bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leishmanicidal effect ofSpiranthera odoratíssima(Rutaceae) and its isolated alkaloid skimmianine occurs by a nitric oxide dependent mechanism
Authors: DOS SANTOS ROGERIO ALEXANDRE NUNES , BATISTA JOÃO , ROSA SUELLEN IARA GUIRRA , TORQUATO HERON FERNANDES , BASSI CARMEN LÚCIA , RIBEIRO TEREZA AUXILIADORA NASCIMENTO , DE SOUSA PAULO TEIXEIRA , BESSERA ÂNGELA MÁRCIA SELHORST E SILVA , FONTES COR JESUS FERNANDES , DA SILVA LUIZ EVERSON , PIUVEZAM MÁRCIA REGINA 
Published: August 2011

SUMMARYLeishmaniasis is one of the neglected diseases. High cost, systemic toxicity, and diminished efficacy due to development of resistance by the parasites has a negative impact on the current treatment options. Thus, the search for a new, effective and safer anti-leishmanial drug becomes of paramount importance. Compounds derived from natural products may be a better and cheaper source in this regard. This study evaluated thein vitroanti-leishmanial activity ofSpiranthera odoratíssima(Rutaceae) fractions and isolated compounds, using promastigote and amastigote forms of differentLeishmaniaspecies. J774 A.1 macrophage was used as the parasite host cell for thein vitroassays. Evaluations of cytoxicity, nitric oxide (NO), interleukin-10 andin silicoanalysis were carried out.In vitroexperiments showed that the fruit hexanic fraction (Fhf) and its alkaloid skimmianine (Skm) have a significant (P<0·001) effect againstL. braziliensis. This anti-L. braziliensisactivity of Fhf and Skm was due to increased production of NO and attenuation of IL-10 production in the macrophages at concentrations ranging from 1·6 to 40·0μg/ml. Thein silicoassay demonstrated significant interaction between Skm and amino acid residues of NOS2. Skm is thus a promising drug candidate forL. braziliensisdue to its potent immunomodulatory activity.
Climate influences parasite-mediated competitive release
Authors: LARSEN MARTIN H. , JENSEN K. THOMAS , MOURITSEN KIM N. 
Published: August 2011

SUMMARYParasitism is believed to play an important role in maintaining species diversity, for instance by facilitating coexistence between competing host species. However, the possibility that environmental factors may govern the outcome of parasite-mediated competition has rarely been considered. The closely related amphipodsCorophium volutatorandCorophium arenariumboth serve as second intermediate host for detrimental trematodes.Corophium volutatoris the superior competitor of the two, but also suffers from higher mortality when exposed to infective trematode stages. Here, we report parasite-mediated competitive release ofC. arenariumin an intertidal habitat, in part triggered by unusually high temperatures linked to the North Atlantic climate oscillation (NAO). The elevated temperatures accelerated the transmission of cercariae from sympatric first intermediate hosts (mud snails) to amphipods, causing a local collapse of the parasite-sensitiveC. volutatorpopulation and concordant increase in the abundance of the competitively inferiorC. arenarium.
The P2′ residue is a key determinant of mesotrypsin specificity: engineering a high-affinity inhibitor with anticancer activity
Authors: Salameh Moh'd A. , Soares Alexei S. , Hockla Alexandra , Radisky Derek C. , Radisky Evette S. 
Published: August 2011

PRSS3/mesotrypsin is an atypical isoform of trypsin, the up-regulation of which has been implicated in promoting tumour progression. Mesotrypsin inhibitors could potentially provide valuable research tools and novel therapeutics, but small-molecule trypsin inhibitors have low affinity and little selectivity, whereas protein trypsin inhibitors bind poorly and are rapidly degraded by mesotrypsin. In the present study, we use mutagenesis of a mesotrypsin substrate, APPI (amyloid precursor protein Kunitz protease inhibitor domain), and of a poor mesotrypsin inhibitor, BPTI (bovine pancreatic trypsin inhibitor), to dissect mesotrypsin specificity at the key P2′ position. We find that bulky and charged residues strongly disfavour binding, whereas acidic residues facilitate catalysis. Crystal structures of mesotrypsin complexes with BPTI variants provide structural insights into mesotrypsin specificity and inhibition. Through optimization of the P1 and P2′ residues of BPTI, we generate a stable high-affinity mesotrypsin inhibitor with an equilibrium binding constant Ki of 5.9 nM, a &gt;2000-fold improvement in affinity over native BPTI. Using this engineered inhibitor, we demonstrate the efficacy of pharmacological inhibition of mesotrypsin in assays of breast cancer cell malignant growth and pancreatic cancer cell invasion. Although further improvements in inhibitor selectivity will be important before clinical potential can be realized, the results of the present study support the feasibility of engineering protein protease inhibitors of mesotrypsin and highlight their therapeutic potential.
SEED: efficient clustering of next-generation sequences
Authors: Bao Ergude , Jiang Tao , Kaloshian Isgouhi , Girke Thomas 
Published: August 2011

