bluuebunny/crossref_metadata_2025_split huggingface dataset:
TAP1 and TAP2 gene polymorphism in rheumatoid arthritis in a population in eastern France
Authors: Zhang S.‐L. , Chabod J. , Penfornis A. , Reviron D. , Tiberghien P. , Wendling D. , Toussirot É. 
Published: March 2003

SummaryThe ‘transporter associated with antigen processing’ (TAP) gene products are involved in the processing of endogenous peptides that bind to class I molecules. Polymorphism within these genes could alter the level of the immune response, a phenomenon relevant to the development of autoimmune diseases. In this study, we examined the polymorphism of TAP1 and TAP2 genes in patients with rheumatoid arthritis (RA). TAP1 and TAP2 typing was performed for 138 Caucasian RA patients and 100 healthy controls, all originating from eastern France. TAP1 polymorphic residues at positions 333 and 637 and amino acid variants 379, 565, 651 and 665 in the TAP2 gene were found using amplification refractory mutation system–polymerase chain reaction (ARMS‐PCR). This method enabled us to determine four TAP1 alleles (TAP1A to TAP1D) and eight TAP2 alleles (TAP2A to TAP2H). All patients and controls had been HLA‐DRB1* genotyped. The polymorphic residues TAP1333 and TAP1637 did not show any difference in their distribution between patients and controls. Similar findings were obtained for TAP2379 and TAP2665. However, we found an increased frequency of Thr homozygosity and heterozygosity at position 565 in the TAP2 gene in RA patients (RA vs. controls: 25.3 vs. 14%; P = 0.032; OR = 2.09; CI = 1.01–4.38). Similarly, the prevalence of subjects who were homozygote and heterozygote for Cys651 was increased in the RA group (RA vs. controls: 36.8 vs. 11%; P = 0.02). The dimorphic site TAP2565 defines TAP2D and TAP2E alleles, while the site at position 651 characterizes TAP2F. Thus, we found that TAP2D and TAP2E alleles were more prevalent in RA, but not significantly so (RA vs. controls: TAP2D: 10 vs. 3.6%; P = 0.24; TAP2E: 3.6 vs. 0%; P = 0.19). Similarly, the frequency of TAP2F was higher in RA patients (24.5%) than in controls (11.3%), but this was not significant after correction (P = 0.029; Pcorr = 0.17). Finally, we found no linkage disequilibrium between DRB1* RA‐associated alleles and amino acid substitution Thr565 or TAP2D and TAP2E alleles, whereas Cys651 (and TAP2F) was not independent of DRB1*04, a strongly RA‐associated allele. Finally, Thr at position 565 in the TAP2 gene was associated with manifestations of disease severity in only a few patients. Examination of TAP1 and TAP2 gene polymorphisms in RA patients revealed an association between a particular amino acid residue, namely Thr565 in the TAP2 gene, and RA. This association was found to be weak and did not seem to be a predictor for the severity of the disease.
Comparison of different techniques for detection of anti‐HLA antibodies in sera from patients awaiting kidney transplantation
Authors: Uboldi de Capei M. , Praticò L. , Curtoni E. S. 
Published: March 2003

SummaryThe aim of the present study was to compare different techniques of HLA antibody detection in patients waiting for a transplant. Two methods of HLA antibody screening were compared: the complement‐dependent cytotoxicity (CDC) test and the enzyme‐linked immunosorbent solubility assay (ELISA). Three different commercial kits for the latter assay were tested: the kits were produced by One Lambda (O.L.) and SANG STAT for prescreening and specificity determination, and GTI only for prescreening. Of the two techniques, only CDC can detect IgM. The study included 207 serum samples selected from 192 patients waiting for a first kidney transplant. The conclusions are that O.L. is more sensitive than CDC and the other ELISA kits and is much faster for analysing a serum (taking only a few hours), but costs about 16 times more than CDC and does not detect IgM antibodies, so can be used only in support of CDC.
Novel single nucleotide polymorphisms in the 3′‐UTR of the TGFβRI and TGFβRIII genes
Authors: Bayat A. , Watson J. S. , Stanley J. K. , Ferguson M. W. J. , Ollier W. E. R. 
Published: March 2003

