenient for formulating the integral equation, does not satisfy the solid wall boundary condition wherever the body surface is not aligned with the uniform mean flow. In this paper, we argue that the proper boundary condition for the acoustic wave should not have its normal velocity be zero everywhere on the solid surfaces, as has been applied in the literature. A careful study of the acoustic energy conservation equation is presented that shows such a boundary condition in fact leads to erroneous source or sink points on solid surfaces not aligned with the mean flow. A new solid wall boundary condition is proposed that conserves the acoustic energy and a new time domain boundary integral equation is derived. In addition to conserving the acoustic energy, another significant advantage of the new equation is that it is considerably simpler than previous formulations. In particular, tangential derivatives of the solution on the solid surfaces are no longer needed in the new formulation, which greatly simplifies numerical implementation. Furthermore, stabilization of the new integral equation by Burton-Miller type reformulation is presented. The stability of the new formulation is studied theoretically as well as numerically by an eigenvalue analysis. Numerical solutions are also presented that demonstrate the stability of the new formulation.
Research priorities for conservation and natural resource management in Oceania's small-island developing states.

PubMed

Weeks, R; Adams, V M

2018-02-01

For conservation science to effectively inform management, research must focus on creating the scientific knowledge required to solve conservation problems. We identified research questions that, if answered, would increase the effectiveness of conservation and natural resource management practice and policy in Oceania's small-island developing states. We asked conservation professionals from academia, governmental, and nongovernmental organizations across the region to propose such questions and then identify which were of high priority in an online survey. We compared the high-priority questions with research questions identified globally and for other regions. Of 270 questions proposed by respondents, 38 were considered high priority, including: What are the highest priority areas for conservation in the face of increasing resource demand and climate change? How should marine protected areas be networked to account for connectivity and climate change? What are the most effective fisheries management policies that contribute to sustainable coral reef fisheries? High-priority questions related to the particular challenges of undertaking conservation on small-island developing states and the need for a research agenda that is responsive to the sociocultural context of Oceania. Research priorities for Oceania relative to elsewhere were broadly similar but differed in specific issues relevant to particular conservation contexts. These differences emphasize the importance of involving local practitioners in the identification of research priorities. Priorities were reasonably well aligned among sectoral groups. Only a few questions were widely considered answered, which may indicate a smaller-than-expected knowledge-action gap. We believe these questions can be used to strengthen research collaborations between scientists and practitioners working to further conservation and natural resource management in this region. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.
Conservation of geo- and -biodiversity in Lithuania: are there conflicts?

NASA Astrophysics Data System (ADS)

Skridlaite, Grazina; Motiejunaite, Jurga

2014-05-01

Lithuanian surface is sculptured by more than five glaciers, which retreated c. 10 000 years ago. After the ice sheets melted in Lithuania, Latvia and Poland, and other neighbouring countries, they left numerous erratic boulders and boulder fields. Hundreds of single boulders and boulder fields are declared as natural monuments in Lithuania and other countries and are variably protected. Tens of single boulders and boulder fields are included into the Geosites database at the Lithuanian Geological Survey. Rapid weather changes in Lithuania cause the weathering of erratic boulders. However, the fastest erosion is by overgrowing cryptogams: lichenized and non-lichenized fungi, algae, cyanobacteria and bryophytes. Lichens are among the first colonizers of rock surfaces, and their impact on stonework heritage is rather well documented. Hard rocks (e.g. granites) are weathering considerably slower than soft or relatively soft sandstones, dolomites or marbles; however serious impact is visible on stones with inscriptions, drawings and open surfaces of the protected nature monuments. Lichens gradually cover whole boulder surfaces obscuring their geological value and contributing to the surface weathering in Lithuania and neighbouring countries where numerous protected stony nature monuments occur. The 73 of the 723 species of lichenized and allied fungi in Lithuania are confined to hard acid rocks. Eight of these acid rock-dwelling species are included in the Lithuanian Red Data Book, some of them have high threat category or are thought to be extinct now. There is no conservation conflict between the red-listed saxicolous lichens and their substrate where the species are confined to wild boulder meadows. Here lichens and their boulder substrate suffer from excessive growth and overshadowing from surrounding vascular plants, also from pollution which change stone surface properties and induce encroachment of more aggressive species than the usual slow-growing acid rock communities. The main conservation conflict occurs when the solitary boulder monuments or open boulder expositions (e.g. V. Intas' Museum of Boulders in Mosedis, the Geology Museum in Vievis) are concerned. These expositions are supposed to serve a basis for geological science and education; however they are almost completely overgrown. Attempts to clean the boulders were met by general public and some scientists rather negatively and caused several conflicts. A wave of negative opinions appeared in media after the second largest boulder Puntukas was cleaned by compressed water streams. Several problems are concerned. First of all, both chemical and mechanical cleaning not only will remove lichens and other cryptogams, but may be damaging to a boulder or to environment and wildlife. The measures should be taken with utmost care, and lichen species as well as stone surfaces are to be examined before applying any treatment. Another problem is to convince general public, caretakers and scientists that the overgrown stone surfaces should be cleaned. Some botanists, foresters, environmental people would prefer to let the nature to do its work and to cover stony surfaces with vegetation. Therefore, in conflict cases, expert opinions, both botanical and geological should be addressed. This is a contribution to the Open Access Centre activities
Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawson,C.; Yung, B.; Barbour, A.

2006-01-01

Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of Borrelia turicatae strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Angstroms. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing Borrelia. The fold featuresmore » an inner stem formed by highly conserved N and C termini and an outer 'dome' formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.« less
Ground-water levels in the alluvial aquifer in Eastern Arkansas, 1989

USGS Publications Warehouse

Westerfield, P.W.; Baxter, C.R.

1990-01-01

This report, prepared by the U.S. Geological Survey in cooperation with the Arkansas Soil and Water Conservation Commission, the U.S. Soil Conservation Service and local Conservation Districts, contains groundwater level measurements of 504 wells that tap the alluvial aquifer in the Quaternary deposits of the Mississippi Alluvial Plain. The measurements were made by district Soil Conservation Service personnel during 1989. The shallowest prepumping season water levels occurred in Clay, Greene, Independence, Mississippi, Phillips, and Randolph Counties where water levels averaged less than 20 ft below the land surface. The deepest water levels occurred in Arkansas, Lonoke, Poinsett, and Prairie Counties where water levels of more than 100 ft were measured. Water levels in the postpumping season averaged about 2.5 ft lower than during the prepumping season. (USGS)
Physics in strong magnetic fields near neutron stars

NASA Technical Reports Server (NTRS)

Harding, Alice K.

1991-01-01

Electromagnetic phenomena occurring in the strong magnetic fields of neutron stars are currently of great interest in high-energy astrophysics. Observations of rotation rate changes and cyclotron lines in pulsars and gamma-ray bursts indicate that surface magnetic fields of neutron stars often exceed a trillion gauss. In fields this strong, where electrons behave much as if they were in bound atomic states, familiar processes undergo profound changes, and exotic processes become important. Strong magnetic fields affect the physics in several fundamental ways: energies perpendicular to the field are quantized, transverse momentum is not conserved, and electron-positron spin is important. Neutron stars therefore provide a unique laboratory for the study of physics in extremely high fields that cannot be generated on earth.
75 FR 66119 - Proposed Information Collection; International Conservation Grant Programs

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

..., great apes, elephants, and many other highly cherished species. The Division of International Conservation administers 11 competitive grant programs funded under the: African Elephant Conservation Act (16 U.S.C. 4201-4245). Asian Elephant Conservation Act of 1997 (16 U.S.C. 4261). Great Apes Conservation...
Expression and mutagenesis of the sea anemone toxin Av2 reveals key amino acid residues important for activity on voltage-gated sodium channels.

PubMed

Moran, Yehu; Cohen, Lior; Kahn, Roy; Karbat, Izhar; Gordon, Dalia; Gurevitz, Michael

2006-07-25

Type I sea anemone toxins are highly potent modulators of voltage-gated Na-channels (Na(v)s) and compete with the structurally dissimilar scorpion alpha-toxins on binding to receptor site-3. Although these features provide two structurally different probes for studying receptor site-3 and channel fast inactivation, the bioactive surface of sea anemone toxins has not been fully resolved. We established an efficient expression system for Av2 (known as ATX II), a highly insecticidal sea anemone toxin from Anemonia viridis (previously named A. sulcata), and mutagenized it throughout. Each toxin mutant was analyzed in toxicity and binding assays as well as by circular dichroism spectroscopy to discern the effects derived from structural perturbation from those related to bioactivity. Six residues were found to constitute the anti-insect bioactive surface of Av2 (Val-2, Leu-5, Asn-16, Leu-18, and Ile-41). Further analysis of nine Av2 mutants on the human heart channel Na(v)1.5 expressed in Xenopus oocytes indicated that the bioactive surfaces toward insects and mammals practically coincide but differ from the bioactive surface of a structurally similar sea anemone toxin, Anthopleurin B, from Anthopleura xanthogrammica. Hence, our results not only demonstrate clear differences in the bioactive surfaces of Av2 and scorpion alpha-toxins but also indicate that despite the general conservation in structure and importance of the Arg-14 loop and its flanking residues Gly-10 and Gly-20 for function, the surface of interaction between different sea anemone toxins and Na(v)s varies.
Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

PubMed

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

Identification of novel binding partners (annexins) for the cell death signal phosphatidylserine and definition of their recognition motif.

PubMed

Rosenbaum, Sabrina; Kreft, Sandra; Etich, Julia; Frie, Christian; Stermann, Jacek; Grskovic, Ivan; Frey, Benjamin; Mielenz, Dirk; Pöschl, Ernst; Gaipl, Udo; Paulsson, Mats; Brachvogel, Bent

2011-02-18

Identification and clearance of apoptotic cells prevents the release of harmful cell contents thereby suppressing inflammation and autoimmune reactions. Highly conserved annexins may modulate the phagocytic cell removal by acting as bridging molecules to phosphatidylserine, a characteristic phagocytosis signal of dying cells. In this study five members of the structurally and functionally related annexin family were characterized for their capacity to interact with phosphatidylserine and dying cells. The results showed that AnxA3, AnxA4, AnxA13, and the already described interaction partner AnxA5 can bind to phosphatidylserine and apoptotic cells, whereas AnxA8 lacks this ability. Sequence alignment experiments located the essential amino residues for the recognition of surface exposed phosphatidylserine within the calcium binding motifs common to all annexins. These amino acid residues were missing in the evolutionary young AnxA8 and when they were reintroduced by site directed mutagenesis AnxA8 gains the capability to interact with phosphatidylserine containing liposomes and apoptotic cells. By defining the evolutionary conserved amino acid residues mediating phosphatidylserine binding of annexins we show that the recognition of dying cells represent a common feature of most annexins. Hence, the individual annexin repertoire bound to the cell surface of dying cells may fulfil opsonin-like function in cell death recognition.
Effects of feral horses in Great Basin landscapes on soils and ants: Direct and indirect mechanisms

USGS Publications Warehouse

Beever, E.A.; Herrick, J.E.

2006-01-01

We compared soil-surface penetration resistance and abundance of ant mounds at 12 western Great Basin sites (composed of 19 plots) either grazed by feral horses (Equus caballus) or having had horses removed for the last 10–14 years. Across this broad spatial domain (3.03 million ha), we minimized confounding due to abiotic factors by selecting horse-occupied and horse-removed sites with similar aspect, slope, fire history, grazing pressure by cattle (minimal to none), and dominant vegetation (Artemisia tridentata). During both 1997 and 1998, we found 2.2–8.4 times greater abundance of ant mounds and 3.0–15.4 times lower penetration resistance in soil surfaces at horse-removed sites. In 1998, thatched Formica ant mounds, which existed predominately at high elevations, were 3.3 times more abundant at horse-removed sites, although abundance varied widely among sites within treatments. Several types of analyses suggested that horses rather than environmental variability were the primary source of treatment differences we observed in ecosystem components. Tests of several predictions suggest that alterations occurred through not only direct effects, but also indirect effects and potentially feedback loops. Free-roaming horses as well as domestic grazers should be considered in conservation planning and land management in the Great Basin, an ecoregion that represents both an outstanding conservation opportunity and challenge.
Prostaglandin D2 Regulates SOX9 Nuclear Translocation during Gonadal Sex Determination in Tammar Wallaby, Macropus eugenii.

PubMed

Chen, Yu; Yu, Hongshi; Pask, Andrew J; Shaw, Geoff; Renfree, Marilyn B

2017-01-01

Sex determination and sexual differentiation pathways are highly conserved between marsupials and eutherians. There are 2 different pathways of prostaglandin D2 (PGD2) synthesis: prostaglandin D synthase (PTGDS) and haematopoietic prostaglandin D synthase (HPGDS). PGD2 regulates the subcellular localization of SOX9 during gonadal sexual differentiation. To investigate the function of PGD2 in the tammar gonad, we cultured undifferentiated male gonads in the presence of the HPGDS inhibitor HQL-79 and female gonads with exogenous PGD2 to mimic activation of the PTGDS-PGD2 pathway. Tammar PTGDS and HPGDS have only 50% similarity with mouse and human orthologues, but functional domains are conserved. The expression of SOX9 was unchanged by the treatments in cultured gonads, but its subcellular localization was markedly affected. SOX9 remained cytoplasmic in the Sertoli cells of testes treated with HQL-79. Treated testes developed a thickened ovary-like surface epithelium. In contrast, SOX9 became nuclear in the granulosa cells of developing ovaries treated with PGD2 and the surface epithelium was thin, as in testes. These results demonstrate that PGD2 regulates the subcellular localization of SOX9 and subsequent gonadal development in the developing marsupial gonads, as it does in mice, and that it must have been an ancestral mechanism. © 2017 S. Karger AG, Basel.
Evaluating the Soil Vulnerability Index (SVI), an index to characterize inherent vulnerability of croplands to runoff and leaching

USDA-ARS?s Scientific Manuscript database

Soil erosion and nutrient loss from surface runoff and sub-surface flows are critical problems for croplands in the United States. Assessing cropland vulnerability to runoff and leaching is needed for watershed or regional land use and land management planning and conservation resources allocation. ...
18 CFR 806.22 - Standards for consumptive uses of water.

Code of Federal Regulations, 2011 CFR

2011-04-01

... consumptive uses of water. 806.22 Section 806.22 Conservation of Power and Water Resources SUSQUEHANNA RIVER... withdrawn for a period of 90 days without impact to surface water flows. (ii) Release water for flow... be withdrawn for a period of 90 days without impact to surface water flows. (iii) Discontinue the...
External insulation of electrified railway and energy saving analysis

NASA Astrophysics Data System (ADS)

Dun, Xiaohong

2018-04-01

Through the analysis of the formation process of insulator surface fouling and the cause of fouling of the insulator, the electrified railway was explored to utilize the coating material on the surface of the insulator to achieve the effect of flashover prevention. At the same time the purpose of energy conservation can be achieved.
Sampling from living organisms: section 3 in Sampling and experiments with biofilms in the environment: chapter 6

USGS Publications Warehouse

Kellogg, Christina A.

2014-01-01

Living organisms, unlike inanimate surfaces, seem to exert some control over their surface microbiota, in many cases maintaining conserved, species-specific microbial communities. Microbial ecologists seek to characterize and identify these microbes to understand the roles they are playing in the larger organism's biology.
Direct k-space imaging of Mahan cones at clean and Bi-covered Cu(111) surfaces

NASA Astrophysics Data System (ADS)

Winkelmann, Aimo; Akin Ünal, A.; Tusche, Christian; Ellguth, Martin; Chiang, Cheng-Tien; Kirschner, Jürgen

2012-08-01

Using a specifically tailored experimental approach, we revisit the exemplary effect of photoemission from quasi-free electronic states in crystals. Applying a momentum microscope, we measure photoelectron momentum patterns emitted into the complete half-space above the sample after excitation from a linearly polarized laser light source. By the application of a fully three-dimensional (3D) geometrical model of direct optical transitions, we explain the characteristic intensity distributions that are formed by the photoelectrons in k-space under the combination of energy conservation and crystal momentum conservation in the 3D bulk as well as at the two-dimensional (2D) surface. For bismuth surface alloys on Cu(111), the energy-resolved photoelectron momentum patterns allow us to identify specific emission processes in which bulk excited electrons are subsequently diffracted by an atomic 2D surface grating. The polarization dependence of the observed intensity features in momentum space is explained based on the different relative orientations of characteristic reciprocal space directions with respect to the electric field vector of the incident light.
Investigations Of Surface-Catalyzed Reactions In A Mars Mixture

NASA Astrophysics Data System (ADS)

Dougherty, Max; Owens, W.; Meyers, J.; Fletcher, D. G.

2011-05-01

In the design of a thermal protection system (TPS) for a planetary entry vehicle, accurate modeling of the trajectory aero-heating poses a significant challenge owing to large uncertainties in chemical processes taking place at the surface. Even for surface-catalyzed reactions, which have been investigated extensively, there is no consensus on how they should be modeled; or, in some cases, on which reactions are likely to occur. Current TPS designs for Mars missions rely on a super-catalytic boundary condition, which assumes that all dissociated species recombine to the free stream composition.While this is recognized to be the the most conservative approach, discrepancies in aero-heating measurements in ground test facilities preclude less conservative design options, resulting in an increased TPS mass at the expense of scientific pay- load.Using two-photon absorption laser induced fluorescence in a 30 kW inductively coupled plasma torch facility, preliminary studies have been performed to obtain spatially-resolved measurements of the dominant species in a plasma boundary layer for a Martian atmosphere mixture over catalytic and non-catalytic surfaces.
Discontinuous Spectral Difference Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Liu, Yen; Vinokur, Marcel; Wang, Z. J.

2004-01-01

A new, high-order, conservative, and efficient method for conservation laws on unstructured grids is developed. The concept of discontinuous and high-order local representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) and the Spectral Volume (SV) methods, but while these methods are based on the integrated forms of the equations, the new method is based on the differential form to attain a simpler formulation and higher efficiency. A discussion on the Discontinuous Spectral Difference (SD) Method, locations of the unknowns and flux points and numerical results are also presented.
High order entropy conservative central schemes for wide ranges of compressible gas dynamics and MHD flows

NASA Astrophysics Data System (ADS)

Sjögreen, Björn; Yee, H. C.

2018-07-01

The Sjogreen and Yee [31] high order entropy conservative numerical method for compressible gas dynamics is extended to include discontinuities and also extended to equations of ideal magnetohydrodynamics (MHD). The basic idea is based on Tadmor's [40] original work for inviscid perfect gas flows. For the MHD four formulations of the MHD are considered: (a) the conservative MHD, (b) the Godunov [14] non-conservative form, (c) the Janhunen [19] - MHD with magnetic field source terms, and (d) a MHD with source terms by Brackbill and Barnes [5]. Three forms of the high order entropy numerical fluxes for the MHD in the finite difference framework are constructed. They are based on the extension of the low order form of Chandrashekar and Klingenberg [9], and two forms with modifications of the Winters and Gassner [49] numerical fluxes. For flows containing discontinuities and multiscale turbulence fluctuations the high order entropy conservative numerical fluxes as the new base scheme under the Yee and Sjogreen [31] and Kotov et al. [21,22] high order nonlinear filter approach is developed. The added nonlinear filter step on the high order centered entropy conservative spatial base scheme is only utilized at isolated computational regions, while maintaining high accuracy almost everywhere for long time integration of unsteady flows and DNS and LES of turbulence computations. Representative test cases for both smooth flows and problems containing discontinuities for the gas dynamics and the ideal MHD are included. The results illustrate the improved stability by using the high order entropy conservative numerical flux as the base scheme instead of the pure high order central scheme.
Evaluation of the Soil Conservation Service curve number methodology using data from agricultural plots

NASA Astrophysics Data System (ADS)

Lal, Mohan; Mishra, S. K.; Pandey, Ashish; Pandey, R. P.; Meena, P. K.; Chaudhary, Anubhav; Jha, Ranjit Kumar; Shreevastava, Ajit Kumar; Kumar, Yogendra

2017-01-01

The Soil Conservation Service curve number (SCS-CN) method, also known as the Natural Resources Conservation Service curve number (NRCS-CN) method, is popular for computing the volume of direct surface runoff for a given rainfall event. The performance of the SCS-CN method, based on large rainfall (P) and runoff (Q) datasets of United States watersheds, is evaluated using a large dataset of natural storm events from 27 agricultural plots in India. On the whole, the CN estimates from the National Engineering Handbook (chapter 4) tables do not match those derived from the observed P and Q datasets. As a result, the runoff prediction using former CNs was poor for the data of 22 (out of 24) plots. However, the match was little better for higher CN values, consistent with the general notion that the existing SCS-CN method performs better for high rainfall-runoff (high CN) events. Infiltration capacity (fc) was the main explanatory variable for runoff (or CN) production in study plots as it exhibited the expected inverse relationship between CN and fc. The plot-data optimization yielded initial abstraction coefficient (λ) values from 0 to 0.659 for the ordered dataset and 0 to 0.208 for the natural dataset (with 0 as the most frequent value). Mean and median λ values were, respectively, 0.030 and 0 for the natural rainfall-runoff dataset and 0.108 and 0 for the ordered rainfall-runoff dataset. Runoff estimation was very sensitive to λ and it improved consistently as λ changed from 0.2 to 0.03.
Characterization of 17 chaperone-usher fimbriae encoded by Proteus mirabilis reveals strong conservation

PubMed Central

Kuan, Lisa; Schaffer, Jessica N.; Zouzias, Christos D.

