bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a functional hypoxia-responsive element that regulates the expression of the egl nine homologue 3 (egln3/phd3) gene
Authors: Pescador Nuria , Cuevas Yolanda , Naranjo Salvador , Alcaide Marisa , Villar Diego , Landázuri Manuel O. , del Peso Luis 
Published: August 2005

Low oxygen levels induce an adaptive response in cells through the activation of HIFs (hypoxia-inducible factors). These transcription factors are mainly regulated by a group of proline hydroxylases that, in the presence of oxygen, target HIF for degradation. The expression of two such enzymes, EGLN1 [EGL nine homologous protein 1, where EGL stands for egg laying defective (Caenorhabditis elegans gene)] and EGLN3, is induced by hypoxia through a negative feedback loop, and we have demonstrated recently that hypoxic induction of EGLN expression is HIF-dependent. In the present study, we have identified an HRE (hypoxia response element) in the region of the EGLN3 gene using a combination of bioinformatics and biological approaches. Initially, we isolated a number of HRE consensus sequences in a region of 40 kb around the human EGLN3 gene and studied their evolutionary conservation. Subsequently, we examined the functionality of the conserved HRE sequences in reporter and chromatin precipitation assays. One of the HREs, located within a conserved region of the first intron of the EGLN3 gene 12 kb downstream of the transcription initiation site, bound HIF in vivo. Furthermore, this sequence was able to drive reporter gene expression under conditions of hypoxia in an HRE-dependent manner. Indeed, we were able to demonstrate that HIF was necessary and sufficient to induce gene expression from this enhancer sequence.
An ordered sequential mechanism for Factor IX and Factor IXa binding to platelet receptors in the assembly of the Factor X-activating complex
Authors: Yang Xia , Walsh Peter N. 
Published: August 2005

To define the contributions of the Ω-loop of the Gla (γ-carboxyglutamic acid) domain and the EGF2 (second epidermal growth factor) domain of FIXa (Factor IXa) in the assembly of the FX-activating complex on activated platelets and phospholipid membranes, three recombinant FIXa chimeras were prepared with corresponding residues from the homologous coagulation protein, FVII: (i) Gly4–Gln11 (FIXa7Ωloop), (ii) Cys88–Cys124 (FIXa7EGF2), and (iii) both Gly4–Gln11 and Cys88–Cys124 (FIXa7Ωloop7EGF2). All three chimeras were similar to wild-type FIXa, as assessed by SDS/PAGE, active-site titration, content of Gla residues, activation rates by FXIa and rates of FXa generation in solution. Titrations of FX or FVIIIa on SFLLRN peptide-activated platelets and on phospholipid vesicles in the presence of FVIIIa revealed normal substrate and cofactor binding to all chimeras. In kinetic assays in the presence of phospholipid vesicles and FVIIIa, compared with wild-type FIXa Kd, app∼4 nM, the FIX7Ωloop chimera showed a 1.6-fold increase in Kd, app, the FIX7EGF2 chimera had a 7.4-fold increase in Kd, app, and the FIX7Ωloop7EGF2 chimera showed a 21-fold increase in Kd, app. In kinetic assays and equilibrium platelet-binding assays with activated platelets and FVIIIa, compared with wild-type FIXa (Vmax∼5 nM min−1; Kd, app∼0.5 nM; Bmax∼550 sites/platelet; Kd∼0.5 nM), the FIX7Ωloop chimera displayed 2-fold decreases in Vmax and Bmax and 2-fold increases in Kd, app and Kd. The FIX7EGF2 chimera displayed 2-fold decreases in Vmax and Bmax and 10-fold increases in Kd, app and Kd. The FIX7Ωloop7EGF2 chimera showed non-saturable curves and severely impaired rates of FXa generation, and non-saturable, non-specific, low-level binding to activated platelets. Thus both the Gla domain Ω-loop (Gly4–Gln11) and the EGF2 domain (Cys88–Cys124) are required to mediate the normal assembly of the FX-activating complex on activated platelets and on phospholipid membranes.
Surface salt bridges modulate the DNA site size of bacterial histone-like HU proteins
Authors: Kamau Edwin , Tsihlis Nick D. , Simmons L. Alice , Grove Anne 
Published: August 2005

