bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Responses of Container‐ versus Ground‐Grown Soybean to Elevated Carbon Dioxide and Ozone
Authors: Booker Fitzgerald L. , Miller Joseph E. , Fiscus Edwin L. , Pursley Walter A. , Stefanski Leonard A.
Published: May 2005

In studies of CO2–enrichment effects on plants, the applicability of results derived from experiments using container‐grown plants for predictions of future crop performance in a CO2–enriched atmosphere has been questioned. Concerns also have been expressed about plant growth studies with the air pollutant O3 in pot‐grown plants. Further, since elevated CO2 and O3 co‐occur, studies are required with the combination of gases. In this 2‐yr experiment, soybean [Glycine max (L.) Merr.] plants grown in large pots (15 and 21 L) and in the ground were exposed to mixtures of CO2 and O3 in open‐top chambers. The CO2 treatments were ambient and CO2 enrichment of approximately 337 μmol mol−1 added 24 h d−1 Ozone treatments were charcoal‐filtered (CF) air (23 nmol mol−1) and approximately 1.5 times ambient O3 levels (71 nmol mol−1) given 12 h d−1 Relative effects of elevated CO2 and O3 on aboveground biomass and seed yield were quite similar for plants grown in pots compared with plants grown in the ground. Elevated CO2 increased total seed mass and O3 suppressed it to similar magnitudes in both rooting environments. Elevated CO2 also reduced the toxic effects of O3 Net photosynthesis (A) was similar while stomatal conductance (gs) was higher in pot‐grown compared with ground‐grown plants, possibly due to better soil moisture status. The results indicated that planting density and rooting environment affected plant morphology, but relative responses of seed yield to elevated CO2 and O3 were not fundamentally different between soybean plants grown in large pots and in the ground in open‐top chambers.
Performance of Crosses among French and Spanish Maize Populations across Environments
Authors: Malvar R. A. , Revilla P. , Butrón A. , Gouesnard B. , Boyat A. , Soengas P. , Álvarez A. , Ordás A.
Published: May 2005

Heterotic patterns among European maize (Zea mays L.) populations are strongly affected by genotype × environment (GE) interactions and no single heterotic pattern has been identified so far that is not influenced by GE interaction. The objectives of this work were to study (i) the mean performance and stability of the heterotic patterns ‘Humid Spain × Southern France’ and ‘Dry Spain × Humid Spain’ and (ii) the influence of some environmental and genotypic covariates on G and E main effects and their interaction. We studied the GE interaction for grain yield in eight environments using Sites Regression (SREG) and factorial regression models. The biplot obtained from the SREG model allowed visual cultivar evaluation. The factorial regression model incorporated genotypic and environmental covariates that enhanced biological interpretation of GE interaction. The heterotic patterns Humid Spain × Southern France and Dry Spain × Humid Spain had similar mean performance across environments, but the former, represented by the cross Lazcano × Millette du Lauragais, was more stable. Effects of G, E, and GE for grain yield were mainly due to earliness, vigor effects, and/or environmental factors related to cold stress. An adequately long vegetative cycle along with early vigor had a great influence on the mean grain yield performance of Lazcano × Millette du Lauragais. Additionally, its intermediate number of days to silking and tolerance to temperature stresses could be related to its stability. Breeding for tolerance to temperature stresses could render more stable maize genotypes.
Population Structure and Evolutionary Dynamics of Wild–Weedy–Domesticated Complexes of Common Bean in a Mesoamerican Region
Authors: Zizumbo-Villarreal Daniel , Colunga-GarcíaMarín Patricia , de la Cruz Emeterio Payró , Delgado-Valerio Patricia , Gepts Paul
Published: May 2005

The diversity, structure, genetic flow, and evolutive relationships within and among three wild–weedy–domesticated complexes and a wild population isolated from crops of common bean (Phaseolus vulgaris L.) were analyzed under traditional agriculture, within a region of the Mesoamerican center of domestication. Their diversity was compared with the diversity of a local commercial variety and a breeding line. A morphological marker and 37 polymorphic ISSR loci were used. Total genetic diversity within the wild, weedy, and domesticated populations across the complexes was very similar (0.24, 0.22, and 0.26, respectively). Weedy populations within each complex were more closely related to the domesticated than to the wild populations, suggesting they originated from introgression of wild‐type alleles into the domesticated populations or predominant gene flow from domesticated to wild populations. The wild population in closest proximity to the crop within its complex was more similar to the domesticated and weedy populations of its complex than to the rest of the wild populations, suggesting displacement of the wild genetic diversity by gene flow from the domesticated population within its complex. The high values of differentiation among wild, weedy, and domesticated populations within each complex suggest high autogamy or genetic drift. However, the values of gene flow among populations within the complexes were close to one, theoretically sufficient to counteract genetic drift and/or autogamy. We therefore assume that human selection is the most important evolutionary mechanism for maintaining the high wild‐domesticated differentiation by negative farmer selection of cultivated plants with morphological characters that suggest introgression. Farmers may influence the magnitude and characteristics of gene flow among populations within each complex by the management of the distance between the crops and the wild populations, the diversity within the landraces sown, and the tolerance and harvesting of weedy populations. The high geographic differentiation of the wild populations, together with the local differences in human selection practices and agronomic management, could have generated multiple evolutionary lineages after domestication. Domesticated populations within complexes were between two and four times more diverse than the local commercial variety and four and nine times more diverse than the breeding line. New conservation and breeding strategies are suggested to maintain and use the gene pools from these complexes.
Characterization of Resistance to Brown Stem Rot of Soybean in Five Accessions from Central China
Authors: Patzoldt M. E. , Carlson S. R. , Diers B. W.
Published: May 2005

