bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cotton Cultivars Evaluated for Tolerance to Reniform Nematode
Authors: Stetina Salliana R. , Sciumbato Gabriel L. , Young Lawrence D. , Blessitt Julie A. 
Published: March 2009

Thirty-nine commercial cotton (Gossypium hirsutum) cultivars were evaluated to identify those with tolerance to reniform nematode (Rotylenchulus reniformis). Trials were conducted for three years at two west-central Mississippi field locations naturally infested with reniform nematode. Main plots were cultivars and subplots were either not treated or treated with nematicide. Reniform nematode soil population densities were assessed throughout the growing season. At harvest, seed cotton yields were determined, and fiber quality was evaluated for select samples. Data were pooled from all years and locations, and t-tests were used to identify tolerant cultivars. Cultivars were judged tolerant if nematicide did not improve yield, although the nematode population was reduced at a midseason sampling interval. Only Deltapine 449 BR, Paymaster 1218 BR, and Suregrow 215 BR met these criteria. Additionally, tolerance indices were calculated for nine cultivars showing suppressed nematode populations in nematicide-treated plots at any point during the growing season. The three tolerant cultivars identified based on the t-tests ranked first (Suregrow 215 BR), second (Paymaster 1218 BR), and fifth (Deltapine 449 BR) with respect to tolerance index. Because they do not appear to suffer significant yield loss due to reniform nematode, these three cultivars may benefit growers. Accepted for publication 12 January 2009. Published 12 March 2009.
Report of a Watermelon mosaic potyvirus Strain in Kentucky Undetected by ELISA
Authors: Vincelli Paul , Seebold Kenneth 
Published: March 2009

These results indicate that a strain of WMV is present in Kentucky which does not react to a widely used assay for detection of this economically important virus. Prior to this report, it has been unknown whether the recent, widespread occurrence of PVG-positive/CVS-negative cucurbit samples was due to a new variant of a previously recognized potyvirus or a new potyvirus. This report identifies the causal agent for at least some of these anomalous cases. Accepted for publication 2 January 2009. Published 13 March 2009.
A severe symptom phenotype in tomato in Mali is caused by a reassortant between a novel recombinant begomovirus (Tomato yellow leaf curl Mali virus) and a betasatellite
Authors: CHEN LI‐FANG , ROJAS MARIA , KON TATSUYA , GAMBY KADIATOU , XOCONOSTLE‐CAZARES BEATRIZ , GILBERTSON ROBERT L. 
Published: March 2009

SUMMARYTomato production in West Africa has been severely affected by begomovirus diseases, including yellow leaf curl and a severe symptom phenotype, characterized by extremely stunted and distorted growth and small deformed leaves. Here, a novel recombinant begomovirus from Mali, Tomato yellow leaf curl Mali virus (TYLCMLV), is described that, alone, causes tomato yellow leaf curl disease or, in combination with a betasatellite, causes the severe symptom phenotype. TYLCMLV is an Old World monopartite begomovirus with a hybrid genome composed of sequences from Tomato yellow leaf curl virus‐Mild (TYLCV‐Mld) and Hollyhock leaf crumple virus (HoLCrV). A TYLCMLV infectious clone induced leaf curl and yellowing in tomato, leaf curl, crumpling and yellowing in Nicotiana benthamiana and common bean, mild symptoms in N. glutinosa, and a symptomless infection in Datura stramonium. In a field‐collected sample from a tomato plant showing the severe symptom phenotype in Mali, TYLCMLV was detected together with a betasatellite, identified as Cotton leaf curl Gezira betasatellite (CLCuGB). Tomato plants co‐agroinoculated with TYLCMLV and CLCuGB developed severely stunted and distorted growth and small crumpled leaves. These symptoms were more severe than those induced by TYLCMLV alone, and were similar to the severe symptom phenotype observed in the field in Mali and in other West African countries. TYLCMLV and CLCuGB also induced more severe symptoms than TYLCMLV in the other solanaceous hosts, but not in common bean. The increased symptom severity was associated with hyperplasia of phloem‐associated cells, but relatively little increase in TYLCMLV DNA levels. In surveys of tomato virus diseases in West Africa, TYLCMLV was commonly detected in plants with leaf curl and yellow leaf curl symptoms, whereas CLCuGB was infrequently detected and always in association with the severe symptom phenotype. Together, these results indicate that TYLCMLV causes tomato yellow leaf curl disease throughout West Africa, whereas TYLCMLV and CLCuGB represent a reassortant that causes the severe symptom phenotype in tomato.
Maintenance of genetic variation in plants and pathogens involves complex networks of gene‐for‐gene interactions
Authors: HALL SHARON A. , ALLEN REBECCA L. , BAUMBER RACHEL E. , BAXTER LAURA A. , FISHER KATE , BITTNER‐EDDY PETER D. , ROSE LAURA E. , HOLUB ERIC B. , BEYNON JIM L. 
Published: March 2009

