WorldWideScience

Sample records for rapid molecular characterization

  1. Rapid Characterization of Molecular Chemistry, Nutrient Make-Up and Microlocation of Internal Seed Tissue

    International Nuclear Information System (INIS)

    Yu, P.; Block, H.; Niu, Z.; Doiron, K.

    2007-01-01

    Wheat differs from corn in biodegradation kinetics and fermentation characteristics. Wheat exhibits a relatively high rate (23% h 01 ) and extent (78% DM) of biodegradation, which can lead to metabolic problems such as acidosis and bloat in ruminants. The objective of this study was to rapidly characterize the molecular chemistry of the internal structure of wheat (cv. AC Barrie) and reveal both its structural chemical make-up and nutrient component matrix by analyzing the intensity and spatial distribution of molecular functional groups within the intact seed using advanced synchrotron-powered Fourier transform infrared (FTIR) microspectroscopy. The experiment was performed at the U2B station of the National Synchrotron Light Source at Brookhaven National Laboratory, New York, USA. The wheat tissue was imaged systematically from the pericarp, seed coat, aleurone layer and endosperm under the peaks at ∼1732 (carbonyl C(double b ond)O ester), 1515 (aromatic compound of lignin), 1650 (amide I), 1025 (non-structural CHO), 1550 (amide II), 1246 (cellulosic material), 1160, 1150, 1080, 930, 860 (all CHO), 3350 (OH and NH stretching), 2928 (CH 2 stretching band) and 2885 cm -1 (CH 3 stretching band). Hierarchical cluster analysis and principal component analysis were applied to analyze the molecular FTIR spectra obtained from the different inherent structures within the intact wheat tissues. The results showed that, with synchrotron-powered FTIR microspectroscopy, images of the molecular chemistry of wheat could be generated at an ultra-spatial resolution. The features of aromatic lignin, structural and non-structural carbohydrates, as well as nutrient make-up and interactions in the seeds, could be revealed. Both principal component analysis and hierarchical cluster analysis methods are conclusive in showing that they can discriminate and classify the different inherent structures within the seed tissue. The wheat exhibited distinguishable differences in the

  2. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  3. Molecular characterization of genetic diversity in some durum wheat ...

    African Journals Online (AJOL)

    Molecular characterization of genetic diversity in some durum wheat ... African Journal of Biotechnology ... Thus, RAPD offer a potentially simple, rapid and reliable method to evaluate genetic variation and relatedness among ten wheat ...

  4. Molecular characterization of Azotobacter spp. nifH gene Isolated ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-15

    Dec 15, 2009 ... Available online at http://www.academicjournals.org/AJB. ISSN 1684–5315 ... Molecular characterization of Azotobacter spp. nifH .... MATERIALS AND METHODS ..... rapidly expanding and is currently composed of over.

  5. Molecular characterization of FXI deficiency.

    Science.gov (United States)

    Berber, Ergul

    2011-02-01

    Factor XI (FXI) deficiency is a rare autosomal bleeding disease associated with genetic defects in the FXI gene. It is a heterogeneous disorder with variable tendency in bleeding and variable causative FXI gene mutations. It is characterized as a cross-reacting material-negative (CRM-) FXI deficiency due to decreased FXI levels or cross-reacting material-positive (CRM+) FXI deficiency due to impaired FXI function. Increasing number of mutations has been reported in FXI mutation database, and most of the mutations are affecting serine protease (SP) domain of the protein. Functional characterization for the mutations helps to better understand the molecular basis of FXI deficiency. Prevalence of the disease is higher in certain populations such as Ashkenazi Jews. The purpose of this review is to give an overview of the molecular basis of congenital FXI deficiency.

  6. Rapid molecular technique to distinguish Fusarium species

    CSIR Research Space (South Africa)

    Lodolo, EJ

    1993-03-01

    Full Text Available The nuclear DNA (nDNA) of different isolates of three closely related, toxin-producing Fusarium species, F. moniliforme, F. nygamai and F. napiforme, was compared to ascertain the sensitivity of a molecular method to distinguish these three species...

  7. A simple and rapid molecular method for Leptospira species identification

    NARCIS (Netherlands)

    Ahmed, Ahmed; Anthony, Richard M.; Hartskeerl, Rudy A.

    2010-01-01

    Serological and DNA-based classification systems only have little correlation. Currently serological and molecular methods for characterizing Leptospira are complex and costly restricting their world-wide distribution and use. Ligation mediated amplification combined with microarray analysis

  8. Molecular characterization of rye cultivars

    Directory of Open Access Journals (Sweden)

    Želmíra Balážová

    2016-01-01

    Full Text Available 14.00 The results of molecular analysis of 45 rye taxa (Secale cereale L. represented by agricultural varieties originated from Central Europe and the Union of Soviet Socialist Republics (SUN are presented. The genetic diversity of rye cultivars by 6 SSR markers was evaluated. Six specific microsatellite primer pairs produced 58 polymorphic alleles with an average of 9.7 alleles per locus. The number of alleles ranged from 6 (SCM2 to 14 (SCM86. Genetic polymorphism was characterized based on diversity index (DI, probability of identity (PI and polymorphic information content (PIC. The diversity index (DI of SSR markers ranged from 0.5478 (SCM2 to 0.887 (SCM86 with an average of 0.778. The lowest value of polymorphic information content was recorded for SCM2 (0.484 and the highest value for SCM86 (0.885 of PIC was detected in SCM86 with an average of 0.760.The dendrogram of genetic similarity was constructed, based on UPGMA algorithm. The hierarchical cluster analysis divided rye genotypes into 4 main clusters. The first cluster of 14 genotypes was subdivided in two subclusters (1a and 1b where 50% of genotypes were Czechoslovak origin. The second cluster contained four genotypes were three (75% of them had Czech or Czechoslovak origin. In the third subcluster separated three rye genotypes of different origin. The rest (24 of rye genotypes in the fourth cluster were divided into two subclusters (4a and 4b where clearly separated group of Polish (4aa and Czech and Czechoslovak (4ab genotypes. Two genotypes of 4aa subcluster (Wojcieszyckie and Dankowskie Nowe from Poland were genetically the closest. In the dendrogram alle genotypes were differentiated and clustering partially reflects geographic origin of studied rye genotypes. In this experiment, SSRs markers proved to be a high informative and usefull tool in genetic diversity research for the distinguishing and characterization of close related varieties. Normal 0 21 false false false CS JA X-NONE

  9. Molecular characterization of opioid receptors

    Energy Technology Data Exchange (ETDEWEB)

    Howard, A.D.

    1986-01-01

    The aim of this research was to purify and characterize active opioid receptors and elucidate molecular aspects of opioid receptor heterogeneity. Purification to apparent homogeneity of an opioid binding protein from bovine caudate was achieved by solubilization in the non-ionic detergent, digitonin, followed by sequential chromatography on the opiate affinity matrix, ..beta..-naltrexylethylenediamine-CH-Sepharose 4B, and on the lectine affinity matrix, wheat germ agglutinin-agarose. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE) followed by autoradiography revealed that radioiodinated purified receptor gave a single band. Purified receptor preparations showed a specific activity of 12,000-15,000 fmol of opiate bound per mg of protein. Radioiodinated human beta-endorphin (/sup 125/I-beta-end/sub H/) was used as a probe to investigate the ligand binding subunits of mu and delta opioid receptors. /sup 125/I-beta-end/sub H/ was shown to bind to a variety of opioid receptor-containing tissues with high affinity and specificity with preference for mu and delta sites, and with little, if any, binding to kappa sites. Affinity crosslinking techniques were employed to covalently link /sup 125/I-beta-end/sub H/ to opioid receptors, utilizing derivatives of bis-succinimidyl esters that are bifunctional crosslinkers with specificities for amino and sulfhydryl groups. This, and competition experiments with high type-selective ligands, permitted the assignment of two labeled peptides to their receptor types, namely a peptide of M/sub r/ = 65,000 for mu receptors and one of M/sub r/ = 53,000 for delta receptors.

  10. Characterization of aluminium alloys rapidly solidified

    International Nuclear Information System (INIS)

    Monteiro, W.A.

    1988-01-01

    This paper discussed the investigation of the microstructural and mechanical properties of the aluminium alloys (3003; 7050; Al-9% Mg) rapidly solidified by melt spinning process (cooling rate 10 4 - 10 6 K/s). The rapidly solidification process of the studied aluminium alloys brought a microcrystallinity, a minimum presence of coarse precipitation and, also, better mechanical properties of them comparing to the same alloys using ingot process. (author) [pt

  11. Molecular characterization of composite interfaces

    International Nuclear Information System (INIS)

    Ishida, H.

    1982-01-01

    The Fourier Transform Infrared Spectroscopy was applied to elucidate the molecular structures of the glass/matrix interface. The various interfaces and interphases were studied. It is found that the structure of the silane in a treating solution is important in determining the structure of the silane on glass fibers, influences the macroscopic properties of composites. The amount of silane on glass fibers, the state of hydrogen bonding, orientation, copolymerization of the organicfunctionality with the matrix, curing of the silane, and effect of water on the interface were investigated. It is shown that the molecular approach is useful to interpret and predict physicomechanical properties of composites

  12. Molecular characterization of rainbow trout, Oncorhynchus mykiss ...

    Indian Academy of Sciences (India)

    Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Bhimtal 263 ... Mir J. I., Ali S., Patiyal R. S. and Singh A. K. 2015 Molecular characterization of rainbow trout, ..... 5 × 106 MCMC repeats for final sampling of data. .... enhancing aquaculture productivity in the coldwater regions. ... simulation study.

  13. Rapid detection and characterization of Salmonella enterica ...

    African Journals Online (AJOL)

    Multiplex polymerase chain reaction (PCR) was used for molecular typing of Salmonella enterica serovars in Egypt. During the summer of 2010, a total of 1075 samples were collected from cattle, sheep and poultry farms to be subjected for isolation of Salmonella (290 rectal swabs from cattle, 335 rectal swabs from sheep ...

  14. Molecular Characterization of Copepod Photoreception.

    Science.gov (United States)

    Porter, Megan L; Steck, Mireille; Roncalli, Vittoria; Lenz, Petra H

    2017-08-01

    Copepod crustaceans are an abundant and ecologically significant group whose basic biology is guided by numerous visually guided behaviors. These behaviors are driven by copepod eyes, including naupliar eyes and Gicklhorn's organs, which vary widely in structure and function among species. Yet little is known about the molecular aspects of copepod vision. In this study we present a general overview of the molecular aspects of copepod vision by identifying phototransduction genes from newly generated and publicly available RNA-sequencing data and assemblies from 12 taxonomically diverse copepod species. We identify a set of 10 expressed transcripts that serve as a set of target genes for future studies of copepod phototransduction. Our more detailed evolutionary analyses of the opsin gene responsible for forming visual pigments found that all of the copepod species investigated express two main groups of opsins: middle-wavelength-sensitive (MWS) opsins and pteropsins. Additionally, there is evidence from a few species (e.g., Calanus finmarchicus, Eurytemora affinis, Paracyclopina nana, and Lernaea cyprinacea) for the expression of two additional groups of opsins-the peropsins and rhodopsin 7 (Rh7) opsins-at low levels or distinct developmental stages. An ontogenetic analysis of opsin expression in Calanus finmarchicus found the expression of a single dominant MWS opsin, as well as evidence for differences in expression across development in some MWS, pteropsin, and Rh7 opsins, with expression peaking in early naupliar through early copepodite stages.

  15. Seismogeodesy for rapid earthquake and tsunami characterization

    Science.gov (United States)

    Bock, Y.

    2016-12-01

    Rapid estimation of earthquake magnitude and fault mechanism is critical for earthquake and tsunami warning systems. Traditionally, the monitoring of earthquakes and tsunamis has been based on seismic networks for estimating earthquake magnitude and slip, and tide gauges and deep-ocean buoys for direct measurement of tsunami waves. These methods are well developed for ocean basin-wide warnings but are not timely enough to protect vulnerable populations and infrastructure from the effects of local tsunamis, where waves may arrive within 15-30 minutes of earthquake onset time. Direct measurements of displacements by GPS networks at subduction zones allow for rapid magnitude and slip estimation in the near-source region, that are not affected by instrumental limitations and magnitude saturation experienced by local seismic networks. However, GPS displacements by themselves are too noisy for strict earthquake early warning (P-wave detection). Optimally combining high-rate GPS and seismic data (in particular, accelerometers that do not clip), referred to as seismogeodesy, provides a broadband instrument that does not clip in the near field, is impervious to magnitude saturation, and provides accurate real-time static and dynamic displacements and velocities in real time. Here we describe a NASA-funded effort to integrate GPS and seismogeodetic observations as part of NOAA's Tsunami Warning Centers in Alaska and Hawaii. It consists of a series of plug-in modules that allow for a hierarchy of rapid seismogeodetic products, including automatic P-wave picking, hypocenter estimation, S-wave prediction, magnitude scaling relationships based on P-wave amplitude (Pd) and peak ground displacement (PGD), finite-source CMT solutions and fault slip models as input for tsunami warnings and models. For the NOAA/NASA project, the modules are being integrated into an existing USGS Earthworm environment, currently limited to traditional seismic data. We are focused on a network of

  16. Molecular characterization and phylogenetic relationships among ...

    African Journals Online (AJOL)

    Molecular characterization and phylogenetic relationships among and within species of Phalaenopsis (Epidendroideae: Orchidaceae) based on RAPD analysis. ... Ph. parishii, Ph. labbi nepal, Ph. speciosa, Ph. lobbi yellow, Ph. venosa, Ph. hieroglyphica, and Ph. maculata; the third group consisted of Ph. minho princess, ...

  17. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma

    NARCIS (Netherlands)

    Fishbein, Lauren; Leshchiner, Ignaty; Walter, Vonn; Danilova, Ludmila; Robertson, A. Gordon; Johnson, Amy R.; Lichtenberg, Tara M.; Murray, Bradley A.; Ghayee, Hans K.; Else, Tobias; Ling, Shiyun; Jefferys, Stuart R.; de Cubas, Aguirre A.; Wenz, Brandon; Korpershoek, Esther; Amelio, Antonio L.; Makowski, Liza; Rathmell, W. Kimryn; Gimenez-Roqueplo, Anne Paule; Giordano, Thomas J.; Asa, Sylvia L.; Tischler, Arthur S.; Akbani, Rehan; Ally, Adrian; Amar, Laurence; Amelio, Antonio L.; Arachchi, Harindra; Asa, Sylvia L.; Auchus, Richard J.; Auman, J. Todd; Baertsch, Robert; Balasundaram, Miruna; Balu, Saianand; Bartsch, Detlef K.; Baudin, Eric; Bauer, Thomas; Beaver, Allison; Benz, Christopher; Beroukhim, Rameen; Beuschlein, Felix; Bodenheimer, Tom; Boice, Lori; Bowen, Jay; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Carter, Suzie; Cassol, Clarissa A.; Cherniack, Andrew D.; Chin, Lynda; Cho, Juok; Chuah, Eric; Chudamani, Sudha; Cope, Leslie; Crain, Daniel; Curley, Erin; Danilova, Ludmila; de Cubas, Aguirre A.; de Krijger, Ronald R.; Demchok, John A.; Deutschbein, Timo; Dhalla, Noreen; Dimmock, David; Dinjens, Winand N M; Else, Tobias; Eng, Charis; Eschbacher, Jennifer; Fassnacht, Martin; Felau, Ina; Feldman, Michael; Ferguson, Martin L.; Fiddes, Ian; Fishbein, Lauren; Frazer, Scott; Gabriel, Stacey B.; Gardner, Johanna; Gastier-Foster, Julie M.; Gehlenborg, Nils; Gerken, Mark; Getz, Gad; Geurts, Jennifer; Ghayee, Hans K.; Gimenez-Roqueplo, Anne Paule; Giordano, Thomas J.; Goldman, Mary; Graim, Kiley; Gupta, Manaswi; Haan, David; Hahner, Stefanie; Hantel, Constanze; Haussler, David; Hayes, D. Neil; Heiman, David I.; Hoadley, Katherine A.; Holt, Robert A.; Hoyle, Alan P.; Huang, Mei; Hunt, Bryan; Hutter, Carolyn M.; Jefferys, Stuart R.; Johnson, Amy R.; Jones, Steven J M; Jones, Corbin D.; Kasaian, Katayoon; Kebebew, Electron; Kim, Jaegil; Kimes, Patrick; Knijnenburg, Theo; Korpershoek, Esther; Lander, Eric; Lawrence, Michael S.; Lechan, Ronald; Lee, Darlene; Leraas, Kristen M.; Lerario, Antonio; Leshchiner, Ignaty; Lichtenberg, Tara M.; Lin, Pei; Ling, Shiyun; Liu, Jia; LiVolsi, Virginia A.; Lolla, Laxmi; Lotan, Yair; Lu, Yiling; Ma, Yussanne; Maison, Nicole; Makowski, Liza; Mallery, David; Mannelli, Massimo; Marquard, Jessica; Marra, Marco A.; Matthew, Thomas; Mayo, Michael; Méatchi, Tchao; Meng, Shaowu; Merino, Maria J.; Mete, Ozgur; Meyerson, Matthew; Mieczkowski, Piotr A.; Mills, Gordon B.; Moore, Richard A.; Morozova, Olena; Morris, Scott; Mose, Lisle E.; Mungall, Andrew J.; Murray, Bradley A.; Naresh, Rashi; Nathanson, Katherine L.; Newton, Yulia; Ng, Sam; Ni, Ying; Noble, Michael S.; Nwariaku, Fiemu; Pacak, Karel; Parker, Joel S.; Paul, Evan; Penny, Robert; Perou, Charles M.; Perou, Amy H.; Pihl, Todd; Powers, James; Rabaglia, Jennifer; Radenbaugh, Amie; Ramirez, Nilsa C.; Rao, Arjun; Rathmell, W. Kimryn; Riester, Anna; Roach, Jeffrey; Robertson, A. Gordon; Sadeghi, Sara; Saksena, Gordon; Salama, Sofie; Saller, Charles; Sandusky, George; Sbiera, Silviu; Schein, Jacqueline E.; Schumacher, Steven E.; Shelton, Candace; Shelton, Troy; Sheth, Margi; Shi, Yan; Shih, Juliann; Shmulevich, Ilya; Simons, Janae V.; Sipahimalani, Payal; Skelly, Tara; Sofia, Heidi J.; Sokolov, Artem; Soloway, Matthew G.; Sougnez, Carrie; Stuart, Josh; Sun, Charlie; Swatloski, Teresa; Tam, Angela; Tan, Donghui; Tarnuzzer, Roy; Tarvin, Katherine; Thiessen, Nina; Thorne, Leigh B.; Timmers, Henri J.; Tischler, Arthur S.; Tse, Kane; Uzunangelov, Vlado; van Berkel, Anouk; Veluvolu, Umadevi; Vicha, Ales; Voet, Doug; Waldmann, Jens; Walter, Vonn; Wan, Yunhu; Wang, Zhining; Wang, Tracy S.; Weaver, Joellen; Weinstein, John N.; Weismann, Dirk; Wenz, Brandon; Wilkerson, Matthew D.; Wise, Lisa; Wong, Tina; Wong, Christopher; Wu, Ye; Yang, Liming; Zelinka, Tomas; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Zhang, Wei; Zhu, Jingchun; Zinzindohoué, Franck; Zmuda, Erik; Pacak, Karel; Nathanson, Katherine L.; Wilkerson, Matthew D.

    2017-01-01

    We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight

  18. Cultural, morphological, pathogenic and molecular characterization ...

    African Journals Online (AJOL)

    Alternaria blotch (Alternaria mali) causes severe foliar damage to apple trees in Kashmir. Twenty one (21) isolates of A. mali were collected from different locations and characterized for cultural, morphological, pathogenic and molecular variations. A. mali colonies varied in their cultural behaviour ranging from velvety to ...

  19. Phenotypic and molecular characterization of Salmonella serotypes ...

    African Journals Online (AJOL)

    The presence of Salmonella and human pathogens in unpasteurized milk remains a public health hazard. The study reported the phenotypic and molecular characterization of Salmonella serotypes in cow raw milk, cheese and traditional yoghurt marketed for man's consumption in Nigeria. Isolation of Salmonella was done ...

  20. Synthesis, characterization, antimicrobial activity and molecular ...

    African Journals Online (AJOL)

    Synthesis, characterization, antimicrobial activity and molecular docking studies of combined pyrazol-barbituric acid pharmacophores. Assem Barakat, Bandar M. Al-Qahtani, Abdullah M. Al-Majid, M. Ali Mohammed Rafi Shaik, Mohamed H.M. Al-Agamy, Abdul Wadood ...

  1. Molecular characterization of rainbow trout, Oncorhynchus mykiss

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Online resources. Molecular characterization of rainbow trout, Oncorhynchus mykiss (Walbaum, 1792) stocks in India. Ashoktaru Barat Prabhati K. Sahoo Rohit Kumar Javaid I. Mir Shahnawaz Ali Rabindar S. Patiyal Atul K. Singh. Volume 94 Online resources 2015 pp e13- ...

  2. Isolation and molecular characterization of phytase producing ...

    African Journals Online (AJOL)

    Isolation and molecular characterization of phytase producing bacteria from Malaysia hot springs. ... The strains were further analyzed in broth culture using sodium phytate as substrate. Among them, strain L3 was selected as the best producer (0.16 U/ml after 72 h of culture). This phytase showed optimal activity at 37 °C ...

  3. Molecular characterization of PCN populations from Serbia

    Directory of Open Access Journals (Sweden)

    Oro Violeta

    2012-01-01

    Full Text Available The morphology of potato cyst nematodes (PCN was until recently almost the only way to identify these quarantine organisms. In the last two decades, molecular analyses contributed to faster and more efficient identification of two Globodera species (Globodera pallida and G. rostochiensis and allowed insight into the genetic structure of those parts that were practically inaccessible by morphological studies. Molecular characterization was performed in ITS1-5.8S-ITS2 region. The comparison was made with sequences of different foreign PCN populations via NCBI GenBank database. The results of molecular studies showed similarities and differences between local and foreign PCN populations in the part of genome that was studied.

  4. Molecular and phenotypic characterization of anamorphic fungi

    OpenAIRE

    Madrid Lorca, Hugo

    2011-01-01

    Anamorphic fungi (those reproducing asexually) are a big part of kingdom Fungi. Most of them occur as saprobes in nature, but numerous species are pathogenic to plants and animals including man. With the aim of contributing to the knowledge of the diversity and distribution of anamorphic fungi, we performed a phenotypic and molecular characterization of environmental and clinical isolates of these fungi. Based on a polyphasic taxonomy approach which included morphology, physiology and DNA seq...

  5. Rapid Molecular Identification of Human Taeniid Cestodes by Pyrosequencing Approach

    Science.gov (United States)

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Tourtip, Somjintana; Yamasaki, Hiroshi; Maleewong, Wanchai

    2014-01-01

    Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse. PMID:24945530

  6. Rapid molecular identification of human taeniid cestodes by pyrosequencing approach.

    Directory of Open Access Journals (Sweden)

    Tongjit Thanchomnang

    Full Text Available Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1 gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.

  7. Molecular diagnostics for the detection and characterization of microbial pathogens.

    Science.gov (United States)

    Procop, Gary W

    2007-09-01

    New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

  8. Rapid Isolation and Molecular Detection of Streptomycin-Producing Streptomycetes

    Directory of Open Access Journals (Sweden)

    M Motovali-bashi

    2006-07-01

    Full Text Available Introduction: Streptomyces species are mycelial, aerobic gram-positive bacteria that are isolated from soil and produce a diverse range of antibiotics. Streptomyces griseus produces the antibiotic, streptomycin and forms spores even in a liquid culture. The gene cluster for the production of Streptomycin antibiotic contains strR gene that encodes StrR, a pathway-specific regulator. Then, this pathway-specific regulator induces transcription of other streptomycin production genes in the gene cluster. The overall aim of this work was rapid isolation and molecular detection of streptomycin-producing Streptomycetes, especially S. griseus, from Iranian soils in order to manipulate them for increased production of streptomycin. Methods: This research used new initiative half-specific medium for isolation of Streptomycetes from natural environments, called FZmsn. The fifty colonies of Streptomyces strains grown on the surface of FZmsn medium isolated from environmental samples were defined on the basis of their morphological characteristics and light microscope studies. A set of primers was designed to detect strR by OLIGO software. Results: In colony-PCR reactions followed by gel electrophoresis, 6 colonies from Streptomyces strains colonies were detected as S. griseus colonies. Conclusion: These native Streptomyces strains will be used for genetic manipulation of S. griseus in order to increase production levels of streptomycin.

  9. Rapid sampling of molecular motions with prior information constraints.

    Science.gov (United States)

    Raveh, Barak; Enosh, Angela; Schueler-Furman, Ora; Halperin, Dan

    2009-02-01

    Proteins are active, flexible machines that perform a range of different functions. Innovative experimental approaches may now provide limited partial information about conformational changes along motion pathways of proteins. There is therefore a need for computational approaches that can efficiently incorporate prior information into motion prediction schemes. In this paper, we present PathRover, a general setup designed for the integration of prior information into the motion planning algorithm of rapidly exploring random trees (RRT). Each suggested motion pathway comprises a sequence of low-energy clash-free conformations that satisfy an arbitrary number of prior information constraints. These constraints can be derived from experimental data or from expert intuition about the motion. The incorporation of prior information is very straightforward and significantly narrows down the vast search in the typically high-dimensional conformational space, leading to dramatic reduction in running time. To allow the use of state-of-the-art energy functions and conformational sampling, we have integrated this framework into Rosetta, an accurate protocol for diverse types of structural modeling. The suggested framework can serve as an effective complementary tool for molecular dynamics, Normal Mode Analysis, and other prevalent techniques for predicting motion in proteins. We applied our framework to three different model systems. We show that a limited set of experimentally motivated constraints may effectively bias the simulations toward diverse predicates in an outright fashion, from distance constraints to enforcement of loop closure. In particular, our analysis sheds light on mechanisms of protein domain swapping and on the role of different residues in the motion.

  10. Rapid sampling of molecular motions with prior information constraints.

    Directory of Open Access Journals (Sweden)

    Barak Raveh

    2009-02-01

    Full Text Available Proteins are active, flexible machines that perform a range of different functions. Innovative experimental approaches may now provide limited partial information about conformational changes along motion pathways of proteins. There is therefore a need for computational approaches that can efficiently incorporate prior information into motion prediction schemes. In this paper, we present PathRover, a general setup designed for the integration of prior information into the motion planning algorithm of rapidly exploring random trees (RRT. Each suggested motion pathway comprises a sequence of low-energy clash-free conformations that satisfy an arbitrary number of prior information constraints. These constraints can be derived from experimental data or from expert intuition about the motion. The incorporation of prior information is very straightforward and significantly narrows down the vast search in the typically high-dimensional conformational space, leading to dramatic reduction in running time. To allow the use of state-of-the-art energy functions and conformational sampling, we have integrated this framework into Rosetta, an accurate protocol for diverse types of structural modeling. The suggested framework can serve as an effective complementary tool for molecular dynamics, Normal Mode Analysis, and other prevalent techniques for predicting motion in proteins. We applied our framework to three different model systems. We show that a limited set of experimentally motivated constraints may effectively bias the simulations toward diverse predicates in an outright fashion, from distance constraints to enforcement of loop closure. In particular, our analysis sheds light on mechanisms of protein domain swapping and on the role of different residues in the motion.

  11. Molecular characterization of apocrine salivary duct carcinoma.

    Science.gov (United States)

    Chiosea, Simion I; Williams, Lindsay; Griffith, Christopher C; Thompson, Lester D R; Weinreb, Ilan; Bauman, Julie E; Luvison, Alyssa; Roy, Somak; Seethala, Raja R; Nikiforova, Marina N

    2015-06-01

    Contemporary classification and treatment of salivary duct carcinoma (SDC) require its thorough molecular characterization. Thirty apocrine SDCs were analyzed by the Ion Ampliseq Cancer HotSpot panel v2 for mutations in 50 cancer-related genes. Mutational findings were corroborated by immunohistochemistry (eg, TP53, BRAF, β-catenin, estrogen, and androgen receptors) or Sanger sequencing/SNaPshot polymerase chain reaction. ERBB2 (HER2), PTEN, FGFR1, CDKN2A/P16, CMET, EGFR, MDM2, and PIK3CA copy number changes were studied by fluorescence in situ hybridization. TP53 mutations (15/27, 56%), PTEN loss (11/29, 38%, including 2 cases with PTEN mutation), PIK3CA hotspot mutations (10/30, 33%), HRAS hotspot mutations (10/29; 34%), and ERBB2 amplification (9/29, 31%, including 1 case with mutation) represented the 5 most common abnormalities. There was no correlation between genetic changes and clinicopathologic parameters. There was substantial overlap between genetic changes: 8 of 9 cases with ERBB2 amplification also harbored a PIK3CA, HRAS, and TP53 mutation and/or PTEN loss. Six of 10 cases with PIK3CA mutation also had an HRAS mutation. These findings provide a molecular rationale for dual targeting of mitogen-activated protein kinase and phosphoinositide 3-kinase pathways in SDC. FGFR1 amplification (3/29, 10%) represents a new potential target. On the basis of studies of breast carcinomas, the efficacy of anti-ERBB2 therapy will likely be decreased in SDC with ERBB2 amplification co-occurring with PIK3CA mutation or PTEN loss. Therefore, isolated ERBB2 testing is insufficient for theranostic stratification of apocrine SDC. On the basis of the prevalence and type of genetic changes, apocrine SDC appears to resemble one subtype of breast carcinoma-"luminal androgen receptor positive/molecular apocrine."

  12. Molecular characterization of the canine HMGB1.

    Science.gov (United States)

    Murua Escobar, H; Meyer, B; Richter, A; Becker, K; Flohr, A M; Bullerdiek, J; Nolte, I

    2003-01-01

    Due to the close similarities of numerous canine diseases to their human counterparts, the dog could join the mouse as the species of choice to unravel the genetic background of complex diseases as e.g. cancer and metabolic diseases. Accordingly, the role of the dog as a model for therapeutic approaches is strongly increasing. However, prerequisite for such studies is the characterization of the corresponding canine genes. Recently, the human high mobility group protein B1 (HMGB1) has attracted considerable interest of oncologists because of what is called its "double life". Besides its function as an architectural transcription factor HMGB1 can also be secreted by certain cells and then acts as a ligand for the receptor for advanced glycation end products (RAGE). The binding of HMGB1 to RAGE can activate key cell signaling pathways, such as p38(MAPK), JNK, and p42/p44(MAPK) emphasizing the important role of HMGB1 in inflammation and tumor metastasis. These results make HMGB1 a very interesting target for therapeutic studies done in model organisms like the dog. In this study we characterized the molecular structure of the canine HMGB1 gene on genomic and cDNA levels, its predicted protein, the gene locus and a basic expression pattern. Copyright 2003 S. Karger AG, Basel

  13. Isolation, cloning and molecular characterization of a thermotolerant ...

    African Journals Online (AJOL)

    Isolation, cloning and molecular characterization of a thermotolerant xylanase from Streptomyces sp. THW31. Thayat Sriyapai, Peechapack Somyoonsap, Supatra Areekit, Paisarn Khawsak, Arda Pakpitcharoen, Kosum Chansiri ...

  14. Introducing molecular selectivity in rapid impedimetric sensing of phthalates

    KAUST Repository

    Zia, Asif I.; Mukhopadhyay, Subhas Chandra; Al-Bahadly, Ibrahim H.; Yu, Paklam; Gooneratne, Chinthaka Pasan; Kosel, Jü rgen

    2014-01-01

    This research article reports a real-time and non-invasive detection technique for phthalates in liquids by Electrochemical Impedance Spectroscopy (EIS), incorporating molecular imprinting technique to introduce selectivity for the phthalate

  15. Rapid characterizing of ferromagnetic materials using spin rectification

    International Nuclear Information System (INIS)

    Fan, Xiaolong; Wang, Wei; Wang, Yutian; Zhou, Hengan; Rao, Jinwei; Zhao, Xiaobing; Gao, Cunxu; Xue, Desheng; Gui, Y. S.; Hu, C.-M.

    2014-01-01

    Spin rectification is a powerful tool for dc electric detections of spin dynamics and electromagnetic waves. Technically, elaborately designed on-chip microwave devices are needed in order to realize that effect. In this letter, we propose a rapid characterizing approach based on spin rectification. By directly sending dynamic current into ferromagnetic films with stripe shape, resonant dc voltages can be detected along the longitudinal or transversal directions. As an example, Fe (010) films with precise crystalline structure and magnetic parameters were used to testify the reliability of such method. We investigated not only the dynamic parameters and the precise anisotropy constants of the Fe crystals but also the principle of spin rectification in this method

  16. Preparation and Characterization of Nonylphenol Magnetic Molecularly Imprinted Polymer

    International Nuclear Information System (INIS)

    Chen, F. Y.; Ba, S. P.; Tang, Y. B.; Wang, X. G.

    2015-01-01

    Nonylphenol (NP) is a toxic xenobiotic compound classified as an endocrine disrupter, which can interface with the hormonal system of numerous organisms, and then cause a series of pathological changes. It is of great significance to remove nonyl phenol from the environment. In this paper, an effective method for the preparation of molecularly imprinted nanoparticles was reported. Firstly, Fe/sub 3/O/sub 4/ at the rate SiO/sub 2/ magnetic carrier material modified by trimethoxysilane was achieved through three-step reaction. After that, the selective magnetic molecularly imprinted polymer sorbent for NP (Fe/sub 3/O/sub 4/ at the rate SiO/sub 2/-MIP) was synthesized by surface molecular imprinting technique, using NP as template, 4-vinyl pyridine(4-Vpy) as functional monomers, ethylene glycol dimethacrylate (EGDMA) as cross linker and azobisisobutyronitrile (AIBN) as initiator. The morphous, composition, structure and performance of polymer adsorbent was characterized by SEM, TEM, FT-IR, XRD, EDS, VSM and nitrogen adsorption-desorption techniques. The results indicated that the polymer adsorbent was successfully prepared. The size of the polymer particle was about 50 nm, the aperture on the surface was 3.71 nm, the BET specific surface area was 61.80 m/sup 2/g and the Langmuir specific surface area was 101.24 m/sup 2/g. The selective adsorption rate for NP of 0.5 mmol/L attained value of 86.5%, and for NP with low concentration (less than 2.0 mg/L), the selective adsorption rate reached more than 90%. The synthesized magnetic molecularly imprinted polymer had higher selective recognition ability towards the template molecule nonylphenol. It has good magnetism and can be rapidly separated after being employed by using adscititious magnetic field. It has potential application value in treatment and enrichment of nonylphenol. (author)

  17. Using molecular techniques for rapid detection of Salmonella ...

    African Journals Online (AJOL)

    PRECIOUS

    2010-02-01

    Feb 1, 2010 ... A total of 152 samples of chicken and chicken products ... detection of Salmonella species in the collected field samples ... that 16 million new cases of typhoid fever occur each ... vative methods for the rapid identification of Salmonella ... saved for the PCR-Non Selective test (PCR-NS) and 1 ml of the.

  18. Using current molecular techniques for rapid differentiation of ...

    African Journals Online (AJOL)

    Typhoid fever is responsible for the deaths of many people annually. However, conventional and timeconsuming detection methods for Salmonella Typhi still dominate. By using a molecular based approach, it was possible to identify Salmonella Typhi by amplifying two specific genes (viaB and tyv) and by using RFLP ...

  19. Introducing molecular selectivity in rapid impedimetric sensing of phthalates

    KAUST Repository

    Zia, Asif I.

    2014-05-01

    This research article reports a real-time and non-invasive detection technique for phthalates in liquids by Electrochemical Impedance Spectroscopy (EIS), incorporating molecular imprinting technique to introduce selectivity for the phthalate molecule in the detection system. A functional polymer with Bis (2-ethylhexyl) phthalate (DEHP) template was immobilized on the sensing surface of the inter-digital (ID) capacitive sensor with sputtered gold sensing electrodes fabricated over a native layer of silicon dioxide on a single crystal silicon substrate. Various concentrations (10 to 200 ppm) of DEHP in deionized MilliQ water were exposed to the sensor surface functionalized with molecular imprinted polymer (MIP) in order to capture the analyte molecule, hence introducing molecular selectivity to the testing system. Impedance spectra were obtained using EIS in order to determine sample conductance for evaluation of phthalate concentration in the solution. Electrochemical Spectrum Analyzer algorithm was used to deduce equivalent circuit and equivalent component parameters from the experimentally obtained impedance spectra employing Randle\\'s cell model curve fitting technique. Experimental results confirmed that the immobilization of the functional polymer on sensing surface introduces selectivity for phthalates in the sensing system. The results were validated by testing the samples using High Performance Liquid Chromatography (HPLC-DAD). © 2014 IEEE.

  20. Molecular Characterization of Bacterial Respiration on Minerals

    Energy Technology Data Exchange (ETDEWEB)

    Blake, Robert C.

    2013-04-26

    The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength

  1. Molecular characterization of intestinal protozoan parasites from ...

    African Journals Online (AJOL)

    Koffi Mathurin

    2014-02-17

    Feb 17, 2014 ... histolytica and C. parvum infection, based on molecular diagnosis, in children .... cytotoxigenic Clostridium difficile ), viruses (Rotavirus,. Noro viruses and ... cost, it gives the true prevalence with respect to its sensi- tivity and ...

  2. Fabrication of Polymerase Chain Reaction Plastic Lab-on-a-Chip Device for Rapid Molecular Diagnoses

    Directory of Open Access Journals (Sweden)

    Kieu The Loan Trinh

    2016-05-01

    Full Text Available Purpose: We aim to fabricate a thermoplastic poly(methylmethacrylate (PMMA Lab-on-a-Chip device to perform continuous- flow polymerase chain reactions (PCRs for rapid molecular detection of foodborne pathogen bacteria. Methods: A miniaturized plastic device was fabricated by utilizing PMMA substrates mediated by poly(dimethylsiloxane interfacial coating, enabling bonding under mild conditions, and thus avoiding the deformation or collapse of microchannels. Surface characterizations were carried out and bond strength was measured. The feasibility of the Lab-on-a-Chip device for performing on-chip PCR utilizing a lab-made, portable dual heater was evaluated. The results were compared with those obtained using a commercially available thermal cycler. Results: A PMMA Lab-on-a-Chip device was designed and fabricated for conducting PCR using foodborne pathogens as sample targets. A robust bond was established between the PMMA substrates, which is essential for performing miniaturized PCR on plastic. The feasibility of on-chip PCR was evaluated using Escherichia coli O157:H7 and Cronobacter condimenti, two worldwide foodborne pathogens, and the target amplicons were successfully amplified within 25 minutes. Conclusions: In this study, we present a novel design of a low-cost and high-throughput thermoplastic PMMA Lab-on-a-Chip device for conducting microscale PCR, and we enable rapid molecular diagnoses of two important foodborne pathogens in minute resolution using this device. In this regard, the introduced highly portable system design has the potential to enable PCR investigations of many diseases quickly and accurately.

  3. Rapid methods for the extraction and archiving of molecular grade fungal genomic DNA.

    Science.gov (United States)

    Borman, Andrew M; Palmer, Michael; Johnson, Elizabeth M

    2013-01-01

    The rapid and inexpensive extraction of fungal genomic DNA that is of sufficient quality for molecular approaches is central to the molecular identification, epidemiological analysis, taxonomy, and strain typing of pathogenic fungi. Although many commercially available and in-house extraction procedures do eliminate the majority of contaminants that commonly inhibit molecular approaches, the inherent difficulties in breaking fungal cell walls lead to protocols that are labor intensive and that routinely take several hours to complete. Here we describe several methods that we have developed in our laboratory that allow the extremely rapid and inexpensive preparation of fungal genomic DNA.

  4. Molecular Characterization of Cocoa, Mango, Banana and Yam ...

    African Journals Online (AJOL)

    Molecular Characterization of Cocoa, Mango, Banana and Yam Isolates of Botryodiplodia theobromae in Ghana. ... A total of 25 fungal isolates were sampled from cocoa, mango, banana and yam within four ... HOW TO USE AJOL.

  5. Morphological and molecular characterization of L-methioninase ...

    African Journals Online (AJOL)

    Six species of L-methioninase producing Aspergillus species, isolated from Egyptian soil, were selected for comprehensive morphotypic and molecular characterization. Based on morphological and physiological features, these isolates were identified as Aspergillus flavipes, Aspergillus carneus, Aspergillus flavus, ...

  6. Rapid molecular identification and characteristics of Lactobacillus strains.

    Science.gov (United States)

    Markiewicz, L H; Biedrzycka, E; Wasilewska, E; Bielecka, M

    2010-09-01

    Eleven type strains and 24 Lactobacillus isolates, preliminarily classified to the species due to phenotypic features, were investigated. Standard methods of identification with species-specific PCRs and typing with PFGE (with ApaI, NotI and SmaI restriction enzymes) allowed us to distinguish 16 unique strains belonging to 5 species (L. acidophilus, L. delbrueckii ssp. bulgaricus, L. plantarum, L. rhamnosus, L. salivarius). Alternative approach with 16S-23S rDNA ARDRA identification (with merely two restrictases, BsuRI and TaqI) and PCR-based typing (RAPD with two random- and rep-PCR with (GTG)(5) primers) showed to be more discriminative, i.e. 21 unique strains were classified in the same species as above. As a result, 7 out of 24 phenotypically species-assigned isolates were reclassified. The alternative procedure of rapid identification and typing of Lactobacillus isolates appeared to be equally effective and shortened from 1 week to 2-3 d (in comparison to the standard methods).

  7. Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

    Science.gov (United States)

    Cazanave, Charles; Greenwood-Quaintance, Kerryl E.; Hanssen, Arlen D.; Karau, Melissa J.; Schmidt, Suzannah M.; Gomez Urena, Eric O.; Mandrekar, Jayawant N.; Osmon, Douglas R.; Lough, Lindsay E.; Pritt, Bobbi S.; Steckelberg, James M.

    2013-01-01

    We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure. PMID:23658273

  8. The rapid evolution of molecular genetic diagnostics in neuromuscular diseases.

    Science.gov (United States)

    Volk, Alexander E; Kubisch, Christian

    2017-10-01

    The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.

  9. Molecular characterization of carbapenem-resistant Acinetobacter ...

    African Journals Online (AJOL)

    Purpose: To survey the molecular characteristics of imipenem-resistant Acinetobacter baumannii obtained from pediatric burns patients in a teaching hospital in Tehran, Iran. Methods: Over a 10-month period, 73 non-duplicate A. baumannii strains were collected from pediatric burns patients admitted to Motahari Burn and ...

  10. Molecular detection and characterization of sustainable intracellular ...

    African Journals Online (AJOL)

    3Centre for Biopolymer and Bio-Molecular Research, Athlone College of Technology, Republic of Ireland. ... cells was associated with the elongation of micro-villar extension that ... Keywords: Intracellular contaminants, cell cultures, bacteria culture, pre-clinical studies. ... production work involving culture technology.

  11. Molecular Characterization of Glucose-6-Phosphate ...

    African Journals Online (AJOL)

    G6PD) deficiency among staff and students of a university community in Malaysia as well as to identify molecular genetics by determination of G6PD mutations. Methods: Cross-sectional and experimental studies were carried out on the staff ...

  12. Isolation, characterization and Molecular weight Determination of ...

    African Journals Online (AJOL)

    Salwee

    2013-07-10

    Jul 10, 2013 ... Cellulose hydrolyzing enzyme from fungus Trichoderma viride was purified and characterized. The cellulase ... the most abundant component of plant biomass, found ... could efficiently and economically convert celluloytic.

  13. Molecular characterization of organic electronic films.

    Science.gov (United States)

    DeLongchamp, Dean M; Kline, R Joseph; Fischer, Daniel A; Richter, Lee J; Toney, Michael F

    2011-01-18

    Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Molecular Characterization of Macrophage-Biomaterial Interactions.

    Science.gov (United States)

    Moore, Laura Beth; Kyriakides, Themis R

    2015-01-01

    Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulation. In this review, we discuss the molecular events that contribute to macrophage activation and fusion with a focus on the role of the inflammasome, signaling pathways such as JAK/STAT and NF-κB, and the putative involvement of micro RNAs in the regulation of these processes.

  15. Isolation, Characterization and Molecular weight determination of ...

    African Journals Online (AJOL)

    Enzyme purification to homogeneity was carried out by anion exchange chromatography on DEAE-Sepharose. SDS-PAGE revealed molecular mass of 87 kDa. Maximal activity of the enzymes was observed at 50°C at pH 4 and was stimulated by Ca2+, Co2+, Mg2+ (test at 10 Mm each) and inhibited by Fe2+. Ethanol at an ...

  16. Molecular Characterization of Macrophage-Biomaterial Interactions

    OpenAIRE

    Moore, Laura Beth; Kyriakides, Themis R.

    2015-01-01

    Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulati...

  17. Comprehensive molecular characterization of gastric adenocarcinoma

    Science.gov (United States)

    Bass, Adam J.; Thorsson, Vesteinn; Shmulevich, Ilya; Reynolds, Sheila M.; Miller, Michael; Bernard, Brady; Hinoue, Toshinori; Laird, Peter W.; Curtis, Christina; Shen, Hui; Weisenberger, Daniel J.; Schultz, Nikolaus; Shen, Ronglai; Weinhold, Nils; Kelsen, David P.; Bowlby, Reanne; Chu, Andy; Kasaian, Katayoon; Mungall, Andrew J.; Robertson, A. Gordon; Sipahimalani, Payal; Cherniack, Andrew; Getz, Gad; Liu, Yingchun; Noble, Michael S.; Pedamallu, Chandra; Sougnez, Carrie; Taylor-Weiner, Amaro; Akbani, Rehan; Lee, Ju-Seog; Liu, Wenbin; Mills, Gordon B.; Yang, Da; Zhang, Wei; Pantazi, Angeliki; Parfenov, Michael; Gulley, Margaret; Piazuelo, M. Blanca; Schneider, Barbara G.; Kim, Jihun; Boussioutas, Alex; Sheth, Margi; Demchok, John A.; Rabkin, Charles S.; Willis, Joseph E.; Ng, Sam; Garman, Katherine; Beer, David G.; Pennathur, Arjun; Raphael, Benjamin J.; Wu, Hsin-Ta; Odze, Robert; Kim, Hark K.; Bowen, Jay; Leraas, Kristen M.; Lichtenberg, Tara M.; Weaver, Stephanie; McLellan, Michael; Wiznerowicz, Maciej; Sakai, Ryo; Getz, Gad; Sougnez, Carrie; Lawrence, Michael S.; Cibulskis, Kristian; Lichtenstein, Lee; Fisher, Sheila; Gabriel, Stacey B.; Lander, Eric S.; Ding, Li; Niu, Beifang; Ally, Adrian; Balasundaram, Miruna; Birol, Inanc; Bowlby, Reanne; Brooks, Denise; Butterfield, Yaron S. N.; Carlsen, Rebecca; Chu, Andy; Chu, Justin; Chuah, Eric; Chun, Hye-Jung E.; Clarke, Amanda; Dhalla, Noreen; Guin, Ranabir; Holt, Robert A.; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Li, Haiyan A.; Lim, Emilia; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen L.; Nip, Ka Ming; Robertson, A. Gordon; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Beroukhim, Rameen; Carter, Scott L.; Cherniack, Andrew D.; Cho, Juok; Cibulskis, Kristian; DiCara, Daniel; Frazer, Scott; Fisher, Sheila; Gabriel, Stacey B.; Gehlenborg, Nils; Heiman, David I.; Jung, Joonil; Kim, Jaegil; Lander, Eric S.; Lawrence, Michael S.; Lichtenstein, Lee; Lin, Pei; Meyerson, Matthew; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Saksena, Gordon; Schumacher, Steven E.; Sougnez, Carrie; Stojanov, Petar; Tabak, Barbara; Taylor-Weiner, Amaro; Voet, Doug; Rosenberg, Mara; Zack, Travis I.; Zhang, Hailei; Zou, Lihua; Protopopov, Alexei; Santoso, Netty; Parfenov, Michael; Lee, Semin; Zhang, Jianhua; Mahadeshwar, Harshad S.; Tang, Jiabin; Ren, Xiaojia; Seth, Sahil; Yang, Lixing; Xu, Andrew W.; Song, Xingzhi; Pantazi, Angeliki; Xi, Ruibin; Bristow, Christopher A.; Hadjipanayis, Angela; Seidman, Jonathan; Chin, Lynda; Park, Peter J.; Kucherlapati, Raju; Akbani, Rehan; Ling, Shiyun; Liu, Wenbin; Rao, Arvind; Weinstein, John N.; Kim, Sang-Bae; Lee, Ju-Seog; Lu, Yiling; Mills, Gordon; Laird, Peter W.; Hinoue, Toshinori; Weisenberger, Daniel J.; Bootwalla, Moiz S.; Lai, Phillip H.; Shen, Hui; Triche, Timothy; Van Den Berg, David J.; Baylin, Stephen B.; Herman, James G.; Getz, Gad; Chin, Lynda; Liu, Yingchun; Murray, Bradley A.; Noble, Michael S.; Askoy, B. Arman; Ciriello, Giovanni; Dresdner, Gideon; Gao, Jianjiong; Gross, Benjamin; Jacobsen, Anders; Lee, William; Ramirez, Ricardo; Sander, Chris; Schultz, Nikolaus; Senbabaoglu, Yasin; Sinha, Rileen; Sumer, S. Onur; Sun, Yichao; Weinhold, Nils; Thorsson, Vésteinn; Bernard, Brady; Iype, Lisa; Kramer, Roger W.; Kreisberg, Richard; Miller, Michael; Reynolds, Sheila M.; Rovira, Hector; Tasman, Natalie; Shmulevich, Ilya; Ng, Santa Cruz Sam; Haussler, David; Stuart, Josh M.; Akbani, Rehan; Ling, Shiyun; Liu, Wenbin; Rao, Arvind; Weinstein, John N.; Verhaak, Roeland G.W.; Mills, Gordon B.; Leiserson, Mark D. M.; Raphael, Benjamin J.; Wu, Hsin-Ta; Taylor, Barry S.; Black, Aaron D.; Bowen, Jay; Carney, Julie Ann; Gastier-Foster, Julie M.; Helsel, Carmen; Leraas, Kristen M.; Lichtenberg, Tara M.; McAllister, Cynthia; Ramirez, Nilsa C.; Tabler, Teresa R.; Wise, Lisa; Zmuda, Erik; Penny, Robert; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Curely, Erin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Shelton, Troy; Shelton, Candace; Sherman, Mark; Benz, Christopher; Lee, Jae-Hyuk; Fedosenko, Konstantin; Manikhas, Georgy; Potapova, Olga; Voronina, Olga; Belyaev, Smitry; Dolzhansky, Oleg; Rathmell, W. Kimryn; Brzezinski, Jakub; Ibbs, Matthew; Korski, Konstanty; Kycler, Witold; ŁaŸniak, Radoslaw; Leporowska, Ewa; Mackiewicz, Andrzej; Murawa, Dawid; Murawa, Pawel; Spychała, Arkadiusz; Suchorska, Wiktoria M.; Tatka, Honorata; Teresiak, Marek; Wiznerowicz, Maciej; Abdel-Misih, Raafat; Bennett, Joseph; Brown, Jennifer; Iacocca, Mary; Rabeno, Brenda; Kwon, Sun-Young; Penny, Robert; Gardner, Johanna; Kemkes, Ariane; Mallery, David; Morris, Scott; Shelton, Troy; Shelton, Candace; Curley, Erin; Alexopoulou, Iakovina; Engel, Jay; Bartlett, John; Albert, Monique; Park, Do-Youn; Dhir, Rajiv; Luketich, James; Landreneau, Rodney; Janjigian, Yelena Y.; Kelsen, David P.; Cho, Eunjung; Ladanyi, Marc; Tang, Laura; McCall, Shannon J.; Park, Young S.; Cheong, Jae-Ho; Ajani, Jaffer; Camargo, M. Constanza; Alonso, Shelley; Ayala, Brenda; Jensen, Mark A.; Pihl, Todd; Raman, Rohini; Walton, Jessica; Wan, Yunhu; Demchok, John A.; Eley, Greg; Mills Shaw, Kenna R.; Sheth, Margi; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean Claude; Davidsen, Tanja; Hutter, Carolyn M.; Sofia, Heidi J.; Burton, Robert; Chudamani, Sudha; Liu, Jia

    2014-01-01

    Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies. PMID:25079317

  18. Molecular cytogenetic characterization of a human thyroid cancercell line

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Tuton, Tiffany B.; Ito, Yuko; Chu, LisaW.; Lu, Chung-Mei; Baumgartner, Adolf; Zitzelsberger, Horst F.; Weier,Jingly F.

    2006-01-04

    The incidence of papillary thyroid carcinoma (PTC) increases significantly after exposure of the head and neck region to ionizing radiation, yet we know neither the steps involved in malignant transformation of thyroid epithelium nor the specific carcinogenic mode of action of radiation. Such increased tumor frequency became most evident in children after the 1986 nuclear accident in Chernobyl, Ukraine. In the twelve years following the accident, the average incidence of childhood PTCs (chPTC) increased over one hundred-fold compared to the rate of about 1 tumor incidence per 10{sup 6} children per year prior to 1986. To study the etiology of radiation-induced thyroid cancer, we formed an international consortium to investigate chromosomal changes and altered gene expression in cases of post-Chernobyl chPTC. Our approach is based on karyotyping of primary cultures established from chPTC specimens, establishment of cell lines and studies of genotype-phenotype relationships through high resolution chromosome analysis, DNA/cDNA micro-array studies, and mouse xenografts that test for tumorigenicity. Here, we report the application of fluorescence in situ hybridization (FISH)-based techniques for the molecular cytogenetic characterization of a highly tumorigenic chPTC cell line, S48TK, and its subclones. Using chromosome 9 rearrangements as an example, we describe a new approach termed ''BAC-FISH'' to rapidly delineate chromosomal breakpoints, an important step towards a better understanding of the formation of translocations and their functional consequences.

  19. Molecular characterization and phylogenetic analysis of Fasciola gigantica from Nigeria.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Tokashiki, Minami; Opara, Maxwell Nwachukwu; Iroh, Gabriel; Hayashi, Kei; Kumar, Uday Mohanta; Itagaki, Tadashi

    2017-02-01

    Fasciola gigantica is considered the major pathogen causing fasciolosis in Africa; however, molecular characterization of this fluke has not been adequately elucidated. It is important to scientifically elucidate the dispersal history of F. gigantica by analyzing its genetic diversity. Fasciola flukes from Nigeria were analyzed using nuclear and mitochondrial DNA markers. A total of 172 Fasciola flukes collected from cattle were identified as F. gigantica because they displayed the F. gigantica fragment pattern in multiplex PCR for the nuclear marker, phosphoenolpyruvate carboxykinase (pepck). In total, 70 haplotypes were detected from Nigerian F. gigantica on the basis of the concatenated sequence of mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase 1 (cox1). The index of neutrality (Fu's Fs) suggests rapid expansion of the Nigerian F. gigantica population. Although four haplogroups, Nigeria 1A, 1B, 2A, and 2B, were detected from Nigerian F. gigantica, a climate-specific genetic structure was not observed among F. gigantica populations from three agro-climatic regions (Sahel, Savannah, and Forest). This is probably because of the frequent transportation of livestock from one part of the country to the other. Nigeria 1A and 1B had close relationships with the Egyptian population of F. gigantica, whereas Nigeria 2A and 2B were comparatively related to the Zambian population. No haplotype was shared among the three countries, and it therefore is difficult to estimate the dispersal route of F. gigantica within the African continent. Copyright © 2016. Published by Elsevier Ireland Ltd.

  20. Physiological and molecular characterization of cowpea [Vigna ...

    African Journals Online (AJOL)

    Diaga Diouf

    Cowpea, Vigna unguiculata (L.) Walp. presents phenotypical variabilities and in order to study the genetic diversity of cultivated Senegalese varieties, two experimental approaches were used. First, a physiological characterization based on nitrogen fixation was used to assess cowpea breeding lines. Inoculation with two ...

  1. Molecular Characterization of the Resistance of Mycobacterium ...

    African Journals Online (AJOL)

    Purpose: To characterize the resistance of Mycobacterium tuberculosis to second line drugs using a line probe assay. Methods: Multi-drug resistant strains of Mycobacterium tuberculosis isolated between December 2008 and December 2009 were tested for resistance to fluoroquinolones and second-line injectable drugs ...

  2. Molecular Characterization of the Resistance of Mycobacterium ...

    African Journals Online (AJOL)

    Abstract. Purpose: To characterize the resistance of Mycobacterium tuberculosis to second line drugs using a line probe assay. Methods: ... Marne-la-Coquette,. France). Bacterial isolates contained in 500 µl of liquid culture were heat- inactivated at 95 °C for 30 min and then sonicated for 12 min. Finally, the suspension was ...

  3. Molecular characterization and expression analysis of chalcone ...

    African Journals Online (AJOL)

    Chalcone synthase (CHS, EC: 2.3.1.74) is a key enzyme in the flavonoid and anthocyanin biosynthesis pathway. In order to investigate the role of CHS in tree peony flower coloration mechanism, we isolated and characterized the CHS gene from Paeonia suffruticosa cv. Yu Ji Yan Zhuang and analyzed its spatial and ...

  4. Isolation, characterization and molecular weight determination of ...

    African Journals Online (AJOL)

    Shanmugam

    2013-01-30

    Jan 30, 2013 ... an attempt was made to isolate and characterize collagen from the marine sponge, Spirastrella inconstans. The total ... major constituent of many connective tissues. It is distributed in skin, bones, cartilage, tendons, ligaments, blood vessels, teeth ..... sponge fiber skeleton: a biomimetic scaffold for human.

  5. Rapid detection, characterization, and enumeration of foodborne pathogens

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey

    2011-01-01

    . The present review discusses the reasons for the increasing interest in rapid methods; current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing...... of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture...... of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based...

  6. Molecular Characterization of Staphylococcus warneri Catalase

    OpenAIRE

    Fukuda, Daisuke; Mizuno, Kouhei; Kohno, Mamiko; Sonomoto, Kenji; Ishizaki, Ayaaki

    2000-01-01

    The catalase gene was cloned by screening a genomic DNA library of S. warneri ISK-1 strain with a strong catalase activity for complementation of the activity in catalase-deficient E. coli strain. Nucleotide sequence analysis of a 2.2-kb DNA fragment revealed an open reading frame, called katA, encoding a peptide of 504 amino acids with a calculated molecular mass of 58kDa. The predicted amino acid sequence showed high similarities with the monofunctional catalases. No similarities were found...

  7. Clinical librarian support for rapid review of clinical utility of cancer molecular biomarkers.

    Science.gov (United States)

    Geng, Yimin; Fowler, Clara S; Fulton, Stephanie

    2015-01-01

    The clinical librarian used a restricted literature searching and quality-filtering approach to provide relevant clinical evidence for the use of cancer molecular biomarkers by institutional policy makers and clinicians in the rapid review process. The librarian-provided evidence was compared with the cited references in the institutional molecular biomarker algorithm. The overall incorporation rate of the librarian-provided references into the algorithm was above 80%. This study suggests the usefulness of clinical librarian expertise for clinical practice. The searching and filtering methods for high-level evidence can be adopted by information professionals who are involved in the rapid literature review.

  8. Implementation of Rapid Molecular Infectious Disease Diagnostics: the Role of Diagnostic and Antimicrobial Stewardship.

    Science.gov (United States)

    Messacar, Kevin; Parker, Sarah K; Todd, James K; Dominguez, Samuel R

    2017-03-01

    New rapid molecular diagnostic technologies for infectious diseases enable expedited accurate microbiological diagnoses. However, diagnostic stewardship and antimicrobial stewardship are necessary to ensure that these technologies conserve, rather than consume, additional health care resources and optimally affect patient care. Diagnostic stewardship is needed to implement appropriate tests for the clinical setting and to direct testing toward appropriate patients. Antimicrobial stewardship is needed to ensure prompt appropriate clinical action to translate faster diagnostic test results in the laboratory into improved outcomes at the bedside. This minireview outlines the roles of diagnostic stewardship and antimicrobial stewardship in the implementation of rapid molecular infectious disease diagnostics. Copyright © 2017 American Society for Microbiology.

  9. Mutant germplasm characterization using molecular markers. A manual

    International Nuclear Information System (INIS)

    2002-01-01

    Plant biotechnology applications must not only respond to the challenge of improving food security and fostering socio-economic development, but in doing so, promote the conservation, diversification and sustainable use of plant genetic resources for food and agriculture. Nowadays the biotechnology toolbox available to plant breeders offers several new possibilities for increasing productivity, crop diversification and production, while developing a more sustainable agriculture. This training course focuses on one of the most promising set of techniques used in modern crop improvement programmes, i.e. on molecular markers. These are rapidly being adopted by plant breeders and molecular biologists as effective and appropriate tools for basic and applied studies addressing biological components in agricultural production systems. Their use in applied breeding programmes can range from facilitating the appropriate choice of parents for crosses, to mapping/tagging of gene blocks associated with economically important traits (often termed 'quantitative trait loci' (QTLs)). Gene tagging and QTL mapping in turn permit marker-assisted selection (MAS) in backcross, pedigree, and population improvement programmes, thereby facilitating more efficient incremental improvement of specific individual target traits. And through comparative genomics, molecular markers can be used in ways that allow us to more effectively discover and efficiently exploit biodiversity and the evolutionary relationships between organisms. Substantial progress has been made in recent years in mapping, tagging and isolating many agriculturally important genes using molecular markers due in large part to improvements in the techniques that have been developed to help find markers of interest. Among the techniques that are particularly promising are Restriction Fragment Length Polymorphism (RFLPs), Amplified Fragment Length Polymorphism (AFLPs), Random Amplified Polymorphic DNA (RAPDs), Microsatellites

  10. Fluorescein isothiocyanate: Molecular characterization by theoretical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Casanovas, Jordi [Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c/Jaume II No 69, Lleida E-25001 (Spain); Jacquemin, Denis [Laboratoire de Chimie Theorique Appliquee, Facultes Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur (Belgium)], E-mail: denis.jacquemin@fundp.ac.be; Perpete, Eric A. [Laboratoire de Chimie Theorique Appliquee, Facultes Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur (Belgium); Aleman, Carlos [Departament d' Enginyeria Quimica, E. T. S. d' Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E-08028 (Spain)], E-mail: carlos.aleman@upc.edu

    2008-12-10

    Quantum mechanical calculations have been used to investigate the conformation, molecular geometry, basicity and spectroscopic properties of fluorescein isothiocyanate in both the gas-phase and aqueous solution. Specifically, calculations have been performed considering the neutral, monoanionic and dianionic forms of this important fluorescent compound. Results reveal that for the neutral form multiple conformational states are possible, all them with significant contributions, and the stability of the different conformers is similar in the gas-phase and aqueous solution. Calculation of the excitation energies revealed that spectroscopic properties are very sensitive to the relaxation effect in solution. A good agreement has been reached obtained between the experimental and theoretical values derived from time-dependent density functional theory methods for the neutral form, whereas for charged species the calculations fail to accurately reproduce the measured trends.

  11. First molecular characterization of Cryptosporidium in Yemen.

    Science.gov (United States)

    Alyousefi, N A; Mahdy, M A K; Lim, Y A L; Xiao, L; Mahmud, R

    2013-05-01

    Cryptosporidium is a protozoan parasite of humans and animals and has a worldwide distribution. The parasite has a unique epidemiology in Middle Eastern countries where the IId subtype family of Cryptosporidium parvum dominates. However, there has been no information on Cryptosporidium species in Yemen. Thus, this study was conducted in Yemen to examine the distribution of Cryptosporidium species and subtype families. Fecal samples were collected from 335 patients who attended hospitals in Sana'a city. Cryptosporidium species were determined by PCR and sequence analysis of the 18 s rRNA gene. Cryptosporidium parvum and C. hominis subtypes were identified based on sequence analysis of the 60 kDa glycoprotein (gp60) gene. Out of 335 samples, 33 (9.9%) were positive for Cryptosporidium. Of them, 97% were identified as C. parvum whilst 1 case (3%) was caused by C. hominis. All 7 C. parvum isolates subtyped belonged to the IIaA15G2R1 subtype. The common occurrence of the zoonotic IIa subtype family of C. parvum highlights the potential occurrence of zoonotic transmission of cryptosporidiosis in Yemen. However, this postulation needs confirmation with future molecular epidemiological studies of cryptosporidiosis in both humans and animals in Yemen.