Brown stem rot (BSR) of soybean [Glycine max (L.) Merr.], caused by Phialophora gregata (Allington & Chamberlain) W. Gams f. sp. sojae Kobayashi, Yamamoto, Negishi, and Ogoshi, can be effectively controlled with genetic resistance. Although three BSR resistance genes have been described, they all map to the same genetic region on linkage group (LG) J. In a previous screening of plant introductions (PIs) for BSR resistance, PI 567296B, PI 567323A, PI 567479, PI 567535B, and PI 567544 from central China were identified as having a high level of resistance. The objective of this study was to determine if resistance in these PIs maps to the same region on LG J where BSR resistance genes were previously identified. To map the resistance genes in these accessions, each PI was crossed to the susceptible cultivar Century 84 and 94 F2:3 lines were developed from each cross. Lines were evaluated for BSR resistance in the greenhouse and screened with molecular markers from LG J. In all five populations, a quantitative trait locus (QTL) conferring BSR resistance was mapped to the same region on LG J where resistance has already been reported. These results suggest that the BSR resistance genes identified in these five PIs from central China are likely allelic with previously reported BSR resistance genes.
Predicting Cation Exchange Capacity for Soil Survey Using Linear Models
Authors: Seybold C. A. , Grossman R. B. , Reinsch T. G.
Published: May 2005

Measuring the cation exchange capacity (CEC) for all horizons of every map unit component in a survey area is very time consuming and costly. The objective of this study was to develop CEC (pH 7 NH4OAc) prediction models that encompass most soils of the United States. The National Soil Survey Characterization database was used to develop the predictive models using general linear models. Data were stratified into more homogeneous groups based on the organic C content, soil pH, taxonomic family mineralogy class and CEC‐activity class, and taxonomic order. Models were developed for each strata or data group. Organic matter and noncarbonate clay contents were the main predictor variables used. Water at −1500 kPa was used in lieu of clay content on four groups. Results indicate that between 43 and 78% of the variation in CEC could be explained for the high organic C data groups; between 53 and 84% could be explained for the mineralogy groups; between 86 and 95% could be explained for the CEC‐activity class groups; and between 53 and 86% could be explained for the taxonomic orders. The same predictive model was applicable for Gelisols and Histosols. Inceptisols and Alfisols (>0.3% organic C) also shared the same model. In general, the mineralogy/CEC‐activity class equations had lower RMSEs than the taxonomic order equations. A decision tree, based on how the data was stratified, guides the selection of which model to use for a soil layer. Validation results indicated that the models, in aggregate, provide a reasonable estimate of CEC for most soils of the United States.
Development of a Water‐Extractable Phosphorus Test for Manure
Authors: Wolf Ann M. , Kleinman Peter J. A. , Sharpley Andrew N. , Beegle Douglas B.
Published: May 2005

The loss of P in runoff from agricultural land to which manure has been applied is related to water extractable P (WEP) in manure. However, a standard method to routinely measure WEP in manures has not been established and variables impacting the measurement have not been widely studied. In this investigation, the impact of manure holding times (1–22 d), WEP extract holding times (0–17 d with and without acidification), and method of P measurement on WEP were evaluated. In addition, four manure samples (one dairy, one swine, two poultry) and proposed WEP method were distributed to seven public and private laboratories to assess inter‐ and intralaboratory variability of WEP test results. The proposed method entailed extracting manures with water at a 1:200 ratio (manure solids/water), shaking for 60 min on a reciprocating shaker, and either filtering or centrifuging before P measurement by inductively coupled plasma atomic emission spectroscopy (ICP). Results show refrigerated (4°C) manure samples can be held up to 22 d and acidified extracts 18 d before analysis. Separation procedures (filtering vs. centrifuging) did not impact WEP measurements. While the method of P measurement (ICP vs. colorimetric) did have a significant impact on test results, the two methods were highly correlated and results within 5 to 10%. The proposed manure WEP method shows a high level of precision (relative standard deviations [RSDs] < 6.5) within laboratories, although greater variability (RSDs of 13.3–28.8) exists among laboratories when compared with other standard manure analyses, such as total P.
Defining Critical Capillary Rise Properties for Growing Media in Nurseries
Authors: Caron J. , Elrick D. E. , Beeson R. , Boudreau J.
Published: May 2005

Water availability for landscape nursery irrigation is foreseen as a major impediment for this industry within the next decade. Among various solutions proposed to increase irrigation efficiency, thereby reducing the water volumes required, are closed and semi‐closed subirrigation systems designed to grow plants potted in organic growing media. These systems, however, require organic substrates that have good capillary properties. However, standards for such capillary properties are not available. This study compared substrates composed of peat, bark, and sand having contrasting capillary properties, in a nursery experiment to establish guideline values for the proper and efficient operation on capillary mat devices. It also proposes a theoretical model of capillary rise using the hydraulic characteristics of growing media to predict the suitability of various substrates. Substrates with 60% (per volume) sphagnum peat were found to provide the best capillary rise and best growth, based on empirical measurements, relative to substrates with 30% sphagnum or 30% sedge peat. The proposed theoretical model concurred with these observations.
Phosphorus Fractions and Release Patterns in Typical Mediterranean Soils
Authors: Saavedra Concepción , Delgado Antonio
Published: May 2005