SUMMARYThe RPP13 [recognition of Hyaloperonospora arabidopsidis (previously known as Peronospora parasitica)] resistance (R) gene in Arabidopsis thaliana exhibits the highest reported level of sequence diversity among known R genes. Consistent with a co‐evolutionary model, the matching effector protein ATR13 (A. thaliana‐recognized) from H. arabidopsidis reveals extreme levels of allelic diversity. We isolated 23 new RPP13 sequences from a UK metapopulation, giving a total of 47 when combined with previous studies. We used these in functional studies of the A. thaliana accessions for their resistance response to 16 isolates of H. arabidopsidis. We characterized the molecular basis of recognition by the expression of the corresponding ATR13 genes from these 16 isolates in these host accessions. This allowed the determination of which alleles of RPP13 were responsible for pathogen recognition and whether recognition was dependent on the RPP13/ATR13 combination. Linking our functional studies with phylogenetic analysis, we determined that: (i) the recognition of ATR13 is mediated by alleles in just a single RPP13 clade; (ii) RPP13 alleles in other clades have evolved the ability to detect other pathogen ATR protein(s); and (iii) at least one gene, unlinked to RPP13 in A. thaliana, detects a different subgroup of ATR13 alleles.
NSAID‐induced antral ulcers are associated with distinct changes in mucosal gene expression
Authors: DESAI J. C. , GOO T. , FUKATA M. , SANYAL S. , DIKMAN A. , MILLER K. , COHEN L. , BROOKS A. , WANG Q. , ABREU M. T. , AISENBERG J. 
Published: March 2009

SummaryBackground  The basis for individual variation in gastroduodenal vulnerability to NSAIDs is not well understood.Aim  To assess whether a gene expression signature is associated with susceptibility to gastroduodenal ulcerations.Methods  Twenty‐five Helicobacter pylori negative adults were treated for 7 days with naproxen 500 mg b.d. Subjects underwent baseline and post‐treatment endoscopy, during which biopsies were taken from antrum and duodenum. RNA extraction and cDNA synthesis were performed, followed by PCR of 23 genes relevant to mucosal injury and repair. Fold changes in gene expression were compared between subjects who developed ulcers and those who did not.Results  Compared with subjects who did not develop ulcers (n = 18), subjects who developed antral ulcers (n = 7) had significantly greater mucosal up‐regulation of interleukin‐8 [Fold change = 33.5 (S.E.M. = 18.5) vs. −7.7 (3.2)] and of cyclo‐oxygenase‐2 [2.3 (1.7) vs. −10.8 (2.2)]. Conversely, non‐ulcer subjects had significantly greater up‐regulation of toll‐like receptor‐4, cyclo‐oxygenase‐1 and hepatocyte growth factor [14.0 (2.2) vs. −0.8 (1.0), 9.8 (2.4) vs. 0.0 (0.7) and 8.2 (2.6) vs. −2.2 (0.3) respectively].Conclusions  NSAID‐induced antral ulcers are associated with a specific pattern of gastroduodenal mucosal gene expression. These patterns may provide an insight into the molecular basis of individual susceptibility to mucosal injury.
Suppressor of cytokine signalling 1 (SOCS1) is a physiological regulator of the asthma response
Authors: Lee C. , Kolesnik T. B. , Caminschi I. , Chakravorty A. , Carter W. , Alexander W. S. , Jones J. , Anderson G. P. , Nicholson S. E. 
Published: March 2009