Abstract
Motivation: Similarity clustering of next-generation sequences (NGS) is an important computational problem to study the population sizes of DNA/RNA molecules and to reduce the redundancies in NGS data. Currently, most sequence clustering algorithms are limited by their speed and scalability, and thus cannot handle data with tens of millions of reads.
Results: Here, we introduce SEED—an efficient algorithm for clustering very large NGS sets. It joins sequences into clusters that can differ by up to three mismatches and three overhanging residues from their virtual center. It is based on a modified spaced seed method, called block spaced seeds. Its clustering component operates on the hash tables by first identifying virtual center sequences and then finding all their neighboring sequences that meet the similarity parameters. SEED can cluster 100 million short read sequences in &lt;4 h with a linear time and memory performance. When using SEED as a preprocessing tool on genome/transcriptome assembly data, it was able to reduce the time and memory requirements of the Velvet/Oasis assembler for the datasets used in this study by 60–85% and 21–41%, respectively. In addition, the assemblies contained longer contigs than non-preprocessed data as indicated by 12–27% larger N50 values. Compared with other clustering tools, SEED showed the best performance in generating clusters of NGS data similar to true cluster results with a 2- to 10-fold better time performance. While most of SEED's utilities fall into the preprocessing area of NGS data, our tests also demonstrate its efficiency as stand-alone tool for discovering clusters of small RNA sequences in NGS data from unsequenced organisms.
Availability: The SEED software can be downloaded for free from this site: http://manuals.bioinformatics.ucr.edu/home/seed.
Contact: thomas.girke@ucr.edu
Supplementary information: Supplementary data are available at Bioinformatics online
Evaluation of Phosphonate Treatments for Control of Phytophthora Crown Rot of Walnut
Authors: Browne G. T. , Prichard T. L. , Schmidt L. S. , Krueger W. H. 
Published: August 2011

Preventive foliar and soil (chemigation) applications of phosphonate were evaluated in a factorial manner for control of cankers caused by Phytophthora citricola in a Persian walnut orchard, cultivar Chandler. In each of two experiments, a foliar treatment was applied once in the second week of September, and a soil chemigation treatment was applied three times at weekly intervals from the last week of August to the second week of September; the treatments were applied separately and in combination to the walnut trees. At 1 and at 7 months after completion of the treatments, the trees were wound inoculated with P. citricola. Treatment efficacy was assessed by measuring the area of resulting trunk cankers. Trees that had received a foliar spray with phosphonate consistently developed less necrotic bark area than trees that had not received the treatment. This effect was evident following the inoculations made 1 and 7 months after phosphonate treatments. Chemigation with phosphonate contributed to canker suppression only following inoculations made 1 month after treatment in experiment 1; the suppression was not evident in experiment 2. The results suggest that a late-summer foliar spray treatment with phosphonate, but not necessarily short-term chemigation treatments, may help to reduce losses caused by P. citricola in Persian walnut. Accepted for publication 4 March 2011. Published 1 June 2011.
First Report of Stem Dieback and Leaf Spot of Leucothoe caused by Cylindrocladium colhounii in North Carolina
Authors: Benson D. M. , Parker K. C. , Ivors K. L. 
Published: August 2011

Leucothoe fontanesiana (L. catesbaei) and L. axillaris are common in the nursery trade for landscape use in USDA Zones 5 to 8. This is the first report of C. colhounii attacking L. axillaris and L. fontanesiana in North Carolina. Accepted for publication 14 April 2011. Published 28 June 2011.
Thousand Cankers Disease is Widespread in Black Walnut in the Western United States
Authors: Tisserat Ned , Cranshaw Whitney , Putnam Melodie L. , Pscheidt Jay , Leslie Charles A. , Murray Marion , Hoffman James , Barkley Yvonne , Alexander Kathleen , Seybold Steven J. 
Published: August 2011