Phosphorus forms dictate the P release potential of soils in agronomic and environmental terms. The main purposes of this work were to study P forms by sequential chemical fractionation in soils typical of Mediterranean areas, establishing correlations between P fractions and soil properties, and identify the relationships of specific P fractions to P release potential as determined using P sinks (anion‐exchange resins). To this end, three different fractionation methods were used. A comparison of the results obtained with the three sequential fractionation schemes provides useful information about P forms in representative Mediterranean soils, allowing the distinction of P fractions which include: (i) the more labile P forms (essentially adsorbed P), (ii) most of pedogenic Ca phosphates, (iii) most of low soluble pedogenic Ca phosphates, (iv) lithogenic Ca phosphates, (v) P occluded in poorly crystalline Fe oxides, and (vi) P occluded in crystalline Fe oxides. The ratio of the P fraction, which includes the more labile P forms (essentially adsorbed) to combined non‐organic P fractions was negatively correlated with soil pH (r= −0.83,P< 0.001) and positively correlated with the portion of combined Fe fractions related to poorly crystalline oxides (r= 0.84,P< 0.001). The greatest of P desorbable from resins (Qmax, in the Johnson–Mehl equation) was related mainly to the combined P fractions including adsorbed P and precipitated Ca phosphates in the studied soils. The amount of P desorbed at 1 h (Q1h) accounted for a sizeable fraction ofQmax(between 29 and 59 %), theQ1h/Qmaxratio being positively correlated with the portion of combined non‐organic P fractions related to adsorbed P (r= 0.66;P< 0.01), and negatively correlated with the portion of combined P fractions related to low soluble pedogenic Ca phosphates (r= −0.67;P< 0.01).
Discontinuous Pore Fluid Distribution under Microgravity‐KC‐135 Flight Investigations
Authors: Reddi Lakshmi N. , Xiao Ming , Steinberg Susan L.
Published: May 2005

Designing a reliable plant growth system for crop production in space requires the understanding of pore fluid distribution in porous media under microgravity. The objective of this experimental investigation, which was conducted aboard NASA KC‐135 reduced gravity flight, is to study possible particle separation and the distribution of discontinuous wetting fluid in porous media under microgravity. KC‐135 aircraft provided gravity conditions of 1, 1.8, and 10−2 g Glass beads of a known size distribution were used as porous media; and Hexadecane, a petroleum compound immiscible with and lighter than water, was used as wetting fluid at residual saturation. Nitrogen freezer was used to solidify the discontinuous Hexadecane ganglia in glass beads to preserve the ganglia size changes during different gravity conditions, so that the blob‐size distributions (BSDs) could be measured after flight. It was concluded from this study that microgravity has little effect on the size distribution of pore fluid blobs corresponding to residual saturation of wetting fluids in porous media. The blobs showed no noticeable breakup or coalescence during microgravity. However, based on the increase in bulk volume of samples due to particle separation under microgravity, groups of particles, within which pore fluid blobs were encapsulated, appeared to have rearranged themselves under microgravity.
Binding of DNA from Bacillus subtilis on Montmorillonite–Humic Acids–Aluminum or Iron Hydroxypolymers
Authors: Crecchio Carmine , Ruggiero Pacifico , Curci Maddalena , Colombo Claudio , Palumbo Giuseppe , Stotzky Guenther
Published: May 2005

The equilibrium adsorption and binding of DNA from Bacillus subtilis on complexes of montmorillonite–humic acids Al or Fe hydroxypolymers (Al–M–HA or Fe–M–HA) at different M/HA ratios, the desorption of DNA, the capacity of bound DNA to transform competent cells of B. subtilis in vitro, and the protection of bound DNA from degradation by free and organomineral‐bound DNase I are reported. Adsorption was rapid (maximal after 2 h), occurred from pH 3 to 10, and was higher on Al–M–HA than on Fe–M–HA. Saturation of the sites on the surface or between the layers of Al– or Fe–M–HA occurred with only some complexes, depending on how the complexes were prepared. Essentially no desorption under stringent conditions was observed. Bound DNA transformed auxotrophic competent cells of B. subtilis, although at a lower frequency than free DNA. Bound DNA was protected more than free DNA against degradation by DNase I, and differences in resistance to degradation between free and bound DNA were more evident when DNase was also bound on the organomineral complexes.
A Laboratory Method for Determining the Unsaturated Hydraulic Properties of Soil Peds
Authors: Meadows Darren G. , Young Michael H. , McDonald Eric V.
Published: May 2005

The ability to estimate soil hydraulic properties of undisturbed soil peds is limited. Most laboratory methods repack samples into soil cores, thus destroying the structure. Most field methods average over multiple peds precluding measurements of individual peds. This article details a method for determining unsaturated soil hydraulic properties of individual highly structured soil peds. The procedure is based on the evaporation method. The peds were first coated in paraffin wax, with the top surface left open to the atmosphere, and then encased in expandable foam to provide extra support. After saturating, both mass (from digital balance) and soil water potential (from tensiometer) data were recorded every 5 min as the ped dried until the soil water potential reached approximately −70 kPa. The van Genuchten parameters (α, n) and saturated hydraulic conductivity (Ks) were estimated with inversion modeling, using the soil water potential data and final water content. Residual and saturated water contents, θr and θs, respectively, were measured independently. A mini‐permeameter provided independent estimates of Ks We compared the areally weighted average of our optimized hydraulic properties with results from a field infiltrometer test conducted at the exact location from where the peds were collected. The two methods compared well, though some disparity existed between the estimates of n and Ks, likely indicating the effects of interped cracks sampled with the tension infiltrometer. The method is potentially valuable for geostatistical and scaling studies because the smallest structural unit, the soil ped, can be sampled and analyzed.
Relationship of Apparent Soil Electrical Conductivity to Claypan Soil Properties
Authors: Jung W. K. , Kitchen N. R. , Sudduth K. A. , Kremer R. J. , Motavalli P. P.
Published: May 2005