2014-01-01

Proteus mirabilis is a Gram-negative enteric bacterium that causes complicated urinary tract infections, particularly in patients with indwelling catheters. Sequencing of clinical isolate P. mirabilis HI4320 revealed the presence of 17 predicted chaperone-usher fimbrial operons. We classified these fimbriae into three groups by their genetic relationship to other chaperone-usher fimbriae. Sixteen of these fimbriae are encoded by all seven currently sequenced P. mirabilis genomes. The predicted protein sequence of the major structural subunit for 14 of these fimbriae was highly conserved (≥95 % identity), whereas three other structural subunits (Fim3A, UcaA and Fim6A) were variable. Further examination of 58 clinical isolates showed that 14 of the 17 predicted major structural subunit genes of the fimbriae were present in most strains (>85 %). Transcription of the predicted major structural subunit genes for all 17 fimbriae was measured under different culture conditions designed to mimic conditions in the urinary tract. The majority of the fimbrial genes were induced during stationary phase, static culture or colony growth when compared to exponential-phase aerated culture. Major structural subunit proteins for six of these fimbriae were detected using MS of proteins sheared from the surface of broth-cultured P. mirabilis, demonstrating that this organism may produce multiple fimbriae within a single culture. The high degree of conservation of P. mirabilis fimbriae stands in contrast to uropathogenic Escherichia coli and Salmonella enterica, which exhibit greater variability in their fimbrial repertoires. These findings suggest there may be evolutionary pressure for P. mirabilis to maintain a large fimbrial arsenal. PMID:24809384
A comparison of global conservation prioritization models with spatial spending patterns of conservation nongovernmental organizations.

PubMed

Holmes, George; Scholfield, Katherine; Brockington, Dan

2012-08-01

In recent decades, various conservation organizations have developed models to prioritize locations for conservation. Through a survey of the spending patterns of 281 conservation nongovernmental organizations (NGOs), we examined the relation between 2 such models and spatial patterns of spending by conservation NGOs in 44 countries in sub-Saharan Africa. We tested whether, at the country level, the proportion of a country designated as a conservation priority was correlated with where NGOs spent money. For one model (the combination of Conservation International's hotspots and High Biodiversity Wilderness Areas, which are areas of high endemism with high or low levels of vegetation loss respectively), there was no relation between the proportion of a country designated as a priority and levels of NGO spending, including by the NGO associated with the model. In the second model (Global 200), the proportion of a country designated as a priority and the amount of money spent by NGOs were significantly and positively related. Less money was spent in countries in northern and western sub-Saharan Africa than countries in southern and eastern Africa, relative to the proportion of the country designated as a conservation priority. We suggest that on the basis of our results some NGOs consider increasing their spending on the areas designated as of conservation priority which are currently relatively underfunded, although there are economic, political, cultural, historical, biological, and practical reasons why current spending patterns may not align with priority sites. ©2012 Society for Conservation Biology.
Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components.

PubMed

Baumstummler, A; Lehmann, D; Janjic, N; Ochsner, U A

2014-10-01

Slow off-rate modified aptamer (SOMAmer) reagents were generated to several Staphylococcus aureus cell surface-associated proteins via SELEX with multiple modified DNA libraries using purified recombinant or native proteins. High-affinity binding agents with sub-nanomolar Kd 's were obtained for staphylococcal protein A (SpA), clumping factors (ClfA, ClfB), fibronectin-binding proteins (FnbA, FnbB) and iron-regulated surface determinants (Isd). Further screening revealed several SOMAmers that specifically bound to Staph. aureus cells from all strains that were tested, but not to other staphylococci or other bacteria. SpA and ClfA SOMAmers proved useful for the selective capture and enrichment of Staph. aureus cells, as shown by culture and PCR, leading to improved limits of detection and efficient removal of PCR inhibitors. Detection of Staph. aureus cells was enhanced by several orders of magnitude when the bacterial cell surface was coated with SOMAmers followed by qPCR of the SOMAmers. Furthermore, fluorescence-labelled SpA SOMAmers demonstrated their utility as direct detection agents in flow cytometry. Significance and impact of the study: Monitoring for microbial contamination of food, water, nonsterile products or the environment is typically based on culture, PCR or antibodies. Aptamers that bind with high specificity and affinity to well-conserved cell surface epitopes represent a promising novel type of reagents to detect bacterial cells without the need for culture or cell lysis, including for the capture and enrichment of bacteria present at low cell densities and for the direct detection via qPCR or fluorescent staining. © 2014 Soma Logic, Inc. published by John Wiley & Sons Ltd On behalf of the society for Applied Microbiology.
Conservation Process Model (cpm): a Twofold Scientific Research Scope in the Information Modelling for Cultural Heritage

NASA Astrophysics Data System (ADS)

Fiorani, D.; Acierno, M.

2017-05-01

The aim of the present research is to develop an instrument able to adequately support the conservation process by means of a twofold approach, based on both BIM environment and ontology formalisation. Although BIM has been successfully experimented within AEC (Architecture Engineering Construction) field, it has showed many drawbacks for architectural heritage. To cope with unicity and more generally complexity of ancient buildings, applications so far developed have shown to poorly adapt BIM to conservation design with unsatisfactory results (Dore, Murphy 2013; Carrara 2014). In order to combine achievements reached within AEC through BIM environment (design control and management) with an appropriate, semantically enriched and flexible The presented model has at its core a knowledge base developed through information ontologies and oriented around the formalization and computability of all the knowledge necessary for the full comprehension of the object of architectural heritage an its conservation. Such a knowledge representation is worked out upon conceptual categories defined above all within architectural criticism and conservation scope. The present paper aims at further extending the scope of conceptual modelling within cultural heritage conservation already formalized by the model. A special focus is directed on decay analysis and surfaces conservation project.
Cloning and characterisation of type 4 fimbrial genes from Actinobacillus pleuropneumoniae.

PubMed

Stevenson, Andrew; Macdonald, Julie; Roberts, Mark

2003-03-20

Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumoniae. Little is known about the mechanisms by which A. pleuropneumoniae colonises the respiratory tract. Fimbriae are common mediators of bacterial adherence to mucosal epithelia and have been observed on the surface of A. pleuropneumoniae cells. Here we report the identification and characterisation of the type 4 fimbrial structural gene (apfA) from A. pleuropneumoniae. In addition a number of open reading frames were identified in A. pleuropneumoniae that have significant homology to type 4 fimbrial biogenesis genes from other species, including a putative leader specific peptidase (apfD). A. pleuropneumoniae apfA codes for a predicted polypeptide of approximately 16kDa, removal of the leader sequence at the predicted cleavage site would yield a 14.5kDa polypeptide. The first 30 residues of the mature polypeptide are well conserved with other members of the group A type 4 fimbriae family. The signal sequence of ApfA is 13 amino acids in length and, unusually, the residue that precedes the cleavage site is alanine rather than glycine which is found in most other type 4 fimbriae. The C-terminus of ApfA possesses cysteine residues that are conserved in type 4 fimbriae of many species. In other type 4 fimbriae the distal C-terminal cysteines form a disulphide bond that produces a loop, which is important for the function of fimbriae and also comprises a major antigenic determinant. A motif within the predicted loop in ApfA was found to be highly conserved in type 4 fimbriae of other HAP organisms (Haemophilus, Actinobacillus, Pasteurella). The A. pleuropneumoniae type 4 fimbrial biogenesis genes showed the strongest homology to putative type 4 fimbrial genes of Haemophilus ducreyi. A. pleuropneumoniae apfA gene was shown to be present and highly conserved in different serotypes of A. pleuropneumoniae. Recombinant ApfA was produced and used to raise anti-ApfA antisera.
Countering resistance to protected-area extension.

PubMed

Lindenmayer, David; Thorn, Simon; Noss, Reed

2018-04-01

The establishment of protected areas is a critical strategy for conserving biodiversity. Key policy directives like the Aichi targets seek to expand protected areas to 17% of Earth's land surface, with calls by some conservation biologists for much more. However, in places such as the United States, Germany, and Australia, attempts to increase protected areas are meeting strong resistance from communities, industry groups, and governments. We examined case studies of such resistance in Victoria, Australia, Bavaria, Germany, and Florida, United States. We considered 4 ways to tackle this problem. First, broaden the case for protected areas beyond nature conservation to include economic, human health, and other benefits, and translate these into a persuasive business case for protected areas. Second, better communicate the conservation values of protected areas. This should include highlighting how many species, communities, and ecosystems have been conserved by protected areas and the counterfactual (i.e., what would have been lost without protected area establishment). Third, consider zoning of activities to ensure the maintenance of effective management. Finally, remind citizens to think about conservation when they vote, including holding politicians accountable for their environmental promises. Without tackling resistance to expanding the protected estate, it will be impossible to reach conservation targets, and this will undermine attempts to stem the global extinction crisis. © 2017 Society for Conservation Biology.
Conserved Regions of Gonococcal TbpB Are Critical for Surface Exposure and Transferrin Iron Utilization

PubMed Central

Ostberg, Karen L.; DeRocco, Amanda J.; Mistry, Shreni D.; Dickinson, Mary Kathryne

2013-01-01

The transferrin-binding proteins TbpA and TbpB enable Neisseria gonorrhoeae to obtain iron from human transferrin. The lipoprotein TbpB facilitates, but is not strictly required for, TbpA-mediated iron acquisition. The goal of the current study was to determine the contribution of two conserved regions within TbpB to the function of this protein. Using site-directed mutagenesis, the first mutation we constructed replaced the lipobox (LSAC) of TbpB with a signal I peptidase cleavage site (LAAA), while the second mutation deleted a conserved stretch of glycine residues immediately downstream of the lipobox. We then evaluated the resulting mutants for effects on TbpB expression, surface exposure, and transferrin iron utilization. Western blot analysis and palmitate labeling indicated that the lipobox, but not the glycine-rich motif, is required for lipidation of TbpB and tethering to the outer membrane. TbpB was released into the supernatant by the mutant that produces TbpB LSAC. Neither mutation disrupted the transport of TbpB across the bacterial cell envelope. When these mutant TbpB proteins were produced in a strain expressing a form of TbpA that requires TbpB for iron acquisition, growth on transferrin was either abrogated or dramatically diminished. We conclude that surface tethering of TbpB is required for optimal performance of the transferrin iron acquisition system, while the presence of the polyglycine stretch near the amino terminus of TbpB contributes significantly to transferrin iron transport function. Overall, these results provide important insights into the functional roles of two conserved motifs of TbpB, enhancing our understanding of this critical iron uptake system. PMID:23836816
DOE Office of Scientific and Technical Information (OSTI.GOV)

Leger, M.; Morvan, J.M.; Thibaut, M.

Restoration of a geologic structure at earlier times is a good means to criticize, and next to improve, its interpretation. Restoration softwares already exist in 2D, but a lot of work remains to be done in 3D. The authors focus on the interbedding slip phenomenon, with bed-length and volume conservation. They unfold a (geometrical) foliation by optimizing following least-squares criteria: horizontalness, bed-length and volume conservation, under equality constraints related to the position of the ``binding`` or ``pin-surface``

Nondestructive evaluation of protective coatings for the conservation of industrial monuments

NASA Astrophysics Data System (ADS)

Welp, Hubert; Lenz, Marcel; Mazzon, Cristian; Dillmann, Christopher; Gerhardt, Nils C.; Prange, Michael; Hofmann, Martin R.

2017-07-01

For the conservation of cultural monuments standard anti-corrosion coatings are not applicable because the historical character of the objects would be lost. Alternative transparent coatings have to be evaluated and monitored nondestructively with respect to their effectiveness in protecting metal surfaces. We demonstrate that Optical Coherence Tomography (OCT) can be an alternative to the currently used method of Electrochemical Impedance Spectroscopy (EIS) for the characterization of coating defects and corrosion processes.
Digital Technology in the protection of cultural heritage Bao Fan Temple mural digital mapping survey

NASA Astrophysics Data System (ADS)

Zheng, Y.

2015-08-01

Peng Xi county, Sichuan province, the Bao Fan temple mural digitization survey mapping project: we use three-dimensional laserscanning, multi-baseline definition digital photography, multi-spectral digital image acquisition and other technologies for digital survey mapping. The purpose of this project is to use modern mathematical reconnaissance mapping means to obtain accurate mural shape, color, quality and other data. Combined with field investigation and laboratory analysis results, and based on a comprehensive survey and study, a comprehensive analysis of the historical Bao Fan Temple mural artistic and scientific value was conducted. A study of the mural's many qualities (structural, material, technique, preservation environment, degradation, etc.) reveal all aspects of the information carried by the Bao Fan Temple mural. From multiple angles (archeology, architecture, surveying, conservation science and other disciplines) an assessment for the Bao Fan Temple mural provides basic data and recommendations for conservation of the mural. In order to achieve the conservation of cultural relics in the Bao Fan Temple mural digitization survey mapping process, we try to apply the advantages of three-dimensional laser scanning equipment. For wall murals this means obtaining three-dimensional scale data from the scan of the building and through the analysis of these data to help determine the overall condition of the settlement as well as the deformation of the wall structure. Survey analysis provides an effective set of conclusions and suggestions for appropriate mural conservation. But before data collection, analysis and research need to first to select the appropriate scanning equipment, set the appropriate scanning accuracy and layout position of stations necessary to determine the scope of required data. We use the fine features of the three-dimensional laser scanning measuring arm to scan the mural surface deformation degradation to reflect the actual state of the mural surface patch model. For the degradation of the surface of the pigment layer, we use the patch model to simulate the scan obtained from an analysis. Statistics calculated relatively objective mural surface area from volume data, providing more accurate quantitative data for the mural conservation, especially, providing a viable technology for accurate monitoring of continued degradation. We believe, in order to make use of the three-dimensional laser scanning technology in a digital heritage conservation application, the technology should not only be used to record the object geometry and play a role in record keeping aspects, but, rather, should be used during the investigation to protect against targeted degradation and a more meaningful interpretation function. Like the development of the medical application of X-ray technology not only retains a picture, but more importantly, through this technical interpretation of patient pathology, guides doctors in carrying out the treatment work. Therefore, in the process of digitization of cultural heritage research, the focus should shift to the use of digital technology in the analysis of heritage object degradation and degradation monitoring surveys can promote the application of digital technology in the conservation of cultural heritage.
How to Go Green: Creating a Conservation Culture in a Public High School through Education, Modeling, and Communication

ERIC Educational Resources Information Center

Schelly, Chelsea; Cross, Jennifer E.; Franzen, William; Hall, Pete; Reeve, Stu

2012-01-01

This case study examines how energy conservation efforts in one public high school contributed to both sustainability education and the adoption of sustainable behavior within educational and organizational practice. Individual role models, school facilities, school governance and school culture together support both conservation and environmental…
High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

PubMed

Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

2014-01-01

Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.
Comparison of conservation metrics in a case study of lemurs.

PubMed

Gudde, Renske; Venditti, Chris

2016-12-01

Conservation planning is important to protect species from going extinct now that natural habitats are decreasing owing to human activity and climate change. However, there is considerable controversy in choosing appropriate metrics to weigh the value of species and geographic regions. For example, the added value of phylogenetic conservation-selection criteria remains disputed because high correlations between them and the nonphylogenetic criteria of species richness have been reported. We evaluated the commonly used conservation metrics species richness, endemism, phylogenetic diversity (PD), and phylogenetic endemism (PE) in a case study on lemurs of Madagascar. This enabled us to identify the conservation target of each metric and consider how they may be used in future conservation planning. We also devised a novel metric that uses a phylogeny scaled according to the rate of phenotypic evolution as a proxy for a species' ability to adapt to change. High rates of evolution may indicate generalization or specialization. Both specialization and low rates of evolution may result in an inability to adapt to changing environments. We examined conservation priorities by using the inverse of the rate of body mass evolution to account for species with low rates of evolution. In line with previous work, we found high correlations among species richness and PD (r = 0.96), and endemism and PE (r = 0.82) in Malagasy lemurs. Phylogenetic endemism in combination with rates of evolution and their inverse prioritized grid cells containing highly endemic and specialized lemurs at risk of extinction, such as Avahi occidentalis and Lepilemur edwardsi, 2 endangered lemurs with high rates of phenotypic evolution and low-quality diets, and Hapalemur aureus, a critically endangered species with a low rate of body mass evolution and a diet consisting of very high doses of cyanide. © 2016 Society for Conservation Biology.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraus, A.; Garner, P.; Hanan, N.

Thermal-hydraulic simulations have been performed using computational fluid dynamics (CFD) for the highly-enriched uranium (HEU) design of the IVG.1M reactor at the Institute of Atomic Energy (IAE) at the National Nuclear Center (NNC) in the Republic of Kazakhstan. Steady-state simulations were performed for both types of fuel assembly (FA), i.e. the FA in rows 1 & 2 and the FA in row 3, as well as for single pins in those FA (600 mm and 800 mm pins). Both single pin calculations and bundle sectors have been simulated for the most conservative operating conditions corresponding to the 10 MW outputmore » power, which corresponds to a pin unit cell Reynolds number of only about 7500. Simulations were performed using the commercial code STAR-CCM+ for the actual twisted pin geometry as well as a straight-pin approximation. Various Reynolds-Averaged Navier-Stokes (RANS) turbulence models gave different results, and so some validation runs with a higher-fidelity Large Eddy Simulation (LES) code were performed given the lack of experimental data. These singled out the Realizable Two-Layer k-ε as the most accurate turbulence model for estimating surface temperature. Single-pin results for the twisted case, based on the average flow rate per pin and peak pin power, were conservative for peak clad surface temperature compared to the bundle results. Also the straight-pin calculations were conservative as compared to the twisted pin simulations, as expected, but the single-pin straight case was not always conservative with regard to the straight-pin bundle. This was due to the straight-pin temperature distribution being strongly influenced by the pin orientation, particularly near the outer boundary. The straight-pin case also predicted the peak temperature to be in a different location than the twisted-pin case. This is a limitation of the straight-pin approach. The peak temperature pin was in a different location from the peak power pin in every case simulated, and occurred at an inner pin just before the enrichment change. The 600 mm case demonstrated a peak clad surface temperature of 370.4 K, while the 800 mm case had a temperature of 391.6 K. These temperatures are well below the necessary temperatures for boiling to occur at the rated pressure. Fuel temperatures are also well below the melting point. Future bundle work will include simulations of the proposed low-enriched uranium (LEU) design. Two transient scenarios were also investigated for the single-pin geometries. Both were “model” problems that were focused on pure thermal-hydraulic behavior, and as such were simple power changes that did not incorporate neutron kinetics modeling. The first scenario was a high-power, ramp increase, while the second scenario was a low-power, step increase. A cylindrical RELAP model was also constructed to investigate its accuracy as compared to the higher-fidelity CFD. Comparisons between the two codes showed good agreement for peak temperatures in the fuel and at the cladding surface for both cases. In the step transient, temperatures at four axial levels were also computed. These showed greater but reasonable discrepancy, with RELAP outputting higher temperatures. These results provide some evidence that RELAP can be used with confidence in modeling transients for IVG.« less
Near grazing scattering from non-Gaussian ocean surfaces

NASA Technical Reports Server (NTRS)

Kim, Yunjin; Rodriguez, Ernesto

1993-01-01

We investigate the behavior of the scattered electromagnetic waves from non-Gaussian ocean surfaces at near grazing incidence. Even though the scattering mechanisms at moderate incidence angles are relatively well understood, the same is not true for near grazing rough surface scattering. However, from the experimental ocean scattering data, it has been observed that the backscattering cross section of a horizontally polarized wave can be as large as the vertical counterpart at near grazing incidence. In addition, these returns are highly intermittent in time. There have been some suggestions that these unexpected effects may come from shadowing or feature scattering. Using numerical scattering simulations, it can be shown that the horizontal backscattering cannot be larger than the vertical one for the Gaussian surfaces. Our main objective of this study is to gain a clear understanding of scattering mechanisms underlying the near grazing ocean scattering. In order to evaluate the backscattering cross section from ocean surfaces at near grazing incidence, both the hydrodynamic modeling of ocean surfaces and an accurate near grazing scattering theory are required. For the surface modeling, we generate Gaussian surfaces from the ocean surface power spectrum which is derived using several experimental data. Then, weakly nonlinear large scale ocean surfaces are generated following Longuet-Higgins. In addition, the modulation of small waves by large waves is included using the conservation of wave action. For surface scattering, we use MOM (Method of Moments) to calculate the backscattering from scattering patches with the two scale shadowing approximation. The differences between Gaussian and non-Gaussian surface scattering at near grazing incidence are presented.
Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf

PubMed Central

Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N. W.; Casewell, Nicholas R.; Undheim, Eivind A. B.; Vidal, Nicolas; Ali, Syed A.; King, Glenn F.; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation. PMID:24312363
Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf.

