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Sample records for amplified fragment length

  1. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Jensen, J.S.

    1999-01-01

    Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including......I restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp, The method was able...

  2. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination......-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal...... whereas others are highly divergent. Conclusions: AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme...

  3. An integrated restriction fragment length polymorphism--amplified fragment length polymorphism linkage map for cultivated sunflower.

    Science.gov (United States)

    Gedil, M A; Wye, C; Berry, S; Segers, B; Peleman, J; Jones, R; Leon, A; Slabaugh, M B; Knapp, S J

    2001-04-01

    Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 x HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 x HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 x HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.

  4. Amplified Fragment Length Polymorphism Diversity in Cephalosporium maydis from Egypt.

    Science.gov (United States)

    Saleh, Amgad A; Zeller, Kurt A; Ismael, Abou-Serie M; Fahmy, Zeinab M; El-Assiuty, Elhamy M; Leslie, John F

    2003-07-01

    ABSTRACT Cephalosporium maydis, the causal agent of late wilt of maize, was first described in Egypt in the 1960s, where it can cause yield losses of up to 40% in susceptible plantings. We characterized 866 isolates of C. maydis collected from 14 governates in Egypt, 7 in the Nile River Delta and 7 in southern (Middle and Upper) Egypt, with amplified fragment length polymorphism (AFLP) markers. The four AFLP primer-pair combinations generated 68 bands, 25 of which were polymorphic, resulting in 52 clonal haplotypes that clustered the 866 isolates into four phylogenetic lineages. Three lineages were found in both the Nile River Delta and southern Egypt. Lineage IV, the most diverse group (20 haplotypes), was recovered only from governates in the Nile River Delta. In some locations, one lineage dominated (up to 98% of the isolates recovered) and, from some fields, only a single haplotype was recovered. Under field conditions in Egypt, there is no evidence that C. maydis reproduces sexually. The nonuniform geographic distribution of the pathogen lineages within the country could be due to differences in climate or in the farming system, because host material differs in susceptibility and C. maydis lineages differ in pathogenicity.

  5. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility

    NARCIS (Netherlands)

    Badali, H.; Yazdanparast, S.A.; Bonifaz, A.; Mousavi, B.; de Hoog, G.S.; Klaassen, C.H.W.; Meis, J.F.G.M.

    2013-01-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated in

  6. Amplified fragment length polymorphism and pulsed field gel electrophoresis for subspecies differentiation of Serpulina pilosicoli

    DEFF Research Database (Denmark)

    Møller, Kristian; Jensen, Tim Kåre; Boye, Mette;

    1999-01-01

    Pulsed field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP) were compared for their ability to differentiate between 50 porcine Serpulina pilosicoli isolates. Both techniques were highly sensitive, dividing the isolates into 36 and 38 groups, respectively. Due...

  7. AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS OF MYCOBACTERIUM AVIUM COMPLEX ISOLATES RECOVERED FROM SOUTHERN CALIFORNIA

    Science.gov (United States)

    Fine-scale genotyping methods are necessary in order to identify possible sources of human exposure to opportunistic pathogens belonging to the Mycobacterium avium complex (MAC). In this study, amplified fragment length polymorphism (AFLP) analysis was evaluated for fingerprintin...

  8. Comparative Analysis of Human and Canine Campylobacter upsaliensis Isolates by Amplified Fragment Length Polymorphism

    DEFF Research Database (Denmark)

    Damborg, Peter; Guardabassi, Luca; Pedersen, Karl;

    2008-01-01

    Human (n = 33) and canine (n = 53) Campylobacter upsaliensis isolates from seven countries were genotyped by a new amplified fragment length polymorphism method. We observed 100% typeability and high overall diversity. The majority of human strains (23/33) clustered separately from canine strains......, indicating that dogs may not be the main source of human infection.......Human (n = 33) and canine (n = 53) Campylobacter upsaliensis isolates from seven countries were genotyped by a new amplified fragment length polymorphism method. We observed 100% typeability and high overall diversity. The majority of human strains (23/33) clustered separately from canine strains...

  9. ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

    DEFF Research Database (Denmark)

    Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir;

    2008-01-01

    A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs in tha...... combining the advantages of the AFLP technique with a simple, rapid and cheap polymerase chain reaction product detection method.......A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs...... for differentiation of the organisms without previous knowledge of their DNA sequence. The usefulness of the method is confirmed by genotyping of 70 previously characterized clinical E. coli isolates. The grouping obtained was identical to the results of REA-PFGE. Versatility of the method is highlighted, i.e. its...

  10. Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Atabay, H.I.; Amisu, K.O.;

    2004-01-01

    Aims: To investigate the potential of amplified fragment length polymorphism (AFLP) profiling for genotyping Arcobacter butzleri and to obtain further data on the genetic diversity of this organism. Methods and Results: Seventy-three isolates of Danish, British, Turkish, Swedish, Nigerian and Nor...

  11. Genomic variations of Mycoplasma capricolum subsp capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Bolske, G.; Ahrens, Peter;

    2000-01-01

    The genetic diversity of Mycoplasma capricolum subsp. capripneumoniae strains based on determination of amplified fragment length polymorphisms (AFLP) is described. AFLP fingerprints of 38 strains derived from different countries in Africa and the Middle East consisted of over 100 bands in the size...... found by 16S rDNA analysis. The present data support previous observations regarding genetic homogeneity of M. capricolum subsp. capripneumoniae, and confirm the two evolutionary lines of descent found by analysis of 16S rRNA genes....

  12. [Recent advances of amplified fragment length polymorphism and its applications in forensic botany].

    Science.gov (United States)

    Li, Cheng-Tao; Li, Li

    2008-10-01

    Amplified fragment length polymorphism (AFLP) is a new molecular marker to detect genomic polymorphism. This new technology has advantages of high resolution, good stability, and reproducibility. Great achievements have been derived in recent years in AFLP related technologies with several AFLP expanded methodologies available. AFLP technology has been widely used in the fields of plant, animal, and microbes. It has become one of the hotspots in Forensic Botany. This review focuses on the recent advances of AFLP and its applications in forensic biology.

  13. Evaluation of genetic diversity in jackfruit (Artocarpus heterophyllus Lam.) based on amplified fragment length polymorphism markers.

    Science.gov (United States)

    Shyamalamma, S; Chandra, S B C; Hegde, M; Naryanswamy, P

    2008-07-22

    Artocarpus heterophyllus Lam., commonly called jackfruit, is a medium-sized evergreen tree that bears high yields of the largest known edible fruit. Yet, it has been little explored commercially due to wide variation in fruit quality. The genetic diversity and genetic relatedness of 50 jackfruit accessions were studied using amplified fragment length polymorphism markers. Of 16 primer pairs evaluated, eight were selected for screening of genotypes based on the number and quality of polymorphic fragments produced. These primer combinations produced 5976 bands, 1267 (22%) of which were polymorphic. Among the jackfruit accessions, the similarity coefficient ranged from 0.137 to 0.978; the accessions also shared a large number of monomorphic fragments (78%). Cluster analysis and principal component analysis grouped all jackfruit genotypes into three major clusters. Cluster I included the genotypes grown in a jackfruit region of Karnataka, called Tamaka, with very dry conditions; cluster II contained the genotypes collected from locations having medium to heavy rainfall in Karnataka; cluster III grouped the genotypes in distant locations with different environmental conditions. Strong coincidence of these amplified fragment length polymorphism-based groupings with geographical localities as well as morphological characters was observed. We found moderate genetic diversity in these jackfruit accessions. This information should be useful for tree breeding programs, as part of our effort to popularize jackfruit as a commercial crop.

  14. Application of fluorescent amplified fragment length polymorphism for comparison of human and animal isolates of Yersinia enterocolitica

    DEFF Research Database (Denmark)

    Fearnley, C.; On, S.L.W.; Kokotovic, Branko

    2005-01-01

    An amplified fragment length polymorphism (AFLP) method, developed to genotype Yersinia enterocolitica, has been used to investigate 70 representative strains isolated from humans, pigs, sheep, and cattle in the United Kingdom. AFLP primarily distinguished Y enterocolitica strains according...

  15. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

    DEFF Research Database (Denmark)

    Kokotovic, Branko; On, Stephen L.W.

    1999-01-01

    A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species...

  16. Genetic variation in hemp and marijuana (Cannabis sativa L.) according to amplified fragment length polymorphisms.

    Science.gov (United States)

    Datwyler, Shannon L; Weiblen, George D

    2006-03-01

    Cannabis sativa L. (Cannabaceae) is one of the earliest known cultivated plants and is important in the global economy today as a licit and an illicit crop. Molecular markers distinguishing licit and illicit cultivars have forensic utility, but no direct comparison of hemp and marijuana amplified fragment length polymorphism (AFLP) has been made to date. Genetic variation was surveyed in three populations of fiber hemp and a potent cultivar of marijuana using AFLP markers. Ten primer pairs yielded 1206 bands, of which 88% were polymorphic. Eighteen bands represented fixed differences between all fiber populations and the drug cultivar. These markers have practical utility for (1) establishing conspiracy in the cultivation and distribution of marijuana, (2) identifying geographic sources of seized drugs, and (3) discriminating illegal, potent marijuana cultivars from hemp where the cultivation of industrial hemp is permitted.

  17. Random amplified polymorphic DNA and amplified fragment length polymorphism assessment of genetic variation in Nicaraguan populations of Pinus oocarpa.

    Science.gov (United States)

    Díaz, V; Muñiz, L M; Ferrer, E

    2001-11-01

    Pinus oocarpa is the most widely distributed pine species of Mexico and Central America. The natural populations of Nicaragua have been affected by extensive human activities. As a consequence, their size has been reduced, and there is a serious threat to the development of mature woodland. Knowledge of population structures and the genetic diversity of the species is required for the design of sustainable use and conservation strategies. Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic variation among 10 populations from three geographical regions of Nicaragua. Both markers revealed high levels of diversity in these populations. G(ST) values and analyses of molecular variance (AMOVA) found that most variation was within populations but there is still a significant differentiation between populations indicating that the populations sampled cannot be considered a single panmictic unit. The partitions created by AMOVA also showed that there was little differentiation between populations of different regions, although cluster analyses based on RAPDs and AFLPs indicated a closer relationship among most of the populations from a same geographical region. Management of P. oocarpa in Nicaragua should be aimed to maintain the high degree of genetic variation within individual populations that is still observed even in some of these highly degraded populations.

  18. A NEW APPROACH TO GENE DIAGNOSIS OF DUCHENNE/BECKER MUSCULAR DYSTROPHY AMPLIFIED FRAGMENT LENGTH POLYMORPHISMS

    Institute of Scientific and Technical Information of China (English)

    许顺斌; 黄尚志; 罗会元

    1994-01-01

    Four (CA), repeats, located in introns,44,45,49 and 50 of the dystrophin gene,were evaluated in Chinese.These loci are highly polymorphic,with polymorphism information contents of 0.872,0.772,0.870 and 0.718,respectively.All four loci can be easily amplified and labelled using two duplex PCR reactions with α-32P-dCTP and can be detected by denaturing polyacrylamide gel electrophoresis.Using these four loci and the two polymorphic(CA)n repeats located at the 5′ and 3′ ends of the dystrophin gene,we have developed a new PCR-based procedure-Amp-FLP( amplified fragment length polymorphism)linkage analysis for the gene diagnosis of DMD/BMD.This method can detect intragenic recombination rapidly and efficiently and greatly improves the success rate of carrier deterction and prenatal diagnosis in non-deletion DMD/BMD families.All of the loci used in this procedure are intragenic.In addition ,the loci in introns 44,45,49 and 50 are located in the deletion-prone region of the dystrophin gene,making them valuable and usefui in the identification of deletion mutations.Here we report one case of deletion detection using these four loci.

  19. Genetic diversity of the edible mushroom Pleurotus sp. by amplified fragment length polymorphism.

    Science.gov (United States)

    Pawlik, Anna; Janusz, Grzegorz; Koszerny, Joanna; Małek, Wanda; Rogalski, Jerzy

    2012-10-01

    Pleurotus strains are the most important fungi used in the agricultural industry. The exact characterization and identification of Pleurotus species is fundamental for correct identification of the individuals and exploiting their full potential in food industry. The amplified fragment length polymorphism (AFLP) method was applied for genomic fingerprinting of 21 Pleurotus isolates of Asian and European origin. Using one PstI restriction endonuclease and four selective primers in an AFLP assay, 371 DNA fragments were generated, including 308 polymorphic bands. The AFLP profiles were found to be highly specific for each strain and they unambiguously distinguished 21 Pleurotus sp. fungi. The coefficient of Jaccard's genome profile similarity between the analyzed strains ranged from 0.0 (Pleurotus sp. I vs. P. sajor-caju 237 and P. eryngii 238) to 0.750 (P. ostreatus 246 vs. P. ostreatus 248), and the average was 0.378. The AFLP-based dendrogram generated by the UPGMA method grouped all the Pleurotus fungi studied into two major clusters and one independent lineage located on the outskirt of the tree occupied by naturally growing Pleurotus species strain I. The results of the present study suggest the possible applicability of the AFLP-PstI method in effective identification and molecular characterization of Pleurotus sp. strains.

  20. High-resolution genotyping of Listeria monocytogenes by fluorescent amplified fragment length polymorphism analysis compared to pulsed-field gel electrophoresis, random amplified polymorphic DNA analysis, ribotyping, and PCR-restriction fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Vogel, Birte Fonnesbech; Fussing, V.; Ojeniyi, B.;

    2004-01-01

    The purpose of this study was to evaluate fluorescent amplified fragment length polymorphism (AFLP) analysis for the inter- and intraspecies differentiation of a collection of 96 strains of Listeria monocytogenes and 10 non- L. monocytogenes strains representing six other Listeria species of diff...

  1. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility.

    Science.gov (United States)

    Badali, Hamid; Yazdanparast, Seyed Amir; Bonifaz, Alexandro; Mousavi, Bita; de Hoog, G Sybren; Klaassen, Corné H W; Meis, Jacques F

    2013-06-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated infection in apparently healthy individuals have been reported worldwide. All tested strains of V. botryosa, identified on the basis of sequencing and phenotypic and physiological criteria prior to our study, were confirmed by AFLP analysis, yielding a clear separation of V. botryosa as a rather homogeneous group from related species. In vitro antifungal susceptibility testing resulted in MIC90s across all strains in increasing order posaconazole (0.25 μg/ml), itraconazole (1 μg/ml), voriconazole (4 μg/ml), terbinafine (4 μg/ml), caspofungin (8 μg/ml), anidulafungin (8 μg/ml), isavuconazole (16 μg/ml), amphotericin B (16 μg/ml), and fluconazole (32 μg/ml). Overall, the isolates showed a uniform pattern of low MICs of itraconazole and posaconazole, but high MICs for remaining agents. The echinocandins (caspofungin and anidulafungin) had no activity against V. botryosa. There was no statistically significant difference between susceptibilities of environmental (n = 11) and clinical (n = 7) isolates of V. botryosa (P > 0.05).

  2. Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism.

    Science.gov (United States)

    Thompson, F L; Hoste, B; Vandemeulebroecke, K; Swings, J

    2001-12-01

    The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Amplified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mollusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacultural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actually known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyticus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoenteri, V. pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with > or =45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (> or =45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described.

  3. Using amplified fragment length polymorphism analysis to differentiate isolates of Pasteurella multocida serotype 1

    Science.gov (United States)

    Blehert, D.S.; Jefferson, K.L.; Heisey, D.M.; Samuel, M.D.; Berlowski, B.M.; Shadduck, D.J.

    2008-01-01

    Avian cholera, an infectious disease caused by the bacterium Pasteurella multocida, kills thousands of North American wild waterfowl annually. Pasteurella multocida serotype 1 isolates cultured during a laboratory challenge study of Mallards (Anas platyrhynchos) and collected from wild birds and environmental samples during avian cholera outbreaks were characterized using amplified fragment length polymorphism (AFLP) analysis, a whole-genome DNA fingerprinting technique. Comparison of the AFLP profiles of 53 isolates from the laboratory challenge demonstrated that P. multocida underwent genetic changes during a 3-mo period. Analysis of 120 P. multocida serotype 1 isolates collected from wild birds and environmental samples revealed that isolates were distinguishable from one another based on regional and temporal genetic characteristics. Thus, AFLP analysis had the ability to distinguish P. multocida isolates of the same serotype by detecting spatiotemporal genetic changes and provides a tool to advance the study of avian cholera epidemiology. Further application of AFLP technology to the examination of wild bird avian cholera outbreaks may facilitate more effective management of this disease by providing the potential to investigate correlations between virulence and P. multocida genotypes, to identify affiliations between bird species and bacterial genotypes, and to elucidate the role of specific bird species in disease transmission. ?? Wildlife Disease Association 2008.

  4. Differentiation of Salmonella enteritidis isolates by fluorescent amplified fragment length polymorphism.

    Science.gov (United States)

    Kober, Márcia Vargas; Abreu, Marina Bystronski; Bogo, Maurício Reis; Ferreira, Carlos Alexandre Sanchez; Oliveira, Sílvia Dias

    2011-01-01

    Salmonella Enteritidis is responsible for human gastroenteritis outbreaks worldwide, and the molecular characterization of isolates is an important tool for epidemiological studies. Fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed on 31 Salmonella Enteritidis strains from South Brazil isolated from human, foods, swine, broiler carcasses, and other poultry-related samples to subtype isolates in comparison to pulsed-field gel electrophoresis (PFGE) analysis. Five strains of Salmonella Enteritidis from different geographical regions, Salmonella Enteritidis ATCC 13076, and four isolates of different Salmonella serovars were also tested. Among the 41 isolates tested, 96 polymorphic AFs and 40 distinct profiles were obtained, displaying a Simpson's index of diversity of 0.99; whereas the PFGE analysis presented 13 patterns and the resulting Simpson's index was 0.55. Nine FAFLP and seven PFGE clusters could be inferred based in Dice similarity coefficient. FAFLP clustering readily identified different serotypes of Salmonella but did not distinguish isolates epidemiologically nonrelated or distinct phage types. Therefore, these results indicate that FAFLP is a rapid method for epidemiological investigations of Salmonella outbreaks, presenting a high discriminatory power for subtyping of Salmonella Enteritidis.

  5. Assessment of intercentre reproducibility and epidemiological concordance of Legionella pneumophila serogroup 1 genotyping by amplified fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Fry, N K; Bangsborg, Jette Marie; Bernander, S;

    2000-01-01

    The aims of this work were to assess (i) the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for epidemiological typing of Legionella pneumophila serogroup 1, and (ii) the suitability of the method for standardisation and implementation...... by members of the European Working Group on Legionella Infections. Fifty coded isolates comprising two panels of well-characterised strains, a "reproducibility" panel (n=20) and an "epidemiologically related" panel (n=30), were sent to 13 centres in 12 European countries. Analysis was undertaken in each...... using gel analysis software yielded R=1.00 and E=1.00, with 12, 13 or 14 types. This method can be used as a simple, rapid screening tool for epidemiological typing of isolates of Legionella pneumophila serogroup 1. Results demonstrate that the method can be highly reproducible (R=1...

  6. Delineation of Campylobacter concisus genomospecies by amplified fragment length polymorphism analysis and correlation of results with clinical data

    DEFF Research Database (Denmark)

    Aabenhus, R.; On, Stephen L.W.; Siemer, Berit L.;

    2005-01-01

    phenotypically indistinguishable but genetically distinct taxa (i.e., genornospecies) that may vary in pathogenicity. We examined 62 C concisus strains by amplified fragment length polymorphism (AFLP) profiling and correlated the results with clinical data. All C. concisus strains gave unique AFLP profiles......, and numerical analysis of these data distributed the strains among four clusters. The clustering was of taxonomic significance: two clusters contained, respectively, the type strain (of oral origin) and a reference strain (from diarrhea) of each of the known genomospecies. Genomospecies 2 strains were more....... All genomospecies 4 strains were of the same protein profile group and failed to react with a C concisus species-specific PCR assay based on 23S rRNA gene sequences: the taxonomic position of this group requires closer investigation. Campylobacter concisus is genetically and taxonomically diverse...

  7. Amplified fragment length polymorphism: an adept technique for genome mapping, genetic differentiation, and intraspecific variation in protozoan parasites.

    Science.gov (United States)

    Kumar, Awanish; Misra, Pragya; Dube, Anuradha

    2013-02-01

    With the advent of polymerase chain reaction (PCR), genetic markers are now accessible for all organisms, including parasites. Amplified fragment length polymorphism (AFLP) is a PCR-based marker for the rapid screening of genetic diversity and intraspecific variation. It is a potent fingerprinting technique for genomic DNAs of any origin or complexity and rapidly generates a number of highly replicable markers that allow high-resolution genotyping. AFLPs are convenient and reliable in comparison to other markers like random amplified polymorphic DNA, restriction fragment length polymorphism, and simple sequence repeat in terms of time and cost efficiency, reproducibility, and resolution as it does not require template DNA sequencing. In addition, AFLP essentially probes the entire genome at random, without prior sequence knowledge. So, AFLP markers have emerged as an advance type of genetic marker with broad application in genomic mapping, population genetics, and DNA fingerprinting and are ideally suited as screening tool for molecular markers linked with biological and clinical traits. This review describes the AFLP procedure and its applications and overview in the fingerprinting of a genome, which has been currently used in parasite genome research. We outline the AFLP procedure adapted for Leishmania genome study and discuss the benefits of AFLPs for assessing genetic variation and genome mapping over other existing molecular techniques. We highlight the possible use of AFLPs as genetic markers with its broad application in parasitological research because it allows random screening of the entire genome for linkage with genetic and clinical properties of the parasite. In this review, we have taken a pragmatic approach on the study of AFLP for genome mapping and polymorphism in protozoan parasites and conclude that AFLP is a very useful tool.

  8. Genetic differentiation of Octopus minor (Mollusca, Cephalopoda) off the northern coast of China as revealed by amplified fragment length polymorphisms.

    Science.gov (United States)

    Yang, J M; Sun, G H; Zheng, X D; Ren, L H; Wang, W J; Li, G R; Sun, B C

    2015-12-02

    Octopus minor (Sasaki, 1920) is an economically important cephalopod that is found in the northern coastal waters of China. In this study, we investigated genetic differentiation in fishery populations using amplified fragment length polymorphisms (AFLPs). A total of 150 individuals were collected from five locations: Dalian (DL), Yan-tai (YT), Qingdao (QD), Lianyungang (LY), and Zhoushan (ZS), and 243 reproducible bands were amplified using five AFLP primer combinations. The percentage of polymorphic bands ranged from 53.33 to 76.08%. Nei's genetic identity ranged from 0.9139 to 0.9713, and the genetic distance ranged from 0.0291 to 0.0900. A phylogenetic tree was constructed using the unweighted pair group method with arithmetic mean, based on the genetic distance. The DL and YT populations originated from one clade, while the QD, LY, and ZS populations originated from another. The results indicate that the O. minor stock consisted of two genetic populations with an overall significantly analogous FST value (0.1088, P octopus fisheries, so that this marine resource can be conserved for its long-term utilization.

  9. Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms.

    Science.gov (United States)

    De Vos, Lieschen; Steenkamp, Emma T; Martin, Simon H; Santana, Quentin C; Fourie, Gerda; van der Merwe, Nicolaas A; Wingfield, Michael J; Wingfield, Brenda D

    2014-01-01

    The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.

  10. Genetic diversity among elite Sorghum lines revealed by restriction fragment length polymorphisms and random amplified polymorphic DNAs.

    Science.gov (United States)

    Vierling, R A; Xiang, Z; Joshi, C P; Gilbert, M L; Nguyen, H T

    1994-02-01

    The genetic diversity of sorghum, as compared to corn, is less well characterized at the genetic and molecular levels despite its worldwide economic importance. The objectives of this study were to: (1) investigate genetic diversity for restriction fragment length polymorphism (RFLPs) and random amplified polymorphic DNAs (RAPDs) in elite sorghum lines, (2) compare similarities based on molecular markers with pedigree relationships, and (3) examine the potential of RFLPs and RAPDs for assigning sorghum lines to the A/B (sterile) and R (restorer) groups. Using four restriction enzymes, polymorphism was detected with 61% of the RFLP probes used, compared to 77% of the random primers. One hundred and sixteen (64%) probe-enzyme combinations yielded multiple-band profiles compared to 98% of the random primers. RFLP profiles generated 290 polymorphic bands compared to 177 polymorphic RAPDs. Pair-wise comparisons of polymorphic RFLPs and RAPDs were used to calculate Nei and Jaccard coefficients. These were employed to generate phenograms using UPGMA and neighborjoining clustering methods. Analysis of RFLP data with Jaccard's coefficient and neighbor-joining clustering produced the phenogram with the closest topology to the known pedigree.

  11. Amplified fragment length polymorphism of Streptococcus suis strains correlates with their profile of virulence-associated genes and clinical background.

    Science.gov (United States)

    Rehm, Thomas; Baums, Christoph G; Strommenger, Birgit; Beyerbach, Martin; Valentin-Weigand, Peter; Goethe, Ralph

    2007-01-01

    Amplified fragment length polymorphism (AFLP) typing was applied to 116 Streptococcus suis isolates with different clinical backgrounds (invasive/pneumonia/carrier/human) and with known profiles of virulence-associated genes (cps1, -2, -7 and -9, as well as mrp, epf and sly). A dendrogram was generated that allowed identification of two clusters (A and C) with different subclusters (A1, A2, C1 and C2) and two heterogeneous groups of strains (B and D). For comparison, three strains from each AFLP subcluster and group were subjected to multilocus sequence typing (MLST) analysis. The closest relationship and lowest diversity were found for patterns clustering within AFLP subcluster A1, which corresponded with sequence type (ST) complex 1. Strains within subcluster A1 were mainly invasive cps1 and mrp+ epf+ (or epf*) sly+ cps2+ strains of porcine or human origin. A new finding of this study was the clustering of invasive mrp* cps9 isolates within subcluster A2. MLST analysis suggested that A2 correlates with a single ST complex (ST87). In contrast to A1 and A2, subclusters C1 and C2 contained mainly pneumonia isolates of genotype cps7 or cps2 and epf- sly-. In conclusion, this study demonstrates that AFLP allows identification of clusters of S. suis strains with clinical relevance.

  12. Validation of phylogenetic signals in amplified fragment length data: testing the utility and reliability in closely related taxa

    Directory of Open Access Journals (Sweden)

    Tolley-Jordan Lori R

    2009-02-01

    Full Text Available Abstract Background Discriminating taxa with the nuclear marker, amplified fragment length polymorphism (AFLP has been accomplished for various organisms in economic, ecological, and evolutionary studies. The protocol available for AFLP generation does not require prior knowledge of the genome; however, it is often extensively modified to fit the needs of the researcher. Modification of this protocol for new labs is intimidating and time-consuming, particularly for taxa in which AFLP have not been previously developed. Furthermore, determining what constitutes quality output during different stages of fragment generation is not well defined and this may further hinder the use AFLP by new researchers. Findings We present a step-by-step AFLP protocol, using flourophore-labeled primers for use with automated sequencers, including examples of both successful and unsuccessful results. We sufficiently normalized peak intensity and standardized allele calling across all samples for each primer combination. Repeatability was assessed with a phylogenetic tree in which replicate samples clustered together using the minimum evolution procedure. We found differences greater than 10% in allele position among replicated samples would cause replicates to no longer cluster. To minimize offset allele positions, we suggest that researchers analyze different primer combinations at the same time using multiple dyes with the automated sequencer to minimize mismatched alleles across replicates. Conclusion For researchers wanting to use AFLP, this molecular technique is difficult and time-consuming to develop. Clarifying what constitutes quality output for each step in AFLP generation will help to reduce redundant trials in protocol development and, in turn, advance the discipline of population genetics.

  13. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: Strain diversity, host range, and recombination

    NARCIS (Netherlands)

    Schouls, L.M.; Reulen, S.; Duim, B.; Wagenaar, J.A.; Willems, R.J.L.; Dingle, K.E.; Colles, F.M.; Embden, van J.D.A.

    2003-01-01

    Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic

  14. Characterization of Mycoplasma hyosynoviae strains by amplified fragment length polymorphism analysis, pulsed-field gel electrophoresis and 16S ribosomal DNA sequencing

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Ahrens, Peter

    2002-01-01

    , were investigated by analysis of amplified fragment length polymorphisms of the Bgl II and Mfe I restriction sites and by pulsed-field gel electrophoresis of a Bss HII digest of chromosomal DNA. Both methods allowed unambiguous differentiation of the analysed strains and showed similar discriminatory...

  15. Genotyping of human and porcine Yersinia enterocolitica, Yersinia intertmedia, and Yersinia bercovieri strains from Switzerland by amplified fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Kuehni-Boghenbor, Kathrin; On, Stephen L.W.; Kokotovic, Branko

    2006-01-01

    In this study, 231 strains of Yersinia enterocolitica, 25 strains of Y. intermedia, and 10 strains of Y. bercovieri from human and porcine sources (including reference strains) were analyzed using amplified fragment length polymorphism (AFLP), a whole-genome fingerprinting method for subtyping ba...

  16. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq.

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    Full Text Available As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive "Yanjiang" variety as the female parent with the salt-tolerant "9901" variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq, leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for "Yanjiang", 47.41-fold for "9901", and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs. The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.

  17. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq).

    Science.gov (United States)

    Zhang, Jian; Yuan, Huwei; Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

    2016-01-01

    As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive "Yanjiang" variety as the female parent with the salt-tolerant "9901" variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for "Yanjiang", 47.41-fold for "9901", and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.

  18. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq)

    Science.gov (United States)

    Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

    2016-01-01

    As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree. PMID:27327501

  19. KARAKTERISTIK GENETIK Kappaphycus alvarezii SEHAT DAN TERINFEKSI PENYAKIT ICE-ICE DENGAN METODE Amplified Fragment Length Polymorphism (AFLP

    Directory of Open Access Journals (Sweden)

    Emma Suryati

    2013-03-01

    Full Text Available Infeksi penyakit ice-ice pada Kappaphycus alvarezii seringkali menyebabkan penurunan produksi yang sangat signifikan. K. alvarezii merupakan alga merah penghasil karaginan yang memiliki nilai ekonomi tinggi dan banyak dimanfaatkan dalam berbagai industri, seperti farmasi, makanan, stabilizer, dan kosmetik. Perbaikan genetik sangat diperlukan untuk meningkatkan produksi. Penelitian ini bertujuan untuk mengetahui karakteristik kemiripan genetik K. alvarezii sehat dan terinfeksi penyakit dari Balai Penelitian dan Pengembangan Budidaya Air Payau (BPPBAP, Maros dengan metode Amplified Fragment Length Polymorphism (AFLP. Pada penelitian ini juga dianalisis K. alvarezii asal Bone (BNE, Gorontalo (GRL, Tambalang (TMB, dan Kendari (KND sebagai kontrol rumput laut sehat. Metode AFLP menggunakan enzim restriksi Psti dan Mset, preamplifikasi dan amplifikasi selektif diawali dengan isolsi DNA, uji genimoc DNA, restriksi dan ligasi. Hasil yang diperoleh menunjukkan penggunaan marker AFLP dengan primer forward P11 dan primer reverse M48, M49 dan M50 terhadap K. alvarezii yang berasal dari Takalar (TKL, dan Mataram (MTR, tanpa infeksi (sehat dan terinfeksi penyakit Takalar ice (TKL+, Mataram ice (MTR+, serta K. alvarezii kontrol (BNE, (GRL, (TMB, dan (KND menghasilkan 519 fragmen dalam 122 lokus dengan ukuran 50 - ~370 pb. Kemiripan genetik K. alvarezii yang terinfeksi penyakit ice-ice lebih rendah jika dibandingkan dengan yang sehat. Kemiripan genetik K. alvarezii dari Takalar sehat (TKL dan terinfeksi ice-ice (TKL+ adalah 0,8176 dan MTR-MTR+ adalah 0,8033.

  20. Female-only sex-linked amplified fragment length polymorphism markers support ZW/ZZ sex determination in the giant freshwater prawn Macrobrachium rosenbergii.

    Science.gov (United States)

    Jiang, Xue-Hui; Qiu, Gao-Feng

    2013-12-01

    Sex determination mechanisms in many crustacean species are complex and poorly documented. In the giant freshwater prawn, Macrobrachium rosenbergii, a ZW/ZZ sex determination system was previously proposed based on sex ratio data obtained by crosses of sex-reversed females (neomales). To provide molecular evidence for the proposed system, novel sex-linked molecular markers were isolated in this species. Amplified fragment length polymorphism (AFLP) using 64 primer combinations was employed to screen prawn genomes for DNA markers linked with sex loci. Approximately 8400 legible fragments were produced, 13 of which were uniquely identified in female prawns with no indication of corresponding male-specific markers. These AFLP fragments were reamplified, cloned and sequenced, producing two reliable female-specific sequence characterized amplified region (SCAR) markers. Additional individuals from two unrelated geographic populations were used to verify these findings, confirming female-specific amplification of single bands. Detection of internal polymorphic sites was conducted by designing new primer pairs based on these internal fragments. The internal SCAR fragments also displayed specificity in females, indicating high levels of variation between female and male specimens. The distinctive feature of female-linked SCAR markers can be applied for rapid detection of prawn gender. These sex-specific SCAR markers and sex-associated AFLP candidates unique to female specimens support a sex determination system consistent with female heterogamety (ZW) and male homogamety (ZZ).

  1. Identification and molecular epidemiology of Campylobacter coli isolates from human gastroenteritis, food, and animal sources by amplified fragment length polymorphism analysis and Penner serotyping

    DEFF Research Database (Denmark)

    Siemer, B.L.; Nielsen, Elsa; On, Stephan L.w.

    2005-01-01

    Campylobacter coli is an infrequently studied but important food-borne pathogen with a wide natural distribution. We investigated its molecular epidemiology by use of amplified fragment length polymorphism (AFLP)-based genotyping and Penner serotyping. Serotype reference strains and 177 Danish...... isolates of diverse origin identified by routine phenotyping as C coli were examined. Molecular tools identified some 12% of field isolates as Campylobacter jejuni, emphasizing the need for improved identification methods in routine laboratories. Cluster analysis of AFLP profiles of 174 confirmed C. coli...

  2. Characterization of Pseudomonas aeruginosa in Burn Patients Using PCR- Restriction Fragment Length Polymorphism and Random Amplified Polymorphic DNA Analysis

    Directory of Open Access Journals (Sweden)

    Abdolaziz Rastegar Lari

    2010-09-01

    Full Text Available One of the major opportunistic pathogens in patients with burninjuries is Pseudomonas aeruginosa, which causes severe infectionsin burned patients. The objective of the study was to examinethe molecular epidemiology of P. aeruginosa colonization inthe burn unit of Shahid Motahari Hospital in Tehran, Iran. Restrictionfragment length polymorphism (RFLP and random amplifiedpolymorphic DNA (RAPD analysis were employed tostudy 127 clinical and two environmental P. aeruginosa isolatescollected from January to June 2008. In RFLP, the PCR productsof 16S rRNA gene were digested with restriction enzyme Alu I,Hae III, and Rsa I, and the fragments generated were analyzed byagarose electrophoresis. Molecular typing by RFLP did show nodiscriminatory power for P. aeruginosa isolates, but RAPD-PCRrevealed eight different genotypes; RAPD1to RAPD8 in clinicaland environmental isolates. RAPD1 was the major genotype inclinical (n=64, 50.4% and environmental isolates (n=1, 50%.The findings suggest that RAPD might have a superior typeabilityand discriminatory power over RFLP to study P. aeruginusa.Moreover, they highlight the need for further attention to the controlof infection sources in Burn Units to prevent the transmissionof the bacterium.

  3. A High-Density Genetic Map for Cucumber (Cucumis Sativus L. Based on Specific Length Amplified Fragment (SLAF Sequencing and QTL Analysis of Fruit Traits in Cucumber

    Directory of Open Access Journals (Sweden)

    Wenying eZhu

    2016-04-01

    Full Text Available High-density genetic linkage map plays an important role in genome assembly and QTL fine mapping. Since the coming of next-generation sequencing (NGS, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000×S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on 7 chromosomes, and spanned 1061.19cM. The average genetic distance is 0.35cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.

  4. Use of pulsed field gel electrophoresis (PFGE and single-enzyme amplified fragment length polymorphism(SE-AFLP to subtype isolates of Salmonella entericaserotype enteritidis

    Directory of Open Access Journals (Sweden)

    Caterina Mammina

    2005-03-01

    Full Text Available

    Serotype Enteritidis is still the main serotype infecting humans and poultry worldwide. Subtyping of isolates belonging to this serotype is difficult, because of the wide clonal circulation of a few bacterial clones.

    This study presents the results of the characterization of 49 isolates of S. Enteritidis identified at the southern Italy Centre for Enteric Pathogens (CEPIM during the years 2002-2003 by the methods of Pulsed Field Gel Electrophoresis (PFGE and Single-Enzyme Amplified Fragment Length Polymorphism (SE-AFLP.

    Clustering of the strains by SE-AFLP and PFGE is very similar, but the first technique is more rapid and user-friendly and does not require sophisticated equipment. Further work is needed for a more accurate assessment of SEAFLP, but preliminary results suggest it could be a promising support to epidemiological investigations.

  5. A comparison of Peronospora parasitica (Downy mildew) isolates from Arabidopsis thaliana and Brassica oleracea using amplified fragment length polymorphism and internal transcribed spacer 1 sequence analyses.

    Science.gov (United States)

    Rehmany, A P; Lynn, J R; Tör, M; Holub, E B; Beynon, J L

    2000-07-01

    Amplified fragment length polymorphism (AFLP) fingerprints and internal transcribed spacer 1 (ITS1) sequences from 27 Peronospora parasitica isolates (collected from Arabidopsis thaliana or Brassica oleracea), 5 Albugo candida isolates (from the same hosts and from Capsella bursa-pastoris), and 1 Bremia lactucae isolate (from Lactuca sativa) were compared. The AFLP analysis divided the isolates into five groups that correlated with taxonomic species and, in most cases, with host origin. The only exception was a group consisting of A. candida isolates from both B. oleracea and C. bursa-pastoris. ITS1 sequence analysis divided the isolates into the same five groups, demonstrated the divergence between P. parasitica isolates from A. thaliana and B. oleracea, and, using previously published ITS1 sequences, clearly showed the relationship between A. candida isolates from different hosts.

  6. Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge.

    Science.gov (United States)

    Zhang, Yuejin; Guo, Lijun; Shu, Zhiming; Sun, Yiyue; Chen, Yuanyuan; Liang, Zongsuo; Guo, Hongbo

    2013-03-22

    Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006-2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246) was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357) was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10-93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1-5.

  7. Identification of Amplified Fragment Length Polymorphism (AFLP Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge

    Directory of Open Access Journals (Sweden)

    Hongbo Guo

    2013-03-01

    Full Text Available Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006–2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA and amplified fragment length polymorphism (AFLP with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246 was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357 was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10−93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1–5.

  8. Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes.

    Science.gov (United States)

    Masuyama, Kotoka; Shojo, Hideki; Nakanishi, Hiroaki; Inokuchi, Shota; Adachi, Noboru

    2017-01-01

    Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted "bidirectional analysis," which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples.

  9. Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers.

    Science.gov (United States)

    Qiu, T; Jiang, L L; Yang, Y F

    2016-08-19

    The genetic and epigenetic diversity and structure of naturally occurring Phragmites australis populations occupying two different habitats on a small spatial scale in the Songnen Prairie in northeastern China were investigated by assessing amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs) through fluorescent capillary detection. The two groups of P. australis were located in a seasonal waterlogged low-lying and alkalized meadow with a pH of 8-8.5 and in an alkaline patch without accumulated rainwater and with a pH greater than 10. These groups showed high levels of genetic diversity at the habitat level based on the percentage of polymorphic bands (90.32, 82.56%), Nei's gene diversity index (0.262, 0.248), and the Shannon diversity index (0.407, 0.383). Although little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale, our results implied significant genetic differentiation between habitats. Extensive epigenetic diversity within habitats, along with clear differentiation, was found. Specifically, the former habitat (Habitat 1, designated H1) harbored higher levels of genetic and epigenetic diversity than the latter (Habitat 2, designated H2), and population-level diversity was also high. This study represents one of few attempts to predict habitat-based genetic differentiation of reeds on a small scale. These assessments of genetic and epigenetic variation are integral aspects of molecular ecological studies on P. australis. Possible causes for within- and between-habitat genetic and epigenetic variations are discussed.

  10. Comparison of genetic diversity of the invasive weed Rubus alceifolius poir. (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers.

    Science.gov (United States)

    Amsellem, L; Noyer, J L; Le Bourgeois, T; Hossaert-McKey, M

    2000-04-01

    Theory predicts that colonization of new areas will be associated with population bottlenecks that reduce within-population genetic diversity and increase genetic differentiation among populations. This should be especially true for weedy plant species, which are often characterized by self-compatible breeding systems and vegetative propagation. To test this prediction, and to evaluate alternative scenarios for the history of introduction, the genetic diversity of Rubus alceifolius was studied with amplified fragment length polymorphism (AFLP) markers in its native range in southeast Asia and in several areas where this plant has been introduced and is now a serious weed (Indian Ocean islands, Australia). In its native range, R. alceifolius showed great genetic variability within populations and among geographically close populations (populations sampled ranging from northern Vietnam to Java). In Madagascar, genetic variability was somewhat lower than in its native range, but still considerable. Each population sampled in the other Indian Ocean islands (Mayotte, La Réunion, Mauritius) was characterized by a single different genotype of R. alceifolius for the markers studied, and closely related to individuals from Madagascar. Queensland populations also included only a single genotype, identical to that found in Mauritius. These results suggest that R. alceifolius was first introduced into Madagascar, perhaps on multiple occasions, and that Madagascan individuals were the immediate source of plants that colonized other areas of introduction. Successive nested founder events appear to have resulted in cumulative reduction in genetic diversity. Possible explanations for the monoclonality of R. alceifolius in many areas of introduction are discussed.

  11. Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods.

    Science.gov (United States)

    Yilancioglu, Kaan; Cetiner, Selim

    2013-05-01

    Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

  12. Genetic Mapping of Laminaria japonica and L. longissima Using Amplified Fragment Length Polymorphism Markers in a "Two-Way Pseudo-Testcross" Strategy

    Institute of Scientific and Technical Information of China (English)

    Yuhui Li; Yingxia Yang; Jidong Liu; Xiuliang Wang; Tianxiang Gao; Delin Duan

    2007-01-01

    With a "two-way pseudo-testcross" mapping strategy, we applied the amplified fragment length polymorphism (AFLP) markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F1 cross family (Laminaria longissima Aresch. x L. japonica Miyabe) with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1:1ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3:1 Mendelian segregation ratio. Among the loci with 1:1 segregating ratios, 79 loci were ordered in 14 linkage groups (648.6 cM) of the paternal map, and 72 loci were ordered in 14 linkage groups (601.9 cM) of the maternal map. The average density of loci was approximately 1 per 8 cM. To investigate the homologies between two parental maps, we used 58 loci segregated 3:1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.

  13. Genetic alteration of penicillin non-susceptible Streptococcus pneumoniae observed throughout recurrence of acute otitis media detected by amplified fragment length polymorphism analysis.

    Directory of Open Access Journals (Sweden)

    Sugata K

    2001-06-01

    Full Text Available The prevalence of penicillin non-susceptible Streptococcus pneumoniae (PNSSP is increasing among isolates from acute otitis media (AOM. Repeated episodes of antibiotic exposure are a well-known risk factor for the isolation of PNSSP although otitis-prone or recurrent AOM cases frequently require repeated courses of antibiotic treatment. In order to evaluate the chronological alteration of S. pneumoniae during recurrences of AOM, strains of S. pneumoniae were isolated from 11 patients, each of whom had experienced 2-4 episodes of AOM, were examined. Every bacterial specimen obtained from a single episode of recurrent AOM was examined by PCR-based penicillin-binding protein (PBP assay, serotyping, and amplified fragment length polymorphism (AFLP, then compared to other samples from the same case. Two cases (18.2% showed strain diversity during repeated antibiotic treatments by serotyping or PBP-assay. By AFLP analysis, 6 cases (54.5% demonstrated heterogeneous strains during recurrent AOM. Clonal survivors of previous episodes of AOM were not always the cause of subsequent episodes of AOM, even in otitis-prone cases.

  14. Genotyping of Madurella mycetomatis by selective amplification of restriction fragments (amplified fragment length polymorphism) and subtype correlation with geographical origin and lesion size.

    Science.gov (United States)

    van de Sande, Wendy W J; Gorkink, Roy; Simons, Guus; Ott, Alewijn; Ahmed, Abdalla O A; Verbrugh, Henri; van Belkum, Alex

    2005-09-01

    One of the causative organisms of mycetoma is the fungus Madurella mycetomatis. Previously, extensive molecular typing studies identified Sudanese isolates of this fungus as clonal, but polymorphic genetic markers have not yet been identified. Here, we report on the selective amplification of restriction fragment (AFLP) analysis of 37 Sudanese clinical isolates of M. mycetomatis. Of 93 AFLP fragments generated, 25 were polymorphic, and 12 of these 25 polymorphic fragments were found in a large fraction of the strains. Comparative analysis resulted into a tree, composed of two main (clusters I and II) and one minor cluster (cluster III). Seventy-five percent of the strains found in cluster I originated from central Sudan, while the origin of the strains in cluster II was more heterogeneous. Furthermore, the strains found in cluster I were generally obtained from lesions larger than those from which the strains found in cluster II were obtained (chi-square test for trend, P = 0.03). Among the 12 more commonly found polymorphisms, 4 showed sequence homology with known genes. Marker A7 was homologous to an endo-1,4-beta-glucanase from Aspergillus oryzae, 97% identical markers A12 and B3 matched a hypothetical protein from Gibberella zeae, and marker B4 was homologous to casein kinase I from Danio rerio. The last marker seemed to be associated with strains originating from central Sudan (P = 0.001). This is the first report on a genotypic study where genetic markers which may be used to study pathogenicity in M. mycetomatis were obtained.

  15. Genotypic identification of some lactic acid bacteria by amplified fragment length polymorphism analysis and investigation of their potential usage as starter culture combinations in Beyaz cheese manufacture.

    Science.gov (United States)

    Karahan, A G; Başyiğit Kiliç, G; Kart, A; Sanlidere Aloğlu, H; Oner, Z; Aydemir, S; Erkuş, O; Harsa, S

    2010-01-01

    In this study, 2 different starter culture combinations were prepared for cheesemaking. Starter culture combinations were formed from 8 strains of lactic acid bacteria. They were identified as Lactococcus lactis ssp. lactis (2 strains), Lactobacillus plantarum (5 strains), and Lactobacillus paraplantarum (1 strain) by amplified fragment length polymorphism analysis. The effects of these combinations on the physicochemical and microbiological properties of Beyaz cheeses were investigated. These cheeses were compared with Beyaz cheeses that were produced with a commercial starter culture containing Lc. lactis ssp. lactis and Lc. lactis ssp. cremoris as control. All cheeses were ripened in brine at 4 degrees C for 90 d. Dry matter, fat in dry matter, titratable acidity, pH, salt in dry matter, total N, water-soluble N, and ripening index were determined. Sodium dodecyl sulfate-PAGE patterns of cheeses showed that alpha(S)-casein and beta-casein degraded slightly during the ripening period. Lactic acid bacteria, total mesophilic aerobic bacteria, yeast, molds, and coliforms were also counted. All analyses were repeated twice during d 7, 30, 60, and 90. The starter culture combinations were found to be significantly different from the control group in pH, salt content, and lactobacilli, lactococci, and total mesophilic aerobic bacteria counts, whereas the cheeses were similar in fat, dry matter content, and coliform, yeast, and mold counts. The sensory analysis of cheeses indicated that textural properties of control cheeses presented somewhat lower scores than those of the test groups. The panelists preferred the tastes of treatment cheeses, whereas cheeses with starter culture combinations and control cheeses had similar scores for appearance and flavor. These results indicated that both starter culture combinations are suitable for Beyaz cheese production.

  16. Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy.

    Science.gov (United States)

    Xu, Xiaomei; Chao, Juan; Cheng, Xueli; Wang, Rui; Sun, Baojuan; Wang, Hengming; Luo, Shaobo; Xu, Xiaowan; Wu, Tingquan; Li, Ying

    2016-01-01

    Phytophthora root rot caused by Phytophthora capsici (P. capsici) is a serious limitation to pepper production in Southern China, with high temperature and humidity. Mapping PRR resistance genes can provide linked DNA markers for breeding PRR resistant varieties by molecular marker-assisted selection (MAS). Two BC1 populations and an F2 population derived from a cross between P. capsici-resistant accession, Criollo de Morelos 334 (CM334) and P. capsici-susceptible accession, New Mexico Capsicum Accession 10399 (NMCA10399) were used to investigate the genetic characteristics of PRR resistance. PRR resistance to isolate Byl4 (race 3) was controlled by a single dominant gene, PhR10, that was mapped to an interval of 16.39Mb at the end of the long arm of chromosome 10. Integration of bulked segregant analysis (BSA) and Specific Length Amplified Fragment sequencing (SLAF-seq) provided an efficient genetic mapping strategy. Ten polymorphic Simple Sequence Repeat (SSR) markers were found within this region and used to screen the genotypes of 636 BC1 plants, delimiting PhR10 to a 2.57 Mb interval between markers P52-11-21 (1.5 cM away) and P52-11-41 (1.1 cM). A total of 163 genes were annotated within this region and 31 were predicted to be associated with disease resistance. PhR10 is a novel race specific gene for PRR, and this paper describes linked SSR markers suitable for marker-assisted selection of PRR resistant varieties, also laying a foundation for cloning the resistance gene.

  17. Fluorescent amplified fragment length polymorphism (FAFLP genotyping demonstrates the role of biofilm-producing methicillin-resistant periocular Staphylococcus epidermidis strains in postoperative endophthalmitis

    Directory of Open Access Journals (Sweden)

    Hasnain Seyed E

    2006-01-01

    Full Text Available Abstract Background An observational case series was used to study the virulence characteristics and genotypes of paired Staphylococcus epidermidis isolates cultured from intraocular samples and from periocular environment of patients with postcataract surgery endophthalmitis. Methods Eight S. epidermidis isolates were obtained from three patients (2 from patients #1 and 2 and 4 from patient #3 whose vitreous and/or anterior chamber (AC specimens and preoperative lid/conjunctiva samples were culture positive. Cultures were identified by API-Staph phenotypic identification system and genotypically characterized by Fluorescent Amplified Fragment Length Polymorphism (FAFLP and checked for their antimicrobial susceptibility. The isolates were tested for biofilm-production and methicillin-resistance (MR by PCR amplification of icaAB and mecA gene respectively. Results Four out of eight S. epidermidis strains showed multiple drug resistance (MDR. All the eight strains were PCR positive for mecA gene whereas seven out of eight strains were positive for icaAB genes. In all three patients FAFLP typing established vitreous isolates of S. epidermidis strains to be indistinguishable from the strains isolated from the patient's conjunctival swabs. However, from patient number three there was one isolate (1030b from lid swab, which appeared to be nonpathogenic and ancestral having minor but significant differences from other three strains from the same patient. This strain also lacked icaAB gene. In silico analysis indicated possible evolution of other strains from this strain in the patient. Conclusion Methicillin-resistant biofilm positive S. epidermidis strains colonizing the conjunctiva and eyelid were responsible for postoperative endophthalmitis (POE.

  18. Molecular Variability Within and Among Verticillium dahliae Vegetative Compatibility Groups Determined by Fluorescent Amplified Fragment Length Polymorphism and Polymerase Chain Reaction Markers.

    Science.gov (United States)

    Collado-Romero, Melania; Mercado-Blanco, Jesús; Olivares-García, Concepción; Valverde-Corredor, Antonio; Jiménez-Díaz, Rafael M

    2006-05-01

    ABSTRACT A degree of genetic diversity may exist among Verticillium dahliae isolates within vegetative compatibility groups (VCGs) that bears phytopathological significance and is worth investigating using molecular tools of a higher resolution than VCG characterization. The molecular variability within and among V. dahliae VCGs was studied using 53 artichoke isolates from eastern-central Spain, 96 isolates from cotton, 7 from cotton soil, and 45 from olive trees in countries of the Mediterranean Basin. Isolates were selected to represent the widest available diversity in cotton- and olive-defoliating (D) and -nondefoliating (ND) pathotypes, as well as for VCG. The VCG of 96 cotton and olive isolates was determined in this present study. Molecular variability among V. dahliae isolates was assessed by fluorescent amplified fragment length polymorphism (AFLP) analysis and by polymerase chain reaction (PCR) assays for DNA fragments associated with the D (462 bp) and ND (824 bp) pathotypes, as well as a 334-bp amplicon associated with D pathotype isolates but also present in some VCG2B isolates. Isolates from cotton were in VCG1A, VCG1B, VCG2A, VCG2B, and VCG4B and those from olive trees were in VCG1A, VCG2A, and VCG4B. Artichoke isolates included representatives of VCG1A, VCG2A, VCG2B (including a newly identified VCG2Ba), and VCG4B. AFLP data were used to generate matrixes of genetic distance among isolates for cluster analysis using the neighbor-joining method and for analysis of molecular variance. Results demonstrated that V. dahliae isolates within a VCG subgroup are molecularly similar, to the extent that clustering of isolates correlated with VCG subgroups regardless of the host source and geographic origin. VCGs differed in molecular variability, with the variability being highest in VCG2B and VCG2A. For some AFLP/VCG subgroup clusterings, V. dahliae isolates from artichoke grouped in subclusters clearly distinct from those comprising isolates from cotton and

  19. Development of fluorescent amplified fragment length polymorphism for Streptococcus suis%猪链球菌荧光DNA扩增片段长度多态性检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    王楷成; Linda van der Graaf; 陆承平; 黄保续; 范伟兴

    2012-01-01

    The fluorescent amplified fragment length for Streptococcus suis was developed using 2 pairs of primers.51 to 98 fragments of highly polymorphic products were obtained by 2 pairs of primers in 12 Streptococcus suis isolates.The fluorescent amplified fragment length technique can be used to detect the DNA polymorphism of Streptococcus suis.Different serotypes or different isolates of the same serotype in Streptococcus suis can be distinguished by the method.It is available in identification or tracking for Streptococcus suis strains.%利用荧光标记技术,采用2对引物初步建立检测猪链球菌荧光DNA扩增片段长度多态性方法,结果表明12株猪链球菌扩增的多态性位点数从51~98条不等,该方法能够检测猪链球菌的多态性,区分不同血清型以及同一血清型不同特性的菌株,可用于菌株鉴定及流行病学研究中细菌源的追踪。

  20. Differentially Expression of Tual, a Tubulin-encoding Gene,during Flowering of Tea Plant Camellia sinensis(L.)O.Kuntze Using cDNA Amplified Fragment Length Polymorphism Technique

    Institute of Scientific and Technical Information of China (English)

    Wan-Ping FANG; Chang-Jun JIANG; Mei YU; Ai-Hua YE; Zhao-Xia WANG

    2006-01-01

    The complementary DNA (cDNA) amplified fragment length polymorphism technique was used to isolate transcript-derived fragments corresponding to genes involved in the flowering of tea plant. Comparative sequence analysis of an approximately 300 bp differential fragment amplified by primer combination E11M11 revealed 80%-84% similarity to the corresponding part of an α-tubulin gene of other species. The complete cDNA sequence of this α-tubulin was cloned by the rapid amplification of cDNA ends technique; its full length is 1537 bp and contains an open reading frame of 450 amino acid residues with two Nglycosylation sites and four protein kinase C phosphorylation sites. The deduced amino acid sequences did show significant homology to the α-tubulin from other plants that has been reported to be a pollen-specific protein and could be correlated with plant cytoplasm-nucleus-interacted male sterility. We named this complete cDNA Tual. The nucleotide and amino acid sequence data of Tual have been recorded in the GenBank sequence database with the accession No. DQ340766. This Tual gene was cloned into the pET-32a expression system and expressed in Escherichia coli BL21trxB(DE3). The molecular weight of expressed protein was deduced to be approximately 49 kDa. Western blot analysis was used to identify the temporal expression of Tual in tea plant. Further studies of the effect of Tual protein on pollen tube growth indicated the Tual solution obviously promoted the growth of tea pollen tube.

