216 results on '"Jacques RA"'
Search Results
152. Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection
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Laxmi Yeruva, Garry S. A. Myers, Nicole Spencer, Heather Huot Creasy, Nancy E. Adams, Anthony T. Maurelli, Grant R. McChesney, Mario A. Cleves, Jacques Ravel, Anne Bowlin, and Roger G. Rank
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Microbiology ,QR1-502 - Abstract
ABSTRACT It is not currently possible to predict the probability of whether a woman with a chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated with distinct chlamydial pathotypes, we utilized two Chlamydia muridarum variants (C. muridarum Var001 [CmVar001] and CmVar004) that differ in their abilities to elicit upper genital tract pathology in a mouse model. CmVar004 has a lower growth rate in vitro and induces pathology in only 20% of C57BL/6 mouse oviducts versus 83.3% of oviducts in CmVar001-infected mice. To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. CmVar004 infection induced significantly lower levels of CXCL1, CXCL2, tumor necrosis factor alpha (TNF-α), and CCL2 in comparison to CmVar001 infection with similar rRNA (rs16) levels for Chlamydiae. A combination of microRNA (miRNA) sequencing and quantitative real-time PCR (qRT-PCR) analysis of 134 inflammation-related miRNAs was performed 24 h postinfection to determine if the chemokine/cytokine responses would also be reflected in miRNA expression profiles. Interestingly, 12 miRNAs (miR-135a-5p, miR298-5p, miR142-3p, miR223-3p, miR299a-3p, miR147-3p, miR105, miR325-3p, miR132-3p, miR142-5p, miR155-5p, and miR-410-3p) were overexpressed during CmVar004 infection compared to CmVar001 infection, inversely correlating with the respective chemokine/cytokine responses. To our knowledge, this is the first report demonstrating that early biomarkers elicited in the host can differentiate between two pathological variants of chlamydiae and be predictive of upper tract disease. IMPORTANCE It is apparent that an infecting chlamydial population consists of multiple genetic variants with differing capabilities of eliciting a pathological response; thus, it may be possible to identify biomarkers specific for a given virulence pathotype. miRNAs are known to regulate genes that in turn regulate signaling pathways involved in disease pathogenesis. Importantly, miRNAs are stable and can reflect a tissue response and therefore have the potential to be biomarkers of disease severity. Currently, with respect to chlamydial infections, there is no way to predict whether an infected patient is more or less likely to develop PID. However, data presented in this study indicate that the expression of a specific miRNA profile associated with a virulent variant early in the infection course may be predictive of an increased risk of pelvic inflammatory disease, allowing more aggressive treatment before significant pathology develops.
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- 2014
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153. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community.
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Naomi F Montalvo, Jeanette Davis, Jan Vicente, Raquel Pittiglio, Jacques Ravel, and Russell T Hill
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Medicine ,Science - Abstract
The bacterial communities of sponges have been studied using molecular techniques as well as culture-based techniques, but the communities described by these two methods are remarkably distinct. Culture-based methods describe communities dominated by Proteobacteria, and Actinomycetes while molecular methods describe communities dominated by predominantly uncultivated groups such as the Chloroflexi, Acidobacteria, and Acidimicrobidae. In this study, we used a wide range of culture media to increase the diversity of cultivable bacteria from the closely related giant barrel sponges, Xestospongia muta collected from the Florida Keys, Atlantic Ocean and Xestospongia testudinaria, collected from Indonesia, Pacific Ocean. Over 400 pure cultures were isolated and identified from X. muta and X. testudinaria and over 90 bacterial species were represented. Over 16,000 pyrosequences were analyzed and assigned to 976 OTUs. We employed both cultured-based methods and pyrosequencing to look for patterns of overlap between the culturable and molecular communities. Only one OTU was found in both the molecular and culturable communities, revealing limitations inherent in both approaches.
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- 2014
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154. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes.
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Ekaterine Khmaladze, Dawn N Birdsell, Amber A Naumann, Christian B Hochhalter, Meagan L Seymour, Roxanne Nottingham, Stephen M Beckstrom-Sternberg, James Beckstrom-Sternberg, Mikeljon P Nikolich, Gvantsa Chanturia, Ekaterine Zhgenti, Mariam Zakalashvili, Lile Malania, Giorgi Babuadze, Nikoloz Tsertsvadze, Natalia Abazashvili, Merab Kekelidze, Shota Tsanava, Paata Imnadze, Holly H Ganz, Wayne M Getz, Ofori Pearson, Pawel Gajer, Mark Eppinger, Jacques Ravel, David M Wagner, Richard T Okinaka, James M Schupp, Paul Keim, and Talima Pearson
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Medicine ,Science - Abstract
Sequence analyses and subtyping of Bacillus anthracis strains from Georgia reveal a single distinct lineage (Aust94) that is ecologically established. Phylogeographic analysis and comparisons to a global collection reveals a clade that is mostly restricted to Georgia. Within this clade, many groups are found around the country, however at least one subclade is only found in the eastern part. This pattern suggests that dispersal into and out of Georgia has been rare and despite historical dispersion within the country, for at least for one lineage, current spread is limited.
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- 2014
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155. Free glycogen in vaginal fluids is associated with Lactobacillus colonization and low vaginal pH.
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Paria Mirmonsef, Anna L Hotton, Douglas Gilbert, Derick Burgad, Alan Landay, Kathleen M Weber, Mardge Cohen, Jacques Ravel, and Gregory T Spear
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Medicine ,Science - Abstract
Lactobacillus dominates the lower genital tract microbiota of many women, producing a low vaginal pH, and is important for healthy pregnancy outcomes and protection against several sexually transmitted pathogens. Yet, factors that promote Lactobacillus remain poorly understood. We hypothesized that the amount of free glycogen in the lumen of the lower genital tract is an important determinant of Lactobacillus colonization and a low vaginal pH.Free glycogen in lavage samples was quantified. Pyrosequencing of the 16S rRNA gene was used to identify microbiota from 21 African American women collected over 8-11 years.Free glycogen levels varied greatly between women and even in the same woman. Samples with the highest free glycogen had a corresponding median genital pH that was significantly lower (pH 4.4) than those with low glycogen (pH 5.8; p
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- 2014
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156. No Resistance Plasmid in Yersinia pestis, North America
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David M. Wagner, Janelle Runberg, Amy J. Vogler, Judy Lee, Elizabeth M. Driebe, Lance B. Price, David M. Engelthaler, W. Florian Fricke, Jacques Ravel, and Paul Keim
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Multidrug resistance ,plague ,North America ,Salmonella ,Yersinia pestis ,bacteria ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Published
- 2010
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157. Male Circumcision Significantly Reduces Prevalence and Load of Genital Anaerobic Bacteria
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Cindy M. Liu, Bruce A. Hungate, Aaron A. R. Tobian, David Serwadda, Jacques Ravel, Richard Lester, Godfrey Kigozi, Maliha Aziz, Ronald M. Galiwango, Fred Nalugoda, Tania L. Contente-Cuomo, Maria J. Wawer, Paul Keim, Ronald H. Gray, and Lance B. Price
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Microbiology ,QR1-502 - Abstract
ABSTRACT Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (n = 77) and from a circumcised intervention group (n = 79) at enrollment and year 1 follow-up in a randomized circumcision trial in Rakai, Uganda. We characterized microbiota using16S rRNA gene-based quantitative PCR (qPCR) and pyrosequencing, log response ratio (LRR), Bayesian classification, nonmetric multidimensional scaling (nMDS), and permutational multivariate analysis of variance (PerMANOVA). At baseline, men in both study arms had comparable coronal sulcus microbiota; however, by year 1, circumcision decreased the total bacterial load and reduced microbiota biodiversity. Specifically, the prevalence and absolute abundance of 12 anaerobic bacterial taxa decreased significantly in the circumcised men. While aerobic bacterial taxa also increased postcircumcision, these gains were minor. The reduction in anaerobes may partly account for the effects of circumcision on reduced HIV acquisition. IMPORTANCE The bacterial changes identified in this study may play an important role in the HIV risk reduction conferred by male circumcision. Decreasing the load of specific anaerobes could reduce HIV target cell recruitment to the foreskin. Understanding the mechanisms that underlie the benefits of male circumcision could help to identify new intervention strategies for decreasing HIV transmission, applicable to populations with high HIV prevalence where male circumcision is culturally less acceptable.