  12. Rapid molecular diagnostics for multi-drug resistant tuberculosis in India.

    Science.gov (United States)

    Ramachandran, Rajeswari; Muniyandi, M

    2018-03-01

    Rapid molecular diagnostic methods help in the detection of TB and Rifampicin resistance. These methods detect TB early, are accurate and play a crucial role in reducing the burden of drug resistant tuberculosis. Areas covered: This review analyses rapid molecular diagnostic tools used in the diagnosis of MDR-TB in India, such as the Line Probe Assay and GeneXpert. We have discussed the burden of MDR-TB and the impact of recent diagnostic tools on case detection and treatment outcomes. This review also discusses the costs involved in establishing these new techniques in India. Expert commentary: Molecular methods have considerable advantages for the programmatic management of drug resistant TB. These include speed, standardization of testing, potentially high throughput and reduced laboratory biosafety requirements. There is a desperate need for India to adopt modern, rapid, molecular tools with point-of-care tests being currently evaluated. New molecular diagnostic tests appear to be cost effective and also help in detecting missing cases. There is enough evidence to support the scaling up of these new tools in India.

  13. Molecular characterization of Cryptosporidium isolates from humans in Equatorial Guinea.

    Science.gov (United States)

    Blanco, María Alejandra; Iborra, Asunción; Vargas, Antonio; Nsie, Eugenia; Mbá, Luciano; Fuentes, Isabel

    2009-12-01

    The aim of the study was to perform a molecular characterization of clinical isolates of Cryptosporidium species from Equatorial Guinea. Standard laboratory methods were used to identify 35 cryptosporidiosis cases among 185 patients. PCR-RFLP successfully identified 34 Cryptosporidium species from these 35 cases, comprising C. parvum (52.9%), C. hominis (44.1%) and C. meleagridis (2.9%); over 90% of the species were isolated from HIV-positive patients. This is the first report of the molecular characterization of Cryptosporidium species isolated from humans in Equatorial Guinea and shows that zoonotic and anthroponotic transmission is present in this country.

  14. Human serum amyloid genes--molecular characterization

    International Nuclear Information System (INIS)

    Sack, G.H.; Lease, J.J.

    1986-01-01

    Three clones containing human genes for serum amyloid A protein (SAA) have been isolated and characterized. Each of two clones, GSAA 1 and 2 (of 12.8 and 15.9 kilobases, respectively), contains two exons, accouting for amino acids 12-58 and 58-103 of mature SAA; the extreme 5' termini and 5' untranslated regions have not yet been defined but are anticipated to be close based on studies of murine SAA genes. Initial amino acid sequence comparisons show 78/89 identical residues. At 4 of the 11 discrepant residues, the amino acid specified by the codon is the same as the corresponding residue in murine SAA. Identification of regions containing coding regions has permitted use of selected subclones for blot hybridization studies of larger human SAA chromosomal gene organization. The third clone, GSAA 3 also contains SAA coding information by DNA sequence analysis but has a different organization which has not yet been fully described. We have reported the isolation of clones of human DNA hybridizing with pRS48 - a plasmid containing a complementary DNA (cDNA) clone for murine serum amyloid A (SAA; 1, 2). We now present more detailed data confirming the identity and defining some of the organizational features of these clones

  15. Rapid detection, characterization, and enumeration of foodborne pathogens.

    Science.gov (United States)

    Hoorfar, J

    2011-11-01

    As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible

  16. Characterization of rapidly solidified powder of high-speed steel

    Czech Academy of Sciences Publication Activity Database

    Miglierini, M.; Lančok, Adriana; Kusý, M.

    2009-01-01

    Roč. 190, 1-3 (2009), s. 51-57 ISSN 0304-3843 R&D Projects: GA ČR GP203/07/P011 Grant - others:GA(SK) VEGA1/3190/06 Institutional research plan: CEZ:AV0Z40320502 Keywords : Rapidly solidified powder * Tool steel * Mössbauer spectroscopy Subject RIV: CA - Inorganic Chemistry Impact factor: 0.209, year: 2007

  17. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Science.gov (United States)

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  18. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Directory of Open Access Journals (Sweden)

    Satish K Guttikonda

    Full Text Available Demand for the commercial use of genetically modified (GM crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  19. Characterizing Air Quality in a Rapidly Changing World

    Science.gov (United States)

    The purpose of this paper is to 1) highlight projects collecting large volumes of unique air quality data; 2) explore how the collection of big data fits into the overall picture of air quality management and characterization; 3) provide an update on the E-Enterprise advanced mon...

  20. Proceedings of the workshop on characterization of molecular assemblies

    International Nuclear Information System (INIS)

    Imae, Toyoko; Furusaka, Michihiro

    1993-08-01

    Molecular condensation system shows the different physical characteristic properties from those of the component molecules, therefore, this workshop was to offer the place of discussion on the future of the research on molecular assembly state from wide visual field. The workshop was held on March 15 and 16, 1993 at the National Laboratory for High Energy Physics (KEK). Lectures were given on future plan of pulsed neutron sources and present state of Wink, characterization by small angle neutron scattering of molecular assemblies that dodecyl dimethylamine oxide constructs, microscopic and macroscopic structures of new surface active molecules, characterization of phospholipid molecular assembly state, crystalline molecular complex formed in surfactant and additives, small angle neutron scattering for phase separation and critical phenomena of micro-emulsion, structural research on hydrophilic composite lipid, associative behavior of bile acid salts in aqueous solution, phase separation and morphology of surfactant system, characterization of macroscopic structure in polymers by ultrasmall angle X-ray scattering and dynamic light scattering, and research on light scattering of glass-forming polymers. (K.I.)

  1. Practical Photoemission Characterization Of Molecular Films And Related Interfaces

    International Nuclear Information System (INIS)

    Ivanco, J.

    2013-01-01

    Even though the term ‘organic electronics’ evokes rather organic devices, a significant part of its scope deals with physical properties of ‘active elements’ such as organic films and interfaces. Examination of the film growth and the evolution of the interface formation are particularly needful for the understanding a mechanism controlling their final properties. Performing such experiments in an ultra-high vacuum allows both to ‘stretch’ the time scale for pseudo real-time observations and to control properties of the probed systems on the atomic level. Photoemission technique probes directly electronic and chemical structure and it has thereby established among major tools employed in the field.This review primarily focuses to electronic properties of oligomeric molecular films and their interfaces examined by photoemission. Yet, it does not aspire after a complete overview on the topic; it rather aims to otherwise standard issues encountered at the photoemission characterization and analysis of the organic materials, though requiring to consider particularities of molecular films in terms of the growth, electronic properties, and their characterization and analysis. In particular, the fundamental electronic parameters of molecular films such as the work function, the ionization energy, and the interfacial energy level alignment, and their interplay, will be pursued with considering often neglected influence of the molecular orientation. Further, the implication on the band bending in molecular films based on photoemission characterization, and a model on the driving mechanism for the interfacial energy level alignment will be addressed. (author)

  2. Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

    Science.gov (United States)

    Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

    2014-07-15

    Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Partial Molecular Characterization Of Cowpea Stunt Isolates Of ...

    African Journals Online (AJOL)

    Partial molecular characterization of the coat protein of the cowpea stunt-causing isolates of Cucumber Mosaic Virus (CMV) from Arkansas and Georgia revealed that both isolates of CMV belong to CMV subgroup I and differ at eight nucleotides positions, resulting in two amino acids difference. There was only one amino ...

  4. Molecular cloning and characterization of pathogenesis-related ...

    African Journals Online (AJOL)

    We described the cloning and characterization of pathogenesis-related protein 5 gene in maize, named ZmPR5 (GenBank Accession Number: HM230665). Molecular and bioinformatic analyses of ZmPR5 revealed an open reading frame (ORF) of 525 bp, encoding a protein of 175 amino acids (aa) and a deduced ...

  5. Molecular cloning and characterization of a novel human testis ...

    Indian Academy of Sciences (India)

    Molecular cloning and characterization of a novel human testis-specific gene by use of ... pared against 70 other libraries, and the hits showing >10- fold differences .... proteins or testis-development-related proteins such as TSP-. NY, TPX1 ...

  6. Molecular characterization and expression analysis of fat mass and ...

    Indian Academy of Sciences (India)

    Keywords. fat mass and obesity-associated gene (FTO); rabbit; mRNA expression patterns; sequence analysis; Oryctolagus cuniculus. ... In this work, the molecular characterization and expression features of rabbit (Oryctolagus cuniculus) FTO cDNA were analysed. The rabbit FTO cDNA with a size of 2158 bp was cloned, ...

  7. Molecular characterization of capsid protein gene of potato virus X ...

    African Journals Online (AJOL)

    Molecular characterization of capsid protein gene of potato virus X from Pakistan. Arshad Jamal, Idrees Ahmad Nasir, Bushra Tabassum, Muhammad Tariq, Abdul Munim Farooq, Zahida Qamar, Mohsin Ahmad Khan, Nadeem Ahmad, Muhammad Shafiq, Muhammad Saleem Haider, M. Arshad Javed, Tayyab Husnain ...

  8. Recent Advances in the Molecular Characterization of Circulating Tumor Cells

    Energy Technology Data Exchange (ETDEWEB)

    Lowes, Lori E. [London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 4L6 (Canada); Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1 (Canada); Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 4L6 (Canada); Allan, Alison L., E-mail: alison.allan@lhsc.on.ca [London Regional Cancer Program, London Health Sciences Centre, London, ON N6A 4L6 (Canada); Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1 (Canada); Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 4L6 (Canada); Lawson Health Research Institute, London, ON N6C 2R5 (Canada)

    2014-03-13

    Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch{sup ®} system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a “real-time liquid biopsy” that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing.

  9. Recent Advances in the Molecular Characterization of Circulating Tumor Cells

    International Nuclear Information System (INIS)

    Lowes, Lori E.; Allan, Alison L.

    2014-01-01

    Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch ® system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a “real-time liquid biopsy” that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing

  10. Rapid Detection and Characterization of Emerging Foreign Animal Disease Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-11-18

    To best safeguard human and animal health requires early detection and characterization of disease events. This must include effective surveillance for emerging infectious diseases. Both deliberate and natural outbreaks have enormous economic and public health impacts, and can present serious threats to national security. In this project, we developed novel next generation detection technologies to protect the agricultural economy and biosecurity. The first technology is a multiplexed assay to simultaneously detection 10 swine viral and bacterial pathogens. The second one is the Lawrence Livermore Microbial Detection Array (LLMDA) which can detect more than 10,000 microbial species including 4219 viruses, 5367 bacteria, 265 fungi, 117 protozoa and 293 archaea. We analyzed a series of swine clinical samples from past disease events to demonstrate the utility of the assays for faster and cheaper detection of emerging and foreign animal disease pathogens, and their utility as s routine diagnosis and surveillance tool. A second goal of the study is to better understand mechanisms of African swine fever virus (ASFV) infection in pigs to aid the development of countermeasures and diagnostics. There is no vaccine available for ASF. ASF outbreak is on the rise on several European countries. Though ASF is not currently in the U.S., a potential outbreak in the U.S. would be detrimental to the swine industry and the US agricultural economy. We pursued a genome-wide approach to characterize the pig immune responses after ASFV infection. We used RNA sequencing and bioinformatics methods to identify genes and pathways that are affected during ASF infection. We have identified a list of most differentially expressed genes that are in the immune response pathways.

  11. Quantum state specific reactant preparation in a molecular beam by rapid adiabatic passage

    Science.gov (United States)

    Chadwick, Helen; Hundt, P. Morten; van Reijzen, Maarten E.; Yoder, Bruce L.; Beck, Rainer D.

    2014-01-01

    Highly efficient preparation of molecules in a specific rovibrationally excited state for gas/surface reactivity measurements is achieved in a molecular beam using tunable infrared (IR) radiation from a single mode continuous wave optical parametric oscillator (cw-OPO). We demonstrate that with appropriate focusing of the IR radiation, molecules in the molecular beam crossing the fixed frequency IR field experience a Doppler tuning that can be adjusted to achieve complete population inversion of a two-level system by rapid adiabatic passage (RAP). A room temperature pyroelectric detector is used to monitor the excited fraction in the molecular beam and the population inversion is detected and quantified using IR bleaching by a second IR-OPO. The second OPO is also used for complete population transfer to an overtone or combination vibration via double resonance excitation using two spatially separated RAP processes.

  12. Characterization of Capsicum species using anatomical and molecular data.

    Science.gov (United States)

    Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

    2013-02-28

    Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

  13. Applying polarity rapid assessment method and ultrafiltration to characterize NDMA precursors in wastewater effluents.

    Science.gov (United States)

    Chen, Chao; Leavey, Shannon; Krasner, Stuart W; Mel Suffet, I H

    2014-06-15

    Certain nitrosamines in water are disinfection byproducts that are probable human carcinogens. Nitrosamines have diverse and complex precursors that include effluent organic matter, some anthropogenic chemicals, and natural (likely non-humic) substances. An easy and selective tool was first developed to characterize nitrosamine precursors in treated wastewaters, including different process effluents. This tool takes advantages of the polarity rapid assessment method (PRAM) and ultrafiltration (UF) (molecular weight distribution) to locate the fractions with the strongest contributions to the nitrosamine precursor pool in the effluent organic matter. Strong cation exchange (SCX) and C18 solid-phase extraction cartridges were used for their high selectivity for nitrosamine precursors. The details of PRAM operation, such as cartridge clean-up, capacity, pH influence, and quality control were included in this paper, as well as the main parameters of UF operation. Preliminary testing of the PRAM/UF method with effluents from one wastewater treatment plant gave very informative results. SCX retained 45-90% of the N-nitrosodimethylamine (NDMA) formation potential (FP)-a measure of the precursors-in secondary and tertiary wastewater effluents. These results are consistent with NDMA precursors likely having a positively charged amine group. C18 adsorbed 30-45% of the NDMAFP, which indicates that a substantial portion of these precursors were non-polar. The small molecular weight (MW) (10 kDa) fractions obtained from UF were the primary contributors to NDMAFP. The combination of PRAM and UF brings important information on the characteristics of nitrosamine precursors in water with easy operation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Characterization of nanoparticle-based contrast agents for molecular magnetic resonance imaging

    International Nuclear Information System (INIS)

    Shan, Liang; Chopra, Arvind; Leung, Kam; Eckelman, William C.; Menkens, Anne E.

    2012-01-01

    The development of molecular imaging agents is currently undergoing a dramatic expansion. As of October 2011, ∼4,800 newly developed agents have been synthesized and characterized in vitro and in animal models of human disease. Despite this rapid progress, the transfer of these agents to clinical practice is rather slow. To address this issue, the National Institutes of Health launched the Molecular Imaging and Contrast Agents Database (MICAD) in 2005 to provide freely accessible online information regarding molecular imaging probes and contrast agents for the imaging community. While compiling information regarding imaging agents published in peer-reviewed journals, the MICAD editors have observed that some important information regarding the characterization of a contrast agent is not consistently reported. This makes it difficult for investigators to evaluate and meta-analyze data generated from different studies of imaging agents, especially for the agents based on nanoparticles. This article is intended to serve as a guideline for new investigators for the characterization of preclinical studies performed with nanoparticle-based MRI contrast agents. The common characterization parameters are summarized into seven categories: contrast agent designation, physicochemical properties, magnetic properties, in vitro studies, animal studies, MRI studies, and toxicity. Although no single set of parameters is suitable to define the properties of the various types of contrast agents, it is essential to ensure that these agents meet certain quality control parameters at the preclinical stage, so that they can be used without delay for clinical studies.

  15. Rapid Molecular detection of citrus brown spot disease using ACT gene in Alternaria alternata

    Directory of Open Access Journals (Sweden)

    Hamid Moghimi

    2017-06-01

    Full Text Available Introduction:Using rapid detection methods is important for detection of plant pathogens and also prevention through spreading pests in agriculture. Citrus brown spot disease caused by pathogenic isolates of Alternaria alternata is a common disease in Iran. Materials and methods: In this study, for the first time a PCR based molecular method was used for rapid diagnosis of brown spot disease. Nine isolates of A. Alternata were isolated in PDA medium from different citrus gardens. The plant pathogenic activity was examined in tangerine leaves for isolates. Results showed that these isolates are the agents of brown spot disease. PCR amplification of specific ACT-toxin gene was performed for DNA extracted from A. alternata isolates, with 11 different fungal isolates as negative controls and 5 DNA samples extracted from soil. Results: Results showed that A. alternata, the causal agent of brown spot disease, can be carefully distinguished from other pathogenic agents by performing PCR amplification with specific primers for ACT toxin gene. Also, the results from Nested-PCR method confirmed the primary reaction and the specificity of A. alternata for brown spot disease. PCR results to control samples of the other standard fungal isolates, showed no amplification band. In addition, PCR with the DNA extracted from contaminated soils confirmed the presence of ACT toxin gene. Discussion and conclusion: Molecular procedure presented here can be used in rapid identification and prevention of brown spot infection in citrus gardens all over the country.

  16. Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

    Science.gov (United States)

    Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

    2018-05-15

    Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

  17. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

    Science.gov (United States)

    Linehan, W Marston; Spellman, Paul T; Ricketts, Christopher J; Creighton, Chad J; Fei, Suzanne S; Davis, Caleb; Wheeler, David A; Murray, Bradley A; Schmidt, Laura; Vocke, Cathy D; Peto, Myron; Al Mamun, Abu Amar M; Shinbrot, Eve; Sethi, Anurag; Brooks, Samira; Rathmell, W Kimryn; Brooks, Angela N; Hoadley, Katherine A; Robertson, A Gordon; Brooks, Denise; Bowlby, Reanne; Sadeghi, Sara; Shen, Hui; Weisenberger, Daniel J; Bootwalla, Moiz; Baylin, Stephen B; Laird, Peter W; Cherniack, Andrew D; Saksena, Gordon; Haake, Scott; Li, Jun; Liang, Han; Lu, Yiling; Mills, Gordon B; Akbani, Rehan; Leiserson, Mark D M; Raphael, Benjamin J; Anur, Pavana; Bottaro, Donald; Albiges, Laurence; Barnabas, Nandita; Choueiri, Toni K; Czerniak, Bogdan; Godwin, Andrew K; Hakimi, A Ari; Ho, Thai H; Hsieh, James; Ittmann, Michael; Kim, William Y; Krishnan, Bhavani; Merino, Maria J; Mills Shaw, Kenna R; Reuter, Victor E; Reznik, Ed; Shelley, Carl S; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Tickoo, Satish; Burnett, Kenneth; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph D; Penny, Robert J; Shelton, Candace; Shelton, W Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Avedon, Melissa T; Bowen, Jay; Gastier-Foster, Julie M; Gerken, Mark; Leraas, Kristen M; Lichtenberg, Tara M; Ramirez, Nilsa C; Santos, Tracie; Wise, Lisa; Zmuda, Erik; Demchok, John A; Felau, Ina; Hutter, Carolyn M; Sheth, Margi; Sofia, Heidi J; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C; Zhang, Jiashan; Ayala, Brenda; Baboud, Julien; Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Ally, Adrian; Balasundaram, Miruna; Balu, Saianand; Beroukhim, Rameen; Bodenheimer, Tom; Buhay, Christian; Butterfield, Yaron S N; Carlsen, Rebecca; Carter, Scott L; Chao, Hsu; Chuah, Eric; Clarke, Amanda; Covington, Kyle R; Dahdouli, Mahmoud; Dewal, Ninad; Dhalla, Noreen; Doddapaneni, Harsha V; Drummond, Jennifer A; Gabriel, Stacey B; Gibbs, Richard A; Guin, Ranabir; Hale, Walker; Hawes, Alicia; Hayes, D Neil; Holt, Robert A; Hoyle, Alan P; Jefferys, Stuart R; Jones, Steven J M; Jones, Corbin D; Kalra, Divya; Kovar, Christie; Lewis, Lora; Li, Jie; Ma, Yussanne; Marra, Marco A; Mayo, Michael; Meng, Shaowu; Meyerson, Matthew; Mieczkowski, Piotr A; Moore, Richard A; Morton, Donna; Mose, Lisle E; Mungall, Andrew J; Muzny, Donna; Parker, Joel S; Perou, Charles M; Roach, Jeffrey; Schein, Jacqueline E; Schumacher, Steven E; Shi, Yan; Simons, Janae V; Sipahimalani, Payal; Skelly, Tara; Soloway, Matthew G; Sougnez, Carrie; Tam, Angela; Tan, Donghui; Thiessen, Nina; Veluvolu, Umadevi; Wang, Min; Wilkerson, Matthew D; Wong, Tina; Wu, Junyuan; Xi, Liu; Zhou, Jane; Bedford, Jason; Chen, Fengju; Fu, Yao; Gerstein, Mark; Haussler, David; Kasaian, Katayoon; Lai, Phillip; Ling, Shiyun; Radenbaugh, Amie; Van Den Berg, David; Weinstein, John N; Zhu, Jingchun; Albert, Monique; Alexopoulou, Iakovina; Andersen, Jeremiah J; Auman, J Todd; Bartlett, John; Bastacky, Sheldon; Bergsten, Julie; Blute, Michael L; Boice, Lori; Bollag, Roni J; Boyd, Jeff; Castle, Erik; Chen, Ying-Bei; Cheville, John C; Curley, Erin; Davies, Benjamin; DeVolk, April; Dhir, Rajiv; Dike, Laura; Eckman, John; Engel, Jay; Harr, Jodi; Hrebinko, Ronald; Huang, Mei; Huelsenbeck-Dill, Lori; Iacocca, Mary; Jacobs, Bruce; Lobis, Michael; Maranchie, Jodi K; McMeekin, Scott; Myers, Jerome; Nelson, Joel; Parfitt, Jeremy; Parwani, Anil; Petrelli, Nicholas; Rabeno, Brenda; Roy, Somak; Salner, Andrew L; Slaton, Joel; Stanton, Melissa; Thompson, R Houston; Thorne, Leigh; Tucker, Kelinda; Weinberger, Paul M; Winemiller, Cynthia; Zach, Leigh Anne; Zuna, Rosemary

    2016-01-14

    Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

  18. Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma

    Science.gov (United States)

    Linehan, W. Marston; Spellman, Paul T.; Ricketts, Christopher J.; Creighton, Chad J.; Fei, Suzanne S.; Davis, Caleb; Wheeler, David A.; Murray, Bradley A.; Schmidt, Laura; Vocke, Cathy D.; Peto, Myron; Al Mamun, Abu Amar M.; Shinbrot, Eve; Sethi, Anurag; Brooks, Samira; Rathmell, W. Kimryn; Brooks, Angela N.; Hoadley, Katherine A.; Robertson, A. Gordon; Brooks, Denise; Bowlby, Reanne; Sadeghi, Sara; Shen, Hui; Weisenberger, Daniel J.; Bootwalla, Moiz; Baylin, Stephen B.; Laird, Peter W.; Cherniack, Andrew D.; Saksena, Gordon; Haake, Scott; Li, Jun; Liang, Han; Lu, Yiling; Mills, Gordon B.; Akbani, Rehan; Leiserson, Mark D.M.; Raphael, Benjamin J.; Anur, Pavana; Bottaro, Donald; Albiges, Laurence; Barnabas, Nandita; Choueiri, Toni K.; Czerniak, Bogdan; Godwin, Andrew K.; Hakimi, A. Ari; Ho, Thai; Hsieh, James; Ittmann, Michael; Kim, William Y.; Krishnan, Bhavani; Merino, Maria J.; Mills Shaw, Kenna R.; Reuter, Victor E.; Reznik, Ed; Shelley, Carl Simon; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Tickoo, Satish; Burnett, Kenneth; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph D.; Penny, Robert J.; Shelton, Candace; Shelton, W. Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Avedon, Melissa T.; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Santos, Tracie; Wise, Lisa; Zmuda, Erik; Demchok, John A.; Felau, Ina; Hutter, Carolyn M.; Sheth, Margi; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Ayala, Brenda; Baboud, Julien; Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Ally, Adrian; Balasundaram, Miruna; Balu, Saianand; Beroukhim, Rameen; Bodenheimer, Tom; Buhay, Christian; Butterfield, Yaron S.N.; Carlsen, Rebecca; Carter, Scott L.; Chao, Hsu; Chuah, Eric; Clarke, Amanda; Covington, Kyle R.; Dahdouli, Mahmoud; Dewal, Ninad; Dhalla, Noreen; Doddapaneni, HarshaVardhan; Drummond, Jennifer; Gabriel, Stacey B.; Gibbs, Richard A.; Guin, Ranabir; Hale, Walker; Hawes, Alicia; Hayes, D. Neil; Holt, Robert A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Steven J.M.; Jones, Corbin D.; Kalra, Divya; Kovar, Christie; Lewis, Lora; Li, Jie; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Meng, Shaowu; Meyerson, Matthew; Mieczkowski, Piotr A.; Moore, Richard A.; Morton, Donna; Mose, Lisle E.; Mungall, Andrew J.; Muzny, Donna; Parker, Joel S.; Perou, Charles M.; Roach, Jeffrey; Schein, Jacqueline E.; Schumacher, Steven E.; Shi, Yan; Simons, Janae V.; Sipahimalani, Payal; Skelly, Tara; Soloway, Matthew G.; Sougnez, Carrie; Tam, Angela; Tan, Donghui; Thiessen, Nina; Veluvolu, Umadevi; Wang, Min; Wilkerson, Matthew D.; Wong, Tina; Wu, Junyuan; Xi, Liu; Zhou, Jane; Bedford, Jason; Chen, Fengju; Fu, Yao; Gerstein, Mark; Haussler, David; Kasaian, Katayoon; Lai, Phillip; Ling, Shiyun; Radenbaugh, Amie; Van Den Berg, David; Weinstein, John N.; Zhu, Jingchun; Albert, Monique; Alexopoulou, Iakovina; Andersen, Jeremiah J; Auman, J. Todd; Bartlett, John; Bastacky, Sheldon; Bergsten, Julie; Blute, Michael L.; Boice, Lori; Bollag, Roni J.; Boyd, Jeff; Castle, Erik; Chen, Ying-Bei; Cheville, John C.; Curley, Erin; Davies, Benjamin; DeVolk, April; Dhir, Rajiv; Dike, Laura; Eckman, John; Engel, Jay; Harr, Jodi; Hrebinko, Ronald; Huang, Mei; Huelsenbeck-Dill, Lori; Iacocca, Mary; Jacobs, Bruce; Lobis, Michael; Maranchie, Jodi K.; McMeekin, Scott; Myers, Jerome; Nelson, Joel; Parfitt, Jeremy; Parwani, Anil; Petrelli, Nicholas; Rabeno, Brenda; Roy, Somak; Salner, Andrew L.; Slaton, Joel; Stanton, Melissa; Thompson, R. Houston; Thorne, Leigh; Tucker, Kelinda; Weinberger, Paul M.; Winemiller, Cythnia; Zach, Leigh Anne; Zuna, Rosemary

    2016-01-01

    Background Papillary renal cell carcinoma, accounting for 15% of renal cell carcinoma, is a heterogeneous disease consisting of different types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal cell carcinoma; no effective forms of therapy for advanced disease exist. Methods We performed comprehensive molecular characterization utilizing whole-exome sequencing, copy number, mRNA, microRNA, methylation and proteomic analyses of 161 primary papillary renal cell carcinomas. Results Type 1 and Type 2 papillary renal cell carcinomas were found to be different types of renal cancer characterized by specific genetic alterations, with Type 2 further classified into three individual subgroups based on molecular differences that influenced patient survival. MET alterations were associated with Type 1 tumors, whereas Type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-ARE pathway. A CpG island methylator phenotype (CIMP) was found in a distinct subset of Type 2 papillary renal cell carcinoma characterized by poor survival and mutation of the fumarate hydratase (FH) gene. Conclusions Type 1 and Type 2 papillary renal cell carcinomas are clinically and biologically distinct. Alterations in the MET pathway are associated with Type 1 and activation of the NRF2-ARE pathway with Type 2; CDKN2A loss and CIMP in Type 2 convey a poor prognosis. Furthermore, Type 2 papillary renal cell carcinoma consists of at least 3 subtypes based upon molecular and phenotypic features. PMID:26536169

  19. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics.

    Science.gov (United States)

    James, Ameh; Macdonald, Joanne

    2015-01-01

    Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.

  20. A two-locus molecular characterization of Paramecium calkinsi.

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Potekhin, Alexey; Rautian, Maria; Prajer, Małgorzata

    2012-03-01

    Paramecium calkinsi (Ciliophora, Protozoa) is a euryhaline species which was first identified in freshwater habitats, but subsequently several strains were also collected from brackish water. It is characterized by clockwise spiral swimming movement and the general morphology of the "bursaria type." The present paper is the first molecular characterization of P. calkinsi strains recently collected in distant regions in Russia using ITS1-5.8S- ITS2-5'LSU rDNA (1100bp) and COI (620bp) mtDNA sequenced gene fragments. For comparison, our molecular analysis includes P. bursaria, exhibiting a similar "bursaria morphotype" as well as species representing the "aurelia type," i.e., P. caudatum, P. multimicronucleatum, P. jenningsi, and P. schewiakoffi, and some species of the P. aurelia species complex (P. primaurelia, P. tetraurelia, P. sexaurelia, and P. tredecaurelia). We also use data from GenBank concerning other species in the genus Paramecium and Tetrahymena (which used as an outgroup). The division of the genus Paramecium into four subgenera (proposed by Fokin et al. 2004) is clearly presented by the trees. There is a clear separation between P. calkinsi strains collected from different regions (races). Consequently, given the molecular distances between them, it seems that these races may represent different syngens within the species. Copyright © 2011 Elsevier GmbH. All rights reserved.

  1. Rapid characterization of superconducting wires and tapes in strong pulsed magnetic fields

    International Nuclear Information System (INIS)

    Bockstal, L. van; Keyser, A. de; Deschagt, J.; Hopkins, S.C.; Glowacki, B.A.

    2007-01-01

    A new measurement system for rapid characterization of superconducting wires and tapes is developed. The CryoPulse-BI is a system to provide a direct measurement of critical material parameters for superconducting materials when high long pulsed magnetic fields and strong currents are applied. In the experiments, synchronized magnetic fields up to 30 T and current pulses up to 5 kA are generated with adjustable timing. Varying the magnetic field strength, the current through the sample and the BI timing allows for a thorough characterization of the sample and the determination of critical currents. The rapid cycle time of the experiments yields a rapid and thorough determination of the critical parameters. The method has been tested on low T c as well as high T c materials with the field parallel or perpendicular to the current. The discussion covers the current state of the art including a comparison of our results to classical DC characterization measurements

  2. [Molecular characterization of heterozygous beta-thalassemia in Lanzarote, Spain].

    Science.gov (United States)

    Calvo-Villas, José Manuel; de la Iglesia Iñigo, Silvia; Ropero Gradilla, Paloma; Zapata Ramos, María Francisca; Cuesta Tovar, Jorge; Sicilia Guillén, Francisco

    2008-04-05

    The aim of this study was to determine the molecular defects of heterozygous beta thalassaemia and to ascertain their distribution in Lanzarote. Molecular characterization was achieved by real time polymerase chain reaction (RT-PCR LightCycler, Roche), PCR-ARMS (PCR-amplification reaction mutations system) and DNA sequencing on an automated DNA sequencer. Two hundred forty-three heterozygous beta thalassaemia carriers were included between July 1991 and February 2007. RT-PCR detected the molecular defect in 81% of the beta thalassaemia chromosomes analyzed [113 codon CD 39 (C --> T); 41 IVS-1-nt-110 (G --> A), 25 IVS 1-nt-1 (G --> A) and 19 IVS 1-nt-6 (T --> C)]. The remaining 12 molecular defects included the deletion 619 bp (7.8%) and the mutations -28 (A --> G), IVS1-nt-2 (T --> G), CD 41/42 (-TTCT), CD 8/9 (+G), CD 51 (-C), CD 22 (G --> T) and CD 24 (T --> A), CD 67 (-TG) and the novel mutation CD 20/21-TGGA. The distribution of the mutations is similar to that found in the Mediterranean area. The increasing migratory flow received in the Canary Islands may explain the emergence of new mutations not reported before in our area.

  3. Biochemical and Molecular Characterization of Plant-Parasitic Nematodes

    Directory of Open Access Journals (Sweden)

    I.M. de O. Abrantes

    2004-08-01

    Full Text Available Nematologists need correct species identification to carry out research, teaching, extension and other activities. Therefore, nematode taxonomy must be pursued diligently at all levels. The identification of plant-parasitic nematodes is not always easy and that of some species is especially difficult. Most of the information that nematologists use when characterizing and identifying specimens is based on morphological and morphometrical characters. Although these characters are of primary importance, in the last three decades they have been supplemented by biochemical/ molecular characters. Biochemical approaches include the separation of proteins (general proteins and isozymes by one-dimensional gel electrophoresis, isoelectric focusing, two-dimensional gel electrophoresis, and sodium dodecyl sulphate-capillary gel electrophoresis. Serology has also been found effective in the identification and quantification of nematodes, monoclonal antibodies being a more useful immunological tool than polyclonal antibodies. Identification based on the direct examination of DNA is potentially a more powerful method to characterize inter- and intra-specific variability. The development of techniques such as the polymerase chain reaction, restriction fragment length polymorphism, randomly amplified polymorphic DNA, and amplified fragment length polymorphism has increased the accuracy and speed of nematode characterization/identification. Progress continues to be made and more and more nematologists are using molecular techniques for diagnostic purposes and to assess genetic variation.

  4. MoCha: Molecular Characterization of Unknown Pathways.

    Science.gov (United States)

    Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

    2016-04-01

    Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

  5. Molecular biophysics: detection and characterization of damage in molecular, cellular, and physiological systems

    International Nuclear Information System (INIS)

    Danyluk, S.S.

    1979-01-01

    This section contains summaries of research on the detection and characterization of damage in molecular, cellular, and physiological systems. Projects under investigation in this section include: chemical synthesis of nucleic acid derivatives; structural and conformational properties of biological molecules in solution; crystallographic and chemical studies of immunoglobulin structure; instrument design and development for x-ray and neutron scattering studies of biological molecules; and chromobiology and circadian regulation

  6. Molecular Recognition: Preparation and Characterization of Two Tripodal Anion Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Shokri, Alireza; Deng, Shihu; Wang, Xue B.; Kass, Steven R.

    2014-03-01

    Two new tripodal hydroxyl-based anion receptors (1 and 2) are reported and their molecular complexes with Cl–, H2PO4 –, and OAc– along with the (M–1)– ion of 1 were characterized by negative ion photoelectron spectroscopy in the gas phase and by binding constant determinations in four solvents (i.e., CDCl3, CD2Cl2, CD3COCD3, and CD3CN). An intramolecular hydrogen bond network (HBN) in hexaol 1 was found to diminish its binding whereas the triol 2 is the strongest aliphatic hydroxyl-based receptor to date.

  7. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

    Science.gov (United States)

    Burgess, Treena I.

    2015-01-01

    Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

  8. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

    Directory of Open Access Journals (Sweden)

    Zhonglou Sun

    Full Text Available The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes. Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma. Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma. Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

  9. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

    Science.gov (United States)

    Sun, Zhonglou; Pan, Tao; Hu, Chaochao; Sun, Lu; Ding, Hengwu; Wang, Hui; Zhang, Chenling; Jin, Hong; Chang, Qing; Kan, Xianzhao; Zhang, Baowei

    2017-01-01

    The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

  10. [Phenotypic and molecular characterization of a Colombian family with phenylketonuria].

    Science.gov (United States)

    Gélvez, Nancy; Acosta, Johana; López, Greizy; Castro, Derly; Prieto, Juan Carlos; Bermúdez, Martha; Tamayo, Marta L

    2016-09-01

    Phenylketonuria is a metabolic disorder characterized by severe neurological involvement and behavioral disorder, whose early diagnosis enables an effective treatment to avoid disease sequelae, thus changing the prognosis. Objective: To characterize a family with phenylketonuria in Colombia at clinical, biochemical and molecular levels. Materials and methods: The population consisted of seven individuals of a consanguineous family with four children with suggestive symptoms of phenylketonuria. After signing an informed consent, blood and urine samples were taken for colorimetric tests and high performance liquid and thin layer chromatographies. DNA extraction and sequencing of the 13 exons of the PAH gene were performed in all subjects. We designed primers for each exon with the Primer 3 software using automatic sequencing equipment Abiprism 3100 Avant. Sequences were analyzed using the SeqScape, v2.0, software. Results: We described the clinical and molecular characteristics of a Colombian family with phenylketonuria and confirmed the presence of the mutation c.398_401delATCA. We established a genotype-phenotype correlation, highlighting the interesting clinical variability found among the affected patients despite having the same mutation in all of them. Conclusions: Early recognition of this disease is very important to prevent its neurological and psychological sequelae, given that patients reach old age without diagnosis or proper management.

  11. Rapid, efficient and selective preconcentration of benzo[a]pyrene (BaP) by molecularly imprinted composite cartridge and HPLC

    Energy Technology Data Exchange (ETDEWEB)

    Çorman, Mehmet Emin, E-mail: mecorman@sinop.edu.tr [Hacettepe University, Department of Chemistry, Ankara (Turkey); Sinop University, Department of Bioengineering, Sinop (Turkey); Armutcu, Canan [Hacettepe University, Department of Chemistry, Ankara (Turkey); Uzun, Lokman, E-mail: lokman@hacettepe.edu.tr [Hacettepe University, Department of Chemistry, Ankara (Turkey); Denizli, Adil [Hacettepe University, Department of Chemistry, Ankara (Turkey)

    2017-01-01

    In this study, cryogel-based molecularly imprinted composite cartridges were designed for the rapid, efficient, and selective preconcentration of benzo[a]pyrene (BaP) from water samples. First, a BaP-imprinted poly(2-hydroxyethyl methacrylate-N-methacryloyl-(L)-phenylalanine) composite cartridge was synthesized under semi-frozen conditions and characterized by scanning electron microscopy, elemental analysis, Fourier transform infrared spectroscopy, and swelling tests. After the optimization of preconcentration parameters, i.e., pH and initial BaP concentration, the selectivity and preconcentration efficiency, and reusability of these cartridges were also evaluated. In selectivity experiments, BaP imprinted composite cartridge exhibited binding capacities 3.09, 9.52, 8.87, and 8.77-fold higher than that of the non-imprinted composite cartridge in the presence of competitors, such as benzo[b]fluoranthene (BbF), benzo[k]fluoranthene (BkF), indeno[1,2,3-cd]pyrene (IcdP), and 1-naphthol, respectively. The method detection limit (MDL), relative standard deviation (RSD) and preconcentration efficiency (PE) of the synthesized composite cartridge were calculated as 24.86 μg/L, 1.60%, and 349.6%, respectively. - Highlights: • Cryogel based molecularly imprinted composite cartridges as solid-phase extraction sorbents • Combination unique structural features of cryogels with MIP • An excellent ability to recognize the BaP molecule even if single-run contact • Rapid, efficient, selective and cost-friendly PAH preconcentration • Hydrophobic interactions via N-methacryloyl-(L)-phenylalanine.

  12. Surface and Electrical Characterization of Conjugated Molecular Wires

    Science.gov (United States)

    Demissie, Abel Tesfahun

    This thesis describes the surface and electrical characterization of ultrathin organic films and interfaces. These films were synthesized on the surface of gold by utilizing layer by layer synthesis via imine condensation. Film growth by imine click (condensation) chemistry is particularly useful for molecular electronics experiments because it provides a convenient means to obtain and extend ?-conjugation in the growth direction. However, in the context of film growth from a solid substrate, the reaction yield per step has not been characterized previously, though it is critically important. To address these issues, my research focused on a comprehensive characterization of oligophenyleneimine (OPI) wires via Rutherford backscattering spectrometry (RBS), X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), reflection-absorption infrared spectroscopy (RAIRS), and cyclic voltammetry (CV). In addition, we had the unique opportunity of developing the first of its kind implementation of nuclear reaction analysis (NRA) to probe the intensity of carbon atoms after each addition step. Overall the combination of various techniques indicated that film growth proceeds in a quantitative manner. Furthermore, the NRA experiment was optimized to measure the carbon content in self-assembled monolayers of alkyl thiols. The results indicated well-resolved coverage values for ultrathin films with consecutive steps of 2 carbon atoms per molecule. Another fundamental problem in molecular electronics is the vast discrepancy in the values of measured resistance per molecule between small and large area molecular junctions. In collaboration with researchers at the National University of Singapore, we addressed these issues by comparing the electrical properties of OPI wires with the eutectic gallium indium alloy (EGaIn) junction (1000 mum2), and conducting probe atomic force microscopy (CP-AFM) junction (50 nm2). Our results showed that intensive (i.e., area

  13. Rapid

    Directory of Open Access Journals (Sweden)

    Nahla M. Wassim

    2013-01-01

    Full Text Available Members of Aedes caspius mosquitoes are incriminated to be a potential reservoir of “Rift Valley Fever Virus” (RVF during interepizootic periods in Egypt. Ae. caspius contains two distinct forms which are morphologically indistinguishable but differ in physiology and behavior; Ae. caspius form (a requires a blood meal for each egg batch(anautogeny, is unable to mate in confined spaces(eurygamous. The second form (b lays egg batch without blood meal (autogenous and can mate in confined spaces (stenogamous. In this work, we collected the autogenous and anautogenous forms of Ae. caspius from two different breeding habitats in the Qalyubia Governorate. Analysis of the Drosophila ace-Orthologous acetylecholinesterase gene revealed that a single polymorphic region characterized each species. Based on this region, specific primers were used to amplify the entire section of intron II, sections of Exon 2 and Exon 3 of ace-2 gene for differentiating the complex species of mosquitoes. The amplicons of anautogenous form sized 441 pb and increase 116 bp than autogenous form of Ae. caspius. High rates of point mutations were addressed; deletion/insertion events are 120 bases. The transversion mutations were 44 bases and were relatively close to the transtion mutations 43 base. The genetic distance was 0.01 between the two forms.

  14. Molecular characterization of lactobacilli isolated from fermented idli batter

    Directory of Open Access Journals (Sweden)

    Perumal Jayaprabha Agaliya

    2013-12-01

    Full Text Available Lactic acid bacteria are non pathogenic organism widely distributed in nature typically involved in a large number of spontaneous food fermentation. The purpose of this study was to characterize the bacteriocinogenic lactobacilli from fermented idli batter which can find application in biopreservation and biomedicine. Eight most promising lactobacilli were chosen from twenty two isolates based on their spectrum of activity against other lactic acid bacteria and pathogens. The eight lactobacilli were characterized based on the various classical phenotypic tests, physiological tests and biochemical tests including various carbohydrate utilization profiles. All isolates were homo fermentative, catalase, and gelatin negative. Molecular characterization was performed by RAPD, 16S rRNA analysis, 16S ARDRA, and Multiplex PCR for species identification. RAPD was carried out using the primer R2 and M13. Five different clusters were obtained based on RAPD indicating strain level variation. 16S rRNA analysis showed 99 to 100% homology towards Lactobacillus plantarum. The restriction digestion pattern was similar for all the isolates with the restriction enzyme AluI. The subspecies were identified by performing Multiplex PCR using species specific primer. Among the five clusters, three clusters were clearly identified as Lactobacillus plantarum subsp. plantarum, Lactobacillus pentosus, and Lactobacillus plantarum subsp. argentoratensis.

  15. Structure–performance characterization for carbon molecular sieve membranes using molecular scale gas probes

    KAUST Repository

    Rungta, Meha

    2015-04-01

    © 2015 Elsevier Ltd. All rights reserved. Understanding the relationship between carbon molecular sieve (CMS) pore structure and corresponding gas separation performance enables optimization for a given gas separation application. The final pyrolysis temperature and starting polymer precursor are the two critical parameters in controlling CMS performance. This study considers structure and performance changes of CMS derived from a commercially available polymer precursor at different pyrolysis temperatures. As reviewed in this paper, most traditional characterization methods based on microscopy, X-ray diffraction, spectroscopy, sorption-based pore size distribution measurements etc. provide limited information for relating separation performance to the CMS morphology and structural changes. A useful alternative approach based on different sized gases as molecular scale probes of the CMS pore structure was successfully used here in conjunction with separation data to provide critical insights into the structure-performance relationships of the engineered CMS.

  16. Near instrument-free, simple molecular device for rapid detection of herpes simplex viruses.

    Science.gov (United States)

    Lemieux, Bertrand; Li, Ying; Kong, Huimin; Tang, Yi-Wei

    2012-06-01

    The first near instrument-free, inexpensive and simple molecular diagnostic device (IsoAmp HSV, BioHelix Corp., MA, USA) recently received US FDA clearance for use in the detection of herpes simplex viruses (HSV) in genital and oral lesion specimens. The IsoAmp HSV assay uses isothermal helicase-dependent amplification in combination with a disposable, hermetically-sealed, vertical-flow strip identification. The IsoAmp HSV assay has a total test-to-result time of less than 1.5 h by omitting the time-consuming nucleic acid extraction. The diagnostic sensitivity and specificity are comparable to PCR and are superior to culture-based methods. The near instrument-free, rapid and simple characteristics of the IsoAmp HSV assay make it potentially suitable for point-of-care testing.

  17. A rapid, one step molecular identification of Trichoderma citrinoviride and Trichoderma reesei.

    Science.gov (United States)

    Saroj, Dina B; Dengeti, Shrinivas N; Aher, Supriya; Gupta, Anil K

    2015-06-01

    Trichoderma species are widely used as production hosts for industrial enzymes. Identification of Trichoderma species requires a complex molecular biology based identification involving amplification and sequencing of multiple genes. Industrial laboratories are required to run identification tests repeatedly in cell banking procedures and also to prove absence of production host in the product. Such demands can be fulfilled by a brief method which enables confirmation of strain identity. This communication describes one step identification method for two common Trichoderma species; T. citrinoviride and T. reesei, based on identification of polymorphic region in the nucleotide sequence of translation elongation factor 1 alpha. A unique forward primer and common reverse primer resulted in 153 and 139 bp amplicon for T. citrinoviride and T. reesei, respectively. Simplification was further introduced by using mycelium as template for PCR amplification. Method described in this communication allows rapid, one step identification of two Trichoderma species.

  18. Expedited Site Characterization: A rapid, cost-effective process for preremedial site characterization

    International Nuclear Information System (INIS)

    Burton, J.C.; Walker, J.L.; Jennings, T.V.; Aggarwal, P.K.; Hastings, B.; Meyer, W.T.; Rose, C.M.; Rosignolo, C.L.

    1993-01-01

    Argonne National Laboratory has developed a unique, cost- and time-effective, technically innovative process for preremedial site characterization, referred to as Expedited Site Characterization (ESC). The cost of the ESC field sampling process ranges from 1/10 to 1/5 of the cost of traditional site characterization. The time required for this ESC field activity is approximately 1/30 of that for current methods. Argonne's preremedial site investigations based on this approach have been accepted by the appropriate regulatory agencies. The ESC process is flexible and neither site nor contaminant dependent. The process has been successfully tested and applied in site investigations of multiple contaminated landfills in New Mexico (for the US Department of the Interior's Bureau of Land Management [BLM]) and at former grain storage facilities in Nebraska and Kansas, contaminated with carbon tetrachloride (for the Department of Agriculture's Commodity Credit Corporation [CCC/USDA]). A working demonstration of this process was sponsored by the US Department of Energy (DOE) Office of Technology Development as a model of the methodology needed to accelerate site characterizations at DOE facilities. This report describes the application of the process in New Mexico, Nebraska and Kansas

  19. Ancient low-molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw.

    Science.gov (United States)

    Drake, Travis W; Wickland, Kimberly P; Spencer, Robert G M; McKnight, Diane M; Striegl, Robert G

    2015-11-10

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high-temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low-molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters.

  20. Ancient low–molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw

    Science.gov (United States)

    Drake, Travis W.; Wickland, Kimberly P.; Spencer, Robert G. M.; McKnight, Diane M.; Striegl, Robert G.

    2015-01-01

    Northern permafrost soils store a vast reservoir of carbon, nearly twice that of the present atmosphere. Current and projected climate warming threatens widespread thaw of these frozen, organic carbon (OC)-rich soils. Upon thaw, mobilized permafrost OC in dissolved and particulate forms can enter streams and rivers, which are important processors of OC and conduits for carbon dioxide (CO2) to the atmosphere. Here, we demonstrate that ancient dissolved organic carbon (DOC) leached from 35,800 y B.P. permafrost soils is rapidly mineralized to CO2. During 200-h experiments in a novel high–temporal-resolution bioreactor, DOC concentration decreased by an average of 53%, fueling a more than sevenfold increase in dissolved inorganic carbon (DIC) concentration. Eighty-seven percent of the DOC loss to microbial uptake was derived from the low–molecular-weight (LMW) organic acids acetate and butyrate. To our knowledge, our study is the first to directly quantify high CO2 production rates from permafrost-derived LMW DOC mineralization. The observed DOC loss rates are among the highest reported for permafrost carbon and demonstrate the potential importance of LMW DOC in driving the rapid metabolism of Pleistocene-age permafrost carbon upon thaw and the outgassing of CO2 to the atmosphere by soils and nearby inland waters.

  1. Molecular characterization of two accessions of Cydonia oblonga

    International Nuclear Information System (INIS)

    Alvarado-Marchena, Luis; Flores-Mora, Dora; Chacon-Cerdas, Randall; Schmidt-Duran, Alexander; Alvarado-Ulloa, Carlos

    2015-01-01

    The use of the trnH-psbA plastid spacer and the matK coding sequence were evaluated as possible markers for the molecular characterization of two accessions quince (C. oblonga) from Argentina and Costa Rica. The research was carried out by the Centro de Investigacion en Biotecnologia del Instituto Tecnologico de Costa Rica (ITCR), during the year 2014. The amplified products were analyzed with MEGA v6.0 software to calculate the genetic distances using the Tamura-Nei model . The matK sequence presented the highest percentage of variable sites and intraspecific distance, indicating the presence of polymorphisms between the accessions. The use of the trnH-psbA spacer for quince had little capacity for discrimination because at the intra-specific level this locus presented less divergence. (author) [es

  2. SYNTHESIS AND CHARACTERIZATION OF NEW STABILIZERS WITH OPTIMAL MOLECULAR WEIGHT

    Institute of Scientific and Technical Information of China (English)

    Jiang-qing Pan

    2001-01-01

    Over 2 × l08 tons of polymers are produced every year, and a large portion of polymers faces the degradation problem. There are many effective methods to protect polymers against degradation and the addition of stabilizers to polymer remains the most convenient and effective way of enhancing polymer life and performance. In this article, a series of effective stabilizers with optimal molecular weight (MW), including common, monomeric and polymeric stabilizers (antioxidant and light stabilizer) were synthesized using isocyanation, controlled isocyanation, hydrosilylation, epoxide addition, macroreaction of stabilizing functional compounds and polymerization of monomeric stabilizers. The sructure and performance of these new stabilizers were characterized by using IR, NMR, MS, UV-spectra, XPS and elemental analysis. The current development of stabilizer synthesis was also reviewed.``

  3. Molecular identification and characterization of prohibitin from Echinococcus granulosus.

    Science.gov (United States)

    Zhong, Xiuqin; Song, Xingju; Wang, Ning; Hu, Dandan; Liu, Tinayu; Wang, Tao; Gu, Xiaobin; Lai, Weimin; Peng, Xuerong; Yang, Guangyou

    2016-02-01

    Prohibitin (PHB) is a widely distributed protein that functions as a molecular chaperone, is involved in the regulation of cell cycle, and maintains mitochondrial structure and functions of the anti-apoptosis, senescence, and proliferation. The aim of this study was to characterize PHB in Echinococcus granulosus (EgPHB), a harmful cestode parasite of humans, many livestock species, and wild animals. We found that EgPHB is a conserved SPFH (stomatin, prohibitin, flotillin, and HflK/C) domain-containing protein, consisting of 289 amino acids, which shares 42.66-99.31% identity with PHBs from other parasites and mammals. EgPHB was located mainly in the tegument issue of protoscoleces, in the inner body of adult worms, and was expressed widely in the germinal layer. This is the first report on prohibitin from E. granulosus, and EgPHB is considered to be a valuable protein to study more in the future.

  4. Molecular characterization of two accessions of Cydonia oblonga.

    Directory of Open Access Journals (Sweden)

    Luis Alvarado-Marchena

    2015-06-01

    Full Text Available The purpose of this research was to evaluate the plastid trnH-psbA spacer and the matK coding sequence as possible markers for the molecular characterization in two accessions of quince (C. oblonga, one from Argentina and the other one from Costa Rica. The study was carried out at Center for Biotechnology Research (CIB in Spanish of the Technological Institute of Costa Rica (ITCR, in Spanish during 2014. Amplified products were analyzed using MEGA v6.0 software to calculate genetic distances using the Tamura-Nei model.The results showed that the matK sequence presented the highest percentage of variable sites and the highest intraspecific distance, suggesting the presence of polymorphisms between the two accessions. On the other hand, the trnH-psbA spacer for quince had a low ability to discriminate because, at intraspecific level, this locus showed less differences.

  5. [Molecular characterization of breast cancer in clinical practice].

    Science.gov (United States)

    Zemmouri, Y; De Croze, D; Vincent Salomon, A; Rouzier, R; Bonneau, C

    2016-05-01

    Breast cancer involves various types of tumors. The objective of this review was to provide a summary of the main methods currently available in clinical practice to characterize breast cancers at a molecular level and to discuss their prognostic and predictive values. Hormonal receptors expression and the HER2 status are prognostic markers and can also predict the response to targeted therapies. Their analysis through immunohistochemistry is systematical. Ki67 is an effective prognostic marker, but its reliability is debated because of its low reproducibility between laboratories and between pathologists. Commercial genomic signatures are all considered valid prognostic tools and may guide physicians to make therapeutic choices. These signatures are costly and should therefore be restricted to situations in which the use of chemotherapy remains equivocal. Copyright © 2016. Published by Elsevier SAS.

  6. Molecular characterization of Marek's disease herpesvirus B antigen

    International Nuclear Information System (INIS)

    Isfort, R.J.; Sithole, I.; Kung, H.J.; Velicer, L.F.

    1986-01-01

    The Marek's disease herpesvirus (MDHV) B antigen (MDHV-B) was identified and molecularly characterized as a set of three glycoproteins of 100,000, 60,000, and 49,000 apparent molecular weight (gp100, gp60, and gp49, respectively) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) after immunoprecipitation from [ 35 S]methionine-labeled infected cells by specific rabbit antiserum directed against MDHV-B (RαB), as previously determined by immunodiffusion. Further identification was accomplished by blocking this immunoprecipitation with highly purified MDHV-B. The same set of three polypeptides was also immunoprecipitated from [ 35 S] methionine- and 14 C-labeled infected cells into two other sera shown to have anti-B activity. These data serve to clarify the molecular identification of the polypeptides found in common between MDHV and HVT by linking them to MDHV-B. Collectively, the data presented here and by others support the conclusion that all three glycoproteins now identified as gp100, gp60, and gp49 have MDHV-B determinants. Finally, detection of the same three polypeptides with well-absorbed RαPM, which was directed against purified infected-cell plasma membranes, suggests that at least one component of the B-antigen complex has a plasma membrane location in the infected cell. These preliminary data point to the future membrane biochemistry and membrane immunology experiments needed to understand the MDHV system, and they may explain the high level of immunogenicity of MDHV-B in the infected chicken, as shown by its immunoprecipitation with immune chicken serum

  7. Molecular Characterization of Brown Carbon in Biomass Burning Aerosol Particles

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Peng; Aiona, Paige K.; Li, Ying; Shiraiwa, Manabu; Laskin, Julia; Nizkorodov, Sergey A.; Laskin, Alexander

    2016-11-01

    Emissions from biomass burning are a significant source of brown carbon (BrC) in the atmosphere. In this study, we investigate the molecular composition of freshly-emitted biomass burning organic aerosol (BBOA) samples collected during test burns of selected biomass fuels: sawgrass, peat, ponderosa pine, and black spruce. We characterize individual BrC chromophores present in these samples using high performance liquid chromatography coupled to a photodiode array detector and a high-resolution mass spectrometer. We demonstrate that both the overall BrC absorption and the chemical composition of light-absorbing compounds depend significantly on the type of biomass fuels and burning conditions. Common BrC chromophores in the selected BBOA samples include nitro-aromatics, polycyclic aromatic hydrocarbon derivatives, and polyphenols spanning a wide range of molecular weights, structures, and light absorption properties. A number of biofuel-specific BrC chromophores are observed, indicating that some of them may be used as potential markers of BrC originating from different biomass burning sources. On average, ~50% of the light absorption above 300 nm can be attributed to a limited number of strong BrC chromophores, which may serve as representative light-absorbing species for studying atmospheric processing of BrC aerosol. The absorption coefficients of BBOA are affected by solar photolysis. Specifically, under typical atmospheric conditions, the 300 nm absorbance decays with a half-life of 16 hours. A “molecular corridors” analysis of the BBOA volatility distribution suggests that many BrC compounds in the fresh BBOA have low volatility (<1 g m-1) and will be retained in the particle phase under atmospherically relevant conditions.

  8. Molecular characterization of Hepatozoon canis in dogs from Colombia.

    Science.gov (United States)

    Vargas-Hernandez, Giovanni; André, Marcos R; Munhoz, Thiago D; Faria, Joice M L; Machado, Rosangela Z; Tinucci-Costa, Mirela

    2012-01-01

    Hepatozoonosis is a tick-borne disease whose transmission to dogs occurs by ingestion of oocysts infected ticks or feeding on preys infested by infected ticks. Until now, there is no previous report of molecular characterization of Hepatozoon sp. in dogs from Colombia. EDTA blood samples were collected from 91 dogs from central-western region of Colombia (Bogotá, Bucaramanga, and Villavicencio cities) and submitted to 18S rRNA Hepatozoon sp. PCR and blood smears confection. Phylogenetic analysis was used to access the identity of Hepatozoon species found in sampled dogs. From 91 sampled dogs, 29 (31.8%) were positive to Hepatozoon sp. (25 dogs were only positive in PCR, 1 was positive only in blood smears, and 3 were positive in both blood smears and PCR). After sequencing, the found Hepatozoon sp. DNA showed 100% of identity with Hepatozoon canis DNA isolates. The phylogenetic tree supported the identity of the found Hepatozoon sp. DNA, showing that the isolates from Colombia were placed in the same clade than other H. canis isolates from Venezuela, Spain, and Taiwan. This is the first molecular detection of H. canis in dogs from Colombia.

  9. Molecular characterization of a novel intracellular ADP-ribosyl cyclase.

    Directory of Open Access Journals (Sweden)

    Dev Churamani

    2007-08-01

    Full Text Available ADP-ribosyl cyclases are remarkable enzymes capable of catalyzing multiple reactions including the synthesis of the novel and potent intracellular calcium mobilizing messengers, cyclic ADP-ribose and NAADP. Not all ADP-ribosyl cyclases however have been characterized at the molecular level. Moreover, those that have are located predominately at the outer cell surface and thus away from their cytosolic substrates.Here we report the molecular cloning of a novel expanded family of ADP-ribosyl cyclases from the sea urchin, an extensively used model organism for the study of inositol trisphosphate-independent calcium mobilization. We provide evidence that one of the isoforms (SpARC1 is a soluble protein that is targeted exclusively to the endoplasmic reticulum lumen when heterologously expressed. Catalytic activity of the recombinant protein was readily demonstrable in crude cell homogenates, even under conditions where luminal continuity was maintained.Our data reveal a new intracellular location for ADP-ribosyl cyclases and suggest that production of calcium mobilizing messengers may be compartmentalized.

  10. Molecular characterization and polymorphisms of butyrylcholinesterase in cynomolgus macaques.

    Science.gov (United States)

    Uno, Yasuhiro; Uehara, Shotaro; Mahadhi, Hassan M D; Ohura, Kayoko; Hosokawa, Masakiyo; Imai, Teruko

    2018-06-01

    Butyrylcholinesterase (BChE), an enzyme essential for drug metabolism, has been investigated as antidotes against organophosphorus nerve agents, and the efficacy and safety have been studied in cynomolgus macaques. BChE polymorphisms partly account for variable BChE activities among individuals in humans, but have not been investigated in cynomolgus macaques. Molecular characterization was carried out by analyzing primary sequence, gene, tissue expression, and genetic variants. In cynomolgus and human BChE, phylogenetically closely related, amino acid residues important for enzyme function were conserved, and gene and genomic structure were similar. Cynomolgus BChE mRNA was most abundantly expressed in liver among the 10 tissue types analyzed. Re-sequencing found 26 non-synonymous genetic variants in 121 cynomolgus and 23 rhesus macaques, indicating that macaque BChE is polymorphic, although none of these variants corresponded to the null or defective alleles of human BChE. These results suggest molecular similarities of cynomolgus and human BChE. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Molecular characterization of some lignicolous species from fungal culture collection

    Directory of Open Access Journals (Sweden)

    Stević Nevena

    2014-01-01

    Full Text Available Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17 obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25°C. BLAST (Basic Local Alignment Search Tool was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity. [Projekat Ministarstva nauke Republike Srbije, br. III43002 and by the Provincial Secretariat for Science and Technological Development, Vojvodina, Serbia APV 114-4513592/2013-03: Molecular and phenotypic diversity of taxa of economical and epidemiological importance, and endangered and endemic species in Europe

  12. Phytochemical evaluation and molecular characterization of some important medicinal plants

    Directory of Open Access Journals (Sweden)

    Varahalarao Vadlapudi

    2012-05-01

    Full Text Available Objective: Phytochemical evaluation and molecular characterization of plants is an important task in medicinal botany and drug discovery. In the current study, Ocimum species, Pimenta officinalis and Piper betel were considered as medicinal plants by evaluation of phytochemical composition like phenol content, Flavonoid content, antioxidant content and other activities like antibacterial, antifungal, lethal dosage (LD 50 of the plant extracts. Among the selected plants P. officinalis shown higher medicinal properties and is selected for molecular characterization. Methods: Antimicrobial activity by agar well diffusion method and also estimated Total phenols, flavonoids content, Total Antioxidants, Cytotoxic assay on Artemia salina for determining lethal dosage (LD50, matK gene was sequenced by using ABI Prism 3700. Leaf extract of P. officinalis plant is further selected for GC-chromatographic analysis to know its chemical composition. DNA was isolated by different protocols, optimized, and is used for the PCR amplification of trnL-gene which is a universal marker among plants in molecular taxonomy. The trnL-gene is amplified by using PCR. The product obtained from PCR is purified and the sample is used for sequencing so that it can be used for comparative studies. Results: P.offcinalis has shown good antimicrobial activity against all organisms . A. flavus is resistant against O. sanctum (B. Phenolic content (26.5 毺 g/g is found to be rich in P. betel where as flavonoid and Antioxidant content are significant in P. betel. The chromatogram revealed the presence of high concentration of Eugenol in the leaf sample. On submitting to BLASTN, the genetic sequence has found similarity with Pimenta dioica plastid partial matK gene and Ugni molinae trnK gene. MatK did not shown any interactions with trnK or trnL genes. MatK has shown interactions with various genes like ycf5, pclpp, psbh, atph, NDVI, rpoc1, ndha, ndhd, psai. Conclusions: we can

  13. Fiber-optic sensors for rapid, inexpensive characterization of soil and ground water contamination

    International Nuclear Information System (INIS)

    Milanovich, F.P.; Yow, J.L. Jr.

