bluuebunny/crossref_metadata_2025 huggingface dataset:
Strong association between DQA1/DQB1 genotype and early‐onset IDDM in Chinese: the association is with alleles rather than specific residues
Authors: Chang Y. W. , Lam K. S. L. , Hawkins B. R.
Published: March 2003

We report on the role of HLA‐DQA1 and DQB1 alleles in determining susceptibility to insulin‐dependent diabetes mellitus (IDDM) in Hong Kong Chinese and investigate whether these alleles affect the age of onset of the disease. We studied 76 unrelated Chinese patients and 250 controls. There was no apparent predisposing effect of non‐aspartic acid residues at position 57 of the DQβ chain (Asp57–) but there was an excess of homozygous genotypes containing arginine at position 52 of the DQα chain (Arg52+). This excess was mainly attributable to the genotype DQA1*0301/ DQA1*05011 in early‐onset disease. There was a significant excess of heterodimers of DQα and DQβ carrying Arg52+ and Asp57– in both early‐onset and late‐onset disease, but the excess in early‐onset disease was mainly attributable to a single heterodimer formed by DQA1*05011 and DQB1*0201. Of three DQA1/ DQB1 genotypes containing a double dose of Arg52+ and Asp57–, only one had a strong association with both early‐onset and late‐onset disease. We show that early‐onset IDDM and late‐onset IDDM in Chinese may be separated on the basis of their associated DQA1 and DQB1 genotypes and we conclude that previously reported associations of IDDM with Arg52+ and Asp57– residues in Chinese are secondary to specific combinations of DQA1 and DQB1 alleles. We also show that DRB1 molecules play a distinct role in determining susceptibility to early‐onset IDDM but the greatest effect is exerted by specific DR/DQ genotypic combinations.
Human cytokine gene nucleotide sequence alignments: supplement 1
Authors: Bidwell J. L. , Wood N. A. P. , Morse H. R. , Olomolaiye O. O. , Keen L. J. , Laundy G. J.
Published: March 2003

Note: The PDF version of this supplement can be downloaded as ten separate PDF files from
HLA‐DPB1 alleles in house dust mite allergic patients
Authors: O’Brien R. M. , Tait B. D. , Varney M. D. , Thomas W. R.
Published: March 2003

Associations were sought between the presence of allergic sensitivity to Der p 1, a major allergen from the house dust mite, and the HLA‐DPB1 genotype. Whilst allergic patients did not differ from controls in DPB1 allelic distribution, there was a correlation of DPB1*11011 with strongly reactive T‐cell proliferative responses to Der p 1 and high titre specific IgE to Dermatophagoides pteronyssinus.
Confirmation of the detection of HLA‐A*0104N in a family: a PCR–SSP reaction for the allelic detection of HLA‐A*0104N
Authors: Moses J. H. , Downes J. , McClenahan W. , Clow N. , Kennedy C. , Greville W. D. , Dunckley H.
Published: March 2003

The allele A*0104N has been detected in a family with a patient requiring a bone marrow transplant. The allele was found as a consequence of a discrepant result when family members were typed using serology and polymerase chain reaction using sequence‐specific primers (PCR–SSP). Serological typing gave an apparent HLA‐A ‘blank’ while PCR–SSP revealed the presence of an A*01 allele in three family members who were serologically negative for A1. Sequencing‐based typing (SBT) was then used to establish that the allele was A*0104N. A PCR–SSP reaction was subsequently designed and used for the allelic detection of A*0104N. The study highlights the potential risks involved if molecular technology is used for typing, unless all non‐expressed alleles are specifically detected.
Towards understanding the origin and dispersal of Austronesians in the Solomon Sea: HLA class II polymorphism in eight distinct populations of Asia‐Oceania
Authors: Zimdahl H. , Schiefenhövel W. , Kayser M. , Roewer L. , Nagy M.
Published: March 2003

HLA class II nucleotide sequence polymorphisms were examined in eight ethnic groups of Asia‐Oceania using DNA typing methods. Allele frequencies and characteristic DR/DQ haplotypes were determined and compared with those of other populations of Asia‐Oceania. Genetic distances were measured to show the genetic relationship within the studied populations as well as between the studied populations and previously published populations. Phylogenetic trees were constructed based on HLA allele frequencies using the neighbour‐joining method. The populations, mainly Trobriand Islanders, Roro, Tolai, Western Samoans and Taiwanese Aborigines, are characterized by a reduced diversity at the HLA loci examined, especially for DPB1. The high frequency of the ‘Asian’‐specific DPB1*0501 allele in Trobrianders and Roro, but also in Western Samoans and Taiwanese Aborigines, was the most striking result. The prevalence of DPB1*0501 and the short genetic distance from Trobriander and Roro to Taiwanese Aborigines provide evidence that the origin of the Austronesian odyssey is south‐east Asia, and Taiwan could be an important part of it. The relatedness of Trobrianders to the Polynesian population from Western Samoa indicates a probable recent common ancestor. The observed lack of diversity may reflect bottleneck(s) and/or limited diversity of the founding population. Analysis of HLA class I antigens, together with mt‐DNA and Y‐chromosomal studies, will give us further information about the settlement of the Trobriand and other islands during the colonization of the Pacific.
Analysis of the phenotypic distribution of HLA class I and class II in atopic and non‐atopic asthma patients
Authors: Torío A. , Sánchez‐Guerrero I. , Muro M. , Herrero N. , Pagán J. , Minguela A. , Marín L. , Moya‐Quiles M. R. , Sanchís M. J. , Álvarez‐López M. R.
Published: March 2003

