bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers
Authors: Herter Sylvia , Piper Derek E. , Aaron Wade , Gabriele Timothy , Cutler Gene , Cao Ping , Bhatt Ami S. , Choe Youngchool , Craik Charles S. , Walker Nigel , Meininger David , Hoey Timothy , Austin Richard J. 
Published: August 2005

Hepsin is a membrane-anchored, trypsin-like serine protease with prominent expression in the human liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1–P4 substrate specificity. Hepsin exhibited strong preference at the P1 position for arginine over lysine, and favoured threonine, leucine or asparagine at the P2, glutamine or lysine at the P3, and proline or lysine at the P4 position. The relative activity of hepsin toward individual AMC (7-amino-4-methylcoumarin)-tetrapeptides was generally consistent with the overall peptide profiling results derived from the PC-SCL screen. The most active tetrapeptide substrate Ac (acetyl)-KQLR-AMC matched with the activation cleavage site of the hepatocyte growth factor precursor sc-HGF (single-chain HGF), KQLR↓VVNG (where ↓ denotes the cleavage site), as identified by a database analysis of trypsin-like precursors. X-ray crystallographic studies with KQLR chloromethylketone showed that the KQLR peptide fits well into the substrate-binding cleft of hepsin. This hepsin-processed HGF induced c-Met receptor tyrosine phosphorylation in SKOV-3 ovarian cancer cells, indicating that the hepsin-cleaved HGF is biologically active. Activation cleavage site mutants of sc-HGF with predicted non-preferred sequences, DPGR↓VVNG or KQLQ↓VVNG, were not processed, illustrating that the P4–P1 residues can be important determinants for substrate specificity. In addition to finding macromolecular hepsin substrates, the extracellular inhibitors of the HGF activator, HAI-1 and HAI-2, were potent inhibitors of hepsin activity (IC50 4±0.2 nM and 12±0.5 nM respectively). Together, our findings suggest that the HGF precursor is a potential in vivo substrate for hepsin in tumours, where hepsin expression is dysregulated and may influence tumorigenesis through inappropriate activation and/or regulation of HGF receptor (c-Met) functions.
Characterization of a recombinant type II 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Helicobacter pylori
Authors: Webby Celia J. , Patchett Mark L. , Parker Emily J. 
Published: August 2005

DAH7P (3-Deoxy-D-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. Previous work has identified two families of DAH7P synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type I paralogues from Escherichia coli. Whereas a number of organisms possess genes encoding both type I and type II DAH7P synthases, the pathogen Helicobacter pylori has only a single, type II, enzyme. Recombinant DAH7P synthase from H. pylori was partially solubilized by co-expression with chaperonins GroEL/GroES in E. coli, and purified to homogeneity. The enzyme reaction follows an ordered sequential mechanism with the following kinetic parameters: Km (PEP), 3 μM; Km (E4P), 6 μM; and kcat, 3.3 s−1. The enzyme reaction involves interaction of the si face of PEP with the re face of E4P. H. pylori DAH7P synthase is not inhibited by phenylalanine, tyrosine, tryptophan or chorismate. EDTA inactivates the enzyme, and activity is restored by a range of bivalent metal ions, including (in order of decreasing effectiveness) Co2+, Mn2+, Ca2+, Mg2+, Cu2+ and Zn2+. Analysis of type II DAH7P synthase sequences reveals several highly conserved motifs, and comparison with the type I enzymes suggests that catalysis by these two enzyme types occurs on a similar active-site scaffold and that the two DAH7P synthase families may indeed be distantly related.
Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus
Authors: Martínez-Fleites Carlos , Ortíz-Lombardía Miguel , Pons Tirso , Tarbouriech Nicolas , Taylor Edward J. , Arrieta Juan G. , Hernández Lázaro , Davies Gideon J. 
Published: August 2005

