bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIF receptor‐gp130 interaction investigated by homology modeling: Implications for LIF binding
Authors: Smith David K. , Treutlein Herbert R. 
Published: July 2010

AbstractLeukemia inhibitory factor (LIF), a member of the gpl30 family of helical cytokines, is involved in the hemopoietic and neural systems. The LIF signal transducing complex contains two receptor molecules, the LIF receptor (LIFR) and gp130. The extracellular region of the LIFR is unique in that it includes three membrane‐proximal fibronectin type III domains and two cytokine binding domains (CBDs) separated by an immunoglobulin‐like domain. Although some mutagenesis data on LIF are available, it is not yet known which regions of LIFR or gp130 bind LIF. Nor is it known whether LIFR contacts gp130 in a manner similar to the growth hormone receptor dimer and, if so, through which of its CBDs. To attempt to elucidate these matters and to investigate the receptor complex, models of the CBDs of LIFR and the CBD of gp130 were constructed. Analyses of the electrostatic isopotential surfaces of the CBD models suggest that gp130 and the membrane‐proximal CBD of LIFR hetero‐dimerize and bind LIF through contacts similar to those seen in the growth hormone receptor dimer. This work further demonstrates the utility of electrostatic analyses of homology models and suggests a strategy for biochemical investigations of the LIF‐receptor complex.
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 Å resolution and 100 K: The role of the water structure and its contribution to binding
Authors: Gregoriou Mary , Noble Martin E. M. , Watson Kimberly A. , Garman Elspeth F. , Johnson Louise N. , Krulle Thomas M. , Fuetene Carmen De La , Fleet George W.J. , Oikonomakos Nikos G. 
Published: July 2010

AbstractA glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopyranose spirohydantoin have been determined at 100 K to 2.0 Å and 1.8 Å resolution, respectively, and refined to crystallographic R values of 0.197 (Rfree 0.248) and 0.182 (Rfree 0.229), respectively. The low temperature structure of GPb is almost identical to that of the previously determined room temperature structure, apart from a decrease in overall atomic temperature factors (〈B〉 room temperature GPb = 34.9 Å2; 〈B〉 100 K GPb = 23.4 Å2). The glucopyranose spirohydantoin inhibitor (Ki = 3.0 μM) binds at the catalytic site and induces small changes in two key regions of the protein: the 280s loop (residues 281‐286) that results in a decrease in mobility of this region, and the 380s loop (residues 377‐385) that undergoes more significant shifts in order to optimize contact to the ligand. The hydantoin group, that is responsible for increasing the affinity of the glucose compound by a factor of 103, makes only one hydrogen bond to the protein, from one of its NH groups to the main chain oxygen of His377. The other polar groups of the hydantoin group form hydrogen bonds to five water molecules. These waters are involved in extensive networks of hydrogen bonds and appear to be an integral part of the protein structure. Analysis of the water structure at the catalytic site of the native enzyme, shows that five waters are displaced by ligand binding and that there is a significant decrease in mobility of the remaining waters on formation of the GPb‐hydantoin complex. The ability of the inhibitor to exploit existing waters, to displace waters and to recruit new waters appears to be important for the high affinity of the inhibitor.
Mapping of the interleukin‐10/interleukin‐10 receptor combining site
Authors: Reineke Ulrich , Sabat Robert , Volk Hans‐Dieter , Schneider‐Mergener Jens 
Published: July 2010

AbstractThe discontinuous interleukin‐10(IL‐10)/interleukin‐10 receptor (IL‐10R) combining site was mapped using sets of overlapping peptides derived from both binding partners bound to continuous cellulose membranes. Low affinity binding of single regions of the discontinuous contact sites on IL‐10 and IL‐10R could be identified due to (1) high peptide density on the membrane support, (2) incubation with high protein concentrations, (3) indirect immunodetection of the ligates after electrotransfer onto polyvinylene difluoride membranes, and (4) use of highly overlapping peptide scans of different length (6‐mers and 15‐mers). The single binding regions identified for each protein species are separated in the protein sequences, but form continuous areas on the surface of IL‐10 (X‐ray structure) and IL‐10R (computer model). Furthermore, four epitopes of neutralizing anti‐IL‐10 and anti‐IL‐10R antibodies were mapped and overlap with these binding regions. Soluble peptides (15‐ to 19‐mers) each spanning one of the three identified IL‐10‐derived receptor binding regions displayed no significant affinity to IL‐10R as expected, whereas a peptide (35‐mer) comprising two of these regions had considerably higher binding activity. The data are consistent with a previously published computer model of the IL‐10/IL‐10R complex. This approach should be generally applicable for the mapping of non‐linear protein‐protein contact sites.
A differential scanning calorimetric study of the thermal unfolding of apo‐ and holo‐cytochrome b562
Authors: Robinson Clifford R. , Sligar Stephen G. , Liu Yufeng , O'Brien Ronan , Sturtevant Julian M. 
Published: July 2010