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- 2013
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158. Twice-Daily Application of HIV Microbicides Alters the Vaginal Microbiota
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Jacques Ravel, Pawel Gajer, Li Fu, Christine K. Mauck, Sara S. K. Koenig, Joyce Sakamoto, Alison A. Motsinger-Reif, Gustavo F. Doncel, and Steven L. Zeichner
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Microbiology ,QR1-502 - Abstract
ABSTRACT Vaginal HIV microbicides offer great promise in preventing HIV transmission, but failures of phase 3 clinical trials, in which microbicide-treated subjects had an increased risk of HIV transmission, raised concerns about endpoints used to evaluate microbicide safety. A possible explanation for the increased transmission risk is that the agents shifted the vaginal bacterial community, resulting in loss of natural protection and enhanced HIV transmission susceptibility. We characterized vaginal microbiota, using pyrosequencing of bar-coded 16S rRNA gene fragments, in samples from 35 healthy, sexually abstinent female volunteer subjects (ages 18 to 50 years) with regular menses in a repeat phase 1 study of twice-daily application over 13.5 days of 1 of 3 gel products: a hydroxyethylcellulose (HEC)-based “universal” placebo (10 subjects), 6% cellulose sulfate (CS; 13 subjects), and 4% nonoxynol-9 (N-9; 12 subjects). We used mixed effects models inferred using Bayesian Markov chain Monte Carlo methods, which showed that treatment with active agents shifted the microbiota toward a community type lacking significant numbers of Lactobacillus spp. and dominated by strict anaerobes. This state of the vaginal microbiota was associated with a low or intermediate Nugent score and was not identical to bacterial vaginosis, an HIV transmission risk factor. The placebo arm contained a higher proportion of communities dominated by Lactobacillus spp., particularly L. crispatus, throughout treatment. The data suggest that molecular evaluation of microbicide effects on vaginal microbiota may be a critical endpoint that should be incorporated in early clinical assessment of microbicide candidates. IMPORTANCE Despite large prevention efforts, HIV transmission and acquisition rates remain unacceptably high. In developing countries, transmission mainly occurs through heterosexual intercourse, where women are significantly more vulnerable to infection than men. Vaginal microbicides are considered to be one of the most promising female-controlled products, in that women themselves insert the microbicides into the vagina to prevent HIV transmission during sexual intercourse. The failure of several microbicides in clinical trials has raised questions concerning the low in vivo efficacy of such anti-HIV molecules. This study was designed to gain insights into the failures of two microbicides by testing the hypothesis that the microbicides negatively affect a critical line of defense against HIV, the vaginal microbiota. The results suggest that in the early assessment of candidate microbicides, culture-independent evaluation of their effect on the vaginal microbiota should be considered and may constitute a critical endpoint.
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- 2012
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159. « Le sac d’école électronique »: un outil technologique pouvant faciliter la mise en place de l’alignement curriculaire / The 'digital school bag': A technological tool to facilitate the implementation of curriculum alignment
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Marie-Pierrette Ntyonga-Pono, Jacques Raynauld, and Olivier Gerbé
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Réforme éducative, situation d'apprentissage et d'évaluation, soutien technologique, alignement curriculaire. ,Education - Abstract
Cet article discute des réformes du système éducatif québécois qui s’inscrivent dans le courant des réformes entreprises un peu partout dans le monde avec des résultats variables. Plusieurs facteurs sont évoqués parmi lesquels le manque de formation et de soutien des enseignants, malgré les actions du ministère de l’Éducation, du Loisir et du Sport du Québec qui a confié la recherche de moyens de soutien à différents organismes dont la Maison des technologies de formation et d'apprentissage Roland-Giguère (MATI Montréal) qui a conçu un logiciel «le sac d’école» peu connu et utilisé. Le but de cet article est de présenter cet outil technologique et comment il peut permettre d’atteindre l’alignement curriculaire, élément clé de toute réussite de réforme éducative. This paper discusses the education-system reforms in Quebec, which follow the same trends as reforms undertaken elsewhere in the world with various results. Several factors are invoked, among which is the lack of training and support for teachers despite the efforts of Quebec’s Ministère de l’Éducation, du Loisir et du Sport, which assigned various organizations to looks into support methods. These organizations included the Maison des technologies de formation et d’apprentissage Roland-Giguère (MATI Montréal), which designed a “school bag” software that is little used. The paper introduces the technological tool and shows how it can help in reaching curriculum alignment, a key element for the success of educational reforms.
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- 2012
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160. Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants.
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Maria Sellitto, Guoyun Bai, Gloria Serena, W Florian Fricke, Craig Sturgeon, Pawel Gajer, James R White, Sara S K Koenig, Joyce Sakamoto, Dustin Boothe, Rachel Gicquelais, Deborah Kryszak, Elaine Puppa, Carlo Catassi, Jacques Ravel, and Alessio Fasano
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Medicine ,Science - Abstract
Celiac disease (CD) is a unique autoimmune disorder in which the genetic factors (DQ2/DQ8) and the environmental trigger (gluten) are known and necessary but not sufficient for its development. Other environmental components contributing to CD are poorly understood. Studies suggest that aspects of gluten intake might influence the risk of CD occurrence and timing of its onset, i.e., the amount and quality of ingested gluten, together with the pattern of infant feeding and the age at which gluten is introduced in the diet. In this study, we hypothesize that the intestinal microbiota as a whole rather than specific infections dictates the switch from tolerance to immune response in genetically susceptible individuals. Using a sample of infants genetically at risk of CD, we characterized the longitudinal changes in the microbial communities that colonize infants from birth to 24 months and the impact of two patterns of gluten introduction (early vs. late) on the gut microbiota and metabolome, and the switch from gluten tolerance to immune response, including onset of CD autoimmunity. We show that infants genetically susceptible to CD who are exposed to gluten early mount an immune response against gluten and develop CD autoimmunity more frequently than at-risk infants in which gluten exposure is delayed until 12 months of age. The data, while derived from a relatively small number of subjects, suggest differences between the developing microbiota of infants with genetic predisposition for CD and the microbiota from infants with a non-selected genetic background, with an overall lack of bacteria of the phylum Bacteriodetes along with a high abundance of Firmicutes and microbiota that do not resemble that of adults even at 2 years of age. Furthermore, metabolomics analysis reveals potential biomarkers for the prediction of CD. This study constitutes a definite proof-of-principle that these combined genomic and metabolomic approaches will be key to deciphering the role of the gut microbiota on CD onset.
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- 2012
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161. Evaluation of methods for the extraction and purification of DNA from the human microbiome.