The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 Å (1 Å=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed β-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339–Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.
An olive pollen protein with allergenic activity, Ole e 10, defines a novel family of carbohydrate-binding modules and is potentially implicated in pollen germination
Authors: Barral Patricia , Suárez Cinthya , Batanero Eva , Alfonso Carlos , Alché Juan de Dios , Rodríguez-García María Isabel , Villalba Mayte , Rivas Germán , Rodríguez Rosalía 
Published: August 2005

CBMs (carbohydrate-binding modules) are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. They have been frequently identified by amino acid sequence alignments, but only a few have been experimentally established to have a carbohydrate-binding activity. A small olive pollen protein, Ole e 10 (10 kDa), has been described as a major inducer of type I allergy in humans. In the present study, the ability of Ole e 10 to bind several polysaccharides has been analysed by affinity gel electrophoresis, which demonstrated that the protein bound 1,3-β-glucans preferentially. Analytical ultracentrifugation studies confirmed binding to laminarin, at a protein/ligand ratio of 1:1. The interaction of Ole e 10 with laminarin induced a conformational change in the protein, as detected by CD and fluorescence analyses, and an increase of 3.6 °C in the thermal denaturation temperature of Ole e 10 in the presence of the glycan. These results, and the absence of alignment of the sequence of Ole e 10 with that of any classified CBM, indicate that this pollen protein defines a novel family of CBMs, which we propose to name CBM43. Immunolocalization of Ole e 10 in mature and germinating pollen by transmission electron microscopy and confocal laser scanning microscopy demonstrated the co-localization of Ole e 10 and callose (1,3-β-glucan) in the growing pollen tube, suggesting a role for this protein in the metabolism of carbohydrates and in pollen tube wall re-formation during germination.
A Reassessment of the SIDS Back to Sleep Campaign
Authors: Pelligra Ralph , Doman Glen , Leisman Gerry 
Published: August 2005

The Back to Sleep Campaign was initiated in 1994 to implement the American Academy of Pediatrics' (AAP) recommendation that infants be placed in the nonprone sleeping position to reduce the risk of the Sudden Infant Death Syndrome (SIDS). This paper offers a challenge to the Back to Sleep Campaign (BTSC) from two perspectives: (1) the questionable validity of SIDS mortality and risk statistics, and (2) the BTSC as human experimentation rather than as confirmed preventive therapy.The principal argument that initiated the BTSC and that continues to justify its existence is the observed parallel declines in the number of infants placed in the prone sleeping position and the number of reported SIDS deaths. We are compelled to challenge both the implied causal relationship between these observations and the SIDS mortality statistics themselves.
Non‐uniform volume and water content changes in swelling clay soil: I. Theoretical analysis
Authors: VOLTZ M. , CABIDOCHE Y.‐M. 
Published: August 2005

SummaryIn many clay soils, drying and wetting cause non‐uniform changes in water content and in the volume of soil and peds. Theoretical relations between total volume of soil, soil thickness and water content are sought for non‐uniformly swelling and shrinking soil. Such soil is assumed to be composed of small elemental volumes, each of which does swell or shrink uniformly. It is also assumed that the non‐uniformity of swelling or shrinking in such soils arises solely from spatial variation brought about by variations in evapotranspiration and infiltration. A constant ratio between movement of the soil in the vertical and horizontal dimensions is assumed for all elements of soil. By averaging over the soil volume the equations describing the volume change of individual elemental volumes, the averaged equations for non‐uniform volume changes may be obtained. They show that the average and the spatial distribution of the changes in soil thickness determine the average changes in water content of the soil. It is concluded that the equations for uniform and non‐uniform volume changing soils, though formally different, should in practice produce nearly identical results for clay soils.
Non‐uniform volume and water content changes in swelling clay soil: II. A field study on a Vertisol
Authors: CABIDOCHE Y.‐M. , VOLTZ M. 
Published: August 2005