In several studies the HLA system has been implicated in the development of asthma, but the importance of the associations between HLA genes and asthma remains unclear. The aim of this study was to determine the HLA class I and II phenotypic frequencies in a population of asthmatics, and to analyse the relationship between these phenotypes and any type of asthma. We typed HLA class I and II antigens in a series of 189 asthmatic individuals (102 atopic and 87 non‐atopic), and in a control population of 150 unrelated healthy Caucasoid donors. When the HLA phenotypic frequencies were compared, no statistical differences were found. Therefore, no definitive HLA association could be established with atopic or non‐atopic asthma in the studied population.

Abbreviations AA, atopic asthma; FEV1, forced expiratory volume in 1 s; NAA, non‐atopic asthma; PCR, polymerase chain reaction; SSOP, sequence‐specific oligonucleotide probes; SPT, skin prick test.
Influence of TNFα and LTα single nucleotide polymorphisms on susceptibility to and prognosis in cutaneous malignant melanoma in the British population
Authors: Howell W. M. , Turner S. J. , Collins A. , Bateman A. C. , Theaker J. M.
Published: March 2003

Cutaneous malignant melanoma (CMM) is a potentially fatal malignancy in which exposure to UV light is the most important risk factor. Several lines of evidence suggest that increased expression of tumour necrosis factor (TNF) α, upregulated by UV exposure, may contribute to tumour escape from the immune response. In this study, we addressed whether single nucleotide polymorphisms (SNPs) in the TNFα promoter and lymphotoxin (LT) α gene are associated with susceptibility to or known prognostic indicators (e.g. initial tumour growth phase, Breslow thickness, mitotic count in vertical growth phase tumours, and tumour regression) in CMM. One hundred and forty‐six British Caucasian CMM patients and 220 controls were typed for TNFα−376, −308 and −238 and LTα+252 SNPs by ARMS‐PCR. Only the TNFα−238 GG (P = 0.05) and GA (P = 0.03) genotypes showed slight, but significant, associations with CMM, while LTα+252 AA was associated with a higher mitotic count in vertical growth phase tumours (P = 0.02). Both TNFα−238 and LTα+252 SNPs showed linkage disequilibrium with HLA‐DQB1*0303 and *0301 alleles, variably implicated in CMM susceptibility/prognosis. In addition, TNFα−238, −308, LTα+252 haplotypes were assigned and compared. The GGA haplotype showed a modest association with CMM (P = 0.04) and with stage of disease (P = 0.03) and initial growth phase in CMM (P = 0.02), but these associations were only significant when P‐values were uncorrected. Unlike basal cell carcinoma, these preliminary findings suggest that genetic variation associated with differential TNFα and LTα production is unlikely to play a major, independent role in susceptibility to, and perhaps prognosis in, CMM.
A PCR‐RFLP typing method for adhesion molecule gene polymorphisms and allele frequencies in a normal UK population
Authors: Gbadegesin R. A. , Watson C. J. , Cotton S. A. , Brenchley P. E. C. , Webb N. J. A.
Published: March 2003

We report simple and reproducible PCR‐RFLP typing methods for the polymorphisms in the ICAM‐1, E‐selectin and PECAM‐1 genes. The genotype and allele frequencies detected in a normal UK population did not deviate significantly from the Hardy–Weinberg equilibrium; neither did they differ from frequencies previously reported using SSP or SSCP methods.
cDNA cloning of the polymeric immunoglobulin receptor of the marsupial Macropus eugenii (tammar wallaby)
Authors: Taylor C. L. , Harrison G. A. , Watson C. M. , Deane E. M.
Published: March 2003

cDNA encoding a marsupial polymeric immunoglobulin receptor (pIgR) was isolated from Macropus eugenii (tammar wallaby) mammary lymph node primarily by reverse transcriptase coupled polymerase chain reaction (RT‐PCR) and rapid amplification of cDNA ends (RACE) PCR. This resulted in a 5′ truncated clone and, in order to obtain the full‐length sequence, genomic walking PCR was utilized. The complete sequence consists of 2696 bp of cDNA and encodes a predicted polypeptide of 732 amino acids. The wallaby sequence is highly conserved in relation to the only other reported marsupial pIgR sequence, that of Trichosurus vulpecula (brushtail possum), having a nucleotide identity of 86.7% and a deduced amino acid identity of 79.9%. The wallaby nucleotide sequence also has a moderate degree of similarity with the pIgR sequences of eutherian mammals, being most similar to that of the rat, with an identity of 63.1%. At the amino acid level, in comparison to eutherian sequences, the wallaby pIgR is most similar to that of humans with an identity of 52.6%. pIgR phylogenetic trees were constructed for tammar wallaby, brushtail possum and several eutherian mammal cDNA and deduced amino acid sequences. In both DNA and protein analyses, the eutherian sequences formed a sister clade to the exclusion of the marsupial sequences, in agreement with the current view of mammalian evolution.
Sequence similarity matching: proposal of a structure‐based rating system for bone marrow transplantation
Authors: Elsner H.‐A. , Blasczyk R.
Published: March 2003