    1994-08-01

    The extent and complexity of worldwide environmental contamination are great enough that characterization, remediation, and performance monitoring will be extremely costly and lengthy. Characterization techniques that are rapid, inexpensive, and simple and that do not generate waste are urgently needed. Towards this end LLNL is developing a fiber-optic chemical sensor technology for use in groundwater and vadose-zone monitoring. We use a colorimetric detection technique, based on an irreversible chemical reaction between a specific reagent and the target compound. The accuracy and sensitivity of the sensor (<5 ppb by weight in water, determined by comparison with gas chromatographic standard measurements) are sufficient for environmental monitoring of trichloroethylene (TCE) and chloroform

  14. Using 3D Printing for Rapid Prototyping of Characterization Tools for Investigating Powder Blend Behavior

    DEFF Research Database (Denmark)

    Hirschberg, Cosima; Boetker, Johan P; Rantanen, Jukka

    2018-01-01

    of complex powder behavior, such as mixing process and segregation phenomenon. An approach based on the fast prototyping of new powder handling geometries and interfacing solutions for process analytical tools is reported. This study utilized 3D printing for rapid prototyping of customized geometries...... the percolation thresholds. Blends with a paracetamol wt% above the percolation threshold were subsequently investigated in relation to their segregation behavior. Rapid prototyping using 3D printing allowed designing two funnels with tailored flow behavior (funnel flow) of model formulations, which could...... blend were monitored during blending. Rapid prototyping allowed for fast modification of powder testing geometries and easy interfacing with process analytical tools, opening new possibilities for more detailed powder characterization....

  15. New strategy for rapid diagnosis and characterization of fungal infections: the example of corneal scrapings.

    Directory of Open Access Journals (Sweden)

    Pablo Goldschmidt

    Full Text Available PURPOSE: The prognosis of people infected with Fungi especially immunocompromised depends on rapid and accurate diagnosis to capitalize on time administration of specific treatments. However, cultures produce false negative results and nucleic-acid amplification techniques require complex post-amplification procedures to differentiate relevant fungal types. The objective of this work was to develop a new diagnostic strategy based on real-time polymerase-chain reaction high-resolution melting analysis (PCR-HRM that a detects yeasts and filamentous Fungi, b differentiates yeasts from filamentous Fungi, and c discriminates among relevant species of yeasts. METHODS: PCR-HRM detection limits and specificity were assessed with a isolated strains; b human blood samples experimentally infected with Fungi; c blood experimentally infected with other infectious agents; d corneal scrapings from patients with suspected fungal keratitis (culture positive and negative and e scrapings from patients with suspected bacterial, viral or Acanthamoeba infections. The DNAs were extracted and mixed with primers diluted in the MeltDoctor® HRM Master Mix in 2 tubes, the first for yeasts, containing the forward primer CandUn (5'CATGCCTGTTTGAGCGTC and the reverse primer FungUn (5'TCCTCCGCTT ATTGATATGCT and the second for filamentous Fungi, containing the forward primer FilamUn (5'TGCCTGTCCGAGCGTCAT and FungUn. Molecular probes were not necessary. The yields of DNA extraction and the PCR inhibitors were systematically monitored. RESULTS: PCR-HRM detected 0.1 Colony Forming Units (CFU/µl of yeasts and filamentous Fungi, differentiated filamentous Fungi from yeasts and discriminated among relevant species of yeasts. PCR-HRM performances were higher than haemoculture and sensitivity and specificity was 100% for culture positive samples, detecting and characterizing Fungi in 7 out 10 culture negative suspected fungal keratitis. CONCLUSIONS: PCR-HRM appears as a new, sensitive

  16. Comparison of Molecular and Phenotypic Methods for the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae.

    Science.gov (United States)

    Somily, Ali M; Garaween, Ghada A; Abukhalid, Norah; Absar, Muhammad M; Senok, Abiola C

    2016-03-01

    In recent years, there has been a rapid dissemination of carbapenem resistant Enterobacteriaceae (CRE). This study aimed to compare phenotypic and molecular methods for detection and characterization of CRE isolates at a large tertiary care hospital in Saudi Arabia. This study was carried out between January 2011 and November 2013 at the King Khalid University Hospital (KKUH) in Saudi Arabia. Determination of presence of extended-spectrum beta-lactamases (ESBL) and carbapenem resistance was in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Phenotypic classification was done by the MASTDISCS(TM) ID inhibitor combination disk method. Genotypic characterization of ESBL and carbapenemase genes was performed by the Check-MDR CT102. Diversilab rep-PCR was used for the determination of clonal relationship. Of the 883 ESBL-positive Enterobacteriaceae detected during the study period, 14 (1.6%) isolates were carbapenem resistant. Both the molecular genotypic characterization and phenotypic testing were in agreement in the detection of all 8 metalo-beta-lactamases (MBL) producing isolates. Of these 8 MBL-producers, 5 were positive for blaNDM gene and 3 were positive for blaVIM gene. Molecular method identified additional blaOXA gene isolates while MASTDISCS(TM) ID detected one AmpC producer isolate. Both methods agreed in identifying 2 carbapenem resistant isolates which were negative for carbapenemase genes. Diversilab rep-PCR analysis of the 9 Klebsiella pneumoniae isolates revealed polyclonal distribution into eight clusters. MASTDISCS(TM) ID is a reliable simple cheap phenotypic method for detection of majority of carbapenemase genes with the exception of the blaOXA gene. We recommend to use such method in the clinical laboratory.

  17. Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

    Science.gov (United States)

    Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

    2010-03-01

    Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

  18. Molecular characterization of radon-induced rat lung tumors

    International Nuclear Information System (INIS)

    Guillet Bastide, K.

    2008-11-01

    The radon gas is a well known lung carcinogenic factor in human at high doses but the cancer risk at low doses is not established. Indeed, epidemiological studies at low doses are difficult to conduct because of the human exposure to other lung carcinogenic factors. These data underlined the necessity to conduct experiments on lung tumors developed on animal model. The aim of this work was to characterize rat lung tumors by working on a series of radon-induced tumors that included adenocarcinomas (A.C.), squamous cell carcinomas (S.C.C.) and adeno-squamous carcinomas (A.S.C.), that are mixed tumors with both A.C. and S.C.C. cellular components. A C.G.H. analysis of the three types of tumors allowed us to define chromosomal recurrent unbalances and to target candidate genes potentially implicated in lung carcinogenesis, as p16Ink4a, p19Arf, Rb1, K-Ras or c-Myc. A more precise analysis of the p16Ink4a/Cdk4/Rb1 and p19Arf/Mdm2/Tp53 pathways was performed and indicated that the Rb1 pathway was frequently inactivated through an absence of p16 Ink4a protein expression, indicating that it has a major role in rat lung carcinogenesis. Finally, a comparative transcriptomic analysis of the three types of tumors allowed us to show for the first time that the complex tumors A.S.C. have a transcriptomic profile in accordance with their mixed nature but that they also display their own expression profiles specificities. This work allowed us to find molecular characteristics common to murine and human lung tumors, indicating that the model of lung tumors in rat is pertinent to search for radiation-induced lung tumors specificities and to help for a better molecular identification of this type of tumors in human. (author)

  19. Primary intraosseous smooth muscle tumor of uncertain malignant potential: original report and molecular characterization

    Directory of Open Access Journals (Sweden)

    Lauren Kropp

    2016-11-01

    Full Text Available We report the first case of primary intraosseous smooth muscle tumor of uncertain malignant potential (STUMP which is analogous to borderline malignant uterine smooth muscle tumors so designated. The tumor presented in the femur of an otherwise healthy 30-year-old woman. Over a 3-year period, the patient underwent 11 biopsies or resections and 2 cytologic procedures. Multiple pathologists reviewed the histologic material including musculoskeletal pathologists but could not reach a definitive diagnosis. However, metastases eventually developed and were rapidly progressive and responsive to gemcitabine and docetaxel. Molecular characterization and ultrastructural analysis was consistent with smooth muscle origin, and amplification of unmutated chromosome 12p and 12q segments appears to be the major genomic driver of this tumor. Primary intraosseous STUMP is thought to be genetically related to leiomyosarcoma of bone, but likely representing an earlier stage of carcinogenesis. Wide excision and aggressive followup is warranted for this potentially life-threatening neoplasm.

  20. Primary Intraosseous Smooth Muscle Tumor of Uncertain Malignant Potential: Original Report and Molecular Characterization.

    Science.gov (United States)

    Kropp, Lauren; Siegal, Gene P; Frampton, Garrett M; Rodriguez, Michael G; McKee, Svetlana; Conry, Robert M

    2016-11-17

    We report the first case of primary intraosseous smooth muscle tumor of uncertain malignant potential (STUMP) which is analogous to borderline malignant uterine smooth muscle tumors so designated. The tumor presented in the femur of an otherwise healthy 30-year-old woman. Over a 3-year period, the patient underwent 11 biopsies or resections and 2 cytologic procedures. Multiple pathologists reviewed the histologic material including musculoskeletal pathologists but could not reach a definitive diagnosis. However, metastases eventually developed and were rapidly progressive and responsive to gemcitabine and docetaxel. Molecular characterization and ultrastructural analysis was consistent with smooth muscle origin, and amplification of unmutated chromosome 12p and 12q segments appears to be the major genomic driver of this tumor. Primary intraosseous STUMP is thought to be genetically related to leiomyosarcoma of bone, but likely representing an earlier stage of carcinogenesis. Wide excision and aggressive follow-up is warranted for this potentially life-threatening neoplasm.

  1. Molecular characterization of misidentified Plasmodium ovale imported cases in Singapore.

    Science.gov (United States)

    Chavatte, Jean-Marc; Tan, Sarah Bee Hui; Snounou, Georges; Lin, Raymond Tzer Pin Valentine

    2015-11-14

    Plasmodium ovale, considered the rarest of the malaria parasites of humans, consists of two morphologically identical but genetically distinct sympatric species, Plasmodium ovale curtisi and Plasmodium ovale wallikeri. These parasites resemble morphologically to Plasmodium vivax with which they also share a tertian periodicity and the ability to cause relapses, making them easily misidentified as P. vivax. Plasmodium ovale infections are rarely reported, but given the likelihood of misidentification, their prevalence might be underestimated. Morphological and molecular analysis of confirmed malaria cases admitted in Singapore in 2012-2014 detected nine imported P. ovale cases that had been misidentified as P. vivax. Since P. ovale had not been previously officially reported in Singapore, a retrospective analysis of available, frozen, archival blood samples was performed and returned two additional misidentified P. ovale cases in 2003 and 2006. These eleven P. ovale samples were characterized with respect to seven molecular markers (ssrRNA, Potra, Porbp2, Pog3p, dhfr-ts, cytb, cox1) used in recent studies to distinguish between the two sympatric species, and to a further three genes (tufa, clpC and asl). The morphological features of P. ovale and the differential diagnosis with P. vivax were reviewed and illustrated by microphotographs. The genetic dimorphism between P. ovale curtisi and P. ovale wallikeri was assessed by ten molecular markers distributed across the three genomes of the parasite (Genbank KP050361-KP050470). The data obtained for seven of these markers were compared with those published and confirmed that both P. ovale species were present. This dimorphism was also confirmed for the first time on: (1) two genes from the apicoplast genome (tufA and clpC genes); and, (2) the asl gene that was used for phylogenetic analyses of other Plasmodium species, and that was found to harbour the highest number of dimorphic loci between the two P. ovale species

  2. Molecular characterization of eimeria species naturally infecting egyptian baldi chickens.

    Directory of Open Access Journals (Sweden)

    Sahar M Gadelhaq

    2015-03-01

    Full Text Available Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated.Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR marker.The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp, E. brunette (626bp, E. tenella (539bp, E. maxima (272bp, E. necatrix (200bp, E. mitis (327bp and E. praecopx (354bp. A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G in compared with the reference sequence.This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens.

  3. Molecular characterization of eimeria species naturally infecting egyptian baldi chickens.

    Science.gov (United States)

    Gadelhaq, Sahar M; Arafa, Waleed M; Aboelhadid, Shawky M

    2015-01-01

    Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated. Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR) marker. The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp), E. brunette (626bp), E. tenella (539bp), E. maxima (272bp), E. necatrix (200bp), E. mitis (327bp) and E. praecopx (354bp). A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G) when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G) in compared with the reference sequence. This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens.

  4. Molecular Characterization of Eimeria Species Naturally Infecting Egyptian Baldi Chickens

    Science.gov (United States)

    GADELHAQ, Sahar M; ARAFA, Waleed M; ABOELHADID, Shawky M

    2015-01-01

    Background: Coccidiosis is a serious protozoal disease of poultry. The identification of Eimeria species has important implications for diagnosis and control as well as for epidemiology. The molecular characterization of Eimeria species infecting Egyptian baladi chickens was investigated. Methods: Eimeria species oocysts were harvested from intestines of naturally infected Egyptian baldi chickens. The morphometry characterization of oocysts along with COCCIMORPH software was done. The DNA was extracted initially by freezing and thawing then the prepared samples was subjected to commercial DNA kits. The DNA products were analyzed through conventional polymerase chain reaction by using amplified region (SCAR) marker. Results: The PCR results confirmed the presence of 7 Eimeria species in the examined fecal samples of Egyptian baldi breed with their specific ampilicon sizes being E. acervulina (811bp), E. brunette (626bp), E. tenella (539bp), E. maxima (272bp), E. necatrix (200bp), E. mitis (327bp) and E. praecopx (354bp). A sequencing of the two most predominant species of Eimeria was done, on E. tenella and E. máxima. Analysis of the obtained sequences revealed high identities 99% between Egyptian isolates and the reference one. Similarly, E. maxima isolated from Egyptian baldi chickens showed 98% nucleotide identities with the reference strain. Only single nucleotide substitution was observed among the Egyptian E. tenella isolates (A181G) when compared to the reference one. The Egyptian isolates acquired 4 unique mutations (A68T, C164T, G190A and C227G) in compared with the reference sequence. Conclusion: This is the first time to identify the 7 species of Eimeria from Egyptian baladi chickens. PMID:25904950

  5. Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

    Science.gov (United States)

    Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

    2016-12-01

    NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

  6. Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing.

    Science.gov (United States)

    Yu, Hui; Zhang, Victor Wei; Stray-Pedersen, Asbjørg; Hanson, Imelda Celine; Forbes, Lisa R; de la Morena, M Teresa; Chinn, Ivan K; Gorman, Elizabeth; Mendelsohn, Nancy J; Pozos, Tamara; Wiszniewski, Wojciech; Nicholas, Sarah K; Yates, Anne B; Moore, Lindsey E; Berge, Knut Erik; Sorte, Hanne; Bayer, Diana K; ALZahrani, Daifulah; Geha, Raif S; Feng, Yanming; Wang, Guoli; Orange, Jordan S; Lupski, James R; Wang, Jing; Wong, Lee-Jun

    2016-10-01

    Primary immunodeficiency diseases (PIDDs) are inherited disorders of the immune system. The most severe form, severe combined immunodeficiency (SCID), presents with profound deficiencies of T cells, B cells, or both at birth. If not treated promptly, affected patients usually do not live beyond infancy because of infections. Genetic heterogeneity of SCID frequently delays the diagnosis; a specific diagnosis is crucial for life-saving treatment and optimal management. We developed a next-generation sequencing (NGS)-based multigene-targeted panel for SCID and other severe PIDDs requiring rapid therapeutic actions in a clinical laboratory setting. The target gene capture/NGS assay provides an average read depth of approximately 1000×. The deep coverage facilitates simultaneous detection of single nucleotide variants and exonic copy number variants in one comprehensive assessment. Exons with insufficient coverage (diagnostic yield of severe primary immunodeficiency. Establishing a molecular diagnosis enables early immune reconstitution through prompt therapeutic intervention and guides management for improved long-term quality of life. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  7. Rapid Evaporation of Water on Graphene/Graphene-Oxide: A Molecular Dynamics Study.

    Science.gov (United States)

    Li, Qibin; Xiao, Yitian; Shi, Xiaoyang; Song, Shufeng

    2017-09-07

    To reveal the mechanism of energy storage in the water/graphene system and water/grapheme-oxide system, the processes of rapid evaporation of water molecules on the sheets of graphene and graphene-oxide are investigated by molecular dynamics simulations. The results show that both the water/graphene and water/grapheme-oxide systems can store more energy than the pure water system during evaporation. The hydroxyl groups on the surface of graphene-oxide are able to reduce the attractive interactions between water molecules and the sheet of graphene-oxide. Also, the radial distribution function of the oxygen atom indicates that the hydroxyl groups affect the arrangement of water molecules at the water/graphene-oxide interface. Therefore, the capacity of thermal energy storage of the water/graphene-oxide system is lower than that of the water/graphene system, because of less desorption energy at the water/graphene-oxide interface. Also, the evaporation rate of water molecules on the graphene-oxide sheet is slower than that on the graphene sheet. The Leidenfrost phenomenon can be observed during the evaporation process in the water/grapheme-oxide system.

  8. Molecular characterization of Hepatozoon canis from farm dogs in Pakistan.

    Science.gov (United States)

    Ahmad, Abdullah S; Saeed, Muhammad A; Rashid, Imran; Ashraf, Kamran; Shehzad, Wasim; Traub, Rebecca J; Baneth, Gad; Jabbar, Abdul

    2018-04-01

    Hepatozoon canis is a tick-borne pathogen of canids, which is distributed worldwide. However, very little is known about this protozoan parasite in Pakistan. This study provides the first molecular evidence of H. canis from farm dogs from three agro-ecological zones of Punjab, Pakistan. A conventional PCR targeting the 18S rRNA gene was used to characterize H. canis from farm dogs from three districts, namely Kasur, Rawalpindi, and Muzaffargarh, in Punjab. Of 341 blood samples tested, 155 (45.5%) were positive for H. canis, 73 (61.3%) from Kasur, 46 (42.5%) from Rawalpindi, and 36 (31.5%) from Muzaffargarh. Phylogenetic analyses revealed that 18S rRNA sequences of H. canis from this study clustered in three clades with those of H. canis from previously published studies to the exclusion of all other Hepatozoon spp. included in the analysis. This study provides the first insight into H. canis from farm dogs in Pakistan. Furthermore, it lays a foundation for future studies of the parasite to assess the impact of canine hepatozoonosis in dogs from various agro-ecological zones in Pakistan where pet ownership of dogs is increasing.

  9. Molecular Characterization of Putative Virulence Determinants in Burkholderia pseudomallei

    Directory of Open Access Journals (Sweden)

    Suat Moi Puah

    2014-01-01

    Full Text Available The Gram-negative saprophyte Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease which is endemic in Southeast Asia and northern Australia. This bacterium possesses many virulence factors which are thought to contribute to its survival and pathogenicity. Using a virulent clinical isolate of B. pseudomallei and an attenuated strain of the same B. pseudomallei isolate, 6 genes BPSL2033, BP1026B_I2784, BP1026B_I2780, BURPS1106A_A0094, BURPS1106A_1131, and BURPS1710A_1419 were identified earlier by PCR-based subtractive hybridization. These genes were extensively characterized at the molecular level, together with an additional gene BPSL3147 that had been identified by other investigators. Through a reverse genetic approach, single-gene knockout mutants were successfully constructed by using site-specific insertion mutagenesis and were confirmed by PCR. BPSL2033::Km and BURPS1710A_1419::Km mutants showed reduced rates of survival inside macrophage RAW 264.7 cells and also low levels of virulence in the nematode infection model. BPSL2033::Km demonstrated weak statistical significance (P=0.049 at 8 hours after infection in macrophage infection study but this was not seen in BURPS1710A_1419::Km. Nevertheless, complemented strains of both genes were able to partially restore the gene defects in both in vitro and in vivo studies, thus suggesting that they individually play a minor role in the virulence of B. pseudomallei.

  10. Characterization of Gladiolus Germplasm Using Morphological, Physiological, and Molecular Markers.

    Science.gov (United States)

    Singh, Niraj; Pal, Ashish K; Roy, R K; Tewari, S K; Tamta, Sushma; Rana, T S

    2018-04-01

    Estimation of variability and genetic relationships among breeding materials is one of the important strategies in crop improvement programs. Morphological (plant height, spike length, a number of florets/spike), physiological (chlorophyll content, chlorophyll fluorescence, and rapid light curve parameters) and Directed amplification of minisatellite DNA (DAMD) markers were used to investigate the relationships among 50 Gladiolus cultivars. Cluster analysis based on morphological data, physiological characteristics, molecular markers, and cumulative data discriminated all cultivars into seven, five, seven, and six clusters in the unweighted pair-group method using arithmetic mean (UPGMA) dendrogram, respectively. The results of the principal coordinate analysis (PCoA) also supported UPGMA clustering. Variations among the Gladiolus cultivars at phenotypic level could be due to the changes in physiology, environmental conditions, and genetic variability. DAMD analysis using 10 primers produced 120 polymorphic bands with 80% polymorphism showing polymorphic information content (PIC = 0.28), Marker index (MI = 3.37), Nei's gene diversity (h = 0.267), and Shannon's information index (I = 0.407). Plant height showed a positive significant correlation with Spike length and Number of florets/spike (r = 0.729, p < 0.001 and r = 0.448, p = 0.001 respectively). Whereas, Spike length showed positive significant correlation with Number of florets/spike (r = 0.688, p < 0.001) and Chlorophyll content showed positive significant correlation with Electron transport rate (r = 0.863, p < 0.001). Based on significant morphological variations, high physiological performance, high genetic variability, and genetic distances between cultivars, we have been able to identify diverse cultivars of Gladiolus that could be the potential source as breeding material for further genetic improvement in this ornamental crop.

  11. Molecular characterization of γ gliadin from durum wheat ( Triticum ...

    African Journals Online (AJOL)

    gliadin protein associated with gluten strength and viscoelasticity of the dough, we performed an in silico molecular and structural analysis in order to define its putative functional properties. The latter could be a valuable candidate as molecular ...

  12. Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS

    Science.gov (United States)

    Zheng, Wei; Wang, Fangxu; Zhao, Yang; Sun, Xinguang; Kang, Liping; Fan, Ziquan; Qiao, Lirui; Yan, Renyi; Liu, Shuchen; Ma, Baiping

    2017-08-01

    A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MSE data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MSE with informatics platform. [Figure not available: see fulltext.

  13. Molecular and immunological characterization of mycobacteria associated with bovine farcy

    International Nuclear Information System (INIS)

    Kwajok, Victor Loku

    2000-01-01

    The aim of the study was to: i.isolate and identify Mycobacterium farcinogenese from the clinical samples (lymph nodes and serum), ii.charcterization of these species including mycobacterium senegalense and the related taxa using molecular biology methods (DNA extraction, PCR amplification, restriction fragment length plymorphism determination using restriction enzymes and DNA sequencing) and iii.immunological analysis of the species (animal pathogenicity tests, ELISA using sera samples from the clinical cases, protein antigen bands determination using SDS-PAGE method, and antigen-antibodies immunoassay using Western blotting and immunodiffusion tests). Seventeen clinical isolates identified as Mycobacterium farcinogenese were obtained from 578 lymph nodes and 36 positive sera samples of the 269 which were tested. Molecular characterization of the test strains was carried out using independent taxonomic criteria derived from the application of morphological, enzymatic and chemotaxonomic methods. DNA extraction method gave clearly resolved bands on agarose gel electrophoresis with clear common bands of 1500 base pairs. The extracted DNA was used as template for pcr amplification with universal primer 27f (5'AGAGTTTGATCCGGCTAG-3') and primer 1525r' (5'AAGGAGGTATCGAGCC-3') with appended restriction sites being ideal primers for amplification. No significant difference in the DNA fingerprints of the farcy agents were reproducible over successive generations and were in line with their placement in the genus Mycobacterium. PCR-DNA fingerprinting using BamHI restriction enzymes for restriction fragment length polymorphism analysis as a means for differentiating between Mycobacterium farcinogenes and Mycobacterium senegalense. The 16SrDNA sequencing of Mycobacterium farcinogenes and Mycobacterium senegalense the farcy sole agents, gave data of variable signals with 1482 nucleotides with 65 corresponding almost complete nucleotide sequences in 1404 positions. Manual

  14. Molecular and immunological characterization of mycobacteria associated with bovine farcy

    Energy Technology Data Exchange (ETDEWEB)

    Kwajok, Victor Loku [Faculty of Veterinary Sciences, University of Khartoum, Khartoum (Sudan)

    2000-07-01

    The aim of the study was to: i.isolate and identify Mycobacterium farcinogenese from the clinical samples (lymph nodes and serum), ii.charcterization of these species including mycobacterium senegalense and the related taxa using molecular biology methods (DNA extraction, PCR amplification, restriction fragment length plymorphism determination using restriction enzymes and DNA sequencing) and iii.immunological analysis of the species (animal pathogenicity tests, ELISA using sera samples from the clinical cases, protein antigen bands determination using SDS-PAGE method, and antigen-antibodies immunoassay using Western blotting and immunodiffusion tests). Seventeen clinical isolates identified as Mycobacterium farcinogenese were obtained from 578 lymph nodes and 36 positive sera samples of the 269 which were tested. Molecular characterization of the test strains was carried out using independent taxonomic criteria derived from the application of morphological, enzymatic and chemotaxonomic methods. DNA extraction method gave clearly resolved bands on agarose gel electrophoresis with clear common bands of 1500 base pairs. The extracted DNA was used as template for pcr amplification with universal primer 27f (5'AGAGTTTGATCCGGCTAG-3') and primer 1525r' (5'AAGGAGGTATCGAGCC-3') with appended restriction sites being ideal primers for amplification. No significant difference in the DNA fingerprints of the farcy agents were reproducible over successive generations and were in line with their placement in the genus Mycobacterium. PCR-DNA fingerprinting using BamHI restriction enzymes for restriction fragment length polymorphism analysis as a means for differentiating between Mycobacterium farcinogenes and Mycobacterium senegalense. The 16SrDNA sequencing of Mycobacterium farcinogenes and Mycobacterium senegalense the farcy sole agents, gave data of variable signals with 1482 nucleotides with 65 corresponding almost complete nucleotide sequences in 1404 positions. Manual

  15. A simple and rapid characterization of influenza virus isolates by monoclonal antibodies in radioimmunoassay

    International Nuclear Information System (INIS)

    Kostolansky, F.; Styk, B.; Russ, G.

    1986-01-01

    Radioimmunoassay is described with infectious allantoic fluid directly bound to solid phase, suitable for the detection and further characterization of influenza virus isolates. This simple and rapid method was applied for the description of isolates obtained from different regions of Czechoslovakia during the influenza epidemic in 1983. The results confirmed that all 13 examined isolates represented influenza A viruses possessing H3 subtype haemagglutinin very similar to haemagglutinin of influenza viruses A/Bangkok/1/79 (H3N2), A/Belgium/2/81 (H3N2) and A/Philippines/2/82 (H3N2). (author)

  16. Performance Characterization and Auto-Ignition Performance of a Rapid Compression Machine

    OpenAIRE

    Hao Liu; Hongguang Zhang; Zhicheng Shi; Haitao Lu; Guangyao Zhao; Baofeng Yao

    2014-01-01

    A rapid compression machine (RCM) test bench is developed in this study. The performance characterization and auto-ignition performance tests are conducted at an initial temperature of 293 K, a compression ratio of 9.5 to 16.5, a compressed temperature of 650 K to 850 K, a driving gas pressure range of 0.25 MPa to 0.7 MPa, an initial pressure of 0.04 MPa to 0.09 MPa, and a nitrogen dilution ratio of 35% to 65%. A new type of hydraulic piston is used to address the problem in which the hydraul...

  17. Rapid degradation of Congo red by molecularly imprinted polypyrrole-coated magnetic TiO2 nanoparticles in dark at ambient conditions

    International Nuclear Information System (INIS)

    Wei, Shoutai; Hu, Xiaolei; Liu, Hualong; Wang, Qiang; He, Chiyang

    2015-01-01

    Highlights: • Molecularly imprinted polypyrrole-coated magnetic TiO 2 catalyst was prepared. • The catalyst degraded Congo red rapidly in dark at ambient conditions. • Degradation mechanism was proposed according to LC–MS analysis. • The catalyst can be easily recycled by a magnet. - Abstract: A novel molecularly imprinted polymer (MIP)-coated magnetic TiO 2 nanocomposite was prepared, using methyl orange (MO) as the dummy template and pyrrole as functional monomer, for degradation of Congo red (CR). The nanocomposite was characterized by Fourier transform infrared spectroscopy, thermo-gravimetric analysis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer. The imprinting efficiency of the imprinted nanoparticles was investigated by static binding test, and their degradation ability toward CR was also studied. Moreover, the effects of pH, temperature, dissolved oxygen and oscillation rate on degradation rate of CR were investigated. Results showed that the imprinted nanocomposite had higher adsorption ability for MO compared with the non-imprinted one. Moreover, it could degrade CR rapidly in dark at room temperature and atmospheric pressure and could be recycled easily by a magnet with a good reusability. A degradation mechanism was proposed according to LC–MS analysis of degradation products of CR. The new imprinted nanoparticles showed high catalytic activity at ambient conditions without light illumination and additional chemicals, and therefore, it can be potentially applied to the rapid, “green” and low-cost degradation of CR in industrial printing and dyeing wastewater

  18. Rapid degradation of Congo red by molecularly imprinted polypyrrole-coated magnetic TiO{sub 2} nanoparticles in dark at ambient conditions

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Shoutai; Hu, Xiaolei; Liu, Hualong; Wang, Qiang; He, Chiyang, E-mail: chiyanghe@hotmail.com

    2015-08-30

    Highlights: • Molecularly imprinted polypyrrole-coated magnetic TiO{sub 2} catalyst was prepared. • The catalyst degraded Congo red rapidly in dark at ambient conditions. • Degradation mechanism was proposed according to LC–MS analysis. • The catalyst can be easily recycled by a magnet. - Abstract: A novel molecularly imprinted polymer (MIP)-coated magnetic TiO{sub 2} nanocomposite was prepared, using methyl orange (MO) as the dummy template and pyrrole as functional monomer, for degradation of Congo red (CR). The nanocomposite was characterized by Fourier transform infrared spectroscopy, thermo-gravimetric analysis, X-ray diffraction, transmission electron microscopy, and vibrating sample magnetometer. The imprinting efficiency of the imprinted nanoparticles was investigated by static binding test, and their degradation ability toward CR was also studied. Moreover, the effects of pH, temperature, dissolved oxygen and oscillation rate on degradation rate of CR were investigated. Results showed that the imprinted nanocomposite had higher adsorption ability for MO compared with the non-imprinted one. Moreover, it could degrade CR rapidly in dark at room temperature and atmospheric pressure and could be recycled easily by a magnet with a good reusability. A degradation mechanism was proposed according to LC–MS analysis of degradation products of CR. The new imprinted nanoparticles showed high catalytic activity at ambient conditions without light illumination and additional chemicals, and therefore, it can be potentially applied to the rapid, “green” and low-cost degradation of CR in industrial printing and dyeing wastewater.

  19. Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil.

    OpenAIRE

    FAJARDO, T. V. M.; NASCIMENTO, M. B.; EIRAS, M.; NICKEL, O.; PIO-RIBEIRO, G.

    2016-01-01

    ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of...

  20. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

    Science.gov (United States)

    Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

    2012-04-01

    Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Multidrug-resistant tuberculosis: Rapid molecular detection with MTBDRplus® assay in clinical samples

    Directory of Open Access Journals (Sweden)

    Rita Macedo

    2009-05-01

    Full Text Available Nowadays, the greatest concern of tuberculosis control programmes is the appearance of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis. Rapid determination of drug resistance in clinical samples, with Mycobacterium tuberculosis complex (MTC, is the prerequisite for initiating effective chemotherapy, ensuring successful treatment of the patient and preventing further spread of drugresistant isolates.The aim of our study was to determine the sensitivity of the new MTBDRplus® assay in comparison to culture, identification and classic DST, directly from smear-positive clinical specimens.A total of 68 smear-positive sputum specimens were processed by both the classical mycobacteriological methods and the molecular assay, MTBDRplus®.MTBDRplus® assay allowed an accurate identification of MTC species by detection of the specific band in all samples, from which we also isolated and identified MTC strains by culture methods. In the samples from which we isolated susceptible strains (63.2%, wild type patterns were found using MTBDRplus® assay. The samples from which we isolated resistant strains (36.8% showed specific mutations associated with the correspondent resistant phenotype.Our study indicated that this assay allows rapid detection of resistance, always in agreement with classic methods. Resumo: Uma das principais problematicas no controlo da tuberculose e o aparecimento de casos de tuberculose multirresistente (TB-MR e tuberculose extensivamente resistente (TB-XDR. A deteccao precoce da resistencia a farmacos, directamente a partir de amostras respiratorias, e essencial para que se assegure o tratamento atempado, adequado e eficaz da tuberculose, bem como para prevenir a disseminacao destes casos de especial gravidade.O nosso objectivo foi avaliar a sensibilidade e comparar os resultados obtidos com um metodo de genetica molecular disponivel comercialmente – MTBDRplus® – e o isolamento

  2. Rapid molecular evolution across amniotes of the IIS/TOR network.

    Science.gov (United States)

    McGaugh, Suzanne E; Bronikowski, Anne M; Kuo, Chih-Horng; Reding, Dawn M; Addis, Elizabeth A; Flagel, Lex E; Janzen, Fredric J; Schwartz, Tonia S

    2015-06-02

    The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

  3. Molecular characterization of the 17D-204 yellow fever vaccine.

    Science.gov (United States)

    Salmona, Maud; Gazaignes, Sandrine; Mercier-Delarue, Severine; Garnier, Fabienne; Korimbocus, Jehanara; Colin de Verdière, Nathalie; LeGoff, Jerome; Roques, Pierre; Simon, François

    2015-10-05

    The worldwide use of yellow fever (YF) live attenuated vaccines came recently under close scrutiny as rare but serious adverse events have been reported. The population identified at major risk for these safety issues were extreme ages and immunocompromised subjects. Study NCT01426243 conducted by the French National Agency for AIDS research is an ongoing interventional study to evaluate the safety of the vaccine and the specific immune responses in HIV-infected patients following 17D-204 vaccination. As a preliminary study, we characterized the molecular diversity from E gene of the single 17D-204 vaccine batch used in this clinical study. Eight vials of lyophilized 17D-204 vaccine (Stamaril, Sanofi-Pasteur, Lyon, France) of the E5499 batch were reconstituted for viral quantification, cloning and sequencing of C/prM/E region. The average rate of virions per vial was 8.68 ± 0.07 log₁₀ genome equivalents with a low coefficient of variation (0.81%). 246 sequences of the C/prM/E region (29-33 per vials) were generated and analyzed for the eight vials, 25 (10%) being defective and excluded from analyses. 95% of sequences had at least one nucleotide mutation. The mutations were observed on 662 variant sites distributed through all over the 1995 nucleotides sequence and were mainly non-synonymous (66%). Genome variability between vaccine vials was highly homogeneous with a nucleotide distance ranging from 0.29% to 0.41%. Average p-distances observed for each vial were also homogeneous, ranging from 0.15% to 0.31%. This study showed a homogenous YF virus RNA quantity in vaccine vials within a single lot and a low clonal diversity inter and intra vaccine vials. These results are consistent with a recent study showing that the main mechanism of attenuation resulted in the loss of diversity in the YF virus quasi-species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Molecular and Genomic Characterization of Enteric Pathogens Circulating during Hajj

    KAUST Repository

    Alsomali, Mona

    2016-05-01

    Hajj, the annual Muslim pilgrimage to Mecca, Saudi Arabia is a unique mass gathering event that attracts approximately 3 million pilgrims from around the globe. This diverse pilgrim population coupled with the nature of the performed activities raise major public health concerns in the host country with potential global implications. Although gastroenteritis and diarrhea are common among the pilgrims performing Hajj, the microbial etiologies of these infections are still unknown. We used molecular and antigenic approaches to identify the main pathogens associated with Hajj diarrhea. 544 fecal samples from pilgrims suffering from diarrhea whilst performing Hajj during three consecutive seasons (2011-2013) and 99 control samples from 2011 were screened for 16 pathogens that include bacterial, parasitic and viral etiologies that are commonly associated with diarrheal infections. At least one of the screened pathogens could be detected in 42% (n=228) of the samples from the diarrheal cases. Bacteria were the main agents detected in 83% (n=189) of the positive samples, followed by viral and parasitic agents detected in 6% (n=14) and 5% (n=12) respectively. We have also standardized a 16S-based metagenomic approach to identify the gut microbiome in diarrheal cases and non-diarrheal controls in 76 samples. Also, we have standardized a shotgun metagenomics protocol for the direct characterization (diagnosis) of enteric pathogens without cultivation. This approach was used successfully to identify viral (adenovirus) and bacterial causes of Enterotoxigenic E. coli diarrhea from Hajj samples. The findings in this study fill in clear gaps in our knowledge of the etiologies associated with diarrheal infections during Hajj. Foodborne bacteria were the major contributors to Hajj-diarrheal infections. This was coupled with the increased incidences of antimicrobial resistance loci associated with the identified bacteria. These findings would help the public health policy makers to

  5. Preliminary molecular characterization of the human pathogen Angiostrongylus cantonensis

    Directory of Open Access Journals (Sweden)

    He Ai

    2009-10-01

    Full Text Available Abstract Background Human angiostrongyliasis is an emerging food-borne public health problem, with the number of cases increasing worldwide, especially in mainland China. Angiostrongylus cantonensis is the causative agent of this severe disease. However, little is known about the genetics and basic biology of A. cantonensis. Results A cDNA library of A. cantonensis fourth-stage larvae was constructed, and ~1,200 clones were sequenced. Bioinformatic analyses revealed 378 cDNA clusters, 54.2% of which matched known genes at a cutoff expectation value of 10-20. Of these 378 unique cDNAs, 168 contained open reading frames encoding proteins containing an average of 238 amino acids. Characterization of the functions of these encoded proteins by Gene Ontology analysis showed enrichment in proteins with binding and catalytic activity. The observed pattern of enzymes involved in protein metabolism, lipid metabolism and glycolysis may reflect the central nervous system habitat of this pathogen. Four proteins were tested for their immunogenicity using enzyme-linked immunosorbent assays and histopathological examinations. The specificity of each of the four proteins was superior to that of crude somatic and excretory/secretory antigens of larvae, although their sensitivity was relatively low. We further showed that mice immunized with recombinant cystatin, a product of one of the four cDNA candidate genes, were partially protected from A. cantonensis infection. Conclusion The data presented here substantially expand the available genetic information about the human pathogen A. cantonensis, and should be a significant resource for angiostrongyliasis researchers. As such, this work serves as a starting point for molecular approaches for diagnosing and controlling human angiostrongyliasis.

  6. Molecular characterization of barley 3H semi-dwarf genes.

    Directory of Open Access Journals (Sweden)

    Haobing Li

    Full Text Available The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace 'TX9425' was crossed with the Australian barley variety 'Franklin' to generate a doubled haploid (DH population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from 'TX9425' was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF2 fine mapping population segregating only for the dwarfing gene from 'TX9425' were developed. The semi-dwarfing gene in 'TX9425' was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the 'TX9425'-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the 'TX9425'/'Franklin' DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.

  7. Multimodal fluorescence molecular imaging for in vivo characterization of skin cancer using endogenous and exogenous fluorophores

    Science.gov (United States)

    Miller, Jessica P.; Habimana-Griffin, LeMoyne; Edwards, Tracy S.; Achilefu, Samuel

    2017-06-01

    Similarity of skin cancer with many benign skin pathologies requires reliable methods to detect and differentiate the different types of these lesions. Previous studies have explored the use of disparate optical techniques to identify and estimate the invasive nature of melanoma and basal cell carcinoma with varying outcomes. Here, we used a concerted approach that provides complementary information for rapid screening and characterization of tumors, focusing on squamous cell carcinoma (SCC) of the skin. Assessment of in vivo autofluorescence lifetime (FLT) imaging of endogenous fluorophores that are excitable at longer wavelengths (480 nm) than conventional NADH and FAD revealed a decrease in the short FLT component for SCC compared to normal skin, with mean values of 0.57±0.026 ns and 0.61±0.021 ns, respectively (p=0.004). Subsequent systemic administration of a near-infrared fluorescent molecular probe in SCC bearing mice, followed by the implementation of image processing methods on data acquired from two-dimensional and three-dimensional fluorescence molecular imaging, allowed us to estimate the tumor volume and depth, as well as quantify the fluorescent probe in the tumor. The result suggests the involvement of lipofuscin-like lipopigments and riboflavin in SCC metabolism and serves as a model for staging SCC.

  8. Characterization of the rapid transcriptional response to long-term sensitization training in Aplysia californica.

    Science.gov (United States)

    Herdegen, Samantha; Holmes, Geraldine; Cyriac, Ashly; Calin-Jageman, Irina E; Calin-Jageman, Robert J

    2014-12-01

    We used a custom-designed microarray and quantitative PCR to characterize the rapid transcriptional response to long-term sensitization training in the marine mollusk Aplysia californica. Aplysia were exposed to repeated noxious shocks to one side of the body, a procedure known to induce a long-lasting, transcription-dependent increase in reflex responsiveness that is restricted to the side of training. One hour after training, pleural ganglia from the trained and untrained sides of the body were harvested; these ganglia contain the sensory nociceptors which help mediate the expression of long-term sensitization memory. Microarray analysis from 8 biological replicates suggests that long-term sensitization training rapidly regulates at least 81 transcripts. We used qPCR to test a subset of these transcripts and found that 83% were confirmed in the same samples, and 86% of these were again confirmed in an independent sample. Thus, our new microarray design shows strong convergent and predictive validity for analyzing the transcriptional correlates of memory in Aplysia. Fully validated transcripts include some previously identified as regulated in this paradigm (ApC/EBP and ApEgr) but also include novel findings. Specifically, we show that long-term sensitization training rapidly up-regulates the expression of transcripts which may encode Aplysia homologs of a C/EBPγ transcription factor, a glycine transporter (GlyT2), and a vacuolar-protein-sorting-associated protein (VPS36). Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Rapid Characterization of Bacterial Electrogenicity Using a Single-Sheet Paper-Based Electrofluidic Array

    Directory of Open Access Journals (Sweden)

    Yang Gao

    2017-07-01

    Full Text Available Electrogenicity, or bacterial electron transfer capacity, is an important application which offers environmentally sustainable advances in the fields of biofuels, wastewater treatment, bioremediation, desalination, and biosensing. Significant boosts in this technology can be achieved with the growth of synthetic biology that manipulates microbial electron transfer pathways, thereby potentially significantly improving their electrogenic potential. There is currently a need for a high-throughput, rapid, and highly sensitive test array to evaluate the electrogenic properties of newly discovered and/or genetically engineered bacterial species. In this work, we report a single-sheet, paper-based electrofluidic (incorporating both electronic and fluidic structure screening platform for rapid, sensitive, and potentially high-throughput characterization of bacterial electrogenicity. This novel screening array uses (i a commercially available wax printer for hydrophobic wax patterning on a single sheet of paper and (ii water-dispersed electrically conducting polymer mixture, poly(3,4-ethylenedioxythiophene:polystyrene sulfonate, for full integration of electronic and fluidic components into the paper substrate. The engineered 3-D, microporous, hydrophilic, and conductive paper structure provides a large surface area for efficient electron transfer. This results in rapid and sensitive power assessment of electrogenic bacteria from a microliter sample volume. We validated the effectiveness of the sensor array using hypothesis-driven genetically modified Pseudomonas aeruginosa mutant strains. Within 20 min, we observed that the sensor platform successfully measured the electricity-generating capacities of five isogenic mutants of P. aeruginosa while distinguishing their differences from genetically unmodified bacteria.

  10. Rapid Colorimetric Detection of Cartap Residues by AgNP Sensor with Magnetic Molecularly Imprinted Microspheres as Recognition Elements

    Directory of Open Access Journals (Sweden)

    Mao Wu

    2018-06-01

    Full Text Available The overuse of cartap in tea tree leads to hazardous residues threatening human health. A colorimetric determination was established to detect cartap residues in tea beverages by silver nanoparticles (AgNP sensor with magnetic molecularly imprinted polymeric microspheres (Fe3O4@mSiO2@MIPs as recognition elements. Using Fe3O4 as supporting core, mesoporous SiO2 as intermediate shell, methylacrylic acid as functional monomer, and cartap as template, Fe3O4@mSiO2@MIPs were prepared to selectively and magnetically separate cartap from tea solution before colorimetric determination by AgNP sensors. The core-shell Fe3O4@mSiO2@MIPs were also characterized by FT-IR, TEM, VSM, and experimental adsorption. The Fe3O4@mSiO2@MIPs could be rapidly separated by an external magnet in 10 s with good reusability (maintained 95.2% through 10 cycles. The adsorption process of cartap on Fe3O4@mSiO2@MIPs conformed to Langmuir adsorption isotherm with maximum adsorption capacity at 0.257 mmol/g and short equilibrium time of 30 min at 298 K. The AgNP colorimetric method semi-quantified cartap ≥5 mg/L by naked eye and quantified cartap 0.1–5 mg/L with LOD 0.01 mg/L by UV-vis spectroscopy. The AgNP colorimetric detection after pretreatment with Fe3O4@mSiO2@MIPs could be successfully utilized to recognize and detect cartap residues in tea beverages.

  11. Hydrodynamic characterization and molecular weight estimation of ultrasonically sheared DNA

    International Nuclear Information System (INIS)

    Casal, J. I.; Garces, F.; Garcia-Sacristan, A.

    1981-01-01

    The sedimentation coefficients and intrinsic viscosities of ultrasonically sheared calf thymus DNA have been determined. The molecular weight estimation according to this parameters have been compared with the ones obtained from the electrophoretic migration rates based on the calibration proposed using the known molecular weight restriction fragments of X-ENA. (Author) 35 refs

  12. Molecular cytogenetic characterization of a new wheat Secale ...

    Indian Academy of Sciences (India)

    A stable, highly fertile wheat Secale africanum substitution line LF24, derived from the F7 generation of a cross between Mianyang11 (MY11) and Triticum durum, S. africanum amphiploid (YF) was identified through molecular cytogenetic analysis. Application of C-banding, in situ hybridization and molecular markers ...

  13. Using rapid diagnostic tests as source of malaria parasite DNA for molecular analyses in the era of declining malaria prevalence

    DEFF Research Database (Denmark)

    Ishengoma, Deus S; Lwitiho, Sudi; Madebe, Rashid A

    2011-01-01

    was conducted to examine if sufficient DNA could be successfully extracted from malaria rapid diagnostic tests (RDTs), used and collected as part of routine case management services in health facilities, and thus forming the basis for molecular analyses, surveillance and quality control (QC) testing of RDTs....... continued molecular surveillance of malaria parasites is important to early identify emerging anti-malarial drug resistance, it is becoming increasingly difficult to obtain parasite samples from ongoing studies, such as routine drug efficacy trials. To explore other sources of parasite DNA, this study...

  14. Vibrational spectroscopy as a probe to rapidly detect, identify, and characterize micro-organisms

    Science.gov (United States)

    Sockalingum, Ganesh D.; Lamfarraj, Hasnae; Beljebbar, Abdelilah; Pina, Patrick; Delavenne, Marc; Witthuhn, Fabienne; Allouch, Pierre; Manfait, Michel

    1999-04-01

    Fast and exact identification of a great number of microorganisms is becoming a serious challenge. Differentiation and identification of microorganisms is today mainly achieved by the use of a variety of distinct techniques based on morphological, serological aspects and a set of biochemical test. Vibrational spectroscopic techniques can be complementary and useful methods in this field due to their rapidity, 'fingerprinting' capabilities, and the molecular information that they can provide. Using SERS at Ag colloids, we have conducted pilot studies to rapidly detect and identify bacterial clinical strains. Using a Raman microspectrometer equipped with a He/Ne laser, a first attempt to record SERS spectra was made on colloidal solutions. Spectra were of good quality but not very reproducible due to the movement of the microorganisms. Strains were then put in presence of Ag colloids and direct on-plate analysis was performed. Spectra were more reproducible, with diminished fluorescence, and reveal characteristic cellular-level information. Different growth conditions and colloid preparations have been tested. Pseudomonas aeruginosa and Escherichia coli clinical strains, responsible for nosocomial infections, have been our first test samples. An attempt has also been made to record SERS data from gold colloids in view of future measurement in the near-IR. Spectroscopic data are compared with ATR-FTIR results.

  15. Molecular Characterization and Cluster Analysis of Field Isolates of Avian Infectious Laryngotracheitis Virus from Argentina

    Directory of Open Access Journals (Sweden)

    María I. Craig

    2017-12-01

    Full Text Available Avian infectious laryngotracheitis (ILT is a worldwide infectious disease that causes important economic losses in the poultry industry. Although it is known that ILT virus (ILTV is present in Argentina, there is no information about the circulating strains. With the aim to characterize them, seven different genomic regions (thymidine kinase, glycoproteins D, G, B, C, and J, and infected cell polypeptide 4 were partially sequenced and compared between field samples. The gJ sequence resulted to be the most informative segment, it allowed the differentiation among field sample strains, and also, between wild and vaccine viruses. Specific changes in selected nucleotidic positions led to the definition of five distinct haplotypes. Tests for detection of clustering were run to test the null hypothesis that ILTV haplotypes were randomly distributed in time in Argentina and in space in the most densely populated poultry region of this country, Entre Rios. From this study, it was possible to identify a 46 km radius cluster in which higher proportions of haplotypes 4 and 5 were observed, next to a provincial route in Entre Rios and a significant decline of haplotype 5 between 2009 and 2011. Results here provide an update on the molecular epidemiology of ILT in Argentina, including data on specific genome segments that may be used for rapid characterization of the virus in the field. Ultimately, results will contribute to the surveillance of ILT in the country.

  16. Molecular characterization of Streptococcus agalactiae strains isolated from fishes in Malaysia.

    Science.gov (United States)

    Amal, M N A; Zamri-Saad, M; Siti-Zahrah, A; Zulkafli, A R; Nur-Nazifah, M

    2013-07-01

    The aim of this study was to characterize Streptococcus agalactiae strains that were isolated from fishes in Malaysia using random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (REP-PCR) techniques. A total of 181 strains of Strep. agalactiae isolated from red hybrid tilapia (Oreochromis sp.) and golden pompano (Trachinotus blochii) were characterized using RAPD and REP-PCR techniques. Both the fingerprinting techniques generated reproducible band patterns, differing in the number and molecular mass amplicons. The RAPD technique displayed greater discriminatory power by its production of more complex binding pattern and divided all the strains into 13 groups, compared to 9 by REP-PCR technique. Both techniques showed the availability to differentiate the genetic profiles of the strains according to their geographical location of origin. Three strains of Strep. agalactiae that were recovered from golden pompano showed a genetic dissimilarity from the strains isolated from red hybrid tilapia, while the strain of ATCC 27956 that recovered from bovine displayed a unique profile for both methods. Both techniques possess excellent discriminative capabilities and can be used as a rapid means of comparing Strep. agalactiae strains for future epidemiological investigation. Framework as the guideline in traceability of this disease and in the search for potential local vaccine candidates for streptococcosis in this country. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

  17. Molecular and biochemical characterization of calmodulin from Echinococcus granulosus.

    Science.gov (United States)

    Wang, Ning; Zhong, Xiuqin; Song, Xingju; Gu, Xiaobin; Lai, Weiming; Xie, Yue; Peng, Xuerong; Yang, Guangyou

    2017-12-04

    Echinococcus granulosus is a harmful cestode parasite that causes cystic echinococcosis in humans as well as various livestock species and wild animals. Calmodulin (CaM), a Ca 2+ sensor protein, is widely expressed in eukaryotes and mediates a variety of cellular signaling activities. In the present study, the cDNA encoding CaM in Echinococcus granulosus (rEgCaM) was successfully cloned and the molecular and biochemical characterizations carried out. The antigenicity and immunoreactivity of rEgCaM was detected and the preliminary enzyme-linked immunosorbent assay (ELISA)-based serodiagnostic potential of EgCaM was assessed. The locations of this protein in the adult worm and larval stage, and the mRNA expression in different states of E. granulosus protoscoleces (PSCs) were defined clearly. Moreover, the Ca 2+ -binding properties of EgCaM were measured. rEgCaM is a highly conserved calcium-binding protein, consisting of 149 amino acids. Immunoblotting analysis revealed that rEgCaM could be identified using E. granulosus infected sheep serum. The use of rEgCaM as an antigen was evaluated by indirect ELISA which exhibited a high sensitivity (90.3%), but low specificity (47.1%). rEgCaM was ubiquitously expressed in protoscoleces and adults of E. granulosus, as well as in the germinal layer of the cyst wall. The mRNA expression level of rEgCaM was increased from the start of H 2 O 2 exposure and then gradually decreased because of the increased apoptosis of PSCs. In electrophoretic mobility tests and 1-anilinonaphthalene-8-sulfonic acid assays, rEgCaM showed a typical characteristic of a calcium-binding protein. To our knowledge, this is the first report on CaM from E. granulosus and rEgCaM is likely to be involved in some important biological function of E. granulosus as a calcium-binding protein.

  18. Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

    Science.gov (United States)

    Paramo, Teresa; East, Alexandra; Garzón, Diana; Ulmschneider, Martin B; Bond, Peter J

    2014-05-13

    Protein cavities and tunnels are critical in determining phenomena such as ligand binding, molecular transport, and enzyme catalysis. Molecular dynamics (MD) simulations enable the exploration of the flexibility and conformational plasticity of protein cavities, extending the information available from static experimental structures relevant to, for example, drug design. Here, we present a new tool (trj_cavity) implemented within the GROMACS ( www.gromacs.org ) framework for the rapid identification and characterization of cavities detected within MD trajectories. trj_cavity is optimized for usability and computational efficiency and is applicable to the time-dependent analysis of any cavity topology, and optional specialized descriptors can be used to characterize, for example, protein channels. Its novel grid-based algorithm performs an efficient neighbor search whose calculation time is linear with system size, and a comparison of performance with other widely used cavity analysis programs reveals an orders-of-magnitude improvement in the computational cost. To demonstrate its potential for revealing novel mechanistic insights, trj_cavity has been used to analyze long-time scale simulation trajectories for three diverse protein cavity systems. This has helped to reveal, respectively, the lipid binding mechanism in the deep hydrophobic cavity of a soluble mite-allergen protein, Der p 2; a means for shuttling carbohydrates between the surface-exposed substrate-binding and catalytic pockets of a multidomain, membrane-proximal pullulanase, PulA; and the structural basis for selectivity in the transmembrane pore of a voltage-gated sodium channel (NavMs), embedded within a lipid bilayer environment. trj_cavity is available for download under an open-source license ( http://sourceforge.net/projects/trjcavity ). A simplified, GROMACS-independent version may also be compiled.

  19. Molecular identification and characterization of Rhizoctonia solani AG-3 isolates causing black scurf of potato

    International Nuclear Information System (INIS)

    Zaidy, M.E.; Othman, M.R.; Mahmoud, M.

    2018-01-01

    Twenty-six isolates of Rhizoctonia solani AG-3 were collected from four potato growing area of Saudi Arabia. Yield damages due to this infection is reported to range from 7-64% (average of 35%), depending on many factors. Molecular identification of R. solani AG-3 isolates by ITS-regions and characterization was done by inter simple sequence repeat (ISSR) markers. Twenty-six isolates of R. solani used in the current study were isolated from potato fields in four major potato-producing regions of Saudi Arabia. All isolates were inoculated on potato and observations on the percentage of disease incidence were recorded. Genomic DNA extraction of R. solani AG-3 isolates was used by A specific and sensitive PCR and ISSR primers. A single splinter of nearly 500 bp was only amplified once genomic DNA from R. solani AG-3 isolates. Amplicon size of three ISSR primers ranged from 0.3 to 2.8 Kb in isolates. Using the three primers, the tested isolates were separated on the basis of genetic similarity coefficients (GSC). The range of the GSC was beginning at 0.62 and ending at 1.00. In unweighted pair-group method arithmetic averages (UPGMA) analysis, the R. solani isolates grouped into five clusters. The present method provided rapid and reliable detection of R. solani AG-3 isolates. Molecular characterization have great genetic variation in the R. solani AG-3 population, without any correlation between aggressiveness, geographical regions and genetic variation based on ISSR markers. (author)

  20. Characterization of nanoparticle mediated laser transfection by femtosecond laser pulses for applications in molecular medicine.

    Science.gov (United States)

    Schomaker, Markus; Heinemann, Dag; Kalies, Stefan; Willenbrock, Saskia; Wagner, Siegfried; Nolte, Ingo; Ripken, Tammo; Murua Escobar, Hugo; Meyer, Heiko; Heisterkamp, Alexander

    2015-02-03

    In molecular medicine, the manipulation of cells is prerequisite to evaluate genes as therapeutic targets or to transfect cells to develop cell therapeutic strategies. To achieve these purposes it is essential that given transfection techniques are capable of handling high cell numbers in reasonable time spans. To fulfill this demand, an alternative nanoparticle mediated laser transfection method is presented herein. The fs-laser excitation of cell-adhered gold nanoparticles evokes localized membrane permeabilization and enables an inflow of extracellular molecules into cells. The parameters for an efficient and gentle cell manipulation are evaluated in detail. Efficiencies of 90% with a cell viability of 93% were achieved for siRNA transfection. The proof for a molecular medical approach is demonstrated by highly efficient knock down of the oncogene HMGA2 in a rapidly proliferating prostate carcinoma in vitro model using siRNA. Additionally, investigations concerning the initial perforation mechanism are conducted. Next to theoretical simulations, the laser induced effects are experimentally investigated by spectrometric and microscopic analysis. The results indicate that near field effects are the initial mechanism of membrane permeabilization. This methodical approach combined with an automated setup, allows a high throughput targeting of several 100,000 cells within seconds, providing an excellent tool for in vitro applications in molecular medicine. NIR fs lasers are characterized by specific advantages when compared to lasers employing longer (ps/ns) pulses in the visible regime. The NIR fs pulses generate low thermal impact while allowing high penetration depths into tissue. Therefore fs lasers could be used for prospective in vivo applications.

  1. Methodology for characterizing the environmental impacts of hydroelectric generating stations : a case study of Farmer Rapids

    International Nuclear Information System (INIS)

    Lemieux, C.; Renaud, S.; Begin, P.; Belzile, L.; Caumartin, J.

    2006-01-01

    This paper described a novel methodology used to characterize the downstream section of a generating station that was not navigable by boat. The method was used as part of a fish habitat characterization study conducted in the Farmers Rapids area of Quebec. The purpose of the study was to identify the discharges and water levels needed to preserve fish habitats in the region. Initially, experimental fishing was undertaken to locate, validate and characterize fish habitats. Habitat models were then developed using a microhabitat modelling method to establish pertinent discharges and water levels. In order to model areas that were not navigable by boat, discharges released by the generating station were reduced to a minimum to temporarily decrease water levels and expose the river. High definition aerial photography and topographic mapping was conducted. The information obtained from the 2 procedures was then used to describe and map the riverbed substrate as well as the bathymetry and aquatic habitats. A 2D hydrodynamic model was then used to simulate water flows in the area at various discharges. The results of the hydrodynamic models and the habitat models were then used to establish appropriate discharges for optimal fish habitats

  2. Design of two molecular methodologies for the rapid identification of Colombian community-acquired methicillin-resistant Staphylococcus aureus isolates

    OpenAIRE

    Escobar, Javier Antonio; Gómez, Ingrid Tatiana; Murillo, Martha Johanna; Castro, Betsy Esperanza; Chavarro, Bibiana; Márquez, Ricaurte Alejandro; Vanegas, Natasha

    2012-01-01

    Introduction. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are found with increasing the frequency, both in healthy individuals in the community and in hospitalized patients. In Colombia and the Andean region, CA-MRSA isolates have a genetic background that is related to the pandemic USA300 clone. Objective. Two molecular methods are designed and standardized for the rapid differentiation of Colombian community-acquired and hospital-acquired methicillin-...

  3. Molecular characterization and assessment of genetic diversity of ...

    African Journals Online (AJOL)

    R Madhusudhana

    genetic diversity available at molecular level among a set of phenotypically different ... allele matching and cluster analysis based on unweighted neighbor- joining (Gascuel, 1997) ..... on isozyme data-a simulation study. Theor. Appl. Genet.

  4. A new fiber-optic sensor technology for rapid and inexpensive characterization of soil contamination

    International Nuclear Information System (INIS)

    Milanovich, F.P.; Brown, S.B.; Colston, B.W. Jr.; Daley, P.F.; Rossabi, J.

    1993-04-01

    The extent and complexity of worldwide environmental contamination are great enough that remediation will be extremely costly and lengthy. There is an urgent need for characterization techniques that are rapid, inexpensive, and simple and that do not generate waste. Towards this end LLNL is developing a fiber-optic chemical sensor technology for use in groundwater and vadose-zone monitoring. We use a colorimetric detection technique, based on an irreversible chemical reaction between a specific reagent and the target compound. The accuracy and sensitivity of the sensor (<5 ppb by weight in water, determined by comparison with gas chromatographic standard measurements) are sufficient for environmental monitoring of at least trichloroethylene (TCE) and chloroform

  5. A novel molecularly imprinted material based on magnetic halloysite nanotubes for rapid enrichment of 2,4-dichlorophenoxyacetic acid in water

    International Nuclear Information System (INIS)

    Zhong, Shian; Zhou, Chengyun; Zhang, Xiaona; Zhou, Hui; Li, Hui; Zhu, Xiaohong; Wang, Yan

    2014-01-01

    Graphical abstract: - Highlights: • Successful preparation of a novel type of magnetic halloysite molecularly imprinted material. • Rapid enrichment for 2,4-dichlorophenoxyacetic acid in water. • This material possesses high adsorption capacity and specific recognition to 2,4-dichlorophenoxyacetic acid. • Magnetic halloysite were synthesized by co-precipitation method. - Abstract: A new type of magnetic halloysite nanotubes molecularly imprinted polymer (MHNTs@MIP) based on halloysite nanotubes (HNTs) with embedded magnetic nanoparticles was introduced in this study. MHNTs@MIP was prepared through surface imprinting technology, using 2,4-dichlorophenoxyacetic acid (2,4-D) as a template, 4-vinylpyridine as the monomer, divinylbenzene as cross-linking agents, and 2,2-azodiisobutyronitrile as initiator. MHNTs@MIP was characterized by Fourier Transform Infrared Spectrometer, transmission electron microscopy, X-ray diffraction, and vibrating sample magnetometer. MHNTs@MIP exhibited rapid and reliable analysis with supermagnetic properties, as well as repeated use and template-specific recognition. The adsorption capacity of magnetic halloysite nanotubes non-imprinted polymer (MHNTs@NIP) and MHNTs@MIP was 10.3 mg/g and 35.2 mg/g, respectively. In the detailed discussion on specific selectivity, MHNTs@MIP can be applied as an adsorbent for sample pretreatment extraction and obtain high recoveries of about 85–94%. After extraction, high-performance liquid chromatography was used to detect 2,4-D residue in water

  6. A novel molecularly imprinted material based on magnetic halloysite nanotubes for rapid enrichment of 2,4-dichlorophenoxyacetic acid in water

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shian; Zhou, Chengyun; Zhang, Xiaona [School of Chemistry and Chemical Engineering, Central South University, Changsha 410083 (China); Zhou, Hui [Cancer Hospital of Xiangya Medical College, Central South University, Changsha 410013 (China); Li, Hui; Zhu, Xiaohong [School of Chemistry and Chemical Engineering, Central South University, Changsha 410083 (China); Wang, Yan, E-mail: yanwangcsu@163.com [School of Chemistry and Chemical Engineering, Central South University, Changsha 410083 (China)

    2014-07-15

    Graphical abstract: - Highlights: • Successful preparation of a novel type of magnetic halloysite molecularly imprinted material. • Rapid enrichment for 2,4-dichlorophenoxyacetic acid in water. • This material possesses high adsorption capacity and specific recognition to 2,4-dichlorophenoxyacetic acid. • Magnetic halloysite were synthesized by co-precipitation method. - Abstract: A new type of magnetic halloysite nanotubes molecularly imprinted polymer (MHNTs@MIP) based on halloysite nanotubes (HNTs) with embedded magnetic nanoparticles was introduced in this study. MHNTs@MIP was prepared through surface imprinting technology, using 2,4-dichlorophenoxyacetic acid (2,4-D) as a template, 4-vinylpyridine as the monomer, divinylbenzene as cross-linking agents, and 2,2-azodiisobutyronitrile as initiator. MHNTs@MIP was characterized by Fourier Transform Infrared Spectrometer, transmission electron microscopy, X-ray diffraction, and vibrating sample magnetometer. MHNTs@MIP exhibited rapid and reliable analysis with supermagnetic properties, as well as repeated use and template-specific recognition. The adsorption capacity of magnetic halloysite nanotubes non-imprinted polymer (MHNTs@NIP) and MHNTs@MIP was 10.3 mg/g and 35.2 mg/g, respectively. In the detailed discussion on specific selectivity, MHNTs@MIP can be applied as an adsorbent for sample pretreatment extraction and obtain high recoveries of about 85–94%. After extraction, high-performance liquid chromatography was used to detect 2,4-D residue in water.