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Sanqing Yuan, Dora B Cohen, Jacques Ravel, Zaid Abdo, and Larry J Forney
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Medicine ,Science - Abstract
DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used.Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.
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- 2012
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162. Comparison of storage conditions for human vaginal microbiome studies.
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Guoyun Bai, Pawel Gajer, Melissa Nandy, Bing Ma, Hongqiu Yang, Joyce Sakamoto, May H Blanchard, Jacques Ravel, and Rebecca M Brotman
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Medicine ,Science - Abstract
The effect of storage conditions on the microbiome and metabolite composition of human biological samples has not been thoroughly investigated as a potential source of bias. We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and (1)H-NMR analyses.Eight women were enrolled and four mid-vaginal swabs were collected by a physician from each woman. The samples were either processed immediately, stored at -80°C for 4 weeks or at -20°C for 1 week followed by transfer to -80°C for another 4 weeks prior to analysis. Statistical methods, including Kolmogorovo-Smirnov and Wilcoxon tests, were performed to evaluate the differences in vaginal bacterial community composition and metabolites between samples stored under different conditions. The results showed that there were no significant differences between samples processed immediately after collection or stored for varying durations. (1)H-NMR analysis of the small molecule metabolites in vaginal secretions indicated that high levels of lactic acid were associated with Lactobacillus-dominated communities. Relative abundance of lactic acid did not appear to correlate with relative abundance of individual Lactobacillus sp. in this limited sample, although lower levels of lactic acid were observed when L. gasseri was dominant, indicating differences in metabolic output of seemingly similar communities.These findings benefit large-scale, field-based microbiome and metabolomic studies of the vaginal microbiota.
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- 2012
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163. Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.
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Mark Eppinger, Lyndsay Radnedge, Gary Andersen, Nicholas Vietri, Grant Severson, Sherry Mou, Jacques Ravel, and Patricia L Worsham
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Medicine ,Science - Abstract
Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.
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- 2012
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164. Association of fecal microbial diversity and taxonomy with selected enzymatic functions.
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Roberto Flores, Jianxin Shi, Mitchell H Gail, Pawel Gajer, Jacques Ravel, and James J Goedert
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Medicine ,Science - Abstract
Few microbial functions have been compared to a comprehensive survey of the human fecal microbiome. We evaluated determinants of fecal microbial β-glucuronidase and β-glucosidase activities, focusing especially on associations with microbial alpha and beta diversity and taxonomy. We enrolled 51 healthy volunteers (26 female, mean age 39) who provided questionnaire data and multiple aliquots of a stool, from which proteins were extracted to quantify β-glucuronidase and β-glucosidase activities, and DNA was extracted to amplify and pyrosequence 16S rRNA gene sequences to classify and quantify microbiome diversity and taxonomy. Fecal β-glucuronidase was elevated with weight loss of at least 5 lb. (P = 0.03), whereas β-glucosidase was marginally reduced in the four vegetarians (P = 0.06). Both enzymes were correlated directly with microbiome richness and alpha diversity measures, directly with the abundance of four Firmicutes Clostridia genera, and inversely with the abundance of two other genera (Firmicutes Lactobacillales Streptococcus and Bacteroidetes Rikenellaceae Alistipes) (all P = 0.05-0.0001). Beta diversity reflected the taxonomic associations. These observations suggest that these enzymatic functions are performed by particular taxa and that diversity indices may serve as surrogates of bacterial functions. Independent validation and deeper understanding of these associations are needed, particularly to characterize functions and pathways that may be amenable to manipulation.
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- 2012
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165. Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils.
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Coralie Damon, Frédéric Lehembre, Christine Oger-Desfeux, Patricia Luis, Jacques Ranger, Laurence Fraissinet-Tachet, and Roland Marmeisse
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Medicine ,Science - Abstract
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)-0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.
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- 2012
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166. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar.
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Amy J Vogler, Fabien Chan, David M Wagner, Philippe Roumagnac, Judy Lee, Roxanne Nera, Mark Eppinger, Jacques Ravel, Lila Rahalison, Bruno W Rasoamanana, Stephen M Beckstrom-Sternberg, Mark Achtman, Suzanne Chanteau, and Paul Keim
- Subjects
Arctic medicine. Tropical medicine ,RC955-962 ,Public aspects of medicine ,RA1-1270 - Abstract
Plague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable variable-number tandem repeat (VNTR) loci to gain insight into the maintenance and spread of Y. pestis in Madagascar.We analyzed a set of 262 Malagasy isolates using a set of 56 SNPs and a 43-locus multi-locus VNTR analysis (MLVA) system. We then analyzed the geographic distribution of the subclades and identified patterns related to the maintenance and spread of plague in Madagascar. We find relatively high levels of VNTR diversity in addition to several SNP differences. We identify two major groups, Groups I and II, which are subsequently divided into 11 and 4 subclades, respectively. Y. pestis appears to be maintained in several geographically separate subpopulations. There is also evidence for multiple long distance transfers of Y. pestis, likely human mediated. Such transfers have resulted in the reintroduction and establishment of plague in the port city of Mahajanga, where there is evidence for multiple transfers both from and to the central highlands.The maintenance and spread of Y. pestis in Madagascar is a dynamic and highly active process that relies on the natural cycle between the primary host, the black rat, and its flea vectors as well as human activity.
- Published
- 2011
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167. A Comunidade Estética
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Jacques Rancière
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Schiller ,comunidade estética ,política ,Arts in general ,NX1-820 ,Visual arts ,N1-9211 ,History of scholarship and learning. The humanities ,AZ20-999 - Abstract
Partindo da décima-quinta carta de Schiller da obra Cartas para a educação estética do homem, Rancière analisa a relação paradoxal entre a subjetividade estética e a comunidade a que ela dá forma. As implicações políticas desta relação e as suas metamorfoses são desenhadas em três grandes cenários, que culminam na construção do que o autor chama de um ressentimento antiestético contemporâneo
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- 2011
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168. Variation in tropical reef symbiont metagenomes defined by secondary metabolism.
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Mohamed S Donia, W Florian Fricke, Jacques Ravel, and Eric W Schmidt
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Medicine ,Science - Abstract
The complex evolution of secondary metabolism is important in biology, drug development, and synthetic biology. To examine this problem at a fine scale, we compared the genomes and chemistry of 24 strains of uncultivated cyanobacteria, Prochloron didemni, that live symbiotically with tropical ascidians and that produce natural products isolated from the animals. Although several animal species were obtained along a >5500 km transect of the Pacific Ocean, P. didemni strains are >97% identical across much of their genomes, with only a few exceptions concentrated in secondary metabolism. Secondary metabolic gene clusters were sporadically present or absent in identical genomic locations with no consistent pattern of co-occurrence. Discrete mutations were observed, leading to new chemicals that we isolated from animals. Functional cassettes encoding diverse chemicals are exchanged among a single population of symbiotic P. didemni that spans the tropical Pacific, providing the host animals with a varying arsenal of secondary metabolites.
- Published
- 2011
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169. Impacts of poultry house environment on poultry litter bacterial community composition.
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Michael D Dumas, Shawn W Polson, Don Ritter, Jacques Ravel, Jack Gelb, Robin Morgan, and K Eric Wommack
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Medicine ,Science - Abstract
Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.
- Published
- 2011
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170. Castor bean organelle genome sequencing and worldwide genetic diversity analysis.