PubMed

Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N W; Casewell, Nicholas R; Undheim, Eivind A B; Vidal, Nicolas; Ali, Syed A; King, Glenn F; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation.
Biogeochemical Proxies in Scleractinian Corals used to Reconstruct Ocean Circulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guilderson, T.P.; Kashgarian, M.; Schrag, D.P.

We utilize monthly {sup 14}C data derived from coral archives in conjunction with ocean circulation models to address two questions: (1) how does the shallow circulation of the tropical Pacific vary on seasonal to decadal time scales and (2) which dynamic processes determine the mean vertical structure of the equatorial Pacific thermocline. Our results directly impact the understanding of global climate events such as the El Nino-Southern Oscillation (ENSO). To study changes in ocean circulation and water mass distribution involved in the genesis and evolution of ENSO and decadal climate variability, it is necessary to have records of climate variablesmore » several decades in length. Continuous instrumental records are limited because technology for continuous monitoring of ocean currents has only recently been available, and ships of opportunity archives such as COADS contain large spatial and temporal biases. In addition, temperature and salinity in surface waters are not conservative and thus can not be independently relied upon to trace water masses, reducing the utility of historical observations. Radiocarbon ({sup 14}C) in sea water is a quasi-conservative water mass tracer and is incorporated into coral skeletal material, thus coral {sup 14}C records can be used to reconstruct changes in shallow circulation that would be difficult to characterize using instrumental data. High resolution {Delta}{sup 14}C timeseries such as these, provide a powerful constraint on the rate of surface ocean mixing and hold great promise to augment onetime surveys such as GEOSECS and WOCE. These data not only provide fundamental information about the shallow circulation of the Pacific, but can be used as a benchmark for the next generation of high resolution ocean models used in prognosticating climate change.« less
Natural selection promotes antigenic evolvability.

PubMed

Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

2013-01-01

The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.
Natural Selection Promotes Antigenic Evolvability

PubMed Central

Graves, Christopher J.; Ros, Vera I. D.; Stevenson, Brian; Sniegowski, Paul D.; Brisson, Dustin

2013-01-01

The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed ‘cassettes’ that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections. PMID:24244173
Towards a universal vaccine for avian influenza: Protective efficacy of modified Vaccinia virus Ankara and Adenovirus vaccines expressing conserved influenza antigens in chickens challenged with low pathogenic avian influenza virus

PubMed Central

Boyd, Amy C.; Ruiz-Hernandez, Raul; Peroval, Marylene Y.; Carson, Connor; Balkissoon, Devanand; Staines, Karen; Turner, Alison V.; Hill, Adrian V.S.; Gilbert, Sarah C.; Butter, Colin

2013-01-01

Current vaccines targeting surface proteins can drive antigenic variation resulting either in the emergence of more highly pathogenic viruses or of antigenically distinct viruses that escape control by vaccination and thereby persist in the host population. Influenza vaccines typically target the highly mutable surface proteins and do not provide protection against heterologous challenge. Vaccines which induce immune responses against conserved influenza epitopes may confer protection against heterologous challenge. We report here the results of vaccination with recombinant modified Vaccinia virus Ankara (MVA) and Adenovirus (Ad) expressing a fusion construct of nucleoprotein and matrix protein (NP + M1). Prime and boost vaccination regimes were trialled in different ages of chicken and were found to be safe and immunogenic. Interferon-γ (IFN-γ) ELISpot was used to assess the cellular immune response post secondary vaccination. In ovo Ad prime followed by a 4 week post hatch MVA boost was identified as the most immunogenic regime in one outbred and two inbred lines of chicken. Following vaccination, one inbred line (C15I) was challenged with low pathogenic avian influenza (LPAI) H7N7 (A/Turkey/England/1977). Birds receiving a primary vaccination with Ad-NP + M1 and a secondary vaccination with MVA-NP + M1 exhibited reduced cloacal shedding as measured by plaque assay at 7 days post infection compared with birds vaccinated with recombinant viruses containing irrelevant antigen. This preliminary indication of efficacy demonstrates proof of concept in birds; induction of T cell responses in chickens by viral vectors containing internal influenza antigens may be a productive strategy for the development of vaccines to induce heterologous protection against influenza in poultry. PMID:23200938
Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI).

PubMed

Niu, Qian; Ybe, Joel A

2008-02-01

Huntington's disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of the huntingtin protein permits HIP1 protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain. Our 2.8-A crystal structure of the HIP1 371-481 subfragment that includes F432 and K474, which is important for HIPPI binding, is not a death-effector domain but is a partially opened coiled coil. The HIP1 371-481 model reveals a basic surface that we hypothesize to be suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R, from different organisms but are not conserved in the yeast homologue of HIP1, sla2p. We have modeled approximately 85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (Protein Data Bank code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a U-shaped HIP1 molecule.
Biogeochemical Proxies in Scleractinian Corals used to Reconstruct Ocean Circulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guilderson, T P; Kashgarian, M; Schrag, D P

2001-02-23

We utilize monthly {sup 14}C data derived from coral archives in conjunction with ocean circulation models to address two questions: (1) how does the shallow circulation of the tropical Pacific vary on seasonal to decadal time scales and (2) which dynamic processes determine the mean vertical structure of the equatorial Pacific thermocline. Our results directly impact the understanding of global climate events such as the El Nino-Southern Oscillation (ENSO). To study changes in ocean circulation and water mass distribution involved in the genesis and evolution of ENSO and decadal climate variability, it is necessary to have records of climate variablesmore » several decades in length. Continuous instrumental records are limited because technology for continuous monitoring of ocean currents has only recently been available, and ships of opportunity archives such as COADS contain large spatial and temporal biases. In addition, temperature and salinity in surface waters are not conservative and thus can not be independently relied upon to trace water masses, reducing the utility of historical observations. Radiocarbon ({sup 14}C) in sea water is a quasi-conservative water mass tracer and is incorporated into coral skeletal material, thus coral {sup 14}C records can be used to reconstruct changes in shallow circulation that would be difficult to characterize using instrumental data. High resolution {Delta}{sup 14}C timeseries such as these, provide a powerful constraint on the rate of surface ocean mixing and hold great promise to augment onetime surveys such as GEOSECS and WOCE. These data not only provide fundamental information about the shallow circulation of the Pacific, but can be used as a benchmark for the next generation of high resolution ocean models used in prognosticating climate change.« less
Phylogenetic analysis of conservation priorities for aquatic mammals and their terrestrial relatives, with a comparison of methods.

PubMed

May-Collado, Laura J; Agnarsson, Ingi

2011-01-01

Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all 'high priority' species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct--and thus 'biodiverse'--species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders.
The city as a refuge for insect pollinators.

PubMed

Hall, Damon M; Camilo, Gerardo R; Tonietto, Rebecca K; Ollerton, Jeff; Ahrné, Karin; Arduser, Mike; Ascher, John S; Baldock, Katherine C R; Fowler, Robert; Frankie, Gordon; Goulson, Dave; Gunnarsson, Bengt; Hanley, Mick E; Jackson, Janet I; Langellotto, Gail; Lowenstein, David; Minor, Emily S; Philpott, Stacy M; Potts, Simon G; Sirohi, Muzafar H; Spevak, Edward M; Stone, Graham N; Threlfall, Caragh G

2017-02-01

Research on urban insect pollinators is changing views on the biological value and ecological importance of cities. The abundance and diversity of native bee species in urban landscapes that are absent in nearby rural lands evidence the biological value and ecological importance of cities and have implications for biodiversity conservation. Lagging behind this revised image of the city are urban conservation programs that historically have invested in education and outreach rather than programs designed to achieve high-priority species conservation results. We synthesized research on urban bee species diversity and abundance to determine how urban conservation could be repositioned to better align with new views on the ecological importance of urban landscapes. Due to insect pollinators' relatively small functional requirements-habitat range, life cycle, and nesting behavior-relative to larger mammals, we argue that pollinators put high-priority and high-impact urban conservation within reach. In a rapidly urbanizing world, transforming how environmental managers view the city can improve citizen engagement and contribute to the development of more sustainable urbanization. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.
Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes.

PubMed

Xu, Qingping; Traag, Bjørn A; Willemse, Joost; McMullan, Daniel; Miller, Mitchell D; Elsliger, Marc-André; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Chruszcz, Maksymilian; Clayton, Thomas; Das, Debanu; Deller, Marc C; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L; Feuerhelm, Julie; Grant, Joanna C; Grzechnik, Anna; Grzechnik, Slawomir K; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K; Klock, Heath E; Knuth, Mark W; Kozbial, Piotr; Krishna, S Sri; Kumar, Abhinav; Marciano, David; Minor, Wladek; Mommaas, A Mieke; Morse, Andrew T; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L; Sefcovic, Natasha; Tien, Henry J; Trame, Christine B; van den Bedem, Henry; Wang, Shuren; Weekes, Dana; Hodgson, Keith O; Wooley, John; Deacon, Ashley M; Godzik, Adam; Lesley, Scott A; Wilson, Ian A; van Wezel, Gilles P

2009-09-11

SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 A resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic "whirly" single-stranded DNA/RNA-binding proteins. However, the electro-negative surface of the SALPs suggests that neither SsgB nor any of the other SALPs are likely to interact with nucleotide substrates. Instead, we show that a conserved hydrophobic surface is likely to be important for SALP function and suggest that proteins are the likely binding partners.
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

PubMed Central

Hopkins, Max; Kailasan, Shweta; Cohen, Allison; Roux, Simon; Tucker, Kimberly Pause; Shevenell, Amelia; Agbandje-McKenna, Mavis; Breitbart, Mya

2014-01-01

The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. PMID:24694711
Lysimetric evaluation of simplified surface energy balance approach in the Texas high plains

USGS Publications Warehouse

Gowda, P.H.; Senay, G.B.; Howell, T.A.; Marek, T.H.

2009-01-01

Numerous energy balance (EB) algorithms have been developed to make use of remote sensing data to estimate evapotranspiration (ET) regionally. However, most EB models are complex to use and efforts are being made to simplify procedures mainly through the scaling of reference ET. The Simplified Surface Energy Balance (SSEB) is one such method. This approach has never been evaluated using measured ET data. In this study, the SSEB approach was applied to 14 Landsat TM images covering a major portion of the Southern High Plains that were acquired during 2006 and 2007 cropping seasons. Performance of the SSEB was evaluated by comparing estimated ET with measured daily ET from four large monolithic lysimeters at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. Statistical evaluation of results indicated that the SSEB accounted for 84% of the variability in the measured ET values with a slope and intercept of 0.75 and 1.1 mm d-1, respectively. Considering the minimal amount of ancillary data required and excellent performance in predicting daily ET, the SSEB approach is a promising tool for mapping ET in the semiarid Texas High Plains and in other parts of the world with similar hydro-climatic conditions.

Lysimetric Evaluation of Simplified Surface Energy Balance Approach in the Texas High Plains

USGS Publications Warehouse

Senay, Gabriel B.; Gowda, P.H.; Howell, T.A.; Marek, T.H.

2009-01-01

Numerous energy balance (EB) algorithms have been developed to make use of remote sensing data to estimate evapotranspiration (ET) regionally. However, most EB models are complex to use and efforts are being made to simplify procedures mainly through the scaling of reference ET. The Simplified Surface Energy Balance (SSEB) is one such method. This approach has never been evaluated using measured ET data. In this study, the SSEB approach was applied to fourteen Landsat TM images covering a major portion of the Southern High Plains that were acquired during 2006 and 2007 cropping seasons. Performance of the SSEB was evaluated by comparing estimated ET with measured daily ET from four large monolithic lysimeters at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. Statistical evaluation of results indicated that the SSEB accounted for 84% of the variability in the measured ET values with a slope and intercept of 0.75 and 1.1 mm d-1, respectively. Considering the minimal amount of ancillary data required and excellent performance in predicting daily ET, the SSEB approach is a promising tool for mapping ET in the semiarid Texas High Plains and in other parts of the world with similar hydro-climatic conditions.
Mechanics and Hydrodynamics of Acrobatics and Aquabatics by Whales and Dolphins

NASA Astrophysics Data System (ADS)

Fish, Frank

2017-11-01

Cetaceans (whales, dolphins) are extremely energetic, fast swimming, and highly maneuverable in both water and air. Behaviors that cross the interface include breaching, porpoising, tail stands, and spin-leaps. The mechanics of breaching and porpoising entails propulsive movements of the caudal flukes to accelerate the animal vertically through the water surface to become airborne. Porpoising is beneficial to reduce the energetic cost of swimming at high speeds. Tail stands have a vertically oriented dolphin with half or more of its body out of the water. Bubble DPIV was used to quantify the propulsive force matching the weight of the animal supported above the water surface. The propulsive movements produced a jet flow and associated vorticity directed downward. Spin-leaps require a rapid vertical ascend from underwater by a rolling dolphin. Out of the water, the spin rate increases due to conservation of angular momentum and an imbalance between driving and resistive torques. The spin rate is associated with the moment of inertia of the animal's morphology. The physics of these high-energy maneuvers have engineering application for understanding ballistic performance across the air/water interface. Funded from ONR-MURI Grant N0001141410533.
Cave Conservation Priority Index to Adopt a Rapid Protection Strategy: A Case Study in Brazilian Atlantic Rain Forest

NASA Astrophysics Data System (ADS)

Souza Silva, Marconi; Martins, Rogério Parentoni; Ferreira, Rodrigo Lopes

2015-02-01

Cave environments are characterized by possessing specialized fauna living in high environmental stability with limited food conditions. These fauna are highly vulnerable to impacts, because this condition can frequently be easily altered. Moreover, environmental determinants of the biodiversity patterns of caves remain poorly understood and protected. Therefore, the main goal of this work is to propose a cave conservation priority index (CCPi) for a rapid assessment for troglobiotic and troglophile protection. Furthermore, the troglobiotic diversity, distribution and threats have been mapped in the Brazilian Atlantic forest. To propose the CCPi, the human impacts and richness of troglobiotic and troglophile species of 100 caves were associated. Data related to troglomorphic/troglobiotic fauna from another 200 caves were used to map the troglobiotic diversity and distribution. The CCPi reveals extremely high conservation priority for 15 % of the caves, high for 36 % and average for 46 % of the caves. Fourteen caves with extremely high priorities should have urgent conservation and management actions. The geographical distribution of the 221 known troglobiotic/troglomorphic species allowed us to select 19 karst areas that need conservation actions. Seven areas were considered to have urgent priority for conservation actions. The two richest areas correspond to the "iron quadrangle" with iron ore caves (67 spp.) and the "Açungui limestone group" (56 spp.). Both areas have several caves and are important aquifers. The use of the CCPi can prevent future losses because it helps assessors to select caves with priorities for conservation which should receive emergency attention in relation to protection, management and conservation actions.
Protecting Important Sites for Biodiversity Contributes to Meeting Global Conservation Targets

PubMed Central

Butchart, Stuart H. M.; Scharlemann, Jörn P. W.; Evans, Mike I.; Quader, Suhel; Aricò, Salvatore; Arinaitwe, Julius; Balman, Mark; Bennun, Leon A.; Bertzky, Bastian; Besançon, Charles; Boucher, Timothy M.; Brooks, Thomas M.; Burfield, Ian J.; Burgess, Neil D.; Chan, Simba; Clay, Rob P.; Crosby, Mike J.; Davidson, Nicholas C.; De Silva, Naamal; Devenish, Christian; Dutson, Guy C. L.; Fernández, David F. Día z; Fishpool, Lincoln D. C.; Fitzgerald, Claire; Foster, Matt; Heath, Melanie F.; Hockings, Marc; Hoffmann, Michael; Knox, David; Larsen, Frank W.; Lamoreux, John F.; Loucks, Colby; May, Ian; Millett, James; Molloy, Dominic; Morling, Paul; Parr, Mike; Ricketts, Taylor H.; Seddon, Nathalie; Skolnik, Benjamin; Stuart, Simon N.; Upgren, Amy; Woodley, Stephen

2012-01-01

Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites). Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs). While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45–1.14% annually since 1950 for IBAs and 0.79–1.49% annually for AZEs). Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends. PMID:22457717
The complete influenza hemagglutinin fusion domain adopts a tight helical hairpin arrangement at the lipid:water interface.

PubMed

Lorieau, Justin L; Louis, John M; Bax, Ad

2010-06-22

All but five of the N-terminal 23 residues of the HA2 domain of the influenza virus glycoprotein hemagglutinin (HA) are strictly conserved across all 16 serotypes of HA genes. The structure and function of this HA2 fusion peptide (HAfp) continues to be the focus of extensive biophysical, computational, and functional analysis, but most of these analyses are of peptides that do not include the strictly conserved residues Trp(21)-Tyr(22)-Gly(23). The heteronuclear triple resonance NMR study reported here of full length HAfp of sero subtype H1, solubilized in dodecylphosphatidyl choline, reveals a remarkably tight helical hairpin structure, with its N-terminal alpha-helix (Gly(1)-Gly(12)) packed tightly against its second alpha-helix (Trp(14)-Gly(23)), with six of the seven conserved Gly residues at the interhelical interface. The seventh conserved Gly residue in position 13 adopts a positive angle, enabling the hairpin turn that links the two helices. The structure is stabilized by multiple interhelical C(alpha)H to C=O hydrogen bonds, characterized by strong interhelical H(N)-H(alpha) and H(alpha)-H(alpha) NOE contacts. Many of the previously identified mutations that make HA2 nonfusogenic are also incompatible with the tight antiparallel hairpin arrangement of the HAfp helices.(15)N relaxation analysis indicates the structure to be highly ordered on the nanosecond time scale, and NOE analysis indicates HAfp is located at the water-lipid interface, with its hydrophobic surface facing the lipid environment, and the Gly-rich side of the helix-helix interface exposed to solvent.
Galectins as self/non-self recognition receptors in innate and adaptive immunity: an unresolved paradox

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Nita-Lazar, Mihai; Banerjee, Aditi; Pasek, Marta; Shridhar, Surekha; Guha, Prasun; Fernández-Robledo, José A.

2012-01-01

Galectins are characterized by their binding affinity for β-galactosides, a unique binding site sequence motif, and wide taxonomic distribution and structural conservation in vertebrates, invertebrates, protista, and fungi. Since their initial description, galectins were considered to bind endogenous (“self”) glycans and mediate developmental processes and cancer. In the past few years, however, numerous studies have described the diverse effects of galectins on cells involved in both innate and adaptive immune responses, and the mechanistic aspects of their regulatory roles in immune homeostasis. More recently, however, evidence has accumulated to suggest that galectins also bind exogenous (“non-self”) glycans on the surface of potentially pathogenic microbes, parasites, and fungi, suggesting that galectins can function as pattern recognition receptors (PRRs) in innate immunity. Thus, a perplexing paradox arises by the fact that galectins also recognize lactosamine-containing glycans on the host cell surface during developmental processes and regulation of immune responses. According to the currently accepted model for non-self recognition, PRRs recognize pathogens via highly conserved microbial surface molecules of wide distribution such as LPS or peptidoglycan (pathogen-associated molecular patterns; PAMPs), which are absent in the host. Hence, this would not apply to galectins, which apparently bind similar self/non-self molecular patterns on host and microbial cells. This paradox underscores first, an oversimplification in the use of the PRR/PAMP terminology. Second, and most importantly, it reveals significant gaps in our knowledge about the diversity of the host galectin repertoire, and the subcellular targeting, localization, and secretion. Furthermore, our knowledge about the structural and biophysical aspects of their interactions with the host and microbial carbohydrate moieties is fragmentary, and warrants further investigation. PMID:22811679
Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin*

PubMed Central

Koiwai, Kotaro; Hartmann, Marcus D.; Linke, Dirk; Lupas, Andrei N.; Hori, Katsutoshi

2016-01-01

Trimeric autotransporter adhesins (TAAs) on the cell surface of Gram-negative pathogens mediate bacterial adhesion to host cells and extracellular matrix proteins. However, AtaA, a TAA in the nonpathogenic Acinetobacter sp. strain Tol 5, shows nonspecific high adhesiveness to abiotic material surfaces as well as to biotic surfaces. It consists of a passenger domain secreted by the C-terminal transmembrane anchor domain (TM), and the passenger domain contains an N-terminal head, N-terminal stalk, C-terminal head (Chead), and C-terminal stalk (Cstalk). The Chead-Cstalk-TM fragment, which is conserved in many Acinetobacter TAAs, has by itself the head-stalk-anchor architecture of a complete TAA. Here, we show the crystal structure of the Chead-Cstalk fragment, AtaA_C-terminal passenger domain (CPSD), providing the first view of several conserved TAA domains. The YadA-like head (Ylhead) of the fragment is capped by a unique structure (headCap), composed of three β-hairpins and a connector motif; it also contains a head insert motif (HIM1) before its last inner β-strand. The headCap, Ylhead, and HIM1 integrally form a stable Chead structure. Some of the major domains of the CPSD fragment are inherently flexible and provide bending sites for the fiber between segments whose toughness is ensured by topological chain exchange and hydrophobic core formation inside the trimer. Thus, although adherence assays using in-frame deletion mutants revealed that the characteristic adhesive sites of AtaA reside in its N-terminal part, the flexibility and toughness of the CPSD part provide the resilience that enables the adhesive properties of the full-length fiber across a wide range of conditions. PMID:26698633
Isothiocyanate from Moringa oleifera seeds mitigates hydrogen peroxide-induced cytotoxicity and preserved morphological features of human neuronal cells

PubMed Central

Shaari, Khozirah; Rosli, Rozita

2018-01-01

Reactive oxygen species are well known for induction of oxidative stress conditions through oxidation of vital biomarkers leading to cellular death via apoptosis and other process, thereby causing devastative effects on the host organs. This effect is believed to be linked with pathological alterations seen in several neurodegenerative disease conditions. Many phytochemical compounds proved to have robust antioxidant activities that deterred cells against cytotoxic stress environment, thus protect apoptotic cell death. In view of that we studied the potential of glucomoringin-isothiocyanate (GMG-ITC) or moringin to mitigate the process that lead to neurodegeneration in various ways. Neuroprotective effect of GMG-ITC was performed on retinoic acid (RA) induced differentiated neuroblastoma cells (SHSY5Y) via cell viability assay, flow cytometry analysis and fluorescence microscopy by means of acridine orange and propidium iodide double staining, to evaluate the anti-apoptotic activity and morphology conservation ability of the compound. Additionally, neurite surface integrity and ultrastructural analysis were carried out by means of scanning and transmission electron microscopy to assess the orientation of surface and internal features of the treated neuronal cells. GMG-ITC pre-treated neuron cells showed significant resistance to H2O2-induced apoptotic cell death, revealing high level of protection by the compound. Increase of intracellular oxidative stress induced by H2O2 was mitigated by GMG-ITC. Thus, pre-treatment with the compound conferred significant protection to cytoskeleton and cytoplasmic inclusion coupled with conservation of surface morphological features and general integrity of neuronal cells. Therefore, the collective findings in the presence study indicated the potentials of GMG-ITC to protect the integrity of neuron cells against induced oxidative-stress related cytotoxic processes, the hallmark of neurodegenerative diseases. PMID:29723199
Crucial nesting habitat for gunnison sage-grouse: A spatially explicit hierarchical approach

USGS Publications Warehouse

Aldridge, Cameron L.; Saher, D.J.; Childers, T.M.; Stahlnecker, K.E.; Bowen, Z.H.