AbstractCytochrome b562 is a four‐helix‐bundle protein containing a non‐covalently bound b‐type heme prosthetic group. In the absence of heme, cytochrome b562 remains highly structured under native conditions. Here we report thermodynamic data for the thermal denaturation of the holo‐ and apoproteins as determined by differential scanning calorimetry. Thermal denaturation of holocytochrome b562 is a highly reversible process, and unexpectedly does not involve dissociation of the heme prosthetic group. Thermal denaturation of the corresponding apoprotein, with the heme group chemically removed, remains a cooperative, reversible process. Apocytochrome b562 is substantially destabilized relative to the holoprotein: the t1/2 is more than ten degrees lower, and enthalpy and heat capacity changes are about one‐half of the holoprotein values. However, the energetic parameters of apocytochrome b562denaturation are within the range of observed values for small proteins.
Conformational diversity of acid‐denatured cytochrome c studied by a matrix analysis of far‐UV CD spectra
Authors: Konno Takashi 
Published: July 2010

AbstractThe singular value decomposition (SVD) analysis was applied to a large set of far‐ultraviolet circular dichroism (far‐UV CD) spectra (100‐400 spectra) of horse heart cytochrome c (cyt c). The spectra were collected at pH 1.7‐5.0 in (NH4)2SO4, sorbitol and 2,2,2‐trifluoroethanol (TFE) solutions. The present purpose is to develop a rigorous matrix method applied to far‐UV CD spectra to resolve in details conformational properties of proteins in the non‐native (or denatured) regions. The analysis established that three basis spectral components are contained in a data set of difference spectra (referred to the spectrum of the native state) used here. By a further matrix transformation, any observed spectrum could be decomposed into fractions of the native (N), the molten‐globule (MG), the highly denatured (D), and the alcohol‐induced helical (H) spectral forms. This method could determine fractional transition curves of each conformer as a function of solution conditions, which gave the results consistent with denaturation curves of cyt c monitored by other spectroscopic methods. The results in sorbitol solutions, for example, suggested that the preferential hydration effect of the co‐solvent stabilizes the MG conformer of cyt c. This report has found that the systematic SVD analysis of the far‐UV CD spectra is a powerful tool for the conformational analysis of the non‐native species of a protein when it is suitably supplemented with other experimental methods.
Complete localization of disulfide bonds in GM2 activator protein
Authors: Schütte Christina G. , Lemm Thorsten , Sandhoff Konrad , Glombitza Gereon J. 
Published: July 2010

AbstractLysosomal degradation of ganglioside GM2 by hexosaminidase A requires the presence of a small, non‐enzymatic cofactor, the GM2‐activator protein (GM2AP). Lack of functional protein leads to the AB variant of GM2‐gangliosidosis, a fatal lysosomal storage disease.Although its possible mode of action and functional domains have been discussed frequently in the past, no structural information about GM2AP is available so far. Here, we determine the complete disulfide bond pattern of the protein. Two of the four disulfide bonds present in the protein were open to classical determination by enzymatic cleavage and mass spectrometry. The direct localization of the remaining two bonds was impeded by the close vicinity of cysteines 136 and 138. We determined the arrangement of these disulfide bonds by MALDI‐PSD analysis of disulfide linked peptides and by partial reduction, cyanylation and fragmentation in basic solution, as described recently (Wu F, Watson JT, 1997, Protein Sci 6:391‐398).
Simultaneous δ15N, δ13C and δ34S measurements of low‐biomass samples using a technically advanced high sensitivity elemental analyzer connected to an isotope ratio mass spectrometer
Authors: Hansen T. , Burmeister A. , Sommer U. 
Published: July 2010