Bacterial histone-like DNA-binding proteins are best known for their role in compacting the genomic DNA. Of these proteins, HU is ubiquitous and highly conserved across the eubacterial kingdom. Using the HBsu (Bacillus subtilis-encoded HU homologue) as a model, we explore here the molecular basis for the ability of some HU homologues to engage a longer approx. 35 bp DNA site as opposed to the much shorter sites reported for other homologues. Using electrophoretic mobility-shift assays, we show that the DNA site size for HBsu is approx. 10–13 bp and that a specific surface salt bridge limits the DNA site size for HBsu. Surface exposure of the highly conserved Lys3, achieved by substitution of its salt-bridging partner Asp26 with Ala, leads to enhanced DNA compaction by HBsu-D26A (where D26A stands for the mutant Asp26→Ala), consistent with the interaction of Lys3 with the ends of a 25 bp duplex. Both HBsu and HBsu-D26A bend DNA, as demonstrated by their equivalent ability to promote ligase-mediated DNA cyclization, indicating that residues involved in mediating DNA kinks are unaltered in the mutant protein. We suggest that Lys3 is important for DNA wrapping due to its position at a distance from the DNA kinks where it can exert optimal leverage on flanking DNA and that participation of Lys3 in a surface salt bridge competes for its interaction with DNA phosphates, thereby reducing the occluded site size.
Investigation of the catalytic triad of arylamine N-acetyltransferases: essential residues required for acetyl transfer to arylamines
Authors: Sandy James , Mushtaq Adeel , Holton Simon J. , Schartau Pamela , Noble Martin E. M. , Sim Edith 
Published: August 2005

The NATs (arylamine N-acetyltransferases) are a well documented family of enzymes found in both prokaryotes and eukaryotes. NATs are responsible for the acetylation of a range of arylamine, arylhydrazine and hydrazine compounds. We present here an investigation into the catalytic triad of residues (Cys-His-Asp) and other structural features of NATs using a variety of methods, including site-directed mutagenesis, X-ray crystallography and bioinformatics analysis, in order to investigate whether each of the residues of the catalytic triad is essential for catalytic activity. The catalytic triad of residues, Cys-His-Asp, is a well defined motif present in several families of enzymes. We mutated each of the catalytic residues in turn to investigate the role they play in catalysis. We also mutated a key residue, Gly126, implicated in acetyl-CoA binding, to examine the effects on acetylation activity. In addition, we have solved the structure of a C70Q mutant of Mycobacterium smegmatis NAT to a resolution of 1.45 Å (where 1 Å=0.1 nm). This structure confirms that the mutated protein is correctly folded, and provides a structural model for an acetylated NAT intermediate. Our bioinformatics investigation analysed the extent of sequence conservation between all eukaryotic and prokaryotic NAT enzymes for which sequence data are available. This revealed several new sequences, not yet reported, of NAT paralogues. Together, these studies have provided insight into the fundamental core of NAT enzymes, and the regions where sequence differences account for the functional diversity of this family. We have confirmed that each of the three residues of the triad is essential for acetylation activity.
Integrating soil map information in modelling the spatial variation of continuous soil properties
Authors: GOOVAERTS P. , JOURNEL A.G. 
Published: August 2005

SummaryThis paper presents two indicator algorithms that integrate soil map information into modelling the spatial variation of continuous soil properties: these are simple indicator kriging with varying means and the Markov–Bayes algorithm. Both methods are used to evaluate probabilities for copper and cobalt deficiencies in the Borders Region of Scotland. Results are compared with maps obtained by the polygonal method (Thiessen polygons) and an indicator kriging algorithm that does not use soil map information. Accounting for soil map information is shown to improve delineation of the deficient areas, especially where the sampling is sparse.Test locations are classified as deficient or not so as to minimize an expected cost of mis‐classification that is derived from local probability distributions of copper or cobalt and functions measuring the cost of overestimating or underestimating metal concentrations. The comparison of classification results with actual copper and cobalt concentrations at test locations shows that the two proposed algorithms can decrease substantially the economic loss attached to misclassification.
Molecular phylogenetic analysis of a soil microbial community in a soybean field
Authors: UEDA T. , SUGA Y. , MATSUGUCHI T. 
Published: August 2005