SummaryBackground
The molecular determinants of the severity and persistence of allergic asthma remain poorly understood. Suppressor of cytokine signalling 1 (SOCS1) is a negative regulator of IL‐4‐dependent pathways in vitro and might therefore control T‐helper type 2 (Th2) immunity associated traits, such as IgE levels, mucin production, IL‐5 and IL‐13 induction, and eosinophilic mucosal inflammation, which are implicated in allergic asthma.Objective
To investigate the role of SOCS1 in regulating Th2‐associated disease traits in a murine sub‐chronic aeroallergen‐driven asthma model.Methods
Following sensitization and challenge with ovalbumin (OVA), bronchoalveolar lavage and serum were collected from mice lacking the Socs1 gene on an IFN‐γ null background (Socs1−/−Ifnγ−/−). The composition of infiltrating cells in the lung, serum IgE and IgG1 levels and cytokine levels were analysed.Results
Serum IgE levels and infiltrating eosinophils were considerably increased in the lungs of OVA‐treated Socs1−/−Ifnγ−/− mice compared with Ifnγ−/− and C57BL/6 controls. Expression of the Th2 cytokines, IL‐4, IL‐5 and IL‐13 was increased in CD4+ cells and lung tissue from OVA‐treated Socs1−/−Ifnγ−/− mice. IgE, IL‐5 levels and infiltrating eosinophils were also elevated in saline‐treated Socs1−/−Ifnγ−/− mice, suggesting that in the absence of SOCS1, mice are already biased towards a Th2 response. It is at present unclear whether the elevated cytokine levels are sufficient to result in the exacerbated Th2 response to OVA challenge or whether enhanced intra‐cellular signalling also contributes. Surprisingly, of the various IL‐4/IL‐13 responsive genes tested, only Arginase I appeared to be modestly up‐regulated in the lungs of OVA‐treated Socs1−/−Ifnγ−/− mice, suggesting that regulation by SOCS1 occurs primarily in haematopoietic cells and not in the airway epithelium.Conclusions
Together these results indicate that SOCS1 is an important regulator of the Th2 response.
Characterization of NVX‐207, a novel betulinic acid‐derived anti‐cancer compound
Authors: Willmann M. , Wacheck V. , Buckley J. , Nagy K. , Thalhammer J. , Paschke R. , Triche T. , Jansen B. , Selzer E. 
Published: March 2009

AbstractBackground Development of betulinic acid derivatives for clinical use has been hampered by adverse pharmacological and physico‐chemical characteristics of this class of compounds. We here present a novel semi‐synthetic betulinic acid‐derived drug candidate well suited for further clinical development.Materials and methods In vitroactivity and mode of action of NVX‐207 were determined using normal as well as cancer cell lines. Gene expression profiling was performed with Affymetrix U133 microarrays. NVX‐207 binding partners were identified using a heterobifunctional chemical crosslinker system. Potential binding proteins were identified by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) analysis. Clinical studies were conducted in canine cancer patients suffering from spontaneously arising pre‐treated tumours.Results NVX‐207 showed anti‐tumour activity (mean IC50 = 3·5 μM) against various human and canine cell lines. NVX‐207‐induced apoptosis was associated with activation of the intrinsic apoptotic pathway via cleavage of caspases ‐9, ‐3, ‐7 and of poly (ADP‐ribose) polymerase (PARP). Global gene expression profiling demonstrated regulation of genes associated with lipid metabolism, most notably an upregulation of genes coding for insulin‐induced gene 1 (Insig‐1), low‐density lipoprotein receptor (LDL‐R) and of 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG‐CoA). NVX‐207 bound to apolipoprotein A‐I, a major regulator of lipid metabolism and cholesterol transport. A phase I/II study in dogs suffering from naturally occurring cancer receiving local treatment of NVX‐207 (10 mg mL−1) showed excellent clinical responses including a complete remission in so far 5/5 treated animals.Conclusions NVX‐207 is well tolerated and has significant anti‐cancer activityin vitroandin vivoin dogs with treatment‐resistant malignancies.
Biodiversity indicators in European ground waters: towards a predictive model of stygobiotic species richness
Authors: STOCH FABIO , ARTHEAU MALVINA , BRANCELJ ANTON , GALASSI DIANA M. P. , MALARD FLORIAN 
Published: March 2009

