bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex interaction between HLA DR and DQ in conferring risk for childhood type 1 diabetes
Authors: Kockum I. , Sanjeevi C. B. , Eastman S. , Landin‐Olsson M. , Dahlquist G. , Lernmark Å. 
Published: March 2003

AbstractType 1 (insulin‐dependent) diabetes mellitus is associated with HLA DR and DQ factors, but the primary risk alleles are difficult to identify because recombination events are rare in the DQ–DR region. The risk of HLA genotypes for type 1 diabetes was therefore studied in more than 420 incident new onset, population‐based type 1 diabetes children and 340 age, sex and geographically matched controls from Sweden. A stepwise approach was used to analyse risk by relative and absolute risks, stratification analysis and the predispositional allele test. The strongest relative and absolute risks were observed for DQB1*02‐DQA1*0501/DQB1*0302‐DQA1*0301 heterozygotes (AR 1/46, P < 0.001) or the simultaneous presence of both DRB1*03 and DQB1*0302 (AR 1/52, P < 0.001). Stratification analysis showed that DQB1*0302 was more frequent among DRB1*04 patients than DRB1*04 controls (P < 0.001), while DRB1*03 was more frequent among both DQA1*0501 (P < 0.001) and DQB1*02 (P < 0.001) patients than respective controls. The predispositional allele test indicated that DRB1*03 (P < 0.001) would be the predominant risk factor on the DRB1*03‐DQA1*0501‐DQB1*02 haplotype. In contrast, although DQB1*0302 (P < 0.001) would be the predominant risk factor on the DRB1*04‐DQA1*0301‐DQB1*0302 haplotype, the predispositional allele test also showed that DRB1*0401, but no other DRB1*04 subtype, had an additive risk to that of DQB1*0302 (P < 0.002). It is concluded that the association between type 1 diabetes and HLA is due to a complex interaction between DR and DQ since (1) DRB1*03 was more strongly associated with the disease than DQA1*0501‐DQB1*02 and (2) DRB1*0401 had an additive effect to DQB1*0302. The data from this population‐based investigation suggest an independent role of DR in the risk of developing type 1 diabetes, perhaps by providing diseases‐promoting transcomplementation molecules.
HLA class II polymorphism in Thai patients with non‐Hodgkin’s lymphoma
Authors: Nathalang O. , Tatsumi N. , Hino M. , Prayoonwiwat W. , Yamane T. , Suwanasophon C. , Sriphaisal T. 
Published: March 2003

AbstractThe distribution of HLA‐DRB1 alleles and DQB1 alleles in 100 Thai patients with non‐Hodgkin’s lymphoma (NHL) was analysed using the polymerase chain reaction with sequence‐specific primer (PCR–SSP) method, and the association between the disease and the presence of certain HLA class II alleles was investigated. The frequencies of HLA‐DRB1*1502 and DRB1*09012 were increased while those of DRB1*0404, DRB1*0803 and DRB1*1106 were decreased. On the other hand, the incidence of HLA‐DQB1 alleles was similar to that in the normal population. Interestingly, only HLA‐DRB1*1502 showed a significant positive association with NHL, especially in patients ≤ 45 years and in male patients. It is concluded that the DRB1*1502 allele may contribute to NHL susceptibility in the Thai population. However, further studies on the functional roles of the HLA class II alleles are necessary to elucidate NHL susceptibility.
Further characterization of MHC haplotypes demonstrates conservation telomeric of HLA‐A: update of the 4AOH and 10IHW cell panels
Authors: Cattley S. K. , Williamson J. F. , Tay G. K. , Martinez O. P. , Gaudieri S. , Dawkins R. L. 
Published: March 2003

AbstractCell panels have been used extensively in studies of polymorphism and disease associations within the major histocompatibility complex (MHC), but the results from these panels require continuous updates with the increasing availability of novel data. We present here an updated table of the typings of the 10IHW and 4AOH panels. Local data included are HFE, HERV‐K(C4) and six microsatellites telomeric of HLA‐A. Typings for class I, MICA (PERB11.1), MICB (PERB11.2), XA, XB, LMP2 and 10 microsatellites reported by others have also been consolidated in this table. The tabulation shows that the length of conservation in the human MHC is even more extensive than previously thought. Human MHC ancestral haplotypes are inherited as a conserved region of genomic sequence spanning some 6–8 megabases from the HLA class II region and beyond the HLA class I region up to and including the HFE gene. Numerous examples of historical recombinations were also observed.
Molecular variation of HLA class I genes in the Corsican population: approach to its origin
Authors: Grimaldi M.‐C. , Crouau‐Roy B. , Contu L. , Amoros J.‐P. 
Published: March 2003

