bluuebunny/crossref_metadata_2025 huggingface dataset:
The growth hormone 1 GH1:c.457C>G mutation is associated with intramuscular and rump fat distribution in a large sample of Australian feedlot cattle
Authors: Barendse W. , Bunch R. J. , Harrison B. E. , Thomas M. B.
Published: March 2006

The GH1:c.457C>G exon 5 missense mutation in the bovine growth hormone 1 (GH1) gene that causes the replacement of leucine (L) with valine (V) was investigated in 1027 cattle with primarily Angus and Shorthorn breeding from Australian feedlots. The allele frequency of the GH1:c.457C allele was 0.77 in Angus and 0.76 in Shorthorn. The GH1:c.457C allele was associated with lower marbling (P = 0.0472), and the average effect of allele substitution was −0.22 of a phenotypic standard deviation. This allele was also associated with slightly higher rump fat (P = 0.0541) and the average effect of allele substitution was 0.11 SD. Marbling and rump fat were not strongly correlated (r = 0.097, P < 0.01) in this data set. This mutation had no significant effect on eye muscle area or hot dressed carcass weight (P > 0.1). Given these relationships, the differences between GH1 alleles could be the result of differential deposition of fat in fat depots.
Characterization of the porcineacyl‐CoA synthetase long‐chain 4gene and its association with growth and meat quality traits
Authors: Mercadé A. , Estellé J. , Pérez‐Enciso M. , Varona L. , Silió L. , Noguera J. L. , Sánchez A. , Folch J. M.
Published: March 2006

Long‐chain acyl‐CoA synthetase (ACSL) catalyses the formation of long‐chain acyl‐CoA from fatty acid, ATP and CoA, activating fatty acids for subsequent reactions. Long‐chain acyl‐CoA synthetase thus plays an essential role in both lipid biosynthesis and fatty acid degradation. TheACSL4gene was evaluated as a positional candidate gene for the quantitative trait loci (QTL) located betweenSW2456andSW1943on chromosome X. We have sequenced 4906 bp of the pigACSL4mRNA. Sequence analysis allowed us to identify 10 polymorphisms located in the 3′‐UTR region and to elucidate twoACSL4haplotypes. Furthermore, a QTL and an association study between polymorphisms of theACSL4gene and traits of interest were carried out in an Iberian × Landrace cross. We report QTL that have not been previously identified, and we describe an association of theACSL4polymorphisms with growth and percentage of oleic fatty acid. Finally, we have determined allelic frequencies in 140 pigs belonging to the Iberian, Landrace, Large White, Meishan, Pietrain, Duroc, Vietnamese, Peccary and Babirusa populations.
Prediction of drug clearance in children from adults: a comparison of several allometric methods
Authors: Mahmood Iftekhar
Published: March 2006

Aims In recent years with the advent of paediatric exclusivity and requirements to conduct clinical studies in children, the current emphasis is to find a safe and efficacious dose of a drug in children. It has been suggested that one can predict the clearance of a drug in children according to the equation: CL in the child = adult CL × (weight of the child/70)0.75. Considering the controversy surrounding the exponent of 0.75 for the prediction of clearance and lack of any systematic evaluation of the aforementioned proposal, the objectives of the study were as follows: (i) to determine if indeed the exponent 0.75 is the most suitable exponent for the prediction of clearance in children from adult data; (ii) to explore and search for other exponents that are more accurate or as good as 0.75; and (iii) to propose a new approach (if any) based on the findings of the current evaluation.

Methods Six methods were used to predict clearance of drugs in children from adult data. Besides evaluating the exponent of 0.75, exponents of 0.80, 0.85 and 1.0 were also evaluated. An empirical approach based on kidney and liver weights was also examined. Based on the results of five methods, a sixth method was introduced.

Results The results of the study indicate that no single method is suitable for all drugs or for all age groups. The exponents 0.75, 0.80, and 0.85 provided the same degree of accuracy or error in the prediction of clearance in children.

Conclusions Since no single method is suitable for all drugs or for all age groups. A combination of approaches is suggested which may help in improving the prediction of clearance in children from adult data.
Structural, immunological and functional properties of natural recombinant Pen a 1, the major allergen of Brown Shrimp, Penaeus aztecus
Authors: Reese G. , Schicktanz S. , Lauer I. , Randow S. , Lüttkopf D. , Vogel L. , Lehrer S. B. , Vieths S.
Published: March 2006

Background
Recombinant allergens are considered the basis for new diagnostic approaches and development of novel strategies of allergen‐specific immunotherapy. As Pen a 1 from brown shrimp Penaeus aztecus is the only major allergen of shrimp and binds up to 75% of all shrimp‐specific IgE antibodies this molecule may be an excellent model for the usage of allergens with reduced IgE antibody‐binding capacity for specific immunotherapy.

Aim
The aim was to clone, express and characterize a full‐length recombinant Pen a 1 molecule and compare it with natural Pen a 1 in regard to structural and immunological parameters such as IgE antibody capacity and ability to induce IgE‐mediated mediator release.