Understanding relationships between sensor‐based measurements and soil properties related to soil quality may help in developing site‐specific management. The primary objective of this research was to examine whether sensor‐based apparent soil electrical conductivity (ECa) could be used to predict soil properties for claypan soil. Soil samples were obtained at three depths intervals (0‐ to 7.5‐, 7.5‐ to 15‐, and 15‐ to 30‐cm depths) at 65 locations within a 4‐ha area of an agricultural field located in north central Missouri in 2002. Samples were analyzed for numerous physical, chemical, and microbiological properties that serve as soil quality indicators. The ECameasurements were also collected at the coring locations with an electromagnetic induction‐based sensor. A combine equipped with a commercial yield‐sensing, GPS based recording system was used to map corn (Zea maysL.) and soybean [Glycine max(L.) Merr.] yields from 1993 to 2002. At the deepest sampling depth, soil bulk density (Db), clay, silt, cation exchange capacity (CEC), and Bray‐1 P were the most significantly correlated (r> 0.55) with ECaSoil properties were regressed against ECa, andR2values were often improved using a quadratic term of ECa, especially at the 0‐ to 7.5‐cm depth. Selected regression models were validated with an independent soil sample data set (n= 20). Soil properties were similar between measured and predicted. Some soil properties (e.g., clay and CEC) and ECathat were positively correlated to yield in years with average or greater than average cumulative July to August precipitation (>15 cm) were negatively correlated to yield for years with less than average precipitation (<15 cm). Our results suggest that sensor‐based ECacan be a quick and economical way of estimating some claypan soil quality measurements.
Recovery of Fertilizer Nitrogen in Crop Residues and Cover Crops on an Irrigated Sandy Soil
Authors: Bundy Larry G. , Andraski Todd W.
Published: May 2005

Nitrogen fertilizer inputs for intensive, irrigated crop production on sandy soils can contribute to elevated NO3 concentrations in groundwater. This study was conducted from 1995 to 1998 to determine the potential of a winter rye (Secale cereale L.) cover crop to recover fertilizer N from soil and crop residues and the availability of this N to corn (Zea mays L.). Nitrogen fertilizer treatments included no N and N‐labeled (15N‐depleted) fertilizer (NLF) applied to sweet corn at 190 kg ha−1 and to potato (Solanum tuberosum L.) at 224 kg ha−1 Cover crop treatments (fallow and winter rye) were established following harvest, plowed the following spring, and corn was grown with unlabeled fertilizer N at 112 kg ha−1 Whole plant fertilizer N recovery averaged 54% for sweet corn and 34% for potato using the NLF (15N isotope) method, and was significantly lower than N recovery determined by the difference method. Total NLF recovery decreased between harvest and the following spring (from 66 to 43% following sweet corn and from 47 to 37% following potato), presumably due to mineralization and leaching of crop residue N. Winter rye NLF uptake averaged 2 kg ha−1 and had no effect on total NLF recovery. Corn grain yields were significantly higher following potato than following sweet corn and following a winter rye cover crop compared with fallow in 2 of 3 yr. Corn NLF uptake averaged 3 kg ha−1 indicating the yield benefit following potato or winter rye was due to a rotation effect rather than a direct N contribution. These results indicate that on irrigated sandy soils in this region most of the N fertilizer not removed in the harvested portion of crops will be lost by leaching during the growing season or by the following spring.
SOIL CARBON CHANGES AFTER 26 YEARS IN A CUMBERLAND PLATEAU HARDWOOD FOREST
Authors: Kelly J. M. , Mays P. A.
Published: May 2005

Concerns about global warming and discussions of possible mitigation measures have generated a need for information on changes in soil C over time. The objective of this study was to determine if there was a change in soil C concentration in an aggrading oak forest over a 26‐yr interval. Using permanently identified points on the Camp Branch Experimental Watershed, soil samples were first collected in July of 1976 and archived. During July of 2002, 11 points covering 6 of the 18 soil series present on the watershed were resampled. The series chosen represent a range in topographic positions and forest cover types. In both 1976 and 2002, a bucket auger was used to collect samples at depth intervals of 0 to 10, 10 to 30, and 30 to 50 cm. Both sample sets were analyzed in 2002 using a loss on combustion technique to determine organic C concentration. A bootstrapping data analysis indicated an increase (95% confidence interval) in the concentration of C in the 0‐ to 10‐cm depth. No change in C concentration occurred in the 10‐ to 30‐ or 30‐ to 50‐cm samples. Average soil C concentration in the 0‐ to 10‐cm samples increased from a mean of 20.8 g kg−1 in 1976 to 35.9 g kg−1 in 2002. Among soil series, concentrations ranged from 9.5 to 28.9 g kg−1 in 1976 and 22.1 to 64.7 g kg−1 in 2002. Although the sample numbers are limited, results indicate that average soil C concentration in the top 10 cm of the mineral soil increased by 73% at this site over a 26‐yr interval.
Testing the Pore‐Solid Fractal Model for the Soil Water Retention Function
Authors: Wang Kang , Zhang Renduo , Wang Fuqin
Published: May 2005