SummaryTransforming growth factor beta (TGFβ) family members are multifunctional cytokines that play a key role in cellular growth, proliferation and differentiation. Transmembrane signalling by TGFβ occurs via a complex of the serine/threonine kinases TGFβ type 1 (TGFβRI), type 2 (TGFβRII), and type 3 (TGFβRIII) receptors. Previous studies have implicated TGFβ receptors (TGFβR) in a variety of important hereditary clinical disorders. Mutations of the TGFβR genes have been observed in several human cancers. The aim of this study was to identify and confirm novel single nucleotide polymorphisms (SNPs) in TGFβRI and RIII and to determine the relative allele and genotype frequencies of these SNPs. SNPs were identified from the examination of sequence alignments held in databases and were confirmed by DNA sequencing. A polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) method was devised for genotyping TGFβ receptor polymorphisms. DNA samples from 91 controls were examined. The observed heterozygosities of TGFβRI and TGFβRIII gene polymorphisms in the control population were 43 and 33%, respectively, suggesting these SNPs could be useful markers in disease association studies.
Modelling SO42– surface complexation on variable charge minerals. II. Competition between SO42–, oxalate and fulvate
Authors: Karltun E. 
Published: March 2003

SummaryThe adsorption of oxalate and fulvate and the competition for surface‐adsorption sites between SO42–‐oxalate and SO42–‐fulvate on goethite and on a soil material from a podzol B horizon were studied in batch titration experiments. The adsorption and competition processes were evaluated with surface complexation modelling using the diffuse‐layer model (DLM). Two different adsorption reactions were tested for oxalate and fulvate adsorption and the reaction giving the largest charge neutralization at the surface gave the best description of experimental data. In the soil solution an Al‐oxalate complex induced a substantial decrease in oxalate adsorption when the pH fell below 4.5. No such effect was found in the soil‐fulvate system. Adsorption constants obtained from binary systems (oxide‐ligand) were used to model adsorption and competition in the two ternary systems oxide‐SO42–‐oxalate and oxide‐SO42–‐fulvate. Experimental data showed that oxalate and fulvate competed with SO42– for adsorption sites. The DLM produced acceptable descriptions of experimental data, although the model slightly underpredicted SO42– adsorption in ternary systems. The competition between adsorbates was attributed mainly to charge neutralization at the surface induced by adsorption of the ligands.
Apparent cation‐exchange equilibria in podzolic forest soils
Authors: Nissinen A. , Ilvesniemi H. , Tanskanen N. 
Published: March 2003

SummaryThe Gaines–Thomas selectivity coefficient, K, was used to express the relation between the cations in solution and the cations in exchange sites in podzolic forest soils. Soil solution was obtained by centrifuging a fresh bulked soil sample. Exchangeable cations HX, AlX, CaX, MgX and KX and effective cation‐exchange capacity, CECe, were determined with 0.1 m BaCl2. Apparent values of K indicated a preference of Ca2+ over Mg2+ and over Al3+ in O, A and B horizons (log KAl–Ca < 0 and log KMg–Ca < 0), whereas log KK–Ca and log KH–Ca exceeded zero. The horizons were similar with respect to log KH–Ca, and the differences in log KMg–Ca were small. Log KK–Ca and log KAl–Ca increased in the horizons in the order O < A < B. Log KAl–Ca was not significantly correlated with the fraction AlX/CECe. Log KMg–Ca was positively correlated with the fractions HX/CECe and AlX/CECe, and negatively correlated with log (CaX/MgX). The selectivity coefficient of binary cation exchange seemed to be applicable to in situ soil solutions. However, the fraction of each cation on exchange sites should be based on the CECe rather than on the sum of the two cations. The latter, also, seemed to be acceptable in cases of exchangeable cations with a large relative content in soil, e.g. in Al3+–Ca2+ exchange in A and B horizons, and in H+–Ca2+ exchange in O and A horizons.
Nitrate leaching: modifying the loss from mineralized organic matter
Authors: GOSS M. J. , HOWSE K. R. , CHRISTIAN D. G. , CATT J. A. , PEPPER T. J. 
Published: March 2003