  7. Molecular cloning and characterization of pathogenesis-related ...

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... Available online at http://www.academicjournals.org/AJB ... November, 2011. We described the cloning and characterization of pathogenesis-related protein 5 gene in maize, named .... in two inbred lines was calculated using the ↵Ct method. .... Of the characterized PRs currently known, PR-1, PR-2,. PR-3 ...

  8. Molecular characterization and expression of DgZFP1, a gene ...

    African Journals Online (AJOL)

    USER

    2010-04-12

    Apr 12, 2010 ... Full Length Research Paper. Molecular characterization and ... stem mainly done by removing the auxiliary flower buds. But cultivars as potted ... DgZFP1 by using the first strand cDNA of chrysanthemum as a template.

  9. Molecular cloning and characterization of a putative OGG_N domain ...

    African Journals Online (AJOL)

    Molecular cloning and characterization of a putative OGG_N domain from the camel, Camelus dromedarius. Farid Shokry Ataya, Mohammad Saud Alanazi, Dalia Fouad, Hehsam Mahmoud Saeed, Mohammad Bazzi ...

  10. Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer

    Science.gov (United States)

    2017-07-01

    AWARD NUMBER: W81XWH-16-1-0274 TITLE: Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer PRINCIPAL INVESTIGATOR...SUBTITLE Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-16-1-0274 5c...organoid technology via collaboration with Dr. Mary Estes (Baylor College of Medicine ) and her lab, via one-on-one visits, has guided Dr. Alex Peniche with

  11. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Science.gov (United States)

    Jarquin, Robin; Hanning, Irene; Ahn, Soohyoun; Ricke, Steven C.

    2009-01-01

    Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered. PMID:22346699

  12. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Directory of Open Access Journals (Sweden)

    Steven C. Ricke

    2009-07-01

    Full Text Available Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered.

  13. Rapid and molecular selective electrochemical sensing of phthalates in aqueous solution

    KAUST Repository

    Zia, Asif I.; Mukhopadhyay, Subhas Chandra; Yu, Paklam; Al-Bahadly, Ibrahim H.; Gooneratne, Chinthaka Pasan; Kosel, Jü rgen

    2015-01-01

    molecular imprinted polymer (MIP) to introduce selectivity for the di(2-ethylhexyl) phthalate (DEHP) molecule. Various concentrations (1-100. ppm) of DEHP in deionized MilliQ water were tested using the functionalized sensing surface to capture the analyte

  14. Infrared spectrophotometry, a rapid and effective tool for characterization of direct distillation naphthas

    International Nuclear Information System (INIS)

    Baldrich Ferrer, Carlos A; Novoa Mantilla, Luz Angela

    2005-01-01

    The characterization of naphtha obtained by direct distillation of medium and heavy crude oils is often limited by the low yield of these fractions. Gas chromatography is a technique that allows a complete determination of the chemical composition of this fraction. However, the prediction of properties such as octane rating and RVP from chromatographic data is a difficult task because there are not adequate models to predict the interaction of the different components, and particularly in the case of heavier fractions, there are some problems for the complete separation of components under the gas chromatographic conditions. The IR technology constitutes a rapid and effective tool to predict several properties of naphtha from the correlation of the spectrum in the infrared area and the properties. In this study, prediction models were developed in a Petrospec Cetane 2000 analyzer, in order to predict in a fast and simple way, the density, the antiknock index and the aromatic content of straight run naphtha obtained in a standard crude oil distillation unit. The equipment used was designed in the factory for the exclusive characterization of medium distillation and not for lighter fractions therefore this work constitutes an innovation given the extensive applications of this type of analyzers

  15. Rapid detailed characterization of concrete shielding blocks utilizing internal natural radionuclides for calibration

    International Nuclear Information System (INIS)

    McDonald, R.J.; Smith, A.R.; Hurley, D.L.; Norman, E.B.; Schoonover, M.R.

    1998-01-01

    Following many years of productive research, the 184-inch Cyclotron, the SuperHILAC, and the BEVALAC accelerators at the Berkeley Laboratory were closed, leaving thousands of concrete shielding blocks available for reuse, recycling, or disposal. The process history of these blocks precludes free release pending radiological characterization. This paper describes a procedure whereby a high efficiency shielded germanium spectrometer is used to rapidly characterize natural and man-made activity within the blocks. The spectrometer is moved up to the block and 5 minutes of data are collected at the point on the block that registers highest on a micro-R meter. Sensitivity is better than 1 pCi/g (0.037 Bq/g) for Co-60 and Eu-152, the prominent man-made activities observed. One-time calibration of the detector system is obtained from a sample of concrete, drilled with a hammer drill, counted in our low-background facility, and compared to crushed rock with known U, Th, and K activity. A simple relationship exists between the counts/minute observed in a characteristic gamma-ray peak and the activity in the block. (author)

  16. A two-step method for rapid characterization of electroosmotic flows in capillary electrophoresis.

    Science.gov (United States)

    Zhang, Wenjing; He, Muyi; Yuan, Tao; Xu, Wei

    2017-12-01

    The measurement of electroosmotic flow (EOF) is important in a capillary electrophoresis (CE) experiment in terms of performance optimization and stability improvement. Although several methods exist, there are demanding needs to accurately characterize ultra-low electroosmotic flow rates (EOF rates), such as in coated capillaries used in protein separations. In this work, a new method, called the two-step method, was developed to accurately and rapidly measure EOF rates in a capillary, especially for measuring the ultra-low EOF rates in coated capillaries. In this two-step method, the EOF rates were calculated by measuring the migration time difference of a neutral marker in two consecutive experiments, in which a pressure driven was introduced to accelerate the migration and the DC voltage was reversed to switch the EOF direction. Uncoated capillaries were first characterized by both this two-step method and a conventional method to confirm the validity of this new method. Then this new method was applied in the study of coated capillaries. Results show that this new method is not only fast in speed, but also better in accuracy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Rapid Separation Methods to Characterize Actinides and Metallic Impurities in Plutonium Scrap Materials at SRS

    International Nuclear Information System (INIS)

    Maxwell, S.L. III; Jones, V.D.

    1998-07-01

    The Nuclear Materials Stabilization and Storage Division at SRS plans to stabilize selected plutonium scrap residue materials for long term storage by dissolution processing and plans to stabilize other plutonium vault materials via high-temperature furnace processing. To support these nuclear material stabilization activities, the SRS Analytical Laboratories Department (ALD) will provide characterization of materials required prior to the dissolution or the high-firing of these materials. Lab renovations to install new analytical instrumentation are underway to support these activities that include glove boxes with simulated-process dissolution and high- pressure microwave dissolution capability. Inductively-coupled plasma atomic emission spectrometry (ICP-AES), inductively- coupled mass spectrometry (ICP-MS) and thermal-ionization mass spectrometry (TIMS) will be used to measure actinide isotopics and metallic impurities. New high-speed actinide separation methods have been developed that will be applied to isotopic characterization of nuclear materials by TIMS and ICP-MS to eliminate isobaric interferences between Pu-238 /U- 238 and Pu-241/Am-241. TEVA Resin, UTEVA Resin, and TRU Resin columns will be used with vacuum-assisted flow rates to minimize TIMS and ICP-MS sample turnaround times. For metallic impurity analysis, rapid column removal methods using UTEVA Resin, AGMP-1 anion resin and AG MP-50 cation resin have also been developed to remove plutonium and uranium matrix interferences prior to ICP-AES and ICP- MS measurements

  18. Rapid detailed characterization of concrete shielding blocks utilizing internal natural radionuclides for calibration

    International Nuclear Information System (INIS)

    McDonald, R.J.; Smith, A.R.; Norman, E.B.; Cowles, D.

    1995-10-01

    Following many years of productive work, the SuperHILAC and Bevalac accelerators at Lawrence Berkeley National Laboratory were closed, leaving thousands of concrete shielding blocks available for reuse or disposal. The process history of these blocks as shielding precludes free release pending radiological characterization. This paper presents a method for the rapid characterization of gamma-ray-emitting radioisotopes in large samples of earth-like materials: concrete shielding blocks in this case. Active regions are identified with a sensitive radiation-survey instrument and then examined in detail with a high-efficiency lead-shielded Ge spectrometer. Naturally-occurring gamma-ray emissions from the decays of uranium, thorium, and potassium are used to calibrate the spectrometer. A simple relationship exists between the observed counting rate in a characteristic gamma ray and the activity in the block. This method, taking only tens of minutes per sample at the nano-Curie/gram sensitivity level, replaces much of the expensive coring and laboratory analysis methods needed otherwise

  19. Molecular characterization of rpoB gene encoding the RNA ...

    African Journals Online (AJOL)

    Polymerase chain reaction (PCR) mediated direct DNA sequencing was evaluated for rapid detection of Rifampicin resistance (RMPr) of Mycobacterium tuberculosis. After amplification of the rpoB gene, the product was sequenced using ABI 310 Genetic Analyzer and the rifampicin resistance in M. tuberculosis were ...

  20. Isolation and molecular genetic characterization of a yeast strain ...

    African Journals Online (AJOL)

    The yeast was identified by molecular genetics technique based on sequence analysis of the variable D1/D2 domain of the large subunit (26S) ribosomal DNA. Subsequent 26S rRNA gene sequencing showed 100% base sequence homology and it was identified as Candida viswanathii. The degradation of PAHs

  1. Molecular and Cytogenetic Characterization of Wild Musa Species

    Czech Academy of Sciences Publication Activity Database

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, I.; Häkkinen, M.; Roux, N.; Swennen, R.; Doležel, Jaroslav

    2015-01-01

    Roč. 10, č. 8 (2015), e0134096 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) LG12021; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : NUCLEAR-DNA CONTENT * GENETIC DIVERSITY * RIBOSOMAL DNA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.057, year: 2015

  2. Molecular characterization of Cymbidium kanran cultivars based on ...

    African Journals Online (AJOL)

    TUOYO

    2010-08-09

    Aug 9, 2010 ... Fifty-four Cymbidium kanran cultivars from China, Japan and Korea were examined and analyzed by using the successive screening of 3′-end extended random primer amplified polymorphic DNA (ERAPD) markers to determine their molecular diversity and relationships. In ERAPD analyses, the strand-.

  3. Molecular characterization of barley ( Hordeum vulgare L.) genome ...

    African Journals Online (AJOL)

    The present work aimed to select drought tolerant barley (Hordeum vulgare L.) cultivars through identification of stress genes responsible for drought tolerance. Several barley genotypes were tested for drought resistance using specific molecular markers, nine out of all the genotypes were chosen for this study; five out of ...

  4. Molecular characterization of olive cultivars grown in Iraq using ...

    African Journals Online (AJOL)

    The results of this research confirmed AFLP and SSR to be useful tools in genetic relationships among olive cultivars, in creating a molecular database for Iraqi olive cultivars, in breeding strategies and in correct cultivar identification. Keywords: Olea europaea, genetic diversity, amplified fragment length polymorphism ...

  5. Molecular characterization of transforming growth factor-beta3

    NARCIS (Netherlands)

    Dijke, ten P.

    1991-01-01

    Normal tissue homeostasis is controlled by a critical balance of positive and negative modulators. Chapter 2 gives an overview of the molecular aspects of growth control, in particular the role of growth factors and oncogene and anti-oncogene products. Uncontrolled growth of cancer cells

  6. Molecular cloning and characterization of a new peroxidase gene ...

    African Journals Online (AJOL)

    length cDNA of O.violaceus peroxidase gene (OvRCI, GenBank. Acc. No. AY428037) was 1220 bp and contained an 1128 bp open reading frame encoding a protein of 375 amino acids. Homology analysis and molecular modeling revealed that ...

  7. PREPARATION AND CHARACTERIZATION OF MOLECULARLY IMPRINTED ELECTROPOLYMERIZED CARBON ELECTRODES

    Science.gov (United States)

    Molecularly imprinted polymers (MIP) selective for fluorescein, rhodamine or 2,4-dichlorophenoxyacetic acid (2,4-D) were electropolymerized onto graphite electrodes using an aqueous solution equimolar in resorsinol/ortho-phenylenediamine and in the presence of the template mole...

  8. Low-molecular-weight chitosans: Preparation and characterization

    Czech Academy of Sciences Publication Activity Database

    Tishchenko, Galina; Šimůnek, Jiří; Brus, Jiří; Netopilík, Miloš; Pekárek, Michal; Walterová, Zuzana; Koppová, Ingrid; Lenfeld, Jiří

    2011-01-01

    Roč. 86, č. 2 (2011), s. 1077-1081 ISSN 0144-8617 R&D Projects: GA ČR(CZ) GA525/08/0803 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z50450515 Keywords : low-molecular-weight chitosans * chitooligosaccharides * oxidative depolymerization Subject RIV: ED - Physiology Impact factor: 3.628, year: 2011

  9. Molecular characterization and expression analysis of a hepcidin ...

    African Journals Online (AJOL)

    Jane

    2011-08-03

    Aug 3, 2011 ... the liver, intestine and brain were 2.4, 1.5 and 2-fold increase, respectively, compared with the control animals after 5 days .... (sex change) of RFE attracted more attention (Cheng et al., 2003 ...... Molecular Biology. New York: ...

  10. Molecular characterization of Cymbidium kanran cultivars based on ...

    African Journals Online (AJOL)

    Fifty-four Cymbidium kanran cultivars from China, Japan and Korea were examined and analyzed by using the successive screening of 3'-end extended random primer amplified polymorphic DNA (ERAPD) markers to determine their molecular diversity and relationships. In ERAPD analyses, the strandspecific DNA ...

  11. Molecular characterization of X chromosome fragility in idiopathic ...

    African Journals Online (AJOL)

    Heba Alla Hosny Omar

    2015-11-23

    Nov 23, 2015 ... Frequency of fragile X syndrome among male siblings and relatives of mentally retarded patients ... hence the wide clinical spectrum of disorders caused by this ... fragile X syndrome, autism and other less well-characterized.

  12. Molecular characterization of WFS1 in patients with Wolfram syndrome

    NARCIS (Netherlands)

    Van den Ouweland, JMW; Cryns, K; Pennings, RJE; Walraven, [No Value; Janssen, GMC; Maassen, JA; Veldhuijzen, BFE; Arntzenius, AB; Lindhout, D; Cremers, CWRJ; Van Camp, G; Dikkeschei, LD

    Wolfram (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness) syndrome is a rare autosomal-recessive neurodegenerative disorder that is characterized by juvenile-onset diabetes mellitus, optic atrophy, diabetes insipidus, and sensorineural hearing impairment. A gene responsible for

  13. Molecular characterization of WFS1 in patients with Wolfram syndrome.

    NARCIS (Netherlands)

    Ouweland, J.M.W. van den; Cryns, K.; Pennings, R.J.E.; Walraven, I.; Janssen, G.M.; Maassen, J.A.; Veldhuijzen, B.F.; Arntzenius, A.B.; Lindhout, D.; Cremers, C.W.R.J.; Camp, G. van; Dikkeschei, L.D.

    2003-01-01

    Wolfram (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness) syndrome is a rare autosomal-recessive neurodegenerative disorder that is characterized by juvenile-onset diabetes mellitus, optic atrophy, diabetes insipidus, and sensorineural hearing impairment. A gene responsible for

  14. Molecular characterization of the thioredoxin system from Methanosarcina acetivorans

    OpenAIRE

    McCarver, Addison C.; Lessner, Daniel J.

    2014-01-01

    The thioredoxin system, composed of thioredoxin reductase (TrxR) and thioredoxin (Trx), is widely distributed in nature, where it serves key roles in electron transfer and in defense against oxidative stress. Although recent evidence reveals Trx homologues are almost universally present among the methane-producing archaea (methanogens), a complete thioredoxin system has not been characterized from any methanogen. We examined the phylogeny of Trx homologues among methanogens and characterized ...

  15. Molecular Characterization of Three Lactobacillus delbrueckii subsp. bulgaricus Phages

    OpenAIRE

    Casey, Eoghan; Mahony, Jennifer; O'Connell-Motherway, Mary; Bottacini, Francesca; Cornelissen, Anneleen; Neve, Horst; Heller, Knut J.; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

    2014-01-01

    In this study, three phages infecting Lactobacillus delbrueckii subsp. bulgaricus, named Ld3, Ld17, and Ld25A, were isolated from whey samples obtained from various industrial fermentations. These phages were further characterized in a multifaceted approach: (i) biological and physical characterization through host range analysis and electron microscopy; (ii) genetic assessment through genome analysis; (iii) mass spectrometry analysis of the structural components of the phages; and (iv), for ...

  16. Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

    Science.gov (United States)

    Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

    2017-08-01

    There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

  17. A rapid PCR-based approach for molecular identification of filamentous fungi.

    Science.gov (United States)

    Chen, Yuanyuan; Prior, Bernard A; Shi, Guiyang; Wang, Zhengxiang

    2011-08-01

    In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal with a large number of filamentous fungal isolates in the same batch, was established. The filamentous fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted DNA also can be used to amplify other protein-coding genes for fungal identification. This method can be used for rapid systematic identification of filamentous fungal isolates.

  18. Laboratory and Molecular Characterization of Dengue Viruses in a 2014 Outbreak in Guangfo Region, Southern China.

    Science.gov (United States)

    Luo, Zhao-Fan; Hu, Bo; Zhang, Feng-Yi; Lin, Xiang-Hua; Xie, Xiao-Ying; Pan, Kun-Yi; Li, Hong-Yu; Ren, Rui-Wen; Zhao, Wen-Zhong

    2017-09-25

    Non-specific symptoms and low viremia levels make early diagnosis of dengue virus (DENV) infection challenging. This study aimed to i) identify laboratory markers that can be used to predict a DENV-positive diagnosis and ii) perform a molecular characterization of DENVs from the 2014 Guangdong epidemic. This retrospective study analyzed 1,044 patients from the Guangdong epidemic who were clinically suspected cases of dengue. Viral RNA was detected by real-time RT-PCR, and viral-specific NS1 antigen was detected using enzyme-linked immuno sorbent assay. A molecular phylogenetic analysis was performed for the with the DENV C-prM gene junction. Patients with dengue infection had leukopenia (2.8 × 10 9 /L), thrombocytopenia (109.0 × 10 9 /L), elevated aspartate aminotransferase (56.0 IU/L) and alanine aminotransferase (43.5 IU/L), and prolonged activated partial thromboplastin time (APTT, 33.5 s) (all P < 0.001) compared to patients without dengue. The positive predictive value of leukopenia and thrombocytopenia for DENV infection were 96.9% and 93.0%, respectively. Leukopenia, thrombocytopenia, elevated aminotransferases, and prolonged APTT were useful predictive markers for an early diagnosis of DENV infection. Phylogenetic analysis indicated that the DENVs from the 2014 epidemic were closely related to a 2010 New Delhi strain and a 2013 Guangzhou strain. The 2014 epidemic consisted of co-circulating DENV-1 genotypes I and V from multiple origins. Efficient dengue surveillance can facilitate rapid response to future outbreaks.

  19. Cloning and molecular characterization of a copper chaperone gene ...

    African Journals Online (AJOL)

    The cDNA encoding a copper chaperone, designated as HbCCH1, was isolated from Hevea brasiliensis. HbCC1 was 589 bp long containing a 261 bp open reading frame encoding a putative protein of 86 amino acids, flanked by a 103 bp 5'UTR and a 225 bp 3'UTR. The predicted molecular mass of HbCCH1 was 9.2 kDa, ...

  20. Comprehensive characterization of molecular interactions based on nanomechanics.

    Directory of Open Access Journals (Sweden)

    Murali Krishna Ghatkesar

    Full Text Available Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6 Da adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.

  1. Isolation and molecular characterization of Clostridium perfringens from healthy Merino lambs in Patagonia region, Argentina

    DEFF Research Database (Denmark)

    Mignaqui, A. C.; Marcellino, R. B.; Ronco, Troels

    2017-01-01

    The presence and molecular characterization of Clostridium perfringens in healthy Merino lambs over a six-month period was investigated in this study. Overall, a high prevalence of C. perfringens was detected, even in day-old lambs. Even though the majority of the isolates were characterized...

  2. Rapid characterization of the biomechanical properties of drug-treated cells in a microfluidic device

    International Nuclear Information System (INIS)

    Zhang, Xiaofei; Zhang, Yang; Bai, Guohua; Tan, Qiulin; Sun, Dong; Chu, Henry K; Wang, Kaiqun

    2015-01-01

    Cell mechanics is closely related to many cell functions. Recent studies have suggested that the deformability of cells can be an effective biomarker to indicate the onset and progression of diseases. In this paper, a microfluidic chip is designed for rapid characterization of the mechanics of drug-treated cells through stretching with dielectrophoresis (DEP) force. This chip was fabricated using PDMS and micro-electrodes were integrated and patterned on the ITO layer of the chip. Leukemia NB4 cells were considered and the effect of all-trans retinoic acid (ATRA) drug on NB4 cells were examined via the microfluidic chip. To induce a DEP force onto the cell, a relatively weak ac voltage was utilized to immobilize a cell at one side of the electrodes. The applied voltage was then increased to 3.5 V pp and the cell started to be stretched along the applied electric field lines. The elongation of the cell was observed using an optical microscope and the results showed that both types of cells were deformed by the induced DEP force. The strain of the NB4 cell without the drug treatment was recorded to be about 0.08 (time t = 180 s) and the drug-treated NB4 cell was about 0.21 (time t = 180 s), indicating a decrease in the stiffness after drug treatment. The elastic modulus of the cell was also evaluated and the modulus changed from 140 Pa to 41 Pa after drug treatment. This microfluidic chip can provide a simple and rapid platform for measuring the change in the biomechanical properties of cells and can potentially be used as the tool to determine the biomechanical effects of different drug treatments for drug discovery and development applications. (paper)

  3. Rapid characterization of seismic sources in Chile: Contribution of the GNSS component

    Science.gov (United States)

    Barrientos, S. E.; Riquelme, S.; Baez, J. C., Sr.

    2017-12-01

    The recently created National Seismological Center (CSN) of the University of Chile was tasked to upgrade the countrýs seismic network in 2013. The upgrade included new 65 collocated accelerometer and broadband instruments together with 130 GNSS devices designed to transmit their data in real time. Forty units of the GNSS devices include the RTX option, a real time 1-Hz positioning capability at 4-cm error level. The observation system is complemented with 297 additional stand-alone strong motion instruments mainly located in basins for seismic engineering purposes. Broadband data can be accessed in real time from IRIS Data Management Service under networks C and C1. Strong motion event data can be retrieved through the CSN database (evtdb.csn.uchile.cl). A server is being established to handle GNSS data requests through an NTRIP Caster. Completion of the connectivity of the GNSS remote units to the main acquisition servers is expected to take place within several months. In addition to the 40 units providing real time positioning through the RTX option, Precise Point Positioning (PPP) algorithms are being tested on the CSN main servers to enable real time estimates every second for all GNSS remote devices. Because of the high earthquake productivity rate in Chile, the RTX system capabilities have been positively tested in two cases already, demonstrating their excellent performance: i) the main aftershock (M7.6) of the April 1, 2014, northern Chile event and ii) the April 24, 2017, (M6.9) event in central Chile. The former produced coastal horizontal static displacements of the order of 30 cm while the latter of the order of 5 cm. In addition to rapid earthquake characterization through static deformation, W-phase displacement waveform inversions are included in the fast analysis providing excellent results. These new applications and methodologies have profoundly impacted the rapid evaluation of the tsunamigenic potential of large earthquakes in the near field.

  4. Performance Characterization and Auto-Ignition Performance of a Rapid Compression Machine

    Directory of Open Access Journals (Sweden)

    Hao Liu

    2014-09-01

    Full Text Available A rapid compression machine (RCM test bench is developed in this study. The performance characterization and auto-ignition performance tests are conducted at an initial temperature of 293 K, a compression ratio of 9.5 to 16.5, a compressed temperature of 650 K to 850 K, a driving gas pressure range of 0.25 MPa to 0.7 MPa, an initial pressure of 0.04 MPa to 0.09 MPa, and a nitrogen dilution ratio of 35% to 65%. A new type of hydraulic piston is used to address the problem in which the hydraulic buffer adversely affects the rapid compression process. Auto-ignition performance tests of the RCM are then performed using a DME–O2–N2 mixture. The two-stage ignition delay and negative temperature coefficient (NTC behavior of the mixture are observed. The effects of driving gas pressure, compression ratio, initial pressure, and nitrogen dilution ratio on the two-stage ignition delay are investigated. Results show that both the first-stage and overall ignition delays tend to increase with increasing driving gas pressure. The driving gas pressure within a certain range does not significantly influence the compressed pressure. With increasing compression ratio, the first-stage ignition delay is shortened, whereas the second-stage ignition delay is extended. With increasing initial pressure, both the first-stage and second-stage ignition delays are shortened. The second-stage ignition delay is shortened to a greater extent than that of the first-stage. With increasing nitrogen dilution ratio, the first-stage ignition delay is shortened, whereas the second-stage is extended. Thus, overall ignition delay presents different trends under various compression ratios and compressed pressure conditions.

  5. Characterization of Metarhizium species and varieties based on molecular analysis, heat tolerance and cold activity

    Science.gov (United States)

    Fernandes, E.K.K.; Keyser, C.A.; Chong, J.P.; Rangel, D.E.N.; Miller, M.P.; Roberts, D.W.

    2010-01-01

    Aims: The genetic relationships and conidial tolerances to high and low temperatures were determined for isolates of several Metarhizium species and varieties. Methods and Results: Molecular-based techniques [AFLP and rDNA (ITS1, ITS2 and 5??8S) gene sequencing] were used to characterize morphologically identified Metarhizium spp. isolates from a wide range of sources. Conidial suspensions of isolates were exposed to wet heat (45 ?? 0??2??C) and plated on potato dextrose agar plus yeast extract (PDAY) medium. After 8-h exposure, the isolates divided clearly into two groups: (i) all isolates of Metarhizium anisopliae var. anisopliae (Ma-an) and Metarhizium from the flavoviride complex (Mf) had virtually zero conidial relative germination (RG), (ii) Metarhizium anisopliae var. acridum (Ma-ac) isolates demonstrated high heat tolerance (c. 70-100% RG). Conidial suspensions also were plated on PDAY and incubated at 5??C for 15 days, during which time RGs for Ma-an and Ma-ac isolates were virtually zero, whereas the two Mf were highly cold active (100% RG). Conclusions: Heat and cold exposures can be used as rapid tools to tentatively identify some important Metarhizium species and varieties. Significance and Impact of the Study: Identification of Metarhizium spp. currently relies primarily on DNA-based methods; we suggest a simple temperature-based screen to quickly obtain tentative identification of isolates as to species or species complexes. ?? 2009 The Society for Applied Microbiology.

  6. Structure–performance characterization for carbon molecular sieve membranes using molecular scale gas probes

    KAUST Repository

    Rungta, Meha; Xu, Liren; Koros, William J.

    2015-01-01

    © 2015 Elsevier Ltd. All rights reserved. Understanding the relationship between carbon molecular sieve (CMS) pore structure and corresponding gas separation performance enables optimization for a given gas separation application. The final

  7. Molecular cloning and functional characterization of avian interleukin-19

    Science.gov (United States)

    The present study describes the cloning and functional characterization of avian interleukin (IL)-19, a cytokine that, in mammals, alters the balance of Th1 and Th2 cells in favor of the Th2 phenotype. The full-length avian IL-19 gene, located on chromosome 26, was amplified from LPS-stimulated chi...

  8. Genetic diversity and molecular characterization of physic nut ...

    African Journals Online (AJOL)

    ajl

    2013-02-27

    Feb 27, 2013 ... 2Department of Plant Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil. ... primers were used to characterize toxicity alleles, and none of the accessions presented patterns ... accessions from India (Gupta et al., 2008; Gohil and. Pandya .... ISSR primers, generally low genetic diversity was.

  9. Molecular characterization of Agrotis segetum nucleopolyhedrovirus from Poland

    NARCIS (Netherlands)

    Jakubowska, A.K.; Oers, van M.M.; Ziemnicka, J.; Lipa, J.J.; Vlak, J.M.

    2005-01-01

    The turnip moth, Agrotis segetum (Lepidoptera, Noctuidae), is an important pest insect in Europe, Asia, and Africa. We have genetically characterized and classified a nucleopolyhedrovirus isolated from A. segetum larvae in Poland (AgseNPV-P). The restriction pattern of AgseNPV-P was distinct from an

  10. Molecular characterization and novel genetic variability in leptin ...

    African Journals Online (AJOL)

    The present study was undertaken with the objectives of sequencing, characterization and single nucleotide polymorphisms (SNPs) identification of mithun leptin gene. The mithun leptin gene (3420 bp) was sequenced, compared with other species and phylogenetic tree were constructed. Single-strand conformation ...

  11. Molecular characterization and diversity analysis in chilli pepper ...

    African Journals Online (AJOL)

    India is considered to be the secondary center of diversity of chilli pepper, especially of Capsicum annuum. Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and diversity analysis especially in cultivated species which have low levels of polymorphism. The diversity ...

  12. Molecular characterization of 26S proteasome regulatory subunit in ...

    African Journals Online (AJOL)

    Trichophyton verrucosum is a zoophilic dermatophyte, which causes dermatophytosis infection in human as well as animals. 26S proteasome is an important protein in eukaryotic cells that is involved with degradation of unneeded or damaged proteins, when tagged with ubiquitin. In this study, we characterized the 26S ...

  13. Molecular cloning and characterization of glucose transporter 1 ...

    African Journals Online (AJOL)

    Glucose transporter type-1 (glut1) and citrate synthase plays crucial role in glucose transport and regulation of tricarboxylic acid cycle (TCA) cycle in mammalian energy metabolism. The present study was aimed to clone and characterize glut1 and citrate synthase cDNA in water buffalo (Bubalus bubalis). Total of 90 ...

  14. Molecular characterization of the plum collection [Prunus domestica ...

    African Journals Online (AJOL)

    Eight Random Amplified Microsatellite markers (RAMs) were used to characterize the genetic diversity found in 14 Prunus materials belonging to the deciduous collection of the Pedagogical and Technological University of Colombia. A total of 121 bands were generated: they range from nine for the GT primer to 26 for the ...

  15. Molecular characterization of bovine trypanosomes from the Kachia ...

    African Journals Online (AJOL)

    The PCR assay allowed detection and characterization of three Trypanosoma livestock species namely T. vivax, 13 of 33 was positive; T. congolense forest, 1 of 2 and 1 T. b. brucei. The sizes of base ... For diagnostic purposes, improvement in primer designs for enhancing T. vivax detection in field samples is suggested.

  16. Molecular Characterization of wheat stem rust races in Kenya

    Science.gov (United States)

    Stem or black rust caused by Puccinia graminis f. sp. tritici (Pgt) Erikss. & Henning causes severe losses to wheat (Triticum aestivum L.), historically threatening global wheat production. Characterizing prevalent isolates of Pgt would enhance the knowledge of population dynamics and evolution of t...

  17. Characterization of molecular and elemental impurities in tungsten hexafluoride

    International Nuclear Information System (INIS)

    Streusand, B.J.; Yost, V.E.; Govorchin, S.W.; Fry, R.C.; Padula, F.J.; Hughes, S.K.

    1990-01-01

    Analysis of WF 6 is a very difficult process because of the reactivity of the compound, the low detection limits required by its use in semiconductor processing, and by the presence of large amounts of tungsten in the analyte. It is not possible to perform elemental analysis with low detection limits directly on WF 6 or on hydrolyzed WF 6 . However, it is possible to remove the interfering tungsten by physical and chemical separation techniques. This paper discusses how the analysis of molecular impurities in WF 6 may be accomplished directly in the gas phase by infrared spectroscopy and by gas chromatography

  18. Molecular Characterization of Salmonella Typhimurium Highly Successful Outbreak Strains

    DEFF Research Database (Denmark)

    Petersen, Randi Føns; Litrup, Eva; Larsson, Jonas T.

    2011-01-01

    we detected changes in three of five MLVA loci in a small fraction of isolates. These changes were mainly due to the gain or loss of single repeats. Optical Mapping of the large cluster strain indicated no increased content of virulence genes; however, Optical Mapping did reveal a large insert......, a probable prophage, in the main cluster. This probable prophage may give the cluster strain a competitive advantage. The molecular methods employed suggested that the four clusters represented four distinct strains, although they seemed to be epidemiologically linked and shared genotypic characteristics....

  19. Molecular Characterization of a Catalase from Hydra vulgaris

    OpenAIRE

    Dash, Bhagirathi; Phillips, Timothy D.

    2012-01-01

    Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp ...

  20. Rapid Discovery and Functional Characterization of Terpene Synthases from Four Endophytic Xylariaceae.

    Directory of Open Access Journals (Sweden)

    Weihua Wu

    Full Text Available Endophytic fungi are ubiquitous plant endosymbionts that establish complex and poorly understood relationships with their host organisms. Many endophytic fungi are known to produce a wide spectrum of volatile organic compounds (VOCs with potential energy applications, which have been described as "mycodiesel". Many of these mycodiesel hydrocarbons are terpenes, a chemically diverse class of compounds produced by many plants, fungi, and bacteria. Due to their high energy densities, terpenes, such as pinene and bisabolene, are actively being investigated as potential "drop-in" biofuels for replacing diesel and aviation fuel. In this study, we rapidly discovered and characterized 26 terpene synthases (TPSs derived from four endophytic fungi known to produce mycodiesel hydrocarbons. The TPS genes were expressed in an E. coli strain harboring a heterologous mevalonate pathway designed to enhance terpene production, and their product profiles were determined using Solid Phase Micro-Extraction (SPME and GC-MS. Out of the 26 TPS's profiled, 12 TPS's were functional, with the majority of them exhibiting both monoterpene and sesquiterpene synthase activity.

  1. FIRST RESULTS FROM THE RAPID-RESPONSE SPECTROPHOTOMETRIC CHARACTERIZATION OF NEAR-EARTH OBJECTS USING UKIRT

    Energy Technology Data Exchange (ETDEWEB)

    Mommert, M.; Trilling, D. E.; Petersen, E. [Department of Physics and Astronomy, Northern Arizona University, Flagstaff, AZ 86001 (United States); Borth, D. [Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI), D-67663 Kaiserslautern (Germany); Jedicke, R. [Institute for Astronomy, University of Hawaii at Manoa, Honolulu, HI 96822 (United States); Butler, N. [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Reyes-Ruiz, M. [Universidad Nacional Autónoma de México, Instituto de Astronomía, Ensenada, B.C. 22860, México (Mexico); Pichardo, B. [Instituto de Astronomía, Universidad Nacional Autónoma de México, Ciudad Universitaria, D.F. 04510, México (Mexico); Axelrod, T. [Steward Observatory, University of Arizona, Tucson, AZ 85721 (United States); Moskovitz, N., E-mail: michael.mommert@nau.edu [Lowell Observatory, Flagstaff, AZ 86001 (United States)

    2016-04-15

    Using the Wide Field Camera for the United Kingdom Infrared Telescope (UKIRT), we measure the near-infrared colors of near-Earth objects (NEOs) in order to put constraints on their taxonomic classifications. The rapid-response character of our observations allows us to observe NEOs when they are close to the Earth and bright. Here we present near-infrared color measurements of 86 NEOs, most of which were observed within a few days of their discovery, allowing us to characterize NEOs with diameters of only a few meters. Using machine-learning methods, we compare our measurements to existing asteroid spectral data and provide probabilistic taxonomic classifications for our targets. Our observations allow us to distinguish between S-complex, C/X-complex, D-type, and V-type asteroids. Our results suggest that the fraction of S-complex asteroids in the whole NEO population is lower than the fraction of ordinary chondrites in the meteorite fall statistics. Future data obtained with UKIRT will be used to investigate the significance of this discrepancy.

  2. Design and performance of a 50mK rapid turnaround detector characterization system

    International Nuclear Information System (INIS)

    Benford, Dominic J.; Dipirro, Michael J.; Forgione, Joshua B.; Jackson, Michael L.; Harvey Moseley, S.; Panek, John; Shirron, Peter J.; Staguhn, Johannes G.

    2006-01-01

    Upcoming major NASA missions such as the Einstein Inflation Probe and the Single Aperture Far-Infrared Observatory will require arrays of detectors with thousands of background-limited elements sensitive to wavelengths from ∼50μm to ∼3mm. Because of the low power levels present in space with cryogenic telescopes, these detectors will likely operate at temperatures below 100mK. In order to make rapid progress on detector development, the cryogenic testing cycle must be made convenient and quick. We have developed a cryogenic detector characterization system capable of testing superconducting detector arrays in formats up to 8x32, read out by SQUID multiplexers. The system relies on the cooling of a two-stage adiabatic demagnetization refrigerator immersed in a liquid helium bath. This approach permits a detector to be cooled from 300K to 50mK in under 6h, so that a test cycle begun in the morning will be over by the end of the day. The system is modular, with two identical immersible units, so that while one unit is cooling, the second can be reconfigured for the next battery of tests

  3. Rapid Large Earthquake and Run-up Characterization in Quasi Real Time

    Science.gov (United States)

    Bravo, F. J.; Riquelme, S.; Koch, P.; Cararo, S.

    2017-12-01

    Several test in quasi real time have been conducted by the rapid response group at CSN (National Seismological Center) to characterize earthquakes in Real Time. These methods are known for its robustness and realibility to create Finite Fault Models. The W-phase FFM Inversion, The Wavelet Domain FFM and The Body Wave and FFM have been implemented in real time at CSN, all these algorithms are running automatically and triggered by the W-phase Point Source Inversion. Dimensions (Large and Width ) are predefined by adopting scaling laws for earthquakes in subduction zones. We tested the last four major earthquakes occurred in Chile using this scheme: The 2010 Mw 8.8 Maule Earthquake, The 2014 Mw 8.2 Iquique Earthquake, The 2015 Mw 8.3 Illapel Earthquake and The 7.6 Melinka Earthquake. We obtain many solutions as time elapses, for each one of those we calculate the run-up using an analytical formula. Our results are in agreements with some FFM already accepted by the sicentific comunnity aswell as run-up observations in the field.

  4. Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns

    Directory of Open Access Journals (Sweden)

    Ojurongbe Olusola

    2012-05-01

    Full Text Available Abstract Background Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility. Methods We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET method to genotype four functional SNPs including -986 G > A (#rs3124952, -602 G > A (#rs3124953, -4A > G (#rs17514136 and +6424 G > T (#rs7851696 in the ficolin-2 (FCN2 gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176, Nigerian (n = 180, Vietnamese (n = 172 and European Caucasian ethnicity (n = 165. Results We observed that the genotype distribution of three functional SNP variants (−986 G > A, -602 G > A and -4A > G differ significantly between the populations investigated (p p  Conclusions The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.

  5. Molecular Characterization of a Catalase from Hydra vulgaris

    Science.gov (United States)

    Dash, Bhagirathi; Phillips, Timothy D.

    2012-01-01

    Catalase, an antioxidant and hydroperoxidase enzyme protects the cellular environment from harmful effects of hydrogen peroxide by facilitating its degradation to oxygen and water. Molecular information on a cnidarian catalase and/or peroxidase is, however, limited. In this work an apparent full length cDNA sequence coding for a catalase (HvCatalase) was isolated from Hydra vulgaris using 3’- and 5’- (RLM) RACE approaches. The 1859 bp HvCatalase cDNA included an open reading frame of 1518 bp encoding a putative protein of 505 amino acids with a predicted molecular mass of 57.44 kDa. The deduced amino acid sequence of HvCatalase contained several highly conserved motifs including the heme-ligand signature sequence RLFSYGDTH and the active site signature FXRERIPERVVHAKGXGA. A comparative analysis showed the presence of conserved catalytic amino acids [His(71), Asn(145), and Tyr(354)] in HvCatalase as well. Homology modeling indicated the presence of the conserved features of mammalian catalase fold. Hydrae exposed to thermal, starvation, metal and oxidative stress responded by regulating its catalase mRNA transcription. These results indicated that the HvCatalase gene is involved in the cellular stress response and (anti)oxidative processes triggered by stressor and contaminant exposure. PMID:22521743

  6. Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

    Science.gov (United States)

    Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

    2012-01-01

    Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

  7. Bayesian semiparametric regression models to characterize molecular evolution

    Directory of Open Access Journals (Sweden)

    Datta Saheli

    2012-10-01

    Full Text Available Abstract Background Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Dirichlet process prior on the distribution of the regression coefficients that describes the relationship between the changes in amino acid distances and natural selection in protein-coding DNA sequence alignments. Results The Bayesian semiparametric approach is illustrated with simulated data and the abalone lysin sperm data. Our method identifies groups of properties which, for this particular dataset, have a similar effect on evolution. The model also provides nonparametric site-specific estimates for the strength of conservation of these properties. Conclusions The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, while taking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.

  8. Molecular Characterization of Three Lactobacillus delbrueckii subsp. bulgaricus Phages

    Science.gov (United States)

    Casey, Eoghan; Mahony, Jennifer; O'Connell-Motherway, Mary; Bottacini, Francesca; Cornelissen, Anneleen; Neve, Horst; Heller, Knut J.; Noben, Jean-Paul; Dal Bello, Fabio

    2014-01-01

    In this study, three phages infecting Lactobacillus delbrueckii subsp. bulgaricus, named Ld3, Ld17, and Ld25A, were isolated from whey samples obtained from various industrial fermentations. These phages were further characterized in a multifaceted approach: (i) biological and physical characterization through host range analysis and electron microscopy; (ii) genetic assessment through genome analysis; (iii) mass spectrometry analysis of the structural components of the phages; and (iv), for one phage, transcriptional analysis by Northern hybridization, reverse transcription-PCR, and primer extension. The three obtained phage genomes display high levels of sequence identity to each other and to genomes of the so-called group b L. delbrueckii phages c5, LL-Ku, and phiLdb, where some of the observed differences are believed to be responsible for host range variations. PMID:25002431

  9. Molecular characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages.

    Science.gov (United States)

    Casey, Eoghan; Mahony, Jennifer; O'Connell-Motherway, Mary; Bottacini, Francesca; Cornelissen, Anneleen; Neve, Horst; Heller, Knut J; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

    2014-09-01

    In this study, three phages infecting Lactobacillus delbrueckii subsp. bulgaricus, named Ld3, Ld17, and Ld25A, were isolated from whey samples obtained from various industrial fermentations. These phages were further characterized in a multifaceted approach: (i) biological and physical characterization through host range analysis and electron microscopy; (ii) genetic assessment through genome analysis; (iii) mass spectrometry analysis of the structural components of the phages; and (iv), for one phage, transcriptional analysis by Northern hybridization, reverse transcription-PCR, and primer extension. The three obtained phage genomes display high levels of sequence identity to each other and to genomes of the so-called group b L. delbrueckii phages c5, LL-Ku, and phiLdb, where some of the observed differences are believed to be responsible for host range variations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  10. Fulleropyrrolidine end-capped molecular wires for molecular electronics--synthesis, spectroscopic, electrochemical, and theoretical characterization

    DEFF Research Database (Denmark)

    Sørensen, Jakob Kryger; Fock, Jeppe; Pedersen, Anders Holmen

    2011-01-01

    In continuation of previous studies showing promising metal-molecule contact properties a variety of C(60) end-capped "molecular wires" for molecular electronics were prepared by variants of the Prato 1,3-dipolar cycloaddition reaction. Either benzene or fluorene was chosen as the central wire...... state. However, the fluorescence of C(60) was quenched by charge transfer from the wire to C(60). Quantum chemical calculations predict and explain the collapse of coherent electronic transmission through one of the fulleropyrrolidine-terminated molecular wires......., and synthetic protocols for derivatives terminated with one or two fullero[c]pyrrolidine "electrode anchoring" groups were developed. An aryl-substituted aziridine could in some cases be employed directly as the azomethine ylide precursor for the Prato reaction without the need of having an electron...

  11. Phenotypical and molecular characterization of portuguese usher syndrome patients

    OpenAIRE

    Nunes, Jóni Luís Soares

    2015-01-01

    Trabalho final de mestrado integrado em Medicina (Oftalmologia), apresentado à Faculdade de Medicina da Universidade de Coimbra. Introduction: Usher syndrome (USH) is a recessive inherited disease characterized by sensorineural hearing loss (HL), visual loss due to retinitis pigmentosa (RP) and, in some cases, vestibular dysfunction. This syndrome is the most common cause that affects those two major senses, vision and hearing and encompasses three clinical sub-types (USH1, USH2 a...

  12. Molecular characterization of the African orthobunyavirus Ilesha virus

    Czech Academy of Sciences Publication Activity Database

    Pachler, K.; Růžek, Daniel; Nowotny, N.

    2013-01-01

    Roč. 20, DEC 2013 (2013), s. 124-130 ISSN 1567-1348 R&D Projects: GA ČR GAP502/11/2116 Grant - others:GA MŠk(CZ) ED0006/01/01 Institutional support: RVO:60077344 Keywords : Ilesha virus * Orthobunyavirus * Genome characterization * Phylogenetic analysis Subject RIV: EE - Microbiology, Virology Impact factor: 3.264, year: 2013

  13. Molecular dynamics characterization of as-implanted damage in silicon

    International Nuclear Information System (INIS)

    Santos, Ivan; Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Barbolla, Juan

    2005-01-01

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions

  14. Molecular dynamics characterization of as-implanted damage in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ivan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)]. E-mail: ivasan@ele.uva.es; Marques, Luis A. [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Pelaz, Lourdes [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Lopez, Pedro [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Aboy, Maria [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Barbolla, Juan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)

    2005-12-05

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions.

  15. Characterization of molecular outflows in the substellar domain

    International Nuclear Information System (INIS)

    Phan-Bao, Ngoc; Dang-Duc, Cuong; Lee, Chin-Fei; Ho, Paul T. P.; Li, Di

    2014-01-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M J , which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10 –6 M ☉ to 2.9 × 10 –5 M ☉ and an outflow mass-loss rate from 2.7 × 10 –9 M ☉ yr –1 to 4.1 × 10 –8 M ☉ yr –1 . These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M J in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M J in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  16. Characterization of molecular outflows in the substellar domain

    Energy Technology Data Exchange (ETDEWEB)

    Phan-Bao, Ngoc; Dang-Duc, Cuong [Department of Physics, International University-Vietnam National University HCM, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City (Viet Nam); Lee, Chin-Fei; Ho, Paul T. P. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 106, Taiwan (China); Li, Di, E-mail: pbngoc@hcmiu.edu.vn, E-mail: pbngoc@asiaa.sinica.edu.tw [National Astronomical Observatories, Chinese Academy of Science, Chaoyang District Datun Rd A20, Beijing (China)

    2014-11-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M {sub J}, which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10{sup –6} M {sub ☉} to 2.9 × 10{sup –5} M {sub ☉} and an outflow mass-loss rate from 2.7 × 10{sup –9} M {sub ☉} yr{sup –1} to 4.1 × 10{sup –8} M {sub ☉} yr{sup –1}. These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M {sub J} in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M {sub J} in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  17. Boronate esters: Synthesis, characterization and molecular base receptor analysis

    Science.gov (United States)

    Gómez-Jaimes, Gelen; Barba, Victor

    2014-10-01

    The synthesis of three boronate esters obtained by reacting 4-fluorophenylboronic (1), 4-iodophenylboronic (2) and 3,4-chlorophenylboronic (3) acids with 2,4,5-trihidroxybenzaldehyde is reported. The structural characterization was determined by spectroscopic and spectrometric techniques. The boron atom was evaluated to acts as Lewis acid center in the reaction with pyridine (Py), triethylamine (TEA) and fluoride anion (F-). The titration method was followed by UV-Vis and 11B NMR spectroscopy; results indicate the good interaction with the fluoride ion but poor coordination towards pyridine in solution.

  18. Synthesis and characterization of lanthanum incorporated mesoporous molecular sieves

    International Nuclear Information System (INIS)

    Pesquera, C.; Gonzalez, F.; Blanco, C.; Sanchez, L.

    2004-01-01

    A series of mesoporous materials under reflux conditions have been synthesized with two silicon sources (fumed silica and sodium silicate) and lanthanum added. The following Si/La molar ratio was used in the samples: 100; 75; 50 and 25. The calcined products were characterized by means of X-ray diffraction, nitrogen adsorption isotherms and energy dispersive X-ray spectrometry (EDS). The BET surface area gradually decreases with an increase in the lanthanum content of the LaxMCM-41 samples. Moreover, the average pore size tends to decrease along with the increase in the La content in the samples

  19. Novel Materials for Molecular Electronics and their Characterization

    Directory of Open Access Journals (Sweden)

    Martin Weis

    2006-01-01

    Full Text Available Defect-free diacetylene (DA Langmuir-Blodgett films polymerized on a air/water interface have various¨applications in biosensors, membrane physics or low-dimensional physics. Polymerization of DA monolayers is in general way characterized by optical spectroscopy. In this study for evaluation of photopolymerization process for the first time the Maxwell displacement current (MDC measuring technique was used. In experiment MDC flows through the metalelectrode/air gap/Langmuir monolayer/water surface structure. The effect of polymerization as well as the phase transition of polymerized DA was observed. Moreover PDA domain creation and homogenization was registered.

  20. Characterizing the Frequency and Elevation of Rapid Drainage Events in West Greenland

    Science.gov (United States)

    Cooley, S.; Christoffersen, P.

    2016-12-01

    Rapid drainage of supraglacial lakes on the Greenland Ice Sheet is critical for the establishment of surface-to-bed hydrologic connections and the subsequent transfer of water from surface to bed. Yet, estimates of the number and spatial distribution of rapidly draining lakes vary widely due to limitations in the temporal frequency of image collection and obscureness by cloud. So far, no study has assessed the impact of these observation biases. In this study, we examine the frequency and elevation of rapidly draining lakes in central West Greenland, from 68°N to 72.6°N, and we make a robust statistical analysis to estimate more accurately the likelihood of lakes draining rapidly. Using MODIS imagery and a fully automated lake detection method, we map more than 500 supraglacial lakes per year over a 63000 km2 study area from 2000-2015. Through testing four different definitions of rapidly draining lakes from previously published studies, we find that the number of rapidly draining lakes varies from 3% to 38%. Logistic regression between rapid drainage events and image sampling frequency demonstrates that the number of rapid drainage events is strongly dependent on cloud-free observation percentage. We then develop three new drainage criteria and apply an observation bias correction that suggests a true rapid drainage probability between 36% and 45%, considerably higher than previous studies without bias assessment have reported. We find rapid-draining lakes are on average larger and disappear earlier than slow-draining lakes, and we also observe no elevation differences for the lakes detected as rapidly draining. We conclude a) that methodological problems in rapid drainage research caused by observation bias and varying detection methods have obscured large-scale rapid drainage characteristics and b) that the lack of evidence for an elevation limit on rapid drainage suggests surface-to-bed hydrologic connections may continue to propagate inland as climate warms.

  1. Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

    Science.gov (United States)

    Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

    2017-11-01

    Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

  2. Rapid molecular assays for the detection of yellow fever virus in low-resource settings.

    Science.gov (United States)

    Escadafal, Camille; Faye, Oumar; Sall, Amadou Alpha; Faye, Ousmane; Weidmann, Manfred; Strohmeier, Oliver; von Stetten, Felix; Drexler, Josef; Eberhard, Michael; Niedrig, Matthias; Patel, Pranav

    2014-03-01

    Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV), is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control. The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA) assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay) to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal. The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction) and rapid processing time (<20 min). Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for YFV detection in low-resource settings.

  3. The SUCCESS model for laboratory performance and execution of rapid molecular diagnostics in patients with sepsis.

    Science.gov (United States)

    Dekmezian, Mhair; Beal, Stacy G; Damashek, Mary Jane; Benavides, Raul; Dhiman, Neelam

    2015-04-01

    Successful performance and execution of rapid diagnostics in a clinical laboratory hinges heavily on careful validation, accurate and timely communication of results, and real-time quality monitoring. Laboratories must develop strategies to integrate diagnostics with stewardship and evidence-based clinical practice guidelines. We present a collaborative SUCCESS model for execution and monitoring of rapid sepsis diagnostics to facilitate timely treatment. Six months after execution of the Verigene Gram-Positive Blood Culture (BC-GP) and the AdvanDx PNA-FISH assays, data were collected on 579 and 28 episodes of bacteremia and fungemia, respectively. Clinical testing was executed using a SUCCESS model comprising the following components: stewardship, utilization of resources, core strategies, concierge services, education, support, and surveillance. Stewardship needs were identified by evaluating the specialty services benefiting from new testing. Utilization of resources was optimized by reviewing current treatment strategies and antibiogram and formulary options. Core strategies consisted of input from infectious disease leadership, pharmacy, and laboratory staff. Concierge services included automated Micro-eUpdate and physician-friendly actionable reports. Education modules were user-specific, and support was provided through a dedicated 24/7 microbiology hotline. Surveillance was performed by daily audit by the director. Using the SUCCESS model, the turnaround time for the detailed report with actionable guidelines to the physician was ∼3 hours from the time of culture positivity. The overall correlation between rapid methods and culture was 94% (546/579). Discrepant results were predominantly contaminants such as a coagulase-negative staphylococci or viridans streptococci in mixed cultures. SUCCESS is a cost-effective and easily adaptable model for clinical laboratories with limited stewardship resources.

  4. Rapid molecular assays for the detection of yellow fever virus in low-resource settings.

    Directory of Open Access Journals (Sweden)

    Camille Escadafal

    2014-03-01

    Full Text Available BACKGROUND: Yellow fever (YF is an acute viral hemorrhagic disease transmitted by Aedes mosquitoes. The causative agent, the yellow fever virus (YFV, is found in tropical and subtropical areas of South America and Africa. Although a vaccine is available since the 1930s, YF still causes thousands of deaths and several outbreaks have recently occurred in Africa. Therefore, rapid and reliable diagnostic methods easy to perform in low-resources settings could have a major impact on early detection of outbreaks and implementation of appropriate response strategies such as vaccination and/or vector control. METHODOLOGY: The aim of this study was to develop a YFV nucleic acid detection method applicable in outbreak investigations and surveillance studies in low-resource and field settings. The method should be simple, robust, rapid and reliable. Therefore, we adopted an isothermal approach and developed a recombinase polymerase amplification (RPA assay which can be performed with a small portable instrument and easy-to-use lyophilized reagents. The assay was developed in three different formats (real-time with or without microfluidic semi-automated system and lateral-flow assay to evaluate their application for different purposes. Analytical specificity and sensitivity were evaluated with a wide panel of viruses and serial dilutions of YFV RNA. Mosquito pools and spiked human plasma samples were also tested for assay validation. Finally, real-time RPA in portable format was tested under field conditions in Senegal. CONCLUSION/SIGNIFICANCE: The assay was able to detect 20 different YFV strains and demonstrated no cross-reactions with closely related viruses. The RPA assay proved to be a robust, portable method with a low detection limit (<21 genome equivalent copies per reaction and rapid processing time (<20 min. Results from real-time RPA field testing were comparable to results obtained in the laboratory, thus confirming our method is suitable for

  5. Isolation and molecular characterization of Newcastle disease viruses from raptors.

    Science.gov (United States)

    Jindal, Naresh; Chander, Yogesh; Primus, Alexander; Redig, Patrick T; Goyal, Sagar M

    2010-12-01

    The present study was undertaken to detect and characterize Newcastle disease virus (NDV) in raptors. Cloacal and oropharyngeal swab samples were collected from 60 casualty raptors during January to March 2009 in Minnesota. Inoculation of all these samples (n=120) in 9-day-old embryonated hens' eggs resulted in isolation of haemagglutinating viruses in three samples from two bald eagles and one great horned owl. These three haemagglutinating viruses were confirmed as NDV by reverse transcription-polymerase chain reaction (RT-PCR) using fusion gene-specific primers, and were negative for avian influenza virus by RT-PCR. Further characterization revealed that all three possessed (112)GKQGRL(117) at the fusion gene cleavage site, indicating that they were lentogenic strains. Phylogenetic analysis revealed that all three isolates clustered with published class II genotype II NDVs. The nucleotide sequence homology of the three NDV isolates among themselves was 98.4 to 99.6% and the sequence homology with lentogenic strains from wild birds used for comparison varied between 94.5 and 100%. Detection of NDV strains from raptors merits further epidemiological studies to determine the prevalence of different NDV strains in raptors and their impact in relation to transmission to domestic poultry.

  6. [Molecular characterization of Echinococcus granulosus isolates obtained from different hosts].

    Science.gov (United States)

    Erdoğan, Emrah; Özkan, Bora; Mutlu, Fatih; Karaca, Serkan; Şahin, İzzet

    2017-01-01

    Echinococcus granulosus is a parasite that can be seen throughout the world. So far, five species of genus Echinococcus have been identified as parasite in people: E.granulosus, E.multilocularis, E.vogeli, E.oligarthrus, E.shiquicus. Larval (metacestod) form of parasite settles in internal organs of hoofed animals (cattle, goats, pigs, horses, sheep, etc.) and human; the adult form is found in small intestine of final host, canine. Disease caused by parasite called as "Cystic echinococcosis" (CE) is an important health problem and causes economic losses in many countries including our country that livestock is common. Infective eggs cause infections in intermediate hosts by taking oral way and rarely inhalation. Received egg opens in the stomach and intestines of intermediate host and oncosphere is released. Oncosphere quickly reaches the lamina propria of the villus epithelium by its histolytic enzymes and hooks. It usually transported from here to the liver and lungs, less frequently, muscle, brain, spleen, kidney and to other organs through the veins. By molecular studies, five species have been validated taxonomically and 10 different variants or strains of E.granulosus have been identified. Host and developmental differences between strains may negatively affect control studies and fight against the parasite. This study aimed to determinate E.granulosus strains obtained from cyst material of different intermediate hosts from different regions of Turkey by molecular methods. In the study, 25 human, 8 cattle, 6 sheep and 2 goat cysts material has been collected. Total genomic DNA was isolated from protoscoleces in cyst fluid and analyzed by PCR with COX-1 (L) and COX-1 (S) genes specific primers. DNA sequence analysis for each PCR product has been made. DNA sequence analysis results evaluated phylogenetically by MEGA analyze and BLAST software. As a result of this study, all isolates were identified as E.granulosus sensu stricto (G1) by DNA sequence analysis. CE

  7. Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Ortiz, Pedro; Cabrera, Maria; Hobán, Cristian; Itagaki, Tadashi

    2016-06-01

    The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru. Copyright © 2015. Published by Elsevier Ireland Ltd.

  8. Rapid and molecular selective electrochemical sensing of phthalates in aqueous solution

    KAUST Repository

    Zia, Asif I.

    2015-05-01

    Reported research work presents real time non-invasive detection of phthalates in spiked aqueous samples by employing electrochemical impedance spectroscopy (EIS) technique incorporating a novel interdigital capacitive sensor with multiple sensing thin film gold micro-electrodes fabricated on native silicon dioxide layer grown on semiconducting single crystal silicon wafer. The sensing surface was functionalized by a self-assembled monolayer of 3-aminopropyltrietoxysilane (APTES) with embedded molecular imprinted polymer (MIP) to introduce selectivity for the di(2-ethylhexyl) phthalate (DEHP) molecule. Various concentrations (1-100. ppm) of DEHP in deionized MilliQ water were tested using the functionalized sensing surface to capture the analyte. Frequency response analyzer (FRA) algorithm was used to obtain impedance spectra so as to determine sample conductance and capacitance for evaluation of phthalate concentration in the sample solution. Spectrum analysis algorithm interpreted the experimentally obtained impedance spectra by applying complex nonlinear least square (CNLS) curve fitting in order to obtain electrochemical equivalent circuit and corresponding circuit parameters describing the kinetics of the electrochemical cell. Principal component analysis was applied to deduce the effects of surface immobilized molecular imprinted polymer layer on the evaluated circuit parameters and its electrical response. The results obtained by the testing system were validated using commercially available high performance liquid chromatography diode array detector system.

  9. Identification and molecular characterization of Parkin in Clonorchis sinensis.

    Science.gov (United States)

    Bai, Xuelian; Kim, Tae Im; Lee, Ji-Yun; Dai, Fuhong; Hong, Sung-Jong

    2015-02-01

    Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to Zn(2+) were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis.

  10. Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

    International Nuclear Information System (INIS)

    Hasan, Nor’Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

    2016-01-01

    Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management

  11. Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

    Science.gov (United States)

    Hasan, Nor'Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

    2016-02-01

    Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

  12. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  13. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

    Science.gov (United States)

    Robertson, A Gordon; Kim, Jaegil; Al-Ahmadie, Hikmat; Bellmunt, Joaquim; Guo, Guangwu; Cherniack, Andrew D; Hinoue, Toshinori; Laird, Peter W; Hoadley, Katherine A; Akbani, Rehan; Castro, Mauro A A; Gibb, Ewan A; Kanchi, Rupa S; Gordenin, Dmitry A; Shukla, Sachet A; Sanchez-Vega, Francisco; Hansel, Donna E; Czerniak, Bogdan A; Reuter, Victor E; Su, Xiaoping; de Sa Carvalho, Benilton; Chagas, Vinicius S; Mungall, Karen L; Sadeghi, Sara; Pedamallu, Chandra Sekhar; Lu, Yiling; Klimczak, Leszek J; Zhang, Jiexin; Choo, Caleb; Ojesina, Akinyemi I; Bullman, Susan; Leraas, Kristen M; Lichtenberg, Tara M; Wu, Catherine J; Schultz, Nicholaus; Getz, Gad; Meyerson, Matthew; Mills, Gordon B; McConkey, David J; Weinstein, John N; Kwiatkowski, David J; Lerner, Seth P

    2017-10-19

    We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Molecular Characterization of Two Major Dengue Outbreaks in Costa Rica.

    Science.gov (United States)

    Soto-Garita, Claudio; Somogyi, Teresita; Vicente-Santos, Amanda; Corrales-Aguilar, Eugenia

    2016-07-06

    Dengue virus (DENV) (Flavivirus, Flaviviridae) is a reemerging arthropod-borne virus with a worldwide circulation, transmitted mainly by Aedes aegypti and Aedes albopictus mosquitoes. Since the first detection of its main transmitting vector in 1992 and the invasion of DENV-1 in 1993, Costa Rica has faced dengue outbreaks yearly. In 2007 and 2013, Costa Rica experienced two of the largest outbreaks in terms of total and severe cases. To provide genetic information about the etiologic agents producing these outbreaks, we conducted phylogenetic analysis of viruses isolated from human samples. A total of 23 DENV-1 and DENV-2 sequences were characterized. These analyses signaled that DENV-1 genotype V and DENV-2 American/Asian genotype were circulating in those outbreaks. Our results suggest that the 2007 and 2013 outbreak viral strains of DENV-1 and DENV-2 originated from nearby countries and underwent in situ microevolution. © The American Society of Tropical Medicine and Hygiene.