The soil water retention curve is an important hydraulic function for the study of flow transport processes in unsaturated soils. To accurately describe and interpret the hydraulic property, a general soil water retention function was developed based on the pore‐solid fractal (PSF) model. The objective of this study was to evaluate the general soil water retention function using data of 65 soils and to compare the PSF function with its special cases, that is, three other soil water retention functions. Defined from the parameters of the PSF, an index of β/θs was used to quantify the relationship between the PSF and the other soil water retention functions. The PSF function fit all the data sets well, whereas the other retention functions only matched the retention data for some soils, ranging from 11 to 72% of the tested soils. Directly fitting these functions with the data sets showed that for 30 to 40% of the tested soils, these functions gave poorer results than the PSF.
Evaluation of the Heat Pulse Ratio Method for Measuring Soil Water Flux
Authors: Ochsner Tyson E. , Horton Robert , Kluitenberg Gerard J. , Wang Quanjiu
Published: May 2005

Soil water flux is an important hydrologic parameter, yet few techniques for measuring it in situ are available. Here we evaluate the heat pulse ratio method for measuring water flux. We conducted heat pulse measurements of flux in packed columns of sand, sandy loam, and silt loam soil. Water fluxes were calculated from the data following both a traditional temperature increase difference method and a new temperature increase ratio method. Both methods yielded similar estimates of flux, agreeing to within 0.84 cm h−1 on average. The low flow detection limits for both methods were also similar and ranged from 0.1 to 0.4 cm h−1 However, the ratio method was superior in that it permitted simpler calculations, reduced the number of required parameters by four, and exhibited two to three times greater precision. We found strong linear relationships (r2 ≥ 0.98, standard error < 0.4 cm h−1) between estimated and imposed water fluxes up to 40 cm h−1 However, the slopes of these relationships were less than one, ranging from 0.739 for the sand to 0.224 for the sandy loam. These slopes indicate that the sensitivity was less than predicted by the standard conduction–convection model. We have not discovered the cause of these errors, but we did find that the errors could not be explained by increasing the magnitude of the conduction term in the model as has been previously suggested. Instead, the errors could be explained by reducing the magnitude of the convection term. This finding can help direct future research efforts to improve the accuracy of the ratio method.
Antagonist of fractalkine (CX3CL1) delays the initiation and ameliorates the progression of lupus nephritis in MRL/lpr mice
Authors: Inoue Atsushi , Hasegawa Hitoshi , Kohno Masashi , Ito Mitsuko R. , Terada Miho , Imai Toshio , Yoshie Osamu , Nose Masato , Fujita Shigeru
Published: May 2005

Objective

Lupus nephritis is characterized by immune complex deposition and inflammatory cell infiltration into the renal glomeruli. Local generation of chemokines and the presence of chemokine receptors on the infiltrating cells may be involved in this process. Fractalkine (Fkn)/CX3CL1 and its receptor, CX3CR1, form one such chemokine system. We therefore undertook this study to investigate whether Fkn antagonist inhibits the initiation and progression of lupus nephritis in MRL/lpr mice.

Methods

NH2‐terminally truncated Fkn/CX3CL1 analogs were transfected into a nonmetastatic fibroblastoid cell line, MRL/N‐1, and injected subcutaneously into MRL/lpr mice.

Results

Fkn analogs truncated by ≥4 amino acid residues from the N‐terminus failed to induce chemotaxis and calcium influx by CX3CR1‐expressing cells. Of these, the most potent antagonist (Fkn‐AT) lacked the 4 N‐terminal amino acid residues. Fkn expression in the glomerulus was significantly increased in 12‐week‐old MRL/lpr mice. Expression was localized predominantly in the glomerular endothelial cells, but was occasionally observed in the mesangial cells and, to a lesser extent, in the interstitial microvasculature. Inoculation of MRL/lpr mice with Fkn‐AT before the onset or during the early stages of lupus nephritis significantly reduced glomerular hypercellularity, glomerulosclerosis, crescent formation, and vasculitis compared with control mice. This seemed to be due to a marked reduction in macrophage accumulation. In contrast, Fkn antagonist did not affect pneumonitis, sialadenitis, lymphadenopathy, or splenomegaly.

Conclusion

We prepared a novel potent Fkn antagonist and demonstrated its ability to delay the initiation and ameliorate the progression of lupus nephritis. This agent may therefore provide a new therapeutic approach to lupus nephritis.
Additive bone‐protective effects of anabolic treatment when used in conjunction with RANKL and tumor necrosis factor inhibition in two rat arthritis models
Authors: Schett Georg , Middleton Scot , Bolon Brad , Stolina Marina , Brown Heather , Zhu Li , Pretorius Jim , Zack Debra J. , Kostenuik Paul , Feige Ulrich
Published: May 2005

Objective

To investigate whether the bone‐preserving effects of a RANKL antagonist or a tumor necrosis factor (TNF) antagonist could be further improved by the addition of a bone anabolic agent in inflammatory arthritis.

