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Sample records for single pcr product

  1. Ligase-free subcloning: a versatile method to subclone polymerase chain reaction (PCR) products in a single day.

    Science.gov (United States)

    Shuldiner, A R; Tanner, K; Scott, L A; Moore, C A; Roth, J

    1991-04-01

    Often, it is convenient to subclone polymerase chain reaction (PCR) products into a plasmid vector for subsequent replication in bacteria, but conventional subcloning methods often fail. We report a rapid and versatile method to subclone PCR products directionally into a specific site of virtually any plasmid vector. The procedure requires only four primers, does not require DNA ligase, and may be accomplished in a single day. Ligase-free subcloning is performed by incorporating into the PCR primers sequences at the 5' ends that result in PCR products whose 3' ends are complementary to the 3' ends of the recipient linearized plasmid. The PCR product and the linearized plasmid are spliced together in a second PCR reaction in which Taq polymerase extends the complementary overlapping 3' ends (ligation by overlap extension). Denaturation followed by heterologous reannealing and cyclization results in a cyclic recombinant plasmid with two nicks that may be used directly to transform competent Escherichia coli. In our hands, ligase-free subcloning is rapid, and offers many advantages over existing strategies.

  2. Genetic control of conventional labeling through the bovine meat production chain by single nucleotide polymorphisms using real-time PCR.

    Science.gov (United States)

    Capoferri, Rossana; Bongioni, Graziella; Galli, Andrea; Aleandri, Riccardo

    2006-08-01

    Since January 2002, the European Union has adopted precise guidelines aimed at protecting the safety of meat and controlling the production chain. To this purpose, the conventional traceability of livestock and meat represents the main tool, but verification of traceability requires genetic support. At present, single nucleotide polymorphisms (SNPs) represent the most innovative molecular markers in genotyping studies. The aim of this study was to verify correct labeling in a bovine meat production chain by a real-time PCR protocol based on SNP analysis. Reference hair samples from 5,000 animals were randomly collected from 22 farms. Twelve hundred meat samples were collected at different steps of the bovine meat production chain. In particular, 1,000 meat samples were collected at the slaughterhouse and 200 samples from the same animals directly at the butcher's shop. The protocol was optimized and validated by testing a set of 16 SNP markers on 95 DNA samples from bovine sires of different breeds. Thereafter, the genotyping of 2,200 samples was conducted with a set of 12 selected SNPs to verify traceability of the meat production chain at three different stages: farm, slaughterhouse, and butcher's shop. Irregularities in conventional traceability were evidenced directly in 1.87% of the samples at the slaughterhouse. This percentage increased to 3.25% when sampling was conducted at the butcher's shop. This study demonstrates that despite the precautions adopted over the meat production chain, some critical points still exist that cause the loss of a correct association between registration numbers and samples.

  3. Detection of hybridization of single-strand DNA PCR products in temperature change process by a novel metal-clamping piezoelectric sensor.

    Science.gov (United States)

    Chen, Qinghai; Bian, Zhiheng; Hua, Xing; Yao, Chunyan; Wu, Wei; Zhang, Xue; Zhang, Bo; Huang, Junfu; Tang, Wanli; Fu, Weiling

    2010-05-15

    Oligonucleotide probes on the sensor surface can be hybridized with single-strand DNA (ssDNA) that is formed from PCR products in ice bath after degeneration. Thus, detection of PCR products by piezoelectric sensors requires the participation of ssDNA PCR products in ice bath. When PCR products in ice bath are added into the buffer of the sensor well at room temperature, there will be a temperature change process during mixing. However, it still remains unclear whether the temperature change affects the frequency baseline stability of the sensor and the result judgment, which is the basic condition for detecting hybridization of nucleic acid. In this study, we detected the hybridization of HPV PCR products during temperature change process by a self-designed adjustable metal-clamping piezoelectric sensor. The study mainly involves sensor adjustment, probe immobilization and ice bath sample addition (at different concentrations and different volumes). The response curve of basic frequency in temperature change process showed three stages, i.e., increase, decrease to baseline, and continuous decrease to stability. The early increase of frequency and duration of the time can reach 55+/-7.4 Hz and 39 min when 40 microL sample (0-1 degrees C) was added into 110 microL buffer (25 degrees C). The frequency increase effect caused by temperature difference at early stage depends on the volume ratio of two liquids and on the temperature difference. The results indicate that we should pay more attention to possibly small volume of PCR products in ice bath and minor temperature difference of two liquids in operation. 2010 Elsevier B.V. All rights reserved.

  4. Enhancement of PCR Detection Limit by Single-Tube Restriction Endonuclease-PCR (RE-PCR).

    Science.gov (United States)

    Datta, Sibnarayan; Budhauliya, Raghvendra; Chatterjee, Soumya; Vanlalhmuaka; Veer, Vijay; Chakravarty, Runu

    2016-06-01

    Polymerase chain reaction (PCR) is widely used in biological research and diagnostics because of its high sensitivity and specificity. However, the sensitivity of PCR is strongly influenced by topological characteristics of the template. Supercoiled templates are known to inhibit PCR, whereas linearized forms of the same supercoiled templates facilitate PCR. This study was conducted to compare the PCR efficiency of circular supercoiled DNA templates to their restriction endonuclease (RE)-mediated linearized forms. Additionally, we also evaluated the possibility of RE digestion of the circular supercoiled templates within the complete PCR buffer. Following a systematic approach, we demonstrated that circular supercoiled templates could be efficiently linearized by RE in the complete PCR buffer itself. This allowed linearization of circular supercoiled templates and their subsequent amplification in the PCR buffer in a single-tube format. Using this extremely simple RE-PCR approach, we documented up to tenfold increases in detection efficiency of PCR with two different circular supercoiled templates of clinical origin, including an international calibration standard. This inexpensive and easy approach to increasing PCR sensitivity can be easily adapted to any standard PCR protocol aimed at amplifying circular supercoiled genomes. Apart from its application in the development of sensitive clinical diagnostic PCR assays for a large number of organisms, this method could also prove to be very useful in simplifying the existing protocols for other applications where pre-PCR restriction digestion is required, such as mutation detection, genotyping, and selective template amplification.

  5. Heterozygote PCR product melting curve prediction.

    Science.gov (United States)

    Dwight, Zachary L; Palais, Robert; Kent, Jana; Wittwer, Carl T

    2014-03-01

    Melting curve prediction of PCR products is limited to perfectly complementary strands. Multiple domains are calculated by recursive nearest neighbor thermodynamics. However, the melting curve of an amplicon containing a heterozygous single-nucleotide variant (SNV) after PCR is the composite of four duplexes: two matched homoduplexes and two mismatched heteroduplexes. To better predict the shape of composite heterozygote melting curves, 52 experimental curves were compared with brute force in silico predictions varying two parameters simultaneously: the relative contribution of heteroduplex products and an ionic scaling factor for mismatched tetrads. Heteroduplex products contributed 25.7 ± 6.7% to the composite melting curve, varying from 23%-28% for different SNV classes. The effect of ions on mismatch tetrads scaled to 76%-96% of normal (depending on SNV class) and averaged 88 ± 16.4%. Based on uMelt (www.dna.utah.edu/umelt/umelt.html) with an expanded nearest neighbor thermodynamic set that includes mismatched base pairs, uMelt HETS calculates helicity as a function of temperature for homoduplex and heteroduplex products, as well as the composite curve expected from heterozygotes. It is an interactive Web tool for efficient genotyping design, heterozygote melting curve prediction, and quality control of melting curve experiments. The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/hets/. © 2013 WILEY PERIODICALS, INC.

  6. Single bovine sperm sex typing by amelogenin nested PCR.

    Science.gov (United States)

    Colley, A; Buhr, M; Golovan, S P

    2008-10-01

    Sex-sorted bovine semen has become a valuable tool in animal production for sex preselection. Development of novel sperm sexing technologies, or evaluation of the quality of existing methods, often requires a single-sperm, sex-typing method that is reliable and easy to perform. In the present study, we report the development, validation, and application of a simple, reliable, and cost-effective method for single-sperm sex typing using nested polymerase chain reaction (PCR), based on the amelogenin gene. Several hundred single sperm were isolated using a simple manual technique, or a high-speed flow-sorter, and were successfully sex-typed using the amelogenin nested PCR. Based on the pooled results of individual sperm, there was no significant difference in the semen sex ratio of unsorted (44.6% X-sperm and 55.4% Y-sperm) or X/Y-sorted semen (91.4% X-sperm and 94.0% Y-sperm), as compared to the expected ratio in unsorted semen or the post-sorting reanalysis data, respectively. The amelogenin single-sperm sexing method was an adaptable, accurate, and reliable tool for single-sperm sex typing.

  7. Comprehensive GMO detection using real-time PCR array: single-laboratory validation.

    Science.gov (United States)

    Mano, Junichi; Harada, Mioko; Takabatake, Reona; Furui, Satoshi; Kitta, Kazumi; Nakamura, Kosuke; Akiyama, Hiroshi; Teshima, Reiko; Noritake, Hiromichi; Hatano, Shuko; Futo, Satoshi; Minegishi, Yasutaka; Iizuka, Tayoshi

    2012-01-01

    We have developed a real-time PCR array method to comprehensively detect genetically modified (GM) organisms. In the method, genomic DNA extracted from an agricultural product is analyzed using various qualitative real-time PCR assays on a 96-well PCR plate, targeting for individual GM events, recombinant DNA (r-DNA) segments, taxon-specific DNAs, and donor organisms of the respective r-DNAs. In this article, we report the single-laboratory validation of both DNA extraction methods and component PCR assays constituting the real-time PCR array. We selected some DNA extraction methods for specified plant matrixes, i.e., maize flour, soybean flour, and ground canola seeds, then evaluated the DNA quantity, DNA fragmentation, and PCR inhibition of the resultant DNA extracts. For the component PCR assays, we evaluated the specificity and LOD. All DNA extraction methods and component PCR assays satisfied the criteria set on the basis of previous reports.

  8. Use PCR and a Single Hair To Produce a "DNA Fingerprint."

    Science.gov (United States)

    Campbell, A. Malcolm; And Others

    1997-01-01

    Presents a laboratory procedure that involves students extracting their own DNA from a single hair follicle, using the polymerase chain reaction (PCR) to amplify a polymorphic locus, performing electrophoresis on the PCR products on an agarose gel, and visualizing the alleles to generate a "DNA fingerprint." Discusses theoretical background,…

  9. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...

  10. Examining Sources of Error in PCR by Single-Molecule Sequencing

    Science.gov (United States)

    Potapov, Vladimir

    2017-01-01

    Next-generation sequencing technology has enabled the detection of rare genetic or somatic mutations and contributed to our understanding of disease progression and evolution. However, many next-generation sequencing technologies first rely on DNA amplification, via the Polymerase Chain Reaction (PCR), as part of sample preparation workflows. Mistakes made during PCR appear in sequencing data and contribute to false mutations that can ultimately confound genetic analysis. In this report, a single-molecule sequencing assay was used to comprehensively catalog the different types of errors introduced during PCR, including polymerase misincorporation, structure-induced template-switching, PCR-mediated recombination and DNA damage. In addition to well-characterized polymerase base substitution errors, other sources of error were found to be equally prevalent. PCR-mediated recombination by Taq polymerase was observed at the single-molecule level, and surprisingly found to occur as frequently as polymerase base substitution errors, suggesting it may be an underappreciated source of error for multiplex amplification reactions. Inverted repeat structural elements in lacZ caused polymerase template-switching between the top and bottom strands during replication and the frequency of these events were measured for different polymerases. For very accurate polymerases, DNA damage introduced during temperature cycling, and not polymerase base substitution errors, appeared to be the major contributor toward mutations occurring in amplification products. In total, we analyzed PCR products at the single-molecule level and present here a more complete picture of the types of mistakes that occur during DNA amplification. PMID:28060945

  11. Development of a reference material of a single DNA molecule for the quality control of PCR testing.

    Science.gov (United States)

    Mano, Junichi; Hatano, Shuko; Futo, Satoshi; Yoshii, Junji; Nakae, Hiroki; Naito, Shigehiro; Takabatake, Reona; Kitta, Kazumi

    2014-09-02

    We developed a reference material of a single DNA molecule with a specific nucleotide sequence. The double-strand linear DNA which has PCR target sequences at the both ends was prepared as a reference DNA molecule, and we named the PCR targets on each side as confirmation sequence and standard sequence. The highly diluted solution of the reference molecule was dispensed into 96 wells of a plastic PCR plate to make the average number of molecules in a well below one. Subsequently, the presence or absence of the reference molecule in each well was checked by real-time PCR targeting for the confirmation sequence. After an enzymatic treatment of the reaction mixture in the positive wells for the digestion of PCR products, the resultant solution was used as the reference material of a single DNA molecule with the standard sequence. PCR analyses revealed that the prepared samples included only one reference molecule with high probability. The single-molecule reference material developed in this study will be useful for the absolute evaluation of a detection limit of PCR-based testing methods, the quality control of PCR analyses, performance evaluations of PCR reagents and instruments, and the preparation of an accurate calibration curve for real-time PCR quantitation.

  12. Species identification and quantification in meat and meat products using droplet digital PCR (ddPCR).

    Science.gov (United States)

    Floren, C; Wiedemann, I; Brenig, B; Schütz, E; Beck, J

    2015-04-15

    Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Removal of PCR error products and unincorporated primers by metal-chelate affinity chromatography.

    Directory of Open Access Journals (Sweden)

    Indhu Kanakaraj

    Full Text Available Immobilized Metal Affinity Chromatography (IMAC has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and "histidine tags" genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu(2+-iminodiacetic acid (IDA agarose spin column, 94-99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu(2+-IDA agarose can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs.