  1. Designation of the European Working Group on Legionella Infection (EWGLI) amplified fragment length polymorphism types of Legionella pneumophila serogroup 1 and results of intercentre proficiency testing Using a standard protocol

    DEFF Research Database (Denmark)

    Fry, N K; Bangsborg, Jette Marie; Bergmans, A;

    2002-01-01

    The utility of amplified fragment length polymorphism (AFLP) analysis as a genotyping method for the epidemiological typing of Legionella pneumophila serogroup 1 has been previously demonstrated. This study (i). reports recommendations for the designation of the European Working Group on Legionella...... (recorded as AFLP type 001-016 or untypeable) was determined by participants with reference to these 16 AFLP types, either visually or using gel analysis software where available, and reported to the coordinating centre. Nine of the 12 strains, including an epidemiologically related pair and two pairs...... Infections (EWGLI) AFLP types, (ii). describes the EWGLI AFLP types identified for the 130 strains in the EWGLI culture collection, and (iii). reports the results of a newly introduced international programme of proficiency testing. Following preliminary analysis of 20 epidemiologically unrelated isolates...

  2. Recent Advances of Amplified Fragment Length Polymorphism and Its Applications in Forensic Botany%AFLP分子标记技术的新进展及其在法医植物学中的应用

    Institute of Scientific and Technical Information of China (English)

    李成涛; 李莉

    2008-01-01

    扩增片段长度多态性(amplified fragment length polymorphism,AFLP)是一种用来检测基因组多态性的新一代分子标记,具有分辨率高、稳定性好、重复性好等特点.近年来,研究人员对该技术进行了不断的优化和完善,并由之衍生出多种相关技术.AFLP技术在动物、植物及微生物等许多研究领域已有广泛应用,在法医植物学中得到初步发展并成为研究热点.本文主要介绍了AFLP技术的新进展以及在法医植物学中的应用情况.

  3. Fragment Length of Circulating Tumor DNA.

    Directory of Open Access Journals (Sweden)

    Hunter R Underhill

    2016-07-01

    Full Text Available Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively. Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively. Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

  4. Fragment Length of Circulating Tumor DNA.

    Science.gov (United States)

    Underhill, Hunter R; Kitzman, Jacob O; Hellwig, Sabine; Welker, Noah C; Daza, Riza; Baker, Daniel N; Gligorich, Keith M; Rostomily, Robert C; Bronner, Mary P; Shendure, Jay

    2016-07-01

    Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

  5. Intestinal carriage of Campylobacter jejuni and Campylobacter coli among cattle from South-western Norway and comparative genotyping of bovine and human isolates by amplified-fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Vardund T

    2006-06-01

    Full Text Available Abstract In a survey conducted in 1999–2001, the carriage of thermotolerant Campylobacters in cattle was investigated, and the genetic diversity of C. jejuni within one herd was examined and compared with human isolates. C. jejuni, C. coli and other thermotolerant Campylobacter spp. were isolated from intestinal contents from 26%, 3% and 2% of 804 cattle, respectively. The carriage rate was higher in calves (46% than in adults (29%. Twenty-nine C. jejuni isolates from one herd and 31 human isolates from the study area were genotyped with amplified-fragment length polymorphism (AFLP. Eighty-three % of the bovine isolates fell into three distinct clusters with 95–100% similarity, persistent in the herd for 5–10 months. Among human isolates, 58% showed >90% similarity with bovine isolates. The results show that cattle are a significant and stable reservoir for C. jejuni in the study area. Transmission between individuals within the herd may be sufficient to maintain a steady C. jejuni population independent of environmental influx. The results of this study have provided new information on C. jejuni and C. coli transmission, and also on the carriage in cattle, genotypes stability and similarity between bovine and human isolates.

  6. Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphism.

    Science.gov (United States)

    Prakash, A; Sharma, C; Singh, A; Kumar Singh, P; Kumar, A; Hagen, F; Govender, N P; Colombo, A L; Meis, J F; Chowdhary, A

    2016-03-01

    Candida auris is a multidrug-resistant nosocomial bloodstream pathogen that has been reported from Asian countries and South Africa. Herein, we studied the population structure and genetic relatedness among 104 global C. auris isolates from India, South Africa and Brazil using multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RPB1, RPB2 and internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal DNA were sequenced for MLST. Further, genetic variation and proteomic assessment was carried out using AFLP and MALDI-TOF MS, respectively. Both MLST and AFLP typing clearly demarcated two major clusters comprising Indian and Brazilian isolates. However, the South African isolates were randomly distributed, suggesting different genotypes. MALDI-TOF MS spectral profiling also revealed evidence of geographical clustering but did not correlate fully with the genotyping methods. Notably, overall the population structure of C. auris showed evidence of geographical clustering by all the three techniques analysed. Antifungal susceptibility testing by the CLSI microbroth dilution method revealed that fluconazole had limited activity against 87% of isolates (MIC90, 64 mg/L). Also, MIC90 of AMB was 4 mg/L. Candida auris is emerging as an important yeast pathogen globally and requires reproducible laboratory methods for identification and typing. Evaluation of MALDI-TOF MS as a typing method for this yeast is warranted.

  7. Most cases of cryptococcal meningitis in HIV-uninfected patients in Vietnam are due to a distinct amplified fragment length polymorphism-defined cluster of Cryptococcus neoformans var. grubii VN1.

    Science.gov (United States)

    Day, Jeremy N; Hoang, Thu N; Duong, Anh V; Hong, Chau T T; Diep, Pham T; Campbell, James I; Sieu, Tran P M; Hien, Tran T; Bui, Tien; Boni, Maciej F; Lalloo, David G; Carter, Dee; Baker, Stephen; Farrar, Jeremy J

    2011-02-01

    Cryptococcal disease most commonly occurs in patients with an underlying immune deficit, most commonly HIV infection, and is due to Cryptococcus neoformans var. grubii. Occasionally disease due to this variety occurs in apparently immunocompetent patients. The relationship between strains infecting immunosuppressed and immunocompetent patients is not clear. Amplified fragment length polymorphism (AFLP) analysis was used to characterize the relationship between strains infecting HIV-infected and uninfected patients. Isolates from 51 HIV-uninfected patients and 100 HIV-infected patients with cryptococcal meningitis were compared. C. neoformans var. grubii VNI was responsible for infections in 73% of HIV-uninfected and 100% of HIV-infected patients. AFLP analysis defined two distinct clusters, VNIγ and VNIδ. The majority (84%) of isolates from HIV-uninfected patients were VNIγ, compared with only 38% of isolates from HIV-infected patients (odds ratio, 8.30; 95% confidence interval [CI], 3.04 to 26.6; P cryptococcal meningitis in Vietnam. The distribution of these clusters differs according to the immune status of the host.

  8. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Science.gov (United States)

    Asadzadeh, Mohammad; Ahmad, Suhail; Hagen, Ferry; Meis, Jacques F; Al-Sweih, Noura; Khan, Ziauddin

    2015-01-01

    Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A

  9. Molecular epidemiology and in-vitro antifungal susceptibility of Aspergillus terreus species complex isolates in Delhi, India: evidence of genetic diversity by amplified fragment length polymorphism and microsatellite typing.

    Directory of Open Access Journals (Sweden)

    Shallu Kathuria

    Full Text Available Aspergillus terreus is emerging as an etiologic agent of invasive aspergillosis in immunocompromised individuals in several medical centers in the world. Infections due to A. terreus are of concern due to its resistance to amphotericin B, in vivo and in vitro, resulting in poor response to antifungal therapy and high mortality. Herein we examined a large collection of molecularly characterized, geographically diverse A. terreus isolates (n = 140 from clinical and environmental sources in India for the occurrence of cryptic A. terreus species. The population structure of the Indian A. terreus isolates and their association with those outside India was determined using microsatellite based typing (STR technique and Amplified Fragment Length Polymorphism analysis (AFLP. Additionally, in vitro antifungal susceptibility of A. terreus isolates was determined against 7 antifungals. Sequence analyses of the calmodulin locus identified the recently described cryptic species A. hortai, comprising 1.4% of Aspergillus section Terrei isolates cultured from cases of aspergilloma and probable invasive aspergillosis not reported previously. All the nine markers used for STR typing of A. terreus species complex proved to be highly polymorphic. The presence of high genetic diversity revealing 75 distinct genotypes among 101 Indian A. terreus isolates was similar to the marked heterogeneity noticed in the 47 global A. terreus population exhibiting 38 unique genotypes mainly among isolates from North America and Europe. Also, AFLP analysis showed distinct banding patterns for genotypically diverse A. terreus isolates. Furthermore, no correlation between a particular genotype and amphotericin B susceptibility was observed. Overall, 8% of the A. terreus isolates exhibited low MICs of amphotericin B. All the echinocandins and azoles (voriconazole, posaconazole and isavuconazole demonstrated high potency against all the isolates. The study emphasizes the need of

  10. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Directory of Open Access Journals (Sweden)

    Mohammad Asadzadeh

    Full Text Available Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp, C. orthopsilosis (109 bp, C. metapsilosis (217 bp and L. elongisporus (258 bp were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380 by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study was performed by amplified fragment length polymorphism (AFLP analysis. Phenotypically identified C. parapsilosis isolates (n = 380 were identified as C. parapsilosis sensu stricto (n = 361, C. orthopsilosis (n = 15, C. metapsilosis (n = 1 and L. elongisporus (n = 3 by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1 comprising 11 isolates recovered from 10

  11. Identification of beef using restriction fragment length polymorphism–

    Directory of Open Access Journals (Sweden)

    R. A. Al-Sanjary

    2009-01-01

    Full Text Available To differentiate the beef from other types of meat consumed by human, DNA markers based on polymerase chain reaction restriction fragment length polymorphism technique is performed by using universal primers designed on mitochondrial cytochrome b gene to obtain amplified band 359 bp, then digested with some of restriction enzymes like Tru91, RsaI, Hinf I, Hae III, Alu I, Taq I, Mob I. The result revealed that, the Hinf I enzyme produce three bands 198, 117, 44 bp and the Hae III enzyme revealed two band 285, 74 bp, the Alu I enzyme also produced two band but the molecular weight are 190, 169 bp. The other enzymes did not reveal any digestion of the amplified bands and this result is a characteristic unique to beef compared with other types of meat when using same enzymes.

  12. Measuring Optimal Length of the Amplifying Fiber in Different Working Conditions of the Amplifier

    Directory of Open Access Journals (Sweden)

    Radek Poboril

    2014-01-01

    Full Text Available The aim of this article is to highlight possible unwanted behaviour of an EDFA optical amplifier during temperature changes. After a brief introduction dealing with amplifiers and doped fibers in general we focus on the assembly of our own EDFA amplifier with standard construction and the IsoGain I-6 amplifying fiber, and on the parameters of its individual components. Since an erbium doped fiber has usually no direct thermal stabilization, temperature changes can affect performance of the entire amplifier. The next part of the article therefore describes the impacts of such changes on behaviour of our amplifier. At the very end we performed a measurement of the amplifier deployed in the actual WDM-PON the description of which can be found in the last chapter.

  13. Optimisation and evaluation of restriction fragment length polimorfism method for apolipoprotein E

    Directory of Open Access Journals (Sweden)

    Drljević Nevena

    2014-01-01

    Full Text Available Introduction. Apolipoprotein E gene polymorphism is characterized by the presence of three common alleles, e2, e3 and e4, which encode three isoforms of apolipoprotein E in plasma E2, E3 and E4. Genetic polymorphisms of apolipoprotein E gene are predictive markers for the development of numerous disorders of lipid metabolism, already proven in a large number of clinical trials. This study was aimed at assessing the success rate of restriction fragment length polymorphism method for the detections of genes coding for isoenzymes E2, E3 and E4. Material and Methods. Deoxyribonucleic acid, used in this study, was extracted from blood by standard procedure using chloroform and phenol. The polymerase chain reaction method was used to amplify the coding sequence of fourth exon of the apolipoprotein E gene. Amplification products were digested with HhaI. The fragments obtained were separated by electrophoresis and visualized with ultraviolet light. Results. Our results showed that the restriction fragment length polymorphism method is optimal for detection of apolipoprotein E polymorphisms. The restriction enzyme HhaI achieved the cleavage of the gene on the specific loci, directly depend of presence or absence of mutations at positions 112 and 158, of different alleles. Conclusion. This method enables simple, rapid and efficient analysis of restriction fragment length polymorphisms, directly determining the patient’s genotype.

  14. Use of single-enzyme amplified fragment length polymorphism for typing Clostridium perfringens isolated from diarrheic piglets Uso do polimorfismo do comprimento de fragmentos amplificados para tipagem de Clostridium perfringens isolados de suínos com diarréia

    Directory of Open Access Journals (Sweden)

    Luciane Tieko Shinya

    2006-09-01

    Full Text Available Clostridium perfringens is an important pathogen in human and veterinary medicine. In swine, the agent is responsible for necrotic enteritis and enterotoxemia characterized by diarrhea, weight loss, delayed development and, in some cases, death. In the present study amplified fragment length polymorphism analyses (AFLP was used to characterize 54 C. perfringens strains isolated from swine presenting diarrhea. Analysis of the results showed 29 distinct profiles with discriminatory index equal to 0.97. Partial correlation between the origin of the isolates and groups was drawn, and correlation was possible in only 18.5% of the samples. Characterization of the strains in biotypes (A, B, C, D and E, production of beta-2 toxin and enterotoxin were performed by means of the polymerase chain reaction (PCR. Biotypes A, C and D were observed among the strains analyzed. All samples were positive for presence of the gene encoding beta-2 toxin and negative for the gene encoding enterotoxin. AFLP have shown to be a simple, fast, low cost method with high discriminative power and good reproducibility, presenting a great potential in epidemiological studies involving C. perfringens strains of animal origin.Clostridium perfringens é um importante agente infeccioso em medicina veterinária e humana. Em suínos, o agente é responsável pela enterite necrótica e enterotoxemia, caracterizadas por diarréia, perda de peso, atraso no desenvolvimento e morte. No presente estudo foi utilizado o polimorfismo do comprimento de fragmentos amplificados (AFLP, para caracterizar 54 isolados de C. perfringens obtidos de suínos com diarréia. A análise dos resultados do AFLP demonstrou 29 perfis distintos com índice discriminatório igual a 0,97. A correlação entre a origem dos isolados e os agrupamentos obtidos foi parcial, sendo apenas possível a correlação total de 18,5% das amostras estudadas. A caracterização das cepas em biotipos (A, B, C, D e E, produ

  15. Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP).

    Science.gov (United States)

    Prakash, Om; Pandey, Prashant K; Kulkarni, Girish J; Mahale, Kiran N; Shouche, Yogesh S

    2014-09-01

    Terminal restriction fragment length polymorphism (T-RFLP) is a rapid, robust, inexpensive and simple tool for microbial community profiling. Methods used for DNA extraction, PCR amplification and digestion of amplified products have a considerable impact on the results of T-RFLP. Pitfalls of the method skew the similarity analysis and compromise its high throughput ability. Despite a high throughput method of data generation, data analysis is still in its infancy and needs more attention. Current article highlights the limitations of the methods used for data generation and analysis. It also provides an overview of the recent methodological developments in T-RFLP which will assist the readers in obtaining real and authentic profiles of the microbial communities under consideration while eluding the inherent biases and technical difficulties.

  16. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

    Directory of Open Access Journals (Sweden)

    Leterrier Christine

    2010-07-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism for genomic DNA, and EST (Expressed Sequence Tag for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

  17. Molecular identification of Giardia duodenalis in Ecuador by polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Richard Atherton

    2013-06-01

    Full Text Available The aim of this study was to determine the genetic diversity of Giardia duodenalis present in a human population living in a northern Ecuadorian rain forest. All Giardia positive samples (based on an ELISA assay were analysed using a semi-nested polymerase chain reaction-restriction fragment length polymorphism assay that targets the glutamate dehydrogenase (gdh gene; those amplified were subsequently genotyped using NlaIV and RsaI enzymes. The gdh gene was successfully amplified in 74 of 154 ELISA positive samples; 69 of the 74 samples were subsequently genotyped. Of these 69 samples, 42 (61% were classified as assemblage B (26 as BIII and 16 as BIV, 22 (32% as assemblage A (3 as AI and 19 as AII and five (7% as mixed AII and BIII types. In this study site we observe similar diversity in genotypes to other regions in Latin America, though in contrast to some previous studies, we found similar levels of diarrheal symptoms in those individuals infected with assemblage B compared with those infected with assemblage A.

  18. Characterisation of Toxoplasma gondii isolates using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the non-coding Toxoplasma gondii (TGR)-gene sequences

    DEFF Research Database (Denmark)

    Høgdall, Estrid; Vuust, Jens; Lind, Peter;

    2000-01-01

    of using TGR gene variants as markers to distinguish among T. gondii isolates from different animals and different geographical sources. Based on the band patterns obtained by restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction (PCR) amplified TGR sequences, the T...

  19. Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems

    Science.gov (United States)

    Tiquia, Sonia M.

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

  20. Biases for detecting arbuscular mycorrhizal fungal mixture by terminal restriction fragment length polymorphism (T-RFLP).

    Science.gov (United States)

    Watanarojanaporn, N; Longtonglang, A; Boonkerd, N; Tittabutr, P; Lee, J; Teaumroong, N

    2014-01-01

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified ribosomal RNA genes is used for profiling microbial communities and sometimes for species richness and relative abundance estimation in environmental samples. However, the T-RFLP fingerprint may be subject to biases during the procedure, influencing the detection of real community structures in the environment. To investigate possible sources of T-RFLP bias, 18S rRNA gene clones derived from two arbuscular mycorrhizal fungal sequences were combined in simple pairwise mixes to assess the effects of polymerase chain reaction cycle number, plant genomic DNA purification method and varying template ratio on the template-to-product ratio as measured by relative T-RF peak area. Varying cycle numbers indicated that amplification was still in the exponential phase at the cycle numbers lower than 18, so these small cycle numbers were used for the comparison of template-to-product quantities. Relative abundance estimated from T-RF peak ratios varied with different purification procedures, but the best results, closest to input ratios, were obtained by using phenol-chloroform purification. The presence of an excess of unpurified non-target plant genomic DNA generated a bias towards lower or overestimation of relative abundance. We conclude that a low number of amplification cycles and stringent DNA purification are necessary for accurate mixed sample analysis by T-RFLP.

  1. Genotypic lineages and restriction fragment length polymorphism of canine distemper virus isolates in Thailand.

    Science.gov (United States)

    Radtanakatikanon, Araya; Keawcharoen, Juthatip; Charoenvisal, Na Taya; Poovorawan, Yong; Prompetchara, Eakachai; Yamaguchi, Ryoji; Techangamsuwan, Somporn

    2013-09-27

    Canine distemper virus (CDV) is known to cause multisystemic disease in all families of terrestrial carnivores. Attenuated live vaccines have been used to control CDV in a variety of species for many decades, yet a number of CDV infections in vaccinated dogs are still observed. The aims of this study were to investigate the genetic diversity of CDV lineages based on phosphoprotein (P), hemagglutinin (H) and fusion protein (F) genes and to develop the restriction fragment length polymorphism (RFLP) technique for effective differentiation among individual wild-type and vaccine lineages in Thailand. Four commercial vaccine products, thirteen conjunctival swabs and various tissues from 9 necropsied dogs suspected of having CDV infections were included. Virus isolation was performed using Vero cell expressing canine signaling lymphocyte activation molecules (Vero-DST cells). Reverse-transcription polymerase chain reaction (RT-PCR) on 3 gene regions from the dog derived specimens and the vaccines were carried out, then RFLP analysis upon F-gene amplified fragments was developed. Nucleotide sequence and phylogenetic analysis were compared with other CDV lineages in Genbank. Phylogenetic relationships revealed that CDV field isolates were separated from the vaccine lineage and could be divided into two clusters; one of which belonged to the Asia-1 lineage and another, not related to any previous recognized lineages was proposed as 'Asia-4'. RFLP patterns demonstrating concordance with phylogenetic trees of the distemper virus allowed for differentiation between the Asia-1, Asia-4 and vaccine lineages. Thus, RFLP technique is able to effectively distinguish individual wild-type canine distemper virus from vaccine lineages in Thailand.

  2. Changes in Mammalian Body Length over 175 Years - Adaptations to a Fragmented Landscape?

    Directory of Open Access Journals (Sweden)

    Niels Martin Schmidt

    2003-12-01

    Full Text Available The potential consequences of anthropogenic habitat fragmentation on species diversity and extinction have drawn considerable attention in recent decades. In many cases, traditional island biogeography theory has been applied to explain the observed patterns. Here, we propose that habitat fragmentation as a selective force can be traced in mammalian body length changes. By exploring historical sources, we are able to show that the body length of Danish mammals has altered over a period of 175 years, possibly in response to increasing habitat fragmentation. The rate of body length change was generally lowest in medium-sized mammals, and increased with both smaller and larger body mass. Small mammals have generally increased, whereas large mammals have decreased in length. In addition to habitat fragmentation, some species may experience other selective forces, such as traffic, and may be trapped in an evolutionary tug-of-war, where the selective forces pull in opposite directions.

  3. An Imaging System for Automated Characteristic Length Measurement of Debrisat Fragments

    Science.gov (United States)

    Moraguez, Mathew; Patankar, Kunal; Fitz-Coy, Norman; Liou, J.-C.; Sorge, Marlon; Cowardin, Heather; Opiela, John; Krisko, Paula H.

    2015-01-01

    The debris fragments generated by DebriSat's hypervelocity impact test are currently being processed and characterized through an effort of NASA and USAF. The debris characteristics will be used to update satellite breakup models. In particular, the physical dimensions of the debris fragments must be measured to provide characteristic lengths for use in these models. Calipers and commercial 3D scanners were considered as measurement options, but an automated imaging system was ultimately developed to measure debris fragments. By automating the entire process, the measurement results are made repeatable and the human factor associated with calipers and 3D scanning is eliminated. Unlike using calipers to measure, the imaging system obtains non-contact measurements to avoid damaging delicate fragments. Furthermore, this fully automated measurement system minimizes fragment handling, which reduces the potential for fragment damage during the characterization process. In addition, the imaging system reduces the time required to determine the characteristic length of the debris fragment. In this way, the imaging system can measure the tens of thousands of DebriSat fragments at a rate of about six minutes per fragment, compared to hours per fragment in NASA's current 3D scanning measurement approach. The imaging system utilizes a space carving algorithm to generate a 3D point cloud of the article being measured and a custom developed algorithm then extracts the characteristic length from the point cloud. This paper describes the measurement process, results, challenges, and future work of the imaging system used for automated characteristic length measurement of DebriSat fragments.

  4. Restriction fragment length polymorphisms of the DNA of selected Naegleria and Acanthamoeba amebae.

    Science.gov (United States)

    McLaughlin, G L; Brandt, F H; Visvesvara, G S

    1988-09-01

    Fourteen strains of Naegleria fowleri, two strains of N. gruberi, and one strain each of N. australiensis, N. jadini, N. lovaniensis, Acanthamoeba sp., A. castellanii, A. polyphaga, and A. comandoni isolated from patients, soil, or water were characterized by restriction fragment length polymorphisms. Total cellular DNA (1 microgram) was digested with either HindIII, BglII, or EcoRI; separated on agarose gels; and stained with ethidium bromide. From 2 to 15 unusually prominent repetitive restriction fragment bands, totaling 15 to 50 kilobases in length and constituting probably more than 30% of the total DNA, were detected for all ameba strains. Each species displayed a characteristic pattern of repetitive restriction fragments. Digests of the four Acanthamoeba spp. displayed fewer, less intensely staining repetitive fragments than those of the Naegleria spp. All N. fowleri strains, whether isolated from the cerebrospinal fluid of patients from different parts of the world or from hot springs, had repetitive restriction fragment bands of similar total lengths (ca. 45 kilobases), and most repetitive bands displayed identical mobilities. However, polymorphic bands were useful in identifying particular isolates. Restriction fragment length polymorphism analysis generally was consistent with taxonomy based on studies of infectivity, morphology, isoenzyme patterns, and antibody reactivity and suggests that this technique may help classify amebae isolated from clinical specimens or from the environment.

  5. Discrimination among individuals using terminal restriction fragment length polymorphism profiling of bacteria derived from forensic evidence.

    Science.gov (United States)

    Nishi, Eiji; Tashiro, Yukihiro; Sakai, Kenji

    2015-05-01

    DNA typing from forensic evidence is commonly used to identify individuals. However, when the quantity of the forensic evidence is insufficient, successful identification using DNA typing is impossible. Such evidence may also contain DNA from bacteria that occur naturally on the skin. In this study, we aimed to establish a profiling method using terminal restriction fragment length polymorphisms (T-RFLPs) of the amplified bacterial 16S ribosomal RNA (rRNA) gene. First, the extraction and digestion processes were investigated, and the T-RFLP profiling method using the 16S rRNA gene amplicon was optimized. We then used this method to compare the profiles of bacterial flora from the hands of 12 different individuals. We found that the T-RFLP profiles from one person on different days displayed higher similarity than those between individuals. In a principal component analysis (PCA), T-RFLPs from each individual were closely clustered in 11 out of 12 cases. The clusters could be distinguished from each other, even when the samples were collected from different conditions. No major change of the profile was observed after six months except in two cases. When handprints on glass plates were compared, 11 of 12 individuals were assigned to a few clusters including the cluster corresponding to the correct individual. In conclusion, a method for reproducible T-RFLP profiling of bacteria from trace amounts of handprints was established. The profiles were obtained for particular individuals clustered in PCA and were experimentally separable from other individuals in most cases. This technique could provide useful information for narrowing down a suspect in a criminal investigation.

  6. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Santos, M S; Souza, E S; S Junior, R M; Talhari, S; Souza, J V B

    2010-08-01

    Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas--FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods.

  7. [Species identification of grouper and snapper in Taiwan Strait using polymerase chain reaction-restriction fragment length polymorphism analysis and lab-on-a-chip system].

    Science.gov (United States)

    Chen, Shuangya; Zhang, Jin; Chen, Weiling; Xu, Dunming; Zhou, Yu

    2011-07-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and lab-on-a-chip system were used to identify grouper and snapper species in Taiwan Strait. A fragment of 464 bp length of mitochondrial cytochrome b gene was amplified by PCR and the products were digested with restriction enzymes Dde I , Hae III and NLa III, individually. The fragments generated after digestion were further resolved on the DNA Chip. Eight grouper species and five snapper species were successfully identified. The results demonstrated that PCR-RFLP analysis and lab-on-a-chip system provide a fast, easy, automated, and reliable analysis approach. This approach is potential for the purpose of fish adulteration control.

  8. Restriction fragment length polymorphism of two HLA-B-associated transcripts genes in five autoimmune diseases

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P;

    1991-01-01

    The restriction fragment length polymorphism of the two human HLA-B-associated transcripts (BATs) genes, BAT1 and BAT2, identifying polymorphic bands of 12, 8, 2.5, and 1.1 kb, and at 3.3, 2.7, 2.3, and 0.9 kb, respectively, was investigated in patients with primary biliary cirrhosis (PBC), syste...

  9. RECONSTRUCTION OF TOTAL LENGTH OF FEMUR FROM ITS PROXIMAL AND DISTAL FRAGMENTS

    Directory of Open Access Journals (Sweden)

    Ajay M. Parmar

    2015-12-01

    Full Text Available Aims and Objectives: To find out the correlation between maximum length of femur and its proximal & distal fragments. and to formulate regression equation for estimation of stature from maximum femoral length. Materials and methods: This study consists 50 femur (27 of right side & 23 of left side. The maximum length of femur, proximal (P1,P2,P3,P4 and distal (D1,D2,D3,D4 measurements was taken with help of osteometric board and by vernier calliper. Results: The correlation found in P1,P2,P3,P4, D1,D4 on right side femur and P2, P3, P4, D1, D4 on left side femur. The strongest correlation observed in the D4 on right femur and P2 of left femur. The result obtained were analysed and derived regression equation between maximum femoral length and its proximal and distal fragments. Conclusion: The positive correlation between maximum femoral length and its proximal and distal fragments and regression equations derived in this study helpful to estimate stature in Medico-legal investigations and in Anthropometry.

  10. Differentiation of Helicobacter pylori isolates by polymerase chain reaction-restriction fragment length polymorphism

    Institute of Scientific and Technical Information of China (English)

    SHI Li; SUN Yong; ZHANG Ya-li; ZHANG Zhen-shu; ZHOU Dian-yuan

    2002-01-01

    Objective: To investigate the association between the diversity of urease gene and urease activity of clinical isolates of Helicobacter pylori (H. pylori). Methods: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of urease gene and rapid urease activity test were used to study the urease activity of different clinical isolates of H. pylori. Results: H. pylori clinical isolates were divided into 4types according to their PCR-RFLP results of urease gene and urease activity. Type I , possessing strong urease activity (0. 11) and presented 1 fragment of 1.7 kb by PCR-RFLP, had close relations with gastric ulcer; type Ⅱ , with the weakest urease activity (0. 07) and 2 fragments (1.3 and 0. 4 kb respectively), was associated with duodenal bulb ulcer; type Ⅱ , with the strongest urease activity (0. 12) and 2 fragments (0. 4and 0. 17 kb) with or without 1 fragment (0. 23 or 0. 37 kb) , was responsible for gastritis; type Ⅳ, with weak urease activity (0. 09) and 2 fragments (1.5 and 0. 2 kb), was shown to be related to both gastric and duodenal bulb ulcers. Conclusion: The diversity of urease gene decides different urease activities of different clinical isolates of H. pylori, hence the different possibilities of pathogenesis due to this bacteria.

  11. Molecular differentiation of Angiostrongylus costaricensis, A. cantonensis, and A. vasorum by polymerase chain reaction- restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2003-01-01

    Full Text Available Angiostrongylus cantonensis, A. costaricensis, and A. vasorum are etiologic agents of human parasitic diseases. Their identification, at present, is only possible by examining the adult worm after a 40-day period following infection of vertebrate hosts with the third-stage larvae. In order to obtain a diagnostic tool to differentiate larvae and adult worm from the three referred species, polymerase chain reaction-restriction fragment length polymorphism was carried out. The rDNA second internal transcribed spacer (ITS2 and mtDNA cytochrome oxidase I regions were amplified, followed by digestion of fragments with the restriction enzymes RsaI, HapII, AluI, HaeIII, DdeI and ClaI. The enzymes RsaI and ClaI exhibited the most discriminating profiles for the differentiation of the regions COI of mtDNA and ITS2 of rDNA respectively. The methodology using such regions proved to be efficient for the specific differentiation of the three species of Angiostrongylus under study.

  12. Evidence of a normal mean telomere fragment length in patients with Ullrich-Turner syndrome

    DEFF Research Database (Denmark)

    Kveiborg, Marie; Gravholt, Claus Højbjerg; Kassem, M

    2001-01-01

    Clinical and epidemiological studies suggest that premature ageing and increased morbidity and mortality is present in Ullrich-Turner syndrome. We studied telomere restriction fragment length (TRFL) in 30 women with Ullrich-Turner syndrome and 30 age-matched control women. All Turner women had...... with excessive telomere loss, at least when studied in peripheral blood leucocytes, and thus quite different from other premature ageing syndromes....

  13. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-06-03

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

  14. Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Xian; Wen-Ming Cong; Shu-Hui Zhang; Meng-Chao Wu

    2005-01-01

    AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments.METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD)with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated,purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data.RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size,histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene.CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcinogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis.

  15. Amplified Fragment Length Polymorphism (AFLP) data obtained for 34 Microtus longicaudus individuals at 91 loci

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Prior to removal of pest species from an area, resource managers must determine if re-immigration from another population is possible. Voles inhabiting Saddle Rock...

  16. Genomic diversity among Danish field strains of Mycoplasma hyosynoviae assessed by amplified fragment length polymorphism analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, Niels F.; Nielsen, Elisabeth O.;

    2002-01-01

    ) were concurrently examined for variance in BglII-MfeI and EcoRI-Csp6I-A AFLP markers. A total of 56 different genomic fingerprints having an overall similarity between 77 and 96% were detected. No correlation between AFLP variability and period of isolation or anatomical site of isolation could...

  17. Apophysomyces elegans: epidemiology, amplified fragment length polymorphism typing, and in vitro antifungal susceptibility pattern.

    NARCIS (Netherlands)

    Chakrabarti, A.; Shivaprakash, M.R.; Curfs-Breuker, I.; Baghela, A.; Klaassen, C.H.; Meis, J.F.G.M.

    2010-01-01

    Apophysomyces elegans is an emerging pathogen in India. We planned the present study to analyze the clinical pattern of the disease, to perform molecular strain typing, and to determine the in vitro activities of eight antifungal drugs against A. elegans. A total of 16 clinical and two environmental

  18. Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Winton, J.; Lorenzen, Niels

    2005-01-01

    -gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes......The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt......) sequences of the VHSV glycoprotein (G) gene, were used to predict restriction fragment length polymorphism (RFLP) patterns that were subsequently grouped and compared with a phylogenetic analysis of the G-gene sequences of the same set of isolates. Digestion of PCR amplicons from the full-length G...

  19. Selection of enzymes for terminal restriction fragment length polymorphism analysis of fungal internally transcribed spacer sequences.

    Science.gov (United States)

    Alvarado, Pablo; Manjón, Jose L

    2009-07-01

    Terminal restriction fragment length polymorphism (TRFLP) profiling of the internally transcribed spacer (ITS) ribosomal DNA of unknown fungal communities is currently unsupported by a broad-range enzyme-choosing rationale. An in silico study of terminal fragment size distribution was therefore performed following virtual digestion (by use of a set of commercially available 135 type IIP restriction endonucleases) of all published fungal ITS sequences putatively annealing to primers ITS1 and ITS4. Different diversity measurements were used to rank primer-enzyme pairs according to the richness and evenness that they showed. Top-performing pairs were hierarchically clustered to test for data dependency. The enzyme set composed of MaeII, BfaI, and BstNI returned much better results than randomly chosen enzyme sets in computer simulations and is therefore recommended for in vitro TRFLP profiling of fungal ITSs.

  20. ESTIMATION OF STATURE FROM FRAGMENT OF FEMUR (POPLITEAL LENGTH IN BENGALEE POPULATION

    Directory of Open Access Journals (Sweden)

    Tapas Ghosh

    2015-09-01

    Full Text Available Introduction: Of the mathematical methods, regression equations have been successfully used for estimation of stature. Population specific formulae produce more accurate results. The present investigation was designed to estimate stature from fragment of femur obtained from a collection of Bengalee population of the state of West Bengal of India. Materials & Methods: The fragment of the femur (Popliteal length of femur was measured by a vertical length from the point where the distance between external borders of both linea aspera lips becomes 10 mm (it was considered as the lower end of linea aspera, where the two lips diverges below, to the ground where lower surfaces of both the condyles were in contact. Results: The following regression equation was obtained: Stature in feet = 0.127[20.1184 + 1.6890x]. (‘x’ stands for popliteal length of femur in centimeter. Discussion: This would help in identification of unknown skeletal remains, as estimation of stature is an important part in establishing the biological profile of skeletal remains.

  1. Genetic diversity among Puntius sophore complex using restriction fragment length polymorphism

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    Smitha Balaraj

    2012-08-01

    Full Text Available Restriction fragment length polymorphism (RFLP analysis of genomic DNA was employed to characterize species of Puntius sophore complex, a benthopelagic freshwater fish species. Samples of five species of Puntius viz, Puntius sophore, Puntius amphibius, Puntius chola, Puntius bimaculatus and Puntius dorsalis from the East-flowing Tamiraparani and Kuzhithurai and West-flowing Tamiraparani river basins (Western Ghats were analyzed. The restriction enzyme employed (Hind III generated species-specific DNA patterns for each of the five species. DNA exhibited considerable polymorphism among species. All samples showed relatively high values of diversity. The relation between species is discussed.

  2. Lactic acid bacterial population dynamics during fermentation and storage of Thai fermented sausage according to restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Wanangkarn, Amornrat; Liu, Deng-Cheng; Swetwiwathana, Adisorn; Jindaprasert, Aphacha; Phraephaisarn, Chirapiphat; Chumnqoen, Wanwisa; Tan, Fa-Jui

    2014-09-01

    This study applied restriction fragment length polymorphism (RFLP) analysis to identify the lactic acid bacteria (LAB) isolated from "mum" Thai fermented sausages during fermentation and storage. A total of 630 lactic acid bacteria were isolated from the sausages prepared using 2 methods. In Method 1, after stuffing, the sausages were stored at 30 °C for 14 days. In Method 2, after stuffing and storage at 30 °C for 3 days, the sausages were vacuum-packed and stored at 4 °C until Day 28. The sausages were sampled on Days 0, 3, 14, and 28 for analyses. The 16S rDNA was amplified and digested using restriction enzymes. Of the restriction enzymes evaluated, Dde I displayed the highest discrimination capacity. The LAB were classified and 7 species were identified For Methods 1 and 2, during fermentation, the Lactobacillus sakei and Lactobacillus plantarum species were dominant. For Method 2, the proportion of Leuconostoc mesenteroides markedly increased during storage, until L. sakei and Ln. mesenteroides represented the dominant species. The identification of LAB in the sausage samples could facilitate the selection of appropriate microorganisms for candidate starter cultures for future controlled mum production.

  3. Simple and rapid human papillomavirus genotyping method by restriction fragment length polymorphism analysis with two restriction enzymes.

    Science.gov (United States)

    Chen, Linghan; Watanabe, Ken; Haruyama, Takahiro; Kobayashi, Nobuyuki

    2013-07-01

    Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low-cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes HpyCH4V and NlaIII. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR-positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non-specific amplifications with PCR. In conclusion, this PCR-RFLP method using restriction enzymes HpyCH4V and NlaIII is simple, non-labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples.

  4. A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker for the identification of Amaranthus cruentus species.

    Science.gov (United States)

    Park, Young-Jun; Nishikawa, Tomotaro; Matsushima, Kenichi; Minami, Mineo; Nemoto, Kazuhiro

    2014-12-01

    A rapid and reliable PCR-restriction fragment length polymorphism (RFLP) marker was developed to identify the Amaranthus cruentus species by comparing sequences of the starch branching enzyme (SBE) locus among the three cultivated grain amaranths. We determined the partial SBE genomic sequence in 72 accessions collected from diverse locations around the world by direct sequence analysis. Then, we aligned the gene sequences and searched for restriction enzyme cleavage sites specific to each species for use in the PCR-RFLP analysis. The result indicated that MseI would recognize the sequence 5'-T/TAA-3' in intron 11 from A. cruentus SBE. A restriction analysis of the amplified 278-bp portion of the SBE gene using the MseI restriction enzyme resulted in species-specific RFLP patterns among A. cruentus, Amaranthus caudatus and Amaranthus hypochondriacus. Two different bands, 174-bp and 104-bp, were generated in A. cruentus, while A. caudatus and A. hypochondriacus remained undigested (278-bp). Thus, we propose that the PCR-RFLP analysis of the amaranth SBE gene provides a sensitive, rapid, simple and useful technique for identifying the A. cruentus species among the cultivated grain amaranths.

  5. Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria

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    Ding Tao

    2013-01-01

    Full Text Available Abstract Background Plant endophytic bacteria play an important role benefiting plant growth or being pathogenic to plants or organisms that consume those plants. Multiple species of bacteria have been found co-inhabiting plants, both cultivated and wild, with viruses and fungi. For these reasons, a general understanding of plant endophytic microbial communities and their diversity is necessary. A key issue is how the distributions of these bacteria vary with location, with plant species, with individual plants and with plant growing season. Results Five common plant species were collected monthly for four months in the summer of 2010, with replicates from four different sampling sites in the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. Metagenomic DNA was extracted from ground, washed plant leaf samples, and fragments of the bacterial 16S rDNA genes were amplified for analysis of terminal restriction fragment length polymorphism (T-RFLP. We performed mono-digestion T-RFLP with restriction endonuclease DdeI, to reveal the structures of leaf endophytic bacterial communities, to identify the differences between plant-associated bacterial communities in different plant species or environments, and to explore factors affecting the bacterial distribution. We tested the impacts of three major factors on the leaf endophytic bacterial communities, including host plant species, sampling dates and sampling locations. Conclusions Results indicated that all of the three factors were significantly related (α = 0.05 to the distribution of leaf endophytic bacteria, with host species being the most important, followed by sampling dates and sampling locations.

  6. Directly transforming PCR-amplified DNA fragments into plant cells is a versatile system that facilitates the transient expression assay.

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    Yuming Lu

    Full Text Available A circular plasmid containing a gene coding sequence has been broadly used for studying gene regulation in cells. However, to accommodate a quick screen plasmid construction and preparation can be time consuming. Here we report a PCR amplified dsDNA fragments (PCR-fragments based transient expression system (PCR-TES for suiting in the study of gene regulation in plant cells. Instead of transforming plasmids into plant cells, transient expression of PCR-fragments can be applicable. The transformation efficiency and expression property of PCR-fragments are comparable to transformation using plasmids. We analyzed the transformation efficiency in PCR-TES at transcription and protein levels. Our results indicate that the PCR-TES is as versatile as the conventional transformation system using plasmid DNA. Through reconstituting PYR1-mediated ABA signaling pathway in Arabidopsis mesophyll protoplasts, we were not only validating the practicality of PCR-TES but also screening potential candidates of CDPK family members which might be involved in the ABA signaling. Moreover, we determined that phosphorylation of ABF2 by CPK4 could be mediated by ABA-induced PYR1 and ABI1, demonstrating a crucial role of CDPKs in the ABA signaling. In summary, PCR-TES can be applicable to facilitate analyzing gene regulation and for the screen of putative regulatory molecules at the high throughput level in plant cells.

  7. Device Length Dependency of Cross Gain Modulation and Cross Phase Modulation in Semiconductor Optical Amplifier

    Institute of Scientific and Technical Information of China (English)

    Tomonori; Yazaki; Ryo; Inohara; Kosuke; Nishimura; Munefumi; Tsurusawa; Masashi; Usami

    2003-01-01

    The cross gain modulation, the cross phase modulation and their recovery time in the SOAs with the various lengths were experimentally investigated. It was found that these values strongly depended on the device length.

  8. Investigating of yeast species in wine fermentation using terminal restriction fragment length polymorphism method.

    Science.gov (United States)

    Sun, Yue; Liu, Yanlin

    2014-04-01

    The objective of this study was to examine the potential of terminal restriction fragment length polymorphism (T-RFLP) in monitoring yeast communities during wine fermentation and to reveal new information on yeast community of Chinese enology. Firstly, terminal restriction fragment (TRF) lengths database was constructed using 32 pure yeast species. Ten of these species were firstly documented. The species except for Candida vini, Issatchenkia orientalis/Candida krusei, Saccharomyces bayanus, Saccharomyces pastorianus, Saccharomyces cerevisiae, Saccharomyces kudriarzevii and Zygosaccharomyces bisporus could be distinguished by the T-RFLP targeting 5.8S-ITS rDNA. Moreover, the yeast communities in spontaneous fermentation of Chardonnay and Riesling were identified by T-RFLP and traditional methods, including colony morphology on Wallerstein Nutrient (WLN) medium and 5.8S-ITS-RFLP analysis. The result showed that T-RFLP profiles of the yeast community correlated well with that of the results identified by the traditional methods. The TRFs with the highest intensity and present in all the samples corresponded to Saccharomyces sp. Other species detected by both approaches were Hanseniaspora uvarum, Metschnikowia pulcherrima, Pichia minuta var. minuta, Saccharomycodes ludwigii/Torulaspora delbrueckii and Candida zemplinina. This study revealed that T-RFLP technique is a rapid and useful tool for monitoring the composition of yeast species during wine fermentation.

  9. Restriction fragment length polymorphism of adhesin gene hpaA from different Helicobacter pylori strains of Chongqing, China

    Institute of Scientific and Technical Information of China (English)

    Yu Hong; Xu-Hu Mao; Wei-Kun Zeng; Li-Ming Ma; Shen-Rong Jing; Quan-Ming Zou

    2005-01-01

    AIM: To assess the variability of adhesin gene hpaA between different Helicobacter pylori ( H pylori) strains with PCR-restriction fragment length polymorphism (RFLP). METHODS: Twelve different H pylori strains were chosento amplify the 710-bp segments of gene hpaA. These strains were NCTC11637, SS1; Chongqing clinical isolates CCS9801, CCS9802, CCS9803, CCS9806, CCS9809,CCS9810, CCS9813, which were gained from patients of gastritis; Mongolia gerbil adapted H pylori strains (abbreviation MG), which were gained from the following steps: gastric mucosal specimens of Mongolia gerbils infected by clinical isolate CCS9803 were cultured and detected, the positive H pylori strains were named as the first generation of Mongolia gerbil adapted H pylori strains(abbreviation MG1) and then were subcultured with healthy Mongolia gerbil to generate MG2, in turn to gain the ninth generation (abbreviation MG9). All hpaA segments, obtained from 12 different H pylori strains,were digested by HhaⅠ and HaeⅢ individually and analyzed by agarose gel electrophoresis. RESULTS: In all 12 strains, the 710-bp PCR products were successfully amplified and products were cloned to pMD18T vector respectively, then the recombinant plasmids were digested simultaneously with NcoⅠ and XhoⅠ to recover the small fragments. The objective fragments from 12 different H pylori strains digested with Hae Ⅲ could be seen as 4 types of bands and 5 types with Hha Ⅰ. According to the hpaA RFLP patterns, the 12 H pylori strains could be divided into 5 groups: group Ⅰ, NCTC11637 and SS1; group Ⅱ, CCS9809, which RFLP type digested with HaeⅢ wasthe same as strains of group Ⅰ, but HhaⅠ RFLP showeddifference compared with the other groups; group Ⅲ,CCS9810; group Ⅳ, CCS9803; group Ⅴ: CCS9801,CCS9802, CCS9806, CCS9813, MG1, MG3 and MG9. The sequence data of 12 hpaA segments were analyzed by DNAsis software and it was observed that: (1) The homologies of base pair and amino acid sequence

  10. Polymerase chain reaction-restriction fragment length polymorphism assays to distinguish Liriomyza huidobrensis (Diptera: Agromyzidae) from associated species on lettuce cropping systems in Italy.

    Science.gov (United States)

    Masetti, Antonio; Luchetti, Andrea; Mantovani, Barbara; Burgio, Giovanni

    2006-08-01

    The pea leafminer, Liriomyza huidobrensis (Blanchard) (Diptera: Agromyzidae), is a serious insect pest infesting open field lettuce plantings in northern Italy. In these cropping systems, it coexists with several other agromyzid species that have negligible economic importance on open field vegetables. The rapid detection of L. huidobrensis is crucial for effective management strategies, but the identification of agromyzids to species can be very difficult at adult as well at immature stages. In this study, a polymerase chain reaction (PCR)-restriction fragment length polymorphism assay is proposed to separate L. huidobrensis from Liriomyza bryoniae (Kaltenbach), Liriomyza trifolii (Burgess), and Chromatomyia horticola (Goureau), which usually occur in the same lettuce plantings. An approximately 1,031-bp region of the mitochondrial genome encompassing the 3' region of cytochrome oxidase I, the whole leucine tRNA, and all of the cytochrome oxidase II was amplified by PCR and digested using the enzymes PvuII and SnaBI separately. Both endonucleases cut the amplicons of L. huidobrensis in two fragments, whereas the original band was not cleaved in the other analyzed species. The presence of Dacnusa spp. DNA does not bias the assay, because the PCR conditions and the primer set here described do not amplify any tract of this endoparasitic wasp genome.

  11. Rapid detection of clarithromycin resistant Helicobacter pylori strains in Spanish patients by polymerase chain reaction-restriction fragment length polymorphism

    Science.gov (United States)

    Agudo, Sonia; Pérez-Pérez, Guillermo; Alarcón, Teresa; López-Brea, Manuel

    2014-01-01

    Introduction The aim of this study was to characterize the mutations types present in the 23S rRNA gene related to H. pylori clarithromycin-resistance strains in Spain and evaluate a novel PCR-RFLP method for detection of the most frequent point mutation in our population. Methods Gastric biopsies were obtained by endoscopy from patients with gastric symptoms. H. pylori was cultured according to standard microbiological procedures and clarithromycin resistance was determined by E-test. DNA extraction was performed by NucliSens platform with the NucliSens magnetic extraction reagents (bioMérieux) according to the manufacturer instructions. Analyses for point mutations in 23S rRNA gene strains were performed by sequence analysis of amplified polymerase chain reaction products. Restriction fragment length polymorphism was performed using BsaI enzyme to detect restriction sites that correspond to the mutation (A2143G). Result We found 42 out of 118 (35.6%) strains resistant to clarithromycin by E-test. E-test results were confirmed for the presence of point mutation in 34 (88.1%) of these strains. Mutation A2143G was found in 85.3% of the strains. Analyses with the restriction enzyme BsaI was able to confirm the presence of A2143G mutation. There were 8 H. pylori strains resistant to clarithromycin by E-test but without any point mutation in the 23 rRNA gene. Conclusion We conclude that PCR-RFLP is a reliable method to detect clarithromycin-resistance H. pylori strains in countries with a high prevalence of clarithromycin-resistance as Spain It may be useful before choosing regimens of H. pylori eradication. PMID:21412667

  12. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP for rapid diagnosis of neonatal sepsis

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    Anusha Rohit

    2016-01-01

    Full Text Available Background & objectives: The difficulties in diagnosis of neonatal sepsis are due to varied clinical presentation, low sensitivity of blood culture which is considered the gold standard and empirical antibiotic usage affecting the outcome of results. Though polymerase chain reaction (PCR based detection of bacterial 16S rRNA gene has been reported earlier, this does not provide identification of the causative agent. In this study, we used restriction fragment length polymorphism (RFLP of amplified 16S rRNA gene to identify the organisms involved in neonatal sepsis and compared the findings with blood culture. Methods: Blood samples from 97 neonates were evaluated for diagnosis of neonatal sepsis using BacT/Alert (automated blood culture and PCR-RFLP. Results: Bacterial DNA was detected by 16S rRNA gene PCR in 55 cases, while BacT/Alert culture was positive in 34 cases. Staphylococcus aureus was the most common organism detected with both methods. Klebsiella spp. was isolated from four samples by culture but was detected by PCR-RFLP in five cases while Acinetobacter spp. was isolated from one case but detected in eight cases by PCR-RFLP. The sensitivity of PCR was found to be 82.3 per cent with a negative predictive value of 85.7 per cent. Eighty of the 97 neonates had prior exposure to antibiotics. Interpretation & conclusions:The results of our study demonstrate that PCR-RFLP having a rapid turnaround time may be useful for the early diagnosis of culture negative neonatal sepsis.

  13. Intestinal microbiota is different in women with preterm birth: results from terminal restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Shiozaki, Arihiro; Yoneda, Satoshi; Yoneda, Noriko; Yonezawa, Rika; Matsubayashi, Takamichi; Seo, Genichiro; Saito, Shigeru

    2014-01-01

    Preterm birth is a leading cause of perinatal morbidity and mortality. Studies using a cultivation method or molecular identification have shown that bacterial vaginosis is one of the risk factors for preterm birth. However, an association between preterm birth and intestinal microbiota has not been reported using molecular techniques, although the vaginal microbiota changes during pregnancy. Our aim here was to clarify the difference in intestinal and vaginal microbiota between women with preterm birth and women without preterm labor. 16S ribosomal ribonucleic acid genes were amplified from fecal and vaginal DNA by polymerase chain reaction. Using terminal restriction fragment length polymorphism (T-RFLP), we compared the levels of operational taxonomic units of both intestinal and vaginal flora among three groups: pregnant women who delivered term babies without preterm labor (non-PTL group) (n = 20), those who had preterm labor but delivered term babies (PTL group) (n = 11), and those who had preterm birth (PTB group) (n = 10). Significantly low levels of Clostridium subcluster XVIII, Clostridium cluster IV, Clostridium subcluster XIVa, and Bacteroides, and a significantly high level of Lactobacillales were observed in the intestinal microbiota in the PTB group compared with those in the non-PTL group. The levels of Clostridium subcluster XVIII and Clostridium subcluster XIVa in the PTB group were significantly lower than those in the PTL group, and these levels in the PTL group were significantly lower than those in non-PTL group. However, there were no significant differences in vaginal microbiota among the three groups. Intestinal microbiota in the PTB group was found to differ from that in the non-PTL group using the T-RFLP method.

  14. Use of restriction fragment length polymorphisms to investigate strain variation within Neisseria meningitidis

    Energy Technology Data Exchange (ETDEWEB)

    Williams, S.D.

    1989-01-01

    Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty-six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P{sup 32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analyzed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population.

  15. A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method.

    Science.gov (United States)

    Kim, Diane Y; Countway, Peter D; Yamashita, Warren; Caron, David A

    2012-12-01

    Microbial eukaryotes in seawater samples collected from two depths (5 m and 500 m) at the USC Microbial Observatory off the coast of Southern California, USA, were characterized by cloning and sequencing of 18S rRNA genes, as well as DNA fragment analysis of these genes. The sequenced genes were assigned to operational taxonomic units (OTUs), and taxonomic information for the sequence-based OTUs was obtained by comparison to public sequence databases. The sequences were then subjected to in silico digestion to predict fragment sizes, and that information was compared to the results of the T-RFLP method applied to the same samples in order to provide taxonomic context for the environmental T-RFLP fragments. A total of 663 and 678 sequences were analyzed for the 5m and 500 m samples, respectively, which clustered into 157 OTUs and 183 OTUs. The sequences yielded substantially fewer taxonomic units as in silico fragment lengths (i.e., following in silico digestion), and the environmental T-RFLP resulted in the fewest unique OTUs (unique fragments). Bray-Curtis similarity analysis of protistan assemblages was greater using the T-RFLP dataset compared to the sequence-based OTU dataset, presumably due to the inability of the fragment method to differentiate some taxa and an inability to detect many rare taxa relative to the sequence-based approach. Nonetheless, fragments in our analysis generally represented the dominant sequence-based OTUs and putative identifications could be assigned to a majority of the fragments in the environmental T-RFLP results. Our empirical examination of the T-RFLP method identified limitations relative to sequence-based community analysis, but the relative ease and low cost of fragment analysis make this method a useful approach for characterizing the dominant taxa within complex assemblages of microbial eukaryotes in large datasets.

  16. Identification of Pork Contamination in Meatballs of Indonesia Local Market Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis.

    Science.gov (United States)

    Erwanto, Yuny; Abidin, Mohammad Zainal; Sugiyono, Eko Yasin Prasetyo Muslim; Rohman, Abdul

    2014-10-01

    This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

  17. Mycobacterium tuberculosis complex differentiation using gyrB-restriction fragment length polymorphism analysis

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    Erica Chimara

    2004-11-01

    Full Text Available Mycobacterium tuberculosis complex (MTBC members are causative agents of human and animal tuberculosis. Differentiation of MTBC members is required for appropriate treatment of individual patients and for epidemiological purposes. Strains from six MTBC species - M. tuberculosis, M. bovis subsp. bovis, M. bovis BCG, M. africanum, M. pinnipedii, and "M. canetti" - were studied using gyrB-restriction fragment length polymorphism (gyrB-RFLP analysis. A table was elaborated, based on observed restriction patterns and published gyrB sequences. To evaluate applicability of gyrB-RFLP at Instituto Adolfo Lutz, São Paulo, Mycobacterial Reference Laboratory, 311 MTBC clinical isolates, previously identified using traditional methods as M. tuberculosis (306, M. bovis (3, and M. bovis BCG (2, were analyzed by gyrB-RFLP. All isolates were correctly identified by the molecular method, but no distinction between M. bovis and M. bovis BCG was obtained. Differentiation of M. tuberculosis and M. bovis is of utmost importance, because they require different treatment schedules. In conclusion, gyrB-RFLP is accurate and easy-to-perform, with potential to reduce time needed for conventional differentiation methods. However, application for epidemiological studies remains limited, because it cannot differentiate M. tuberculosis from M. africanum subtype II, and "M. canetti", M. africanum subtype I from M. pinnipedii, and. M. bovis from M. bovis BCG.

  18. Generation of a Restriction Fragment Length Polymorphism Linkage Map for Toxoplasma Gondii

    Science.gov (United States)

    Sibley, L. D.; LeBlanc, A. J.; Pfefferkorn, E. R.; Boothroyd, J. C.