2012-01-01

Gunnison sage-grouse (Centrocercus minimus) is a species of special concern and is currently considered a candidate species under Endangered Species Act. Careful management is therefore required to ensure that suitable habitat is maintained, particularly because much of the species' current distribution is faced with exurban development pressures. We assessed hierarchical nest site selection patterns of Gunnison sage-grouse inhabiting the western portion of the Gunnison Basin, Colorado, USA, at multiple spatial scales, using logistic regression-based resource selection functions. Models were selected using Akaike Information Criterion corrected for small sample sizes (AIC c) and predictive surfaces were generated using model averaged relative probabilities. Landscape-scale factors that had the most influence on nest site selection included the proportion of sagebrush cover >5%, mean productivity, and density of 2 wheel-drive roads. The landscape-scale predictive surface captured 97% of known Gunnison sage-grouse nests within the top 5 of 10 prediction bins, implicating 57% of the basin as crucial nesting habitat. Crucial habitat identified by the landscape model was used to define the extent for patch-scale modeling efforts. Patch-scale variables that had the greatest influence on nest site selection were the proportion of big sagebrush cover >10%, distance to residential development, distance to high volume paved roads, and mean productivity. This model accurately predicted independent nest locations. The unique hierarchical structure of our models more accurately captures the nested nature of habitat selection, and allowed for increased discrimination within larger landscapes of suitable habitat. We extrapolated the landscape-scale model to the entire Gunnison Basin because of conservation concerns for this species. We believe this predictive surface is a valuable tool which can be incorporated into land use and conservation planning as well the assessment of future land-use scenarios. ?? 2011 The Wildlife Society.
Characterization of a highly conserved human homolog to the chicken neural cell surface protein Bravo/Nr-CAM that maps to chromosome band 7q31

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, R.P.; Vielmetter, J.; Dreyer, W.J.

1996-08-01

The neuronal cell adhesion molecule Bravo/Nr-CAM is a cell surface protein of the immunoglobulin (Ig) superfamily and is closely related to the L1/NgCAM and neurofascin molecules, all of which contain six immunoglobulin domains, five fibronectin repeats, a transmembrane region, and an intracellular domain. Chicken Bravo/Nr-CAM has been shown to interact with other cell surface molecules of the Ig superfamily and has been implicated in specific pathfinding roles of axonal growth cones in the developing nervous system. We now report the characterization of cDNA clones encoding the human Bravo/Nr-CAM protein, which, like its chicken homolog, is composed of six V-like Igmore » domains and five fibronectin type III repeats. The human Bravo/Nr-CAM homolog also contains a transmembrane and intracellular domain, both of which are 100% conserved at the amino acid level compared to its chicken homolog. Overall, the human Bravo/Nr-CAM homolog is 82% identical to the chicken Bravo/Nr-CAM amino acid sequence. Independent cDNAs encoding four different isoforms were also identified, all of which contain alternatively spliced variants around the fifth fibronectin type III repeat, including one isoform that had been previously identified for chicken Bravo/Nr-CAM. Northern blot analysis reveals one mRNA species of approximately 7.0 kb in adult human brain tissue. Fluorescence in situ hybridization maps the gene for human Bravo/Nr-CAM to human chromosome 7q31.1-q31.2. This chromosomal locus has been previously identified as containing a tumore suppressor candidate gene commonly deleted in certain human cancer tissues. 38 refs., 5 figs.« less
A novel thromboxane A2 receptor N42S variant results in reduced surface expression and platelet dysfunction.

PubMed

Nisar, Shaista P; Lordkipanidzé, Marie; Jones, Matthew L; Dawood, Ban; Murden, Sherina; Cunningham, Margaret R; Mumford, Andrew D; Wilde, Jonathan T; Watson, Steve P; Mundell, Stuart J; Lowe, Gillian C

2014-05-05

A small number of thromboxane receptor variants have been described in patients with a bleeding history that result in platelet dysfunction. We have identified a patient with a history of significant bleeding, who expresses a novel heterozygous thromboxane receptor variant that predicts an asparagine to serine substitution (N42S). This asparagine is conserved across all class A GPCRs, suggesting a vital role for receptor structure and function.We investigated the functional consequences of the TP receptor heterozygous N42S substitution by performing platelet function studies on platelet-rich plasma taken from the patient and healthy controls. We investigated the N42S mutation by expressing the wild-type (WT) and mutant receptor in human embryonic kidney (HEK) cells. Aggregation studies showed an ablation of arachidonic acid responses in the patient, whilst there was right-ward shift of the U46619 concentration response curve (CRC). Thromboxane generation was unaffected. Calcium mobilisation studies in cells lines showed a rightward shift of the U46619 CRC in N42S-expressing cells compared to WT. Radioligand binding studies revealed a reduction in BMax in platelets taken from the patient and in N42S-expressing cells, whilst cell studies confirmed poor surface expression. We have identified a novel thromboxane receptor variant, N42S, which results in platelet dysfunction due to reduced surface expression. It is associated with a significant bleeding history in the patient in whom it was identified. This is the first description of a naturally occurring variant that results in the substitution of this highly conserved residue and confirms the importance of this residue for correct GPCR function.
Isothiocyanate from Moringa oleifera seeds mitigates hydrogen peroxide-induced cytotoxicity and preserved morphological features of human neuronal cells.

PubMed

Jaafaru, Mohammed Sani; Nordin, Norshariza; Shaari, Khozirah; Rosli, Rozita; Abdull Razis, Ahmad Faizal

2018-01-01

Reactive oxygen species are well known for induction of oxidative stress conditions through oxidation of vital biomarkers leading to cellular death via apoptosis and other process, thereby causing devastative effects on the host organs. This effect is believed to be linked with pathological alterations seen in several neurodegenerative disease conditions. Many phytochemical compounds proved to have robust antioxidant activities that deterred cells against cytotoxic stress environment, thus protect apoptotic cell death. In view of that we studied the potential of glucomoringin-isothiocyanate (GMG-ITC) or moringin to mitigate the process that lead to neurodegeneration in various ways. Neuroprotective effect of GMG-ITC was performed on retinoic acid (RA) induced differentiated neuroblastoma cells (SHSY5Y) via cell viability assay, flow cytometry analysis and fluorescence microscopy by means of acridine orange and propidium iodide double staining, to evaluate the anti-apoptotic activity and morphology conservation ability of the compound. Additionally, neurite surface integrity and ultrastructural analysis were carried out by means of scanning and transmission electron microscopy to assess the orientation of surface and internal features of the treated neuronal cells. GMG-ITC pre-treated neuron cells showed significant resistance to H2O2-induced apoptotic cell death, revealing high level of protection by the compound. Increase of intracellular oxidative stress induced by H2O2 was mitigated by GMG-ITC. Thus, pre-treatment with the compound conferred significant protection to cytoskeleton and cytoplasmic inclusion coupled with conservation of surface morphological features and general integrity of neuronal cells. Therefore, the collective findings in the presence study indicated the potentials of GMG-ITC to protect the integrity of neuron cells against induced oxidative-stress related cytotoxic processes, the hallmark of neurodegenerative diseases.
Analysis of the ionic interaction between the hydrophobin RodA and two cutinases of Aspergillus nidulans obtained via an Aspergillus oryzae expression system.

PubMed

Tanaka, Takumi; Nakayama, Mayumi; Takahashi, Toru; Nanatani, Kei; Yamagata, Youhei; Abe, Keietsu

2017-03-01

Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1. We also reported that hydrophobin RodA of the model fungus Aspergillus nidulans, which was obtained via an A. oryzae expression system, interacted via ionic interactions with CutL1. In the present study, phylogenetic and alignment analyses revealed that the N-terminal regions of several RolA orthologs contained positively charged residues and that the corresponding negatively charged residues on the surface of CutL1 that were essential for the RolA-CutL1 interaction were highly conserved in several CutL1 orthologs. A PBSA microparticle degradation assay, a pull-down assay using a dispersion of Teflon particles, and a kinetic analysis using a quartz crystal microbalance revealed that recombinant A. nidulans RodA interacted via ionic interactions with two recombinant A. nidulans cutinases. Together, these results imply that ionic interactions between hydrophobins and cutinases may be common among aspergilli and other filamentous fungi.
7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2010 CFR

2010-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...
7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2011 CFR

2011-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...
Assessment of lesser prairie-chicken use of wildlife water guzzlers

USGS Publications Warehouse

Boal, Clint W.; Borsdorf, Philip K.; Gicklhorn, Trevor S.

2014-01-01

Man-made water sources have been used as a management tool for wildlife, especially in arid regions, but the value of these water sources for wildlife populations is not well understood. In particular, the value of water as a conservation tool for Lesser Prairie-Chickens (Tympanuchus pallidicinctus) is unknown. However, this is a relevant issue due to a heightened conservation concern for the species and its occupancy of an arid landscape anticipated to experience warmer, drier springs and winters. We assessed if Lesser Prairie-Chickens would use commercially available wildlife water guzzlers and if there was any apparent selection between two design types. We confirmed that Lesser Prairie-Chickens would use bird friendly designed wildlife water guzzlers. Use was primarily during the lekking-nesting period (March–May) and the brood rearing period (June–July) and primarily by males. Although both designs were used, we found significantly greater use of a design that had a wider water trough and ramp built into the tank cover compared to a design that had a longer, narrower trough extending from the tank.Although we were unable to assess the physiological need of surface water by Lesser Prairie-Chickens, we were able to verify that they will use wildlife water guzzlers to access surface water. If it is found surface water is beneficial for Lesser Prairie-Chickens, game bird friendly designed guzzlers may be a useful conservation tool for the species.
Localization of functional receptor epitopes on the structure of ciliary neurotrophic factor indicates a conserved, function-related epitope topography among helical cytokines.

PubMed

Panayotatos, N; Radziejewska, E; Acheson, A; Somogyi, R; Thadani, A; Hendrickson, W A; McDonald, N Q

1995-06-09

By rational mutagenesis, receptor-specific functional analysis, and visualization of complex formation in solution, we identified individual amino acid side chains involved specifically in the interaction of ciliary neurotrophic factor (CNTF) with CNTFR alpha and not with the beta-components, gp130 and LIFR. In the crystal structure, the side chains of these residues, which are located in helix A, the AB loop, helix B, and helix D, are surface accessible and are clustered in space, thus constituting an epitope for CNTFR alpha. By the same analysis, a partial epitope for gp130 was also identified on the surface of helix A that faces away from the alpha-epitope. Superposition of the CNTF and growth hormone structures showed that the location of these epitopes on CNTF is analogous to the location of the first and second receptor epitopes on the surface of growth hormone. Further comparison with proposed binding sites for alpha- and beta-receptors on interleukin-6 and leukemia inhibitory factor indicated that this epitope topology is conserved among helical cytokines. In each case, epitope I is utilized by the specificity-conferring component, whereas epitopes II and III are used by accessory components. Thus, in addition to a common fold, helical cytokines share a conserved order of receptor epitopes that is function related.
A new approach to assess the chemical composition of powder deposits damaging the stone surfaces of historical monuments.

PubMed

Fermo, Paola; Turrion, Raquel Gonzalez; Rosa, Mario; Omegna, Alessandra

2015-04-01

The issue of conservation of the monumental heritage worldwide is mainly related to atmospheric pollution that causes the degradation of stone surfaces. The powder deposits present on the stone monuments reflect the composition of the aerosol particulate matter (PM) to which the surfaces are exposed, so the chemical characterization of the outermost damaged layers is necessary in order to adopt mitigation measurements to reduce PM emissions. In the present paper, a new analytical approach is proposed to investigate the chemical composition of powder deposits present on Angera stone, a dolomitic rock used in the Richini courtyard, a masterpiece of Lombard Baroque and placed in Milan. Inorganic and organic components present in these deposits have been analyzed by IC (ion chromatography) and a new approach mainly bases on thermal analyses, respectively. Gypsum is the main inorganic constituent indicating a composition similar to that of black crusts, hard black patina covering the degraded building surfaces. Ammonium nitrate present in the powder is able to react with the stone substrate to form magnesium nitrate which can migrate into the porous stone. The carbonaceous fraction powder deposits (i.e. OC = Organic Carbon and EC = Elemental Carbon) have been quantified by a new simple thermal approach based on carbon hydrogen nitrogen (CHN) analysis. The presence of high concentration of EC confirms that the powder deposits are evolving to black crust. Low values of water-soluble organic carbon (WSOC, determined by total organic carbon-TOC), with respect to what is normally found in PM, may indicate a migration process of organic substances into the stone with a worsening of the conservation conditions. The presence of heavy metals of anthropogenic origin and acting as catalysts in the black crust formation process has been highlighted by SEM-EDS (electron microscopy coupled with an energy dispersive spectrometer) as well.
Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region

USGS Publications Warehouse

Bowker, M.A.; Miller, M.E.; Belnap, J.; Sisk, T.D.; Johnson, N.C.

2008-01-01

Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.
Emerging technologies for removing nonpoint phosphorus from surface water and groundwater: introduction

USDA-ARS?s Scientific Manuscript database

The long-term application of phosphorus (P) to agricultural lands has led to P accumulation in soils around the world. The build-up of soil P, also known as legacy P, poses a continued risk to ground and surface water quality that may be difficult to mitigate using traditional conservation and nutri...

Generic E. coli levels in surface and nontraditional irrigation water in the mid Atlantic in relation to FSMA water quality standards: A CONSERVE study

USDA-ARS?s Scientific Manuscript database

Introduction: The use of surface (pond and river) and nontraditional (reclaimed wastewater, produce wash water) irrigation water (SNIW) could reduce stress on ground water resources. However, it is essential to understand how these irrigation sources may influence the microbiological safety of fresh...
Selective deuterium ion acceleration using the Vulcan petawatt laser

NASA Astrophysics Data System (ADS)

Krygier, A. G.; Morrison, J. T.; Kar, S.; Ahmed, H.; Alejo, A.; Clarke, R.; Fuchs, J.; Green, A.; Jung, D.; Kleinschmidt, A.; Najmudin, Z.; Nakamura, H.; Norreys, P.; Notley, M.; Oliver, M.; Roth, M.; Vassura, L.; Zepf, M.; Borghesi, M.; Freeman, R. R.

2015-05-01

We report on the successful demonstration of selective acceleration of deuterium ions by target-normal sheath acceleration (TNSA) with a high-energy petawatt laser. TNSA typically produces a multi-species ion beam that originates from the intrinsic hydrocarbon and water vapor contaminants on the target surface. Using the method first developed by Morrison et al. [Phys. Plasmas 19, 030707 (2012)], an ion beam with >99% deuterium ions and peak energy 14 MeV/nucleon is produced with a 200 J, 700 fs, > 10 20 W / cm 2 laser pulse by cryogenically freezing heavy water (D2O) vapor onto the rear surface of the target prior to the shot. Within the range of our detectors (0°-8.5°), we find laser-to-deuterium-ion energy conversion efficiency of 4.3% above 0.7 MeV/nucleon while a conservative estimate of the total beam gives a conversion efficiency of 9.4%.
Identification of the psaA Gene, Coding for Pneumococcal Surface Adhesin A, in Viridans Group Streptococci other than Streptococcus pneumoniae

PubMed Central

Jado, Isabel; Fenoll, Asunción; Casal, Julio; Pérez, Amalia

2001-01-01

The gene encoding the pneumococcal surface adhesin A (PsaA) protein has been identified in three different viridans group streptococcal species. Comparative studies of the psaA gene identified in different pneumococcal isolates by sequencing PCR products showed a high degree of conservation among these strains. PsaA is encoded by an open reading frame of 930 bp. The analysis of this fragment in Streptococcus mitis, Streptococcus oralis, and Streptococcus anginosus strains revealed a sequence identity of 95, 94, and 90%, respectively, to the corresponding open reading frame of the previously reported Streptococcus pneumoniae serotype 6B strain. Our results confirm that psaA is present and detectable in heterologous bacterial species. The possible implications of these results for the suitability and potential use of PsaA in the identification and diagnosis of pneumococcal diseases are discussed. PMID:11527799
A reentrant loop domain in the glutamate carrier EAAT1 participates in substrate binding and translocation.

PubMed

Seal, R P; Amara, S G

1998-12-01

To investigate the structural determinants underlying transport by the glutamate transporter EAAT1, we mutated each of 24 highly conserved residues (P392 to Q415) to cysteine. A majority of these substituted cysteines react with the sulfhydryl-modifying reagent MTSEA, suggesting that they reside in an aqueous environment. The impermeant reagents MTSES and MTSET react with residues at each end of the domain (A395C and A414C), supporting a model that places these residues near the extracellular surface. Substrates and inhibitors block the reaction between MTS derivatives and A395C, and the cosubstrate, sodium, slows reaction of MTSEA with Y405C and E406C. From these results, we propose that this domain forms a reentrant membrane loop at the cell surface and may comprise part of the translocation pore for substrates and cotransported ions.
The structure of cell adhesion molecule uvomorulin. Insights into the molecular mechanism of Ca2+-dependent cell adhesion.

PubMed Central

Ringwald, M; Schuh, R; Vestweber, D; Eistetter, H; Lottspeich, F; Engel, J; Dölz, R; Jähnig, F; Epplen, J; Mayer, S

1987-01-01

We have determined the amino acid sequence of the Ca2+-dependent cell adhesion molecule uvomorulin as it appears on the cell surface. The extracellular part of the molecule exhibits three internally repeated domains of 112 residues which are most likely generated by gene duplication. Each of the repeated domains contains two highly conserved units which could represent putative Ca2+-binding sites. Secondary structure predictions suggest that the putative Ca2+-binding units are located in external loops at the surface of the protein. The protein sequence exhibits a single membrane-spanning region and a cytoplasmic domain. Sequence comparison reveals extensive homology to the chicken L-CAM. Both uvomorulin and L-CAM are identical in 65% of their entire amino acid sequence suggesting a common origin for both CAMs. Images Fig. 1. Fig. 4. Fig. 7. PMID:3501370
Range expansion through fragmented landscapes under a variable climate

PubMed Central

Bennie, Jonathan; Hodgson, Jenny A; Lawson, Callum R; Holloway, Crispin TR; Roy, David B; Brereton, Tom; Thomas, Chris D; Wilson, Robert J

2013-01-01

Ecological responses to climate change may depend on complex patterns of variability in weather and local microclimate that overlay global increases in mean temperature. Here, we show that high-resolution temporal and spatial variability in temperature drives the dynamics of range expansion for an exemplar species, the butterfly Hesperia comma. Using fine-resolution (5 m) models of vegetation surface microclimate, we estimate the thermal suitability of 906 habitat patches at the species' range margin for 27 years. Population and metapopulation models that incorporate this dynamic microclimate surface improve predictions of observed annual changes to population density and patch occupancy dynamics during the species' range expansion from 1982 to 2009. Our findings reveal how fine-scale, short-term environmental variability drives rates and patterns of range expansion through spatially localised, intermittent episodes of expansion and contraction. Incorporating dynamic microclimates can thus improve models of species range shifts at spatial and temporal scales relevant to conservation interventions. PMID:23701124
The next-generation ESL continuum gyrokinetic edge code

NASA Astrophysics Data System (ADS)

Cohen, R.; Dorr, M.; Hittinger, J.; Rognlien, T.; Collela, P.; Martin, D.

