bluuebunny/crossref_metadata_2025_split huggingface dataset:
Powdery Mildew Resistance Conferred by Loss of the ENHANCED DISEASE RESISTANCE1 Protein Kinase Is Suppressed by a Missense Mutation in KEEP ON GOING, a Regulator of Abscisic Acid Signaling
Authors: Wawrzynska Anna , Christiansen Katy M. , Lan Yinan , Rodibaugh Natalie L. , Innes Roger W. 
Published: September 2008

Abstract
Loss-of-function mutations in the Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE1 (EDR1) gene confer enhanced resistance to infection by powdery mildew (Golovinomyces cichoracearum). EDR1 encodes a protein kinase, but its substrates and the pathways regulated by EDR1 are unknown. To identify components of the EDR1 signal transduction pathway(s), we conducted a forward genetic screen for mutations that suppressed edr1-mediated disease resistance. Genetic mapping and cloning of one of these suppressor mutations revealed a recessive missense mutation in the KEEP ON GOING gene (KEG; At5g13530), which we designated keg-4. KEG encodes a multidomain protein that includes a RING E3 ligase domain, a kinase domain, ankyrin repeats, and HERC2-like repeats. The KEG protein has previously been shown to have ubiquitin ligase activity and to negatively regulate protein levels of the transcription factor ABCISIC ACID INSENSITIVE5. KEG mRNA levels were found to be 3-fold higher in edr1 mutant plants compared to wild type. Loss-of-function mutations in KEG are seedling lethal and are hypersensitive to glucose and abscisic acid (ABA). The keg-4 mutation, in contrast, conferred resistance to 6% glucose and suppressed edr1-mediated hypersensitivity to ABA, suggesting that the keg-4 mutation suppresses ABA signaling by altering KEG function. Several ABA-responsive genes were found to be further up-regulated in the edr1 mutant following ABA treatment, and this up-regulation was suppressed by the keg-4 mutation. We conclude that edr1-mediated resistance to powdery mildew is mediated, in part, by enhanced ABA signaling.
Further Evidence for the Mandatory Nature of Polysaccharide Debranching for the Aggregation of Semicrystalline Starch and for Overlapping Functions of Debranching Enzymes in Arabidopsis Leaves
Authors: Wattebled Fabrice , Planchot Véronique , Dong Ying , Szydlowski Nicolas , Pontoire Bruno , Devin Aline , Ball Steven , D'Hulst Christophe 
Published: September 2008

Abstract
Four isoforms of debranching enzymes are found in the genome of Arabidopsis (Arabidopsis thaliana): three isoamylases (ISA1, ISA2, and ISA3) and a pullulanase (PU1). Each isoform has a specific function in the starch pathway: synthesis and/or degradation. In this work we have determined the levels of functional redundancy existing between these isoforms by producing and analyzing different combinations of mutations: isa3-1 pu1-1, isa1-1 isa3-1, and isa1-1 isa3-1 pu1-1. While the starch content strongly increased in the isa3-1 pu1-1 double mutant, the latter decreased by over 98% in the isa1-1 isa3-1 genotype and almost vanished in triple mutant combination. In addition, whereas the isa3-1 pu1-1 double mutant synthesizes starch very similar to that of the wild type, the structure of the residual starch present either in isa1-1 isa3-1 or in isa1-1 isa3-1 pu1-1 combination is deeply affected. In the same way, water-soluble polysaccharides that accumulate in the isa1-1 isa3-1 and isa1-1 isa3-1 pu1-1 genotypes display strongly modified structure compared to those found in isa1-1. Taken together, these results show that in addition to its established function in polysaccharide degradation, the activity of ISA3 is partially redundant to that of ISA1 for starch synthesis. Our results also reveal the dual function of pullulanase since it is partially redundant to ISA3 for degradation and to ISA1 for synthesis. Finally, x-ray diffraction analyses suggest that the crystallinity and the presence of the 9- to 10-nm repetition pattern in starch precisely depend on the level of debranching enzyme activity.
Solution structure of the extraterminal domain of the bromodomain‐containing protein BRD4
Authors: Lin Yi‐Jan , Umehara Takashi , Inoue Makoto , Saito Kohei , Kigawa Takanori , Jang Moon‐Kyoo , Ozato Keiko , Yokoyama Shigeyuki , Padmanabhan Balasundaram , Güntert Peter 
Published: September 2008