  14. Detection of Brucella melitensis and Brucella abortus strains using a single-stage PCR method

    Directory of Open Access Journals (Sweden)

    Alamian, S.

    2015-04-01

    Full Text Available Brucella melitensis and Brucella abortus are of the most important causes of brucellosis, an infectious disease which is transmitted either directly or indirectly including consuming unpasteurized dairy products. Both strains are considered endemic in Iran. Common diagnostic methods such as bacteriologic cultures are difficult and time consuming regarding the bacteria. The aim of this study was to suggest a single-stage PCR method using a pair of primers to detect both B. melitensis and B. abortus. The primers were named UF1 and UR1 and the results showed that the final size of PCR products were 84 bp and 99 bp for B. melitensis and B. abortus, respectively. Therefore the method could be useful for rapid detection of B. melitensis and B. abortus simultaneously.

  15. Sensitive simultaneous detection of seven sexually transmitted agents in semen by multiplex-PCR and of HPV by single PCR.

    Directory of Open Access Journals (Sweden)

    Fabrícia Gimenes

    Full Text Available Sexually transmitted diseases (STDs may impair sperm parameters and functions thereby promoting male infertility. To date limited molecular studies were conducted to evaluate the frequency and type of such infections in semen Thus, we aimed at conceiving and validating a multiplex PCR (M-PCR assay for the simultaneous detection of the following STD pathogens in semen: Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Trichomonas vaginalis, Herpes virus simplex (HSV -1 and -2, and Treponema pallidum; We also investigated the potential usefulness of this M-PCR assay in screening programs for semen pathogens. In addition, we aimed: to detect human Papillomavirus (HPV and genotypes by single PCR (sPCR in the same semen samples; to determine the prevalence of the seven STDs, HPV and co-infections; to assess the possibility that these infections affect semen parameters and thus fertility. The overall validation parameters of M-PCR were extremely high including agreement (99.2%, sensitivity (100.00%, specificity (99.70%, positive (96.40% and negative predictive values (100.00% and accuracy (99.80%. The prevalence of STDs was very high (55.3%. Furthermore, associations were observed between STDs and changes in semen parameters, highlighting the importance of STD detection in semen. Thus, this M-PCR assay has great potential for application in semen screening programs for pathogens in infertility and STD clinics and in sperm banks.

  16. Single-step blood direct PCR: A robust and rapid method to diagnose triplet repeat disorders.

    Science.gov (United States)

    Singh, Inder; Swarup, Vishnu; Shakya, Sunil; Goyal, Vinay; Faruq, Mohammed; Srivastava, Achal Kumar

    2017-08-15

    DNA extraction prior to polymerase chain reaction (PCR) amplification in genetic diagnoses of triplet repeat disorders (TRDs) is tedious and labour-intensive and has the limitations of sample contamination with foreign DNA, including that from preceding samples. Therefore, we aimed to develop a rapid, robust, and cost-effective method for expeditious genetic investigation of TRDs from whole blood as a DNA template. Peripheral blood samples were collected from 70 clinically suspected patients of progressive ataxia. The conventional method using genomic DNA and single-step Blood-Direct PCR (BD-PCR) method with just 2μl of whole blood sample were tested to amplify triplet repeat expansion in genes related to spinocerebellar ataxia (SCA) types 1, 2, 3, 12 and Friedreich's ataxia (FRDA). Post-PCR, the allele sizes were mapped and repeat numbers were calculated using GeneMapper and macros run in Microsoft Excel programmes. Successful amplification of target regions was achieved in all samples by both methods. The frequency of the normal and mutated allele was concordant between both methods, diagnosing 37% positive for a mutation in either of the candidate genes. The BD-PCR resulted in higher intensities of product peaks of normal and pathogenic alleles. The nearly-accurate sizing of the normal and expanded allele was achieved in a shorter time (4-5h), without DNA extraction and any risk of cross contamination, which suggests the BD-PCR to be a reliable, inexpensive, and rapid method to confirm TRDs. This technique can be introduced in routine diagnostic procedures of other tandem repeat disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. PCR

    African Journals Online (AJOL)

    Jane

    2011-07-11

    Jul 11, 2011 ... then in age group 31 to 40 years, 2.25% (2/89) CMV DNA were detected by PCR and 0% was recorded in age group of above 40 years. The overall prevalence of human cytomegalovirus (HCMV) infection in 16 ..... genome revisited: Comparison with the chimpanzee cytomegalovirus genome. J. Gen. Virol.

  18. Simple and fast multiplex PCR method for detection of species origin in meat products.

    Science.gov (United States)

    Izadpanah, Mehrnaz; Mohebali, Nazanin; Elyasi Gorji, Zahra; Farzaneh, Parvaneh; Vakhshiteh, Faezeh; Shahzadeh Fazeli, Seyed Abolhassan

    2018-02-01

    Identification of animal species is one of the major concerns in food regulatory control and quality assurance system. Different approaches have been used for species identification in animal origin of feedstuff. This study aimed to develop a multiplex PCR approach to detect the origin of meat and meat products. Specific primers were designed based on the conserved region of mitochondrial Cytochrome C Oxidase subunit I ( COX1 ) gene. This method could successfully distinguish the origin of the pig, camel, sheep, donkey, goat, cow, and chicken in one single reaction. Since PCR products derived from each species represent unique molecular weight, the amplified products could be identified by electrophoresis and analyzed based on their size. Due to the synchronized amplification of segments within a single PCR reaction, multiplex PCR is considered to be a simple, fast, and inexpensive technique that can be applied for identification of meat products in food industries. Nowadays, this technique has been considered as a practical method to identify the species origin, which could further applied for animal feedstuffs identification.

  19. A novel and highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus.

    Science.gov (United States)

    Shen, Xin-Xin; Qiu, Fang-Zhou; Zhao, Huai-Long; Yang, Meng-Jie; Hong, Liu; Xu, Song-Tao; Zhou, Shuai-Feng; Li, Gui-Xia; Feng, Zhi-Shan; Ma, Xue-Jun

    2018-03-01

    The sensitivity of qRT-PCR assay is not adequate for the detection of the samples with lower viral load, particularly in the cerebrospinal fluid (CSF) of patients. Here, we present the development of a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of human enterovirus (HEV). The clinical performance of both RTN RT-PCR and qRT-PCR was also tested and compared using 140 CSF and fecal specimens. The sensitivities of RTN RT-PCR assay for EV71, Coxsackievirus A (CVA)16, CVA6 and CVA10 achieved 10 -8 dilution with a corresponding Ct value of 38.20, 36.45, 36.75, and 36.45, respectively, which is equal to traditional two-step nested RT-PCR assay and approximately 2-10-fold lower than that of qRT-PCR assay. The specificity of RTN RT-PCR assay was extensively analyzed insilico and subsequently verified using the reference isolates and clinical samples. Sixteen qRT-PCR-negative samples were detected by RTN RT-PCR and a variety of enterovirus serotypes was identified by sequencing of inner PCR products. We conclude RTN RT-PCR is more sensitive than qRT-PCR for the detection of HEV in clinical samples. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Cloning flanking sequence by single-primer PCR in transgenic plants.

    Science.gov (United States)

    Ma, J; Wang, Y P; Ren, S; Zhang, Z; Lu, S; Wang, P W

    2014-10-20

    The insertion position of exogenous genes in plant genomes is usually identified by adapter ligation-mediated polymerase chain reaction (PCR), thermal asymmetric interlaced PCR, and restriction site extension PCR in transgenic plant research. However, these methods have various limitations, such as the complexity of designing primers and time-consuming and multiple-step procedures. The goal of this study was to establish an easier, more rapid, and more accurate method to clone flanking sequence using single-primer PCR in transgenic plants. Unknown flanking genome sequences in transgenic plants, including those in tobacco, soybean, rice, and maize, were cloned using the single-primer PCR method established in this study, with the Bar gene as the anchor gene. The primer 1 (P1), P2, and P3 PCRs obtained 4 sequences, and the completely correct flanking sequence of 508 bp that was obtained in the P3 PCR was verified by sequencing analysis. The single-primer PCR is more rapid and accurate than conventional methods, justifying its application widely in cloning flanking sequences in transgenic plants.

  1. Purification of nanoparticle PCR products and their topography observed with AFM

    International Nuclear Information System (INIS)

    Mi Lijuan; Wang Hubin; Chinese Academy of Sciences, Beijing; Li Bin; Zhou Hualan; Hu Jun

    2007-01-01

    Nanoparticle PCR (NP-PCR) is a new method to optimize PCR amplification. Suitable amount of Au nanoparticles can improve specificity, sensitivity and extension rate of PCR. In this paper, we compare efficiency of purifying NP-PCR products with different methods. In addition, topographies of DNA products in NP-PCR were observed with atomic force microscope (AFM). The results show that most of DNA products purified directly by routing method remain almost free due to less effect of nanoparticales. The yields decrease when the AuNPs were removed by high-speed centrifugation. A little amount of DNA subsided with AuNPs. (authors)

  2. PCR amplification of microsatellites from single cells of Karenia brevis preserved in Lugol's iodine solution.

    Science.gov (United States)

    Henrichs, D W; Renshaw, M A; Santamaria, C A; Richardson, B; Gold, J R; Campbell, L

    2008-01-01

    A simple and effective protocol is described for multiplex polymerase chain reaction (PCR) amplification of single cells of Karenia brevis. The protocol requires minimum processing, avoids additions that might dilute target DNA template, and can be used on cells preserved in Lugol's iodine preservative. Destaining of Lugol's-preserved cells with sodium thiosulfate allowed successful amplification of single-copy, nuclear-encoded microsatellites in single cells of K. brevis that have been preserved for up to 6 years.

  3. Detection of fowl adenovirus DNA from formalin-fixed and paraffin-embedded sections by PCR and classification of serotypes by sequencing of PCR products.

    Science.gov (United States)

    Ohizumi, Takuya; Nakamura, Kikuyasu; Yamamoto, Yu; Mase, Masaji; Yamada, Manabu

    2012-12-01

    Detection of fowl adenovirus (FAV) DNA from formalin-fixed and paraffin-embedded (FFPE) sections was attempted by PCR. Serotypes of FAV were classified by sequencing the PCR products. In trials of PCR using a positive control infected with serotype 2 FAV, the best primer set was 57F forward primer (5'-CAARTTCAGRCAGACGGT-3') and 26R reverse primer (5'-GGCTTGACGTACGCTCCGTA-3'). A second PCR with the same primer set revealed a clearer band in the electrophoresis of generated PCR products. Generated PCR products were confirmed to be derived from infected FAV. In addition, PCR and sequencing of PCR products of the liver FFPE sections, from two natural inclusion body hepatitis cases that were not examined for virologic isolation, suggested that the detected FAV was serotype 8a. The PCR of FFPE sections, and serotyping by the sequencing of PCR products, are useful for diagnosis and epidemiologic analysis of FAV infections.

  4. Detecting the Presence of Nora Virus in "Drosophila" Utilizing Single Fly RT-PCR

    Science.gov (United States)

    Munn, Bethany; Ericson, Brad; Carlson, Darby J.; Carlson, Kimberly A.

    2015-01-01

    A single fly RT-PCR protocol has recently been developed to detect the presence of the persistent, horizontally transmitted Nora virus in "Drosophila." Wild-caught flies from Ohio were tested for the presence of the virus, with nearly one-fifth testing positive. The investigation presented can serve as an ideal project for biology…

  5. RT-qPCR work-flow for single-cell data analysis

    Czech Academy of Sciences Publication Activity Database

    Stahlberg, A.; Rusňáková, Vendula; Forootan, A.; Anděrová, Miroslava; Kubista, Mikael

    2013-01-01

    Roč. 59, č. 1 (2013), s. 80-88 ISSN 1046-2023 R&D Projects: GA MŠk(CZ) ME10052; GA ČR GAP303/10/1338 Institutional research plan: CEZ:AV0Z50520701 Institutional support: RVO:68378041 Keywords : RT-qPCR * Single-cell biology * Single-cell data analysis Subject RIV: EB - Genetics ; Molecular Biology; FH - Neurology (UEM-P) Impact factor: 3.221, year: 2013

  6. Flow-through PCR on a 3D qiandu-shaped polydimethylsiloxane (PDMS) microdevice employing a single heater: toward microscale multiplex PCR.

    Science.gov (United States)

    Wu, Wenming; Loan, Kieu The Loan; Lee, Nae Yoon

    2012-05-07

    Consistent temperature control in an on-chip flow-through polymerase chain reaction (PCR) employing two or more heaters is one of the main obstacles for device miniaturization and integration when realizing micro total analysis systems (μTAS), and also leads to operational complexity. In this study, we propose a qiandu (right triangular prism)-shaped polydimethylsiloxane (PDMS) microdevice with serpentine microchannels fabricated on its slanted plane, and apply the device for an on-chip flow-through PCR employing a single heater. The inclined nature of the qiandu-shaped microdevice enables the formation of a surface temperature gradient along the slanted plane of the microdevice in a height-dependent manner by the use of a single heater, and enables liquid to traverse over wide ranges of temperatures, including the three temperature zones--denaturation, annealing, and extension temperatures--required in a typical PCR. The feasibility of the qiandu-shaped PDMS microdevice as a versatile platform for performing a flow-through PCR was examined by employing multiple templates and varying the inclination angle of the device. In addition, the potential of performing a multiplex PCR using a single qiandu-shaped PDMS microdevice was explored. A 409 bp long gene fragment effective as a marker for diagnosing lung cancer and a 230 bp long gene fragment from a plasmid vector were simultaneously amplified in less than 25 min on a single microdevice, paving the way for a microscale, multiplex PCR on a single device employing a single heater.