Recent advances in DNA‐based typing have led to the detection of a continuously growing number of HLA alleles. For this reason, HLA matching in transplantation of hematopoietic stem cells from unrelated donors has become increasingly complicated. When there is no genotypically identical sibling and there are several alternative potential donors that all have a mismatch at a relevant HLA locus, until now no rating system has existed indicating different levels of allogenicity. In order to find a theoretical approach to this problem we propose a rating system (‘dissimilarity index’) based on structural data of HLA class I molecules, and on published data about frequencies of naturally occurring amino acid exchanges. For demonstration we employ our rating system for the comparison of the HLA‐A*23 and A*24 groups, both of which allelic products are subdivisions of the serological HLA‐A9 family. Remarkable differences between the subtypes were revealed, which were superior to a simple sequence comparison. More surprisingly, it was uncovered that some alleles of the A*24 group showed fewer differences to A*2301 than to alleles within their own subtype group. Sequence similarity matching may serve as a starting point for the clinical evaluation of acceptable mismatches within the HLA‐A9 family and serve as a model for other HLA class I groups.
The interleukin‐1 receptor antagonist gene: a single‐copy variant of the intron 2 variable number tandem repeat (VNTR) polymorphism
Authors: Vamvakopoulos J. E. , Taylor C. J. , Morris‐Stiff G. J. , Green C. , Metcalfe S.
Published: March 2003

A variable number tandem repeat (VNTR) polymorphism exists within intron 2 of the human interleukin‐1 receptor antagonist gene, consisting of perfect repeats of an 86‐bp sequence. Five allelic variants have been identified wherein the number of repeats varies from two to six. This is the first report of a rare, single‐copy allele designated IL1RN*0.
Integrating properties of soil map delineations into ordinary kriging
Authors: BOUCNEAU  , VAN MEIRVENNE  , THAS  , HOFMAN
Published: March 2003

Stratification of a region based on soil map delineations followed by within‐stratum interpolation is sometimes used to combine soil maps and spatial interpolation. However, not all delineations are equally suitable to subdivide an area into precisely located mutually exclusive strata. This paper proposes a flow‐path to characterize the nature of soil map delineations and a methodology to integrate the properties of map delineations into ordinary kriging.Four types of delineations were distinguished based on three criteria: the nature of transition (discontinuous or gradual), the mapping accuracy, and the structure of the within‐unit spatial variation. For each type of delineation the ordinary kriging algorithm was modified to integrate its properties in the interpolation.As a test case, the sand content of the topsoil in the province of West‐Flanders (Belgium) was mapped, using independent test data for validation. Inside the mapping units and at delineations identified as gradual transitions, our procedure, termed ordinary kriging integrating properties of map delineations (OKPD) , performed similarly to stratified ordinary kriging (SOK). However, close to the delineations identified as inaccurately mapped discontinuities the mean square prediction error of OKPD was 0.64 times that of SOK. Moreover, near these delineations, the prediction variance was largely underestimated by SOK (relative variance = 5.1), whereas OKPD produced a more realistic value (relative variance = 1.5).
Capillary electrophoretic behaviour of humic substances from Sphagnum peats of various geographical origin: relation with the degree of decomposition
Authors: BRAGATO G. , MORI A. , DE NOBILI M.
Published: March 2003

Humic substances (HS) extracted from 14 Sphagnum peats of various geographical origin were submitted tocapillary electrophoresis (CE) in free solution and in entangled polymer solutions (25 gl‐1 and 50 gl−1) of polyethylene glycol (PEG). Electrophoretic runs were made in uncoated capillaries (75 μm internal diameter) using a tris‐hydroxymethylaminomethane (TRIS)‐phosphate buffer (pH 8.3) eventually containing PEG and applying a voltage of 10 kV. The HS extract of a Lithuanian peat was fractionated by ultrafiltration into five fractions with a nominal mean relative molecular mass (M) of 3000, 7500, 20 000, 75 000 and 200 000 Da. Without PEG, migration times were not correlated with the logarithm of M, but linear relations were obtained with 25gl−1 and 50gl−1 PEG solutions. Both solutions separated the different fractions by size; the best regression and the largest interval of linearity, M from 3000 to 200 000 Da, was obtained with the 25gl−1 PEG solution. At 10kV and without PEG, migration times ranged from 6.5 to 8.1 min and did not differentiate the peats, whereas at 25gl−1 PEG, migration times ranged from 3.3 to 6.5 min and, when plotted as a function of either the r value or the von Post index (H), which are used to evaluate the degree of decomposition of horticultural peats, they separated samples on the basis of their geographical origin and probable type of mire complex. At 25gl−1 PEG, migration times also showed a well‐defined linear decreasing trend with the increase of mean annual temperatures. These relations suggest the hypothesis that humification in mires goes along with an increase in the average size of humic molecules.
Chlordane transport in a sandy soil: effects of suspended soil material and pig slurry
Authors: HESKETH N. , BROOKES P. C. , ADDISCOTT T. M.
Published: March 2003