2009-05-01

The Edge Simulation Laboratory (ESL) project is developing continuum-based approaches to kinetic simulation of edge plasmas. A new code is being developed, based on a conservative formulation and fourth-order discretization of full-f gyrokinetic equations in parallel-velocity, magnetic-moment coordinates. The code exploits mapped multiblock grids to deal with the geometric complexities of the edge region, and utilizes a new flux limiter [P. Colella and M.D. Sekora, JCP 227, 7069 (2008)] to suppress unphysical oscillations about discontinuities while maintaining high-order accuracy elsewhere. The code is just becoming operational; we will report initial tests for neoclassical orbit calculations in closed-flux surface and limiter (closed plus open flux surfaces) geometry. It is anticipated that the algorithmic refinements in the new code will address the slow numerical instability that was observed in some long simulations with the existing TEMPEST code. We will also discuss the status and plans for physics enhancements to the new code.
A stewardship approach to grassland bird habitat conservation in Saskatchewan, Canada

Treesearch

Stephen K. Davis; Bob Springer; Jennifer Lohmeyer; Lesley Hall; Tom Harrison

2005-01-01

Saskatchewan provides habitat for a number of grassland specialists that are of high conservation concern. For example, 10 of 12 “primary endemic,” and 17 of 25 “secondary endemic” species of the Great Plains identified by Mengel (1970) regularly breed in Saskatchewan. In addition, each of the 30 species of high conservation...
A framework for addressing bird conservation priorities in high-elevation vegetation communities of the Appalachian Mountains

Treesearch

Brian W. Smith; Dean Demarest; Ed. Laurent

2010-01-01

The Appalachian Mountains Joint Venture (AMJV) is a self-directed, nonregulatory bird conservation partnership with the mission of restoring and sustaining native bird populations and their habitats throughout Appalachia. In 2008, the AMJV formed an ad hoc "high-elevation" technical working group to identify and address conservation priorities of bird species...
Vegetation Fraction Mapping with High Resolution Multispectral Data in the Texas High Plains

NASA Astrophysics Data System (ADS)

Oshaughnessy, S. A.; Gowda, P. H.; Basu, S.; Colaizzi, P. D.; Howell, T. A.; Schulthess, U.

2010-12-01

Land surface models use vegetation fraction to more accurately partition latent, sensible and soil heat fluxes from a partially vegetated surface as it affects energy and moisture exchanges between the earth’s surface and atmosphere. In recent years, there is interest to integrate vegetation fraction data into intelligent irrigation scheduling systems to avoid false positive signals to irrigate. Remote sensing can facilitate the collection of vegetation fraction information on individual fields over large areas in a timely and cost-effective manner. In this study, we developed and evaluated a set of vegetation fraction models using least square regression and artificial neural network (ANN) techniques using RapidEye satellite data (6.5 m spatial resolution and on-demand temporal resolution). Four images were acquired during the 2010 summer growing season, covering bare soil to full crop cover conditions, over the USDA-ARS-Conservation and Production Research Laboratory in Bushland, Texas [350 11' N, 1020 06' W; 1,170 m elevation MSL]. Spectral signatures were extracted from 25 ground truth locations with geographic coordinates. Vegetation fraction information was derived from digital photos taken at the time of image acquisition using a supervised classification technique. Comparison of performance statistics indicate that ANN performed slightly better than least square regression models.
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

PubMed Central

Laine, Elodie; Carbone, Alessandra

2015-01-01

Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforward way three sequence- and structure-based descriptors of protein residues: evolutionary conservation, physico-chemical properties and local geometry. The implemented strategy yields very precise predictions for a wide range of protein-protein interfaces and discriminates them from small-molecule binding sites. Beyond its predictive power, the approach permits to dissect interaction surfaces and unravel their complexity. We show how the analysis of the predicted patches can foster new strategies for PPIs modulation and interaction surface redesign. The approach is implemented in JET2, an automated tool based on the Joint Evolutionary Trees (JET) method for sequence-based protein interface prediction. JET2 is freely available at www.lcqb.upmc.fr/JET2. PMID:26690684
A conserved motif in the linker domain of STAT1 transcription factor is required for both recognition and release from high-affinity DNA-binding sites.

PubMed

Hüntelmann, Bettina; Staab, Julia; Herrmann-Lingen, Christoph; Meyer, Thomas

2014-01-01

Binding to specific palindromic sequences termed gamma-activated sites (GAS) is a hallmark of gene activation by members of the STAT (signal transducer and activator of transcription) family of cytokine-inducible transcription factors. However, the precise molecular mechanisms involved in the signal-dependent finding of target genes by STAT dimers have not yet been very well studied. In this study, we have characterized a sequence motif in the STAT1 linker domain which is highly conserved among the seven human STAT proteins and includes surface-exposed residues in close proximity to the bound DNA. Using site-directed mutagenesis, we have demonstrated that a lysine residue in position 567 of the full-length molecule is required for GAS recognition. The substitution of alanine for this residue completely abolished both binding to high-affinity GAS elements and transcriptional activation of endogenous target genes in cells stimulated with interferon-γ (IFNγ), while the time course of transient nuclear accumulation and tyrosine phosphorylation were virtually unchanged. In contrast, two glutamic acid residues (E559 and E563) on each monomer are important for the dissociation of dimeric STAT1 from DNA and, when mutated to alanine, result in elevated levels of tyrosine-phosphorylated STAT1 as well as prolonged IFNγ-stimulated nuclear accumulation. In conclusion, our data indicate that the kinetics of signal-dependent GAS binding is determined by an array of glutamic acid residues located at the interior surface of the STAT1 dimer. These negatively charged residues appear to align the long axis of the STAT1 dimer in a position perpendicular to the DNA, thereby facilitating the interaction between lysine 567 and the phosphodiester backbone of a bound GAS element, which is a prerequisite for transient gene induction.
Characterization of Microbial Community in Lascaux Cave by High Throughput Sequencing

NASA Astrophysics Data System (ADS)

Alonso, Lise; Dubost, Audrey; Luis, Patricia; Pommier, Thomas; Moënne-Loccoz, Yvan

2017-04-01

The Lascaux Cave in South-Est France is an archeological landmark renowned for its Paleolithic paintings dating back c.18.000 years. Extensive touristic frequenting and repeated chemical treatments have resulted in the development of microbial stains on cave walls, which is a major issue in terms of art conservation. Therefore, it is of prime importance to better understand the microbial ecology of Lascaux Cave. Like many other caves, Lascaux is quite heterogeneous in terms of the nature and surface properties of rock walls within cave rooms, as well as the succession of rooms/galleries from the entrance to deeper areas of the cave. Lascaux Cave displays an additional levels of heterogeneity related to the presence of discontinuous stains on certain types of cave walls. We compared the microbial community (i.e. both prokaryotic and eukaryotic microbial populations) colonizing cave walls of different rooms/galleries, in and outside stains and in different cave layers, in successive years. Quantitative PCR analysis of cave wall samples gave in the order of 102 copies of 18S rRNA genes and 105 copies of 16S rRNA genes per ng of DNA, indicating significant colonization of all cave walls by micro-eukaryotes and especially bacteria. Illumina metagenomic analyses of cave wall samples was carried out based on four ribosomal DNA markers targeting bacteria, archaea, fungi, and other micro-eukaryotes. The results showed that the four microbial communities were highly diverse in and outside stains, as several hundred genera of microorganisms were identified in each. Proteobacteria were more prominent within stains whereas Bacteroidetes and Sordariomycetes were more prominent outside stains. High-throughput sequencing also showed that the nature/surface properties of cave walls were the main factor determining the structure and composition of microbial communities, ahead of the other heterogeneity factors studied i.e. location within the cave, presence of stain and sampling season. This work provides a global view of the microbial community of Lascaux Cave, which could be useful to guide conservation efforts.
Filtering fens: mechanisms explaining phosphorus-limited hotspots of biodiversity in wetlands adjacent to heavily fertilized areas.

PubMed

Cusell, Casper; Kooijman, Annemieke; Fernandez, Filippo; van Wirdum, Geert; Geurts, Jeroen J M; van Loon, E Emiel; Kalbitz, Karsten; Lamers, Leon P M

2014-05-15

The conservation of biodiverse wetland vegetation, including that of rich fens, has a high priority at a global scale. Although P-eutrophication may strongly decrease biodiversity in rich fens, some well-developed habitats do still survive in highly fertilized regions due to nutrient filtering services of large wetlands. The occurrence of such nutrient gradients is well-known, but the biogeochemical mechanisms that determine these patterns are often unclear. We therefore analyzed chemical speciation and binding of relevant nutrients and minerals in surface waters, soils and plants along such gradients in the large Ramsar nature reserve Weerribben-Wieden in the Netherlands. P-availability was lowest in relatively isolated floating rich fens, where plant N:P ratios indicated P-limitation. P-limitation can persist here despite high P-concentrations in surface waters near the peripheral entry locations, because only a small part of the P-input reaches the more isolated waters and fens. This pattern in P-availability appears to be primarily due to precipitation of Fe-phosphates, which mainly occurs close to entry locations as indicated by decreasing concentrations of Fe- and Al-bound P in the sub-aquatic sediments along this gradient. A further decrease of P-availability is caused by biological sequestration, which occurs throughout the wetland as indicated by equal concentrations of organic P in all sub-aquatic sediments. Our results clearly show that the periphery of large wetlands does indeed act as an efficient P-filter, sustaining the necessary P-limitation in more isolated parts. However, this filtering function does harm the ecological quality of the peripheral parts of the reserve. The filtering mechanisms, such as precipitation of Fe-phosphates and biological uptake of P, are crucial for the conservation and restoration of biodiverse rich fens in wetlands that receive eutrophic water from their surroundings. This seems to implicate that biodiverse wetland vegetation requires larger areas, as long as eutrophication has not been seriously tackled. Copyright © 2014 Elsevier B.V. All rights reserved.
Polymorphism of the Pv200L Fragment of Merozoite Surface Protein-1 of Plasmodium vivax in Clinical Isolates from the Pacific Coast of Colombia

PubMed Central

Valderrama-Aguirre, Augusto; Zúñiga-Soto, Evelin; Mariño-Ramírez, Leonardo; Moreno, Luz Ángela; Escalante, Ananías A.; Arévalo-Herrera, Myriam; Herrera, Sócrates

2011-01-01

Merozoite surface protein 1 (MSP-1) is a polymorphic malaria protein with functional domains involved in parasite erythrocyte interaction. Plasmodium vivax MSP-1 has a fragment (Pv200L) that has been identified as a potential subunit vaccine because it is highly immunogenic and induces partial protection against infectious parasite challenge in vaccinated monkeys. To determine the extent of genetic polymorphism and its effect on the translated protein, we sequenced the Pv200L coding region from isolates of 26 P. vivax-infected patients in a malaria-endemic area of Colombia. The extent of nucleotide diversity (π) in these isolates (0.061 ± 0.004) was significantly lower (P ≤ 0.001) than that observed in Thai and Brazilian isolates; 0.083 ± 0.006 and 0.090 ± 0.006, respectively. We found two new alleles and several previously unidentified dimorphic substitutions and significant size polymorphism. The presence of highly conserved blocks in this fragment has important implications for the development of Pv200L as a subunit vaccine candidate. PMID:21292880
Characterization of recombinant MSP5 Anaplasma marginale Havana isolate

PubMed Central

Corona, B.; Machado, H.; Rodríguez, M.; Martínez, S.

2009-01-01

Anaplasma marginale is the causative agent of bovine anaplasmosis, a disease of worldwide economic importance. Major surface proteins (MSPs) are involved in host-pathogen and tick-pathogen interactions and they have been used as markers for the genetic characterization of A. marginale strains and phylogenetic studies. The major surface protein 5 (MSP5) is highly conserved in the genus Anaplasma and in all isolates of A. marginale. The aim of the present work was to carry out the cloning, sequencing and characterization of the recombinant MSP5 Anaplasma marginale Havana isolate. The sequence of the msp5 gene of Anaplasma marginale Havana isolate with a size of 633 pb was determined (Acc. No. AY527217). This gene was cloned into pRSETB vector and expressed in Escherichia coli. The MSP5 protein was recognized by the monoclonal antibody ANAF16C1 and it showed a high similitude percent with the gene sequence described for other Anaplasma marginale isolates. These data are very important for the development of a diagnostic test for A. marginale using the MSP5 recombinant protein. PMID:24031449
7 CFR 12.23 - Conservation plans and conservation systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... to produce agricultural commodities prior to December 23, 1985, the applicable conservation systems... available conservation technology; cost-effective; and shall not cause undue economic hardship on the person... containing highly erodible cropland which was used to produce an agricultural commodity prior to December 23...
Conservative Protestantism and attitudes toward corporal punishment, 1986-2014.

PubMed

Hoffmann, John P; Ellison, Christopher G; Bartkowski, John P

2017-03-01

Research indicates that conservative Protestants are highly supportive of corporal punishment. Yet, Americans' support for this practice has waned during the past several decades. This study aggregates repeated cross-sectional data from the General Social Surveys (GSS) to consider three models that address whether attitudes toward spanking among conservative Protestants shifted relative to those of other Americans from 1986 to 2014. Although initial results reveal a growing gap between conservative Protestants and the broader American public, we find that average levels of support have remained most robust among less educated conservative Protestants, with some erosion among more highly educated conservative Protestants. Moreover, trends in variability suggest that conservative Protestants exhibit more cohesive support for this practice than do others. These results provide a window into the cultural contours of religious change and the social factors that facilitate such change. Copyright © 2016 Elsevier Inc. All rights reserved.
Structural assessment of the impact of environmental constraints on Arabidopsis thaliana leaf growth: a 3D approach.

PubMed

Wuyts, Nathalie; Massonnet, Catherine; Dauzat, Myriam; Granier, Christine

2012-09-01

Light and soil water content affect leaf surface area expansion through modifications in epidermal cell numbers and area, while effects on leaf thickness and mesophyll cell volumes are far less documented. Here, three-dimensional imaging was applied in a study of Arabidopsis thaliana leaf growth to determine leaf thickness and the cellular organization of mesophyll tissues under moderate soil water deficit and two cumulative light conditions. In contrast to surface area, thickness was highly conserved in response to water deficit under both low and high cumulative light regimes. Unlike epidermal and palisade mesophyll tissues, no reductions in cell number were observed in the spongy mesophyll; cells had rather changed in volume and shape. Furthermore, leaf features of a selection of genotypes affected in leaf functioning were analysed. The low-starch mutant pgm had very thick leaves because of unusually large palisade mesophyll cells, together with high levels of photosynthesis and stomatal conductance. By means of an open stomata mutant and a 9-cis-epoxycarotenoid dioxygenase overexpressor, it was shown that stomatal conductance does not necessarily have a major impact on leaf dimensions and cellular organization, pointing to additional mechanisms for the control of CO(2) diffusion under high and low stomatal conductance, respectively. © 2012 Blackwell Publishing Ltd.
Development of a locally mass flux conservative computer code for calculating 3-D viscous flow in turbomachines

NASA Technical Reports Server (NTRS)

Walitt, L.

1982-01-01

The VANS successive approximation numerical method was extended to the computation of three dimensional, viscous, transonic flows in turbomachines. A cross-sectional computer code, which conserves mass flux at each point of the cross-sectional surface of computation was developed. In the VANS numerical method, the cross-sectional computation follows a blade-to-blade calculation. Numerical calculations were made for an axial annular turbine cascade and a transonic, centrifugal impeller with splitter vanes. The subsonic turbine cascade computation was generated in blade-to-blade surface to evaluate the accuracy of the blade-to-blade mode of marching. Calculated blade pressures at the hub, mid, and tip radii of the cascade agreed with corresponding measurements. The transonic impeller computation was conducted to test the newly developed locally mass flux conservative cross-sectional computer code. Both blade-to-blade and cross sectional modes of calculation were implemented for this problem. A triplet point shock structure was computed in the inducer region of the impeller. In addition, time-averaged shroud static pressures generally agreed with measured shroud pressures. It is concluded that the blade-to-blade computation produces a useful engineering flow field in regions of subsonic relative flow; and cross-sectional computation, with a locally mass flux conservative continuity equation, is required to compute the shock waves in regions of supersonic relative flow.

Theoretical analysis of multiphase flow during oil-well drilling by a conservative model

NASA Astrophysics Data System (ADS)

Nicolas-Lopez, Ruben

2005-11-01

In order to decrease cost and improve drilling operations is necessary a better understood of the flow mechanisms. Therefore, it was carried out a multiphase conservative model that includes three mass equations and a momentum equation. Also, the measured geothermal gradient is utilized by state equations for estimating physical properties of the phases flowing. The mathematical model is solved by numerical conservative schemes. It is used to analyze the interaction among solid-liquid-gas phases. The circulating system consists as follow, the circulating fluid is pumped downward into the drilling pipe until the bottom of the open hole then it flows through the drill bit, and at this point formation cuttings are incorporated to the circulating fluid and carried upward to the surface. The mixture returns up to the surface by an annular flow area. The real operational conditions are fed to conservative model and the results are matched up to field measurements in several oil wells. Mainly, flow rates, drilling rate, well and tool geometries are data to estimate the profiles of pressure, mixture density, equivalent circulating density, gas fraction and solid carrying capacity. Even though the problem is very complex, the model describes, properly, the hydrodynamics of drilling techniques applied at oil fields. *Authors want to thank to Instituto Mexicano del Petroleo and Petroleos Mexicanos for supporting this research.
Perforated Duodenal Ulcer in High Risk Patients: Is Percutaneous Drainage Justified?

PubMed Central

Saber, Aly; Gad, Mohammad A; Ellabban, Gouda M

2012-01-01

Background: Conservative treatment was recommended as the treatment of choice in perforated acute peptic ulcer. Here, we adjunct percutaneous peritoneal drainage with nonoperative conservative treatment in high risk elderly patients with perforated duodenal ulcer. Aim: The work was to study the efficacy of percutaneous peritoneal drainage under local anesthesia supported by conservative measures in high risk elderly patients, according to the American Society of Anesthesiologists grading, with perforated duodenal ulcer. Patients and Methods: Twenty four high risk patients with age >65 years having associated medical illness with evidence of perforated duodenal ulcer. Results: The overall morbidity and mortality were comparable with those treated by conservative measures alone. Conclusion: In high risk patients with perforated peptic ulcer and established peritonitis, percutaneous peritoneal drainage under local anesthesia seems to be effective with least operative trauma and mortality rate. PMID:22393546
Pulsed Nd:YAG laser selective ablation of surface enamel caries: II. Histology and clinical trials

NASA Astrophysics Data System (ADS)

Harris, David M.; Goodis, Harold E.; White, Joel M.; Arcoria, Charles J.; Simon, James; Burkart, John; Yessik, Michael J.; Myers, Terry D.

2000-03-01

High intensity infrared light from the pulsed Nd:YAG dental laser is absorbed by pigmented carious enamel and not absorbed by normal enamel. Therefore, this system is capable of selective removal of surface enamel caries. Safety and efficacy of the clinical procedure was evaluated in two sets of clinical trials at three dental schools. Carious lesions were randomized to drill or laser treatment. Pulp vitality, surface condition, preparations and restorations were evaluated by blinded evaluators. In Study 1 surface caries were removed from 104 third molars scheduled for extraction. One week post-treatment teeth were extracted and the pulp was examined histologically. In Study 2 90 patients with 422 lesions on 376 teeth were randomized to laser or drill and followed for six months. There were no adverse events and both clinical and histological evaluations of pulp vitality showed no abnormalities. Caries were removed in all conditions. A significantly greater number of preparations in the drill groups vs. laser groups entered dentin (drill equals 11, laser equals 1, p less than 0.001). This indicates that the more conservative laser treatment removed the caries but not the sound enamel below the lesion.
Slanted snaking of localized Faraday waves

NASA Astrophysics Data System (ADS)

Pradenas, Bastián; Araya, Isidora; Clerc, Marcel G.; Falcón, Claudio; Gandhi, Punit; Knobloch, Edgar

2017-06-01

We report on an experimental, theoretical, and numerical study of slanted snaking of spatially localized parametrically excited waves on the surface of a water-surfactant mixture in a Hele-Shaw cell. We demonstrate experimentally the presence of a hysteretic transition to spatially extended parametrically excited surface waves when the acceleration amplitude is varied, as well as the presence of spatially localized waves exhibiting slanted snaking. The latter extend outside the hysteresis loop. We attribute this behavior to the presence of a conserved quantity, the liquid volume trapped within the meniscus, and introduce a universal model based on symmetry arguments, which couples the wave amplitude with such a conserved quantity. The model captures both the observed slanted snaking and the presence of localized waves outside the hysteresis loop, as demonstrated by numerical integration of the model equations.
Conserving migratory mule deer through the umbrella of sage-grouse

USGS Publications Warehouse

Copeland, H. E.; Sawyer, H.; Monteith, K. L.; Naugle, D.E.; Pocewicz, Amy; Graf, N.; Kauffman, Matthew J.