SummaryWe report here the phylogenetic characterization of small subunit rRNA gene sequences obtained by polymerase chain reaction (PCR) amplification of mixed population DNA extracted directly from soil in a soybean field without culturing the organisms. The phylogenetic analysis of 17 soil clones by the neighbour‐joining method shows that the soil sample contained broadly diverse prokaryotes; a clone related to archaea, a clone to gram‐positive bacteria with high G+C contents, two clones to green sulphur bacteria, four clones to proteobacteria, and nine clones were not in clusters of any previously reported bacterial groups, which suggests they belong to members of novel groups in Bacteria. In addition, the archaeal sequence, FIE16, is phylogenetically similar to ANTARCTIC 12, a clone obtained from surface waters of Antarctica by PCR. Their occurrence in both the ocean and soil suggests a global distribution of this archaeal group. In conclusion, rRNA gene sequences recovered from soil biomass document the occurrence of many more bacterial lingeages than have been recognized previously through cultivation‐based techniques.
Adsorption mechanisms of thiazafluron in mineral soil clay components
Authors: COX L. , HERMOSIN M.C. , CORNEJO J. 
Published: August 2005

SummaryThe adsorption of the herbicide thiazafluron, 1,3‐dimethyl‐1‐(5‐trifluoromethyl‐1,3,4‐thiadiazol‐2‐yl)urea, by three smectites, illite, kaolinite, ferrihydrite and the clay fraction of an illitic soil (54.9% illite, 17.0% montmorillonite and 24.9% kaolinite) and a montmorillonitic soil (33.9% illite, 55.0% montmorillonite and 11.1% kaolinite) has been determined. Thiazafluron adsorbed on neither kaolinite nor iron oxide. The adsorption isotherms on smectites and illite conformed to the Freundlich equation. Values of Kf‐obtained for smectites were larger than for the illite and increased as the layer charge of the smectite decreased. Desorption of thiazafluron on smectites was shown to be highly irreversible. Adsorption isotherms of thiazafluron on different homoionic montmorillonite samples suggest an important role of the exchangeable cations in the adsorption. Infrared spectra and X‐ray diffraction analysis of the complexes of thiazafluron with homoionic montmorillonites indicated that thiazafluron adsorbs in the interlamellar space of the smectites, mainly by substitution of water molecules associated with the exchangeable cations through the carbonyl‐amide group and formation of H‐bonds or waterbridge between the NH group of the amide and the basal oxygens of the montmorillonite. The illitic soil clay adsorbed more of the herbicide than the montmorillonitic one did, suggesting that illite and montmorillonite may be present in soils in altered forms giving rise to different adsorption capacities from those of the pure minerals.
Total and young organic matter distributions in aggregates of silty cultivated soils
Authors: PUGET P. , CHENU C. , BALESDENT J. 
Published: August 2005

SummaryThe distribution of organic matter in soil aggregates was investigated by fractionating aggregates and measuring carbon contents. The distribution of recently incorporated organic carbon was analyzed using 13C natural abundance. The soils of the experiment, which previously only had C3 vegetation, were cropped to maize, aC4 plant, for 6 or 23 years.Aggregate size distributions were determined for silty soils with different organic matter contents. Slaking‐resistant macroaggregates were enriched in C as compared to dry‐sieved macroaggregates or to microaggregates, and the C content increased with the size of aggregates. The δ13C value was used to calculate the amount of C3‐derived and C4‐derived organic carbon in the fractions. The larger carbon contents in stable macroaggregates were due to young C4‐derived organic carbon (<6 or 23 years), and we concluded that young organic matter was responsible for macroaggregate stability.
Medium‐term transformations of organic N in a cultivated soil
Authors: BALABANE M. , BALESDENT J. 
Published: August 2005

SummaryWe followed in situ the evolution of nitrogen recently incorporated into a soil under maize culture for 4 years. Each year, a different pair of plots treated by removal or return of maize crop residues received a single pulse of 15N‐labelled fertilizer. Unlabelled fertilizer was otherwise supplied. In parallel, plots supplied with unlabelled fertilizer received a single pulse of 15N‐labelled maize crop residues.Varying weather affected total and fertilizer‐derived N in the crop and residual inorganic N in the topsoil, but it did not affect fertilizer‐N immobilization and remineralization. There was no consistent effect of crop residue return on total soil N, immobilization of fertilizer N, or the decay kinetics of recently immobilized N.Recently incorporated organic N from crop residues and microbial immobilization of inorganic N displayed similar mid‐term decay kinetics. Crop residue N and immobilized N enter a labile compartment with an average residence time of a few months. A proportion, estimated at 28%, enters a more stable compartment from which the mineralization was imperceptible in 4 years. Particle‐size fractions >50 um, which receive most of the crop residue N, retained it for only a short time. The mid‐term stabilization of N was mainly in soil fractions <50 um.
Nitrous oxide fluxes from grassland in the Netherlands: II. Effects of soil type, nitrogen fertilizer application and grazing
Authors: VELTHOF G.L. , OENEMA O. 
Published: August 2005