Summary1. Estimates of species richness obtained from exhaustive field inventories over large spatial scales are expensive and time‐consuming. For this reason, efficiency demands the use of indicators as ‘surrogates’ of species richness. Biodiversity indicators are defined herein as a limited suite of taxonomic groups the species richness of which is correlated with the species richness of all other taxonomic groups present in the survey area.2. Species richness in ground water was assessed at different spatial scales using data collected from six regions in Europe. In total, 375 stygobiotic species were recorded across 1157 sites and 96 aquifers. The taxonomic groups collected from more than one site and with more than two species (Oligochaeta, Gastropoda, Cyclopoida, Harpacticoida, Ostracoda, Isopoda, Amphipoda, Bathynellacea and Acari) were used to develop nonparametric models to predict stygobiotic biodiversity at the aquifer scale.3. Pair‐wise correlations between taxonomic groups were low, i.e. variation in species richness of a single taxonomic group did not usually reflect variation of the other groups. In contrast, multiple regressions calculated between species richness of any combination of taxa and extra‐group species richness along the six regions resulted in a number of significant relationships.4. These results suggest that some taxonomic groups (mainly Copepoda and Amphipoda and, to a lesser extent, Oligochaeta and Gastropoda) combined in different ways across the regions, were good biodiversity indicators in European groundwater ecosystems. However, the uneven distribution of taxonomic groups prevented selection of a common set of indicators for all six regions. Faunal differences among regions are presumably related to both historical and ecological factors, including palaeogeography, palaeoecology, geology, aquifer fragmentation and isolation, and, less clearly, anthropogenic disturbance.
Environmental flows and the European Water Framework Directive
Authors: ACREMAN M. C. , FERGUSON A. J. D. 
Published: March 2009

Summary1. Environmental flows is now a widely accepted term that covers the quantity, timing, duration, frequency and quality of water flows required to sustain freshwater, estuarine and near‐shore ecosystems and the human livelihoods and well‐being that depend on them.2. The Water Framework Directive (WFD) of the European Union does not use the term environmental flows explicitly, but requires member states to achieve good ecological status (GES) in all waterbodies, which is assessed by reference to aquatic biology. Nevertheless, it is accepted that ecologically appropriate hydrological regimes are necessary to meet this status. Implementing environmental flows will be a key measure for restoring and managing river ecosystems.3. The WFD explicitly requires stakeholder involvement, but this has been interpreted as largely a dissemination exercise by national government agencies. Stakeholders are no longer involved in negotiation over ecological objectives as these are pre‐set in the WFD. However, stakeholders may be more involved in reviewing standards and agreeing to measures to restore river ecosystems to the status required by the WFD.4. The U.K. has undertaken two major projects to set environmental standards for water resources (i) to define water abstraction limits that maintain a healthy river ecosystem and (ii) to define ecologically appropriate flow releases from reservoirs.5. Implementation of environmental flows remains a major issue, but new ideas such as time‐limited licences and licence trading are being tried.
Reserve selection for conserving groundwater biodiversity
Authors: MICHEL GEORGES , MALARD FLORIAN , DEHARVENG LOUIS , DI LORENZO TIZIANA , SKET BORIS , DE BROYER CLAUDE 
Published: March 2009

Summary1. A possible conservation strategy to minimise the risk of groundwater biodiversity loss due to human activities consists in designing a network of reserve areas at the continental scale that collectively include most groundwater species. To this end, we compared the efficiency of three area selection methods (species richness hotspots, endemism hotspots and complementarity) and examined the influence of spatial constraints (reduced extent and increased aggregation of reserve areas) on the representation of 1059 groundwater species in six European regions.2. Presence data from a data base elaborated as part of a European initiative on groundwater biodiversity, the PASCALIS project, were referenced onto 4675 grid cells (0.2 by 0.2°). Complementary performed much better than traditional selection methods for maximising species representation in a reserve network arbitrarily limited to 10% of all the cells containing groundwater fauna. It captured 155 more species than areas selected on richness and 77 more species than areas selected on endemism hotspots.3. Representing species in a specified proportion of their area of occupancy (i.e. 100%, 50% and 10% of the area of occupancy of species occurring in 1, ≤10, and >10 cells, respectively) required inclusion of 46% of the cells containing groundwater fauna. The reserve network needed to achieve this level of coverage may be too large and fragmented to be implemented and managed in practice.4. Reduction of the reserve areas to 10% of the landscape containing groundwater fauna and their aggregation into a smaller number of cell clusters resulted in a more realistic reserve network that represented 73.8% (782 species) and 59.1% (274 endemics) of the total number of species and endemics, respectively.5. We propose several research priorities to improve the design of effective groundwater reserve networks in Europe: (i) devising sampling strategies that reduce uncertainties in the placement of reserves and increase the number of alternative reserve networks and (ii) shifting from a grid‐cell selection approach to an aquifer‐selection approach that incorporates species representation targets, minimum space requirement and also socio‐economic costs related to the vulnerability of aquifers and degree of human activity in the catchment.
Influence of geographical extent on typology‐ and model‐based assessments of taxonomic completeness of river macroinvertebrates
Authors: AROVIITA JUKKA , MYKRÄ HEIKKI , MUOTKA TIMO , HÄMÄLÄINEN HEIKKI 
Published: March 2009