2014-01-01

Conserving migratory ungulates in increasingly human-dominated landscapes presents a difficult challenge to land managers and conservation practitioners. Nevertheless, ungulates may receive ancillary benefits from conservation actions designed to protect species of greater conservation priority where their ranges are sympatric. Greater Sage-Grouse (Centrocerus urophasianus), for example, have been proposed as an umbrella species for other sagebrush (Artemesia spp.)-dependent fauna. We examined a landscape where conservation efforts for sage-grouse overlap spatially with mule deer (Odocoileus hemionus) to determine whether sage-grouse conservation measures also might protect important mule deer migration routes and seasonal ranges. We conducted a spatial analysis to determine what proportion of migration routes, stopover areas, and winter ranges used by mule deer were located in areas managed for sage-grouse conservation. Conservation measures overlapped with 66–70% of migration corridors, 74–75% of stopovers, and 52–91% of wintering areas for two mule deer populations in the upper Green River Basin of Wyoming. Of those proportions, conservation actions targeted towards sage-grouse accounted for approximately half of the overlap in corridors and stopover areas, and nearly all overlap on winter ranges, indicating that sage-grouse conservation efforts represent an important step in conserving migratory mule deer. Conservation of migratory species presents unique challenges because although overlap with conserved lands may be high, connectivity of the entire route must be maintained as barriers to movement anywhere within the migration corridor could render it unviable. Where mule deer habitats overlap with sage-grouse core areas, our results indicate that increased protection is afforded to winter ranges and migration routes within the umbrella of sage-grouse conservation, but this protection is contingent on concentrated developments within core areas not intersecting with high-priority stopovers or corridors, and that the policy in turn does not encourage development on deer ranges outside of core areas. With the goal of protecting entire migration routes, our analysis highlights areas of potential conservation focus for mule deer, which are characterized by high exposure to residential development and use by a large proportion of migrating deer.
Immunity to Intracellular Salmonella Depends on Surface-associated Antigens

PubMed Central

Claudi, Beatrice; Mazé, Alain; Schemmer, Anne K.; Kirchhoff, Dennis; Schmidt, Alexander; Burton, Neil; Bumann, Dirk

2012-01-01

Invasive Salmonella infection is an important health problem that is worsening because of rising antimicrobial resistance and changing Salmonella serovar spectrum. Novel vaccines with broad serovar coverage are needed, but suitable protective antigens remain largely unknown. Here, we tested 37 broadly conserved Salmonella antigens in a mouse typhoid fever model, and identified antigen candidates that conferred partial protection against lethal disease. Antigen properties such as high in vivo abundance or immunodominance in convalescent individuals were not required for protectivity, but all promising antigen candidates were associated with the Salmonella surface. Surprisingly, this was not due to superior immunogenicity of surface antigens compared to internal antigens as had been suggested by previous studies and novel findings for CD4 T cell responses to model antigens. Confocal microscopy of infected tissues revealed that many live Salmonella resided alone in infected host macrophages with no damaged Salmonella releasing internal antigens in their vicinity. In the absence of accessible internal antigens, detection of these infected cells might require CD4 T cell recognition of Salmonella surface-associated antigens that could be processed and presented even from intact Salmonella. In conclusion, our findings might pave the way for development of an efficacious Salmonella vaccine with broad serovar coverage, and suggest a similar crucial role of surface antigens for immunity to both extracellular and intracellular pathogens. PMID:23093937
Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raymond, Donald D.; Bajic, Goran; Ferdman, Jack

Antigenic variation requires frequent revision of annual influenza vaccines. Next-generation vaccine design strategies aim to elicit a broader immunity by directing the human immune response toward conserved sites on the principal viral surface protein, the hemagglutinin (HA). We describe a group of antibodies that recognize a hitherto unappreciated, conserved site on the HA of H1 subtype influenza viruses. Mutations in that site, which required a change in the H1 component of the 2017 vaccine, had not previously “taken over” among circulating H1 viruses. Our results encourage vaccine design strategies that resurface a protein to focus the immune response on amore » specific region.« less
Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Treesearch

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...
Hydrologic connectivity of geographically isolated wetlands to surface water systems

NASA Astrophysics Data System (ADS)

Creed, I. F.; Ameli, A.

2016-12-01

Hydrologic connectivity of wetlands is poorly characterized and understood. Our inability to quantify this connectivity compromises our understanding of the potential impacts of land use (e.g., wetland drainage) and climate changes on watershed structure, function and water supplies. We develop a computationally efficient physically-based subsurface-surface hydrological model to map both the subsurface and surface hydrologic connectivity of geographically isolated wetlands (i.e., wetlands without surface outlets) and explore the time and length variations in these connections to a river within the Prairie Pothole Region of North America. Despite a high density of geographically isolated wetlands, modeled connections show that these wetlands are not hydrologically isolated. Hydrologic subsurface connectivity differs significantly from surface connectivity in terms of timing and length of connections. Slow subsurface connections between wetlands and the downstream river originate from wetlands throughout the watershed, whereas fast surface connections were limited to large events and originate from wetlands located near the river. Results also suggest that prioritization of protection of wetlands that relies on shortest distance of wetland to the river or surface connections alone can lead to unintended consequences in terms of loss of attending wetland ecosystem functions, services and their benefits to society. This modeling approach provides first ever insight on the nature of geographically isolated wetland subsurface and surface hydrological connections to rivers, and can provide guidance on the development of watershed management and conservation plans (e.g., wetlands drainage/restoration) under different climate and land management scenarios.
A model of the ground surface temperature for micrometeorological analysis

NASA Astrophysics Data System (ADS)

Leaf, Julian S.; Erell, Evyatar

2017-07-01

Micrometeorological models at various scales require ground surface temperature, which may not always be measured in sufficient spatial or temporal detail. There is thus a need for a model that can calculate the surface temperature using only widely available weather data, thermal properties of the ground, and surface properties. The vegetated/permeable surface energy balance (VP-SEB) model introduced here requires no a priori knowledge of soil temperature or moisture at any depth. It combines a two-layer characterization of the soil column following the heat conservation law with a sinusoidal function to estimate deep soil temperature, and a simplified procedure for calculating moisture content. A physically based solution is used for each of the energy balance components allowing VP-SEB to be highly portable. VP-SEB was tested using field data measuring bare loess desert soil in dry weather and following rain events. Modeled hourly surface temperature correlated well with the measured data (r 2 = 0.95 for a whole year), with a root-mean-square error of 2.77 K. The model was used to generate input for a pedestrian thermal comfort study using the Index of Thermal Stress (ITS). The simulation shows that the thermal stress on a pedestrian standing in the sun on a fully paved surface, which may be over 500 W on a warm summer day, may be as much as 100 W lower on a grass surface exposed to the same meteorological conditions.
Two types of Cassie-to-Wenzel wetting transitions on superhydrophobic surfaces during drop impact.

PubMed

Lee, Choongyeop; Nam, Youngsuk; Lastakowski, Henri; Hur, Janet I; Shin, Seungwon; Biance, Anne-Laure; Pirat, Christophe; Kim, Chang-Jin C J; Ybert, Christophe

2015-06-21

Despite the fact that superhydrophobic surfaces possess useful and unique properties, their practical application has remained limited by durability issues. Among those, the wetting transition, whereby a surface gets impregnated by the liquid and permanently loses its superhydrophobicity, certainly constitutes the most limiting aspect under many realistic conditions. In this study, we revisit this so-called Cassie-to-Wenzel transition (CWT) under the broadly encountered situation of liquid drop impact. Using model hydrophobic micropillar surfaces of various geometrical characteristics and high speed imaging, we identify that CWT can occur through different mechanisms, and at different impact stages. At early impact stages, right after contact, CWT occurs through the well established dynamic pressure scenario of which we provide here a fully quantitative description. Comparing the critical wetting pressure of surfaces and the theoretical pressure distribution inside the liquid drop, we provide not only the CWT threshold but also the hardly reported wetted area which directly affects the surface spoiling. At a later stage, we report for the first time to our knowledge, a new CWT which occurs during the drop recoil toward bouncing. With the help of numerical simulations, we discuss the mechanism underlying this new transition and provide a simple model based on impulse conservation which successfully captures the transition threshold. By shedding light on the complex interaction between impacting water drops and surface structures, the present study will facilitate designing superhydrophobic surfaces with a desirable wetting state during drop impact.
Orbits on a Concave Frictionless Surface

DTIC Science & Technology

2007-01-01

resistance. Because mechanical energy is conserved (for the system of ball and earth), the sum of the kinetic (K) and gravitational potential (U) energies...effects occur when a ball rolls without slipping on the surface of a rotating flat plate ,7 on the inner surface of a vertical cylinder such as a golf...The simple example of a ball in vertical freefall illustrates why this is necessary and how to perform the conversion. The method is then applied to
SR-XRD and SR-FTIR study of the alteration of silver foils in medieval paintings.

PubMed

Salvadó, Nati; Butí, Salvador; Labrador, Ana; Cinque, Gianfelice; Emerich, Hermann; Pradell, Trinitat

2011-03-01

Altarpieces and polychrome carved wood from the fifteenth century AD usually exhibit golden and silvery areas by the application of a very thin foil of metal. The metal foils were normally protected from the atmosphere by a varnish or resin which maybe either preserved or absent. Moreover, they were glued to the background surface by adhesive substances (egg yolk, drying oil or animal glue). The high proportion of the glueing substances often renders the development of reaction compounds. With time, silver alters blacken or simply disappear completely. In this paper, we study the alterations to metal foils from a selection of fifteenth century artworks showing different glueing agents, organic coatings and several degrees of conservation of the organic coatings and metal leafs. The submillimetric layered structure and the high variability and low amount of most of the compounds present in the different layers, as well as their differing nature (organic and inorganic) make the use of micron-sensitive high-resolution techniques essential for their study. In particular, the high resolution, high brilliance and small footprint renders synchrotron radiation most adequate for their study. SR-XRD was performed to identify the reaction compounds formed in the different layers; μFTIR was used at to identify the silver protecting organic coatings, the metal foil glueing layers and the corresponding reaction compounds. The results obtained suggest that atmospheric corrosion is the dominant mechanism, and therefore that the degree of corrosion of the metal foils is mainly related to the conservation state of the protecting coatings.
Tracking leatherback turtles from the world's largest rookery: assessing threats across the South Atlantic

PubMed Central

Witt, Matthew J.; Augowet Bonguno, Eric; Broderick, Annette C.; Coyne, Michael S.; Formia, Angela; Gibudi, Alain; Mounguengui Mounguengui, Gil Avery; Moussounda, Carine; NSafou, Monique; Nougessono, Solange; Parnell, Richard J.; Sounguet, Guy-Philippe; Verhage, Sebastian; Godley, Brendan J.

2011-01-01

Despite extensive work carried out on leatherback turtles (Dermochelys coriacea) in the North Atlantic and Indo-Pacific, very little is known of the at-sea distribution of this species in the South Atlantic, where the world's largest population nests in Gabon (central Africa). This paucity of data is of marked concern given the pace of industrialization in fisheries with demonstrable marine turtle bycatch in African/Latin American waters. We tracked the movements of 25 adult female leatherback turtles obtaining a range of fundamental and applied insights, including indications for methodological advancement. Individuals could be assigned to one of three dispersal strategies, moving to (i) habitats of the equatorial Atlantic, (ii) temperate habitats off South America or (iii) temperate habitats off southern Africa. While occupying regions with high surface chlorophyll concentrations, these strategies exposed turtles to some of the world's highest levels of longline fishing effort, in addition to areas with coastal gillnet fisheries. Satellite tracking highlighted that at least 11 nations should be involved in the conservation of this species in addition to those with distant fishing fleets. The majority of tracking days were, however, spent in the high seas, where effective implementation of conservation efforts is complex to achieve. PMID:21208949
A new flow model for highly separated airfoil flows at low speeds

NASA Technical Reports Server (NTRS)

Zumwalt, G. W.; Naik, S. N.

1979-01-01

An analytical model for separated airfoil flows is presented which is based on experimentally observed physical phenomena. These include a free stagnation point aft of the airfoil and a standing vortex in the separated region. A computer program is described which iteratively matches the outer potential flow, the airfoil turbulent boundary layer, the separated jet entrainment, mass conservation in the separated bubble, and the rear stagnation pressure. Separation location and pressure are not specified a priori. Results are presented for surface pressure coefficient and compared with experiment for three angles of attack for a GA(W)-1, 17% thick airfoil.
Trajectory characteristics and heating of hypervelocity projectiles having large ballistic coefficients

NASA Technical Reports Server (NTRS)

Tauber, Michael E.

1986-01-01

A simple, approximate equation describing the velocity-density relationship (or velocity-altitude) has been derived from the flight of large ballistic coefficient projectiles launched at high speeds. The calculations obtained by using the approximate equation compared well with results for numerical integrations of the exact equations of motion. The flightpath equation was used to parametrically calculate maximum body decelerations and stagnation pressures for initial velocities from 2 to 6 km/s. Expressions were derived for the stagnation-point convective heating rates and total heat loads. The stagnation-point heating was parametrically calculated for a nonablating wall and an ablating carbon surface. Although the heating rates were very high, the pulse decayed quickly. The total nose-region heat shield weight was conservatively estimated to be only about 1 percent of the body mass.
7 CFR 12.22 - Highly erodible field determination criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of changing field boundaries. When field boundaries are changed to include areas of land that were... Section 12.22 Agriculture Office of the Secretary of Agriculture HIGHLY ERODIBLE LAND AND WETLAND CONSERVATION Highly Erodible Land Conservation § 12.22 Highly erodible field determination criteria. (a...
Energy Analysis.

ERIC Educational Resources Information Center

Bazjanac, Vladimir

1981-01-01

The Aquatic Center at Corvallis (Oregon) is analyzed for energy use. Energy conservation in the building would be accomplished best through heavy insulation of exterior surfaces and the maximization of passive solar gain. (Author/MLF)
7 CFR 1491.22 - Conservation easement deeds.

Code of Federal Regulations, 2011 CFR

2011-01-01

... versus impervious surfaces on the easement area; the impact to water quality concerns in the area; the... OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS FARM AND RANCH LANDS PROTECTION PROGRAM...
Water Wisdom: 23 Stand-Alone Activities on Water Supply and Water Conservation for High School Students. 2nd Edition.

ERIC Educational Resources Information Center

Massachusetts State Water Resources Authority, Boston.

This water conservation education program for high schools consists of both stand-alone activities and teacher support materials. Lessons are divided into six broad categories: (1) The Water Cycle; (2) Water and Society; (3) Keeping Water Pure; (4) Visualizing Volumes; (5) The Economics of Water Use; and (6) Domestic Water Conservation. The…

Porphyromonas gingivalis Uses Specific Domain Rearrangements and Allelic Exchange to Generate Diversity in Surface Virulence Factors.

PubMed

Dashper, Stuart G; Mitchell, Helen L; Seers, Christine A; Gladman, Simon L; Seemann, Torsten; Bulach, Dieter M; Chandry, P Scott; Cross, Keith J; Cleal, Steven M; Reynolds, Eric C

2017-01-01

Porphyromonas gingivalis is a keystone pathogen of chronic periodontitis. The virulence of P. gingivalis is reported to be strain related and there are currently a number of strain typing schemes based on variation in capsular polysaccharide, the major and minor fimbriae and adhesin domains of Lys-gingipain (Kgp), amongst other surface proteins. P. gingivalis can exchange chromosomal DNA between strains by natural competence and conjugation. The aim of this study was to determine the genetic variability of P. gingivalis strains sourced from international locations over a 25-year period and to determine if variability in surface virulence factors has a phylogenetic basis. Whole genome sequencing was performed on 13 strains and comparison made to 10 previously sequenced strains. A single nucleotide polymorphism-based phylogenetic analysis demonstrated a shallow tri-lobed phylogeny. There was a high level of reticulation in the phylogenetic network, demonstrating extensive horizontal gene transfer between the strains. Two highly conserved variants of the catalytic domain of the major virulence factor the Kgp proteinase (Kgp cat I and Kgp cat II) were found. There were three variants of the fourth Kgp C-terminal cleaved adhesin domain. Specific variants of the cell surface proteins FimA, FimCDE, MfaI, RagAB, Tpr, and PrtT were also identified. The occurrence of all these variants in the P. gingivalis strains formed a mosaic that was not related to the SNP-based phylogeny. In conclusion P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors.
The conserved transmembrane RING finger protein PLR-1 downregulates Wnt signaling by reducing Frizzled, Ror and Ryk cell-surface levels in C. elegans

PubMed Central

Moffat, Laura L.; Robinson, Ryan E.; Bakoulis, Anastasia; Clark, Scott G.

2014-01-01

Wnts control a wide range of essential developmental processes, including cell fate specification, axon guidance and anteroposterior neuronal polarization. We identified a conserved transmembrane RING finger protein, PLR-1, that governs the response to Wnts by lowering cell-surface levels of the Frizzled family of Wnt receptors in Caenorhabditis elegans. Loss of PLR-1 activity in the neuron AVG causes its anteroposterior polarity to be symmetric or reversed because signaling by the Wnts CWN-1 and CWN-2 are inappropriately activated, whereas ectopic PLR-1 expression blocks Wnt signaling and target gene expression. Frizzleds are enriched at the cell surface; however, when PLR-1 and Frizzled are co-expressed, Frizzled is not detected at the surface but instead is colocalized with PLR-1 in endosomes. The Frizzled cysteine-rich domain (CRD) and invariant second intracellular loop lysine are crucial for PLR-1 downregulation. The PLR-1 RING finger and protease-associated (PA) domain are essential for activity. In a Frizzled-dependent manner, PLR-1 reduces surface levels of the Wnt receptors CAM-1/Ror and LIN-18/Ryk. PLR-1 is a homolog of the mammalian transmembrane E3 ubiquitin ligases RNF43 and ZNRF3, which control Frizzled surface levels in an R-spondin-sensitive manner. We propose that PLR-1 downregulates Wnt receptor surface levels via lysine ubiquitylation of Frizzled to coordinate spatial and temporal responses to Wnts during neuronal development. PMID:24401370
Detection of latent fingerprints using high-resolution 3D confocal microscopy in non-planar acquisition scenarios

NASA Astrophysics Data System (ADS)

Kirst, Stefan; Vielhauer, Claus

2015-03-01

In digitized forensics the support of investigators in any manner is one of the main goals. Using conservative lifting methods, the detection of traces is done manually. For non-destructive contactless methods, the necessity for detecting traces is obvious for further biometric analysis. High resolutional 3D confocal laser scanning microscopy (CLSM) grants the possibility for a detection by segmentation approach with improved detection results. Optimal scan results with CLSM are achieved on surfaces orthogonal to the sensor, which is not always possible due to environmental circumstances or the surface's shape. This introduces additional noise, outliers and a lack of contrast, making a detection of traces even harder. Prior work showed the possibility of determining angle-independent classification models for the detection of latent fingerprints (LFP). Enhancing this approach, we introduce a larger feature space containing a variety of statistical-, roughness-, color-, edge-directivity-, histogram-, Gabor-, gradient- and Tamura features based on raw data and gray-level co-occurrence matrices (GLCM) using high resolutional data. Our test set consists of eight different surfaces for the detection of LFP in four different acquisition angles with a total of 1920 single scans. For each surface and angles in steps of 10, we capture samples from five donors to introduce variance by a variety of sweat compositions and application influences such as pressure or differences in ridge thickness. By analyzing the present test set with our approach, we intend to determine angle- and substrate-dependent classification models to determine optimal surface specific acquisition setups and also classification models for a general detection purpose for both, angles and substrates. The results on overall models with classification rates up to 75.15% (kappa 0.50) already show a positive tendency regarding the usability of the proposed methods for LFP detection on varying surfaces in non-planar scenarios.
Food Supply and Seawater pCO2 Impact Calcification and Internal Shell Dissolution in the Blue Mussel Mytilus edulis

PubMed Central

Melzner, Frank; Stange, Paul; Trübenbach, Katja; Thomsen, Jörn; Casties, Isabel; Panknin, Ulrike; Gorb, Stanislav N.; Gutowska, Magdalena A.

2011-01-01

Progressive ocean acidification due to anthropogenic CO2 emissions will alter marine ecosytem processes. Calcifying organisms might be particularly vulnerable to these alterations in the speciation of the marine carbonate system. While previous research efforts have mainly focused on external dissolution of shells in seawater under saturated with respect to calcium carbonate, the internal shell interface might be more vulnerable to acidification. In the case of the blue mussel Mytilus edulis, high body fluid pCO2 causes low pH and low carbonate concentrations in the extrapallial fluid, which is in direct contact with the inner shell surface. In order to test whether elevated seawater pCO2 impacts calcification and inner shell surface integrity we exposed Baltic M. edulis to four different seawater pCO2 (39, 142, 240, 405 Pa) and two food algae (310–350 cells mL−1 vs. 1600–2000 cells mL−1) concentrations for a period of seven weeks during winter (5°C). We found that low food algae concentrations and high pCO2 values each significantly decreased shell length growth. Internal shell surface corrosion of nacreous ( = aragonite) layers was documented via stereomicroscopy and SEM at the two highest pCO2 treatments in the high food group, while it was found in all treatments in the low food group. Both factors, food and pCO2, significantly influenced the magnitude of inner shell surface dissolution. Our findings illustrate for the first time that integrity of inner shell surfaces is tightly coupled to the animals' energy budget under conditions of CO2 stress. It is likely that under food limited conditions, energy is allocated to more vital processes (e.g. somatic mass maintenance) instead of shell conservation. It is evident from our results that mussels exert significant biological control over the structural integrity of their inner shell surfaces. PMID:21949698
Food supply and seawater pCO2 impact calcification and internal shell dissolution in the blue mussel Mytilus edulis.

