bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mouse models for genetic dissection of polygenic gastrointestinal diseases
Authors: Hillebrandt S. , Matern S. , Lammert F. 
Published: March 2003

AbstractMany diseases with a major public health impact are the result of complex interactions between environmental factors and multiple genes. In the past decade, methods for genome analysis, in particular quantitative trait locus (QTL) analysis in animal models, were developed to identify and localize the genes responsible for multifactorial (polygenic) diseases; QTL analysis is based on experimental crosses between inbred strains with high and low genetic susceptibility. Recently the genes underlying several QTLs could be cloned successfully. Here we describe the impact of these genomic approaches in mice on our understanding of the multifactorial genetics of three gastrointestinal diseases related to metabolism (cholesterol cholelithiasis), development (gastroschisis), and colorectal cancer. The examples demonstrate how mouse models continue to be an invaluable tool in unravelling complex pathomechanisms and unlocking our understanding of human diseases.
Low‐density‐lipoprotein peak particle size in a Mediterranean population
Authors: M. Rizzo , Barbagallo C. M. , Severino M. , Polizzi F. , Onorato F. , Noto D. , Cefalù A. B. , Pace A. , Marino G. , Notarbartolo A. , Averna R. M. 
Published: March 2003

AbstractBackground The predominance of small, dense low‐density lipoprotein (LDL) particles (‘LDL phenotype B’) has been associated with a three‐fold increased risk of myocardial infarction, but the feasibility of the identification of small, dense LDL as independent predictors of coronary artery disease risk in population studies remains questioned.Design We evaluated the LDL peak particle size and its relation with other established risk factors for coronary heart disease in a group of 156 randomized subjects living on the Mediterranean island of Ustica (71 males and 85 women, range of age 20–69 years), representing approximately 30% of the total population.Results The prevalence of LDL phenotype B subjects was low (approximately 15% in both men and women) and there was a clear trend for both genders in reducing the LDL peak particle size with age. Moreover, LDL phenotype B subjects had higher BMI values, prevalence of diabetes and plasma triglyceride (TG) levels and lower plasma HDL‐C concentrations in comparison with LDL phenotype A individuals; in a multivariate analysis, plasma TG levels were the only variable independently associated with LDL peak particle size.Conclusions In this population, which appears to be somewhat protected by premature coronary artery disease, a low prevalence of the LDL pattern B was found in both men and women, and plasma TG could have a key role in regulating the LDL peak particle size. The follow up, still ongoing, will provide useful information on the predictive role of LDL peak particle size on cardiovascular risk, at least in a low‐risk population.
Differential expression of MHC class II genes in lung tumour cell lines
Authors: Redondo M. , Ruiz‐Cabello F. , Concha A. , Hortas M. L. , Serrano A. , Morell M. , Garrido F. 
Published: March 2003

Molecular characterization of HLA class II expression was investigated in five lung tumour cell lines at the protein and mRNA levels. The cell lines exhibited a differential expression of HLA‐DR, HLA‐DP and HLA‐DQ products and also showed differences in the inducibility of HLA class II genes by γ‐IFN. Gamma‐IFN stimulation induced only HLA‐DR expression to varying degrees in three cell lines, while only one cell line showed stimulation for HLA‐DP and none for HLA‐DQ antigens. These results suggest locus‐specific regulation for the three loci. The presence of DR protein on the cell‐surface membrane was always positively correlated with the presence of HLA‐DR mRNA in the cells. After treatment with 5‐azacytidine in the A549 cell line, which expressed the lowest values, there was no effect on HLA class II levels. This suggested that methylation does not play an important role in the lack of MHC class II antigen expression.In addition to studying mRNA levels of HLA class II antigens, we analysed mRNA of the proto‐oncogene c‐myc and observed a positive correlation of two mRNA: the increments in HLA‐DR expression were associated with increments in c‐myc expression. This suggests a relationship between the regulatory mechanisms which control the expression of c‐myc and HLA‐DR antigens in lung tumour cell lines.
Rapid and simultaneous HLA class I (‐A, ‐B and ‐C loci) DNA typing using the microtitre plate–reverse hybridization assay (MRHA)
Authors: Moribe T. , Hirai H. , Kimura M. , Inagawa A. , Nakatani S. , Kaneshige T. , Inoko H. 
Published: March 2003