AbstractConventional simultaneous CNS stable isotope abundance measurements of solid samples usually require high sample amounts, up to 1 mg carbon, to achieve exact analytical results. This rarely used application is often impaired by high C:S element ratios when organic samples are analyzed and problems such as incomplete conversion into sulphur dioxide occur during analysis. We introduce, as a technical innovation, a high sensitivity elemental analyzer coupled to a conventional isotope ratio mass spectrometer, with which CNS‐stable isotope ratios can be determined simultaneously in samples with low carbon content (<40 µg C corresponding to ∼100 µg dry weight). The system includes downsized reactors, a temperature program‐controlled gas chromatography (GC) column and a cryogenic trap to collect small amounts of sulphur dioxide. This modified application allows for highly sensitive measurements in a fully automated operation with standard deviations better than ±0.47‰ for δ15N and δ34S and ±0.12‰ for δ13C (n = 127). Samples collected from one sampling site in a Baltic fjord within a short time period were measured with the new system to get a first impression of triple stable isotope signatures. The results confirm the potential of using δ34S as a stable isotope tracer in combination with δ15N and δ13C measurements to improve discrimination of food sources in aquatic food webs. Copyright © 2009 John Wiley & Sons, Ltd.
Bioremediation of Dinitrotoluene in Aged Clay and Sandy Soils Using Pseudomonas Organisms, Spizizen Nutrient Medium and Prairie Silt Loam
Authors: Kornguth Steven , Chambliss Glenn , Gehring Kristine , Wible Lyman , Anderson Jack , Shalabi George , Unversagt Louis , Brodman Bruce W. 
Published: July 2010

AbstractThis article describes the utility of Spizizen medium in effecting the release of 2,4 dinitrotoluene (DNT) from plasticized propellant in aged clay soil and of added Pseudomonas organisms in enhancing the rate of degradation of DNT in clay and sandy soils. DNT is an environmental problem because of its toxicity to mammals. It is proposed that the citrate in Spizizen medium chelates metals that form the aggregates of humin in aged clay soils, thereby releasing propellant components. Lack of awareness of DNT mobilization by citrate or other polyanions may lead to a potential underestimation of the 2,4 DNT present in aged contaminated soil and a potential increased release of DNT following exposure to solvents containing citrate or other polyanions. DNT in contaminated sandy soils was rapidly degraded when Pseudomonas and Spizizen medium were added (85% degraded in 20 days). Pseudomonas isolated/Torn soils at the Badger Plant have particular utility for the in situ degradation of 2,4 DNT in clay and sandy soils because they metabolize Spizizen medium, thrive in diverse climates, and have been selected for their ability to grow in soils contaminated with DNT. Mixture of either the contaminated clay soil or the contaminated sandy soil with uncontaminated prairie silt loam (20:80 ratio) facilitated management of the treatment process. This observation is important because of the widespread distribution, and hence low cost, of this soil type in the central United States.
Accounting for Science and Uncertainty in Cleanup Levels: The Use of 1 μg/kg as the Cleanup Criterion for Dioxin in Soil
Authors: LaGoy Peter K. 
Published: July 2010

AbstractAt hazardous waste sites, a 1 μg/kg (ppb) cleanup level has commonly been used for dioxin in residential soil. This article outlines reasons for the continued use of this value in site remediation. Dioxin, one of the most toxic compounds known, has been a focus of scientific study for many years. However, controversy continues to surround its regulation, with some scientists arguing that new scientific results support decreasing risk estimates for dioxin and others taking the opposite view. Part of this controversy appears to involve a decreasing emphasis on cancer and an increased concern about non‐cancer and ecological impacts of dioxin. The 1 ppb soil cleanup level represents a reasonable generic value for dioxin, with higher or lower values required on a case‐by‐case basis to protect specific populations.
Remediation of the Radioactive Waste Landfill and Chemical Disposal Pits Sites at Sandia National Laboratories
Authors: Conway Rarilee , Aas Chris 
Published: July 2010

AbstractSandia National Laboratories' Environmental Restoration (ER) Project remediated the Radioactive Waste Landfill and Chemical Disposal Pits (RWL/CDPs) sites located in Albuquerque, New Mexico. The remediation was conducted in 1996 using conventional excavation, as well as hybrid remote robotic manipulation technology at a cost of approximately $3 million. Wastes generated included approximately 73 cubic meters (m3) of debris (including thermal batteries, spark gap tubes, radioactive sources, weapons components, and some classified material), 535 m3 of plutonium‐contaminated soil, and 2,294 m3 of soil contaminated with thorium, cesium, uranium, and tritium. The remediation was successful since the project goal of risk reduction was accomplished and no injuries or negative occurrences resulted. This cleanup is one example of the Department of Energy's (DOE's) accelerated approach to environmental restoration. The remediation was performed as a voluntary corrective measure to reduce schedule and budget, compared with the traditional approach following Resource Conservation and Recovery Act (RCRA) regulations.
Remediation Technologies Screening Matrix and Reference Guide: Version III
Authors: Teefy Dennis A. 
Published: July 2010