Methods
Total RNA was isolated from P. aztecus and a rapid amplification of cDNA ends (5′ RACE) was performed to obtain full‐length cDNA coding for Pen a 1. Using a gene‐specific primer, PCR was performed and full‐length cDNA was cloned and sequenced. Recombinant His‐tagged Pen a 1 was isolated from Escherichia coli under native conditions by immobilized metal affinity chromatography. Secondary structure of natural and recombinant Pen a 1 was compared by circular dichroism (CD) spectroscopy, and the IgE antibody‐binding capacity evaluated by RAST. The allergenic potency was tested by the capability of natural and recombinant Pen a 1 to induce mediator release in a murine and human in vitro model of IgE‐mediated type I allergy.

Results
The deduced amino‐acid sequence was 284 residues long and amino‐acid sequence identities with allergenic and non‐allergenic tropomyosins ranged from 80% to 99% and 51% to 58%, respectively. The analysis of the secondary structure of natural and recombinant Pen a 1 by CD spectroscopic analysis showed that both nPen a 1 and rPen a 1 had α‐helical conformation that is typical for tropomyosin. The IgE antibody binding capacities of nPen a 1 and r Pen a1 were found to be essentially identical by RAST. The mediator release experiments using both wild‐type and humanized rat basophilic leukaemia 30/25 cells showed that rPen a 1 and nPen a 1 induced a similar level of mast cell activation.

Conclusions
Recombinant Pen a 1 and natural Pen a 1 are structurally and immunologically identical and rPen a 1 may be used as the basis for component‐resolved diagnosis and the generation of modified shrimp tropomyosin for allergen‐specific immunotherapy. The results of the animal studies indicate that C3H/HeJ mice that were sensitized with shrimp extract in combination with cholera toxin as adjuvant may be a suitable model to study shrimp allergy.
The α4bβ7‐integrin is dynamically expressed on murine eosinophils and involved in eosinophil trafficking to the intestine
Authors: Brandt E. B. , Zimmermann N. , Muntel E. E. , Yamada Y. , Pope S. M. , Mishra A. , Hogan S. P. , Rothenberg M. E.
Published: March 2006

Background
Of the numerous adhesion molecules expressed by eosinophils, the α4‐integrin has been identified as critically involved in eosinophil trafficking in the lung. Most studies have focused on the role of the α4β1‐adhesion complex, but eosinophils also express the α4β7‐integrin complex.

Objective
To investigate the role of α4β7, by assessing its membrane expression on eosinophils from different compartments using allergen‐challenged mice and IL‐4/IL‐5 bi‐transgenic mice. In addition, we aim to determine the impact of β7‐integrin deficiency on eosinophil recruitment to the lungs and intestine in specific experimental allergic models.

Results
Evaluation of α4β7 expression on bronchoalveolar lavage fluid (BALF) and lung tissue eosinophils revealed a down‐regulation of this integrin as eosinophils migrate through the lungs. Indeed eosinophils isolated from the BALF and lung of allergic mice had low expression of the α4β7‐complex. While expression of the α4‐chain remained unchanged, a significant decrease in β7‐surface expression was observed. Intestinal eosinophils, isolated from Peyer's patches, also displayed a down‐regulation of the α4β7‐integrin, albeit only modest. In contrast, circulating eosinophils, isolated from the blood and spleen, expressed high levels of the α4β7‐integrin. However, eosinophil trafficking into the lungs of β7‐integrin‐deficient mice was not significantly impaired in response to respiratory allergen challenges. In contrast, β7‐deficient mice had impaired eosinophil recruitment to the intestine.

Conclusion
Taken together, these results identify differential expression of the α4β7‐integrin on eosinophils and its critical role in regulating eosinophil responses in the intestine.
Genetic polymorphisms of major house dust mite allergens
Authors: Piboonpocanun S. , Malainual N. , Jirapongsananuruk O. , Vichyanond P. , Thomas W. R.
Published: March 2006

Background
Polymorphic sequence substitutions in the major mite allergens can markedly affect immunoglobulin E binding and T cell responses, but there are few studies on environmental isolates from Dermatophagoides pteronyssinus and none for D. farinae.

Objective
To determine the sequence variation of the group 1 and 2 allergens from environmental D. pteronyssinus and D. farinae.

Methods
RNA from each species was isolated from homes in Bangkok and the sequence of Der p 1, Der p 2, Der f 1, and Der f 2 determined from cDNA produced by high fidelity polymerase chain reactions.

Results
The enlarged data set revealed preferred amino acid substitutions in residues 19, 81, and 215 of Der p 1 as well as sporadic changes. Der p 2 showed frequent variations with clusters of amino acid substitutions, but the canonical Der p 2.0101 was not found in any of 17 sequences. Der f 2 showed variants with clusters of substitutions similar to Der p 2 but in different amino acid positions and without any structural concordance. Der f 1 in contrast to the other allergens had few amino acid sequence substitutions.

Conclusions
The sequence information on variants provides data important for the optimal design of allergen formulations and useful for the genetic engineering and structure–function analyses of the major allergens.
Induction of interleukin‐10 and suppressor of cytokine signalling‐3 gene expression following peptide immunotherapy
Authors: Tarzi M. , Klunker S. , Texier C. , Verhoef A. , Stapel S. O. , Akdis C. A. , Maillere B. , Kay A. B. , Larché M.
Published: March 2006

Background
Allergen‐derived (T cell epitope) peptides may be safer for immunotherapy than native allergen, as they do not cross‐link immunoglobulin (Ig)E. However, HLA polymorphism results in multiple potential epitopes. Synthetic peptides of phospholipase (PL) A2 were selected for a peptide vaccine, on the basis of binding affinity for commonly expressed HLA‐DR molecules.