  7. Detection of mandarin in orange juice by single-nucleotide polymorphism qPCR assay.

    Science.gov (United States)

    Aldeguer, Miriam; López-Andreo, María; Gabaldón, José A; Puyet, Antonio

    2014-02-15

    A dual-probe real time PCR (qPCR) DNA-based analysis was devised for the identification of mandarin in orange juice. A single nucleotide polymorphism at the trnL-trnF intergenic region of the chloroplast chromosome was confirmed in nine orange (Citrus sinensis) and thirteen commercial varieties of mandarin, including Citrus reticulata and Citrus unshiu species and a mandarin × tangelo hybrid. Two short minor-groove binding fluorescent probes targeting the polymorphic sequence were used in the dual-probe qPCR, which allowed the detection of both species in single-tube reactions. The similarity of PCR efficiencies allowed a simple estimation of the ratio mandarin/orange in the juice samples, which correlated to the measured difference of threshold cycle values for both probes. The limit of detection of the assay was 5% of mandarin in orange juice, both when the juice was freshly prepared (not from concentrate) or reconstituted from concentrate, which would allow the detection of fraudulently added mandarin juice. The possible use of the dual-probe system for quantitative measurements was also tested on fruit juice mixtures. qPCR data obtained from samples containing equal amounts of mandarin and orange juice revealed that the mandarin target copy number was approximately 2.6-fold higher than in orange juice. The use of a matrix-adapted control as calibrator to compensate the resulting C(T) bias allowed accurate quantitative measurements to be obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. A multiplex PCR mini-barcode assay to identify processed shark products in the global trade.

    Directory of Open Access Journals (Sweden)

    Diego Cardeñosa

    Full Text Available Protecting sharks from overexploitation has become global priority after widespread population declines have occurred. Tracking catches and trade on a species-specific basis has proven challenging, in part due to difficulties in identifying processed shark products such as fins, meat, and liver oil. This has hindered efforts to implement regulations aimed at promoting sustainable use of commercially important species and protection of imperiled species. Genetic approaches to identify shark products exist but are typically based on sequencing or amplifying large DNA regions and may fail to work on heavily processed products in which DNA is degraded. Here, we describe a novel multiplex PCR mini-barcode assay based on two short fragments of the cytochrome oxidase I (COI gene. This assay can identify to species all sharks currently listed on the Convention of International Trade of Endangered Species (CITES and most shark species present in the international trade. It achieves species diagnosis based on a single PCR and one to two downstream DNA sequencing reactions. The assay is capable of identifying highly processed shark products including fins, cooked shark fin soup, and skin-care products containing liver oil. This is a straightforward and reliable identification method for data collection and enforcement of regulations implemented for certain species at all governance levels.

  9. Development of single step RT-PCR for detection of Kyasanur forest disease virus from clinical samples

    Directory of Open Access Journals (Sweden)

    Gouri Chaubal

    2018-02-01

    Discussion and conclusion: The previously published sensitive real time RT-PCR assay requires higher cost in terms of reagents and machine setup and technical expertise has been the primary reason for development of this assay. A single step RT-PCR is relatively easy to perform and more cost effective than real time RT-PCR in smaller setups in the absence of Biosafety Level-3 facility. This study reports the development and optimization of single step RT-PCR assay which is more sensitive and less time-consuming than nested RT-PCR and cost effective for rapid diagnosis of KFD viral RNA.

  10. Ion pair-reversed phase HPLC approach facilitates subcloning of PCR products and screening of recombinant colonies.

    Science.gov (United States)

    Shaw-Bruha, C M; Lamb, K A

    2000-04-01

    The isolation of a single DNA molecule for cloning is technically difficult, and the subsequent screening of colonies for recombinant DNA clones is time consuming. Ion pair-reversed phase HPLC (IP-RP-HPLC) analysis of nucleic acids improves the resolution and isolation of PCR products to be cloned. We demonstrate that PCR products analyzed and collected using the IP-RP-HPLC approach (WAVE DNA Fragment Analysis System) can be cloned directly into a plasmid vector. In addition, we demonstrate that when IP-RP-HPLC analysis is extended to the colony screening process, the time required for these procedures is reduced.

  11. ddpcRquant: threshold determination for single channel droplet digital PCR experiments.

    Science.gov (United States)

    Trypsteen, Wim; Vynck, Matthijs; De Neve, Jan; Bonczkowski, Pawel; Kiselinova, Maja; Malatinkova, Eva; Vervisch, Karen; Thas, Olivier; Vandekerckhove, Linos; De Spiegelaere, Ward

    2015-07-01

    Digital PCR is rapidly gaining interest in the field of molecular biology for absolute quantification of nucleic acids. However, the first generation of platforms still needs careful validation and requires a specific methodology for data analysis to distinguish negative from positive signals by defining a threshold value. The currently described methods to assess droplet digital PCR (ddPCR) are based on an underlying assumption that the fluorescent signal of droplets is normally distributed. We show that this normality assumption does not likely hold true for most ddPCR runs, resulting in an erroneous threshold. We suggest a methodology that does not make any assumptions about the distribution of the fluorescence readouts. A threshold is estimated by modelling the extreme values in the negative droplet population using extreme value theory. Furthermore, the method takes shifts in baseline fluorescence between samples into account. An R implementation of our method is available, allowing automated threshold determination for absolute ddPCR quantification using a single fluorescent reporter.

  12. Single-tube nested PCR for detection of tritrichomonas foetus in feline feces.

    Science.gov (United States)

    Gookin, Jody L; Birkenheuer, Adam J; Breitschwerdt, Edward B; Levy, Michael G

    2002-11-01

    Tritrichomonas foetus, a venereal pathogen of cattle, was recently identified as an inhabitant of the large intestine in young domestic cats with chronic diarrhea. Recognition of the infection in cats has been mired by unfamiliarity with T. foetus in cats as well as misdiagnosis of the organisms as Pentatrichomonas hominis or Giardia sp. when visualized by light microscopy. The diagnosis of T. foetus presently depends on the demonstration of live organisms by direct microscopic examination of fresh feces or by fecal culturing. As T. foetus organisms are fastidious and fragile, routine flotation techniques and delayed examination and refrigeration of feces are anticipated to preclude the diagnosis in numerous cases. The objective of this study was to develop a sensitive and specific PCR test for the diagnosis of feline T. foetus infection. A single-tube nested PCR was designed and optimized for the detection of T. foetus in feline feces by using a combination of novel (TFITS-F and TFITS-R) and previously described (TFR3 and TFR4) primers. The PCR is based on the amplification of a conserved portion of the T. foetus internal transcribed spacer (ITS) region (ITS1 and ITS2) and the 5.8S rRNA gene. The absolute detection limit of the single-tube nested PCR was 1 organism, while the practical detection limit was 10 organisms per 200 mg of feces. Specificity was examined by using P. hominis, Giardia lamblia, and feline genomic DNA. Our results demonstrate that the single-tube nested PCR is ideally suited for (i) diagnostic testing of feline fecal samples that are found negative by direct microscopy and culturing and (ii) definitive identification of microscopically observable or cultivated organisms.

  13. The workflow of single-cell expression profiling using quantitative real-time PCR

    Czech Academy of Sciences Publication Activity Database

    Stahlberg, A.; Kubista, Mikael

    2014-01-01

    Roč. 14, č. 3 (2014), s. 323-331 ISSN 1473-7159 R&D Projects: GA ČR GA13-02154S; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : single-cell workflow * gene expression profiling * RT-qPCR Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.516, year: 2014

  14. Single-cell qPCR on dispersed primary pituitary cells -an optimized protocol

    Directory of Open Access Journals (Sweden)

    Haug Trude M

    2010-11-01

    Full Text Available Abstract Background The incidence of false positives is a potential problem in single-cell PCR experiments. This paper describes an optimized protocol for single-cell qPCR measurements in primary pituitary cell cultures following patch-clamp recordings. Two different cell harvesting methods were assessed using both the GH4 prolactin producing cell line from rat, and primary cell culture from fish pituitaries. Results Harvesting whole cells followed by cell lysis and qPCR performed satisfactory on the GH4 cell line. However, harvesting of whole cells from primary pituitary cultures regularly produced false positives, probably due to RNA leakage from cells ruptured during the dispersion of the pituitary cells. To reduce RNA contamination affecting the results, we optimized the conditions by harvesting only the cytosol through a patch pipette, subsequent to electrophysiological experiments. Two important factors proved crucial for reliable harvesting. First, silanizing the patch pipette glass prevented foreign extracellular RNA from attaching to charged residues on the glass surface. Second, substituting the commonly used perforating antibiotic amphotericin B with β-escin allowed efficient cytosol harvest without loosing the giga seal. Importantly, the two harvesting protocols revealed no difference in RNA isolation efficiency. Conclusion Depending on the cell type and preparation, validation of the harvesting technique is extremely important as contaminations may give false positives. Here we present an optimized protocol allowing secure harvesting of RNA from single cells in primary pituitary cell culture following perforated whole cell patch clamp experiments.

  15. Prevalence of tick-borne haemoparasites in small ruminants in Turkey and diagnostic sensitivity of single-PCR and RLB.

    Science.gov (United States)

    Bilgic, Huseyin Bilgin; Bakırcı, Serkan; Kose, Onur; Unlu, Ahmet Hakan; Hacılarlıoglu, Selin; Eren, Hasan; Weir, William; Karagenc, Tulin

    2017-04-27

    Tick-borne haemoparasitic diseases (TBHDs), caused by Theileria, Babesia, Anaplasma and Ehrlichia, are common in regions of the world where the distributions of host, pathogen and vector overlap. Many of these diseases threaten livestock production and some also represent a concern to human public health. The primary aim of this study was to determine the prevalence of the above-mentioned pathogens in a large number of blood samples (n = 1979) collected from sheep (n = 1727) and goats (n = 252) in Turkey. A secondary aim was to assess the diagnostic sensitivity of a number of species-specific polymerase chain reaction (PCR) tests and the reverse line blotting (RLB) assay. DNA samples were screened using species-specific PCR for the presence of Theileria ovis, Theileria sp. MK, T. lestoquardi, T. uilenbergi, T. luwenshuni, Babesia ovis, Anaplasma ovis and A. phagocytophilum while RLB was undertaken to test for the presence of all known Theileria, Babesia, Anaplasma and Ehrlichia species. The diagnostic sensitivity of these two approaches was then compared in terms of their ability to detect single species and mixed infections. Overall, 84 and 74.43% of the small ruminants sampled were identified as hosting one or more pathogen(s) by species-specific PCR and RLB respectively. The presence of Theileria sp. OT1, T. luwenshuni and T. uilenbergi in Turkey was revealed for the first time while the presence of Babesia motasi, B. crassa and T. separata in Turkish small ruminants was confirmed using molecular methods. A high prevalence of mixed infection was evident, with PCR and RLB approaches indicating that 52.24 and 35.42% of animals were co-infected with multiple species, respectively. More than 80% of the mixed infections contained T. ovis and/or A. ovis. The RLB approach was found to be capable of detecting mixed infections with species such as Theileria sp. OT1, Theileria sp. OT3, T. separata, B. crassa and Babesia spp. The results indicated that

  16. Single cell PCR amplification of diatoms using fresh and preserved samples

    Science.gov (United States)

    Hamilton, Paul B.; Lefebvre, Keely E.; Bull, Roger D.

    2015-01-01

    Single cell Chelex® DNA extraction and nested PCR amplification were used to examine partial gene sequences from natural diatom populations for taxonomic and phylogenetic studies at and above the level of species. DNA was extracted from cells that were either fresh collected or stored in RNAlater. Extractions from Lugol's fixation were also attempted with limited success. Three partial gene sequences (rbcL, 18S, and psbA) were recovered using existing and new primers with a nested or double nested PCR approach with amplification and success rates between 70 and 96%. An rbcL consensus tree grouped morphologically similar specimens and was consistent across the two primary sample treatments: fresh and RNAlater. This tool will greatly enhance the number of microscopic diatom taxa (and potentially other microbes) available for barcoding and phylogenetic studies. The near-term increase in sequence data for diatoms generated via routine single cell extractions and PCR will act as a multiproxy validation of longer-term next generation genomics. PMID:26528252

  17. Scarless and sequential gene modification in Pseudomonas using PCR product flanked by short homology regions

    Directory of Open Access Journals (Sweden)

    Liang Rubing

    2010-08-01

    Full Text Available Abstract Background The lambda Red recombination system has been used to inactivate chromosomal genes in various bacteria and fungi. The procedure consists of electroporating a polymerase chain reaction (PCR fragment containing antibiotic cassette flanked by homology regions to the target locus into a strain that can express the lambda Red proteins (Gam, Bet, Exo. Results Here a scarless gene modification strategy based on the Red recombination system has been developed to modify Pseudomonas genome DNA via sequential deletion of multiple targets. This process was mediated by plasmid pRKaraRed encoding the Red proteins regulated by PBAD promoter, which was functional in P. aeruginosa as well as in other bacteria. First the target gene was substituted for the sacB-bla cassette flanked by short homology regions (50 bp, and then this marker gene cassette could be replaced by the PCR fragment flanking itself, generating target-deleted genome without any remnants and no change happened to the surrounding region. Twenty genes involved in the synthesis and regulation pathways of the phenazine derivate, pyocyanin, were modified, including one single-point mutation and deletion of two large operons. The recombination efficiencies ranged from 88% to 98%. Multiple-gene modification was also achieved, generating a triple-gene deletion strain PCA (PAO1, ΔphzHΔphzMΔphzS, which could produce another phenazine derivate, phenazine-1-carboxylic acid (PCA, efficiently and exclusively. Conclusions This lambda Red-based technique can be used to generate scarless and sequential gene modification mutants of P. aeruginosa efficiently, using one-step PCR product flanked by short homology regions. Single-point mutation, scarless deletion of genes can be achieved easily in less than three days. This method may give a new way to construct genetically modified P. aeruginosa strains more efficiently and advance the regulatory network study of this organism.