SummaryA theoretical model of volume change in swelling clay soil is applied in a field study to determine the swelling‐shrinking behaviour of a Vertisol in Guadeloupe (French West Indies). The field experiment estimated the spatial averages of vertical soil movements and soil water content changes by measurements at the intersections of a sampling grid. The geometry of volume change was found to be anisotropic with vertical soil movements slightly larger than horizontal ones. The observed anisotropy seems to arise because the peds slide along oblique slickensides whereas individual peds shrink and expand isotropically. The discrepancy with earlier field results which indicated strictly isotropic volume changes is thought to arise in part from a difference in the nature of the clay soils investigated. An uncertainty analysis of the experiment shows that the main source of error is due to the estimation of the spatial averages of soil elevation.
Variation of textural porosity of a clay‐loam soil during compaction
Authors: BRUAND A. , COUSIN I. 
Published: August 2005

SummaryThe effect of compaction on the porosity of aggregates was studied in the laboratory using mercury porosimetry and backscattered electron scanning images (BESI) of polished thin sections. Porosity was divided into structural and textural porosity, and then textural porosity into lacunar and clayey porosity.For aggregates equilibrated at a water potential of −1 kPa and pressures of 50 and 200 kPa, compaction of structural porosity resulted in an increase of textural porosity. For aggregates equilibrated at a water potential of −1 kPa and an applied pressure of 600 kPa, the structural porosity strongly decreased but did not result in a variation of textural porosity. For aggregates equilibrated at water potentials of −63 and −103 kPa and the three values of pressure studied, textural porosity was unaffected by compaction whatever the evolution of structural porosity. The BESI indicated that the increase in textural porosity which was recorded by mercury porosimetry for aggregates equilibrated at a water potential of −1 kPa and applied pressures of 50 and 200 kPa was due to the formation of relict structural pores during compaction. The relict structural pores resulted from partial distortion of the structural pores within the original aggregates. These relict structural pores still had the morphology of structural pores on BESI, but they were accessible to mercury through the necks of textural pores identified as lacunar pores.Results also indicate that massive structure frequently seen in the field for these soils and interpreted as resulting either from structural collapse during rewetting or from compaction actually resulted mainly from wheel compaction.
The influence of increased NH4+ deposition rates on aluminium chemistry in the percolate of acid soils
Authors: EGLI M. , FITZE P. 
Published: August 2005

SummaryThe influence of different NH4+ loads on aluminium speciation in percolating water was studied on acid luvisols with similar soil‐pH values but with different soil adsorption surface characteristics. All of the applied NH4+ was nitrified and therefore led to proton production. Thus, Al displacement in the percolate was increased. The extent of this enhanced translocation was found to be chiefly a function of the amount of exchangeable base cations which buffered the protons produced by nitrification.The proportion of the different Al species in the percolate was altered at large NH4+ loads. Very large A13+ concentrations eliminated Al species bound to dissolved organic matter and particles, presumably because of flocculation and precipitation of organic ligands. Furthermore, increased NO3− and A13+ concentrations enhanced the desorption of F− giving rise to an additional increase in Al displacement by the formation of Al fluoro complexes in the aqueous phase.
Radio‐caesium fixation dynamics: measurement in six Cumbrian soils
Authors: ABSALOM J.P. , YOUNG S.D. , CROUT N.M.J. 
Published: August 2005

SummaryFive peat soils and a mineral soil were artificially contaminated with 137Cs. Soil solution activity and radio–lability of 137Cs were monitored over 709 days to quantify progressive 137Cs fixation. The peat soils fixed large amounts of 137Cs, but less than the mineral soil did. Distribution coefficients (Kd, cm3 g−1) ranged from 30 to 5000 at the end of equilibration. A labile 137Cs distribution coefficient, Kdt, was estimated by a method involving solid ⇌ solution equilibration in dilute solution.In a separate study several concentrations of KCl were added to soils in increasing concentration both before and after the addition of 137Cs. Differences in apparent adsorption strength of radiocaesium indicated that K+ induced the collapse of expanded mineral interlayers, thereby trapping ions. It seemed that I37Cs adsorbs at sites in the small micaceous clay fraction of the peat soils.The different rates of 137Cs adsorption and fixation in the peat and mineral soils, in which the rate of access of 137Cs to fixation sites in peat soils is less, seems to have been caused partly by lack of K, and partly by the scarcity of fixation sites.
Simplified models of anoxia and denitrification in aggregated and simple‐structured soils
Authors: ARAH J.R.M. , VINTEN A.J.A. 
Published: August 2005

