bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea
Authors: Narihiro Takashi , Sekiguchi Yuji 
Published: January 2011

SummaryFor the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.
Disruption of the siderophore‐binding desE receptor gene in Streptomyces coelicolor A3(2) results in impaired growth in spite of multiple iron–siderophore transport systems
Authors: Tierrafría Víctor H. , Ramos‐Aboites Hilda E. , Gosset Guillermo , Barona‐Gómez Francisco 
Published: January 2011

SummaryFerrioxamines‐mediated iron acquisition by Streptomyces coelicolor A3(2) has recently received increased attention. In addition to the biological role of desferrioxamines (dFOs) as hydroxamate siderophores, and the pharmaceutical application of dFO‐B as an iron‐chelator, the ferrioxamines have been shown to mediate microbial interactions. In S. coelicolor the siderophore‐binding receptors DesE (Sco2780) and CdtB (Sco7399) have been postulated to specifically recognize and uptake FO‐E (cyclic) and FO‐B (linear) respectively. Here, disruption of the desE gene in S. coelicolor, and subsequent phenotypic analysis, is used to demonstrate a link between iron metabolism and physiological and morphological development. Streptomyces coelicolor desE mutants, isolated in both wild‐type (M145) and a coelichelin biosynthesis and transport minus background (mutant W3), a second hydroxamate siderophore system only found in S. coelicolor and related species, resulted in impaired growth and lack of sporulation. This phenotype could only be partially rescued by expression in trans of either desE and cdtB genes, which contrasted with the ability of FO‐E, and to a lesser extent of FO‐B, to fully restore growth at µM concentrations, with a concomitant induction of a marked phenotypic response involving precocious synthesis of actinorhodin and sporulation. Moreover, growth restoration of the desE mutant by complementation with desE and cdtB showed that DesE, which is universally conserved in Streptomyces, and CdtB, only present in certain streptomycetes, have partial equivalent functional roles under laboratory conditions, implying overlapping ferrioxamine specificities. The biotechnological and ecological implications of these observations are discussed.
Adenoid ameloblastoma with dentinoid and ghost cells. A composite odontogenic tumour: a rare case report and review of the literature
Authors: Sonone A. , Hande A. , Chaudhary M. , Bonde R. , Sheorain A. , Agni N. 
Published: January 2011

AbstractIn this article we report a case of rare composite odontogenic tumor, having features similar to adenoid ameloblastoma with dentinoid described previously. The histological features are similar to both ameloblastoma and AOT and show evidence of induction in the form of dentinoid. The patient was a 35 years old female. The lesion was located on right side of the mandible in premolar‐molar area. Radiograph revealed unilocular radiolucency with foci of radio‐opacities. On gross examination the tumor was cystic at places. The histopathological features consists of two patterns, one resembling AOT and other plexiform ameloblastoma. The formation of dentinoid like material was observed in association with odontogenic epithelium. Apart from this the presence of ghost cells was a unique histopathological feature.This article also reviews the various cases reported in literature and provides an insight into the nature of composite odontogenic tumor. To date only 12 cases of this uncommon composite odontogenic tumor are reported in the literature.
Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
Authors: HELYAR S. J. , HEMMER‐HANSEN J. , BEKKEVOLD D. , TAYLOR M. I. , OGDEN R. , LIMBORG M. T. , CARIANI A. , MAES G. E. , DIOPERE E. , CARVALHO G. R. , NIELSEN E. E. 
Published: January 2011

AbstractRecent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.
Effect of Acute Posttrauma Propranolol on PTSD Outcome and Physiological Responses During Script‐Driven Imagery
Authors: Hoge Elizabeth A. , Worthington John J. , Nagurney John T. , Chang Yuchiao , Kay Elaine B. , Feterowski Christine M. , Katzman Anna R. , Goetz Jared M. , Rosasco Maria L. , Lasko Natasha B. , Zusman Randall M. , Pollack Mark H. , Orr Scott. P. , Pitman Roger K. 
Published: January 2011