Summary1. River InVertebrate Prediction and Classification System (RIVPACS)‐type predictive models are increasingly used to assess the biological condition of freshwaters, but management schemes may also be based on a priori groupings of similar water bodies (typologies) to control for natural variation in biota. The two approaches may lead to disagreements of the biological status of a site, depending on, for example, the spatial scale at which assessments are conducted.2. We used data from 96 reference and 134 potentially impacted sites from Western and Central Finland to compare RIVPACS‐type models and a simple size‐based typology of rivers for the assessment of taxonomic completeness (the quotient of the Observed‐to‐Expected number of predicted taxa, O / E) of riffle macroinvertebrates. We specifically examined how geographical extent influences bioassessment performance (accuracy, precision and sensitivity to detect impact) of the two approaches. To fully examine the behaviour of the O / E‐index with the two approaches at differing spatial scales, we performed all assessments with a full range of thresholds for predicted taxa occurrence probabilities (pt from 0+ to 0.9).3. Both approaches performed consistently better than the corresponding null models. At the larger extent (i.e. assessment encompassing the whole study area), the RIVPACS‐approach performed in all aspects better than the typology‐approach. However, at the smaller extent (i.e. regional assessments) the RIVPACS‐type models and the typologies showed similar accuracy to predict the actual fauna (mean E), similar precision (SD) of cross‐validated O / E and similar sensitivity to detect sites with human impairment.4. SD(O / E) decreased (i.e. precision increased) consistently with increasing pt. However, both approaches were most sensitive at intermediate pt:s (c. 0.2–0.6) when taxa with low predicted occurrence probabilities were excluded.5. Our results show that RIVPACS‐type predictive models are less susceptible to variations in spatial scale, whereas the performance of a priori typologies increases with decreasing spatial extent. Thus, RIVPACS‐type models are more efficient for large‐scale bioassessments, but at restricted spatial scales, or with an otherwise biologically meaningful stratification, simple a priori classifications can be equally useful for the assessment of taxonomic completeness of river macroinvertebrates.
Overexpression of chromatin assembly factor‐1 (CAF‐1) p60 is predictive of adverse behaviour of prostatic cancer
Authors: Staibano Stefania , Mascolo Massimo , Mancini Francesco Paolo , Kisslinger Annamaria , Salvatore Gaetano , Di Benedetto Maria , Chieffi Paolo , Altieri Vincenzo , Prezioso Domenico , Ilardi Gennaro , De Rosa Gaetano , Tramontano Donatella 
Published: March 2009

Aims:  Prostatic cancer may remain organ‐confined indefinitely; in a number of patients, however it gives rise to clinical symptoms and death. The biological behaviour of this tumour mostly remains difficult to predict. A promising tool for diagnosis and prognosis of some human tumours is the chromatin assembly factor‐1 (CAF‐1), involved in the control of higher order chromatin organization. The aim was to explore the role of CAF‐1/p60 protein as a new prognostic marker for prostatic cancer.Methods and results:  The expression of CAF‐1/p60 was evaluated by immunohistochemistry and Western blotting in a selected series of prostatic cancers and in prostatic cancer cell lines. Results were compared with clinicopathological data and outcome of patients. CAF‐1/p60 was expressed in all cases, with a linear increase from low‐grade tumours (Gleason score <7) to high‐grade prostatic cancers (Gleason score >7). By comparing results with follow‐up data, a significant association between overexpression of CAF‐1/p60 and unfavourable behaviour of prostatic cancer emerged, and its predictive value was independent of classical prognostic factors.Conclusions:  In our series of cases, overexpression of CAF‐1/p60 characterized prostatic cancers with a worse prognosis. CAF‐1/p60 has a potential role as a new reliable prognostic biomarker for prostatic cancer.