SummaryThree human leucocyte antigen (HLA) class I loci (HLA‐A, ‐B and ‐Cw) were typed for the first time at the DNA level in the Corsican population. This analysis was performed on 100 individuals of Corsican origin living in central Corsica (46 individuals) and in south‐western Corsica (54 individuals). The genetic structure of these two subpopulations was analysed on the basis of the molecular polymorphisms of the HLA‐A, ‐B and ‐Cw genes. A phylogenetic and a haplotypic analysis were performed. The genotypic analysis did not detect genetic differentiation. Examination of the allelic and haplotypic frequencies did, however, reveal some significant differences between the two zones. Similarities with the Sardinian population were found, and were particularly evident in the south‐western sample. However, Corsica has probably been subject to greater West European influence, which can be seen in the Corte sample (Haute Corse).
Asthma and IL‐4 receptor alpha gene variants
Authors: Wjst M. , Kruse S. , Illig T. , Deichmann K. 
Published: March 2003

SummaryLinkage of allergy to chromosome 16 has been described in several studies, together with a positive association with interleukin 4 receptor α gene variants. Our aim was to replicate these findings in a sample of German and Swedish families recruited through sib‐pairs affected by bronchial asthma. None of the markers showed linkage with the main phenotype of asthma or with total serum IgE. Seropositivity to D. pteronyssinus showed borderline significance in a region flanking the IL4Rα location. Single nucleotide polymorphisms (SNPs) leading to the protein exchanges I50V, E375A, C406R, S478P and Q551R in the IL‐4 receptor α were examined for allele sharing in sibs with asthma. Multiple regression analysis was performed for association with total serum IgE and specific IgE. Allele sharing of IL4Rα SNPs in asthmatic children was not significantly increased for any of the examined SNPs except for the intracytoplasmatic polymorphism 551R (0.79 vs. 0.84 expected, P = 0.044). The variants 50V, 478P and 551R were associated with slightly increased, and 375A and 406R with decreased total IgE levels, all at a non‐significant level. None of the examined IL4Rα variants were correlated to asthma severity. In summary, a single gene effect of IL4Rα variants or any other gene on chromosome 16 could not be shown in this selected population of children with asthma. As there could be interactions with multiple genetic and environmental factors, IL4Rα could still be involved in asthma pathogenesis.
Frequencies of the ‐330 (T → G) IL‐2 and ‐590 (T → C) IL‐4 gene polymorphisms in a population from south‐eastern Brazil
Authors: Scarel‐Caminaga R. M. , Trevilatto P. C. , Souza A. P. , Brito R. B. , Line S. R. P. 
Published: March 2003

SummaryPolymorphisms in the promoter regions of cytokine genes may affect their transcription. A T/G substitution at position −330 of the interleukin‐2 (IL‐2) gene and a T/C substitution at position −590 of the interleukin‐4 (IL‐4) gene have been described previously. The −590 (T → C) IL‐4 gene polymorphism was associated with asthma and atopy in US and Japanese populations. Population genetics is a useful tool for determination of the biological significance of genetic polymorphisms. The aim of this study was to investigate the frequencies of polymorphisms in the promoter regions of the IL‐2 and IL‐4 genes in a population from south‐eastern Brazil and to compare them with those published for other populations. Allele frequencies were estimated in 114 unrelated individuals from São Paulo State. These subjects had an average age of 41.2 years (± 12.4 years) and the ethnic composition of the sample was: 78.07% Caucasian, 11.4% Black and 10.53% Mulatto. DNA from subjects was extracted from epithelial buccal cells, and the PCR‐RFLP technique was employed to investigate the −330 (T → G) IL‐2 and −590 (T → C) IL‐4 gene polymorphisms. The allele frequency of the IL‐2 gene polymorphism obtained in our study was similar to that found in UK Caucasoid groups. The T allele frequency of the IL‐4 gene polymorphism observed in the Caucasian Brazilian group was similar to that found in UK and Australian populations, while the frequency observed for the Black Brazilian group was similar to that found in Japanese and Kuwaiti Arab populations. The results for the −330 (T → G) IL‐2 and −590 (T → C) IL‐4 polymorphisms are consistent with the high contribution of European lineages to the population in south‐eastern Brazil.
Soil organic matter pools in a volcanic‐ash soil under fallow or cultivation with applied chicken manure
Authors: GIJSMAN A. J. , SANZ J. I. 
Published: March 2003