AbstractBRD4, which is a member of the BET (bromodomains and extraterminal) protein family, interacts preferentially with acetylated chromatin and possesses multiple cellular functions in meiosis, embryonic development, the cell cycle, and transcription. BRD4 and its family members contain two bromodomains known to bind acetylated lysine, and a conserved ET domain whose function is unclear. Here we show the solution structure of the ET domain of mouse BRD4, which provides the first three‐dimensional structure of an ET domain in the BET family. We determined the NMR structure of BRD4‐ET with a root‐mean‐square deviation of 0.41 Å for the backbone atoms in the structured region of residues 608–676 on the basis of 1793 upper distance limits derived from NOE intensities measured in three‐dimensional NOESY spectra. The structure of the BRD4‐ET domain comprises three α‐helices and a characteristic loop region of an irregular but well‐defined structure. A DALI search revealed no close structural homologs in the current Protein Data Bank. The BRD4‐ET structure has an acidic patch that forms a continuous ridge with a hydrophobic cleft, which may interact with other proteins and/or DNA.
Association of polymorphisms in CASP10 and CASP8 with FEV1/FVC and bronchial hyperresponsiveness in ethnically diverse asthmatics
Authors: Smith Alicia K. , Lange Leslie A. , Ampleford Elizabeth J. , Meyers Deborah A. , Bleecker Eugene R. , Howard Timothy D. 
Published: September 2008

SummaryBackground
Several chromosomal regions have been identified using family‐based linkage analysis to contain genes contributing to the development of asthma and allergic disorders. One of these regions, chromosome 2q32‐q33, contains a gene cluster containing CFLAR, CASP10 and CASP8. These genes regulate the extrinsic apoptosis pathway utilized by several types of immune and structural cells that have been implicated in the pathogenesis of asthma.Objective
To assess the role of genetic variation in CFLAR, CASP10 and CASP8 in asthma and related phenotypes in individuals of diverse ethnic backgrounds.Methods
We tested 26 single nucleotide polymorphisms (SNPs) in the CFLAR, CASP10 and CASP8 gene cluster for association with asthma and related phenotypes in African‐American, non‐Hispanic whites, and Hispanic case–control populations (cases, N=517, controls, N=644).Results
Five CASP10 SNPS were associated with forced expiratory volume in 1 s (FEV1)/forced expiration volume capacity (FVC) in the African‐American subjects with asthma (P=0.0009–0.047). Nine SNPs, seven in CASP10 and two in CASP8, were also associated with the degree of bronchial hyperresponsiveness (BHR) (as determined by PC20) in race‐specific analysis, predominately in the Non‐Hispanic white cases. Two SNPs, rs6750157 in CASP10 and rs1045485 in CASP8 were modestly associated with asthma in the African‐American (P=0.025) and Hispanic (P=0.033) populations, respectively.Conclusion
These data suggest a role for CASP10 as a potential modifier of the asthma phenotype, specifically with measures of airway obstruction and BHR.
Allergens to wheat and related cereals
Authors: Tatham A. S. , Shewry P. R. 
Published: September 2008

SummaryWheat is one of the major crops grown, processed and consumed by humankind and is associated with both intolerances (notably coeliac disease) and allergies.Two types of allergy are particularly well characterized. The first is bakers' asthma, which results from the inhalation of flour and dust during grain processing. Although a number of wheat proteins have been shown to bind IgE from patients with bakers' asthma, there is no doubt a well‐characterized group of inhibitors of α‐amylase (also called chloroform methanol soluble, or CM, proteins) are the major components responsible for this syndrome. The second well‐characterized form of allergy to wheat proteins is wheat‐dependent exercise‐induced anaphylaxis (WDEIA), with the ω5‐gliadins (part of the gluten protein fraction) being the major group of proteins which are responsible. Other forms of food allergy have also been reported, with the proteins responsible including gluten proteins, CM proteins and non‐specific lipid transfer proteins.Processing of wheat and of related cereals (barley and rye, which may contain related allergens) may lead to decreased allergenicity while genetic engineering technology offers opportunities to eliminate allergens by suppressing gene expression.
Renin‐angiotensin system gene polymorphisms and diastolic heart failure
Authors: Wu C.‐K. , Tsai C.‐T. , Hwang J.‐J. , Luo J.‐L. , Juang J. J.‐M. , Hsu K.‐L. , Lai L.‐P. , Lin J.‐L. , Tseng C.‐D. , Chiang F.‐T. 
Published: September 2008