SummaryWe have established a precise, rapid, simple and practical HLA class I DNA typing method using the microtitre plate–reverse hybridization assay (MRHA), which enables us to perform simultaneous DNA typing of the HLA‐A, ‐B and ‐C loci using the same PCR parameters and hybridization conditions. PCR‐amplified products for the HLA‐A, ‐B and ‐C loci were hybridized, respectively, with sequence‐specific oligonucleotide (SSO) probes, which were immobilized covalently onto a microtitre plate, in hybridization buffer containing formamide at 37 °C. After washing at room temperature, the bound PCR products were detected by peroxidase‐conjugate streptavidine followed by colour development such as enzyme immunoassay (EIA). In addition to the simple thermoregulation for hybridization and postwashing, strong positive signals, low background and high reproducibility, this DNA typing method enabled simultaneous typing of the HLA‐A, ‐B and ‐C loci using a single microtitre plate as in HLA serotyping. The assignment of the HLA genotype was easily achieved by automated colorimetric reading and computer software, based on the cut‐off value (threshold) established for each probe. For routine HLA class I typing, it may be possible to replace serological typing with the HLA class I DNA typing system using our MRHA method.
Allele frequencies of polymorphisms of TNFA, IL‐6, IL‐10 and IFNG in an Italian Caucasian population
Authors: Poli F. , Nocco A. , Berra S. , Scalamogna M. , Taioli E. , Longhi E. , Sirchia G. 
Published: March 2003

SummaryPolymorphisms in the regulatory and intronic regions of several cytokines have been associated with differential cytokine production. In this paper we genotyped, using the polymerase chain reaction–sequence‐specific primers (PCR‐SSP) method, a series of 363 healthy Italian Caucasians with the aim of obtaining a reference population for further studies on the role of cytokines in the inflammatory and immune responses. We also compared the results to those for other populations. The polymorphisms analysed were those of tumour necrosis factor alpha (TNFA), interleukin 6 (IL‐6), interleukin 10 (IL‐10) and interferon gamma (IFNG). We found that the frequency of allele TNFA*1 at position −380 was 87.7% and that of TNFA*2 was 12.4%, significantly different from those of the UK and Japanese populations but not different from that of a population in Gambia. For IL‐10 the frequencies of alleles −1082A and −1082G were 63.0% and 37.0% and those of alleles −819C, − 819T, −592C and −592A were 70.8, 29.2, 70.8 and 29.2%, respectively, significantly different from those observed in south‐east England, in Manchester and in an Oriental population from southern China. The frequencies of IL‐6 alleles − 174C and −174G were 29.0 and 71.0%, respectively; for IFNG polymorphisms at position −874, in the population under evaluation, the alleles −874T and −874A were present in 44.7 and 55.3% of the subjects, respectively. Genotype frequencies of IL‐6 were significantly different from those observed in populations from Germany and from the UK. The analysis carried out by our group indicates that there is heterogeneity in the frequencies of the cytokine polymorphisms among the different Caucasian populations, and this underlines the importance of a ‘local’ reference population when evaluating the clinical relevance of cytokine gene polymorphisms.
Iron oxide mineralogy of Terre Rosse and Rendzinas in relation to their moisture and temperature regimes
Authors: SINGER A. , SCHWERTMANN U. , FRIEDL J. 
Published: March 2003

SummaryTerre Rosse and Rendzinas occur on limestones close together under the same climatic conditions. Their differences in iron oxide mineralogy are believed to be due to differences in the pedoclimate. We monitored the soil moisture tension and the soil temperature over nearly 3 years in Terra Rossa‐Rendzina pairs on hard limestone and soft chalk in Israel. The Terre Rosse dried out more rapidly than the Rendzinas mainly because of their smaller water‐holding capacity. In summer, average soil temperatures in the Rendzinas were significantly lower than in the Terre Rosse.Haematite dominates the red Terre Rosse and goethite the yellower Rendzinas. This difference appears to be related to the soil climate, specifically the moisture regime of the two soils, and supports the hypothesis that release of Fe and formation of ferrihydrite in Terre Rosse during the wet winter is followed by transformation to haematite during marked desiccation in the dry summer. By contrast, wetter soil conditions in the Rendzinas direct the formation of Fe oxides more towards goethite. either directly or by transformation of ferrihydrite via solution.
Sorption of organic acids in acid soils and its implications in the rhizosphere
Authors: JONES D. L. , BRASSINGTON D. S. 
Published: March 2003

