bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyphenoloxidase Silencing Affects Latex Coagulation in Taraxacum Species
Authors: Wahler Daniela , Gronover Christian Schulze , Richter Carolin , Foucu Florence , Twyman Richard M. , Moerschbacher Bruno M. , Fischer Rainer , Muth Jost , Prüfer Dirk 
Published: July 2009

Abstract
Latex is the milky sap that is found in many different plants. It is produced by specialized cells known as laticifers and can comprise a mixture of proteins, carbohydrates, oils, secondary metabolites, and rubber that may help to prevent herbivory and protect wound sites against infection. The wound-induced browning of latex suggests that it contains one or more phenol-oxidizing enzymes. Here, we present a comprehensive analysis of the major latex proteins from two dandelion species, Taraxacum officinale and Taraxacum kok-saghyz, and enzymatic studies showing that polyphenoloxidase (PPO) is responsible for latex browning. Electrophoretic analysis and amino-terminal sequencing of the most abundant proteins in the aqueous latex fraction revealed the presence of three PPO-related proteins generated by the proteolytic cleavage of a single precursor (pre-PPO). The laticifer-specific pre-PPO protein contains a transit peptide that can target reporter proteins into chloroplasts when constitutively expressed in dandelion protoplasts, perhaps indicating the presence of structures similar to plastids in laticifers, which lack genuine chloroplasts. Silencing the PPO gene by constitutive RNA interference in transgenic plants reduced PPO activity compared with wild-type controls, allowing T. kok-saghyz RNA interference lines to expel four to five times more latex than controls. Latex fluidity analysis in silenced plants showed a strong correlation between residual PPO activity and the coagulation rate, indicating that laticifer-specific PPO plays a major role in latex coagulation and wound sealing in dandelions. In contrast, very little PPO activity is found in the latex of the rubber tree Hevea brasiliensis, suggesting functional divergence of latex proteins during plant evolution.
RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice
Authors: Lee Tae-Ho , Kim Yeon-Ki , Pham Thu Thi Minh , Song Sang Ik , Kim Ju-Kon , Kang Kyu Young , An Gynheung , Jung Ki-Hong , Galbraith David W. , Kim Minkyun , Yoon Ung-Han , Nahm Baek Hie 
Published: July 2009

AbstractMicroarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. However, there have been no reports, to date, of such a database being constructed for rice (Oryza sativa). Here, we describe the construction of such a database, called RiceArrayNet (RAN; http://www.ggbio.com/arraynet/), which provides information on coexpression between genes in terms of correlation coefficients (r values). The average number of coexpressed genes is 214, with sd of 440 at r ≥ 0.5. Given the correlation between genes in a gene pair, the degrees of closeness between genes can be visualized in a relational tree and a relational network. The distribution of correlated genes according to degree of stringency shows how each gene is related to other genes. As an application of RAN, the 16-member L7Ae ribosomal protein family was explored for coexpressed genes and gene expression values within and between rice and Arabidopsis (Arabidopsis thaliana), and common and unique features in coexpression partners and expression patterns were observed for these family members. We observed a correlation pattern between Os01g0968800, a drought-responsive element-binding transcription factor, Os02g0790500, a trehalose-6-phosphate synthase, and Os06g0219500, a small heat shock factor, reflecting the fact that genes responding to the same biological stresses are regulated together. The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners.
Physiological and Transcriptome Analysis of Iron and Phosphorus Interaction in Rice Seedlings
Authors: Zheng Luqing , Huang Fangliang , Narsai Reena , Wu Jiaojiao , Giraud Estelle , He Fei , Cheng Longjun , Wang Fang , Wu Ping , Whelan James , Shou Huixia 
Published: July 2009