SummaryThe impact on nitrate leaching of agronomic practices designed to immobilize nitrogen in autumn and winter was investigated over 4 years. Experimental treatments (reducing tillage depth, incorporating harvest residues, reducing fertilizer N by growing unfertilized grass or by spring‐sown rather than autumn‐sown crops) were compared with a control treatment in which autumn crops were sown after burning harvest residues, mouldboard ploughing and seedbed preparation. Winter cover cropping was also compared with winter fallowing. In the first year, incorporation of harvest residues or reducing tillage depth significantly decreased nitrate leaching compared with the control. Unfertilized grass did not affect leaching in the first winter but significantly decreased it in years 2 and 3. When winter cover crops were grown, nitrate leaching was never less than that under an autumn‐sown cereal, and in the subsequent year leaching could be significantly greater. Winter fallowing caused the most nitrate leaching over the year. In the winter following a spring‐sown crop, leaching under an autumn‐sown crop greatly increased. Summed over 4 years, most leaching occurred with the winter fallow—spring cropping treatment; it was 18% more than where a winter cover crop preceded the spring crop. Reducing tillage depth or incorporating harvest residues did not significantly decrease leaching. Unfertilized grass ley followed by an autumn‐sown cereal in the fourth year was the only treatment that significantly decrease leaching. Unfertilized grass ley followed by an autumn‐sown cereal in the fourth year was the only treatment that significantly reduced leaching loss compared with the control. Incorporating harvest residues resulted in a balance between annual N inputs and outputs. All other treatments required substantial net annual N mineralization to balance annual inputs and outputs.
Movement, adsorption and mineralization of atrazine in two soils with and without switchgrass (Panicum virgatum) roots
Authors: Mersie W. , Seybold C. , Tsegaye T. 
Published: March 2003

SummaryA study was conducted to determine the influence of switchgrass roots on the mobility, adsorption–desorption and mineralization of atrazine in Cullen clay loam and Emporia loamy sand soils. Bromide and atrazine distribution profiles in the leachates indicated greater preferential movement in columns with roots than in columns without roots. Larger concentrations of atrazine were detected at lower depths of Emporia soil with switchgrass roots than without. Adsorption of atrazine was greater in Cullen than in Emporia soil and conformed to Freundlich isotherms. In both Cullen and Emporia soils, adsorption and desorption were not different between soil with or without switchgrass roots. After 84 days of incubation, less than 6% of the applied atrazine was mineralized in the Cullen soil and 2% in Emporia soil. Mineralization was greater in the Cullen soil than in the Emporia soil at 42, 56, 70 and 84 days of sampling. The presence of switchgrass roots did not affect the mineralization of atrazine in Emporia soil. The presence of switchgrass roots caused preferential movement of atrazine, but did not affect its adsorption and mineralization in either soil type.
Management effects on forms of phosphorus in soil and leaching losses
Authors: Leinweber P. , Meissner R. , Eckhardt K. ‐U. , Seeger J. 
Published: March 2003