Methods

Lewis rats with either adjuvant‐induced arthritis (AIA) or collagen‐induced arthritis (CIA) were treated for 10 days with PEGylated soluble tumor necrosis factor receptor type I (PEG sTNFRI), interleukin‐1 receptor antagonist (IL‐1Ra), osteoprotegerin (OPG), parathyroid hormone (PTH), or combinations of these agents starting on day 4 after disease onset. Treatment effects were assessed clinically, radiologically, and histologically, and by morphometry for the extent of paw swelling, bone erosive changes, and synovial inflammation.

Results

Paw swelling and synovial inflammation were significantly inhibited by PEG sTNFRI in AIA and CIA, and by IL‐1Ra in CIA. OPG and PTH had no significant effect on these parameters. Analysis of bone erosion revealed a significant bone‐sparing effect of monotherapy with PEG sTNFRI or OPG in both models, whereas IL‐1Ra was only effective in CIA. PTH treatment alone did not show a bone‐protective effect in either model. With the combination of PEG sTNFRI and PTH, erosion scores (−74% in AIA and −61% in CIA versus controls) were significantly lower than those elicited by PEG sTNFRI alone (−41% and −29%, respectively, versus controls). Similar results were also obtained with the combination of OPG and PTH (−88% in AIA and −73% in CIA, compared with −70% and −55%, respectively, with OPG monotherapy). Coadministration of IL‐1Ra and PTH had no synergistic bone‐sparing effect. Morphometric analysis revealed that the addition of PTH to PEG sTNFRI or OPG resulted in higher bone volume and higher osteoblast numbers in both AIA and CIA.

Conclusion

The bone‐protective effects resulting from RANKL or TNF antagonism can be further improved by the addition of a bone anabolic agent.
Skewed X chromosome inactivation in blood cells of women with scleroderma
Authors: Özbalkan Zeynep , Baǧışlar Sevgi , Kiraz Sedat , Akyerli Cemaliye Boylu , Özer Hüseyin T. E. , Yavuz Şule , Birlik A. Merih , Çalgüneri Meral , Özçelik Tayfun
Published: May 2005

Objective

Scleroderma (SSc) is an autoimmune disease of unknown etiology. The disease is 3–8 times more frequent in women than in men. The role of X chromosome inactivation (XCI) in the predisposition of women to autoimmunity has been questioned. Until now this has not been illustrated experimentally. This study was undertaken to test the hypothesis that disturbances in XCI mosaicism may be involved in the pathogenesis of the disease in female patients with SSc.

Methods

Seventy female SSc patients and 160 female controls were analyzed for the androgen receptor locus by theHpaII/polymerase chain reaction assay to assess XCI patterns in DNA extracted from peripheral blood cells. Furthermore, skin biopsy samples were obtained from 5 patients whose blood revealed an extremely skewed pattern of XCI, and the analysis repeated. Since microchimerism in SSc was reported, Y chromosome sequences were investigated in all samples.

Results

Skewed XCI was observed in DNA from peripheral blood cells in 35 of 55 informative patients (64%), as compared with 10 of 124 informative controls (8%) (P< 0.0001). Extreme skewing was present in 27 of the patient group (49%), as compared with only 3 of the controls (2.4%) (P< 0.0001). However, XCI was random in all skin biopsy samples. The potential contribution of microchimerism to the random XCI pattern is highly unlikely based on the medical histories of the patients.

Conclusion

Skewed XCI mosaicism may play a significant role in the pathogenesis of SSc.
Relationship of radiographic and clinical variables to pinch and grip strength among individuals with osteoarthritis
Authors: Dominick Kelli L. , Jordan Joanne M. , Renner Jordan B. , Kraus Virginia B.
Published: May 2005

Objective

Little is known about how specific radiographic features are related to hand strength in osteoarthritis (OA). This study examined associations of radiographic variables with pinch and grip strength among individuals with radiographic hand OA.

Methods

Participants (n = 700, 80% female, mean age 69 years) were part of a study on the genetics of generalized OA. All had bilateral radiographic hand OA. Linear models were used to examine associations of grip and pinch strength with 1) OA in joint groups (proximal interphalangeal, metacarpophalangeal [MCP], carpometacarpal [CMC]), 2) OA in rays (first through fifth), and 3) summed Kellgren/Lawrence (K/L) grades for severity of OA in all joints. Adjusted models controlled for age, sex, hand pain, chondrocalcinosis, and hand hypermobility. Mixed models accounted for clustering within families.

Results

In bivariate analyses, all joint groups, all rays, and total summed K/L grades were significantly negatively associated with grip and pinch strength (P < 0.05). In adjusted models, the only joint group significantly associated with grip strength was the CMCs, and only OA in the MCP joint was significantly associated with pinch strength (P < 0.05). The only ray significantly associated with grip strength (P < 0.05) was ray 1, and no individual rays were significantly associated with pinch strength. A higher summed K/L grade was significantly associated with both lower grip strength and lower pinch strength.

Conclusion

Among individuals with radiographic hand OA, increasing radiographic severity is associated with reduced grip and pinch strength, even when controlling for self‐reported pain. Individuals with radiographic OA in specific locations (CMC joints, MCP joints, and ray 1) may be at particular risk for reduced hand strength.
Analysis of immune reconstitution after autologous bone marrow transplantation in systemic sclerosis
Authors: Farge Dominique , Henegar Corneliu , Carmagnat Maryvonnick , Daneshpouy Marjan , Marjanovic Zora , Rabian Claire , Ilie Doina , Douay Corinne , Mounier Nicolas , Clave Emmanuel , Bengoufa Djaouida , Cabane Jean , Marolleau Jean Pierre , Gluckman Eliane , Charron Dominique , Toubert Antoine ,   for the Intensification et Autogreffe dans les Maladies Auto Immunes Résistantes (ISAMAIR) Study Group
Published: May 2005

Objective

To analyze hematopoietic and immune reconstitution after autologous hematopoietic stem cell transplantation (HSCT) in 7 patients with systemic sclerosis (SSc).