AbstractThe antagonistic interaction between iron (Fe) and phosphorus (P) has been noted in the area of plant nutrition. To understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under four different nutrient conditions: (1) full strength of Fe and P (+Fe+P); (2) full strength of P and no Fe (−Fe+P); (3) full strength of Fe and no P (+Fe−P); and (4) without both Fe and P (−Fe−P). While removal of Fe in the growth medium resulted in very low shoot and root Fe concentrations, the chlorotic symptoms and retarded seedling growth were only observed on seedlings grown in the presence of P. Microarray data showed that in roots, 7,628 transcripts were significantly changed in abundance in the absence of Fe alone. Interestingly, many of these changes were reversed if P was also absent (−Fe−P), with only approximately 15% overlapping with –Fe alone (–Fe+P). Analysis of the soluble Fe concentration in rice seedling shoots showed that P deficiency resulted in significantly increased Fe availability within the plants. The soluble Fe concentration under –Fe–P conditions was similar to that under +Fe+P conditions. These results provide evidence that the presence of P can affect Fe availability and in turn can influence the regulation of Fe-responsive genes.
The Role of Oxophytodienoate Reductases in the Detoxification of the Explosive 2,4,6-Trinitrotoluene by Arabidopsis
Authors: Beynon Emily R. , Symons Zoe C. , Jackson Rosamond G. , Lorenz Astrid , Rylott Elizabeth L. , Bruce Neil C. 
Published: July 2009

Abstract
The explosive 2,4,6-trinitrotoluene (TNT) is a significant environmental pollutant that is both toxic and recalcitrant to degradation. Phytoremediation is being increasingly proposed as a viable alternative to conventional remediation technologies to clean up explosives-contaminated sites. Despite the potential of this technology, relatively little is known about the innate enzymology of TNT detoxification in plants. To further elucidate this, we used microarray analysis to identify Arabidopsis (Arabidopsis thaliana) genes up-regulated by exposure to TNT and found that the expression of oxophytodienoate reductases (OPRs) increased in response to TNT. The OPRs share similarity with the Old Yellow Enzyme family, bacterial members of which have been shown to transform explosives. The three predominantly expressed forms, OPR1, OPR2, and OPR3, were recombinantly expressed and affinity purified. Subsequent biochemical characterization revealed that all three OPRs are able to transform TNT to yield nitro-reduced TNT derivatives, with OPR1 additionally producing the aromatic ring-reduced products hydride and dihydride Meisenheimer complexes. Arabidopsis plants overexpressing OPR1 removed TNT more quickly from liquid culture, produced increased levels of transformation products, and maintained higher fresh weight biomasses than wild-type plants. In contrast, OPR1,2 RNA interference lines removed less TNT, produced fewer transformation products, and had lower biomasses. When grown on solid medium, two of the three OPR1 lines and all of the OPR2-overexpressing lines exhibited significantly enhanced tolerance to TNT. These data suggest that, in concert with other detoxification mechanisms, OPRs play a physiological role in xenobiotic detoxification.
Metabolic adaptation of Phytophthora infestans during growth on leaves, tubers and artificial media
Authors: JUDELSON HOWARD S. , TANI SHUJI , NARAYAN REENA D. 
Published: July 2009

SUMMARYEfficient nutrient acquisition is critical to the fitness of plant pathogens. To address how the late blight agent Phytophthora infestans adapts to nutrients offered by its hosts, genes in glycolytic, gluconeogenic and amino acid pathways were mined from its genome and their expression in different plant tissues and artificial media was measured. Evidence for conventional glycolytic and gluconeogenic processes was obtained, although several steps involved pyrophosphate‐linked transformations which are uncommon in eukaryotes. In media manipulation studies, nearly all genes in the pathways were subject to strong transcriptional control. However in rye–sucrose media, tomato leaflets, potato tubers and, at both early and late stages of infection, most glycolytic genes were expressed similarly, which indicated that each plant tissue presented a nutrient‐rich environment. Biochemical analyses also demonstrated that sporulation occurred from host material in which sugars were abundant, with fructose and glucose increasing at the expense of sucrose late in the disease cycle. The expression of only a few genes changed late in infection, with the most notable example being lower invertase levels in the sucrose‐reduced leaves. Interestingly, most gluconeogenic genes were up‐regulated in tubers compared with other tissues. Rather than reflecting a starvation response, this probably reveals the role of such enzymes in converting carbon skeletons from the abundant free amino acids of tubers into citric acid cycle and glycolysis intermediates, as genes involved in amino acid catabolism were also more highly expressed in tubers. The corresponding enzymes also displayed higher activities in defined media when amino acids were abundant, as in tubers.
Pliocene onset of rapid exhumation in Taiwan during arc–continent collision: new insights from detrital thermochronometry
Authors: Kirstein L. A. , Fellin M. G. , Willett S. D. , Carter A. , Chen Y.‐ G. , Garver J. I. , Lee D. C. 
Published: July 2009