SummaryWe should know the effects of soil use and management on the contents and forms of soil phosphorus (P) and the resulting potential for leaching losses of P to prevent eutrophication of surface water. We determined P test values, amounts of sequentially extracted forms of P, P sorption capacities and degrees of P saturation in 20 differently treated soils and compared these data with leaching losses in lysimeters. One‐way analyses of variance indicated that most fractions of P were significantly influenced by soil texture, land use (grassland, arable or fallow or reafforestation), mineral fertilization and intensity of soil management. Generally, sandy soils under grass and given large amounts of P fertilizer contained the most labile P and showed the largest P test values. Fallow and reafforestation led to smallest labile P fractions and relative increases of P extractable by H2SO4 and residual P. Arable soils with organic and mineral P fertilization given to crop rotations had the largest amounts of total P, labile P fractions and P test values. The mean annual concentrations of P in the lysimeter leachates varied from 0 to 0.81 mg l–1 (mean 0.16 mg l–1) and the corresponding leaching losses of P from < 0.01 to 3.2 kg ha–1 year–1 (mean 0.3 kg P ha–1 year–1). These two sets of data were correlated and a significant exponential function (R2 = 0.676) described this relation. Different soil textures, land uses and management practices resulted in similar values for P leaching losses as those for the amounts of labile P fractions. Surprisingly, larger rates of mineral P fertilizer did not necessarily result in greater leaching losses. The contents of P extracted by NaHCO3 and acid oxalate and the degrees of P saturation were positively correlated with the concentrations of P in leachates and leaching losses. As the P sorption capacity and degree of P saturation predicted leaching losses of P better than did routinely determined soil P tests, they possibly can be developed as novel P tests that meet the requirements of plant nutrition and of water protection.
Particle size fractionation of soil containing coal and combusted particles
Authors: Schmidt M. W. I. , Rumpel C. , Kögel‐Knabner I. 
Published: March 2003

SummaryStandard procedure for dispersing natural soils for particle size fractionation can be too aggressive for soil containing coal and other organic particles from coal industries. We have investigated ultrasonic dispersion for the latter in four soils differing in pedogenesis (Phaeozem, Podzol, reclaimed mine soils), carbon content (27.5–138.6 g kg–1), clay content (80–153 g kg–1) and sources of particles (airborne coal dust, combustion residues, lignite particles). As we found previously for natural soils, the ultrasonic energy needed for complete dispersion varies between 450 and 500 J ml–1, but the resulting particle size distributions differ from those obtained by standard textural analysis. This is probably related to the different properties of native soil organic matter and coal and combusted particles. Coal and soot particles may partly resist oxidation with hydrogen peroxide, depending on material and particle size. The diameter of lignite particles, remaining after oxidation, is overestimated in sedimentation analysis by a factor of 1.66. Sand‐sized lignite particles can be disrupted by ultrasonication and redistributed to finer particle size fractions. The ultrasonic dispersion and particle size fractionation procedure can be applied to soils containing coal and combusted particles, but caution is needed in interpreting the results if they contain large proportions of coal particles.
From local hydraulic properties to effective transport in soil
Authors: Kasteel R. , Vogel H. ‐J. , Roth K. 
Published: March 2003

SummaryThe inability to predict flow and transport behaviour based on a priori information demonstrates the lack of knowledge we currently have concerning transport‐relevant properties or processes, or both. We present an approach in which the behaviour of effective solute transport at the scale of a soil column (100 mm) is predicted by taking into account the spatial structure of the hydraulic properties at the local scale (1 mm). The local absorption coefficients obtained from X‐ray tomography, which are linearly related to bulk density, are used as local proxy for hydraulic properties. As a first approximation, two density classes were distinguished, and the three‐dimensional structure of the hydraulic properties was implemented in a model of flow and transport. The local hydraulic properties were obtained from a network model, except for the absolute value of the hydraulic conductivity function which was measured. Model simulations were compared with a measured breakthrough curve determined on the same soil sample. The two agreed well, although the local hydraulic properties and parameter structure were determined independently with respect to a breakthrough experiment. Predictions of solute transport at the column scale were sensitive to the difference in saturated hydraulic conductivities of both materials, but not to the local dispersivities. The simulations demonstrate that (i) assuming validity of the Richards equation and the convection–dispersion equation on the local scale leads to a good description of the effective flow and transport behaviour at the column scale without making any assumptions about the governing processes at that scale; (ii) the dispersion parameters, which are notoriously difficult to determine, need not be determined since their effect is included explicitly; and (iii) local absorption coefficients can be used as a local proxy for the parameter field of the hydraulic properties.
Simulation of water retention and hydraulic conductivity in soil using a three‐dimensional network
Authors: Peat D. M. W. , Matthews G. P. , Worsfold P. J. , Jarvis S. C. 
Published: March 2003