ABSTRACTBackground  Diastolic heart failure (DHF) refers to an abnormality of diastolic distensibility, filling or relaxation of the left ventricle. The genetic study of DHF is scarce in the literature. The association of renin‐angiotensin system (RAS) and DHF are well known. We hypothesized that RAS genes might be the susceptible genes for DHF and conducted a case‐control study to prove the hypothesis.Materials and methods  A total of 1452 consecutive patients were analysed and 148 patients with a diagnosis of DHF confirmed by echocardiography were recruited. We had two control populations. The first controls consisted of 286 normal subjects while the second were 148 matched controls selected on a 1‐to‐1 basis by age, sex, hypertension, diabetes and medication use. The angiotensin‐converting enzyme (ACE) gene insertion/deletion polymorphism; multilocus polymorphisms of the angiotensinogen gene; and the A1166C polymorphisms of the angiotensin II type I receptor (AT1R) gene were genotyped.Results  In a single‐locus analysis, the odds ratios (ORs) for DHF were significant with the ACE DD genotype and the AT1R 1166 CC plus AC genotype. In addition, the concomitant presence of ACE DD and AT1R 1166 CC/AC genotypes synergistically increased the predisposition to DHF.Conclusions  Genetic variants in the RAS genes may determine an individual's risk to develop DHF. There is also a synergistic gene‐gene interaction between the RAS genes in the development of DHF.
Effect of obesity and insulin sensitivity on adiponectin isoform distribution
Authors: Kaser S. , Tatarczyk T. , Stadlmayr A. , Ciardi C. , Ress C. , Tschoner A. , Sandhofer A. , Paulweber B. , Ebenbichler C. F. , Patsch J. R. 
Published: September 2008

ABSTRACTBackground  Adiponectin is an insulin‐sensitizing, antiatherogenic and anti‐inflammatory adipocytokine that circulates in three isoforms: a trimer [low‐molecular weight (LMW)], a hexamer (trimer‐dimer) of medium molecular weight (MMW) and a multimeric high molecular weight (HMW) isoform. Evidence is accumulating that HMW adiponectin is the active isoform of the adipocytokine. We investigated the impact of adipose tissue and insulin sensitivity on adiponectin isoform distribution.Materials and methods  One hundred and eighty‐seven normolipidaemic, non‐diabetic lean or obese subjects with or without insulin resistance participating in the Salzburg Atherosclerosis Prevention program in subjects at High Individual Risk (SAPHIR) were included in the study. Insulin sensitivity was determined by the short insulin tolerance test and the homeostasis model assessment (HOMA) index. Serum adiponectin isoform distribution was determined by an enzyme immunoassay.Results  Total adiponectin as well as HMW/total adiponectin ratio was significantly increased in female subjects. Circulating total adiponectin levels were lowest in obese patients due to reduced concentrations of HMW adiponectin. As determined by stepwise regression analysis, besides age and high density lipoprotein (HDL) cholesterol, visceral fat area and waist‐to‐hip ratio predicted concentrations of HMW adiponectin, while insulin sensitivity had no influence on either total adiponectin or its isoforms.Conclusions  Our results underline that determination of adiponectin isoforms are more useful than measurement of total adiponectin in clinical settings. Our data suggest that adiponectin concentrations are strongly associated with visceral fat area but not with insulin sensitivity. Thus, we hypothesize that insulin resistance is a consequence rather than the cause of hypoadiponectinaemia in obese subjects.
Presence of hepatitis C Virus DNA sequences in the DNA of infected patients
Authors: Zemer R. , Cohen Y. Kitay , Naftaly T. , Klein A. 
Published: September 2008

ABSTRACTBackground  Hepatitis C virus (HCV) consists of a single positive RNA molecule. In the present study we investigated the possibility that HCV may undergo integration into the genomic DNA of infected cells.Materials and methods  HCV(+) patients (n = 51) and 21 HCV(–) controls were investigated for HCV integration. RNase treated DNA samples of mononuclear cells (MNC) and liver biopsies of the patients were screened by PCR and seminested PCR processes for detection of integration. Positive results were further investigated by means of Southern analysis of patient's DNA as well as sequencing of PCR products of patient's DNA.Results  Positive PCR results were detected in 4/51 of the HCV(+) patients and in none of the control group. Southern analysis showed the presence of HCV sequence in a 23 kbp band of the patient which is much larger than the viral genome itself (9·646 kbp). Sequencing of cloned PCR products showed an identity of over 95·0% to HCV.Conclusions  As much as we are aware this is the first demonstration of the possible integration of HCV sequences into the DNA of HCV(+) patients.
A curve fitting approach to estimate the extent of fermentation of indigestible carbohydrates
Authors: Wang H. , Weening D. , Jonkers E. , Boer T. , Stellaard F. , Small A. C. , Preston T. , Vonk R. J. , Priebe M. G. 
Published: September 2008