Thousand cankers disease of black walnut is caused by aggressive feeding by the walnut twig beetle and subsequent canker development around beetle galleries caused the fungus Geosmithia morbida. The authors We confirmed the presence of G. morbida from symptomatic black walnut or hybrids in California, Colorado, Idaho, New Mexico, Oregon, Utah, and Washington. Thousand cankers disease continues to cause extensive mortality to black walnut over a wide geographic region and is intensifying in the western United States. Accepted for publication 2 June 2011. Published 30 June 2011.
Expansion of Groundnut ringspot virus Host and Geographic Ranges in Solanaceous Vegetables in Peninsular Florida
Authors: Webster Craig G. , Turechek William W. , Mellinger H. Charles , Frantz Galen , Roe Nancy , Yonce Henry , Vallad Gary E. , Adkins Scott 
Published: August 2011

To the best of our knowledge, this is the first report of GRSV infecting tomatillo and eggplant, and it is the first report of GRSV infecting pepper in the United States. This first identification of GRSV-infected crop plants in commercial fields in Palm Beach and Manatee Counties demonstrates the continuing geographic spread of the virus into additional vegetable production areas of Florida. This information indicates that a wide range of solanaceous plants is likely to be infected by this emerging viral pathogen in Florida and beyond. Accepted for publication 27 June 2011. Published 25 July 2011.
Evolution of theS-Locus Region in Arabidopsis Relatives
Authors: Guo Ya-Long , Zhao Xuan , Lanz Christa , Weigel Detlef 
Published: August 2011

AbstractThe S locus, a single polymorphic locus, is responsible for self-incompatibility (SI) in the Brassicaceae family and many related plant families. Despite its importance, our knowledge of S-locus evolution is largely restricted to the causal genes encoding the S-locus receptor kinase (SRK) receptor and S-locus cysteine-rich protein (SCR) ligand of the SI system. Here, we present high-quality sequences of the genomic region of six S-locus haplotypes: Arabidopsis (Arabidopsis thaliana; one haplotype), Arabidopsis lyrata (four haplotypes), and Capsella rubella (one haplotype). We compared these with reference S-locus haplotypes of the self-compatible Arabidopsis and its SI congener A. lyrata. We subsequently reconstructed the likely genomic organization of the S locus in the most recent common ancestor of Arabidopsis and Capsella. As previously reported, the two SI-determining genes, SCR and SRK, showed a pattern of coevolution. In addition, consistent with previous studies, we found that duplication, gene conversion, and positive selection have been important factors in the evolution of these two genes and appear to contribute to the generation of new recognition specificities. Intriguingly, the inactive pseudo-S-locus haplotype in the self-compatible species C. rubella is likely to be an old S-locus haplotype that only very recently became fixed when C. rubella split off from its SI ancestor, Capsella grandiflora.
Functional Analysis of All AGAMOUS Subfamily Members in Rice Reveals Their Roles in Reproductive Organ Identity Determination and Meristem Determinacy
Authors: Dreni Ludovico , Pilatone Alessandro , Yun Dapeng , Erreni Stefano , Pajoro Alice , Caporali Elisabetta , Zhang Dabing , Kater Martin M. 
Published: August 2011

AbstractReproductive organ development is one of the most important steps in the life cycle of plants. Studies using core eudicot species like thale cress (Arabidopsis thaliana) and snapdragon (Antirrhinum majus) have shown that MADS domain transcription factors belonging to the AGAMOUS (AG) subfamily regulate the identity of stamens, carpels, and ovules and that they are important for floral meristem determinacy. Here, we investigate the genetic interactions between the four rice (Oryza sativa) AG subfamily members, MADS3, MADS13, MADS21, and MADS58. Our data show that, in contrast with previous reports, MADS3 and MADS58 determine stamen and carpel identity and, together with MADS13, are important for floral meristem determinacy. In the mads3 mads58 double mutant, we observed a complete loss of reproductive organ identity and massive accumulation of lodicules in the third and fourth floral whorls. MADS21 is an AGL11 lineage gene whose expression is not restricted to ovules. Instead, its expression profile is similar to those of class C genes. However, our genetic analysis shows that MADS21 has no function in stamen, carpel, or ovule identity determination.
Differences in both prevalence and titre of specific immunoglobulin E among children with asthma in affluent and poor communities within a large town in Ghana
Authors: Stevens W. , Addo‐Yobo E. , Roper J. , Woodcock A. , James H. , Platts‐Mills T. , Custovic A. 
Published: August 2011