In experiments in lysimeters of sandy soil chlordane was transported in water flows only when sorbed on suspended soil material. A chlordane ‘concentration’ was calculated by dividing this sorbed chlordane by the volume of the water sample in which the suspended matter was carried. In all but one lysimeter the first peak in this ‘concentration’ appeared in the drainage well ahead of the first peak in the concentration of bromide applied at the same time as the chlordane. Chlordane also persisted in the drainage for less time than bromide. The transport of chlordane was most closely associated with that of the largest category of suspended soil material (> 1.2 μm), possibly because that category contained the most organic matter. It was not associated with the transport of colloidal matter for either of the two possible size limits applied to the latter (< 0.22 μm or < 0.45 μm). In the lysimeters to which pig slurry was applied the evidence that it enhanced the transport of chlordane was limited and equivocal; the chlordane was probably sorbed strongly by the soil's organic matter before the slurry was applied. The application of chlordane was 100 times greater than in normal agricultural practice and it was followed by a substantial volume of water. Nevertheless, only 0.00002% of it was transported from the lysimeters, and its ‘concentration’, calculated as above, never exceeded the EU limit of 0.1 μg1−1 for any one pesticide.
Phosphorus retention and release of anions and organic carbon by two Andisols
Authors: Beck M. A. , Robarge W. P. , Buol S. W.
Published: March 2003

Andisols can absorb large amounts of phosphorus rapidly, and then release it slowly, yet the mechanisms by which they retain P and release it for plant growth are poorly understood. Ligand exchange of organic compounds from Al–humic complexes by P and/or Si release – due to breakdown of allophanic microstructure to provide sorption sites – might account for the retention of P, but its extent is not known. We applied a soil column flow‐through technique to quantify the release of anions and organic carbon (C) associated with P sorption by two andic soils, and we related the anion release to possible mechanisms for the retention of P. Phosphate (H2PO4–, HPO42–) sorption and concurrent anion desorption were obtained by passing a 1‐g P 1–1 (32 mmol KH2PO4 in 1 mm CaCl2) solution through the soil columns (25 cm3). Total dissolved P, Fe, Al, S, Ca, Mg, K, Mn, organic C and pH were determined in the eluent. Changes in eluent pH and the patterns of the retention of P and corresponding concentrations of Al, Si and organic C in the eluent were similar for the two Andisols. The general pattern and changes in pH of the eluent coincided with changes in the patterns of release of organic C and Si and the rate of P retention. Release of silica accounted for < 6% of the P sorbed and had only a minor role in P retention in these two Andisols. Release of organic C, however, accounted on a molar basis for 40% and 83%, respectively, of the P sorbed. Direct measurements of the pH of the eluent and release of anions and organic C concurrent to P retention contribute to rapid assessment of the controlling mechanisms of P retention. The results indirectly confirm the hypothesis of ligand exchange of solution P with organic complexes held on allophanic surfaces. The organic C release, however, is not specifically related to either the fast or the slow P retention phase. The shift in the controlling P retention reaction associated with a change from the fast to the slow P retention phase is clearly indicated by an abrupt change of the pH of the eluent. This shift, in previous studies identified graphically by a change in slope of the P sorption isotherm, can be identified directly by measuring the pH of the matrix.
Fixation of radiocaesium traces in a weathering sequence mica → vermiculite → hydroxy interlayered vermiculite
Authors: Maes E. , Vielvoye L. , Stone W. , Delvaux B.
Published: March 2003

Radiocaesium fixation in soils is reported to occur on frayed edge sites of micaceous minerals. The weathering of mica in acid soils may therefore influence the Cs+ fixation process and thereby the mobility of the radiopollutant. We produced a laboratory weathering model biotite → trioctahedral vermiculite → oxidized vermiculite → hydroxy interlayered vermiculite (HIV) and quantified the Cs+ fixation of each mineral both in a fixed K+–Ca2+ background and in acid conditions. The transformation process was achieved through K depletion by Na‐tetraphenylboron, oxidation with Br2 and Al‐intercalation using NaOH and AlCl3. In a constant K+–Ca2+ background, vermiculite fixed 92–95% of the initial 137Cs+ contamination while biotite and HIV fixed only 18–33%. In acid conditions, the interlayer occupancy by either potassium (biotite) or hydroxy‐Al groups (HIV) strongly limited Cs+ fixation to 1–4% of the initial 137Cs+ contamination. Cs+ fixation occurred on vermiculitic sites associated with micaceous wedge zones. Though both oxidized and trioctahedral vermiculites fixed similar Cs+ amounts in a constant K+–Ca2+ background (92–95%), the oxidized vermiculite retained much more radiocaesium in acid conditions (78–84% against 54–59%), because of its dioctahedral character.
Modelling particle mobilization and leaching in macroporous soil
Authors: Jarvis N. J. , Villholth K. G. , Ulén B.
Published: March 2003

The migration of colloidal particles in the unsaturated zone may enhance leaching of sorbing contaminants to surface waters and groundwaters. This paper describes a simple model of particle leaching and translocation based on the dual‐porosity model MACRO. The model includes descriptions of processes such as ‘source‐limited’ particle detachment due to the kinetic energy of rain, replenishment of the depleted store of particles up to a maximum value determined by the amount of dispersible clay in the soil, and convective transport of particles in macropores subject to a filter sink term varying as a function of pore water velocity. Estimates of model parameter values are obtained by comparing simulations with measurements of particle concentrations in the discharge from tile drains made in a silty clay soil in southwest Sweden. Calibrated in this way, the model is shown to reproduce satisfactorily the observations. A sensitivity analysis suggests that the critical parameters in the model are those related to particle filtering during vertical transport in soil macropores.
Transformation and binding of 13C and 14C‐labelled atrazine in relation to straw decomposition in soil
Authors: Benoit P. , Preston C. M.
Published: March 2003