SUMMARYIntroduction: Animal and human research suggests that the development of posttraumatic stress disorder (PTSD) may involve the overconsolidation of memories of a traumatic experience. Previous studies have attempted to use pharmaceutical agents, especially the β‐adrenergic blocker propranolol, to reduce this overconsolidation. Aims: In this randomized, placebo‐controlled study of the efficacy of propranolol in reducing the development of PTSD, we optimized dosages and conducted both psychophysiological and clinical assessments 1 and 3 months after the traumatic event. Forty‐one emergency department patients who had experienced a qualifying acute psychological trauma were randomized to receive up to 240 mg/day of propranolol or placebo for 19 days. At 4 and 12 weeks post‐trauma, PTSD symptoms were assessed. One week later, participants engaged in script‐driven imagery of their traumatic event while psychophysiological responses were measured. Results: Physiological reactivity during script‐driven traumatic imagery, severity of PTSD symptoms, and the rate of the PTSD diagnostic outcome were not significantly different between the two groups. However, post hoc subgroup analyses showed that in participants with high drug adherence, at the 5‐week posttrauma assessment, physiological reactivity was significantly lower during script‐driven imagery in the propranolol than in the placebo subjects. Conclusions: The physiological results provide some limited support for a model of PTSD in which a traumatic conditioned response is reduced by posttrauma propranolol. However, the clinical results from this study do not support the preventive use of propranolol in the acute aftermath of a traumatic event.
Management challenges in psychiatric patients with severe mandibular pain: a case report
Authors: Cheng A , Kunchur R , Goss AN 
Published: January 2011

AbstractA 68‐year‐old man was admitted to the psychiatric unit of a major hospital as he was threatening self‐harm due to uncontrolled left mandibular pain. Although he had significant psychiatric issues, psychiatric treatment did not help him. Further review at three weeks post‐admission showed that he had had many months of unsuccessful dental treatment and this had triggered his psychiatric crisis. Multidisciplinary investigation and communication showed that he had trigeminal neuralgia secondary to vascular changes in his temporal lobe. He responded well to explanation and anti‐neuralgic medication. Simple guidelines on how dental practitioners can cope with such patients are presented.
A New
Technique to Determine Convection Coefficients With Flow Through Particle
Beds
Authors: Nie Xiaodong , Evitts Richard , Besant Robert , Bolster John 
Published: January 2011

Abstract
A new method for determining the heat transfer coefficient for air flowing steadily through beds of particles is presented. In this technique, a step change in the inlet air temperature is applied to a small test bed and temperature distributions in the bed and at the air outlet are sampled over a short time period. The convective heat transfer coefficient is determined using data from the convective heat transfer process in the bed where the analysis includes the partial differential equation that describes the transient energy storage in the particles within the bed. The analysis is performed for a short time duration when the temperature distribution in the particle bed is almost linear along the axis of the bed. This time period permits the most accurate determination of the heat transfer coefficient using the data. Using beds of spherical particles a new correlation is developed for the Nusselt number versus the Reynolds number (5&lt;Redh&lt;280) and includes the uncertainty bounds. This new correlation compares well with correlations developed by some other researchers for similar spherical particle beds.
Mutational Analyses of Open Reading Frames within the
vraSR
Operon and Their Roles in the Cell Wall Stress Response of
Staphylococcus aureus
Authors: McCallum N. , Meier P. Stutzmann , Heusser R. , Berger-Bächi B. 
Published: January 2011