Summary
Background Reports from several African countries have noted an increasing prevalence of asthma in areas of extensive urbanization.
Objective To investigate the relevance of allergen‐specific sensitization and body mass index (BMI) to asthma/wheezing and exercise‐induced bronchospasm (EIB) among children from affluent and poorer communities within a large town in Ghana.
Methods Children with physician‐diagnosed asthma and/or current wheezing aged 9–16 years (n=99; cases) from three schools with differing socio‐economic backgrounds [urban affluent (UA), urban poor (UP) or suburban/rural (SR)] were recruited from a cross‐sectional study (n=1848) in Kumasi, Ghana, and matched according to age, sex and area of residence with non‐asthmatic/non‐wheezy controls. We assayed sera for IgE antibodies to mite, cat, dog, cockroach, Ascaris and galactose‐α‐1,3‐galactose.
Results Children from the UA school had the lowest total serum IgE. However, cases from the UA school had a higher prevalence and mean titre of sIgE to mite (71.4%, 21.2 IU/mL) when compared with controls (14.3%, 0.8 IU/mL) or cases from UP (30%, 0.8 IU/mL) and SR community (47.8%, 1.6 IU/mL). While similar findings were observed with EIB in the whole population, among cases there was no difference in IgE antibody prevalence or titre between children with or without EIB. BMI was higher among UA children with and without asthma; in UP and SR communities, children with EIB (n=14) had a significantly higher BMI compared with children with asthma/wheezing without EIB (n=38) (18.2 vs. 16.4, respectively, P<0.01).
Conclusions and Clinical Relevance In the relatively affluent school, asthma/wheezing and EIB were associated with high titre IgE antibodies to mite, decreased total IgE, and increased BMI. This contrasted with children in the urban poor school and suggests that changes relevant to a Western model of childhood asthma can occur within a short geographical distance within a large city in Africa.
Cite this as: W. Stevens, E. Addo‐Yobo, J. Roper, A. Woodcock, H. James, T. Platts‐Mills and A. Custovic, Clinical & Experimental Allergy, 2011 (41) 1587–1594.
Lymphangioma of the pancreas: a multimodal approach to pre‐operative diagnosis
Authors: Fonseca R. , Pitman M. B. 
Published: August 2011

Background:  Lymphangioma of the pancreas is an extremely rare benign tumour of lymphatic origin, with only four cases diagnosed by EUS‐FNA reported to date.Methods and materials:  Five cases of either cytologically or histologically diagnosed pancreatic lymphangioma with pre‐operative cytological analysis by EUS‐FNAC were reviewed.Results:  All patients were female, with a mean age of 56.4 years. By imaging, the cystic lesions ranged in size from 2 to 7 cm (mean 4.5 cm) and were mainly located in the head of the pancreas. All cysts had thin walls and no cyst demonstrated a mural nodule. Diagnosis based on imaging features was benign in all cases due to the absence of high‐risk features. Four samples were sent for biochemical analysis, which showed low CEA levels (range, <0.5–19.4 ng/ml; mean, 5.45 ng/ml) and CA 19.9 and CA 72.4 levels within normal range. All cyst fluids showed numerous small lymphocytes with no atypia; no epithelial cells were present, including no gastrointestinal contamination. Flow cytometry in two cases showed T lymphocytes with a mature phenotype. Surgical resection in two patients confirmed the cytological diagnosis. Benign clinical follow‐up was available in three patients at 2, 3 and 3.5 years.Conclusion:  A multimodal approach to cytological diagnosis (combining clinical, radiological and cyst fluid gross, biochemical and cytological characteristics) can lead to the diagnosis of this cystic neoplasm and distinguish it from other more common cysts in the pancreas, potentially avoiding the need for unnecessary surgery.
Effects of soil moisture on the temperature sensitivity of heterotrophic respiration vary seasonally in an old‐field climate change experiment
Authors: Suseela Vidya , Conant Richard T. , Wallenstein Matthew D. , Dukes Jeffrey S. 
Published: August 2011