  18. Single top quark production with CMS

    Directory of Open Access Journals (Sweden)

    Piccolo Davide

    2013-11-01

    Full Text Available Measurements of single top quark production performed using the CMS experiment [1] data collected in 2011 at centre-of-mass energies of 7 TeV and in 2012 at 8 TeV, are presented. The cross sections for the electroweak production of single top quarks in the t-channel and in association with W-bosons is measured and the results are used to place constraints on the CKM matrix element Vtb. Measurements of top quark properties in single top quark production are also presented. The results include the measurement of the charge ratio in the single top t-channel.

  19. Search for Single Top Production at LEP

    CERN Document Server

    Achard, P; Aguilar-Benítez, M; Alcaraz, J; Alemanni, G; Allaby, James V; Aloisio, A; Alviggi, M G; Anderhub, H; Andreev, V P; Anselmo, F; Arefev, A; Azemoon, T; Aziz, T; Bagnaia, P; Bajo, A; Baksay, G; Baksay, L; Baldew, S V; Banerjee, S; Banerjee, Sw; Barczyk, A; Barillère, R; Bartalini, P; Basile, M; Batalova, N; Battiston, R; Bay, A; Becattini, F; Becker, U; Behner, F; Bellucci, L; Berbeco, R; Berdugo, J; Berges, P; Bertucci, B; Betev, B L; Biasini, M; Biglietti, M; Biland, A; Blaising, J J; Blyth, S C; Bobbink, Gerjan J; Böhm, A; Boldizsar, L; Borgia, B; Bottai, S; Bourilkov, D; Bourquin, Maurice; Braccini, S; Branson, J G; Brochu, F; Burger, J D; Burger, W J; Cai, X D; Capell, M; Cara Romeo, G; Carlino, G; Cartacci, A M; Casaus, J; Cavallari, F; Cavallo, N; Cecchi, C; Cerrada, M; Chamizo-Llatas, M; Chang, Y H; Chemarin, M; Chen, A; Chen, G; Chen, G M; Chen, H F; Chen, H S; Chiefari, G; Cifarelli, Luisa; Cindolo, F; Clare, I; Clare, R; Coignet, G; Colino, N; Costantini, S; de la Cruz, B; Cucciarelli, S; van Dalen, J A; De Asmundis, R; Déglon, P L; Debreczeni, J; Degré, A; Dehmelt, K; Deiters, K; Della Volpe, D; Delmeire, E; Denes, P; De Notaristefani, F; De Salvo, A; Diemoz, M; Dierckxsens, M; Dionisi, C; Dittmar, M; Doria, A; Dova, M T; Duchesneau, D; Echenard, B; Eline, A; El-Mamouni, H; Engler, A; Eppling, F J; Ewers, A; Extermann, P; Falagán, M A; Falciano, S; Favara, A; Fay, J; Fedin, O; Felcini, M; Ferguson, T; Fesefeldt, H S; Fiandrini, E; Field, J H; Filthaut, Frank; Fisher, P H; Fisher, W; Fisk, I; Forconi, G; Freudenreich, Klaus; Furetta, C; Galaktionov, Yu; Ganguli, S N; García-Abia, P; Gataullin, M; Gentile, S; Giagu, S; Gong, Z F; Grenier, G; Grimm, O; Grünewald, M W; Guida, M; van Gulik, R; Gupta, V K; Gurtu, A; Gutay, L J; Haas, D; Hakobyan, R S; Hatzifotiadou, D; Hebbeker, T; Hervé, A; Hirschfelder, J; Hofer, H; Hohlmann, M; Holzner, G; Hou, S R; Hu, Y; Jin, B N; Jones, L W; de Jong, P; Josa-Mutuberria, I; Käfer, D; Kaur, M; Kienzle-Focacci, M N; Kim, J K; Kirkby, Jasper; Kittel, E W; Klimentov, A; König, A C; Kopal, M; Koutsenko, V F; Kräber, M H; Krämer, R W; Krenz, W; Krüger, A; Kunin, A; Ladrón de Guevara, P; Laktineh, I; Landi, G; Lebeau, M; Lebedev, A; Lebrun, P; Lecomte, P; Lecoq, P; Le Coultre, P; Le Goff, J M; Leiste, R; Levtchenko, M; Levchenko, P M; Li, C; Likhoded, S A; Lin, C H; Lin, W T; Linde, Frank L; Lista, L; Liu, Z A; Lohmann, W; Longo, E; Lü, Y S; Lübelsmeyer, K; Luci, C; Luminari, L; Lustermann, W; Ma Wen Gan; Malgeri, L; Malinin, A; Maña, C; Mangeol, D J J; Mans, J; Martin, J P; Marzano, F; Mazumdar, K; McNeil, R R; Mele, S; Merola, L; Meschini, M; Metzger, W J; Mihul, A; Milcent, H; Mirabelli, G; Mnich, J; Mohanty, G B; Muanza, G S; Muijs, A J M; Musicar, B; Musy, M; Nagy, S; Natale, S; Napolitano, M; Nessi-Tedaldi, F; Newman, H; Niessen, T; Nisati, A; Nowak, H; Ofierzynski, R A; Organtini, G; Palomares, C; Pandoulas, D; Paolucci, P; Paramatti, R; Passaleva, G; Patricelli, S; Paul, T; Pauluzzi, M; Paus, C; Pauss, Felicitas; Pedace, M; Pensotti, S; Perret-Gallix, D; Petersen, B; Piccolo, D; Pierella, F; Pioppi, M; Piroué, P A; Pistolesi, E; Plyaskin, V; Pohl, M; Pozhidaev, V; Pothier, J; Prokofiev, D O; Prokofev, D; Quartieri, J; Rahal-Callot, G; Rahaman, M A; Raics, P; Raja, N; Ramelli, R; Rancoita, P G; Ranieri, R; Raspereza, A V; Razis, P A; Ren, D; Rescigno, M; Reucroft, S; Riemann, S; Riles, K; Roe, B P; Romero, L; Rosca, A; Rosier-Lees, S; Roth, S; Rosenbleck, C; Roux, B; Rubio, Juan Antonio; Ruggiero, G; Rykaczewski, H; Sakharov, A; Saremi, S; Sarkar, S; Salicio, J; Sánchez, E; Sanders, M P; Schäfer, C; Shchegelskii, V; Schmidt-Kärst, S; Schmitz, D; Schopper, Herwig Franz; Schotanus, D J; Schwering, G; Sciacca, C; Servoli, L; Shevchenko, S; Shivarov, N; Shoutko, V; Shumilov, E; Shvorob, A V; Siedenburg, T; Son, D; Souga, C; Spillantini, P; Steuer, M; Stickland, D P; Stoyanov, B; Strässner, A; Sudhakar, K; Sultanov, G G; Sun, L Z; Sushkov, S V; Suter, H; Swain, J D; Szillási, Z; Tang, X W; Tarjan, P; Tauscher, Ludwig; Taylor, L; Tellili, B; Teyssier, D; Timmermans, C; Ting, Samuel C C; Ting, S M; Tonwar, S C; Tóth, J; Tully, C; Tung, K L; Ulbricht, J; Valente, E; Van de Walle, R T; Vásquez, R P; Veszpremi, V; Vesztergombi, G; Vetlitskii, I; Vicinanza, D; Viertel, Gert M; Villa, S; Vivargent, M; Vlachos, S; Vodopyanov, I; Vogel, H; Vogt, H; Vorobev, I; Vorobyov, A A; Wadhwa, M; Wallraff, W; Wang, X L; Wang, Z M; Weber, M; Wienemann, P; Wilkens, H; Wynhoff, S; Xia, L; Xu, Z Z; Yamamoto, J; Yang, B Z; Yang, C G; Yang, H J; Yang, M; Yeh, S C; Zalite, A; Zalite, Yu; Zhang, Z P; Zhao, J; Zhu, G Y; Zhu, R Y; Zhuang, H L; Zichichi, A; Zimmermann, B; Zöller, M

    2002-01-01

    Single top production in e^+e^- annihilations is searched for in data collected by the L3 detector at centre-of-mass energies from 189 to 209 GeV, corresponding to a total integrated luminosity of 634 pb-1. Investigating hadronic and semileptonic top decays, no evidence of single top production at LEP is obtained and upper limits on the single top cross section as a function of the centre-of-mass energy are derived. Limits on possible anomalous couplings, as well as on the scale of contact interactions responsible for single top production are determined.

  20. Evaluation of digital real-time PCR assay as a molecular diagnostic tool for single-cell analysis.

    Science.gov (United States)

    Chang, Chia-Hao; Mau-Hsu, Daxen; Chen, Ke-Cheng; Wei, Cheng-Wey; Chiu, Chiung-Ying; Young, Tai-Horng

    2018-02-21

    In a single-cell study, isolating and identifying single cells are essential, but these processes often require a large investment of time or money. The aim of this study was to isolate and analyse single cells using a novel platform, the PanelChip™ Analysis System, which includes 2500 microwells chip and a digital real-time polymerase chain reaction (dqPCR) assay, in comparison with a standard PCR (qPCR) assay. Through the serial dilution of a known concentration standard, namely pUC19, the accuracy and sensitivity levels of two methodologies were compared. The two systems were tested on the basis of expression levels of the genetic markers vimentin, E-cadherin, N-cadherin and GAPDH in A549 lung carcinoma cells at two known concentrations. Furthermore, the influence of a known PCR inhibitor commonly found in blood samples, heparin, was evaluated in both methodologies. Finally, mathematical models were proposed and separation method of single cells was verified; moreover, gene expression levels during epithelial-mesenchymal transition in single cells under TGFβ1 treatment were measured. The drawn conclusion is that dqPCR performed using PanelChip™ is superior to the standard qPCR in terms of sensitivity, precision, and heparin tolerance. The dqPCR assay is a potential tool for clinical diagnosis and single-cell applications.

  1. Detection and quantification of beef and pork materials in meat products by duplex droplet digital PCR

    OpenAIRE

    Cai, Yicun; He, Yuping; Lv, Rong; Chen, Hongchao; Wang, Qiang; Pan, Liangwen

    2017-01-01

    Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos t...

  2. PCR assay for the detection of Campylobacter in marinated and non-marinated poultry products

    OpenAIRE

    Katzav, Marianne; Isohanni, Pauliina; Lund, Marianne; Hakkinen, Marjaana; Lyhs, Ulrike

    2008-01-01

    During a period of 9 months, 194 marinated and non-marinated poultry products were collected from retail shops in a defined area in Western Finland and tested for Campylobacter spp. using a conventional enrichment culture and Polymerase Chain Reaction (PCR) method. For marinated poultry products, the study involved modification of a commercial DNA isolation method. Using either a conventional culture or PCR method, a total of 25 (12.9%) of all investigated samples were Campylobacter positive....

  3. Figure 1. T. tor species. Figure 2. Long PCR products of ...

    Indian Academy of Sciences (India)

    Annam

    Figure 2. Long PCR products of mitochondrial DNA from the fish T. tor. Lane 1, amplified product using L-12321-Leu and S-LA-16S-H primers. Lane 2, amplified product using H-12321 –Leu and S-LA-16S-L primers. Lane M, 1-Kb DNA ladder. 8 kb ...

  4. CP Violation in Single Top Quark Production

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Weigang [Michigan State Univ., East Lansing, MI (United States)

    2012-01-01

    We present a search for CP violation in single top quark production with the DØ experiment at the Tevatron proton-antiproton collider. CP violation in the top electroweak interaction results in different single top quark production cross sections for top and antitop quarks. We perform the search in the single top quark final state using 5.4 fb-1 of data, in the s-channel, t-channel, and for both combined. At this time, we do not see an observable CP asymmetry.

  5. Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.

    Science.gov (United States)

    Jordan, Michael R; Kearney, Mary; Palmer, Sarah; Shao, Wei; Maldarelli, Frank; Coakley, Eoin P; Chappey, Colombe; Wanke, Christine; Coffin, John M

    2010-09-01

    To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. Copyright 2010 Elsevier B.V. All rights reserved.

  6. PCR assay for the detection of Campylobacter in marinated and non-marinated poultry products.

    Science.gov (United States)

    Katzav, Marianne; Isohanni, Pauliina; Lund, Marianne; Hakkinen, Marjaana; Lyhs, Ulrike

    2008-10-01

    During a period of 9 months, 194 marinated and non-marinated poultry products were collected from retail shops in a defined area in Western Finland and tested for Campylobacter spp. using a conventional enrichment culture and Polymerase Chain Reaction (PCR) method. For marinated poultry products, the study involved modification of a commercial DNA isolation method. Using either a conventional culture or PCR method, a total of 25 (12.9%) of all investigated samples were Campylobacter positive. In marinated poultry products, Campylobacter was detected at a prevalence of 21.1% and 9.5% in turkey and chicken products, respectively. In August, there was a peak with 28.9% positive Campylobacter samples. Campylobacter inoculation tests were carried out to test the detection limit of both methods. The PCR method used is faster than microbiological analyses. However, enrichment of the samples is necessary due to the low occurrence of Campylobacter spp. in retail Finnish poultry products.

  7. Simultaneous identification of seven foodborne pathogens and Escherichia coli (pathogenic and nonpathogenic) using capillary electrophoresis-based single-strand conformation polymorphism coupled with multiplex PCR.