Objective
To evaluate treatment with an HLA‐DR‐based PLA2 peptide vaccine in subjects with mild honeybee allergy in an open, controlled study.

Methods
Twelve volunteers with allergy to bee venom received nine intradermal injections of PLA2 peptides, with six untreated subjects serving as controls. Outcome was assessed by the size of the late‐phase cutaneous reaction to allergen, peripheral blood mononuclear cell (PBMC) proliferation, cytokine release, and expression of genes associated with immune regulation.

Results
Subjects receiving peptides showed a decrease in the magnitude of the late‐phase cutaneous reaction to bee venom compared with controls (P=0.03). The proliferation of venom‐stimulated PBMCs decreased in treated subjects compared with controls (P=0.01). Peptide treatment reduced the production of IL‐13 by PLA2‐stimulated PBMCs (P<0.01) and IFN‐γ (P<0.01), and increased the production of IL‐10 (P=0.02). Transcription of the suppressor of cytokine signalling (Socs)3 gene was significantly increased following therapy. A transient, but modest, increase in allergen‐specific IgG was also observed.

Conclusion
HLA‐DR‐based T cell epitopes modify surrogate markers associated with successful immunotherapy and induction of immune regulation, supporting the concept that this form of treatment may be efficacious in human allergic disease.
Inhibitory effects of fluvastatin on cytokine and chemokine production by peripheral blood mononuclear cells in patients with allergic asthma
Authors: Samson K. T. R. , Minoguchi K. , Tanaka A. , Oda N. , Yokoe T. , Yamamoto Y. , Yamamoto M. , Ohta S. , Adachi M.
Published: March 2006

Background
Statins have anti‐inflammatory effects on immune cells.

Objective
To investigate the immunomodulatory effects of fluvastatin on peripheral blood mononuclear cells (PBMCs) after allergen‐specific and non‐allergen‐specific stimulation in patients with asthma and in healthy subjects.

Methods
PBMCs from seven patients with asthma who showed elevated immunoglobulin (Ig)E to house dust mite were isolated and stimulated with Dermatofagoides farinae, purified protein derivative, and phytohaemagglutinin (PHA) in the presence or absence of fluvastatin. PBMCs from seven healthy subjects were stimulated with PHA. The effects of fluvastatin on cell proliferation and production of cytokines (interferon [IFN]‐γ and interleukin [IL]‐5) and chemokines (chemokine CXC motif, ligand [CXCL10], and CC chemokine ligand [CCL17]) were measured. Migration of T helper (Th)1 and Th2 cell lines was also investigated. The expression of CXCR3 and CCR4 was analysed with flow cytometry. Steroid‐insensitive PBMCs induced by preculture with IL‐2 and IL‐4 were also evaluated. Some experiments were performed in the presence of mevalonic acid.

Results
Fluvastatin inhibited the proliferation of PBMCs and decreased the production of IL‐5, IFN‐γ, CCL17, and CXCL10 after allergen‐specific and non‐allergen‐specific stimulation; all these effects, except for decreased CXCL10 production, were partially reversed by mevalonic acid. Culture supernatants obtained in the presence of fluvastatin prevented the migration of Th1 and Th2 cell lines in a dose‐dependent manner. In addition, CCR4 and CXCR3 expression on CD4+ T cells was not affected by the presence of fluvastatin. Fluvastatin inhibited the proliferative response of steroid‐insensitive PBMCs to phytohaemagglutinin.

Conclusion
Fluvastatin has inhibitory effects on cytokine and chemokine production, and thus might be used as a potential therapeutic agent in severe asthma.
Do parents with an atopic family history adopt a ‘prudent’ lifestyle for their infant? (KOALA Study)
Authors: Kummeling I. , Thijs C. , Stelma F. , Huber M. , van den Brandt P. A. , Dagnelie P. C
Published: March 2006

Background
Atopic parents may adopt lifestyle characteristics that allegedly protect against atopic disease. If this is true, infants from atopic parents will be characterized by low‐risk behaviour. Consequently, aetiologic studies on lifestyle factors and allergic disease in childhood may be biased by confounding by indication.

Objective
We explored whether the prevalence of ‘prudent’ lifestyle characteristics differs between atopic and non‐atopic families.

Methods
Information about a family history of atopic manifestations and lifestyle characteristics was collected by repeated questionnaires in the Dutch KOALA Birth Cohort Study in 2469 infants from families with divergent lifestyle practices (conventional vs. alternative).

Results
In conventional lifestyle families, infants were less often exposed to environmental tobacco smoke when parents were atopic than when they were non‐atopic (10.0% vs. 14.7%, P=0.001). In alternative lifestyle families, exposure to smoking was very rare in both groups (1.7% vs. 2.6%). Pets were less often present in families with than without parental atopy (38.8% vs. 51.1%, P=0.008 for conventional lifestyle families; 43.0% vs. 48.4%, P=0.014 for alternative lifestyle families). Infants with atopic siblings had less often been vaccinated according to the standard scheme than infants with non‐atopic siblings in conventional lifestyle families (76.6% vs. 85.5%, P<0.001). In alternative lifestyle families, the difference was in the same direction but not statistically significant (30.1% vs. 40.5%, P=0.143). Antibiotic use, breastfeeding and consumption of organic foods were unrelated to a family history of atopic manifestations.