SummaryThe conduction of water by soil is fundamental to the way in which soils transport nutrients and pollutants into groundwater. The derivation of relations between water flow and void structure has relied on the implicit assumption that water flows through aligned unconnected cylindrical capillary tubes. We describe a three‐dimensionally interconnected model of void structure, called Pore‐Cor, which simulates the intrusion of a non‐wetting fluid and drainage of a wetting fluid. The model is calibrated by fitting it to the water retention curves of a sandy soil at four depths. The experimental drainage pressures are related to the radii of the entries to the voids by the Laplace equation. The necessities of using this equation, and of employing a simplified void geometry, introduce major approximations into the modelling. Nevertheless, the model is sufficiently precise and versatile to predict trends in other properties usefully. It is illustrated in this work by a close correlation between a predicted and experimental change in saturated hydraulic conductivity with depth, and a realistic unsaturated hydraulic conductivity curve. The saturated and unsaturated hydraulic values are shown to be much more realistic than those predicted by the aligned cylinders model. In addition, the simulations by Pore‐Cor indicate that the void network within the sandy soil is acting in a structured rather than a random manner. The Pore‐Cor model is currently being used to explain the matrix‐flow characteristics of tracers and pollutants.
Particulate organic matter as a source of variation in denitrification in clods of soil
Authors: Parry S. , Renault P. , Chadœuf J. , Chenu C. , Lensi R. 
Published: March 2003

SummaryExisting mechanistic models of denitrification in clods of soil describe the anaerobic activity in the centres of the clods, but they neglect the role of particulate organic materials. We therefore studied the effect of particulate organic matter on denitrification in soil both under pasture and in arable cultivation. Clods were separated into two compartments: (i) particulate organic matter and adhering soil exceeding 200 μm (coated POM), and (ii) the matrix (the rest of the soil). Potential denitrification and production of CO2 were then estimated on coated POM, matrix and unfractionated soil. The quantity and the quality of coated POM were assessed individually in 100 clods from the pasture and 100 from the arable land. The rate of potential denitrification was similar in unfractionated soil from these treatments. However, it was 70 times greater in the coated POM than in the matrix from the arable soil. Production of CO2 was nine times greater in the coated POM than in the matrix from the pasture soil and 33 times greater in the arable soils. These observations were the basis for a mechanistic model of denitrification, taking into account contributions from coated POM and the matrix. Denitrification rates in a computerized representation of clods from both pasture and arable soil had approximately the same distribution as experimental data both in the matrix and coated POM contributions in the cropped soil and in the matrix alone in the pasture soil. Coated particulate organic matter can explain more than half of the denitrification and most of the variation in denitrification when it increases microbial activity sufficiently and the soil structure limits the supply of O2.
Simulation of calcium leaching and desorption in an acid forest soil
Authors: Van Praag H. J. , De Smedt F. , Thanh T. vu 
Published: March 2003

SummaryThe aim of the study was to evaluate effects of mobile and immobile water and diffusion‐limited transport on the binding and release of ions in soils. The desorption and leaching of calcium in a humic layer of a densely rooted acid forest soil under a beech stand was studied in laboratory experiments by leaching soil columns with a desorption solution and recycling the leachate through the columns. Radioactive tracers were added and monitored in the leachate to evaluate desorption and leaching characteristics of the soil. Parallel experiments were conducted with chloride and calcium to determine transport and desorption parameters independently. The experimental data were then analysed with a transport model, taking into account effects of mobile and immobile soil water fractions, and in the case of calcium assuming an equilibrium Langmuir adsorption isotherm.The transport was highly dependent on the mobility of the soil water, and in particular the fraction of the soil water to which the chemical was confined as a result of ionic properties. For chloride an excluded soil water phase had to be taken into account to explain the experimental findings. Immobile or mobile water and solute transfer and transport properties were not sufficient to explain non‐equilibrium effects in the adsorption reactions. Desorption curves agreed with results from batch experiments, provided the leaching experiments were done in such a way that equilibration between the soil solution and the solid matrix adsorption sites was reached, otherwise desorption was delayed and the calculated isotherms do not represent actual equilibrium adsorption–desorption conditions.