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Maximo Rivarola, Jeffrey T Foster, Agnes P Chan, Amber L Williams, Danny W Rice, Xinyue Liu, Admasu Melake-Berhan, Heather Huot Creasy, Daniela Puiu, M J Rosovitz, Hoda M Khouri, Stephen M Beckstrom-Sternberg, Gerard J Allan, Paul Keim, Jacques Ravel, and Pablo D Rabinowicz
- Subjects
Medicine ,Science - Abstract
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
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- 2011
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171. Repensando la noción de ‘comunidad’ en contextos de alta migración: el caso de Pepinales
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Jacques Ramírez
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COMUNIDAD ,MIGRACIÓN ,TRANSNACIONALISMOS ,REDES ,ARCHIPIÉLAGO ,Anthropology ,GN1-890 ,Archaeology ,CC1-960 - Abstract
El presente artículo tiene como objetivo central rastrear y repensar el concepto de ‘comunidad’ en contextos de alta migración. A partir de un trabajo etnográfico realizado sobre pepinales, el cual ha experimentado flujos migratorios internos e internacionales por más de cuatro décadas, cuestionamos las nociones clásicas de comunidad así como señalamos las limitantes de las propuestas de los estudios migratorios al hablar de ‘comunidades transnacionales’ y el uso del término ‘comunidades fantasmas’. Luego de realizar un recorrido teórico por este concepto, proponemos ver a las comunidades, en contextos de alta migración, como re-desterrritorializadas formando un archipiélago activo en movimiento.
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- 2010
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172. The effects of circumcision on the penis microbiome.
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Lance B Price, Cindy M Liu, Kristine E Johnson, Maliha Aziz, Matthew K Lau, Jolene Bowers, Jacques Ravel, Paul S Keim, David Serwadda, Maria J Wawer, and Ronald H Gray
- Subjects
Medicine ,Science - Abstract
Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners.We assessed the penile (coronal sulci) microbiota in 12 HIV-negative Ugandan men before and after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA gene pyrosequencing targeting the V3-V4 hypervariable regions. Taxonomic classification was performed using the RDP Naïve Bayesian Classifier. Among the 42 unique bacterial families identified, Pseudomonadaceae and Oxalobactericeae were the most abundant irrespective of circumcision status. Circumcision was associated with a significant change in the overall microbiota (PerMANOVA p = 0.007) and with a significant decrease in putative anaerobic bacterial families (Wilcoxon Signed-Rank test p = 0.014). Specifically, two families-Clostridiales Family XI (p = 0.006) and Prevotellaceae (p = 0.006)-were uniquely abundant before circumcision. Within these families we identified a number of anaerobic genera previously associated with bacterial vaginosis including: Anaerococcus spp., Finegoldia spp., Peptoniphilus spp., and Prevotella spp.The anoxic microenvironment of the subpreputial space may support pro-inflammatory anaerobes that can activate Langerhans cells to present HIV to CD4 cells in draining lymph nodes. Thus, the reduction in putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases.
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- 2010
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173. Recent Advances in Understanding the Microbiology of the Female Reproductive Tract and the Causes of Premature Birth
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Xia Zhou, Rebecca M. Brotman, Pawel Gajer, Zaid Abdo, Ursel Schüette, Sam Ma, Jacques Ravel, and Larry J. Forney
- Subjects
Gynecology and obstetrics ,RG1-991 ,Infectious and parasitic diseases ,RC109-216 - Abstract
Data derived from molecular microbiological investigations of the human vagina have led to the discovery of resident bacterial communities that exhibit marked differences in terms of species composition. All undergo dynamic changes that are likely due to intrinsic host and behavioral factors. Similar types of bacteria have been found in both amniotic fluid and the vagina, suggesting a potential route of colonization. Given that not all of the species involved in intrauterine infections are readily cultivated, it is important that culture-independent methods of analysis must be used to understand the etiology of these infections. Further research is needed to establish whether an ascending pathway from the vagina to the amniotic cavity enables the development of intrauterine infections.
- Published
- 2010
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174. The role of genomics in the identification, prediction, and prevention of biological threats.
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W Florian Fricke, David A Rasko, and Jacques Ravel
- Subjects
Biology (General) ,QH301-705.5 - Abstract
In all likelihood, it is only a matter of time before our public health system will face a major biological threat, whether intentionally dispersed or originating from a known or newly emerging infectious disease. It is necessary not only to increase our reactive "biodefense," but also to be proactive and increase our preparedness. To achieve this goal, it is essential that the scientific and public health communities fully embrace the genomic revolution, and that novel bioinformatic and computing tools necessary to make great strides in our understanding of these novel and emerging threats be developed. Genomics has graduated from a specialized field of science to a research tool that soon will be routine in research laboratories and clinical settings. Because the technology is becoming more affordable, genomics can and should be used proactively to build our preparedness and responsiveness to biological threats. All pieces, including major continued funding, advances in next-generation sequencing technologies, bioinformatics infrastructures, and open access to data and metadata, are being set in place for genomics to play a central role in our public health system.
- Published
- 2009
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175. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.
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Lance B Price, Cindy M Liu, Johan H Melendez, Yelena M Frankel, David Engelthaler, Maliha Aziz, Jolene Bowers, Rogan Rattray, Jacques Ravel, Chris Kingsley, Paul S Keim, Gerald S Lazarus, and Jonathan M Zenilman
- Subjects
Medicine ,Science - Abstract
BackgroundBacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota.Methodology/principal findingsWe prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007) and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics.Conclusions/significanceThe 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.
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- 2009
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176. Pre-Columbian origins for North American anthrax.
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Leo J Kenefic, Talima Pearson, Richard T Okinaka, James M Schupp, David M Wagner, Alex R Hoffmaster, Carla B Trim, Wai-Kwan Chung, Jodi A Beaudry, Lingxia Jiang, Pawel Gajer, Jeffrey T Foster, James I Mead, Jacques Ravel, and Paul Keim
- Subjects
Medicine ,Science - Abstract
Disease introduction into the New World during colonial expansion is well documented and had a major impact on indigenous populations; however, few diseases have been associated with early human migrations into North America. During the late Pleistocene epoch, Asia and North America were joined by the Beringian Steppe ecosystem which allowed animals and humans to freely cross what would become a water barrier in the Holocene. Anthrax has clearly been shown to be dispersed by human commerce and trade in animal products contaminated with Bacillus anthracis spores. Humans appear to have brought B. anthracis to this area from Asia and then moved it further south as an ice-free corridor opened in central Canada approximately 13,000 ybp. In this study, we have defined the evolutionary history of Western North American (WNA) anthrax using 2,850 single nucleotide polymorphisms (SNPs) and 285 geographically diverse B. anthracis isolates. Phylogeography of the major WNA B. anthracis clone reveals ancestral populations in northern Canada with progressively derived populations to the south; the most recent ancestor of this clonal lineage is in Eurasia. Our phylogeographic patterns are consistent with B. anthracis arriving with humans via the Bering Land Bridge. This northern-origin hypothesis is highly consistent with our phylogeographic patterns and rates of SNP accumulation observed in current day B. anthracis isolates. Continent-wide dispersal of WNA B. anthracis likely required movement by later European colonizers, but the continent's first inhabitants may have seeded the initial North American populations.
- Published
- 2009
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177. Correction: Pre-Columbian Origins for North American Anthrax.