As a source of organic matter, crop residues affect the behaviour of pesticides in agricultural soils. The fate of [U‐ring‐13C] and [U‐ring‐14C] atrazine (6‐chloro‐N‐ethyl‐N‐isopropyl‐1,3,5‐triazine‐2,4‐diamine) was investigated during laboratory incubation under controlled conditions in a loamy soil amended with wheat straw at two different states of decomposition: no preliminary decomposition or 6 months’ preliminary decomposition. After 3 months, non‐extractable, so‐called ‘bound’, 13C‐atrazine residues were recovered in three particle‐size fractions (> 200, 50–200 and < 50 μm), and investigated with solid‐state 13C‐NMR spectroscopy. Parallel incubations with [U‐ring‐14C] atrazine were carried out to quantify the bound residues as well as the extractable and mineralized fractions. The effect of straw residues on atrazine behaviour depended on whether they had been previously decomposed or not. When straw was decomposed for 6 months prior to incubation, atrazine mineralization was enhanced to 50% of the initial 14C in contrast to 15% of the initial 14C in soil alone and soil amended with fresh straw. In parallel, atrazine bound residues were formed in greater amount representing up to 20% of the initial 14C. CP/MAS 13C‐NMR on soil size fractions of soil–straw mixtures after incubation with 13C‐atrazine showed that bound residues contained mostly triazinic C, corresponding to atrazine or primary metabolites. Non‐humified organic materials recovered in size fractions > 200 and 50–200 μm contained significant amounts of bound residues, especially when straw was added to the soil. CP/MAS 13C‐NMR analysis of humic acids obtained from < 50‐μm fractions was difficult due to overlapping of the native carboxyl 13C signal with the 13C‐atrazine signal.
Nutrient concentrations and acidity in ferralitic soil under perennial cropping, fallow and primary forest in central Amazonia
Authors: Schroth G. , Seixas R. , Da Silva L. F. , Teixeira W. G. , Zech W.
Published: March 2003

The long‐term productivity on the acidic, nutrient‐poor upland soils of central Amazonia depends to a large extent on the chemical soil fertility as influenced by vegetation type and management. We compared soil and soil solution data from permanent cropping, fallow and primary forest on a Xanthic Ferralsol in central Amazonia to evaluate changes of soil fertility following forest conversion, agricultural use at different intensities and setting aside agricultural land. The agricultural systems included a perennial polyculture at two fertilizer inputs and a monoculture plantation. Soil and soil solution were collected to 2 m depth, and the soil solution was monitored over 2 years. Both soil and soil solution data showed decreasing soil fertility in the sequence: monoculture and polyculture at large input, polyculture at small input, forest and fallow. The soil solution data were more sensitive to effects of systems and fertilizer inputs on subsoil fertility. Fractionation of the N in the soil solution showed a larger proportion of dissolved organic N in the N‐poor fallow soil than in the soil under forest and agriculture. The soil under fallow, forest and low‐input agriculture had larger exchangeable acidity than that under high‐input agriculture, but the Al concentrations in the soil solution were very small because there were few cations with which to exchange and less nitrification. In high‐input agriculture, pronounced acidification peaks in the topsoil solution followed fertilization. The comparison of soil and soil solution data explained why the spontaneous vegetation thrives at very large exchangeable acidity in these soils, whereas agricultural systems often depend on liming to reduce the concentration of toxic Al in the soil.
Characterization of β‐d‐glucosidase extracted from soil fractions
Authors: Busto M. D. , Perez‐Mateos M.
Published: March 2003

One way to study the state in which stabilized extracellular enzymes persist and are active in the soil is by extraction from the soil, with subsequent fractionation of enzyme–organomineral complexes and characterization of such complexes. In order to investigate the location and characteristics of soil β‐glucosidase, three soil fractions were obtained both from real (undisturbed) soil aggregates and from structural (dispersed in water and physically disrupted) aggregates using two different granulometric procedures. The β‐glucosidase activity of the fraction was then assayed. When the aggregates were dispersed, more than 73% of activity was in the soil microaggregates with diameters of less than 50 μm (SF50). These aggregates were associated with strongly humified organic matter. Solutions of diluted pyrophosphate at neutral pH liberated active β‐glucosidase from all fractions, although the efficacy of extraction varied according to the type of fraction. The SF50fraction and aggregates of 2000–100 μm obtained by sieving (SF2000) showed the greatest β‐glucosidase activity (34.5 and 36.0%, respectively). Micro‐ and ultrafiltration of SF50extracts increased the total β‐glucosidase activity, whereas these procedures, applied to the RF2000fraction, decreased it. Humus–β‐glucosidase complexes in the SF50fraction, between 0.45 μm and 105nominal molecular weight limit (nmwl) (SF50II) and < 105nmwl(SF50III) showed an optimum pH at 5.4, and in the SF50I fraction (> 0.45 μm) the optimum was 4.0. The stability of β‐glucosidase in the aggregates of the smallest size SF50II and SF50III decreased at acid pHs. The presence of two enzymes (or two forms of the same enzyme) catalysing the same reaction with different values of Michaelis constant and maximum velocity was observed in all but one of the β‐glucosidase complexes extracted and partially purified from the SF50aggregates.
The effect of aging biosolids on the availability of cadmium and zinc in soil
Authors: Stacey S. , Merrington G. , McLaughlin M. J.
Published: March 2003