  15. Rapid radiological characterization method based on the use of dose coefficients

    International Nuclear Information System (INIS)

    Dulama, C.; Toma, Al.; Dobrin, R.; Valeca, M.

    2010-01-01

    Intervention actions in case of radiological emergencies and exploratory radiological surveys require rapid methods for the evaluation of the range and extent of contamination. When simple and homogeneous radionuclide composition characterize the radioactive contamination, surrogate measurements can be used to reduce the costs implied by laboratory analyses and to speed-up the process of decision support. A dose-rate measurement-based methodology can be used in conjunction with adequate dose coefficients to assess radionuclide inventories and to calculate dose projections for various intervention scenarios. The paper presents the results obtained for dose coefficients in some particular exposure geometries and the methodology used for deriving dose rate guidelines from activity concentration upper levels specified as contamination limits. All calculations were performed by using the commercial software MicroShield from Grove Software Inc. A test case was selected as to meet the conditions from EPA Federal Guidance Report no. 12 (FGR12) concerning the evaluation of dose coefficients for external exposure from contaminated soil and the obtained results were compared to values given in the referred document. The geometries considered as test cases are: contaminated ground surface; - infinite extended homogeneous surface contamination and soil contaminated to a depth of 15 cm. As shown by the results, the values agree within 50% relative difference for most of the cases. The greatest discrepancies were observed for depth contamination simulation and in the case of radionuclides with complicated gamma emission and this is due to the different approach from MicroShield and FGR12. A case study is presented for validation of the methodology, where both dose rate measurements and laboratory analyses were performed on an extended quasi-homogeneous NORM contamination. The dose rate estimations obtained by applying the dose coefficients to the radionuclide concentrations

  16. Molecular characterization of novel sulfotransferases from the tick, Ixodes scapularis

    Directory of Open Access Journals (Sweden)

    King Roberta S

    2011-06-01

    Full Text Available Abstract Background Ixodes scapularis, commonly known as the blacklegged or deer tick, is the main vector of Lyme disease in the United States. Recent progress in transcriptome research has uncovered hundreds of different proteins expressed in the salivary glands of hard ticks, the majority of which have no known function, and include many novel protein families. We recently identified transcripts coding for two putative cytosolic sulfotransferases in these ticks which recognized phenolic monoamines as their substrates. In this current study, we characterize the genetic expression of these two cytosolic sulfotransferases throughout the tick life cycle as well as the enzymatic properties of the corresponding recombinant proteins. Interestingly, the resultant recombinant proteins showed sulfotransferase activity against both neurotransmitters dopamine and octopamine. Results The two sulfotransferase genes were coded as Ixosc SULT 1 & 2 and corresponding proteins were referred as Ixosc Sult 1 and 2. Using gene-specific primers, the sulfotransferase transcripts were detected throughout the blacklegged tick life cycle, including eggs, larvae, nymphs, adult salivary glands and adult midgut. Notably, the mRNA and protein levels were altered upon feeding during both the larval and nymphal life stages. Quantitative PCR results confirm that Ixosc SULT1 was statistically increased upon blood feeding while Ixosc SULT 2 was decreased. This altered expression led us to further characterize the function of these proteins in the Ixodid tick. The sulfotransferase genes were cloned and expressed in a bacterial expression system, and purified recombinant proteins Ixosc Sult 1(R and 2(R showed sulfotransferase activity against neurotransmitters dopamine and octopamine as well as the common sulfotransferase substrate p-nitrophenol. Thus, dopamine- or octopamine-sulfonation may be involved in altering the biological signal for salivary secretion in I. scapularis

  17. Molecular and biochemical characterization of carbonic anhydrases of Paracoccidioides

    Directory of Open Access Journals (Sweden)

    Mariana Vieira Tomazett

    Full Text Available Abstract Carbonic anhydrases (CA belong to the family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the present work, we characterized the cDNAs of four Paracoccidioides CAs (CA1, CA2, CA3, and CA4. In the presence of CO2, there was not a significant increase in fungal ca1, ca2 and ca4 gene expression. The ca1 transcript was induced during the mycelium-to-yeast transition, while ca2 and ca4 gene expression was much higher in yeast cells, when compared to mycelium and mycelium-to-yeast transition. The ca1 transcript was induced in yeast cells recovered directly from liver and spleen of infected mice, while transcripts for ca2 and ca4 were down-regulated. Recombinant CA1 (rCA1 and CA4 (rCA4, with 33 kDa and 32 kDa respectively, were obtained from bacteria. The enzymes rCA1 (β-class and rCA4 (α-class were characterized regarding pH, temperature, ions and amino acids addition influence. Both enzymes were stable at pHs 7.5-8.5 and temperatures of 30-35 °C. The enzymes were dramatically inhibited by Hg+2 and activated by Zn+2, while only rCA4 was stimulated by Fe2+. Among the amino acids tested (all in L configuration, arginine, lysine, tryptophan and histidine enhanced residual activity of rCA1 and rCA4.

  18. Molecular and biochemical characterization of carbonic anhydrases of Paracoccidioides.

    Science.gov (United States)

    Tomazett, Mariana Vieira; Zanoelo, Fabiana Fonseca; Bailão, Elisa Flávia Cardoso; Bailão, Alexandre Melo; Borges, Clayton Luiz; Soares, Célia Maria de Almeida

    2016-01-01

    Carbonic anhydrases (CA) belong to the family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide to bicarbonate. In the present work, we characterized the cDNAs of four Paracoccidioides CAs (CA1, CA2, CA3, and CA4). In the presence of CO2, there was not a significant increase in fungal ca1, ca2 and ca4 gene expression. The ca1 transcript was induced during the mycelium-to-yeast transition, while ca2 and ca4 gene expression was much higher in yeast cells, when compared to mycelium and mycelium-to-yeast transition. The ca1 transcript was induced in yeast cells recovered directly from liver and spleen of infected mice, while transcripts for ca2 and ca4 were down-regulated. Recombinant CA1 (rCA1) and CA4 (rCA4), with 33 kDa and 32 kDa respectively, were obtained from bacteria. The enzymes rCA1 (β-class) and rCA4 (α-class) were characterized regarding pH, temperature, ions and amino acids addition influence. Both enzymes were stable at pHs 7.5-8.5 and temperatures of 30-35 °C. The enzymes were dramatically inhibited by Hg+2 and activated by Zn+2, while only rCA4 was stimulated by Fe2+. Among the amino acids tested (all in L configuration), arginine, lysine, tryptophan and histidine enhanced residual activity of rCA1 and rCA4.

  19. Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): Evidence for rapid diversification and host shifts in spider wasps.

    Science.gov (United States)

    Rodriguez, Juanita; Pitts, James P; Florez, Jaime A; Bond, Jason E; von Dohlen, Carol D

    2016-01-01

    Pompilinae is one of the largest subfamilies of spider wasps (Pompilidae). Most pompilines are generalist spider predators at the family level, but some taxa exhibit ecological specificity (i.e., to spider-host guild). Here we present the first molecular phylogenetic analysis of Pompilinae, toward the aim of evaluating the monophyly of tribes and genera. We further test whether changes in the rate of diversification are associated with host-guild shifts. Molecular data were collected from five nuclear loci (28S, EF1-F2, LWRh, Wg, Pol2) for 76 taxa in 39 genera. Data were analyzed using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results were compared with previous hypotheses of subfamilial and tribal classification, as well as generic relationships in the subfamily. The classification of Pompilus and Agenioideus is also discussed. A Bayesian relaxed molecular clock analysis was used to examine divergence times. Diversification rate-shift tests accounted for taxon-sampling bias using ML and BI approaches. Ancestral host family and host guild were reconstructed using MP and ML methods. Ancestral host guild for all Pompilinae, for the ancestor at the node where a diversification rate-shift was detected, and two more nodes back in time was inferred using BI. In the resulting phylogenies, Aporini was the only previously proposed monophyletic tribe. Several genera (e.g., Pompilus, Microphadnus and Schistonyx) are also not monophyletic. Dating analyses produced a well-supported chronogram consistent with topologies from BI and ML results. The BI ancestral host-use reconstruction inferred the use of spiders belonging to the guild "other hunters" (frequenting the ground and vegetation) as the ancestral state for Pompilinae. This guild had the highest probability for the ML reconstruction and was equivocal for the MP reconstruction; various switching events to other guilds occurred throughout the evolution of the group. The diversification of

  20. Molecular characterization of dissolved organic matter (DOM): a critical review.

    Science.gov (United States)

    Nebbioso, Antonio; Piccolo, Alessandro

    2013-01-01

    Advances in water chemistry in the last decade have improved our knowledge about the genesis, composition, and structure of dissolved organic matter, and its effect on the environment. Improvements in analytical technology, for example Fourier-transform ion cyclotron (FT-ICR) mass spectrometry (MS), homo and hetero-correlated multidimensional nuclear magnetic resonance (NMR) spectroscopy, and excitation emission matrix fluorimetry (EEMF) with parallel factor (PARAFAC) analysis for UV-fluorescence spectroscopy have resulted in these advances. Improved purification methods, for example ultrafiltration and reverse osmosis, have enabled facile desalting and concentration of freshly collected DOM samples, thereby complementing the analytical process. Although its molecular weight (MW) remains undefined, DOM is described as a complex mixture of low-MW substances and larger-MW biomolecules, for example proteins, polysaccharides, and exocellular macromolecules. There is a general consensus that marine DOM originates from terrestrial and marine sources. A combination of diagenetic and microbial processes contributes to its origin, resulting in refractory organic matter which acts as carbon sink in the ocean. Ocean DOM is derived partially from humified products of plants decay dissolved in fresh water and transported to the ocean, and partially from proteinaceous and polysaccharide material from phytoplankton metabolism, which undergoes in-situ microbial processes, becoming refractory. Some of the DOM interacts with radiation and is, therefore, defined as chromophoric DOM (CDOM). CDOM is classified as terrestrial, marine, anthropogenic, or mixed, depending on its origin. Terrestrial CDOM reaches the oceans via estuaries, whereas autochthonous CDOM is formed in sea water by microbial activity; anthropogenic CDOM is a result of human activity. CDOM also affects the quality of water, by shielding it from solar radiation, and constitutes a carbon sink pool. Evidence in support

  1. Rapid and Accurate Molecular Identification of the Emerging Multidrug-Resistant Pathogen Candida auris.

    Science.gov (United States)

    Kordalewska, Milena; Zhao, Yanan; Lockhart, Shawn R; Chowdhary, Anuradha; Berrio, Indira; Perlin, David S

    2017-08-01

    Candida auris is an emerging multidrug-resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper, we present fast, robust, easy-to-perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii , Candida haemulonii , and Candida lusitaniae Targeting rDNA region nucleotide sequences, primers specific for C. auris only or C. auris and related species were designed. A panel of 140 clinical fungal isolates was used in both PCR and real-time PCR assays followed by electrophoresis or melting temperature analysis, respectively. The identification results from the assays were 100% concordant with DNA sequencing results. These molecular assays overcome the deficiencies of existing phenotypic tests to identify C. auris and related species. Copyright © 2017 Kordalewska et al.

  2. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Peter Eastman

    2017-07-01

    Full Text Available OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.

  3. Synthesis and Characterization of Magnesium Substituted Aluminophosphate Molecular Sieves with AEL Structure

    Institute of Scientific and Technical Information of China (English)

    Benjing Xu; Ling Qian; Xinmei Liu; Chunmin Song; Zifeng Yan

    2004-01-01

    MAPO-11 molecular sieves were synthesized by hydrothermal methods. The influence of precursor of magnesium, Mg/Al ratio, synthesis temperature, synthesis time and the type of template on the formation and properties of MAPO-11 molecular sieves was examined. The samples were characterized by the techniques of X-ray diffraction (XRD), scanning electron microscopy (SEM), thermogravimetric/differential thermogravimetric analysis (TG-DGA), etc. The results show that the shape and size of crystal were influenced by the precursor of Mg, the Mg/Al ratio and the type of template, and the TG-DGA analysis shows that MAPO-11 molecular sieves as-synthesized have poor thermal stability.

  4. Molecular characterization of enolase gene from Taenia multiceps.

    Science.gov (United States)

    Li, W H; Qu, Z G; Zhang, N Z; Yue, L; Jia, W Z; Luo, J X; Yin, H; Fu, B Q

    2015-10-01

    Taenia multiceps is a cestode parasite with its larval stage, known as Coenurus cerebralis, mainly encysts in the central nervous system of sheep and other livestocks. Enolase is a key glycolytic enzyme and represents multifunction in most organisms. In the present study, a 1617bp full-length cDNA encoding enolase was cloned from T. multiceps and designated as TmENO. A putative encoded protein of 433 amino acid residues that exhibited high similarity to helminth parasites. The recombinant TmENO protein (rTmENO) showed the catalytic and plasminogen-binding characteristics after the TmENO was subcloned and expressed in the pET30a(+) vector. The TmENO gene was transcribed during the adult and larval stages and was also identified in both cyst fluid and as a component of the adult worms and the metacestode by western blot analysis. Taken together, our results will facilitate further structural characterization for TmENO and new potential control strategies for T. multiceps. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Molecular characterization and analysis of the porcine NURR1 gene

    Directory of Open Access Journals (Sweden)

    Knud Larsen

    2016-12-01

    Here we report the isolation and characterization of porcine NURR1 cDNA. The NURR1 cDNA was RT-PCR cloned using NURR1-specific oligonucleotide primers derived from in silico sequences. The porcine NURR1 cDNA encodes a polypeptide of 598 amino acids, displaying a very high similarity with bovine, human and mouse (99% NURR1 protein. Expression analysis revealed a differential NURR1 mRNA expression in various organs and tissues. NURR1 transcripts could be detected as early as at 60 days of embryo development in different brain tissues. A significant increase in NURR1 transcript in the cerebellum and a decrease in NURR1 transcript in the basal ganglia was observed during embryo development. The porcine NURR1 gene was mapped to chromosome 15. Two missense mutations were found in exon 3, the first coding exon of NURR1. Methylation analysis of the porcine NURR1 gene body revealed a high methylation degree in brain tissue, whereas methylation of the promoter was very low. A decrease in DNA methylation in a discrete region of the NURR1 promoter was observed in pig frontal cortex during pig embryo development. This observation correlated with an increase in NURR1 transcripts. Therefore, methylation might be a determinant of NURR1 expression at certain time points in embryo development.

  6. Molecular characterization of canine parvovirus in Vientiane, Laos.

    Science.gov (United States)

    Vannamahaxay, Soulasack; Vongkhamchanh, Souliya; Intanon, Montira; Tangtrongsup, Sahatchai; Tiwananthagorn, Saruda; Pringproa, Kidsadagon; Chuammitri, Phongsakorn

    2017-05-01

    The global emergence of canine parvovirus type 2c (CPV-2c) has been well documented. In the present study, 139 rectal swab samples collected from diarrheic dogs living in Vientiane, Laos, in 2016 were tested for the presence of the canine parvovirus (CPV) VP2 gene by PCR. The results showed that 82.73% (115/139) of dogs were CPV positive by PCR. The partial VP2 gene was sequenced in 94 of the positive samples; 91 samples belonged to CPV-2c (426Glu) subtype, while 3 samples belonged to the CPV-2a (426Asn) subtype. Notably, phylogenetic analysis of amino acid sequences revealed a close relationship between Laotian isolates and novel Chinese CPV-2c isolates. In Laotian CPV isolates, aligned protein sequences indicated a high rate of residue substitutions at positions 305, 324, 345, 370, 375, and 426 in the GH loop. The mutation at residue 370 (Q370R), a single mutation, was characterized as a unique mutant residue specific to the Laotian CPV-2c variant.

  7. Molecular Characterization of Cryptosporidium spp. in Children from Mexico

    Science.gov (United States)

    Valenzuela, Olivia; González-Díaz, Mariana; Garibay-Escobar, Adriana; Burgara-Estrella, Alexel; Cano, Manuel; Durazo, María; Bernal, Rosa M.; Hernandez, Jesús; Xiao, Lihua

    2014-01-01

    Cryptosporidiosis is a parasitic disease caused by Cryptosporidium spp. In immunocompetent individuals, it usually causes an acute and self-limited diarrhea; in infants, infection with Cryptosporidium spp. can cause malnutrition and growth retardation, and declined cognitive ability. In this study, we described for the first time the distribution of C. parvum and C. hominis subtypes in 12 children in Mexico by sequence characterization of the 60-kDa glycoprotein (GP60) gene of Cryptosporidium. Altogether, 7 subtypes belonging to 4 subtype families of C. hominis (Ia, Ib, Id and Ie) and 1 subtype family of C. parvum (IIa) were detected, including IaA14R3, IaA15R3, IbA10G2, IdA17, IeA11G3T3, IIaA15G2R1 and IIaA16G1R1. The frequency of the subtype families and subtypes in the samples analyzed in this study differed from what was observed in other countries. PMID:24755606

  8. Molecular cloning and characterization of Aspergillus nidulans cyclophilin B.

    Science.gov (United States)

    Joseph, J D; Heitman, J; Means, A R

    1999-06-01

    Cyclophilins are an evolutionarily conserved family of proteins which serve as the intracellular receptors for the immunosuppressive drug cyclosporin A. Here we report the characterization of the first cyclophilin cloned from the filamentous fungus Aspergillus nidulans (CYPB). Sequence analysis of the cypB gene predicts an encoded protein with highest homology to the murine cyclophilin B protein. The sequence similarity includes an N-terminal sequence predicted to target the protein to the endoplasmic reticulum (ER) as well as a C-terminal sequence predicted to retain the mature protein in the ER. The bacterially expressed hexa-histidine tagged protein displays peptidyl-prolyl isomerase activity which is inhibited by cyclosporin A. In the presence of cyclosporin A, the expressed protein also inhibits purified calcineurin. When the endogenous cypB gene was disrupted and placed under the control of the regulatable alcohol dehydrogenase promoter, the strain demonstrated no detectable growth phenotype under conditions which induce or repress cypB transcription. Induction or repression of the cypB gene also did not effect sensitivity of A. nidulans to cyclosporin A. cypB mRNA levels were significantly elevated under severe heat shock conditions, indicating a possible role for the A. nidulans cyclophilin B protein during growth in high stress environments. Copyright 1999 Academic Press.

  9. Physicochemical characterization of irradiated high molecular weight chitosan

    International Nuclear Information System (INIS)

    Rapado, Manuel; Paredes, Mayte; Altanes, Sonia; Barrera, Gisela; Otero, Isabel; Peniche, Carlos; Gonzalez, Maykel

    2006-01-01

    Chitosan is obtained by mean of partial deacetylation of chitin. Due to the diverse biological properties of this polymer it has valuable medical applications. Some of these applications require sterile materials. For this purpose irradiation techniques seem to have advantages since they do not require any additives, which could contaminate the final sterile product with toxic residuals. The aims of the present study were to determinate the bio burden for assessing the sterilization dose and to identify the influence of the absorbed dose of gamma radiation on the molar mass and chemical structure of chitosan. Changes in polymer features were evaluated by comparing the results obtained from the characterization of treated and raw polymers. The obtained results have been shown chain cleavage caused by irradiation. It was revealed by a decrease in the intrinsic viscosities of the polymers. The invariance of the infrared spectra of polymer indicates that chain degradation occurs without significant change of the chemical structure. The results obtained have practical implication in the field of radiation sterilization of chitosan used for biotechnology, medicine and pharmacy

  10. Molecular Characterization and Mortality From Breast Cancer in Men.

    Science.gov (United States)

    Massarweh, Suleiman Alfred; Sledge, George W; Miller, Dave P; McCullough, Debbie; Petkov, Valentina I; Shak, Steven

    2018-05-10

    Purpose Limited data exist on the molecular biology, treatment, and outcomes of breast cancer in men, and much of our understanding in this area remains largely an extrapolation from data in women with breast cancer. Materials and Methods We studied men and women with hormone receptor-positive breast cancer and the 21-gene Breast Recurrence Score (RS) results. Differences in clinical characteristics and gene expression were determined, and distribution of RS results was correlated with 5-year breast cancer-specific survival (BCSS) and overall survival. Results There were 3,806 men and 571,115 women. Men were older than women (mean age, 64.2 v 59.1 years; P < .001). RS < 18 predominated in both genders, but RS ≥ 31 was more frequent in men (12.4% v 7.4%; P < .001), as were very low scores (RS < 11; 33.8% v 22.1%; P < .001). Mean gene expression was higher in men for the estrogen receptor (ER), proliferation, and invasion groups. ER was lowest and progesterone receptor was highest in women younger than 50 years of age, with a progressive increase in ER with age. Men younger than 50 years of age had slightly lower ER and progesterone receptor compared with older men. Survival data were available from SEER for 322 men and 55,842 women. Five-year BCSS was 99.0% (95% CI, 99.3% to 99.9%) and 95.9% (95% CI, 87.6% to 98.7%) for men with RS < 18 and RS 18-30, respectively, and for women, it was 99.5% (95% CI, 99.4% to 99.6%) and 98.6% (95% CI, 98.4% to 98.8%), respectively. RS ≥ 31 was associated with an 81.0% 5-year BCSS in men (95% CI, 53.3% to 93.2%) and 94.9% 5-year BCSS (95% CI, 93.9% to 95.7%) in women. Five-year BCSS and overall survival were lower in men than in women. Conclusion This study reveals some distinctive biologic features of breast cancer in men and an important prognostic role for RS testing in both men and women.

  11. Frequency and Molecular Characterization of Watermelon Mosaic Virus from Serbia

    Directory of Open Access Journals (Sweden)

    Ana Vučurović

    2010-01-01

    Full Text Available Watermelon mosaic virus (WMV is widespread in cucurbit crops, most commonly occuring in temperate and Mediterranean regions. In Serbia WMV has been detected in single and mixed infections with Zucchini yellow mosaic virus and Cucumber mosaic virus in field-grown pumpkin and squash crops. Among pumpkin-affecting viruses WMV is the most frequent one, both by the number of localities and its incidence at each location. During the growing season of 2009, samples from 583 plants of Cucurbita pepo cvs. Olinka, Belgrade zucchini and Tosca (Zucchini group, as well as from C. maxima and C. moschata showing symptoms of virus infection were collected from 12 commercial fields at eight localities and analyzed by DAS-ELISA using polyclonal antisera specific to six most important cucurbit viruses. Interestingly, WMV was detected at fewer sites and had lower ncidence rate than in two previous years. In single infections, WMV was found in 11% of tested plants in three fields; in mixed infections with ZYMV, it was recorded in 9.9% of plants in five fields and with CMV in only 0.2% in one field. The partial coat protein gene and 3’ non-translated region from two representativeisolates of WMV originating from different localities and host plant species were amplified by RT-PCR, sequenced, and compared with the sequences available in GenBank database. The PCR-amplified fragment of predicted size of approximately 1017 bp was obtained. The sequences of isolates 137-08 (Acc. No. GQ259958 and 159-08 (GU144020 proved to be 94-99% identical at the nucleotide level with those from other parts of the world. The sequences of these two isolates differed from each other only at two nucleotide positions, without any amino acid substitution. Phylogenetic analysis of 57 isolates based on 750 bp sequences of the coat protein gene showed no correlation between isolates and their geographic origin, and italso indicated that these isolates fell into three molecular groups of

  12. Molecular characterization and interactome analysis of Trypanosoma cruzi tryparedoxin II.

    Science.gov (United States)

    Arias, Diego G; Piñeyro, María Dolores; Iglesias, Alberto A; Guerrero, Sergio A; Robello, Carlos

    2015-04-29

    Trypanosoma cruzi, the causative agent of Chagas disease, possesses two tryparedoxins (TcTXNI and TcTXNII), belonging to the thioredoxin superfamily. TXNs are oxidoreductases which mediate electron transfer between trypanothione and peroxiredoxins. This constitutes a difference with the host cells, in which these activities are mediated by thioredoxins. These differences make TXNs an attractive target for drug development. In a previous work we characterized TcTXNI, including the redox interactome. In this work we extend the study to TcTXNII. We demonstrate that TcTXNII is a transmembrane protein anchored to the surface of the mitochondria and endoplasmic reticulum, with a cytoplasmatic orientation of the redox domain. It would be expressed during the metacyclogenesis process. In order to continue with the characterization of the redox interactome of T. cruzi, we designed an active site mutant TcTXNII lacking the resolving cysteine, and through the expression of this mutant protein and incubation with T. cruzi proteins, heterodisulfide complexes were isolated by affinity chromatography and identified by mass spectrometry. This allowed us to identify sixteen TcTXNII interacting proteins, which are involved in a wide range of cellular processes, indicating the relevance of TcTXNII, and contributing to our understanding of the redox interactome of T. cruzi. T. cruzi, the causative agent of Chagas disease, constitutes a major sanitary problem in Latin America. The number of estimated infected persons is ca. 8 million, 28 million people are at risk of infection and ~20,000 deaths occur per year in endemic regions. No vaccines are available at present, and most drugs currently in use were developed decades ago and show variable efficacy with undesirable side effects. The parasite is able to live and prolipherate inside macrophage phagosomes, where it is exposed to cytotoxic reactive oxygen and nitrogen species, derived from macrophage activation. Therefore, T. cruzi

  13. Molecular characterization of bacteriophages for microbial source tracking in Korea.

    Science.gov (United States)

    Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo

    2009-11-01

    We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

  14. Molecular identification, immunolocalization, and characterization of Clonorchis sinensis triosephosphate isomerase.

    Science.gov (United States)

    Zhou, Juanjuan; Liao, Hua; Li, Shan; Zhou, Chenhui; Huang, Yan; Li, Xuerong; Liang, Chi; Yu, Xinbing

    2015-08-01

    Clonorchis sinensis triosephosphate isomerase (CsTIM) is a key regulatory enzyme of glycolysis and gluconeogenesis, which catalyzes the interconversion of glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. In this study, the biochemical characterizations of CsTIM have been examined. A full-length complementary DNA (cDNA; Cs105350) sequence encoding CsTIM was obtained from our C. sinensis cDNA library. The open reading frame of CsTIM contains 759 bp which encodes 252 amino acids. The amino acid sequence of CsTIM shares 60-65% identity with other species. Western blot analysis displayed that recombinant CsTIM (rCsTIM) can be probed by anti-rCsTIM rat serum and anti-C. sinensis excretory/secretory products (anti-CsESPs) rat serum. Quantitative reverse transcription (RT)-PCR and western blotting analysis revealed that CsTIM messenger RNA (mRNA) and protein were differentially expressed in development cycle stages of the parasite, including adult worm, metacercaria, excysted metacercaria, and egg. In addition, immunolocalization assay showed that CsTIM was located in the seminal vesicle, eggs, and testicle. Moreover, rCsTIM exhibited active enzyme activity in catalytic reactions. The Michaelis constant (K m) of rCsTIM was 0.33 mM, when using glyceraldehyde 3-phosphate as the substrate. The optimal temperature and pH of CsTIM were 37 °C and 7.5-9.5, respectively. Collectively, these results suggest that CsTIM is an important protein involved in glycometabolism, and CsTIM possibly take part in many biological functions in the growth and development of C. sinensis.

  15. Molecular and functional characterization of a human ATM gene analogue at Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Garcia, V.

    2001-12-01

    The human ATM gene, whose inactivation is responsible for the human disease ataxia telangiectasia is conserved throughout the Eukaryotes and plays an important role in the cellular responses to DNA damage, in particular to DNA double-strand breaks (DSBs). Here we describe the identification of an Arabidopsis thaliana homologue of ATM (AtATM), and the molecular and cytological characterization of plants, hereafter called atm, carrying a disrupting T-DNA insertion in this gene. AtATM covers a 32 kb region on chromosome 3. The AtATM transcript has a complex structure, is 12 kb long and formed by 79 exons. The transcriptional level of AtATM is very low in all the tissues tested, and does not vary after exposure to ionizing radiations (IR). In atm plants, the protein is not detected suggesting the mutants are null. The atm mutants are partially sterile. Aberrant segregation of chromosomes during meiosis I on both male and female sides account for this sterility. However, meiotic recombination frequency is normal. Mutant plants are also hypersensitive to gamma rays and methyl methane sulfonate, but not to UV-B, pointing to a specific defect of atm mutants in the response to DNA DSBs. In plants, ionizing radiations induce a strong, rapid and transient transcriptional activation of genes involved in the cellular response to or the repair of DSBs. This transcriptional regulation of AtRAD51, AtPARP1, atGR1 and AtL1G4 is lost in the atm mutants . The absence of AtRAD51 induction associated with ionizing radiation sensitivity suggest that AtAtm play an important function in DSB repair by homologous recombination. In addition we show that homologous intra-chromosomal recombination frequency is elevated in the mutant comparing to wild-type, with or without gamma irradiation. These results show the implication of AtAtm in the genomic stability. (author)

  16. Interaction of pathology and molecular characterization of thyroid cancers

    International Nuclear Information System (INIS)

    Williams, E.D.; Cherstvoy, E.; Egloff, B.; Hoefler, H.; Vecchio, G.; Bogdanova, T.; Bragarnik, M.; Tronko, N.D.

    1996-01-01

    This paper presents the results of joint studies of thyroid cancer in children under 15 years of age between departments in Cambridge, Brussels, Naples and Munich in the European Union, and departments in Minsk, Kiev and Obninsk in the newly independent states of Eastern Europe. The pathology of 264 cases of childhood thyroid cancer out of 430 that have occurred since 1990 in the 3 countries in which high levels of fallout from the Chernobyl accident occurred has been restudied by NIS and EU pathologists. The overall level of agreement reached was about 97%. The diagnosis was supported by immunocytochemistry and ISH for the differentiation markers, thyroglobulin and calcitonin, and the tumors were classified according to the WHO, with papillary carcinomas being further subclassified. 99% of the 134 Belarussian cases were papillary carcinomas, as were 94% of the 114 Ukrainian tumors. All 9 of the Russian cases available for study were papillary in type. 76 of 154 cases of childhood thyroid cancer reviewed over a 30 year period in England and Wales and were also studied, 68% of these were papillary carcinoma. Histological study showed that a subtype of papillary carcinoma, rarely found in adults, with a solid/follicular architecture occurred in children. It was found in 72% of the Belarussian papillary carcinomas, 76% of the Ukrainian cases, but only 40% of the England and Wales cases. Molecular biological studies showed that the proportion of cases of papillary carcinoma expressing the ret gene was not significantly different in the exposed and the unexposed tumors, studies of the type of translocation leading to ret gene expression are not yet conclusive. Ras gene mutations were found as expected in follicular carcinoma, but were absent from any papillary carcinoma, whether from exposed or unexposed cases. TSH receptor mutations, normally found in follicular tumors were not found in any papillary carcinomas, nor were any p53 mutations identified. All these results

  17. Microbiological and molecular characterization of Staphylococcus hominis isolates from blood.

    Directory of Open Access Journals (Sweden)

    Soraya Mendoza-Olazarán

    Full Text Available BACKGROUND: Among Coagulase-Negative Staphylococci (CoNS, Staphylococcus hominis represents the third most common organism recoverable from the blood of immunocompromised patients. The aim of this study was to characterize biofilm formation, antibiotic resistance, define the SCCmec (Staphylococcal Chromosomal Cassette mec type, and genetic relatedness of clinical S. hominis isolates. METHODOLOGY: S. hominis blood isolates (n = 21 were screened for biofilm formation using crystal violet staining. Methicillin resistance was evaluated using the cefoxitin disk test and the mecA gene was detected by PCR. Antibiotic resistance was determined by the broth microdilution method. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE and SCCmec typed by multiplex PCR using two different methodologies described for Staphylococcus aureus. RESULTS: Of the S. hominis isolates screened, 47.6% (10/21 were categorized as strong biofilm producers and 23.8% (5/21 as weak producers. Furthermore, 81% (17/21 of the isolates were methicillin resistant and mecA gene carriers. Resistance to ampicillin, erythromycin, and trimethoprim was observed in >70% of isolates screened. Each isolate showed a different PFGE macrorestriction pattern with similarity ranging between 0-95%. Among mecA-positive isolates, 14 (82% harbored a non-typeable SCCmec type: eight isolates were not positive for any ccr complex; four contained the mec complex A ccrAB1 and ccrC, one isolate contained mec complex A, ccrAB4 and ccrC, and one isolate contained the mec complex A, ccrAB1, ccrAB4, and ccrC. Two isolates harbored the association: mec complex A and ccrAB1. Only one strain was typeable as SCCmec III. CONCLUSIONS: The S. hominis isolates analyzed were variable biofilm producers had a high prevalence of methicillin resistance and resistance to other antibiotics, and high genetic diversity. The results of this study strongly suggested that S. hominis isolates harbor

  18. Molecular characterization of a novel cryptic virus infecting pigeonpea plants.

    Directory of Open Access Journals (Sweden)

    Surender Kumar

    Full Text Available A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L. Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1. The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5' non-coding region (5'-GATAATGATCCAAGGA-3'. The largest dsRNA (dsRNA-1 was identified as the viral RNA dependent RNA polymerase (replicase, predicted to encode a putative 55.34 kDa protein (P1. The two other smaller dsRNAs (dsRNA-2 and dsRNA-3 predicted to encode for putative capsid proteins of 38.50kDa (P2 and 38.51kDa (P3, respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3Dpol structure revealed several interesting features. The 3Dpol in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A, not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb encodes a protein (P4, with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants.

  19. Investigation on microstructure characterization and property of rapidly solidified Mg-Zn-Ca-Ce-La alloys

    Energy Technology Data Exchange (ETDEWEB)

    Zhou Tao, E-mail: tzhou1118@163.com [College of Material Science and Engineering, Chongqing University of Technology, Chongqing 400054 (China); Chen Zhenhua, E-mail: chenzhenhua45@hotmail.com [College of Material Science and Engineering, Hunan University, Changsha 410082 (China); Yang Mingbo, E-mail: yangmingbo@cqit.edu.cn [College of Material Science and Engineering, Chongqing University of Technology, Chongqing 400054 (China); Hu Jianjun, E-mail: hujj@qq.com [College of Material Science and Engineering, Chongqing University of Technology, Chongqing 400054 (China); Xia Hua, E-mail: xiahua@cqut.edu.cn [College of Material Science and Engineering, Chongqing University of Technology, Chongqing 400054 (China)

    2012-01-15

    Rapidly solidified (RS) Mg-Zn-Ca-Ce-La (wt.%) alloys have been produced via atomizing the alloy melt and subsequent splat-quenching on the water-cooled copper twin-rollers in the form of flakes. Microstructure characterization, phase compositions and thermal stability of the alloys have been systematically investigated. The results showed that with addition of RE (Ce and La) to the Mg-6Zn-5Ca alloy, the stable intermetallic compounds i.e. the Mg{sub x}Zn{sub y}RE{sub z} phase with a few Ca (about 3 at.%), shortened as the T Prime phase, were formed at the expense of the binary Mg-Zn and Ca{sub 2}Mg{sub 6}Zn{sub 3} phases, which was possibly beneficial to the enhanced thermal stability of the alloy. In the Mg-6Zn-5Ca-3Ce-0.5La alloy, the composition of the T Prime phase in the grain interior was different from that at the grain boundaries, in which the segregation of the La elements was found, and the atomic percentage ratio of Zn to Ce in the T Prime phase within the grains was close to 2. Moreover, the stable Mg{sub 2}Ca phases were detected around the T Prime phases at the grain boundaries in the alloy. - Research Highlights: Black-Right-Pointing-Pointer The phase constitution of RS Mg-6Zn-5Ca alloy can be improved by RE additions. Black-Right-Pointing-Pointer In the Mg-Zn-Ca-Ce-La alloys, the Mg{sub x}Zn{sub y}RE{sub z} phase with a few Ca (T Prime phase) is formed. Black-Right-Pointing-Pointer The formation of the T Prime phase leads to the loss of the Mg-Zn and Ca{sub 2}Mg{sub 6}Zn{sub 3} phases. Black-Right-Pointing-Pointer The composition of the T Prime phase differs from the grain interior to the grain boundary.

  20. Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program.

    Science.gov (United States)

    Walker, Douglas G; Whetzel, Alexis M; Serrano, Geidy; Sue, Lucia I; Lue, Lih-Fen; Beach, Thomas G

    2016-09-01

    Many factors affect the integrity of messenger RNA from human autopsy tissues including postmortem interval (PMI) between death and tissue preservation and the pre-mortem agonal and disease states. In this communication, we describe RNA isolation and characterization of 389 samples from 18 different tissues from elderly donors who were participants in a rapid whole-body autopsy program located in Sun City, Arizona ( www.brainandbodydonationprogram.org ). Most tissues were collected within a PMI of 2-6 h (median 3.15 h; N = 455), but for this study, tissue from cases with longer PMIs (1.25-29.25 h) were included. RNA quality was assessed by RNA integrity number (RIN) and total yield (ng RNA/mg tissue). RIN correlated with PMI for heart (r = -0.531, p = 0.009) and liver (r = -558, p = 0.0017), while RNA yield correlated with PMI for colon (r = -485, p = 0.016) and skin (r = -0.460, p = 0.031). RNAs with the lowest integrity were from skin and cervix where 22.7 and 31.4 % of samples respectively failed to produce intact RNA; by contrast all samples from esophagus, lymph node, jejunum, lung, stomach, submandibular gland and kidney produced RNA with measurable RINs. Expression levels in heart RNA of 4 common housekeeping normalization genes showed significant correlations of Ct values with RIN, but only one gene, glyceraldehyde-3 phosphate dehydrogenase, showed a correlation of Ct with PMI. There were no correlations between RIN values obtained for liver, adrenal, cervix, esophagus and lymph node and those obtained from corresponding brain samples. We show that high quality RNA can be produced from most human autopsy tissues, though with significant differences between tissues and donors. The RNA stability and yield did not depend solely on PMI; other undetermined factors are involved, but these do not include the age of the donor.

  1. Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis.

    Science.gov (United States)

    Perreten, Vincent; Endimiani, Andrea; Thomann, Andreas; Wipf, Juliette R K; Rossano, Alexandra; Bodmer, Michèle; Raemy, Andreas; Sannes-Lowery, Kristin A; Ecker, David J; Sampath, Rangarajan; Bonomo, Robert A; Washington, Cicely

    2013-06-01

    Bovine mastitis, an inflammatory disease of the mammary gland, is one of the most costly diseases affecting the dairy industry. The treatment and prevention of this disease is linked heavily to the use of antibiotics in agriculture and early detection of the primary pathogen is essential to control the disease. Milk samples (n=67) from cows suffering from mastitis were analyzed for the presence of pathogens using PCR electrospray-ionization mass spectrometry (PCR/ESI-MS) and were compared with standard culture diagnostic methods. Concurrent identification of the primary mastitis pathogens was obtained for 64% of the tested milk samples, whereas divergent results were obtained for 27% of the samples. The PCR/ESI-MS failed to identify some of the primary pathogens in 18% of the samples, but identified other pathogens as well as microorganisms in samples that were negative by culture. The PCR/ESI-MS identified bacteria to the species level as well as yeasts and molds in samples that contained a mixed bacterial culture (9%). The sensitivity of the PCR/ESI-MS for the most common pathogens ranged from 57.1 to 100% and the specificity ranged from 69.8 to 100% using culture as gold standard. The PCR/ESI-MS also revealed the presence of the methicillin-resistant gene mecA in 16.2% of the milk samples, which correlated with the simultaneous detection of staphylococci including Staphylococcus aureus. We demonstrated that PCR/ESI-MS, a more rapid diagnostic platform compared with bacterial culture, has the significant potential to serve as an important screening method in the diagnosis of bovine clinical mastitis and has the capacity to be used in infection control programs for both subclinical and clinical disease. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  2. Phenotypic, Molecular, and Pathological Characterization of Colletotrichum acutatum Associated with Andean Lupine and Tamarillo in the Ecuadorian Andes

    NARCIS (Netherlands)

    Falconi, C.; Visser, R.G.F.; Heusden, van A.W.

    2013-01-01

    Anthracnose is a serious problem of both Andean lupine and tamarillo in Ecuador. Morphological features, internal transcribed spacer (ITS) sequences, and host specificity were used to characterize Colletotrichum isolates from lupine and tamarillo. Based on phenotypic and molecular characterization,

  3. Rapid molecular detection of rifampicin resistance facilitates early diagnosis and treatment of multi-drug resistant tuberculosis: case control study.

    Directory of Open Access Journals (Sweden)

    Philly O'Riordan

    2008-09-01

    Full Text Available Multi-drug resistant tuberculosis (MDR-TB is a major public health concern since diagnosis is often delayed, increasing the risk of spread to the community and health care workers. Treatment is prolonged, and the total cost of treating a single case is high. Diagnosis has traditionally relied upon clinical suspicion, based on risk factors and culture with sensitivity testing, a process that can take weeks or months. Rapid diagnostic molecular techniques have the potential to shorten the time to commencing appropriate therapy, but have not been put to the test under field conditions.This retrospective case-control study aimed to identify risk factors for MDR-TB, and analyse the impact of testing for rifampicin resistance using RNA polymerase B (rpoB mutations as a surrogate for MDR-TB. Forty two MDR-TB cases and 84 fully sensitive TB controls were matched by date of diagnosis; and factors including demographics, clinical presentation, microbiology findings, management and outcome were analysed using their medical records. Conventionally recognised risk factors for MDR-TB were absent in almost half (43% of the cases, and 15% of cases were asymptomatic. A significant number of MDR-TB cases were identified in new entrants to the country. Using rpoB mutation testing, the time to diagnosis of MDR-TB was dramatically shortened by a median of 6 weeks, allowing patients to be commenced on appropriate therapy a median of 51days earlier than those diagnosed by conventional culture and sensitivity testing.MDR-TB is frequently an unexpected finding, may be asymptomatic, and is particularly prevalent among TB infected new entrants to the country. Molecular resistance testing of all acid fast bacilli positive specimens has the potential to rapidly identify MDR-TB patients and commence them on appropriate therapy significantly earlier than by conventional methods.

  4. Molecular characterization of phytoplasmas in lilies with fasciation in the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Bertaccini, A.; Fránová, Jana; Botti, S.; Tabanelli, D.

    2005-01-01

    Roč. 249, - (2005), s. 79-85 ISSN 0378-1097 R&D Projects: GA AV ČR(CZ) IBS5051014 Institutional research plan: CEZ:AV0Z50510513 Keywords : phytoplasma * Lilium spp. * molecular characterization Subject RIV: EE - Microbiology, Virology Impact factor: 2.057, year: 2005

  5. Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Causing Fatal Purulent Pericarditis.

    Science.gov (United States)

    Kumar, Vasudevan Anil; Nair, Nisha; Thachathodiyl, Rajesh; Nandakumar, Aswathy; Dinesh, Kavitha R; Thatcher, Eileen; Karim, Shamsul; Biswas, Raja

    2013-07-01

    Though pericardial disease is common in patients with renal disease, purulent pericarditis is very rare. We report a fatal case of purulent pericarditis and sepsis due to methicillin-resistant Staphylococcus aureus in a 78-year-old male with systemic hypertension and renal disease along with the molecular characterization of its resistant mechanism.

  6. Molecular-beam epitaxy growth and characterization of 5-μm quantum cascade laser

    International Nuclear Information System (INIS)

    Mamutin, V V; Ustinov, V M; Ilyinskaya, N D; Baydakova, M V; Ber, B Ya; Kasantsev, D Yu

    2011-01-01

    Molecular-beam epitaxy growth of 5 μm emitting strain-compensated quantum semiconductor laser (QCL) is reported. The QCL structure is characterized by complementary techniques: high-resolution X-ray diffraction and dynamical secondary-ion mass-spectrometry, that reveal the high quality of QCL structure and in-depth distribution of chemical composition, respectively.

  7. Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

    Science.gov (United States)

    Ateş Sönmezoğlu, Özlem; Terzi, Begüm

    2018-02-01

    Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

  8. Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

    Directory of Open Access Journals (Sweden)

    Thor Vinícius Martins Fajardo

    2015-12-01

    Full Text Available ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV, except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP and coat (CP protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

  9. Molecular Detection and Characterization of Goat Isolate of Taenia hydatigena in Turkey

    Directory of Open Access Journals (Sweden)

    Armagan Erdem Utuk

    2012-01-01

    Full Text Available The aim of this study was to provide molecular detection and characterization of the goat isolate of Taenia hydatigena from Ankara province of Turkey. For this purpose, PCR amplification of small subunit ribosomal RNA (rrnS and partial sequencing of mitochondrial cytochrome c oxidase subunit 1 (mt-CO1 genes were performed in a one-month-old dead goat. According to rrnS-PCR results, parasites were identified as Taenia spp., and partial sequence of mt-CO1 gene was corresponding to T. hydatigena. At the end of the study, we concluded that molecular tools can be used to define species of parasites in cases where the key morphologic features cannot be detected. Nucleotide sequence data of Turkish goat isolate of T. hydatigena was submitted to GenBank for other researchers interested in this subject. By this study, molecular detection and characterization of T. hydatigena was done for the first time in Turkey.

  10. Using a Microscale Approach to Rapidly Separate and Characterize Three Photosynthetic Pigment Species from Fern

    Science.gov (United States)

    Ayudhya, Theppawut Israsena Na; Posey, Frederick T.; Tyus, Jessica C.; Dingra, Nin N.

    2015-01-01

    A rapid separation of three photosynthetic pigments (chlorophyll "a" and "b" and xanthophyll) from fern ("Polystichum acrostichoides") is described using microscale solvent extraction and traditional thin layer chromatography that minimizes use of harmful chemicals and lengthy procedures. The experiment introduces…

  11. Southern-by-Sequencing: A Robust Screening Approach for Molecular Characterization of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Gina M. Zastrow-Hayes

    2015-03-01

    Full Text Available Molecular characterization of events is an integral part of the advancement process during genetically modified (GM crop product development. Assessment of these events is traditionally accomplished by polymerase chain reaction (PCR and Southern blot analyses. Southern blot analysis can be time-consuming and comparatively expensive and does not provide sequence-level detail. We have developed a sequence-based application, Southern-by-Sequencing (SbS, utilizing sequence capture coupled with next-generation sequencing (NGS technology to replace Southern blot analysis for event selection in a high-throughput molecular characterization environment. SbS is accomplished by hybridizing indexed and pooled whole-genome DNA libraries from GM plants to biotinylated probes designed to target the sequence of transformation plasmids used to generate events within the pool. This sequence capture process enriches the sequence data obtained for targeted regions of interest (transformation plasmid DNA. Taking advantage of the DNA adjacent to the targeted bases (referred to as next-to-target sequence that accompanies the targeted transformation plasmid sequence, the data analysis detects plasmid-to-genome and plasmid-to-plasmid junctions introduced during insertion into the plant genome. Analysis of these junction sequences provides sequence-level information as to the following: the number of insertion loci including detection of unlinked, independently segregating, small DNA fragments; copy number; rearrangements, truncations, or deletions of the intended insertion DNA; and the presence of transformation plasmid backbone sequences. This molecular evidence from SbS analysis is used to characterize and select GM plants meeting optimal molecular characterization criteria. SbS technology has proven to be a robust event screening tool for use in a high-throughput molecular characterization environment.

  12. High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

    Directory of Open Access Journals (Sweden)

    Daniel Petras

    2017-12-01

    Full Text Available Dissolved organic matter (DOM is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 1015 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR and mass spectrometry (MS. To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC, molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the

  13. Molecular characterization of cultivated species of the genus Pachyrhizus Rich. ex DC. by AFLP markers

    DEFF Research Database (Denmark)

    Santayana, Monica; Rossel, Genoveva; Núñez, Jorge

    2014-01-01

    ) molecular markers in order to estimate genetic diversity and interspecific relationships. To complement molecular marker information, individuals from each accession were analyzed in order to confirmploidy levels. Eight AFLP primer combinations detected 136 (68.7 %) polymorphic bands. Shannon’s diversity...... indices (Hs) for each species were 1.04 (P. ahipa), 1.07 (P. tuberosus), and 2.42 (P. erosus), while the total diversity index was 2.45. Phylogenetic analysis, principal coordinate analysis and analysis of molecular variance (FST=0.796) all showed significant species differentiation. All accessions were...... diploid (2n=2x=22), which is characteristic of the tribe Phaseoleae. Finally, a misclassified accession of P. tuberosus was identified. Molecular characterization of accessions is necessary for efficient management of germplasm collections....

  14. Molecular Characterization of Gastric Carcinoma: Therapeutic Implications for Biomarkers and Targets

    Directory of Open Access Journals (Sweden)

    Lionel Kankeu Fonkoua

    2018-03-01

    Full Text Available Palliative chemotherapy is the mainstay of treatment of advanced gastric carcinoma (GC. Monoclonal antibodies including trastuzumab, ramucirumab, and pembrolizumab have been shown to provide additional benefits. However, the clinical outcomes are often unpredictable and they can vary widely among patients. Currently, no biomarker is available for predicting treatment response in the individual patient except human epidermal growth factor receptor 2 (HER2 amplification and programmed death-ligand 1 (PD-L1 expression for effectiveness of trastuzumab and pembrolizumab, respectively. Multi-platform molecular analysis of cancer, including GC, may help identify predictive biomarkers to guide selection of therapeutic agents. Molecular classification of GC by The Cancer Genome Atlas Research Network and the Asian Cancer Research Group is expected to identify therapeutic targets and predictive biomarkers. Complementary to molecular characterization of GC is molecular profiling by expression analysis and genomic sequencing of tumor DNA. Initial analysis of patients with gastroesophageal carcinoma demonstrates that the ratio of progression-free survival (PFS on molecular profile (MP-based treatment to PFS on treatment prior to molecular profiling exceeds 1.3, suggesting the potential value of MP in guiding selection of individualized therapy. Future strategies aiming to integrate molecular classification and profiling of tumors with therapeutic agents for achieving the goal of personalized treatment of GC are indicated.

  15. Molecular Characterization of Gastric Carcinoma: Therapeutic Implications for Biomarkers and Targets.

    Science.gov (United States)

    Kankeu Fonkoua, Lionel; Yee, Nelson S

    2018-03-09

    Palliative chemotherapy is the mainstay of treatment of advanced gastric carcinoma (GC). Monoclonal antibodies including trastuzumab, ramucirumab, and pembrolizumab have been shown to provide additional benefits. However, the clinical outcomes are often unpredictable and they can vary widely among patients. Currently, no biomarker is available for predicting treatment response in the individual patient except human epidermal growth factor receptor 2 (HER2) amplification and programmed death-ligand 1 (PD-L1) expression for effectiveness of trastuzumab and pembrolizumab, respectively. Multi-platform molecular analysis of cancer, including GC, may help identify predictive biomarkers to guide selection of therapeutic agents. Molecular classification of GC by The Cancer Genome Atlas Research Network and the Asian Cancer Research Group is expected to identify therapeutic targets and predictive biomarkers. Complementary to molecular characterization of GC is molecular profiling by expression analysis and genomic sequencing of tumor DNA. Initial analysis of patients with gastroesophageal carcinoma demonstrates that the ratio of progression-free survival (PFS) on molecular profile (MP)-based treatment to PFS on treatment prior to molecular profiling exceeds 1.3, suggesting the potential value of MP in guiding selection of individualized therapy. Future strategies aiming to integrate molecular classification and profiling of tumors with therapeutic agents for achieving the goal of personalized treatment of GC are indicated.

  16. An ion cooling and state characterization apparatus for studies of molecular ion dissociative interactions

    International Nuclear Information System (INIS)

    Deng, Shihu; Vane, C R; Bannister, M E; Havener, C C; Meyer, F W; Krause, H F; Hettich, R L; Goeringer, D E; Van Berkel, G J

    2009-01-01

    An experimental capability is being developed at the Oak Ridge National Laboratory Multi-Charged Ion Research Facility (ORNL MIRF) to enable stored cooling and state characterization of molecular ions of essentially any mass. Ions selected from a variety of available sources are injected from the side into a 1.5 meter long electrostatic mirror trap, where excited internal states are cooled by radiative cooling. An electron beam target located near the middle of the ion-trap region, coupled with neutral fragment imaging detector systems at each end of the trap, permits state-specific studies of electron-molecular ion dissociation.

  17. Microstructure characterization of rapidly solidified Al-Fe-Cr-Ce alloy by positron annihilation spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Michalcová, A.; Vojtěch, D.; Čízek, J.; Procházka, I.; Drahokoupil, Jan; Novák, P.

    2011-01-01

    Roč. 509, č. 7 (2011), s. 3211-3218 ISSN 0925-8388 Institutional research plan: CEZ:AV0Z10100520 Keywords : metals and alloy s * nanostructured materials * rapid solidification * positron spectroscopies * transmission electron microscopy * x-ray diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.289, year: 2011

  18. A metric for characterizing the bistability of molecular quantum-dot cellular automata

    International Nuclear Information System (INIS)

    Lu Yuhui; Lent, Craig S

    2008-01-01

    Much of molecular electronics involves trying to use molecules as (a) wires, (b) diodes or (c) field-effect transistors. In each case the criterion for determining good performance is well known: for wires it is conductance, for diodes it is conductance asymmetry, while for transistors it is high transconductance. Candidate molecules can be screened in terms of these criteria by calculating molecular conductivity in forward and reverse directions, and in the presence of a gating field. Hence so much theoretical work has focused on understanding molecular conductance. In contrast a molecule used as a quantum-dot cellular automata (QCA) cell conducts no current at all. The keys to QCA functionality are (a) charge localization, (b) bistable charge switching within the cell and (c) electric field coupling between one molecular cell and its neighbor. The combination of these effects can be examined using the cell-cell response function which relates the polarization of one cell to the induced polarization of a neighboring cell. The response function can be obtained by calculating the molecular electronic structure with ab initio quantum chemistry techniques. We present an analysis of molecular QCA performance that can be applied to any candidate molecule. From the full quantum chemistry, all-electron ab initio calculations we extract parameters for a reduced-state model which reproduces the cell-cell response function very well. Techniques from electron transfer theory are used to derive analytical models of the response function and can be employed on molecules too large for full ab initio treatment. A metric is derived which characterizes molecular QCA performance the way transconductance characterizes transistor performance. This metric can be assessed from absorption measurements of the electron transfer band or quantum chemistry calculations of appropriate sophistication

  19. Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

    Science.gov (United States)

    Drenscko, Mihaela

    Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

  20. A novel molecularly imprinted material based on magnetic halloysite nanotubes for rapid enrichment of 2,4-dichlorophenoxyacetic acid in water.

    Science.gov (United States)

    Zhong, Shian; Zhou, Chengyun; Zhang, Xiaona; Zhou, Hui; Li, Hui; Zhu, Xiaohong; Wang, Yan

    2014-07-15

    A new type of magnetic halloysite nanotubes molecularly imprinted polymer (MHNTs@MIP) based on halloysite nanotubes (HNTs) with embedded magnetic nanoparticles was introduced in this study. MHNTs@MIP was prepared through surface imprinting technology, using 2,4-dichlorophenoxyacetic acid (2,4-D) as a template, 4-vinylpyridine as the monomer, divinylbenzene as cross-linking agents, and 2,2-azodiisobutyronitrile as initiator. MHNTs@MIP was characterized by Fourier Transform Infrared Spectrometer, transmission electron microscopy, X-ray diffraction, and vibrating sample magnetometer. MHNTs@MIP exhibited rapid and reliable analysis with supermagnetic properties, as well as repeated use and template-specific recognition. The adsorption capacity of magnetic halloysite nanotubes non-imprinted polymer (MHNTs@NIP) and MHNTs@MIP was 10.3mg/g and 35.2mg/g, respectively. In the detailed discussion on specific selectivity, MHNTs@MIP can be applied as an adsorbent for sample pretreatment extraction and obtain high recoveries of about 85-94%. After extraction, high-performance liquid chromatography was used to detect 2,4-D residue in water. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Rapid preparation process of antiparkinsonian drug Mucuna pruriens silver nanoparticle by bioreduction and their characterization

    Science.gov (United States)

    Arulkumar, Subramanian; Sabesan, Muthukumaran

    2010-01-01

    Backgorund: Development of biologically inspired experimental processes for the synthesis of nanoparticles is evolving an important branch of nanotechnology. Methods: The bioreduction behavior of plant seed extract of Mucuna pruriens in the synthesis of silver nanoparticles was investigated employing UV/visible spectrophotometry, X-ray diffraction (XRD), and transmission electron microscopy (TEM), Fourier transform – infra red (FT- IR). Result: M. pruriens was found to exhibit strong potential for rapid reduction of silver ions. The formation of nanoparticles by this method is extremely rapid, requires no toxic chemicals, and the nanoparticles are stable for several months. Conclusion: The main conclusion is that the bioreduction method to produce nanoparticles is a good alternative to the electrochemical methods and it is expected to be biocompatible. PMID:21808573

  2. Molecular characterization of canine parvovirus (CPV) infection in dogs in Turkey.

    Science.gov (United States)

    Timurkan, Mehmet; Oğuzoğlu, Tuba

    2015-01-01

    This study provides data about canine parvovirus (CPV) types circulating among dogs in Turkey. Sixty-five samples from dogs with and without clinical signs of parvovirus infection were collected between April 2009 and February 2010. The samples were subsequently tested for CPV using polymerase chain reaction (PCR). Twenty-five samples (38.4%) were positive; when positive samples were characterized by sequence analysis, results showed that both CPV-2a (17/25, 68%) and CPV-2b (8/25, 32%) strains are circulating among domestic dogs in Turkey. This is the first molecular characterization study of CPVs from dogs based on partial VP2 gene sequences in Turkey.

  3. Molecular Characterization of the Skate Peripherin/rds Gene: Relationship to Its Orthologues and Paralogues

    Science.gov (United States)

    Li, Chibo; Ding, Xi-Qin; O’Brien, John; Al-Ubaidi, Muayyad R.

    2010-01-01

    PURPOSE A great deal of information about functionally significant domains of a protein may be obtained by comparison of primary sequences of gene homologues over a broad phylogenetic base. This study was designed to identify evolutionarily conserved domains of the photoreceptor disc membrane protein peripherin/rds by analysis of the homologue in a primitive vertebrate, the skate. METHODS A skate retinal cDNA library was screened using a mouse peripherin/rds clone. The 5′ and 3′ untranslated regions of the skate peripherin/rds (srds) cDNA were isolated by the rapid amplification of cDNA ends (RACE) approach. The gene structure was characterized by PCR amplification and sequencing of genomic fragments. Northern and Western blot analyses were used to identify srds transcript and protein, respectively. RESULTS A new homologue of peripherin/rds was identified from the skate retinal cDNA library. SRDS is a glycoprotein with a predicted molecular mass of 40.2 kDa. The srds gene consists of two exons and one small intron and transcribes into a single 6-kb message. Phylogenetic analysis places SRDS at the base of peripherin/rds family and near the division of that group and the branch leading to rds-like and rom-1 genes. SRDS protein is 54.5% identical with peripherin/rds across species. Identity is significantly higher (73%) in the intradiscal domains. Sequence comparison revealed the conservation of all residues that have been shown, on mutation, to associate with retinitis pigmentosa and showed conservation of most residues associated with macular dystrophies. Comparison with ROM-1 and other rds-like proteins revealed the presence of a highly conserved domain in the large intradiscal loop. CONCLUSIONS Srds represents the skate orthologue of mammalian peripherin/rds genes. Conservation of most of the residues associated with human retinal diseases indicates that these residues serve important functional roles. The high degree of conservation of a short stretch within

  4. Molecular characterization of a proteolysis-resistant lipase from Bacillus pumilus SG2

    Directory of Open Access Journals (Sweden)

    R. Sangeetha

    2014-06-01

    Full Text Available Proteolysis-resistant lipases can be well exploited by industrial processes which employ both lipase and protease as biocatalysts. A proteolysis resistant lipase from Bacillus pumilus SG2 was isolated, purified and characterized earlier. The lipase was resistant to native and commercial proteases. In the present work, we have characterized the lip gene which encodes the proteolysis-resistant lipase from Bacillus pumilus SG2. The parameters and structural details of lipase were analysed. The lip gene consisted of 650 bp. The experimental molecular weight of SG2 lipase was nearly double that of its theoretical molecular weight, thus suggesting the existence of the functional lipase as a covalent dimer. The proteolytic cleavage sites of the lipase would have been made inaccessible by dimerisation, thus rendering the lipase resistant to protease.

  5. Molecular characterization of a patient presumed to have prader-willi syndrome.

    Science.gov (United States)

    Falaleeva, Marina; Sulsona, Carlos R; Zielke, Horst R; Currey, Kathleen M; de la Grange, Pierre; Aslanzadeh, Vahid; Driscoll, Daniel J; Stamm, Stefan

    2013-01-01

    Prader-Willi syndrome (PWS) is caused by the loss of RNA expression from an imprinted region on chromosome 15 that includes SNRPN, SNORD115, and SNORD116. Currently, there are no mouse models that faithfully reflect the human phenotype and investigations rely on human post-mortem material. During molecular characterization of tissue deposited in a public brain bank from a patient diagnosed with Prader-Willi syndrome, we found RNA expression from SNRPN, SNORD115, and SNORD116 which does not support a genetic diagnosis of Prader-Willi syndrome. The patient was a female, Caucasian nursing home resident with history of morbid obesity (BMI 56.3) and mental retardation. She died at age of 56 from pulmonary embolism. SNORD115 and SNORD116 are unexpectedly stable in post mortem tissue and can be used for post-mortem diagnosis. Molecular characterization of PWS tissue donors can confirm the diagnosis and identify those patients that have been misdiagnosed.

  6. Characterization of rapid recovery from γ-ray damage in plateau-phase human diploid fibroblasts

    International Nuclear Information System (INIS)

    Malcolm, A.W.; Tomkinson, K.N.; Little, J.B.

    1982-01-01

    Rapid recovery was investigated in density-inhibited, stationary-phase human diploid cells subcultured to low density at various times after a single dose of radiation. The influence of total dose, postirradiation temperature, and cell-to-cell contact on recovery was examined. The cultures were exposed to 60 Co γ rays at a dose rate of 50 rad per second. When the irradiation and postirradiation temperatures were maintained at 25 or 37 0 C, recovery, as manifested by an enhancement in survival, was similar during the first 30 min, whereas it was reduced at later times in the 25 0 C compared with the 37 0 C cultures. This result suggests the existence of different rapidly and slowly acting components to recovery. No recovery was noted at any time with incubation at 4 0 C. The recovery observed in density-inhibited cultures was consistently greater than that in less dense cultures, suggesting an effect of cell-to-cell contact and cell cycle distribution. Following single doses of 200 to 900 rad, progressive enhancement in relative recovery occurred with increasing doses over a period of 2 to 90 min, illustrating the importance of the relationship of the dose to the rapid recovery process

  7. Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

    Science.gov (United States)

    Sokullu Urkac, E.; Oztarhan, A.; Tihminlioglu, F.; Kaya, N.; Ila, D.; Muntele, C.; Budak, S.; Oks, E.; Nikolaev, A.; Ezdesir, A.; Tek, Z.

    2007-08-01

    Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 1017 ion/cm2 and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

  8. Thermal characterization of Ag and Ag + N ion implanted ultra-high molecular weight polyethylene (UHMWPE)

    Energy Technology Data Exchange (ETDEWEB)

    Sokullu Urkac, E. [Department of Materials Science, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey)]. E-mail: emelsu@gmail.com; Oztarhan, A. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Tihminlioglu, F. [Department of Chemical Engineering, Izmir High Technology Institute, Gulbahcekoyu Urla, Izmir (Turkey); Kaya, N. [Bioengineering Department, Ege University, Bornova, Izmir 35100 (Turkey); Ila, D. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Muntele, C. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Budak, S. [Center for Irradiation of Materials, Alabama A and M University, Normal AL 35762 (United States); Oks, E. [H C Electronics Institute, Tomsk (Russian Federation); Nikolaev, A. [H C Electronics Institute, Tomsk (Russian Federation); Ezdesir, A. [R and D Department, PETKIM Holding A.S., Aliaga, Izmir 35801 (Turkey); Tek, Z. [Department of Physics, Celal Bayar University, Manisa (Turkey)

    2007-08-15

    Most of total hip joints are composed of ultra-high molecular weight polyethylene (UHMWPE ). However, as ultra-high molecular weight polyethylene is too stable in a body, wear debris may accumulate and cause biological response such as bone absorption and loosening of prosthesis. In this study, ultra-high molecular weight polyethylene samples were Ag and Ag + N hybrid ion implanted by using MEVVA ion implantation technique to improve its surface properties. Samples were implanted with a fluence of 10{sup 17} ion/cm{sup 2} and extraction voltage of 30 kV. Implanted and unimplanted samples were investigated by thermo-gravimetry analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (XRD) analysis, scanning electron microscopy (SEM), optical microscopy (OM) and contact Angle measurement. Thermal characterization results showed that the ion bombardment induced an increase in the % crystallinity, onset and termination degradation temperatures of UHMWPE.