    Science.gov (United States)

    Oh, Mi-Hwa; Paek, Se-Hee; Shin, Gi Won; Kim, Hae-Yeong; Jung, Gyoo Yeol; Oh, Sangsuk

    2009-06-01

    The objective of this study was to develop a novel technique for parallel analysis of eight important foodborne microbes using capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP) coupled with multiplex PCR. Specific primers for multiplex PCR amplification of the 16S rRNA gene were designed, corresponding to eight species of bacteria, including Escherichia coli, Clostridium perfringens, Campylobacter jejuni, Salmonella enterica, Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, and Bacillus cereus, for the species-specific identification and optimal separation of their PCR products in subsequent analysis by CE-SSCP. Multiplex PCR conditions including annealing temperature, extension time, the number of PCR cycles, and primer concentrations were then optimized for simultaneous detection of all target foodborne bacteria. The diagnostic system using CE-SSCP combined with multiplex PCR developed here can be used for rapid investigation of causative agents of foodborne illness. The simplicity and high sensitivity of the method may lead to improved management of safety and illness related to food.

  8. Single-Step Multiplex PCR Assay for Characterization of New World Leishmania Complexes

    Science.gov (United States)

    Harris, Eva; Kropp, Gerald; Belli, Alejandro; Rodriguez, Betzabé; Agabian, Nina

    1998-01-01

    We have developed a PCR assay for one-step differentiation of the three complexes of New World Leishmania (Leishmania braziliensis, Leishmania mexicana, and Leishmania donovani). This multiplex assay is targeted to the spliced leader RNA (mini-exon) gene repeats of these organisms and can detect all three complexes simultaneously, generating differently sized products for each complex. The assay is specific to the Leishmania genus and does not recognize related kinetoplastid protozoa, such as Trypanosoma cruzi, Trypanosoma brucei, and Crithidia fasciculata. It correctly identified Leishmania species with a broad geographic distribution in Central and South America. The sensitivity of the PCR amplification ranged from 1 fg to 10 pg of DNA (0.01 to 100 parasites), depending on the complex detected. Crude extracts of cultured parasites, prepared simply by boiling diluted cultures, served as excellent templates for amplification. Crude preparations of clinical material were also tested. The assay detected L. braziliensis in dermal scrapings from cutaneous leishmanial lesions, Leishmania chagasi in dermal scrapings of atypical cutaneous leishmaniasis, and L. mexicana from lesion aspirates from infected hamsters. We have minimized the material requirements and maximized the simplicity, rapidity, and informative content of this assay to render it suitable for use in laboratories in countries where leishmaniasis is endemic. This assay should be useful for rapid in-country identification of Leishmania parasites, particularly where different Leishmania complexes are found in the same geographical area. PMID:9650950

  9. PCR assay for the detection of Campylobacter in marinated and non-marinated poultry products

    DEFF Research Database (Denmark)

    Katzav, Marianne; Isohanni, Pauliina; Lund, Marianne

    2008-01-01

    During a period of 9 months, 194 marinated and non-marinated poultry products were collected from retail shops in a defined area in Western Finland and tested for Campylobacter spp. using a conventional enrichment culture and Polymerase Chain Reaction (PCR) method. For marinated poultry products......, the study involved modification of a commercial DNA isolation method. Using either a conventional culture or PCR method, a total of 25 (12.9%) of all investigated samples were Campylobacter positive. In marinated poultry products, Campylobacter was detected at a prevalence of 21.1% and 9.5% in turkey...

  10. Evaluation of a new single-tube multiprobe real-time PCR for diagnosis of Entamoeba histolytica and Entamoeba dispar.

    Science.gov (United States)

    Liang, Shih-Yu; Hsia, Kan-Tai; Chan, Yun-Hsien; Fan, Chia-Kwung; Jiang, Donald Dah-Shyong; Landt, Olfert; Ji, Dar-Der

    2010-08-01

    A single-tube multiprobe real-time PCR assay for simultaneous detection of Entamoeba histolytica and Entamoeba dispar was developed. One primer pair with 2 species-specific probes was designed based on new SSU RNA regions of the ribosomal DNA-containing episome. The sensitivity is 1 parasite per milliliter of feces and thus superior to the conventional nested PCR and comparable to other published real-time PCR protocols. The applicability for clinical diagnosis was validated with 218 stool specimens from patients. A total of 51 E. histolytica and 39 E. dispar positive samples was detected by the multiprobe real-time PCR compared to 39 and 22 by routine nested PCR diagnosis. The detection rate of Entamoeba species for the multiprobe real-time PCR assays was significantly higher than the nested PCR (40.8% vs. 28.0%, P Entamoeba moshkovskii, Giardia lamblia , Cryptosporidium sp., Escherichia coli , or other nonpathogenic enteric parasites. The multiprobe real-time PCR assay is simple and rapid and has high specificity and sensitivity. The assay could streamline the laboratory diagnosis procedure and facilitate epidemiological investigation.

  11. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy

    Science.gov (United States)

    2012-01-01

    Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN) promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i) rapid and highly efficient; (ii) native DNA cloning without introduction of extra bases; (iii) restriction-free; (iv) easy positioning of directional and site-specific recombination owing to formulated primer design. ABI-REC is a novel approach to

  12. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy

    Directory of Open Access Journals (Sweden)

    Bi Yanzhen

    2012-07-01

    Full Text Available Abstract Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i rapid and highly efficient; (ii native DNA cloning without introduction of extra bases; (iii restriction-free; (iv easy positioning of directional and site-specific recombination owing to formulated primer design. ABI

  13. Search for single top production at HERA

    International Nuclear Information System (INIS)

    Brandt, G.

    2008-01-01

    A search for single top production in e p collisions using the complete high-energy data from HERA is presented. This search is based on the analysis of events containing isolated leptons (electronic or muons) and missing transverse momentum P T miss . In the absence of a signal, an upper limit on the top production cross-section σ ep→etX tuγ T miss and the measurements of W boson polarisation fractions.

  14. New device and method for capture, reverse transcription and nested PCR in a single closed-tube.

    Science.gov (United States)

    Olmos, A; Cambra, M; Esteban, O; Gorris, M T; Terrada, E

    1999-01-01

    A device and improved method based on the use of a compartmentalized Eppendorf tube that allows capture, reverse transcription and nested-PCR in a single closed-tube has been developed and patented. The main advantages of the system are the high sensitivity obtained, the simplicity, the low risk of contamination and the easy establishment of adequate conditions for nested-PCR. The method has been successfully applied to the detection and characterization of citrus tristeza closterovirus and plum pox potyvirus isolates in plant tissues and single aphids squashed on paper. This device and methodology could be easily adapted to the detection of other targets. PMID:10037824

  15. Figure 1. T. tor species. Figure 2. Long PCR products of ...

    Indian Academy of Sciences (India)

    Annam

    Long PCR products of mitochondrial DNA from the fish T. tor. Lane 1, amplified product using L-12321-Leu and S-LA-16S-H primers. Lane 2, amplified product using H-12321 –Leu and S-LA-16S-L ... The structure of complete mitochondrial genome of Tor tor. Position of 13 protein coding genes, 22 tRNA genes, 2 rRNA ...

  16. Mutation Scanning in a Single and a Stacked Genetically Modified (GM) Event by Real-Time PCR and High Resolution Melting (HRM) Analysis

    Science.gov (United States)

    Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G.; Brandes, Christian

    2014-01-01

    Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017 × MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

  17. Survey of Campylobacter jejuni in retail chicken meat products by application of a quantitative PCR protocol.

    Science.gov (United States)

    Rantsiou, Kalliopi; Lamberti, Cristina; Cocolin, Luca

    2010-07-31

    Campylobacter-contaminated food products are currently the cause of the highest number of gastroenteritis cases in developed countries. Apart for biosafety measures at the primary production level, no other official control measures are currently in place for its control. This is partly due to the lack of quantitative data regarding the prevalence and contamination level of different food products by Campylobacter spp. that does not allow for quantitative risk assessment. PCR-based methods, applied without prior enrichment, in food samples circumvent limitations associated with the quantification of foodborne pathogens by traditional, culture-dependent methods. In this study, we report the development of a protocol, based on the amplification of the rpoB gene of Campylobacter jejuni, by quantitative PCR (qPCR), directly in food samples. The quantification limit of the protocol was determined to be in the order of 10 colony forming units (cfu)/g or ml of food sample. The optimized protocol was applied for the survey of C. jejuni in naturally contaminated poultry samples. In parallel, traditional sampling was also performed. A high percentage of samples (87%) resulted to be positive by qPCR, while no C. jejuni was detected by traditional analysis. Furthermore, important differences were observed in the detection by qPCR between samples before and after enrichment. Copyright 2010 Elsevier B.V. All rights reserved.

  18. Simultaneous detection of five notifiable viral diseases of cattle by single-tube multiplex real-time RT-PCR.

    Science.gov (United States)

    Wernike, Kerstin; Hoffmann, Bernd; Beer, Martin

    2015-06-01

    Multiplexed real-time PCR (qPCR) assays enable the detection of several target genes in a single reaction, which is applicable for simultaneous testing for the most important viral diseases in samples obtained from ruminants with unspecific clinical symptoms. Here, reverse transcription qPCR (RT-qPCR) systems for the detection of bovine viral diarrhoea virus (BVDV) and bluetongue virus (BTV) were combined with an internal control system based on the beta-actin gene. Additionally, a background screening for three further major pathogens of cloven-hoofed animals reportable to the World Organisation for Animal Health, namely foot-and-mouth disease virus, epizootic haemorrhagic disease virus, and Rift Valley fever virus, was integrated using the identical fluorophore for the respective RT-qPCR assays. Every pathogen-specific assay had an analytical sensitivity of at least 100 genome copies per reaction within the multiplex approach, and a series of reference samples and clinical specimens obtained from cattle, but also from small ruminants, were detected reliably. The qPCR systems integrated in the background screening were even not influenced by the simultaneous amplification of very high BVDV and BTV genome copy numbers. The newly developed multiplex qPCR allows the specific and sensitive detection of five of the most important diseases of ruminants and could be used in the context of monitoring programs or for differential diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Improved in situ hybridization to HIV with RNA probes derived from PCR products.

    Science.gov (United States)

    Cone, R W; Schlaepfer, E

    1997-05-01

    These experiments tested the hypothesis that a pool of PCR-derived RNA probes with defined length and even representation of the target sequences could produce more specific and intense in situ hybridization signals than randomly size-reduced, plasmid-derived RNA probes. In situ hybridization was performed with sense and anti-sense HIV-1 RNA probes that were derived from PCR products tailed with the T7 RNA polymerase promoter or from plasmid DNA. In situ hybridization using a pool of seven anti-sense or sense PCR-derived RNA probes (1805 nucleotides of HIV sequence, 257 nucleotides average probe length) was compared with hybridization using anti-sense or sense RNA probes made from a plasmid representing the HIV-1 env gene (3151 nucleotides of HIV-1 target). The pooled PCR-derived probes resulted in stronger in situ hybridization signals and less background than those produced with plasmid-derived RNA probes. This method for creating PCR-derived RNA probes improves the feasibility of synthesizing multiple, discrete RNA probes for studies of specific mRNA expression because it does not require the subcloning steps used to construct plasmids. PCR-derived RNA probes may provide a viable alternative to the use of plasmid-derived RNA probes for in situ hybridization.

  20. Comparison between single PCR and nested PCR in detection of human papilloma viruses in paraffin-embedded OSCC and fresh oral mucosa.

    Science.gov (United States)

    Jalouli, Miranda; Jalouli, Jamshid; Ibrahim, Salah O; Hirsch, Jan-Michaél; Sand, Lars

    2015-01-01

    Infection with human papilloma virus (HPV) has been implicated as one of the risk factors for the development of oropharyngeal cancer. Many different HPV tests exist, and information regarding their specific technical, analytical, and clinical properties is increasing. This study aimed to compare the level of detection of HPV using two reliable polymerase chain reaction (PCR) methods, nested PCR (NPCR) and single PCR (SPCR), in archival paraffin-embedded oral squamous cell carcinoma (OSCC) samples and fresh oral mucosa specimens. The presence of HPV genome in two groups of tissue samples was analyzed: (i) 57 paraffin-embedded OSCC samples from Sudan and (ii) eight healthy fresh oral mucosal samples from Swedish volunteers. The specimens were tested by SPCR with primer pair MY9/MY11 and NPCR using GP5+/GP6+ primer sets. Eighteen (32%) out of the 57 paraffin-embedded OSCC samples, and five (62%) out of the eight fresh clinically healthy samples were found to be HPV-positive with NPCR. With SPCR, four (7%) out of the paraffin-embedded OSCC samples were HPV-positive. A statistically significant difference between HPV-positive and -negative samples was found when comparing NPCR and SPCR in OSCC and fresh oral mucosa (p<0.0001). The comparative test between SPCR and NPCR showed 100% sensitivity and 69% specificity for OSCC. The use of the GP5+/GP6+ nested PCR increased the positivity rate, efficiency rate and sensitivity of HPV detection in oral samples significantly and should be considered as the method of choice. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  1. Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR)

    NARCIS (Netherlands)

    Ruiz-Villalba, Adrián; van Pelt-Verkuil, Elizabeth; Gunst, Quinn D.; Ruijter, Jan M.; van den Hoff, Maurice J. B.

    2017-01-01

    Quantitative PCR allows the precise measurement of DNA concentrations and is generally considered to be straightforward and trouble free. However, a survey with 93 validated assays for genes in the Wnt-pathway showed that the amplification of nonspecific products occurs frequently and is unrelated

  2. Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products.

    Science.gov (United States)

    Agrimonti, Caterina; Bottari, Benedetta; Sardaro, Maria Luisa Savo; Marmiroli, Nelson

    2017-09-08

    Dairy foods represent an important sector of the food market for their nutritional qualities and their organoleptic characteristics, which are often linked to tradition and to region. These products are typically protected by labels such as PDO (Protected Designation of Origin) and PGI (Protected Geographical Indication). Real-time PCR (qPCR) is a fundamental tool in "Food Genomics;" a discipline concerned with the residual DNA in food, which, alongside traditional physical and chemical methods, is frequently used to determine product safety, quality and authenticity. Compared to conventional or "end-point" PCR, qPCR incorporates continuous monitoring of reaction progress, thereby enabling quantification of target DNA. This review describes qPCR applications to the analysis of microbiota, and to the identification of the animal species source of milk from which dairy products have been made. These are important aspects for ensuring safety and authenticity. The various applications of qPCR are discussed, as well as advantages and disadvantages in comparison with other analytical methods.