SummaryOrganic acids have been implicated in many soil‐forming and rhizosphere processes, but their fate in soil is poorly understood. We examined the sorption of four simple short‐chain organic acids (citric, oxalic, malic and acetic) in five acid soils and on synthetic iron hydroxide (ferrihydrite). The results for both soils and ferrihydrite indicated that the sorption depended on concentration in the following order of strength: phosphate >> oxalate > citrate > malate >> acetate. The sorption reactions in soil were shown to be little influenced by pH, whereas for ferrihydrite, sorption of all ligands increased strongly with decreasing pH. The sorption of organic anions onto ferrihydrite was influenced to a lesser extent by the presence of metal cations in solution. From the results we calculated that when organic acids enter solution they rapidly become sorbed onto the soil's exchange complex (> 80% within 10 min), and we believe that this sorption will greatly diminish their effectiveness to mobilize nutrients from the rhizosphere.
Reduced CO2 release from decomposing wheat straw under N‐limiting conditions: simulation of carbon turnover
Authors: HADAS A. , PARKIN T. B. , STAHL P. D. 
Published: March 2003

SummaryThe turnover of residue carbon in soil containing little available N can affect the management of crop residues. The effects of N deficiency on CO2 release from decomposing wheat straw were measured in an incubation experiment and interpreted by computer simulation. Straw with a C:N ratio of 91, incubated for 460 days in sand that was inoculated with a soil suspension, released CO2 much more slowly than when inorganic N was added to obtain a C:N ratio of 5. The evolution of CO2 continued longer without added N, approaching the amount released in the high N treatment with time. The simulation model NCSOIL was modified to simulate reduced CO2 release from decomposing residue when N limits microbial growth by (i) including the decomposers' biomass in the rate of residue decomposition in the form of a Monod‐type equation, where the biomass reduced the rate when its concentration was small compared with a saturation constant, and (ii) including formation of a polysaccharide‐like pool that received the decomposed C that could not be assimilated by the biomass because of insufficient N. The modified model simulated the reduced CO2 production in the absence of sufficient N, as a result of a smaller microbial biomass that reduced the rate of residue decomposition, and the formation of polysaccharides as long as N limited synthesis of microbial biomass.
The nature and kinetics of organic matter release from soil by salt solutions
Authors: Reemtsma T. , Bredow A. , Gehring M. 
Published: March 2003

SummaryLaboratory experiments in soil columns were performed to study the influence of dissolved salts on the amount and composition of organic matter (OM) released from soil. Samples of two surface soils from former wastewater infiltration sites were leached with solutions containing dissolved salts (NaH2PO4, NaNO3, CaCl2) and by deionized water. The NaH2PO4 solution induced strongest release with 0.6% of soil organic carbon (Corg) with 700 ml for 100 g of soil, while CaCl2 released the least, summing to 0.1–0.2% of Corg. The OM released was characterized by UV absorbance (aromaticity), ultrafiltration (molecular size distribution) and solid‐phase extraction (polarity). The results suggest that CaCl2 preferentially released readily soluble OM. For the other solutions we assume solubilization by enhanced electrostatic repulsion (water), sodium exchange (NaNO3), and sodium exchange and calcium decomplexation and displacement of sorbed organic anions (NaH2PO4) to be the major mechanisms of release. In all experiments a phase of spontaneous desorption was observed, followed by a phase of steady‐state desorption. Activation energies for steady‐state release were estimated from kinetic investigations and suggest that the release is controlled by diffusion towards the phase boundary. These investigations emphasize the influence of dissolved salts on the nature and quantity of organic matter released from soil. The method presented seems able to characterize soil organic matter with respect to its availability and its mode of association with the soil matrix.
Changes to water repellence of soil aggregates caused by substrate‐induced microbial activity
Authors: Hallett P. D. , Young I. M. 
Published: March 2003