A major concern with the safe re‐use of biosolids on land is the potential for release of metals from organic matter in the biosolids, due to decomposition proceeding as biosolids age. To quantify the effects of biosolid aging on Cd and Zn bioavailability, two sewage sludges (Lagoon sludge and Filtered sludge) and a garden compost were incubated at 25°C and 35°C for 100 days. Changes in availability of Cd and Zn were determined using isotope dilution principles, with the materials being labelled with carrier‐free 109Cd and 65Zn. We determined isotopically exchangeable metal pools (E values) and plant available metal pools (L values) by measuring specific activities of Cd and Zn in soil extracts and in wheat plants, respectively. Changes in carbon content over time were determined using 13C‐NMR spectroscopy and chemical extraction methods, and related to changes in availability of metal pools as determined by isotopic procedures.

Hot‐water‐extractable carbon content, assumed to represent easily decomposable organic matter, decreased during the 100 days by 80–190 mg kg−1. The Compost and Lagoon sludge showed no change in L values for Cd or Zn with time, but in the Filtered sludge the L values for Cd and Zn increased significantly, by 43% and 56%, respectively. The isotopically exchangeable pools of Cd and Zn did not change with incubation treatment of the biosolids.

These data indicate that the potential for metal release from biosolids as organic matter decomposes depends to a large extent on the biosolid composition.
Influence of the rhizosphere on microbial biomass and recently formed organic matter
Authors: De Neergaard A. , Magid J.
Published: March 2003

We have aimed to quantify the effect of roots on the size of the soil microbial biomass, and their influence on the turnover of soil organic matter and on the extent of the rhizosphere. We sampled a sandy clay loam topsoil from two subplots with different treatment histories. One had a normal arable fertilization record, the other had received only inorganic nitrogen fertilizer but no phosphorus and potassium for 30 years.

Glucose labelled with14C was added to both samples which were then incubated for 4 weeks before the soil was packed in cylinders and planted with ryegrass. In both soils, microbial biomass at the root surface doubled during the first 8 days. At day 15, the microbial biomass had further increased in the fertile soil, and the rhizosphere effect had extended 2.5 mm into the fertile soil, but to only 1 mm in the infertile soil.

The microbial14C increased threefold near the roots in the fertile soil as a result of assimilation of previously formed microbial residues, but in the infertile soil there was no increase. There was a close relation between the increase in microbial14C and a decrease in14C soluble in 2 mKCl, indicating that the microbial residues were more weakly adsorbed in the fertile soil. We conclude that the increased microbial population living near the root surfaces re‐assimilated part of the14C‐labelled microbial residues in the fertile soil. In the infertile soil, microbial residues resisted decomposition because they were more strongly sorbed on to soil surfaces.
The effects of temperature, water‐filled pore space and land use on N2O emissions from an imperfectly drained gleysol
Authors: Dobbie K. E. , Smith K. A.
Published: March 2003

To investigate the effect of soil physical conditions and land use on emissions of nitrous oxide (N2O) to the atmosphere, soil cores of an imperfectly drained gleysol were taken from adjacent fields under perennial ryegrass and winter wheat. The cores were fertilized with ammonium nitrate and incubated at three different temperatures and water‐filled pore space (WFPS) values, and N2O emissions were measured by gas chromatography. Emissions showed a very large response to temperature. Apparent values of Q10 (emission rate at (T + 10)°C/emission rate at T°C) for the arable soil were about 50 for the 5–12°C interval and 8.9 for 12–18°C; the corresponding Q10s for the grassland soil were 3.7 and 2.3. Emissions from the grassland soil were always greater than those from the arable soil, although the ratio narrowed with increasing temperature. Changes in soil WFPS also had a profound effect on emissions. Those from the arable soil increased about 30‐fold as the WFPS increased from 60 to 80%, while that from the grassland soil increased 12‐fold. This latter response was similar to earlier field measurements. The N2O emissions were considered to be produced primarily by denitrification. We concluded that the impacts of temperature and WFPS on emissions could both be explained on the basis of existing models relating increasing respiration or decreased oxygen diffusivity, or both, to the development of anaerobic zones within the soil.
Retention and release of dissolved organic matter in Podzol B horizons
Authors: Zysset M. , Berggren D.
Published: March 2003

The main objectives were to study the effects of pH on the retention and release of organic matter in acid soil, and to determine the main differences in results obtained from batch experiments and experiments in columns. We took soil material from the B horizons of a Podzol at Skånes Värsjö (southern Sweden). In batch experiments, soil was equilibrated with solutions varying in pH and concentration of dissolved organic C. In Bh samples, the release of dissolved C gradually increased with increase in pH. In the Bs1 material there was a minimum at pH 4.1, and in the Bs2 soil the minimum occurred at pH 4.6. The ability to retain added dissolved C increased in the order Bh < Bs1 < Bs2.