AbstractMicrobial decomposition of soil organic matter produces a major flux of CO2 from terrestrial ecosystems and can act as a feedback to climate change. Although climate‐carbon models suggest that warming will accelerate the release of CO2 from soils, the magnitude of this feedback is uncertain, mostly due to uncertainty in the temperature sensitivity of soil organic matter decomposition. We examined how warming and altered precipitation affected the rate and temperature sensitivity of heterotrophic respiration (Rh) at the Boston‐Area Climate Experiment, in Massachusetts, USA. We measured Rh inside deep collars that excluded plant roots and litter inputs. In this mesic ecosystem, Rh responded strongly to precipitation. Drought reduced Rh, both annually and during the growing season. Warming increased Rh only in early spring. During the summer, when Rh was highest, we found evidence of threshold, hysteretic responses to soil moisture: Rh decreased sharply when volumetric soil moisture dropped below ~15% or exceeded ~26%, but Rh increased more gradually when soil moisture rose from the lower threshold. The effect of climate treatments on the temperature sensitivity of Rh depended on the season. Apparent Q10 decreased with high warming (~3.5 °C) in spring and fall. Presumably due to limiting soil moisture, warming and precipitation treatments did not affect apparent Q10 in summer. Drought decreased apparent Q10 in fall compared to ambient and wet precipitation treatments. To our knowledge, this is the first field study to examine the response of Rh and its temperature sensitivity to the combined effects of warming and altered precipitation. Our results highlight the complex responses of Rh to soil moisture, and to our knowledge identify for the first time the seasonal variation in the temperature sensitivity of microbial respiration in the field. We emphasize the importance of adequately simulating responses such as these when modeling trajectories of soil carbon stocks under climate change scenarios.
Cellular Immune Responses in Mice Induced by M. tuberculosis PE35‐DNA Vaccine Construct
Authors: Hanif S. N. M. , Al‐Attiyah R. , Mustafa A. S. 
Published: August 2011

AbstractThe PE35 (Rv3872) gene of Mycobacterium tuberculosis is present in the region of difference (RD) one that is deleted in all vaccine strains of Mycobacterium bovis bacillus Calmette Guerin. The aim of this study was to clone PE35 DNA into a DNA vaccine plasmid with CMV promoter and interleukin‐2 secretory signal and evaluate the recombinant plasmid for induction of antigen‐specific cellular responses in mice. DNA corresponding to PE35 was PCR amplified from the genomic DNA of M. tuberculosis H37Rv, cloned into pGEMT‐Easy vector and sub‐cloned into the DNA vaccine vector pUMVC6. BALB/c mice were immunized with recombinant pUMVC6/PE35 and spleen cells were tested for T‐helper (Th)1‐type (antigen‐induced proliferation and secretion of IFN‐γ) and Th2‐type (IL‐5), and anti‐inflammatory (IL‐10) cytokine responses to pure recombinant PE35 protein and its synthetic peptides. Mice immunized with the recombinant plasmid DNA (pUMVC6/PE35) showed positive Th1‐type cellular responses to pure PE35, but not to an irrelevant antigen, i.e. PPE68 (Rv3873). However, the vaccine construct did not induce antigen‐specific Th2‐type (IL‐5) or anti‐inflammatory (IL‐10) reactivity to PE35. Testing with synthetic peptides showed that Th1‐type cells recognizing various epitopes of PE35 were induced in mice immunized with pUMVC6/PE35 DNA. These results suggest that pUMVC6/PE35 may be useful as a safer vaccine candidate against TB.
Classical biological control of Fallopia japonica in the United Kingdom – lessons for Europe
Authors: SHAW R H , TANNER R , DJEDDOUR D , CORTAT G 
Published: August 2011

Shaw RH, Tanner R, Djeddour D & Cortat G (2011). Classical biological control of Fallopia japonica in the United Kingdom – lessons for Europe. Weed Research51, 552–558.SummaryThe programme for the biological control of Fallopia japonica in the United Kingdom has provided some valuable insights into the practicalities of delivering a classical biological control programme against a weed in the European Union. In the absence of tailored legislation, the licensing process was complex but not prohibitive. It involved the production of a pest risk analysis (PRA; based on the EPPO template), an application through national legislation (the UK Wildlife and Countryside Act), the production of peer‐reviewed publications, expert committee consideration, further commissioned peer review and public consultations prior to final Ministerial judgement, which was granted in March 2010. Although there is room for some streamlining in the process, this approach has proved to be effective and robust and should be applicable to similar programmes in Europe. This is important, because classical biological control has considerable potential for the management of F. japonica and other weed targets throughout Europe, especially those impacting habitats where chemical use is all but impossible. The lessons learned from the knotweed biocontrol programme are discussed, and current weed biocontrol activities in Europe are briefly summarised. A classical biocontrol programme needs to deliver more than just pure science, because effective communication and negotiations in the public and political arena can provide more challenges than the traditional scientific ones.