  9. First isolation and molecular characterization of Ehrlichia canis in Costa Rica, Central America.

    Science.gov (United States)

    Romero, L E; Meneses, A I; Salazar, L; Jiménez, M; Romero, J J; Aguiar, D M; Labruna, M B; Dolz, G

    2011-08-01

    The present study investigated Ehrlichia species in blood samples from dogs suspected of clinical ehrlichiosis, using molecular and isolation techniques in cell culture. From a total of 310 canine blood samples analyzed by 16S rRNA nested PCR, 148 (47.7%) were positive for Ehrlichia canis. DNA from Ehrlichia chaffeensis or Ehrlichia ewingii was not detected in any sample using species-specific primers in separated reactions. Leukocytes from five PCR-positive dogs were inoculated into DH82 cells; successful isolation of E. canis was obtained in four samples. Partial sequence of the dsb gene of eight canine blood samples (including the five samples for in vitro isolation) was obtained by PCR and their analyses through BLAST showed 100% of identity with the corresponding sequence of E. canis in GenBank. This study represents the first molecular diagnosis, isolation, and molecular characterization of E. canis in dogs from Costa Rica. Copyright © 2010 Elsevier Ltd. All rights reserved.

  10. Impact of rapid molecular diagnostic tests on time to treatment initiation and outcomes in patients with multidrug-resistant tuberculosis, Tamil Nadu, India.

    Science.gov (United States)

    Nair, Dina; Navneethapandian, Pooranaganga D; Tripathy, Jaya Prasad; Harries, Anthony D; Klinton, Joel S; Watson, Basilea; Sivaramakrishnan, Gomathi N; Reddy, Devarajulu S; Murali, Lakshmi; Natrajan, Mohan; Swaminathan, Soumya

    2016-09-01

    India is replacing culture and drug sensitivity testing (CDST) with rapid molecular tests for diagnosing MDR-TB. We assessed the impact of rapid tests on time to initiation of treatment and outcomes in patients with MDR-TB compared with CDST. A retrospective cohort study involving MDR-TB patients from six districts in Tamil Nadu state, who underwent CDST (2010-2011) and rapid tests (2012-2013). There were 135 patients in the CDST group and 389 in the rapid diagnostic test group. Median time from sputum receipt at the laboratory to initiation of MDR-TB treatment was 130 days (IQR 75-213) in the CDST group and 22 days (IQR 14-38) in the rapid diagnostic test group (p30% in both groups and missing data were higher in CDST (13%) compared with rapid tests (3%). There were significantly higher risks of unfavourable treatment outcomes in males (aRR 1.3, 95% CI 1.1-1.5) and those with treatment initiation delays >30 days (aRR 1.3, 95% CI 1.0-1.6). Rapid molecular diagnostic tests shortened the time to initiate treatment which was associated with reduced unfavourable outcomes in MDR-TB patients. This supports the policy to scale up these tests in India. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Molecular characterization of Giardia intestinalis assemblage E from goat kids in Bangladesh

    OpenAIRE

    Mohammad Alamgir Hossain; Sohana Akter Mina; Lolo Wal Marzan; Mohammad Asif Imran Khan Emon; Rasel Das; AMAM Zonaed Siddiki

    2015-01-01

    Objective: To molecularly characterize Giardia in goat kids to elucidate the possible zoonotic hazards in Bangladesh and find out the role of Giardia protozoan parasite as a source of human infection. Methods: Fecal samples of 100 goat kids were genotyped by nested PCR amplification of β-giardin gene fragment followed by sequencing and analysis. Results: The total prevalence of Giardia in goat kids was 3% (3/100) and the infection is more widespread in younger (P = 0.36), Bl...

  12. Cutaneous Pythiosis in calves: An epidemiologic, pathologic, serologic and molecular characterization

    Directory of Open Access Journals (Sweden)

    Guilherme Konradt

    2016-12-01

    Full Text Available This study reports the epidemiological, pathological and mycological findings of cutaneous pythiosis in cattle in southern Brazil. 23 calves, that were kept next to a river with extensive marshy regions, presented ulcerated cutaneous lesions in thoracic and pelvic limbs, sometimes extending to the ventral thoracic region. Histopathological examination revealed multifocal pyogranulomas in the superficial and deep dermis. The Grocott-Methenamine silver, immunohistochemistry anti-Pythium insidiosum, ELISA serology and molecular characterization demonstrated the agent P. insidiosum in these cases.

  13. Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou, E-mail: eatonch@gmail.com

    2014-10-01

    Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast β-relaxation is followed by a much slower α-relaxation. There is a little change in the structural properties in the β-relaxation region, while major configuration rearrangements occurred in the α-relaxation range and the crystallization process was completed at the end of α-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.

  14. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    Energy Technology Data Exchange (ETDEWEB)

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  15. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    International Nuclear Information System (INIS)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R.

    2014-01-01

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  16. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    Directory of Open Access Journals (Sweden)

    Li Hai-Long

    2011-06-01

    Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  17. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

    Science.gov (United States)

    Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

    2011-06-10

    Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  18. Molecular characterization of Mycobacterium bovis strains isolated from cattle slaughtered at two abattoirs in Algeria

    Directory of Open Access Journals (Sweden)

    Ouzrout Rachid

    2009-01-01

    Full Text Available Abstract Background Bovine Tuberculosis is prevalent in Algeria despite governmental attempts to control the disease. The objective of this study was to conduct, for the first time, molecular characterization of a population sample of Mycobacterium bovis strains isolated from slaughter cattle in Algeria. Between August and November 2007, 7250 animals were consecutively screened at the abattoirs of Algiers and Blida. In 260 animals, gross visible granulomatous lesions were detected and put into culture. Bacterial isolates were subsequently analysed by molecular methods. Results Altogether, 101 bacterial strains from 100 animals were subjected to molecular characterization. M. bovis was isolated from 88 animals. Other bacteria isolated included one strain of M. caprae, four Rhodococcus equi strains, three Non-tuberculous Mycobacteria (NTM and five strains of other bacterial species. The M. bovis strains isolated showed 22 different spoligotype patterns; four of them had not been previously reported. The majority of M. bovis strains (89% showed spoligotype patterns that were previously observed in strains from European cattle. Variable Number of Tandem Repeat (VNTR typing supported a link between M. bovis strains from Algeria and France. One spoligotype pattern has also been shown to be frequent in M. bovis strains from Mali although the VNTR pattern of the Algerian strains differed from the Malian strains. Conclusion M. bovis infections account for a high amount of granulomatous lesions detected in Algerian slaughter cattle during standard meat inspection at Algiers and Blida abattoir. Molecular typing results suggested a link between Algerian and European strains of M. bovis.

  19. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

    2014-06-10

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  20. Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

    Directory of Open Access Journals (Sweden)

    Subin eHada

    2014-06-01

    Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  1. The evolution of advanced molecular diagnostics for the detection and characterization of Mycoplasma pneumoniae

    Directory of Open Access Journals (Sweden)

    Maureen H. Diaz

    2016-03-01

    Full Text Available Over the past several years there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis and sequencing typing (MLVA and MLST, respectively, matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS, single nucleotide polymorphism (SNP typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

  2. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

    Science.gov (United States)

    Diaz, Maureen H; Winchell, Jonas M

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

  3. Molecular characterization of multidrug-resistant Shigella spp. of food origin.

    Science.gov (United States)

    Ahmed, Ashraf M; Shimamoto, Tadashi

    2015-02-02

    Shigella spp. are the causative agents of food-borne shigellosis, an acute enteric infection. The emergence of multidrug-resistant clinical isolates of Shigella presents an increasing challenge for clinicians in the treatment of shigellosis. Several studies worldwide have characterized the molecular basis of antibiotic resistance in clinical Shigella isolates of human origin, however, to date, no such characterization has been reported for Shigella spp. of food origin. In this study, we characterized the genetic basis of multidrug resistance in Shigella spp. isolated from 1600 food samples (800 meat products and 800 dairy products) collected from different street venders, butchers, retail markets, and slaughterhouses in Egypt. Twenty-four out of 27 Shigella isolates (88.9%) showed multidrug resistance phenotypes to at least three classes of antimicrobials. The multidrug-resistant Shigella spp. were as follows: Shigella flexneri (66.7%), Shigella sonnei (18.5%), and Shigella dysenteriae (3.7%). The highest resistance was to streptomycin (100.0%), then to kanamycin (95.8%), nalidixic acid (95.8%), tetracycline (95.8%), spectinomycin (93.6%), ampicillin (87.5%), and sulfamethoxazole/trimethoprim (87.5%). PCR and DNA sequencing were used to screen and characterize integrons and antibiotic resistance genes. Our results indicated that 11.1% and 74.1% of isolates were positive for class 1 and class 2 integrons, respectively. Beta-lactamase-encoding genes were identified in 77.8% of isolates, and plasmid-mediated quinolone resistance genes were identified in 44.4% of isolates. These data provide useful information to better understand the molecular basis of antimicrobial resistance in Shigella spp. To the best of our knowledge, this is the first report of the molecular characterization of antibiotic resistance in Shigella spp. isolated from food. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Use of FTA® card methodology for sampling and molecular characterization of Echinococcus granulosus sensu lato in Africa.

    Science.gov (United States)

    Boué, Franck; El Berbri, Ikhlass; Hormaz, Vanessa; Boucher, Jean-Marc; El Mamy, Ahmed Bezeid; Traore, Abdallah; Fihri, Ouafaa Fassi; Petavy, Anne-Françoise; Dakkak, Allal; Umhang, Gérald

    2017-02-01

    Cystic Echinococcosis is a parasitic disease caused by the cestode Echinococcus granulosus widely distributed in Africa. Monitoring of this parasite requires access to cyst samples on intermediate hosts observed at the slaughterhouse. In order to facilitate sampling in the field and analysis, the French National Reference Laboratory for Echinococcus spp. has developed a tissue derived from DNA sampling with FTA ® card technology. The DNA samples were taken by applying the FTA ® paper on the germinal layer after opening the cysts. The sampling technique was validated using frozen cysts (n = 76) stored in the laboratory and from field samples (n = 134) taken at the slaughterhouse by veterinarian technicians during meat inspection in Morocco, Mali and Mauritania. DNA was extracted after several weeks of storage at room temperature. PCR assays were performed using primers for generic cestode (cox1) and amplified fragments were sequenced. All samples taken in the lab and 80% of field samples were capable of molecular characterization. Cyst-derived DNA from FTA ® samples can be useful for easy sampling, storage and rapid, safe and cheap shipment. The use of the FTA methodology will facilitate studies in the field to investigate the presence and genetic characterization of E. granulosus sensu lato in African countries. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Molecular cloning and characterization of a novel pyrethroid-hydrolyzing esterase originating from the Metagenome

    Directory of Open Access Journals (Sweden)

    Liu Yu

    2008-12-01

    , purified and characterized. The molecular mass of the native enzyme was approximately 31 kDa as determined by gel filtration. The results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the deduced amino acid sequence of the Pye3 indicated molecular mass of 31 kDa and 31.5 kDa, respectively, suggesting that the Pye3 is a monomer. The purified Pye3 not only degraded all pyrethroid pesticides tested, but also hydrolyzed ρ-nitrophenyl esters of medium-short chain fatty acids, indicating that the Pye3 is an esterase with broader specificity. The Km values for trans-Permethrin and cis-permethrin are 0.10 μM and 0.18 μM, respectively, and these catalytic properties were superior to carboxylesterases from resistant insects and mammals. The catalytic activity of the Pye3 was strongly inhibited by Hg2+, Ag+, ρ-chloromercuribenzoate, whereas less pronounced effect was observed in the presence of divalent cations, the chelating agent EDTA and phenanthroline. Conclusion A novel pyrethroid-hydrolyzing esterase gene was successfully cloned using metagenomic DNA combined with activity-based functional screening from soil, the broader substrate specificities and higher activity of the pyrethroid-hydrolyzing esterase (Pye3 make it an ideal candidate for in situ for detoxification of pyrethroids where they cause environmental contamination problems. Consequently, metagenomic DNA clone library offers possibilities to discover novel bio-molecules through the expression of genes from uncultivated bacteria.

  6. Real-time polymerase chain reaction assay for the rapid detection and characterization of chloroquine-resistant Plasmodium falciparum malaria in returned travelers.

    Science.gov (United States)

    Farcas, Gabriella A; Soeller, Rainer; Zhong, Kathleen; Zahirieh, Alireza; Kain, Kevin C

    2006-03-01

    Imported drug-resistant malaria is a growing problem in industrialized countries. Rapid and accurate diagnosis is essential to prevent malaria-associated mortality in returned travelers. However, outside of a limited number of specialized centers, the microscopic diagnosis of malaria is slow, unreliable, and provides little information about drug resistance. Molecular diagnostics have the potential to overcome these limitations. We developed and evaluated a rapid, real-time polymerase chain reaction (PCR) assay to detect Plasmodium falciparum malaria and chloroquine (CQ)-resistance determinants in returned travelers who are febrile. A real-time PCR assay based on detection of the K76T mutation in PfCRT (K76T) of P. falciparum was developed on a LightCycler platform (Roche). The performance characteristics of the real-time assay were compared with those of the nested PCR-restriction fragment-length polymorphism (RFLP) and the sequence analyses of samples obtained from 200 febrile returned travelers, who included 125 infected with P. falciparum (48 of whom were infected CQ-susceptible [K76] and 77 of whom were CQ-resistant [T76] P. falciparum), 22 infected with Plasmodium vivax, 10 infected with Plasmodium ovale, 3 infected with Plasmodium malariae malaria, and 40 infected with other febrile syndromes. All patient samples were coded, and all analyses were performed blindly. The real-time PCR assay detected multiple pfcrt haplotypes associated with CQ resistance in geographically diverse malaria isolates acquired by travelers. Compared with nested-PCR RFLP (the reference standard), the real-time assay was 100% sensitive and 96.2% specific for detection of the P. falciparum K76T mutation. This assay is rapid, sensitive, and specific for the detection and characterization of CQ-resistant P. falciparum malaria in returned travelers. This assay is automated, standardized, and suitable for routine use in clinical diagnostic laboratories.

  7. Characterization of molecularly imprinted polymers using a new polar solvent titration method.

    Science.gov (United States)

    Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

    2014-07-01

    A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

  8. Rapid affinity-purification and physicochemical characterization of pumpkin (Cucurbita maxima) phloem exudate lectin.

    Science.gov (United States)

    Narahari, Akkaladevi; Swamy, Musti J

    2010-04-21

    The chito-oligosaccharide-specific lectin from pumpkin (Cucurbita maxima) phloem exudate has been purified to homogeneity by affinity chromatography on chitin. After SDS/PAGE in the presence of 2-mercaptoethanol, the pumpkin phloem lectin yielded a single band corresponding to a molecular mass of 23.7 kDa, whereas ESI-MS (electrospray ionization MS) gave the molecular masses of the subunit as 24645 Da. Analysis of the CD spectrum of the protein indicated that the secondary structure of the lectin consists of 9.7% alpha-helix, 35.8% beta-sheet, 22.5% beta-turn and 32.3% unordered structure. Saccharide binding did not significantly affect the secondary and tertiary structures of the protein. The haemagglutinating activity of pumpkin phloem lectin was mostly unaffected in the temperature range 4-70 degrees C, but a sharp decrease was seen between 75 and 85 degrees C. Differential scanning calorimetric and CD spectroscopic studies suggest that the lectin undergoes a co-operative thermal unfolding process centred at approx. 81.5 degrees C, indicating that it is a relatively stable protein.

  9. Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria.

    Science.gov (United States)

    Zait, Houria; Kouidri, Mokhtaria; Grenouillet, Florence Elisabeth; Umhang, Gérald; Millon, Laurence; Hamrioui, Boussad; Grenouillet, Frédéric

    2016-06-01

    In Algeria, previous studies investigated genotypes of Echinococcus granulosus sensu lato in animals and identified E. granulosus sensu stricto (s.s.) genotypes G1 and G3 whereas Echinococcus canadensis genotype G6 was only reported from dromedary cysts. Molecular data on human cystic echinococcosis (CE) were limited. We implemented a large genotyping study of hydatid cysts from humans and livestock animals to specify CE's molecular epidemiology and the genetic diversity in Algeria. Fifty-four human CE cysts from patients predominantly admitted in surgical units from Mustapha Hospital, Algiers, and 16 cysts from livestock animals gathered in two geographically distinct slaughterhouses, Tiaret and Tamanrasset, were collected. Molecular characterization was performed using sequencing of two mitochondrial genes, cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit I (NDI). In humans, G1 of E. granulosus s.s. was the main genotype (90.7 %); four samples (7.4 %) were characterized as E. granulosus s.s. G3 and one cyst as E. canadensis G6 (1.8 %). This molecular confirmation of E. canadensis G6 human infection in Algeria was observed in a Tuareg female living in a desertic area in Tamanrasset. All cysts from sheep, cattle, and goat were identified as E. granulosus s.s. G1 and the two cysts originating from dromedary as E. canadensis G6. Twenty concatenated haplotypes (COI + NDI) were characterized. Among E. granulosus s.s., one haplotype (HL1) was highly predominant in both humans and animals cysts (71.6 %). This study revealed main occurrence of E. granulosus s.s. in humans and livestock animals, with description of a predominant shared haplotype corresponding to the main worldwide observed haplotype E.granulosus s.s. G1. E. canadensis G6 was limited to South Algeria, in dromedary as well as in human.

  10. The vaginal microbiota: what have we learned after a decade of molecular characterization?

    Science.gov (United States)

    van de Wijgert, Janneke H H M; Borgdorff, Hanneke; Verhelst, Rita; Crucitti, Tania; Francis, Suzanna; Verstraelen, Hans; Jespers, Vicky

    2014-01-01

    We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.

  11. The vaginal microbiota: what have we learned after a decade of molecular characterization?

    Directory of Open Access Journals (Sweden)

    Janneke H H M van de Wijgert

    Full Text Available We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A to determine if consistent molecular vaginal microbiota (VMB composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV, and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.

  12. MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex.

    Directory of Open Access Journals (Sweden)

    Carolina Firacative

    Full Text Available BACKGROUND: The Cryptococcus neoformans/C. gattii species complex comprises two sibling species that are divided into eight major molecular types, C. neoformans VNI to VNIV and C. gattii VGI to VGIV. These genotypes differ in host range, epidemiology, virulence, antifungal susceptibility and geographic distribution. The currently used phenotypic and molecular identification methods for the species/molecular types are time consuming and expensive. As Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS offers an effective alternative for the rapid identification of microorganisms, the objective of this study was to examine its potential for the identification of C. neoformans and C. gattii strains at the intra- and inter-species level. METHODOLOGY: Protein extracts obtained via the formic acid extraction method of 164 C. neoformans/C. gattii isolates, including four inter-species hybrids, were studied. RESULTS: The obtained mass spectra correctly identified 100% of all studied isolates, grouped each isolate according to the currently recognized species, C. neoformans and C. gattii, and detected potential hybrids. In addition, all isolates were clearly separated according to their major molecular type, generating greater spectral differences among the C. neoformans molecular types than the C. gattii molecular types, most likely reflecting a closer phylogenetic relationship between the latter. The number of colonies used and the incubation length did not affect the results. No spectra were obtained from intact yeast cells. An extended validated spectral library containing spectra of all eight major molecular types was established. CONCLUSIONS: MALDI-TOF MS is a rapid identification tool for the correct recognition of the two currently recognized human pathogenic Cryptococcus species and offers a simple method for the separation of the eight major molecular types and the detection of hybrid strains within this

  13. Rapid biosynthesis and characterization of silver nanoparticles: an assessment of antibacterial and antimycotic activity

    Science.gov (United States)

    Kanawaria, Sajjan Kumar; Sankhla, Aryan; Jatav, Pradeep Kumar; Yadav, Raghvendra Singh; Verma, Kumar Sambhav; Velraj, Parthiban; Kachhwaha, Sumita; Kothari, Shanker Lal

    2018-04-01

    Bioassisted synthesis provides a facile, convenient, and promising approach to produce many inorganic nanostructures. Herein, we report a rapid biosynthesis of silver nanoparticles (AgNPs) using Thuja occidentalis (L.) leaf extract with an emphasis on their antibacterial and antimycotic activity. Interestingly, the synthesis of AgNPs was completed in a short duration of 35-40 min. The electron micrographs showed AgNPs with particles Bacillus subtilis. An AgNP solution with 30 µg/ml concentration arrested the growth of bacterial strains making a zone of inhibition > 15 mm. The antimycotic activity against Aspergillus niger, Fusarium spp., and Alternaria alternata species increased monotonically with nanoparticle concentration in the growth media. A 10 ppm solution of AgNP was detrimental to fungal growth. Thus, the technique provides an avenue to synthesize antibiotic AgNPs without use of other external agents.

  14. Characterizing millisecond intermediates in hemoproteins using rapid-freeze-quench resonance Raman spectroscopy.

    Science.gov (United States)

    Matsumura, Hirotoshi; Moënne-Loccoz, Pierre

    2014-01-01

    The combination of rapid freeze quenching (RFQ) with resonance Raman (RR) spectroscopy represents a unique tool with which to investigate the nature of short-lived intermediates formed during the enzymatic reactions of metalloproteins. Commercially available equipment allows trapping of intermediates within a millisecond to second time scale for low-temperature RR analysis resulting in the direct detection of metal-ligand vibrations and porphyrin skeletal vibrations in hemoproteins. This chapter briefly discusses RFQ-RR studies carried out previously in our laboratory and presents, as a practical example, protocols for the preparation of RFQ samples of the reaction of metmyoglobin with nitric oxide (NO) under anaerobic conditions. Also described are important controls and practical procedures for the analysis of these samples by low-temperature RR spectroscopy.

  15. Rapid characterization of a nanomaterial structure using X-ray reciprocal-lattice-space imaging

    International Nuclear Information System (INIS)

    Sakata, Osami; Yoshimoto, Mamoru; Miki, Kazushi

    2006-01-01

    The X-ray reciprocal-lattice-space imaging method is able to record the reciprocal-lattice-space of nanostructure by sample-and-detector fixed geometry. This method was developed by the surface structure analysis beam line BL13XU of SPring-8. Outline of the X-ray diffraction method and basic principles of the X-ray reciprocal-lattice-space imaging method, and application examples are stated. The method is able to find out the Bragg conditions of nanostructure of surface in the atmosphere. The reciprocal-lattice of the embedded trace atomic wires was observed. The trace atoms of Bi atomic wires embedded in silicone showed the diffraction signal and image by a short exposure time. This method is useful at rapid non-destructive measurement of nanostructure. (S.Y.)

  16. Characterization of reaction conditions providing rapid and specific cysteine alkylation for peptide-based mass spectrometry.

    Science.gov (United States)

    Paulech, Jana; Solis, Nestor; Cordwell, Stuart J

    2013-01-01

    Alkylation converts Cys thiols to thioethers and prevents unwanted side reactions, thus facilitating mass spectrometric identification of Cys-containing peptides. Alkylation occurs preferentially at Cys due to its high nucleophilicity, however reactions at other such sites are possible. N-ethylmaleimide (NEM) shows rapid reaction kinetics with Cys and careful definition of reaction conditions results in little reactivity at other sites. Analysis of a protein standard alkylated under differing reaction conditions (pH, NEM concentrations and reaction times) was performed using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and selected reaction monitoring (SRM) of NEM-modified and unmodified peptide pairs. Mis-alkylation sites at primary and secondary amines were identified and limited to one equivalent of NEM. No evidence for hydroxyl or thioether alkylation was observed. Improved specificity was achieved by restricting the pH below neutral, NEM concentration below 10mM and/or reaction time to below 5min. Maximal removal of Cys activity was observed in tissue homogenates at 40mM NEM within 1min, dependent upon efficient protein denaturation. SRM assays identified peptide-specific levels of mis-alkylation, indicating that NEM-modified to unmodified ratios did not exceed 10%, with the exception of Cys alkylation that proceeded to 100%, and some Lys residues that resulted in tryptic missed cleavages. High reactivity was observed for His residues considering their relatively low abundance. These data indicate that rapid and specific Cys alkylation is possible with NEM under relatively mild conditions, with more abrasive conditions leading to increased non-specific alkylation without appreciable benefit for MS-based proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. [Molecular characterization of resistance mechanisms: methicillin resistance Staphylococcus aureus, extended spectrum β-lactamases and carbapenemases].

    Science.gov (United States)

    Oteo, Jesús; Belén Aracil, María

    2015-07-01

    Multi-drug resistance in bacterial pathogens increases morbidity and mortality in infected patients and it is a threat to public health concern by their high capacity to spread. For both reasons, the rapid detection of multi-drug resistant bacteria is critical. Standard microbiological procedures require 48-72 h to provide the antimicrobial susceptibility results, thus there is emerging interest in the development of rapid detection techniques. In recent years, the use of selective and differential culture-based methods has widely spread. However, the capacity for detecting antibiotic resistance genes and their low turnaround times has made molecular methods a reference for diagnosis of multidrug resistance. This review focusses on the molecular methods for detecting some mechanisms of antibiotic resistance with a high clinical and epidemiological impact: a) Enzymatic resistance to broad spectrum β-lactam antibiotics in Enterobacteriaceae, mainly extended spectrum β-lactamases (ESBL) and carbapenemases; and b) methicillin resistance in Staphylococcus aureus. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  18. Characterizing Urban Household Waste Generation and Metabolism Considering Community Stratification in a Rapid Urbanizing Area of China.

    Directory of Open Access Journals (Sweden)

    Lishan Xiao

    Full Text Available The relationship between social stratification and municipal solid waste generation remains uncertain under current rapid urbanization. Based on a multi-object spatial sampling technique, we selected 191 households in a rapidly urbanizing area of Xiamen, China. The selected communities were classified into three types: work-unit, transitional, and commercial communities in the context of housing policy reform in China. Field survey data were used to characterize household waste generation patterns considering community stratification. Our results revealed a disparity in waste generation profiles among different households. The three community types differed with respect to family income, living area, religious affiliation, and homeowner occupation. Income, family structure, and lifestyle caused significant differences in waste generation among work-unit, transitional, and commercial communities, respectively. Urban waste generation patterns are expected to evolve due to accelerating urbanization and associated community transition. A multi-scale integrated analysis of societal and ecosystem metabolism approach was applied to waste metabolism linking it to particular socioeconomic conditions that influence material flows and their evolution. Waste metabolism, both pace and density, was highest for family structure driven patterns, followed by lifestyle and income driven. The results will guide community-specific management policies in rapidly urbanizing areas.

  19. Characterizing Urban Household Waste Generation and Metabolism Considering Community Stratification in a Rapid Urbanizing Area of China.

    Science.gov (United States)

    Xiao, Lishan; Lin, Tao; Chen, Shaohua; Zhang, Guoqin; Ye, Zhilong; Yu, Zhaowu

    2015-01-01

    The relationship between social stratification and municipal solid waste generation remains uncertain under current rapid urbanization. Based on a multi-object spatial sampling technique, we selected 191 households in a rapidly urbanizing area of Xiamen, China. The selected communities were classified into three types: work-unit, transitional, and commercial communities in the context of housing policy reform in China. Field survey data were used to characterize household waste generation patterns considering community stratification. Our results revealed a disparity in waste generation profiles among different households. The three community types differed with respect to family income, living area, religious affiliation, and homeowner occupation. Income, family structure, and lifestyle caused significant differences in waste generation among work-unit, transitional, and commercial communities, respectively. Urban waste generation patterns are expected to evolve due to accelerating urbanization and associated community transition. A multi-scale integrated analysis of societal and ecosystem metabolism approach was applied to waste metabolism linking it to particular socioeconomic conditions that influence material flows and their evolution. Waste metabolism, both pace and density, was highest for family structure driven patterns, followed by lifestyle and income driven. The results will guide community-specific management policies in rapidly urbanizing areas.

  20. Combining nanocalorimetry and dynamic transmission electron microscopy for in situ characterization of materials processes under rapid heating and cooling

    Energy Technology Data Exchange (ETDEWEB)

    Grapes, Michael D., E-mail: mgrapes1@jhu.edu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Materials Measurement Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States); LaGrange, Thomas; Reed, Bryan W.; Campbell, Geoffrey H. [Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Friedman, Lawrence H.; LaVan, David A., E-mail: david.lavan@nist.gov [Materials Measurement Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899 (United States); Weihs, Timothy P., E-mail: weihs@jhu.edu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    2014-08-15

    Nanocalorimetry is a chip-based thermal analysis technique capable of analyzing endothermic and exothermic reactions at very high heating and cooling rates. Here, we couple a nanocalorimeter with an extremely fast in situ microstructural characterization tool to identify the physical origin of rapid enthalpic signals. More specifically, we describe the development of a system to enable in situ nanocalorimetry experiments in the dynamic transmission electron microscope (DTEM), a time-resolved TEM capable of generating images and electron diffraction patterns with exposure times of 30 ns–500 ns. The full experimental system consists of a modified nanocalorimeter sensor, a custom-built in situ nanocalorimetry holder, a data acquisition system, and the DTEM itself, and is capable of thermodynamic and microstructural characterization of reactions over a range of heating rates (10{sup 2} K/s–10{sup 5} K/s) accessible by conventional (DC) nanocalorimetry. To establish its ability to capture synchronized calorimetric and microstructural data during rapid transformations, this work describes measurements on the melting of an aluminum thin film. We were able to identify the phase transformation in both the nanocalorimetry traces and in electron diffraction patterns taken by the DTEM. Potential applications for the newly developed system are described and future system improvements are discussed.

  1. Rapid Source Characterization of the 2011 Mw 9.0 off the Pacific coast of Tohoku Earthquake

    Science.gov (United States)

    Hayes, Gavin P.

    2011-01-01

    On March 11th, 2011, a moment magnitude 9.0 earthquake struck off the coast of northeast Honshu, Japan, generating what may well turn out to be the most costly natural disaster ever. In the hours following the event, the U.S. Geological Survey National Earthquake Information Center led a rapid response to characterize the earthquake in terms of its location, size, faulting source, shaking and slip distributions, and population exposure, in order to place the disaster in a framework necessary for timely humanitarian response. As part of this effort, fast finite-fault inversions using globally distributed body- and surface-wave data were used to estimate the slip distribution of the earthquake rupture. Models generated within 7 hours of the earthquake origin time indicated that the event ruptured a fault up to 300 km long, roughly centered on the earthquake hypocenter, and involved peak slips of 20 m or more. Updates since this preliminary solution improve the details of this inversion solution and thus our understanding of the rupture process. However, significant observations such as the up-dip nature of rupture propagation and the along-strike length of faulting did not significantly change, demonstrating the usefulness of rapid source characterization for understanding the first order characteristics of major earthquakes.

  2. Single-shot T1 mapping of the corpus callosum: A rapid characterization of fiber bundle anatomy

    Directory of Open Access Journals (Sweden)

    Sabine eHofer

    2015-05-01

    Full Text Available Using diffusion-tensor MRI and fiber tractography the topographic organization of the corpus callosum (CC has been described to comprise 5 segments with fibers projecting into prefrontal (I, premotor and supplementary motor (II, primary motor (III, and primary sensory areas (IV, as well as into parietal, temporal, and occipital cortical areas (V. In order to more rapidly characterize the underlying anatomy of these segments, this study used a novel single-shot T1 mapping method to quantitatively determine T1 relaxation times in the human CC. A region-of-interest analysis revealed a tendency for the lowest T1 relaxation times in the genu and the highest T1 relaxation times in the somatomotor region of the CC. This observation separates regions dominated by myelinated fibers with large diameters (somatomotor area from densely packed smaller axonal bundles (genu with less myelin. The results indicate that characteristic T1 relaxation times in callosal profiles provide an additional means to monitor differences in fiber anatomy, fiber density, and gray matter in respective neocortical areas. In conclusion, rapid T1 mapping allows for a characterization of the axonal architecture in an individual CC in less than 10 s. The approach emerges as a valuable means for studying neocortical brain anatomy with possible implications for the diagnosis of neurodegenerative processes.

  3. Rapid earthquake characterization using MEMS accelerometers and volunteer hosts following the M 7.2 Darfield, New Zealand, Earthquake

    Science.gov (United States)

    Lawrence, J. F.; Cochran, E.S.; Chung, A.; Kaiser, A.; Christensen, C. M.; Allen, R.; Baker, J.W.; Fry, B.; Heaton, T.; Kilb, Debi; Kohler, M.D.; Taufer, M.

    2014-01-01

    We test the feasibility of rapidly detecting and characterizing earthquakes with the Quake‐Catcher Network (QCN) that connects low‐cost microelectromechanical systems accelerometers to a network of volunteer‐owned, Internet‐connected computers. Following the 3 September 2010 M 7.2 Darfield, New Zealand, earthquake we installed over 180 QCN sensors in the Christchurch region to record the aftershock sequence. The sensors are monitored continuously by the host computer and send trigger reports to the central server. The central server correlates incoming triggers to detect when an earthquake has occurred. The location and magnitude are then rapidly estimated from a minimal set of received ground‐motion parameters. Full seismic time series are typically not retrieved for tens of minutes or even hours after an event. We benchmark the QCN real‐time detection performance against the GNS Science GeoNet earthquake catalog. Under normal network operations, QCN detects and characterizes earthquakes within 9.1 s of the earthquake rupture and determines the magnitude within 1 magnitude unit of that reported in the GNS catalog for 90% of the detections.

  4. Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

    Science.gov (United States)

    Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

    2016-09-16

    The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

  5. Rapid-Response Characterization of Near-Earth Asteroids Using KMTNet-SAAO

    Science.gov (United States)

    Erasmus, Nicolas; Mommert, Michael; Trilling, David E.; Sickafoose, Amanda A.; van Gend, Carel; Hora, Joseph L.; Worters, Hannah L.

    2017-10-01

    We present here VRI spectrophotometry of 39 near-Earth asteroids (NEAs) observed with the Sutherland, South Africa, node of the Korea Microlensing Telescope Network (KMTNet). Of the 39 NEAs, 19 were targeted, but because of KMTNet’s large 2 deg × 2 deg field of view, 20 serendipitous NEAs were also captured in the observing fields. Our rapid-response approach meant targeted observations were performed within 44 days (median: 16 days, min: 4 days) of each NEA’s discovery date. Our broadband spectrophotometry is reliable enough to distinguish among four asteroid taxonomies and we were able to confidently categorize 31 of the 39 observed targets as either a S-, C-, X- or D-type asteroid. Our data suggest that the ratio between “stony” S-type NEAs and “not- stony” (C+X+D)-type NEAs, with H magnitudes between 15 and 25, is roughly 1:1. Additionally, we report ~1-hour light curve data for each NEA. Of the 39 targets, we were able to resolve the complete rotation period and amplitude for six and place lower limits for the remaining targets.Based on the success of this pilot study we plan to continue KMTNet observations but also make use of Lesedi, a new 1-meter remotely-operable telescope also situated in Sutherland, to perform similar spectrophotometric observations in the future. As before, we plan to target newly discovered NEAs in order to continue the rapid-response approach. With Lesedi, observations will take place throughout the year and we plan to include smaller NEAs (larger H magnitudes) in our sample. We will also increase the observed duration of each NEA to 2-3 hours so we are more likely to observe a complete rotation period for our observed NEAs.This study was facilitated by observations made at the South African Astronomical Observatory (SAAO) and this work is partially supported by the South African National Research Foundation (NRF). This work is supported in part by the National Aeronautics and Space Administration (NASA) under grant

  6. Caracterização molecular de butiazeiro por marcadores RAPD Molecular characterization of Pindo palm by RAPD markers

    Directory of Open Access Journals (Sweden)

    Adrise Medeiros Nunes

    2008-09-01

    Full Text Available O grupo botânico Arecaceae é de extremo interesse por compreender plantas em extinção e por apresentar um grande potencial de exploração econômica. O butiazeiro (Butia capitata (Mart. Becc. ocorre naturalmente no Sul do Brasil. Sua caracterização molecular é de extremo interesse para futuros trabalhos de melhoramento genético. Assim sendo, verificou-se a variabilidade genética existente entre vinte e dois genótipos de butiazeiro da espécie (Butia capitata, pertencentes ao BAG (Banco Ativo de Germoplasma de frutíferas nativas do Centro Agropecuário da Palma - UFPel. Esses genótipos foram analisados usando marcadores do tipo RAPD (Random Amplified Polymorphic DNA. Um total de 136 fragmentos foram obtidos, sendo 77 polimórficos. O primer OPA11 apresentou maior polimorfismo, produzindo 9 perfis diferentes. A análise de agrupamento, realizada pelo método UPGMA, produziu um dendrograma que permitiu a clara separação dos genótipos em dois grupos principais. Verificou-se que, com a técnica de marcadores de RAPD, foi possível obter um perfil molecular único e uma estimativa da variabilidade existente entre os genótipos de butiazeiro avaliados.The study of the botanical group Arecaceae is of extreme interest for evolving several endangered species of plants and for presenting a great potential of economical exploration. The Pindo palm (or wine palm, jelly palm (Butia capitata (Mart. Becc. is natural from the south of Brazil. Its molecular characterization is of extreme interest for future researches of genetic improvement. Since little is known about the variability of the species, the existent genetic variability was verified among twenty-two genotypes of Pindo palm (or wine palm, jelly palm, from BAG (Germoplasm Assets Bank of fruit trees native from the Agricultural Center of the Palma - UFPEL, which were analyzed using markers RAPD (Random Amplified Polymorphic DNA with Operon Technologies' decamers primers. With 21 primers

  7. Preparation, Characterization, and UV Irradiation of Mars Soil Analogues Under Simulated Martian Conditions to Support Detection of Molecular Biomarkers

    Science.gov (United States)

    Fornaro, T.; Brucato, J. R.; ten Kate, I. L.; Siljeström, S.; Steele, A.; Cody, G. D.; Hazen, R. M.

    2018-04-01

    We present laboratory activities of preparation, characterization, and UV irradiation processing of Mars soil analogues, which are key to support both in situ exploration and sample return missions devoted to detection of molecular biomarkers on Mars.

  8. Molecular Characterization of Clostridium difficile Isolates in China From 2010 to 2015

    Directory of Open Access Journals (Sweden)

    Xiao-shu Liu

    2018-04-01

    Full Text Available Clostridium difficile infection (CDI has become a worldwide public health problem causing high mortality and a large disease burden. Molecular typing and analysis is important for surveillance and infection control of CDI. However, molecular characterization of C. difficile across China is extremely rare. Here, we report on the toxin profiles, molecular subtyping with multilocus sequence typing (MLST and PCR ribotyping, and epidemiological characteristics of 199 C. difficile isolates collected between 2010 through 2015 from 13 participating centers across China. We identified 35 STs and 27 ribotypes (RTs among the 199 C. difficile isolates: ST35 (15.58%, ST3 (15.08%, ST37 (12.06%, and RT017 (14.07%, RT001 (12.06%, RT012 (11.56% are the most prevalent. One isolate with ST1 and 8 isolates with ST 11 were identified. We identified a new ST in this study, denoted ST332. The toxin profile tcdA+tcdB+tcdC+tcdR+tcdE+CDT- (65.83% was the predominant profile. Furthermore, 11 isolates with positive binary toxin genes were discovered. According to the PCR ribotyping, one isolate with RT 027, and 6 isolates with RT 078 were confirmed. The epidemiological characteristics of C. difficile in China shows geographical differences, and both the toxin profile and molecular types exhibit great diversity across the different areas.

  9. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

  10. Intact molecular characterization of cord factor (trehalose 6,6'-dimycolate) from nine species of mycobacteria by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Fujita, Yukiko; Naka, Takashi; McNeil, Michael R; Yano, Ikuya

    2005-10-01

    Cord factor (trehalose 6,6'-dimycolate, TDM) is an unique glycolipid with a trehalose and two molecules of mycolic acids in the mycobacterial cell envelope. Since TDM consists of two molecules of very long branched-chain 3-hydroxy fatty acids, the molecular mass ranges widely and in a complex manner. To characterize the molecular structure of TDM precisely and simply, an attempt was made to determine the mycolic acid subclasses of TDM and the molecular species composition of intact TDM by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for the first time. The results showed that less than 1 microg mycolic acid methyl ester of TDM from nine representative species of mycobacteria and TDM from the same species was sufficient to obtain well-resolved mass spectra composed of pseudomolecular ions [M+Na]+. Although the mass ion distribution was extremely diverse, the molecular species of each TDM was identified clearly by constructing a molecular ion matrix consisting of the combination of two molecules of mycolic acids. The results showed a marked difference in the molecular structure of TDM among mycobacterial species and subspecies. TDM from Mycobacterium tuberculosis (H37Rv and Aoyama B) showed a distinctive mass pattern and consisted of over 60 molecular ions with alpha-, methoxy- and ketomycolate. TDM from Mycobacterium bovis BCG Tokyo 172 similarly showed over 35 molecular ions, but that from M. bovis BCG Connaught showed simpler molecular ion clusters consisting of less than 35 molecular species due to a complete lack of methoxymycolate. Mass ions due to TDM from M. bovis BCG Connaught and Mycobacterium kansasii showed a biphasic distribution, but the two major peaks of TDM from M. kansasii were shifted up two or three carbon units higher compared with M. bovis BCG Connaught. Within the rapid grower group, in TDM consisting of alpha-, keto- and wax ester mycolate from Mycobacterium phlei and Mycobacterium flavescens, the

  11. Rapid characterization of transgenic and non-transgenic soybean oils by chemometric methods using NIR spectroscopy

    Science.gov (United States)

    Luna, Aderval S.; da Silva, Arnaldo P.; Pinho, Jéssica S. A.; Ferré, Joan; Boqué, Ricard

    Near infrared (NIR) spectroscopy and multivariate classification were applied to discriminate soybean oil samples into non-transgenic and transgenic. Principal Component Analysis (PCA) was applied to extract relevant features from the spectral data and to remove the anomalous samples. The best results were obtained when with Support Vectors Machine-Discriminant Analysis (SVM-DA) and Partial Least Squares-Discriminant Analysis (PLS-DA) after mean centering plus multiplicative scatter correction. For SVM-DA the percentage of successful classification was 100% for the training group and 100% and 90% in validation group for non transgenic and transgenic soybean oil samples respectively. For PLS-DA the percentage of successful classification was 95% and 100% in training group for non transgenic and transgenic soybean oil samples respectively and 100% and 80% in validation group for non transgenic and transgenic respectively. The results demonstrate that NIR spectroscopy can provide a rapid, nondestructive and reliable method to distinguish non-transgenic and transgenic soybean oils.

  12. Lock-in thermography as a rapid and reproducible thermal characterization method for magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Lemal, Philipp; Geers, Christoph; Monnier, Christophe A.; Crippa, Federica; Daum, Leopold; Urban, Dominic A.; Rothen-Rutishauser, Barbara [Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg (Switzerland); Bonmarin, Mathias, E-mail: mathias.bonmarin@zhaw.ch [Institute of Computational Physics, Zurich University of Applied Sciences, Technikumstrasse 9, 8400 Winterthur (Switzerland); Petri-Fink, Alke, E-mail: alke.fink@unifr.ch [Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg (Switzerland); Chemistry Department, University of Fribourg, Chemin du Museé 9, CH-1700 Fribourg (Switzerland); Moore, Thomas L., E-mail: thomaslee.moore@unifr.ch [Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg (Switzerland)

    2017-04-01

    Lock-in thermography (LIT) is a sensitive imaging technique generally used in engineering and materials science (e.g. detecting defects in composite materials). However, it has recently been expanded for investigating the heating power of nanomaterials, such as superparamagnetic iron oxide nanoparticles (SPIONs). Here we implement LIT as a rapid and reproducible method that can evaluate the heating potential of various sizes of SPIONs under an alternating magnetic field (AMF), as well as the limits of detection for each particle size. SPIONs were synthesized via thermal decomposition and stabilized in water via a ligand transfer process. Thermographic measurements of SPIONs were made by stimulating particles of varying sizes and increasing concentrations under an AMF. Furthermore, a commercially available SPION sample was included as an external reference. While the size dependent heating efficiency of SPIONs has been previously described, our objective was to probe the sensitivity limits of LIT. For certain size regimes it was possible to detect signals at concentrations as low as 0.1 mg Fe/mL. Measuring at different concentrations enabled a linear regression analysis and extrapolation of the limit of detection for different size nanoparticles. - Highlights: • A multi-sample screening assessment of magnetic nanoparticle thermal characteristics is shown via lock-in thermography. • Lower concentration limit of nanoparticle detection based on particle size is proposed. • A commercially available reference sample indicates the stability and reproducibility of LIT.

  13. Rapid Characterization of Fatty Acids in Oleaginous Microalgae by Near-Infrared Spectroscopy

    Directory of Open Access Journals (Sweden)

    Bin Liu

    2015-03-01

    Full Text Available The key properties of microalgal biodiesel are largely determined by the composition of its fatty acid methyl esters (FAMEs. The gas chromatography (GC based techniques for fatty acid analysis involve energy-intensive and time-consuming procedures and thus are less suitable for high-throughput screening applications. In the present study, a novel quantification method for microalgal fatty acids was established based on the near-infrared spectroscopy (NIRS technique. The lyophilized cells of oleaginous Chlorella containing different contents of lipids were scanned by NIRS and their fatty acid profiles were determined by GC-MS. NIRS models were developed based on the chemometric correlation of the near-infrared spectra with fatty acid profiles in algal biomass. The optimized NIRS models showed excellent performances for predicting the contents of total fatty acids, C16:0, C18:0, C18:1 and C18:3, with the coefficient of determination (R2 being 0.998, 0.997, 0.989, 0.991 and 0.997, respectively. Taken together, the NIRS method established here bypasses the procedures of cell disruption, oil extraction and transesterification, is rapid, reliable, and of great potential for high-throughput applications, and will facilitate the screening of microalgal mutants and optimization of their growth conditions for biodiesel production.

  14. Strategy for identification & characterization of Bartonella henselae with conventional & molecular methods

    Directory of Open Access Journals (Sweden)

    Kavita Diddi

    2013-01-01

    Full Text Available Background & objectives: Bartonella henselae is a fastidious gram-negative bacterium usually causing self limiting infections in immunocompetent individuals but often causes potentially life threatening infection, such as bacillary angiomatosis in immunocompromised patients. Both diagnosis of infections and research into molecular mechanisms of pathogenesis have been hindered by lack of appropriate and reliable diagnostic techniques. We undertook this study to standardize methods to characterize B. henselae in clinical samples to diagnose Bartonella infection correctly. Methods: B. henselae ATCC 49882 strain was procured from American type culture collection, USA. This strain was revived and maintained in the laboratory, and identification and characterization of this strain was done by conventional and molecular techniques, which included culture on various media, staining by different methods including electron microscopy, biochemical analysis by conventional methods and API, polymerase chain reaction (PCR for amplification of citrate synthase gene followed by restriction fragment length polymorphism (RFLP. Results: This organism was biochemically inert due to slow growth and generated unique identification code with API. The amplification of the citrate-synthase gene with primers yielded a 381 bp product followed by specific RFLP profile for B. henselae. Interpretation & conclusions: Bartonella is fastidious and fragile organism and should be handled carefully. Extra effort and careful observation are required to isolate and characterize this organism.

  15. Full-length genomic and molecular characterization of Canine parvovirus in dogs from North of Brazil.

    Science.gov (United States)

    Silva, S P; Silva, L N P P; Rodrigues, E D L; Cardoso, J F; Tavares, F N; Souza, W M; Santos, C M P; Martins, F M S; Jesus, I S; Brito, T C; Moura, T P C; Nunes, M R T; Casseb, L M N; Silva Filho, E; Casseb, A R

    2017-09-21

    With the objective of characterizing Canine parvovirus (CPV) from some suspected fecal samples of dogs collected from the Veterinarian Hospital in Belém city, five positive samples were found by PCR assay and an update molecular characterization was provided of the CPV-2 circulation in Belém. Through sequencing of the complete DNA sequences (NS1, NS2, VP1, and VP2 genes), the CPV-2 strain was identified as CPV-2b (Asn426Asp) circulating in Belém. The CPV-2b strain with a different change at the position Tyr324Leu was detected in all samples assessed and thus reported for the first time for the scientific community. Phylogenetic analysis indicated that Belém CPV-2b and CPV-2a strains would be related to a cluster with samples after the 1990s, suggesting that CPV-2b in Belém originated from CPV-2a circulating in Brazil after the 1990s. Potential recombination events were analyzed using RDP4 and SplitsTree4; therefore, results suggest that CPV-2 sequences here described were not potentially recombination events. Continuous monitoring and molecular characterization of CPV-2 samples are needed not only to identify possible genetic and antigenic changes that may interfere with the effectiveness of vaccines but also to bring a better understanding of the mechanisms that drive the evolution of CPV-2 in Brazil.

  16. Physiological and Molecular Characterization of Cephaleuros virescens Occurring in Mango Trees.

    Science.gov (United States)

    Vasconcelos, Camila Vilela; Pereira, Fabíola Teodoro; Duarte, Elizabeth Amélia Alves; de Oliveira, Thiago Alves Santos; Peixoto, Nei; Carvalho, Daniel Diego Costa

    2018-06-01

    The objective of this work was to accomplish the isolation, molecular identification and characterizing the physiology of the causal agent of the algal spot in mango trees. For this purpose, the pathogen growth was assessed in different culture media, with subsequent observation and measurements of the filamentous cells. The molecular identification was made using mycelium obtained from leaf lesions and pure algae colonies grown in culture medium. Descriptions based on DNA sequencing indicated that the algae is Cephaleuros virescens . The algae must be isolated primarily in liquid medium for further pricking into agar medium. The highest mycelial growth average in Petri dishes occurred when the algae were grown in Trebouxia and BBM. Trebouxia enabled larger cells in the filamentous cells when compared to other culture media.

  17. Molecular-level characterization of elastin-like constructs and human aortic elastin

    DEFF Research Database (Denmark)

    Heinz, Andrea; Schräder, Christoph U; Baud, Stéphanie

    2014-01-01

    This study aimed to characterize the structures of two elastin-like constructs, one composed of a cross-linked elastin-like polypeptide and the other one of cross-linked tropoelastin, and native aortic elastin. The structures of the insoluble materials and human aortic elastin were investigated...... quantification revealed that the cross-linking degree of the two in vitro cross-linked materials was significantly lower than that of native elastin. Molecular dynamics simulations were performed, based on molecular species identified in the samples, to follow the formation of elastin cross-links. The results...... provide evidence for the significance of the GVGTP hinge region of domain 23 for the formation of elastin cross-links. Overall, this work provides important insight into structural similarities and differences between elastin-like constructs and native elastin. Furthermore, it represents a step toward...

  18. Synthesis and Characterization of Magnetic-Graphene Molecularly Imprinted Polymers for Selective Recognition of Ltryptophan

    Directory of Open Access Journals (Sweden)

    Zhang Yi

    2017-01-01

    Full Text Available In this paper, a novel molecular imprinted polymer using L-tryptophan(L-Trp as the template, dopamine(DA as both functional monomer and cross linking agent, magnetic graphene as the supporting matrix was synthesized. The prepared magnetic-graphene molecularly imprinted polymers(Fe3O4@GO-MIPs were characterized by Fourier transform infrared spectrometer(FT-IR, transmission electron microscopy (TEM, vibrating sample magnetometer (VSM, respectively. The results showed that when the molar ratio of L- tryptophan and dopamine was 1:4 and the reaction temperature was 60 °C, Fe3O4@GO-MIPs had the best adsorption quantity of 31.9 mg/g. The rebinding experiments indicated that Fe3O4@GO-MIPs not only have outstanding affinity and selectivity towards L-Trp over structurally related compounds but also easily reach the magnetic separation under an external magnetic field.

  19. In vitro cross-linking of elastin peptides and molecular characterization of the resultant biomaterials

    DEFF Research Database (Denmark)

    Heinz, Andrea; Ruttkies, Christoph K H; Jahreis, Günther

    2013-01-01

    -link desmosine or isodesmosine was unexpected, however, could be confirmed by tandem mass spectrometry and molecular dynamics simulations. CONCLUSIONS: The study demonstrated that it is possible to produce biopolymers containing polyfunctional cross-links characteristic of mature elastin from small elastin......BACKGROUND: Elastin is a vital protein and the major component of elastic fibers which provides resilience to many vertebrate tissues. Elastin's structure and function are influenced by extensive cross-linking, however, the cross-linking pattern is still unknown. METHODS: Small peptides containing...... and the insoluble polymers, after digestion with pancreatic elastase or trypsin, were furthermore comprehensively characterized on the molecular level using MALDI-TOF/TOF mass spectrometry. RESULTS: MS(2) data was used to develop the software PolyLinX, which is able to sequence not only linear and bifunctionally...

  20. Molecular characterization of kerogens by mild selective chemical degradation - ruthenium tetroxide oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Boucher, R.J.; Standen, G.; Eglinton, G. (University of Bristol, Bristol (UK). Organic Geochemistry Unit)

    1991-06-01

    Molecular characterization of two kerogen isolates (Messel and Kimmeridge Clay), two kerogen-rich shales (green River and Maoming) and a coal, (Loy Yang) was undertaken using selective chemical degradation with ruthenium tetroxide (RuO{sub 4}). The RuO{sub 4} oxidation gave extracts which were soluble in dichloromethane and contained series of straight chain monocarboxylic acids, {alpha},{omega}-dicarboxylic acids, branched mono- and dicarboxylic acids, isoprenoid and cyclic acids. Straight chain carboxylic acids were predominant (65-87% of quantified chromatogram components for the range of sedimentary organic matter studied), reflecting the major content of polymethylene chains in these kerogens. This mild, oxidative technique serves to differentiate kerogens at a molecular level, thereby supplementing existing conventional chemical, pyrolytic, n.m.r. and other techniques. 39 refs., 3 figs., 5 tabs.

  1. Molecular characterization of hemoglobin D Punjab traits and clinical-hematological profile of the patients

    Directory of Open Access Journals (Sweden)

    Sanjay Pandey

    Full Text Available CONTEXT AND OBJECTIVE: Hemoglobin (Hb D hemoglobinopathies are widespread diseases in northwestern India and usually present with mild hemolytic anemia and mild to moderate splenomegaly. The heterozygous form of Hb D is clinically silent, but coinheritance of Hb D with Hb S or beta-thalassemia produces clinically significant conditions like thalassemia intermedia of moderate severity. Under heterozygous conditions with coinheritance of alpha and beta-thalassemia, patients show a degree of clinical variability. Thus, our aim was to molecularly characterize the Hb D trait among individuals who were clinically symptomatic because of co-inheritance of alpha deletions or any beta-globin gene mutations. DESIGN AND SETTING: This was a cross-sectional study conducted in an autonomous tertiary-care hospital. METHODS: Complete blood count and red cell indices were measured using an automated cell analyzer. Quantitative assessment of hemoglobin Hb F, Hb A, Hb A2 and Hb D was performed by means of high performance liquid chromatography (HPLC. DNA extraction was done using the phenol-chloroform method. Molecular analyses on common alpha deletions and common beta mutations were done using the Gap polymerase chain reaction and Amplification Refractory Mutation System, respectively. RESULTS: We evaluated 30 patients and found clinical variation in the behavior of Hb D traits. In six patients, the Hb D traits were clinically symptomatic and behaved like those of thalassemia intermedia. Molecular characterization showed that three out of these six were IVS-1-5 positive. CONCLUSIONS: HPLC may not be the gold standard for diagnosing symptomatic Hb D Punjab traits. Hence, standard confirmation should include molecular studies.

  2. Molecular and cytogenetic characterization of radon-induced lung tumors in the rat

    International Nuclear Information System (INIS)

    Dano, Laurent

    2000-01-01

    Radon is a natural radioactive gas. This radioelement, which is an α-particle emitter, is omnipresent in the environment. Inhalation of atmospheric radon is the major exposure route in man of natural radioactivity which results in respiratory tract contamination. An increased lung cancer risk associated with radon inhalation has been shown both in humans and animals by epidemiological and experimental studies, respectively. In rats, characterization of dose-effect relationships has led to the construction of statistical models that may help theoretically in the prediction of human health involvements of both occupational and domestic chronic exposure to radon. However, little is known about the cellular and molecular mechanisms of radon-induced lung carcinogenesis. In the laboratory, a model of lung cancers induced in rats after radon inhalation is available. This model represents a good tool to identify and characterize the genetic events contributing to the development of radon-induced lung tumors. Carrying out a global approach based on the combined use of classical and molecular cytogenetic methods, the analysis of 17 neoplasms allowed the identification of chromosomal regions frequently altered in these tumors. Numerous similarities have been found between our results and the cytogenetic data for human lung cancers, suggesting common underlying genetic molecular mechanisms for lung cancer development in both species. Moreover, our study has allowed to point to tumor suppressor genes and proto-oncogenes potentially involved in radon-induced lung carcinogenesis. Thus, our results may aid further molecular studies aimed either at confirming the role of these candidate genes or at demonstrating the involvement of yet to be identified genes. (author) [fr

  3. A hybrid thermal video and FTIR spectrometer system for rapidly locating and characterizing gas leaks

    Science.gov (United States)

    Williams, David J.; Wadsworth, Winthrop; Salvaggio, Carl; Messinger, David W.

    2006-08-01

    Undiscovered gas leaks, known as fugitive emissions, in chemical plants and refinery operations can impact regional air quality and present a loss of product for industry. Surveying a facility for potential gas leaks can be a daunting task. Industrial leak detection and repair programs can be expensive to administer. An efficient, accurate and cost effective method for detecting and quantifying gas leaks would both save industries money by identifying production losses and improve regional air quality. Specialized thermal video systems have proven effective in rapidly locating gas leaks. These systems, however, do not have the spectral resolution for compound identification. Passive FTIR spectrometers can be used for gas compound identification, but using these systems for facility surveys is problematic due to their small field of view. A hybrid approach has been developed that utilizes the thermal video system to locate gas plumes using real time visualization of the leaks, coupled with the high spectral resolution FTIR spectrometer for compound identification and quantification. The prototype hybrid video/spectrometer system uses a sterling cooled thermal camera, operating in the MWIR (3-5 μm) with an additional notch filter set at around 3.4 μm, which allows for the visualization of gas compounds that absorb in this narrow spectral range, such as alkane hydrocarbons. This camera is positioned alongside of a portable, high speed passive FTIR spectrometer, which has a spectral range of 2 - 25 μm and operates at 4 cm -1 resolution. This system uses a 10 cm telescope foreoptic with an onboard blackbody for calibration. The two units are optically aligned using a turning mirror on the spectrometer's telescope with the video camera's output.

  4. Rapid and simple immunophenotypic characterization of lymphocytes using a new test.

    Science.gov (United States)

    Bellido, M; Rubiol, E; Ubeda, J; Estivill, C; López, O; Manteiga, R; Nomdedéu, J F

    1998-08-01

    In this paper, we report our experience of lymphocyte phenotyping of a series of 108 consecutive samples using a simple flow cytometry test (Lymphogram). The kit consists of a combination of 5 different markers conjugated with three fluorochromes (CD8-FITC, CD19-FITC, CD56-PE, CD3-PE, CD4-PECy5) in the same tube. This allows identification of different T-cells, NK subpopulations and B lymphocytes. The samples were divided into three groups: samples with absolute lymphocytosis (> 5 x 10(9)/L) (n = 50), samples with relative lymphocytosis (> 50%) (n = 24) and other categories for which a lymphocyte immunophenotype was required (T-cell lymphoma and estimation of blood involvement in chronic lymphoproliferative disorders (CLPD) (n = 34). When CD19+ cells exceeded the normal range or there was a suspicion of CLPD without B-cell lymphopenia, clonality was investigated by means of light chain restriction analysis. In the first group, 29 samples were abnormal (10 CLPD, 3 polyclonal B-cell lymphocytosis, 13 inversions of the CD4/CD8 ratio and 3 cases with CD4 lymphocytosis) and 21 samples were regarded as normal. In the second group 7 samples showed abnormalities (2 CLPD, 3 inverted CD4/CD8 ratios and 2 with a relative increase in CD4 cells). In one sample from the third group B-cell clonality without lymphocytosis was detected whereas in 18 samples a polyclonal pattern was observed. The presence of B-cell lymphopenia precluded further clonality study in 13 samples. Lymphogram associated with clonality analysis is a rapid, easy and cheap method of assessing lymphocyte phenotypes in the majority of clinically relevant situations.

  5. Development and characterization of a handheld hyperspectral Raman imaging probe system for molecular characterization of tissue on mesoscopic scales.

    Science.gov (United States)

    St-Arnaud, Karl; Aubertin, Kelly; Strupler, Mathias; Madore, Wendy-Julie; Grosset, Andrée-Anne; Petrecca, Kevin; Trudel, Dominique; Leblond, Frédéric

    2018-01-01

    Raman spectroscopy is a promising cancer detection technique for surgical guidance applications. It can provide quantitative information relating to global tissue properties associated with structural, metabolic, immunological, and genetic biochemical phenomena in terms of molecular species including amino acids, lipids, proteins, and nucleic acid (DNA). To date in vivo Raman spectroscopy systems mostly included probes and biopsy needles typically limited to single-point tissue interrogation over a scale between 100 and 500 microns. The development of wider field handheld systems could improve tumor localization for a range of open surgery applications including brain, ovarian, and skin cancers. Here we present a novel Raman spectroscopy implementation using a coherent imaging bundle of fibers to create a probe capable of reconstructing molecular images over mesoscopic fields of view. Detection is performed using linear scanning with a rotation mirror and an imaging spectrometer. Different slits widths were tested at the entrance of the spectrometer to optimize spatial and spectral resolution while preserving sufficient signal-to-noise ratios to detect the principal Raman tissue features. The nonbiological samples, calcite and polytetrafluoroethylene (PTFE), were used to characterize the performance of the system. The new wide-field probe was tested on ex vivo samples of calf brain and swine tissue. Raman spectral content of both tissue types were validated with data from the literature and compared with data acquired with a single-point Raman spectroscopy probe. The single-point probe was used as the gold standard against which the new instrument was benchmarked as it has already been thoroughly validated for biological tissue characterization. We have developed and characterized a practical noncontact handheld Raman imager providing tissue information at a spatial resolution of 115 microns over a field of view >14 mm 2 and a spectral resolution of 6 cm -1 over

  6. Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

    Science.gov (United States)

    Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

    2018-01-01

    Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

  7. Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

    Science.gov (United States)

    Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

    2018-05-01

    Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

  8. Rapid characterization of the chemical constituents of Sijunzi decoction by UHPLC coupled with Fourier transform ion cyclotron resonance mass spectrometry.