ABSTRACT

The exposure of
Staphylococcus aureus
to a broad range of cell wall-damaging agents triggers the induction of a cell wall stress stimulon (CWSS) controlled by the VraSR two-component system. The
vraSR
genes form part of the four-cistron autoregulatory operon
orf1-yvqF-vraS-vraR
. The markerless inactivation of each of the genes within this operon revealed that
orf1
played no observable role in CWSS induction and had no influence on resistance phenotypes for any of the cell envelope stress-inducing agents tested. The remaining three genes were all essential for the induction of the CWSS, and mutants showed various degrees of increased susceptibility to cell wall-active antibiotics. Therefore, the role of YvqF in
S. aureus
appears to be opposite that in other Gram-positive bacteria, where YvqF homologs have all been shown to inhibit signal transduction. This role, as an activator rather than repressor of signal transduction, corresponds well with resistance phenotypes of ΔYvqF mutants, which were similar to those of ΔVraR mutants in which CWSS induction also was completely abolished. Resistance profiles of ΔVraS mutants differed phenotypically from those of ΔYvqF and ΔVraR mutants on many non-ß-lactam antibiotics. ΔVraS mutants still became more susceptible than wild-type strains at low antibiotic concentrations, but they retained larger subpopulations that were able to grow on higher antibiotic concentrations than ΔYvqF and ΔVraR mutants. Subpopulations of ΔVraS mutants could grow on even higher glycopeptide concentrations than wild-type strains. The expression of a highly sensitive CWSS-luciferase reporter gene fusion was up to 2.6-fold higher in a ΔVraS than a ΔVraR mutant, which could be linked to differences in their respective antibiotic resistance phenotypes. Bacterial two-hybrid analysis indicated that the integral membrane protein YvqF interacted directly with VraS but not VraR, suggesting that it plays an essential role in sensing the as-yet unknown trigger of CWSS induction.
Artemether and Artesunate Show the Highest Efficacies in Rescuing Mice with Late-Stage Cerebral Malaria and Rapidly Decrease Leukocyte Accumulation in the Brain
Authors: Clemmer L. , Martins Y. C. , Zanini G. M. , Frangos J. A. , Carvalho L. J. M. 
Published: January 2011

ABSTRACT

The murine model of cerebral malaria (ECM) caused by
Plasmodium berghei
ANKA (PbA) infection in susceptible mice has been extensively used for studies of pathogenesis and identification of potential targets for human CM therapeutics. However, the model has been seldom explored to evaluate adjunctive therapies for this malaria complication. A first step toward this goal is to define a treatment protocol with an effective antimalarial drug able to rescue mice presenting late-stage ECM. We evaluated the efficacy of artemisinin, artemether, artesunate, and quinine given intraperitoneally once a day, and combinations with mefloquine, in suppressing PbA infection in mice with moderate parasitemia. Artemether, artesunate, and quinine were then evaluated for efficacy in rescuing PbA-infected mice with ECM, strictly defined by using objective criteria based on the presentation of clinical signs of neurological involvement, degree of hypothermia, and performance in a set of six motor behavior tests. Artemether at 25 mg/kg presented the fastest parasite killing ability in 24 h and fully avoided recrudescence in a 5-day treatment protocol. Artemether and artesunate were equally effective in rescuing mice with late-stage ECM (46 and 43% survival, respectively), whereas quinine had a poor performance (12.5% survival). Artemether caused a marked decrease in brain leukocyte accumulation 24 h after the first dose. In conclusion, artemether and artesunate are effective in rescuing mice with late-stage ECM and decrease brain inflammation. In addition, the described protocols for more strict clinical evaluation and for rescue treatment provide a framework for studies of CM adjunctive therapies using this mouse model.
In Vitro
Activities of New 2-Substituted Quinolines against
Leishmania donovani
Authors: Loiseau Philippe M. , Gupta Suman , Verma Aditya , Srivastava Saumya , Puri S. K. , Sliman Faten , Normand-Bayle Marie , Desmaele Didier 
Published: January 2011

ABSTRACT

A series of 9 quinolines and 18 styrylquinolines was evaluated for the drugs'
in vitro
antileishmanial activities and cytotoxicities. The 7-aroylstyrylquinoline scaffold appeared to be the most promising one, with the most interesting compound, no. 35, exhibiting a 50% inhibitory concentration (IC
50
) of 1.2 μM and a selectivity index value of 121.5. Compound 35 was 10-fold and 8-fold more active than miltefosine and sitamaquine, the reference compounds, with selectivity indexes 607-fold and 60-fold higher, respectively.
Identification of the Minimal Active Sequence of an Anti-Influenza Virus Peptide
Authors: Jones Jeremy C. , Settles Erik W. , Brandt Curtis R. , Schultz-Cherry Stacey 
Published: January 2011