    1992-01-01

    We have constructed a genetic linkage map for the parasitic protozoan, Toxoplasma gondii, using randomly selected low copy number DNA markers that define restriction fragment length polymorphisms (RFLPs). The inheritance patterns of 64 RFLP markers and two phenotypic markers were analyzed among 19 recombinant haploid progeny selected from two parallel genetic crosses between PLK and CEP strains. In these first successful interstrain crosses, these RFLP markers segregated into 11 distinct genetic linkage groups that showed close correlation with physical linkage groups previously defined by molecular karyotype. Separate linkage maps, constructed for each of the 11 chromosomes, indicated recombination frequencies range from approximately 100 to 300 kb per centimorgan. Preliminary linkage assignments were made for the loci regulating sinefungin resistance (snf-1) on chromosome IX and adenine arabinoside (ara-1) on chromosome V by linkage to RFLP markers. Despite random segregation of separate chromosomes, the majority of chromosomes failed to demonstrate internal recombination events and in 3/19 recombinant progeny no intramolecular recombination events were detected. The relatively low rate of intrachromosomal recombination predicts that tight linkage for unknown genes can be established with a relatively small set of markers. This genetic linkage map should prove useful in mapping genes that regulate drug resistance and other biological phenotypes in this important opportunistic pathogen. PMID:1360931

  19. Differentiation of Candida glabrata, C. nivariensis and C. bracarensis based on fragment length polymorphism of ITS1 and ITS2 and restriction fragment length polymorphism of ITS and D1/D2 regions in rDNA

    DEFF Research Database (Denmark)

    Mirhendi, H; Bruun, B; Schønheyder, H C

    2011-01-01

    Different molecular methods for the discrimination of Candida glabrata, C. bracarensis and C. nivariensis were evaluated and the prevalence of these species among Danish blood isolates investigated. Control strains were used to determine fragment length polymorphism in the ITS1, ITS2, ITS1-5.8S...

  20. Polymerase chain reaction-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment for authentication of four clam species.

    Science.gov (United States)

    Fernandez, Alicia; García, Teresa; Gonzalez, Isabel; Asensio, Luis; Rodriguez, Miguel Angel; Hernández, Pablo E; Martin, Rosario

    2002-04-01

    Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction-restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose gel electrophoresis when amplicons were digested with endonucleases BsmAI and BsrI allowed unequivocal identification of the four clam species. This approach would be less costly, simpler, and quicker than conventional sequencing of polymerase chain reaction products followed by detailed comparison of individual sequences, especially when large numbers of samples need to be analyzed.

  1. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

    Science.gov (United States)

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  2. Expression of tumor related gene NAG6 in gastric cancer and restriction fragment length polymorphism analysis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Mei Zhang; Shou-Rong Sheng; Xiao-Yan Wang; Liang-Hua Bin; Jie-Ru Wang; Gui-Yuan Li

    2004-01-01

    AIM: NAG6 gene is a novel tumor related gene identified recently. This study was designed to examine the expression of this gene in gastric cancer and corresponding normal tissues, and to investigate its role in the occurrence and development of gastric cancer, also to study if the genetic structure of NAG6 was altered in gastric cancer.METHODS: Reverse transcription-polymerase chain reaction (RT-PCR), Northern blot analysis and dot hybridization were used to compare the expression level of NAG6 gene in 42cases of gastric cancer tissues with their corresponding normal tissues of the same patients respectively. In addition,restriction fragment length polymorphism (RFLP) analysis was adopted to study if the genetic structure of NAG6 was altered in gastric carcinomas.RESULTS: The expression of NAG6 in 57.1% gastric cancer tissues (25/42) was absent by RT-PCR analysis. The downregulation rate of NAG6 in gastric cancer tissues was significantly higher than that in corresponding normal tissues (P<0.01). However no correlation between the downregulation of NAG6 and lymph-node and/or distance metastasis was found in this study (P>0.05). Dot hybridization confirmed the results of RT-PCR. Furthermore,the results of EcoRI RFLP analysis of NAG6 gene demonstrated that 3 of 7 cases of gastric cancer showed loss of 5 kb fragment in comparison with their corresponding normal tissues.CONCLUSION: NAG6 gene is significantly down regulated in gastric cancer. The loss of genetic materials may be the cause of down-regulation of NAG6 expression. This seems to suggest that NAG6 may represent a candidate of putative tumor suppressor gene at 7q31-32 loci associated with gastric carcinoma. The down-regulation of this gene may play a role in occurrence and development of this disease, however it may not be associated with lymph node and/or distance metastasis.

  3. MULTIPLE ENZYME RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS FOR HIGH RESOLUTION DISTINCTION OF PSEUDOMONAS (SENSU STRICTO) 16S RRNA GENES

    Science.gov (United States)

    Pseudomonas specific 16S rDNA PCR amplification and multiple enzyme restriction fragment length polymorphism (MERFLP) analysis using a single digestion mixture of Alu I, Hinf I, Rsa I, and Tru 9I distinguished 150 published sequences and reference strains of authentic Pseudomonas...

  4. Rapid detection of dihydropteroate polymorphism in AIDS-related Pneumocystis carinii pneumonia by restriction fragment length polymorphism

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Eugen-Olsen, Jesper; Lundgren, B

    2000-01-01

    are associated with failure of sulpha prophylaxis and increased mortality in HIV-1 positive patients with PCP, suggesting that DHPS mutations may cause sulpha resistance. To facilitate detection of DHPS mutations we developed a restriction fragment length polymorphism (RFLP) assay, detecting mutations at codon...

  5. Analysis of length distribution of short DNA fragments induced by 7Li ions using the random-breakage model

    Institute of Scientific and Technical Information of China (English)

    KONG Fuquan; ZHAO Kui; ZHAN Yong; CAO Tianguang; NI Meinan; SUI Li; CAI Minghui; ZHUO Yizhong

    2005-01-01

    Deoxyribonucleic acid (DNA) is an important bio-macromolecule. DNA double strand breaks (DSBs) are considered to be the most important initial damage responsible for all biological effects induced by ionizing radiation. In this paper the length distribution of DNA fragments induced by 7Li ionizing radiation is fitted with the random breakage model. In this model, the parameter u is the average number of DSBs on every DNA molecule induced by ionizing radiation. The fitting result shows that the random breakage model cannot describe the distribution of DNA fragments in lower doses, while the random breakage model is in better accordance with the experimental data in higher doses. It is shown that the length distribution of DNA fragments has random statistical feature in higher doses. In this situation, the random breakage model looks like a model without any parameter since the u has specific physical meaning and can directly be obtained from experimental data.

  6. Typing and clustering of Yersinia pseudotuberculosis isolates by restriction fragment length polymorphism analysis using insertion sequences.

    Science.gov (United States)

    Voskresenskaya, E; Savin, C; Leclercq, A; Tseneva, G; Carniel, E

    2014-06-01

    Yersinia pseudotuberculosis is an enteropathogen that has an animal reservoir and causes human infections, mostly in temperate and cold countries. Most of the methods previously used to subdivide Y. pseudotuberculosis were performed on small numbers of isolates from a specific geographical area. One aim of this study was to evaluate the typing efficiency of restriction fragment length polymorphism of insertion sequence hybridization patterns (IS-RFLP) compared to other typing methods, such as serotyping, ribotyping, and multilocus sequence typing (MLST), on the same set of 80 strains of Y. pseudotuberculosis of global origin. We found that IS100 was not adequate for IS-RFLP but that both IS285 and IS1541 efficiently subtyped Y. pseudotuberculosis. The discriminatory index (DI) of IS1541-RFLP (0.980) was superior to those of IS285-RFLP (0.939), ribotyping (0.944), MLST (0.861), and serotyping (0.857). The combination of the two IS (2IS-RFLP) further increased the DI to 0.998. Thus, IS-RFLP is a powerful tool for the molecular typing of Y. pseudotuberculosis and has the advantage of exhibiting well-resolved banding patterns that allow for a reliable comparison of strains of worldwide origin. The other aim of this study was to assess the clustering power of IS-RFLP. We found that 2IS-RFLP had a remarkable capacity to group strains with similar genotypic and phenotypic markers, thus identifying robust populations within Y. pseudotuberculosis. Our study thus demonstrates that 2IS- and even IS1541-RFLP alone might be valuable tools for the molecular typing of global isolates of Y. pseudotuberculosis and for the analysis of the population structure of this species.

  7. Restriction fragment length polymorphism of the HLA-DP subregion and correlations to HLA-DP phenotypes

    DEFF Research Database (Denmark)

    Hyldig-Nielsen, J J; Morling, Niels; Ødum, Niels;

    1987-01-01

    The restriction fragment length polymorphism (RFLP) of the class II HLA-DP subregion of the major histocompatibility complex (MHC) of humans has been unraveled by Southern blotting using DP alpha and DP beta probes in a study of 46 unrelated individuals with known HLA-DP types. Contrary to earlier...... preliminary findings with a limited number of enzymes, the RFLP appears to be quite extensive both with the DP beta (14 different DNA markers defined by individual fragments or clusters thereof) and the DP alpha (8 markers) probes, especially when enzymes recognizing only four base pairs were used. A few...

  8. Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays

    Directory of Open Access Journals (Sweden)

    Malloff Chad A

    2004-01-01

    Full Text Available Abstract Background The recent development of array based comparative genomic hybridization (CGH technology provides improved resolution for detection of genomic DNA copy number alterations. In array CGH, generating spotting solution is a multi-step process where bacterial artificial chromosome (BAC clones are converted to replenishable PCR amplified fragments pools (AFP for use as spotting solution in a microarray format on glass substrate. With completion of the human and mouse genome sequencing, large BAC clone sets providing complete genome coverage are available for construction of whole genome BAC arrays. Currently, Southern hybridization, fluorescent in-situ hybridization (FISH, and BAC end sequencing methods are commonly used to identify the initial BAC clone but not the end product used for spotting arrays. The AFP sequencing technique described in this study is a novel method designed to verify the identity of array spotting solution in a high throughput manner. Results We show here that Southern hybridization, FISH, and AFP sequencing can be used to verify the identity of final spotting solutions using less than 10% of the AFP product. Single pass AFP sequencing identified over half of the 960 AFPs analyzed. Moreover, using two vector primers approximately 90% of the AFP spotting solutions can be identified. Conclusions In this feasibility study we demonstrate that current methods for identifying initial BAC clones can be adapted to verify the identity of AFP spotting solutions used in printing arrays. Of these methods, AFP sequencing proves to be the most efficient for large scale identification of spotting solution in a high throughput manner.

  9. Characterization of Campylobacter jejuni and Campylobacter coli genotypes in poultry flocks by restriction fragment length polymorphism (RFLP) analysis.

    Science.gov (United States)

    Carreira, Ana Cláudia; Cunha, Mónica V

    2015-01-01

    We describe a simple, rapid, and discriminatory methodology that allows the routine molecular characterization of Campylobacter jejuni and Campylobacter coli isolates. The proposed approach is built on one of the earliest and simplest molecular typing methods ever, consisting on the analysis of the fragments of different lengths generated by digestion of homologous DNA sequences with specific restriction endonucleases, a process known as restriction fragment length polymorphism (RFLP) analysis. The strategy underneath the workflow reported here is meant to explore the polymorphisms of Campylobacter spp. flaA gene (flaA-RFLP) that allows the local investigation of the genetic diversity and distribution of C. coli and C. jejuni isolates from different sources, namely, chickens' caeca. Although not appropriate for global and long-term epidemiological studies as a single approach, flaA-RFLP analysis can be very useful in surveys limited in space and time and, for specific epidemiological settings, an alternative to more modern and resource-demanding techniques.

  10. Chemoattractive capacity of different lengths of nerve fragments bridging regeneration chambers for the repair of sciatic nerve defects

    Institute of Scientific and Technical Information of China (English)

    Jiren Zhang; Yubo Wang; Jincheng Zhang

    2012-01-01

    A preliminary study by our research group showed that 6-mm-long regeneration chamber bridging is equivalent to autologous nerve transplantation for the repair of 12-mm nerve defects.In this study,we compared the efficacy of different lengths (6,8,10 mm) of nerve fragments bridging 6-mm regeneration chambers for the repair of 12-mm-long nerve defects.At 16 weeks after the regeneration chamber was implanted,the number,diameter and myelin sheath thickness of the regenerated nerve fibers,as well as the conduction velocity of the sciatic nerve and gastrocnemius muscle wet weight ratio,were similar to that observed with autologous nerve transplantation.Our results demonstrate that 6-,8-and 10-mm-long nerve fragments bridging 6-mm regeneration chambers effectively repair 12-mm-long nerve defects.Because the chemoattractive capacity is not affected by the length of the nerve fragment,we suggest adopting 6-mm-long nerve fragments for the repair of peripheral nerve defects.

  11. Typing of Human Mycobacterium avium Isolates in Italy by IS1245-Based Restriction Fragment Length Polymorphism Analysis

    Science.gov (United States)

    Lari, Nicoletta; Cavallini, Michela; Rindi, Laura; Iona, Elisabetta; Fattorini, Lanfranco; Garzelli, Carlo

    1998-01-01

    All but 2 of 63 Mycobacterium avium isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS1245 restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS1245 patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS1245 RFLP pattern. PMID:9817900

  12. Processing of Phonemic Consonant Length: Semantic and Fragment Priming Evidence from Bengali.

    Science.gov (United States)

    Kotzor, Sandra; Wetterlin, Allison; Roberts, Adam C; Lahiri, Aditi

    2016-03-01

    Six cross-modal lexical decision tasks with priming probed listeners' processing of the geminate-singleton contrast in Bengali, where duration alone leads to phonemic contrast ([pata] 'leaf' vs. [pat:a] 'whereabouts'), in order to investigate the phonological representation of consonantal duration in the lexicon. Four form-priming experiments (auditory fragment primes and visual targets) were designed to investigate listeners' sensitivity to segments of conflicting duration. Each prime derived from a real word ([k(h)[symbol: see text]m]/[g(h)en:]) was matched with a mispronunciation of the opposite duration (*[k(h)[symbol: see text]m:]/*[g(h)en]) and both were used to prime the full words [k(h)[symbol: see text]ma] ('forgiveness') and [g(h)en:a] ('disgust') respectively. Although all fragments led to priming, the results showed an asymmetric pattern. The fragments of words with singletons mispronounced as geminates led to equal priming, while those with geminates mispronounced as singletons showed a difference. The priming effect of the real-word geminate fragment was significantly greater than that of its corresponding nonword singleton fragment. In two subsequent semantic priming tasks with full-word primes a stronger asymmetry was found: nonword geminates (*[k(h)[symbol: see text]m:a]) primed semantically related words ([marjona] 'forgiveness') but singleton nonword primes (*[ghena]) did not show priming. This overall asymmetry in the tolerance of geminate nonwords in place of singleton words is attributed to a representational mismatch and points towards a moraic representation of duration. While geminates require a mora which cannot be derived from singleton input, the additional information in geminate nonwords does not create a similar mismatch.

  13. Use of restriction fragment length polymorphism to identify Candida species, related to onychomycosis

    Science.gov (United States)

    Mohammadi, Rasoul; Badiee, Parisa; Badali, Hamid; Abastabar, Mahdi; Safa, Ahmad Hosseini; Hadipour, Mahboubeh; Yazdani, Hajar; Heshmat, Farnaz

    2015-01-01

    Background: Onychomycosis is one of the most common clinical forms of fungal infections due to both filamentous fungi and yeasts. The genus of Candida is one of the most prominent causes of onychomycosis in all around the world. Although Candida albicans is still the most frequent cause of nail infections, use of broad-spectrum antifungal agents has led to a shift in the etiology of C. albicans to non-albicans species. The aim of the present study is rapid and precise identification of candida species isolated from nail infection by using of PCR-RFLP technique. Materials and Methods: A total of 360 clinical yeast strains were collected from nail infections in Iran. Genomic DNA was extracted using FTA; cards. ITS1-5.8SrDNA-ITS2 region was amplified using universal primers and subsequently products were digested with the restriction enzyme MspI. For identification of newly described species (C. parapsilosis complex), the SADH gene was amplified, followed by digestion with Nla III restriction enzyme. Results: Candida albicans was the most commonly isolated species (41.1%), followed by C. parapsilosis (21.4%), C. tropicalis (12.8%), C. kefyr (9.4%), C. krusei (5.5%), C. orthopsilosis (4.1%), C. glabrata (2.8%), C. guilliermondii (1.4%), C. rugosa (0.8%), and C. lusitaniae (0.5%). Patients in the age groups of 51-60 and 81-90 years had the highest and lowest distribution of positive specimens, respectively. Conclusion: Rapid and precise identification of Candida species from clinical specimens lead to appropriate therapeutic plans. PMID:26015921

  14. Rapid detection of dihydropteroate polymorphism in AIDS-related Pneumocystis carinii pneumonia by restriction fragment length polymorphism

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Eugen-Olsen, J; Lundgren, B

    2000-01-01

    Sulpha agents, which act by inhibiting the enzyme dihydropteroate synthase (DHPS), are used widely for the treatment and prophylaxis of Pneumocystis carinii pneumonia (PCP). Recently, we have shown that mutations in the dihydropteroate synthase (DHPS) gene of Pneumocystis carinii f.sp hominis...... are associated with failure of sulpha prophylaxis and increased mortality in HIV-1 positive patients with PCP, suggesting that DHPS mutations may cause sulpha resistance. To facilitate detection of DHPS mutations we developed a restriction fragment length polymorphism (RFLP) assay, detecting mutations at codon...

  15. Restriction fragment length polymorphism analysis of rotavirus VP7-encoding gene from humans and animals of Northeast India: a relative study of Indian and global isolates.

    Science.gov (United States)

    Chakraborty, P; Barman, N N; Sharma, I

    2015-09-01

    A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic relationship between 67 (29 Indian, 38 global) rotavirus isolates of human, bovine and porcine neonates. The assay involved direct digestion of RT-PCR amplified VP7 cDNAs with three restriction enzymes (VspI, HaeIII, NlaIV) independently. Forty-eight RFLP patterns were identified for all 67 strains, and of these 20 patterns were associated with Indian isolates. A correlation between the restriction patterns and G type was apparent through deduction of enzyme restriction sites from known sequences. Major G serotypes (G1, G2, G6, G8) with a few mixed types could be differentiated where there was a positive assortment of intrinsic serotypes from multiple host origin, and certain single or combined enzyme profiles were highly dominant in the population. Significant genetic variations were established between global and Indian isolates and none of the RFLP patterns were shared between them. These data suggest that the Indian wild-type rotavirus population is distinguishable based on the VP7 gene, and co-circulation of distinct strains in different hosts is foremost, indicating the possible likelihood of inter-species transmission.

  16. Analysis of the bacterial diversity existing on animal hide and wool: development of a preliminary PCR-restriction fragment length polymorphism fingerprint database for identifying isolates.

    Science.gov (United States)

    Chen, Yu; Gao, Hongwei; Zhang, Yanming; Deng, Mingjun; Wu, Zhenxing; Zhu, Laihua; Duan, Qing; Xu, Biao; Liang, Chengzhu; Yue, Zhiqin; Xiao, Xizhi

    2012-01-01

    Twenty-one bacterial strains were isolated from imported cattle hide and rabbit wool using two types of media, nutrient broth, and nutrient broth with serum. The bacteria identified were Brevibacillus laterosporus, Leclercia adecarboxylata, Peptococcus niger, Bacillus circulans, Raoultella ornithinolytica, Bacillus subtilis, Bacillus cereus, Bacillus thermobacillus, Bacillus choshinensis, Bacillus sphaericus, Acinetobacter haemolyticus, Sphingomonas paucimobilis, Bacillus thuringiensis, Staphylococcus intermedius, Mycobacteria, Moraxella, Klebsiella pneumoniae, Ralstonia pickettii, Staphylococcus chromogenes, Comamonas testosteroni, and Cupriavidus pauculus. The 16s rDNA gene of each bacterium was amplified using the universal primers 27f and 1492r. The amplicons were digested with AvaI, BamHI, BgII, DraI, EcoRI, EcoRV, HindIII, HinfI, HpaI, PstI, SmaI, TaqII, XbaI, XmaI, AluI, XhoI, and PvuI individually. A specific fingerprint from the PCR-restriction fragment length polymorphism method based on 16s rDNA was obtained for each bacterium. The results showed that the method developed was useful not only for bacterial identification but also for the etiological investigation of pathogens in imported animal hair and wool.

  17. Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism.

    Science.gov (United States)

    Fortuna, Ann-Marie; Marsh, Terence L; Honeycutt, C Wayne; Halteman, William A

    2011-08-01

    Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments' relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.

  18. Use of amplified fragment length polymorphism analysis to identify medically important Candida spp., including C-dubliniensis

    NARCIS (Netherlands)

    Borst, A; Theelen, B; Reinders, E; Boekhout, T; Fluit, AC; Savelkoul, PHM

    2003-01-01

    Non-Candida albicans Candida species are increasingly being isolated. These species show differences in levels of resistance to antimycotic agents and mortality. Therefore, it is important to be able to correctly identify the causative organism to the species level. Identification of C. dubliniensis

  19. Exploration of amplified fragment length polymorphism analysis as an effective tool for discriminating pathogenic strains of bacteria

    OpenAIRE

    Allen, Robert; Weinbrecht,; Taylor,, Patrick A.; Beaumann,

    2012-01-01

    K Weinbrecht,1 A Taylor,2 C Beaumann,3 RW Allen11Department of Forensic Sciences, Center for Health Sciences, Oklahoma State University, Tulsa, OK; 2Centers for Disease Control, Atlanta, GA; 3PharmaNet-i3, Indianapolis, IN, USABackground: The detrimental effect pathogens used as bioweapons could have on the US is sufficient to warrant extensive efforts to establish preparedness to prevent, and, if necessary, respond to such an event. The objective of this research was to adapt and refine ampl...

  20. Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, Mia; Skov, Marianne N.; Sandvang, Dorthe

    2005-01-01

    Molecular typing is an important tool in surveillance and outbreak investigations Of human Salmonella infections. In this study, three molecular typing methods were used to investigate the discriminatory ability, reproducibility and the genetic relationship between 110 Salmonella enterica subspec...

  1. GENETIC DIVERSITY OF CLINICAL AND ENVIRONMENTAL ISOLATES OF VIBRIO CHOLERAE DETERMINED BY AMPLIFIED FRAGMENT LENGTH POLYMORPHISM FINGERPRINTING. (R824995)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  2. GENETIC DIVERSITY OF VIBRIO CHOLERAE IN CHESAPEAKE BAY DETERMINED BY AMPLIFIED FRAGMENT LENGTH POLYMORPHISM FINGERPRINTING. (R824995)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  3. The PML gene is linked to a megabase-scale insertion/deletion restriction fragment length polymorphism

    Energy Technology Data Exchange (ETDEWEB)

    Goy, A.; Xiao, Y.H.; Passalaris, T. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others

    1995-03-20

    The PML gene located on chromosome band 15q22 is involved with the RAR{alpha} locus (17q21) in a balanced reciprocal translocation uniquely observed in acute promyelocytic leukemia. Physical mapping studies by pulsed-field gel electrophoresis revealed that the PML gene is flanked by two CpG islands that are separated by a variable distance in normal individuals. Several lines of evidence demonstrate that this is the consequence of a large insertion/deletion polymorphism linked to the PML locus: (1) overlapping fragments obtained with a variety of rare-cutting restriction enzymes demonstrated the same variability in distance between the flanking CpG islands; (2) mapping with restriction enzymes insensitive to CpG methylation confirmed that the findings were not a consequence of variable methylation of CpG dinucleotides; (3) the polymorphism followed a Mendelian inheritance pattern. This polymorphism is localized 3{prime} to the PML locus. There are five common alleles, described on the basis of BssHII fragments, ranging from 220 to 350 kb with increments of approximately 30 kb between alleles. Both heterozygous (61%) and homozygous (391%) patterns were observed in normal individuals. Mega-base-scale insertion/deletion restriction fragment length polymorphisms are very rare and have been described initially in the context of multigene families. Such structures have been also reported as likely regions of genetic instability. High-resolution restriction mapping of this particular structure linked to the PML locus is underway. 47 refs., 4 figs., 1 tab.

  4. SIMULATIVE ANALYSIS OF OSNR AND RECEIVED ELECTRIC RF POWER OF A ROF SYSTEM HAVING VARIABLE FIBER LENGTH, USING DIFFERENT MODULATION TECHNIQUES AND OPTICAL AMPLIFIERS

    Directory of Open Access Journals (Sweden)

    KARANBIR SINGH,

    2011-05-01

    Full Text Available In this paper, we analyzed OSNR and received electric RF power of a RoF communication system having variable fiber length, using direct and external modulation techniques and different optical amplifiers. In this work, we have compared and measured the OSNR and received optical power of the RoF system for different modulation techniques, i.e. direct and external modulation. Further, we also compared the received electric RF power for variable fiber lengths for direct and external modulation using different optical amplifiers, i.e. EDFAand SOA. We observe an increase of –11 dB (approx. in the received RF power for External modulation compared to direct modulation with EDFA.

  5. NcoI restriction fragment length polymorphism (RFLP) of the tumour necrosis factor (TNF alpha) region in primary biliary cirrhosis and in healthy Danes

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P;

    1989-01-01

    The restriction fragment length polymorphism of the human tumour necrosis factor (TNF alpha) region was investigated by means of 20 different restriction enzymes and a human TNF alpha cDNA probe. Only one of the enzymes, NcoI, revealed a polymorphic pattern consisting of fragments of 10.5 and 5...

  6. Regulation of chain length in two diatoms as a growth-fragmentation process

    Science.gov (United States)

    Gherardi, Marco; Amato, Alberto; Bouly, Jean-Pierre; Cheminant, Soizic; Ferrante, Maria Immacolata; d'Alcalá, Maurizio Ribera; Iudicone, Daniele; Falciatore, Angela; Cosentino Lagomarsino, Marco

    2016-08-01

    Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statistical physics model of chain growth and separation in combination with experimental evaluation of chain-length distributions. Applying this combined analysis to data from Chaetoceros decipiens and Phaeodactylum tricornutum, we find that cells of the first species control chain separation, likely through a cell-to-cell communication process, while the second species only modulates the separation rate. These results promote quantitative methods for characterizing chain formation in several chain-forming species and in diatoms in particular.

  7. A Population Genetics Study of Anopheles Darlingi (Diptera: Culicidae) from Colombia Based on Random Amplified Polymorphic DNA-Polymerase Chain Reaction and Amplified Fragment Length Polymorphism Markers

    Science.gov (United States)

    2007-06-01

    biogeographic province population from those of rhe Choco -MagdCllena. In this lasr region. Choco Clnd Cordoba populations showed the Ilighest genetic flow. Key...Atrato, Choco Province; Granada (030 32’ 19" N and 73° W) in the municipality of Granada, Meta Province; and Tai in the municipality of lierralta...darling; popu- lalions: Rete ( Choco ), Tierrallll (Cordoba), and Granada (Meta). PERU ~ uo u u:: i3 ~ ECUADOR 1996, Rafael & Tadei 1998,2000, 1999

  8. Restriction fragment length polymorphism (RFLP) of two HLA-B-associated transcripts (BATs) genes in healthy Danes

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P;

    1990-01-01

    The restriction fragment length polymorphism (RFLP) of the two human HLA-B-associated transcripts (BATs) genes, BAT1 and BAT2, was investigated using 5 different restriction enzymes and two human BAT1 and BAT2 cDNA probes. Two of the enzymes, NcoI and RsaI, revealed polymorphic patterns which were...... investigated in healthy Danes. The cDNA/restriction enzyme combination BAT1/NcoI identifies polymorphic bands at 12 kb, 8 kb, 2.5 kb, and 1.1 kb, while the BAT2/RsaI combination identifies polymorphic bands at 3.3 kb, 2.7 kb, 2.3 kb, and 0.9 kb. The frequencies of these markers were determined in 90 unrelated...

  9. Species determination within Staphylococcus genus by extended PCR-restriction fragment length polymorphism of saoC gene.

    Science.gov (United States)

    Bukowski, Michal; Polakowska, Klaudia; Ilczyszyn, Weronika M; Sitarska, Agnieszka; Nytko, Kinga; Kosecka, Maja; Miedzobrodzki, Jacek; Dubin, Adam; Wladyka, Benedykt

    2015-01-01

    Genetic methods based on PCR-restriction fragment length polymorphism (RFLP) are widely used for microbial species determination. In this study, we present the application of saoC gene as an effective tool for species determination and within-species diversity analysis for Staphylococcus genus. The unique sequence diversity of saoC allows us to apply four restriction enzymes to obtain RFLP patterns, which appear highly distinctive even among closely related species as well as atypical isolates of environmental origin. Such patterns were successfully obtained for 26 species belonging to Staphylococcus genus. What is more, tracing polymorphisms detected by different restriction enzymes allowed for basic phylogeny analysis for Staphylococcus aureus, which is potentially applicable for other staphylococcal species.

  10. Genotypic change of porcine circovirus type 2 on Japanese pig farms as revealed by restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Takahagi, Yoichi; Nishiyama, Yasutaka; Toki, Shinji; Yonekita, Taro; Morimatsu, Fumiki; Murakami, Hiroshi

    2008-06-01

    Porcine circovirus type 2 (PCV2) has been recognized as the causal agent of postweaning multisystemic wasting syndrome and can be divided into two major genotypic groups. We developed a method of restriction fragment length polymorphism (RFLP) analysis of PCV2 open reading frame 2 for easy discrimination between the two major groups. Genotyping of PCV2 isolates from 10 Japanese commercial pig farms was performed, and the analysis revealed that both PCV2 groups and at least five RFLP types of PCV2 are prevalent in Japan. On two farms, the genotypes of the PCV2 isolates in the spring of 2007 were different from those in the autumn of 2006. One genotype may have become dominant within only six months on these farms.

  11. Leishmania spp. identification by polymerase chain reaction-restriction fragment length polymorphism analysis and its applications in French Guiana.

    Science.gov (United States)

    Simon, Stéphane; Veron, Vincent; Carme, Bernard

    2010-02-01

    Leishmania (Viannia) guyanensis was for many years the only species commonly identified in French Guiana, but precise species identifications were quite rare. We describe a new restriction fragment length polymorphism-polymerase chain reaction technique using a 615-bp fragment of the RNA polymerase II gene and 2 restriction enzymes, TspRI and HgaI. Seven reference strains (Leishmania (Leishmania) amazonensis, Leishmania (Viannia) lainsoni, Leishmania (Viannia) braziliensis, L. (V.) guyanensis, Leishmania (Viannia) naiffi, Leishmania (Leishmania) major, Leishmania (Leishmania) infantum) and 112 clinical samples from positive lesions were used for the development of the technique. The rates of positive species identification were 85.7% for punch skin biopsy specimens, 93.1% for positive Giemsa-stained smears, and 100% for positive culture supernatants. In the framework of cutaneous leishmaniasis species surveillance for the 2006 to 2008 period, parasite identification was carried out for 199 samples from different patients. The prevalence of the various Leishmania spp. was 84.4% for L. (V.) guyanensis, 8.0% for L. (V.) braziliensis, 5.0% for L. (L.) amazonensis, and 2.6% for L. (V.) lainsoni. L. (V.) braziliensis seems to be locally an emerging pathogen.

  12. Taenia saginata: differential diagnosis of human taeniasis by polymerase chain reaction-restriction fragment length polymorphism assay.

    Science.gov (United States)

    Nunes, Cáris Maroni; Dias, Ana Karina Kerche; Dias, Francisca Elda Ferreira; Aoki, Sérgio Moraes; de Paula, Henrique Borges; Lima, Luis Gustavo Ferraz; Garcia, José Fernando

    2005-08-01

    Speciation of Taenia in human stool is important because of their different clinical and epidemiological features. DNA analysis has recently become possible which overcomes the problems of differentiating human taeniid cestodes morphologically. In the present study, we evaluated PCR coupled to restriction fragment length polymorphism to differentiate Taenia solium from Taenia saginata eggs present in fecal samples from naturally infected patients. A different DraI-RFLP pattern: a two-band pattern (421 and 100 bp) for T. saginata and a three-band pattern (234, 188, and 99 bp) for T. solium was observed allowing the two species to be separated. The lower detection limit of the PCR-RFLP using a non-infected fecal sample prepared with a given number of T. saginata eggs was 34 eggs in 2 g stool sediment. The 521 bp mtDNA fragment was detected in 8 out of 12 Taenia sp. carriers (66.6%). Of these, three showed a T. solium pattern and five a T. saginata pattern.

  13. A unique restriction site in the flaA gene allows rapid differentiation of group I and group II Clostridium botulinum strains by PCR-restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Paul, Catherine J; Tran, Shulin; Tam, Kevin J; Austin, John W

    2007-09-01

    Clostridium botulinum produces the potent botulinum neurotoxin, the causative agent of botulism. Based on distinctive physiological traits, strains of C. botulinum can be divided into four groups: however, only groups I and II are associated with human illness. Alignment of the flaA gene sequences from 40 group I and 40 group II strains identified a single BsrG1 restriction cut site that was present at base pair 283 in all group II flaA sequences and was not found in any group I sequence. The flaA gene was amplified by rapid colony PCR from 22 group I strains and 18 group II strains and digested with BsrGI restriction enzyme. Standard agarose gel electrophoresis with ethidium bromide staining showed two fragments, following restriction digestion of group II flaA gene amplicons with BsrGI, but only a single band of uncut flaA from group I strains. Combining rapid colony PCR with BsrGI restriction digest of the flaA gene at 60 degrees C is a significant improvement over current methods, such as meat digestion or amplified fragment length polymorphism, as a strain can be identified as either group I or group II in under 5 h when starting with a visible plated C. botulinum colony.

  14. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction

    Science.gov (United States)

    Birla, Bhagyashree S.; Chou, Hui-Hsien

    2015-01-01

    Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly. PMID:26716828

  15. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

    Directory of Open Access Journals (Sweden)

    Bhagyashree S Birla

    Full Text Available Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

  16. Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

    Science.gov (United States)

    Birla, Bhagyashree S; Chou, Hui-Hsien

    2015-01-01

    Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

  17. Distribution Study of Chlamydia trachomatis Serovars among High-Risk Women in China Performed Using PCR-Restriction Fragment Length Polymorphism Genotyping▿

    Science.gov (United States)

    Gao, Xing; Chen, Xiang-Sheng; Yin, Yue-Ping; Zhong, Ming-Ying; Shi, Mei-Qin; Wei, Wan-Hui; Chen, Qiang; Peeling, Rosanna W.; Mabey, David

    2007-01-01

    This was one of the first epidemiological studies in China focused on genital Chlamydia trachomatis serotype distribution in high-risk female populations using omp1 gene-based restriction fragment length polymorphism analysis. One thousand seven hundred seventy cervical swab samples from women attending sexually transmitted disease clinics and female sex workers in six cities in China (Shenzhen and Guangzhou in southern China, Nanjing and Shanghai in eastern China, and Nanning and Chengdu in southwestern China) were subjected to serovar genotyping. The proportion of omp1 genes successfully amplified in 240 C. trachomatis plasmid-positive samples was 94.2% (226/240). Serotypes E (n = 63; 27.9%), F (n = 53; 23.5%), G (n = 28; 12.4%), and D (n = 25; 11.1%) were most prevalent. Though there was no significant difference in the geographic distribution of C. trachomatis, serotype E was predominant in the South (32.1%) and East (27.1%), while serotype F was predominant in the Southwest (28.3%). Serotype F infection was associated with young age and single status. Serovar G was associated with lower abdominal pain; 47.5% of asymptomatic patients were infected with serovar E. These results provide information on distribution of genital C. trachomatis serotypes among high-risk women in China and indicate that high-risk women, including those who are asymptomatic, can be infected with multiple serovars of C. trachomatis, revealing exposure to multiple sources of infection. Although the scope for generalizations is limited by our small sample size, our results showing clinical correlations with genotypes are informative. PMID:17301282

  18. Detection of low-abundance KRAS mutations in colorectal cancer using microfluidic capillary electrophoresis-based restriction fragment length polymorphism method with optimized assay conditions.

    Directory of Open Access Journals (Sweden)

    Huidan Zhang

    Full Text Available Constitutively active KRAS mutations have been found to be involved in various processes of cancer development, and render tumor cells resistant to EGFR-targeted therapies. Mutation detection methods with higher sensitivity will increase the possibility of choosing the correct individual therapy. Here, we established a highly sensitive and efficient microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP platform for low-abundance KRAS genotyping with the combination of µCE and RFLP techniques. By using our self-built sensitive laser induced fluorescence (LIF detector and a new DNA intercalating dye YOYO-1, the separation conditions of µCE for ΦX174 HaeIII DNA marker were first optimized. Then, a Mav I digested 107-bp KRAS gene fragment was directly introduced into the microfluidic device and analyzed by µCE, in which field amplified sample stacking (FASS technique was employed to obtain the enrichment of the RFLP digestion products and extremely improved the sensitivity. The accurate analysis of KRAS statuses in HT29, LS174T, CCL187, SW480, Clone A, and CX-1 colorectal cancer (CRC cell lines by µCE-based RFLP were achieved in 5 min with picoliter-scale sample consumption, and as low as 0.01% of mutant KRAS could be identified from a large excess of wild-type genomic DNA (gDNA. In 98 paraffin-embedded CRC tissues, KRAS codon 12 mutations were discovered in 28 (28.6%, significantly higher than that obtained by direct sequencing (13, 13.3%. Clone sequencing confirmed these results and showed this system could detect at least 0.4% of the mutant KRAS in CRC tissue slides. Compared with direct sequencing, the new finding of the µCE-based RFLP platform was that KRAS mutations in codon 12 were correlated with the patient's age. In conclusion, we established a sensitive, fast, and cost-effective screening method for KRAS mutations, and successfully detected low-abundance KRAS mutations in clinical

  19. Structures and bonding on a colloidal silver surface of the various length carboxyl terminal fragments of bombesin.

    Science.gov (United States)

    Podstawka, Edyta; Ozaki, Yukihiro; Proniewicz, Leonard M

    2008-10-07

    Raman (RS) and surface-enhanced Raman scattering spectra (SERS) were measured for various length carboxyl terminal fragments (X-14 of amino acid sequence) of bombesin ( BN): BN13-14, BN12-14, BN11-14, BN10-14, BN9-14, and BN8-14 in silver colloidal solutions. Density functional theory (DFT) calculations of Raman wavenumbers and intensities with extended basis sets (B3LYP/6-31++G**) were performed with the aim of providing the definitive band allocations to the normal coordinates. The proposed band assignment is consistent with the assignment for similar compounds reported in the literature. The nonadsorbed and adsorbed molecular structures were deducted by detailed spectral analysis of the RS and SERS spectra, respectively. This analysis also allowed us to propose the particular surface geometry and orientation of these peptides on silver surface, and their specific interaction with the surface. For example, a SERS spectrum of BN8-14 indicates that the interaction of a thioether atom and Trp8 with the silver surface is favorable and may dictate the orientation and conformation of adsorbed peptide. One of the most prominent and common features in all of the fragments' SERS spectra is a approximately 692 cm (-1) band due to nu(C-S) accompanied by two or three bands of different C-S conformers for all, except BN8-14, which suggests that all of the above-mentioned compounds adsorb on the silver surface through the thioether atom and that the attachment of Trp8 produces limitation in a number of possible C-S conformers adopted on this surface. Our results also show clearly that His12 and CO do not interact with the colloid surface, which supports our earlier results.

  20. 16S rRNA terminal restriction fragment length polymorphism for the characterization of the nasopharyngeal microbiota.

    Directory of Open Access Journals (Sweden)

    Silvio D Brugger

    Full Text Available A novel non-culture based 16S rRNA Terminal Restriction Fragment Length Polymorphism (T-RFLP method using the restriction enzymes Tsp509I and Hpy166II was developed for the characterization of the nasopharyngeal microbiota and validated using recently published 454 pyrosequencing data. 16S rRNA gene T-RFLP for 153 clinical nasopharyngeal samples from infants with acute otitis media (AOM revealed 5 Tsp509I and 6 Hpy166II terminal fragments (TFs with a prevalence of >10%. Cloning and sequencing identified all TFs with a prevalence >6% allowing a sufficient description of bacterial community changes for the most important bacterial taxa. The conjugated 7-valent pneumococcal polysaccharide vaccine (PCV-7 and prior antibiotic exposure had significant effects on the bacterial composition in an additive main effects and multiplicative interaction model (AMMI in concordance with the 16S rRNA 454 pyrosequencing data. In addition, the presented T-RFLP method is able to discriminate S. pneumoniae from other members of the Mitis group of streptococci, which therefore allows the identification of one of the most important human respiratory tract pathogens. This is usually not achieved by current high throughput sequencing protocols. In conclusion, the presented 16S rRNA gene T-RFLP method is a highly robust, easy to handle and a cheap alternative to the computationally demanding next-generation sequencing analysis. In case a lot of nasopharyngeal samples have to be characterized, it is suggested to first perform 16S rRNA T-RFLP and only use next generation sequencing if the T-RFLP nasopharyngeal patterns differ or show unknown TFs.

  1. Genotyping of Candida orthopsilosis Clinical Isolates by Amplification Fragment Length Polymorphism Reveals Genetic Diversity among Independent Isolates and Strain Maintenance within Patients▿

    OpenAIRE

    Tavanti, Arianna; Hensgens, Lambert A. M.; Ghelardi, Emilia; Campa, Mario; Senesi, Sonia

    2007-01-01

    Candida parapsilosis former groups II and III have recently been established as independent species named C. orthopsilosis and C. metapsilosis, respectively. In this report, 400 isolates (290 patients) previously classified as C. parapsilosis by conventional laboratory tests were screened by BanI digestion profile analysis of the secondary alcohol dehydrogenase gene fragment and by amplification fragment length polymorphism (AFLP). Thirty-three strains collected from 13 patients were identifi...

  2. PCR-restriction fragment length polymorphism assay for detection of gyrA mutations associated with fluoroquinolone resistance in Campylobacter coli.

    Science.gov (United States)

    Alonso, Rodrigo; Mateo, Estibaliz; Girbau, Cecilia; Churruca, Estibaliz; Martinez, Irati; Fernández-Astorga, Aurora

    2004-12-01

    A fragment of the gyrA gene was sequenced from 34 isolates of Campylobacter coli, including 23 isolates resistant to ciprofloxacin. All ciprofloxacin-resistant isolates examined by DNA sequencing carried a point mutation at position Thr-86 on the gyrA gene product, involving the replacement of Thr-86 by Ile. A combined PCR-restriction fragment length polymorphism technique using RsaI was developed to detect this mutation.

  3. Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti

    Energy Technology Data Exchange (ETDEWEB)

    Severson, D.W.; Thathy, V.; Mori, A. [Univ. of Wisconsin, Madison, WI (United States)] [and others

    1995-04-01

    Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F{sub 2} populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs [2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI], is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filaria nematode Brugia malayi and the yellow fever virus. 35 refs., 2 figs., 3 tabs.

  4. Transmission of tuberculosis in Havana, Cuba: a molecular epidemiological study by IS6110 restriction fragment length polymorphism typing

    Directory of Open Access Journals (Sweden)

    Diaz R

    2001-01-01

    Full Text Available The combination of molecular and conventional epidemiological methods has improved the knowledge about the transmission of tuberculosis in urban populations. To examine transmission of tuberculosis in Havana, Cuba, with DNA fingerprinting, we studied 51 out of 92 Mycobacterium tuberculosis strains isolated from tuberculosis patients who resided in Havana and whose infection was culture-confirmed in the period from September 1997 to March 1998. Isolates from 28 patients (55% had unique IS6110 restriction fragment length polymorphism (RFLP patterns, while isolates from 23 others (45% had identical patterns and belonged to 7 clusters. Three clusters consisting of six, five and two cases were each related to small outbreaks that occurred in a closed setting. Three other clustered cases were linked to a large outbreak that occurred in another institution. Younger patients were more correlated to clustering than older ones. The finding that 45% of the isolates had clustered RFLP patterns suggests that recent transmission is a key factor in the tuberculosis cases in Havana. The IS6110 RFLP typing made it possible to define the occurrence of outbreaks in two closed institutions.

  5. A novel hepatitis B virus genotyping system by using restriction fragment length polymorphism patterns of S gene amplicons

    Institute of Scientific and Technical Information of China (English)

    Guo-Bing Zeng; Shu-Juan Wen; Zhan-Hui Wang; Li Yan; Jian Sun; Jin-Lin Hou

    2004-01-01

    AIM: Traditional hepatitis B virus (HBV) genotyping methods using restriction fragment length polymorphism (RFLP) can reliably identify genotypes A to F. As HBV genotypes G and H have been recently identified, this study was to establish an accurate and simple genotyping method for all eight HBV genotypes (A to H).METHODS: Two hundred and forty HBV small S sequences obtained from GeneBank were analysed for restriction enzyme sites that would be genotype-specific. Restriction patterns following digestion with restriction enzymes BsrⅠ,StyⅠ, DpnⅠ, HpaⅡ, and EaeⅠ, were determined to identify all eight HBV genotypes. Mixed genotype infections were confirmed by cloning and further RFLP analysis.RESULTS: The new genotyping method could identify HBV genotypes A to H. Genotypes B and C could be determined by a single step digestion with BsrⅠ and StyⅠ in parallel. This was particularly useful in the Far East where genotypes B and C are predominant. Serum samples from 187 Chinese HBV carriers were analysed with this genotyping system, and the genotype distribution was 1.1% (2), 51.9% (97), 40.6% (76) and 4.8%(9) for genotypes A, B, C, and D, respectively. Mixed genotypes were found in only 3 patients (1.6%). Sequence data analysis confirmed the validity of this new method.CONCLUSION: This HBV genotyping system can identify all eight HBV genotypes. It is accurate and simple, and can be widely used for studies on HBV genotyping.

  6. Usefulness of restriction fragment length polymorphism and spoligotyping for epidemiological studies of Mycobacterium bovis in Madagascar: description of new genotypes.

    Science.gov (United States)

    Rasolofo Razanamparany, Voahangy; Quirin, René; Rapaoliarijaona, Andriampenomaka; Rakotoaritahina, Hugues; Vololonirina, Elie Jeanne; Rasolonavalona, Tiana; Ferdinand, Séverine; Sola, Christophe; Rastogi, Nalin; Ramarokoto, Herimanana; Chanteau, Suzanne

    2006-04-16

    Tuberculosis is highly prevalent in cattle in Madagascar. An epidemiological study based on genotyping of Mycobacterium bovis and its transmission to humans was carried out. The restriction fragment length polymorphism (IS6110 and DR markers) and spoligotyping were used to assess the genetic diversity of strains from different regions of Madagascar. One of these strains was isolated from goat, the other strains were isolated from zebu cattle. Nine IS6110 profiles, 20 DR profiles and 12 spoligotypes were obtained. About 90% of all isolates gave a single IS6110 band at about 1.8 kb. Most strains had the same spoligotype. M. bovis strains commonly lack spacers 39-43, and all Malagasy strains also lacked spacers 3-5, 8-10 and 16. This pattern has not been reported elsewhere. DR was the most discriminatory of the three markers. The patterns obtained with the three markers were combined to identify 34 different genotypes, one of which was found in 35% of the strains. No region-specific M. bovis genotype was identified, but the genotyping of 18 M. bovis strains isolated from patients showed that the human and bovine strains were identical, suggesting possible human contamination from zebu cattle.

  7. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

    Directory of Open Access Journals (Sweden)

    Azzedine Bounamous

    2014-07-01

    Full Text Available A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b, t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin.

  8. Identification of Echinococcus granulosus strains using polymerase chain reaction-restriction fragment length polymorphism amongst livestock in Moroto district, Uganda.

    Science.gov (United States)

    Chamai, Martin; Omadang, Leonard; Erume, Joseph; Ocaido, Michael; Oba, Peter; Othieno, Emmanuel; Bonaventure, Straton; Kitibwa, Annah

    2016-07-29

    A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus-positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda.

  9. Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Miyaguchi, Hajime

    2016-09-20

    An improved version of a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method for genotyping toxic pufferfish species by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is described. DNA extraction is carried out using a silica membrane-based DNA extraction kit. After the PCR amplification using a detergent-free PCR buffer, restriction enzymes are added to the solution without purifying the reaction solution. A reverse-phase silica monolith column and a Fourier transform high resolution mass spectrometer having a modified Kingdon trap analyzer are employed for separation and detection, respectively. The mobile phase, consisting of 400 mM 1,1,1,3,3,3-hexafluoro-2-propanol, 15 mM triethylamine (pH 7.9) and methanol, is delivered at a flow rate of 0.4 ml/min. The cycle time for LC/ESI-MS analysis is 8 min including equilibration of the column. Deconvolution software having an isotope distribution model of the oligonucleotide is used to calculate the corresponding monoisotopic mass from the mass spectrum. For analysis of oligonucleotides (range 26-79 nucleotides), mass accuracy was 0.62 ± 0.74 ppm (n = 280) and excellent accuracy and precision were sustained for 180 hr without use of a lock mass standard.

  10. Polymerase chain reaction-restriction fragment length polymorphism method for differentiation of uropathogenic specific protein gene types.

    Science.gov (United States)

    Lai, Yun Mei; Zaw, Myo Thura; Shamsudin, Shamsul Bahari; Lin, Zaw

    2016-08-01

    The putative pathogenicity island (PAI) containing the uropathogenic specific protein (usp) gene and three small open reading frames (orfU1, orfU2, and orfU3) encoding 98, 97, and 96 amino acid proteins is widely distributed among uropathogenic Escherichia coli (UPEC) strains. This PAI was designated as PAIusp. Sequencing analysis of PAIusp has revealed that the usp gene can be divided into two types - uspI and uspII - based on sequence variation at the 3' terminal region and the number and position of orfUs differ from strain to strain. Based on usp gene types and orfU sequential patterns, PAIusp can be divided into four subtypes. Subtyping of PAIusp is a useful method to characterize UPEC strains. In this study, we developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to differentiate usp gene types. This method could correctly identify the usp gene type in usp-positive UPEC strains in our laboratory.

  11. Characterization of field strains of infectious laryngotracheitis virus in China by restriction fragment length polymorphism and sequence analysis.

    Science.gov (United States)

    Yan, Zhuanqiang; Li, Shengpeng; Xie, Qingmei; Chen, Feng; Bi, Yingzuo

    2016-01-01

    Nineteen strains of infectious laryngotracheitis virus (ILTV; Gallid herpesvirus 1) were isolated from dead or diseased birds in chicken flocks from different areas of China between 2010 and 2014 and used to investigate ILTV epidemiology. These strains were characterized using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns and sequence analysis of the thymidine kinase (TK) gene. PCR-RFLP analysis showed that the TK gene generated 2 patterns when digested with restriction endonuclease enzymes. Pattern A corresponded to 2 virulent field strains, while pattern B was characteristic of 2 virulent field strains, 15 low pathogenicity field strains, and all vaccine strains. Sequence analysis of the TK gene indicated that the messenger RNA polyadenylation signals could be identified in some isolates where amino acid 252 was threonine, and in those with methionine at that position. The present study has demonstrated that most of the outbreaks of ILT in China were caused either by low virulence strains or by vaccine-related strains, and also emphasizes the importance of reinforcing ILTV surveillance in both vaccinated and nonvaccinated flocks.

  12. Prevalence of Trichomonas spp. in domestic pigeons in Shandong Province, China, and genotyping by restriction fragment length polymorphism.

    Science.gov (United States)

    Jiang, Xiyue; Sun, Jingjing; Wang, Fangkun; Li, Hongmei; Zhao, Xiaomin

    2016-05-01

    Oropharyngeal swabs (n = 609) were collected randomly from 80,000 domestic pigeons (Columba livia domestica) on five pigeon farms and at one pigeon slaughterhouse in Shandong Province, China, from September 2012 to July 2013. Trichomonas spp. were detected in 206/609 (33.8%) samples. The prevalence was 14.9-31.1%, depending on different levels of sanitation and management, and was 4.8% in nestling pigeons, 13.6% in breeding pigeons and 35.2% in adolescent pigeons. Trichomonas gallinae genotypes A and B, and Trichomonas tenax-like isolates were identified by PCR-restriction fragment length polymorphism (RFLP) analysis and sequencing of the 5.8S rDNA-internal transcribed spacer (ITS) regions. RFLP analysis with the restriction enzyme BsiEI generated different RFLP band patterns between T. gallinae and T.tenax-like isolates. When BsiEI RFLP analysis was combined with HaeIII RFLP analysis, all infection types of T. gallinae and T.tenax-like isolates could be identified.

  13. An improved PCR-restriction fragment length polymorphism (RFLP) method for the identification of cry1-type genes.

    Science.gov (United States)

    Shu, Changlong; Liu, Dongming; Zhou, Zishan; Cai, Jilin; Peng, Qi; Gao, Jiguo; Song, Fuping; Zhang, Jie

    2013-11-01

    The cry1-type genes of Bacillus thuringiensis represent the largest cry gene family, which contains 50 distinct holotypes. It is becoming more and more difficult to identify cry1-type genes using current methods because of the increasing number of cry1-type genes. In the present study, an improved PCR-restriction fragment length polymorphism (PCR-RFLP) method which can distinguish 41 holotypes of cry1-type genes was developed. This improved method was used to identify cry1-type genes in 20 B. thuringiensis strains that are toxic to lepidoptera. The results showed that the improved method can efficiently identify single and clustered cry1-type genes and can be used to evaluate cry1-type genes in novel strain collections of B. thuringiensis. Among the detected cry1-type genes, we identified four novel genes, cry1Ai, cry1Bb, cry1Ja, and cry1La. The bioassay results from the expressed products of the four novel cry genes showed that Cry1Ai2, Cry1Bb2, and Cry1Ja2 were highly toxic against Plutella xylostella, whereas Cry1La2 exhibited no activity. Moreover, Cry1Ai2 had good lethal activity against Ostrinia furnacalis, Hyphantria cunea, Chilo suppressalis, and Bombyx mori larvae and considerable weight loss activity against Helicoverpa armigera.

  14. Use of PCR-restriction fragment length polymorphism analysis for identification of yeast species isolated from bovine intramammary infection.

    Science.gov (United States)

    Fadda, M E; Pisano, M B; Scaccabarozzi, L; Mossa, V; Deplano, M; Moroni, P; Liciardi, M; Cosentino, S

    2013-01-01

    This study reports a rapid PCR-based technique using a one-enzyme RFLP for discrimination of yeasts isolated from bovine clinical and subclinical mastitis milk samples. We analyzed a total of 1,486 milk samples collected over 1 yr in south Sardinia and northern Italy, and 142 yeast strains were preliminarily grouped based on their cultural morphology and physiological characteristics. Assimilation tests were conducted using the identification kit API ID 32C and APILAB Plus software (bioMérieux, Marcy l'Etoile, France). For PCR-RFLP analysis, the 18S-ITS1-5.8S ribosomal(r)DNA region was amplified and then digested with HaeIII, and dendrogram analysis of RFLP fragments was carried out. Furthermore, within each of the groups identified by the API or PCR-RFLP methods, the identification of isolates was confirmed by sequencing of the D1/D2 region using an ABI Prism 310 automatic sequencer (Applied Biosystems, Foster City, CA). The combined phenotypic and molecular approach enabled the identification of 17 yeast species belonging to the genera Candida (47.9%), Cryptococcus (21.1%), Trichosporon (19.7%), Geotrichum (7.1%), and Rhodotorula (4.2%). All Candida species were correctly identified by the API test and their identification confirmed by sequencing. All strains identified with the API system as Geotrichum candidum, Cryptococcus uniguttulatus, and Rhodotorula glutinis also produced characteristic restriction patterns and were confirmed as Galactomyces geotrichum (a teleomorph of G. candidum), Filobasidium uniguttulatum (teleomorph of Crypt. uniguttulatus), and R. glutinis, respectively, by D1/D2 rDNA sequencing. With regard to the genus Trichosporon, preliminary identification by API was problematic, whereas the RFLP technique used in this study gave characteristic restriction profiles for each species. Moreover, sequencing of the D1/D2 region allowed not only successful identification of Trichosporon gracile where API could not, but also correct identification of

  15. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

    NARCIS (Netherlands)

    Coolen, MJL; Post, E; Davis, CC; Forney, LJ

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the h

  16. Analysis of ORF 1 in European porcine reproductive and respiratory syndrome virus by long RT-PCR and restriction fragment length polymorphism (RFLP) analysis

    DEFF Research Database (Denmark)

    Nielsen, H. S.; Storgaard, Torben; Oleksiewicz, M.B.

    2000-01-01

    A rapid method was developed for partial characterization of the replicase-encoding open reading frame 1 (ORF 1) of porcine reproductive and respiratory syndrome virus (PRRSV). It comprised long RT-PCR amplification of 11.1 kb (94%) of ORF 1, followed by restriction fragment length polymorphism...

  17. Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing.

    NARCIS (Netherlands)

    Huyen, M.N.; Kremer, K.; Lan, N.T.; Buu, T.N.; Cobelens, F.G.; Tiemersma, E.W.; Haas, P. de; Soolingen, D. van

    2013-01-01

    BACKGROUND: In comparison to restriction fragment length polymorphism (RFLP) typing, variable number of tandem repeat (VNTR) typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard i

  18. Terminal Restriction Fragment Length Polymorphism for the Identification of Spirorchiid Ova in Tissues from the Green Sea Turtle, Chelonia mydas.