Conclusion
Some ‘prudent’ lifestyle characteristics differed between atopic and non‐atopic families, depending on whether atopic manifestations were present in parents or older siblings. This has important consequences for the validity in epidemiological studies on the aetiology of allergy in children. Confounding by indication because of a family history of atopic manifestations can best be controlled for by considering atopy in parents and siblings as separate confounders.
The analysis and quantification of a clonal B cell response in a hyperimmunized anti-D donor
Authors: Dohmen S E , Verhagen O J H M , De Groot S M , Stott L M , Aalberse R C , Urbaniak S J , Van Der Schoot C E
Published: March 2006

Healthy volunteers are hyperimmunized with RhD-positive red cells in order to obtain plasma containing high titres of anti-D immunoglobulin, which is used for the prevention of haemolytic disease of the fetus and newborn. We analysed the anti-D immune response in a donor who had been hyperimmunized for 7 years and who showed declining anti-D titres despite re-immunization. A phage display library representing the complete immunorepertoire and a second library representing the IGHV3 superspecies family genes (IGHV3s) repertoire in the donor were constructed and analysed. A clonal Ig-gene rearrangement was quantified in the peripheral blood by limiting dilution polymerase chain reaction (PCR) All RhD-binding phages from both libraries, except one, had heavy chains with IGH–VDJ rearrangements of the same clonal origin, but with different patterns of somatic mutations and joined with different light chains. Limiting dilution PCR performed on mRNA and genomic DNA showed a frequency of 1 clonal B cell in 2000 IgG1/3-positive B cells. We show the presence of clonally related RhD-specific B cells in a hyperimmunized anti-D donor who had declining anti-D titres and who was unresponsive to re-immunization. Furthermore, we found a high frequency of clonal B cells. These results contribute to the understanding of the immune response against RhD in hyperimmunized anti-D donors.
Skewing of X‐chromosome inactivation in three generations of carriers with X‐linked chronic granulomatous disease within one family
Authors: Köker M. Y. , Sanal Ö. , De Boer M. , Tezcan I. , Metin A. , Tan Ç. , Ersoy F. , Roos D.
Published: March 2006

Background  Chronic granulomatous disease (CGD) is an inherited disorder of the innate immune system characterized by impairment of intracellular microbicidal activity of phagocytes. Mutations in one of the four known NADPH‐oxidase components preclude generation of superoxide and related antimicrobial oxidants, leading to the phenotype of CGD. Defects in gp91‐phox, encoded by CYBB, lead to X‐linked CGD, responsible for approximately 70% of all CGD cases. The aim of the study was to evaluate the hypothesis that age‐related skewing of X‐chromosome inactivation, as described in several CGD families, is caused by preferential survival of bone marrow clones with an inactive NADPH oxidase.

Materials and methods  We studied the neutrophils from three patients and four carriers in three generations of a Turkish family with X‐linked CGD. Carrier detection was carried out by the dihydrorhodamine (DHR)‐1,2,3 assay, which measures on a per‐cell basis the NADPH oxidase‐dependent oxidation of DHR by phagocytes. The X‐chromosome inactivation pattern was determined with the HUMARA assay in DNA from leucocytes as well as in DNA from a buccal smear of the four carriers.

Results  The three patients were identified by a negative DHR test, and the mutation in their CYBB gene was characterized by DNA sequencing. Moreover, we found an age‐related degree of skewing of X‐chromosome inactivation in the leucocytes of the four X‐CGD carriers, both at the protein level (NADPH oxidase activity) and at the DNA level (HUMARA assay). However, similar skewing of X‐chromosome inactivation was found in the buccal DNA from these women.

Conclusions  These novel findings indicate that the age‐related degree of skewing was probably a chance finding, not related to preferential survival of NADPH oxidase‐deficient precursor cells, because this enzyme is not expressed in (buccal) epithelial cells.
Markers of eosinophilic inflammation and risk prediction in patients with coronary artery disease
Authors: Falcone C. , Minoretti P. , D’Angelo A. , Buzzi M. P. , Coen E. , Emanuele E. , Aldeghi A. , Olivieri V. , Geroldi D.
Published: March 2006

Background  The eotaxin family comprises three distinct peptides (eotaxin, eotaxin‐2 and eotaxin‐3) which have been implicated in eosinophilic inflammation. In vitro and clinical studies suggest that eotaxins could play a role in vascular inflammation, but no data are available on their prognostic significance in patients with angiographically documented coronary artery disease (CAD).

Materials and methods  Baseline plasma samples were obtained from 1014 patients with documented CAD. We tested the predictive effect of markers of eosinophilic inflammation and C‐reactive protein (CRP) on death from cardiovascular causes and nonfatal myocardial infarction over a 2·7–4·1‐year follow‐up period.

Results  Unexpectedly, lower eotaxin‐3 concentrations were observed in patients with adverse cardiovascular events, whereas both eotaxin and eotaxin‐2 showed no association with risk. After adjustment for most potential confounders, patients in the upper‐quartile of eotaxin‐3 levels had a 0·42 hazard‐ratio (95% CI, 0·29–0·61, P < 0·001) for adverse events compared with subjects in the lower‐quartile. The highest risk of future cardiovascular events was observed in subjects with combined elevation of CRP and reduction of eotaxin‐3; 4·4 hazard‐ratio (95% CI, 2·1–9·5, P < 0·001). Importantly, receiver‐operating‐characteristic curves analysis suggested a superior prognostic value of eotaxin‐3 compared with CRP for predicting cardiac events in patients with CAD.