SummaryIntensively managed grasslands are potentially a large source of nitrous oxide (N2O) in the Netherlands because of the large nitrogen (N) input and the fairly wet soil conditions. To quantify the effects of soil type, N‐fertilizer application and grazing on total N2O losses from grassland, fluxes of N2O were measured weekly from unfertilized and mown, N fertilized and mown, and N fertilized and predominantly grazed grassland on a sand soil, a clay soil, and two peat soils during the growing season of 1992.Total N2O losses from unfertilized grassland were 2.5–13.5 times more from the peat soils than from the sand and clay soils. Application of calcium ammonium nitrate fertilizer significantly increased N2O flux on all sites, especially when the soil was wet. The percentage of fertilizer N applied lost to the atmosphere as N2O during the season ranged from 0.5 on the sand soil to 3.9 on one of the peat soils. Total N2O losses were 1.5–2.5 times more from grazed grassland than from mown grassland, probably because of the extra N input from urine and dung. From 1.0 to 7.7% of the calculated total amount of N excreted in urine and dung was emitted as N2O on grazed grassland. The large N2O losses measured from the peat soils, combined with the large proportion of grassland on peat in the Netherlands, mean that these grasslands contribute significantly to the total emission from the country.
Fertilization effects on organic matter in physically fractionated soils as studied by 13C NMR: Results from two long‐term field experiments
Authors: RANDALL E.W. , MAHIEU N. , POWLSON D.S. , CHRISTENSEN B.T. 
Published: August 2005

Summary l3C–nuclear magnetic resonance (NMR) spectra taken using magic–angle spinning (MAS), cross polarization (CP) and with total suppression of side bands (TOSS) are reported for soils from two long–term field experiments. One set of soils was from the Broadbalk Experiment at Rothamsted, UK (monoculture of winter wheat since 1843) and the other was from the Lermarken site of the Askov Long–Term Experiment on Animal Manure and Mineral Fertilizers (arable rotation since 1894). At both sites soil samples were taken from three fertilizer treatments: nil, inorganic fertilizers, animal manure. Spectra were obtained from whole soil samples and from the size fractions clay (<2 μrn), silt (2–20 μm) and, in some cases, sand (20–2000 μm).Comparison of the total strengths of the 13C–NMR signal for each size separate in relation to its total organic C content shows that clay, particularly, contains large percentages of C not detected by NMR because of the large magnetic susceptibilities of the soil minerals. It is proposed that the observed signals come from the more labile pools of soil organic matter (SOM), on the presumption that these pools are less closely associated with soil minerals and iron oxides and are likely to be less protected from microbial or enzymic decomposition.For both Rothamsted and Askov, functional groups in the 45–110 ppm region (N– and O–alkyls) dominate in the spectra for whole soils, with aromatics (110–160 ppm) and alkyls (0–45 ppm) signals being the next prominent. In the Askov whole soil samples 13C–NMR revealed no differences between nil, inorganic fertilizer and animal manure treatments but in the Rothamsted whole soil there were some small differences.Clay and silt fractions from Askov contain more alkyls and less aromatics than those from Rothamsted. For both sites clay in enriched in alkyls and depleted in aromatics relative to silt. Clay from Askov, but not Rothamsted, contains more N–alkyls (45–65 ppm) and less acetals (90–110 ppm) than silt. O–alkyls (65–90 ppm) account for more than 20% of the total signal in clay and silt from both sites. Fertilization regimes have not significantly affected the chemical composition of SOM associated with clay– and silt–sized fractions in the soils at either site. We conclude that the chemical composition of SOM is determined primarily by the interaction between the organisms responsible for decomposition and the mineral soil matrix rather than the nature of substrate input.
Dynamic programming analysis of pore space
Authors: EGGLESTON J.R. , PEIRCE J.J. 
Published: August 2005