    Science.gov (United States)

    Chapman, Phoebe A; Traub, Rebecca J; Kyaw-Tanner, Myat T; Owen, Helen; Flint, Mark; Cribb, Thomas H; Mills, Paul C

    2016-01-01

    Blood flukes are among the most common disease causing pathogens infecting vertebrates, including humans and some of the world's most globally endangered fauna. Spirorchiid blood flukes are parasites of marine turtles, and are associated with pathology, strandings and mortalities worldwide. Their ova embolize in tissues and incite significant inflammatory responses, however attempts to draw correlations between species and lesions are frustrated by difficulties in identifying ova beyond the genus level. In this study, a newly developed terminal restriction fragment length polymorphism (T-RFLP) method was validated as a tool for differentiating between mixed spirorchiid ova in turtle tissue. Initially, a multiplex PCR was used to differentiate between the five genera of spirorchiid flukes. Following this, PCR was performed using genus/genera-specific fluorescently tagged primer pairs and PCR products digested analysis using restriction endonucleases. Using capillary electrophoresis, this T-RFLP method could differentiate between twelve species and genotypes of spirorchiid flukes in turtles. It was applied to 151 tissue samples and successfully identified the spirorchiid species present. It was found to be more sensitive than visual diagnosis, detecting infections in 28 of 32 tissues that were negative on histology. Spirorchiids were present in 96.7% of tissues tested, with Neospirorchis genotype 2 being the most prevalent, present in 93% of samples. Mixed infections were common, being present in 60.7% of samples tested. The method described here is, to our knowledge, the first use of the T-RFLP technique on host tissues or in an animal ecology context, and describes a significant advancement in the clinical capacity to diagnose a common cause of illness in our environment. It is proven as a sensitive, specific and cost-efficient means of identifying spirorchiid flukes and ova in turtles, with the potential to contribute valuable information to epidemiological and

  19. M protein typing of Thai group A streptococcal isolates by PCR-Restriction fragment length polymorphism analysis

    Directory of Open Access Journals (Sweden)

    Good Michael F

    2005-10-01

    Full Text Available Abstract Background Group A streptococcal (GAS infections can lead to the development of severe post-infectious sequelae, such as rheumatic fever (RF and rheumatic heart disease (RHD. RF and RHD are a major health concern in developing countries, and in indigenous populations of developed nations. The majority of GAS isolates are M protein-nontypeable (MNT by standard serotyping. However, GAS typing is a necessary tool in the epidemiologically analysis of GAS and provides useful information for vaccine development. Although DNA sequencing is the most conclusive method for M protein typing, this is not a feasible approach especially in developing countries. To overcome this problem, we have developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP-based assay for molecular typing the M protein gene (emm of GAS. Results Using one pair of primers, 13 known GAS M types showed one to four bands of PCR products and after digestion with Alu I, they gave different RFLP patterns. Of 106 GAS isolates examined from the normal Thai population and from patients with GAS-associated complications including RHD, 95 isolates gave RFLP patterns that corresponded to the 13 known M types. Only 11 isolates gave RFLP patterns that differed from the 13 known M types. These were then analyzed by DNA sequencing and six additional M types were identified. In addition, we found that M93 GAS was the most common M type in the population studied, and is consistent with a previous study of Thai GAS isolates. Conclusion PCR-RFLP analysis has the potential for the rapid screening of different GAS M types and is therefore considerably advantageous as an alternative M typing approach in developing countries in which GAS is endemic.

  20. Terminal Restriction Fragment Length Polymorphism for the Identification of Spirorchiid Ova in Tissues from the Green Sea Turtle, Chelonia mydas

    Science.gov (United States)

    Chapman, Phoebe A.; Traub, Rebecca J.; Kyaw-Tanner, Myat T.; Owen, Helen; Flint, Mark; Cribb, Thomas H.; Mills, Paul C.

    2016-01-01

    Blood flukes are among the most common disease causing pathogens infecting vertebrates, including humans and some of the world's most globally endangered fauna. Spirorchiid blood flukes are parasites of marine turtles, and are associated with pathology, strandings and mortalities worldwide. Their ova embolize in tissues and incite significant inflammatory responses, however attempts to draw correlations between species and lesions are frustrated by difficulties in identifying ova beyond the genus level. In this study, a newly developed terminal restriction fragment length polymorphism (T-RFLP) method was validated as a tool for differentiating between mixed spirorchiid ova in turtle tissue. Initially, a multiplex PCR was used to differentiate between the five genera of spirorchiid flukes. Following this, PCR was performed using genus/genera-specific fluorescently tagged primer pairs and PCR products digested analysis using restriction endonucleases. Using capillary electrophoresis, this T-RFLP method could differentiate between twelve species and genotypes of spirorchiid flukes in turtles. It was applied to 151 tissue samples and successfully identified the spirorchiid species present. It was found to be more sensitive than visual diagnosis, detecting infections in 28 of 32 tissues that were negative on histology. Spirorchiids were present in 96.7% of tissues tested, with Neospirorchis genotype 2 being the most prevalent, present in 93% of samples. Mixed infections were common, being present in 60.7% of samples tested. The method described here is, to our knowledge, the first use of the T-RFLP technique on host tissues or in an animal ecology context, and describes a significant advancement in the clinical capacity to diagnose a common cause of illness in our environment. It is proven as a sensitive, specific and cost-efficient means of identifying spirorchiid flukes and ova in turtles, with the potential to contribute valuable information to epidemiological and

  1. Molecular characterization of Mycobacterium tuberculosis isolates from Tehran, Iran by restriction fragment length polymorphism analysis and spoligotyping.

    Science.gov (United States)

    Feyisa, Seifu Gizaw; Haeili, Mehri; Zahednamazi, Fatemeh; Mosavari, Nader; Taheri, Mohammad Mohammad; Hamzehloo, Gholamreza; Zamani, Samin; Feizabadi, Mohammad Mehdi

    2016-04-01

    INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB) isolates by DNA fingerprinting has contributed to tuberculosis (TB) control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan TB patients were fingerprinted by standard IS6110-restriction fragment length polymorphism (RFLP) analysis and spoligotyping. RESULTS The copy number of IS6110 ranged from 10-24 per isolate. The isolates were classified into 22 clusters showing ≥ 80% similarity by RFLP analysis. Fourteen multidrug-resistant (MDR) isolates were grouped into 4 IS6110-RFLP clusters, with 10 isolates [71% (95% CI: 45-89%)] in 1 cluster, suggesting a possible epidemiological linkage. Eighteen Iranian isolates showed ≥ 80% similarity with Afghan isolates. There were no strains with identical fingerprints. Spoligotyping of 70 isolates produced 23 distinct patterns. Sixty (85.7%) isolates were grouped into 13 clusters, while the remaining 10 isolates (14.2%) were not clustered. Ural (formerly Haarlem4) (n = 22, 31.4%) was the most common family followed by Central Asian strain (CAS) (n = 18, 25.7%) and T (n = 9, 12.8%) families. Only 1strain was characterized as having the Beijing genotype. Among 60 Iranian and 10 Afghan MTB isolates, 25% (95% CI: 16-37) and 70% (95% CI: 39-89) were categorized as Ural lineage, respectively. CONCLUSIONS A higher prevalence of Ural family MTB isolates among Afghan patients than among Iranian patients suggests the possible transmission of this lineage following the immigration of Afghans to Iran.

  2. Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.

    Science.gov (United States)

    Said, Halima M; Krishnamani, Keshav; Omar, Shaheed V; Dreyer, Andries W; Sansom, Bianca; Fallows, Dorothy; Ismail, Nazir A

    2016-10-01

    The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.

  3. Comparison between terminal-restriction fragment length polymorphism (T-RFLP) and quantitative culture for analysis of infants' gut microbiota.

    Science.gov (United States)

    Sjöberg, Fei; Nowrouzian, Forough; Rangel, Ignacio; Hannoun, Charles; Moore, Edward; Adlerberth, Ingegerd; Wold, Agnes E

    2013-07-01

    The infantile intestinal microbiota is a major stimulus for immune maturation. Both culture and DNA-based methods can be used for microbiota characterization, but few studies have systematically compared their performance for analysis of the gut microbiota. Here, we examined fecal samples obtained on six occasions between one week and 12 months of age from six vaginally delivered infants. After quantitative aerobic and anaerobic culture of the samples on selective and non-selective media, DNA was extracted from the fecal samples and analyzed regarding 16S rRNA gene polymorphism by terminal-restriction fragment length polymorphism (T-RFLP). A database was constructed for direct identification of T-RFLP peaks by analysis of pure-culture bacteria and analysis of a limited number of samples by 16S rRNA cloning and sequencing. Bacterial genera present at >10⁶ CFU/g feces, as determined by quantitative culture, were generally readily detected by T-RFLP, while culture on selective media was more sensitive in detecting facultative anaerobes with lower population counts. In contrast, T-RFLP more readily than culture detected several anaerobic species, also taxa that could not be identified using the database. T-RFLP readily identified bacteria to the genus level and also provided some sub-genus discrimination. Both T-RFLP and culture identified Bifidobacterium, Clostridium and Bacteroides spp. among the most common colonizers of the infantile microbiota throughout the first year of life. T-RFLP analysis showed that microbiota complexity was high in the first weeks of life, declined to a minimum at 1-2 months of age, and thereafter increased again. Principal component analysis revealed that early samples (1 week-6 months) chiefly differed between individual infants, while 12-month samples were similar between children, but different from the early samples. Our results indicate that T-RFLP has high sensitivity and adequate taxonomic discrimination capacity for analysis of

  4. Isolation and characterization of DNA probes from a flow-sorted human chromosome 8 library that detect restriction fragment length polymorphism (RFLP).

    OpenAIRE

    Wood, S.; Starr, T V; Shukin, R J

    1986-01-01

    We have used a recombinant DNA library constructed from flow-sorted human chromosome 8 as a source of single-copy human probes. These probes have been screened for restriction fragment length polymorphism (RFLP) by hybridization to Southern transfers of genomic DNA from five unrelated individuals. We have detected six RFLPs distributed among four probes after screening 741 base pairs for restriction site variation. These RFLPs all behave as codominant Mendelian alleles. Two of the probes dete...

  5. Identification of Carnobacterium Species by Restriction Fragment Length Polymorphism of the 16S-23S rRNA Gene Intergenic Spacer Region and Species-Specific PCR

    OpenAIRE

    Rachman, Cinta; Kabadjova, Petia; Valcheva, Rosica; Prévost, Hervé; Dousset, Xavier

    2004-01-01

    The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in ord...

  6. ISOLATION AND IDENTIFICATION OF cDNA FRAGMENTS AND FULL-LENGTH cDNA DIFFERENTIALLY EXPRESSED IN HUMAN GLIOBLASTOMA CELL LINE BT-325 VERSUS ALL-TRANS RETINOIC ACID INDUCTION

    Institute of Scientific and Technical Information of China (English)

    金虎林; 胡松年; 李光涛; 涂纯; 袁建刚; 强伯勤

    2000-01-01

    Objective. To investigate the differentiation process of the human glioblastoma cells. Methods. Differential display reverse transcribed-PCR(DDRT-PCR) was used to isolate the genes differentially expressed in control and all-trans retinoic acid treated human glioblastoma cell line BT-325. Routine method of cDNA library screening was performed to clone full-length cDNA. Results. Thirty-six RT-PCR reactions were performed and 64 differentially expressed fragments were recovered, amplified and cloned. Of them,46 ESTs were sequenced and delivered into the GenBank. The homology comparison us ing BLAST algorithm revealed that 22ESTs are highly homologous with the known genes and many of them play impor tant roles in the cell differentiation progress. A dot-blot hybridization was conducted to certify the differentiation expres sion. The result showed that 27 EST clones are expressed at different level in control and all-trans retinoi c acid treated BT-325 cells. A full-length cDNA was cloned using the ES T-HGBB098. Conclusion. DDRT-PCR was a simple and effective method to serially analyze the differentially expressed genes.

  7. ISOLATION AND IDENTIFICATION OF cDNA FRAGMENTS AND FULL-LENGTH cDNA DIFFERENTIALLY EXPRESSEDIN HUMAN GLIOBLASTOMA CELL LINE BT-325 VERSUS ALL-TRANS RETINOIC ACID INDUCTION

    Institute of Scientific and Technical Information of China (English)

    金虎林; 胡松年; 李光涛; 涂纯; 袁建刚; 强伯勤

    2000-01-01

    Objective. To investigate the differentiation process of the human glioblastoma cells. Methods. Differential display reverse transcribed-PCR(DDRT-PCR) was used to isolate the genes differentially expressed in control and all-trans retinoic acid treated human glioblastoma cell line BT-325. Routine method of cDNA library screening was performed to clone full-length cDNA. Results. Thirty-six RT-PCR reactions were performed and 64 differentially expressed fragments were recovered, amplified and cloned. Of them,46 ESTs were sequenced and delivered into the GenBank. The homology comparison us-ing BLAST algorithm revealed that 22ESFs are highly homologous with the known genes and many of them play impor-tant roles in the cell differentiation progress. A dot-blot hybridization was conducted to certify the differemiation expres-sion. The result showed that 27 EST clones are expressed at different level in control and all-traus retinoic acid treated BT-325 cells. A full-length cDNA was cloned using the EST-HGBB098.Conclusion. DDRT-PCR was a simple and effective method to segally analyze the differentially expressed genes.

  8. Development of a polymerase chain reaction-restriction fragment length polymorphism method for identification of the Fusarium genus using the transcription elongation factor-1α gene.

    Science.gov (United States)

    Zarrin, Majid; Ganj, Farzaneh; Faramarzi, Sama

    2016-12-01

    Fusarium species are well-known plant pathogens and food contaminants that have also appeared as one of the most important groups of medically significant fungi. The sequences of the translation elongation factor (TEF)-1α gene have been broadly employed for species detection. A total of 50 strains of Fusarium spp., including environmental, clinical and reference isolates were used for the current study. The primer sets, Fu3f and Fu3r, were used to amplify an ~420-bp DNA fragment of the TEF-1α gene. Double digestion with two restriction enzymes, XhoI and SduI was used for discrimination of the Fusarium species in the TEF-1α gene fragment. Double digestion of the TEF-1α gene fragment from five clinically important Fusarium species were clearly differentiated from each other: The F. solani species complex, F. oxysporum species complex, F. verticillioides, F. proliferatum and F. fujikuroi. This method facilitates detection and enables verification of the Fusarium genus; therefore, it may be applied for disease control.

  9. HLA-DPB1 typing with polymerase chain reaction and restriction fragment length polymorphism technique in Danes

    DEFF Research Database (Denmark)

    Hviid, T V; Madsen, H O; Morling, N

    1992-01-01

    endonucleases: RsaI, FokI, ApaI, SacI, BstUI, EcoNI, and DdeI, and the DNA fragments were separated by electrophoresis in agarose gels. Altogether, 71 individuals were investigated and 16 different HLA-DPB1 types were observed in 26 different heterozygotic combinations, as well as five possible homozygotes...

  10. Studies of nontarget-mediated distribution of human full-length IgG1 antibody and its FAb fragment in cardiovascular and metabolic-related tissues.

    Science.gov (United States)

    Davidsson, Pia; Söderling, Ann-Sofi; Svensson, Lena; Ahnmark, Andrea; Flodin, Christine; Wanag, Ewa; Screpanti-Sundqvist, Valentina; Gennemark, Peter

    2015-05-01

    Tissue distribution and pharmacokinetics (PK) of full-length nontargeted antibody and its antigen-binding fragment (FAb) were evaluated for a range of tissues primarily of interest for cardiovascular and metabolic diseases. Mice were intravenously injected with a dose of 10 mg/kg of either human IgG1or its FAb fragment; perfused tissues were collected at a range of time points over 3 weeks for the human IgG1 antibody and 1 week for the human FAb antibody. Tissues were homogenized and antibody concentrations were measured by specific immunoassays on the Gyros system. Exposure in terms of maximum concentration (Cmax ) and area under the curve was assessed for all nine tissues. Tissue exposure of full-length antibody relative to plasma exposure was found to be between 1% and 10%, except for brain (0.2%). Relative concentrations of FAb antibody were the same, except for kidney tissue, where the antibody concentration was found to be ten times higher than in plasma. However, the absolute tissue uptake of full-length IgG was significantly higher than the absolute tissue uptake of the FAb antibody. This study provides a reference PK state for full-length whole and FAb antibodies in tissues related to cardiovascular and metabolic diseases that do not include antigen or antibody binding.

  11. Screening of cytoplasmic DNA diversity between and within Lupinus mutabilis Sweet and Lupinus albus sensu lato by restriction fragment length polymorphism (RFLP).

    Science.gov (United States)

    Olczak, T; Rurek, M; Jańska, H; Augustyniak, H; Sawicka-Sienkiewicz, E J

    2001-01-01

    Seven populations and five mutant lines of the Andean lupin and four species from the section Albus were screened for their mitochondrial and chloroplast polymorphisms. For this purpose the RFLP method with EcoRI as a restriction enzyme was used. Lupinus luteus, Lupinus albus and Phaseolus vulgaris organellar clones as well as amplified fragments were used as probes. We found that mitochondrial probes were more suitable than chloroplast probes for identification of inter- and intra-specific variations within the examined material. Most mitochondrial probes differentiate the two species investigated. A high level of mitochondrial polymorphism was observed among the populations of L. mutabilis in contrast to monomorphism among the species in the section Albus. A limited polymorphism was detected between the mutant lines of L. mutabilis. We conclude from this study that the mitochondrial RFLP analysis is a valuable tool for identification of variability among Andean lupin populations.

  12. RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) ANALYSIS OF GENOMIC DNA OF 5 STRAINS OF TRICHINELLA SPIRALIS IN CHINA

    Institute of Scientific and Technical Information of China (English)

    王虹; 张月清; 劳为德; 吴赵永

    1995-01-01

    Five restriction endonucleases were used to digest genomic DNA from 5 isolates of Trichinella spiralis obtained from Changchun,Tianjin,Xian,Henan and Yunnan.All the isolates were secured from pigs ex-cept the Changchun strain which came from dog.The DNA fragments digested by endonuclease were sepa-mted by agarose gel electrophoesis.The DNA fragments digested by endonuclease were sepa-rated by agarose gel electrophoresis.The Changchun is olate had a EcoRI band at 1.12kb and a Dral band at 1.97kb which were unique to this isolate.A cloned specific repetitive DNA sequence(1.12kb) from the Changchun strain was selected to prepare a probe for the Southern blotting of EcoRI restriction DNA frag-ments for the 5 isolates.The 1.12kb hybridizing band did not appear except in the Changchun isolate.These results seem to indicate that there are differences between the isolates obtained from hosts in differ-ent geographical regions.

  13. Identification of planorbids from Venezuela by polymerase chain reaction amplification and restriction fragment length polymorphism of internal transcriber spacer of the RNA ribosomal gene

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2000-01-01

    Full Text Available Snails of the genus Biomphalaria from Venezuela were subjected to morphological assessment as well as polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP analysis. Morphological identification was carried out by comparison of characters of the shell and the male and female reproductive apparatus. The PCR-RFLP involved amplification of the internal spacer region ITS1 and ITS2 of the RNA ribosomal gene and subsequent digestion of this fragment by the restriction enzymes DdeI, MnlI, HaeIII and MspI. The planorbids were compared with snails of the same species and others reported from Venezuela and present in Brazil, Cuba and Mexico. All the enzymes showed a specific profile for each species, that of DdeI being the clearest. The snails were identified as B. glabrata, B. prona and B. kuhniana.

  14. Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.

    Science.gov (United States)

    Bengtsson, Johan; Hartmann, Martin; Unterseher, Martin; Vaishampayan, Parag; Abarenkov, Kessy; Durso, Lisa; Bik, Elisabeth M; Garey, James R; Eriksson, K Martin; Nilsson, R Henrik

    2012-07-01

    Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

  15. Direct and accurate measurement of CAG repeat configuration in the ataxin-1 (ATXN-1) gene by "dual-fluorescence labeled PCR-restriction fragment length analysis".

    Science.gov (United States)

    Lin, Jiang X; Ishikawa, Kinya; Sakamoto, Masaki; Tsunemi, Taiji; Ishiguro, Taro; Amino, Takeshi; Toru, Shuta; Kondo, Ikuko; Mizusawa, Hidehiro

    2008-01-01

    Spinocerebellar ataxia type 1 (SCA1; OMIM: #164400) is an autosomal dominant cerebellar ataxia caused by an expansion of CAG repeat, which encodes polyglutamine, in the ataxin-1 (ATXN1) gene. Length of polyglutamine in the ATXN1 protein is the critical determinant of pathogenesis of this disease. Molecular diagnosis of SCA1 is usually undertaken by assessing the length of CAG repeat configuration using primers spanning this configuration. However, this conventional method may potentially lead to misdiagnosis in assessing polyglutamine-encoding CAG repeat length, since CAT interruptions may be present within the CAG repeat configuration, not only in normal controls but also in neurologically symptomatic subjects. We developed a new method for assessing actual CAG repeat numbers not interrupted by CAT sequences. Polymerase chain reaction using a primer pair labeled with two different fluorescences followed by restriction enzyme digestion with SfaNI which recognizes the sequence "GCATC(N)(5)", lengths of actual CAG repeats that encode polyglutamine were directly detected. We named this method "dual fluorescence labeled PCR-restriction fragment length analysis". We found that numbers of actual CAG repeat encoding polyglutamine do not overlap between our cohorts of normal chromosomes (n=385) and SCA1 chromosomes (n=5). We conclude that the present method is a useful way for molecular diagnosis of SCA1.

  16. Meat speciation by restriction fragment length polymorphism analysis using an α-actin cDNA probe.

    Science.gov (United States)

    Fairbrother, K S; Hopwood, A J; Lockley, A K; Bardsley, R G

    1998-09-01

    Classical DNA fingerprinting is based on separation of DNA restriction fragments by electrophoresis and hybridisation to nucleic acid probes containing repetitive nucleotide sequences. The use of such mini- or micro-satellite probes tends to yield patterns specific to an individual rather than to a species, hence their value in forensic analysis but general unsuitability for meat speciation. In the present study, a cDNA probe based on conserved sequences contained in members of the actin multigene family has been evaluated for potential application in meat speciation. Genomic DNA was extracted from muscle and digested with BamHI before electrophoresis and hybridisation to a murine α-actin cDNA probe. Beef, pork, lamb, horse, chicken and fish DNA restriction fragments formed characteristic 'fingerprints' which were reproducible and varied sufficiently to allow discrimination even between closely-related species. However no major differences were seen between individuals of the same breed or between different breeds within a species. When DNA obtained from fresh tissue and also from meat heated at 120 °C was analysed, the gel patterns were essentially the same. An attractive feature of this approach is that it employs a single cross-reacting probe and set of conditions, and gives different patterns with all species so far studied. This simplicity suggests applications in meat speciation or related areas of biology.

  17. Identification of weakly beta-hemolytic porcine spirochetes by biochemical reactions, PCR-based restriction fragment length polymorphism analysis and species-specific PCR.

    Science.gov (United States)

    Ohya, Tatsuo; Araki, Hiroshi; Sueyoshi, Masuo

    2008-08-01

    We examined the usefulness of PCR-based restriction fragment length polymorphism (PCR-RFLP) and species-specific PCR combined with a newly devised rapid biochemical test using microplates for identifying weakly beta-hemolytic intestinal spirochetes (WBHIS) isolated from pigs. WBHIS strains showing atypical biochemical characteristics were decisively identified at the species level by PCR-RFLP and species-specific PCR. Identification of WBHIS at the species level in routine diagnostic work will certainly contribute to clarifying the pathogenicity of WBHIS.

  18. Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus.

    Science.gov (United States)

    Costa, Jean-Marc; Garcia-Hermoso, Dea; Olivi, Martine; Cabaret, Odile; Farrugia, Cécile; Lecellier, Gaël; Dromer, Françoise; Bretagne, Stéphane

    2010-03-01

    Microsatellite length polymorphism (MLP) typing is a PCR-based method used for genotyping of the diploid yeast Candida albicans. However, MLP is subject to homoplasia which can hamper the accuracy of the results. We combined fragment length analysis, high-resolution DNA melting (HRM) analysis, and SNaPshot minisequencing after a single amplification of the CDC3 locus to study 95 epidemiologically independent C. albicans isolates. HRM analysis for a given electrophoretic group led to a maximum of three different curves due to the presence of a SNP upstream of the tandem repeat which could be characterized using the SNaPshot assay. The combination of the three methods had a discriminatory index of 0.88 in complete congruence with previous MLP typing (Mantel test R=0.99, P<10(-)(4)). HRM is a useful tool of adding resolving power to MLP genotyping in identifying SNPs.

  19. Effect of linker length between variable domains of single chain variable fragment antibody against daidzin on its reactivity.

    Science.gov (United States)

    Yusakul, Gorawit; Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-07-01

    The peptide linker between variable domains of heavy (VH) and light (VL) chains is one of important factors that influence the characteristics of scFv, including binding activity and specificity against target antigen. The scFvs against daidzin (DZ-scFvs) with different linker lengths were constructed in the format of VH-(GGGGS)n-VL (n = 1, 3, 5, and 7). They were expressed in the hemolymph of silkworm larvae using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system, and their reactivity against daidzin and related compounds were evaluated using an indirect competitive enzyme-linked immunosorbent assay (icELISA), which is applicable for quantitative analysis of daidzin. The results showed that the reactivity of scFvs against daidzin was increased, whereas specificity slightly decreased when their peptide linker was lengthened. These results suggested that the linker length of DZ-scFvs contributes to its reactivity. In addition, the results emphasize that the linker length could control the reactivity of DZ-scFvs.

  20. Ligation-based assembly for constructing mouse synthetic scFv libraries by chain shuffling with in vivo-amplified VH and VL fragments.

    Science.gov (United States)

    Nishi, Michiru; Jian, Nan; Yamamoto, Keiko; Seto, Haruyo; Nishida, Yuichi; Tonoyama, Yasuhiro; Shimizu, Nobuyoshi; Nishi, Yoshisuke

    2014-10-01

    In vitro assembly of two or three PCR fragments using primers is a common method of constructing scFv fragments for display on the surface of phage. However, mismatch annealing often occurs during in this step, leading to cloning and display of incomplete Fab or scFv fragments. To overcome this limitation, we developed a ligation-based two-fragment assembly (LTFA) protocol that involved separately cloning VH and Vκ fragments into the high-copy-number plasmid pUC18. The VH and Vκ fragments had randomized complementarity-determining region 3 (CDR3) and were joined with a peptidyl linker composed of (G4S)3. Using this approach, complete sequences of scFv fragments were successfully constructed, and the sequencing of 83 scFv clones revealed that none of the sequences, including the linker region, contained deletions or mutations. In contrast, linker sequences generated using a conventional two-fragment PCR assembly (TFPA) protocol often contained sequence anomalies, including large truncations. Using the LTFA protocol, a final library size of 1.0×10(8)cfu was achieved. Examination of the amino acid profiles of the generated scFv fragments within the randomized regions introduced using degenerate codons did not detect any bias from that expected based on stochastic distribution. After several cycles of panning with this library, antigen-specific scFvs against two reference antigens, hen egg lysozyme and streptavidin were detected. In addition, scFvs with specificity against peptidyl antigens in the loop region of the Medaka ortholog of human C6orf89, which encodes a histone deacetylase enhancer that interacts with the bombesin receptor, were also obtained. The LTFA protocol developed here is robust and allows for the easy construction of integral scFv fragments compared with conventional TFPA. Utilizing LTFA, other CDRs can be readily combined. This approach also allows for the in vitro maturation of scFv fragments by separately introducing randomization in CDRs or

  1. A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae

    Directory of Open Access Journals (Sweden)

    Austin M. Wofford

    2014-04-01

    Full Text Available Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences ofycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group.

  2. A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)1

    Science.gov (United States)

    Wofford, Austin M.; Finch, Kristen; Bigott, Adam; Willyard, Ann

    2014-01-01

    • Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid simple sequence repeat (cpSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. • Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compared interspecific variation between cpSSRs and nucleotide sequences of ycf1 and tested intraspecific variation for cpSSRs using 911 samples in the P. ponderosa species complex. • Results: The cpSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions, and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. • Discussion: The protocol allows efficient genotyping of many samples. The cpSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for cpSSR loci in a plastome alignment for the target group. PMID:25202625

  3. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    Science.gov (United States)

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  4. The human tyrosine aminotransferase gene: characterization of restriction fragment length polymorphisms and haplotype analysis in a family with tyrosinemia type II.

    Science.gov (United States)

    Westphal, E M; Natt, E; Grimm, T; Odievre, M; Scherer, G

    1988-07-01

    Deficiency in hepatic tyrosine aminotransferase (TAT) causes tyrosinemia type II, an autosomal recessively inherited disorder. Using a TAT cosmid clone, we have identified an MspI restriction fragment length polymorphism (RFLP) 5' to the TAT gene, with allele frequencies of 0.63 and 0.37. Analysis of the cloned maternal and paternal TAT alleles from a patient with tyrosinemia type II led to the identification of a HaeIII RFLP at the 3' end of the TAT gene, with allele frequencies of 0.94 and 0.06. The two RFLPs are 27 kb apart and in no allelic association. From haplotype frequencies, a polymorphism information content (PIC) value of 0.44 was obtained. The two RFLPs have allowed the unambiguous identification of the mutant TAT alleles in the patient's pedigree by haplotype analysis.

  5. Performance of PCR-restriction fragment length polymorphism analysis of the Helicobacter pylori ureB gene in differentiating gene variants

    DEFF Research Database (Denmark)

    Colding, H; Hartzen, S H; Mohammadi, M;

    2003-01-01

    unrelated clinical H. pylori isolates with PCR-RFLP typing of the ureB gene (933 bp), combining the results obtained with restriction enzymes HaeIII and Sau3A, and a mixture of the enzymes. We therefore find that PCR-RFLP typing of the ureB gene of H. pylori with restriction enzymes HaeIII and Sau3A......Recently, PCR-restriction fragment length polymorphism (PCR-RFLP) of the urease genes of Helicobacter pylori was evaluated in a meta-analysis; acceptable discriminatory indices of the ureAB and C genes were found. In the present investigation, we found a discriminatory index of 0.95 for 191...

  6. Association of restriction fragment length polymorphism at the atrial natriuretic peptide gene locus with aldosterone responsiveness to angiotensin in aldosterone-producing adenoma.

    Science.gov (United States)

    Tunny, T J; Jonsson, J R; Klemm, S A; Ballantine, D M; Stowasser, M; Gordon, R D

    1994-11-15

    Primary aldosteronism is an important, potentially curable, form of hypertension. We examined the possible association between restriction fragment length polymorphisms in the atrial natriuretic peptide (ANP) gene and responsiveness of aldosterone to angiotensin II in 59 patients with primary aldosteronism due to aldosterone-producing adenoma (APA). Significant differences in the allelic frequencies of the BglI, TaqI and XhoI polymorphic sites at the ANP gene locus (chromosome 1; 1p36) between angiotensin II-unresponsive and angiotensin II-responsive tumors were observed. Variation in the ANP gene between the two groups may result in altered expression of ANP within the adrenal gland, and may contribute to the biochemical regulation of aldosterone production of these two subgroups of patients with APA.

  7. Genetic Typing of Bovine Viral Diarrhoea Virus (BVDV by Restriction Fragment Length Polymorphism (RFLP and Identification of a New Subtype in Poland

    Directory of Open Access Journals (Sweden)

    Kuta Aleksandra

    2015-04-01

    Full Text Available Restriction fragment length polymorphism (RFLP analysis was developed for genetic typing of Polish strains of bovine viral diarrhoea virus (BVDV. The method was applied using 60 BVDV isolates, which included BVDV genotype 1, subtypes a, b, d, e, f, and g, and genotype 2a. RT-PCR products of the 5’untranslated region (5’UTR were digested using three enzymes. Restriction patterns classified the strains into seven groups, each with a specific and different pattern from other subtypes. These findings were confirmed by nucleotide sequencing and phylogenetic analysis. The results suggest that RFLP analysis is a simple, reliable, and fast genotyping method for BVDV strains in comparison with sequencing. This method can distinguish six subtypes of BVDV-1 including a new subtype 1e, identified exclusively by this method, and it allows differentiation of BVDV-1 from BVDV-2 genotype.

  8. Genotyping of Candida orthopsilosis clinical isolates by amplification fragment length polymorphism reveals genetic diversity among independent isolates and strain maintenance within patients.

    Science.gov (United States)

    Tavanti, Arianna; Hensgens, Lambert A M; Ghelardi, Emilia; Campa, Mario; Senesi, Sonia

    2007-05-01

    Candida parapsilosis former groups II and III have recently been established as independent species named C. orthopsilosis and C. metapsilosis, respectively. In this report, 400 isolates (290 patients) previously classified as C. parapsilosis by conventional laboratory tests were screened by BanI digestion profile analysis of the secondary alcohol dehydrogenase gene fragment and by amplification fragment length polymorphism (AFLP). Thirty-three strains collected from 13 patients were identified as C. orthopsilosis, thus giving the first retrospective evidence that C. orthopsilosis was responsible for 4.5% of the infections/colonization attributed to C. parapsilosis. AFLP was proven to unambiguously identify C. orthopsilosis at the species level and efficiently delineate intraspecific genetic relatedness. A high percentage of polymorphic AFLP bands was observed for independent isolates collected from each patient. Statistical analysis of the pairwise genetic distances and bootstrapping revealed that clonal reproduction and recombination both contribute to C. orthopsilosis genetic population structure. AFLP patterns of sequential isolates obtained from two patients demonstrated that a successful strain colonization within the same patient occurred, as revealed by strain maintenance in various body sites. No association between AFLP markers and drug resistance was observed, and none of the clinical C. orthopsilosis isolates were found to produce biofilm in vitro.

  9. Amplification of a single-locus variable-number direct repeats with restriction fragment length polymorphism (DR-PCR/RFLP) for genetic typing of Acinetobacter baumannii strains.

    Science.gov (United States)

    Nowak-Zaleska, Alicja; Krawczyk, Beata; Kotłowski, Roman; Mikucka, Agnieszka; Gospodarek, Eugenia

    2008-01-01

    In search of an effective DNA typing technique for Acinetobacter baumannii strains for hospital epidemiology use, the performance and convenience of a new target sequence was evaluated. Using known genomic sequences of Acinetobacter baumannii strains AR 319754 and ATCC 17978, we developed single-locus variable-number direct-repeat analysis using polymerase chain reaction-restriction fragment length polymorphism (DR-PCR/RFLP) method. A total of 90 Acinetobacter baumannii strains isolated from patients of the Clinical Hospital in Bydgoszcz, Poland, were examined. Initially, all strains were typed using macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE). Digestion of the chromosomal DNA with the ApaI endonuclease and separation of the fragments by PFGE revealed 21 unique types. Application of DR-PCR/RFLP resulted in recognition of 12 clusters. The results showed that the DR-PCR/RFLP method is less discriminatory than REA-PFGE, however, the novel genotyping method can be used as an alternative technique for generating DNA profiles in epidemiological studies of intra-species genetic relatedness of Acinetobacter baumannii strains.

  10. Molecular characterization of the U.S. Phaseolus acutifolius A. Gray collection using Amplified Fragment Length Polymorphism (AFLP) and Targeted Region Amplification Polymorphism (TRAP) markers.

    Science.gov (United States)

    Tepary bean (Phaseolus acutifolius A. Gray), a truly Native American crop, is a short life-cycle annual desert legume indigenous to northwestern Mexico and the southwestern USA and is considered drought and heat tolerant. The Western Regional Plant Introduction Station currently maintains 211 acce...

  11. Genetic relatedness among Campylobacter jejuni serotyped isolates of diverse origin as determined by numerical analysis of amplified fragment length polymorphism (AFLP) profiles

    DEFF Research Database (Denmark)

    Siemer, B.L.; Harrington, C.S.; Nielsen, E.M.;

    2004-01-01

    health. The remaining 30 groups contained isolates from humans, chickens and associated food products, cattle, sheep, turkeys, ostriches and/or dogs. Strains assigned to serotypes 2, 6/7, 11 and 12 formed major clusters at the 77.6% S-level. Most other serotypes did not form homogeneous clusters...... of the Study: The genetic relatedness among all 'Penner' serotypes of C. jejuni is assessed by AFLP analysis. In addition, further evidence of epidemic and host-specific clones of C. jejuni is provided....

  12. Molecular epidemiology of contagious bovine pleuropneumonia in Tanzania based on amplified fragment length polymorphism and pulsed-field gel electrophoresis analysis

    DEFF Research Database (Denmark)

    Kusiluka, L.J.M.; Ojeniyi, B.; Friis, N.F.;

    2001-01-01

    The genetic diversity of 60 field strains of Mycoplasma mycoides ssp. mycoides, small colony type (M,. mycoides), comprising 56 isolates from cattle in Tanzania, one from Kenya, two from Botswana and one from Portugal, as well as the type (PG1(T)) and vaccine (T-1-SR49) strains, was ivestigated. ......, this study; has demonstrated that AFLP and PFGE are potential tools for molecular epidemiological studies of M. mycoides SC infections....

  13. DNA Polymorphism Detection of Cannabis Using Amplified Fragment Length Polymorphism%应用AFLP检测大麻遗传多样性

    Institute of Scientific and Technical Information of China (English)

    郭佳; 裴黎; 彭建雄; 翟红; 张贵芹; 揭琴; 涂政

    2008-01-01

    目的 筛选对于大麻多态性好的AFLP引物标记来区分大麻品种.方法 利用AFLP技术用55对引物组合对12个大麻地域品种进行初筛.结果 选出5对多态性好的引物组合进行了遗传多样性研究.每对AFLP引物组合扩增出47~76务带.共获得285条带,其中多态性条带为99条以及10条品种特异带.结论 AFLP对于大麻具有很高的分辨率,为今后深入地研究大麻植物遗传多样性奠定了很好的基础.

  14. Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

    Science.gov (United States)

    Kerkhof, L.; Santoro, M.; Garland, J.

    2000-01-01

    In this report, we describe an experiment conducted at Kennedy Space Center in the biomass production chamber (BPC) using soybean plants for purification and processing of human hygiene water. Specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. Plants were grown in hydroponics media corresponding to four different treatments: control (Hoagland's solution), artificial gray water (Hoagland's+surfactant), filtered gray water collected from human subjects on site, and unfiltered gray water. Differences in rhizosphere microbial populations in all experimental treatments were observed when compared to the control treatment using both community level physiological profiles (BIOLOG) and molecular fingerprinting of 16S rRNA genes by terminal restriction fragment length polymorphism analysis (TRFLP). Furthermore, screening of a clonal library of 16S rRNA genes by TRFLP yielded nearly full length SSU genes associated with the various treatments. Most 16S rRNA genes were affiliated with the Klebsiella, Pseudomonas, Variovorax, Burkholderia, Bordetella and Isosphaera groups. This molecular approach demonstrated the ability to rapidly detect and identify microorganisms unique to experimental treatments and provides a means to fingerprint microbial communities in the biosystems being developed at NASA for optimizing advanced life support operations.

  15. TARC: Carlo Rubbia's Energy Amplifier

    CERN Multimedia

    Laurent Guiraud

    1997-01-01

    Transmutation by Adiabatic Resonance Crossing (TARC) is Carlo Rubbia's energy amplifier. This CERN experiment demonstrated that long-lived fission fragments, such as 99-TC, can be efficiently destroyed.

  16. Rapid identification of rumen protozoa by restriction analysis of amplified 18S rRNA gene

    NARCIS (Netherlands)

    Regensbogenova, M.; Kisidayova, S.; Michalowski, T.; Javorsky, P.; Moon-van der Staay, S.Y.; Hackstein, J.H.P.; McEwan, N.R.; Jouany, J.P.; Newbold, J.C.; Pristas, P.

    2004-01-01

    A rapid method has been developed for molecular identification of rumen ciliates without the need for cultivation. Total DNA was isolated from single protozoal cells by the Chelex method and nearly complete protozoal 18S rRNA genes were amplified and subjected to restriction fragment length polymorp

  17. Towards the molecular characterisation of parasitic nematode assemblages: an evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis.

    Science.gov (United States)

    Lott, M J; Hose, G C; Power, M L

    2014-09-01

    Identifying factors which regulate temporal and regional structuring within parasite assemblages requires the development of non-invasive techniques which facilitate both the rapid discrimination of individual parasites and the capacity to monitor entire parasite communities across time and space. To this end, we have developed and evaluated a rapid fluorescence-based method, terminal restriction fragment length polymorphism (T-RFLP) analysis, for the characterisation of parasitic nematode assemblages in macropodid marsupials. The accuracy with which T-RFLP was capable of distinguishing between the constituent taxa of a parasite community was assessed by comparing sequence data from two loci (the ITS+ region of nuclear ribosomal DNA and the mitochondrial CO1) across ∼20 species of nematodes (suborder Strongylida). Our results demonstrate that with fluorescent labelling of the forward and reverse terminal restriction fragments (T-RFs) of the ITS+ region, the restriction enzyme Hinf1 was capable of generating species specific T-RFLP profiles. A notable exception was within the genus Cloacina, in which closely related species often shared identical T-RFs. This may be a consequence of the group's comparatively recent evolutionary radiation. While the CO1 displayed higher sequence diversity than the ITS+, the subsequent T-RFLP profiles were taxonomically inconsistent and could not be used to further differentiate species within Cloacina. Additionally, several of the ITS+ derived T-RFLP profiles exhibited unexpected secondary peaks, possibly as a consequence of the restriction enzymes inability to cleave partially single stranded amplicons. These data suggest that the question of T-RFLPs utility in monitoring parasite communities cannot be addressed without considering the ecology and unique evolutionary history of the constituent taxa.

  18. In vivo Dopamine Efflux is Decreased in Striatum of both Fragment (R6/2) and Full-Length (YAC128) Transgenic Mouse Models of Huntington's Disease.

    Science.gov (United States)

    Callahan, Joshua W; Abercrombie, Elizabeth D

    2011-01-01

    Huntington's disease (HD) is characterized by numerous alterations within the corticostriatal circuitry. The striatum is innervated by a dense array of dopaminergic (DA) terminals and these DA synapses are critical to the proper execution of motor functions. As motor disturbances are prevalent in HD we examined DA neurotransmission in the striatum in transgenic (tg) murine models of HD. We used in vivo microdialysis to compare extracellular concentrations of striatal DA in both a fragment (R6/2) model, which displays a rapid and severe phenotype, and a full-length (YAC128) model that expresses a more progressive phenotype. Extracellular striatal DA concentrations were significantly reduced in R6/2 mice and decreased concomitantly with age-dependent increasing motor impairments on the rotarod task (7, 9, and 11 weeks). In a sample of 11-week-old R6/2 mice, we also measured tissue concentrations of striatal DA and found that total levels of DA were significantly depleted. However, the loss of total DA content (<50%) was insufficient to account for the full extent of DA depletion in the extracellular fluid (ECF; ∼75%). We also observed a significant reduction in extracellular DA concentrations in the striatum of 7-month-old YAC128 mice. In a separate set of experiments, we applied d-amphetamine (AMPH; 10 μm) locally into the striatum to stimulate the release of intracellular DA into the ECF. The AMPH-induced increase in extracellular DA levels was significantly blunted in 9-week-old R6/2 mice. There also was a decrease in AMPH-stimulated DA efflux in 7-month-old YAC128 mice in comparison to WT controls, although the effect was milder. In the same cohort of 7-month-old YAC128 mice we observed a significant reduction in the total locomotor activity in response to systemic AMPH (2 mg/kg). Our data demonstrate that extracellular DA release is attenuated in both a fragment and full-length tg mouse model of HD and support the concept of DA involvement in aspects of

  19. Unusual sequence length-dependent gold nanoparticles aggregation of the ssDNA sticky end and its application for enzyme-free and signal amplified colorimetric DNA detection

    Science.gov (United States)

    He, Hongfei; Dai, Jianyuan; Duan, Zhijuan; Zheng, Baozhan; Meng, Yan; Guo, Yong; Dan Xiao, A1"/>

    2016-08-01

    It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

  20. Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates.

    Science.gov (United States)

    Duffy, Lesley L; Blackall, Patrick J; Cobbold, Rowland N; Fegan, Narelle

    2015-06-01

    Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute.

  1. Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay.

    Science.gov (United States)

    Zhang, Yi; Guo, Gang; Huang, Hetian; Lu, Lu; Wang, Lijie; Fang, Lingzhao; Liu, Lin; Wang, Yachun; Zhang, Shengli

    2015-09-01

    An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene.

  2. A semester-long project for teaching basic techniques in molecular biology such as restriction fragment length polymorphism analysis to undergraduate and graduate students.

    Science.gov (United States)

    DiBartolomeis, Susan M

    2011-01-01

    Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky(73). Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers.

  3. Restriction Fragment Length Polymorphism Analysis of Large Subunit rDNA of Symbiotic Dinoflagellates from Scleractinian Corals in the Zhubi Coral Reef of the Nansha Islands

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Zooxanthellae are very important for the coral reef ecosystem. The diversity of coral hosts is high in the South China Sea, but the diversity of zooxanthellae has not yet been investigated. We chose the Zhubi Coral Reef of the Nansha Islands as the region to be surveyed in the present study because it represents a typical tropical coral reef of the South China Sea and we investigated zooxanthellae diversity in 10 host scleractinian coral species using polymerase chain reaction (PCR) of the large subunit rRNA and restriction fragment length polymorphism (RFLP) patterns. Pocillopora verrucosa, Acropora pelifera, Acropora millepora, Fungia fungites, Galaxea fascicularis, and Acropora pruinosa harbor Clade C, Goniastrea aspera harbors Clade D, and Acropora formosa harbors Clades D and C. Therefore, the Clade C is the dominant type in the Zhubi Coral Reef of the NanshaIslands. Furthermore, the results of the present also disprove what has been widely accepted, namely that one coral host harbors only one algal symbiont. The coral-algal symbiosis is flexible, which may be an important mechanism for surviving coral bleaching. Meanwhile, on the basis of the results of the present study, we think that Symbiodinium Clade D may be more tolerant to stress than Symbiodinium Clade C.

  4. Restriction fragment length polymorphism of ovine casein genes: close linkage between the alpha s1-, alpha s2-, beta- and kappa-casein loci.

    Science.gov (United States)

    Leveziel, H; Metenier, L; Guerin, G; Cullen, P; Provot, C; Bertaud, M; Mercier, J C

    1991-01-01

    Restriction fragment length polymorphism (RFLP) of ovine casein genes was investigated. Genomic DNA from 56 rams was digested with 10 restriction endonucleases and Southern blots probed with the four ovine casein cDNAs (alpha s1-, beta-, alpha s2- and kappa-Cn). Five enzymes, namely, BglI, PvuII, RsaI, TaqI and HindIII revealed nine different RFLPs. The inheritance of six of these polymorphisms was studied by segregation analysis of gametes in nine rams' families, and each of them could be related to the existence of alleles at the relevant casein locus. A close linkage between the four ovine casein genes was demonstrated since no recombination within the four pairs of loci examined, alpha s1-beta-Cn, alpha s1-kappa-Cn, beta-kappa-Cn and alpha s2-kappa-Cn, was observed in the progeny of double heterozygous rams. The casein genes are thus clustered in the ovine species as in the case of other mammals.

  5. Distribution of genes encoding putative virulence factors and fragment length polymorphisms in the vrrA gene among Brazilian isolates of Bacillus cereus and Bacillus thuringiensis.

    Science.gov (United States)

    Zahner, Viviane; Cabral, Diana Aparecida; Régua-Mangia, Adriana Hamond; Rabinovitch, Leon; Moreau, Gaétan; McIntosh, Douglas

    2005-12-01

    One hundred twenty-one strains of the Bacillus cereus complex, of which 80 were isolated from a variety of sources in Brazil, were screened by PCR for the presence of sequences (bceT, hblA, nheBC, plc, sph, and vip3A) encoding putative virulence factors and for polymorphisms in variable-number tandem repeats (VNTR), using a variable region of the vrrA open reading frame as the target. Amplicons were generated from isolates of B. cereus and Bacillus thuringiensis for each of the sequences encoding factors suggested to play a role in infections of mammals. Intriguingly, the majority of these sequences were detected more frequently in Bacillus thuringiensis than in B. cereus. The vip3A sequence, which encodes an insecticidal toxin, was detected exclusively in B. thuringiensis. VNTR analysis demonstrated the presence of five different fragment length categories in both species, with two of these being widely distributed throughout both taxa. In common with data generated from previous studies examining European, Asian, or North American populations, our investigation of Brazilian isolates supports the notion that B. cereus and B. thuringiensis should be considered to represent a single species.

  6. Amplification refractory mutation system polymerase chain reaction versus optimized polymerase chain reaction restriction-fragment length polymorphism for apolipoprotein E genotyping of majorly depressed patients.

    Science.gov (United States)

    You, Hongmin; Chen, Jin; Zhou, Jingjing; Huang, Hua; Pan, Junxi; Wang, Ziye; Lv, Lin; Zhang, Lujun; Li, Juan; Qin, Bin; Yang, Yongtao; Xie, Peng

    2015-11-01

    Major depressive disorder (MDD) is a prevalent, debilitating mood disorder that has been associated with several genetic polymorphisms. One such polymorphism, namely that of apolipoprotein E (APOE), has three allelic forms (ε2, ε3 and ε4) that encode for six unique isoforms of the APOE protein. A growing number of techniques have been developed for APOE genotyping; however, not all polymerase chain reaction (PCR)‑based genotyping techniques are equally accurate or cost‑effective. In order to find a more accurate and cost‑effective APOE genotyping method for MDD screening in large populations, the present study comparatively evaluated two genotyping methods, amplification refractory mutation system PCR (ARMS‑PCR) and optimized PCR restriction‑fragment length polymorphism (PCR‑RFLP), in blood samples taken from a population of 708 MDD patients. Although either of the two methods were able to detect all six unique APOE genotypes, comparisons of the two methods with Sanger sequencing demonstrated that ARMS‑PCR (94%) was significantly more accurate than optimized PCR‑RFLP (82%). ARMS‑PCR should prove useful in quickly verifying ambiguous results obtained by other APOE genotyping methods and can be cost-effectively performed in the setting of a small laboratory or a population-based screening program.

  7. Evaluation of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay for molecular epidemiological study of Shiga toxin-producing Escherichia coli.

    Science.gov (United States)

    Sugimoto, Norihiko; Shima, Kensuke; Hinenoya, Atsushi; Asakura, Masahiro; Matsuhisa, Akio; Watanabe, Haruo; Yamasaki, Shinji

    2011-07-01

    In this study, we have evaluated our recently developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for the molecular subtyping of Shiga toxin-producing Escherichia coli (STEC). A total of 200 STEC strains including O157 (n=100), O26 (n=50), O111 (n=10), and non-O26/O111/O157 (n=40) serogroups isolated during 2005-2006 in Japan, which were identified to be clonally different by pulsed-field gel electrophoresis (PFGE) were further analyzed by the PCR-RFLP assay in comparison to PFGE. Ninety-five of O157, 48 of O26, five of O111 and 19 of non-O26/O111/O157 STEC strains yielded one to three amplicons ranging from 6.0 to 15.5 kb in size by the specific primer set targeting region V which is located in the upstream of stx genes. These strains were classified into 41 (O157), 8 (O26), 4 (O111) and 17 (non-O26/O111/O157) groups based on the RFLP patterns obtained by subsequent restriction digestion, respectively. Although the discriminatory power of PCR-RFLP assay was somewhat less than that of PFGE, it is more convenient for molecular subtyping of STEC strains especially for O157, the most important serogroup implicated in human diseases, as well as to identify the outbreak-associated isolates because of its simplicity, rapidity, ease and good reproducibility.

  8. Application of restriction fragment length polymorphism analysis to simple and rapid genotyping of bovine viral diarrhea virus strains isolated in Japan.

    Science.gov (United States)

    Seki, Yoshihisa; Seimiya, Yukio M; Motokawa, Masato; Yaegashi, Gakuji; Nagai, Makoto; Hayashi, Michiko

    2008-04-01

    The E2 regions of 177 bovine viral diarrhea virus (BVDV) strains isolated in Japan between 1957 and 2006 were analyzed for genotyping. The strains were classified into 8 genotypes (1a, 1b, 1c, 1d, 1e, 1f, So and 2a) based on the phylogenetic analysis. The restriction fragment length polymorphism (RFLP) analysis of the RT-PCR products using 6 selected enzymes (Apo I, Mly I, BstAP I, Pvu II, Ear I, EcoR V) disclosed the cutting patterns classified into 11 groups (I-XI), each of that consisted of strains belonging to a single genotype. Namely, groups-I and -II were composed by genotype-1a strains, groups-III and -IV by 1b strains, and groups-V and -VI by 1c strains. Other groups-VII, -VIII, -IX, -X and -XI comprised genotypes-1d, -1e, -1f, -So and -2a strains, respectively. The results suggest that the RFLP analysis can simply and rapidly differentiate the 8 genotypes of BVDV strains.

  9. Genotypic characterization of Indian isolates of infectious bursal disease virus strains by reverse transcription-polymerase chain reaction combined with restriction fragment length polymorphism analysis.

    Science.gov (United States)

    Priyadharsini, C V; Senthilkumar, T M A; Raja, P; Kumanan, K

    2016-03-01

    The reverse transcription PCR (RT-PCR) combined with restriction fragment length polymorphism (RFLP) is used for the differentiation of classical virulent (cv), virulent (v) and very virulent (vv) strains of infectious bursal disease virus (IBDV) isolates from chicken bursal tissues in southern states of India. In the present study, six different isolates (MB11, HY12, PY12, BGE14, VCN14 and NKL14) of IBDV strains were subjected for genotyping along with vaccine virus (Georgia, intermediate strain) using RT-PCR for amplification of a 743 bp sequence in the hypervariable region of VP2 gene followed by restriction enzyme digestion with 5 different restriction enzymes (BspMI, SacI, HhaI, StuI and SspI). The RT-PCR products obtained from vvIBDV strains were digested by SspI enzyme except PY12, BGE14 and MB11 isolates. The SacI digested the isolate MB11, PY12 and the vaccine strain, but it did not cleave the very virulent isolates of IBDV. HhaI cleaved all the isolates with different restriction profile patterns. StuI digested all the vvIBDV isolates and BspMI was not able to differentiate field isolates from vaccine strain. Though RT-PCR combined with RFLP is a genotypic method, further confirmation of serotypes to distinguish the vvIBDV from cvIBDV has to be carried out using pathogenicity studies.

  10. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene.

    Science.gov (United States)

    Yadegar, Abbas; Alebouyeh, Masoud; Lawson, Andy J; Mirzaei, Tabassom; Nazemalhosseini Mojarad, Ehsan; Zali, Mohammad Reza

    2014-06-01

    Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.

  11. Pros and cons of ion-torrent next generation sequencing versus terminal restriction fragment length polymorphism T-RFLP for studying the rumen bacterial community.

    Science.gov (United States)

    de la Fuente, Gabriel; Belanche, Alejandro; Girwood, Susan E; Pinloche, Eric; Wilkinson, Toby; Newbold, C Jamie

    2014-01-01

    The development of next generation sequencing has challenged the use of other molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP). Although absolute number differed, there was a high correlation between NGS and T-RFLP in terms of richness and diversity with R values of 0.836 and 0.781 for richness and Shannon-Wiener index, respectively. Dendrograms for both datasets were also highly correlated (Mantel test = 0.742). Eighteen OTUs and ten genera were significantly impacted by the addition of rumen protozoa, with an increase in the relative abundance of Prevotella, Bacteroides and Ruminobacter, related to an increase in free ammonia levels in the rumen. Our findings suggest that classic fingerprinting methods are still valuable tools to study microbial diversity and structure in complex environments but that NGS techniques now provide cost effect alternatives that provide a far greater level of information on the individual members of the microbial population.

  12. DNA sequence analysis and restriction fragment length polymorphisms of the P1 gene of Haemophilus influenzae biogroup aegyptius associated with Brazilian purpuric fever.

    Science.gov (United States)

    Reed, R B; Frost, J B; Kort, K; Myers, S D; Lesse, A J

    1996-09-01

    Brazilian purpuric fever (BPF) is a fulminant pediatric disease caused by specific strains of Haemophilus influenzae biogroup aegyptius. A conserved epitope on the P1 protein of strains of H. influenzae biogroup aegyptius is seen on most virulent isolates. The P1 protein from a Brazilian case-clone strain of H. influenzae biogroup aegyptius was analyzed by cloning and sequencing the gene. Three major variable regions are present within the P1 gene of the BPF clone in an architecture similar to that of the previously sequenced P1 genes from H. influenzae. The DNA sequence data of the P1 gene provided information for restriction fragment length polymorphism analyses among strains of H. influenzae biogroup aegyptius. Using PCR for amplification of the P1 gene, we found that AlwI restriction of this gene allowed for a highly accurate segregation of virulent strains of H. influenzae biogroup aegyptius associated with BPF. The strong association of virulent phenotypes with specific AlwI restriction patterns of the P1 gene provides a basis for the convenient and accurate identification of strains of H. influenzae biogroup aegyptius which cause BPF.