SummaryTwo complementary approaches to modelling soil anoxia and denitrification are compared. The first postulates a structurally and biologically heterogeneous soil matrix (physical aggregates) and Michaelis—Menten kinetics; the second a random distribution of cylindrical air‐filled pores, a uniform metabolic activity and zero‐order reaction kinetics. Simple functional approximations to both models are developed, allowing their differences to be explored. At water contents corresponding to aggregate saturation the anoxic fractions and denitrification rates predicted by the aggregate model exceed those predicted by the simple‐structure model. In drier soils the predictions of the latter model typically exceed those of the former by between one and three orders of magnitude, the discrepancy lessening as the oxygen reaction potential and the mean radius of the aggregates increase. The aggregate model is much more sensitive to air‐filled porosity, and shows a decreased denitrification efficiency when nitrate concentrations are low. It is likely to predict sharper rainfall‐induced denitrification events, and a smaller background activity, than the distri‐buted‐pore treatment. Whichever of these or other process‐based treatments of denitrification is adopted, simple approximations like those presented here greatly facilitate inclusion in larger‐volume systems models.
Anaerobiosis in saturated soil aggregates: modelling and experiment
Authors: SIERRA J. , RENAULT P. , VALLES V. 
Published: August 2005

SummaryA model of anaerobiosis based on gas diffusion and microbial respiration is proposed for soil aggregates. Unlike previous models, it accounts for the dependency of O2 consumption on O2 and CO2 concentrations and, consequently, on chemical reactions of CO2 in soil solution. The model is tested with experimental data of respiration and O2 distribution within spherical remoulded aggregates of different sizes saturated with water. Most of the model parameters were estimated experimentally.Fick's law could describe O2 diffusion inside the saturated aggregates. The model agreed well with O2 profiles measured soon after saturation. Later, the model underestimated anaerobiosis, probably because of changes in radial distribution of microbial activity inside the aggregates. Respiration as a function of O2 concentration was satisfactorily described by the model. Nevertheless, each size of aggregate was analysed separately because of an apparent relation between size and maximal aerobic respiration. This seems to be associated with a non‐homogeneous distribution of aerobic respiration. The model represents an improvement on those currently used to estimate anaerobiosis inside aggregates.
Pyrolysis methylation—mass spectrometry of whole soils
Authors: SCHULTEN H.‐R. , SORGE C. 
Published: August 2005