AbstractThe U. S. Army Environmental Center (USAEC) is leading an effort to update the Remediation Technologies Screening Matrix and Reference Guide, Third Edition under the auspices of the Federal Remediation Technologies Roundtable (FRTR). Its purpose is to create a comprehensive “Remediation Technologies Yellow Pages” for use by those responsible for environmental cleanup. The Guide is being produced as a multiagency cooperative effort published under the FRTR. Members of this effort include USAEC, the U. S. Army Corps of Engineers (USACE), the Naval Facilities Engineering Service Center (NFESC), the Air Force Center for Environmental Excellence (AFCEE), the Environmental Protection Agency (EPA), the Department of Energy (DOE), the Department of the Interior (DOI), and the Interstate Technologies Regulation Cooperative (ITRC). This article provides a comprehensive look at environmental technology information provided in the electronic user‐defined Remediation Technologies Screening Matrix and Reference Guide.
Almost all graphs with 1.44n edges are 3‐colorable
Authors: Chvátal V. 
Published: July 2010

AbstractWe establish a uniform asymptotic approximation of certain probabilities arising in the coupon collector's problem. Then we use this approximation to prove that almost all graphs with n vertices and 1.44 n edges contain no subgraph with minimum degree at least three, and hence are 3‐colorable.
A power law for connectedness of some random graphs at the critical point
Authors: Zhang Yu 
Published: July 2010

AbstractWe consider P(G is connected) when G is a graph with vertex set Z+ = {1,2, …}, and the edge between i and j is present with probability p(i, j) = min(λ h(i, j), 1) for certain functions h(i, j) homogeneous of degree ‐1. It is known that there is a critical value λc of λ such that magnified image.We show that the probability, at the critical point λc, that n1, and n2 are connected satisfies a power law, in the sense that for n2 ≧ nt ≧ 1 magnified image for any δ > 0 and certain constants c1 and c2.
On generalized independent subsets of trees
Authors: Drmota Michael , Kirschenhofer Peter 
Published: July 2010

AbstractA natural generalization of the widely discussed independent (or “internally stable”) subsets of graphs is to consider subsets of vertices where no two elements have distance less or equal to a fixed numberk(“k‐independent subsets”). In this paper we give asymptotic results on the average number of ˆ‐independent subsets for trees of sizen, where the trees are taken from a so‐called simply generated family. This covers a lot of interesting examples like binary trees, general planted plane trees, and others.
Proportional graphs
Authors: Janson Svante , Kratochvil Jan 
Published: July 2010

AbstractLet S be a finite set of graphs and t a real number, 0 < t < 1. A (deterministic) graph G is (t, 5)‐proportional if for every H ∈ S, the number of induced subgraphs of G isomorphic to H equals the expected number of induced copies of H in the random graph Gn, t where n = |V(G)|. Let Sk = {all graphs on k vertices}, in particular S3 = {K3, P2, K2Kt, D3}. The notion of proportional graphs stems from the study of random graphs (Barbour, Karoński, and Ruciński, J Combinat. Th. Ser. B, 47, 125‐145, 1989; Janson and Nowicki, Prob. Th. Rel. Fields, to appear, Janson, Random Struct. Alg., 1, 15‐37, 1990) where it is shown that (t, S3)‐proportional graphs play a very special role; we thus call them simply t‐proportional. However, only a few ½‐proportional graphs on 8 vertices were known and it was an open problem whether there are any f‐proportional graphs with t ≠ ½ at all. In this paper, we show that there are infinitely many ½‐proportional graphs and that there are t‐proportional graphs with t≠. Both results are proved constructively. [We are not able to provide the latter construction for all f∈ Q∩(0,1), but the set of ts for which our construction works is dense in (0,1).] To support a conviction that the existence of (t, S3)‐proportional graphs was not quite obvious, we show that there are no (t, S4)‐proportional graphs.
Spanning maximal planar subgraphs of random graphs
Authors: Bollobás B. , Frieze A. M. 
Published: July 2010