  3. New Physics in Single-Top Production

    CERN Document Server

    Lohse, T; The ATLAS collaboration

    2014-01-01

    In this paper an overview of recent results on the search for physics beyond the Standard Model in the electro-weak top-quark production from the ATLAS, D0 , CDF and CMS collaborations is given. This includes searches for W' and b$^∗$ resonances as well as measurements of CP violation, the W helicity fractions and the top-quark polarisation in single-top production. A brief review on the search for flavour-changing neutral currents and cross-section measurements with respect to the CKM matrix element $V_{tb}$ is given.

  4. Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR.

    Science.gov (United States)

    Furet, Jean-Pierre; Quénée, Pascal; Tailliez, Patrick

    2004-12-15

    Real-time quantitative PCR assays were developed for the absolute quantification of lactic acid bacteria (LAB) (Streptococcus thermophilus, Lactobacillus delbrueckii, L. casei, L. paracasei, L. rhamnosus, L. acidophilus and L. johnsonii) in fermented milk products. The results of molecular quantification and classic bacterial enumeration did not differ significantly with respect to S. thermophilus and the species of the L. casei group which were detected in the six commercial fermented products tested, thus showing that DNA extraction was efficient and that genomic DNA solutions were free of PCR inhibitors. For L. delbrueckii, the results of bacterial enumeration were generally lower by a factor 10 to 100 than those of PCR quantification, suggesting a loss of viability during storage of the dairy products at 1-8 degrees C for most of the strains in this species. Real-time quantitative assays enabled identification of the species of lactic acid bacterial strains initially present in commercial fermented milk products and their accurate quantification with a detection threshold of 10(3) cells per ml of product.

  5. On-chip single-copy real-time reverse-transcription PCR in isolated picoliter droplets

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Wheeler, E; Lee-Houghton, L; Watkins, N; Nasarabadi, S; Hebert, N; Leung, P; Arnold, D; Bailey, C; Colston, B

    2007-12-19

    The first lab-on-chip system for picoliter droplet generation and RNA isolation, followed by reverse transcription, and PCR amplification with real-time fluorescence detection in the trapped droplets has been developed. The system utilized a shearing T-junction in a fused silica device to generate a stream of monodisperse picoliter-scale droplets that were isolated from the microfluidic channel walls and each other by the oil phase carrier. An off-chip valving system stopped the droplets on-chip, allowing thermal cycling for reverse transcription and subsequent PCR amplification without droplet motion. This combination of the established real-time reverse transcription-PCR assay with digital microfluidics is ideal for isolating single-copy RNA and virions from a complex environment, and will be useful in viral discovery and gene-profiling applications.

  6. Simple Objective Detection of Human Lyme Disease Infection Using Immuno-PCR and a Single Recombinant Hybrid Antigen

    Science.gov (United States)

    Halpern, Micah D.; Molins, Claudia R.; Schriefer, Martin

    2014-01-01

    A serology-based tiered approach has, to date, provided the most effective means of laboratory confirmation of clinically suspected cases of Lyme disease, but it lacks sensitivity in the early stages of disease and is often dependent on subjectively scored immunoblots. We recently demonstrated the use of immuno-PCR (iPCR) for detecting Borrelia burgdorferi antibodies in patient serum samples that were positive for Lyme disease. To better understand the performance of the Lyme disease iPCR assay, the repeatability and variability of the background of the assay across samples from a healthy population (n = 36) were analyzed. Both of these parameters were found to have coefficients of variation of Lyme disease patient serum samples (n = 12) demonstrated a strong correlation with that of 2-tier testing. Furthermore, a simplified iPCR approach using a single hybrid antigen and detecting only IgG antibodies confirmed the 2-tier diagnosis in the Lyme disease patient serum samples (n = 12). Validation of the hybrid antigen IgG iPCR assay using a blinded panel of Lyme disease and non-Lyme disease patient serum samples (n = 92) resulted in a sensitivity of 69% (95% confidence interval [CI], 50% to 84%), compared to that of the 2-tier analysis at 59% (95% CI, 41% to 76%), and a specificity of 98% (95% CI, 91% to 100%) compared to that of the 2-tier analysis at 97% (95% CI, 88% to 100%). A single-tier hybrid antigen iPCR assay has the potential to be an improved method for detecting host-generated antibodies against B. burgdorferi. PMID:24899074

  7. Observation of Single Top Quark Production

    Energy Technology Data Exchange (ETDEWEB)

    Gerber, Cecilia E.; /Illinois U., Chicago

    2009-09-01

    The author reports on the observation of electroweak production of single top quarks in p{bar p} collisions at {radical}s = 1.96 Tev using 2.3 fb{sup -1} of data collected with the D0 detector at the fermilab Tevatron Collider. Using events containing an isolated electron or muon, missing transverse energy, two, three or four jets, with one or two of them identified as originating from the fragmentation of a b quark, the measured cross section for the process p{bar p} {yields} tb + X, tqb + X is 3.94 {+-} 0.88 pb (for a top quark mass of 170 GeV). the probability to measure a cross section at this value or higher in the absence of signal is 2.5 x 10{sup -7}, corresponding to a 5.0 standard deviation significance. Using the same dataset, the measured cross sections for the t- and the s-channel processes when determined simultaneously with no assumption on their relative production rate are 3.14{sub -0.80}{sup +0.94} pb and 1.05 {+-} 0.81 pb respectively, consistent with standard model expectations. The measured t-channel cross section has a significance of 4.8 standard deviations, representing the first evidence for the production of an individual single top process to be detected.

  8. Whole Blood PCR Amplification with Pfu DNA Polymerase and Its Application in Single-Nucleotide Polymorphism Analysis.

    Science.gov (United States)

    Liu, Er-Ping; Wang, Yan; He, Xiao-Hui; Guan, Jun-Jie; Wang, Jin; Qin, Zheng-Hong; Sun, Wan-Ping

    2015-11-01

    Point-of-care genetic analysis may require polymerase chain reaction (PCR) to be carried out on whole blood. However, human blood contains natural inhibitors of PCR such as hemoglobin, immunoglobulin G, lactoferrin, and proteases, as well as anticoagulant agents, including EDTA and heparin that can reduce whole blood PCR efficiency. Our purpose was to develop a highly specific, direct whole blood single-nucleotide polymorphism (SNP) analysis method based on allele-specific (AS) PCR that is mediated by Pfu DNA polymerase and phosphorothioate-modified AS primers. At high Mg(2+) concentrations, Pfu DNA polymerase efficiently amplified genomic DNA in a reaction solution containing up to 14% whole blood. Among the three anticoagulants tested, Pfu DNA polymerase showed the highest activity with sodium citrate. Meanwhile, Triton X-100 and betaine inhibited Pfu DNA polymerase activity in whole blood PCR, whereas trehalose had virtually no effect. These findings provided for the development of a low-cost, simple, and fast direct whole blood genotyping method that uses Pfu DNA polymerase combined with phosphorothioate AS primers for CYP2C9*3 and VKORC1(-1639) loci. With its high DNA amplification efficiency and tolerance of various blood conditions, Pfu DNA polymerase can be used in clinical laboratories to analyze SNPs in whole blood samples.

  9. Discovery of single top quark production

    Energy Technology Data Exchange (ETDEWEB)

    Gillberg, Dag [Simon Fraser Univ., Burnaby, BC (Canada)

    2009-04-01

    The top quark is by far the heaviest known fundamental particle with a mass nearing that of a gold atom. Because of this strikingly high mass, the top quark has several unique properties and might play an important role in electroweak symmetry breaking - the mechanism that gives all elementary particles mass. Creating top quarks requires access to very high energy collisions, and at present only the Tevatron collider at Fermilab is capable of reaching these energies. Until now, top quarks have only been observed produced in pairs via the strong interaction. At hadron colliders, it should also be possible to produce single top quarks via the electroweak interaction. Studies of single top quark production provide opportunities to measure the top quark spin, how top quarks mix with other quarks, and to look for new physics beyond the standard model. Because of these interesting properties, scientists have been looking for single top quarks for more than 15 years. This thesis presents the first discovery of single top quark production. An analysis is performed using 2.3 fb-1 of data recorded by the D0 detector at the Fermilab Tevatron Collider at centre-of-mass energy √s = 1.96 TeV. Boosted decision trees are used to isolate the single top signal from background, and the single top cross section is measured to be σ(p$\\bar{p}$ → tb + X, tqb + X) = 3.74-0.74+0.95 pb. Using the same analysis, a measurement of the amplitude of the CKM matrix element Vtb, governing how top and b quarks mix, is also performed. The measurement yields: |V{sub tb}|f1L| = 1.05 -0.12+0.13, where f1L is the left-handed Wtb coupling. The separation of signal from background is improved by combining the boosted decision trees with two other multivariate techniques. A new cross section measurement is performed, and the significance for the excess over the predicted background exceeds 5

  10. Gene transcription analysis of carrot allergens by relative quantification with single and duplex reverse transcription real-time PCR.

    Science.gov (United States)

    Zagon, Jutta; Jansen, Bärbel; Knoppik, Meike; Ehlers, Anke; Kroh, Lothar W; Holzhauser, Thomas; Vieths, Stefan; Broll, Hermann

    2010-01-01

    Single and duplex real-time polymerase chain reaction (PCR) systems have been developed to quantify specific mRNA transcription of genes coding for the major Daucus carota allergen isoforms Dau c 1.01 and Dau c 1.02. Methods were tested with samples from the local market. Whereas the gene transcription levels for Dau c 1.01 were consistently high in all investigated samples, significant differences for the Dau c 1.02 transcription could be demonstrated in randomly collected market samples. The gene transcription level for the minor Dau c 1.02 variant is about one log below Dau c 1.01. Both formats, single or duplex real-time methods, exhibit ideal cycle threshold (CT) ranges and good reproducibility. In particular, the easily performed duplex real-time PCR system is potentially suited for the selection of hypoallergenic varieties and studying the impact of post-harvesting or environmental conditions.

  11. Evidence for production of single top quarks

    Energy Technology Data Exchange (ETDEWEB)

    Abazov, V.M.; /Dubna, JINR; Abbott, B.; /Oklahoma U.; Abolins, M.; /Michigan State U.; Acharya, B.S.; /Tata Inst.; Adams, M.; /Illinois U., Chicago; Adams, T.; /Florida State U.; Aguilo, E.; /Simon Fraser U.; Ahn, S.H.; /Korea U., KODEL; Ahsan, M.; /Kansas State U.; Alexeev, G.D.; /Dubna, JINR; Alkhazov, G.; /St. Petersburg, INP /Michigan U.

    2008-03-01

    We present first evidence for the production of single top quarks in the D0 detector at the Fermilab Tevatron p{bar p} collider. The standard model predicts that the electroweak interaction can produce a top quark together with an antibottom quark or light quark, without the antiparticle top quark partner that is always produced from strong coupling processes. Top quarks were first observed in pair production in 1995, and since then, single top quark production has been searched for in ever larger datasets. In this analysis, we select events from a 0.9 fb{sup -1} dataset that have an electron or muon and missing transverse energy from the decay of a W boson from the top quark decay, and two, three, or four jets, with one or two of the jets identified as originating from a b hadron decay. The selected events are mostly backgrounds such as W+jets and t{bar t} events, which we separate from the expected signals using three multivariate analysis techniques: boosted decision trees, Bayesian neural networks, and matrix element calculations. A binned likelihood fit of the signal cross section plus background to the data from the combination of the results from the three analysis methods gives a cross section for single top quark production of {sigma}(p{bar p} {yields} tb + X, tqb + X) = 4.7 {+-} 1.3 pb. The probability to measure a cross section at this value or higher in the absence of signal is 0.014%, corresponding to a 3.6 standard deviation significance. The measured cross section value is compatible at the 10% level with the standard model prediction for electroweak top quark production. We use the cross section measurement to directly determine the Cabibbo-Kobayashi-Maskawa quark mixing matrix element that describes the Wtb coupling and find |V{sub tb}f{sub 1}{sup L}| = 1.31{sub -0.21}{sup +0.25}, where f{sub 1}{sup L} is a generic vector coupling. This model-independent measurement translates into 0.68 < |V{sub tb}| {le} 1 at the 95% C.L. in the standard model.

  12. Development of an immunoFET biosensor for the detection of biotinylated PCR product

    Directory of Open Access Journals (Sweden)

    Wannaporn Muangsuwan

    2016-10-01

    Full Text Available ImmunoFET (IMFET biosensor is a simple platform for the detection of biotinylated products of polymerase chain reaction (PCR. Construction of the IMFET biosensor started with adsorption of 1.5 mg/mL of protein A (PA onto the insulated gate surface of ISFET for 90 min. Next, the immobilized 1/500 dilution of anti-biotin antibody was adsorbed onto the PA layer for 60 min. The IMFET biosensor was subsequently ready for detection of the biotinylated amplicon. The IMFET biosensor showed highly specific binding to the biotinylated PCR product of the phaE gene of Haloquadratum walsbyi DSM 16854. The phaE gene is a biomarker of polyhydroxyalkanoate (PHA producers that contain PHA synthase class III. The lowest amount of DNA template of H. walsbyi DSM 16854 that the IMFET biosensor could detect was 125 fg. The IMFET biosensor has a lower amount of detection compared with a DNA lateral flow biosensor from our previous study. The degree of linearity of the biosensor signal was influenced by the concentration of the biotinylated amplicon. The IMFET biosensor also has a short response time (approximately 30 times to detect the phaE amplicon compared to an agarose gel electrophoresis. The IMFET biosensor is a promising tool for the detection of the biotinylated PCR product, and it can be integrated into a micro total analysis system (μTAS.