  13. Clustering of Beijing genotype Mycobacterium tuberculosis isolates from the Mekong delta in Vietnam on the basis of variable number of tandem repeat versus restriction fragment length polymorphism typing

    Directory of Open Access Journals (Sweden)

    Huyen Mai NT

    2013-02-01

    Full Text Available Abstract Background In comparison to restriction fragment length polymorphism (RFLP typing, variable number of tandem repeat (VNTR typing is easier to perform, faster and yields results in a simple, numerical format. Therefore, this technique has gained recognition as the new international gold standard in typing of Mycobacterium tuberculosis. However, some reports indicated that VNTR typing may be less suitable for Beijing genotype isolates. We therefore compared the performance of internationally standardized RFLP and 24 loci VNTR typing to discriminate among 100 Beijing genotype isolates from the Southern Vietnam. Methods Hundred Beijing genotype strains defined by spoligotyping were randomly selected and typed by RFLP and VNTR typing. The discriminatory power of VNTR and RFLP typing was compared using the Bionumerics software. Results Among 95 Beijing strains available for analysis, 14 clusters were identified comprising 34 strains and 61 unique profiles in 24 loci VNTR typing ((Hunter Gaston Discrimination Index (HGDI = 0.994. 13 clusters containing 31 strains and 64 unique patterns in RFLP typing (HGDI = 0.994 were found. Nine RFLP clusters were subdivided by VNTR typing and 12 VNTR clusters were split by RFLP. Five isolates (5% revealing double alleles or no signal in two or more loci in VNTR typing could not be analyzed. Conclusions Overall, 24 loci VNTR typing and RFLP typing had similar high-level of discrimination among 95 Beijing strains from Southern Vietnam. However, loci VNTR 154, VNTR 2461 and VNTR 3171 had hardly added any value to the level of discrimination.

  14. Molecular identification of Candida species isolated from cases of neonatal candidemia using polymerase chain reaction-restriction fragment length polymorphism in a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    Akeela Fatima

    2017-01-01

    Full Text Available Context: Candida spp. is an emerging cause of bloodstream infections worldwide. Delay in speciation of Candida isolates by conventional methods and resistance to antifungal drugs in various Candida species are responsible for the increase in morbidity and mortality due to candidemia. Hence, the rapid identification of Candida isolates is very important for the proper management of patients with candidemia. Aims: The aim was to re-evaluate the identification of various Candida spp. by polymerase chain reaction (PCR-restriction fragment length polymorphism (RFLP and to evaluate the accuracy, speed, and cost of phenotypic methodology versus PCR-RFLP. Settings and Design: Hospital-based cross-sectional study. Materials and Methods: Ninety consecutive clinical isolates of seven Candida species, isolated from blood of neonates and identified by routine phenotypic methods, were re-evaluated using universal primers internal transcribed spacer 1 (ITS1 and ITS4 for PCR amplification and Msp I restriction enzyme for RFLP. Statistical Analysis Used: Kappa test for agreement. Results: The results of PCR-RFLP were 100% in agreement with those obtained using conventional phenotypic methods. Identification could be achieved within 3 work days by both the methods. Our routine methods proved to be cost effective than PCR-RFLP. Conclusions: We can continue with our routine phenotypic methods and PCR-RFLP can be used for periodic quality control or when conventional methods fail to identify a species.

  15. IR action spectroscopy shows competitive oxazolone and diketopiperazine formation in peptides depends on peptide length and identity of terminal residue in the departing fragment.

    Science.gov (United States)

    Morrison, L J; Chamot-Rooke, J; Wysocki, V H

    2014-05-01

    The interplay between the entropically and enthalpically favored products of peptide fragmentation is probed using a combined experimental and theoretical approach. These b2 ion products can take either an oxazolone or diketopiperazine structure. Cleavage after the second amide bond is often a favorable process because the products are small ring structures that are particularly stable. These structures are structurally characterized by action IRMPD spectroscopy and semi-quantified using gas-phase hydrogen-deuterium exchange. The formation of the oxazolone and diketopiperazine has been thought to be largely governed by the identity of the first two residues at the N-terminus of the peptide. We show here that the length of the precursor peptide and identity of the third residue play a significant role in the formation of the diketopiperazine structure in peptides containing an N-terminal asparagine residue. This is additionally the first instance showing an N-terminal residue with an amide side chain can promote formation of the diketopiperazine b2 ion structure.

  16. Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The characterization of microbial communities of different depth sediment samples was examined by a culture-independent method and compared with physicochemical parameters, those are organic matter (OM), total nitrogen (TN), total phosphorus (TP), pH and redox potential (Eh). Total genomic DNA was extracted from samples derived from different depths. After they were amplified with the GC-341f/907r primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis (DGGE). The profile of DGGE fingerprints of different depth sediment samples revealed that the community structure remained relatively stable along the entire 45 cm sediment core, however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. The principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into two groups, which were located 0-20 cm and 21-45 cm, respectively. The sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belonged to Bacillus, Bacterium, Brevibacillus, Exiguobacterium, γ-Proteobacterium, Acinetobacter sp. And some uncultured or unidentified bacteria. The results indicated the existence of highly diverse bacterial community in the lake sediment core.

  17. Chain-amplified photochemical fragmentation of N-alkoxypyridinium salts: proposed reaction of alkoxyl radicals with pyridine bases to give pyridinyl radicals.

    Science.gov (United States)

    Shukla, Deepak; Adiga, Shashishekar P; Ahearn, Wendy G; Dinnocenzo, Joseph P; Farid, Samir

    2013-03-01

    Photoinduced electron transfer to N-alkoxypyridiniums, which leads to N–O bond cleavage and alkoxyl radical formation, is highly chain amplified in the presence of a pyridine base such as lutidine. Density functional theory calculations support a mechanism in which the alkoxyl radicals react with lutidine via proton-coupled electron transfer (PCET) to produce lutidinyl radicals (BH•). A strong electron donor, BH• is proposed to reduce another alkoxypyridinium cation, leading to chain amplification, with quantum yields approaching 200. Kinetic data and calculations support the formation of a second, stronger reducing agent: a hydrogen-bonded complex between BH• and another base molecule (BH•···B). Global fitting of the quantum yield data for the reactions of four pyridinium salts (4-phenyl and 4-cyano with N-methoxy and N-ethoxy substituents) led to a consistent set of kinetic parameters. The chain nature of the reaction allowed rate constants to be determined from steady-state kinetics and independently determined chain-termination rate constants. The rate constant of the reaction of CH3O• with lutidine to form BH•, k1, is ~6 × 10(6) M(–1) s(–1); that of CH3CH2O• is ~9 times larger. Reaction of CD3O• showed a deuterium isotope effect of ~6.5. Replacing lutidine by 3-chloropyridine, a weaker base, decreases k1 by a factor of ~400.

  18. Utility of MtCOI polymerase chain reaction-restriction fragment length polymorphism in differentiating between Q and B whitefly Bemisia tabaci biotypes

    Institute of Scientific and Technical Information of China (English)

    Wei-Hua Ma; Xian-Chun Li; Timothy J. Dennehy; Chao-Liang Lei; Mo Wang; Benjamin A. Degain; Robert L. Nichols

    2009-01-01

    The invasive, insecticide-resistant, Q whitefly biotype, has gradually spread to other countries including the US via human-mediated movement of plant materials. We assessed the utility of the VspI-based mtCOl (mitochondrion cytochrome oxidase I) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) tech-nique as a rapid, cost-effective, and reliable alternative for differentiating the Q from the dominant B biotype in Arizona. Using the standard mtCOI gene sequencing and mtCOI PCR-RFLP techniques, we biotyped eight whitefly strains of five individuals each collected from poinsettia and cotton at different locations in Arizona. Complete concordance was observed between the two methods, with three strains being identified as the Q biotype and five samples as the B biotype. We also scanned the mtCOI gene sequences for VspI polymorphisms in the B and Q biotype whiteflies currently available in the GenBank database. This global screening revealed the existence of three and four VspI polymorphic types for the Q and B biotypes, respectively. Nevertheless, all three VspI polymorphic Q biotype whiteflies shared a common and unique VspI site that can be used to differentiate Q biotype from the four VspI polymorphic B biotype whiteflies identified. These results demonstrate that the VspI-based mtCOI gene PCR-RFLP provides a reliable diagnostic tool for differentiating the Q and B biotype whiteflies in the US and elsewhere.

  19. Development of a PCR-restriction fragment length polymorphism assay for detection and subtyping of cholix toxin variant genes of Vibrio cholerae.

    Science.gov (United States)

    Awasthi, Sharda Prasad; Asakura, Masahiro; Neogi, Sucharit Basu; Hinenoya, Atsushi; Ramamurthy, T; Yamasaki, Shinji

    2014-05-01

    Cholix toxin (ChxA) is an exotoxin reported in Vibrio cholerae non-O1/non-O139. Apart from its prototype (ChxA I) we have recently identified two novel variants of this toxin, ChxA II and ChxA III. Our previous investigations indicated that the first two variants may instigate extra-intestinal infections and ChxA II can be more lethal than ChxA I in mice. However, all three cholix toxins (ChxA I to III) failed to show any enterotoxicity in rabbit ileal loops. In this study we developed a PCR-restriction fragment length polymorphism (RFLP) assay to differentiate all three chxA variants to further understand the importance of each subtype. By using 53 V. cholerae non-O1/non-O139 strains harbouring chxA genes, which were previously categorized by sequencing, and various other strains as negative controls, the PCR-RFLP assay showed 100 % typability and specificity. Furthermore, when applied to differentiate additional V. cholerae strains, which were also screened for the chxA gene by colony hybridization, this assay identified chxA I and chxA II genes among 18.5 % and 4.5 % of non-O1/non-O139 strains (n = 178), respectively. One non-O1/non-O139 strain was untypable due to the insertion of an IS911-like element. Interestingly, the chxA I gene was detected in 10 out of 137 cholera toxin gene-negative V. cholerae O1 strains. These results suggest that the PCR-RFLP assay developed in this study can be a rapid and simple method to differentiate the chxA subtypes.

  20. Evaluation of antiviral resistant hepatitis B virus subpopulations in patients with chronic hepatitis B by using terminal restriction fragment length polymorphism.

    Science.gov (United States)

    Şahin, Ergin

    2015-12-01

    Antiviral therapies with nucleotide analogues (NA) is crucial in the treatment of chronic hepatitis B as it substantially protects patients from the complications of the disease . However in most of the available NA therapies, resistance emerges in the patients' HBV populations. Therefore, detection of antiviral resistance as early as possible by means of genotypically monitoring the patients' HBV pool during NA therapy is critical to manage treatment regime. In this research study we have investigated the sensitivity and specificity of the terminal restriction fragment length polymorphism (T-RFLP) method in detecting HBV subpopulations carrying antiviral resistance mutations. For this aim, differentiation of mutant strains from wild type strains was demonstrated by PCR-RFLP method. With using recombinant plasmids containing mutant and wild type HBV genomes, we constructed artificial HBV genome populations in order to determine the sensitivity of PCR-T-RFLP method in detecting antiviral resistant minor HBV populations. Finally by comparing with the DNA sequencing method, we demonstrated the specificity of T-RFLP method in genotyping HBV populations. As a result we showed that T-RFLP is able to detect HBV subpopulations representing as low as 1 % of the whole viral population. Additionally T-RFLP showed 100 % concordance with the DNA sequencing method in genotyping HBV populations. As a conclusion, considering the other genotyping methods used in evaluating HBV populations, T-RFLP showed high sensitivity and specificity profiles in detecting antiviral resistant HBV subpopulations. Therefore T-RFLP method can be easily employed in genotypic evaluation of patients' HBV populations during the course of antiviral treatment.

  1. Comparison of human gut microbiota in control subjects and patients with colorectal carcinoma in adenoma: Terminal restriction fragment length polymorphism and next-generation sequencing analyses.

    Science.gov (United States)

    Kasai, Chika; Sugimoto, Kazushi; Moritani, Isao; Tanaka, Junichiro; Oya, Yumi; Inoue, Hidekazu; Tameda, Masahiko; Shiraki, Katsuya; Ito, Masaaki; Takei, Yoshiyuki; Takase, Kojiro

    2016-01-01

    Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in Japan. The etiology of CRC has been linked to numerous factors including genetic mutation, diet, life style, inflammation, and recently, the gut microbiota. However, CRC-associated gut microbiota is still largely unexamined. This study used terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing (NGS) to analyze and compare gut microbiota of Japanese control subjects and Japanese patients with carcinoma in adenoma. Stool samples were collected from 49 control subjects, 50 patients with colon adenoma, and 9 patients with colorectal cancer (3/9 with invasive cancer and 6/9 with carcinoma in adenoma) immediately before colonoscopy; DNA was extracted from each stool sample. Based on T-RFLP analysis, 12 subjects (six control and six carcinoma in adenoma subjects) were selected; their samples were used for NGS and species-level analysis. T-RFLP analysis showed no significant differences in bacterial population between control, adenoma and cancer groups. However, NGS revealed that i), control and carcinoma in adenoma subjects had different gut microbiota compositions, ii), one bacterial genus (Slackia) was significantly associated with the control group and four bacterial genera (Actinomyces, Atopobium, Fusobacterium, and Haemophilus) were significantly associated with the carcinoma-in-adenoma group, and iii), several bacterial species were significantly associated with each type (control: Eubacterium coprostanoligens; carcinoma in adenoma: Actinomyces odontolyticus, Bacteroides fragiles, Clostridium nexile, Fusobacterium varium, Haemophilus parainfluenzae, Prevotella stercorea, Streptococcus gordonii, and Veillonella dispar). Gut microbial properties differ between control subjects and carcinoma-in-adenoma patients in this Japanese population, suggesting that gut microbiota is related to CRC prevention and development.

  2. Community analysis of ammonia oxidizer in the oxygen-limited nitritation stage of OLAND system by DGGE of PCR amplified 16S rDNA Fragments and FISH

    Institute of Scientific and Technical Information of China (English)

    ZHANG Dan; ZHANG De-min; LIU Yao-ping; CAO Wen-wei; CHEN Guan-xiong

    2004-01-01

    OLAND(oxygen limited autotrophic nitrification and denitrification) nitrogen removal system was constructed by coupling with oxygen limited nitritation stage and anaerobic ammonium oxidation stage. Ammonia oxidizer, as a kind of key bacteria in N cycle, plays an important role at the oxygen limited nitritation stage of OLAND nitrogen removal system. In this study, specific amplification of 16S rDNA fragment of ammonia oxidizer by nested PCR, separation of mixed PCR samples by denaturing gradient gel electrophoresis(DGGE), and the quantification of ammonia oxidizer by Fluorescence in situ hybridization(FISH) were combined to investigate the shifts of community composition and quantity of ammonia oxidizer of the oxygen limited nitritation stage in OLAND system. It showed that the community composition of ammonia oxidizer changed drastically when dissolved oxygen was decreased gradually, and the dominant ammonia oxidizer of the steady nitrite accumulation stage were completely different from that of the early stage of oxygen limited nitritation identified by DGGE . It was concluded that the Nitrosomonas may be the dominant genus of ammonia oxidizer at the oxygen limited nitritation stage of OLAND system characterized by nested PCR-DGGE and FISH, and the percentage of Nitrosomonas was 72.5% ( 0.8% of ammonia oxidizer at the steady nitrite accumulation stage detected by FISH.

  3. Operational amplifiers

    CERN Document Server

    Dostal, Jiri

    1993-01-01

    This book provides the reader with the practical knowledge necessary to select and use operational amplifier devices. It presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits.Provides the reader with practical knowledge necessary to select and use operational amplifier devices. Presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits

  4. Ground Wood Fiber Length Distributions

    OpenAIRE

    Lauri Ilmari Salminen; Sari Liukkonen; Alava, Mikko J.

    2014-01-01

    This study considers ground wood fiber length distributions arising from pilot grindings. The empirical fiber length distributions appear to be independent of wood fiber length as well as feeding velocity. In terms of mathematics the fiber fragment distributions of ground wood pulp combine an exponential distribution for high-length fragments and a power-law distribution for smaller lengths. This implies that the fiber length distribution is influenced by the stone surface. A fragmentation-ba...

  5. The Complexity of DRw6 DR5 Haplotypes in American Blacks Demonstrated by Serology, Cellular Typing, and Restriction Fragment Length Polymorphism Analysis

    Science.gov (United States)

    1990-11-01

    A second, less polymorphic 8 gene, DRB3 , controls the expression of DRw52a, 52b, and 52c molecules [7]. The third is a pseudogene, DRB2. The DQ...well as nonexpressed genes (DQA2 and DQB2) [6]. The DRB 1, DRB3 and DQ alleles are often nonrandomly associated with each other forming haplotypes, a...Haplotypes expressing DRw52b carry a 12-kb Taql/DR133 DNA restriction fragment while haplotypes expressing DRw52a or DRw52c carry a 9.6-kb Taql/ DRB3 fragment

  6. Dynamic changes of telomeric restriction fragment (TRF) lengths in cells during the developmental process from embryos to seedlings and a comparison with the embryonal calli in Ginkgo biloba L.

    Institute of Scientific and Technical Information of China (English)

    Liu Di; Zhang Xiao-mei; Hua Xin; Qiao Nan; Song Han; Lu Hai; Guo Hui-hong; Li Feng-lan

    2007-01-01

    Telomeres are the structures that locate at the terminals of linear eukaryotic chromosomes. They can play essential roles in many cellular processes. The terminal location of Arabidopsis-type TTTAGGG tandem repeats were thought to be highly conserved.The terminal location of Ginkgo biloba L. consisting of TTTAGGG tandem repeats, were confirmed by Bal31 exonuclease degradation and Southern blotting. By comparing telomeric restriction fragment (TRF) lengths at different developmental stages from embryos to seedlings, a fluctuant tendency towards variation was found in these samples. The TRF length of embryos was also compared with that of embryonal calli and an upward trend was discovered in callus culture. The results suggest that there should be a telomerase mechanism or/and ALT mechanism for the maintenance of telomere length.

  7. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils

    DEFF Research Database (Denmark)

    Priemé, Anders; Braker, Gesche; Tiedje, James M.

    2002-01-01

    The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from...... the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one...... marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall...

  8. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    Directory of Open Access Journals (Sweden)

    Pooja H. Gupta

    2015-05-01

    Full Text Available Aim: An attempt has been made to study the toll-like receptors 4 (TLR4 gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR, respectively from Kankrej (22 and Triple cross (24 cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p˂0.05. Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05. Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

  9. Polymerase chain reaction-restriction fragment length polymorphism method to distinguish three mealybug groups within the Planococcus citri-P. minor species complex (Hemiptera: Coccoidea: Pseudococcidae).

    Science.gov (United States)

    Rung, A; Miller, D R; Scheffer, S J

    2009-02-01

    The mealybug species Planococcus citri (Risso) and Planococcus minor (Maskell) (Hemiptera: Coccoidea: Pseudococcidae) have special significance to U.S. quarantine and U.S. agriculture. Commonly intercepted at U.S. ports-of-entry, they are difficult to identify based on morphological characters. This study presents a molecular method for distinguishing P. citri, P. minor, and a genetically distinct group that is morphologically identical to P. citri, from Hawaii. This method uses polymerase chain reaction (PCR) followed by restriction fragment polymorphism analysis (RFLP) using the restriction enzymes BspH1, BsmH1, and HpH1. The resulting band patterns can be visualized in a 2% agarose gel and are sufficient to differentiate between the three entities mentioned above. PCR-RFLP diagnostics can be used for all life stages and is cheaper and faster than DNA sequencing.

  10. Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

    Directory of Open Access Journals (Sweden)

    Zhao Jianjun

    2011-02-01

    Full Text Available Abstract In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV, a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR and restriction fragment length polymorphism (RFLP. We selected an 829 bp fragment of the nucleoprotein (N gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively.

  11. Species identification of grouper and snapper in Taiwan Strait using polymerase chain reaction-restriction fragment length polymorphism analysis and lab-on-a-chip system%聚合酶链式反应-限制性片段长度多态性和芯片生物分析技术用于台湾海峡常见石斑鱼和鲷鱼的品种鉴定

    Institute of Scientific and Technical Information of China (English)

    陈双雅; 张津; 陈伟玲; 徐敦明; 周昱

    2011-01-01

    Polymerase chain reaction-restriction fragment length polymorphism ( PCR-RFLP )analysis and lab-on-a-chip system were used to identify grouper and snapper species in Taiwan Strait. A fragment of 464 bp length of mitochondrial cytochrome b gene was amplified by PCR and the products were digested with restriction enzymes Dde Ⅰ, Hae Ⅲ and Nla Ⅲ , individually. The fragments generated after digestion were further resolved on the DNA Chip. Eight grouper species and five snapper species were successfully identified. The results demonstrated that PCR-RFLP analysis and lab-on-a-chip system provide a fast , easy, automated, and reliable analysis approach. This approach is potential for the purpose of fish adulteration control.%应用聚合酶链式反应-限制性片段长度多态性分析(PCR-RFLP)和芯片生物分析系统建立了台湾海峡常见石斑鱼和鲷鱼的分子生物学品种鉴定新方法.首先提取鱼的基因组脱氧核糖核酸(DNA)进行细胞色素b基因特定片段的PCR扩增,然后用Dde Ⅰ、Hae Ⅲ和Nla Ⅲ 3种限制性内切酶进行酶切,在Agilent DNA 1000芯片上对酶切片段进行分离.该方法成功鉴定了台湾海峡常见的8种石斑鱼品种和5种鲷鱼品种,是一种快速、简便、有效的鱼类品种鉴定分析手段.

  12. Restriction fragment length polymorphism and multiple copies of DNA sequences homologous with probes for P-fimbriae and hemolysin genes among uropathogenic Escherichia coli.

    Science.gov (United States)

    Hull, S I; Bieler, S; Hull, R A

    1988-03-01

    Hemolysin and P-fimbriae are two virulence traits frequently found together in uropathogenic Escherichia coli. Previous studies have discovered evidence both for linkage between the genes for these traits and for their duplication in the chromosomes of a limited number of strains. To test whether these observations are characteristic of uropathogenic Escherichia coli, the method of DNA hybridization to DNA restriction fragments separated by electrophoresis and transferred to nylon was used to determine copy number of genes for P-fimbriae (pap) among 51 E. coli strains isolated from symptomatic urinary tract infections. Twenty percent of the strains had more than one copy of pap homologous sequences. Fifteen strains, each representing a unique clone, were examined for the presence of sequences homologous with cloned hemolysin genes (hly). Samples of DNA from 14 of the 15 strains hybridized with hly probes. In eight strains the number of copies of pap equalled the number of copies of hly, including one strain with two apparent copies of each. Five strains appeared to have one more copy of pap than of hly, and one strain had an extra copy of hly.

  13. Ground Wood Fiber Length Distributions

    Directory of Open Access Journals (Sweden)

    Lauri Ilmari Salminen

    2014-01-01

    Full Text Available This study considers ground wood fiber length distributions arising from pilot grindings. The empirical fiber length distributions appear to be independent of wood fiber length as well as feeding velocity. In terms of mathematics the fiber fragment distributions of ground wood pulp combine an exponential distribution for high-length fragments and a power-law distribution for smaller lengths. This implies that the fiber length distribution is influenced by the stone surface. A fragmentation-based model is presented that allows reproduction of the empirical results.

  14. Variation of clonal, mesquite-associated rhizobial and bradyrhizobial populations from surface and deep soils by symbiotic gene region restriction fragment length polymorphism and plasmid profile analysis.

    Science.gov (United States)

    Thomas, P M; Golly, K F; Zyskind, J W; Virginia, R A

    1994-04-01

    Genetic characteristics of 14 Rhizobium and 9 Bradyrhizobium mesquite (Prosopis glandulosa)-nodulating strains isolated from surface (0- to 0.5-m) and deep (4- to 6-m) rooting zones were determined in order to examine the hypothesis that surface- and deep-soil symbiont populations were related but had become genetically distinct during adaptation to contrasting soil conditions. To examine genetic diversity, Southern blots of PstI-digested genomic DNA were sequentially hybridized with the nodDABC region of Rhizobium meliloti, the Klebsiella pneumoniae nifHDK region encoding nitrogenase structural genes, and the chromosome-localized ndvB region of R. meliloti. Plasmid profile and host plant nodulation assays were also made. Isolates from mesquite nodulated beans and cowpeas but not alfalfa, clover, or soybeans. Mesquite was nodulated by diverse species of symbionts (R. meliloti, Rhizobium leguminosarum bv. phaseoli, and Parasponia bradyrhizobia). There were no differences within the groups of mesquite-associated rhizobia or bradyrhizobia in cross-inoculation response. The ndvB hybridization results showed the greatest genetic diversity among rhizobial strains. The pattern of ndvB-hybridizing fragments suggested that surface and deep strains were clonally related, but groups of related strains from each soil depth could be distinguished. Less variation was found with nifHDK and nodDABC probes. Large plasmids (>1,500 kb) were observed in all rhizobia and some bradyrhizobia. Profiles of plasmids of less than 1,000 kb were related to the soil depth and the genus of the symbiont. We suggest that interacting selection pressures for symbiotic competence and free-living survival, coupled with soil conditions that restrict genetic exchange between surface and deep-soil populations, led to the observed patterns of genetic diversity.

  15. Bridging the Gap Between Large-scale Data Sets and Analyses: Semi-automated Methods to Facilitate Length Polymorphism Scoring and Data Analyses.

    Science.gov (United States)

    Amplified fragment length polymorphism (AFLP) markers can be developed more quickly and at a lower cost than microsatellite and single nucleotide polymorphism markers, which makes them ideal markers for large-scale studies of understudied taxa — such as species at risk. However,...

  16. In Vivo Dopamine Efflux is Decreased in Striatum of both Fragment (R6/2 and Full-length (YAC128 Transgenic Mouse Models of Huntington’s Disease

    Directory of Open Access Journals (Sweden)

    Joshua W Callahan

    2011-07-01

    Full Text Available Huntington’s disease (HD is characterized by alterations within the corticostriatal circuitry. The striatum is innervated by a dense array of dopaminergic (DA terminals and these DA synapses are critical to the proper execution of motor functions. As motor disturbances are prevalent in HD we examined DA neurotransmission in the striatum in transgenic (tg murine models of HD. We used in vivo microdialysis to compare extracellular concentrations of striatal DA in both a fragment (R6/2 model, which displays a rapid and severe phenotype, and a full-length (YAC128 model that expresses a more progressive phenotype. Extracellular striatal DA concentrations were significantly reduced in R6/2 mice and decreased concomitantly with age-dependent increasing motor impairments on the rotarod task (7, 9, and 11 weeks. In a sample of 11-week-old R6/2 mice, we also measured tissue concentrations of striatal DA and found that total levels of DA were significantly depleted. However, the loss of total DA content (<50% was insufficient to account for the full extent of DA depletion in the extracellular fluid (ECF (~75%. We also observed a significant reduction in extracellular DA concentrations in the striatum of 7-month-old YAC128 mice. In a separate set of experiments, we applied d-amphetamine (AMPH (10 μm locally into the striatum to stimulate the release of intracellular DA into the ECF. The AMPH-induced increase in extracellular DA levels was significantly blunted in 9-week-old R6/2 mice. There also was a decrease in AMPH-stimulated DA efflux in 7-month-old YAC128 mice in comparison to WT controls, although the effect was milder. In the same cohort of 7-month-old YAC128 mice we observed a significant reduction in the total locomotor activity in response to systemic AMPH (2 mg/kg. Our data demonstrate that extracellular DA release is attenuated in both a fragment and full-length tg mouse model of HD and support the concept of DA involvement in aspects of the

  17. Nanoscale electromechanical parametric amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Aleman, Benjamin Jose; Zettl, Alexander

    2016-09-20

    This disclosure provides systems, methods, and apparatus related to a parametric amplifier. In one aspect, a device includes an electron source electrode, a counter electrode, and a pumping electrode. The electron source electrode may include a conductive base and a flexible conductor. The flexible conductor may have a first end and a second end, with the second end of the flexible conductor being coupled to the conductive base. A cross-sectional dimension of the flexible conductor may be less than about 100 nanometers. The counter electrode may be disposed proximate the first end of the flexible conductor and spaced a first distance from the first end of the flexible conductor. The pumping electrode may be disposed proximate a length of the flexible conductor and spaced a second distance from the flexible conductor.

  18. Quantification of DNA fragmentation in processed foods using real-time PCR.

    Science.gov (United States)

    Mano, Junichi; Nishitsuji, Yasuyuki; Kikuchi, Yosuke; Fukudome, Shin-Ichi; Hayashida, Takuya; Kawakami, Hiroyuki; Kurimoto, Youichi; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Takabatake, Reona; Kitta, Kazumi

    2017-07-01

    DNA analysis of processed foods is performed widely to detect various targets, such as genetically modified organisms (GMOs). Food processing often causes DNA fragmentation, which consequently affects the results of PCR analysis. In order to assess the effects of DNA fragmentation on the reliability of PCR analysis, we investigated a novel methodology to quantify the degree of DNA fragmentation. We designed four real-time PCR assays that amplified 18S ribosomal RNA gene sequences common to various plants at lengths of approximately 100, 200, 400, and 800 base pairs (bp). Then, we created an indicator value, "DNA fragmentation index (DFI)", which is calculated from the Cq values derived from the real-time PCR assays. Finally, we demonstrated the efficacy of this method for the quality control of GMO detection in processed foods by evaluating the relationship between the DFI and the limit of detection.

  19. Analysis and identification of SCAR molecular markers associated with birch fiber length trait

    Institute of Scientific and Technical Information of China (English)

    WANG Dan; WEI Zhi-gang; YANG Chuan-ping; LIU Guan-jun

    2008-01-01

    The fiber length trait (FLT) of 538 individuals from nature birch population in Maorshan region,Heilongjang,China were measured,of which 100 individuals were selected as representative variety of correlated fragments screening with random amplified polymorphism DNA (RAPD) technique.In total of 20 RAPD primers were tested through multiple regression analysis between amplified strip and the character behaviors,and a correlative segment BFLR-16 was obtained.The correlation coefficient between BFLI-16 and FLT was 0.6144,with the significant level of 1%.BFLI-16 was then cloned,sequenced and transformed into SCAR marker.The percentage of identifying long fiber birches by this SCAR was more than 92.The result indicates that the SCAR markers has high specificity for the long fiber individuals and is highly linked with the gene controlling the character of fiber length,and its existence is significantly correlative with the increase in the fiber length.

  20. A mechanism of gene amplification driven by small DNA fragments.

    Directory of Open Access Journals (Sweden)

    Kuntal Mukherjee

    Full Text Available DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s. Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation

  1. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA.

    Science.gov (United States)

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-04-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories.

  2. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    Directory of Open Access Journals (Sweden)

    Leonardo Silva Barbedo

    2016-04-01

    Full Text Available Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories.

  3. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    Science.gov (United States)

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-01-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories. PMID:27074256

  4. Cross-differential amplifier

    Science.gov (United States)

    Hajimiri, Seyed-Ali (Inventor); Kee, Scott D. (Inventor); Aoki, Ichiro (Inventor)

    2013-01-01

    A cross-differential amplifier is provided. The cross-differential amplifier includes an inductor connected to a direct current power source at a first terminal. A first and second switch, such as transistors, are connected to the inductor at a second terminal. A first and second amplifier are connected at their supply terminals to the first and second switch. The first and second switches are operated to commutate the inductor between the amplifiers so as to provide an amplified signal while limiting the ripple voltage on the inductor and thus limiting the maximum voltage imposed across the amplifiers and switches.

  5. High fragmentation characterizes tumour-derived circulating DNA.

    Directory of Open Access Journals (Sweden)

    Florent Mouliere

    Full Text Available BACKGROUND: Circulating DNA (ctDNA is acknowledged as a potential diagnostic tool for various cancers including colorectal cancer, especially when considering the detection of mutations. Certainly due to lack of normalization of the experimental conditions, previous reports present many discrepancies and contradictory data on the analysis of the concentration of total ctDNA and on the proportion of tumour-derived ctDNA fragments. METHODOLOGY: In order to rigorously analyse ctDNA, we thoroughly investigated ctDNA size distribution. We used a highly specific Q-PCR assay and athymic nude mice xenografted with SW620 or HT29 human colon cancer cells, and we correlated our results by examining plasma from metastatic CRC patients. CONCLUSION/SIGNIFICANCE: Fragmentation and concentration of tumour-derived ctDNA is positively correlated with tumour weight. CtDNA quantification by Q-PCR depends on the amplified target length and is optimal for 60-100 bp fragments. Q-PCR analysis of plasma samples from xenografted mice and cancer patients showed that tumour-derived ctDNA exhibits a specific amount profile based on ctDNA size and significant higher ctDNA fragmentation. Metastatic colorectal patients (n = 12 showed nearly 5-fold higher mean ctDNA fragmentation than healthy individuals (n = 16.

  6. Numerical Analysis of Modal Instability Onset in Fiber Amplifiers

    Science.gov (United States)

    2014-03-11

    Evolution of the logarithmic frequency spectrum of the off-center optical intensity probe along the length of the co-pumped amplifier for the case of...Evolution of the logarithmic frequency spectrum of the off-center optical intensity probe along the length of the counter-pumped amplifier for the...ABSTRACT 16. SECURITY CLASSIFICATION OF: Numerical analysis of the onset of modal instability in fiber amplifiers is presented. Specifically calculations

  7. Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica.

    Science.gov (United States)

    Matsumoto, A; Tsumura, Y

    2004-12-01

    We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (approximately 30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (Pobtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.

  8. Portable musical instrument amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Christian, David E. (Danbury, CT)

    1990-07-24

    The present invention relates to a musical instrument amplifier which is particularly useful for electric guitars. The amplifier has a rigid body for housing both the electronic system for amplifying and processing signals from the guitar and the system's power supply. An input plug connected to and projecting from the body is electrically coupled to the signal amplifying and processing system. When the plug is inserted into an output jack for an electric guitar, the body is rigidly carried by the guitar, and the guitar is operatively connected to the electrical amplifying and signal processing system without use of a loose interconnection cable. The amplifier is provided with an output jack, into which headphones are plugged to receive amplified signals from the guitar. By eliminating the conventional interconnection cable, the amplifier of the present invention can be used by musicians with increased flexibility and greater freedom of movement.

  9. Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease.

    Science.gov (United States)

    Emoto, Takuo; Yamashita, Tomoya; Kobayashi, Toshio; Sasaki, Naoto; Hirota, Yushi; Hayashi, Tomohiro; So, Anna; Kasahara, Kazuyuki; Yodoi, Keiko; Matsumoto, Takuya; Mizoguchi, Taiji; Ogawa, Wataru; Hirata, Ken-Ichi

    2017-01-01

    The association between atherosclerosis and gut microbiota has been attracting increased attention. We previously demonstrated a possible link between gut microbiota and coronary artery disease. Our aim of this study was to clarify the gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism (T-RFLP). This study included 39 coronary artery disease (CAD) patients and 30 age- and sex- matched no-CAD controls (Ctrls) with coronary risk factors. Bacterial DNA was extracted from their fecal samples and analyzed by T-RFLP and data mining analysis using the classification and regression algorithm. Five additional CAD patients were newly recruited to confirm the reliability of this analysis. Data mining analysis could divide the composition of gut microbiota into 2 characteristic nodes. The CAD group was classified into 4 CAD pattern nodes (35/39 = 90 %), while the Ctrl group was classified into 3 Ctrl pattern nodes (28/30 = 93 %). Five additional CAD samples were applied to the same dividing model, which could validate the accuracy to predict the risk of CAD by data mining analysis. We could demonstrate that operational taxonomic unit 853 (OTU853), OTU657, and OTU990 were determined important both by the data mining method and by the usual statistical comparison. We classified the gut microbiota profiles in coronary artery disease patients using data mining analysis of T-RFLP data and demonstrated the possibility that gut microbiota is a diagnostic marker of suffering from CAD.

  10. Mitochondrial DNA restriction fragment length polymorphism (RFLP) and 18S small-subunit ribosomal DNA PCR-RFLP analyses of Acanthamoeba isolated from contact lens storage cases of residents in southwestern Korea.

    Science.gov (United States)

    Kong, Hyun-Hee; Shin, Ji-Yeol; Yu, Hak-Sun; Kim, Jin; Hahn, Tae-Won; Hahn, Young-Ho; Chung, Dong-Il

    2002-04-01

    We applied ribosomal DNA PCR-restriction fragment length polymorphism (RFLP) and mitochondrial DNA (mtDNA) RFLP analyses to 43 Acanthamoeba environmental isolates (KA/LH1 to KA/LH43) from contact lens storage cases in southwestern Korea. These isolates were compared to American Type Culture Collection strains and clinical isolates (KA/E1 to KA/E12) from patients with keratitis. Seven riboprint patterns were seen. To identify the species of the isolates, a phylogenetic tree was constructed based on the comparison of riboprint patterns with reference strains. Four types accounted for 39 of the isolates belonging to the A. castellanii complex. The most predominant (48.8%) type was A. castellanii KA/LH2 type, which had identical riboprint and mtDNA RFLP patterns to those of A. castellanii Castellani, KA/E3 and KA/E8. The riboprint and mtDNA RFLP patterns of the KA/LH7 (20.9%) type were identical to those of A. castellanii Ma, a corneal isolate from the United States. The riboprint and mtDNA RFLP patterns of the KA/LH1 (18.6%) type were the same as those of A. lugdunensis L3a, KA/E2, and KA/E12. The prevalent pattern for each type of Acanthamoeba in southwestern Korea was very different from that from southeastern Korea and Seoul, Korea. It is noteworthy that 38 (88.4%) out of 43 isolates from contact lens storage cases of the residents in southwestern Korea revealed mtDNA RFLP and riboprint patterns identical to those found for clinical isolates in our area. This indicates that most isolates from contact lens storage cases in the surveyed area are potential keratopathogens. More attention should be paid to the disinfection of contact lens storage cases to prevent possible amoebic keratitis.

  11. Quantum fragmentation

    CERN Document Server

    Peschanski, R

    1993-01-01

    Phenomenological and theoretical aspects of fragmentation for elementary particles (resp. nuclei) are discussed. It is shown that some concepts of classical fragmentation remain relevant in a microscopic framework, exhibiting non-trivial properties of quantum relativistic field theory (resp. lattice percolation). Email contact: pesch@amoco.saclay.cea.fr

  12. Experimental design of laminar proportional amplifiers

    Science.gov (United States)

    Hellbaum, R. F.

    1976-01-01

    An experimental program was initiated at Langley Research Center to study the effects of various parameters on the design of laminar proportional beam deflection amplifiers. Matching and staging of amplifiers to obtain high-pressure gain was also studied. Variable parameters were aspect ratio, setback, control length, receiver distance, receiver width, width of center vent, and bias pressure levels. Usable pressure gains from 4 to 19 per stage can now be achieved, and five amplifiers were staged together to yield pressure gains up to 2,000,000.

  13. SPS RF System Amplifier plant

    CERN Multimedia

    1977-01-01

    The picture shows a 2 MW, 200 MHz amplifier plant with feeder lines. The main RF-system of the SPS comprises four cavities: two of 20 m length and two of 16.5 m length. They are all installed in one long straight section (LSS 3). These cavities are of the travelling-wave type operating at a centre frequency of 200.2 MHz. They are wideband, filling time about 700 ns and untuned. The power amplifiers, using tetrodes are installed in a surface building 200 m from the cavities. Initially only two cavities were installed, a third cavity was installed in 1978 and a forth one in 1979. The number of power amplifiers was also increased: to the first 2 MW plant a second 2 MW plant was added and by end 1979 there were 8 500 kW units combined in pairs to feed each of the 4 cavities with up to about 1 MW RF power, resulting in a total accelerating voltage of about 8 MV. See also 7412016X, 7412017X, 7411048X.

  14. 胃癌粘膜基因不稳与染色体端粒长度改变的研究%Analysis on genetic instability and telomeric restriction fragment length of gastric cancer in vitro

    Institute of Scientific and Technical Information of China (English)

    房殿春; 杨仕明; 罗元辉

    2001-01-01

    Objective To explore the relationship of the telomere length tomicrosatellite instability (MSI) and to loss of heterozygosity (LOH) of APC, MCC and DCC genes in gastric carcinomas. Methods The specimens were collected from 68 cases of gastric cancer. The length of telomeric restriction fragment (TRF) was measured with Southern blot. LOH of APC, MCC and DCC genes, MSI and frameshift mutation of hMSH6, TGF-βRⅡ and BAX genes were analyzed with PCR-based methods. Results Among all 68 samples, MSI was found in 17 (25%), including 8 of MSI-High (≥2 loci) and 9 of MSI-Low (only one locus). The left 51 samples were found to be lacking MSI or microsatellite stability (MSS). Out of the 8 cases of MSI-High, frameshift mutation of TGF-βRⅡ, BAX and hMSH6 genes was showed in 6, 3 and 2 cases respectively, but no mutation of these genes was found in MSI-Low and MSS samples. In 35 cases, including all MSI-High and MSI-Low studied for TRF, TRF length was shown to be shorter in 20 cases (57.1%), similar in 12 (34.3%) and elongated in 3 (8.6%). The mean TRF length had no correlation with clinicopatho-logical parameters. No association was observed between TRF length and MSI or frameshift mutation. But LOH at the DCC locus were associated with telomere shortening (P<0.01). This tendency was also observed in APC and MCC genes although there was no statistical significance. Conclusion The development of gastric cancer can occur through 2 different genetic pathways. In MSI-High gastric cancers, defective mismatch repair leads the accumulation of mononucleotide mutation and the demostration of MSI-High phenotype. In gastric cancers showing MSI-Low or MSS, multiple deletions may represent the LOH pathway. Telomere erosion might participate in the LOH pathway but be unassociated with MSI-High phenotype in gastric cancer.%目的 探讨端粒长度与微卫星不稳定(MSI)和APC/MCC及DCC基因杂合丢失(LOH)的关系。方法 采用Southern杂交检测端粒限制性片段

  15. Identification of Elymus (Triticeae, Poaceae) and its related genera genomes by RFLP analysis of PCR-amplified Adh genes.

    Science.gov (United States)

    Liu, QuanLan; Zhang, NingNing; Li, Lei; Liu, Jie

    2010-10-01

    Elymus L. is the largest genus in Triticeae, containing about 150 species with four recognized genome donors (St, H, P, and W). Traditionally, the genome compound of this genus is identified based on cytological data. Recently, molecular phylogenetic analysis was used to investigate its genomic combination. Here we describe a restriction fragment length polymorphism (RFLP) assay based on digesting alcohol dehydrogenase (Adh) amplicons with two restriction enzyme combinations, EcoRI-HindIII and EcoRI-PstI, which easily can be used to distinguish Elymus and its closely related genera genomes. The method includes only four steps: (1) amplifying nuclear Adh genes with universal primers; (2) purifying and cloning PCR products; (3) digesting plasmids with restriction enzymes that identify a given genome; (4) running the digested products on an agarose gel and identify the sample based on the restriction profiles. Results showed that: (1) PCR products ranged from 1,200 to 2,000 bp; (2) Adh2 gene was amplified from all the tested genomes; Adh1 gene was amplified from almost all of the tested genomes except the W genome; Adh3 gene was amplified only from the St genome; (3) the EcoRI-HindIII combination was effective to distinguish different Adh gene types (Adh1, Adh2, and Adh3); (4) the Adh2-EcoRI-PstI fragments could be used to distinguish Elymus and its closely related genera genomes. Therefore, This RFLP assay provides an inexpensive and simple means of identifying Elymus genomes.

  16. Wireless Josephson amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Narla, A.; Sliwa, K. M.; Hatridge, M.; Shankar, S.; Frunzio, L.; Schoelkopf, R. J.; Devoret, M. H. [Department of Applied Physics, Yale University, New Haven, Connecticut 06511 (United States)

    2014-06-09

    Josephson junction parametric amplifiers are playing a crucial role in the readout chain in superconducting quantum information experiments. However, their integration with current 3D cavity implementations poses the problem of transitioning between waveguide, coax cables, and planar circuits. Moreover, Josephson amplifiers require auxiliary microwave components, like directional couplers and/or hybrids, that are sources of spurious losses and impedance mismatches that limit measurement efficiency and amplifier tunability. We have developed a wireless architecture for these parametric amplifiers that eliminates superfluous microwave components and interconnects. This greatly simplifies their assembly and integration into experiments. We present an experimental realization of such a device operating in the 9–11 GHz band with about 100 MHz of amplitude gain-bandwidth product, on par with devices mounted in conventional sample holders. The simpler impedance environment presented to the amplifier also results in increased amplifier tunability.

  17. Oscillators and operational amplifiers

    DEFF Research Database (Denmark)

    Lindberg, Erik

    2005-01-01

    A generalized approach to the design of oscillators using operational amplifiers as active elements is presented. A piecewise-linear model of the amplifier is used so that it make sense to investigate the eigenvalues of the Jacobian of the differential equations. The characteristic equation...... of the general circuit is derived. The dynamic nonlinear transfer characteristic of the amplifier is investigated. Examples of negative resistance oscillators are discussed....

  18. Sequence-Related Amplified Polymorphism (SRAP Markers: A Potential Resource for Studies in Plant Molecular Biology

    Directory of Open Access Journals (Sweden)

    Daniel W. H. Robarts

    2014-07-01

    Full Text Available In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR, random-amplified polymorphic DNA (RAPD, and amplified fragment length polymorphism (AFLP to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use. highly variable marker with inherent biological significance.

  19. Magma Fragmentation

    Science.gov (United States)

    Gonnermann, Helge M.

    2015-05-01

    Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

  20. Laser Cooled High-Power Fiber Amplifier

    CERN Document Server

    Nemova, Galina

    2009-01-01

    A theoretical model for laser cooled continuous-wave fiber amplifier is presented. The amplification process takes place in the Tm3+-doped core of the fluoride ZBLAN (ZrF4-BaF2-LaF3-AlF3-NaF) glass fiber. The cooling process takes place in the Yb3+:ZBLAN fiber cladding. It is shown that for each value of the pump power and the amplified signal there is a distribution of the concentration of the Tm3+ along the length of the fiber amplifier, which provides its athermal operation. The influence of a small deviation in the value of the amplified signal on the temperature of the fiber with the fixed distribution of the Tm3+ions in the fiber cladding is investigated.

  1. Fragmented Authoritarianism or Integrated Fragmentation

    DEFF Research Database (Denmark)

    Brødsgaard, Kjeld Erik

    of these business leaders prompts the question of whether we are seeing the development of distinct interest groups that could challenge Party and state authority and create a fragmented polity. However, through the nomenklatura system the Party has an important instrument of control to wield over business groups....... Through this system the Party controls the appointment and promotion of the heads of the most important state-owned enterprises. The nomenklatura system also enables the Party to rotate leaders in big business from a position as CEO in one company to a similar position in another state-owned company...... and the Party-state, I suggest the notion of integrated fragmentation....

  2. Optoisolators simplify amplifier design

    Science.gov (United States)

    Ting, Joseph Wee

    2007-09-01

    Simplicity and low parts count are key virtues to this high voltage amplifier. Optoisolators replace complex high voltage transistor biasing schemes. This amplifier employs only 2 optoisolators, 16 high voltage mosfets transistors, 2 low voltage ones, 6 linear IC's and a score of passive components. Yet it can amplify opamp signals to 5 kV peak-to-peak from DC to sine waves up to 20 kHz. Resistor feedback guarantees the fidelity of the signal. It can source and sink 10 mA of output current. This amplifier was conceived to power ion traps for biological whole cell mass measurements. It is a versatile tool for a variety of applications.

  3. RF Power Amplifier Analysis

    Directory of Open Access Journals (Sweden)

    M. Lokay

    1993-04-01

    Full Text Available The special program is presented for the demonstration of RF power transistor amplifiers for the purposes of the high-school education in courses of radio transmitters. The program is written in Turbo Pascal 6. 0 and enables to study the waveforms in selected points of the amplifier and to draw the trajectories of the working point in a plot of output transistor characteristics.

  4. Charge-sensitive amplifier

    Directory of Open Access Journals (Sweden)

    Startsev V. I.

    2008-02-01

    Full Text Available The authors consider design and circuit design techniques of reduction of the influence of the pyroelectric effect on operation of the charge sensitive amplifiers. The presented experimental results confirm the validity of the measures taken to reduce the impact of pyroelectric currents. Pyroelectric currents are caused by the influence of the temperature gradient on the piezoelectric sensor and on the output voltage of charge sensitive amplifiers.

  5. Polymerase Chain Reaction- Restriction Fragment Length Polymorphism in the Detection of Leu262Val Polymorphism of PARL Gene%PCR-RFLP方法检测PARL基因Leu262Val多态性的实验研究

    Institute of Scientific and Technical Information of China (English)

    代莉; 李会芳; 王玉明; 宋滇平

    2011-01-01

    Objective To determine the optimum experimental conditions of the Leu262Val polymorphism of PARL gene detected by polymerase chain reaction-restriction fragment length polymorphism ( PCR-RFLP).Method In the PCR, PCR program was optimized by touchdown PCR (TD-PCR) ; four kinds of primers'concentration (0.32 umol/l, 0.4μmol/L, 0.6μmol/L, 0.8 μmol/L) were used, PCR products were observed in 2% agarose. In the RFLP, three kinds of PCR product quantity (5 μL, 10μL, 15 μL) and five kinds of incubation time (12 h, 8 h, 4 h, 2 h,1 h) were set when the incision enzyme quantity was unchanging, PCR products were observed in 2% agarose. Results (1) TD-PCR showed no non-specific band and simplified the process for seeking the optimum annealing temperature in ordinary amplification. ( 2) When the primers concentration was 0.4 μ mol/L. PCR production level was higher than others and had less dimer of primers. (3) It was 10 μl PCR production amount that was digested could creat a clear digested electropherogram. (4) It was 4 hours that was demanded in incubated reaction at 37 ℃ . Conclusions The design of primers is the key of PCR, the optimum primer's concentration is 0.4 μmol/L. TD-PCR can optimize connditions of ordinary PCR, it is more simple and effective than the ordinary PCR; The effective RFLP protocol: the system is 20 μL including 10μL PCR reaction mixture and 10 U enzyme are incubated at 37 ℃ for 4 hours.%目的 探讨聚合酶链反应-限制性片段长度多态性方法(PCR-RFLP)检测PARL基因Leu262Val多态性的最适实验条件.方法 在PCR实验中,运用降落PCR(touchdown PCR,TD-PCR)方法优化PCR条件;对引物终浓度设定0.8 μmol/L、0.6 μmol/L、0.4 μmol/L和0.32 μmol/L四个浓度梯度进行扩增;通过2%琼脂糖凝胶电泳观察结果.在RFLP实验中,在内切酶量10 U不变的情况下,PCR产物量分别设定为5 μL、10 μL、15 μL;酶切时间分别设定为12 h、8 h、4 h、2 h、1 h

  6. Double Clad Er-doped Fiber Amplifier

    Institute of Scientific and Technical Information of China (English)

    FU Yong-jun; MAO Xiang-qiao; WEI Huai; LI jian

    2007-01-01

    Presented is a theoretical study of double-clad Er-doped fiber power amplifier(EDFA). Two kinds of double clad fibers(DCF) with rectangular and "flower" inner clad shapes are studied, and these fibers have different coupling constants and propagation losses. We calculate the effective pump power absorption ratio along the fiber with different coupling constants from the first cladding to the doped core and with different propagation losses for the power in the inner cladding. Then the gains of the double clad Er-doped fiber amplifiers versus fiber lengths are calculated using the EDFA model based on propagation and rate equations of a homogeneous, two-level medium.

  7. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2016-01-01

    The Ph.D. -project Bespoke Fragments seeks to explore and utilise the space emerging between the potentials of digital drawing and fabrication and the field of materials and their properties and capacities. Within this span, the project is situated in a shuttling between the virtual and the actual......, the emergence of virtual space is no longer limited to the computer's digital world, but extends into the materials' world. Creation and uncertainty are allowed as virtual parameters in both the digital and reality. Based on this notion the project suggests utilising that exact potential to develop...

  8. Flame Length

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — Flame length was modeled using FlamMap, an interagency fire behavior mapping and analysis program that computes potential fire behavior characteristics. The tool...

  9. Terminal-restriction fragment length polymorphism analysis of diversity of mucosa-associated microbiota in patients with Crohn's disease%克罗恩病患者黏膜相关细菌群落多样性分析

    Institute of Scientific and Technical Information of China (English)

    冉文斌; 欧阳钦; 史维

    2013-01-01

    线菌属含量增加可能在克罗恩病的发生及发展中扮演重要作用.%Objective To explore the differences of colonic mucosal-associate bacterial diversity between the patients with Crohn's disease (CD) and healthy controls.Methods Eight CD patients and 23 healthy controls were recruited from September 2010 to December 2011 at West China Hospital.One biopsy were taken from cecum of every patient with CD and healthy control by endoscopic examination.The diversity of colonic mucosa-associated microbiota was detected by terminal-restriction fragment length polymorphism (T-RFLP).Hierarchical cluster analysis were performed to compare the similarity of microbial communities between CD patients and healthy controls.Differences of bacterial diversity between two groups were also evaluated.The difference of predominant terminal-restrict fragments (T-RF) were analyzed and the bacterium predicted by predominant T-RFs were identified according to MiCA database.Results Hierarchical cluster analysis showed that the mucosal microbial community of CD patients differed from healthy controls.And there were more similarities in the samples of same group than that of different groups.Compared with healthy control group,the richness of mocosal microbiota in CD patients was lower (HaeⅢ:7 ± 4 vs 10 ± 8,P =0.048 ; Msp I + Hae Ⅲ..20 ± 10 vs 24 ± 12,P =0.036).Shannon-Wiener index of CD patients was lower than healthy control(1.7 ± 0.7 vs 2.0 ± 0.5,P =0.220) with no significant difference.Species evenness and Simpson index of CD patients were significantly greater than healthy controls (0.84 ±0.14vs0.77±0.13,P=0.045; 0.25±0.16 vs0.22±0.15,P=0.038).The T-RFof37,40 and 66 bp digested with Msp Ⅰ enzyme predominated in CD patients.Relative quantitative analysis showed 35 bp T-RF digested with Msp Ⅰ was significantly higher in CD patients than that in healthy controls (36.8% (23.0%,55.4%) vs 14.3% (9.5%,19.5%),P =0.001),and 74,141,486,490 bp T-RFs were

  10. Comparison of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay to pulsed-field gel electrophoresis to determine the effect of repeated subculture and prolonged storage on RFLP patterns of Shiga toxin-producing Escherichia coli O157:H7.

    Science.gov (United States)

    Shima, Kensuke; Wu, Yuluo; Sugimoto, Norihiko; Asakura, Masahiro; Nishimura, Kazuhiko; Yamasaki, Shinji

    2006-11-01

    In this study, we compared a recently developed PCR-restriction fragment length polymorphism (PCR-RFLP) assay with pulsed-field gel electrophoresis (PFGE) using three different Shiga toxin-producing Escherichia coli (STEC) strains to understand whether repeated subculture in vitro and prolonged storage at room temperature affect the RFLP patterns of STEC. The PFGE profiles of the STEC strains changed by 1 to 8 fragments after repeated subculture and prolonged storage; one strain was no longer clonal after repeated subculture compared to the original isolate according to the Tenover criteria. In contrast, RFLP patterns obtained by PCR-RFLP were identical after repeated subculture and prolonged storage. These data clearly indicate that the PCR-RFLP assay which is based on the diversity of region V, a regulatory region of Stx-phage, was not affected by repeated subculture and prolonged storage and is a more practical and reliable method for molecular typing of STEC strains.