The column experiment was run for 160 days under unsaturated flow conditions. Columns were packed with Bh, Bh + Bs1 or Bh + Bs1 + Bs2 samples to calculate mass balances for each horizon. Solutions either without any dissolved organic C or ones containing 49 mg C dm−3 with pH of 4.0 or 3.6 were used to leach columns. The pH of input solutions only little affected the concentration of dissolved C in the effluent. Relative proportions of hydrophobic substances decreased with increasing column length and decreasing pH. For input solutions containing dissolved C, near steady state was achieved for both the Bs1 and Bs2 horizons with approximately 25% dissolved organic matter retention. Thus, no maximum sorption capacity for dissolved C could be defined for these horizons. This behaviour could not have been predicted by batch data, showing that column experiments provide useful additional information on interactions between organic compounds and solid soil material.
The impact of long‐term cultivation and management history on the status and dynamics of cobalt in a savanna Alfisol in Nigeria
Authors: Agbenin J. O.
Published: March 2003

The status of cobalt (Co) in savanna soils of Nigeria is largely unknown, and a long‐term experiment including inorganic fertilizer (NPK) and farmyard manure (FYM) and uncultivated land provided information on the way management affected the dynamics of Co in the soil. Total Co increased with increasing depth, whereas readily extractable Co decreased. The mean concentration of Co (5.6–7.9 mg kg−1) was close to the mean value of 8 mg kg−1reported for soils worldwide, whereas the concentration of extractable Co was less than that reported in most soils. Regression analysis indicated that total Fe predicted up to 78% of the soil Co. The potentially available Co correlated strongly with pedogenic or reducible Mn oxides extracted with dithionite–citrate–bicarbonate. Mass balance calculations showed that fertilization with either NPK or FYM caused losses of between 0.8 and 1.1 g Co m−2after 50 years of cultivation against the uncultivated site as a reference. However, Co increased by 1.8 g m−2in the soil receiving FYM + NPK, suggesting that the Co of the soil was best maintained under this management probably because of incidental additions of Co in the manures. Furthermore, the positive Co balance in the FYM + NPK plot was partly enhanced by its larger contents of clay, Fe and pedogenic Mn oxides than in either the FYM or NPK plots. Clay, Fe and pedogenic oxides served as Co sinks in this particular savanna soil.
Generalized linear models in soil science
Authors: Lane P. W.
Published: March 2003

Classical linear models are easy to understand and fit. However, when assumptions are not met, violence should not be used on the data to force them into the linear mould. Transformation of variables may allow successful linear modelling, but it affects several aspects of the model simultaneously. In particular, it can interfere with the scientific interpretation of the model. Generalized linear models are a wider class, and they retain the concept of additive explanatory effects. They provide generalizations of the distributional assumptions of the response variable, while at the same time allowing a transformed scale on which the explanatory effects combine. These models can be fitted reliably with standard software, and the analysis is readily interpreted in an analogous way to that of linear models. Many further generalizations to the generalized linear model have been proposed, extending them to deal with smooth effects, non‐linear parameters, and extra components of variation. Though the extra complexity of generalized linear models gives rise to some additional difficulties in analysis, these difficulties are outweighed by the flexibility of the models and ease of interpretation. The generalizations allow the intuitively more appealing approach to analysis of adjusting the model rather than adjusting the data.
Cation exchange properties of acid forest soils of the northeastern USA
Authors: Johnson C. E.
Published: March 2003

Negative correlations between soil pH and cation exchange capacity (CEC) or base saturation in soils of the northeastern USA and Scandinavia have raised questions regarding the nature of cation exchange in acid forest soils. Using data from three small‐catchment studies and an extensive regional survey of soils in the northeastern USA, I examined relationships among total carbon, effective CEC (CECe), soil pHs(in 0.01 mCaCl2) and base saturation. Organic matter is the predominant source of soil surface charge in these coarse‐grained, glacially derived soils. Correlation coefficients (r) between total carbon and CECeranged from 0.43 to 0.74 in organic horizons and from 0.46 to 0.83 in mineral horizons. In all cases, the intercepts of functional relations between CECeand total C were near zero. In O horizons, the CECeper unit mass of organic carbon (CECe:C) was positively correlated with pHsin three of the four data sets, consistent with the weak‐acid behaviour of the organic matter. However, CECe:C was negatively correlated with pHsin mineral soils in two data sets, and uncorrelated in the other two. The CECein mineral soils represents the portion of total CEC not occupied by organically bound Al. The negative correlations between CECe:C and pHscan therefore be explained by increased Al binding at higher pHs. Aluminium behaves like a base cation in these soils. When Al was considered a base cation, the relation between base saturation and pHscould be effectively modelled by the extended Henderson–Hasselbalch equation. When modelled without Al as a base cation, however, there were no consistent relationships between pHsand base saturation across sites or soil horizons. Because of the non‐acidic behaviour of Al, it is difficult to predict the effect of ongoing reductions in acid deposition on the base status of soils in the northeastern USA.
Interpretation of humic acid coagulation and soluble soil organic matter using a calculated electrostatic potential
Authors: Weng L. , Temminghoff E. J.M. , Van Riemsdijk W. H.
Published: March 2003