ABSTRACTThe Coastal Range in eastern Taiwan contains the remnants of the Pliocene–Pleistocene retro‐foredeep basin of the ongoing Penglai orogeny. These sedimentary successions record the earliest exhumation of the Central Range, Taiwan. We dated detrital Plio‐Pleistocene sediments in the Coastal Range using multiple thermochronometers [fission‐track, zircon (U–Th)/He and U/Pb dating] to document changes in exhumation rate through time. Fission‐track grain ages in 2–4‐Myr‐old sediments were not reset by the Penglai orogeny and reflect the early stage removal of the sedimentary cover. This early stage, when exhumation rates were low, could encompass both the accretionary wedge phase of the orogen and the early arc–continent collision. Sediments younger than 2‐Myr‐old yield Pliocene zircon fission‐track grain ages and suggest that exhumation, transport and deposition occurred within 0.4–1.5 Myr. The recorded onset of rapid exhumation in the Pliocene is contemporaneous with other major tectonic changes in the region, including an increase in subsidence rate in both the pro‐ and retro‐foredeep basins and a change in the wedge kinematics from internal shortening to underplating.
Association of G‐protein‐coupled receptor 154 with asthma and total IgE in a population of the Caribbean coast of Colombia
Authors: Vergara C. , Jiménez S. , Acevedo N. , Martínez B. , Mercado D. , Gusmão L. , Rafaels N. , Hand T. , Barnes K. C. , Caraballo L. 
Published: July 2009

SummaryBackground
G protein‐coupled receptor 154 was described as an asthma susceptibility gene by positional cloning. It has been subsequently associated with asthma and other inflammatory diseases in several populations with different ethnic origin. Replication of associations adds reliability to these findings.Objective
To analyze the association of G protein‐coupled receptor 154 with asthma and total and mite‐specific IgE levels in a population of the Caribbean Coast of Colombia.Methods
We genotyped seven single nucleotide proteins (SNPs) in GPR154 in 475 asthmatics, 394 controls and 116 families from Cartagena, Colombia using either SnaPshot or TaqMan. Total and specific IgE against Blomia tropicalis and Dermatophagoides pteronyssinus were determined by ELISA. Hardy–Weinberg equilibrium was assessed and case–control and family‐based analyses were performed to evaluate the association between the SNPs and their haplotypes and asthma and IgE. Association analyses in the case–control dataset were corrected by population stratification using 52 ancestry informative markers.Results
Allelic distribution was similar to that described in other populations. Two SNPs were associated with the same direction of the effect in both datasets. Allele A of Hopo546333 was protective for asthma (case–control OR: 0.42; 95% CI: 0.17–0.99, P=0.042; P=0.043; families Z score=−2,236; P=0.025). Similarly, allele C of rs740347 conferred low risk for asthma (OR: 0.44; 95% CI: 0.28–0.70, P=0.00017; Pc=0.00037) and total IgE (OR: 0.29; 95% CI: 0.09–0.88, P=0.015; Pc=0.030) in the case–control study and families (Z score=−3.207, P=0.0013; Z score=−3.182, P=0.0014, respectively). Haplotype CCAGGT was associated with total IgE (OR: 1.76; 95% CI: 1.14–2.71, P=0.006, Pc=0.007) in the case–controls group and CGCGGT with both phenotypes (P=0.044 and P=0.032, respectively) in families. Neither SNPs nor haplotypes were associated with levels of mite‐specific IgE.Conclusions
Our findings in a sample of asthmatics from Colombia suggest a relevant role of G protein‐coupled receptor 154 in the pathogenesis of asthma and allergy.
On the putative role of transient receptor potential cation channels in asthma
Authors: Colsoul B. , Nilius B. , Vennekens R. 
Published: July 2009