  13. Development and evaluation of one step single tube multiplex RT-PCR for rapid detection and typing of dengue viruses

    OpenAIRE

    Parida Manmohan; Shrivastava Ambuj; Santhosh SR; Dash Paban; Saxena Parag; Rao PV

    2008-01-01

    Abstract Background Dengue is emerging as a major public health concern in many parts of the world. The development of a one-step, single tube, rapid, and multiplex reverse transcription polymerase chain reaction (M-RT-PCR) for simultaneous detection and typing of dengue virus using serotype specific primers during acute phase of illness is reported. Results An optimal assay condition with zero background was established having no cross-reaction with closely related members of flavivirus (Jap...

  14. Optimization of the Divergent method for genotyping single nucleotide variations using SYBR Green-based single-tube real-time PCR.

    Science.gov (United States)

    Gentilini, Fabio; Turba, Maria E

    2014-01-01

    A novel technique, called Divergent, for single-tube real-time PCR genotyping of point mutations without the use of fluorescently labeled probes has recently been reported. This novel PCR technique utilizes a set of four primers and a particular denaturation temperature for simultaneously amplifying two different amplicons which extend in opposite directions from the point mutation. The two amplicons can readily be detected using the melt curve analysis downstream to a closed-tube real-time PCR. In the present study, some critical aspects of the original method were specifically addressed to further implement the technique for genotyping the DNM1 c.G767T mutation responsible for exercise-induced collapse in Labrador retriever dogs. The improved Divergent assay was easily set up using a standard two-step real-time PCR protocol. The melting temperature difference between the mutated and the wild-type amplicons was approximately 5°C which could be promptly detected by all the thermal cyclers. The upgraded assay yielded accurate results with 157pg of genomic DNA per reaction. This optimized technique represents a flexible and inexpensive alternative to the minor grove binder fluorescently labeled method and to high resolution melt analysis for high-throughput, robust and cheap genotyping of single nucleotide variations. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Expansion during PCR of short single-stranded DNA fragments carrying nonselfcomplementary dinucleotide or trinucleotide repeats

    Czech Academy of Sciences Publication Activity Database

    Reichová, Naďa; Kypr, Jaroslav

    2003-01-01

    Roč. 30, č. 3 (2003), s. 155-163 ISSN 0301-4851 R&D Projects: GA ČR GA301/01/0590 Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA * PCR * expansion Subject RIV: BO - Biophysics Impact factor: 0.565, year: 2003

  16. Rapid restriction enzyme-free cloning of PCR products: a high-throughput method applicable for library construction.

    Directory of Open Access Journals (Sweden)

    Vijay K Chaudhary

    Full Text Available Herein, we describe a novel cloning strategy for PCR-amplified DNA which employs the type IIs restriction endonuclease BsaI to create a linearized vector with four base-long 5'-overhangs, and T4 DNA polymerase treatment of the insert in presence of a single dNTP to create vector-compatible four base-long overhangs. Notably, the insert preparation does not require any restriction enzyme treatment. The BsaI sites in the vector are oriented in such a manner that upon digestion with BsaI, a stuffer sequence along with both BsaI recognition sequences is removed. The sequence of the four base-long overhangs produced by BsaI cleavage were designed to be non-palindromic, non-compatible to each other. Therefore, only ligation of an insert carrying compatible ends allows directional cloning of the insert to the vector to generate a recombinant without recreating the BsaI sites. We also developed rapid protocols for insert preparation and cloning, by which the entire process from PCR to transformation can be completed in 6-8 h and DNA fragments ranging in size from 200 to 2200 bp can be cloned with equal efficiencies. One protocol uses a single tube for insert preparation if amplification is performed using polymerases with low 3'-exonuclease activity. The other protocol is compatible with any thermostable polymerase, including those with high 3'-exonuclease activity, and does not significantly increase the time required for cloning. The suitability of this method for high-throughput cloning was demonstrated by cloning batches of 24 PCR products with nearly 100% efficiency. The cloning strategy is also suitable for high efficiency cloning and was used to construct large libraries comprising more than 108 clones/µg vector. Additionally, based on this strategy, a variety of vectors were constructed for the expression of proteins in E. coli, enabling large number of different clones to be rapidly generated.

  17. High-efficiency nuclear transformation of the oleaginous marine Nannochloropsis species using PCR product.

    Science.gov (United States)

    Li, Fengjuan; Gao, Dawen; Hu, Hanhua

    2014-01-01

    Nannochloropsis are model species for investigating biofuel production by algae. To develop them into an integrated photons-to-fuel production platform, high efficiency transformation methods are necessary. Here, we obtained the β-tubulin promoter regions of all recognized species of genus Nannochloropsis, and successfully transformed all five marine species by electroporation. In addition, the PCR amplified double stranded DNA fragments (PCR fragments) based transformation system was established in these Nannochloropsis species, which showed much higher transformation efficiency (10.7-61.2 × 10(-6), 1.5-13-fold) than that of linearized plasmid based transformation. The cotransformation of N. salina using a circular plasmid containing a non-selectable GUS gene and a PCR fragment containing only a selection marker cassette was also achieved and found to be very efficient (over 50%). This simple and highly efficient transformation protocol reported in our study provided a useful tool for gene functional analysis and genetic engineering of the oleaginous Nannochloropsis species.

  18. Penerapan Metode Diagnosis Cepat Virus Avian Influenza H5N1 dengan Metode Single Step Multiplex RT-PCR

    Directory of Open Access Journals (Sweden)

    Aris Haryanto

    2010-12-01

    Full Text Available Avian influenza (AI virus is a segmented single stranded (ss RNA virus with negative polarity andbelong to the Orthomyxoviridae family. Diagnose of AI virus can be performed using conventional methodsbut it has low sensitivity and specificity. The objective of the research was to apply rapid, precise, andaccurate diagnostic method for AI virus and also to determine its type and subtype based on the SingleStep Multiplex Reverse Transcriptase-Polymerase Chain Reaction targeting M, H5, and N1 genes. In thismethod M, H5 and NI genes were simultaneously amplified in one PCR tube. The steps of this researchconsist of collecting viral RNAs from 10 different AI samples originated from Maros Disease InvestigationCenter during 2007. DNA Amplification was conducted by Simplex RT-PCR using M primer set. Then, bysingle step multiplex RT-PCR were conducted simultaneously using M, H5 and N1 primers set. The RTPCRproducts were then separated on 1.5% agarose gel, stained by ethidum bromide and visualized underUV transilluminator. Results showed that 8 of 10 RNA virus samples could be amplified by Simplex RTPCRfor M gene which generating a DNA fragment of 276 bp. Amplification using multiplex RT-PCRmethod showed two of 10 samples were AI positive using multiplex RT-PCR, three DNA fragments weregenerated consisting of 276 bp for M gene, 189 bp for H5 gene, and 131 bp for N1. In this study, rapid andeffective diagnosis method for AI virus can be conducted by using simultaneous Single Step Multiplex RTPCR.By this technique type and subtype of AI virus, can also be determined, especially H5N1.

  19. Ultra-sensitive Single Fluorescence-labeled Probe-mediated SUP-M-ddPCR for High-throughput GMO Screening.

    Science.gov (United States)

    Niu, Chenqi; Xu, Yuancong; Zhang, Chao; Zhu, Pengyu; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2018-04-13

    As genetically modified (GM) technology develops and genetically modified organisms (GMOs) become more available, GMOs face increasing regulations and pressure to adhere to strict labeling guidelines. A singleplex detection method cannot perform the high-throughput analysis necessary for optimal GMO detection. Combining the advantages of multiplex detection and droplet digital polymerase chain reaction (ddPCR), a single universal primer-multiplex-ddPCR (SUP-M-ddPCR) strategy was proposed for accurate broad-spectrum screening and quantification. The SUP increases efficiency of the primers in PCR and plays an important role in establishing a high-throughput, multiplex detection method. Emerging ddPCR technology has been used for accurate quantification of nucleic acid molecules without a standard curve. Using maize as a reference point, four heterologous genes (35S, NOS, NPTII, and PAT) were selected to evaluate the feasibility and applicability of this strategy. Surprisingly, these four genes cover more than 93% of the transgenic maize lines and serve as preliminary screening sequences. All screening probes were labeled with FAM fluorescence, which allows the signals from the samples with GMO content and those without to be easily differentiated. This fiveplex screening method is a new development in GMO screening. Utilizing an optimal amplification assay, the specificity, limit of detection (LOD) and limit of quantitation (LOQ) were validated. The LOD and LOQ of this GMO screening method were 0.1 % and 0.01 %, respectively, with a relative standard deviation (RSD) <25 %. This method could serve as an important tool for the detection of GM maize from different processed, commercially available products. Further, this screening method could be applied to other fields that require reliable and sensitive detection of DNA targets.

  20. Development and evaluation of one step single tube multiplex RT-PCR for rapid detection and typing of dengue viruses

    Directory of Open Access Journals (Sweden)

    Parida Manmohan

    2008-01-01

    Full Text Available Abstract Background Dengue is emerging as a major public health concern in many parts of the world. The development of a one-step, single tube, rapid, and multiplex reverse transcription polymerase chain reaction (M-RT-PCR for simultaneous detection and typing of dengue virus using serotype specific primers during acute phase of illness is reported. Results An optimal assay condition with zero background was established having no cross-reaction with closely related members of flavivirus (Japanese encephalitis, West Nile, Yellow fever and alphavirus (Chikungunya. The feasibility of M-RT-PCR assay for clinical diagnosis was validated with 620 acute phase dengue patient sera samples of recent epidemics in India. The comparative evaluation vis a vis conventional virus isolation revealed higher sensitivity. None of the forty healthy serum samples screened in the present study revealed any amplification, thereby establishing specificity of the reported assay for dengue virus only. Conclusion These findings clearly suggested that M-RT-PCR assay reported in the present study is the rapid and cost-effective method for simultaneous detection as well as typing of the dengue virus in acute phase patient serum samples. Thus, the M-RT-PCR assay developed in this study will serve as a very useful tool for rapid diagnosis and typing of dengue infections in endemic areas.

  1. Comparison of culture, single and multiplex real-time PCR for detection of Sabin poliovirus shedding in recently vaccinated Indian children.

    Science.gov (United States)

    Giri, Sidhartha; Rajan, Anand K; Kumar, Nirmal; Dhanapal, Pavithra; Venkatesan, Jayalakshmi; Iturriza-Gomara, Miren; Taniuchi, Mami; John, Jacob; Abraham, Asha Mary; Kang, Gagandeep

    2017-08-01

    Although, culture is considered the gold standard for poliovirus detection from stool samples, real-time PCR has emerged as a faster and more sensitive alternative. Detection of poliovirus from the stool of recently vaccinated children by culture, single and multiplex real-time PCR was compared. Of the 80 samples tested, 55 (68.75%) were positive by culture compared to 61 (76.25%) and 60 (75%) samples by the single and one step multiplex real-time PCR assays respectively. Real-time PCR (singleplex and multiplex) is more sensitive than culture for poliovirus detection in stool, although the difference was not statistically significant. © 2017 Wiley Periodicals, Inc.

  2. Observation of Single Top Quark Production

    Energy Technology Data Exchange (ETDEWEB)

    Heinson, Ann; /UC, Riverside; Junk, Tom R.; /Fermilab

    2011-01-01

    The field of experimental particle physics has become more sophisticated over time, as fewer, larger experimental collaborations search for small signals in samples with large components of background. The search for and the observation of electroweak single top quark production by the CDF and D0 collaborations at Fermilab's Tevatron collider are an example of an elaborate effort to measure the rate of a very rare process in the presence of large backgrounds and to learn about the properties of the top quark's weak interaction. We present here the techniques used to make this groundbreaking measurement and the interpretation of the results in the context of the Standard Model.

  3. Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees.

    Science.gov (United States)

    Bertolini, E; Olmos, A; Martínez, M C; Gorris, M T; Cambra, M

    2001-07-01

    A single-step multiplex RT-PCR was developed for the simultaneous and colourimetric detection of six RNA viruses (Cucumber mosaic virus, Cherry leaf roll virus, strawberry latent ringspot virus, Arabis mosaic virus, Olive latent-1 virus and Olive latent-2 virus) which infect olive trees. Six compatible primer set for one-step RT-PCR amplification in a single closed-tube and 3' digoxigenin labelled probes were designed in optimal, specific and conserved regions. The method has been assessed with 195 Spanish field olive trees, suggesting that approximately 1.5% of the tested material was infected by Cucumber mosaic virus and 0.5% by Cherry leaf roll virus. This method saves time and reagent costs compared with monospecific RT-PCR which needs several reactions for the same number of tests. Using colourimetric detection, it is possible to analyse many samples, it increases sensitivity 10-fold, and whilst facilitating the interpretation of results, it avoids the use of gels and the toxic ethidium bromide. The method could be used routinely for sanitary and certification programmes.

  4. Cloning of Single-Chain Antibody Variants by Overlap-Extension PCR for Evaluation of Antibody Expression in Transient Gene Expression.