The coagulation of humic substances and its role in controlling the solubility of organic matter in soils are not well understood. We therefore studied the physico‐chemical behaviour of purified humic acid from forest soil coagulated with Na, Ca, Cu, Al at pH 4 and 6, and then modelled the behaviour with the Non‐Ideal Consistent Competitive Adsorption Donnan (NICA‐Donnan) model. We found that the coagulation of humic acid occurs when the Donnan potential is less negative than −0.08 V. Based on this result, an empirical relation between the Donnan potential of humic acid and its concentration in solution was derived. In addition, the Donnan potential of the dissolved organic matter in the soil solution of six soil profiles from forests was calculated using the NICA‐Donnan model under the assumption that all the dissolved organic matter behaves as humic acid. The measured concentration of dissolved organic matter also decreases in a soil profile, as the calculated potential becomes less negative. The results are in many cases in semi‐quantitative agreement with the predicted concentration based on the humic acid coagulation experiment. Acid soils contain more dissolved organic matter, which may result from the presence of a fairly large fraction of more soluble organic molecules, such as fulvic acid.
Modelling the turnover of 15N‐labelled fertilizer and cover crop in soil and its recovery by maize
Authors: Hadas A. , Doane T. A. , Kramer A. W. , Van Kessel C. , Horwath W. R.
Published: March 2003

The rate at which available nitrogen (N) is released from organic materials in soil is often measured by applying 15N and following its recovery by the growing crop. However, the turnover of labelled N in soil modifies the ratio of labelled to unlabelled available N and thereby affects the uptake of 15N by plants. The recovery of labelled N by maize was measured in a field experiment under three management systems, with one 15N‐labelled input in each: (1) conventional, with fertilizer side dressing, (2) low input, with vetch as a cover crop and fertilizer side dressing, and (3) organic, with vetch and composted manure. The NCSOIL model, which simulates C and N turnover in soil, was modified to include relevant processes related to the maize crop, and used to estimate the decomposition rate constant of vetch in the field by optimizing the simulated dynamics of labelled N uptake by maize against the measured results. A large input of C from mineralizable soil organic matter and root deposition was necessary to account for the recovery of fertilizer N by maize. Optimization of labelled N recovery in the low input system resulted in two optional rate constants for the decomposition of vetch: rapid decomposition (0.4 day−1) of a labile vetch pool (49% of total vetch N), or slow decomposition (0.008 day−1) of a single vetch pool. In the simulated organic system, where manure and vetch were incorporated at the same time, only a rapid decomposition of the labile component of vetch accounted well for the recovery of vetch N by maize. The prolonged recycling of N mineralized from the vetch, and its mixing with fertilizer side dressing in the low input system, reduced the recovery of vetch N even though it was mineralized rapidly. This demonstrates the difficulty in assessing the availability of N from organic materials.
Hydraulic and transport properties of the plant–soil system estimated by inverse modelling
Authors: Sonnleitner M. A. , Abbaspour K. C. , Schulin R.
Published: March 2003

Modelling soil water flow and solute transport under field conditions requires the knowledge of many parameters that are difficult to determine directly. Values determined on small isolated samples in the laboratory are often not representative of field situations. We investigated the applicability of inverse modelling to a soil–plant system in lysimeter experiments. We also tested whether parameters obtained from one experiment could be applied to another with the same soil. In a lysimeter planted with young trees, we first did a multistep drainage experiment and then a long‐term bromide tracer experiment with atmospheric boundary conditions at the soil surface. To estimate the unsaturated hydraulic properties, we linked the inverse program SUFI (Sequential Uncertainty FItting) to the flow and transport model HYDRUS5. A comparison of several scenarios showed that the resulting values of parameters depended strongly on the data used for calibration and the formulation of the objective function. The results suggested that inverse modelling could be used to identify important processes. Inversely obtained parameters gave better predictions for a second experiment when more variables were considered in the objective function and when the range of hydraulic conditions was wider. Furthermore, with retention curves directly fitted to measured water retention data we achieved acceptable results. Despite some limitations, the inverse approach was found to be a sound and useful procedure for estimating parameters of a complex system involving water uptake by roots, solute transport and unsaturated flow.
Changes in river fish assemblages associated with vegetated and degraded banks, upstream of and within nutrient‐enriched zones
Authors: GROWNS  , POLLARD  , GEHRKE
Published: March 2003

Fish assemblages in two reaches of the Hawkesbury–Nepean River were studied to determine the separate and combined effects of modifications to the riparian vegetation and nutrient enrichment on the composition of fish assemblages. Fish were sampled along vegetated and degraded banks where no vegetation was present, and upstream of and within zones of nutrient enrichment, associated with discharge of treated sewage effluent into the river and run‐off from nearby urban areas. Although the species composition differed between river reaches, both the number of fish species and total fish abundance were significantly greater in habitats adjacent to vegetated banks. Five species [Anguilla reinhardtii Steindachner, Macquaria novemaculeata (Steindachner), Cyprinus carpio L., Hypseleotris compressa (Krefft) and Myxus petardi (Castelnau)] were significantly (P < 0.05) affected by riparian degradation, with mean abundances ranging from 3.3 to 13.0 times larger than adjacent to vegetated banks. Species richness, total abundance and abundance of M. novemaculeata and H. compressa were also higher in zones with low levels of nutrient enrichment. Multivariate analyses showed that while eutrophication has a major effect on fish assemblages in the Hawkesbury–Nepean River, even greater effects may result from clearing of riparian vegetation leading to bank degradation.