Conclusions  Low levels of eotaxin‐3 are an independent predictor of future adverse cardiovascular events in patients with CAD and may be useful for risk stratification.
T‐lymphocyte subset distribution in human spleen
Authors: Langeveld M. , Gamadia L. E. , Ten Berge I. J. M.
Published: March 2006

Background  When analyzing human cellular immune responses, most focus is placed on the peripheral blood (PB) and, to a lesser extent, the lymph nodes. To date the spleen has not been analyzed with regard to its role in adaptive cellular immunity and more notably not with respect to T‐cell immune responses.

Materials and methods  We analyzed the splenic lymphocyte compartment in comparison with the PB lymphocyte compartment regarding the number of NK cells, B cells, CD4+, CD8+ T cells and CMV‐specific CD8+ T cells. Furthermore, we analyzed the distribution of naive, memory and effector subsets of CD4+ and CD8+ T cells in these compartments.

Results  The spleen contains proportionally more B cells and less CD4+ and CD8+ T cells than PB. The percentage of CD8+ T cells is greater in the spleen, leading to an inverse CD4/CD8 ratio. Both splenic CD4+ and CD8+ T‐cell populations show a greater number of activated cells, and splenic CD8+ T cells show a more differentiated cytotoxic CD27−CD45RA+ memory phenotype.

Conclusions  Our findings show that the distribution of the different lymphocyte subsets is markedly different between the spleen and the PB, thus inferring an important and distinct role for the spleen in CD4+ and CD8+ T‐cell activation.
Land‐use history and fire effects on soil fertility in eastern Spain
Authors: Duguy B. , Rovira P. , Vallejo R.
Published: March 2006

Changes in land use and fire directly affect the physico‐chemical properties of the soil. In an eastern Spanish area, we analysed the effects of land‐use history and fire frequency prior to fire on soil fertility 9 years after fire. The results showed that long‐term cultivation caused decreases in soil organic matter, total nitrogen (N) and C/N. Between 20 and 40 years after cropping ceased, soil organic carbon (C) and total N had generally not recovered values similar to those found in soils that were never cropped. Total phosphorus and available phosphorus contents were larger in the latest abandoned plots than in the earliest abandoned plots and the uncropped ones, which was interpreted as a result of fertilization. Increasing fire frequency from one to two fires generally caused a decrease in soil organic C, total N, C/N, total phosphorus and available phosphorus. We observed that the losses of organic C in the soil caused by fire were larger among the uncropped plots and hypothesized that fuel loads and thus fire intensities were larger in these ecosystems. Our results also suggested that both long‐term cultivation and fire would tend to separate C and P cycles.
Aggregate‐occluded black carbon in soil
Authors: Brodowski S. , John B. , Flessa H. , Amelung W.
Published: March 2006

The great stability of black carbon (BC) in soils may not be solely attributable to its refractory structure but also to poor accessibility when physically enveloped by soil particles. Our aim was to elucidate the intensity of physical entrapment of BC within soil aggregates. For this purpose, the A horizon of a forest, and of a grassland soil, and of three soils under tillage, were sampled at the experimental station Rotthalmünster, Germany. Black carbon was assessed in water‐stable aggregates and aggregate‐density fractions using benzene polycarboxylic acids as specific markers. The greatest BC concentrations made up 7.2% of organic carbon and were found in the < 53 μm fraction. The smallest BC concentrations occurred in the large macroaggregate fractions (> 2 mm). This pattern has been sustained even after tillage. The C‐normalized BC concentrations were significantly greater (P < 0.05) in the occluded particulate organic matter (OPOM) fractions than in the free particulate organic matter (FPOM) and the mineral fractions. This enrichment of BC compared with organic carbon in the OPOM fractions amounted to factors of 1.5–2.7. Hence, BC was embedded within microaggregates in preference to other organic carbon compounds. Only 2.5–3.5% of BC was located in the OPOM fraction < 1.6 g cm−3, but 22–24% in the OPOM fraction with a density of 1.6–2.0 g cm−3. This suggests that BC possibly acted as a binding agent or was selectively enriched during decomposition of protected SOM, or both. Physical inclusion, particularly within microaggregates, could therefore contribute to the long mean‐residence times of soil‐inherent BC.
The use of periphytic diatoms as a means of assessing impacts of point source inorganic nutrient pollution in south‐eastern Australia
Authors: DELA‐CRUZ JOCELYN , PRITCHARD TIM , GORDON GEOFFREY , AJANI PENELOPE
Published: March 2006

1. Periphytic diatoms are used as indicators of water quality because their ecological tolerances or preferences to environmental variables are thought to be predictable. However, much of the present autecological information for periphytic diatoms has been derived from studies conducted in the northern hemisphere. In this present study we used periphytic diatoms to determine the impacts of inorganic nutrient pollution in a tidal river system in the temperate latitudes of south‐east Australia. In so doing, we assess the suitability of the use of the ‘northern hemisphere’ ecological tolerance/preference data for periphytic diatoms.