SummaryA method based on the principles of dynamic programming is developed and applied to digital soil images to determine tortuosity, effective porosity, and the shortest paths available for flow. Pathways for flow are determined by minimizing a resistance factor. Analysis of two numerically simulated soils finds that a platy soil has greater effective porosity and smaller tortuosity than a layered soil. The ability of the dynamic programming model to analyse large digital images with complex pore structure is subsequently demonstrated by the analysis of a digital image of an agricultural soil. The results from the agricultural soil point to the need for digital soil image analysis to be three–dimensional if convective and diffusive soil properties are to be examined. It is demonstrated that, because determination of flow paths can be treated as a routing problem solved by applying a few simple rules, dynamic programming analysis is not limited by complexity of pore structures.
A fuzzy allocation scheme for the Australian Great Soil Groups Classification system
Authors: MAZAHERI S.A. , KOPPI A.J. , McBRATNEY A.B. 
Published: August 2005

SummaryConventional methods of soil classification are based largely on hierarchies and treat soil attribute value ranges as exactly specifiable quantities. Misclassification may result from ignoring the continuous complex nature of soil variation, and the inability to sample and measure every aspect of soil. The Australian Great Soil Groups (GSG) system of classification is essentially a fuzzy classification, and for the most part central concepts have not been defined explicitly.Centroids were generated, together with fuzzy group membership, using data from the 147 soil profile descriptions in The Handbook of Australian Soils. Some of the GSG, such as Siliceous Sands and Red and Brown Hardpan Soils, were divided into their component parts for better and easier quantification and allocation. The centroids of GSG were examined, and the method of fuzzy κ‐means was then used to allocate unknown profiles to the GSG. The results show that the system is intuitively reasonable.
Aluminium chemistry of the soil solution in an acid forest soil as influenced by percolation rate and soil structure
Authors: FRANKEN G. , PIJPERS M. , MATZNER E. 
Published: August 2005

SummaryThe predicted activity of Al in the soil solutions of acid forest soils often differs from that observed in the field. We have investigated the influence of soil structure and flow rate of the soil solution on the aluminum release to explain this divergence. Disturbed and undisturbed samples of soil were collected from the A and B horizons of a dystric cambisol at Waldstein (Fichtelgebirge, Germany). The samples were irrigated with solutions mixed according to field data on throughfall or soil solution composition with pH 3.5 with flow rates of 4 mm d−1, 12 mm d−1 and 36 mm d−1. The percolates were analysed for major ions. Resulting relations between pH and pAl were compared with batch experiments. In neither the A horizon nor in the B horizon did soil structure influence the relation between pH and pAl. The apparent equilibrium between pH and pAl was described as the pKapp value with pKapp= pAl—a pH (where a is an empirical constant). It was found that the pKapp values for the column percolates were in the range of variation of those found in batch experiments.Flow rate had no influence on pKapp at 4 and 12 mm d−1. At 36 mm d−1 a significant increase of pKapp was observed. This relative undersaturation of Al was more pronounced in the A horizon than in the B horizon. When flow is fast Al release into the percolating soil solution might be limited by diffusion.
Characterizing heavy‐metal adsorption on oxides and oxyhydroxides
Authors: SPARK K.M. , JOHNSON B.B. , WELLS J.D. 
Published: August 2005

SummaryAdsorption of Cu(II), Zn(II), Co(II) and Cd(II) on three different substrates: goethite, alumina and silica, was investigated over the pH range from 3.5 to 10. The consistent variation in the pH at which 50% of the metal is adsorbed (pH50) indicates that the identity of the adsorbing ion is the principal factor determining the pH range over which adsorption occurs. However, the nature of the substrate does play a lesser role. The proton coefficient, χ, ranged from about 0.5 to 1.8, and was correlated with the difference between pH50 and the pH for 50% precipitation. It is suggested that for most metal‐substrate systems, for which χ is about 1, MOH+ plays a dominant role in adsorption. Increasing the substrate concentration decreased pH50 for adsorption of metals on goethite, but there was little change in χ. The change in pH50 was inversely related to χ. While the effect of the nature and concentration of the background electrolyte on Cu(II), Zn(II) and Co(II) adsorption depended on the substrate, increased ionic strength was found to decrease Cd(II) adsorption on all substrates.