SummarySoil microbes produce exudates which upon drying become water‐repellent, thus altering hydraulic properties. The influence of microbial activity caused by adding plant nutrients on the hydraulic characteristics of soil aggregates is reported. Soil aggregates were collected from a field that had been fertilized with different amounts of nitrogen. Aggregates were also incubated with different nutrient treatments in the laboratory. Their sorptivity, hydraulic conductivity and water repellency were measured with a new device. Adding nitrogen was found to decrease sorptivity and hydraulic conductivity because of increased water repellency in the field. In the laboratory studies, the addition of nutrients caused severe water repellency in the soil aggregates. Respiration studies identified a large increase in biological activity following nutrient amendment which produces water‐repellent materials.
Charred organic carbon in German chernozemic soils
Authors: Schmidt M. W. I. , Skjemstad J. O. , Gehrt E. , Kögel‐Knabner I. 
Published: March 2003

SummaryBurning vegetation produces partly charred plant material which subsequently could contribute to the highly refractory proportion of soil organic matter. The presence of charred organic carbon (COC) was investigated in 17 horizons originating from nine soils from Germany and the Netherlands using a suite of complementary methods (high‐energy ultraviolet photo‐oxidation, scanning electron microscopy, solid‐state 13C nuclear magnetic resonance, lignin analysis by CuO oxidation). Charred organic carbon could not be detected in the A horizons of an Alisol and a Gleysol, but it contributed up to 45% of the organic carbon and up to about 8 g kg–1 of the soil in a range of grey to black soils (Cambisol, Luvisol, Phaeozem, Chernozem and Greyzem). All these soils have chernozemic soil properties (dark colour, A–C profile, high base saturation, bioturbation). A 10‐km colour sequence of four chernozemic soils, which were very similar in chemical and physical properties, showed a strong relation between colour and the content of COC. This suggests that the COC affects mainly soil colour in the sequence studied. Finely divided COC seems to be a major constituent of many chernozemic soils in Germany. These results suggest that besides climate, vegetation and bioturbation, fire has played an important role in the pedogenesis of chernozemic soils.
Using regression models in design‐based estimation of spatial means of soil properties
Authors: Brus D. J. 
Published: March 2003

SummaryThe precision of design‐based sampling strategies can be increased by using regression models at the estimation stage. A general regression estimator is given that can be used for a wide variety of models and any well‐defined sampling design. It equals the π estimator plus an adjustment term that accounts for the differences between the π estimators for the spatial means of the auxiliary variables and the true spatial means of these variables. The regression estimator and ratio estimator follow from certain assumptions on the model and the sampling design. These are compared with the π estimator in two case studies.In one study a bivariate field of linearly related variables was simulated and repeatedly sampled by Simple Random Sampling without replacement and sample sizes 10, 25, 50, 100 and 200. For all sample sizes the ratio of the standard error of the simple regression estimator to that of the π estimator was approximately 55%. The bias of the simple regression estimator was negligibly small. The confidence interval estimators were valid for all sample sizes except for n = 10. Also the ratio estimator was approximately unbiased, and the confidence interval estimators were valid for all sample sizes, even for n = 10. This is remarkable because the ratio estimator assumes that the intercept of the regression line is 0 which was incorrect for the simulated field. On the other hand, only approximately 55% of the potential gain was achieved because the model was inappropriate.In a second study the spatial means of the Mean Highest Watertable of map units were estimated by Stratified Simple Random Sampling and the combined (multiple) regression estimator. The NAP elevation, the local elevation, the Easting and the Northing were used as auxiliary variables. For all map units except one the combined (multiple) regression estimator was more precise than the π estimator. The ratio of the standard errors varied from 0.36 to 1.04. The domain for which the regression estimator was less precise than the π estimator showed strong variation between strata. For this domain it was more efficient to group the strata into two groups and to fit simple models for these groups separately.
An explanation of linear increases in gas concentration under closed chambers used to measure gas exchange between soil and the atmosphere
Authors: Conen F. , Smith K. A. 
Published: March 2003