ABSTRACTBackground  Information about the extent of carbohydrate digestion and fermentation is critical to our ability to explore the metabolic effects of carbohydrate fermentation in vivo. We used cooked 13C‐labelled barley kernels, which are rich in indigestible carbohydrates, to develop a method which makes it possible to distinguish between and to assess carbohydrate digestion and fermentation.Materials and methods  Seventeen volunteers ingested 86 g (dry weight) of cooked naturally 13C enriched barley kernels after an overnight fast. 13CO2 and H2 in breath samples were measured every half hour for 12 h. The data of 13CO2 in breath before the start of the fermentation were used to fit the curve representing the digestion phase. The difference between the area under curve (AUC) of the fitted digestion curve and the AUC of the observed curve was regarded to represent the fermentation part. Different approaches were applied to determine the proportion of the 13C‐dose available for digestion and fermentation.Results  Four hours after intake of barley, H2‐excretion in breath started to rise. Within 12 h, 24–48% of the 13C‐dose was recovered as 13CO2, of which 18–19% was derived from colonic fermentation and the rest from digestion. By extrapolating the curve to baseline, it was estimated that eventually 24–25% of the total available 13C in barley would be derived from colon fermentation.Conclusion  Curve fitting, using 13CO2‐ and H2‐breath data, is a feasible and non‐invasive method to assess carbohydrate digestion and fermentation after consumption of 13C enriched starchy food.
Diversity and activity of aquatic fungi under low oxygen conditions
Authors: MEDEIROS A. O. , PASCOAL C. , GRAÇA M. A. S. 
Published: September 2008

Summary1. The objective was to test whether a decrease in oxygen concentration in streams affects the diversity and activity of aquatic hyphomycetes and consequently leaf litter decomposition.2. Senescent leaves of Alnus glutinosa were immersed for 7 days in a reference stream, for fungal colonization, and then incubated for 18 days in microcosms at five oxygen concentrations (4%, 26%, 54%, 76% and 94% saturation). Leaf decomposition (as loss of leaf toughness), fungal diversity, reproduction (as spore production) and biomass (ergosterol content) were determined.3. Leaf toughness decreased by 70% in leaves exposed to the highest O2 concentration, whereas the decrease was substantially less (from 25% to 45%) in treatments with lower O2. Fungal biomass decreased from 99 to 12 mg fungi g−1 ash‐free dry mass on exposure to 94% and 4% O2 respectively. Sporulation was strongly inhibited by reduction of dissolved O2 in water (3.1 × 104 versus 1.3 × 103 spores per microcosms) for 94% and 4% saturation respectively.4. A total of 20 species of aquatic hyphomycetes were identified on leaves exposed to 94% O2, whereas only 12 species were found in the treatment with 4% O2 saturation. Multidimensional scaling revealed that fungal assemblages exposed to 4% O2 were separated from all the others. Articulospora tetracladia, Cylindrocarpon sp. and Flagellospora curta were the dominant species in microcosms with 4% O2, while Flagellospora curvula and Anguillospora filiformis were dominant at higher O2 concentrations.5. Overall results suggest that the functional role of aquatic hyphomycetes as decomposers of leaf litter is limited when the concentration of dissolved oxygen in streams is low.
Plant diversity positively affects short‐term soil carbon storage in experimental grasslands
Authors: STEINBEISS SIBYLLE , BEßLER HOLGER , ENGELS CHRISTOF , TEMPERTON VICKY M. , BUCHMANN NINA , ROSCHER CHRISTIANE , KREUTZIGER YVONNE , BAADE JUSSI , HABEKOST MAIKE , GLEIXNER GERD 
Published: September 2008