2. Artificial substrates were used to collect periphytic diatoms at 35 sites, which were positioned along the riverbanks and the middle of the river at various distances upstream and downstream of the sewage outfall. The sampling design took into account tidal excursions and the observed sewage plume dynamics. Periphytic diatoms were collected during the austral winter month of August and the austral spring months of September and October. We deployed the artificial substrates for 4 weeks to allow the periphytic diatoms to recruit and colonise, before identifying and enumerating the assemblages.

3. Data analysis included two approaches: multivariate visualisations of combinations of environmental and biological data to investigate shifts in species structure of the periphytic diatom assemblage and multimetric indices based on ecological tolerance/preference data.

4. We found that the spatial patterns inferred from multivariate and multimetric analyses were consistent. Temporal variation in the composition of the periphytic diatom assemblage was greater than the spatial variation along horizontal sections of the river (in any one deployment) due mainly to shifts between winter and spring species.

5. Outfall effects were most apparent in winter, possibly because subsequent deployments were swamped by growth of spring periphytic diatoms. The outfall effects included a shift towards pollutant tolerant species and a reduction in the variability of the periphytic diatom assemblage across the river.

6. We conclude that the use of periphytic diatoms and associated ecological tolerance/preference data as a means of assessing impacts of point source inorganic nutrient pollution is effective. An understanding of river and sewage flow patterns is essential to the design of appropriate monitoring programmes and to the interpretation of results, especially as periphytic diatoms are sensitive to many environmental variables.
Structural insight of human DEAD‐box protein rck/p54 into its substrate recognition with conformational changes
Authors: Matsui Tsutomu , Hogetsu Keita , Usukura Jiro , Sato Takao , Kumasaka Takashi , Akao Yukihiro , Tanaka Nobuo
Published: March 2006

Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B‐cell lymphoma, is a member of the DEAD‐box RNA helicase family. Here, the crystal structure of Nc‐rck/p54, the N‐terminal core domain of rck/p54, revealed that the P‐loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P‐loop. The results of dynamic light scattering revealed to ATP‐induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N‐terminal core and C‐terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c‐myc IRES RNA, whose secondary structure regulates IRES‐dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over‐expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down‐regulation of c‐myc expression. These findings altogether suggest that rck/p54 may affect the IRES‐dependent translation of c‐myc even in the cells.
Combining meteorology, eddy fluxes, isotope measurements, and modeling to understand environmental controls of carbon isotope discrimination at the canopy scale
Authors: ARANIBAR J. N. , BERRY J. A. , RILEY W. J. , PATAKI D. E. , LAW B. E. , EHLERINGER J. R.
Published: March 2006

Estimates of terrestrial carbon isotope discrimination are useful to quantify the terrestrial carbon sink. Carbon isotope discrimination by terrestrial ecosystems may vary on seasonal and interannual time frames, because it is affected by processes (e.g. photosynthesis, stomatal conductance, and respiration) that respond to variable environmental conditions (e.g. air humidity, temperature, light). In this study, we report simulations of the temporal variability of canopy‐scale C3 photosynthetic carbon isotope discrimination obtained with an ecophysiologically based model (ISOLSM) designed for inclusion in global models. ISOLSM was driven by half‐hourly meteorology, and parameterized with eddy covariance measurements of carbon and energy fluxes and foliar carbon isotope ratios from a pine forest in Metolius (OR). Comparing simulated carbon and energy fluxes with observations provided a range of parameter values that optimized the simulated fluxes. We found that the sensitivity of photosynthetic carbon isotope discrimination to the slope of the stomatal conductance equation (m, Ball–Berry constant) provided an additional constraint to the model, reducing the wide parameter space obtained from the fluxes alone. We selected values of m that resulted in similar simulated long‐term discrimination as foliar isotope ratios measured at the site. The model was tested with 13C measurements of ecosystem (δR) and foliar (δf) respiration. The daily variability of simulated 13C values of assimilated carbon (δA) was similar to that of observed δf, and higher than that of observed and simulated δR. We also found similar relationships between environmental factors (i.e. vapor pressure deficit) and simulated δR as measured in ecosystem surveys of δR. Therefore, ISOLSM reasonably simulated the short‐term variability of δA controlled by atmospheric conditions at the canopy scale, which can be useful to estimate the variability of terrestrial isotope discrimination. Our study also shows that including the capacity to simulate carbon isotope discrimination, together with simple ecosystem isotope measurements, can provide a useful constraint to land surface and carbon balance models.
Iron limits primary productivity during spring bloom development in the central North Atlantic
Authors: MOORE C. MARK , MILLS MATTHEW M. , MILNE ANGELA , LANGLOIS REBECCA , ACHTERBERG ERIC P. , LOCHTE KARIN , GEIDER RICHARD J. , LA ROCHE JULIE
Published: March 2006