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Leo J. Kenefic, Talima Pearson, Richard T. Okinaka, James M. Schupp, David M. Wagner, Alex R. Hoffmaster, Carla B. Trim, Wai-Kwan Chung, Jodi A. Beaudry, Lingxia Jiang, Pawel Gajer, Jeffrey T. Foster, James I. Mead, Jacques Ravel, and Paul Keim
- Subjects
Medicine ,Science - Published
- 2009
- Full Text
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178. Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists.
- Author
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Steven E Schutzer, Linda R K Schlater, Catherine M Ronning, David DeShazer, Benjamin J Luft, John J Dunn, Jacques Ravel, Claire M Fraser-Liggett, and William C Nierman
- Subjects
Medicine ,Science - Abstract
Burkholderia mallei is an understudied biothreat agent responsible for glanders which can be lethal in humans and animals. Research with this pathogen has been hampered in part by constraints of Select Agent regulations for safety reasons. Whole genomic sequencing (WGS) is an apt approach to characterize newly discovered or poorly understood microbial pathogens.We performed WGS on a strain of B. mallei, SAVP1, previously pathogenic, that was experimentally infected in 6 equids (4 ponies, 1 mule, 1 donkey), natural hosts, for purposes of producing antibodies. Multiple high inocula were used in some cases. Unexpectedly SAVP1 appeared to be avirulent in the ponies and mule, and attenuated in the donkey, but induced antibodies. We determined the genome sequence of SAVP1 and compared it to a strain that was virulent in horses and a human. In comparison, this phenotypic avirulent SAVP1 strain was missing multiple genes including all the animal type III secretory system (T3SS) complex of genes demonstrated to be essential for virulence in mice and hamster models. The loss of these genes in the SAVP1 strain appears to be the consequence of a multiple gene deletion across insertion sequence (IS) elements in the B. mallei genome. Therefore, the strain by itself is unlikely to revert naturally to its virulent phenotype. There were other genes present in one strain and not the other and vice-versa.The discovery that this strain of B. mallei was both avirulent in the natural host ponies, and did not possess T3SS associated genes may be fortuitous to advance biodefense research. The deleted virulence-essential T3SS is not likely to be re-acquired naturally. These findings may provide a basis for exclusion of SAVP1 from the Select Agent regulation or at least discussion of what else would be required for exclusion. This exclusion could accelerate research by investigators not possessing BSL-3 facilities and facilitate the production of reagents such as antibodies without the restraints of Select Agent regulation.
- Published
- 2008
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179. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America.
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Raymond K Auerbach, Apichai Tuanyok, William S Probert, Leo Kenefic, Amy J Vogler, David C Bruce, Christine Munk, Thomas S Brettin, Mark Eppinger, Jacques Ravel, David M Wagner, and Paul Keim
- Subjects
Medicine ,Science - Abstract
Yersinia pestis, the etiologic agent of plague, was responsible for several devastating epidemics throughout history and is currently of global importance to current public heath and biodefense efforts. Y. pestis is widespread in the Western United States. Because Y. pestis was first introduced to this region just over 100 years ago, there has been little time for genetic diversity to accumulate. Recent studies based upon single nucleotide polymorphisms have begun to quantify the genetic diversity of Y. pestis in North America.To examine the evolution of Y. pestis in North America, a gapped genome sequence of CA88-4125 was generated. Sequence comparison with another North American Y. pestis strain, CO92, identified seven regions of difference (six inversions, one rearrangement), differing IS element copy numbers, and several SNPs.The relatively large number of inverted/rearranged segments suggests that North American Y. pestis strains may be undergoing inversion fixation at high rates over a short time span, contributing to higher-than-expected diversity in this region. These findings will hopefully encourage the scientific community to sequence additional Y. pestis strains from North America and abroad, leading to a greater understanding of the evolutionary history of this pathogen.
- Published
- 2007
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180. The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever.
- Author
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Mark Eppinger, M J Rosovitz, Wolfgang Florian Fricke, David A Rasko, Galina Kokorina, Corinne Fayolle, Luther E Lindler, Elisabeth Carniel, and Jacques Ravel
- Subjects
Genetics ,QH426-470 - Abstract
The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci. The causative agent was later identified as Yersinia pseudotuberculosis, although the range of morbidities was vastly different from classical pseudotuberculosis symptoms. To understand the origin and emergence of the peculiar clinical features of FESLF, we have sequenced the genome of the FESLF-causing strain Y. pseudotuberculosis IP31758 and compared it with that of another Y. pseudotuberculosis strain, IP32953, which causes classical gastrointestinal symptoms. The unique gene pool of Y pseudotuberculosis IP31758 accounts for more than 260 strain-specific genes and introduces individual physiological capabilities and virulence determinants, with a significant proportion horizontally acquired that likely originated from Enterobacteriaceae and other soil-dwelling bacteria that persist in the same ecological niche. The mobile genome pool includes two novel plasmids phylogenetically unrelated to all currently reported Yersinia plasmids. An icm/dot type IVB secretion system, shared only with the intracellular persisting pathogens of the order Legionellales, was found on the larger plasmid and could contribute to scarlatinoid fever symptoms in patients due to the introduction of immunomodulatory and immunosuppressive capabilities. We determined the common and unique traits resulting from genome evolution and speciation within the genus Yersinia and drew a more accurate species border between Y. pseudotuberculosis and Y. pestis. In contrast to the lack of genetic diversity observed in the evolutionary young descending Y. pestis lineage, the population genetics of Y. pseudotuberculosis is more heterogenous. Both Y. pseudotuberculosis strains IP31758 and the previously sequenced Y. pseudotuberculosis strain IP32953 have evolved by the acquisition of specific plasmids and by the horizontal acquisition and incorporation of different genetic information into the chromosome, which all together or independently seems to potentially impact the phenotypic adaptation of these two strains.
- Published
- 2007
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181. Global genetic population structure of Bacillus anthracis.
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Matthew N Van Ert, W Ryan Easterday, Lynn Y Huynh, Richard T Okinaka, Martin E Hugh-Jones, Jacques Ravel, Shaylan R Zanecki, Talima Pearson, Tatum S Simonson, Jana M U'Ren, Sergey M Kachur, Rebecca R Leadem-Dougherty, Shane D Rhoton, Guenevier Zinser, Jason Farlow, Pamala R Coker, Kimothy L Smith, Bingxiang Wang, Leo J Kenefic, Claire M Fraser-Liggett, David M Wagner, and Paul Keim
- Subjects
Medicine ,Science - Abstract
Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064-6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated.
- Published
- 2007
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182. Multiple antimicrobial resistance in plague: an emerging public health risk.
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Timothy J Welch, W Florian Fricke, Patrick F McDermott, David G White, Marie-Laure Rosso, David A Rasko, Mark K Mammel, Mark Eppinger, M J Rosovitz, David Wagner, Lila Rahalison, J Eugene Leclerc, Jeffrey M Hinshaw, Luther E Lindler, Thomas A Cebula, Elisabeth Carniel, and Jacques Ravel
- Subjects
Medicine ,Science - Abstract
Antimicrobial resistance in Yersinia pestis is rare, yet constitutes a significant international public health and biodefense threat. In 1995, the first multidrug resistant (MDR) isolate of Y. pestis (strain IP275) was identified, and was shown to contain a self-transmissible plasmid (pIP1202) that conferred resistance to many of the antimicrobials recommended for plague treatment and prophylaxis. Comparative analysis of the DNA sequence of Y. pestis plasmid pIP1202 revealed a near identical IncA/C plasmid backbone that is shared by MDR plasmids isolated from Salmonella enterica serotype Newport SL254 and the fish pathogen Yersinia ruckeri YR71. The high degree of sequence identity and gene synteny between the plasmid backbones suggests recent acquisition of these plasmids from a common ancestor. In addition, the Y. pestis pIP1202-like plasmid backbone was detected in numerous MDR enterobacterial pathogens isolated from retail meat samples collected between 2002 and 2005 in the United States. Plasmid-positive strains were isolated from beef, chicken, turkey and pork, and were found in samples from the following states: California, Colorado, Connecticut, Georgia, Maryland, Minnesota, New Mexico, New York and Oregon. Our studies reveal that this common plasmid backbone is broadly disseminated among MDR zoonotic pathogens associated with agriculture. This reservoir of mobile resistance determinants has the potential to disseminate to Y. pestis and other human and zoonotic bacterial pathogens and therefore represents a significant public health concern.