  11. Productivity and biochemical properties of green tea in response to full-length and functional fragments of HpaGXooc, a harpin protein from the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

    Indian Academy of Sciences (India)

    Xiaojing Wu; Tingquan Wu; Juying Long; Qian Yin; Yong Zhang; Lei Chen; Ruoxue Liu; Tongchun Gao; Hansong Dong

    2007-09-01

    Harpin proteins from plant pathogenic bacteria can stimulate hypersensitive cell death (HCD), drought tolerance, defence responses against pathogens and insects in plants, as well as enhance plant growth. Recently, we identified nine functional fragments of HpaGXooc, a harpin protein from Xanthomonas oryzae pv. oryzicola, the pathogen that causes bacterial leaf streak in rice. Fragments HpaG1–94, HpaG10–42, and HpaG62–138, which contain the HpaGXooc regions of the amino acid sequence as indicated by the number spans, exceed the parent protein in promoting growth, pathogen defence and HCD in plants. Here we report improved productivity and biochemical properties of green tea (Camellia sinensis) in response to the fragments tested in comparison with HpaGXooc and an inactive protein control. Field tests suggested that the four proteins markedly increased the growth and yield of green tea, and increased the leaf content of tea catechols, a group of compounds that have relevance in the prevention and treatment of human diseases. In particular, HpaG1–94 was more active than HpaGXooc in expediting the growth of juvenile buds and leaves used as green tea material and increased the catechol content of processed teas. When tea shrubs were treated with HpaHXooc and HpaG1–94 compared with a control, green tea yields were over 55% and 39% greater, and leaf catechols were increased by more than 64% and 72%, respectively. The expression of three homologues of the expansin genes, which regulate plant cell growth, and the CsCHS gene encoding a tea chalcone synthase, which critically regulates the biosynthesis of catechols, were induced in germinal leaves of tea plants following treatment with HpaG1–94 or HpaGXooc. Higher levels of gene expression were induced by the application of HpaG1–94 than HpaGXooc. Our results suggest that the harpin protein, especially the functional fragment HpaG1–94, can be used to effectively increase the yield and improve the biochemical

  12. Electrospun amplified fiber optics.

    Science.gov (United States)

    Morello, Giovanni; Camposeo, Andrea; Moffa, Maria; Pisignano, Dario

    2015-03-11

    All-optical signal processing is the focus of much research aiming to obtain effective alternatives to existing data transmission platforms. Amplification of light in fiber optics, such as in Erbium-doped fiber amplifiers, is especially important for efficient signal transmission. However, the complex fabrication methods involving high-temperature processes performed in a highly pure environment slow the fabrication process and make amplified components expensive with respect to an ideal, high-throughput, room temperature production. Here, we report on near-infrared polymer fiber amplifiers working over a band of ∼20 nm. The fibers are cheap, spun with a process entirely carried out at room temperature, and shown to have amplified spontaneous emission with good gain coefficients and low levels of optical losses (a few cm(-1)). The amplification process is favored by high fiber quality and low self-absorption. The found performance metrics appear to be suitable for short-distance operations, and the large variety of commercially available doping dyes might allow for effective multiwavelength operations by electrospun amplified fiber optics.

  13. Framing Fragmentation

    DEFF Research Database (Denmark)

    Bundgaard, Charlotte

    2009-01-01

    , contain distinctive architectural traits, not only based on rational repetition, but also supporting composition and montage as dynamic concepts. Prefab architecture is an architecture of fragmentation, individualization and changeability, and this sets up new challenges for the architect. This paper...... tries to develop a strategy for the architect dealing with industrially based architecture; a strategy which exploits architectural potentials in industrial building, which recognizes the rules of mass production and which redefines the architect’s position among the agents of building. If recent...... developments within the construction sector imply a marginalized role for the architect, this strategy suggests a strong repositioning. In Danish building practice the construction industry is increasingly organized within terms like ”systemized prefab delivery” and ”digital building”. The building is divided...

  14. Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

    Institute of Scientific and Technical Information of China (English)

    SHI Hong-liang; LI Xin-hai; ZHANG De-gui; XIE Chuan-xiao; HAO Zhuan-fang; LI Ming-shun; PAN Guang-tang; ZHANG Shi-huang

    2009-01-01

    Head smut of maize (Zea mays L.), which was caused by Sporisorium reiliana, occurred in most of the maize growing areas of the world. The purpose of this study was to develop SCAR markers for map-based cloning of resistance genes and MAS. Two sets of BC3 progenies, one (BC3Q) derived from the cross Qi319 (resistance)x Huangzao 4 (susceptible),the other (BC3M) from Mol 7 (resistance)x Huangzao 4 (susceptible), were generated. Huangzao 4 was the recurrent parent in both progenies. A combination of BSA (bulked segregant analysis) with AFLP (amplified fragment length polymorphism) method was applied to map the genes involving the resistance to S. Reiliana, and corresponding resistant and susceptible bulks and their parental lines were used for screening polymorphic AFLP primer pairs. One fragment of P13M61-152 was converted into SCAR (sequence charactered amplified fragment) marker S130. The marker was mapped at chromosome bin 2.09, the interval of a major QTL region previously reported to contribute to S. Reiliana resistance.Furthermore, S130 was highly associated with resistance to S. Reiliana, and could be useful for marker-assisted selection and facilitate map-based cloning of resistance genes.

  15. CLONING AND SEQUENCING OF MATURED FRAGMENT OF HUMAN NEVER GROWTH FACTOR GENE

    Institute of Scientific and Technical Information of China (English)

    马巍; 吴玲; 王德利; 刘淼; 任惠民; 杨广笑; 王全颖

    2003-01-01

    Objective Molecular cloning and sequencing of the human matured fragment of human nerve growth factor(NGF) gene. Methods Extracting the human genomic DNA from the white blood cells as templates, the gene of NGF was cloned by using PCR and T-vector cloning method. Screening the positive clones and identified by the restriction enzymes, and then the cloned amplified fragment was sequenced and analyzed. Results DNA sequence comparison the cloned gene of NGF with the GenBank (V01511) sequence demonstrated that both of sequences were identical, 354bp length. Conclusion Cloning the NGF gene from the human genomic DNA has paved the way for further study on gene therapy of nerve system injury.

  16. Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis.

    Science.gov (United States)

    Álvarez-Sandoval, Brenda A; Manzanilla, Linda R; Montiel, Rafael

    2014-01-01

    Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.

  17. Sex determination in highly fragmented human DNA by high-resolution melting (HRM analysis.

    Directory of Open Access Journals (Sweden)

    Brenda A Álvarez-Sandoval

    Full Text Available Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM. HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.

  18. Diversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences Diversidad de las picocianobacterias marinas Prochlorococcus y Synechococcus por medio de polimorfismos de longitud de fragmentos de restricción terminal en secuencias del espaciador transcrito interno del ARNr 16S - 23S

    Directory of Open Access Journals (Sweden)

    PARIS LAVIN

    2008-12-01

    Full Text Available In order to assess the appropriateness of the use of internal transcribed spacer (ITS sequences for the study of population genetics of marine cyanobacteria, we amplified and cloned the 16S rRNA gene plus the 16S-23S ITS regions of six strains of Prochlorococcus and Synechococcus. We analyzed them by denaturing gradient gel electrophoresis (DGGE and terminal restriction fragment length polymorphisms (T-RFLP. When using the standard application of these techniques, we obtained more than one band or terminal restriction fragment (T-RF per strain or cloned sequence. Reports in literature have suggested that these anomalies can result from the formation of secondary structures. Secondary structures of the ITS sequences of Prochlorococcus and Synechococcus strains were computationally modelled at the different temperatures that were used during the polymerase chain reaction (PCR. Modelling results predicted the existence of hairpin loops that would still be present at the extensión temperature; it is likely that these loops produced incomplete and single stranded PCR products. We modified the standard T-RFLP procedure by adding the labelled ITS primer in the last two cycles of the PCR reaction; this resulted, in most cases, in only one T-RF per ribotype. Application of this technique to a natural picoplankton community in marine waters off northern Chile, showed that it was possible to identify the presence, and determine the relative abundance, of several phylogenetic lineages within the genera Prochlorococcus and Synechococcus inhabiting the euphotic zone. Phylogenetic analysis of ITS sequences obtained by cloning and sequencing DNA from the same sample confirmed the presence of the different genotypes. With the proposed modification, T-RFLP profiles should therefore be suitable for studying the diversity of natural populations of cyanobacteria, and should become an important tool to study the factors influencing the genetic structure and

  19. Enterocytozoon bieneusi Identification Using Real-Time Polymerase Chain Reaction and Restriction Fragment Length Polymorphism in HIV-Infected Humans from Kinshasa Province of the Democratic Republic of Congo

    Directory of Open Access Journals (Sweden)

    Roger Wumba

    2012-01-01

    in 242 HIV-infected patients. Typing was based on DNA polymorphism of the ribosomal DNA ITS region of E. bieneusi. PCRRFLP generated with two restriction enzymes (Nla III and Fnu 4HI in PCR-amplified ITS products for classifying strains into different lineages. The diagnosis performance of the indirect immune-fluorescence-monoclonal antibody (IFI-AcM was defined in comparison with real-time PCR as the gold standard. Results. Out of 242 HIV-infected patients, using the real-time PCR, the prevalence of E. bieneusi was 7.9% (n=19 among the 19 E. bieneusi, one was coinfected with E. intestinalis. In 19 E. bieneusi persons using PCR-RFLP method, 5 type I strains of E. bieneusi (26.3% and 5 type IV strains of E. bieneusi (26.3% were identified. The sensitivity of IFI-AcM was poor as estimated 42.1%. Conclusion. Despite different PCR methods, there is possible association between HIVinfection, geographic location (France, Cameroun, Democratic Republic of Congo, and the concurrence of type I and type IV strains.

  20. Fourier plane image amplifier

    Science.gov (United States)

    Hackel, L.A.; Hermann, M.R.; Dane, C.B.; Tiszauer, D.H.

    1995-12-12

    A solid state laser is frequency tripled to 0.3 {micro}m. A small portion of the laser is split off and generates a Stokes seed in a low power oscillator. The low power output passes through a mask with the appropriate hole pattern. Meanwhile, the bulk of the laser output is focused into a larger stimulated Brillouin scattering (SBS) amplifier. The low power beam is directed through the same cell in the opposite direction. The majority of the amplification takes place at the focus which is the fourier transform plane of the mask image. The small holes occupy large area at the focus and thus are preferentially amplified. The amplified output is now imaged onto the multichip module where the holes are drilled. Because of the fourier plane amplifier, only about 1/10th the power of a competitive system is needed. This concept allows less expensive masks to be used in the process and requires much less laser power. 1 fig.

  1. Fourier plane image amplifier

    Science.gov (United States)

    Hackel, Lloyd A.; Hermann, Mark R.; Dane, C. Brent; Tiszauer, Detlev H.

    1995-01-01

    A solid state laser is frequency tripled to 0.3 .mu.m. A small portion of the laser is split off and generates a Stokes seed in a low power oscillator. The low power output passes through a mask with the appropriate hole pattern. Meanwhile, the bulk of the laser output is focused into a larger stimulated Brillouin scattering (SBS) amplifier. The low power beam is directed through the same cell in the opposite direction. The majority of the amplification takes place at the focus which is the fourier transform plane of the mask image. The small holes occupy large area at the focus and thus are preferentially amplified. The amplified output is now imaged onto the multichip module where the holes are drilled. Because of the fourier plane amplifier, only .about.1/10th the power of a competitive system is needed. This concept allows less expensive masks to be used in the process and requires much less laser power.

  2. Dual-pump wave mixing in semiconductor optical amplifiers: performance enhancement with long amplifiers

    Science.gov (United States)

    Tomkos, Ioannis; Zacharopoulos, Ioannis; Syvridis, Dimitrios

    1999-05-01

    We demonstrate experimentally the improvement of the performance of the dual pump wave mixing scheme in semiconductor optical amplifiers, using long amplifier chips and high optical pump powers. The optical amplifiers used in the experiment had a ridge waveguide structure with bulk active layer and antireflective-coated angled facets. Measurements of the conversion efficiency and SBR as a function of wavelength shift are presented for a wavelength shift of more than 40 nm. The above measurements are carried out for three amplifier lengths (500 micrometers , 1000 micrometers , and 1500 micrometers ) and for different levels of the optical power of the two pumps. It will be shown that an increase in the amplifier length from 500 micrometers to 1500 micrometers results to an increase of more than 25 dB for the efficiency and more than 20 dB for the SBR. This improvement combined with the inherent advantages of the dual pump scheme (almost constant SBR and high efficiency for large wavelength shifts) results in a highly performing wavelength converter/phase conjugator, suitable for many applications.

  3. A new and improved method based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for the determination of A1298C mutation in the methylenetetrahydrofolate reductase (MTHFR) gene.

    Science.gov (United States)

    Machnik, Grzegorz; Zapala, Malgorzata; Pelc, Ewa; Gasecka-Czapla, Monika; Kaczmarczyk, Grzegorz; Okopien, Boguslaw

    2013-01-01

    Intracellular folate homeostasis and metabolism is regulated by numerous genes. Among them, 5,10-methylenetetrahydrofolate reductase (MTHFR) is of special interest because of its involvement in regulation of the homocysteine level in the body as a result of folate metabolism. Moreover, some studies demonstrated that the homocysteine plasma level in individuals may be influenced by polymorphisms present in the MTHFR gene. Two common, clinically relevant mutations have been described: MTHFR C677T and MTHFR A1298C. Although several laboratory techniques allow genotyping of both polymorphisms, PCR-RFLP analysis is simple to perform, relatively cheap, and thus one of the most utilized. In the case of A1298C, the PCR-RFLP technique that utilizes MboII endonuclease class II requires an acrylamide gel electrophoresis, since agarose gel electrophoresis is unable to resolve short deoxyribonucleic acid (DNA) fragments after restriction digestion. Agarose gel electrophoresis is commonly preferred over that of acrylamide. To resolve this inconvenience, a novel PCR-RFLP, AjuI-based method to genotype A1298C alleles has been developed that can be performed on standard agarose gel.

  4. Mappability and Read Length

    Directory of Open Access Journals (Sweden)

    Wentian eLi

    2014-11-01

    Full Text Available Power-law distributions are the main functional form forthe distribution of repeat size and repeat copy number in the human genome. When the genome is broken into fragments for sequencing, the limited size offragments and reads may prevent an unique alignment of repeatsequences to the reference sequence. Repeats in the human genome canbe as long as $10^4$ bases, or $10^5-10^6$ bases when allowing for mismatches between repeat units. Sequence reads from these regions are therefore unmappable when the read length is in the range of $10^3$ bases.With the read length of exactly 1000 bases, slightly more than 1% of theassembled genome, and slightly less than 1% of the 1kbreads, are unmappable, excluding the unassembled portion of the humangenome (8% in GRCh37. The slow decay (long tail ofthe power-law function implies a diminishing return in convertingunmappable regions/reads to become mappable with the increase of theread length, with the understanding that increasing read length willalways move towards the direction of 100% mappability.

  5. Overview of bunch length measurements.

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A. H.

    1999-02-19

    An overview of particle and photon beam bunch length measurements is presented in the context of free-electron laser (FEL) challenges. Particle-beam peak current is a critical factor in obtaining adequate FEL gain for both oscillators and self-amplified spontaneous emission (SASE) devices. Since measurement of charge is a standard measurement, the bunch length becomes the key issue for ultrashort bunches. Both time-domain and frequency-domain techniques are presented in the context of using electromagnetic radiation over eight orders of magnitude in wavelength. In addition, the measurement of microbunching in a micropulse is addressed.

  6. STABILIZED TRANSISTOR AMPLIFIER

    Science.gov (United States)

    Noe, J.B.

    1963-05-01

    A temperature stabilized transistor amplifier having a pair of transistors coupled in cascade relation that are capable of providing amplification through a temperature range of - 100 un. Concent 85% F to 400 un. Concent 85% F described. The stabilization of the amplifier is attained by coupling a feedback signal taken from the emitter of second transistor at a junction between two serially arranged biasing resistances in the circuit of the emitter of the second transistor to the base of the first transistor. Thus, a change in the emitter current of the second transistor is automatically corrected by the feedback adjustment of the base-emitter potential of the first transistor and by a corresponding change in the base-emitter potential of the second transistor. (AEC)

  7. Polarization effect in parametric amplifier

    Institute of Scientific and Technical Information of China (English)

    Junhe Zhou; Jianping Chen; Xinwan Li; Guiling Wu; Yiping Wang

    2005-01-01

    @@ Polarization effect in parametric amplifiers is studied. Coupled equations are derived from the basic propagation equations and numerical solutions are given for both one-wavelength-pump and two-wavelengthpump systems. Several parametric amplifiers driven by pumps at one wavelength and two wavelengths are analyzed and the polarization independent parametric amplifier is proposed.

  8. Radio Frequency Solid State Amplifiers

    CERN Document Server

    Jacob, J

    2015-01-01

    Solid state amplifiers are being increasingly used instead of electronic vacuum tubes to feed accelerating cavities with radio frequency power in the 100 kW range. Power is obtained from the combination of hundreds of transistor amplifier modules. This paper summarizes a one hour lecture on solid state amplifiers for accelerator applications.

  9. Multiple pass laser amplifier system

    Science.gov (United States)

    Brueckner, Keith A.; Jorna, Siebe; Moncur, N. Kent

    1977-01-01

    A laser amplification method for increasing the energy extraction efficiency from laser amplifiers while reducing the energy flux that passes through a flux limited system which includes apparatus for decomposing a linearly polarized light beam into multiple components, passing the components through an amplifier in delayed time sequence and recombining the amplified components into an in phase linearly polarized beam.

  10. A modular assembly cloning technique (aided by the BIOF software tool for seamless and error-free assembly of long DNA fragments

    Directory of Open Access Journals (Sweden)

    Orlova Nadezhda A

    2012-06-01

    Full Text Available Abstract Background Molecular cloning of DNA fragments >5 kbp is still a complex task. When no genomic DNA library is available for the species of interest, and direct PCR amplification of the desired DNA fragment is unsuccessful or results in an incorrect sequence, molecular cloning of a PCR-amplified region of the target sequence and assembly of the cloned parts by restriction and ligation is an option. Assembled components of such DNA fragments can be connected together by ligating the compatible overhangs produced by different restriction endonucleases. However, designing the corresponding cloning scheme can be a complex task that requires a software tool to generate a list of potential connection sites. Findings The BIOF program presented here analyzes DNA fragments for all available restriction enzymes and provides a list of potential sites for ligation of DNA fragments with compatible overhangs. The cloning scheme, which is called modular assembly cloning (MAC, is aided by the BIOF program. MAC was tested on a practical dataset, namely, two non-coding fragments of the translation elongation factor 1 alpha gene from Chinese hamster ovary cells. The individual fragment lengths exceeded 5 kbp, and direct PCR amplification produced no amplicons. However, separation of the target fragments into smaller regions, with downstream assembly of the cloned modules, resulted in both target DNA fragments being obtained with few subsequent steps. Conclusions Implementation of the MAC software tool and the experimental approach adopted here has great potential for simplifying the molecular cloning of long DNA fragments. This approach may be used to generate long artificial DNA fragments such as in vitro spliced cDNAs.

  11. Simplified design of IC amplifiers

    CERN Document Server

    Lenk, John

    1996-01-01

    Simplified Design of IC Amplifiers has something for everyone involved in electronics. No matter what skill level, this book shows how to design and experiment with IC amplifiers. For experimenters, students, and serious hobbyists, this book provides sufficient information to design and build IC amplifier circuits from 'scratch'. For working engineers who design amplifier circuits or select IC amplifiers, the book provides a variety of circuit configurations to make designing easier.Provides basics for all phases of practical design.Covers the most popular forms for amplif

  12. Electronic amplifiers for automatic compensators

    CERN Document Server

    Polonnikov, D Ye

    1965-01-01

    Electronic Amplifiers for Automatic Compensators presents the design and operation of electronic amplifiers for use in automatic control and measuring systems. This book is composed of eight chapters that consider the problems of constructing input and output circuits of amplifiers, suppression of interference and ensuring high sensitivity.This work begins with a survey of the operating principles of electronic amplifiers in automatic compensator systems. The succeeding chapters deal with circuit selection and the calculation and determination of the principal characteristics of amplifiers, as

  13. Building valve amplifiers

    CERN Document Server

    Jones, Morgan

    2013-01-01

    Building Valve Amplifiers is a unique hands-on guide for anyone working with tube audio equipment--as an electronics hobbyist, audiophile or audio engineer. This 2nd Edition builds on the success of the first with technology and technique revisions throughout and, significantly, a major new self-build project, worked through step-by-step, which puts into practice the principles and techniques introduced throughout the book. Particular attention has been paid to answering questions commonly asked by newcomers to the world of the valve, whether audio enthusiasts tackling their first build or

  14. REGENERATIVE TRANSISTOR AMPLIFIER

    Science.gov (United States)

    Kabell, L.J.

    1958-11-25

    Electrical circults for use in computers and the like are described. particularly a regenerative bistable transistor amplifler which is iurned on by a clock signal when an information signal permits and is turned off by the clock signal. The amplifier porforms the above function with reduced power requirements for the clock signal and circuit operation. The power requirements are reduced in one way by employing transformer coupling which increases the collector circuit efficiency by eliminating the loss of power in the collector load resistor.

  15. Wideband amplifier design

    CERN Document Server

    Hollister, Allen L

    2007-01-01

    In this book, the theory needed to understand wideband amplifier design using the simplest models possible will be developed. This theory will be used to develop algebraic equations that describe particular circuits used in high frequency design so that the reader develops a ""gut level"" understanding of the process and circuit. SPICE and Genesys simulations will be performed to show the accuracy of the algebraic models. By looking at differences between the algebraic equations and the simulations, new algebraic models will be developed that include parameters originally left out of the model

  16. Microfluidic DNA fragmentation for on-chip genomic analysis

    NARCIS (Netherlands)

    Shui, Lingling; Bomer, Johan G.; Jin, Mingliang; Carlen, Edwin T.; Berg, van den Albert

    2011-01-01

    We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions

  17. Optical amplifier exhibiting net phase-mismatch selected to at least partially reduce gain-induced phase-matching during operation and method of operation

    Science.gov (United States)

    Feve, Jean-Philippe; Kliner, Dahv A. V.; Farrow; Roger L.

    2011-02-01

    An optical amplifier, such as an optical waveguide amplifier (e.g., an optical fiber amplifier or a planar waveguide) or a non-guiding optical amplifier, that exhibits a net phase-mismatch selected to at least partially reduce gain-induced phase-matching during operation thereof is disclosed. In one aspect of the invention, an optical amplifier structure includes at least one optical amplifier having a length and a gain region. The at least one optical amplifier exhibits a net phase-mismatch that varies along at least part of the length thereof selected to at least partially reduce gain-induced phase-matching during operation thereof.

  18. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...

  19. Microfluidic DNA fragmentation for on-chip genomic analysis.

    Science.gov (United States)

    Shui, Lingling; Bomer, Johan G; Jin, Mingliang; Carlen, Edwin T; van den Berg, Albert

    2011-12-09

    We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼ 5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions positioned in larger microfluidic channels that create point-sink flow with large velocity gradients near the constriction entrance. Long constrictions (100 µm) produce shorter fragment lengths compared to shorter constrictions (10 µm), while increasing the hydrodynamic pressure requirement. Sample recirculation (10 ×) in short constrictions reduces the mean fragment length and fragment length variation, and improves yield compared to single-pass experiments without increasing the hydrodynamic pressure.

  20. Modeling of Yb3+-sensitized Er3+-doped silica waveguide amplifiers

    DEFF Research Database (Denmark)

    Lester, Christian; Bjarklev, Anders Overgaard; Rasmussen, Thomas;

    1995-01-01

    A model for Yb3+-sensitized Er3+-doped silica waveguide amplifiers is described and numerically investigated in the small-signal regime. The amplified spontaneous emission in the ytterbium-band and the quenching process between excited erbium ions are included in the model. For pump wavelengths...... between 860 and 995 nm, the amplified spontaneous emission in the ytterbium-band is found to reduce both the gain and the optimum length of the amplifier significantly. The achievable gain of the Yb3+-sensitized amplifier is found to be higher than in an Er3+-doped silica waveguide without Yb 3+ (18 d...

  1. Modeling of semiconductor optical amplifiers

    DEFF Research Database (Denmark)

    Mørk, Jesper; Bischoff, Svend; Berg, Tommy Winther

    We discuss the modelling of semiconductor optical amplifiers with emphasis on their high-speed properties. Applications in linear amplification as well as ultrafast optical signal processing are reviewed. Finally, the possible role of quantum-dot based optical amplifiers is discussed.......We discuss the modelling of semiconductor optical amplifiers with emphasis on their high-speed properties. Applications in linear amplification as well as ultrafast optical signal processing are reviewed. Finally, the possible role of quantum-dot based optical amplifiers is discussed....

  2. PCR typing of DNA fragments of the two short tandem repeat (STR) systems upstream of the human myelin basic protein (MBP) gene in Danes and Greenland Eskimos

    DEFF Research Database (Denmark)

    Nellemann, L J; Frederiksen, J; Morling, N

    1996-01-01

    DNA from the double short tandem repeat (STR) system MBP (locus 18q23-pter) was amplified by the polymerase chain reaction (PCR) and the two polymorphic repeat systems were separated by cutting with the restriction enzyme NlaIII. The lengths of the DNA fragments of the two MBP STR systems MBP......-A and MBP-B were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 112 unrelated Danes, 140 unrelated Greenland Eskimos, and 88 Danish mother/child pairs were analyzed. The distributions of MBP phenotypes were in Hardy-Weinberg equilibrium in both...

  3. The Gain Dependence of the Power Transient in Raman Amplifier

    Institute of Scientific and Technical Information of China (English)

    Zheng Lei; Zhang Jiahong; Chen Zhangyuan; Wu Deming; Xu Anshi

    2003-01-01

    It is observed that the amplitude of the power transient overshoot depends on the gain of the amplifier when the input signal powers are the same. The other system parameters, such as the input pump power and fiber length, have no effects on it.

  4. Two stage dual gate MESFET monolithic gain control amplifier for Ka-band

    Science.gov (United States)

    Sokolov, V.; Geddes, J.; Contolatis, A.

    A monolithic two stage gain control amplifier has been developed using submicron gate length dual gate MESFETs fabricated on ion implanted material. The amplifier has a gain of 12 dB at 30 GHz with a gain control range of over 30 dB. This ion implanted monolithic IC is readily integrable with other phased array receiver functions such as low noise amplifiers and phase shifters.

  5. A Secreted Slit2 Fragment Regulates Adipose Tissue Thermogenesis and Metabolic Function.

    Science.gov (United States)

    Svensson, Katrin J; Long, Jonathan Z; Jedrychowski, Mark P; Cohen, Paul; Lo, James C; Serag, Sara; Kir, Serkan; Shinoda, Kosaku; Tartaglia, Julia A; Rao, Rajesh R; Chédotal, Alain; Kajimura, Shingo; Gygi, Steven P; Spiegelman, Bruce M

    2016-03-01

    Activation of brown and beige fat can reduce obesity and improve glucose homeostasis through nonshivering thermogenesis. Whether brown or beige fat also secretes paracrine or endocrine factors to promote and amplify adaptive thermogenesis is not fully explored. Here we identify Slit2, a 180 kDa member of the Slit extracellular protein family, as a PRDM16-regulated secreted factor from beige fat cells. In isolated cells and in mice, full-length Slit2 is cleaved to generate several smaller fragments, and we identify an active thermogenic moiety as the C-terminal fragment. This Slit2-C fragment of 50 kDa promotes adipose thermogenesis, augments energy expenditure, and improves glucose homeostasis in vivo. Mechanistically, Slit2 induces a robust activation of PKA signaling, which is required for its prothermogenic activity. Our findings establish a previously unknown peripheral role for Slit2 as a beige fat secreted factor that has therapeutic potential for the treatment of obesity and related metabolic disorders.

  6. Capacities of quantum amplifier channels

    Science.gov (United States)

    Qi, Haoyu; Wilde, Mark M.

    2017-01-01

    Quantum amplifier channels are at the core of several physical processes. Not only do they model the optical process of spontaneous parametric down-conversion, but the transformation corresponding to an amplifier channel also describes the physics of the dynamical Casimir effect in superconducting circuits, the Unruh effect, and Hawking radiation. Here we study the communication capabilities of quantum amplifier channels. Invoking a recently established minimum output-entropy theorem for single-mode phase-insensitive Gaussian channels, we determine capacities of quantum-limited amplifier channels in three different scenarios. First, we establish the capacities of quantum-limited amplifier channels for one of the most general communication tasks, characterized by the trade-off between classical communication, quantum communication, and entanglement generation or consumption. Second, we establish capacities of quantum-limited amplifier channels for the trade-off between public classical communication, private classical communication, and secret key generation. Third, we determine the capacity region for a broadcast channel induced by the quantum-limited amplifier channel, and we also show that a fully quantum strategy outperforms those achieved by classical coherent-detection strategies. In all three scenarios, we find that the capacities significantly outperform communication rates achieved with a naive time-sharing strategy.

  7. Small signal microwave amplifier design

    CERN Document Server

    Grosch, Theodore

    2000-01-01

    This book explains techniques and examples for designing stable amplifiers for high-frequency applications in which the signal is small and the amplifier circuit is linear. An in-depth discussion of linear network theory provides the foundation needed to develop actual designs. Examples throughout the book will show you how to apply the knowledge gained in each chapter leading to the complex design of low noise amplifiers. Many exercises at the end of each chapter will help students to practice their skills. The solutions to these design problems are available in an accompanying solutions book

  8. Governmentally amplified output volatility

    Science.gov (United States)

    Funashima, Yoshito

    2016-11-01

    Predominant government behavior is decomposed by frequency into several periodic components: updating cycles of infrastructure, Kuznets cycles, fiscal policy over business cycles, and election cycles. Little is known, however, about the theoretical impact of such cyclical behavior in public finance on output fluctuations. Based on a standard neoclassical growth model, this study intends to examine the frequency at which public investment cycles are relevant to output fluctuations. We find an inverted U-shaped relationship between output volatility and length of cycle in public investment. This implies that periodic behavior in public investment at a certain frequency range can cause aggravated output resonance. Moreover, we present an empirical analysis to test the theoretical implication, using the U.S. data in the period from 1968 to 2015. The empirical results suggest that such resonance phenomena change from low to high frequency.

  9. International Standardization Activities for Optical Amplifiers

    Institute of Scientific and Technical Information of China (English)

    Haruo Okamura

    2003-01-01

    International standardization activities for Optical Amplifiers at IECTC86 and ITU-T SG15 are reviewed. Current discussions include Optical Amplifier safety guideline, Reliability standard, Rest methods of Noise and PMD, Definitions of Raman amplifier parameters and OA classification.

  10. Characterization of SLUG microwave amplifiers

    Science.gov (United States)

    Hoi, I.-C.; Zhu, S.; Thorbeck, T.; McDermott, R.; Mutus, J.; Jeffrey, E.; Barends, R.; Chen, Y.; Roushan, P.; Fowler, A.; Sank, D.; White, T.; Campbell, B.; Chen, Z.; Chiaro, B.; Dunsworth, A.; Kelly, J.; Megrant, A.; Neill, C.; O'Malley, P. J. J.; Quintana, C.; Vainsencher, A.; Wenner, J.; Martinis, J. M.

    2015-03-01

    With the rapid growth of superconducting circuits quantum technology, a near quantum-limited amplifier at GHz frequency is needed to enable high fidelity measurements. We describe such an amplifier, the SQUID based, superconducting low inductance undulatory galvanometer (SLUG) amplifier. We measure the full scattering matrix of the SLUG. In particular, we measure both forward and reverse gain, as well as reflection. We see 15dB forward gain with added noise from one quanta to several quanta. The -1 dB compression point is around -95 dBm, about two orders of magnitude higher than that of typical Josephson parametric amplifiers. With these properties, SLUG is well suited for the high fidelity, simultaneous multiplexed readout of superconducting qubits.

  11. PID Controller with Operational Amplifier

    Directory of Open Access Journals (Sweden)

    Cristian Paul Chioncel

    2009-01-01

    Full Text Available The paper presents a PID controller made with LM741 operational amplifier that implement the PID controllers laws and allow for a widerange of applications of in the field of automatic control of technicalprocesses and systems.

  12. New Packaging for Amplifier Slabs

    Energy Technology Data Exchange (ETDEWEB)

    Riley, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thorsness, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Suratwala, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Steele, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Rogowski, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-03-18

    The following memo provides a discussion and detailed procedure for a new finished amplifier slab shipping and storage container. The new package is designed to maintain an environment of <5% RH to minimize weathering.

  13. Operational amplifiers theory and design

    CERN Document Server

    Huijsing, Johan

    2017-01-01

    This proven textbook guides readers to a thorough understanding of the theory and design of operational amplifiers (OpAmps). The core of the book presents systematically the design of operational amplifiers, classifying them into a periodic system of nine main overall configurations, ranging from one gain stage up to four or more stages. This division enables circuit designers to recognize quickly, understand, and choose optimal configurations. Characterization of operational amplifiers is given by macro models and error matrices, together with measurement techniques for their parameters. Definitions are given for four types of operational amplifiers depending on the grounding of their input and output ports. Many famous designs are evaluated in depth, using a carefully structured approach enhanced by numerous figures. In order to reinforce the concepts introduced and facilitate self-evaluation of design skills, the author includes problems with detailed solutions, as well as simulation exercises. Provides te...

  14. A KIND OF NEW AMPLIFIER

    Institute of Scientific and Technical Information of China (English)

    YIN XUN-HE; FENG RU-PENG; REN YONG

    2000-01-01

    Chaotic characteristics in the iteration of logistic map (one-dimensional discrete dynamic system) are simulatedand analyzed. The circuit implementation of a kind of chaotic amplifier model is based on the chaotic characteristicsthat chaos is sensitively dependent on its initial conditions, and the circuit simulation result is given using simulationprogram with integrated circuit emphasis for personal computer (PSPICE), and is compared with linear amplifier.Advantages and disadvantages of such a model are indicated.

  15. Gain and noise penalty for detuned 980 nm pumping or erbium-doped fiber power amplifiers

    DEFF Research Database (Denmark)

    Pedersen, B.; Chirravuri, J.; Miniscalco, W. J.

    1992-01-01

    The impact of altering the fiber length and pump wavelength on the gain and noise performance of erbium-doped fiber power amplifiers pumped in the 980-nm band is examined. A gain penalty of......The impact of altering the fiber length and pump wavelength on the gain and noise performance of erbium-doped fiber power amplifiers pumped in the 980-nm band is examined. A gain penalty of...

  16. Generation of sub-50 fs pulses from a high-power Yb-doped fiber amplifier.

    Science.gov (United States)

    Deng, Yujun; Chien, Ching-Yuan; Fidric, Bernard G; Kafka, James D

    2009-11-15

    We demonstrate the generation of 48 fs pulses with 18 W average power and 226 nJ of pulse energy from a Yb-doped fiber amplifier. The system uses a simple stretcher-free single-stage amplifier configuration operating in the parabolic pulse regime. The gain fiber length and pump wavelength are chosen in order to reduce the gain per unit length and generate both shorter pulses and higher pulse energy.

  17. Dispersion-Engineered Traveling Wave Kinetic Inductance Parametric Amplifier

    Science.gov (United States)

    Zmuidzinas, Jonas (Inventor); Day, Peter K. (Inventor)

    2014-01-01

    A traveling wave kinetic inductance parametric amplifier comprises a superconducting transmission line and a dispersion control element. The transmission line can include periodic variations of its dimension along its length. The superconducting material can include a high normal state resistivity material. In some instances the high normal state resistivity material includes nitrogen and a metal selected from the group consisting of titanium, niobium and vanadium. The traveling wave kinetic inductance parametric amplifier is expected to exhibit a noise temperature below 100 mK/GHz.

  18. AFLP fragment isolation technique as a method to produce random sequences for single nucleotide polymorphism discovery in the green turtle, Chelonia mydas.

    Science.gov (United States)

    Roden, Suzanne E; Dutton, Peter H; Morin, Phillip A

    2009-01-01

    The green sea turtle, Chelonia mydas, was used as a case study for single nucleotide polymorphism (SNP) discovery in a species that has little genetic sequence information available. As green turtles have a complex population structure, additional nuclear markers other than microsatellites could add to our understanding of their complex life history. Amplified fragment length polymorphism technique was used to generate sets of random fragments of genomic DNA, which were then electrophoretically separated with precast gels, stained with SYBR green, excised, and directly sequenced. It was possible to perform this method without the use of polyacrylamide gels, radioactive or fluorescent labeled primers, or hybridization methods, reducing the time, expense, and safety hazards of SNP discovery. Within 13 loci, 2547 base pairs were screened, resulting in the discovery of 35 SNPs. Using this method, it was possible to yield a sufficient number of loci to screen for SNP markers without the availability of prior sequence information.

  19. rDNA-ITS restriction fragment length polymorphism of cereal cyst nematodes in some regions of Qinghai, Shaanxi and Henan Province, China%青海、陕西部分地区禾谷孢囊线虫rDNA-ITS-RFLP的特征分析

    Institute of Scientific and Technical Information of China (English)

    欧师琪; 彭德良; 李玉

    2011-01-01

    Eleven populations of cereal cyst nematode (CCN) from wheat were collected in collected in Qinghai and Shaanxi Provinc, all morphologically identified as Heterodera avenae. The rDNA-US regions of the populations were amplified with the universal primers AB28 and TW81, a fragment of approximately 1 060 bp was yielded. The fragments were digested with Hinf Ⅰ , TaqⅠ , Hpa Ⅱ , Hae Ⅲ, Pst Ⅰ and Alu Ⅰ . The identical digestion patterns were obtained from CCN populations (YBT10A, HY65A, HY61B, ZHZ162B, HY5B, HHX8A, GH132A, HY92A, HY127B and DT142A) of Qinghai and which were the same species. The digestion patterns were the same between YL4A population of Shaanxi and the ones of Qinghai by Hae Ⅲ ,Hinf Ⅰ and Hpa Ⅱ. The digestion patterns of Pst I and Alu I showed that the YL4A CCN population was differed from the ones of Qinghai, because it had an extra 1 060 bp fragment. The Taq I restriction pattern of YL4A CCN population was complex. The obvious difference could be observed in the Taq I RFLP pattern, a 520 bp fragment was not presented in the Qinghai CCN populations but in the Henan populations. According to the known conclusions, the analysis results restriction profiles showed that 10 populations of Qinghai were the identical RFLP patterns of H. Avenae from China. Alu I profile of YL4A population was the same as H. Avenae from France, then digestion of YL4A population by Pst I and Taq I were different with either members of Avenae group because of its complex profiles. The Henan CCN populations were the similar as Qinghai ones except RFLP profile by Taq I , and identical with H. Avenae from Australia.%采自我国青海、陕西等省地11个寄生小麦的孢囊线虫群体经形态学鉴定为禾谷孢囊线虫(Heterodera avenae).用PCR技术扩增获得的rDNA-ITS片段长度约为l 060 bp.用HinfⅠ、TaqⅠ、HpaⅡ、HaeⅢ、PstⅠ、AluⅠ等6种限制性内切酶酶切ITS扩增产物;青海10群体YBT10A、HY65A、HY61B、ZHZ162B、HY5B

  20. Broadband amplified spontaneous emission from Er3+-doped single-mode tellurite fibre

    Institute of Scientific and Technical Information of China (English)

    Chen Dong-Dan; Zhang Qin-Yuan; Liu Yue-Hui; Xu Shan-Hui; Yang Zhong-Min; Deng Zai-De; Jiang Zhong-Hong

    2006-01-01

    This paper reports on the fabrication and characterization of a newly erbium-doped single-mode tellurite glass-fibre applicable for 1.5-μm optical amplifiers. A very broad erbium amplified spontaneous emission in the range 1450-1650 nm from erbium-doped single-mode tclluritc glass-fibre is obtained upon excitation of a 980-nm laser diode. The effects of the length of glass-fibre and the pumping power of laser diode on the amplified spontaneous emission are discussed.The result indicates that the tellurite glass-fibre is a promising candidate for designing fibre-optic amplifiers and lasers.

  1. Mechanisms in Impact Fragmentation

    OpenAIRE

    Wittel, Falk K.; Carmona, Humberto A.; Kun, Ferenc; Herrmann, Hans J.

    2015-01-01

    The brittle fragmentation of spheres is studied numerically by a 3D Discrete Element Model. Large scale computer simulations are performed with models that consist of agglomerates of many spherical particles, interconnected by beam-truss elements. We focus on a detailed description of the fragmentation process and study several fragmentation mechanisms involved. The evolution of meridional cracks is studied in detail. These cracks are found to initiate in the inside of the specimen with quasi...

  2. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  3. Modification of the full-length cDNA clone of Newcastle disease virus Isolated from an outbreak In the goose

    Institute of Scientific and Technical Information of China (English)

    LIU Yuliang; HU Shunli; ZHANG Yanmei; WU Yantao; LIU Xiufan; R(o)emer-Oberdoerfer Angela; Veits Jutta; Lange Martina

    2006-01-01

    A 6.5-kb specific fragment containing the T7 promoter and the transcription vector was excised from the full-length eDNA clone of the Newcastle disease virus (NDV) strain ZJI of goose origin,and thereafter it was self-ligated to form a high quality plasmid for mutagenesis.Site-directed mutagenesis was used for inserting three additional G nucleotides (nts) into the region between the T7 promoter and the leader sequence of the NDV genome.RT-PCR was employed to amplify the F/HN gene fragments,and then they were ligated by the shared restriction enzyme BsmBI.Finally,the corresponding fragment in the mutant full-length eDNA was substituted with the new one.The sequencing results showed that the three additional Gnts were successfully inserted and the mutant nts in the full-length eDNA were corrected.This study lays a good foundation for research on the reverse genetics of NDV strain ZJI.

  4. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  5. EMI-resilient amplifier circuits

    CERN Document Server

    van der Horst, Marcel J; Linnenbank, André C

    2014-01-01

    This book enables circuit designers to reduce the errors introduced by the fundamental limitations and electromagnetic interference (EMI) in negative-feedback amplifiers.  The authors describe a systematic design approach for application specific negative-feedback amplifiers, with specified signal-to-error ratio (SER).  This approach enables designers to calculate noise, bandwidth, EMI, and the required bias parameters of the transistors used in  application specific amplifiers in order to meet the SER requirements.   ·         Describes design methods that incorporate electromagnetic interference (EMI) in the design of application specific negative-feedback amplifiers; ·         Provides designers with a structured methodology to avoid the use of trial and error in meeting signal-to-error ratio (SER) requirements; ·         Equips designers to increase EMI immunity of the amplifier itself, thus avoiding filtering at the input, reducing the number of components and avoiding detr...

  6. Fragmentation characteristics analysis of sandstone fragments based on impact rockburst test

    Institute of Scientific and Technical Information of China (English)

    Dongqiao Liu; Dejian Li; Fei Zhao; Chengchao Wang

    2014-01-01

    Impact rockburst test on sandstone samples with a central hole is carried out under true triaxial static loads and vertical dynamic load conditions, and rock fragments after the test are collected. The fragments of sandstone generated from strain rockburst test and uniaxial compression test are also collected. The fragments are weighed and the length, width and thickness of each piece of fragments are measured respectively. The fragment quantities with coarse, medium, fine and micro grains in different size ranges, mass and particles distributions are also analyzed. Then, the fractal dimension of fragments is calculated by the methods of size-frequency, mass-frequency and length-to-thickness ratio-frequency. It is found that the crushing degree of impact rockburst fragments is higher, accompanied with blocky character-istics observably. The mass percentage of small grains, including fine and micro grains, in impact rock-burst test is higher than those in strain rockburst test and uniaxial compression test. Energy dissipation from rockburst tests is more than that from uniaxial compression test, as the quantity of micro grains generated does.

  7. Design criteria for ultrafast optical parametric amplifiers

    Science.gov (United States)

    Manzoni, C.; Cerullo, G.

    2016-10-01

    Optical parametric amplifiers (OPAs) exploit second-order nonlinearity to transfer energy from a fixed frequency pump pulse to a variable frequency signal pulse, and represent an easy way of tuning over a broad range the frequency of an otherwise fixed femtosecond laser system. OPAs can also act as broadband amplifiers, transferring energy from a narrowband pump to a broadband signal and thus considerably shortening the duration of the pump pulse. Due to these unique properties, OPAs are nowadays ubiquitous in ultrafast laser laboratories, and are employed by many users, such as solid state physicists, atomic/molecular physicists, chemists and biologists, who are not experts in ultrafast optics. This tutorial paper aims at providing the non-specialist reader with a self-consistent guide to the physical foundations of OPAs, deriving the main equations describing their performance and discussing how they can be used to understand their most important working parameters (frequency tunability, bandwidth, pulse energy/repetition rate scalability, control over the carrier-envelope phase of the generated pulses). Based on this analysis, we derive practical design criteria for OPAs, showing how their performance depends on the type of the nonlinear interaction (crystal type, phase-matching configuration, crystal length), on the characteristics of the pump pulse (frequency, duration, energy, repetition rate) and on the OPA architecture.

  8. A CMOS current-mode operational amplifier

    DEFF Research Database (Denmark)

    Kaulberg, Thomas

    1993-01-01

    current-mode feedback amplifier or a constant bandwidth in a transimpedance feedback amplifier. The amplifier is found to have a gain-bandwidth product of 3 MHz, an offset current of 0.8 μA (signal range ±700 μA), and a (theoretically) unlimited slew rate. The amplifier is realized in a standard CMOS 2...

  9. Telomere Length and Mortality

    DEFF Research Database (Denmark)

    Kimura, Masayuki; Hjelmborg, Jacob V B; Gardner, Jeffrey P

    2008-01-01

    Leukocyte telomere length, representing the mean length of all telomeres in leukocytes, is ostensibly a bioindicator of human aging. The authors hypothesized that shorter telomeres might forecast imminent mortality in elderly people better than leukocyte telomere length. They performed mortality...

  10. Stochastic phenomena in a fiber Raman amplifier

    CERN Document Server

    Kalashnikov, Vladimir; Ania-Castanón, Juan Diego; Jacobsen, Gunnar; Popov, Sergei

    2016-01-01

    The interplay of such cornerstones of modern nonlinear fiber optics as a nonlinearity, stochasticity and polarization leads to variety of the noise induced instabilities including polarization attraction and escape phenomena harnessing of which is a key to unlocking the fiber optic systems specifications required in high resolution spectroscopy, metrology, biomedicine and telecommunications. Here, by using direct stochastic modeling, the mapping of interplay of the Raman scattering-based nonlinearity, the random birefringence of a fiber, and the pump-to-signal intensity noise transfer has been done in terms of the fiber Raman amplifier parameters, namely polarization mode dispersion, the relative intensity noise of the pump laser, fiber length, and the signal power. The obtained results reveal conditions for emergence of the random birefringence-induced resonance-like enhancement of the gain fluctuations (stochastic anti-resonance) accompanied by pulse broadening and rare events in the form of low power outpu...

  11. Gain Characteristics of Fiber Optical Parametric Amplifier

    Institute of Scientific and Technical Information of China (English)

    高明义; 姜淳; 胡卫生

    2004-01-01

    The theory model of fiber optical parametric amplifier (FOPA) was introduced, which is based on optical nonlinear effect. And then numerical simulation was done to analyze and discuss the gain spectral characteristics of one-pump and two-pump FOPA. The results show that for one-pump FOPA, when pump wavelength is near to fiber zero-dispersion wavelength(ZDW), the gain flatness is better, and with the increase of the pump power, fiber length and its nonlinear coefficient, the gain value will increase while the gain bandwidth will become narrow. For two-pump FOPA, when the pump central wavelength is near to fiber ZDW, the gain flatness is better. Moreover, by decreasing the space of two pumps wavelength, the gain flatness can be improved. Finally, some problems existing in FOPA were addressed.

  12. Morphological and sequence-related amplified polymorphism-based molecular diversity of local and exotic wheat genotypes.

    Science.gov (United States)

    Abdelkhalik, S M; Salem, A K M; Abdelaziz, A R; Ammar, M H

    2016-04-28

    Assessing genetic diversity is a prerequisite for the genetic improvement of wheat. Molecular markers offer accurate and reproducible means for assessing genetic diversity. Field performance and sequence-related amplified polymorphism (SRAP)-based assessment of molecular diversity was carried out on a set of 10 local and introduced bread wheat (Triticum sativum L.) genotypes grown in the middle arid region of Saudi Arabia. The results revealed highly significant differences among the studied phenological traits and revealed a significant amount of genetic diversity across the tested genotypes. The overall performance revealed the superiority of KSU 102 in terms of yield and its components, with a yield potential of 8.7 tons/ha. Highly significant and positive correlations were observed among grain yield and biological yield, and also, spike length and spike weight. Thirteen SRAP primer combinations successfully amplified 954 fragments. The total number of genetic loci analyzed was 312. The overall polymorphism ratio was 99.67%, ranging from 98 to 100%. The polymorphic information content values ranged from 0.67 for ME11 x EM5 to 0.97 for ME9 x EM4 and ME11 x EM6, respectively. The wheat genotypes were clustered based on their genetic constitution and origin. The results demonstrate the power of SRAP primers for detecting molecular diversity and for varietal discrimination. The results show that high levels of genetic diversity exist, and suggest the potential of the tested materials for wheat crop improvement in the arid central region of Saudi Arabia.

  13. Capacitively-coupled chopper amplifiers

    CERN Document Server

    Fan, Qinwen; Huijsing, Johan H

    2017-01-01

    This book describes the concept and design of the capacitively-coupled chopper technique, which can be used in precision analog amplifiers. Readers will learn to design power-efficient amplifiers employing this technique, which can be powered by regular low supply voltage such as 2V and possibly having a +\\-100V input common-mode voltage input. The authors provide both basic design concepts and detailed design examples, which cover the area of both operational and instrumentation amplifiers for multiple applications, particularly in power management and biomedical circuit designs. Discusses basic working principles and details of implementation for proven designs; Includes a diverse set of applications, along with measurement results to demonstrate the effectiveness of the technique; Explains advantages and drawbacks of the technique, given particular circumstances.

  14. Supported PCR: an efficient procedure to amplify sequences flanking a known DNA segment

    OpenAIRE

    Rudenko, George N.; Rommens, Caius M.T.; Nijkamp, H. John J.; Hille, Jacques

    1993-01-01

    We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of genomic DNA on streptavidin-containing support. Subsequently, following ligation with a second universal linker primer, the selected fragments can be amplified to amounts suitable for further molecula...

  15. Flying between sky islands: the effect of naturally fragmented habitat on butterfly population structure.

    Science.gov (United States)

    Sekar, Sandhya; Karanth, Praveen

    2013-01-01

    High elevation montane areas are called "sky islands" when they occur as a series of high mountains separated by lowland valleys. Different climatic conditions at high elevations makes sky islands a specialized type of habitat, rendering them naturally fragmented compared to more continuous habitat at lower elevations. Species in sky islands face unsuitable climate in the intervening valleys when moving from one montane area to another. The high elevation shola-grassland mosaic in the Western Ghats of southern India form one such sky island complex. The fragmented patches make this area ideal to study the effect of the spatial orientation of suitable habitat patches on population genetic structure of species found in these areas. Past studies have suggested that sky islands tend to have genetically structured populations, possibly due to reduced gene flow between montane areas. To test this hypothesis, we adopted the comparative approach. Using Amplified Fragment Length Polymorphisms, we compared population genetic structures of two closely related, similar sized butterfly species: Heteropsis oculus, a high elevation shola-grassland specialist restricted to the southern Western Ghats, and Mycalesis patnia, found more continuously distributed in lower elevations. In all analyses, as per expectation the sky island specialist H. oculus exhibited a greater degree of population genetic structure than M. patnia, implying a difference in geneflow. This difference in geneflow in turn appears to be due to the natural fragmentation of the sky island complexes. Detailed analysis of a subset of H. oculus samples from one sky island complex (the Anamalais) showed a surprising genetic break. A possible reason for this break could be unsuitable conditions of higher temperature and lower rainfall in the intervening valley region. Thus, sky island species are not only restricted by lack of habitat continuity between montane areas, but also by the nature of the intervening habitat.

  16. Fluorescent amplified fragment length polymorphism (fAFLP)analysis of population genetic diversity and species relationships of four species of cultured clams in family Veneridae (Mollusca: Bivalvia)%帘蛤科4种养殖蛤群体遗传多样性和种间关系的fAFLP分析

    Institute of Scientific and Technical Information of China (English)

    彭永兴; 程汉良; 夏德全; 吴婷婷; 孟学平; 吉红九; 董志国

    2008-01-01

    利用荧光标记扩增片段长度多态性(fAFLP)技术对文蛤(Meretrix meretrix)、青蛤(Cyclina sinensis)、菲律宾蛤仔(Ruditapes philippinarum)和硬壳蛤(Mercenaria mercenaria)4种帘蛤科贝类的群体遗传多样性和种间关系进行了研究.选择EcoR Ⅰ/Mse Ⅰ进行酶切,使用6个E+3/M+3引物组合进行扩增,共获得1096个位点,多态位点比率95.1%,片段长度50~456 bp.其中,文蛤、青蛤、菲律宾蛤仔和硬壳蛤分别得到681,715,702和694个位点,相应的多态位点比率为76.8%,81.7%,83.0%和75.1%,得到17个种特异性位点,可作为4物种特征标记.分析了群体遗传相似系数和遗传多样性指数以及种间遗传相似系数.结果表明,硬壳蛤群体遗传相似系数最高(0.670 9),遗传多样性指数最低(0.236 0);菲律宾蛤仔群体遗传相似系数最低(0.592 5),遗传多样性指数最高(0.261 8);根据遗传相似系数采用UPGMA法构建了4物种32个体的聚类图,表明文蛤与菲律宾蛤仔遗传关系最近,青蛤与其他3物种遗传关系较远.

  17. String fragmentation; La fragmentation des cordes

    Energy Technology Data Exchange (ETDEWEB)

    Drescher, H.J.; Werner, K. [Laboratoire de Physique Subatomique et des Technologies Associees - SUBATECH, Centre National de la Recherche Scientifique, 44 - Nantes (France)

    1997-10-01

    The classical string model is used in VENUS as a fragmentation model. For the soft domain simple 2-parton strings were sufficient, whereas for higher energies up to LHC, the perturbative regime of the QCD gives additional soft gluons, which are mapped on the string as so called kinks, energy singularities between the leading partons. The kinky string model is chosen to handle fragmentation of these strings by application of the Lorentz invariant area law. The `kinky strings` model, corresponding to the perturbative gluons coming from pQCD, takes into consideration this effect by treating the partons and gluons on the same footing. The decay law is always the Artru-Menessier area law which is the most realistic since it is invariant to the Lorentz and gauge transformations. For low mass strings a manipulation of the rupture point is necessary if the string corresponds already to an elementary particle determined by the mass and the flavor content. By means of the fragmentation model it will be possible to simulate the data from future experiments at LHC and RHIC 3 refs.

  18. Optical steganography based on amplified spontaneous emission noise.

    Science.gov (United States)

    Wu, Ben; Wang, Zhenxing; Tian, Yue; Fok, Mable P; Shastri, Bhavin J; Kanoff, Daniel R; Prucnal, Paul R

    2013-01-28

    We propose and experimentally demonstrate an optical steganography method in which a data signal is transmitted using amplified spontaneous emission (ASE) noise as a carrier. The ASE serving as a carrier for the private signal has an identical frequency spectrum to the existing noise generated by the Erbium doped fiber amplifiers (EDFAs) in the transmission system. The system also carries a conventional data channel that is not private. The so-called "stealth" or private channel is well-hidden within the noise of the system. Phase modulation is used for both the stealth channel and the public channel. Using homodyne detection, the short coherence length of the ASE ensures that the stealth signal can only be recovered if the receiver closely matches the delay-length difference, which is deliberately changed in a dynamic fashion that is only known to the transmitter and its intended receiver.

  19. DETECÇÃO DO COMPLEXO Mycobacterium tuberculosis NO LEITE PELA REAÇÃO EM CADEIA DA POLIMERASE SEGUIDA DE ANÁLISE DE RESTRIÇÃO DO FRAGMENTO AMPLIFICADO (PRA DETECTION OF Mycobacterium tuberculosis COMPLEX BY PCR-RESTRICTION FRAGMENT LENGTH POLYMORFISM ANALYSIS OF THE HSP65 GENE

    Directory of Open Access Journals (Sweden)

    Joab Trajano Silva

    2008-12-01

    , up to species level, is time consuming and difficult. In this work, the objective was to standardize a polymerase chain reaction followed by an enzyme restriction analysis in order to identify the M. tuberculosis complex in milk, without a microbiological isolation step. Reference strains and raw milk seeded with M. Bovis, were used as the starting material.  A 441pb fragment of the hsp65 gene was amplified and digested by two restriction enzymes BstEII and HaeIII. The obtained profile was used to identify the M. tuberculosis complex in milk. The minimum limit of detection of M. bovis in milk was 10CFU/mL. PRA methodology proved to be a specific and sensible method. It can be used to assist the microbiological and biochemical methods commonly used to identifying the bacilli in clinical samples, as milk 

    Key word: Detection limit (PRA, Mycobacterium tuberculosis complex, milk Mycobacterium bovis, Restriction Enzyme Analysis (PCR,

  20. Thermal recovery of NIF amplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, S.; Marshall, C.; Petty, C.; Smith, L.; van Wonterghem, B.; Mills, S.