SummaryThe mammalian transient receptor potential (TRP) superfamily consists of 28 mammalian TRP cation channels, which can be subdivided into six main subfamilies: the TRPC (‘Canonical’), TRPV (‘Vanilloid’), TRPM (‘Melastatin’), TRPP (‘Polycystin’), TRPML (‘Mucolipin’) and the TRPA (‘Ankyrin’) groups. Increasing evidence has accumulated during the previous few years that links TRP channels to the cause of several diseases or to critically influence and/or determine their progress. This review focuses on the possible role of TRP channels in the aetiology of asthmatic lung disease.
Genetic allergen modification in the development of novel approaches to specific immunotherapy
Authors: Mutschlechner S. , Deifl S. , Bohle B. 
Published: July 2009

SummaryIn the recent past, multiple allergens from relevant allergen sources have been cloned, sequenced and produced as recombinant proteins. The availability of recombinant allergens with immunological characteristics similar to their natural counterparts has improved the diagnosis of allergic disorders and increased our knowledge of the biochemical, structural and immunological characteristics of proteins with allergenic potential. Moreover, the use of defined recombinant proteins as vaccines substituting currently used total protein extracts from allergen sources may improve specific immunotherapy (SIT) of Type I allergy. In addition to producing well‐defined batches of wild‐type allergens, the recombinant technology offers the possibility to easily and selectively modify their properties or functions. Diverse modifications of allergens can be genetically engineered, e.g. variants with reduced IgE‐binding capacity, multi‐mers of single allergens or hybrids consisting of different allergens. Furthermore, allergens can be genetically fused with proteins that promote immune responses, which counterregulate the disease‐eliciting T‐helper type 2‐dominated immune response in allergic individuals and may therefore, improve the efficacy of SIT. This review will introduce different concepts of allergen modification using genetic engineering to improve vaccines for SIT of Type I allergy.
Is CSF cytology a useful diagnostic procedure in staging paediatric CNS tumours?
Authors: Cohen N. R. , Phipps K. , Harding B. , Jacques T. S. 
Published: July 2009

Objectives:  To evaluate whether there are any factors that predict malignant cells being found in paediatric cerebrospinal fluid (CSF) samples. To determine whether CSF provides useful staging information not provided by magnetic resonance imaging (MRI) in paediatric patients with primary central nervous system (CNS) malignancy.Methods:  We compared the CSF cytology and spinal MRI staging results in paediatric patients with primary CNS malignancy at a UK tertiary referral centre, over a decade.Results:  Of 159 CSF samples, 72 samples were from 72 patients with primary CNS malignancy with spinal MRI available for comparison. Eight of these 72 had positive cytology (seven malignant and one suspicious). All had a high clinical suspicion of tumour at the time of sampling. Of the 72 patients, only two had evidence of CSF spread on MRI spinal staging and CSF cytology; ten had MRI without cytological evidence and six had cytological without MRI evidence.Conclusions:  In paediatric patients with primary CNS tumours, CSF cytology provides useful staging information. Spinal MRI alone may miss some patients with CSF spread who would be identified with CSF cytology.
Sexual division of antibacterial resource defence in breeding burying beetles, Nicrophorus vespilloides
Authors: Cotter Sheena C. , Kilner Rebecca M. 
Published: July 2009