SummaryIn‐source pyrolysis field ionization mass spectrometry (Py‐FIMS) and Curie–point pyrolysis gas chromatography/mass spectrometry (Py‐GC/MS) have been applied to the characterization of whole soils methylated off–line and on–line by two methylation reagents. Samples of a gleysolic Ap–horizon and a podzolic Bh horizon (Corg concentrations 2–3%) were investigated by conventional on–line and developed off–line methylation with tetramethylammonium hydroxide (TMAH) and by off–line methylation with diazomethane. For the first method, the soils were dried, milled and pretreated with TMAH for 10 min at 250°C at ambient pressure outside the pyrolyzers. For the second method, the dried and milled soils were methylated with an ether solution of diazomethane for 12 h at room temperature (∼20°C). Pyrolysis methylation with TMAH enabled aliphatic C2–C39 monocarboxylic acid methyl esters, C4–C30 dicarboxylic acid dimethyl esters and benzenecarboxylic acid methyl esters to be detected. Methoxybenzenes from phenols, benzenediols and benzenetriols, methoxybenzenecarboxylic acid methyl esters from phenolic acids and furancarboxylic acid methyl esters from carbohydrates were also identified. Nitrogen–containing compounds in soil organic matter were obtained as N,N–dimethylamides. Using diazomethane as methylation reagent, distinct Py‐FIMS signals were observed for aliphatic C2–C32 monocarboxylic acid methyl esters and C3–C24 dicarboxylic acid dimethyl esters. Additionally, methoxybenzenes originating from lignins, methoxybenzenecarboxylic acid methyl esters from phenolic acids and N,N–dimethylamides from amides were detected. The more acid podzolic Bh horizon showed higher relative intensities for dicarboxylic acid dimethyl esters and methylated phenolic acids compared to the gleysolic Ap horizon. Similarly, benzenecarboxylic acids are connected mainly by ester linkages to the macromolecular network of soil organic matter. Both methylation procedures support conventional Py‐FIMS and Py‐GC/MS and give valuable additional information on the occurrence of aliphatic and aromatic carboxylic acids, substituted phenols, benzenediols, benzenetriols, phenolic acids and amides in soil organic matter.
Characterizing trace metal adsorption on kaolinite
Authors: SPARK K.M. , WELLS J.D. , JOHNSON B.B. 
Published: August 2005

SummaryAdsorption of Cu(II), Zn(II), Co(II) and Cd(II) on kaolinite has been investigated at 25°C as a function of pH, concentration of the substrate, and the nature and concentration of the supporting electrolyte. The adsorption edges for three metals (Zn(II), Co(II) and Cd(II)) showed clear evidence of two distinct adsorption processes. As the pH was increased adsorption began at pH 4.5 for all metals, but the fraction of metal adsorbed at the completion of the first stage differed, the order being Zn(II)>Co(II)∼Cd(II). The second stage of adsorption had characteristics similar to those for adsorption of the metals on alumina and silica. Type 1 adsorption (the first stage) probably occurs on the permanent negatively charged kaolinite faces, while Type 2 (the second stage) is associated with the variable‐charge surfaces.Increasing the concentration of supporting electrolyte (KNO3 or NaCl) dramatically reduced the extent of Type 1 adsorption: at 0.1 m no evidence of this process existed. At intermediate concentrations electrolytes containing K+ suppressed Type 1 adsorption more than those containing Na+.
Speciation and calcium competition effects on cadmium sorption by sandy soil at various pHs
Authors: TEMMINGHOFF E.J.M. , VAN DER ZEE S.E.A.T.M. , DE HAAN F.A.M. 
Published: August 2005

SummaryThe effects of Ca competition, ionic strength, inorganic complexation and pH on cadmium adsorption by a sandy soil were studied. Sorption of Cd was measured using four different electrolytes CaCl2, Ca(NO3)2, NaNO3 and NaCl at a constant ionic strength (I) of 0.003 M at three different pHs, at variable Ca/Na ratio with a constant ionic strength of 0.03 and at variable ionic strengths between 0.003 and 0.3 M for two different pHs for Ca(NO3)2 and NaNO3. The measured Cd sorption isotherms were non‐linear. In the case of Cl as electrolyte anion, 13% of the Cd in solution is complexed at I= 0.003 (0.002 M Cl) and 91% of Cd is complexed at I= 0.3 (0.2 M Cl). If NO3 is the anion, none of Cd is complexed at I= 0.003 and 11% at I= 0.3. The Cd complexes do not adsorb significantly. Calcium competition, at an ionic strength of 0.03, reduced the Cd adsorption by 60–80% compared with the case that Na is the cation. Increasing the ionic strength from 0.003 to 0.3 decreased Cd sorption by 60% for Ca(NO3)2 and 25% for NaNO3 due to a decrease of the activity coefficient, increase of inorganic complexation and increase of Ca competition. A decrease of one pH unit reduces Cd sorption of about 75%. Sorption of Cd by soil could be described adequately with the three‐species Freundlich (3SF) equation in which pH, complexation, Ca competition and ionic strength effects were taken into account.