SummaryFrequent applications of chicken manure to a volcanic‐ash soil resulted in an increased crop yield several years after the applications ceased. Improved nutrient cycling through the soil organic matter (SOM) was thought be the cause of this. An area that for several years had been under either unimproved fallow or continuous bean‐maize intercropping (with chicken manure application) was planted with maize intercropped with the legume Arachis pintoi. Soil samples were fractionated into several sizes of aggregates and incubated for 6 weeks in intact form and after crushing the aggregates. Between 1.2 and 3.1% of the C in any aggregate size class exited in easily decomposable (i.e. not physically or chemically protected) form. Less than 0.8% of the macroaggregate C was physically protected by the aggregate structure. More than 97% of the C in any aggregate size class can be considered resistant. The large‐or small‐macroaggregate‐protected SOM (i.e. in aggregates > 2000 μm and 250–2000 μm, respectively). once made available, was more easily decomposed than the unprotected SOM. The large SOM content (45.8–57.3 g C kg−1) but yet limited mineralizability indicates that mechanisms other than soil macroaggregation are important for protecting SOM in this soil. Binding of organic molecules onto allophane minerals is likely to be such a mechanism.The larger yield and nutrient uptake by the maize in the former bean‐maize plots compared with the former fallow plots could not be explained by differences in SOM decomposition. We think that the frequent application of chicken manure to the former bean‐maize plots increased the available phosphorus in these strongly P‐sorbing soils by increasing the cycling of organic‐P or by blocking some of the P‐reactive sites. This, however, needs to be further investigated.
Comparing the effects of pH on the sorption of metals by soil and by goethite, and on uptake by plants
Authors: BARROW N. J. , WHELAN B. R. 
Published: March 2003

SummaryThe effects of soil pH on sorption of cadmium, zinc, nickel and cobalt were studied by changing the pH of a soil and measuring sorption. Results were compared with published results for effects of pH on sorption of cadmium, zinc and nickel by goethite. In a further experiment, the effects of pH on the uptake of zinc and cobalt by subterranean clover were measured.Effects of pH on sorption were described in terms of the concentration of metal ions required to produce equal sorption. Where the metal ions were incubated with the soil, unit increase in pH decreased the concentration of metal ions required about 10‐fold for zinc, about 7‐fold for nickel, about 6‐fold for cobalt, and about 4‐fold for cadmium. When the soil was mixed with a large volume of solution, the effects were similar for zinc and cadmium but slightly smaller for cobalt and slightly larger for nickel. In all cases, the magnitude of the effect varied somewhat with pH. Sorption was greater with a dilute background electroiyte than with a concentrated one and the effects of pH were greater. The effects for soil were smaller than effects of pH on sorption by iron oxides for which unit increase in pH can decrease the required concentration of Zinc 35‐fold and cadmium 11‐fold.These results are consistent with adsorption of divalent ions on a variable charge surface that is negatively charged. They are not consistent with the adsorption of monovalent metal ions on a variable charge surface. This mechanism requires at least a 10‐fold effect of pH. They show that the change in electric potential with change in pH is smaller for reacting surfaces in soil than for goethite. The effects of changing pH on the amounts of zinc and cobalt fertilizer required for equal uptake by plants was even smaller with unit increase in pH, causing a 1.4‐fold increase in the amount of fertilizer required, that is, a 1.4‐fold decrease in fertilizer effectiveness.
A modified Kjeldahl procedure for determining strongly fixed NH4+‐N
Authors: Corti G. , Agnelli A. , Ugolini F. C. 
Published: March 2003