    Science.gov (United States)

    Guan, Zhibo; Wang, Miao; Cai, Yi; Yang, Hongmei; Zhao, Min; Zhao, Chunjie

    2018-06-01

    Sijunzi decoction, a renowned Chinese prescription has long been utilized to treat gastrointestinal problems. In the context of this research work, the use of Ultra high performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry was made to separate and characterize the components of Sijunzi decoction. The performance of Liquid chromatography was carried out on a C8 column (150 mm × 2.1 mm, 1.8 μm); moreover, the mobile phase were consisted of 0.2% formic acid (A) and acetonitrile (B). In accordance with the findings, characterization of 120 chemical compounds was performed by liquid chromatography with mass spectrometry. The key constituents among them included ginsenosides (in Radix Ginseng), 16 triterpene carboxylic acids (in Poria), sesquiterpenes (in Rhizoma Atractylodis Macrocephalae), triterpenesaponins (in Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle) as well as flavonoids (in Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle) in Sijunzi decoction. This research developed the bases for prospective research associated with Sijunzi decoction, together with being expected to be useful to rapidly extract and characterize the constituents in other Traditional Chinese herbal formulations. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Molecular cloning and characterization of Izumo1 gene from bovine testis

    OpenAIRE

    Kim, Ekyune

    2015-01-01

    A well-characterized sperm specific protein of the Member of immunoglobulin superfamily, IZUMO1, has crucial role in fertilization by mediating sperm binding to the egg plasma membrane in the mouse. However little is known about IZUMO1 in bovine. Here, we describe the molecular cloning and expression analysis of bovine IZUMO1 (bIZUMO1). RT-PCR and Western blot analysis of the bovine tissues indicated that bIZUMO1 was specifically expressed in the testis and sperm, Furthermore, the result of o...

  10. First molecular identification and characterization of classical swine fever virus isolates from Nepal.

    Science.gov (United States)

    Postel, Alexander; Jha, Vijay C; Schmeiser, Stefanie; Becher, Paul

    2013-01-01

    Classical swine fever (CSF) is a major constraint to pig production worldwide, and in many developing countries, the epidemiological status is unknown. Here, for the first time, molecular identification and characterization of CSFV isolates from two recent outbreaks in Nepal are presented. Analysis of full-length E2-encoding sequences revealed that these isolates belonged to CSFV subgenotype 2.2 and had highest genetic similarity to isolates from India. Hence, for CSFV, Nepal and India should be regarded as one epidemiological unit. Both Nepalese isolates exhibited significant sequence differences, excluding a direct epidemiological connection and suggesting that CSFV is endemic in that country.

  11. Molecular and stable carbon isotopic characterization of PAH contaminants at McMurdo Station, Antarctica

    International Nuclear Information System (INIS)

    Kim, Moonkoo . E-mail moonkoo.kim@wmich.edu; Kennicutt, Mahlon C.; Qian Yaorong

    2006-01-01

    The molecular and stable carbon isotopic compositions of contaminant polycyclic aromatic hydrocarbons (PAHs) at McMurdo Station, Antarctica were analyzed in samples collected from land and sub-tidal area. PAHs in the study areas were characterized by high amounts of naphthalene and alkylated naphthalenes from petroleum products introduced by human activities in the area. Principal component analysis (PCA) of PAH composition data identified multiple sources of PAH contamination in the study area. Compositional assignments of origins were confirmed using compound specific stable carbon isotopic analysis

  12. Phenotypic, genetic and molecular characterization of a maize low phytic acid mutant (lpa241)

    DEFF Research Database (Denmark)

    Pilu, R.; Panzeri, D.; Gavazzi, G.

    2003-01-01

    -nutritional factor for animals, and isolation of maize low phytic acid (lpa) mutants provides a novel approach to study its biochemical pathway and to tackle the nutritional problems associated with it. Following chemical mutagenesis of pollen, we have isolated a viable recessive mutant named lpa 241 showing about...... 90% reduction of phytic acid and about a tenfold increase in seed-free phosphate content. Although germination rate was decreased by about 30% compared to wild-type, developement of mutant plants was apparentely unaffected. The results of the genetic, biochemical and molecular characterization...

  13. Preparation and Characterization of High Silica Molecular Sieve from Rice Husk

    International Nuclear Information System (INIS)

    Hnaung Hnaung Win; Tin Tin Aye; Kyaw Myo Naing; Nyunt Wynn

    2008-03-01

    A mordenite type of hight silica molecular sieve with a formula composition Na32 (ALO2)32 (SiO2)176 192H2O having a high molar ratio of SiO2 /Al2O3 (5.4) with a percent yield of 98.76% has been prepared from synthesized zeolite NaY and glycolato silicate on the basis of hydrothermal condition.Zeolicate NaY and glycolato silicate were synthesized by using 98.34% purified silica which was extracted from rice husk.The characterizations with XRD, FT-IR, EDXRF,TG-DTA and SEM techniques were studied.

  14. Molecular characterization of a novel family VIII esterase from burkholderia multivorans UWC10

    CSIR Research Space (South Africa)

    Rashamuse, KJ

    2007-02-01

    Full Text Available et al., 1992). Here we report the cloning, purification, and 3D model of a novel family VIII esterase from Burkholderia multivorans UWC10. To our knowledge no report of esterolytic activity from B. multivorans is currently available. METHODOLOGY... stream_source_info Rashamuse1_2007_d.pdf.txt stream_content_type text/plain stream_size 9884 Content-Encoding UTF-8 stream_name Rashamuse1_2007_d.pdf.txt Content-Type text/plain; charset=UTF-8 Molecular Characterization...

  15. Identification and Molecular Characterization of the cDNA Encoding Cucumis melo Allergen, Cuc m 3, a Plant Pathogenesis-Related Protein

    Directory of Open Access Journals (Sweden)

    Mojtaba Sankian

    2014-05-01

    Full Text Available Background: Melon (Cucumis melo allergy is one of the most common food allergies, characterized by oral allergy syndrome. To date, two allergen molecules, Cuc m 1 and Cuc m 2, have been fully characterized in melon pulp, but there are few reports about the molecular characteristics of Cuc m 3. Methods:The Cuc m 3 cDNA has been characterized by rapid amplification of cDNA ends (RACE, which revealed a 456 base-pair (bp fragment encoding a 151-amino acid polypeptide with a predicted molecular mass of 16.97 kDa, and identified 79 and 178 bp untranslated sequences at the 5′ and 3´ ends, respectively. Results: In silico analysis showed strong similarities between Cuc m 3 and other plant pathogen-related protein 1s from cucumber, grape, bell pepper, and tomato. Conclusion: Here we report the identification and characterization of the Cuc m 3 cDNA, which will be utilized for further analyses of structural and allergenic features of this allergen

  16. Frequency-domain Harman technique for rapid characterization of bulk and thin film thermoelectric materials

    Science.gov (United States)

    Moran, Samuel

    Nanostructured thermoelectrics, often in the form of thin films, may potentially improve the generally poor efficiency of bulk thermoelectric power generators and coolers. In order to characterize the efficiency of these new materials it is necessary to measure their thermoelectric figure of merit, ZT. The only direct measurement of ZT is based on the Harman technique and relies on measuring the voltage drop across a sample subjected to a passing continuous current. Application of this technique to thin films is currently carried out as a time-domain measurement of the voltage as the thermal component decays after switching off an applied voltage. This work develops a technique for direct simultaneous measurement of figure of merit and Seebeck coefficient from the harmonic response of a thermoelectric material under alternating current excitation. A thermocouple mounted on the top surface measures voltage across the device as the frequency of the applied voltage is varied. A thermal model allows the sample thermal conductivity to also be determined and shows good agreement with measurements. This technique provides improved signal-to-noise ratio and accuracy compared to time-domain ZT measurements for comparable conditions while simultaneously measuring Seebeck coefficient. The technique is applied to both bulk and thin film thermoelectric samples.

  17. Generation and characterization of neurogenin1-GFP transgenic medaka with potential for rapid developmental neurotoxicity screening

    International Nuclear Information System (INIS)

    Fan Chunyang; Simmons, Steven O.; Law, Sheran H.W.; Jensen, Karl; Cowden, John; Hinton, David; Padilla, Stephanie; Ramabhadran, Ram

    2011-01-01

    Fish models such as zebrafish and medaka are increasingly used as alternatives to rodents in developmental and toxicological studies. These developmental and toxicological studies can be facilitated by the use of transgenic reporters that permit the real-time, noninvasive observation of the fish. Here we report the construction and characterization of transgenic medaka lines expressing green fluorescent protein (GFP) under the control of the zebrafish neurogenin 1 (ngn1) gene promoter. Neurogenin (ngn1) is a helix-loop-helix transcription factor expressed in proliferating neuronal progenitor cells early in neuronal differentiation and plays a crucial role in directing neurogenesis. GFP expression was detected from 24 h post-fertilization until hatching, in a spatial pattern consistent with the previously reported zebrafish ngn1 expression. Temporal expression of the transgene parallels the expression profile of the endogenous medaka ngn1 transcript. Further, we demonstrate that embryos from the transgenic line permit the non-destructive, real-time screening of ngn1 promoter-directed GFP expression in a 96-well format, enabling higher throughput studies of developmental neurotoxicants. This strain has been deposited with and maintained by the National BioResource Project and is available on request ( (http://www.shigen.nig.ac.jp/medaka/strainDetailAction.do?quickSearch=true and strainId=5660)).

  18. Infrared Spectroscopy for Rapid Characterization of Drill Core and Cutting Mineralogy

    Science.gov (United States)

    Calvin, W. M.; Kratt, C.; Kruse, F. A.

    2009-12-01

    Water geochemistry can vary with depth and location within a geothermal reservoir, owing to natural factors such as changing rock type, gas content, fluid source and temperature. The interaction of these variable fluids with the host rock will cause well known changes in alteration mineral assemblages that are commonly factored into the exploration of hydrothermal systems for economic metals, but are less utilized with regard to mapping borehole geology for geothermal energy production. Chemistry of geothermal fluids and rock alteration products can impact production factors such as pipeline corrosion and scaling and early studies explored the use of both silica and chlorites as geothermometers. Infrared spectroscopy is particularly good at identifying a wide variety of alteration minerals, especially in discrimination among clay minerals, with no sample preparation. The technique has been extensively used in the remote identification of materials, but is not commonly used on drill core or chips. We have performed several promising pilot studies that suggest the power of the technique to sample continuously and provide mineral logs akin to geophysical ones. We have surveyed a variety of samples, including drill chip boards, boxed core, and drill cuttings from envelopes, sample bottles and chip trays. This work has demonstrated that core and drill chips can be rapidly surveyed, acquiring spectra every few to tens of cm of section, or the vertical resolution of the chip tray (typically 10 feet). Depending on the sample type we can acquire spectral data over thousands of feet depth at high vertical resolution in a fraction of the time that is needed for traditional analytical methods such as XRD or TEM with better accuracy than traditional geologic drill or chip logging that uses visual inspection alone. We have successfully identified layered silicates such as illite, kaolinite, montmorillonite chlorite and prehnite, zeolites, opal, calcite, jarosite and iron oxides

  19. Separation and characterization of resins and asphaltenes coming from Castilla crude Evaluation of their molecular interaction

    International Nuclear Information System (INIS)

    Navarro, Lina; Alvarez, Mario; Grosso, Jorge Luis; Navarro, Uriel

    2004-01-01

    The study of resins and asphaltenes, the heaviest fractions of oil, has become an area of interest due to the abundance of heavy crude oils in Colombia and Latin America. We studied the chemical composition of the heavy fractions of Castilla crude oil, evaluated some of its molecular parameters and found evidence of the interaction between the resins extracted from the crude with the asphaltenes of the original crude. With this objective, we carried out at the pilot plant level precipitation of the resin-asphaltene (R-A) aggregate by adding and mixing under controlled conditions, a paraffin solvent, from the Apiay refinery, called Apiasol. By extracting Soxhlet with the same solvent, resin 1 of aggregate R-A was separated. Resin ll defined as the soluble fraction that is part of the maltenes, was separated from the deasphalted crude by open column chromatography, using alumina as support, according to the SAR method (Saturated, Aromatics, Resins). The fractions of resins and the asphaltenes obtained, were characterized by: Nuclear Magnetic Resonance (NMR), FT-lR, DRX, elementary analysis (C, H, N, S), metal content (Ni and V), distribution of molecular weight by GPC, and average molecular weight by VPO. The results obtained show evidence that resin l which is part of the aggregate has less average molecular weight than resin ll which is present in the fraction of maltenes. In addition, some changes were found in the elementary analysis of among the resins. On the one hand, and taking into account the existing theories of molecular interactions among these fractions, it was found that the resins l separated from the R-A aggregate, when added to the crude, they stabilize their asphaltenes. This evaluation was carried out by analyzing the flocculation point of the crude and its mixtures with 1,9% and 3,8% of resin l, when they are titrated with a precipitating agent in an NIR cell that works with high pressure and temperature

  20. Molecular characterization of the first leptospires isolated from goats in Brazil

    Directory of Open Access Journals (Sweden)

    Walter Lilenbaum

    2014-12-01

    Full Text Available Two Leptospira sp. isolates were obtained by the first time from goats in Brazil and characterized by sequencing rrs, rpoB and secY genes, PFGE and typing with monoclonal antibodies. Both isolates are identical and belong to Leptospira santarosai. Analysis of the rrs and the rpoB genes sequences revealed 100% identity between the goat isolates and the Bananal reference strain. When secY sequences of the two isolates were compared to each other, it was observed that they had identical sequences. However, when compared to that of the Bananal reference strain, there were 15 mismatches along the 549 bp secY sequence. In conclusion, molecular methods are increasingly useful for the characterization of leptospires and allowed to identify those isolates of caprine origin as closely related but not identical to serovar Bananal, and constitute a new type named Carioca.

  1. Molecular characterization of dissolved organic matter in freshwater wetlands of the Florida Everglades.

    Science.gov (United States)

    Lu, X Q; Maie, N; Hanna, J V; Childers, D L; Jaffé, R

    2003-06-01

    In this study, the molecular composition of dissolved organic matter (DOM), collected from wetlands of the Southern Everglades, was examined using a variety of analytical techniques in order to characterize its sources and transformation in the environment. The methods applied for the characterization of DOM included fluorescence spectroscopy, solid state 13C CPMAS NMR spectroscopy, and pyrolysis-GC/MS. The relative abundance of protein-like components and carbohydrates increased from the canal site to more remote freshwater marsh sites suggesting that significant amounts of non-humic DOM are autochthonously produced within the freshwater marshes, and are not exclusively introduced through canal inputs. Such in situ DOM production is important when considering how DOM from canals is processed and transported to downstream estuaries of Florida Bay.

  2. Morphological, biochemical, and molecular characterization of Meloidogyne spp. populations from Brazilian soybean production regions

    Directory of Open Access Journals (Sweden)

    Camilla Martins de Oliveira

    Full Text Available ABSTRACT: Soybean is a commodity of great economic importance worldwide, particularly in Brazil, world’s second largest producer. Nematodes, especially those of the Meloidogyne genus, severely limit productivity. Identification of nematode species is important for effective soybean management. Here, 26 populations of root-knot nematode (Meloidogyne spp. from 15 municipalities in the states of Bahia, Mato Grosso, Goias, and Minas Gerais were characterized based on the morphology of the female perineal region, esterase profile, and identification based on amplification of specific regions of the population genome. Among the Meloidogyne spp. populations obtained, M. incognita and M. javanica, were identified. No mixed populations were present in the samples. Diagnosis based on molecular analysis was shown to be reliable and the fastest for characterization of nematode populations compared to other methods analyzed.

  3. Synthesis, characterization, and catalytic properties of stable mesoporous molecular sieve MCM-41 prepared from zeolite mordenite

    International Nuclear Information System (INIS)

    Wang Shan; Dou Tao; Li Yuping; Zhang Ying; Li Xiaofeng; Yan Zichun

    2004-01-01

    Mesoporous molecular sieves (denoted as M-MCM-41) with ordered hexagonal structure have been successfully synthesized from the assembly of precursors from preformed zeolite Mordenite with CTAB surfactant micelle in alkaline media. The samples were characterized by XRD, N 2 adsorption, IR and DTG. The materials exhibit highly hydrothermal stability, as compared with conventional MCM-41. Characterization results indicate that the mesoporous walls of M-MCM-41 contain the secondary building units similar to those in microporous crystal of zeolite Mordenite. In catalytic dealkylation of C10 + aromatic hydrocarbon, M-MCM-41 shows higher activities in comparison with Mordenite and MCM-41, which would be ascribed to the combination of advantages of both MCM-41 (large pores) and Mordenite (strong acidity). Furthermore, this synthesis strategy could be used as a new general method for the preparation of hydrothermally stable mesoporous aluminosilicate materials under alkaline conditions

  4. Molecular design and theoretical characterization of benzodithiophene based organic photovoltaic materials

    Science.gov (United States)

    Bhattacharya, Labanya; Sahu, Sridhar

    2018-05-01

    Two different oligomers, containing methyl substituted Benzodithiophene (BDT) as donor unit, fluorinated thiophene as the π-bridge unit and two different kinds of acceptors based on fluorinated benzothiadiazole, fluorinated benzoselenadiazole units are designed for bulk heterojunction (BHJ) organic solar cell (OSC). The ground and excited state properties of those donor-π-acceptor-π-donor (D-π-A-π-D) oligomeric configurations are characterized via density functional (DFT) and time dependent density functional theory (TD-DFT). The parameters such as dipole moment (ρ), chemical potential (µ), electronegativity (χ), frontier molecular orbital (FMO) analysis, HOMO-LUMO gap, open circuit voltage (Voc) and driving force (ΔE) are calculated to analyze geometrical, electronic structural, quantum chemical and photovoltaic properties of the compounds. In addition, optical absorption spectra are also presented for the optical characterization of the compounds.

  5. MOLECULAR CLONING AND CHARACTERIZATION OF NOVEL THERMOSTABLE LIPASE FROM SHEWANELLA PUTREFACIENS AND USING ENZYMATIC BIODIESEL PRODUCTION

    Directory of Open Access Journals (Sweden)

    Fahri Akbas

    2015-02-01

    Full Text Available A novel thermostable lipase from Shewanella putrefaciens was identified, expressed in Escherichia coli, characterized and used in biodiesel production. Enzyme characterization was carried out by enzyme assay, SDS-PAGE and other biochemical reactions. The recombinant lipase was found to have a molecular mass of 29 kDa and exhibited lipase activity when Tween 80 was used as the substrate. The purified enzyme showed maximum activity at pH 5.0 and at 80°C. The recombinant lipase was used for the transesterification of canola oil and waste oil. The enzyme retains 50% of its activity at 90°C for 30 minutes. It is also able to retain 20% of its activity even at 100 °C for 20 minutes. These properties of the obtained new recombinant thermostable lipase make it promising as a biocatalyst for industrial processes.

  6. Structural characterization of a recombinant fusion protein by instrumental analysis and molecular modeling.

    Directory of Open Access Journals (Sweden)

    Zhigang Wu

    Full Text Available Conbercept is a genetically engineered homodimeric protein for the treatment of wet age-related macular degeneration (wet AMD that functions by blocking VEGF-family proteins. Its huge, highly variable architecture makes characterization and development of a functional assay difficult. In this study, the primary structure, number of disulfide linkages and glycosylation state of conbercept were characterized by high-performance liquid chromatography, mass spectrometry, and capillary electrophoresis. Molecular modeling was then applied to obtain the spatial structural model of the conbercept-VEGF-A complex, and to study its inter-atomic interactions and dynamic behavior. This work was incorporated into a platform useful for studying the structure of conbercept and its ligand binding functions.

  7. Molecular and biochemical characterization of Pseudomonas putida isolated from bottled uncarbonated mineral drinking water

    Directory of Open Access Journals (Sweden)

    Tasić S.

    2014-01-01

    Full Text Available Pseudomonas putida belongs to a group of opportunistic pathogens that can cause disease in people with weakened or damaged immune systems. Some strains have medical significance, and for most ingestion is not the primary route of infection. If water used by predisposed subjects is contaminated by P. putida, they may become ill. The aim of this work was the biochemical and molecular characterization of strain ST3 of P. putida isolated from non-carbonated bottled drinking water from Jakov Do 4 on Mt. Vlasina. Characterization of P. putida was performed to assess the risk to human health of the indigenous strains present in the water. Biochemical characterization of strains was performed using the manual identification system ID 32 GN (BioMérieux. Identification was obtained using the database identification software ATB System (Bio-Mérieux. Molecular characterization was performed by PCR amplification and 16S rDNA “thermal cycling sequencing”. Biochemical identification of the strain ST3 was accurate (Id = 99.8%. Comparing the sequences obtained for strain ST3 with NCBI gene bank sequences for 16S rRNA, the highest similarity of our strain (96% identity with a strain of P. putida, designated as biotype A (gi|18076625|emb|AJ308311.1|.PPU308311 isolated in New Zealand, was obtained. While comparison with the NCBI collection of all deposited sequences showed that the 16S rRNA gene sequence of strain ST3 has very high homology, it is not identical, indicating indirectly that strain ST3 is an indigenous strain.

  8. Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content.

    Directory of Open Access Journals (Sweden)

    Maria Sulli

    Full Text Available After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum and diploid (S. phureja and S. chacoense genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2 gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP recessive allele. Novel CHY2 and ZEP alleles were identified in the collection. Multivariate analysis identified several groups of co-regulated non-polar compounds, and resulted in the grouping of the genotypes according to flesh color, suggesting that extensive cross-talk exists between the carotenoid pathway and other metabolite pathways in tubers. Postharvest traits like tuber dormancy and weight loss during storage showed little correlation with tuber carotenoid content, with the exception of zeaxanthin and its esters. Other tuber metabolites, such as glucose, monogalactosyldiacyglycerol (a glycolipid, or suberin precursors, showed instead significant correlations with both traits.

  9. Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content

    Science.gov (United States)

    Sulli, Maria; Mandolino, Giuseppe; Sturaro, Monica; Onofri, Chiara; Diretto, Gianfranco; Parisi, Bruno

    2017-01-01

    After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum) and diploid (S. phureja and S. chacoense) genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2) gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP) recessive allele. Novel CHY2 and ZEP alleles were identified in the collection. Multivariate analysis identified several groups of co-regulated non-polar compounds, and resulted in the grouping of the genotypes according to flesh color, suggesting that extensive cross-talk exists between the carotenoid pathway and other metabolite pathways in tubers. Postharvest traits like tuber dormancy and weight loss during storage showed little correlation with tuber carotenoid content, with the exception of zeaxanthin and its esters. Other tuber metabolites, such as glucose, monogalactosyldiacyglycerol (a glycolipid), or suberin precursors, showed instead significant correlations with both traits. PMID:28898255

  10. Complete characterization by Raman spectroscopy of the structural properties of thin hydrogenated diamond-like carbon films exposed to rapid thermal annealing

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Franck, E-mail: franck.rose@hgst.com; Wang, Na; Smith, Robert; Xiao, Qi-Fan; Dai, Qing; Marchon, Bruno [HGST, A Western Digital Company, San Jose Research Center, 3403, Yerba Buena Rd, San Jose, California 95135 (United States); Inaba, Hiroshi; Matsumura, Toru; Saito, Yoko; Matsumoto, Hiroyuki [HGST, A Western Digital Company, Japan Research Laboratory, 2880 Kozu, Odawara, Kanagawa 256-8510 (Japan); Mangolini, Filippo [Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States); Carpick, Robert W. [Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6315 (United States)

    2014-09-28

    We have demonstrated that multi-wavelength Raman and photoluminescence spectroscopies are sufficient to completely characterize the structural properties of ultra-thin hydrogenated diamond-like carbon (DLC:H) films subjected to rapid thermal annealing (RTA, 1 s up to 659 °C) and to resolve the structural differences between films grown by plasma-enhanced chemical vapor deposition, facing target sputtering and filtered cathodic vacuum arc with minute variations in values of mass density, hydrogen content, and sp³ fraction. In order to distinguish unequivocally between films prepared with different density, thickness, and RTA treatment, a new method for analysis of Raman spectra was invented. This newly developed analysis method consisted of plotting the position of the Raman G band of carbon versus its full width at half maximum. Moreover, we studied the passivation of non-radiative recombination centers during RTA by performing measurements of the increase in photoluminescence in conjunction with the analysis of DLC:H networks simulated by molecular dynamics. The results show that dangling bond passivation is primarily a consequence of thermally-induced sp² clustering rather than hydrogen diffusion in the film.

  11. Complete characterization by Raman spectroscopy of the structural properties of thin hydrogenated diamond-like carbon films exposed to rapid thermal annealing

    International Nuclear Information System (INIS)

    Rose, Franck; Wang, Na; Smith, Robert; Xiao, Qi-Fan; Dai, Qing; Marchon, Bruno; Inaba, Hiroshi; Matsumura, Toru; Saito, Yoko; Matsumoto, Hiroyuki; Mangolini, Filippo; Carpick, Robert W.

    2014-01-01

    We have demonstrated that multi-wavelength Raman and photoluminescence spectroscopies are sufficient to completely characterize the structural properties of ultra-thin hydrogenated diamond-like carbon (DLC:H) films subjected to rapid thermal annealing (RTA, 1 s up to 659 °C) and to resolve the structural differences between films grown by plasma-enhanced chemical vapor deposition, facing target sputtering and filtered cathodic vacuum arc with minute variations in values of mass density, hydrogen content, and sp 3 fraction. In order to distinguish unequivocally between films prepared with different density, thickness, and RTA treatment, a new method for analysis of Raman spectra was invented. This newly developed analysis method consisted of plotting the position of the Raman G band of carbon versus its full width at half maximum. Moreover, we studied the passivation of non-radiative recombination centers during RTA by performing measurements of the increase in photoluminescence in conjunction with the analysis of DLC:H networks simulated by molecular dynamics. The results show that dangling bond passivation is primarily a consequence of thermally-induced sp 2 clustering rather than hydrogen diffusion in the film.

  12. Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013.

    Directory of Open Access Journals (Sweden)

    Sook-Young Lee

    Full Text Available Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica and two Gentoo penguins (Pygoscelis papua. The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9% in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3 in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%, and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%. Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population.

  13. Molecular characterization and expression profiles of nicotinic acetylcholine receptors in the rice striped stem borer, Chilo suppressalis (Lepidoptera: Crambidae).

    Science.gov (United States)

    Xu, Gang; Wu, Shun-Fan; Teng, Zi-Wen; Yao, Hong-Wei; Fang, Qi; Huang, Jia; Ye, Gong-Yin

    2017-06-01

    Nicotinic acetylcholine receptors (nAChRs) are members of the cys-loop ligand-gated ion channel (cysLGIC) superfamily, mediating fast synaptic cholinergic transmission in the central nervous system in insects. Insect nAChRs are the molecular targets of economically important insecticides, such as neonicotinoids and spinosad. Identification and characterization of the nAChR gene family in the rice striped stem borer, Chilo suppressalis, could provide beneficial information about this important receptor gene family and contribute to the investigation of the molecular modes of insecticide action and resistance for current and future chemical control strategies. We searched our C. suppressalis transcriptome database using Bombyx mori nAChR sequences in local BLAST searches and obtained the putative nAChR subunit complementary DNAs (cDNAs) via reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends methods. Similar to B. mori, C. suppressalis possesses 12 nAChR subunits, including nine α-type and three β-type subunits. Quantitative RT-PCR analysis revealed the expression profiles of the nAChR subunits in various tissues, including the brain, subesophageal ganglion, thoracic ganglion, abdominal ganglion, hemocytes, fat body, foregut, midgut, hindgut and Malpighian tubules. Developmental expression analyses showed clear differential expression of nAChR subunits throughout the C. suppressalis life cycle. The identification of nAChR subunits in this study will provide a foundation for investigating the diverse roles played by nAChRs in C. suppressalis and for exploring specific target sites for chemicals that control agricultural pests while sparing beneficial species. ©2016 The Authors Insect Science published by John Wiley & Sons Australia, Ltd on behalf of Institute of Zoology, Chinese Academy of Sciences.

  14. Characterizing the rapid spread of porcine epidemic diarrhea virus (PEDV through an animal food manufacturing facility.

    Directory of Open Access Journals (Sweden)

    Loni L Schumacher

    Full Text Available New regulatory and consumer demands highlight the importance of animal feed as a part of our national food safety system. Porcine epidemic diarrhea virus (PEDV is the first viral pathogen confirmed to be widely transmissible in animal food. Because the potential for viral contamination in animal food is not well characterized, the objectives of this study were to 1 observe the magnitude of virus contamination in an animal food manufacturing facility, and 2 investigate a proposed method, feed sequencing, to decrease virus decontamination on animal food-contact surfaces. A U.S. virulent PEDV isolate was used to inoculate 50 kg swine feed, which was mixed, conveyed, and discharged into bags using pilot-scale feed manufacturing equipment. Surfaces were swabbed and analyzed for the presence of PEDV RNA by quantitative real-time polymerase chain reaction (qPCR. Environmental swabs indicated complete contamination of animal food-contact surfaces (0/40 vs. 48/48, positive baseline samples/total baseline samples, positive subsequent samples/total subsequent samples, respectively; P < 0.05 and near complete contamination of non-animal food-contact surfaces (0/24 vs. 16/18, positive baseline samples/total baseline samples, positive subsequent samples/total subsequent samples, respectively; P < 0.05. Flushing animal food-contact surfaces with low-risk feed is commonly used to reduce cross-contamination in animal feed manufacturing. Thus, four subsequent 50 kg batches of virus-free swine feed were manufactured using the same system to test its impact on decontaminating animal food-contact surfaces. Even after 4 subsequent sequences, animal food-contact surfaces retained viral RNA (28/33 positive samples/total samples, with conveying system being more contaminated than the mixer. A bioassay to test infectivity of dust from animal food-contact surfaces failed to produce infectivity. This study demonstrates the potential widespread viral contamination of

  15. Computational modeling and experimental characterization of bacterial microcolonies for rapid detection using light scattering

    Science.gov (United States)

    Bai, Nan

    A label-free and nondestructive optical elastic forward light scattering method has been extended for the analysis of microcolonies for food-borne bacteria detection and identification. To understand the forward light scattering phenomenon, a model based on the scalar diffraction theory has been employed: a bacterial colony is considered as a biological spatial light modulator with amplitude and phase modulation to the incoming light, which continues to propagate to the far-field to form a distinct scattering 'fingerprint'. Numerical implementation via angular spectrum method (ASM) and Fresnel approximation have been carried out through Fast Fourier Transform (FFT) to simulate this optical model. Sampling criteria to achieve unbiased and un-aliased simulation results have been derived and the effects of violating these conditions have been studied. Diffraction patterns predicted by these two methods (ASM and Fresnel) have been compared to show their applicability to different simulation settings. Through the simulation work, the correlation between the colony morphology and its forward scattering pattern has been established to link the number of diffraction rings and the half cone angle with the diameter and the central height of the Gaussian-shaped colonies. In order to experimentally prove the correlation, a colony morphology analyzer has been built and used to characterize the morphology of different bacteria genera and investigate their growth dynamics. The experimental measurements have demonstrated the possibility of differentiating bacteria Salmonella, Listeria, Escherichia in their early growth stage (100˜500 µm) based on their phenotypic characteristics. This conclusion has important implications in microcolony detection, as most bacteria of our interest need much less incubation time (8˜12 hours) to grow into this size range. The original forward light scatterometer has been updated to capture scattering patterns from microcolonies. Experiments have

  16. Diphtheria in the Republic of Georgia: Use of Molecular Typing Techniques for Characterization of Corynebacterium diphtheriae Strains

    Science.gov (United States)

    Sulakvelidze, Alexander; Kekelidze, Merab; Gomelauri, Tsaro; Deng, Yingkang; Khetsuriani, Nino; Kobaidze, Ketino; De Zoysa, Aruni; Efstratiou, Androulla; Morris, J. Glenn; Imnadze, Paata

    1999-01-01

    Sixty-six Corynebacterium diphtheriae strains (62 of the gravis biotype and 4 of the mitis biotype) isolated during the Georgian diphtheria epidemic of 1993 to 1998 and 13 non-Georgian C. diphtheriae strains (10 Russian and 3 reference isolates) were characterized by (i) biotyping, (ii) toxigenicity testing with the Elek assay and PCR, (iii) the randomly amplified polymorphic DNA (RAPD) technique, and (iv) pulsed-field gel electrophoresis (PFGE). Fifteen selected strains were ribotyped. Six RAPD types and 15 PFGE patterns were identified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribotyped. The Georgian epidemic apparently was caused by one major clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epidemic strain(s) isolated during the concurrent diphtheria epidemic in Russia. A dendrogram based on the PFGE patterns revealed profound differences between the minor (nonpredominant) epidemic strains found in Georgia and Russia. The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains were improved to enable rapid and convenient molecular typing of the strains. The RAPD technique was adequate for biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at discriminating between epidemiologically related and unrelated isolates. PMID:10488190

  17. A member of the HSP90 family from ovine Babesia in China: molecular characterization, phylogenetic analysis and antigenicity.

    Science.gov (United States)

    Guan, Guiquan; Liu, Junlong; Liu, Aihong; Li, Youquan; Niu, Qingli; Gao, Jinliang; Luo, Jianxun; Chauvin, Alain; Yin, Hong; Moreau, Emmanuelle

    2015-09-01

    Heat shock protein 90 (HSP90) is a key component of the molecular chaperone complex essential for activating many signalling proteins involved in the development and progression of pathogenic cellular transformation. A Hsp90 gene (BQHsp90) was cloned and characterized from Babesia sp. BQ1 (Lintan), an ovine Babesia isolate belonging to Babesia motasi-like group, by screening a cDNA expression library and performing rapid amplification of cDNA ends. The full-length cDNA of BQHsp90 is 2399 bp with an open reading frame of 2154 bp encoding a predicted 83 kDa polypeptide with 717 amino acid residues. It shows significant homology and similar structural characteristics to Hsp90 of other apicomplex organisms. Phylogenetic analysis, based on the HSP90 amino acid sequences, showed that the Babesia genus is clearly separated from other apicomplexa genera. Five Chinese ovine Babesia isolates were divided into 2 phylogenetic clusters, namely Babesia sp. Xinjiang (previously designated a new species) cluster and B. motasi-like cluster which could be further divided into 2 subclusters (Babesia sp. BQ1 (Lintan)/Babesia sp. Tianzhu and Babesia sp. BQ1 (Ningxian)/Babesia sp. Hebei). Finally, the antigenicity of rBQHSP90 protein from prokaryotic expression was also evaluated using western blot and enzyme-linked immunosorbent assay (ELISA).

  18. Nanofabrication and characterization of ZnO nanorod arrays and branched microrods by aqueous solution route and rapid thermal processing

    International Nuclear Information System (INIS)

    Lupan, Oleg; Chow, Lee; Chai, Guangyu; Roldan, Beatriz; Naitabdi, Ahmed; Schulte, Alfons; Heinrich, Helge

    2007-01-01

    This paper presents an inexpensive and fast fabrication method for one-dimensional (1D) ZnO nanorod arrays and branched two-dimensional (2D), three-dimensional (3D) - nanoarchitectures. Our synthesis technique includes the use of an aqueous solution route and post-growth rapid thermal annealing. It permits rapid and controlled growth of ZnO nanorod arrays of 1D - rods, 2D - crosses, and 3D - tetrapods without the use of templates or seeds. The obtained ZnO nanorods are uniformly distributed on the surface of Si substrates and individual or branched nano/microrods can be easily transferred to other substrates. Process parameters such as concentration, temperature and time, type of substrate and the reactor design are critical for the formation of nanorod arrays with thin diameter and transferable nanoarchitectures. X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, transmission electron microscopy and Micro-Raman spectroscopy have been used to characterize the samples

  19. Molecular characterization of a GA-inducible gene, Cvsus1, in developing watermelon seeds.

    Science.gov (United States)

    Kim, Joonyul; Jun, Sung-Hoon; Kang, Hong-Gyu; Lee, Jinwon; An, Gynheung

    2002-10-31

    To understand the molecular mechanisms that control seed development, we isolated a seed-preferential gene from ESTs of developing watermelon seeds. The gene Cvsus1 encodes a protein that is 86% identical to the Vicia faba sucrose synthase expressed in developing seeds. RNA blot analysis showed that Cvsus1 was preferentially expressed in watermelon seeds. We also investigated gene expression levels both in pollinated seeds and in parthenocarpic seeds, which lack zygotic tissues. Whereas the transcript level of Cvsus1 was rapidly increased during normal seed development, the expression was not significantly increased in the parthenocarpic seeds. However, treating the parthenocarpic fruits with GA3 strongly induced Cvsus1 expression, up to the level accumulated in pollinated seeds. These results suggest that Cvsus1 is induced in maternal tissues via signals from the zygotic tissues, and that GA may be one of those signals.

  20. Molecular Characterization and Antioxidant Potential of Three Wild Culinary-Medicinal Mushrooms from Tripura, Northeast India.

    Science.gov (United States)

    Das, Aparajita Roy; Borthakur, Madhusmita; Saha, Ajay Krishna; Joshi, Santa Ram; Das, Panna

    2017-01-01

    The aim of this study was to characterize 3 wild culinary-medicinal mushrooms using molecular tools and to analyze their antioxidant activity. Antioxidant properties were studied by evaluating free radical scavenging, reducing power, and chelating effect. The mushrooms were identified as Lentinus squarrosulus, L. tuber-regium, and Macrocybe gigantean by amplifying internal transcribed spacer regions of ribosomal DNA. The results demonstrated that the methanolic extract of M. gigantean has the highest free radical scavenging effect and chelating effect, whereas the methanolic extract of L. squarrosulus has the highest reducing power. The highest total phenol content and the most ascorbic acid were found in the M. gigantean extracts. Among the 3 mushroom extracts, M. gigantean displayed the most potent antioxidant activity. Molecular characterization using the nuclear ribosomal internal transcribed spacer region as a universal DNA marker was an effective tool in the identification and phylogenetic analysis of the studied mushrooms. The study also indicated that these wild macrofungi are rich sources of natural antioxidants.

  1. Molecular Characterization and Germination Analysis of Cotton (Gossypium hirsutum L. Genotypes under Water Deficit Irrigation

    Directory of Open Access Journals (Sweden)

    Eminur ELÇİ

    2016-09-01

    Full Text Available Cotton is an important crop in terms of economic and strategic impacts. Drought stress is one of the most important environmental stress factors which negatively affects growth and yield of plants in Turkey as occurred in many countries in the world. In this study, 11 different cotton cultivars selected based on their agronomical characters were tested under water deficit irrigation strategies. Thus, it was aimed to select and/or determine appropriate new varieties for breeding new national materials resistant to drought stress, and to characterize with the molecular microsatellite markers. According to the different irrigation levels (25%, 50%, 75% and 100% plants were observed under the stressed conditions at the irrigation levels of 50% and 25%. Among the tested varieties, Tamcot Sphinx, Tamcot 94, Tamcot CamdEs and BA525 varieties were found to be more water stress tolerant than others in terms of germination time and germinated plant. The UPGMA (Unweighted Pair-Group Method Using Arithmetic Averages analysis was carried out using 28 markers with average 0.306 polymorphism information content (PIC for molecular characterization studies. Based on the UPGMA results, the varieties were clustered into two groups. It is expected that the results obtained from this study might provide considerable data for improving new drought tolerant varieties.

  2. Analysis of sulfates on low molecular weight heparin using mass spectrometry: structural characterization of enoxaparin.

    Science.gov (United States)

    Gupta, Rohitesh; Ponnusamy, Moorthy P

    2018-05-21

    Structural characterization of Low Molecular Weight Heparin (LMWH) is critical to meet biosimilarity standards. In this context, the review focuses on structural analysis of labile sulfates attached to the side-groups of LMWH using mass spectrometry. A comprehensive review of this topic will help readers to identify key strategies for tackling the problem related to sulfate loss. At the same time, various mass spectrometry techniques are presented to facilitate compositional analysis of LMWH, mainly Enoxaparin. Areas covered: This review summarizes findings on mass spectrometry application for LMWH, including modulation of sulfates, using enzymology and sample preparation approaches. Furthermore, popular open-source software packages for automated spectral data interpretation are also discussed. Successful use of LC/MS can decipher structural composition for LMWH and help evaluate their sameness or biosimilarity with the innovator molecule. Overall, the literature has been searched using PubMed by typing various search queries such as "enoxaparin", "mass spectrometry", "low molecular weight heparin", "structural characterization", etc. Expert commentary: This section highlights clinically relevant areas that need improvement to achieve satisfactory commercialization of LMWHs. It also primarily emphasizes the advancements in instrumentation related to mass spectrometry, and discusses building automated software for data interpretation and analysis.

  3. Characterization and molecular profiling of PSEN1 familial Alzheimer's disease iPSC-derived neural progenitors.

    Directory of Open Access Journals (Sweden)

    Andrew A Sproul

    Full Text Available Presenilin 1 (PSEN1 encodes the catalytic subunit of γ-secretase, and PSEN1 mutations are the most common cause of early onset familial Alzheimer's disease (FAD. In order to elucidate pathways downstream of PSEN1, we characterized neural progenitor cells (NPCs derived from FAD mutant PSEN1 subjects. Thus, we generated induced pluripotent stem cells (iPSCs from affected and unaffected individuals from two families carrying PSEN1 mutations. PSEN1 mutant fibroblasts, and NPCs produced greater ratios of Aβ42 to Aβ40 relative to their control counterparts, with the elevated ratio even more apparent in PSEN1 NPCs than in fibroblasts. Molecular profiling identified 14 genes differentially-regulated in PSEN1 NPCs relative to control NPCs. Five of these targets showed differential expression in late onset AD/Intermediate AD pathology brains. Therefore, in our PSEN1 iPSC model, we have reconstituted an essential feature in the molecular pathogenesis of FAD, increased generation of Aβ42/40, and have characterized novel expression changes.

  4. Molecular Characterization of Hypoderma SPP. in Domestic Ruminants from Turkey and Pakistan.

    Science.gov (United States)

    Ahmed, Haroon; Simsek, Sami; Saki, Cem Ecmel; Kesik, Harun Kaya; Kilinc, Seyma Gunyakti

    2017-08-01

    The aim of this study was to determine the morphological and molecular characterization of Hypoderma spp. in cattle and yak from provinces in Turkey and Pakistan. In total, 78 Hypoderma larvae were collected from slaughtered animals in Turkey and Pakistan from October 2015 to January 2016. Thirty-eight of these 78 Hypoderma larvae were morphologically classified as third instar larvae (L3s) of Hypoderma bovis, 37 were classified as Hypoderma lineatum, and 3 were classified as suspected or unidentified. The restriction enzyme TaqI was used to differentiate the Hypoderma spp. by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). According to the sequences and the PCR-RFLP results, all larval samples from cattle from Turkey were classified as H. bovis, except for 1 sample classified as H. lineatum. All Hypoderma larvae from Pakistan were classified as H. lineatum from cattle and as Hypoderma sinense from yak. This study provides the first molecular characterization of H. lineatum (cattle) and H. sinense (yak) in Pakistan based on PCR-RFLP and sequencing results.

  5. Molecular, biochemical, and morphometric characterization of Fasciola species potentially causing zoonotic disease in Egypt.

    Science.gov (United States)

    El-Rahimy, Hoda H; Mahgoub, Abeer M A; El-Gebaly, Naglaa Saad M; Mousa, Wahid M A; Antably, Abeer S A E

    2012-09-01

    Fascioliasis is an important disease caused by Fasciola hepatica and Fasciola gigantica. The distributions of both species overlap in many areas of Asia and Africa including Egypt. Fifty adult Fasciola worms were collected from livers of cattle and sheep slaughtered in abattoirs, Cairo, Egypt. They were subjected to morphological and metric assessment of external features of fresh adults, morphological and metric assessment of internal anatomy of stained mounted worms, determination of electrophorezed bands of crude adult homogenates using SDS-PAGE, and molecular characterization of species-specific DNA segments using RFLP-PCR. It was found that the correlation between conventional morphology and its morphotype was statistically significant (P value = 0.00). Using SDS-PAGE, 13 bands were detected among both genotypes of Fasciola (35.7, 33.6, 32.4, 29.3, 27.5, 26, 24.4, 23, 21.45, 19, 16.75, 12.5, and 9.1 kDa).The most prevalent bands were that with a molecular weight of 29.3, 26, and 19 kDa. Bands detected were common for both species, but protein bands could not distinguish between F. hepatica and F. gigantica. The result of PCR for the amplification of the selected 28S rDNA fragment with the designed primer set yielded 618 bp long PCR products for F. hepatica and F. gigantica. Different band patterns generated after digestion of the 618 bp segment by the enzyme AvaII obtained with F. hepatica showed segments of the length 529, 62, 27 bp, while with F. gigantica 322, 269, 27 bp bands were obtained. Genotyping revealed no equivocal results. The conventional morphological parameters for species determination of Fasciola spp. endemic in Egypt were evaluated versus protein bands characterization and genotyping. It was concluded that conventional morphological and metric assessments were not useful for differentiation between F. gigantica and F. hepatica due to extensive overlap in the relative ranges. Similar conclusion was reached concerning protein band

  6. Synthesis and characterization of montmorillonite clay intercalated with molecular magnetic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Marcel G.; Martins, Daniel O.T.A.; Carvalho, Beatriz L.C. de [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil); Mercante, Luiza A. [Laboratório Nacional de Nanotecnologia para o Agronegócio (LNNA), Embrapa Instrumentação, São Carlos, SP 13560 970 (Brazil); Soriano, Stéphane [Instituto de Física, Universidade Federal Fluminense, Niterói, RJ 24.210 346 (Brazil); Andruh, Marius [Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Bucharest, Str. Dumbrava Rosie nr. 23, Bucharest (Romania); Vieira, Méri D., E-mail: gqimeri@vm.uff.br [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil); Vaz, Maria G.F., E-mail: mariavaz@vm.uff.br [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil)

    2015-08-15

    In this work montmorillonite (MMT) clay, whose matrix was modified with an ammonium salt (hexadecyltrimethylammonium bromide – CTAB), was employed as an inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange: a nitronyl nitroxide derivative 2-[4-(N-ethyl)-pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (p-EtRad{sup +}) and two binuclear coordination compounds, [Ni(valpn)Ln]{sup 3+}, where H{sub 2}valpn stands for 1,3-propanediyl-bis(2-iminomethylene-6-methoxy-phenol), and Ln=Gd{sup III}; Dy{sup III}. The pristine MMT and the intercalated materials were characterized by X-ray powder diffraction (XRD), infrared spectroscopy (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and magnetic measurements. The X-ray diffraction data analysis showed an increase of the interlamellar space of the intercalated MMT, indicating the intercalation of the magnetic compounds. Furthermore, the magnetic properties of the hybrid compounds were investigated, showing similar behavior as the pure magnetic guest species. - Graphical abstract: Montmorillonite clay was employed as inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange - Highlights: • Montmorillonite was employed as a host material. • Three molecular magnetic compounds were intercalated through ion exchange. • The compounds were successful intercalated maintaining the layered structure. • The hybrid materials exhibited similar magnetic behavior as the pure magnetic guest.

  7. Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

    Science.gov (United States)

    Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

    2017-04-01

    The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Molecular characterization of the transition to mid-life in Caenorhabditis elegans.

    Science.gov (United States)

    Eckley, D Mark; Rahimi, Salim; Mantilla, Sandra; Orlov, Nikita V; Coletta, Christopher E; Wilson, Mark A; Iser, Wendy B; Delaney, John D; Zhang, Yongqing; Wood, William; Becker, Kevin G; Wolkow, Catherine A; Goldberg, Ilya G

    2013-06-01

    We present an initial molecular characterization of a morphological transition between two early aging states. In previous work, an age score reflecting physiological age was developed using a machine classifier trained on images of worm populations at fixed chronological ages throughout their lifespan. The distribution of age scores identified three stable post-developmental states and transitions. The first transition occurs at day 5 post-hatching, where a significant percentage of the population exists in both state I and state II. The temperature dependence of the timing of this transition (Q 10 ~ 1.17) is too low to be explained by a stepwise process with an enzymatic or chemical rate-limiting step, potentially implicating a more complex mechanism. Individual animals at day 5 were sorted into state I and state II groups using the machine classifier and analyzed by microarray expression profiling. Despite being isogenic, grown for the same amount of time, and indistinguishable by eye, these two morphological states were confirmed to be molecularly distinct by hierarchical clustering and principal component analysis of the microarray results. These molecular differences suggest that pharynx morphology reflects the aging state of the whole organism. Our expression profiling yielded a gene set that showed significant overlap with those from three previous age-related studies and identified several genes not previously implicated in aging. A highly represented group of genes unique to this study is involved in targeted ubiquitin-mediated proteolysis, including Skp1-related (SKR), F-box-containing, and BTB motif adaptors.

  9. Genetic and molecular characterization of photoperiod and thermo-sensitive male sterility in rice.

    Science.gov (United States)

    Fan, Yourong; Zhang, Qifa

    2018-03-01

    A review on photoperiod and temperature-sensitive genic male sterility in rice. Male sterility in plants, facilitating the development of hybrid crops, has made great contribution to crop productivity worldwide. Environment-sensitive genic male sterility (EGMS), including photoperiod-sensitive genic male sterility (PGMS) and temperature-sensitive genic male sterility (TGMS), has provided a special class of germplasms for the breeding of "two-line" hybrids in several crops. In rice, the finding of the PGMS NK58S mutant in 1973 started the journey of research and breeding of two-line hybrids. Genetic and molecular characterization of these germplasms demonstrated diverse genes and molecular mechanisms of male sterility regulation. Two loci identified from NK58S, PMS1 and PMS3, both encode long noncoding RNAs. A major TGMS locus, TMS5, found in the TGMS line Annong S-1, encodes an RNase Z. A reverse PGMS mutant carbon starved anther encodes an R2R3 MYB transcription factor. Breeding efforts in the last three decades have resulted in hundreds of EGMS lines and two-line hybrids released to rice production, which have greatly elevated the yield potential and grain quality of rice varieties. The enhanced molecular understanding will offer new strategies for the development of EGMS lines thus further improving two-line hybrid breeding of rice as well as other crops.

  10. Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolated in Nepal.

    Science.gov (United States)

    Poudel, Ajay; Nakajima, Chie; Fukushima, Yukari; Suzuki, Haruka; Pandey, Basu Dev; Maharjan, Bhagwan; Suzuki, Yasuhiko

    2012-06-01

    Despite the fact that Nepal is one of the first countries globally to introduce multidrug-resistant tuberculosis (MDR-TB) case management, the number of MDR-TB cases is continuing to rise in Nepal. Rapid molecular tests applicable in this setting to identify resistant organisms would be an effective tool in reversing this trend. To develop such tools, information about the frequency and distribution of mutations that are associated with phenotypic drug resistance in Mycobacterium tuberculosis is required. In the present study, we investigated the prevalence of mutations in rpoB and katG genes and the inhA promoter region in 158 M. tuberculosis isolates (109 phenotypically MDR and 49 non-MDR isolates collected in Nepal) by DNA sequencing. Mutations affecting the 81-bp rifampin (RIF) resistance-determining region (RRDR) of rpoB were identified in 106 of 109 (97.3%) RIF-resistant isolates. Codons 531, 526, and 516 were the most commonly affected, at percentages of 58.7, 15.6, and 15.6%, respectively. Of 113 isoniazid (INH)-resistant isolates, 99 (87.6%) had mutations in the katG gene, with Ser315Thr being the most prevalent (81.4%) substitution. Mutations in the inhA promoter region were detected in 14 (12.4%) INH-resistant isolates. The results from this study provide an overview of the current situation of RIF and INH resistance in M. tuberculosis in Nepal and can serve as a basis for developing or improving rapid molecular tests to monitor drug-resistant strains in this country.

  11. Rapid Determination of Six Low Molecular Carbonyl Compounds in Tobacco Smoke by the APCI-MS/MS Coupled to Data Mining

    Directory of Open Access Journals (Sweden)

    Wuduo Zhao

    2017-01-01

    Full Text Available A simple method was established for the rapid determination of low molecular carbonyl compounds by the combination of atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS and data mining. The ionization was carried out in positive mode, and six low molecular carbonyl compounds of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde were analyzed by both full scan mode and daughter scan mode. To overcome the quantitative difficulties from isomer of acetone/propionaldehyde and butanone/butyraldehyde, the quantitation procedure was performed with the characteristic ion of [CH3O]+ under CID energy of 5 and 15 eV. Subsequently, the established method was successfully applied to analysis of six low molecular carbonyl compounds in tobacco smoke with analytical period less than four minutes. The contents of acrolein, acetone, propionaldehyde, crotonaldehyde, butanone, and butyraldehyde for a cigarette were about 63±5.8, 325±82, 55±9.7, 11±1.4, 67±5.9, and 12±1.8 μg/cig, respectively. The experimental results indicated that the established method had the potential application in rapid determination of low molecular carbonyl compounds.

  12. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

    Science.gov (United States)

    Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

    2018-01-31

    In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Synthesis of molecularly imprinted dye-silica nanocomposites with high selectivity and sensitivity: Fluorescent imprinted sensor for rapid and efficient detection of τ-fluvalinate in vodka.

    Science.gov (United States)

    Wang, Yunyun; Wang, Jixiang; Cheng, Rujia; Sun, Lin; Dai, Xiaohui; Yan, Yongsheng

    2018-04-01

    An imprinted fluorescent sensor was fabricated based on SiO 2 nanoparticles encapsulated with a molecularly imprinted polymer containing allyl fluorescein. High fluorine cypermethirin as template molecules, methyl methacrylate as functional monomer, and allyl fluorescein as optical materials synthesized a core-shell fluorescent molecular imprinted sensor, which showed a high and rapid sensitivity and selectivity for the detection of τ-fluvalinate. The sensor presented appreciable sensitivity with a limit of 13.251 nM, rapid detection that reached to equilibrium within 3 min, great linear relationship in the relevant concentration range from 0 to 150 nM, and excellent selectivity over structural analogues. In addition, the fluorescent sensor demonstrated desirable regeneration ability (eight cycling operations). The molecularly imprinted polymers ensured specificity, while the fluorescent dyes provided the stabile sensitivity. Finally, an effective application of the sensor was implemented by the detection of τ-fluvalinate in real samples from vodka. The molecularly imprinted fluorescent sensor showed a promising potential in environmental monitoring and food safety. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

    Science.gov (United States)

    Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

    2016-02-01

    The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

  15. Molecular typing and characterization of a new serotype of human enterovirus (EV-B111) identified in China.

    Science.gov (United States)

    Zhang, Yong; Hong, Mei; Sun, Qiang; Zhu, Shuangli; Tsewang; Li, Xiaolei; Yan, Dongmei; Wang, Dongyan; Xu, Wenbo

    2014-04-01

    Molecular methods, based on sequencing the region encoding the complete VP1 or P1 protein, have enabled the rapid identification of new enterovirus serotypes. In the present study, the complete genome of a newly discovered enterovirus serotype, strain Q0011/XZ/CHN/2000 (hereafter referred to as Q0011), was sequenced and analyzed. The virus, isolated from a stool sample from a patient with acute flaccid paralysis in the Tibet region of China in 2000, was characterized by amplicon sequencing and comparison to a GenBank database of enterovirus nucleotide sequences. The nucleotide sequence encoding the complete VP1 capsid protein is most closely related to the sequences of viruses within the species enterovirus B (EV-B), but is less than 72.1% identical to the homologous sequences of the recognized human enterovirus serotypes, with the greatest homology to EV-B101 and echovirus 32. Moreover, the deduced amino acid sequence of the complete VP1 region is less than 84.7% identical to those of the recognized serotypes, suggesting that the strain is a new serotype of enterovirus within EV-B. The virus was characterized as a new enterovirus type, named EV-B111, by the Picornaviridae Study Group of the International Committee on Taxonomy of Viruses. Low positive rate and titer of neutralizing antibody against EV-B111 were found in the Tibet region of China. Nearly 50% of children ≤5 years had no neutralizing antibody against EV-B111. So the extent of transmission and the exposure of the population to this new EV are very limited. This is the first identification of a new serotype of human enterovirus in China, and strain Q0011 was designated the prototype strain of EV-B111. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Molecular characterization of a heterothallic mating system in Pseudogymnoascus destructans, the Fungus causing white-nose syndrome of bats.

    Science.gov (United States)

    Palmer, Jonathan M; Kubatova, Alena; Novakova, Alena; Minnis, Andrew M; Kolarik, Miroslav; Lindner, Daniel L

    2014-07-21

    White-nose syndrome (WNS) of bats has devastated bat populations in eastern North America since its discovery in 2006. WNS, caused by the fungus Pseudogymnoascus destructans, has spread quickly in North America and has become one of the most severe wildlife epidemics of our time. While P. destructans is spreading rapidly in North America, nothing is known about the sexual capacity of this fungus. To gain insight into the genes involved in sexual reproduction, we characterized the mating-type locus (MAT) of two Pseudogymnoascus spp. that are closely related to P. destructans and homothallic (self-fertile). As with other homothallic Ascomycota, the MAT locus of these two species encodes a conserved α-box protein (MAT1-1-1) as well as two high-mobility group (HMG) box proteins (MAT1-1-3 and MAT1-2-1). Comparisons with the MAT locus of the North American isolate of P. destructans (the ex-type isolate) revealed that this isolate of P. destructans was missing a clear homolog of the conserved HMG box protein (MAT1-2-1). These data prompted the discovery and molecular characterization of a heterothallic mating system in isolates of P. destructans from the Czech Republic. Both mating types of P. destructans were found to coexist within hibernacula, suggesting the presence of mating populations in Europe. Although populations of P. destructans in North America are thought to be clonal and of one mating type, the potential for sexual recombination indicates that continued vigilance is needed regarding introductions of additional isolates of this pathogen. Copyright © 2014 Palmer et al.

  17. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    Science.gov (United States)

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-06-28

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  18. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    Directory of Open Access Journals (Sweden)

    Charles W. Ross

    2016-06-01

    Full Text Available Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI, sheath flow electrospray ionization (ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS and high-field nuclear magnetic resonance (NMR analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  19. Clinical characterization and molecular classification of 12 Korean patients with pseudohypoparathyroidism and pseudopseudohypoparathyroidism.

    Science.gov (United States)

    Cho, S Y; Yoon, Y A; Ki, C-S; Huh, H J; Yoo, H-W; Lee, B H; Kim, G-H; Yoo, J-H; Kim, S-Y; Kim, S J; Sohn, Y B; Park, S W; Huh, R; Chang, M S; Lee, J; Kwun, Y; Maeng, S H; Jin, D-K

    2013-10-01

    Pseudohypoparathyroidism (PHP) is defined as resistance toward parathyroid hormones. PHP and pseudopseudohypoparathyroidism (PPHP) are rare disorders resulting from genetic and epigenetic aberrations within or upstream of the GNAS locus. This study investigated the clinical characteristics and performed a molecular analysis of PHP and PPHP. A total of 12 patients with (P)PHP from 11 unrelated families (4 with PHP-Ia, 6 with PHP-Ib, and 2 with PPHP) were characterized using both clinical and molecular methods. Clinical features included the presenting symptoms, Albright hereditary osteodystrophy features, and resistance to hormones. Comprehensive analysis of the GNAS and STX16 loci was undertaken to investigate the molecular defects underlying (P)PHP. All PHP-Ib patients displayed hypocalcemic symptoms. All PHP-Ia patients showed resistance toward TSH, in addition to PTH. In most patients with PHP, when the diagnosis of PHP was first established, hypocalcemia and hyperphosphatemia were associated with a significant increase in serum PTH levels. One patient with PHP-Ia was diagnosed with growth hormone deficiency and showed a good response to human recombinant growth hormone therapy. 6 patients with PHP-Ia and PPHP showed 5 different mutations in the GNAS gene. 5 patients with PHP-Ib displayed a loss of differentially methylated region (DMR) imprints of the maternal GNAS. One PHP-Ib patient showed a de novo microdeletion in STX16 and a loss of methylation of exon A/B on the maternal allele. No patients revealed paternal disomy among 4 patients with PHP-Ib. Identification of the molecular causes of PHP and PPHP explains their distinctive clinical features and enables confirmation of the diagnosis and exact genetic counseling. © J. A. Barth Verlag in Georg Thieme Verlag KG Stuttgart · New York.

  20. Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues.

    Science.gov (United States)

    Almeida, Tânia; Menéndez, Esther; Capote, Tiago; Ribeiro, Teresa; Santos, Conceição; Gonçalves, Sónia

    2013-01-15

    The molecular processes associated with cork development in Quercus suber L. are poorly understood. A previous molecular approach identified a list of genes potentially important for cork formation and differentiation, providing a new basis for further molecular studies. This report is the first molecular characterization of one of these candidate genes, QsMYB1, coding for an R2R3-MYB transcription factor. The R2R3-MYB gene sub-family has been described as being involved in the phenylpropanoid and lignin pathways, both involved in cork biosynthesis. The results showed that the expression of QsMYB1 is putatively mediated by an alternative splicing (AS) mechanism that originates two different transcripts (QsMYB1.1 and QsMYB1.2), differing only in the 5'-untranslated region, due to retention of the first intron in one of the variants. Moreover, within the retained intron, a simple sequence repeat (SSR) was identified. The upstream regulatory region of QsMYB1 was extended by a genome walking approach, which allowed the identification of the putative gene promoter region. The relative expression pattern of QsMYB1 transcripts determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR) revealed that both transcripts were up-regulated in cork tissues; the detected expression was several times higher in newly formed cork harvested from trees producing virgin, second or reproduction cork when compared with wood. Moreover, the expression analysis of QsMYB1 in several Q. suber organs showed very low expression in young branches and roots, whereas in leaves, immature acorns or male flowers, no expression was detected. These preliminary results suggest that QsMYB1 may be related to secondary growth and, in particular, with the cork biosynthesis process with a possible alternative splicing mechanism associated with its regulatory function. Copyright © 2012 Elsevier GmbH. All rights reserved.

  1. Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences.

    Science.gov (United States)

    Amor, Nabil; Farjallah, Sarra; Salem, Mohamed; Lamine, Dia Mamadou; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

    2011-10-01

    Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n=60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene. Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries. Copyright © 2011 Elsevier Inc. All

  2. Isolation and biochemical and molecular characterization of Listeria monocytogenes in food

    International Nuclear Information System (INIS)

    Helel, Salma

    2008-01-01

    monocytogenes is a Gram-positive bacteria, saprophytic, non-spore. This is an extremely resistant seeds to environmental conditions outside, especially since the cold psychrotrophic. It can contaminate raw vegetables, cooked meals ready for consumption or foods to be stored in the refrigerator, such as cheese or meat. It is the bacteria responsible for listeriosis. It threatens first unborn children, infants, pregnant women, the elderly and people whose immune system is weakened. Strains of Listeria spp isolated from foods (seafood, meat, meat) were first identified at the stage of the genus by classical tests (Gram staining, catalase test, oxidase test and mobility) and stage of the test case by hemolysis, CAMP test and the gallery Api Listeria. Biochemical characterization allowed after a numerical analysis, to assign 100% of isolates to the genus Listeria. Molecular characterization was performed by PCR amplification of genes coding for protein p60 (iap), the listeriolysine O (hly), the Phosphatidylinositol Phospholipase C (PI-PLC plca) Phosphatidylcholine Phospholipase C (plcB). The result showed an amplification of the iap gene of 100% of the hly gene, plca, plcB of 31.81%. This characterization represents an identification of the collection on the genetic level and shows that 31.81% of isolates, is likely to express the genes responsible for virulence factors of L. monocytogenes, to produce listeriolysine O, phospholipase C and Lecithinase. The molecular identification was performed by microarray technique and identified isolates L. September monocytogenes (five original clinical isolates and two food-borne), fourteen L. innocua (of food) and a strain not identified by DNA chip.. (Author)

  3. Morphological and Molecular Characterization of Bova Olive Cultivar and Aroma Fingerprint of Its Oil

    Directory of Open Access Journals (Sweden)

    Marin Krapac

    2014-01-01

    Full Text Available This interdisciplinary study aims to contribute to the characterization of Istrian (Croatia olive cultivars and oil, giving for the first time the morphological and genetic profile of Bova cultivar, and chemical and sensorial characteristics of its oil. Morphological features of Bova cv. were determined according to the International Olive Council methodology, while molecular characterization was performed using eleven microsatellite markers. Bova cultivar was morphologically and genetically different from other described Istrian olive cultivars. The microsatellite profile of Bova was also unique when compared to more than 200 different Italian genotypes using the same set of markers. In order to characterize the oil from Bova cv., fruits from three trees at the same ripening stage were harvested and processed separately under the same conditions. Volatile composition of the obtained oil samples was determined using solid-phase microextraction with gas chromatography/mass spectrometry. About 50 volatiles were detected, mostly hydrocarbons (34.69 % of total peak area, followed by aldehydes (25.80 %, alcohols (22.24 %, ketones (8.76 %, organic acids (4.08 %, terpenes (2.10 %, esters (2.18 % and furans (0.26 %. Bova oil was rich in total C6 (39.87 % and C5 volatiles (13.85 %, biogenerated through the lipoxygenase pathway. The most prevalent volatile compound was C6 aldehyde E-2-hexenal. Quantitative descriptive sensory analysis of the investigated olive oil samples was carried out by a sensory panel. The sensory profile was characterized by medium intensities of olive fruity, green leaves and grass, light tomato and aromatic herbs flavours with mild apple and other ripe fruit notes. The taste was characterized by medium to strong bitterness, followed by medium pungency and mild sweetness.