ABSTRACTThe antiviral peptide, entry blocker (EB), inhibits influenza virus replication by preventing attachment to cells. Here, we identified the minimal and optimal EB sequence that retained antiviral activity with a 50% inhibitory concentration (IC50) and 50% effective concentration (EC50) similar to those of the full-length EB peptide and several truncated variants that possessed up to 10-fold lower IC50s. These data have implications for improving the antiviral efficacy of EB-derived peptides while decreasing production costs and easing synthesis.
Interleukin-4-Inducing Principle from
Schistosoma mansoni
Eggs Contains a Functional C-Terminal Nuclear Localization Signal Necessary for Nuclear Translocation in Mammalian Cells but Not for Its Uptake
Authors: Kaur Ishwinder , Schramm Gabriele , Everts Bart , Scholzen Thomas , Kindle Karin B. , Beetz Christian , Montiel-Duarte Cristina , Blindow Silke , Jones Arwyn T. , Haas Helmut , Stolnik Snjezana , Heery David M. , Falcone Franco H. 
Published: January 2011

ABSTRACT

Interleukin-4-inducing principle from schistosome eggs (IPSE/alpha-1) is a protein produced exclusively by the eggs of the trematode
Schistosoma mansoni
. IPSE/alpha-1 is a secretory glycoprotein which activates human basophils via an IgE-dependent but non-antigen-specific mechanism. Sequence analyses revealed a potential nuclear localization signal (NLS) at the C terminus of IPSE/alpha-1. Here we show that this sequence (125-PKRRRTY-131) is both necessary and sufficient for nuclear localization of IPSE or IPSE-enhanced green fluorescent protein (EGFP) fusions. While transiently expressed EGFP-IPSE/alpha-1 was exclusively nuclear in the Huh7 and U-2 OS cell lines, a mutant lacking amino acids 125 to 134 showed both nuclear and cytoplasmic staining. Moreover, insertion of the IPSE/alpha-1 NLS into a tetra-EGFP construct rendered the protein nuclear. Alanine scanning mutagenesis revealed a requirement for the KRRR residues. Fluorescence microscopy depicted, and Western blotting further confirmed, that recombinant IPSE/alpha-1 protein added exogenously is rapidly internalized by CHO cells and accumulates in nuclei in an NLS-dependent manner. A mutant protein in which the NLS motif was disrupted by triple mutation (RRR to AAA) was able to penetrate CHO cells but did not translocate to the nucleus. Furthermore, the uptake of native glycosylated IPSE/alpha-1 was confirmed in human primary monocyte-derived dendritic cells and was found to be a calcium- and temperature-dependent process. Live-cell imaging showed that IPSE/alpha-1 is not targeted to lysosomes. In contrast, peripheral blood basophils do not take up IPSE/alpha-1 and do not require the presence of an intact NLS for activation. Taken together, our results suggest that IPSE/alpha-1 may have additional nuclear functions in host cells.
Transient PI3K Inhibition Induces Apoptosis and Overcomes HGF-Mediated Resistance to EGFR-TKIs inEGFRMutant Lung Cancer
Authors: Donev Ivan S. , Wang Wei , Yamada Tadaaki , Li Qi , Takeuchi Shinji , Matsumoto Kunio , Yamori Takao , Nishioka Yasuhiko , Sone Saburo , Yano Seiji 
Published: January 2011