- Published
- 2007
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183. Litteraturens politik
- Author
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Jacques Rancière
- Subjects
Language and Literature - Abstract
Denna artikel kan endast läsas i tidskriftens pappersupplaga vilken kan beställas via redaktionen.
- Published
- 2007
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184. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
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Derrick E Fouts, Emmanuel F Mongodin, Robert E Mandrell, William G Miller, David A Rasko, Jacques Ravel, Lauren M Brinkac, Robert T DeBoy, Craig T Parker, Sean C Daugherty, Robert J Dodson, A Scott Durkin, Ramana Madupu, Steven A Sullivan, Jyoti U Shetty, Mobolanle A Ayodeji, Alla Shvartsbeyn, Michael C Schatz, Jonathan H Badger, Claire M Fraser, and Karen E Nelson
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.
- Published
- 2005
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185. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
- Author
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Naomi Ward, Øivind Larsen, James Sakwa, Live Bruseth, Hoda Khouri, A Scott Durkin, George Dimitrov, Lingxia Jiang, David Scanlan, Katherine H Kang, Matt Lewis, Karen E Nelson, Barbara Methé, Martin Wu, John F Heidelberg, Ian T Paulsen, Derrick Fouts, Jacques Ravel, Hervé Tettelin, Qinghu Ren, Tim Read, Robert T DeBoy, Rekha Seshadri, Steven L Salzberg, Harald B Jensen, Nils Kåre Birkeland, William C Nelson, Robert J Dodson, Svenn H Grindhaug, Ingeborg Holt, Ingvar Eidhammer, Inge Jonasen, Susan Vanaken, Terry Utterback, Tamara V Feldblyum, Claire M Fraser, Johan R Lillehaug, and Jonathan A Eisen
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.
- Published
- 2004
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186. Reactivity of Allenes towards Iron Carbonyl Complexes
- Author
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Albert M. Kuonen, Jacques Raemy, and Titus A. Jenny
- Subjects
Chemistry ,QD1-999 - Abstract
A series of monosubstituted allenes was reacted with Fe2(CO)9 to give dinuclear iron-carbonyl complexes containing organic ligands derived either from monomeric or dimerized allene. A mechanism of formation is proposed based on isolated intermediates. These intermediates point to an allene dimerization via addition of a reactive allene iron complex to free allene. Unusual chemical shifts were observed for many resonances in the 1H- and 13C-NMR spectra of the new compounds.
- Published
- 1994
187. Pour un système intégré de gestion du processus d’éducation et de formation
- Author
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Jacques Raynauld, Christian Martel, Emmanuelle Villiot-Leclercq, Olivier Gerbé, Jean-Michel Jullien, and Ricardo Camarero
- Subjects
Education ,Special aspects of education ,LC8-6691 - Abstract
L’adoption par la Communauté européenne d’un cadre européen des qualifications (European Qualification Framework [EQF], 2008) a recentré les processus d’éducation et de formation sur la certification des compétences. Pour opérationnaliser ces intentions, le milieu universitaire doit se doter d’environnements intégrés de gestion pédagogique. OpenScenario et OpenSyllabus constituent conjointement une solution possible en offrant à la fois des outils de création, de gestion et de diffusion de plans de cours Web structurés et d’activités d’apprentissage et d’évaluation reposant sur des scénarios et menant à des certifications qui pourraient à terme être diffusées dans des réseaux sociaux professionnels.
- Published
- 2009
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188. Ce que « medium » peut vouloir dire : l’exemple de la photographie
- Author
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Jacques Rancière
- Subjects
Philosophy (General) ,B1-5802 ,Sociology (General) ,HM401-1281 - Full Text
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189. El concepto de anacronismo y la verdad del historiador
- Author
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Jacques Rancière
- Subjects
Literature (General) ,PN1-6790 ,French literature - Italian literature - Spanish literature - Portuguese literature ,PQ1-3999 - Full Text
- View/download PDF
190. Analytical and chemometric strategies for elucidation of yerba mate composition.
- Author
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Dos Santos Polidoro A, Peixoto CN, de Souza VCP, Dos Santos AL, de Araújo Gomes A, and Jacques RA
- Subjects
- Chemometrics, Phenols analysis, Flavonoids analysis, Plant Extracts chemistry, Chromatography, High Pressure Liquid methods, Ilex paraguariensis chemistry
- Abstract
Yerba mate, a popular plant consumed mainly as an infusion, possesses nutritional and medicinal properties attributed to its secondary metabolites. This study aimed to develop strategies to elucidate the phenolic composition of yerba mate samples from Brazil, Argentina, Uruguay, and Paraguay. Optimization of ultrasonic-assisted extraction (UAE) was performed, and the extracted compounds were characterized using ultra-high-pressure liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry (UHPLC-QTOF-MS), molecular fluorescence and high-pressure liquid chromatography with diode-array detection (HPLC-DAD). Chemometric analysis, including parallel factor analysis (PARAFAC) and principal component analysis (PCA) explored metabolite profiles and identify patterns. PARAFAC modelling of the molecular fluorescence results revealed higher pigment content in Brazilian samples, while other countries' samples exhibited higher phenolic content. PCA modeling of HPLC-DAD results indicated that cultivated yerba mate contained higher chlorogenic acids levels, and samples from Argentina, Paraguay, and Uruguay exhibited higher concentrations of chlorogenic acids and flavonoids., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
- Published
- 2023
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191. Production of volatile compounds by yeasts using hydrolysed grape seed oil obtained by immobilized lipases in continuous packed-bed reactors.
- Author
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Castiglioni GZ, Bettio G, Matte CR, Jacques RA, Dos Santos Polidoro A, Rosa CA, and Ayub MAZ
- Subjects
- Hydrolysis, Plant Oils chemistry, Enzymes, Immobilized chemistry, Geotrichum growth & development, Lipase chemistry, Plant Oils metabolism, Seeds chemistry, Vitis chemistry, Volatile Organic Compounds metabolism
- Abstract
Lipases CAL-B, TLL, and RML were used in the synthesis of free fatty acids of grape seed oil as heterogeneous substrate. The best enzyme was used to optimize the reaction variables temperature, enzyme content, and molar ratio of water:oil in batch reactions using experimental planning. The ideal conditions to produce free fatty acids using pure RML were 45 °C, 12:1 substrate molar ratio, and 15% enzyme, resulting in 66% of oil hydrolysis and a productivity of 0.54 mol L
-1 min-1 in 4 h of reaction at 180 rpm. Repeated batches of reaction were performed testing the operational stability of RML, results showing that this enzyme could be used for at least 20 cycles keeping more than 80% of its initial activity, suggesting its potential use in industrial processes. The synthesis of free fatty acids was then evaluated in continuous reactions using packed-bed reactor (PBR). The highest productivity in the continuous process was 6.85 mol L-1 min-1 , using only RML, showing an operational stability higher than 80% of its initial conversion capacity after 11 days of operation, at a flow rate of 0.13 mL min-1 at 45 °C. We evaluated the use of this hydrolyzed oil as substrate for lactone bioproduction using Galactomyces geotrichum UFMG-CM-Y3276, G. geotrichum UFMG-CM-Y3558, and Geotrichum klebahnii UFMG-CM-Y3014 screened for their oil-hydrolysis ability. Volatile compounds were qualitatively identified in GC-MS as γ-octalactone and γ-nonalactone.- Published
- 2020
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192. Wine lees from the 1st and 2nd rackings: valuable by-products.