SummaryThis paper reports a procedure for determining the content of strongly fixed NH4+ in soil. The procedure consists of a Kjeldahl digestion followed by an acid attack of the residue with a 5 m HF:1 m HCl solution. Distillations after each of the two treatments recover different forms of NH4+. The procedure was tested on fine earth (< 2 mm) and skeleton (> 2 mm) fractions of two forest soils developed on sandstone parent material. In both soil fractions we evaluated three different forms of NH4+‐N: (i) Kjeldahl, (ii) non‐exchangeable and (iii) micaceous. The last is located in the interlayer of mica flakes larger than 50 μm that resist the Kjeldahl digestion and is considered strongly fixed. The total NH4+‐N content of a soil is obtained by the summation of the Kjeldahl and the micaceous NH4+‐N. In the soils under consideration, the micaceous form prevails in the skeleton because this fraction is richer in micas of sand size (> 50 μm). Following the proposed procedure, we found that micas (muscovite and biotite) contain about 3000 mg kg–1 of NH4+‐N in the interlayer. The presence of micaceous NH4+‐N in soil is generally ignored because the skeleton is usually excluded from analyses, and the micas larger than 50 μm cannot be dissolved by the Kjeldahl treatments. The micaceous NH4+ is the least extractable form of NH4+‐N, and we infer that it is the least available to plants.
Content and bioavailability of organic forms of nitrogen in the O horizon of a podzol
Authors: Johnsson L. , Berggren D. , Kårén O. 
Published: March 2003

SummaryIt is often thought that the most important source of nitrogen for plants and microorganisms comes from amino acids and amino sugars when they are hydrolysed in acid conditions. We did a microcosm experiment to test the hypothesis. In the experiment spruce seedlings (Picea abies L. Karst) were grown for 145 days in soil taken from a podzol Oa horizon under a long‐term nitrogen fertilization experiment (control and N‐treated soil). Net changes in different pools of organic N were determined using standard fractionation (acid hydrolysis and pyrophosphate extraction). During the experiment the amino acid and amino sugar pools decreased significantly (14% and 15% for the control and 10% and 17% for the N treatment), whereas no significant change was observed in the non‐amino acid plus non‐amino sugar fraction. On a per organic C basis there was even a significant increase in the non‐amino acid plus non‐amino sugar fraction of 11% for the control and 8% for the N treatment. Pyrophosphate extractions suggest that amino acids or amino sugars associated with the humin fraction were more accessible to microbes and plants than those associated with the humic acid, fulvic acid and hydrophilic substances. The long‐term N fertilization (about 73 kg N ha−1 was added annually as NH4NO3 during a 24‐year period) resulted in an enrichment of all major fractions of organic N, i.e. amino acids, amino sugars and non‐amino acids plus non‐amino sugars. This enrichment was largely the result of small increases in all of the amino acids rather than large increases in just a few.
The utility of Burns’s equation to describe solute movement through soil under various boundary and initial conditions
Authors: Magesan G. N. , Scotter D. R. , White R. E. 
Published: March 2003

SummaryBurns’s equation for describing solute movement through soil is attractive because it is simple and predicts adequately in many instances. However, the assumptions implicit in it are not inconsistent with preferential solute flow. We have explored the consequences of this by leaching initially resident chloride and surface‐applied tritium and nitrate through 250‐mm‐long intact cores of a silt loam soil. The applied flow rates of 3 and 5 mm h−1 (realistic rainfall intensities) produced unsaturated soil conditions, except near the base where free water dripped out. Burns’s equation described the movement of the three solutes fairly successfully with the water content parameter having values between 0.29 and 0.48, similar to the actual volumetric water content of 0.47.The leaching of resident chloride to 450‐mm‐deep mole drains in the field was also successfully simulated using Burns’s equation. However, simulation of the leaching of bromide applied to the soil surface as a solid salt was problematic. This resulted from uncertainty as to whether to treat the application as a pulse input to the flux or resident concentration. The observed behaviour fell about midway between the simulations for these contrasting initial conditions.
A 13C‐NMR study of the interactions of soil organic matter with aluminium and allophane in podzols
Authors: Parfitt R. L. , Yuan G. , Theng B. K. G. 
Published: March 2003