    1997-02-01

    The issue of thermal recovery of the NIF amplifiers has taken on increased emphasis as program goals move toward increasing the shot rate to once every four hours. This paper addresses the technical issues associated with achieving thermal recovery in the NIF amplifiers. We identify two temperature related thermal recovery quantities: (1) the difference between the average slab temperature and the temperature of other surfaces in the amplifier cavity, and (2) the temperature difference in the slab over the aperture. The first quantity relates to optical disturbances in the gas column in the system, while the second quantity is associated with optical aberrations in the laser media itself. Calculations and experiments are used to quantify recovery criteria, and develop cooling approaches. The cooling approaches discussed are (1) active cooling of the flashlamps with ambient gas and chilled gas, and (2) active cooling of the slab edge cladding. Calculations indicate that the NIF baseline cooling approach of 20 cfm per lamp ambient temperature gas flow in both the central and side flashlamp cassettes is capable of meeting thermal recovery requirements for an 8 hour shot period, while to achieve a 4 hour shot period requires use of chilled gas and edge cladding cooling. In addition, the effect of changing the amplifier cavity and beamtube fill gas from nitrogen to helium is addressed, showing that a factor of 8 reduction in the sensitivity to thermal disturbances is possible. 6 refs., 9 figs., 1 tab.

  1. Computer Aided Design and Analysis of a 2-4 GHz Broadband Balanced Microstrip Amplifier

    Directory of Open Access Journals (Sweden)

    S. H. Ibrahim

    2012-07-01

    Full Text Available In this paper, a computer-aided design and analysis of a 2-4 GHz broadband balanced microstrip amplifier using a full computer simulation program developed by the author and others is presented. A short and efficient CAD procedure for broadband amplifier design is introduced. The first step is to design an initial narrow-band high gain microstrip amplifier at 3-GHz central frequency. The second step is to optimize the initial lengths and widths of the input and output microstrip-matching circuits to get the broadband amplifier over the range 2-4 GHz. The analysis of both narrow and broadband amplifiers is investigated. In addition, with the design and analysis of a low-pass microstrip filter, the paper introduces the design and analysis of a Lange coupler. The final AC schematic diagram of the designed amplifier with the lengths and widths of microstrip lines is presented.Key Words: Computer-Aided Design and Analysis, Microstrip Amplifier, Microwave Amplifier.

  2. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  3. Fragmented Work Stories

    DEFF Research Database (Denmark)

    Humle, Didde Maria; Reff Pedersen, Anne

    2015-01-01

    Following a strand of narrative studies pointing to the living conditions of storytelling and the micro-level implications of working within fragmented narrative perspectives, this article contributes to narrative research on work stories by focusing on how meaning is created from fragmented...... by exploring how different types of fragmentation create meanings. This is done by studying the work stories of job and personnel consultants and by drawing on the results of a narrative, ethnographic study of a consultancy. The analysis demonstrates how work stories are social practices negotiated, retold...... stories. We argue that meaning by story making is not always created by coherence and causality; meaning is created by different types of fragmentation: discontinuities, tensions and editing. The objective of this article is to develop and advance antenarrative practice analysis of work stories...

  4. Fragmentation in Biaxial Tension

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, G H; Archbold, G C; Hurricane, O A; Miller, P L

    2006-06-13

    We have carried out an experiment that places a ductile stainless steel in a state of biaxial tension at a high rate of strain. The loading of the ductile metal spherical cap is performed by the detonation of a high explosive layer with a conforming geometry to expand the metal radially outwards. Simulations of the loading and expansion of the metal predict strain rates that compare well with experimental observations. A high percentage of the HE loaded material was recovered through a soft capture process and characterization of the recovered fragments provided high quality data, including uniform strain prior to failure and fragment size. These data were used with a modified fragmentation model to determine a fragmentation energy.

  5. Fragmentation Main Model

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — The fragmentation model combines patch size and patch continuity with diversity of vegetation types per patch and rarity of vegetation types per patch. A patch was...

  6. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  7. Matricryptins and matrikines: biologically active fragments of the extracellular matrix.

    Science.gov (United States)

    Ricard-Blum, Sylvie; Salza, Romain

    2014-07-01

    Numerous extracellular proteins and glycosaminoglycans (GAGs) undergo limited enzymatic cleavage resulting in the release of fragments exerting biological activities, which are usually different from those of the full-length molecules. In this review, we define matrikines and matricryptins, which are bioactive fragments released from the extracellular matrix proteins, proteoglycans and GAGs and report their major biological activities. These fragments regulate a number of physiopathological processes including angiogenesis, cancer, fibrosis, inflammation, neurodegenerative diseases and wound healing. The challenges to translate these fragments from molecules biologically active in vitro and in experimental models to potential drugs are discussed in the last part of the review.

  8. CMOS Current-mode Operational Amplifier

    DEFF Research Database (Denmark)

    Kaulberg, Thomas

    1992-01-01

    current-mode feedback amplifier or a constant bandwidth in a transimpedance feedback amplifier. The amplifier is found to have a gain bandwidth product of 8 MHz, an offset current of 0.8 ¿A (signal-range ±700¿A) and a (theoretically) unlimited slew-rate. The amplifier is realized in a standard CMOS 2......A fully differential-input differential-output current-mode operational amplifier (COA) is described. The amplifier utilizes three second generation current-conveyors (CCII) as the basic building blocks. It can be configured to provide either a constant gain-bandwidth product in a fully balanced...

  9. 棘阿米巴土壤分离株CB/S1的线粒体DNA限制性片段长度多态性%MITOCHONDRIAL DNA RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) OF ACANTHAMOEBA SP. CB/S1 ISOLAT ED FROM SOIL

    Institute of Scientific and Technical Information of China (English)

    崔春权; 玄英花; 郑善子; 金松竹; 杨香

    2012-01-01

    [目的]观察棘阿米巴土壤分离株CB/S1的线粒体DNA限制性片段长度多态性(RFLP).[方法]从棘阿米巴CB/S1提取线粒体DNA用Eco RI酶切,与土壤分离株CJY/S4比较观察限制性片段长度多态性.用地衣红-卡红染色观察棘阿米巴内共生细菌.[结果]棘阿米巴土壤分离株CB/S1线粒体DNA RFLP与CJY/S4相比除了额外的片段(extra bands),两个分离株具有相同的片段模式.经地衣红染色观察CB/S1内共生细菌呈黑色、棒状、不规则的分布在胞质内.[结论]额外的片段表明棘阿米巴CB/S1内含有内共生细菌的环状DNA,并且除了内共生细菌的存在棘阿米巴CB/S1与土壤分离株CJY/S4具有密切的亲缘关系.线粒体DNA限制性片段长度多态性是棘阿米巴分类及发现内共生细菌的简便而有效的方法.%[Objective] To survey characterization of Mitochondrial DNA Restriction Fragment Length Polymorphism (MtDNA RFLP) of Aeanthamoeba sp. CB/SI isolated from soil of china. [Methods] The extracted MlDNA was digested with the Eco RI restriction enzyme, electrophoresed in 0.7% agarose gel. The endosymbiont of Acanthamoeba sp. was characterized with orcein-camiime staining [Results] Acanthamoeba sp. CB/SI showED extra bands as weli as common bands with the other Aeanthamoeba sp. CJY/S4 strain isolated from soil, rode-shaped endosymbionts were randomly distributed within the cytoplasm of trophozoite of Aeanthamoeba sp. CB/SI. [Conclusion] These results indicated that the.Acanlhamoeba sp. CB/SI may possi-bly harbor intracellular endosymbiotic bacteria containing circular DNAs. With the exception of the presence of endosymbionts, Aeanthamoeba sp. CB/S1 with Aeanthamoeba CJY/S4 were found to be closely phylogenetically related.

  10. IDENTIFICATION OF GYMNEMA SPECIES BY RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE AND CHLOROPLAST trnK GENE

    Directory of Open Access Journals (Sweden)

    Subashini Sekar

    2014-12-01

    Full Text Available Gymnema is one of the important anti-diabetic medicinal plants used from ancient times and is commonly known as ‘sugar killer’. Most of its species have been used in many applications in Indian traditional medicine. Nevertheless, their efficiency is critically dependent on the use of the correct material. The sharing of similar vernacular name and morphological features make confusion in the usage of Gymnema species. In the present study, Gymnema sp. were identified through random amplified polymorphic DNA (RAPD technique and species specific markers were generated for easy identification of G. elegans, G. montanum and G. sylvestre. Using the RAPD techniques of 3 species specific markers for G. sylvestre, 7 markers for G. elegans and 4 markers for G. montanum had been generated. Highest genetic identity was found between G. sylvestre and G. montanum and highest genetic distance was found between G. sylvestre and G. elegans. Further, DNA barcode was developed by sequencing chloroplast partial trnK DNA of these three species. No significant variation was found in partial trnK gene sequences between Gymnema species. But these sequences can efficiently differentiate the Gymnema and Mandevilla species. In-silico sequence–restriction fragment length polymorphism (RFLP analysis revealed three fragments measuring G. sylvestre - 204, G. elegans - 174, and G. montanum - 168 bp Gymnema species. The present study concluded that RAPD markers were highly efficient for species detection than the partial trnK gene sequences. This could be used to confirm the Gymnema sp. identities and to ensure their safe application in pharmaceuticals.

  11. CAG-encoded polyglutamine length polymorphism in the human genome

    Directory of Open Access Journals (Sweden)

    Hayden Michael R

    2007-05-01

    Full Text Available Abstract Background Expansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority of individuals clinically diagnosed with spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to be caused by this common mutational mechanism. We set out to determine the length distributions of CAG-polyglutamine tracts for the entire human genome in a set of healthy individuals in order to characterize the nature of polyglutamine repeat length variation across the human genome, to establish the background against which pathogenic repeat expansions can be detected, and to prioritize candidate genes for repeat expansion disorders. Results We found that repeats, including those in known disease genes, have unique distributions of glutamine tract lengths, as measured by fragment analysis of PCR-amplified repeat regions. This emphasizes the need to characterize each distribution and avoid making generalizations between loci. The best predictors of known disease genes were occurrence of a long CAG-tract uninterrupted by CAA codons in their reference genome sequence, and high glutamine tract length variance in the normal population. We used these parameters to identify eight priority candidate genes for polyglutamine expansion disorders. Twelve CAG-polyglutamine repeats were invariant and these can likely be excluded as candidates. We outline some confusion in the literature about this type of data, difficulties in comparing such data between publications, and its application to studies of disease prevalence in different populations. Analysis of Gene Ontology-based functions of CAG-polyglutamine-containing genes provided a visual framework for interpretation of these genes' functions. All nine known disease genes were involved in DNA

  12. Linearisation of RF Power Amplifiers

    DEFF Research Database (Denmark)

    Nielsen, Per Asbeck

    2001-01-01

    This thesis deals with linearisation techniques of RF power amplifiers (PA), PA design techniques and integration of the necessary building blocks in a CMOS technology. The opening chapters introduces the theory of transmitter architectures, RF-signal representation and the principles of digital...... modulation. Furthermore different types of power amplifiers, models and measures of non-linearities are presented. A chapter is also devoted to different types of linearisation systems. The work carried out and described in this thesis can be divided into a more theoretical and system oriented treatment...... the polar loop architecture and it’s suitability to modern digital transmitters is discussed. A proposal of an architecture that is suitable for digital transmitters, which means that it has an interface to the digital back-end, defined by low-pass signals in polar form, is presented. Simulation guidelines...

  13. Single conversion stage amplifier - SICAM

    Energy Technology Data Exchange (ETDEWEB)

    Ljusev, P.

    2005-12-15

    This Ph.D. thesis presents a thorough analysis of the so called SICAM - SIngle Converter stage AMplifier approach to building direct energy conversion audio power amplifiers. The mainstream approach for building isolated audio power amplifiers today consists of isolated DC power supply and Class D amplifier, which essentially represents a two stage solution, where each of the components can be viewed as separate and independent part. The proposed SICAM solution strives for direct energy conversion from the mains to the audio output, by dedicating the operation of the components one to another and integrating their functions, so that the final audio power amplifier represents a single-stage topology with higher efficiency, lower volume, less board space, lower component count and subsequently lower cost. The SICAM approach is both applicable to non-isolated and isolated audio power amplifiers, but the problems encountered in these two cases are different. Non-isolated SICAM solutions are intended for both AC mains-connected and battery-powered devices. In non-isolated mains-connected SICAMs the main idea is to simplify the power supply or even provide integrated power factor correction (PFC) functions, while still maintaining low component stress and good audio performance by generally decreasing the input voltage level to the Class D audio power amplifier. On the other hand, non-isolated battery-powered SICAMs have to cope with the ever changing battery voltage and provide output voltage levels which are both lower and higher than the battery voltage, while still being simple and single-stage energy conversion solutions. In isolated SICAMs the isolation transformer adjusts the voltage level on the secondary side to the desired level, so the main challenges here are decreasing the size of the magnetic core and reducing the number and size of bulky reactive components as much as possible. The main focus of this thesis is directed towards the isolated SICAMs and

  14. 338-GHz Semiconductor Amplifier Module

    Science.gov (United States)

    Samoska, Lorene A.; Gaier, Todd C.; Soria, Mary M.; Fung, King Man; Rasisic, Vesna; Deal, William; Leong, Kevin; Mei, Xiao Bing; Yoshida, Wayne; Liu, Po-Hsin; Uyeda, Jansen; Lai, Richard

    2010-01-01

    Research findings were reported from an investigation of new gallium nitride (GaN) monolithic millimeter-wave integrated circuit (MMIC) power amplifiers (PAs) targeting the highest output power and the highest efficiency for class-A operation in W-band (75-110 GHz). W-band PAs are a major component of many frequency multiplied submillimeter-wave LO signal sources. For spectrometer arrays, substantial W-band power is required due to the passive lossy frequency multipliers.

  15. Cloning and Sequencing of a Full-Length cDNA Encoding the RuBPCase Small Subunit (RbcS)in Tea (Camellia sinensis)

    Institute of Scientific and Technical Information of China (English)

    YE Ai-hua; JIANG Chang-jun; ZHU Lin; YU Mei; WANG Zhao-xia; DENG Wei-wei; WEI Chao-lin

    2009-01-01

    This study was aimed to isolate ribulose-l,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) from tea plant [Camellia sinensis (L.) O. Kuntze]. In the study of transcriptional profiling of gene expression from tea flower bud development stage by cDNA-AFLP (cDNA amplified fragment length polymorphism), we have isolated some transcript-derived fragments (TDFs) occurring in both the young and mature flower bud. One of them showed a high degree of similarity to RbcS. Based on the fragment, the full length of RbcS with 769-bp (EF011075) cDNA was obtained via rapid amplification of cDNA ends (RACE). It contained an open reading frame of 176 amino acids consisting of a chloroplast transit peptide with 52 amino acids and a mature protein of 124 amino acids. The amino acids sequence presented a high identity to those of other plant RbcS genes. It also contains three conserved domains and a protein kinase C phosphorylation site, one tyrosine kinase phosphorylation site and two N-myristoylation sites. Analysis by RT-PCR showed that the expression of RbcS in tea from high to low was leaf, young stem, young flower bud and mature flower bud, respectively. The isolation of the tea Rubisco small subunit gene establishes a good foundation for further study on the photosynthesis of tea plant.

  16. Small and lightweight power amplifiers

    Science.gov (United States)

    Shams, Qamar A.; Barnes, Kevin N.; Fox, Robert L.; Moses, Robert W.; Bryant, Robert G.; Robinson, Paul C.; Shirvani, Mir

    2002-07-01

    The control of u wanted structural vibration is implicit in most of NASA's programs. Currently several approaches to control vibrations in large, lightweight, deployable structures and twin tail aircraft at high angles of attack are being evaluated. The Air Force has been examining a vertical tail buffet load alleviation system that can be integrated onboard an F/A-18 and flown. Previous wind tunnel and full-scale ground tests using distributed actuators have shown that the concept works; however, there is insufficient rom available onboard an F/A-18 to store current state-of- the-art system components such as amplifiers, DC-to-DC converter and a computer for performing vibration suppression. Sensor processing, power electronics, DC-to-DC converters, and control electronics that may be collocated with distributed actuators, are particularly desirable. Such electronic system would obviate the need for complex, centralized, control processing and power distribution components that will eliminate the weight associated with lengthy wiring and cabling networks. Several small and lightweight power amplifiers ranging from 300V pp to 650V pp have been designed using off the shelf components for different applications. In this paper, the design and testing of these amplifiers will be presented under various electrical loads.

  17. High power regenerative laser amplifier

    Science.gov (United States)

    Miller, J.L.; Hackel, L.A.; Dane, C.B.; Zapata, L.E.

    1994-02-08

    A regenerative amplifier design capable of operating at high energy per pulse, for instance, from 20-100 Joules, at moderate repetition rates, for instance from 5-20 Hertz is provided. The laser amplifier comprises a gain medium and source of pump energy coupled with the gain medium; a Pockels cell, which rotates an incident beam in response to application of a control signal; an optical relay system defining a first relay plane near the gain medium and a second relay plane near the rotator; and a plurality of reflectors configured to define an optical path through the gain medium, optical relay and Pockels cell, such that each transit of the optical path includes at least one pass through the gain medium and only one pass through the Pockels cell. An input coupler, and an output coupler are provided, implemented by a single polarizer. A control circuit coupled to the Pockels cell generates the control signal in timed relationship with the input pulse so that the input pulse is captured by the input coupler and proceeds through at least one transit of the optical path, and then the control signal is applied to cause rotation of the pulse to a polarization reflected by the polarizer, after which the captured pulse passes through the gain medium at least once more and is reflected out of the optical path by the polarizer before passing through the rotator again to provide an amplified pulse. 7 figures.

  18. Analog circuit design designing high performance amplifiers

    CERN Document Server

    Feucht, Dennis

    2010-01-01

    The third volume Designing High Performance Amplifiers applies the concepts from the first two volumes. It is an advanced treatment of amplifier design/analysis emphasizing both wideband and precision amplification.

  19. Higher order mode optical fiber Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Friis, Søren Michael Mørk; Usuga Castaneda, Mario A.;

    2016-01-01

    We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations.......We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations....

  20. Challenges in higher order mode Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Nielsen, Kristian; Friis, Søren Michael Mørk;

    2015-01-01

    A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed......A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed...

  1. Improved charge amplifier using hybrid hysteresis compensation

    Science.gov (United States)

    Amin-Shahidi, Darya; Trumper, David L.

    2013-08-01

    We present a novel charge amplifier, with a robust feedback circuit and a method for compensating piezoelectric actuator's hysteresis at low frequencies. The amplifier uses a modified feedback circuit which improves robustness to the addition of series load impedance such as in cabling. We also describe a hybrid hysteresis compensation method for enabling the charge amplifier to reduce hysteresis at low frequencies. Experimental results demonstrate the utility of the new amplifier design.

  2. European Research on THz Vacuum Amplifiers

    DEFF Research Database (Denmark)

    Brunetti, F.; Cojocarua, C.-S.; de Rossi, A.

    2010-01-01

    The OPTHER (OPtically Driven TeraHertz AmplifiERs) project represents a considerable advancement in the field of high frequency amplification. The design and realization of a THz amplifier within this project is a consolidation of efforts at the international level from the main players of the Eu...... of the European research, academy and industry in vacuum electronics. This paper describes the status of the project and progress towards the THz amplifier realization....

  3. Performance analysis of a concatenated erbium-doped fiber amplifier supporting four mode groups

    Science.gov (United States)

    Qin, Zujun; Fan, Di; Zhang, Wentao; Xiong, Xianming

    2016-05-01

    An erbium-doped fiber amplifier (EDFA) supporting four mode groups has been theoretically designed by concatenating two sections of erbium-doped fibers (EDFs). Each EDF has a simple erbium doping profile for the purpose of reducing its fabrication complexity. We propose a modified genetic algorithm (GA) to provide detailed investigations on the concatenated amplifier. Both the optimal fiber length and erbium doping radius in each EDF have been found to minimize the gain difference between signal modes. Results show that the parameters of the central-doped EDF have a greater impact on the amplifier performance compared to those of the annular-doped one. We then investigate the influence of the small deviations of the erbium fiber length, doping radius and doping concentration of each EDF from their optimal values upon the amplifier performance, and discuss their design tolerances in obtaining a desirable amplification characteristics.

  4. low pump power photonic crystal fibre amplifiers

    DEFF Research Database (Denmark)

    Hougaard, Kristian G.; Broeng, Jes; Bjarklev, Anders Overgaard

    2003-01-01

    Designs of low pump power optical amplifiers, based on photonic crystal fibres are presented. The potential of these fibre amplifiers is investigated, and it is demonstrated that such amplifiers may deliver gains of more than 15 dB at 1550 nm with less than 1 mW of optical pump power....

  5. A High-performance Small Signal Amplifier

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    According to questions in the design of high quality small signal amplifier, this paper gave a new-type high performance small signal amplifier. The paper selected the operational amplifier of ICL Company and designed a new-type circuit with simple, low cost and excellent performance.

  6. Influences of finite gain bandwidth on pulse propagation in parabolic fiber amplifiers with distributed gain profiles

    Institute of Scientific and Technical Information of China (English)

    Zhao Jia-Sheng; Li Pan; Chen Xiao-Dong; Feng Su-Juan; Mao Qing-He

    2012-01-01

    The evolutions of the pulses propagating in decreasing and increasing gain distributed fiber amplifiers with finite gain bandwidths are investigated by simulations with the nonlinear Schrodinger equation.The results show that the parabolic pulse propagations in both the decreasing and the increasing gain amplifiers are restricted by the finite gain bandwidth.For a given input pulse,by choosing a small initial gain coefficient and gain variation rate,the whole gain for the pulse amplification limited by the gain bandwidth may be higher,which is helpful for the enhancement of the output linearly chirped pulse energy.Compared to the decreasing gain distributed fiber amplifier,the increasing gain distributed amplifier may be more conducive to suppress the pulse spectral broadening and increase the critical amplifier length for achieving a larger output linearly chirped pulse energy.

  7. Bandwidth enhancement for parametric amplifiers operated in chirped multi-beam mode

    CERN Document Server

    Terranova, F; Pegoraro, F

    2008-01-01

    In this paper we discuss the bandwidth enhancement that can be achieved in multi-Joule OPCPA systems exploiting the tunability of parametric amplification. In particular, we consider a pair of single pass amplifiers based on DKDP, pumped by the second harmonic of Nd:glass and tuned to amplify adjacent regions of the signal spectrum. We demonstrate that a bandwidth enhancement up to 50% is possible in two configurations; in the first case, one of the two amplifiers is operated near its non-collinear broadband limit; to allow for effective recombination and recompression of the outgoing signals this configuration requires filtering and phase manipulation of the spectral tail of the amplified pulses. In the second case, effective recombination can be achieved simply by spectral filtering: in this configuration, the optimization of the parameters of the amplifiers (pulse, crystal orientation and crystal length) does not follow the recipes of non-collinear OPCPA.

  8. Wavelength-Dependent Transient Characteristics Caused by Gain Saturation in Highly Nonlinear Fiber-Based Raman Amplifiers

    Institute of Scientific and Technical Information of China (English)

    Shinobu; Tamaoki; Tetsufumi; Tsuzaki; Motoki; Kakui; Masayuki; Shigematsu

    2003-01-01

    We have investigated the transient characteristics of discrete Raman Amplifiers and found that the response time caused by gain saturation is dependent upon the wavelength, which corresponds to the effective length of the pump light.

  9. Amplify Errors to Minimize Them

    Science.gov (United States)

    Stewart, Maria Shine

    2009-01-01

    In this article, the author offers her experience of modeling mistakes and writing spontaneously in the computer classroom to get students' attention and elicit their editorial response. She describes how she taught her class about major sentence errors--comma splices, run-ons, and fragments--through her Sentence Meditation exercise, a rendition…

  10. Fluctuations of fragment observables

    CERN Document Server

    Gulminelli, F

    2006-01-01

    This contribution presents a review of our present theoretical as well as experimental knowledge of different fluctuation observables relevant to nuclear multifragmentation. The possible connection between the presence of a fluctuation peak and the occurrence of a phase transition or a critical phenomenon is critically analyzed. Many different phenomena can lead both to the creation and to the suppression of a fluctuation peak. In particular, the role of constraints due to conservation laws and to data sorting is shown to be essential. From the experimental point of view, a comparison of the available fragmentation data reveals that there is a good agreement between different data sets of basic fluctuation observables, if the fragmenting source is of comparable size. This compatibility suggests that the fragmentation process is largely independent of the reaction mechanism (central versus peripheral collisions, symmetric versus asymmetric systems, light ions versus heavy ion induced reactions). Configurationa...

  11. Measuring Thermodynamic Length

    Energy Technology Data Exchange (ETDEWEB)

    Crooks, Gavin E

    2007-09-07

    Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interestin understanding matter out of equilibrium. In this Letter, we will consider how to denethermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.

  12. Fragments of Time

    DEFF Research Database (Denmark)

    Christiansen, Steen Ledet

    Time travel films necessarily fragment linear narratives, as scenes are revisited with differences from the first time we saw it. Popular films such as Back to the Future mine comedy from these visitations, but there are many different approaches. One extreme is Chris Marker's La Jetée - a film...... made almost completely of still images, recounting the end of the world. These stills can be viewed as fragments that have survived the end of the world and now provide the only access to the events that occured. Shane Carruth's Primer has a different approach to time travel, the narrative diegesis...

  13. IMPACT fragmentation model developments

    Science.gov (United States)

    Sorge, Marlon E.; Mains, Deanna L.

    2016-09-01

    The IMPACT fragmentation model has been used by The Aerospace Corporation for more than 25 years to analyze orbital altitude explosions and hypervelocity collisions. The model is semi-empirical, combining mass, energy and momentum conservation laws with empirically derived relationships for fragment characteristics such as number, mass, area-to-mass ratio, and spreading velocity as well as event energy distribution. Model results are used for several types of analysis including assessment of short-term risks to satellites from orbital altitude fragmentations, prediction of the long-term evolution of the orbital debris environment and forensic assessments of breakup events. A new version of IMPACT, version 6, has been completed and incorporates a number of advancements enabled by a multi-year long effort to characterize more than 11,000 debris fragments from more than three dozen historical on-orbit breakup events. These events involved a wide range of causes, energies, and fragmenting objects. Special focus was placed on the explosion model, as the majority of events examined were explosions. Revisions were made to the mass distribution used for explosion events, increasing the number of smaller fragments generated. The algorithm for modeling upper stage large fragment generation was updated. A momentum conserving asymmetric spreading velocity distribution algorithm was implemented to better represent sub-catastrophic events. An approach was developed for modeling sub-catastrophic explosions, those where the majority of the parent object remains intact, based on estimated event energy. Finally, significant modifications were made to the area-to-mass ratio distribution to incorporate the tendencies of different materials to fragment into different shapes. This ability enabled better matches between the observed area-to-mass ratios and those generated by the model. It also opened up additional possibilities for post-event analysis of breakups. The paper will discuss

  14. A Novel Method for High Efficiency Amplification of Short DNA Fragments%一种高效扩增小片段DNA方法的建立

    Institute of Scientific and Technical Information of China (English)

    李岩; 李珊珊; 张玉祥

    2011-01-01

    目的 建立一种高效扩增小片段DNA的方法.方法 本方法利用单链DNA连接酶(single strand DNA ligase,ssDNA ligase)可以连接单链DNA的性质将小片段DNA自连成环,随后利用phi29 DNA聚合酶进行恒温的滚环复制,将扩增产物进行酶切,得到了扩增后的小片段DNA.结果 单链DNA连接酶可以有效的将30 bp的小片段DNA自连成环,phi29 DNA聚合酶可以扩增出大于10 kb的DNA片段,扩增产物经酶切后又可进行第二轮扩增,并且证明了其成环方式为自成环.结论 通过单链成环后滚环复制的这种方法可以有效的将小片段 DNA进行扩增,解决了PCR无法扩增小片段DNA的问题,并有着广阔的应用前景.%Objective To establish a method for highly efficient amplification of small fragment DNA. Methods Single-strand DNA intramolecular ligation was made by using single-stranded DNA ligase( ssDNA ligase), which can link small DNA fragments into a ring, and then isothermal rolling circle replication was carried out by using phi29 DNA polymerase. The amplified products were cut by incision enzyme. In this way, the small fragment DNA can be amplified at high efficiency. Results SsDNA ligase can make 30 bp oligonucleotide DNA cyclization, and phi29 DNA polymerase can make amplification products more than 10 kb in length. Amplification products can be amplified second times after being cut by incision enzyme. It was also proved that the way of single strand DNA cyclization was intramolecular. Conclusion This method can effectively amplify the small DNA fragments, and has broad prospects of application.

  15. Design of Raman-parametric fiber amplifier for wavelength division multiplex transmission system

    Institute of Scientific and Technical Information of China (English)

    Xiaohong Jiang; Chun Jiang; Xiaoming Zhang

    2008-01-01

    We optimize the novel configuration of a hybrid fiber amplifier-Raman assisted-fiber-based optical parametric amplifier (R-FOPA), in which the parametric gain and Raman gain profiles are combined to achieve a flat composite gain profile.The pump powers and the fiber length in the hybrid amplifier are effectively optimized by genetic algorithm (GA) scheme.The optimization results indicate that the R-FOPA can achieve a 200-nm flat bandwidth spectrum with the gain of 20 dB and ripple of less than 4 dB.

  16. Experimental design studies and flow visualization of proportional laminar-flow fluidic amplifiers

    Science.gov (United States)

    Hellbaum, R. F.; Mcdermon, J. N.

    1977-01-01

    The effects of certain parameter variations on the performance characteristics of laminar, proportional, jet-deflection fluidic amplifiers were studied. The matching and staging of amplifiers to obtain high pressure gain was included, but dynamic effects were not. The parameter variations considered were aspect ratio, setback, control length, splitter distance, receiver-duct width, width of center-vent duct, and bias pressure. Usable pressure gains of 19 per stage were achieved, and 5 amplifier stages were integrated to yield an overall pressure gain of 2,000,000.

  17. Computer Aided Design and Analysis of a 2-4 GHz Broadband Balanced Microstrip Amplifier

    OpenAIRE

    S. H. Ibrahim

    2012-01-01

    In this paper, a computer-aided design and analysis of a 2-4 GHz broadband balanced microstrip amplifier using a full computer simulation program developed by the author and others is presented. A short and efficient CAD procedure for broadband amplifier design is introduced. The first step is to design an initial narrow-band high gain microstrip amplifier at 3-GHz central frequency. The second step is to optimize the initial lengths and widths of the input and output microstrip-matching circ...

  18. Single Strand Conformation Polymorphism analysis of PCR-amplified rDNA to differentiate medically important Aspergillus Species

    Directory of Open Access Journals (Sweden)

    K Diba

    2008-09-01

    Full Text Available "nBackground: Aspergillus species are associated with allergic bronchopulmonary disease, mycotic keratitis, otomycosis, na­sal sinusitis and invasive infection. In this study, we developed a PCR-Single Strand Confomational Polymorphism method to identify the most common Aspergillus species and we showed some advantages of this method comparing a PCR-Restric­tion Fragment Length Polymorphism with our designed restriction enzyme. "nMethods: We selected ITS2, as a short fragment within the rDNA region (length size: 330 bp to be amplified as small size PCR product. We mixed 5 ml of the PCR product with an equal volume of loading buffer and followed by incubation for 5 min at 95º C and quenching in an ice bath. The mixture was applied to a 6%-12% Gradient Poly acryl amide gel to run in a verti­cal electrophoresis, then gel was stained with ethidium bromide and silver nitrate which followed by an ethidium bro­mide staining. "nResults: Our results of restriction digestion showed a fine identification of 7 tested Aspergillus species dur­ing 5-6 hours af­ter an overnight mycelial growth. As our results some of tested Aspergillus species: A. nidulans, A. fisheri, A. quad­ricincta, (A. fumigatus and A. niger as a group and (A. flavus, A. tereus and A. ochraceus as another group, can be dis­criminated. More­over SSCP analysis enabled us to identify above Aspergillus species within 8-12 h after an over night growth without us­ing an expensive restriction enzyme."nConclusion: It is concluded that Single Strand Conformational Polymorphism is a simple and rapid method for identifica­tion of some medically important Aspergillus.

  19. Performance study of macro-bending EDFA/Raman hybrid optical fiber amplifiers

    Science.gov (United States)

    Mahran, O.

    2015-10-01

    In this paper, we present an analytical study of a (macro-bending EDFA)/Raman hybrid optical amplifier. The bending radius is 4 mm with EDFA length 10 m with forward pump power in the range (100-500 mW) and Raman amplifier length (12-55 km) with backward pump power variations (80-200 mW) is considered in our model. Due to bending loss in EDFA, the gain of hybrid amplifier is increased to ~7 dB more than the normal EDFA/Raman hybrid amplifier and the noise figure is decreased by ~2 dB rather than without macro-bending EDFA/Raman hybrid amplifier. The signal to noise ratio (OSNR) calculations shows a better performance of macro-bending EDFA/Raman hybrid amplifier than without macro-bending one. A flat gain is obtained in the signal wavelength region (1560-1600 nm), which is the L-band. The calculated results for macro-bending case are compared with experimental results of normal case by Lee et al., in the L-band showing an increase in the gain, reduction in the noise figure and more gain flatness at the input signal -20 dBm for macro-bending EDFA/Raman hybrid amplifier.

  20. Log amplifier with pole-zero compensation

    Science.gov (United States)

    Brookshier, William

    1987-01-01

    A logarithmic amplifier circuit provides pole-zero compensation for improved stability and response time over 6-8 decades of input signal frequency. The amplifier circuit includes a first operational amplifier with a first feedback loop which includes a second, inverting operational amplifier in a second feedback loop. The compensated output signal is provided by the second operational amplifier with the log elements, i.e., resistors, and the compensating capacitors in each of the feedback loops having equal values so that each break point or pole is offset by a compensating break point or zero.

  1. Semiconductor quantum-dot lasers and amplifiers

    DEFF Research Database (Denmark)

    Hvam, Jørn Märcher; Borri, Paola; Ledentsov, N. N.

    2002-01-01

    -power surface emitting VCSELs. We investigated the ultrafast dynamics of quantum-dot semiconductor optical amplifiers. The dephasing time at room temperature of the ground-state transition in semiconductor quantum dots is around 250 fs in an unbiased amplifier, decreasing to below 50 fs when the amplifier...... is biased to positive net gain. We have further measured gain recovery times in quantum dot amplifiers that are significantly lower than in bulk and quantum-well semiconductor optical amplifiers. This is promising for future demonstration of quantum dot devices with high modulation bandwidth...

  2. An Implantable CMOS Amplifier for Nerve Signals

    DEFF Research Database (Denmark)

    Nielsen, Jannik Hammel; Lehmann, Torsten

    2003-01-01

    In this paper, a low noise high gain CMOS amplifier for minute nerve signals is presented. The amplifier is constructed in a fully differential topology to maximize noise rejection. By using a mixture of weak- and strong inversion transistors, optimal noise suppression in the amplifier is achieved....... A continuous-time current-steering offset-compensation technique is utilized in order to minimize the noise contribution and to minimize dynamic impact on the amplifier input nodes. The method for signal recovery from noisy nerve signals is presented. A prototype amplifier is realized in a standard digital 0...

  3. High temperature charge amplifier for geothermal applications

    Science.gov (United States)

    Lindblom, Scott C.; Maldonado, Frank J.; Henfling, Joseph A.

    2015-12-08

    An amplifier circuit in a multi-chip module includes a charge to voltage converter circuit, a voltage amplifier a low pass filter and a voltage to current converter. The charge to voltage converter receives a signal representing an electrical charge and generates a voltage signal proportional to the input signal. The voltage amplifier receives the voltage signal from the charge to voltage converter, then amplifies the voltage signal by the gain factor to output an amplified voltage signal. The lowpass filter passes low frequency components of the amplified voltage signal and attenuates frequency components greater than a cutoff frequency. The voltage to current converter receives the output signal of the lowpass filter and converts the output signal to a current output signal; wherein an amplifier circuit output is selectable between the output signal of the lowpass filter and the current output signal.

  4. Audio power amplifier design handbook

    CERN Document Server

    Self, Douglas

    2013-01-01

    This book is essential for audio power amplifier designers and engineers for one simple reason...it enables you as a professional to develop reliable, high-performance circuits. The Author Douglas Self covers the major issues of distortion and linearity, power supplies, overload, DC-protection and reactive loading. He also tackles unusual forms of compensation and distortion produced by capacitors and fuses. This completely updated fifth edition includes four NEW chapters including one on The XD Principle, invented by the author, and used by Cambridge Audio. Cro

  5. Picking Up (On) Fragments

    NARCIS (Netherlands)

    Ellis, Phil

    2015-01-01

    abstractThis article discusses the implications for archival and media archaeological research and reenactment artwork relating to a recent arts practice project: reenacttv: 30 lines / 60 seconds. It proposes that archival material is unstable but has traces and fragments that are full of creative p

  6. Fragments of the Past

    Directory of Open Access Journals (Sweden)

    Peter Szende

    2016-10-01

    Full Text Available With travel being made more accessible throughout the decades, the hospitality industry constantly evolved their practices as society and technology progressed. Hotels looked for news ways up service their customers, which led to the invention of the Servidor in 1918. Once revolutionary innovations have gone extinct, merely becoming fragments of the past.

  7. A Partial Double-Pass S-Band Erbium-Doped Fibre Amplifier

    Institute of Scientific and Technical Information of China (English)

    Sulaiman Wadi Harun; Nor Kamilah Saat; Harith Ahmad

    2005-01-01

    @@ An efficient and low noise short wavelength band erbium-doped fibre amplifier (S-band EDFA) is proposed and demonstrated using double-pass configuration. This amplifier provides a gain of 1500 nm signal as high as 26.9 dB,which is 9.6 dB higher than the two-stage single-pass amplifier. The corresponding noise figure obtained is 7.5 dB,which is of the same level as in the single-pass amplifier and more than 2dB lower than the previously reported double-pass amplifier [IEICE Electron. Express 2 (2005) 182]. The gain enhancement is due to the double pass-propagation of the test signal in the second stage, which increases the effective erbium-doped fibre (EDF)length. The low noise is attributed to the optical circulator between EDFs, which prevents the backward amplified spontaneous emission from propagating into the input part of the amplifier. The proposed amplifier is expected to play an important role in the development of a practical S-band EDFA.

  8. Atomic Dipole Traps with Amplified Spontaneous Emission: A Proposal

    CERN Document Server

    Clément, Jean-François; Garreau, Jean Claude; Szriftgiser, Pascal

    2010-01-01

    We propose what we believe to be a novel type of optical source for ultra-cold atomic Far Off-Resonance optical-dipole Traps (FORTs). The source is based on an Erbium Amplified Spontaneous Emission (ASE) source that seeds a high power Erbium Doped Fiber Amplifier (EDFA). The main interest of this source is its very low coherence length, thus allowing an incoherent superposition of several trapping beams without any optical interference. The behavior of the superimposed beams is then a scalar sum greatly simplifying complex configurations. As an illustration, we report an estimation of the intensity noise of this source and an estimation of the atomic excess heating rate for an evaporative cooling experiment application. They are both found to be suitable for cold atoms experiments.

  9. High power RF solid state power amplifier system

    Science.gov (United States)

    Sims, III, William Herbert (Inventor); Chavers, Donald Gregory (Inventor); Richeson, James J. (Inventor)

    2011-01-01

    A high power, high frequency, solid state power amplifier system includes a plurality of input multiple port splitters for receiving a high-frequency input and for dividing the input into a plurality of outputs and a plurality of solid state amplifier units. Each amplifier unit includes a plurality of amplifiers, and each amplifier is individually connected to one of the outputs of multiport splitters and produces a corresponding amplified output. A plurality of multiport combiners combine the amplified outputs of the amplifiers of each of the amplifier units to a combined output. Automatic level control protection circuitry protects the amplifiers and maintains a substantial constant amplifier power output.

  10. Fragment mass analyzer project

    Energy Technology Data Exchange (ETDEWEB)

    Davids, C.N.; Back, B.B.; Blumenthal, D.J. [and others

    1995-08-01

    The FMA is now in routine operation, with about half the ATLAS experiments using the instrument. The beam time is split equally between target and focal-plane experiments. New spectroscopy-grade electronics for the FMA implantation system were acquired. This consists of 96 charge-sensitive preamps, 192 Gaussian shaping amplifier/discriminators, 96 channels of high-resolution ADCs, and 96 channels of medium resolution ADCs. This system is currently undergoing commissioning tests, and will be used in future proton radioactivity experiments.

  11. Quantum Noise in Amplifiers and Hawking/Dumb-Hole Radiation as Amplifier Noise

    CERN Document Server

    Unruh, W G

    2011-01-01

    The quantum noise in a linear amplifier is shown to be thermal noise. The theory of linear amplifiers is applied first to the simplest, single or double oscillator model of an amplifier, and then to linear model of an amplifier with continuous fields and input and outputs. Finally it is shown that the thermal noise emitted by black holes first demonstrated by Hawking, and of dumb holes (sonic and other analogs to black holes), arises from the same analysis as for linear amplifiers. The amplifier noise of black holes acting as amplifiers on the quantum fields living in the spacetime surrounding the black hole is the radiation discovered by Hawking. For any amplifier, that quantum noise is completely characterized by the attributes of the system regarded as a classical amplifier, and arises out of those classical amplification factors and the commutation relations of quantum mechanics.

  12. YANG-MILLS FIELD AMPLIFIER

    Directory of Open Access Journals (Sweden)

    Trunev A. P.

    2015-09-01

    Full Text Available The article presents a project of the Yang-Mills amplifier. Amplifier model is a multilayer spherical shell with increasing density towards the center. In the center of the amplifier is the core of high-density material. It is shown that in such a system, the amplitude of the Yang-Mills waves rises from the periphery to the center of several orders of magnitude. The role of the Yang-Mills field in the processes occurring in the nuclei of galaxies, stars and planets is discussed. The data modeling to strengthen the Yang-Mills field in the bowels of the planet, with an atomic explosion, and in some special devices such as the voltaic pile. To describe the mechanism of amplification chromodynamics field used as accurate results in Yang-Mills theory and numerical models developed based on an average and the exact equations as well. Among the exact solutions of the special role played by the centralsymmetric metric describing the contribution of the Yang-Mills field in the speed of recession of galaxies. Among the approximate numerical models can be noted the eight-scalar model we have developed for the simulation of non-linear color oscillations and chaos in the Yang-Mills theory. Earlier models were investigated spatio-temporal oscillations of the YangMills theory in the case of three and eight colors. The results of numerical simulation show that the nonlinear interaction does not lead to a spatial mixing of colors as it might be in the case of turbulent diffusion. Depending on the system parameters there is a suppression of the amplitude of the oscillations the first three by five colors or vice versa. The kinetic energy fluctuations or shared equally between the color components, or dominated by the kinetic energy of repressed groups of colors. In the present study, we found that amplification chromodynamic field leads to a sharp increase in the amplitude of the suppressed color, which can lead to an increase in entropy, excitation of nuclear

  13. Application of Reverse Transcription-Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Method to Identify H1 Genotype of Measles Virus Infection and Measles Vaccine Related Cases%应用限制性片段长度多态性分析方法鉴别H1基因型麻疹野病毒感染病例和麻疹疫苗相关病例

    Institute of Scientific and Technical Information of China (English)

    李立群; 余文; 赵智娴; 丁峥嵘

    2012-01-01

    Objective Application the method to rapid identify the wild measles strain and China measles vaccine strain in Yunnan province. Method To apply method of reverse transcription-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) and sequence analysis method to detect 8 strains of measles virus. Results The RT-PCR-RFLP method for H1 genotype was used for identifying 8 strains of measles virus, the 5 specimens of wild-type, measles viruses RT-PCR products were cut into 2 fragments, 408 bp and 159 bp, the results showed that 5 specimens of wild-type measles viruses were caused by H1 genotype. The RT-PCR-RFLP method for China vaccine strain identification was used for identifying 3 specimen of measles. 1 specimen RT-PCR products were cut into 2 fragments, 287 bp and 151 bp, which showed that this case was caused by China vaccine strain. 2 specimens of measles were non-H1 wild-type measles viruses. Conclusion The RT-PCR-RFLP method can be used to identify H1 genotype of measles virus and measles vaccine strain. The results are same as the method of nucleoprotein gene sequencing.%目的 在云南省应用H1基因型麻疹野病毒鉴定方法,鉴别H1基因型麻疹野病毒感染病例,应用中国麻疹疫苗株病毒鉴定方法,鉴别接种麻疹疫苗后出现的麻疹样病例是否为麻疹疫苗相关病例.方法 采用逆转录-聚合酶链反应-限制性片段长度多态性分析(Reverse Transcription-Polymerase Chain Reaction-Restriction Fragment Length Polymorphism,RT-PCR-RFLP)方法、序列分析方法鉴别8株麻疹病毒.结果 应用H1基因型麻疹野病毒RT-PCR-RFLP方法对8份标本进行鉴定,其中5份标本RT-PCR产物经 Sal I酶切后,被切成两个片段,分别为408个碱基对(base pair,bp)和159bp,显示5个病例是由H1基因型麻疹野病毒引起的.应用中国麻疹疫苗株病毒RT-PCR-RFLP方法对3份标本进行鉴定,其中1份标本RT-PCR产物经Af1Ⅱ酶切,被切成两个片段,分别为287

  14. Effect of Er+3 Concentration on the Small Signal Gain Coefficient and the Gain in the Erbium Doped Fiber Amplifier

    Directory of Open Access Journals (Sweden)

    O. Mahran

    2014-04-01

    Full Text Available The small signal gain coefficient and the gain of Erbium-Doped Fiber Amplifier (EDFA in the wavelength range (1400-1700 nm for different erbium concentrations and different amplifier lengths are calculated and studied. A core graded-index and erbium-doped concentration, are optimized for an EDFA in simplified two-level model. There is evidence to show that, the gain increases with the erbium concentration and the amplifier length. Where the relation between the gain and the amplifier length at different wavelengths is linear with the maximum gain at &lambda = 1530 nm. Also the temperature dependence of the small signal gain coefficient and the gain at the peak wavelength of EDFA was studied which shows, slightly increase in the values of both with temperature. The value of the signal wavelength was chosen in the gain window of EDFA at 1530 nm.

  15. Locoregional MYCN-amplified neuroblastoma.

    Science.gov (United States)

    Morales La Madrid, Andres; Volchenboum, Samuel; Gastier-Foster, Julie M; Pyatt, Robert; Liu, Don; Pytel, Peter; Lavarino, Cinzia; Rodriguez, Eva; Cohn, Susan L

    2012-10-01

    MYCN-amplification is strongly associated with other high-risk prognostic factors and poor outcome in neuroblastoma. Infrequently, amplification of MYCN has been identified in localized tumors with favorable biologic features. Outcome for these children is difficult to predict and optimal treatment strategies remain unclear. We report a 5-month-old who presented with an MYCN-amplified INSS stage 3, pelvic neuroblastoma. The tumor had favorable histology, hyperdiploidy, and lacked 1p36 and 11q23 aberrations. Although the patient met the criteria for high-risk neuroblastoma, because of the discordant prognostic markers we elected to treat her according to an intermediate-risk protocol. She remains event-free more than 18 months.

  16. Transverse pumped laser amplifier architecture

    Science.gov (United States)

    Bayramian, Andrew James; Manes, Kenneth; Deri, Robert; Erlandson, Al; Caird, John; Spaeth, Mary

    2013-07-09

    An optical gain architecture includes a pump source and a pump aperture. The architecture also includes a gain region including a gain element operable to amplify light at a laser wavelength. The gain region is characterized by a first side intersecting an optical path, a second side opposing the first side, a third side adjacent the first and second sides, and a fourth side opposing the third side. The architecture further includes a dichroic section disposed between the pump aperture and the first side of the gain region. The dichroic section is characterized by low reflectance at a pump wavelength and high reflectance at the laser wavelength. The architecture additionally includes a first cladding section proximate to the third side of the gain region and a second cladding section proximate to the fourth side of the gain region.

  17. Reflection amplifiers in self-regulated learning

    NARCIS (Netherlands)

    Verpoorten, Dominique

    2012-01-01

    Verpoorten, D. (2012). Reflection amplifiers in self-regulated learning. Doctoral thesis. November, 9, 2012, Heerlen, The Netherlands: Open Universiteit (CELSTEC). Datawyse / Universitaire Pers Maastricht.

  18. Enhanced Gain in Photonic Crystal Amplifiers

    DEFF Research Database (Denmark)

    Ek, Sara; Semenova, Elizaveta; Hansen, Per Lunnemann;

    2012-01-01

    study of a 1 QW photonic crystal amplifier. Net gain is achieved which enables laser oscillation in photonic crystal micro cavities. The ability to freely tailor the dispersion in a semiconductor optical amplifier makes it possible to raise the optical gain considerably over a certain bandwidth......We experimentally demonstrate enhanced gain in the slow-light regime of quantum well photonic crystal amplifiers. A strong gain enhancement is observed with the increase of the group refractive index, due to light slow-down. The slow light enhancement is shown in a amplified spontaneous emission...

  19. Design of an 1800nm Raman amplifier

    DEFF Research Database (Denmark)

    Svane, Ask Sebastian; Rottwitt, Karsten

    2013-01-01

    We present the experimental results for a Raman amplifier that operates at 1810 nm and is pumped by a Raman fiber laser at 1680 nm. Both the pump laser and the Raman amplifier is polarization maintaining. A challenge when scaling Raman amplifiers to longer wavelengths is the increase...... performance of the amplifier is also investigated for both configurations. Our results show an on/off gain exceeding 20 dB at 1810 nm for which the obtained effective noise figure is below 3 dB....

  20. Dynamics of Soliton Cascades in Fiber Amplifiers

    CERN Document Server

    Arteaga-Sierra, F R; Agrawal, Govind P

    2016-01-01

    We study numerically the formation of cascading solitons when femtosecond optical pulses are launched into a fiber amplifier with less energy than required to form a soliton of equal duration. As the pulse is amplified, cascaded fundamental solitons are created at different distances, without soliton fission, as each fundamental soliton moves outside the gain bandwidth through the Raman-induced spectral shifts. As a result, each input pulse creates multiple, temporally separated, ultrashort pulses of different wavelengths at the amplifier output. The number of pulses depends not only on the total gain of the amplifier but also on the width of input pulses.

  1. Critical Features of Fragment Libraries for Protein Structure Prediction.

    Science.gov (United States)

    Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

  2. Critical Features of Fragment Libraries for Protein Structure Prediction

    Science.gov (United States)

    dos Santos, Karina Baptista

    2017-01-01

    The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

  3. Minimum Length - Maximum Velocity

    CERN Document Server

    Panes, Boris

    2011-01-01

    We study a framework where the hypothesis of a minimum length in space-time is complemented with the notion of reference frame invariance. It turns out natural to interpret the action of the obtained reference frame transformations in the context of doubly special relativity. As a consequence of this formalism we find interesting connections between the minimum length properties and the modified velocity-energy relation for ultra-relativistic particles. For example we can predict the ratio between the minimum lengths in space and time using the results from OPERA about superluminal neutrinos.

  4. Heavy meson fragmentation at LHC

    Directory of Open Access Journals (Sweden)

    M. A. Gomshi Nobary

    2003-06-01

    Full Text Available   Large Hadron Collider (LHC at CERN will provide excellent opportunity to study the production and decay of heavy mesons and baryons with high statistics. We aim at the heavy mesons in this work and calculate their fragmentation functions consistent with this machine and present their total fragmentation probabilities and average fragmentation parameters.

  5. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

  6. Telomere length and depression

    DEFF Research Database (Denmark)

    Wium-Andersen, Marie Kim; Ørsted, David Dynnes; Rode, Line

    2016-01-01

    BACKGROUND: Depression has been cross-sectionally associated with short telomeres as a measure of biological age. However, the direction and nature of the association is currently unclear. AIMS: We examined whether short telomere length is associated with depression cross-sectionally as well...... as prospectively and genetically. METHOD: Telomere length and three polymorphisms, TERT, TERC and OBFC1, were measured in 67 306 individuals aged 20-100 years from the Danish general population and associated with register-based attendance at hospital for depression and purchase of antidepressant medication....... RESULTS: Attendance at hospital for depression was associated with short telomere length cross-sectionally, but not prospectively. Further, purchase of antidepressant medication was not associated with short telomere length cross-sectionally or prospectively. Mean follow-up was 7.6 years (range 0...

  7. Myofilament length dependent activation

    Energy Technology Data Exchange (ETDEWEB)

    de Tombe, Pieter P.; Mateja, Ryan D.; Tachampa, Kittipong; Mou, Younss Ait; Farman, Gerrie P.; Irving, Thomas C. (IIT); (Loyola)

    2010-05-25

    The Frank-Starling law of the heart describes the interrelationship between end-diastolic volume and cardiac ejection volume, a regulatory system that operates on a beat-to-beat basis. The main cellular mechanism that underlies this phenomenon is an increase in the responsiveness of cardiac myofilaments to activating Ca{sup 2+} ions at a longer sarcomere length, commonly referred to as myofilament length-dependent activation. This review focuses on what molecular mechanisms may underlie myofilament length dependency. Specifically, the roles of inter-filament spacing, thick and thin filament based regulation, as well as sarcomeric regulatory proteins are discussed. Although the 'Frank-Starling law of the heart' constitutes a fundamental cardiac property that has been appreciated for well over a century, it is still not known in muscle how the contractile apparatus transduces the information concerning sarcomere length to modulate ventricular pressure development.

  8. Genetic differentiation of Liparus glabrirostris (Curculionidae: Molytinae) populations from the fragmented habitats of the Alps and Carpathian Mountains.

    Science.gov (United States)

    Mitrović, M; Tomanović, Ž; Jakovljević, M; Radović, D; Havelka, J; Stary, P

    2016-10-01

    Populations of Liparus glabrirostris (Curculionidae: Molytinae), a weevil inhabiting higher altitudes of Central Europe, were sampled from 24 localities in the Alps and Carpathian Mountains, and the geographical structuring of genetic variation was analyzed. Comparison of the concatenated mitochondrial cytochrome oxidase subunit I and subunit II sequences revealed consistent genetic divergence between the populations of L. glabrirostris from different mountain ranges. In phylogenetic analysis using maximum parsimony and median-joining networks, concatenated mitochondrial haplotypes from the Alps and Carpathians clustered as separate lineages, with high bootstrap support. Substantial genetic distances determined between the separated groups ranged from 2.6 to 3.0%, with divergence estimated to have initiated approximately 0.85-0.98 million years ago. The nuclear elongation factor 1α gene was additionally amplified and haplotype analysis showed very low evolutionary divergence (0.2%), with separate clustering as well. The observed divergence suggests that the populations have been isolated for a long time, as a consequence of environmental changes resulting in varying fragmentation of habitats in the Alps and Carpathians, interrupting genetic exchange events and altering the genetic structure of L. glabrirostris populations. On the other hand, comparison of morphological characteristics showed no differences to confirm genetically well differentiated groups of populations. A polymerase chain reaction and restriction fragment length polymorphism-based method was therefore developed to discriminate between the Alpine and Carpathian lineages.

  9. Construction of a human recombinant polyclonal Fab fragment antibody library using peripheral blood lymphocytes of snake bitten victims

    Directory of Open Access Journals (Sweden)

    Motedayen, M.H.

    2015-12-01

    Full Text Available Human snake bitten poisoning is a serious threat in many tropical and subtropical countries such as Iran. The best acceptable treatment of envenomated humans is antivenoms; however they have a series of economic and medical problems and need more improvements. In this study a combinatorial human immunoglobulin gene library against some of Iranian snakes venoms was constructed. Total RNA prepared from peripheral blood lymphocytes of two recovered snake victims. RT-PCR was used for cDNA synthesis and amplification of the heavy (Fd segment and kappa light chains of IgG antibody. After digestion of the heavy chain with SpeI and XhoI and light chain with XbaI and SacI enzymes, inserted successively into the cloning vector pComb3x, and then recombinant vector transformed to TG1 bacteria to construct the Fab library. For determination insertion rate of Fab segment into cloning vector, plasmids of 12 clones of library were extracted and digested with SfiI. Length of amplified Fd and κ chains, were 650 - 750 bp. Primary library size was determined to contain 4.9×105 members out of which half of them contained the same size of Fab fragment. This result is comparable to some researchers and shows that this method could be appropriate tool for the production of human polyclonal Fab fragment antibodies for management of poisonous snake bitted victims.