We present in situ biophysical measurements and bioassay experiments that demonstrate iron limitation of primary productivity during the spring bloom in the central North Atlantic. Mass balance calculations indicate that nitrate drawdown is iron (Fe)‐limited and that aeolian Fe supply to this region cannot support maximal phytoplankton growth during the bloom. Using a simple simulation model, we show that relief of Fe limitation during the spring bloom can increase nitrate drawdown and, hence, new primary production, by 70%. We conclude that the episodic nature of iron supplied by dust deposition is an important factor controlling the dynamics of the spring bloom. From this, we hypothesize that variability in the timing and magnitude of the spring bloom in response to aeolian Fe supply will affect carbon drawdown and food web dynamics in the central North Atlantic.
Estimating the uncertainty in annual net ecosystem carbon exchange: spatial variation in turbulent fluxes and sampling errors in eddy‐covariance measurements
Authors: OREN RAM , HSIEH CHENG‐I , STOY PAUL , ALBERTSON JOHN , MCCARTHY HEATHER R , HARRELL PETER , KATUL GABRIEL G
Published: March 2006

Above forest canopies, eddy covariance (EC) measurements of mass (CO2, H2O vapor) and energy exchange, assumed to represent ecosystem fluxes, are commonly made at one point in the roughness sublayer (RSL). A spatial variability experiment, in which EC measurements were made from six towers within the RSL in a uniform pine plantation, quantified large and dynamic spatial variation in fluxes. The spatial coefficient of variation (CV) of the scalar fluxes decreased with increasing integration time, stabilizing at a minimum that was independent of further lengthening the averaging period (hereafter a ‘stable minimum’). For all three fluxes, the stable minimum (CV=9–11%) was reached at averaging times (τp) of 6–7 h during daytime, but higher stable minima (CV=46–158%) were reached at longer τp (>12 h) during nighttime. To the extent that decreasing CV of EC fluxes reflects reduction in micrometeorological sampling errors, half of the observed variability at τp=30 min is attributed to sampling errors. The remaining half (indicated by the stable minimum CV) is attributed to underlying variability in ecosystem structural properties, as determined by leaf area index, and perhaps associated ecosystem activity attributes. We further assessed the spatial variability estimates in the context of uncertainty in annual net ecosystem exchange (NEE). First, we adjusted annual NEE values obtained at our long‐term observation tower to account for the difference between this tower and the mean of all towers from this experiment; this increased NEE by up to 55 g C m−2 yr−1. Second, we combined uncertainty from gap filling and instrument error with uncertainty because of spatial variability, producing an estimate of variability in annual NEE ranging from 79 to 127 g C m−2 yr−1. This analysis demonstrated that even in such a uniform pine plantation, in some years spatial variability can contribute ∼50% of the uncertainty in annual NEE estimates.
Impacts of climate change on natural forest productivity – evidence since the middle of the 20th century
Authors: BOISVENUE CÉLINE , RUNNING STEVEN W.
Published: March 2006

Changes to forest production drivers (light, water, temperature, and site nutrient) over the last 55 years have been documented in peer‐reviewed literature. The main objective of this paper is to review documented evidence of the impacts of climate change trends on forest productivity since the middle of the 20th century. We first present a concise overview of the climate controls of forest production, provide evidence of how the main controls have changed in the last 55 years, followed by a core section outlining our findings of observed and documented impacts on forest productivity and a brief discussion of the complications of interpreting trends in net primary production (NPP). At finer spatial scales, a trend is difficult to decipher, but globally, based on both satellite and ground‐based data, climatic changes seemed to have a generally positive impact on forest productivity when water was not limiting. Of the 49 papers reporting forest production levels we reviewed, 37 showed a positive growth trend, five a negative trend, three reported both a positive and a negative trend for different time periods, one reported a positive and no trend for different geographic areas, and two reported no trend. Forests occupy ≈52% of the Earth's land surface and tend to occupy more temperature and radiation‐limited environments. Less than 7% of forests are in strongly water‐limited systems. The combined and interacting effects of temperature, radiation, and precipitation changes with the positive effect of CO2, the negative effects of O3 and other pollutants, and the presently positive effects of N will not be elucidated with experimental manipulation of one or a few factors at a time. Assessments of the greening of the biosphere depend on both accurate measurements of rates (net ecosystem exchange, NPP), how much is stored at the ecosystem level (net ecosystem production) and quantification of disturbances rates on final net biome production.
Climatic signals in growth and its relation to ENSO events of two Prosopis species following a latitudinal gradient in South America
Authors: LÓPEZ BERNAT C. , RODRÍGUEZ RODOLFO , GRACIA CARLOS A. , SABATÉ SANTIAGO
Published: March 2006

Semiarid environments throughout the world have lost a major part of their woody vegetation and biodiversity due to the effects of wood cutting, cattle grazing and subsistence agriculture. The resulting state is typically used for cattle production, but the productivity of these systems is often very low, and erosion of the unprotected soil is a common problem. Such dry‐land degradation is of great international concern, not only because the resulting state is hardly productive but also because it paves the way to desertification. The natural distribution of the genus Prosopis includes arid and semiarid zones of the Americas, Africa and Asia, but the majority of the Prosopis species are, however, native to the Americas. In order to assess a likely gradient in the response of tree species to precipitation, temperature and their connection to El Niño southern oscillation (ENSO) events, two Prosopis species were chosen along a latitudinal gradient in Latin America, from northern Peru to central Chile: Prosopis pallida from a semi‐arid land in northern and southern Peru and P. chilensis from a semiarid land in central Chile. Growth rings of each species were crossdated at each sampling site using classical dendrochronological techniques. Chronologies were related with instrumental climatic records in each site, as well as with SOI and N34 series. Cross‐correlation, spectral and wavelet analysis techniques were used to assess the relation of growth with precipitation and temperature. Despite the long distance among sites, the two Prosopis species presented similar responses. Thus, the two species' growth is positively correlated to precipitation, while with temperature it is not. In northern Peru, precipitation and growth of P. pallida present a similar cyclic pattern, with a period of around 3 years. On the other hand, P. pallida in southern Peru, and P. chilensis also present this cyclic pattern, but also another one with lower frequency, coinciding with the pattern of precipitation. Both cycles are within the range of the ENSO band.
A UK‐based investigation of inter‐ and intra‐observer reproducibility of Gleason grading of prostatic biopsies
Authors: Melia J , Moseley R , Ball R Y , Griffiths D F R , Grigor K , Harnden P , Jarmulowicz M , McWilliam L J , Montironi R , Waller M , Moss S , Parkinson M C
Published: March 2006