SummaryThe stabilization of organic matter in soil by interaction with aluminium (Al) or allophane is important in maintaining soil quality, and in retarding the decomposition of soil organic matter. Complexation of Al by soil organic matter may also ameliorate Al toxicity. Here we use 13C‐NMR spectroscopy to assess the interaction of soil organic matter with both Al and allophane in two poorly drained podzols containing only trace amounts of iron. The 13C‐NMR spectrum of the subsoil of the allophane‐rich One Tree Point podzol shows an intense peak at 179 p.p.m., assigned to carbon in carboxylic acids. This peak shifts to 177 p.p.m. after removal of allophane (11% of the soil mass) by treatment with HF. We infer that the carboxyl groups in the organic matter are bonded to structural Al on the surface of allophane spherules. In the non‐allophanic Te Kopuru podzol, on the other hand, the organic matter apparently interacts with Al ions in the soil solution. This soil also has more aromatic carbon and fewer carbons in carboxyl and carbohydrate structures than the allophanic sample. There is an indication that allophane stabilizes carbohydrate groups as well as carboxyl groups.
Methods for determining labile cadmium and zinc in soil
Authors: Young S. D. , Tye A. , Carstensen A. , Resende L. , Crout N. 
Published: March 2003

SummaryIsotopically exchangeable cadmium and zinc (‘E values’) were measured on soils historically contaminated by sewage sludge and ones on zinc‐rich mine spoil. The E‐value assay involves determining the distribution of an added metal isotope, e.g. 109Cd, between the solid and solution phases of a soil suspension. The E values for both metals were found to be robust to changes in the position of the metal solid⇔solution equilibrium, even though the concentration of dissolved metal varied substantially with electrolyte composition and soil:solution ratio. Concentration of labile metal was also invariant over isotope equilibration times of 2–6 days. The use of a submicron filtration procedure, in addition to centrifuging at 2200 g, proved unnecessary if 0.1 m Ca electrolyte was used to suspend the soils.The proportion of ‘fixed’ metal, in non‐labile forms, apparently increased with increasing pH, although there was considerable variation in both sets of contaminated soil. Zinc and cadmium in the sludged soils were similarly labile. Several possible methods for the measurement of chemically reactive metal were explored for comparison with E values, including single extraction with 1 m CaCl2 and a ‘pool depletion’ (PD) method. The latter involves comparing solid⇔solution metal equilibria in two electrolytes with differing degrees of (solution) complex formation, 0.1 m Ca(NO3)2 and CaCl2. Both the single extraction and the PD method gave good estimates of E value for Cd, although the single extraction was more consistent. Neither technique was a useful substitute for determining labile Zn, because of weak chloro‐complexation of Zn2+. We therefore suggest that 1 m CaCl2 extraction of Cd alone be used as an alternative to E values to avoid the inconvenience of isotopic dilution procedures.
Effect of nitrogen fertilization, cropping and irrigation on soil air composition and nitrous oxide emission in a loamy clay
Authors: Simojoki A. , Jaakkola A. 
Published: March 2003

SummaryMost of the nitrous oxide (N2O) in the atmosphere, thought to be involved in global warming, is emitted from soil. Although the main factors controlling the production of N2O in soil are well known, we need more quantitative data on the interactions of soil and the environment in the soil that affect the emission. We therefore studied the effects of irrigation, cropping (fallow, barley with grass undersown) and N fertilization (unfertilized, 103 kg N ha−1) on the composition of soil air and direct N2O emission from soil (using the closed chamber method) in a factorial field experiment on a well‐structured loamy clay soil during 1 June−22 October 1993. The measurements were made weekly during the growing season and three times after harvesting. The composition of the soil air did not indicate severe anoxia in any treatment or combination of treatments, but the accumulation of N2O in the soil air indicated that hypoxia was common. At the start of the irrigation the emissions were small, even though there was much ammonium and nitrate in the soil and therefore a potential for emission of N2O produced by both nitrification and denitrification. Larger emissions occurred later. The largest emissions were found when 60–90% of the soil pore space was filled with water. Irrigation and fertilization with N both roughly doubled the cumulative N2O emission. Growing a crop decreased it by a factor of 3–7. Most N2O was lost from the irrigated fertilized soil under fallow (3.5 kg N ha−1), and least from the unirrigated unfertilized soil under barley (0.1 kg N ha−1).