  10. Picking Up (On Fragments

    Directory of Open Access Journals (Sweden)

    Phil Ellis

    2015-09-01

    Full Text Available This article discusses the implications for archival and media archaeological research and reenactment artwork relating to a recent arts practice project: reenacttv: 30 lines / 60 seconds. It proposes that archival material is unstable but has traces and fragments that are full of creative potential to re-think and re-examine past media historical events through a media archaeological approach to reenactment. The article contains images and links to videos from the final reenactment artworks as well as from rehearsals in Vienna and Bradford.

  11. An Archeology of Fragments

    Directory of Open Access Journals (Sweden)

    Gerald L. Bruns

    2014-10-01

    Full Text Available This is a short (fragmentary history of fragmentary writing from the German Romantics (F. W. Schlegel, Friedrich Hölderlin to modern and contemporary concrete or visual poetry. Such writing is (often deliberately a critique of the logic of subsumption that tries to assimilate whatever is singular and irreducible into totalities of various categorical or systematic sorts. Arguably, the fragment (parataxis is the distinctive feature of literary Modernism, which is a rejection, not of what precedes it, but of what Max Weber called “the rationalization of the world” (or Modernity whose aim is to keep everything, including all that is written, under surveillance and control.

  12. A Characteristic Particle Length

    CERN Document Server

    Roberts, Mark D

    2015-01-01

    It is argued that there are characteristic intervals associated with any particle that can be derived without reference to the speed of light $c$. Such intervals are inferred from zeros of wavefunctions which are solutions to the Schr\\"odinger equation. The characteristic length is $\\ell=\\beta^2\\hbar^2/(8Gm^3)$, where $\\beta=3.8\\dots$; this length might lead to observational effects on objects the size of a virus.

  13. Distributed feedback laser amplifiers combining the functions of amplifiers and channel filters

    DEFF Research Database (Denmark)

    Wang, Z.; Durhuus, T.; Mikkelsen, Benny;

    1994-01-01

    A dynamic model for distributed feedback amplifiers, including the mode coupled equations and the carrier rate equation, is established. The presented mode coupled equations have taken into account the interaction between fast changing optical signal and the waveguide with corrugations. By showin...... the possibility of amplifying 100 ps pulses without pulse broadening, we anticipate that a distributed feedback amplifier can be used as a combined amplifier and channel filter in high bit rate transmission systems....

  14. Amplified spontaneous emission and its restraint in a terawatt Ti:sapphire amplifier

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Amplified spontaneous emission (ASE) and its restraint in a femtosecond Ti: sapphire chirped_pulse amplifier were investigated. The noises arising from ASE were effectively filtered out in the spatial, temporal and spectral domain. Pulses as short as 38 fs were amplified to peak power of 1.4 TW. The power ratio between the amplified femtosecond pulse and the ASE was higher than 106:1.

  15. Observations on oesophageal length.

    Science.gov (United States)

    Kalloor, G J; Deshpande, A H; Collis, J L

    1976-01-01

    The subject of oesophageal length is discussed. The great variations in the length of the oesophagus in individual patients is noted, and the practical use of its recognition in oesophageal surgery is stressed. An apprasial of the various methods available for this measurement is made; this includes the use of external chest measurement, endoscopic measurement, and the measurement of the level of the electrical mucosal potential change. Correlative studies of these various methods are made, and these show a very high degree of significance. These studies involved simultaneous measurement of external and internal oesophageal length in 26 patients without a hiatal hernia or gastro-oesophageal length in 26 patients without a hiatal hernia or gastro-oesophageal reflux symptoms, 42 patients with sliding type hiatal hernia, and 17 patients with a peptic stricture in association with hiatal hernia. The method of measuring oesophageal length by the use of the external chest measurement, that is, the distance between the lower incisor teeth and the xiphisternum, measured with the neck fully extended and the patient lying supine, is described in detail, its practical application in oesophageal surgery is illustrated, and its validity tested by internal measurements. The findings of this study demonstrate that the external chest measurement provides a mean of assessing the true static length of the oesophagus, corrected for the size of the individual. Images PMID:941114

  16. Equilibrium CO bond lengths

    Science.gov (United States)

    Demaison, Jean; Császár, Attila G.

    2012-09-01

    Based on a sample of 38 molecules, 47 accurate equilibrium CO bond lengths have been collected and analyzed. These ultimate experimental (reEX), semiexperimental (reSE), and Born-Oppenheimer (reBO) equilibrium structures are compared to reBO estimates from two lower-level techniques of electronic structure theory, MP2(FC)/cc-pVQZ and B3LYP/6-311+G(3df,2pd). A linear relationship is found between the best equilibrium bond lengths and their MP2 or B3LYP estimates. These (and similar) linear relationships permit to estimate the CO bond length with an accuracy of 0.002 Å within the full range of 1.10-1.43 Å, corresponding to single, double, and triple CO bonds, for a large number of molecules. The variation of the CO bond length is qualitatively explained using the Atoms in Molecules method. In particular, a nice correlation is found between the CO bond length and the bond critical point density and it appears that the CO bond is at the same time covalent and ionic. Conditions which permit the computation of an accurate ab initio Born-Oppenheimer equilibrium structure are discussed. In particular, the core-core and core-valence correlation is investigated and it is shown to roughly increase with the bond length.

  17. Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

    Directory of Open Access Journals (Sweden)

    Adriaenssens Sandy

    2011-08-01

    Full Text Available Abstract Background Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium. We also studied whether seed viability and populations size were correlated with genetic diversity. Results Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10. In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. Conclusions In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.

  18. Self-pulsation in Raman fiber amplifiers

    DEFF Research Database (Denmark)

    Pedersen, Martin Erland Vestergaard; Ott, Johan Raunkjær; Rottwitt, Karsten

    2009-01-01

    Dynamic behavior caused by Brillouin scattering in Raman fiber amplifiers is studied. Modes of self-pulsation steady state oscillations are found. Their dependence on amplification scheme is demonstrated.......Dynamic behavior caused by Brillouin scattering in Raman fiber amplifiers is studied. Modes of self-pulsation steady state oscillations are found. Their dependence on amplification scheme is demonstrated....

  19. BROADBAND TRAVELLING WAVE SEMICONDUCTOR OPTICAL AMPLIFIER

    DEFF Research Database (Denmark)

    2010-01-01

    Broadband travelling wave semiconductor optical amplifier (100, 200, 300, 400, 800) for amplification of light, wherein the amplifier (100, 200, 300, 400, 800) comprises a waveguide region (101, 201, 301, 401, 801) for providing confinement of the light in transverse directions and adapted...

  20. HIERARCHICAL FRAGMENTATION OF THE ORION MOLECULAR FILAMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Satoko; Ho, Paul T. P.; Su, Yu-Nung [Academia Sinica Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 10617, Taiwan (China); Teixeira, Paula S. [Institut fuer Astrophysik, Universitaet Wien, Tuerkenschanzstrasse 17, A-1180, Wien (Austria); Zapata, Luis A., E-mail: satoko_t@asiaa.sinica.edu.tw [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Morelia, Michoacan 58090 (Mexico)

    2013-01-20

    We present a high angular resolution map of the 850 {mu}m continuum emission of the Orion Molecular Cloud-3 (OMC 3) obtained with the Submillimeter Array (SMA); the map is a mosaic of 85 pointings covering an approximate area of 6.'5 Multiplication-Sign 2.'0 (0.88 Multiplication-Sign 0.27 pc). We detect 12 spatially resolved continuum sources, each with an H{sub 2} mass between 0.3-5.7 M {sub Sun} and a projected source size between 1400-8200 AU. All the detected sources are on the filamentary main ridge (n{sub H{sub 2}}{>=}10{sup 6} cm{sup -3}), and analysis based on the Jeans theorem suggests that they are most likely gravitationally unstable. Comparison of multi-wavelength data sets indicates that of the continuum sources, 6/12 (50%) are associated with molecular outflows, 8/12 (67%) are associated with infrared sources, and 3/12 (25%) are associated with ionized jets. The evolutionary status of these sources ranges from prestellar cores to protostar phase, confirming that OMC-3 is an active region with ongoing embedded star formation. We detect quasi-periodical separations between the OMC-3 sources of Almost-Equal-To 17''/0.035 pc. This spatial distribution is part of a large hierarchical structure that also includes fragmentation scales of giant molecular cloud ( Almost-Equal-To 35 pc), large-scale clumps ( Almost-Equal-To 1.3 pc), and small-scale clumps ( Almost-Equal-To 0.3 pc), suggesting that hierarchical fragmentation operates within the Orion A molecular cloud. The fragmentation spacings are roughly consistent with the thermal fragmentation length in large-scale clumps, while for small-scale cores it is smaller than the local fragmentation length. These smaller spacings observed with the SMA can be explained by either a helical magnetic field, cloud rotation, or/and global filament collapse. Finally, possible evidence for sequential fragmentation is suggested in the northern part of the OMC-3 filament.

  1. Ultrafast disk lasers and amplifiers

    Science.gov (United States)

    Sutter, Dirk H.; Kleinbauer, Jochen; Bauer, Dominik; Wolf, Martin; Tan, Chuong; Gebs, Raphael; Budnicki, Aleksander; Wagenblast, Philipp; Weiler, Sascha

    2012-03-01

    Disk lasers with multi-kW continuous wave (CW) output power are widely used in manufacturing, primarily for cutting and welding applications, notably in the automotive industry. The ytterbium disk technology combines high power (average and/or peak power), excellent beam quality, high efficiency, and high reliability with low investment and operating costs. Fundamental mode picosecond disk lasers are well established in micro machining at high throughput and perfect precision. Following the world's first market introduction of industrial grade 50 W picosecond lasers (TruMicro 5050) at the Photonics West 2008, the second generation of the TruMicro series 5000 now provides twice the average power (100 W at 1030 nm, or 60 W frequency doubled, green output) at a significantly reduced footprint. Mode-locked disk oscillators achieve by far the highest average power of any unamplified lasers, significantly exceeding the 100 W level in laboratory set-ups. With robust long resonators their multi-microjoule pulse energies begin to compete with typical ultrafast amplifiers. In addition, significant interest in disk technology has recently come from the extreme light laser community, aiming for ultra-high peak powers of petawatts and beyond.

  2. Design and performance of the beamlet amplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Erlandson, A.C.; Rotter, M.D.; Frank, M.D.; McCracken, R.W.

    1996-06-01

    In future laser systems, such as the National Ignition Facility (NIF), multi-segment amplifiers (MSAs) will be used to amplify the laser beam to the required levels. As a prototype of such a laser architecture, the authors have designed, built, and tested flash-lamp-pumped, Nd:Glass, Brewster-angle slab MSAs for the Beamlet project. In this article, they review the fundamentals of Nd:Glass amplifiers, describe the MSA geometry, discuss parameters that are important in amplifier design, and present our results on the characterization of the Beamlet MSAs. In particular, gain and beam steering measurements show that the Beamlet amplifiers meet all optical performance specifications and perform close to model predictions.

  3. Amplified OTDR systems for multipoint corrosion monitoring.

    Science.gov (United States)

    Nascimento, Jehan F; Silva, Marcionilo J; Coêlho, Isnaldo J S; Cipriano, Eliel; Martins-Filho, Joaquim F

    2012-01-01

    We present two configurations of an amplified fiber-optic-based corrosion sensor using the optical time domain reflectometry (OTDR) technique as the interrogation method. The sensor system is multipoint, self-referenced, has no moving parts and can measure the corrosion rate several kilometers away from the OTDR equipment. The first OTDR monitoring system employs a remotely pumped in-line EDFA and it is used to evaluate the increase in system reach compared to a non-amplified configuration. The other amplified monitoring system uses an EDFA in booster configuration and we perform corrosion measurements and evaluations of system sensitivity to amplifier gain variations. Our experimental results obtained under controlled laboratory conditions show the advantages of the amplified system in terms of longer system reach with better spatial resolution, and also that the corrosion measurements obtained from our system are not sensitive to 3 dB gain variations.

  4. Amplified OTDR Systems for Multipoint Corrosion Monitoring

    Directory of Open Access Journals (Sweden)

    Joaquim F. Martins-Filho

    2012-03-01

    Full Text Available We present two configurations of an amplified fiber-optic-based corrosion sensor using the optical time domain reflectometry (OTDR technique as the interrogation method. The sensor system is multipoint, self-referenced, has no moving parts and can measure the corrosion rate several kilometers away from the OTDR equipment. The first OTDR monitoring system employs a remotely pumped in-line EDFA and it is used to evaluate the increase in system reach compared to a non-amplified configuration. The other amplified monitoring system uses an EDFA in booster configuration and we perform corrosion measurements and evaluations of system sensitivity to amplifier gain variations. Our experimental results obtained under controlled laboratory conditions show the advantages of the amplified system in terms of longer system reach with better spatial resolution, and also that the corrosion measurements obtained from our system are not sensitive to 3 dB gain variations.

  5. Detection of Non-Amplified Genomic DNA

    CERN Document Server

    Corradini, Roberto

    2012-01-01

    This book offers a state-of-the-art overview on non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. The importance of non-amplified DNA sequencing technologies will be also discussed. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specifi...

  6. An Implantable CMOS Amplifier for Nerve Signals

    DEFF Research Database (Denmark)

    Nielsen, Jannik Hammel; Lehmann, Torsten

    2001-01-01

    In this paper, a low noise high gain CMOS amplifier for minute nerve signals is presented. By using a mixture of weak- and strong inversion transistors, optimal noise suppression in the amplifier is achieved. A continuous-time offset-compensation technique is utilized in order to minimize impact...... on the amplifier input nodes. The method for signal recovery from noisy nerve signals is presented. A prototype amplifier is realized in a standard digital 0.5 μm CMOS single poly, n-well process. The prototype amplifier features a gain of 80 dB over a 3.6 kHz bandwidth, a CMRR of more than 87 dB and a PSRR...

  7. Fractal characteristics of cracks and fragments generated in unloading rockburst tests

    Institute of Scientific and Technical Information of China (English)

    Li Dejian; Zhao Fei; Zheng Maojiong

    2014-01-01

    True triaxial rockburst experiments with four different unloading rates were performed on four prism specimens of granite sampled from Beishan, China. The damage evolution in the rockburst test was investigated from two aspects including fracture surface crack and fragment characteristics. The scanning electron microscopy was used to observe the micro crack information on fragment surface. Combing binarization and box counting dimensions, the fractal dimensions of cracks were obtained. Meanwhile, the fragments were collected and a sieving experiment was conducted. We weighed the fragments qualities, counted the amount of fragments and measured the fragments length, width and thickness. Utilizing four methods to calculate damage fractal dimensions of fragments, the trend of fractal value changing with unloading rates can be roughly described. It can be concluded from these experiments that the fractal dimension either for crack or for fragment holds a decreasing trend with the decreasing unloading rate, indicating a reduction of damage level.

  8. The Serendipity of Fragmentation

    DEFF Research Database (Denmark)

    Leixnering, Stephan; Meyer, Renate E.

    Reform approaches in the public sector led to significant changes in the sector’s design. Especially NPM-inspired reform measures which had largely aimed at organizational disaggregation created pluriform landscapes of public sector organizations (PSOs). Following a core public governance principle......, it was the central government’s task to coordinate, steer and control the newly emerged decentralized organizations. This raises questions about the overall design of the public sector at present. Our paper engages with the prevalent public governance phenomenon of fragmentation from a design perspective in order...... insights in how structures and relations were formally designed. Second, we interviewed top officials and executives who performed key tasks in the coordination and management of the city’s autonomous units....

  9. Stone fragmentation by ultrasound

    Indian Academy of Sciences (India)

    S K Shrivastava; Kailash

    2004-08-01

    The presence of kidney stone in the kidney causes discomfort to patients. Hence, removal of such stones is important which is commonly done these days, non-destructively, with lithotripters without surgery. Commercially, lithotripters like extra-corporeal shock wave lithotripters (ESWL) made by Siemens etc are in routine use. These methods are very cumbersome and expensive. Treatment of the patients also takes comparatively more time because of more number of sittings. Some delicate nerves and fibres in the surrounding areas of the stones present in the kidney are also damaged by high ultrasonic intensity used in such systems. In the present work, enhancement of the kidney stone fragmentation by using ultrasound is studied. The cavitation bubbles are found to implode faster, with more disintegration efficiency of the lithotripters, which give better treatment to the patients.

  10. Saturating representation of loop conformational fragments in structure databanks

    Directory of Open Access Journals (Sweden)

    Fiser András

    2006-07-01

    Full Text Available Abstract Background Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments in structure databanks. Results We studied the representation of protein loop fragments up to 14 residues in length. All possible query fragments found in sequence databases (Sequence Space were clustered and cross referenced with available structural fragments in Protein Data Bank (Structure Space. We found that the expansion of PDB in the last few years resulted in a dense coverage of loop conformational fragments. For each loops of length 8 in the current Sequence Space there is at least one loop in Structure Space with 50% or higher sequence identity. By correlating sequence and structure clusters of loops we found that a 50% sequence identity generally guarantees structural similarity. These percentages of coverage at 50% sequence cutoff drop to 96, 94, 68, 53, 33 and 13% for loops of length 9, 10, 11, 12, 13, and 14, respectively. There is not a single loop in the current Sequence Space at any length up to 14 residues that is not matched with a conformational segment that shares at least 20% sequence identity. This minimum observed identity is 40% for loops of 12 residues or shorter and is as high as 50% for 10 residue or shorter loops. We also assessed the impact of rapidly growing sequence databanks on the estimated number of new loop conformations and found that while the number of sequentially unique sequence segments increased about six folds during the last five years there are almost no unique conformational segments among these up to 12 residues long fragments. Conclusion The results suggest that fragment based prediction approaches are not limited any more by the completeness of fragments in databanks but

  11. High power Ka band TWT amplifier

    Energy Technology Data Exchange (ETDEWEB)

    Golkowski, C.; Ivers, J.D.; Nation, J.A.; Wang, P.; Schachter, L.

    1999-07-01

    Two high power 35 GHz TWT amplifiers driven by a relativistic pencil, 850 kV, 200A electron beam have been assembled and tested. The first had a dielectric slow wave structure and was primarily used to develop diagnostics, and to gain experience in working with high power systems in Ka band. The source of the input power for the amplifier was a magnetron producing a 30 kW, 200ns long pulse of which 10 kW as delivered to the experiment. The 30 cm long dielectric (Teflon) amplifier produced output power levels of about 1 MW with a gain of about 23 dB. These results are consistent with expectations from PIC code simulations for this arrangement. The second amplifier, which is a single stage disk loaded slow wave structure, has been designed. It consists of one hundred uniform cells with two sets of ten tapered calls at the ends to lower the reflection coefficient. The phase advance per cell is {pi}/2. The amplifier passband extends from 28 to 40 GHz. It is designed to increase the output power to about 20 MW. The amplifier is in construction and will be tested in the near future. Details of the design of both systems will be provided and initial results from the new amplifier presented.

  12. CONTROL OF FRAGMENTATION BY BLASTING

    Directory of Open Access Journals (Sweden)

    Branko Božić

    1998-12-01

    Full Text Available The degree of fragmentation influences the economy of the excavation operations. Characteristics of blasted rock such as fragment size, volume and mass are fundamental variables effecting the economics of a mining operation and are in effect the basis for evaluating the quality of a blast. The properties of fragmentation, such as size and shape, are very important information for the optimization of production. Three factors control the fragment size distribution: the rock structure, the quantity of explosive and its distribution within the rock mass. Over the last decade there have been considerable advances in our ability to measure and analyze blasting performance. These can now be combined with the continuing growth in computing power to develop a more effective description of rock fragmentation for use by future blasting practitioners. The paper describes a view of the fragmentation problem by blasting and the need for a new generation of engineering tools to guide the design and implementation of blasting operations.

  13. An Envelope Hammerstein Model for Power Amplifiers

    Institute of Scientific and Technical Information of China (English)

    Hua-Dong Wang; Song-Bai He; Jing-Fu Bao; Zheng-De Wu

    2007-01-01

    In this paper, an envelope Hammerstein(EH) model is introduced to describe dynamic inputoutput characteristics of RF power amplifiers. In the modeling approach, we use a new truncation method and an established nonlinear time series method to determine model structure. Then, we discuss the process of model parameter extraction in detailed. Finally, a 2 W WCDMA power amplifier is measured to verify the performance of EH model, and good agreement between model output and measurement result shows our model can accurately predict output characteristic of the power amplifier.

  14. Quantum electronics maser amplifiers and oscillators

    CERN Document Server

    Fain, V M; Sanders, J H

    2013-01-01

    Quantum Electronics, Volume 2: Maser Amplifiers and Oscillators deals with the experimental and theoretical aspects of maser amplifiers and oscillators which are based on the principles of quantum electronics. It shows how the concepts and equations used in quantum electronics follow from the basic principles of theoretical physics.Comprised of three chapters, this volume begins with a discussion on the elements of the theory of quantum oscillators and amplifiers working in the microwave region, along with the practical achievements in this field. Attention is paid to two-level paramagnetic ma

  15. Effect of Soliton Propagation in Fiber Amplifiers

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The propagation of optical solitons in fiber amplifiers is discussed by considering a model that includes linear high order dispersion, two-photon absorption, nonlinear high-order dispersion, self-induced Ramam and five-order nonlinear effects. Based on travelling wave method, the solutions of the nonlinear Schrdinger equations, and the influence on soliton propagation as well as high-order effect in the fiber amplifier are discussed in detail. It is found that because of existing five-order nonlinear effect, the solution is not of secant hyperbola type, but shows high gain state of the fiber amplifier which is very favourable to the propagation of solitons.

  16. High Efficiency Microwave Power Amplifier (HEMPA) Design

    Science.gov (United States)

    Sims, W. Herbert

    2004-01-01

    This paper will focus on developing an exotic switching technique that enhances the DC-to-RF conversion efficiency of microwave power amplifiers. For years, switching techniques implemented in the 10 kHz to 30 MHz region have resulted in DC-to-RF conversion efficiencies of 90-95-percent. Currently amplifier conversion efficiency, in the 2-3 GHz region approaches, 10-20-percent. Using a combination of analytical modeling and hardware testing, a High Efficiency Microwave Power Amplifier was built that demonstrated conversion efficiencies four to five times higher than current state of the art.

  17. Fundamentals of RF and microwave transistor amplifiers

    CERN Document Server

    Bahl, Inder J

    2009-01-01

    A Comprehensive and Up-to-Date Treatment of RF and Microwave Transistor Amplifiers This book provides state-of-the-art coverage of RF and microwave transistor amplifiers, including low-noise, narrowband, broadband, linear, high-power, high-efficiency, and high-voltage. Topics covered include modeling, analysis, design, packaging, and thermal and fabrication considerations. Through a unique integration of theory and practice, readers will learn to solve amplifier-related design problems ranging from matching networks to biasing and stability. More than 240 problems are included to help read

  18. Phase noise in RF and microwave amplifiers.

    Science.gov (United States)

    Boudot, Rodolphe; Rubiola, Enrico

    2012-12-01

    Understanding amplifier phase noise is a critical issue in many fields of engineering and physics, such as oscillators, frequency synthesis, telecommunication, radar, and spectroscopy; in the emerging domain of microwave photonics; and in exotic fields, such as radio astronomy, particle accelerators, etc. Focusing on the two main types of base noise in amplifiers, white and flicker, the power spectral density of the random phase φ(t) is Sφ(f) = b(0) + b(-1)/f. White phase noise results from adding white noise to the RF spectrum in the carrier region. For a given RF noise level, b(0) is proportional to the reciprocal of the carrier power P(0). By contrast, flicker results from a near-dc 1/f noise-present in all electronic devices-which modulates the carrier through some parametric effect in the semiconductor. Thus, b(-1) is a parameter of the amplifier, constant in a wide range of P(0). The consequences are the following: Connecting m equal amplifiers in parallel, b(-1) is 1/m times that of one device. Cascading m equal amplifiers, b(-1) is m times that of one amplifier. Recirculating the signal in an amplifier so that the gain increases by a power of m (a factor of m in decibels) as a result of positive feedback (regeneration), we find that b(-1) is m(2) times that of the amplifier alone. The feedforward amplifier exhibits extremely low b(-1) because the carrier is ideally nulled at the input of its internal error amplifier. Starting with an extensive review of the literature, this article introduces a system-oriented model which describes the phase flickering. Several amplifier architectures (cascaded, parallel, etc.) are analyzed systematically, deriving the phase noise from the general model. There follow numerous measurements of amplifiers using different technologies, including some old samples, and in a wide frequency range (HF to microwaves), which validate the theory. In turn, theory and results provide design guidelines and give suggestions for CAD and

  19. Achieving and maintaining cleanliness in NIF amplifiers

    Energy Technology Data Exchange (ETDEWEB)

    Burnham, A. K.; Horvath, J. A.; Letts, S. A.; Menapace, J. A.; Stowers, I. F.

    1998-07-28

    Cleanliness measurements made on AMPLAB prototype National Ignition Facility (NIF) laser amplifiers during assembly, cassette transfer, and amplifier operation are summarized. These measurements include particle counts from surface cleanliness assessments using filter swipe techniques and from airborne particle monitoring. Results are compared with similar measurements made on the Beamlet and Nova lasers and in flashlamp test fixtures. Observations of Class 100,000 aerosols after flashlamp firings are discussed. Comparisons are made between typical damage densities on laser amplifier optics from Novette, NOVA, Beamlet, and AMPLAB.

  20. Fragment Identification and Statistics Method of Hypervelocity Impact SPH Simulation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiaotian; JIA Guanghui; HUANG Hai

    2011-01-01

    A comprehensive treatment to the fragment identification and statistics for the smoothed particle hydrodynamics (SPH) simulation of hypervelocity impact is presented.Based on SPH method, combined with finite element method (FEM), the computation is performed.The fragments are identified by a new pre- and post-processing algorithm and then converted into a binary graph.The number of fragments and the attached SPH particles are determined by counting the quantity of connected domains on the binary graph.The size, velocity vector and mass of each fragment are calculated by the particles' summation and weighted average.The dependence of this method on finite element edge length and simulation terminal time is discussed.An example of tungsten rods impacting steel plates is given for calibration.The computation results match experiments well and demonstrate the effectiveness of this method.

  1. Typing Candida Species Using Microsatellite Length Polymorphism and Multilocus Sequence Typing.

    Science.gov (United States)

    Garcia-Hermoso, Dea; Desnos-Ollivier, Marie; Bretagne, Stéphane

    2016-01-01

    To gain more insight into the epidemiological relationships between isolates of Candida spp. obtained from various origins, several molecular typing techniques have been developed. Two methods have emerged in the 2000s as soon as enough knowledge of the Candida spp. genomes was available to choose adequate loci and primers, namely microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST). To contrast with previous PCR-based methods, specific amplifications with stringent conditions easily reproducible are the basis of MLP and MLST. MLST relies on Sanger sequencing to detect single-nucleotide polymorphisms within housekeeping genes. MLP needs a first in silico step to select tandemly repeated stretches of two to five nucleotides. One of the two primers used to amplify a microsatellite locus is labeled and fragment sizing is automatically performed using high-resolution electrophoresis platforms. MLST provides results easily comparable between laboratories and active MLST schemes are publicly available for the main Candida species. For comparative studies, MLP needs standards to compensate for the electrophoretic variations depending on the platforms used. Both methods can help us gain insight into the genetic relatedness of fungal isolates, both with advantages and drawbacks, and the choice of one method rather than the other depends on the task in question.

  2. Self-pulsation in Raman fiber amplifiers

    OpenAIRE

    Pedersen, Martin Erland Vestergaard; Ott, Johan Raunkjær; Rottwitt, Karsten

    2009-01-01

    Dynamic behavior caused by Brillouin scattering in Raman fiber amplifiers is studied. Modes of self-pulsation steady state oscillations are found. Their dependence on amplification scheme is demonstrated.

  3. High Energy Single Frequency Resonant Amplifier Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR phase I project proposes a single frequency high energy resonant amplifier for remote sensing. Current state-of-art technologies can not provide all...

  4. Sequence length variation, indel costs, and congruence in sensitivity analysis

    DEFF Research Database (Denmark)

    Aagesen, Lone; Petersen, Gitte; Seberg, Ole

    2005-01-01

    the cost of indels was varied. Indels were treated either as a fifth character state, or strings of contiguous gaps were considered single events by using linear affine gap cost. Congruence consistently improved when indels were treated as single events, but no congruence measure appeared as the obviously...... preferable one. However, when combining enough data, all congruence measures clearly tended to select the same alignment cost set as the optimal one. Disagreement among congruence measures was mostly caused by a dominant fragment or a data partition that included all or most of the length variation...... in the data set. Dominance was easily detected, as the character-based congruence measures approached their optimal value when indel costs were incremented. Dominance of a fragment or data partition was overwhelmed when new sequence length-variable fragments or data partitions were added....

  5. Thermodynamical string fragmentation

    Science.gov (United States)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  6. Thermodynamical String Fragmentation

    CERN Document Server

    Fischer, Nadine

    2016-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from...

  7. Fragmentation Considered Poisonous

    CERN Document Server

    Herzberg, Amir

    2012-01-01

    We present practical poisoning and name-server block- ing attacks on standard DNS resolvers, by off-path, spoofing adversaries. Our attacks exploit large DNS responses that cause IP fragmentation; such long re- sponses are increasingly common, mainly due to the use of DNSSEC. In common scenarios, where DNSSEC is partially or incorrectly deployed, our poisoning attacks allow 'com- plete' domain hijacking. When DNSSEC is fully de- ployed, attacker can force use of fake name server; we show exploits of this allowing off-path traffic analy- sis and covert channel. When using NSEC3 opt-out, attacker can also create fake subdomains, circumvent- ing same origin restrictions. Our attacks circumvent resolver-side defenses, e.g., port randomisation, IP ran- domisation and query randomisation. The (new) name server (NS) blocking attacks force re- solver to use specific name server. This attack allows Degradation of Service, traffic-analysis and covert chan- nel, and also facilitates DNS poisoning. We validated the attac...

  8. Efficient Power Amplifier for Motor Control

    Science.gov (United States)

    Brown, R. J.

    1986-01-01

    Pulse-width-modulated amplifier supplies high current as efficiently as low current needed for starting and running motor. Key to efficiency of motor-control amplifier is V-channel metal-oxide/semiconductor transistor Q1. Device has low saturation resistance. However, has large gate input capacitance and small margin between its turn-on voltage and maximum allowable gate-to-source voltage. Circuits for output stages overcome limitations of VMOS device.

  9. Quantum cloning with an optical fiber amplifier

    CERN Document Server

    Fasel, S; Ribordy, G; Scarani, V; Zbinden, H; Fasel, Sylvain; Gisin, Nicolas; Ribordy, Gregoire; Scarani, Valerio; Zbinden, Hugo

    2002-01-01

    It has been shown theoretically that a light amplifier working on the physical principle of stimulated emission should achieve optimal quantum cloning of the polarization state of light. We demonstrate close-to-optimal universal quantum cloning of polarization in a standard fiber amplifier for telecom wavelengths. For cloning $1\\to 2$ we find a fidelity of 0.82, the optimal value being ${5/6}=0.83$.

  10. CMOS current amplifiers : speed versus nonlinearity

    OpenAIRE

    2000-01-01

    This work deals with analogue integrated circuit design using various types of current-mode amplifiers. These circuits are analysed and realised using modern CMOS integration technologies. The dynamic nonlinearities of these circuits are discussed in detail as in the literature only linear nonidealities and static nonlinearities are conventionally considered. For the most important open-loop current-mode amplifier, the second-generation current-conveyor (CCII), a macromodel is derived tha...

  11. MMIC Amplifiers for 90 to 130 GHz

    Science.gov (United States)

    Samoska, Lorene; Pukala, David; Peralta, Alejandro; Bryerton, Eric; Morgan, Matt; Boyd, T.; Hu, Ming; Schmitz, Adele

    2007-01-01

    This brief describes two monolithic microwave integrated-circuit (MMIC) amplifier chips optimized to function in the frequency range of 90 to 130 GHz, covering nearly all of F-band (90 - 140 GHz). These amplifiers were designed specifically for local-oscillator units in astronomical radio telescopes such as the Atacama Large Millimeter Array (ALMA). They could also be readily adapted for use in electronic test equipment, automotive radar systems, and communications systems that operate between 90 and 130 GHz.

  12. Fragment Merger: An Online Tool to Merge Overlapping Long Sequence Fragments

    Directory of Open Access Journals (Sweden)

    Anna Kramvis

    2013-03-01

    Full Text Available While PCR amplicons extend to a few thousand bases, the length of sequences from direct Sanger sequencing is limited to 500–800 nucleotides. Therefore, several fragments may be required to cover an amplicon, a gene or an entire genome. These fragments are typically sequenced in an overlapping fashion and assembled by manually sliding and aligning the sequences visually. This is time-consuming, repetitive and error-prone, and further complicated by circular genomes. An online tool merging two to twelve long overlapping sequence fragments was developed. Either chromatograms or FASTA files are submitted to the tool, which trims poor quality ends of chromatograms according to user-specified parameters. Fragments are assembled into a single sequence by repeatedly calling the EMBOSS merger tool in a consecutive manner. Output includes the number of trimmed nucleotides, details of each merge, and an optional alignment to a reference sequence. The final merge sequence is displayed and can be downloaded in FASTA format. All output files can be downloaded as a ZIP archive. This tool allows for easy and automated assembly of overlapping sequences and is aimed at researchers without specialist computer skills. The tool is genome- and organism-agnostic and has been developed using hepatitis B virus sequence data.

  13. Some Notes on Wideband Feedback Amplifiers

    Science.gov (United States)

    Fitch, V.

    1949-03-16

    The extension of the passband of wideband amplifiers is a highly important problem to the designer of electronic circuits. Throughout the electronics industry and in many research programs in physics and allied fields where extensive use is made of video amplifiers, the foremost requirement is a passband of maximum width. This is necessary if it is desired to achieve a more faithful reproduction of transient wave forms, a better time resolution in physical measurements, or perhaps just a wider band gain-frequency response to sine wave signals. The art of electronics is continually faced with this omnipresent amplifier problem. In particular, the instrumentation techniques of nuclear physics require amplifiers with short rise times, a high degree of gain stability, and a linear response to high signal levels. While the distributed amplifier may solve the problems of those seeking only a wide passband, the requirements of stability and linearity necessitate using feedback circuits. This paper considers feedback amplifiers from the standpoint of high-frequency performance. The circuit conditions for optimum steady-state (sinusoidal) and transient response are derived and practical circuits (both interstage and output) are presented which fulfill these conditions. In general, the results obtained may be applied to the low-frequency end.

  14. Relativistic length agony continued

    Directory of Open Access Journals (Sweden)

    Redžić D.V.

    2014-01-01

    Full Text Available We made an attempt to remedy recent confusing treatments of some basic relativistic concepts and results. Following the argument presented in an earlier paper (Redžić 2008b, we discussed the misconceptions that are recurrent points in the literature devoted to teaching relativity such as: there is no change in the object in Special Relativity, illusory character of relativistic length contraction, stresses and strains induced by Lorentz contraction, and related issues. We gave several examples of the traps of everyday language that lurk in Special Relativity. To remove a possible conceptual and terminological muddle, we made a distinction between the relativistic length reduction and relativistic FitzGerald-Lorentz contraction, corresponding to a passive and an active aspect of length contraction, respectively; we pointed out that both aspects have fundamental dynamical contents. As an illustration of our considerations, we discussed briefly the Dewan-Beran-Bell spaceship paradox and the ‘pole in a barn’ paradox. [Projekat Ministarstva nauke Republike Srbije, br. 171028

  15. An Algebra for Program Fragments

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun; Madsen, Ole Lehrmann; Møller-Pedersen, Birger

    1985-01-01

    Program fragments are described either by strings in the concrete syntax or by constructor applications in the abstract syntax. By defining conversions between these forms, both may be intermixed. Program fragments are constructed by terminal and nonterminal symbols from the grammar and by variab...

  16. Complete axiomatizations for XPath fragments

    NARCIS (Netherlands)

    ten Cate, B.; Litak, T.; Marx, M.

    2010-01-01

    We provide complete axiomatizations for several fragments of Core XPath, the navigational core of XPath 1.0 introduced by Gottlob, Koch and Pichler. A complete axiomatization for a given fragment is a set of equivalences from which every other valid equivalence is derivable; equivalences can be thou

  17. 123 km Φ-OTDR system based on bidirectional erbium-doped fiber amplifier

    Science.gov (United States)

    Tian, Xiaozhong; Dang, Rui; Tan, Dongjie; Liu, Lu; Wang, Haiming

    2016-10-01

    Based on bidirectional Erbium-doped fiber amplifier (B-EDFA), which can amplify not only forward pulse light but also backward Rayleigh scattering light, a long distance (123 km) Φ-OTDR system is demonstrate. In this system, four B-EDFAs are employed to extend sensing length. Meanwhile, by using the difference value of upper-envelope and lower-envelope of Rayleigh scattering trace, the intrusion with SNR of 5.45 dB, 3.64 dB and 4.51 dB at three test points of sensing fiber is extracted.

  18. Dynamic Gain-Clamped Amplifier with Backward-Injection of a Fabry-Perot Laser

    Institute of Scientific and Technical Information of China (English)

    Chien-Hung Yeh; Chih-Yang Chen; Chien-Chung Lee; Sien Chi

    2003-01-01

    We have been experimentally demonstrated an active control technique of dynamic gain-clamped spectra for the erbium-doped fiber amplifiers (EDFA's) by a backward-injected Fabry-Perot (F-P) laser into this EDFA. In addition, employing a short length erbium-doped fiber (EDF) that not cause any gain saturation for preamplification in front of this amplifier module, it can reduce the noise figure degradation and simultaneously achieve gain variation from 11.1 dB to 0.5 dB for 10 dB input power level change.

  19. Dynamic Gain-Clamped Amplifier with Backward-Injection of a Fabry-Perot Laser

    Institute of Scientific and Technical Information of China (English)

    Chien-Hung; Yeh; Chih-Yang; Chen; Chien-Chung; Lee; Sien; Chi

    2003-01-01

    We have been experimentally demonstrated an active control technique of dynamic gain-clamped spectra for theerbium-doped fiber amplifiers (EDFA's) by a backward-injected Fabry-Perot (F-P) laser into this EDFA. In addition, employing a short length erbium-doped fiber (EDF) that not cause any gain saturation for preamplification in front of this amplifier module, it can reduce the noise figure degradation and simultaneously achieve gain variation from 11.1 dB to 0.5 dB for 10 dB input power level change.

  20. Properties of dysprosium-doped gallium lanthanum sulfide fiber amplifiers operating at 1.3 microm.

    Science.gov (United States)

    Samson, B N; Schweizer, T; Hewak, D W; Laming, R I

    1997-05-15

    In light of recent progress in the fabrication of gallium lanthanum sulfide (GaLaS) fibers, we have modeled the performance of dysprosium-doped GaLaS fiber amplifiers operating at 1.3 microm . Based on experimental data, we find that the incorporation of a codopant (terbium) in the fiber core significantly shortens the optimum amplifier length from >30 m to approximately 3 m . Such a device may be practical, given the fiber losses currently achieved in GaLaS fibers.

  1. Low Noise Optically Pre-amplified Lightwave Receivers and Other Applications of Fiber Optic Parametric Amplifiers

    Science.gov (United States)

    2010-07-27

    noise performance, optical gain bandwidth, and power efficiency. An interesting alternative to the mature Erbium-doped fiber amplifier ( EDFA ) is the...fibers (HNLF) and high power booster EDFAs . The FOPA can provide a very wide gain bandwidth [2], very high gain (70 dB was demonstrated in [3]), and...amplified spontaneous emission (ASE) noise in EDFAs is also generated. It is sometimes referred to as amplified quantum noise. Maximum gain (at the gain

  2. Branching Markov processes on fragmentation trees generated from the paintbox process

    CERN Document Server

    Crane, Harry

    2011-01-01

    A fragmentation of a set $A$ is a graph with vertices labeled by subsets of $A$ which obey a certain parent-child relationship. A random fragmentation tree is a probability distribution on the space of fragmentations of a set. It is often convenient to regard a fragmentation tree as a collection of subsets such that each subset is associated with a non-trivial partition of itself, called its children. In this paper, we study a Markov process on the space of fragmentation trees whose transition probabilities are a product of consistent transition probabilities on the space of partitions. The result is a consistent family of transition probabilities on fragmentation trees which characterizes an infinitely exchangeable process on trees labeled by subsets of the natural numbers. We show that this process possesses a unique stationary measure and can be extended to a process on weighted trees, or trees with edge lengths, as well as mass fragmentations.

  3. Dissection of SARS Coronavirus Spike Protein into Discrete Folded Fragments

    Institute of Scientific and Technical Information of China (English)

    LI Shuang; CAI Zhen; CHEN Yong; LIN Zhanglin

    2006-01-01

    The spike protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) mediates cell fusion by binding to target cell surface receptors. This paper reports a simple method for dissecting the viral protein and for searching for foldable fragments in a random but systematic manner. The method involves digestion by DNase I to generate a pool of short DNA segments, followed by an additional step of reassembly of these segments to produce a library of DNA fragments with random ends but controllable lengths. To rapidly screen for discrete folded polypeptide fragments, the reassembled gene fragments were further cloned into a vector as N-terminal fusions to a folding reporter gene which was a variant of green fluorescent protein. Two foldable fragments were identified for the SARS-CoV spike protein, which coincide with various anti-SARS peptides derived from the hepated repeat (HR) region 2 of the spike protein. The method should be applicable to other viral proteins to isolate antigen or vaccine candidates, thus providing an alternative to the full-length proteins (subunits) or linear short peptides.

  4. Isolation of the sex-associated fragments in the Chinese mitten crab(Eriocheir sinensis) using AFLP technique%利用AFLP方法筛选中华绒螯蟹性别相关标记

    Institute of Scientific and Technical Information of China (English)

    吕慧锋; 江学慧; 邱高峰

    2012-01-01

    利用AFLP(amplified fragment length polymorphism)技术筛选中华绒螯蟹性别相关标记,共使用192对引物组合检测中华绒螯蟹雌、雄和雌雄混合3个基因组池的多态性,共扩增出5 376条多态性条带,平均每对引物组合扩增出28条多态性条带,获得88条雌雄差异条带。利用雌雄各10个个体再次进行AFLP验证,共62条差异条带具有性别差异,包括两种情况:(1)有49条条带在雌性的4~6个个体中存在,在雄性全部个体中缺失;(2)有13条条带在雄性4~6个个体中存在,在所有的雌性个体中缺失;其余的26条没有性别差异性。差异条带经回收、克隆、测序,结果发现有些条带包含多个序列,共得到77条DNA序列,其中31条序列与鸟类、两栖类和哺乳类等脊椎动物性染色体DNA部分片段具有同源性,相似区间在22~212 bp不等,其中6条DNA序列与命中序列之间具有生物学相关性。设计特异性的引物在基因组中检测,没有获得性别特异SCAR标记。%In the present study,amplified fragment length polymorphism(AFLP) was used for the isolation of sex-associated markers in the genome of Chinese mitten crab,Eriocheir sinensis.By screening the male,female and male/female mix bulks with 192 selective AFLP primer combinations,we obtained 5 376 polymorphic fragments in total,each combination generated 28 fragments on average.A total of 88 sex difference AFLP candidates were retrieved.Subsequently,the candidates were further verified in 10 female and 10 male individuals by AFLP again.Sixty-two sex difference fragments were obtained finally,and they could be classified into two groups:(1) Thirteen bands were present in four to six male crabs and absent in all female crabs;(2) Forty-nine bands were present in four to six female crabs,but absent in all male crabs.No sex difference was found in the other 26 bands.The sex difference fragments were recovered,cloned and sequenced.The results showed

  5. Long Coherence Length 193 nm Laser for High-Resolution Nano-Fabrication

    Science.gov (United States)

    2008-06-27

    laser spectral bandwidth to coherence length and the measurement method used. A Michelson interferometer was used to directly measure the coherence...Using the SNLO non-linear optics modeling program and new fiber laser models both developed at Sandia National Labs, we were able to analyze pulsed and...scattering preclude pulsed fiber laser amplifiers from meeting our required power and coherence specifications. While CW fiber laser amplifiers are

  6. discouraged by queue length

    Directory of Open Access Journals (Sweden)

    P. R. Parthasarathy

    2001-01-01

    Full Text Available The transient solution is obtained analytically using continued fractions for a state-dependent birth-death queue in which potential customers are discouraged by the queue length. This queueing system is then compared with the well-known infinite server queueing system which has the same steady state solution as the model under consideration, whereas their transient solutions are different. A natural measure of speed of convergence of the mean number in the system to its stationarity is also computed.

  7. Driven fragmentation of granular gases.

    Science.gov (United States)

    Cruz Hidalgo, Raúl; Pagonabarraga, Ignacio

    2008-06-01

    The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the long velocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f(c) approximately exp(-cn) , with n approximately 1.2 , regarding less the fragmentation mechanisms.

  8. Transpermeance Amplifier Applied to Magnetic Bearings

    Directory of Open Access Journals (Sweden)

    Jossana Ferreira

    2017-02-01

    Full Text Available The most conventional approach of controlling magnetic forces in active magnetic bearings (AMBs is through current feedback amplifiers: transconductance. This enables the operation of the AMB to be understood in terms of a relatively simple current-based model as has been widely reported on in the literature. The alternative notion of using transpermeance amplifiers, which approximate the feedback of gap flux rather than current, has been in commercial use in some form for at least thirty years, however is only recently seeing more widespread acceptance as a commercial standard. This study explores how such alternative amplifiers should be modeled and then examines the differences in behavior between AMBs equipped with transconductance and transpermeance amplifiers. The focus of this study is on two aspects. The first is the influence of rotor displacement on AMB force, commonly modeled as a constant negative equivalent mechanical stiffness, and it is shown that either scheme actually leads to a finite bandwidth effect, but that this bandwidth is much lower when transpermeance is employed. The second aspect is the influence of eddy currents. Using a very simple model of eddy currents (a secondary short-circuited coil, it is demonstrated that transpermeance amplifiers can recover significant actuator bandwidth compared with transconductance, but at the cost of needing increased peak current headroom.

  9. High power, high beam quality regenerative amplifier

    Science.gov (United States)

    Hackel, L.A.; Dane, C.B.

    1993-08-24

    A regenerative laser amplifier system generates high peak power and high energy per pulse output beams enabling generation of X-rays used in X-ray lithography for manufacturing integrated circuits. The laser amplifier includes a ring shaped optical path with a limited number of components including a polarizer, a passive 90 degree phase rotator, a plurality of mirrors, a relay telescope, and a gain medium, the components being placed close to the image plane of the relay telescope to reduce diffraction or phase perturbations in order to limit high peak intensity spiking. In the ring, the beam makes two passes through the gain medium for each transit of the optical path to increase the amplifier gain to loss ratio. A beam input into the ring makes two passes around the ring, is diverted into an SBS phase conjugator and proceeds out of the SBS phase conjugator back through the ring in an equal but opposite direction for two passes, further reducing phase perturbations. A master oscillator inputs the beam through an isolation cell (Faraday or Pockels) which transmits the beam into the ring without polarization rotation. The isolation cell rotates polarization only in beams proceeding out of the ring to direct the beams out of the amplifier. The diffraction limited quality of the input beam is preserved in the amplifier so that a high power output beam having nearly the same diffraction limited quality is produced.

  10. The spectroscopy of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, W.R. [Department of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom); Collaboration: La Direction des Sciences de la Matiere du CEA (FR); Le Fonds National de la Recherche Scientifique de Belgique (BE)

    1998-12-31

    High-resolution measurements on {gamma} rays from fission fragments have provided a rich source of information, unobtainable at the moment in any other way, on the spectroscopy of neutron-rich nuclei. In recent years important data have been obtained on the yrast- and near yrast-structure of neutron-rich fission fragments. We discuss the scope of measurements which can be made on prompt gamma rays from secondary fission fragments, the techniques used in the experiments and some results recently obtained. (author) 24 refs., 8 figs., 1 tab.

  11. Transmission, reflection and localization of waves in one-dimensional amplifying media with nonlinear gain

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Ba Phi [Central University of Construction, Tuy Hoa (Viet Nam); Kim, Ki Hong [Ajou University, Suwon (Korea, Republic of)

    2014-06-15

    We study theoretically the influence of nonlinear gain effects on the transmission and the Anderson localization of waves in both uniform and random one-dimensional amplifying media by using the discrete nonlinear Schroedinger equation. In uniform amplifying media with nonlinear gain, we find that the strong oscillatory behavior of the transmittance and the reflectance for odd and even values of the sample length disappears for large nonlinearities. The exponential decay rate of the transmittance in the asymptotic limit is found to be independent of nonlinear gain. In random amplifying media, we find that the maximum values of the disorder-averaged logarithmic transmittance and reflectance depend nonmonotonically on the strength of nonlinear gain. We also find that the localization length is independent of nonlinear gain. In other words, the Anderson localization is neither enhanced nor weakened due to nonlinear gain. In both the uniform and the random cases, the crossover length, which is the critical length for the amplification to be efficient, is strongly reduced by the nonlinear nature of the gain.

  12. Determination of Arabidopsis thaliana telomere length by PCR.

    Science.gov (United States)

    Vaquero-Sedas, María I; Vega-Palas, Miguel A

    2014-07-02

    In humans, telomere length studies have acquired great relevance because the length of telomeres has been related to natural processes like disease, aging and cancer. However, very little is known about the influence of telomere length on the biology of wild type plants. The length of plant telomeres has been usually studied by Terminal Restriction Fragment (TRF) analyses. This technique requires high amounts of tissue, including multiple cell types, which might be the reason why very little is known about the influence of telomere length on plant natural processes. In contrast, many of the human telomere length studies have focused on homogenous cell populations. Most of these studies have been performed by PCR, using telomeric degenerated primers, which allow the determination of telomere length from small amounts of human cells. Here, we have adapted the human PCR procedure to analyze the length of Arabidopsis thaliana telomeres. This PCR approach will facilitate the analysis of telomere length from low amounts of tissue. We have used it to determine that CG and non CG DNA methylation positively regulates Arabidopsis telomere length.

  13. Spheromak reactor with poloidal flux-amplifying transformer

    Science.gov (United States)

    Furth, Harold P.; Janos, Alan C.; Uyama, Tadao; Yamada, Masaaki

    1987-01-01

    An inductive transformer in the form of a solenoidal coils aligned along the major axis of a flux core induces poloidal flux along the flux core's axis. The current in the solenoidal coil is then reversed resulting in a poloidal flux swing and the conversion of a portion of the poloidal flux to a toroidal flux in generating a spheromak plasma wherein equilibrium approaches a force-free, minimum Taylor state during plasma formation, independent of the initial conditions or details of the formation. The spheromak plasma is sustained with the Taylor state maintained by oscillating the currents in the poloidal and toroidal field coils within the plasma-forming flux core. The poloidal flux transformer may be used either as an amplifier stage in a moving plasma reactor scenario for initial production of a spheromak plasma or as a method for sustaining a stationary plasma and further heating it. The solenoidal coil embodiment of the poloidal flux transformer can alternately be used in combination with a center conductive cylinder aligned along the length and outside of the solenoidal coil. This poloidal flux-amplifying inductive transformer approach allows for a relaxation of demanding current carrying requirements on the spheromak reactor's flux core, reduces plasma contamination arising from high voltage electrode discharge, and improves the efficiency of poloidal flux injection.

  14. Performance Optimization of the Multi-Pumped Raman Optical Amplifier using MOICA

    Directory of Open Access Journals (Sweden)

    Mohsen Katebi Jahromi

    2016-08-01

    Full Text Available In order to achieve the best gain profile for multi pump distributed Raman amplifiers in Wavelength Division Multiplexing (WDM transmission systems, the power and wavelength of pumps, the type of pumping configuration and the number of pump signals are the most important factors. In this paper, using a Multi-Objective Imperialist Competition Optimization Algorithm (MOICA with lowest power consumption and lowest number of pumps, we propose the most uniform gain profile for two types of pumping configurations in S- band and compare the results. Considering the design conditions including the type of pumping configuration, fiber length, fiber type and number of pump signals and using the multi-objective algorithm, we propose a method which can be used to achieve a gain level in which the amplifier has the lowest power consumption and lowest gain ripple. According to this, we can design a powerful WDM transmission system by Distributed Raman Amplifier (DRA with a good performance and efficiency.

  15. The OPTHER Project: Progress toward the THz Amplifier

    DEFF Research Database (Denmark)

    Paoloni, C; Brunetti, F; Di Carlo, A

    2011-01-01

    This paper describes the status of the OPTHER (OPtically driven TeraHertz AmplifiERs) project and progress toward the THz amplifier realization. This project represents a considerable advancement in the field of high frequency amplification. The design and realization of a THz amplifier within th...

  16. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

    Science.gov (United States)

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C. T.; Shui, Lingling

    2017-01-01

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

  17. Computer-aided design of broad band reflection type amplifiers

    DEFF Research Database (Denmark)

    Hammershaimb, Edgar; Jeppesen, Palle; Schjær-Jacobsen, Hans

    1974-01-01

    . At the same time the impedance of unpackaged devices are obtained by on-line correction for the package parasitics. The microwave circuit chosen is a multiple slug coaxial cavity, that is modelled by sections of lossy transmission lines including step susceptances. The measured small signal impedance...... of the packaged TED's and the cavity model are used in a direct optimization procedure, in which the calculated minimum gain in the prescribed frequency range is progressively maximized by adjusting the lengths, characteristic impedances and positions of the slugs. The computed results are displayed...... on a datascreen, which allows for interactive programming. Comparisons of predicted amplifier performance for packaged and unpackaged devices form a basis for evaluating the possible degrading effect of package parasitics. The predictions of the computer-aided design are in good agreement with experimental...

  18. Amplifier Noise Based Optical Steganography with Coherent Detection

    Science.gov (United States)

    Wu, Ben; Chang, Matthew P.; Caldwell, Naomi R.; Caldwell, Myles E.; Prucnal, Paul R.

    2014-12-01

    We summarize the principle and experimental setup of optical steganography based on amplified spontaneous emission (ASE) noise. Using ASE noise as the signal carrier, optical steganography effectively hides a stealth channel in both the time domain and the frequency domain. Coherent detection is used at the receiver of the stealth channel. Because ASE noise has short coherence length and random phase, it only interferes with itself within a very short range. Coherent detection requires the stealth transmitter and stealth receiver to precisely match the optical delay,which generates a large key space for the stealth channel. Several methods to further improve optical steganography, signal to noise ratio, compatibility with the public channel, and applications of the stealth channel are also summarized in this review paper.

  19. Gender determination of the Linne's two-toed sloth (Choloepus didactylus) using SRY amplified from hair.

    Science.gov (United States)

    Murata, K; Masuda, R

    1996-12-01

    Polymerase chain reaction (PCR) amplification of a partial fragment of the sex determining region Y (SRY) gene was used for sexing a young Linne's two-toed sloth (Choloepus didactylus), a species in which gender determination from the external genitalia is difficult. DNA was extracted from hairs of a 5-month-old sloth as well as the dam and sire as external controls. A SRY fragment (216 bases) was PCR-amplified both from the offspring and the sire, but not amplified from the dam. The DNA sequence (166 bases without primers) of the sloth PCR product was determined and compared with SRY sequences of other mammals previously reported. High homology of their nucleotide (74.1-86.8%) and deduced amino acid (63.6-85.5%) sequences indicates that the PCR product of the sloth was amplified from a region of the SRY gene, and that SRY sequences are conserved throughout mammalian orders. From the result the sex of the young sloth was determined as a male. The PCR method using hairs for sexing the sloth provides an advantageous tool for captive propagation plan in zoos. To the authors' knowledge, no report regarding SRY sequences in the order Xenarthra (Edentata) has been published.

  20. Wideband pulse amplifiers for the NECTAr chip

    Science.gov (United States)

    Sanuy, A.; Delagnes, E.; Gascon, D.; Sieiro, X.; Bolmont, J.; Corona, P.; Feinstein, F.; Glicenstein, J.-F.; Naumann, C. L.; Nayman, P.; Ribó, M.; Tavernet, J.-P.; Toussenel, F.; Vincent, P.; Vorobiov, S.

    2012-12-01

    The NECTAr collaboration's FE option for the camera of the CTA is a 16 bits and 1-3 GS/s sampling chip based on analog memories including most of the readout functions. This works describes the input amplifiers of the NECTAr ASIC. A fully differential wideband amplifier, with voltage gain up to 20 V/V and a BW of 400 MHz. As it is impossible to design a fully differential OpAmp with an 8 GHz GBW product in a 0.35 CMOS technology, an alternative implementation based on HF linearized transconductors is explored. The output buffer is a class AB miller operational amplifier, with special non-linear current boost.