PubMed

Melzner, Frank; Stange, Paul; Trübenbach, Katja; Thomsen, Jörn; Casties, Isabel; Panknin, Ulrike; Gorb, Stanislav N; Gutowska, Magdalena A

2011-01-01

Progressive ocean acidification due to anthropogenic CO(2) emissions will alter marine ecosystem processes. Calcifying organisms might be particularly vulnerable to these alterations in the speciation of the marine carbonate system. While previous research efforts have mainly focused on external dissolution of shells in seawater under saturated with respect to calcium carbonate, the internal shell interface might be more vulnerable to acidification. In the case of the blue mussel Mytilus edulis, high body fluid pCO(2) causes low pH and low carbonate concentrations in the extrapallial fluid, which is in direct contact with the inner shell surface. In order to test whether elevated seawater pCO(2) impacts calcification and inner shell surface integrity we exposed Baltic M. edulis to four different seawater pCO(2) (39, 142, 240, 405 Pa) and two food algae (310-350 cells mL(-1) vs. 1600-2000 cells mL(-1)) concentrations for a period of seven weeks during winter (5°C). We found that low food algae concentrations and high pCO(2) values each significantly decreased shell length growth. Internal shell surface corrosion of nacreous ( = aragonite) layers was documented via stereomicroscopy and SEM at the two highest pCO(2) treatments in the high food group, while it was found in all treatments in the low food group. Both factors, food and pCO(2), significantly influenced the magnitude of inner shell surface dissolution. Our findings illustrate for the first time that integrity of inner shell surfaces is tightly coupled to the animals' energy budget under conditions of CO(2) stress. It is likely that under food limited conditions, energy is allocated to more vital processes (e.g. somatic mass maintenance) instead of shell conservation. It is evident from our results that mussels exert significant biological control over the structural integrity of their inner shell surfaces.
Broadly neutralizing antibodies from human survivors target a conserved site in the Ebola virus glycoprotein HR2-MPER region.

PubMed

Flyak, Andrew I; Kuzmina, Natalia; Murin, Charles D; Bryan, Christopher; Davidson, Edgar; Gilchuk, Pavlo; Gulka, Christopher P; Ilinykh, Philipp A; Shen, Xiaoli; Huang, Kai; Ramanathan, Palaniappan; Turner, Hannah; Fusco, Marnie L; Lampley, Rebecca; Kose, Nurgun; King, Hannah; Sapparapu, Gopal; Doranz, Benjamin J; Ksiazek, Thomas G; Wright, David W; Saphire, Erica Ollmann; Ward, Andrew B; Bukreyev, Alexander; Crowe, James E

2018-05-07

Ebola virus (EBOV) in humans causes a severe illness with high mortality rates. Several strategies have been developed in the past to treat EBOV infection, including the antibody cocktail ZMapp, which has been shown to be effective in nonhuman primate models of infection 1 and has been used under compassionate-treatment protocols in humans 2 . ZMapp is a mixture of three chimerized murine monoclonal antibodies (mAbs) 3-6 that target EBOV-specific epitopes on the surface glycoprotein 7,8 . However, ZMapp mAbs do not neutralize other species from the genus Ebolavirus, such as Bundibugyo virus (BDBV), Reston virus (RESTV) or Sudan virus (SUDV). Here, we describe three naturally occurring human cross-neutralizing mAbs, from BDBV survivors, that target an antigenic site in the canonical heptad repeat 2 (HR2) region near the membrane-proximal external region (MPER) of the glycoprotein. The identification of a conserved neutralizing antigenic site in the glycoprotein suggests that these mAbs could be used to design universal antibody therapeutics against diverse ebolavirus species. Furthermore, we found that immunization with a peptide comprising the HR2-MPER antigenic site elicits neutralizing antibodies in rabbits. Structural features determined by conserved residues in the antigenic site described here could inform an epitope-based vaccine design against infection caused by diverse ebolavirus species.
Redox-regulated dynamic interplay between Cox19 and the copper-binding protein Cox11 in the intermembrane space of mitochondria facilitates biogenesis of cytochrome c oxidase

PubMed Central

Bode, Manuela; Woellhaf, Michael W.; Bohnert, Maria; van der Laan, Martin; Sommer, Frederik; Jung, Martin; Zimmermann, Richard; Schroda, Michael; Herrmann, Johannes M.

2015-01-01

Members of the twin Cx9C protein family constitute the largest group of proteins in the intermembrane space (IMS) of mitochondria. Despite their conserved nature and their essential role in the biogenesis of the respiratory chain, the molecular function of twin Cx9C proteins is largely unknown. We performed a SILAC-based quantitative proteomic analysis to identify interaction partners of the conserved twin Cx9C protein Cox19. We found that Cox19 interacts in a dynamic manner with Cox11, a copper transfer protein that facilitates metalation of the Cu(B) center of subunit 1 of cytochrome c oxidase. The interaction with Cox11 is critical for the stable accumulation of Cox19 in mitochondria. Cox19 consists of a helical hairpin structure that forms a hydrophobic surface characterized by two highly conserved tyrosine-leucine dipeptides. These residues are essential for Cox19 function and its specific binding to a cysteine-containing sequence in Cox11. Our observations suggest that an oxidative modification of this cysteine residue of Cox11 stimulates Cox19 binding, pointing to a redox-regulated interplay of Cox19 and Cox11 that is critical for copper transfer in the IMS and thus for biogenesis of cytochrome c oxidase. PMID:25926683
A Neuron-Specific Antiviral Mechanism Prevents Lethal Flaviviral Infection of Mosquitoes

PubMed Central

Xiao, Xiaoping; Zhang, Rudian; Pang, Xiaojing; Liang, Guodong; Wang, Penghua; Cheng, Gong

2015-01-01

Mosquitoes are natural vectors for many etiologic agents of human viral diseases. Mosquito-borne flaviviruses can persistently infect the mosquito central nervous system without causing dramatic pathology or influencing the mosquito behavior and lifespan. The mechanism by which the mosquito nervous system resists flaviviral infection is still largely unknown. Here we report that an Aedes aegypti homologue of the neural factor Hikaru genki (AaHig) efficiently restricts flavivirus infection of the central nervous system. AaHig was predominantly expressed in the mosquito nervous system and localized to the plasma membrane of neural cells. Functional blockade of AaHig enhanced Dengue virus (DENV) and Japanese encephalitis virus (JEV), but not Sindbis virus (SINV), replication in mosquito heads and consequently caused neural apoptosis and a dramatic reduction in the mosquito lifespan. Consistently, delivery of recombinant AaHig to mosquitoes reduced viral infection. Furthermore, the membrane-localized AaHig directly interfaced with a highly conserved motif in the surface envelope proteins of DENV and JEV, and consequently interrupted endocytic viral entry into mosquito cells. Loss of either plasma membrane targeting or virion-binding ability rendered AaHig nonfunctional. Interestingly, Culex pipien pallens Hig also demonstrated a prominent anti-flavivirus activity, suggesting a functionally conserved function for Hig. Our results demonstrate that an evolutionarily conserved antiviral mechanism prevents lethal flaviviral infection of the central nervous system in mosquitoes, and thus may facilitate flaviviral transmission in nature. PMID:25915054
Assessing the shelf life of cost-efficient conservation plans for species at risk across gradients of agricultural land use.

PubMed

Robillard, Cassandra M; Kerr, Jeremy T

2017-08-01

High costs of land in agricultural regions warrant spatial prioritization approaches to conservation that explicitly consider land prices to produce protected-area networks that accomplish targets efficiently. However, land-use changes in such regions and delays between plan design and implementation may render optimized plans obsolete before implementation occurs. To measure the shelf life of cost-efficient conservation plans, we simulated a land-acquisition and restoration initiative aimed at conserving species at risk in Canada's farmlands. We accounted for observed changes in land-acquisition costs and in agricultural intensity based on censuses of agriculture taken from 1986 to 2011. For each year of data, we mapped costs and areas of conservation priority designated using Marxan. We compared plans to test for changes through time in the arrangement of high-priority sites and in the total cost of each plan. For acquisition costs, we measured the savings from accounting for prices during site selection. Land-acquisition costs and land-use intensity generally rose over time independent of inflation (24-78%), although rates of change were heterogeneous through space and decreased in some areas. Accounting for spatial variation in land price lowered the cost of conservation plans by 1.73-13.9%, decreased the range of costs by 19-82%, and created unique solutions from which to choose. Despite the rise in plan costs over time, the high conservation priority of particular areas remained consistent. Delaying conservation in these critical areas may compromise what optimized conservation plans can achieve. In the case of Canadian farmland, rapid conservation action is cost-effective, even with moderate levels of uncertainty in how to implement restoration goals. © 2016 Society for Conservation Biology.
A conservative approach for restoring anterior guidance: a case report.

PubMed

Pontons-Melo, Juan Carlos; Pizzatto, Eduardo; Furuse, Adilson Yoshio; Mondelli, José

2012-06-01

One of the most common dental problems in today's clinics is tooth wear, specifically when related to bruxism. In such cases, the esthetics of anterior teeth may be compromised when excessive wear to the incisal surfaces occurs. Anterior tooth wear resulting from parafunctional bruxism can be conservatively treated with the use of direct resin composite restorations. This restorative approach has the advantages of presenting good predictability, load resistance, acceptable longevity, preservation of healthy dental tissues, and lower cost when compared with indirect restorations. The use of resin composites to solve esthetic problems, however, requires skill and practice. Thus, the present article demonstrates a conservative approach for restoring the esthetics and function of worn anterior teeth with the aid of direct resin composite restorations and selective occlusal adjustment. A conservative approach to restore anterior teeth with excessive wear is possible with direct resin composites. © 2011 Wiley Periodicals, Inc.
Conserved Structural Elements in the V3 Crown of HIV-1 gp120

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, X.; Burke, V; Totrov, M

2010-01-01

Binding of the third variable region (V3) of the HIV-1 envelope glycoprotein gp120 to the cell-surface coreceptors CCR5 or CXCR4 during viral entry suggests that there are conserved structural elements in this sequence-variable region. These conserved elements could serve as epitopes to be targeted by a vaccine against HIV-1. Here we perform a systematic structural analysis of representative human anti-V3 monoclonal antibodies in complex with V3 peptides, revealing that the crown of V3 has four conserved structural elements: an arch, a band, a hydrophobic core and the peptide backbone. These are either unaffected by or are subject to minimal sequencemore » variation. As these regions are targeted by cross-clade neutralizing human antibodies, they provide a blueprint for the design of vaccine immunogens that could elicit broadly cross-reactive protective antibodies.« less
Evaluating relationships between urban land cover composition and evapotranspiration in semi-arid regions

NASA Astrophysics Data System (ADS)

Manago, K. F.; Hogue, T. S.; Litvak, E.; Pataki, D. E.

2016-12-01

California experienced its most severe drought on record in 2013 and 2014, forcing the governor to call for the first statewide reductions in urban water use. This led to numerous water conservation efforts including turf removal and restrictions on outdoor irrigation. The decrease in irrigation across the city of Los Angeles has had major effects on regional hydrologic fluxes. Previous studies have found that conservation efforts have decreased streamflow but little work has been done on the impact of reduced irrigation on Evapotranspiration (ET). ET is one of the most difficult variables to measure as a result of its heterogeneity both spatially and temporally; yet, it is imperative in characterizing energy and hydrologic processes and in aiding water management decisions. Estimating ET is further complicated in urban regions where land cover composition is extremely variable, even at small scales. Irrigated landscape and impervious surfaces are two of the most common land cover types associated with urbanization, but they have opposite effects on ET. While numerous studies have evaluated changes in ET caused by urbanization, they have all produced varying results. This is expected as changes to ET are highly dependent on land cover composition. In this study, we modeled the relationship between ET and urban land cover change in Los Angeles. We utilized empirical equations derived from in situ measurements to calculate tree and irrigated turfgrass ET and compared the results to estimates based on remote-sensing and California Irrigation Management Information System (CIMIS) network of weather stations. We found that unshaded turfgrass largely increased ET compared to impervious surfaces, which reveals lavish irrigation practices. Trees also increased ET, but they provided shade that decreased ET from turf grass. With much of the western United States facing drought and water supply uncertainty due to climate change, understanding and predicting how land cover impacts ET under various scenarios is imperative for informed water management and efficient conservation solutions.
Crystal Structure of the Botulinum Neurotoxin Type G Binding Domain: Insight into Cell Surface Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stenmark, Pål; Dong, Min; Dupuy, Jérôme

2011-11-02

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-{angstrom} X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantlymore » reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent.« less
Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.

PubMed

Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R; Stevens, Raymond C

2010-04-16

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-A X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent. Copyright (c) 2010. Published by Elsevier Ltd.
Polyester synthases: natural catalysts for plastics.

PubMed Central

Rehm, Bernd H A

2003-01-01

Polyhydroxyalkanoates (PHAs) are biopolyesters composed of hydroxy fatty acids, which represent a complex class of storage polyesters. They are synthesized by a wide range of different Gram-positive and Gram-negative bacteria, as well as by some Archaea, and are deposited as insoluble cytoplasmic inclusions. Polyester synthases are the key enzymes of polyester biosynthesis and catalyse the conversion of (R)-hydroxyacyl-CoA thioesters to polyesters with the concomitant release of CoA. These soluble enzymes turn into amphipathic enzymes upon covalent catalysis of polyester-chain formation. A self-assembly process is initiated resulting in the formation of insoluble cytoplasmic inclusions with a phospholipid monolayer and covalently attached polyester synthases at the surface. Surface-attached polyester synthases show a marked increase in enzyme activity. These polyester synthases have only recently been biochemically characterized. An overview of these recent findings is provided. At present, 59 polyester synthase structural genes from 45 different bacteria have been cloned and the nucleotide sequences have been obtained. The multiple alignment of the primary structures of these polyester synthases show an overall identity of 8-96% with only eight strictly conserved amino acid residues. Polyester synthases can been assigned to four classes based on their substrate specificity and subunit composition. The current knowledge on the organization of the polyester synthase genes, and other genes encoding proteins related to PHA metabolism, is compiled. In addition, the primary structures of the 59 PHA synthases are aligned and analysed with respect to highly conserved amino acids, and biochemical features of polyester synthases are described. The proposed catalytic mechanism based on similarities to alpha/beta-hydrolases and mutational analysis is discussed. Different threading algorithms suggest that polyester synthases belong to the alpha/beta-hydrolase superfamily, with a conserved cysteine residue as catalytic nucleophile. This review provides a survey of the known biochemical features of these unique enzymes and their proposed catalytic mechanism. PMID:12954080
Structural Aspects of N-Glycosylations and the C-terminal Region in Human Glypican-1*

PubMed Central

Awad, Wael; Adamczyk, Barbara; Örnros, Jessica; Karlsson, Niclas G.; Mani, Katrin; Logan, Derek T.

2015-01-01

Glypicans are multifunctional cell surface proteoglycans involved in several important cellular signaling pathways. Glypican-1 (Gpc1) is the predominant heparan sulfate proteoglycan in the developing and adult human brain. The two N-linked glycans and the C-terminal domain that attach the core protein to the cell membrane are not resolved in the Gpc1 crystal structure. Therefore, we have studied Gpc1 using crystallography, small angle x-ray scattering, and chromatographic approaches to elucidate the composition, structure, and function of the N-glycans and the C terminus and also the topology of Gpc1 with respect to the membrane. The C terminus is shown to be highly flexible in solution, but it orients the core protein transverse to the membrane, directing a surface evolutionarily conserved in Gpc1 orthologs toward the membrane, where it may interact with signaling molecules and/or membrane receptors on the cell surface, or even the enzymes involved in heparan sulfate substitution in the Golgi apparatus. Furthermore, the N-glycans are shown to extend the protein stability and lifetime by protection against proteolysis and aggregation. PMID:26203194
Type IV pili of Acidithiobacillus ferrooxidans can transfer electrons from extracellular electron donors.

PubMed

Li, Yongquan; Li, Hongyu

2014-03-01

Studies on Acidithiobacillus ferrooxidans accepting electrons from Fe(II) have previously focused on cytochrome c. However, we have discovered that, besides cytochrome c, type IV pili (Tfp) can transfer electrons. Here, we report conduction by Tfp of A. ferrooxidans analyzed with a conducting-probe atomic force microscope (AFM). The results indicate that the Tfp of A. ferrooxidans are highly conductive. The genome sequence of A. ferrooxidans ATCC 23270 contains two genes, pilV and pilW, which code for pilin domain proteins with the conserved amino acids characteristic of Tfp. Multiple alignment analysis of the PilV and PilW (pilin) proteins indicated that pilV is the adhesin gene while pilW codes for the major protein element of Tfp. The likely function of Tfp is to complete the circuit between the cell surface and Fe(II) oxides. These results indicate that Tfp of A. ferrooxidans might serve as biological nanowires transferring electrons from the surface of Fe(II) oxides to the cell surface. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Characterization of structural response to hypersonic boundary-layer transition

DOE PAGES

Riley, Zachary B.; Deshmukh, Rohit; Miller, Brent A.; ...

2016-05-24

The inherent relationship between boundary-layer stability, aerodynamic heating, and surface conditions makes the potential for interaction between the structural response and boundary-layer transition an important and challenging area of study in high-speed flows. This paper phenomenologically explores this interaction using a fundamental two-dimensional aerothermoelastic model under the assumption of an aluminum panel with simple supports. Specifically, an existing model is extended to examine the impact of transition onset location, transition length, and transitional overshoot in heat flux and fluctuating pressure on the structural response of surface panels. Transitional flow conditions are found to yield significantly increased thermal gradients, and theymore » can result in higher maximum panel temperatures compared to turbulent flow. Results indicate that overshoot in heat flux and fluctuating pressure reduces the flutter onset time and increases the strain energy accumulated in the panel. Furthermore, overshoot occurring near the midchord can yield average temperatures and peak displacements exceeding those experienced by the panel subject to turbulent flow. Lastly, these results suggest that fully turbulent flow does not always conservatively predict the thermo-structural response of surface panels.« less
77 FR 18963 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-29

... the Framework Document for High-Intensity Discharge Lamps AGENCY: Office of Energy Efficiency and... availability of framework document for high-intensity discharge (HID) lamps, initiating the rulemaking and data... Availability of Framework Document Regarding Energy Conservation Standards for High-Intensity Discharge (HID...
78 FR 6232 - Energy Conservation Program: Test Procedures for Conventional Cooking Products With Induction...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-30

... Surface efficiency deviation interval technology unit % % ( ) % Large A Electric Coil... 1 69.79 1.59 1.97... Surface efficiency deviation interval technology unit % % ( ) % Large A Electric Coil... 1 64.52 0.87 1.08... technology unit % % ( ) % Large A Electric Coil... 1 79.81 1.66 2.06 B Electric........ 1 61.81 2.83 3.52...

Theory of fracture mechanics based upon plasticity

NASA Technical Reports Server (NTRS)

Lee, J. D.

1976-01-01

A theory of fracture mechanics is formulated on the foundation of continuum mechanics. Fracture surface is introduced as an unknown quantity and is incorporated into boundary and initial conditions. Surface energy is included in the global form of energy conservation law and the dissipative mechanism is formulated into constitutive equations which indicate the thermodynamic irreversibility and the irreversibility of fracture process as well.
The role of Listeria monocytogenes cell wall surface anchor protein LapB in virulence, adherence, and intracellular replication

USDA-ARS?s Scientific Manuscript database

Lmof2365_2117 is a Listeria monocytogenes putative cell wall surface anchor protein with a conserved domain found in collagen binding proteins. We constructed a deletion mutation in lmof2365_2117 in serotype 4b strain F2365, evaluated its virulence, and determined its ability to adhere and invade co...
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

PubMed

Schneider, T D

2001-12-01

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.
The Finite-Surface Method for incompressible flow: a step beyond staggered grid

NASA Astrophysics Data System (ADS)

Hokpunna, Arpiruk; Misaka, Takashi; Obayashi, Shigeru

2017-11-01

We present a newly developed higher-order finite surface method for the incompressible Navier-Stokes equations (NSE). This method defines the velocities as a surface-averaged value on the surfaces of the pressure cells. Consequently, the mass conservation on the pressure cells becomes an exact equation. The only things left to approximate is the momentum equation and the pressure at the new time step. At certain conditions, the exact mass conservation enables the explicit n-th order accurate NSE solver to be used with the pressure treatment that is two or four order less accurate without loosing the apparent convergence rate. This feature was not possible with finite volume of finite difference methods. We use Fourier analysis with a model spectrum to determine the condition and found that the range covers standard boundary layer flows. The formal convergence and the performance of the proposed scheme is compared with a sixth-order finite volume method. Finally, the accuracy and performance of the method is evaluated in turbulent channel flows. This work is partially funded by a research colloaboration from IFS, Tohoku university and ASEAN+3 funding scheme from CMUIC, Chiang Mai University.
Summer Study Program in Geophysical Fluid Dynamics 1989. General Circulation of the Oceans

DTIC Science & Technology

1989-11-01

Description of the Surface Circulation 2.2 A Description of the Interior Circulation 2.3 Formation Sites and Circulation of Deepwater Masses 2.4 Mode...and atmosphere, we have to follow basic laws of physics which lead us to try to solve a series of conservation equations, Mass : Dp*+ P() Du. - , ’ O.j...r~--~)(18) where,= vorticity 0 - 1 Vertically integrated mass conservation gives which leads to T.3) (19) Using the fact that Ro, ;<<I, the lowest
Multiphase wavetrains, singular wave interactions and the emergence of the Korteweg–de Vries equation

PubMed Central

Bridges, Thomas J.