Methods

Two groups of patients were retrospectively constituted according to whether they had a favorable clinical response (group A; n = 4) or no response or a relapse of disease (group B; n = 3) after HSCT. Immune reconstitution was analyzed every 3 months using lymphocyte immunophenotyping, α/β T cell receptor (TCR) diversity analysis, and ex vivo thymic function analysis by quantification of TCR rearrangement excision circles (TRECs).

Results

Patients had similar characteristics at study entry, except for a lower modified Rodnan skin thickness score (P = 0.03) and a lower Health Assessment Questionnaire score (P = 0.05) in group A than in group B. The number of reinjected cells and the time to hematopoietic reconstitution were similar in both groups. The absolute numbers of CD19+ and CD20+ B cells were lower in group A than in normal controls (P < 0.05) and within the normal range in group B. Absolute numbers of T and natural killer lymphocytes were normal before HSCT. Numbers of CD3+ cells remained low thereafter. Numbers of CD8+ cells were back to normal 3 months after HSCT in both groups. B cell counts were low until 6 months after HSCT in group A and stayed in the normal range in group B. The CD3+ defect was sustained in group A, with an opposite trend and a faster CD4+ reconstitution profile in group B. The T cell repertoire was skewed before and until 1 year after HSCT, with shared expansions before and after transplant in a given individual. TREC values correlated negatively with C‐reactive protein levels (rs = −0.41, P = 0.001) and positively with CD19+ (rs = 0.35, P = 0.001) and CD20+ (rs = 0.34, P = 0.002) lymphocyte counts.

Conclusion

B and T lymphocyte populations remained disturbed for at least 1 year after HSCT in SSc patients, which may reflect the persistence of an underlying disease mechanism.
Eigenvalue‐based model selection during latent semantic indexing
Authors: Efron Miles
Published: May 2005

In this study amended parallel analysis (APA), a novel method for model selection in unsupervised learning problems such as information retrieval (IR), is described. At issue is the selection ofk, the number of dimensions retained under latent semantic indexing (LSI). Amended parallel analysis is an elaboration of Horn's parallel analysis, which advocates retaining eigenvalues larger than those that we would expect under term independence. Amended parallel analysis operates by deriving confidence intervals on these “null” eigenvalues. The technique amounts to a series of nonparametric hypothesis tests on the correlation matrix eigenvalues. In the study, APA is tested along with four established dimensionality estimators on six standard IR test collections. These estimates are evaluated with regard to two IR performance metrics. Additionally, results from simulated data are reported. In both rounds of experimentation APA performs well, predicting the best values ofkon 3 of 12 observations, with good predictions on several others, and never offering the worst estimate of optimal dimensionality.
Secalonic acid D blocks embryonic palatal mesenchymal cell‐cycle by altering the activity of CDK2 and the expression of p21 and cyclin E
Authors: Dhulipala V.C. , Maddali K.K. , Welshons W.V. , Reddy C.S.
Published: May 2005

BACKGROUND: The mycotoxin, secalonic acid D (SAD), a known animal and potential human cleft palate (CP)‐inducing agent, is produced by Pencillium oxalicum in corn. SAD selectively inhibits proliferation of murine embryonic palatal mesenchymal (MEPM) cells leading to a reduction in cell numbers. These effects can explain the reduction in shelf size and the resulting CP seen in the offspring of SAD‐exposed mice. Ability of SAD to inhibit proliferation as well as to block the progression of cells from G1‐ to S‐phase of the cell‐cycle were also shown in the human embryonic palatal mesenchymal (HEPM) cells suggesting the potential CP‐inducing effect of SAD in human beings METHODS: Gestation day (GD) 12 mouse embryos and HEPM cells were used to test the hypothesis that the cell‐cycle block induced by SAD results from a disruption of stage‐specific regulatory components both in vivo and in vitro. The effects of SAD on the activity of various cyclin dependent kinases (CDK) and on the levels of various positive (cyclins and CDK) and negative (CDK inhibitors p15, 16, 18, 19, 21, 27, 57) cell‐cycle regulators were assessed by performing kinase assays and immunoblots, respectively. RESULTS: In the murine embryonic palates, SAD specifically inhibited G1/S‐phase‐specific CDK2 activity, reduced the level of cyclin E and tended to increase the level of the CIP/kip CDK inhibitor, p21. In the HEPM cell cultures, exposure to IC50 of SAD significantly affected all of the above targets. In addition, a reduction in the levels/activity of CDK 4/6, a reduction in the levels of cyclins D1, D2, D3, E, A, and all INK4 family proteins, and an increase in the level of the CIP/kip CDK inhibitor, p57, were also seen. CONCLUSIONS: These results suggest that the S‐phase‐specific cell‐cycle proteins CDK2, cyclin E and possibly p21 are the common targets of SAD in murine palatal shelves in vivo and in human embryonic palatal mesenchymal cells in vitro and may be relevant to the pathogenesis of SAD‐induced CP. Birth Defects Res B 2005. © 2005 Wiley‐Liss, Inc.
Control of protein functional dynamics by peptide linkers
Authors: Wriggers Willy , Chakravarty Sugoto , Jennings Patricia A.
Published: May 2005