Aims:  The frequency of prostatic core biopsies to detect cancer has been increasing with more widespread prostate specific antigen (PSA) testing. Gleason score has important implications for patient management but morphological reproducibility data for British practice are limited. Using literature‐based criteria nine uropathologists took part in a reproducibility study.

Methods:  Each of the nine participants submitted slides from consecutive cases of biopsy‐diagnosed cancer assigned to the Gleason score groups 2–4, 5–6, 7 and 8–10 in the original report. A random selection of slides was taken within each group and examined by all pathologists, who were blind to the original score. Over six circulations, new slides were mixed with previously read slides, resulting in a total of 47 of 81 slides being read more than once.

Results:  For the first readings of the 81 slides, the agreement with the consensus score was 78% and overall interobserver agreement was κ 0.54 for Gleason score groups 2–4, 5–6, 7, 8–10. Kappa values for each category were 0.33, 0.56, 0.44 and 0.68, respectively. For the 47 slides read more than once, intra‐observer agreement was 77%, κ 0.66. The study identified problems in core biopsy interpretation of Gleason score at levels 2–4 and 7. Patterns illustrated by Gleason as 2 tended to be categorized as 3 because of the variable acinar size and unassessable lesional margin. In slides with consensus Gleason score 7, 13% of readings were scored 6 and in slides with consensus 6, 18% of readings were scored 7.

Conclusions:  Recommendations include the need to increase objectivity of the Gleason criteria but limits of descriptive morphology may have to be accepted.
Interstitial fibrosis in the heart: differences in extracellular matrix proteins and matrix metalloproteinases in end‐stage dilated, ischaemic and valvular cardiomyopathy
Authors: Herpel E , Pritsch M , Koch A , Dengler T J , Schirmacher P , Schnabel Ph A
Published: March 2006

Aims:  To investigate whether or not there are differences in the distribution of extracellular matrix (ECM) proteins and matrix metalloproteinases (MMPs) in end‐stage heart failure underlying different cardiomyopathies.

Methods and results:  Thirty‐nine explanted human hearts were investigated: 15 with dilated cardiomyopathy (DCM), 17 with ischaemic cardiomyopathy (ICM) and seven with valvular cardiomyopathy (VCM). Transmural samples from four different sites were investigated. Frozen sections were processed for immunohistochemistry for collagens type I, III, IV, laminin and fibronectin, as well as MMP‐1, ‐2 and ‐9. Volume densities were determined. All ECM components were expressed more frequently in DCM than in ICM. Comparing ICM with VCM, all proteins were found more frequently in VCM than in ICM except for type III collagen, which was significantly more frequent in ICM. Comparing DCM and VCM, VCM showed significantly higher volume densities for type III collagen and laminin. MMPs showed only slight variations between the cardiomyopathies.

Conclusion:  The distribution of ECM proteins differs between DCM, ICM and VCM, which suggests that they can be morphologically discriminated by interstitial fibrosis, especially by their expression of matrix proteins.
Expression of ETV6‐NTRK in classical, cellular and mixed subtypes of congenital mesoblastic nephroma
Authors: Anderson J , Gibson S , Sebire N J
Published: March 2006

Aim:  Congenital mesoblastic nephroma (CMN) is the commonest renal tumour of infancy, with classical, cellular and mixed histological subtypes described. A specific ETV6‐NTRK3 fusion‐gene product is reported in association with the cellular variant. The aim was to investigate the relationship between the presence of this product and morphological phenotype using paraffin‐embedded archival material.

Methods and results:  Cases of CMN from a single centre during a 15‐year period (1989–1994) were identified, anonymized and blindly classified using morphological criteria. RNA was extracted from frozen and paraffin sections for both conventional reverse transcriptase‐polymerase chain reaction (RT‐PCR) and quantitative real‐time RT‐PCR. Fifteen samples were analysed; two were non‐informative and three expressed ETV6‐NTRK3 using both techniques, two showing similar expression, whilst one showed expression two orders of magnitude lower, from a cellular tumour. All fusion positive cases were previously classified as cellular subtype. Six patients had mixed‐subtype tumours in which the cellular components, morphologically indistinguishable from cellular tumours, were fusion negative, as were all classical cases.

Conclusions:  Real‐time PCR Taqman assays, using both fixed and frozen tissue, provide highly reproducible detection and quantification of fusion transcript expression. Differences in expression levels may explain previous conflicting data on fusion gene detection in these tumours.