AbstractIncreasing atmospheric CO2concentration and related climate change have stimulated much interest in the potential of soils to sequester carbon. In ‘The Jena Experiment’, a managed grassland experiment on a former agricultural field, we investigated the link between plant diversity and soil carbon storage. The biodiversity gradient ranged from one to 60 species belonging to four functional groups. Stratified soil samples were taken to 30 cm depth from 86 plots in 2002, 2004 and 2006, and organic carbon contents were determined. Soil organic carbon stocks in 0–30 cm decreased from 7.3 kg C m−2in 2002 to 6.9 kg C m−2in 2004, but had recovered to 7.8 kg C m−2by 2006. During the first 2 years, carbon storage was limited to the top 5 cm of soil while below 10 cm depth, carbon was lost probably as short‐term effect of the land use change. After 4 years, carbon stocks significantly increased within the top 20 cm. More importantly, carbon storage significantly increased with sown species richness (log‐transformed) in all depth segments and even carbon losses were significantly smaller with higher species richness. Although increasing species diversity increased root biomass production, statistical analyses revealed that species diversityper sewas more important than biomass production for changes in soil carbon. Below 20 cm depth, the presence of one functional group, tall herbs, significantly reduced carbon losses in the beginning of the experiment. Our analysis indicates that plant species richness and certain plant functional traits accelerate the build‐up of new carbon pools within 4 years. Additionally, higher plant diversity mitigated soil carbon losses in deeper horizons. This suggests that higher biodiversity might lead to higher soil carbon sequestration in the long‐term and therefore the conservation of biodiversity might play a role in greenhouse gas mitigation.
Microarray analysis of acaricide‐inducible gene expression in the southern cattle tick, Rhipicephalus (Boophilus) microplus
Authors: Saldivar L. , Guerrero F. D. , Miller R. J. , Bendele K. G. , Gondro C. , Brayton K. A. 
Published: September 2008

AbstractAcaricide‐inducible differential gene expression was studied in larvae of Rhipicephalus (Boophilus) microplus using a microarray‐based approach. The acaricides used were: coumaphos, permethrin, ivermectin, and amitraz. The microarrays contained over 13 000 probes, having been derived from a previously described R. microplus gene index (BmiGI Version 2; Wang et al., 2007). Relative quantitative reverse transcriptase‐PCR, real time PCR, and serial analysis of gene expression data was used to verify microarray data. Among the differentially expressed genes with informative annotation were legumain, glutathione S‐transferase, and a putative salivary gland‐associated protein.
Impact of outdoor winter sports on the abundance of a key indicator species of alpine ecosystems
Authors: Patthey Patrick , Wirthner Sven , Signorell Natalina , Arlettaz Raphaël 
Published: September 2008

Summary

Tourism and leisure activities have increased continuously all over the world during the past decades, exerting a growing pressure upon naturally fragile ecosystems, such as mountainous habitats. Recent studies have established that disturbance by outdoor winter sports (e.g. skiing, snowboarding and snowshoeing) is a source of stress for wildlife. This may in turn affect its abundance, but we still lack quantitative evidence.
We tested the effect of outdoor winter sports (ski lifts and related recreational activities) on the abundance of the alpine black grouse Tetrao tetrix, a vulnerable indicator species of the timberline ecosystem, the favoured habitat for outdoor winter sports in the European Alps.
Generalized linear models and a model selection approach were used to rank environmental factors influencing black grouse abundance and to make predictions about population status in the theoretical absence of ski resorts. We modelled the number of displaying cocks along census transects in spring, as a function of habitat characteristics (vegetation structure and typology), ski lift density and hunting pressure at 15 natural sites (none or a very low level of anthropogenic disturbance) and 15 ski resorts in the south‐western Swiss Alps.
Ski lift density and habitat typology were the principal determinants of black grouse abundance, whereas hunting pressure had no discernable effect. Ski lifts and related winter sport activities had a strong negative effect on the number of displaying cocks, which may have led to a mean 36% reduction of local abundance in ski lift areas, as determined after controlling for the confounding effect of habitat type.
Synthesis and applications. Conservation action plans for black grouse should aim at reducing the multiple negative effects generated by outdoor winter sports (ski facilities and related winter sport activities). First, vegetation patchiness (i.e. a mosaic of grassy shrubland with scattered trees) should be maintained along ski runs. Secondly, wintering preserves where human access is banned or strictly limited should be promoted within ski resorts. Spatially explicit human–wildlife conflict maps can be constructed from the present model to allow delineation of those areas likely to become effective protection areas.