AbstractPurpose: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI), such as gefitinib and erlotinib, show favorable response to EGFR mutant lung cancer. However, the responders acquire resistance almost without exception. We recently reported that hepatocyte growth factor (HGF) induces EGFR-TKI resistance by activating MET that restores downstream mitogen activated protein kinase (MAPK)/extracellular signal regulated kinase (ERK)1/2 and phosphoinositide 3-kinase (PI3K)/Akt signaling. The purpose of this study was to determine whether inhibition of PI3K, a downstream molecule of both EGFR and MET, could overcome HGF-mediated EGFR-TKI resistance in EGFR mutant lung cancer cells PC-9 and HCC827.Experimental Design: We explored therapeutic effect of a class I PI3K inhibitor PI-103 on HGF-induced EGFR-TKI resistance in vitro and in vivo.Results: Unlike gefitinib or erlotinib, continuous exposure with PI-103 inhibited proliferation of PC-9 and HCC827 cells, even in the presence of HGF. On the other hand, in gefitinib-resistant xenograft model by using PC-9 cells mixed with HGF high producing fibroblasts, PI-103 monotherapy did not inhibit tumor growth. However, PI-103 combined with gefitinib successfully regressed gefitinib-resistant tumor. In vitro experiments by considering short half-life of PI-103 reveal that transient exposure of PI-103 combined with gefitinib caused sustained inhibition of Akt phosphorylation, but not ERK1/2 phosphorylation, resulting in induction of tumor cell apoptosis even in the presence of HGF.Conclusions: These results indicate that transient blockade of PI3K/Akt pathway by PI-103 and gefitinib could overcome HGF-mediated resistance to EGFR-TKIs by inducing apoptosis in EGFR mutant lung cancer. Clin Cancer Res; 17(8); 2260–9. ©2011 AACR.
Acquisition of Chemoresistance and EMT Phenotype Is Linked with Activation of the Endothelin A Receptor Pathway in Ovarian Carcinoma Cells
Authors: Rosanò Laura , Cianfrocca Roberta , Spinella Francesca , Di Castro Valeriana , Nicotra Maria Rita , Lucidi Alessandro , Ferrandina Gabriella , Natali Pier Giorgio , Bagnato Anna 
Published: January 2011

AbstractPurpose: Emerging evidence suggests molecular and phenotypic association between chemoresistance and epithelial–mesenchymal transition (EMT) in cancer. Endothelin-1 (ET-1)/endothelin A receptor (ETAR) axis is implicated in the pathobiology of epithelial ovarian cancer (EOC) by driving tumor-promoting effects, including EMT. Here, we analyzed how ETAR regulates chemoresistance and EMT in EOC.Experimental Design: The effects of ET-1 axis on cell proliferation, drug-induced apoptosis, invasiveness, and EMT were analyzed in cultured EOC cells sensitive and resistant to cisplatinum and taxol. Tumor growth in response to ETAR antagonist was examined in EOC xenografts. ETAR expression was examined in 60 human EOC tumors by immunohistochemistry and correlated with chemoresistance and EMT.Results: In resistant EOC cells ET-1 and ETAR are upregulated, paralleled by enhanced mitogen activated protein kinase (MAPK) and Akt phosphorylation and cell proliferation. Moreover, in these cells the expression of E-cadherin transcriptional repressors, including Snail, Slug, and Twist, as well as of mesenchymal markers, such as vimentin and N-cadherin, were upregulated and linked with enhanced invasive behavior. Interestingly, ETAR blockade with zibotentan, a specific ETAR antagonist, or its silencing, downregulated Snail activity, restored drug sensitivity to cytotoxic-induced apoptosis, and inhibited the invasiveness of resistant cells. In vivo, zibotentan inhibited tumor growth of sensitive and resistant EOC xenografts, and sensitized to chemotherapy. Analysis of EOC human tissues revealed that ETAR is overexpressed in resistant tumors and is associated with EMT phenotype.Conclusions: Our data provide the first evidence that blockade of ETAR-driven EMT can overcome chemoresistance and inhibit tumor progression, improving the outcome of EOC patients' treatment. Clin Cancer Res; 17(8); 2350–60. ©2011 AACR.