Control of structural flexibility is essential for the proper functioning of a large number of proteins and multiprotein complexes. At the residue level, such flexibility occurs due to local relaxation of peptide bond angles whose cumulative effect may result in large changes in the secondary, tertiary or quaternary structures of protein molecules. Such flexibility, and its absence, most often depends on the nature of interdomain linkages formed by oligopeptides. Both flexible and relatively rigid peptide linkers are found in many multidomain proteins. Linkers are thought to control favorable and unfavorable interactions between adjacent domains by means of variable softness furnished by their primary sequence. Large‐scale structural heterogeneity of multidomain proteins and their complexes, facilitated by soft peptide linkers, is now seen as the norm rather than the exception. Biophysical discoveries as well as computational algorithms and databases have reshaped our understanding of the often spectacular biomolecular dynamics enabled by soft linkers. Absence of such motion, as in so‐called molecular rulers, also has desirable functional effects in protein architecture. We review here the historic discovery and current understanding of the nature of domains and their linkers from a structural, computational, and biophysical point of view. A number of emerging applications, based on the current understanding of the structural properties of peptides, are presented in the context of domain fusion of synthetic multifunctional chimeric proteins. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 80: 736–746, 2005

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Engineering mammalian cell factories for improved recombinant monoclonal antibody production: lessons from nature?
Authors: Dinnis Diane M. , James David C.
Published: May 2005

In this review we consider how cell specific recombinant monoclonal antibody (Mab) production by engineered mammalian cells can be improved. Whilst it is generally recognized that Mab production is limited post‐transcriptionally at folding and assembly reactions, genetic engineering strategies based on overexpression of individual chaperones or foldases in mammalian cells have not reliably increased cell specific Mab production. Given that recent studies have established that chaperones and foldases themselves exist in a large multiprotein complex, which may coordinate the sequential processing of Mabs, we propose that global expansion of all components of the secretory pathway will likely be necessary to generically improve recombinant Mab production by mammalian cells. In this context, what can be learnt from nature? Important recent studies have delineated some of the main cellular pathways involved in the differentiation of B‐cells into nature's own high level Mab producers, plasma cells. This is achieved by a dramatic re‐programming of cellular function where the coordinated expansion of metabolic and secretory machinery precedes Ig production, then is maintained by induction of a key intracellular signaling pathway, the unfolded protein response (UPR). Here we review genetic engineering strategies to increase cell specific production rate and discuss whether manipulation of intracellular signaling systems such as the UPR will provide a novel means to engineer mammalian cells for high level recombinant Mab production. © 2005 Wiley Periodicals, Inc.
The effect of whole cell immobilisation on the biotransformation of benzonitrile and the use of direct electric current for enhanced product removal
Authors: Mustacchi Roberta , Knowles Christopher J. , Li Hong , Dalrymple Ian , Sunderland Garry , Skibar Wolfgang , Jackman Simon A.
Published: May 2005

The nitrilase of Rhodococcus rhodochrous performs a one‐step biotransformation of nitriles to their corresponding carboxylic acids. Application of a direct electric current moves the charged carboxylic acid towards an anode, across an anion exchange membrane, into a separate compartment. Cells encapsulated within alginate beads (2.9 mm diameter) for protection against the current biotransformed benzonitrile to benzoic acid with a 26% reduction in the biotransformation rate, from 0.054 mmol/min/g dcw with free cells to 0.040 mmol/min/g dcw with immobilised cells. When the electric current was applied, the biotransformation rate increased to 0.047 mmol/min/g dcw and product recovery increased from 19% to 79%. © 2005 Wiley Periodicals, Inc.
Clinical outcomes after sirolimus‐eluting stent implantation for de novo saphenous vein graft lesions
Authors: Price Matthew J. , Sawhney Neil , Kao John A. , Madrid Antonio , Schatz Richard A. , Teirstein Paul S.
Published: May 2005

The purpose of this study was to evaluate the clinical outcome of patients undergoing sirolimus‐eluting stent implantation for de novo lesions within saphenous vein grafts (SVGs). Although the incidence of restenosis following sirolimus‐eluting stenting (SES) of native coronary arteries is low, the efficacy of SES to treat de novo lesions within SVGs has not been well studied. A total of 35 patients underwent SES implantation of 39 lesions during 36 procedures. All patients had a minimum follow‐up of 6 months following the index procedure. The mean bypass graft age was 10.1 ± 6.5 years (range, 0–23 years). In‐hospital major adverse cardiac events [death, myocardial infarction, thrombosis, or target vessel revascularization (TVR)] occurred in four patients (11%). Clinical follow‐up was obtained in 100% of patients (mean follow‐up, 7.5 ± 2.2 months). There was one cardiac death, presumed due to stent thrombosis. TVR occurred in only two patients (6%). Myocardial infarction (MI) occurred in four patients (11%), all attributable to a nontarget vessel. The combined endpoint of death, MI, or TVR occurred in seven patients (20%). Freedom from death, nonfatal MI, thrombosis, or any revascularization was 65%. Early experience indicates sirolimus‐eluting stents for de novo saphenous vein graft lesions have a low (6%) rate of clinically driven target vessel revascularization. By 7‐month follow‐up, event‐free survival is limited primarily by disease in nontarget vessels. © 2005 Wiley‐Liss, Inc.