Summary 1. A key component of parental care involves defending resources destined for offspring from a diverse array of potential interspecific competitors, such as social parasites, fungi and bacteria. 2. Just as with other aspects of parental care, such as offspring provisioning or brood defence, sexual conflict between parents may arise over how to share the costs of this form of care. There has been little previous work, however, to investigate how this particular burden might be shared. 3. Here, we describe a hitherto uncharacterized form of parental care in burying beetles Nicrophorus vespilloides, a species which prepares carrion for its young and faces competition from microbes for this resource. We found that parents defend the carcass with antibacterial anal exudates, and that the antibacterial activity of these exudates is only upregulated following the discovery of a corpse. At the same time, phenoloxidase activity in the anal exudates is downregulated, indicating parallels with the internal insect immune system. 4. In unmanipulated breeding pairs, females had higher antibacterial activity in their anal exudates than males, suggesting sex‐specific roles in this aspect of parental care. 5. When we experimentally widowed males, we found that they increased levels of antibacterial activity in their anal exudates. Experimentally widowing females, however, led them to decrease levels of antibacterial activity in their anal exudates. Widowed beetles of each sex thus produced anal exudates of comparable antibacterial activity. We suggest that this flexible division of antibacterial activity may be coordinated by Juvenile Hormone.
Effects of atorvastatin on circulating CD34+/CD133+/ CD45− progenitor cells and indices of angiogenesis (vascular endothelial growth factor and the angiopoietins 1 and 2) in atherosclerotic vascular disease and diabetes mellitus
Authors: Jaumdally R. J. , Goon P. K. Y. , Varma C. , Blann A. D. , Lip G. Y. H. 
Published: July 2009

Abstract.  Jaumdally RJ, Goon PKY, Varma C, Blann AD, Lip GYH (City Hospital, Birmingham, United Kingdom). Effects of atorvastatin on circulating CD34+/CD133+/CD45− progenitor cells and indices of angiogenesis (vascular endothelial growth factor and the angiopoietins 1 and 2) in atherosclerotic vascular disease and diabetes mellitus. J Intern Med 2010; 267: 385–393.Background.  Cardiovascular disease (CVD) remains a major cause of morbidity and mortality, especially in the presence of diabetes, possibly because of endothelial damage. Increased circulating progenitor cells (CPCs) and increased plasma markers of angiogenesis [vascular endothelial growth factor (VEGF) and the angiopoietins (Ang‐1 and ‐2)] may be evidence of this damage. Treatment with hydroxy‐methyl‐glutaryl (HMG‐CoA) reductase inhibitors (‘statins’) improves outcomes in patients with vascular disease, including diabetic patients. We hypothesized that 80 mg per day atorvastatin influences CPC counts of VEGF and the angiopoietins in patients with atherosclerotic CVD with or without diabetes mellitus.Methods.  Cardiovascular disease patients with diabetes mellitus (Group A, n = 14) and nondiabetic patients with CVD only (Group B, n = 10) took atorvastatin 80 mg per day for a period of 8–10 weeks. CPCs (CD34+/CD133+/CD45−) were defined by flow cytometry, plasma levels VEGF and Ang‐1 and Ang‐2 by ELISA).Results.  Circulating progenitor cell counts increased (P < 0.001) in Group A compared with a nonsignificant change in Group B (P = 0.37). VEGF levels fell significantly in Group A (P = 0.04) but no significant change was seen in Group B (P = 0.16). Whilst Ang‐1 remained unchanged (P = 0.41), Ang‐2 levels increased markedly in both groups (P < 0.05). These effects were independent of LDL and total cholesterol changes but were associated with HDL changesConclusion.  High‐dose atorvastatin increased circulating CPCs, reduced VEGF and increased Ang‐2 in patients with diabetes and CVD, providing another possible pathophysiological mechanism for the beneficial effects of statins in CVD.
Two methods of random seed generation to avoid over‐segmentation with stochastic watershed: application to nuclear fuel micrographs
Authors: TOLOSA S. CATIVA , BLACHER S. , DENIS A. , MARAJOFSKY A. , PIRARD J.‐P. , GOMMES C.J. 
Published: July 2009

SummaryA stochastic version of the watershed algorithm is obtained by choosing randomly in the image the seeds from which the watershed regions are grown. The output of the procedure is a probability density function corresponding to the probability that each pixel belongs to a boundary. In the present paper, two stochastic seed‐generation processes are explored to avoid over‐segmentation. The first is a non‐uniform Poisson process, the density of which is optimized on the basis of opening granulometry. The second process positions the seeds randomly within disks centred on the maxima of a distance map. The two methods are applied to characterize the grain structure of nuclear fuel pellets. Estimators are proposed for the total edge length and grain number per unit area, LA and NA, which take advantage of the probabilistic nature of the probability density function and do not require segmentation.