- Author
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Giacobbo A, Dias BB, Onorevoli B, Bernardes AM, de Pinho MN, Caramão EB, Rodrigues E, and Jacques RA
- Abstract
Phenolic compounds of the first and second racking wine lees, including anthocyanins, were qualitatively and quantitatively analyzed by HPLC-DAD-MS. Wine lees from both rackings displayed similar chromatographic profiles. Therefore, it was impossible to differentiate the qualitative results regarding phenolic compounds. On the other hand, those from the second racking presented, on average, concentration of polyphenols twice as high. While the ones from the first racking displayed ca. 1600 mg phenolic compounds and 400 mg anthocyanins per kg of dry matter, those from the second racking have shown ca. 3300 mg phenolic compounds and 700 mg anthocyanins per kg of dry matter. These outcomes indicate that, although the wine lees from the first racking can be employed as a resource for phenolic compounds recovery, those from the second racking are more appropriate for this purpose.
- Published
- 2019
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193. GC×GC/qMS analyses of Campomanesia guazumifolia (Cambess.) O. Berg essential oils and their antioxidant and antimicrobial activity.
- Author
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Dos Santos AL, Polidoro ADS, Cardoso CAL, Batistote M, do Carmo Vieira M, Jacques RA, and Caramão EB
- Subjects
- Anti-Infective Agents chemistry, Anti-Infective Agents pharmacology, Antioxidants chemistry, Antioxidants pharmacology, Brazil, Candida albicans drug effects, Escherichia coli drug effects, Gas Chromatography-Mass Spectrometry, Microbial Sensitivity Tests, Oils, Volatile analysis, Oils, Volatile chemistry, Plant Extracts chemistry, Plant Extracts pharmacology, Plant Oils chemistry, Plant Oils pharmacology, Sesquiterpenes analysis, Staphylococcus aureus drug effects, Terpenes analysis, Terpenes chemistry, Anti-Infective Agents isolation & purification, Antioxidants isolation & purification, Myrtaceae chemistry, Oils, Volatile pharmacology
- Abstract
The present study investigated the essential oil obtained from Campomanesia guazumifolia (Cambess.) O. Berg, an aromatic plant used in Brazilian folk medicine. The chemical composition was performed by GC×GC/qMS. The antioxidant and antimicrobial activities were evaluated by DPPH and BCB and, MIC assays, respectively. Sixty-eight compounds were identified in the oil, where the major compounds were bicyclogermacrene (15%), globulol (5%) and spathulenol (5%). Sesquiterpene hydrocarbons (29 compounds) and oxygenated sesquiterpenes (20 compounds) were the most representative classes of terpenes. DPPH (IC
50 value 26.1 ± 0.5 μg/mL) and BCB (68.3 ± 1.5%) values indicated a significant antioxidant activity. The essential oil strongly inhibited Staphylococcus aureus (MIC 15 ± 0.1 μg/mL), Escherichia coli (MIC 25 ± 0.2 μg/mL) and Candida albicans (MIC 5 ± 0.1 μg/mL). The results give a deeper understanding of the chemical composition and report for the first time the antioxidant and antimicrobial potential of the C. guazumifolia essential oil.- Published
- 2019
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- View/download PDF
194. Chemical characterisation of Piper amalago (Piperaceae) essential oil by comprehensive two-dimensional gas chromatography coupled with rapid-scanning quadrupole mass spectrometry (GC×GC/qMS) and their antilithiasic activity and acute toxicity.
- Author
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Dos Santos AL, Novaes ADS, Polidoro ADS, de Barros ME, Mota JS, Lima DBM, Krause LC, Cardoso CAL, Jacques RA, and Caramão EB
- Subjects
- Administration, Oral, Animals, Calcium Oxalate chemistry, Crystallization, Humans, Oils, Volatile administration & dosage, Oils, Volatile toxicity, Plant Leaves chemistry, Plant Stems chemistry, Rats, Wistar, Toxicity Tests, Acute, Gas Chromatography-Mass Spectrometry methods, Kidney Calculi drug therapy, Oils, Volatile chemistry, Oils, Volatile therapeutic use, Piper chemistry
- Abstract
Introduction: Piper amalago has a distribution from Mexico to Brazil; their aerial parts have been used in folk medicine to treat diuretic and kidney diseases., Objective: The purpose of this study was to obtain a deeper understanding of the chemical composition of essential oils (EOs) extracted from both the leaves and stems of P. amalago, compare them, and evaluate their antilithiasic activity and acute toxicity., Methodology: Extraction was performed by hydrodistillation, whereas chemical characterisation by two-dimensional gas chromatography coupled with rapid-scanning quadrupole mass spectrometry (GC×GC/qMS). The antilithiasic activity was evaluated by the effect of the EOs on calcium oxalate crystallisation in vitro. The turbidity index and the number of crystals formed were determined and used as an estimative of the activity. In the acute toxicity assay, the effects of a single oral dose of the EOs in Wistar rats were determined. General behaviour, adverse effects, and mortality were determined., Results: A total of 322 compounds were identified in the EOs. The sesquiterpenes displayed the highest contribution in leaves EOs among which included bicyclogermacrene and δ-cadinene. Sesquiterpenes and oxygenated sesquiterpenes displayed the highest contribution in EOs from stems, among which included bicyclogermacrene and α-cadinol. The EOs demonstrated an excellent action on the crystals growth inhibition, and the oral dose tested did not induce significant changes in the parameters for acute toxicity., Conclusion: The oils have a high chemical complexity, and there are differences between their compositions, which could explain the observed differences in antilithiasic activity. The findings support the use of this plant in folk medicine to treat kidney diseases., (Copyright © 2018 John Wiley & Sons, Ltd.)
- Published
- 2018
- Full Text
- View/download PDF
195. Quantification of nitrogen compounds in diesel fuel samples by comprehensive two-dimensional gas chromatography coupled with quadrupole mass spectrometry.
- Author
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Maciel GP, Machado ME, da Cunha ME, Lazzari E, da Silva JM, Jacques RA, Krause LC, Barros JA, and Caramão EB
- Abstract
Although several methods for the analysis of nitrogen compounds in diesel fuel have been described in the literature, the demand for rapid, sensitive, and robust analyses has increased in recent years. In this study, a comprehensive two-dimensional gas chromatographic method was developed for the identification and quantification of nitrogen compounds in diesel fuel samples. The quantification was performed using the standard addition method and the analysis was conducted using comprehensive two-dimensional gas chromatography coupled with fast quadrupole mass spectrometry. This study is the first to report quantification of nitrogen compounds in diesel fuel samples using the standard addition method without fractionation. This type of analysis was previously performed using many laborious separation steps, which can lead to errors and losses. The proposed method shows good linearity for target nitrogen compounds evaluated (m-toluidine, 4-ethylaniline, indole, 7-methylindole, 7-ethylindole, carbazole, isoquinoline, 4-methylquinoline, benzo[h]quinolone, and acridine) over a range from 0.05 to 2.0 mg/L, and limits of detection and quantification of <0.06 and 0.16 mg/L, respectively, for all nitrogen compounds studied., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2015
- Full Text
- View/download PDF
196. Comprehensive two dimensional gas chromatography with fast-quadrupole mass spectrometry detector analysis of polar compounds extracted from the bio-oil from the pyrolysis of sawdust.