2016-01-01

Multiphase wavetrains are multiperiodic travelling waves with a set of distinct wavenumbers and distinct frequencies. In conservative systems, such families are associated with the conservation of wave action or other conservation law. At generic points (where the Jacobian of the wave action flux is non-degenerate), modulation of the wavetrain leads to the dispersionless multiphase conservation of wave action. The main result of this paper is that modulation of the multiphase wavetrain, when the Jacobian of the wave action flux vector is singular, morphs the vector-valued conservation law into the scalar Korteweg–de Vries (KdV) equation. The coefficients in the emergent KdV equation have a geometrical interpretation in terms of projection of the vector components of the conservation law. The theory herein is restricted to two phases to simplify presentation, with extensions to any finite dimension discussed in the concluding remarks. Two applications of the theory are presented: a coupled nonlinear Schrödinger equation and two-layer shallow-water hydrodynamics with a free surface. Both have two-phase solutions where criticality and the properties of the emergent KdV equation can be determined analytically. PMID:28119546
[Diversity of soil fauna in corn fields in Huang-Huai-Hai Plain of China under effects of conservation tillage].

PubMed

Zhu, Qiang-Gen; Zhu, An-Ning; Zhang, Jia-Bao; Zhang, Huan-Chao; Huang, Ping; Zhang, Cong-Zhi

2009-10-01

An investigation was made on the abundance and diversity of soil fauna in the corn fields under conventional and conservation tillage in Huang-Huai-Hai Plain of China. The abundance and diversity of soil fauna were higher at corn maturing (September) than at its jointing stage (July), and higher at jointing stage under conservation tillage than under conventional tillage. Soil fauna mainly distributed in surface soil layer (0-10 cm), but still had a larger number in 10-20 cm layer under conservation tillage. The individuals of acari, diptera, diplura, and microdrile oligochaetes, especially those of acari, were higher under conservation tillage than under conventional tillage. At maturing stage, an obvious effect of straw-returning under conservation tillage was observed, i. e., the more the straw returned, the higher the abundance of soil fauna, among which, the individuals of collembola, acari, coleopteran, and psocoptera, especially those of collembolan, increased significantly. The abundance of collembola at both jointing and maturing stages was significantly positively correlated with the quantity of straw returned, suggesting that collembola played an important role in straw decomposition and nutrient cycling.
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

PubMed

Graham, Sarah E; Smith, Richard D; Carlson, Heather A

2018-02-26

Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between the protein and ligand. Depending on the specific interactions made by the ligand, displacing waters can yield a gain in binding affinity. The extent to which binding affinity may increase is difficult to predict, as the favorable displacement of a water molecule is dependent on the site-specific interactions made by the water and the potential ligand. Several methods have been developed to predict the location of water sites on a protein's surface, but the majority of methods are not able to take into account both protein dynamics and the interactions made by specific functional groups. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that explicitly accounts for the interaction of both water and small molecule probes with a protein's surface, allowing for their direct competition. This method has previously been shown to identify both active and allosteric sites on a protein's surface. Using a test set of eight systems, we have developed a method using MixMD to identify conserved and displaceable water sites. Conserved sites can be determined by an occupancy-based metric to identify sites which are consistently occupied by water even in the presence of probe molecules. Conversely, displaceable water sites can be found by considering the sites which preferentially bind probe molecules. Furthermore, the inclusion of six probe types allows the MixMD method to predict which functional groups are capable of displacing which water sites. The MixMD method consistently identifies sites which are likely to be nondisplaceable and predicts the favorable displacement of water sites that are known to be displaced upon ligand binding.
[The importance of C-terminal aspartic acid residue (D141) to the antirestriction activity of the ArdB (R64) protein].

PubMed

Kudryavtseva, A A; Osetrova, M S; Livinyuk, V Ya; Manukhov, I V; Zavilgelsky, G B

2017-01-01

Antirestriction proteins of the ArdB/KlcA family are specific inhibitors of restriction (endonuclease) activity of type-I restriction/modification enzymes. The effect of conserved amino acid residues on the antirestriction activity of the ArdB protein encoded by the transmissible R64 (IncI1) plasmid has been investigated. An analysis of the amino acid sequences of ArdB homologues demonstrated the presence of four groups of conserved residues ((1) R16, E32, and W51; (2) Y46 and G48; (3) S81, D83 and E132, and (4) N77, L(I)140, and D141) on the surface of the protein globule. Amino acid residues of the fourth group showed a unique localization pattern with the terminal residue protruding beyond the globule surface. The replacement of two conserved amino acids (D141 and N77) located in the close vicinity of each other on the globule surface showed that the C-terminal D141 is essential for the antirestriction activity of ArdB. The deletion of this residue, as well as replacement by a hydrophobic threonine residue (D141T), completely abolished the antirestriction activity of ArdB. The synonymous replacement of D141 by a glutamic acid residue (D141E) caused an approximately 30-fold decrease of the antirestriction activity of ArdB, and the point mutation N77A caused an approximately 20-fold decrease in activity. The residues D141 and N77 located on the surface of the protein globule are presumably essential for the formation of a contact between ArdB and a currently unknown factor that modulates the activity of type-I restriction/modification enzymes.
Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning.

PubMed

Heredia, Jeremiah D; Park, Jihye; Brubaker, Riley J; Szymanski, Steven K; Gill, Kevin S; Procko, Erik

2018-06-01

Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors. Chemokine CXCL12 was found to interact with residues extending asymmetrically into the CXCR4 ligand-binding cavity, similar to the binding surface of CXCR4 recognized by an antagonistic viral chemokine previously observed crystallographically. CXCR4 mutations distal from the chemokine binding site were identified that enhance chemokine recognition. This included disruptive mutations in the G protein-coupling site that diminished calcium mobilization, as well as conservative mutations to a membrane-exposed site (CXCR4 residues H79 2.45 and W161 4.50 ) that increased ligand binding without loss of signaling. Compared with CXCR4-CXCL12 interactions, CCR5 residues conserved for gp120 (HIV-1 BaL strain) interactions map to a more expansive surface, mimicking how the cognate chemokine CCL5 makes contacts across the entire CCR5 binding cavity. Acidic substitutions in the CCR5 N terminus and extracellular loops enhanced gp120 binding. This study demonstrates how comprehensive mutational scanning can define functional interaction sites on receptors, and novel mutations that enhance receptor activities can be found simultaneously. Copyright © 2018 by The American Association of Immunologists, Inc.
Bioinformatics Reveal Five Lineages of Oleosins and the Mechanism of Lineage Evolution Related to Structure/Function from Green Algae to Seed Plants1[OPEN

PubMed Central

Huang, Ming-Der; Huang, Anthony H.C.

2015-01-01

Plant cells contain subcellular lipid droplets with a triacylglycerol matrix enclosed by a layer of phospholipids and the small structural protein oleosin. Oleosins possess a conserved central hydrophobic hairpin of approximately 72 residues penetrating into the lipid droplet matrix and amphipathic amino- and carboxyl (C)-terminal peptides lying on the phospholipid surface. Bioinformatics of 1,000 oleosins of green algae and all plants emphasizing biological implications reveal five oleosin lineages: primitive (in green algae, mosses, and ferns), universal (U; all land plants), and three in specific organs or phylogenetic groups, termed seed low-molecular-weight (SL; seed plants), seed high-molecular-weight (SH; angiosperms), and tapetum (T; Brassicaceae) oleosins. Transition from one lineage to the next is depicted from lineage intermediates at junctions of phylogeny and organ distributions. Within a species, each lineage, except the T oleosin lineage, has one to four genes per haploid genome, only approximately two of which are active. Primitive oleosins already possess all the general characteristics of oleosins. U oleosins have C-terminal sequences as highly conserved as the hairpin sequences; thus, U oleosins including their C-terminal peptide exert indispensable, unknown functions. SL and SH oleosin transcripts in seeds are in an approximately 1:1 ratio, which suggests the occurrence of SL-SH oleosin dimers/multimers. T oleosins in Brassicaceae are encoded by rapidly evolved multitandem genes for alkane storage and transfer. Overall, oleosins have evolved to retain conserved hairpin structures but diversified for unique structures and functions in specific cells and plant families. Also, our studies reveal oleosin in avocado (Persea americana) mesocarp and no acyltransferase/lipase motifs in most oleosins. PMID:26232488
High-Throughput Genetic Identification of Functionally Important Regions of the Yeast DEAD-Box Protein Mss116p

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohr, Georg; Del Campo, Mark; Turner, Kathryn G.

The Saccharomyces cerevisiae DEAD-box protein Mss116p is a general RNA chaperone that functions in splicing mitochondrial group I and group II introns. Recent X-ray crystal structures of Mss116p in complex with ATP analogs and single-stranded RNA show that the helicase core induces a bend in the bound RNA, as in other DEAD-box proteins, while a C-terminal extension (CTE) induces a second bend, resulting in RNA crimping. Here, we illuminate these structures by using high-throughput genetic selections, unigenic evolution, and analyses of in vivo splicing activity to comprehensively identify functionally important regions and permissible amino acid substitutions throughout Mss116p. The functionallymore » important regions include those containing conserved sequence motifs involved in ATP and RNA binding or interdomain interactions, as well as previously unidentified regions, including surface loops that may function in protein-protein interactions. The genetic selections recapitulate major features of the conserved helicase motifs seen in other DEAD-box proteins but also show surprising variations, including multiple novel variants of motif III (SAT). Patterns of amino acid substitutions indicate that the RNA bend induced by the helicase core depends on ionic and hydrogen-bonding interactions with the bound RNA; identify a subset of critically interacting residues; and indicate that the bend induced by the CTE results primarily from a steric block. Finally, we identified two conserved regions - one the previously noted post II region in the helicase core and the other in the CTE - that may help displace or sequester the opposite RNA strand during RNA unwinding.« less
Factors Affecting Diet Variation in the Pyrenean Rock Ptarmigan (Lagopus muta pyrenaica): Conservation Implications.

PubMed

García-González, Ricardo; Aldezabal, Arantza; Laskurain, Nere Amaia; Margalida, Antoni; Novoa, Claude

2016-01-01

The Pyrenean rock ptarmigan (Lagopus muta pyrenaica) lives at one of the southernmost limits of the ptarmigan range. Their small population sizes and the impacts of global changes are limiting factors in the conservation of this threatened subspecies. An effective conservation policy requires precise basic knowledge of a species' food and habitat requirements, information that is practically non-existent for this Pyrenean population. Here, we describe the diet of a ptarmigan population in the Eastern Pyrenees, the environmental factors influencing its variability and the relationship between diet floristic composition and quality. Diet composition was determined by microhistological analysis of faeces and diet quality was estimated from free-urate faecal N content. Our results show that grouse diet is based mainly on arctic-alpine shrubs of the Ericaceae family, as well as dwarf willows (Salix spp.) and Dryas octopetala. The most frequently consumed plant species was Rhododendron ferrugineum, but its abundance in the diet was negatively related to the diet nitrogen content. Conversely, the abundance of Salix spp., grass leaves and arthropods increased the nitrogen content of the diet. Seasonality associated with snow-melting contributed the most to variability in the Pyrenean ptarmigan diet, differentiating winter from spring/summer diets. The latter was characterised by a high consumption of dwarf willows, flowers, arthropods and tender forb leaves. Geographic area and sex-age class influenced diet variability to a lesser extent. Current temperature increases in the Pyrenees due to global warming may reduce the persistence and surface area of snow-packs where preferred plants for rock ptarmigan usually grow, thus reducing food availability. The high consumption of Rh. ferrugineum characterised the diet of the Pyrenean population. Given the toxicity of this plant for most herbivores, its potential negative effect on Pyrenean ptarmigan populations should be evaluated.
Factors Affecting Diet Variation in the Pyrenean Rock Ptarmigan (Lagopus muta pyrenaica): Conservation Implications

PubMed Central

García-González, Ricardo; Aldezabal, Arantza; Laskurain, Nere Amaia; Margalida, Antoni; Novoa, Claude

2016-01-01

The Pyrenean rock ptarmigan (Lagopus muta pyrenaica) lives at one of the southernmost limits of the ptarmigan range. Their small population sizes and the impacts of global changes are limiting factors in the conservation of this threatened subspecies. An effective conservation policy requires precise basic knowledge of a species' food and habitat requirements, information that is practically non-existent for this Pyrenean population. Here, we describe the diet of a ptarmigan population in the Eastern Pyrenees, the environmental factors influencing its variability and the relationship between diet floristic composition and quality. Diet composition was determined by microhistological analysis of faeces and diet quality was estimated from free-urate faecal N content. Our results show that grouse diet is based mainly on arctic-alpine shrubs of the Ericaceae family, as well as dwarf willows (Salix spp.) and Dryas octopetala. The most frequently consumed plant species was Rhododendron ferrugineum, but its abundance in the diet was negatively related to the diet nitrogen content. Conversely, the abundance of Salix spp., grass leaves and arthropods increased the nitrogen content of the diet. Seasonality associated with snow-melting contributed the most to variability in the Pyrenean ptarmigan diet, differentiating winter from spring/summer diets. The latter was characterised by a high consumption of dwarf willows, flowers, arthropods and tender forb leaves. Geographic area and sex-age class influenced diet variability to a lesser extent. Current temperature increases in the Pyrenees due to global warming may reduce the persistence and surface area of snow-packs where preferred plants for rock ptarmigan usually grow, thus reducing food availability. The high consumption of Rh. ferrugineum characterised the diet of the Pyrenean population. Given the toxicity of this plant for most herbivores, its potential negative effect on Pyrenean ptarmigan populations should be evaluated. PMID:26863532
Role of a highly conserved electrostatic interaction on the surface of cytochrome C in control of the redox function.

PubMed

Tai, Hulin; Mikami, Shin-ichi; Irie, Kiyofumi; Watanabe, Naoki; Shinohara, Naoya; Yamamoto, Yasuhiko

2010-01-12

In Hydrogenobacter thermophilus cytochrome c(552), an electrostatic interaction between Lys8 and Glu68 in the N- and C-terminal helices, respectively, stabilizes its protein structure [Travaglini-Allocatelli, C., Gianni, S., Dubey, V. K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K. L., and Brunori, M. (2005) J. Biol. Chem. 280, 25729-25734], this electrostatic interaction being a highly conserved structural feature of the cytochrome c family. In the present study, the functional consequences of removal of the interaction through replacement of Lys8 by Ala have been investigated in order to elucidate the molecular mechanisms responsible for functional control of the protein. The mutation resulted in a decrease in protein stability, as reflected in lowering of the denaturation temperature by approximately 2-9 degrees C, and a negative shift by approximately 8 mV of the redox potential (E(m)) of the protein. The decrease in the protein stability was attributed to the enthalpic loss due to the removal of the intramolecular interaction. The negative shift of the E(m) value was shown to be due to the effect of the mutation on the entropic contribution to the E(m) value. The small, but subtle, effects of removal of the conserved electrostatic interaction, occurring at approximately 1.4 nm away from heme iron, on the thermodynamic properties of the protein demonstrated not only that the interaction is important for maintaining the functional properties of the protein but also that amino acid residues relatively remote from the heme active site play sizable roles in functional control of the protein.
3D model for Cancerous Inhibitor of Protein Phosphatase 2A armadillo domain unveils highly conserved protein-protein interaction characteristics.

PubMed

Dahlström, Käthe M; Salminen, Tiina A

2015-12-07

Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is a human oncoprotein, which exerts its cancer-promoting function through interaction with other proteins, for example Protein Phosphatase 2A (PP2A) and MYC. The lack of structural information for CIP2A significantly prevents the design of anti-cancer therapeutics targeting this protein. In an attempt to counteract this fact, we modeled the three-dimensional structure of the N-terminal domain (CIP2A-ArmRP), analyzed key areas and amino acids, and coupled the results to the existing literature. The model reliably shows a stable armadillo repeat fold with a positively charged groove. The fact that this conserved groove highly likely binds peptides is corroborated by the presence of a conserved polar ladder, which is essential for the proper peptide-binding mode of armadillo repeat proteins and, according to our results, several known CIP2A interaction partners appropriately possess an ArmRP-binding consensus motif. Moreover, we show that Arg229Gln, which has been linked to the development of cancer, causes a significant change in charge and surface properties of CIP2A-ArmRP. In conclusion, our results reveal that CIP2A-ArmRP shares the typical fold, protein-protein interaction site and interaction patterns with other natural armadillo proteins and that, presumably, several interaction partners bind into the central groove of the modeled CIP2A-ArmRP. By providing essential structural characteristics of CIP2A, the present study significantly increases our knowledge on how CIP2A interacts with other proteins in cancer progression and how to develop new therapeutics targeting CIP2A. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
Phylogenetic Analysis of Conservation Priorities for Aquatic Mammals and Their Terrestrial Relatives, with a Comparison of Methods

PubMed Central

May-Collado, Laura J.; Agnarsson, Ingi

2011-01-01

Background Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. Methodology/Principal Findings A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all ‘high priority’ species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. Conclusions/Significance These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct—and thus ‘biodiverse’—species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders. PMID:21799899
Crystal Structures of Mite Allergens Der f 1 and Der p 1 Reveal Differences in Surface-Exposed Residues that May Influence Antibody Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chruszcz, Maksymilian; Chapman, Martin D.; Vailes, Lisa D.

2009-12-01

The Group 1 mite allergens, Der f 1 and Der p 1, are potent allergens excreted by Dermatophagoides farinae and Dermatophagoides pteronyssinus, respectively. The human IgE antibody responses to the Group 1 allergens show more cross-reactivity than the murine IgG antibody responses which are largely species-specific. Here, we report the crystal structure of the mature form of Der f 1, which was isolated from its natural source, and a new, high-resolution structure of mature recombinant Der p 1. Unlike Der p 1, Der f 1 is monomeric both in the crystalline state and in solution. Moreover, no metal binding ismore » observed in the structure of Der f 1, despite the fact that all amino acids involved in Ca{sup 2+} binding in Der p 1 are completely conserved in Der f 1. Although Der p 1 and Der f 1 share extensive sequence identity, comparison of the crystal structures of both allergens revealed structural features which could explain the differences in murine and human IgE antibody responses to these allergens. There are structural differences between Der f 1 and Der p 1 which are unevenly distributed on the allergens' surfaces. This uneven spatial arrangement of conserved versus altered residues could explain both the specificity and cross-reactivity of antibodies against Der f 1 and Der p 1.« less
High-level systemic expression of conserved influenza epitope in plants on the surface of rod-shaped chimeric particles.

PubMed

Petukhova, Natalia V; Gasanova, Tatiana V; Ivanov, Peter A; Atabekov, Joseph G

2014-04-21

Recombinant viruses based on the cDNA copy of the tobacco mosaic virus (TMV) genome carrying different versions of the conserved M2e epitope from influenza virus A cloned into the coat protein (CP) gene were obtained and partially characterized by our group previously; cysteines in the human consensus M2e sequence were changed to serine residues. This work intends to show some biological properties of these viruses following plant infections. Agroinfiltration experiments on Nicotiana benthamiana confirmed the efficient systemic expression of M2e peptides, and two point amino acid substitutions in recombinant CPs significantly influenced the symptoms and development of viral infections. Joint expression of RNA interference suppressor protein p19 from tomato bushy stunt virus (TBSV) did not affect the accumulation of CP-M2e-ser recombinant protein in non-inoculated leaves. RT-PCR analysis of RNA isolated from either infected leaves or purified TMV-M2e particles proved the genetic stability of TMV‑based viral vectors. Immunoelectron microscopy of crude plant extracts demonstrated that foreign epitopes are located on the surface of chimeric virions. The rod‑shaped geometry of plant-produced M2e epitopes is different from the icosahedral or helical filamentous arrangement of M2e antigens on the carrier virus-like particles (VLP) described earlier. Thereby, we created a simple and efficient system that employs agrobacteria and plant viral vectors in order to produce a candidate broad-spectrum flu vaccine.
Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes

PubMed Central

Nandy, Suman Kumar; Seal, Alpana

2016-01-01

Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases. PMID:27764212

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