AbstractWe study the threshold for the existence of a spanning maximal planar subgraph in the random graph Gn, p . We show that it is very near p = 1/n⅓ We also discuss the threshold for the existence of a spanning maximal outerplanar subgraph. This is very near p = 1/n½.
Acyclic coloring of graphs
Authors: Alon Noga , Mcdiarmid Colin , Reed Bruce 
Published: July 2010

AbstractA vertex coloring of a graph G is called acyclic if no two adjacent vertices have the same color and there is no two‐colored cycle in G. The acyclic chromatic number of G, denoted by A(G), is the least number of colors in an acyclic coloring of G. We show that if G has maximum degree d, then A(G) = 0(d4/3) as d → ∞. This settles a problem of Erdös who conjectured, in 1976, that A(G) = o(d2) as d → ∞. We also show that there are graphs G with maximum degree d for which A(G) = Ω(d4/3/(log d)1/3); and that the edges of any graph with maximum degree d can be colored by 0(d) colors so that no two adjacent edges have the same color and there is no two‐colored cycle. All the proofs rely heavily on probabilistic arguments.
Probabilities in first—order logic of a unary function and a binary relation
Authors: Tyszkiewicz Jerzy 
Published: July 2010

AbstractWe settle the question of the behavior of probabilities of sentences of first—order logic about a unary function and a binary relation. We show that there are sentences of this logic without asymptotic probability. This settles the last open case in the problem of establishing the behavior of asymptotic probabilities for classes of labeled structures corresponding to natural signatures. © 1995 John Wiley & Sons, Inc.
The general birthday problem
Authors: Holst Lars 
Published: July 2010

AbstractThe general birthday problem with unlike birth probabilities and the waiting time N until c people with the same birthday have been obtained is studied in this article. It is shown that N is stochastically largest when the birth probabilities are equal. By embedding in Poisson processes it is shown how the moments of N can be expressed in moments of the minimum of gamma random variables. © 1995 John Wiley & Sons, Inc.
On uncrowded hypergraphs
Authors: Duke Richard A. , Lefmann Hanno , Rödl Vojtech 
Published: July 2010

AbstractIn this note we will show that every k—uniform hypergraph ℋ︁ on n vertices with average degree ik‐1 containing no 2—cycles has independence number α(ℋ︁)≧ck n/t(lnt)1/(k‐1) for t ≧ t0(k). This confirms a conjecture of Spencer. © 1995 John Wiley & Sons, Inc.
Coverings of r—graphs by complete r—partite subgraphs
Authors: Erdös Paul , Rödl Vojtech 
Published: July 2010

AbstractLet G be an (r + l)—uniform hypergraph of n vertices. Let f(r + 1, G) denote the minimum number of complete (r + l)—partite subgraphs necessary to cover all edges of G. We note that f(r+ 1, G) ≦ T(r, r + 1, n); the corresponding Turán number, and prove that up to a factor of 1 + o(l) this bound is best possible. © 1995 John Wiley & Sons, Inc.
Conservation partnerships and biodiversity governance: fulfilling governance functions through interaction
Authors: Visseren‐Hamakers Ingrid Jacoba , Leroy Pieter , Glasbergen Pieter 
Published: July 2010

ABSTRACTOver the last decades, new governance mechanisms such as partnerships have been increasingly accepted as instruments for sustainable development. This article contributes to an improved understanding of the contributions of partnerships, and their interactions with and consequences for intergovernmental regimes. It answers the question to what extent the roles of international intersectoral partnerships in biodiversity governance can be assessed using a positive, negative, or utilitarian qualification. To answer this question, the article develops and applies a methodology to analyze the governance functions that partnerships fulfill, and the institutional interaction (in terms of content, discourses, and rules) between the partnerships and intergovernmental regimes. Two case studies are analyzed: the Great Apes Survival Project (GRASP), and the Critical Ecosystem Partnership Fund (CEPF), which works on biodiversity hotspots. Contrary to most partnerships, these conservation partnerships do not use the market as a steering mechanism for sustainable development, but focus on enhancing international policy processes. The article concludes that the partnerships reinvent biodiversity policy and politics, which is necessary to improve the effectiveness of the biodiversity governance system, and that they complement intergovernmental regimes, albeit with varying effectiveness. Recommendations are developed for governments to strategically enhance public–private interaction. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.