- Author
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Schneider JK, da Cunha ME, dos Santos AL, Maciel GP, Brasil MC, Pinho AR, Mendes FL, Jacques RA, and Caramão EB
- Subjects
- Gas Chromatography-Mass Spectrometry methods, Wood chemistry, Biofuels analysis, Dust analysis, Ketones isolation & purification, Phenols isolation & purification, Wood analysis
- Abstract
In this paper it is studied the most polar fractions of bio-oil produced by fast pyrolysis of Lignocel BK40-90 (sawdust from forest timber). The biomass was submitted to the pyrolysis in an existing FCC pilot plant that was adapted for this procedure. The equipment consists of a fluidized bed reactor with nitrogen injection. The unit operates with continuous biomass feeding and continuous solids circulation. The produced bio-oil was submitted to an aqueous alkaline extraction, isolating the acidic compounds that were analyzed by one-dimensional gas chromatography and comprehensive two-dimensional gas chromatography with quadrupole mass spectrometry detection (qMS). One hundred and thirty compounds (mainly phenols and ketones) were tentatively identified in the extract, some of them by the use of retention indexes. The main differences between chromatographic techniques were the substantial increasing in the peak capacity of GC×GC and the resolution of some co-elutions that occurred in GC/qMS. It is also possible to conclude that this extract is rich in important raw materials for the chemical industry and can be used for this end., (Copyright © 2014 Elsevier B.V. All rights reserved.)
- Published
- 2014
- Full Text
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197. Characterization of the yerba mate (Ilex paraguariensis) volatile fraction using solid-phase microextraction-comprehensive 2-D GC-MS.
- Author
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Purcaro G, Tranchida PQ, Jacques RA, Caramão EB, Moret S, Conte L, Dugo P, Dugo G, and Mondello L
- Subjects
- Plant Extracts isolation & purification, Volatilization, Gas Chromatography-Mass Spectrometry methods, Ilex chemistry, Plant Extracts chemistry
- Abstract
The present research is focused on the use of a solid-phase microextraction-comprehensive 2-D GC methodology, in the analysis of the volatile fraction of yerba mate. Yerba mate is used for the generation of a tea-like beverage, widely consumed in South America. A rapid-scanning quadrupole mass spectrometer (qMS), employed as a detection system and operated at a 25 Hz scanning frequency, supplied high-quality mass spectra. The effectiveness of the 3-D comprehensive 2-D GC-qMS experiment was compared to that of GC-qMS analysis on the same sample. Peak identification, in both applications, was achieved through MS library matching, with the support of linear retention index data. Apart from a great increase in the number of analytes separated (approx. by a factor of 5) and identified (approx. by a factor of 3.5), the comprehensive 2-D GC-qMS approach enabled the determination of a high number of hazardous contaminants (aliphatic hydrocarbons, polycyclic aromatic hydrocarbons, and plasticizers), barely visible in the GC-qMS analysis.
- Published
- 2009
- Full Text
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198. High efficiency liquid chromatography techniques coupled to mass spectrometry for the characterization of mate extracts.
- Author
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Dugo P, Cacciola F, Donato P, Jacques RA, Caramão EB, and Mondello L
- Subjects
- Antioxidants analysis, Food Analysis methods, Plant Leaves chemistry, Polyphenols, Chromatography, Liquid methods, Flavonoids analysis, Ilex paraguariensis chemistry, Mass Spectrometry methods, Phenols analysis, Plant Extracts chemistry, Xanthines analysis
- Abstract
There is growing interest related to rapid screening and full characterization of the constituents of plants with medicinal properties; among these, "Mate" or Yerba Maté is a tea-like beverage widely consumed in South America, obtained from the dried leaves of Ilex paraguariensis. The high content in polyphenols accounts for in vitro and in vivo antioxidant activity of the extracts obtained from this plant; on the other hand, the high complexity of the samples extracted, depending on the method employed, may preclude complete resolution by conventional HPLC techniques. For this purpose, a comprehensive two-dimensional liquid chromatography (LC x LC) system, comprised of an RP-Amide first dimension and a partially porous octadecylsilica column in the second dimension, has been compared with a one-dimensional system. The latter was operated using a partially porous octadecylsilica column, with diode array (DAD) and electrospray/ion trap-time of flight (ESI/IT-TOF) detection for the most complex extracts. The employment of the hybrid mass spectrometer allowed unequivocal identification of several compounds in the mate extracts. Using LC x LC-MS(3), it was possible to discriminate between congeners of chlorogenic acids, along with monoacyl- and diacylchlorogenic acid esters.
- Published
- 2009
- Full Text
- View/download PDF
199. Pressurized liquid extraction of mate tea leaves.
- Author
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Jacques RA, Dariva C, de Oliveira JV, and Caramão EB
- Subjects
- Gas Chromatography-Mass Spectrometry, Pressure, Solvents chemistry, Temperature, Time Factors, Beverages analysis, Ilex paraguariensis chemistry, Plant Extracts chemistry, Plant Leaves chemistry
- Abstract
The objective of this work is to investigate the influence of process parameters on the pressurized liquid extraction (PLE) of Ilex paraguariensis leaves. A factorial 2(6-2) experimental design was employed using responses as the extraction yield and the chromatographic profile of the extracts. The extraction time, polarity of solvent, amount of sample, numbers of PLE cycles, flushing volume and extraction temperature were selected as independent variables (factors). Results obtained indicated that the solvent polarity was the most significant variable in the study, while the amount of sample and extraction temperature also showed significant effect. The other variables did not present significant influence in the yield of extraction. GC/MS analysis of the extract enabled the identification of saturated hydrocarbons, fatty acids, fatty acid methyl esters, phytosterols and theobromine in the extracts. Quantitative analysis of four compounds presented in the extracts (caffeine, phytol, vitamin E and squalene) was performed by the GC/MS in the SIM mode.
- Published
- 2008
- Full Text
- View/download PDF
200. Pressurized liquid extraction of vitamin E from Brazilian grape seed oil.
- Author
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Dos Santos Freitas L, Jacques RA, Richter MF, Silva AL, and Caramão EB
- Subjects
- Chromatography, High Pressure Liquid, Pressure, Reference Standards, Plant Oils chemistry, Vitamin E isolation & purification, Vitis embryology
- Abstract
The goal of this paper is to optimize the pressurized liquid extraction (PLE) of vitamin E from grape seed oil from residues of the wine industry. For this purpose an experimental planning to optimize the extraction of Brazilian grape seed oil by means of PLE with hexane as solvent was applied and the results are compared with conventional methods (Soxhlet and mechanical press extraction). Vitamin E was separated and analyzed using HPLC with UV detection. This study demonstrates the ability of the PLE in extracting grape seed oil rich in vitamin E.
- Published
- 2008
- Full Text
- View/download PDF
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