SummaryEarlier models describing the accumulation of gases under closed chambers are based on the assumption of a constant concentration source that does not change during the time of chamber deployment. A new model is proposed which is based on the assumption of a constant production source, and takes into account possible changes in gas concentrations at the source during chamber deployment. Using N2O as an example, simulations have been carried out for different source strength and depth, diffusivities and air porosities. The main finding was a chamber‐induced increase in gas concentrations in the upper part of the soil profile, including the depth where the N2O source is located. The increase started immediately after chamber closure. Nevertheless, fluxes calculated from increasing concentrations within the chamber's headspace were always less than those expected under undisturbed conditions, i.e. in the absence of a chamber. This was due to a proportion of the gas produced being stored within the soil profile while the chamber was in place. The discrepancy caused by this effect increased with increasing air‐filled porosity and decreasing height of the chamber, and a procedure for correcting chamber flux measurements accordingly is proposed. The increase in soil gas concentrations after chamber closure was confirmed in a laboratory experiment.
A prototype osmotic tensiometer with polymeric gel grains
Authors: Biesheuvel P. M. , Van Loon A. P. , Raangs R. , Verweij H. , Dirksen C. 
Published: March 2003

SummaryAn accurate field method that directly measures the entire range of relevant soil water potentials for periods of months to years is not yet available. The osmotic tensiometer (OT) has the potential to fulfil these demands but is still in an early stage of development. We have designed a novel OT that should overcome several drawbacks of former designs by the use of cross‐linked polymeric gel grains instead of an aqueous solution of linear chain polymers inside the porous ceramic cup. For this reason, the cup can have large pores without polymer leakage. This ensures that water exchanges rapidly with the soil, resulting in a negligible pressure lag with changing temperatures, which is the most important source of a systematic measurement error of an OT. A second reason for better performance might be the inherent elasticity of the grains which should inhibit formation of a polymer cake at the filter. To study several of the key variables of the new sensor, transient and stationary experiments were performed in an aqueous solution the temperature, salt type and salt concentration of which were varied. Under similar conditions the swelling of the polymer grains was studied in more detail. The OT that we developed responds rapidly to changes in water potential, but is very susceptible to the influence of salts. To study and minimize salt influence, swelling tests of unconfined grains are proposed in combination with tests of the OT itself.
Using time domain reflectometry for monitoring mineralization of nitrogen from soil organic matter
Authors: De Neve S. , Van de Steene J. , Hartmann R. , Hofman G. 
Published: March 2003

SummaryThe mineralization of nitrogen from soil organic matter is important when one tries to optimize nitrogen fertilization and assess risks of N losses to the environment, but its measurement is laborious and expensive. We have explored the possibilities for monitoring N mineralization directly using time domain reflectometry (TDR). Net N and S mineralization were monitored over a 101‐day period in two layers (0–30 and 30–60 cm) of a loamy sand soil during aerobic incubation in a laboratory experiment. At the same time electrical conductivity of the bulk soil, σa, was measured by TDR. A series of calibration measurements with different amounts of KNO3 at different soil moisture contents was made with the topsoil to calculate the electrical conductivity, σw, of the soil solution from σa and θ. The actual σw was determined from the conductivity of 1:2 soil:water extracts (σ1:2) with a mass balance approach using measured NO3– concentrations, after correction for ions present prior to the addition of KNO3. The average N mineralization rate in the topsoil was small (0.12 mg N kg−1 day−1), and, as expected, very small in the subsoil (0.023 mg N kg−1 day−1). In the top layer NO3– concentrations calculated from σa determined by TDR slightly underestimated measured concentrations in the first 4 weeks, and in the second half of the incubation there was a significant overestimation of measured NO3–. Using the sum of both measured NO3– and SO42– reduced the overestimation. In the subsoil calculated NO3– concentrations strongly and consistently overestimated measured concentrations, although both followed the same trend. As S mineralization in the subsoil was very small, and initial SO42– concentrations were largely taken into account in the calibration relations, SO42– concentrations could not explain the overestimation. The very small NO3– and SO42– concentrations in the B layer, at the lower limit of the concentrations used in the calibrations, are a possible explanation for the discrepancies. A separate calibration for the subsoil could also be required to improve estimates of NO3– concentrations.