  4. MRI characterization of temporal lobe epilepsy using rapidly measurable spatial indices with hemisphere asymmetries and gender features

    International Nuclear Information System (INIS)

    Datta, Siddhartha; Chakrabarti, Nilkanta; Sarkar, Sudipta; Chakraborty, Sumit; Basu, Swadhapriya; Mulpuru, Sai Krishna; Tiwary, Basant K.; Roy, Prasun Kumar

    2015-01-01

    The paucity of morphometric markers for hemispheric asymmetries and gender variations in hippocampi and amygdalae in temporal lobe epilepsy (TLE) calls for better characterization of TLE by finding more useful prognostic MRI parameter(s). T1-weighted MRI (3 T) morphometry using multiple parameters of hippocampus-parahippocampus (angular and linear measures, volumetry) and amygdalae (volumetry) including their hemispheric asymmetry indices (AI) were evaluated in both genders. The cutoff values of parameters were statistically estimated from measurements of healthy subjects to characterize TLE (57 patients, 55 % male) alterations. TLE had differential categories with hippocampal atrophy, parahippocampal angle (PHA) acuteness, and several other parametric changes. Bilateral TLE categories were much more prevalent compared to unilateral TLE categories. Female patients were considerably more disposed to bilateral TLE categories than male patients. Male patients displayed diverse categories of unilateral abnormalities. Few patients (both genders) had combined bilateral appearances of hippocampal atrophy, amygdala atrophy, PHA acuteness, and increase in hippocampal angle (HA) where medial distance ratio (MDR) varied among genders. TLE had gender-specific and hemispheric dominant alterations in AI of parameters. Maximum magnitude of parametric changes in TLE includes (a) AI increase in HA of both genders, (b) HA increase (bilateral) in female patients, and (c) increase in ratio of amygdale/hippocampal volume (unilateral, right hemispheric), and AI decrease in MDR, in male patients. Multiparametric MRI studies of hippocampus and amygdalae, including their hemispheric asymmetry, underscore better characterization of TLE. Rapidly measurable single-slice parameters (HA, PHA, MDR) can readily delineate TLE in a time-constrained clinical setting, which contrasts with customary three-dimensional hippocampal volumetry that requires many slice computation. (orig.)

  5. MRI characterization of temporal lobe epilepsy using rapidly measurable spatial indices with hemisphere asymmetries and gender features

    Energy Technology Data Exchange (ETDEWEB)

    Datta, Siddhartha; Chakrabarti, Nilkanta [University of Calcutta, Department of Physiology and UGC-CPEPA Centre for ' ' Electro-physiological and Neuro-imaging studies including Mathematical Modelling' ' , Kolkata (India); Sarkar, Sudipta; Chakraborty, Sumit; Basu, Swadhapriya [IPGME and R, SSKM Hospital, Department of Radiodiagnosis, Kolkata (India); Mulpuru, Sai Krishna [National Brain Research Centre, National Neuro-Imaging Facility, Manesar (India); Tiwary, Basant K. [Pondicherry University, Centre for Bioinformatics, School of Life Sciences, Pondicherry (India); Roy, Prasun Kumar [National Brain Research Centre, Computational Neuroimaging Division, Manesar (India); National Brain Research Centre, Clinical Neuroscience Unit, Gurgaon (India)

    2015-09-15

    The paucity of morphometric markers for hemispheric asymmetries and gender variations in hippocampi and amygdalae in temporal lobe epilepsy (TLE) calls for better characterization of TLE by finding more useful prognostic MRI parameter(s). T1-weighted MRI (3 T) morphometry using multiple parameters of hippocampus-parahippocampus (angular and linear measures, volumetry) and amygdalae (volumetry) including their hemispheric asymmetry indices (AI) were evaluated in both genders. The cutoff values of parameters were statistically estimated from measurements of healthy subjects to characterize TLE (57 patients, 55 % male) alterations. TLE had differential categories with hippocampal atrophy, parahippocampal angle (PHA) acuteness, and several other parametric changes. Bilateral TLE categories were much more prevalent compared to unilateral TLE categories. Female patients were considerably more disposed to bilateral TLE categories than male patients. Male patients displayed diverse categories of unilateral abnormalities. Few patients (both genders) had combined bilateral appearances of hippocampal atrophy, amygdala atrophy, PHA acuteness, and increase in hippocampal angle (HA) where medial distance ratio (MDR) varied among genders. TLE had gender-specific and hemispheric dominant alterations in AI of parameters. Maximum magnitude of parametric changes in TLE includes (a) AI increase in HA of both genders, (b) HA increase (bilateral) in female patients, and (c) increase in ratio of amygdale/hippocampal volume (unilateral, right hemispheric), and AI decrease in MDR, in male patients. Multiparametric MRI studies of hippocampus and amygdalae, including their hemispheric asymmetry, underscore better characterization of TLE. Rapidly measurable single-slice parameters (HA, PHA, MDR) can readily delineate TLE in a time-constrained clinical setting, which contrasts with customary three-dimensional hippocampal volumetry that requires many slice computation. (orig.)

  6. Isolation, molecular and biochemical characterization of oil degrading bacteria from contaminated soil at an oil refinery

    International Nuclear Information System (INIS)

    AL-Deeb, T.M.; Malkawi, H.I.

    2009-01-01

    Biodegradation using microorganisms is considered to be cost-effective and environmentally friendly treatment of oil-contaminated sites. Oil-biodegrading bacterial strains were isolated, identified and characterized from oil contaminated soil samples at oil refinery in Zarqa (Jordan). Thirty four bacterial isolates were grown on mineral salt media supplemented with crude oil, but 16 showed positive biodegradation of diesel. All the 34 bacterial isolates were characterized at the molecular and bio-chemical levels, and showed positive polymerase chain reaction (PCR) amplification product size of 1500 bp when 16s rDNA bacterial universal primers were used. Eighteen bacterial isolates showed positive PCR amplification product size of 150 bp specific for the genus Pseudomonas and 3 bacterial isolates showed positive amplification product size of 1500 bp specific for the genus Acinetobacter. Biochemical and physiological characterization performed on the 34 bacterial isolates revealed the presence of oil biodegrading bacterial genera and species of Pseudomonas Acidovorans, P. aeruginosa, P. vesicularis, Acinetobacter calcoaceticus, Ac. lowffii, Micro-ococcus luteus, M. varians, M. lylae, M. roseus, Alcaligenes denitrificians, Bacillus megaterium, Comamonas sp., Moralxella sp., Bordetella sp., P. putida, P. stutzeri and P. mallei. (au)

  7. Molecular and serological characterization of the first Leptospira santarosai strain isolated from a dog.

    Science.gov (United States)

    Miotto, Bruno Alonso; Moreno, Luisa Zanolli; Guilloux, Aline Gil Alves; Sousa, Gisele Oliveira de; Loureiro, Ana Paula; Moreno, Andrea Micke; Lilenbaum, Walter; Vasconcellos, Silvio Arruda; Heinemann, Marcos Bryan; Hagiwara, Mitika Kuribayashi

    2016-10-01

    Leptospirosis is a zoonotic disease of global importance caused by pathogenic Leptospira species. Dogs can become asymptomatically infected, acting like reservoir hosts for pathogenic Leptospira, notably Leptospira interrogans serovar Canicola. Identification of such individuals and characterization of leptospires involved in chronic infections may unravel the role of dogs in the epidemiology of particular leptospiral strains. The aim of the present work was to describe the first Leptospira santarosai strain isolated from a dog. The dog was kept in a public shelter in São Paulo city, Brazil, and presented asymptomatic urinary shedding detected by PCR. Prospective evaluation was performed to fully characterize its chronic carrier state. The dog did not present anti-Leptospira titles or clinical/laboratorial abnormalities during the evaluations; nevertheless long-term urinary shedding was confirmed by PCR and leptospires were recovered from two occasions. The isolated strain was molecularly characterized by partial 16S rRNA and secY gene sequencing and MLST analysis. Serogroup identification was performed using polyclonal antibodies. The strain was identified as Leptospira santarosai, serogroup Sejroe. This is the first evidence in the literature of the isolation of L. santarosai in dogs. Our findings show that dogs can persistently harbor leptospires other than L. interrogans. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Feline urine metabolomic signature: characterization of low-molecular-weight substances in urine from domestic cats.

    Science.gov (United States)

    Rivera-Vélez, Sol-Maiam; Villarino, Nicolas F

    2018-02-01

    Objectives This aim of this study was to characterize the composition and content of the feline urine metabolome. Methods Eight healthy domestic cats were acclimated at least 10 days before starting the study. Urine samples (~2 ml) were collected by ultrasound-guided cystocentesis. Samples were centrifuged at 1000 × g for 8 mins, and the supernatant was analyzed by gas chromatography/time-of-flight mass spectrometery. The urine metabolome was characterized using an untargeted metabolomics approach. Results Three hundred and eighteen metabolites were detected in the urine of the eight cats. These molecules are key components of at least 100 metabolic pathways. Feline urine appears to be dominated by carbohydrates, carbohydrate conjugates, organic acid and derivatives, and amino acids and analogs. The five most abundant molecules were phenaceturic acid, hippuric acid, pseudouridine phosphate and 3-(4-hydroxyphenyl) propionic acid. Conclusions and relevance This study is the first to characterize the feline urine metabolome. The results of this study revealed the presence of multiple low-molecular-weight substances that were not known to be present in feline urine. As expected, the origin of the metabolites detected in urine was diverse, including endogenous compounds and molecules biosynthesized by microbes. Also, the diet seemed to have had a relevant role on the urine metabolome. Further exploration of the urine metabolic phenotype will open a window for discovering unknown, or poorly understood, metabolic pathways. In turn, this will advance our understanding of feline biology and lead to new insights in feline physiology, nutrition and medicine.

  9. Morphological and molecular characterization of Fusarium spp pathogenic to pecan tree in Brazil.

    Science.gov (United States)

    Lazarotto, M; Milanesi, P M; Muniz, M F B; Reiniger, L R S; Beltrame, R; Harakava, R; Blume, E

    2014-11-11

    The occurrence of Fusarium spp associated with pecan tree (Carya illinoinensis) diseases in Brazil has been observed in recent laboratory analyses in Rio Grande do Sul State. Thus, in this study, we i) obtained Fusarium isolates from plants with disease symptoms; ii) tested the pathogenicity of these Fusarium isolates to pecan; iii) characterized and grouped Fusarium isolates that were pathogenic to the pecan tree based on morphological characteristics; iv) identified Fusarium spp to the species complex level through TEF-1α sequencing; and v) compared the identification methods used in the study. Fifteen isolates collected from the inflorescences, roots, and seeds of symptomatic plants (leaf necrosis or root rot) were used for pathogenicity tests. Morphological characterization was conducted using only pathogenic isolates, for a total of 11 isolates, based on the mycelial growth rate, sporulation, colony pigmentation, and conidial length and width variables. Pathogenic isolates were grouped based on morphological characteristics, and molecular characterization was performed by sequencing TEF-1α genes. Pathogenic isolates belonging to the Fusarium chlamydosporum species complex, Fusarium graminearum species complex, Fusarium proliferatum, and Fusarium oxysporum were identified based on the TEF-1α region. Morphological characteristics were used to effectively differentiate isolates and group the isolates according to genetic similarity, particularly conidial width, which emerged as a key morphological descriptor in this study.

  10. Molecular characterization of circulating plasma cells in patients with active systemic lupus erythematosus.

    Directory of Open Access Journals (Sweden)

    Patricia L Lugar

    Full Text Available Systemic lupus erythematosus (SLE is a generalized autoimmune disease characterized by abnormal B cell activation and the occurrence of increased frequencies of circulating plasma cells (PC. The molecular characteristics and nature of circulating PC and B cells in SLE have not been completely characterized. Microarray analysis of gene expression was used to characterize circulating PC in subjects with active SLE. Flow cytometry was used to sort PC and comparator B cell populations from active SLE blood, normal blood and normal tonsil. The gene expression profiles of the sorted B cell populations were then compared. SLE PC exhibited a similar gene expression signature as tonsil PC. The differences in gene expression between SLE PC and normal tonsil PC and tonsil plasmablasts (PB suggest a mature Ig secreting cell phenotype in the former population. Despite this, SLE PC differed in expression of about half the genes from previously published gene expression profiles of normal bone marrow PC, indicating that these cells had not achieved a fully mature status. Abnormal expression of several genes, including CXCR4 and S1P(1, suggests a mechanism for the persistence of SLE PC in the circulation. All SLE B cell populations revealed an interferon (IFN gene signature previously only reported in unseparated SLE peripheral blood mononuclear cells. These data indicate that SLE PC are a unique population of Ig secreting cells with a gene expression profile indicative of a mature, but not fully differentiated phenotype.

  11. Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

    International Nuclear Information System (INIS)

    Ali, M. S.; Latif, Z.

    2016-01-01

    Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

  12. Detection and Molecular Characterization of Gemycircularvirus from Environmental Samples in Brazil.

    Science.gov (United States)

    da Silva Assis, Matheus Ribeiro; Vieira, Carmen Baur; Fioretti, Julia Monassa; Rocha, Mônica Simões; de Almeida, Pedro Ivo Neves; Miagostovich, Marize Pereira; Fumian, Tulio Machado

    2016-12-01

    Gemycircularvirus (GemyCV) is a group of viruses which has been recently proposed as a new viral genus detected in fecal and environmental samples around the world. GemyCVs have been detected in human blood, brain tissue, cerebrospinal fluid, and stool sample. In the present study, we demonstrate for the first time, through molecular detection and characterization, the presence of GemyCVs in environmental samples from Brazil. Our results show a percentage of positivity ranging from 69 (25/36) to 97 % (35/36) in river water samples collected in Manaus, Amazon region, and wastewater from a wastewater treatment plant located in Rio de Janeiro, respectively, revealing GemyCVs as an important environmental contaminant.

  13. Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents

    Science.gov (United States)

    Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang

    2013-05-01

    Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

  14. Molecular characterization of putative Hepatozoon sp. from the sedge warbler (Acrocephalus schoenobaenus).

    Science.gov (United States)

    Biedrzycka, Aleksandra; Kloch, Agnieszka; Migalska, Magdalena; Bielański, Wojciech

    2013-05-01

    We characterized partial sequences of 18S rDNA from sedge warblers infected with a parasite described previously as Hepatozoon kabeeni. Prevalence was 47% in sampled birds.We detected 3 parasite haplotypes in 62 sequenced samples from infected animals. In phylogenetic analyses, 2 of the putative Hepatozoon haplotypes closely resembled Lankesterella minima and L. valsainensis. The third haplotype grouped in a wider clade composed of Caryospora and Eimeria. None of the haplotypes showed resemblance to sequences of Hepatozoon from reptiles and mammals. Molecular detection results were consistent with those from microscopy of stained blood smears, confirming that the primers indeed amplified the parasite sequences. Here we provide evidence that the avian Hepatozoon-like parasites are most likely Lankesterella, supporting the suggestion that the systematic position of avian Hepatozoon-like species needs to be revised.

  15. Molecular Characterization of Microbial Communities in a JP-4 Fuel Contaminated Soil

    International Nuclear Information System (INIS)

    Barcelona, M.J.; Chang, Y.-J.; Gan, Y.D.; Macnaughton, S.J.; Peacock, A.; Stephen, J.R.; White, D.C.

    1999-01-01

    In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and saturated-soils were taken from cores within, up- and down-gradient of the contaminant plume. Significant differences in biomass and proportion of Gram negative bacteria were found inside and outside the plume. Sequence analysis of DGGE bands from within the spill site suggested dominance by a limited number of phylogenetically diverse bacteria. Used in tandem with pollutant quantification, these molecular techniques should facilitate significant improvements over current assessment procedures for determination of remediation end points

  16. Molecular-beam epitaxial growth and characterization of quaternary III-nitride compounds

    International Nuclear Information System (INIS)

    Monroy, E.; Gogneau, N.; Enjalbert, F.; Fossard, F.; Jalabert, D.; Bellet-Amalric, E.; Dang, Le Si; Daudin, B.

    2003-01-01

    We report on the controlled growth and characterization of quaternary AlGaInN compounds by plasma-assisted molecular beam epitaxy. Two-dimensional growth is achieved with a monolayer of In segregating at the growth front. In incorporation is hindered by increasing growth temperature and Al mole fraction, which is explained by the lower binding energy of InN compared to GaN and AlN. The mosaicity of the layers is determined by the substrate quality, whereas the alloy disorder increases with the Al content, independent of the In mole fraction. Room temperature photoluminescence is dominated by a narrow band-edge emission, whose Stokes shift and activation energy increase with the In content. This behavior is interpreted in terms of carrier localization in self-formed alloy inhomogeneities. An In-related band bowing parameter of 2.5 eV has been estimated

  17. Molecular characterization of AI viruses from poultry and wild bird surveillance in Denmark

    DEFF Research Database (Denmark)

    Larsen, Lars Erik; Krog, Jesper Schak; Madsen, Jesper J.

    Infection with avian influenza virus (AIV) in poultry may cause devastating disease although the same virus may not cause disease in wild birds. Since AI viruses can be exchanged between poultry and wild birds, surveillance in wild birds provides important knowledge for control of disease...... in poultry. AIV’s from the Danish wild bird active surveillance were characterized, focusing on viruses from 2012, and from outbreaks of AI in poultry in Denmark. The matrix (M) gene from more than 50 viruses of different subtypes and the hemagglutinin (HA) gene from more than 30 subtype H5 low pathogenic...... viruses were sequenced and compared by alignment and phylogenetic analyses. The aim was to evaluate: the origin of viruses from outbreaks of AI in Danish poultry, the design of active surveillance in Denmark, and the suitability of the molecular diagnostic RT-PCR tests employed. All M-genes from Danish...

  18. Molecular clocks and the human condition: approaching their characterization in human physiology and disease.

    Science.gov (United States)

    Fitzgerald, G A; Yang, G; Paschos, G K; Liang, X; Skarke, C

    2015-09-01

    Molecular clockworks knit together diverse biological networks and compelling evidence from model systems infers their importance in metabolism, immunological and cardiovascular function. Despite this and the diurnal variation in many aspects of human physiology and the phenotypic expression of disease, our understanding of the role and importance of clock function and dysfunction in humans is modest. There are tantalizing hints of connection across the translational divide and some correlative evidence of gene variation and human disease but most of what we know derives from forced desynchrony protocols in controlled environments. We now have the ability to monitor quantitatively ex vivo or in vivo the genome, metabolome, proteome and microbiome of humans in the wild. Combining this capability, with the power of mobile telephony and the evolution of remote sensing, affords a new opportunity for deep phenotyping, including the characterization of diurnal behaviour and the assessment of the impact of the clock on approved drug function. © 2015 John Wiley & Sons Ltd.

  19. Molecular and phylogenetic characterization of Cryptosporidium and Giardia from pigs and cattle in Denmark

    DEFF Research Database (Denmark)

    Langkjær, Rikke Breinhold; Vigre, Håkan; Enemark, Heidi L.

    2007-01-01

    The genetic diversity of Cryptosporidium spp. and Giardia duodenalis from dairy cattle and pigs in Denmark was determined in the present study. Faecal samples from 1237 pigs and 1150 cattle originating from 50 sow herds and 50 dairy herds, respectively, were analysed for the presence of the two...... parasites by immunofluorescence microscopy. A large proportion of the (oo)cyst containing samples were selected for molecular characterization. Sequencing and phylogenetic analysis of the 18S rDNA locus and/or the HSP70 gene of 183 pig and 154 cattle isolates of Cryptosporidium revealed the presence of C....... suis, pig genotype II, C. parvum (cattle genotype), C. bovis, Cryptosporidium deer-like genotype and a novel C. suis-like genotype. For both cattle and pigs, a host age-related change in distribution of species/genotypes was observed. The zoonotic C. parvum (cattle genotype) was most prevalent in young...

  20. Synthesis and molecular characterization of chitosan based polyurethane elastomers using aromatic diisocyanate.

    Science.gov (United States)

    Zia, Khalid Mahmood; Anjum, Sohail; Zuber, Mohammad; Mujahid, Muhammad; Jamil, Tahir

    2014-05-01

    The present research work was performed to synthesize a new series of chitosan based polyurethane elastomers (PUEs) using poly(ɛ-caprolactone) (PCL). The chitosan based PUEs were prepared by step-growth polymerization technique using poly(ɛ-caprolactone) (PCL) and 2,4-toluene diisocyanate (TDI). In the second step the PU prepolymer was extended with different mole ratios of chitosan and 1,4-butane diol (BDO). Molecular engineering was carried out during the synthesis. The conventional spectroscopic characterization of the synthesized samples using FT-IR confirms the existence of the proposed chitosan based PUEs structure. Internal morphology of the prepared PUEs was studied using SEM analysis. The SEM images confirmed the incorporation of chitosan molecules into the PU backbone. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Biological and molecular characterization of Brazilian isolates of Zucchini yellow mosaic virus

    Directory of Open Access Journals (Sweden)

    David Marques de Almeida Spadotti

    2015-02-01

    Full Text Available Zucchini yellow mosaic virus (ZYMV causes substantial economic losses in cucurbit crops. Although ZYMV has been present in Brazil for more than 20 years, there is little information about the biological and molecular characteristics of the isolates found in the country. This study aimed to characterize the experimental hosts, pathotypes and genetic diversity of a collection of eleven Brazilian ZYMV isolates within the coat protein gene. For biological analysis, plant species from Amaranthaceae, Chenopodiaceae, Cucurbitaceae, Fabaceae, Solanaceae, and Pedaliaceae were mechanically inoculated and pathotypes were identified based on the reaction of a resistant Cucumis melo, accession PI414723. All of the cucurbit species/varieties and Sesamum indicum were systemically infected with all isolates. The nucleotide sequence variability of the coat protein gene ranged from 82 % to 99 % compared to the corresponding sequences of ZYMV isolates from different geographical locations. No recombination event was detected in the coat protein gene of the isolates.

  2. Advances on the molecular characterization, clinical relevance, and detection methods of Gadiform parvalbumin allergens.

    Science.gov (United States)

    Fernandes, Telmo J R; Costa, Joana; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P; Mafra, Isabel

    2017-10-13

    Gadiform order includes several fish families, from which Gadidae and Merlucciidae are part of, comprising the most commercially important and highly appreciated fish species, such as cod, pollock, haddock, and hake. Parvalbumins, classified as calcium-binding proteins, are considered the main components involved in the majority of fish allergies. Nine and thirteen parvalbumins were identified in different fish species from Gadidae and Merlucciidae families, respectively. This review intends to describe their molecular characterization and the clinical relevance, as well as the prevalence of fish allergy. In addition, the main protein- and DNA-based methods to detect fish allergens are fully reviewed owing to their importance in the safeguard of sensitized/allergic individuals.

  3. Fabrication of dissimilar metal electrodes with nanometer interelectrode distance for molecular electronic device characterization

    International Nuclear Information System (INIS)

    Guillorn, Michael A.; Carr, Dustin W.; Tiberio, Richard C.; Greenbaum, Elias; Simpson, Michael L.

    2000-01-01

    We report a versatile process for the fabrication of dissimilar metal electrodes with a minimum interelectrode distance of less than 6 nm using electron beam lithography and liftoff pattern transfer. This technique provides a controllable and reproducible method for creating structures suited for the electrical characterization of asymmetric molecules for molecular electronics applications. Electrode structures employing pairs of Au electrodes and non-Au electrodes were fabricated in three different patterns. Parallel electrode structures 300 μm long with interelectrode distances as low as 10 nm, 75 nm wide electrode pairs with interelectrode distances less than 6 nm, and a multiterminal electrode structure with reproducible interelectrode distances of 8 nm were realized using this technique. The processing issues associated with the fabrication of these structures are discussed along with the intended application of these devices. (c) 2000 American Vacuum Society

  4. Cryptosporidiosis in broiler chickens in Zhejiang Province, China: molecular characterization of oocysts detected in fecal samples

    Directory of Open Access Journals (Sweden)

    Wang Lengmei

    2014-01-01

    Full Text Available Cryptosporidium is one of the most important parasites in poultry, and this pathogen can infect more than 30 avian species. The present study investigated the infection rate of Cryptosporidium among broiler chicken flocks. A total of 385 fecal samples from broiler chickens in 7 regions of Zhejiang Province collected from November 2010 to January 2012 were examined by microscopy. Thirty-eight (10% samples were positive for Cryptosporidium infection, and 3 genotypes (Cryptosporidium baileyi, Cryptosporidium meleagridis, and avian genotype II were identified by PCR and sequencing. A phylogenetic tree of the isolates was analyzed. These results suggest that cryptosporidiosis is widespread in poultry in Zhejiang Province, and is a potential threat to public health as well as the economy. This is the first report about the infection rate and molecular characterization of Cryptosporidium in broiler chickens in Zhejiang.

  5. Pigments Characterization and Molecular Identification of Bacterial Symbionts of Brown Algae Padinasp. Collected from Karimunjawa Island

    Directory of Open Access Journals (Sweden)

    Damar Bayu Murti

    2016-06-01

    Full Text Available The search for carotenoids in nature has been extensively studied because of their applications in foods. One treasure of the biopigment source is symbiotic-microorganisms with marine biota. The advantages of symbiont bacteria are easy to culture and sensitize pigments. The use of symbiont bacteria helps to conserve fish, coral reefs, seagrass, and seaweed. Therefore, the bacteria keeps their existence in their ecosystems. In this study, bacterial symbionts were successfully isolated from brown algae Padina sp. The bacterial symbionts had yellow pigment associated with carotenoids. The pigments were characterized using High Performance Liquid Chromatography (HPLC with a Photo Diode Array (PDA detector. The carotenoid pigments in the bacterial symbionts were identified as dinoxanthin, lutein and neoxanthin. Molecular identification by using a 16S rRNA gene sequence method, reveals that the bacterial symbionts were closely related to Bacillus marisflavi with a homology of 99%. Keywords :carotenoid pigments, brown algae, Padina, bacterial symbionts, 16S rRNA

  6. Detailed molecular characterization of castor oil ethoxylates by liquid chromatography multistage mass spectrometry.

    Science.gov (United States)

    Nasioudis, Andreas; van Velde, Jan W; Heeren, Ron M A; van den Brink, Oscar F

    2011-10-07

    The molecular characterization of castor oil ethoxylates (CASEOs) was studied by reverse-phase liquid chromatography (RPLC) mass spectrometry (MS) and multistage mass spectrometry (MS(n)). The developed RPLC method allowed the separation of the various CASEO components, and especially, the baseline separation of multiple nominal isobars (same nominal mass) and isomers (same exact mass). MS and MS(n) were used for the determination and structure elucidation of various structures and for the discrimination of the isobars and isomers. Different ionization techniques and adduct ions were also tested for optimization of the MS detection and the MS(n) fragmentation. A unique fragmentation pathway of ricinoleic acid is proposed, which can be used as a marker of the polymerization process and the topology of ethoxylation in the CASEO. In addition, characteristic neutral losses of ricinoleic acid reveal its (terminal or internal) position in the molecule. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Characterization of Low-Molecular-Weight Heparins by Strong Anion-Exchange Chromatography.

    Science.gov (United States)

    Sadowski, Radosław; Gadzała-Kopciuch, Renata; Kowalkowski, Tomasz; Widomski, Paweł; Jujeczka, Ludwik; Buszewski, Bogusław

    2017-11-01

    Currently, detailed structural characterization of low-molecular-weight heparin (LMWH) products is an analytical subject of great interest. In this work, we carried out a comprehensive structural analysis of LMWHs and applied a modified pharmacopeial method, as well as methods developed by other researchers, to the analysis of novel biosimilar LMWH products; and, for the first time, compared the qualitative and quantitative composition of commercially available drugs (enoxaparin, nadroparin, and dalteparin). For this purpose, we used strong anion-exchange (SAX) chromatography with spectrophotometric detection because this method is more helpful, easier, and faster than other separation techniques for the detailed disaccharide analysis of new LMWH drugs. In addition, we subjected the obtained results to statistical analysis (factor analysis, t-test, and Newman-Keuls post hoc test).

  8. First Identification and Molecular Characterization of Avian metapneumovirus Subtype B from Chickens in Greece.

    Science.gov (United States)

    Tucciarone, Claudia Maria; Andreopoulou, Marianna; Franzo, Giovanni; Prentza, Zoi; Chaligiannis, Ilias; Cecchinato, Mattia

    2017-09-01

    Avian metapneumovirus (aMPV) is considered a major pathogen for turkeys but its impact on chicken production is still partially neglected, even though it is fully acknowledged as a primary pathogen in chickens as well. The lack of structured diagnostic surveys does not allow a pervasive understanding of aMPV epidemiology. Being that aMPV is almost an everyday challenge for farmers and veterinarians, a more accurate report of its presence should be detailed, posing the basis for a deep and global epidemiologic analysis. With these premises, the present work aims to report the first detection and molecular characterization of aMPV subtype B field strains from unvaccinated chickens in Greece. The Greek strains appear to be phylogenetically related among each other and with other recent Mediterranean strains while being distant from the currently applied vaccines, thus stressing once more the necessity to evaluate aMPV diffusion and evolution.

  9. Synthesis and characterization of arylamine derivatives of rauwolscine as molecular probes for alpha 2-adrenergic receptors

    International Nuclear Information System (INIS)

    Lanier, S.M.; Graham, R.M.; Hess, H.J.; Grodski, A.; Repaske, M.G.; Nunnari, J.M.; Limbird, L.E.; Homcy, C.J.

    1987-01-01

    The selective alpha 2-adrenergic receptor antagonist rauwolscine was structurally modified to yield a series of arylamine carboxamide derivatives, which were investigated as potential molecular probes for the localization and structural characterization of alpha 2-adrenergic receptors. The arylamine carboxamides differ in the number of carbon atoms separating the reactive phenyl moiety from the fused ring structure of the parent compound, rauwolscine carboxylate. Competitive inhibition studies with [ 3 H]rauwolscine in rat kidney membranes indicate that the affinity for the carboxamide derivatives is inversely related to the length of the carbon spacer arm with rauwolscine 4-aminophenyl carboxamide exhibiting the highest affinity (Kd = 2.3 +/- 0.2 nM). Radioiodination of rau-AMPC yields a ligand, 125 I-rau-AMPC, which binds to rat kidney alpha 2-adrenergic receptors with high affinity, as determined by both kinetic analysis (Kd = k2/k1 = 0.016 min-1/2.1 X 10(7) M-1 min-1 = 0.76 nM) and equilibrium binding studies (Kd = 0.78 +/- 0.16 nM). 125 I-rau-AMPC was quantitatively converted to the photolabile arylazide derivative 17 alpha-hydroxy-20 alpha-yohimban-16 beta-(N-4-azido-3-[ 125 I]iodophenyl) carboxamide ( 125 I-rau-AZPC). In a partially purified receptor preparation from porcine brain, this compound photolabels a major (Mr = 62,000) peptide. The labeling of this peptide is inhibited by adrenergic agonists and antagonists with a rank order of potency consistent with an alpha 2-adrenergic receptor binding site. Both 125 I-rau-AMPC and the photolabile arylazide derivative, 125 I-rau-AZPC, should prove useful as molecular probes for the structural and biochemical characterization of alpha 2-adrenergic receptors

  10. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin.

    Science.gov (United States)

    Khan, Naima A; Engle, Mark; Dungan, Barry; Holguin, F Omar; Xu, Pei; Carroll, Kenneth C

    2016-04-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Molecular characterization of Hepatozoon spp. infection in endangered Indian wild felids and canids.

    Science.gov (United States)

    Pawar, Rahul Mohanchandra; Poornachandar, Anantula; Srinivas, Pasham; Rao, Kancharapu Ramachandra; Lakshmikantan, Uthandaraman; Shivaji, Sisinthy

    2012-05-25

    Hepatozoon species are parasites that infect a wide variety of domestic and wild animals. The objective of this study was to perform the molecular detection and characterization of Hepatozoon spp. in Asiatic lion, Indian tiger, Indian leopard, Indian wild dog, Indian domestic dog and cat based on partial 18S rRNA gene sequences from Hepatozoon spp. in the naturally infected animals. Hepatozoon spp. could be detected in blood samples of 5 out of 9 Asiatic lions, 2 out of 5 Indian tigers, 2 out of 4 Indian leopards and 2 out of 2 Indian wild dogs and, 2 out of 4 domestic cats and 2 out of 3 domestic dog samples by PCR. Sequencing of PCR amplicon and BLAST analysis of partial 18S rRNA gene sequences indicated that the Hepatozoon spp. in Asiatic lion, Bengal tiger, Indian leopard and domestic cat was Hepatozoon felis (98-99% similarity) and in the Indian wild and domestic dog the phylogenetic neighbour was Hepatozoon canis (97-100% similarity). Presence of H. felis and H. canis in both domestic and wild animals suggested that they are not host specific and the same parasite causes infection in domestic and wild felids and canids in India and from different parts of the world. To our knowledge, this is the first report on detection and molecular characterization of H. felis infection in Asiatic lions, Indian tigers, Indian leopards and H. canis in Indian wild dog. Hepatozoon spp. may be a potential pathogen and an opportunistic parasite in immuno-compromised animals and could thus represent a threat to endangered Indian wild felids and canids. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers.

    Science.gov (United States)

    Coutinho, João Paulo; Carvalho, Ana; Martín, Antonio; Lima-Brito, José

    2018-04-01

    Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

  13. Prevalence and molecular characterization of abnormal hemoglobin in eastern Guangdong of southern China.

    Science.gov (United States)

    Lin, M; Wang, Q; Zheng, L; Huang, Y; Lin, F; Lin, C P; Yang, L Y

    2012-02-01

    Abnormal hemoglobins (Hbs) are the most commonly inherited disorders in humans. Their frequency and types change considerably with geographic location and ethnic group. To investigate the molecular epidemiological characterization of abnormal Hbs in eastern Guangdong of southern China, a total of 11,450 'healthy' subjects were subjected to hemoglobin electrophoresis screening. Samples of EDTA-K(2) blood with abnormal Hbs were analyzed by CELL-DYN1700 blood analyzer; thalassemia genotypes and Hb E variant were identified by gap-PCR and/or reverse dot blot (RDB). The genotypes of Hb variants were detected by PCR and sequencing. The incidence of abnormal Hbs was 0.358%(41/11,450) in Chaozhou, including 12.2% (5/41) Hb J, 4.9% (2/41) Hb K, 9.7% (4/41) Hb Q, 31.7% (13/41) Hb G/D and 41.5% (17/41) Hb E. Eight types of Hb variants were found, including 3 cases of Hb J-Bangkok, 2 cases of Hb J-Wenchang-Wuming, 2 cases of Hb New York, 4 cases of Hb Q-Thailand, 5 cases of Hb G-Waimanalo, 4 cases of Hb Ottawa, 4 cases of Hb G-Chinese and 17 cases of Hb E. In comparison with other areas of Guangdong, Chaozhou had a different pattern of abnormal Hbs with a high prevalence of Hb G/D. This study describes the prevalence and molecular characterization of abnormal Hbs in eastern Guangdong. © 2011 John Wiley & Sons A/S.

  14. Clinical and molecular characterization of 112 single-center patients with Neurofibromatosis type 1.

    Science.gov (United States)

    Corsello, Giovanni; Antona, Vincenzo; Serra, Gregorio; Zara, Federico; Giambrone, Clara; Lagalla, Luca; Piccione, Maria; Piro, Ettore

    2018-04-04

    The aim of this retrospective study was to define clinical and molecular characteristics of a large sample of neurofibromatosis type 1 (NF1) patients, as well as to evaluate mutational spectrum and genotype-phenotype correlation. NF1 is a relatively common neurogenetic disorder (1:2500-1:3000 individuals). It is caused by mutations of the NF1 gene on chromosome 17ql1.2, with autosomal dominant pattern of inheritance and wide phenotypical variability. Café-au-lait spots (CALs), cutaneous and/or subcutaneous neurofibromas (CNFs/SCNFs), skinfold freckling, skeletal abnormalities, Lisch nodules of the iris and increased risk of learning and intellectual disabilities, as well as tumors of the nervous system and other organs are its main clinical features. The preliminary group collected 168 subjects with clinical suspicion of NF1. They were evaluated following the National Institutes of Health (NIH) criteria for NF1, revised by Gutmann et al. 1997, integrated for 67 of them by molecular testing. According to these references, 112 of 168 patients were diagnosed as NF1. The sample was characterized by an equal sex ratio (57 males, 55 females) and age distribution ranging from 10 days to 60 years of age (mean age, 13 years). A wide spectrum of clinical features has been observed in our patients. Mutational analysis resulted positive in 51 cases (76%). Twenty-four mutations detected in our cohort have not been reported to date. This study may contribute to a better definition of genotypic and phenotypic features of NF1 patients, with respect to further insights into the clinical characterization of the disease. In addition, an amplification of the spectrum of mutations in the NF1 gene has been documented.

  15. Peroxiredoxin 6 from the Antarctic emerald rockcod: molecular characterization of its response to warming.

    Science.gov (United States)

    Tolomeo, A M; Carraro, A; Bakiu, R; Toppo, S; Place, S P; Ferro, D; Santovito, G

    2016-01-01

    In the present study, we describe the purification and molecular characterization of two peroxiredoxins (Prdxs), referred to as Prdx6A and Prdx6B, from Trematomus bernacchii, a teleost widely distributed in many areas of Antarctica, that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with Prdx6 orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase and phospholipase activities of these enzymes. Phylogenetic analyses suggest the appearance of the two prdx6 genes through a duplication event before the speciation that led to the differentiation of fish families and that the evolution of the two gene variants seems to proceed together with the evolution of fish orders and families. The temporal expression of Prdx6 mRNA in response to short-term thermal stress showed a general upregulation of prdx6b and inhibition of prdx6a, suggesting that the latter is the variant most affected by temperature increase. The variations of mRNA accumulation are more conspicuous in heart than the liver, probably related to behavioral changes of the specimens in response to elevated temperature. These data, together with the peculiar differences between the molecular structures of the two Prdx6s in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges.

  16. Molecular characterization of Als1, an acetohydroxyacid synthase mutation conferring resistance to sulfonylurea herbicides in soybean.

    Science.gov (United States)

    Ghio, Cecilia; Ramos, María Laura; Altieri, Emiliano; Bulos, Mariano; Sala, Carlos A

    2013-12-01

    The AHAS gene family in soybean was characterized. The locus Als1 for sulfonylurea resistance was mapped and the resistant allele was characterized at the molecular level. Sulfonylurea (SU) resistance in soybean is controlled by Als1, a semi-dominant allele obtained by EMS mutagenesis over the cultivar Williams 82. The overall objective of this research was to map Als1 in the soybean genome and to determine the nucleotidic changes conferring resistance to SU. Four nucleotide sequences (GmAhas1-4) showing high homology with the Arabidopsis thaliana acetohydroxyacid synthase (AHAS, EC 4.1.3.18) gene sequence were identified by in silico analysis, PCR-amplified from the SU-resistant line BTK323STS and sequenced. Expression analysis showed that GmAhas1, located on chromosome 4 by in silico analysis, is the most expressed sequence in true leaves. F2:3 families derived from the cross between susceptible and resistant lines were evaluated for SU resistance. Mapping results indicate that the locus als1 is located on chromosome 4. Sequence comparison of GmAhas1 between BTK323STS and Williams 82 showed a single nucleotide change from cytosine to thymine at position 532. This transversion generates an amino acid change from proline to serine at position 197 (A. thaliana nomenclature) of the AHAS catalytic subunit. An allele-specific marker developed for the GmAhas1 mutant sequence cosegregated with SU resistance in the F2 population. Taking together, the mapping, expression and sequencing results indicate that the GmAhas1 sequence corresponds to the Als1 gene sequence controlling SU resistance in soybean. The molecular breeding tools described herein create the basis to speed up the identification of new mutations in soybean AHAS leading to enhanced levels of resistance to SU or to other families of AHAS inhibitor herbicides.

  17. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin

    Science.gov (United States)

    Khan, Naima A.; Engle, Mark A.; Dungan, Barry; Holguin, F. Omar; Xu, Pei; Carroll, Kenneth C.

    2016-01-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production.

  18. Molecular Characterization of Vibrio cholerae Isolated From Clinical Samples in Kurdistan Province, Iran.

    Science.gov (United States)

    Ramazanzadeh, Rashid; Rouhi, Samaneh; Shakib, Pegah; Shahbazi, Babak; Bidarpour, Farzam; Karimi, Mohammad

    2015-05-01

    Vibrio cholerae causes diarrhoeal disease that afflicts thousands of people annually. V. cholerae is classified on the basis of somatic antigens into serovars or serogroups and there are at least 200 known serogroup. Two serogroups, O1 and O139 have been associated with epidemic diseases. Virulence genes of these bacteria are OmpW, ctxA and tcpA. Due to the importance of V. cholerae infection and developing molecular diagnostics of this organism in medical and microbiology sciences, this study aimed to describe molecular characterization of V. cholerae isolated from clinical samples using a molecular method. In this study, 48 samples were provided during summer 2013 (late August and early September) by reference laboratory. Samples were assessed using biochemical tests initially. The primer of OmpW, ctxA and tcpA genes was used in Polymerase Chain Reaction (PCR) protocols. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and Repetitive Extragenic Palindromic (REP)-PCR methods were used to subtype V. cholerae. In this study, from a total of 48 clinical stool samples 39 (81.2 %) were positive for V. cholerae in biochemical tests and bacteria culture tests. The PCR results showed that of 39 positive isolates 35 (89.7%), 34 (87.1%) and 37 (94.8%) were positive for ctxA, tcpA and OmpW gene, respectively. Also, in the REP-PCR method with ERIC primer strains were divided into 10 groups. In the REP-PCR method with REP primer, strains were divided into 13 groups. Polymerase chain reaction has specificity and accuracy for identification of the organism and is able to differentiate biotypes. Enterobacterial repetitive intergenic consensus sequence is one of the informative and discriminative methods for the analysis of V. cholerae diversity. The REP-PCR is a less informative and discriminative method compared to other methods for the analysis of V. cholerae diversity.

  19. Electrospinning and characterization of polyamide 66 nanofibers with different molecular weights

    Directory of Open Access Journals (Sweden)

    Lilia Muller Guerrini

    2009-06-01

    Full Text Available Polyamide 66 (PA66 nanofibers of different molecular weights were obtained by electrospinning of formic acid solutions. An ionic salt, NaCl, was also added to the solutions to increase the conductivity. PA66 concentrations between 15-17 wt.(%/v and electrical fields between 2.0 and 2.5 kV/cm were the best conditions to produce the smallest nanofibers; however, the addition of NaCl increased the fibers average diameters.The characterization of the fibers was done by scanning electron microscopy (SEM, differential scanning calorimetry (DSC, wide angle X rays diffraction (WAXD and Fourier Transformed Infrared (FTIR. As the molecular weight decreased, the nanofibers average diameters also decreased; however, critical number average and weight average molecular weights were necessary for electrospinning. As the amounts of carboxyl terminal groups (CTG increased, the nanofibers average diameters decreased; however, above CTG's critical values of 8.7 x 10-5 mol.g-1 no electrospinning was possible. The addition of ionic salt increased the electrical conductivity of the solutions and increased the nanofibers' average diameters. By DSC, residual solvent in all the electrospun mats was found; two melting endotherms, one between 248 and 258 °C and the other one between 258 and 267 °C, depending on the sample were also observed. These endotherms were attributed to the melting, re-crystallization and re-melting of the PA66 α-phase. The nanofibers had low % of crystallinity compared to a textile fiber. By WAXS and FTIR, confirmation of the presence of α-phase crystals, of small dimensions and highly imperfect and of a very small amount of β and γ-phases crystals in the nanofibers structure was obtained.

  20. Molecular characterization of Cryptococcus neoformans isolated from the environment in Beijing, China.

    Science.gov (United States)

    Dou, Hongtao; Wang, Huizhu; Xie, Shaowei; Chen, Xinxin; Xu, Zhipeng; Xu, Yingchun

    2017-10-01

    The molecular type of environmental Cryptococcus neoformans in Beijing was not clear. Our study aims to reveal the molecular characterization of C. neoformans complex from environment in Beijing, China. A total of 435 samples of pigeon droppings from 11 different homes in Beijing were collected from August to November in 2015. Pigeon droppings were inoculated onto caffeic acid cornmeal agar (CACA) to screen C. neoformans complex. Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was performed for species identification. Serotype and mating type was determined by specific primers. Restriction fragment length polymorphisms of URA5 (URA5-RFLP) were applied to genotype. Multi-locus sequence typing (MLST) was done for further identification and sequence type (ST) determination. Altogether, 81 isolates of C. neoformans AFLP1/VNI were recognized from 435 pigeon droppings in this study. The positive rate for C. neoformans AFLP1/VNI from pigeon droppings in different homes varied from 5.0% to 52.6%, the average was 20.2%. All of these cryptococcal strains were serotype A, MATα. They were genotyped as VNI by URA5-RFLP and were confirmed by MLST. No other molecular types of C. neoformans and Cryptococcus gattii isolates were isolated. Their STs were identified as ST 31 (n = 54, 66.7%), followed by ST 53 (n = 10), ST 191 (n = 8), ST 5 (n = 5), ST 57 (n = 3), and ST 38 (n = 1). We concluded that not only clinical but also environmental isolates of C. neoformans need to be investigated more deeply and more extensively. The virulence difference between ST 5 and ST 31 need to be explored in the future. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Living Behaviors and Molecular Characterization of Benthic Foraminifera in the Arabian Gulf

    Science.gov (United States)

    Arslan, Muhammad; Kaminski, Michael; Khalil, Amjad; Holzmann, Maria

    2016-04-01

    The benthic foraminifera are among the major carbonate producers in modern Arabian Gulf waters and are found living in all marine habitats. They have been recognized as proxies to assess paleoenvironmental changes, however, their biological behaviors in modern environments needs to be further studied. The current study attempts to explain the biology of benthic foraminifera in terms of their living behaviors and molecular characterization, from different regions of the western side of the Arabian Gulf. Accordingly, two major groups of benthic foraminifera, namely rotaliids and miliolids, are examined under laboratory conditions. Results illustrate that the rotaliids are more resistant to environmental changes than miliolids, as their granular reticulopodial network is stronger than among the miliolids, with high cytoplasmic streaming. The pseudopodia extend out from both primary and secondary apertures, and aid the organism in locomotion by attaching to the wall of hard substrate. As a result they drag their whole bodies toward the direction of motion. In rotaliids, the movement rate is high and is attributed to the extension of pseudopodia through all apertures, compared with miliolids in which pseudopodia extend out from the primary aperture only. The innate behavior of both groups was observed as a function of external stimulus, i.e., light, nutrients, and availability of substrate. The observation on average life span reflected that the rotaliids was able to survive longer than miliolids. Molecular analysis reveals the presence of four groups, i.e., Ammonia, Murrayinella, Glabratellina, and Elphidium which support the morphological taxonomy at the genus level. However, BLAST analysis contradicts the species level taxonomy, which challenges the classification based upon hard-shell morphology. Nevertheless, monophyletic clustering is observed among all major groups. The study concludes that the morphological taxonomy needs to be augmented by molecular analysis

  2. Molecular marker studies in riverine buffaloes, for characterization and diagnosis of genetic defects

    International Nuclear Information System (INIS)

    Yadav, B.R.

    2005-01-01

    The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide probes showed species-specific bands useful for identification of carcass or other unknown samples. Use of RAPD revealed band frequencies, band sharing frequencies, genetic distances, and genetic and identity indexes in different breeds. Bovine microsatellite primers indicate that 70.9% of bovine loci were conserved in buffalo. Allele numbers, sizes, frequencies, heterozygosity and polymorphism information content showed breed-specific patterns. Different marker types - genomic and oligonucleotide probes, RAPD and microsatellites - are useful in parent identification. Individual specific DNA fingerprinting techniques were applied with twin-born animal (XX/XY) chimerism, sex identification, anatomically defective and XO individuals. Molecular markers are a potential tool for geneticists and breeders to evaluate existing germplasm and to manipulate it to develop character-specific strains and to provide the basis for effective genetic conservation. (author)

  3. A New Experimental Polytrauma Model in Rats: Molecular Characterization of the Early Inflammatory Response

    Directory of Open Access Journals (Sweden)

    Sebastian Weckbach

    2012-01-01

    Full Text Available Background. The molecular mechanisms of the immune response after polytrauma are highly complex and far from fully understood. In this paper, we characterize a new standardized polytrauma model in rats based on the early molecular inflammatory and apoptotic response. Methods. Male Wistar rats (250 g, 6–10/group were anesthetized and exposed to chest trauma (ChT, closed head injury (CHI, or Tib/Fib fracture including a soft tissue trauma (Fx + STT or to the following combination of injuries: (1 ChT; (2 ChT + Fx + STT; (3 ChT + CHI; (4 CHI; (5 polytrauma (PT = ChT + CHI + Fx + STT. Sham-operated rats served as negative controls. The inflammatory response was quantified at 2 hours and 4 hours after trauma by analysis of “key” inflammatory mediators, including selected cytokines and complement components, in serum and bronchoalveolar (BAL fluid samples. Results. Polytraumatized (PT rats showed a significant systemic and intrapulmonary release of cytokines, chemokines, and complement anaphylatoxins, compared to rats with isolated injuries or selected combinations of injuries. Conclusion. This new rat model appears to closely mimic the early immunological response of polytrauma observed in humans and may provide a valid basis for evaluation of the complex pathophysiology and future therapeutic immune modulatory approaches in experimental polytrauma.

  4. A New Experimental Polytrauma Model in Rats: Molecular Characterization of the Early Inflammatory Response

    Science.gov (United States)

    Weckbach, Sebastian; Perl, Mario; Heiland, Tim; Braumüller, Sonja; Stahel, Philip F.; Flierl, Michael A.; Ignatius, Anita; Gebhard, Florian; Huber-Lang, Markus

    2012-01-01

    Background. The molecular mechanisms of the immune response after polytrauma are highly complex and far from fully understood. In this paper, we characterize a new standardized polytrauma model in rats based on the early molecular inflammatory and apoptotic response. Methods. Male Wistar rats (250 g, 6–10/group) were anesthetized and exposed to chest trauma (ChT), closed head injury (CHI), or Tib/Fib fracture including a soft tissue trauma (Fx + STT) or to the following combination of injuries: (1) ChT; (2) ChT + Fx + STT; (3) ChT + CHI; (4) CHI; (5) polytrauma (PT = ChT + CHI + Fx + STT). Sham-operated rats served as negative controls. The inflammatory response was quantified at 2 hours and 4 hours after trauma by analysis of “key” inflammatory mediators, including selected cytokines and complement components, in serum and bronchoalveolar (BAL) fluid samples. Results. Polytraumatized (PT) rats showed a significant systemic and intrapulmonary release of cytokines, chemokines, and complement anaphylatoxins, compared to rats with isolated injuries or selected combinations of injuries. Conclusion. This new rat model appears to closely mimic the early immunological response of polytrauma observed in humans and may provide a valid basis for evaluation of the complex pathophysiology and future therapeutic immune modulatory approaches in experimental polytrauma. PMID:22481866

  5. Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

    Science.gov (United States)

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

    Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

  6. Development and characterization of an electrochemical sensor for furosemide detection based on electropolymerized molecularly imprinted polymer.

    Science.gov (United States)

    Kor, Kamalodin; Zarei, Kobra

    2016-01-01

    A novel electrochemical sensor based on a molecularly imprinted polymer, poly(o-phenylenediamine) (PoPD), has been developed for selective and sensitive detection of furosemide. The sensor was prepared by incorporating of furosemide as template molecules during the electropolymerization of o-phenylenediamine on a gold electrode. To develop the molecularly imprinted polymer (MIP), the template molecules were removed from the modified electrode's surface by washing it with 0.25 mol L(-1) NaOH solution. The imprinted layer was characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM). The sensor's preparation conditions including furosemide concentration, the number of CV cycles in the electropolymerization process, extraction solution of the template from the imprinted film, the incubation time and the pH level were optimized. The incubation of the MIP-modified electrode, with respect to furosemide concentration, resulted in a suppression of the K4[Fe(CN)6] oxidation process. Under the optimal experimental conditions, the response of the imprinted sensor was linear in the range of 1.0×10(-7)-7.0×10(-6) mol L(-1) of furosemide. The detection limit was obtained as 7.0×10(-8) mol L(-1) for furosemide by using this sensor. The sensor was successfully used to determine the furosemide amount in the tablet and in human urine samples with satisfactory results. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Retracted: Molecular Characterization and Biological Activity of Interferon-α in Indian Peafowl (Pavo cristatus).

    Science.gov (United States)

    Zhao, Hongjing; Wang, Yu; Liu, Juanjuan; Shao, Yizhi; Li, Jinglun; Chai, Hongliang; Xing, Mingwei

    2017-08-07

    DNA and Cell Biology (DNA&CB) is officially retracting the paper by Zhao H, Wang Y, Liu J, Shao Y, Li J, Chai H, Xing M, entitled, "Molecular Characterization and Biological activity of Interferon-α in Indian Peafowl (Pavo cristatus)," [Epub ahead of print]; 2017, DOI: 10.1089/dna.2017.3798. The Editor-in-Chief of DNA&CB, Dr. Carol Shoshkes Reiss, was alerted to a discrepancy between the findings in the article by Zhao et al., and those of others, about the absence of expression of ISG15 in chickens. Dr. Reiss requested from the authors a clarification in their observations and inquired about the failure to include relevant citations in the reference section of the paper. Based on the response from the authors, it appeared that they did not have the confidence in the data as they were not able to repeat the experiments, and were also unsure of the molecular probes that were used in the study. Therefore, the Editor has determined that the paper should be officially retracted from DNA and Cell Biology.

  8. Molecular characterization of 45 kDa aspartic protease of Trichinella spiralis.

    Science.gov (United States)

    Park, Jong Nam; Park, Sang Kyun; Cho, Min Kyoung; Park, Mi-Kyung; Kang, Shin Ae; Kim, Dong-Hee; Yu, Hak Sun

    2012-12-21

    In a previous study, we identified an aspartic protease gene (Ts-Asp) from the Trichinella spiralis muscle stage larva cDNA library. The gene sequence of Ts-Asp was 1281 bp long and was found to encode a protein consisting of 405 amino acids, with a molecular mass of 45.248 kD and a pI of 5.95. The deduced Ts-Asp has a conserved catalytic motif with catalytic aspartic acid residues in the active site, a common characteristic of aspartic proteases. In addition, the deduced amino acid sequence of Ts-Asp was found to possess significant homology (above 50%) with aspartic proteases from nematode parasites. Results of phylogenetic analysis indicated a close relationship of Ts-Asp with cathepsin D aspartic proteases. For production of recombinant Ts-Asp (rTs-Asp), the pGEX4T expression system was used. Like other proteases, the purified rTs-Asp was able to digest collagen matrix in vitro. Abundant expression of Ts-Asp was observed in muscle stage larva. Ts-Asp was detected in ES proteins, and was able to elicit the production of specific antibodies. It is the first report of molecular characterization of aspartic protease isolated from T. spiralis. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Biological and molecular characterization of silkworm strains from the Brazilian germplasm bank of Bombyx mori.

    Science.gov (United States)

    Pereira, N C; Munhoz, R E F; Bignotto, T S; Bespalhuk, R; Garay, L B; Saez, C R N; Fassina, V A; Nembri, A; Fernandez, M A

    2013-06-28

    Brazil has only one public genetic pool of Bombyx mori strains, which was established in 2005 at Universidade Estadual de Maringá, Maringá, Paraná State. This genetic bank has been maintained, and the strains have been characterized using genetic and morphological tools. The quantitative and qualitative traits, directly or indirectly related to productivity, were evaluated in 14 silkworm strains. In addition to biological and productivity analyses, DNA markers related to susceptibility to the B. mori nucleopolyhedrovirus (BmNPV) were analyzed. BmNPV is a major cause of production loss and is a serious problem for Paraná sericulture. The silkworm strains from diverse geographic origins were found to have different characteristics, including body weight, larval stage duration, cocoon weight, and other biological traits. In terms of productivity, the raw silk percentages were almost uniform, with an overall average of 16.28%. Overall, the Chinese strain C37 gave the best performance in many of the quantitative traits, and it surpassed the other strains in productivity traits. Therefore, it can be used as one of the strains that compose the elite germplasm for silkworm breeding programs. Additionally, genetic molecular markers were efficient in discriminating between B. mori strains that had been identified based on their geographical origin. We found that all Japanese strains produced a 400-bp molecular marker that has been associated with susceptibility to BmNPV.

  10. Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa.

    Science.gov (United States)

    Ueno, Hiroki; Matsumoto, Etsuo; Aruga, Daisuke; Kitagawa, Satoshi; Matsumura, Hideo; Hayashida, Nobuaki

    2012-12-01

    Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.

  11. Molecular Characterization of Foot-and-Mouth Disease Viruses Collected in Tanzania Between 1967 and 2009.

    Science.gov (United States)

    Kasanga, C J; Wadsworth, J; Mpelumbe-Ngeleja, C A R; Sallu, R; Kivaria, F; Wambura, P N; Yongolo, M G S; Rweyemamu, M M; Knowles, N J; King, D P

    2015-10-01

    This paper describes the molecular characterization of foot-and-mouth disease viruses (FMDV) recovered from outbreaks in Tanzania that occurred between 1967 and 2009. A total of 44 FMDV isolates, containing representatives of serotypes O, A, SAT 1 and SAT 2 from 13 regions of Tanzania, were selected from the FAO World Reference Laboratory for FMD (WRLFMD) virus collection. VP1 nucleotide sequences were determined for RT-PCR amplicons, and phylogenetic reconstructions were determined by maximum likelihood and neighbour-joining methods. These analyses showed that Tanzanian type O viruses fell into the EAST AFRICA 2 (EA-2) topotype, type A viruses fell into the AFRICA topotype (genotype I), type SAT 1 viruses into topotype I and type SAT 2 viruses into topotype IV. Taken together, these findings reveal that serotypes O, A, SAT 1 and SAT 2 that caused FMD outbreaks in Tanzania were genetically related to lineages and topotypes occurring in the East African region. The close genetic relationship of viruses in Tanzania to those from other countries suggests that animal movements can contribute to virus dispersal in sub-Saharan Africa. This is the first molecular description of viruses circulating in Tanzania and highlights the need for further sampling of representative viruses from the region so as to elucidate the complex epidemiology of FMD in Tanzania and sub-Saharan Africa. © 2014 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

  12. Molecular characterization of Escherichia coli recovered from traditional milk products in Kashan, Iran

    Directory of Open Access Journals (Sweden)

    Farhad Sharafati Chaleshtori

    2017-10-01

    Full Text Available Aim: Shiga toxigenic Escherichia coli (STEC strains as emerging groups of foodborne pathogens are responsible for most foodborne illnesses. The aim of this study was to determine the antibiotic resistance pattern in STEC isolated from traditional milk products and their molecular characterization. Materials and Methods: A total of 116 samples were randomly purchased from local markets in Kashan, Iran, and evaluated for the occurrence of STEC by culturing and molecular methods. The antibiotic resistance of obtained isolates was determined by Kirby Bauer method. Furthermore, isolates were assayed for the presence of Shiga toxins (stx1 and stx2 and intimin gene (eae. Results: The incidence of E. coli in 60 ice cream, 30 yoghurt, and 26 cheese samples was 8.33%, 10%, and 11.54%, respectively. The findings showed that 11 out of 11 (100% E. coli had both stx1 and stx2 while eae gene was not found in E. coli isolated of traditional milk products. For E. coli strains carrying stx1 and stx2, highest antibiotic sensitive levels were related to trimethoprim/sulfamethoxazole, norfloxacin, chloramphenicol, and ciprofloxacin, respectively. Conclusion: The results showed relationship between the presence of virulence factors and antimicrobial resistance. These results can be used for further studies on STEC as an emerging foodborne pathogen.

  13. First Molecular Characterization of Feline Immunodeficiency Virus in Domestic Cats from Mainland China.

    Science.gov (United States)

    Zhang, Jilei; Wang, Liang; Li, Jing; Kelly, Patrick; Price, Stuart; Wang, Chengming

    2017-01-01

    The feline immunodeficiency virus (FIV) is a retrovirus of the Lentivirus genus that was initially isolated from a colony of domestic cats in California in 1986 and has now been recognized as a common feline pathogen worldwide. To date, there is only one recent serology-based report on FIV in mainland China which was published in 2016. We designed this study to investigate the molecular prevalence and diversity of feline immunodeficiency virus (FIV) in domestic cats from mainland China. We studied the prevalence of FIV in whole blood samples of 615 domestic cats in five cities (Beijing, Guangzhou, Nanjing, Shanghai and Yangzhou) of mainland China and examined them using FRET-PCR (Fluorescence Resonance Energy Transfer-Polymerase Chain Reaction) and regular PCRs for the gag and env genes. Overall, 1.3% (8/615) of the cats were positive for provirus DNA with nucleotide analysis using PCRs for the gag and env sequences showing the cats were infected with FIV subtype A. This is the first molecular characterization of FIV in mainland China and the first description of subtype A in continental Asia.

  14. Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis.

    Science.gov (United States)

    Albufera, U; Bhugaloo-Vial, P; Issack, M I; Jaufeerally-Fakim, Y

    2009-05-01

    Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram.

  15. Moving toward rapid and low-cost point-of-care molecular diagnostics with a repurposed 3D printer and RPA.

    Science.gov (United States)

    Chan, Kamfai; Wong, Pui-Yan; Parikh, Chaitanya; Wong, Season

    2018-03-15

    Traditionally, the majority of nucleic acid amplification-based molecular diagnostic tests are done in centralized settings. In recent years, point-of-care tests have been developed for use in low-resource settings away from central laboratories. While most experts agree that point-of-care molecular tests are greatly needed, their availability as cost-effective and easy-to-operate tests remains an unmet goal. In this article, we discuss our efforts to develop a recombinase polymerase amplification reaction-based test that will meet these criteria. First, we describe our efforts in repurposing a low-cost 3D printer as a platform that can carry out medium-throughput, rapid, and high-performing nucleic acid extraction. Next, we address how these purified templates can be rapidly amplified and analyzed using the 3D printer's heated bed or the deconstructed, low-cost thermal cycler we have developed. In both approaches, real-time isothermal amplification and detection of template DNA or RNA can be accomplished using a low-cost portable detector or smartphone camera. Last, we demonstrate the capability of our technologies using foodborne pathogens and the Zika virus. Our low-cost approach does not employ complicated and high-cost components, making it suitable for resource-limited settings. When integrated and commercialized, it will offer simple sample-to-answer molecular diagnostics. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. Structure characterization of the central repetitive domain of high molecular weight gluten proteins .2. Characterization in solution and in the dry state

    NARCIS (Netherlands)

    van Dijk, A.A.; De Boef, E.; Bekkers, A.; van Wijk, L.L.; van Swieten, E.; Hamer, R.J.; Robillard, G.T.

    The structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins was characterized in solution and in the dr