    Science.gov (United States)

    Mayrhofer, Patrick; Kunert, Renate

    2017-01-01

    Single-chain fragment variable-fragment crystallizable antibody constructs (scFv-Fc) are homodimeric proteins representing valuable alternatives to heterotetrameric full-length IgG molecules to study protein properties and product-dependent cellular behavior. In contrast to naturally occurring antibodies, these artificial molecules are assembled from functional antibody domains to reduce molecule complexity and enhance antibody expression levels. The scFv-Fc format retains critical antibody functions such as antigen binding affinity and antibody effector functions. Here, we present a protocol to convert the full-length anti-HIV-1 IgG1 antibody 2F5 into a scFv-Fc construct. Variable and constant regions are amplified by conventional PCR reactions and assembled by a single overlap-extension PCR reaction. The amplified product is then cloned into a mammalian expression vector suitable for high-titer transient gene expression. This workflow can be applied to any antibody sequence by adapting the specific primer sequences to the antibody of choice.

  5. Single Neutralino production at CERN LHC

    CERN Document Server

    Gounaris, George J; Porfyriadis, P I; Renard, F M

    2005-01-01

    The common belief that the lightest supersymmetric particle (LSP) might be a neutralino, providing also the main Dark Matter (DM) component, calls for maximal detail in the study of the neutralino properties. Motivated by this, we consider the direct production of a single neutralino $\\tchi^0_i$ at a high/energy hadron collider, focusing on the $\\tchi^0_1$ and $\\tchi^0_2$ cases. At Born level, the relevant subprocesses are $q\\bar q\\to \\tchi^0_i \\tilde g$, $g q\\to \\tchi^0_i \\tilde q_{L,R}$ and $q\\bar q'\\to \\tchi^0_i\\tchi^\\pm_j$; while at 1-loop, apart from radiative corrections to these processes, we consider also $gg\\to \\tchi^0_i\\tilde{g}$, for which a numerical code named PLATONgluino is released. The relative importance of these channels turns out to be extremely model dependent. Combining these results with an analogous study of the direct $\\tchi^0_i\\tchi^0_j$ pair production, should provide very sensitive tests of the SUSY models and the Dark Matter assignment.

  6. QCM-based rapid detection of PCR amplification products of Ehrlichia canis.

    Science.gov (United States)

    Bunroddith, Kespunyavee; Viseshakul, Nareerat; Chansiri, Kosum; Lieberzeit, Peter

    2018-02-25

    Ehrlichia canis is an intracellular parasitic bacterium and arthropod-borne pathogen that receives growing attention, because it leads to increasing morbidity and mortality in animals. It does so by causing canine monocytotropic ehrlichiosis (CME). Infected canines may lack obvious clinical signs and stay in chronic stage. Herein we report a rapid screening method based on PCR assay combined with quartz crystal microbalance (QCM) to design a DNA sensor for detecting E. canis in early stages of infection. The test relies on DNA amplification of target nucleotide sequences via PCR followed by detecting DNA-DNA hybridization using QCM. The approach did not result in any cross-hybridization toward other blood bacteria or parasites in dogs, such as Anaplasma platys, Babesia canis and Trypanosoma spp, but turned out selective for the target species. The limit of detection of QCM was as low as 4.1 × 10 9 molecules/μl of 289 bp E. canis PCR products corresponding to 22 copy numbers/μl of E. canis. Furthermore, the technique is also simple, does not require complicated equipment and can in principle be reused. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Pork detection in binary meat mixtures and some commercial food products using conventional and real-time PCR techniques.

    Science.gov (United States)

    Al-Kahtani, Hassan A; Ismail, Elsayed A; Asif Ahmed, Mohammed

    2017-03-15

    Pork DNA was detected in meat mixtures using both conventional PCR and real-time PCR (RT-PCR). Thirty meat mixtures containing beef, chicken, camel, rabbit, goat and sheep with varying percentage of pork (0%, 1%, 5%, 10%, and 20%) and 75 commercial food products, were analyzed using conventional and RT-PCR to determine the presence of pork DNA. Pork DNA standard curves and cycle threshold (Ct) values were used for quantification. The detection limits for pork DNA in the mixtures were 0.22, 0.047, 0.048, 0.0000037, 0.015ng/μl respectively. Unlike conventional PCR, RT-PCR detected pork DNA in nine processed food samples [chicken sausages (2), chicken luncheon (2), turkey meat loaf, milk chocolate with soft nougat, jelly, cake, and candies] at pork DNA concentrations of 0.0001ng/μl or less. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Detection of bovine central nervous system tissues in rendered animal by-products by one-step real-time reverse transcription PCR assay.

    Science.gov (United States)

    Andrievskaia, Olga; Tangorra, Erin

    2014-12-01

    Contamination of rendered animal byproducts with central nervous system tissues (CNST) from animals with bovine spongiform encephalopathy is considered one of the vehicles of disease transmission. Removal from the animal feed chain of CNST originated from cattle of a specified age category, species-labeling of rendered meat products, and testing of rendered products for bovine CNST are tasks associated with the epidemiological control of bovine spongiform encephalopathy. A single-step TaqMan real-time reverse transcriptase (RRT) PCR assay was developed and evaluated for specific detection of bovine glial fibrillary acidic protein (GFAP) mRNA, a biomarker of bovine CNST, in rendered animal by-products. An internal amplification control, mammalian b -actin mRNA, was coamplified in the duplex RRT-PCR assay to monitor amplification efficiency, normalize amplification signals, and avoid false-negative results. The functionality of the GFAP mRNA RRT-PCR was assessed through analysis of laboratory-generated binary mixtures of bovine central nervous system (CNS) and muscle tissues treated under various thermal settings imitating industrial conditions. The assay was able to detect as low as 0.05 % (wt/wt) bovine brain tissue in binary mixtures heat treated at 110 to 130°C for 20 to 60 min. Further evaluation of the GFAP mRNA RRT-PCR assay involved samples of industrial rendered products of various species origin and composition obtained from commercial sources and rendering plants. Low amounts of bovine GFAP mRNA were detected in several bovine-rendered products, which was in agreement with declared species composition. An accurate estimation of CNS tissue content in industrial-rendered products was complicated due to a wide range of temperature and time settings in rendering protocols. Nevertheless, the GFAP mRNA RRT-PCR assay may be considered for bovine CNS tissue detection in rendered products in combination with other available tools (for example, animal age

  9. Detection and identification of food-borne pathogens of the genera Campylobacter, Arcobacter and Helicobacter by multiplex PCR in poultry and poultry products.

    Science.gov (United States)

    Neubauer, C; Hess, M

    2006-10-01

    The objective of this study was to develop a multiplex polymerase chain reaction (PCR) to detect and differentiate food-borne pathogens of the three genera Campylobacter, Arcobacter and Helicobacter in a single step procedure. One common reverse primer and three genus-specific forward primers were designed by hybridizing to the 16S rRNA of selected reference strains. Besides the species with significance as food-borne pathogens isolated from poultry meat--Campylobacter jejuni, Campylobacter coli, Arcobacter butzleri and Helicobacter pullorum--several other members of these genera were tested to determine the specificity of the designed multiplex PCR. In total, 20 ATCC and NCTC reference strains of Campyobacter, Arcobacter and Helicobacter were used to evaluate the PCR. Specific amplificates were obtained from all thermophilic species of Campylobacter as well as from species of Arcobacter and Helicobacter. No amplification product was obtained from the non-thermophilic Campylobacter, C. hyointestinalis and C. fetus. Furthermore, a total of 43 field strains of the three genera isolated from poultry, pigs, cattle and humans were investigated using this PCR. To confirm the classification of 10 H. pullorum strains the 16S rRNAs were sequenced. The developed PCR is a helpful diagnostic tool to detect and differentiate Campylobacter, Arcobacter and Helicobacter isolated from poultry and poultry products.

  10. Setup of a PCR laboratory.

    Science.gov (United States)

    Khan, Zaheer

    2011-01-01

    PCR represents an extremely powerful and central molecular biology method. At the heart of its power is the exquisite sensitivity offered: single molecule detection in certain contexts. However, with great power comes great responsibility. Contamination of reagents or test samples with amplifiable material, such as previous reaction products, can be crippling to scientists applying PCR protocols. Prevention of PCR contamination is far and away preferred over eradication. This chapter sets out to offer guidance as to how to use PCR while minimising contamination problems.

  11. Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.

    Science.gov (United States)

    Girard, Laurie D; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G

    2015-02-07

    The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design

  12. Strain prioritization for natural product discovery by a high-throughput real-time PCR method.

    Science.gov (United States)

    Hindra; Huang, Tingting; Yang, Dong; Rudolf, Jeffrey D; Xie, Pengfei; Xie, Guangbo; Teng, Qihui; Lohman, Jeremy R; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Duan, Yanwen; Shen, Ben

    2014-10-24

    Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered.

  13. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

    DEFF Research Database (Denmark)

    Pereira, Rui; Pereira, Vania; Gomes, Iva

    2012-01-01

    Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility...

  14. Single-cell duplex RT-LATE-PCR reveals Oct4 and Xist RNA gradients in 8-cell embryos

    Directory of Open Access Journals (Sweden)

    Hartung Odelya

    2007-12-01

    Full Text Available Abstract Background The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass are pluripotent and express high levels of Oct4 mRNA, which is down-regulated in the surrounding trophectoderm. In contrast, the trophectoderm of female embryos contains Xist mRNA, which is absent from cells of the inner mass. Prior to blastocyst formation, all blastomeres of female embryos still express both of these RNAs. We, thus, postulated that simultaneous quantification of Oct4 and Xist transcripts in individual blastomeres at the 8-cell stage could be informative as to their subsequent fate. Testing this hypothesis, however, presented numerous technical challenges. We overcame these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR. Results We constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy with different methods. We then undertook analysis of sets of blastomeres isolated from embryos at the 8-cell stage. At this stage, all cells in the embryo are still pluripotent and morphologically equivalent. Our results demonstrate, however, that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. Analysis of multiple embryos also shows that Xist and Oct4 expression levels are not correlated at the 8-cell stage, although transcription of both genes is up-regulated at this time in development. In addition, comparison of data from males and females allowed us to determine that the efficiency of the Oct4/Xist assay is unaffected by sex-related differences in gene expression. Conclusion This paper describes the first example of multiplex RT-LATE-PCR and its utility, when

  15. Single-Step qPCR and dPCR Detection of Diverse CRISPR-Cas9 Gene Editing Events In Vivo

    Directory of Open Access Journals (Sweden)

    Micol Falabella

    2017-10-01

    Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-CRISPR-associated protein 9 (Cas9-based technology is currently the most flexible means to create targeted mutations by recombination or indel mutations by nonhomologous end joining. During mouse transgenesis, recombinant and indel alleles are often pursued simultaneously. Multiple alleles can be formed in each animal to create significant genetic complexity that complicates the CRISPR-Cas9 approach and analysis. Currently, there are no rapid methods to measure the extent of on-site editing with broad mutation sensitivity. In this study, we demonstrate the allelic diversity arising from targeted CRISPR editing in founder mice. Using this DNA sample collection, we validated specific quantitative and digital PCR methods (qPCR and dPCR, respectively for measuring the frequency of on-target editing in founder mice. We found that locked nucleic acid (LNA probes combined with an internal reference probe (Drop-Off Assay provide accurate measurements of editing rates. The Drop-Off LNA Assay also detected on-target CRISPR-Cas9 gene editing in blastocysts with a sensitivity comparable to PCR-clone sequencing. Lastly, we demonstrate that the allele-specific LNA probes used in qPCR competitor assays can accurately detect recombinant mutations in founder mice. In summary, we show that LNA-based qPCR and dPCR assays provide a rapid method for quantifying the extent of on-target genome editing in vivo, testing RNA guides, and detecting recombinant mutations.

  16. Single-Step qPCR and dPCR Detection of Diverse CRISPR-Cas9 Gene Editing Events in Vivo

    Science.gov (United States)

    Falabella, Micol; Sun, Linqing; Barr, Justin; Pena, Andressa Z.; Kershaw, Erin E.; Gingras, Sebastien; Goncharova, Elena A.; Kaufman, Brett A.

    2017-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based technology is currently the most flexible means to create targeted mutations by recombination or indel mutations by nonhomologous end joining. During mouse transgenesis, recombinant and indel alleles are often pursued simultaneously. Multiple alleles can be formed in each animal to create significant genetic complexity that complicates the CRISPR-Cas9 approach and analysis. Currently, there are no rapid methods to measure the extent of on-site editing with broad mutation sensitivity. In this study, we demonstrate the allelic diversity arising from targeted CRISPR editing in founder mice. Using this DNA sample collection, we validated specific quantitative and digital PCR methods (qPCR and dPCR, respectively) for measuring the frequency of on-target editing in founder mice. We found that locked nucleic acid (LNA) probes combined with an internal reference probe (Drop-Off Assay) provide accurate measurements of editing rates. The Drop-Off LNA Assay also detected on-target CRISPR-Cas9 gene editing in blastocysts with a sensitivity comparable to PCR-clone sequencing. Lastly, we demonstrate that the allele-specific LNA probes used in qPCR competitor assays can accurately detect recombinant mutations in founder mice. In summary, we show that LNA-based qPCR and dPCR assays provide a rapid method for quantifying the extent of on-target genome editing in vivo, testing RNA guides, and detecting recombinant mutations. PMID:28860183

  17. High-throughput Characterization of HIV-1 Reservoir Reactivation Using a Single-Cell-in-Droplet PCR Assay

    Directory of Open Access Journals (Sweden)

    Robert W. Yucha

    2017-06-01

    Full Text Available Reactivation of latent viral reservoirs is on the forefront of HIV-1 eradication research. However, it is unknown if latency reversing agents (LRAs increase the level of viral transcription from cells producing HIV RNA or harboring transcriptionally-inactive (latent infection. We therefore developed a microfluidic single-cell-in-droplet (scdPCR assay to directly measure the number of CD4+ T cells that produce unspliced (usRNA and multiply spliced (msRNA following ex vivo latency reversal with either an histone deacetylase inhibitor (romidepsin or T cell receptor (TCR stimulation. Detection of HIV-1 transcriptional activity can also be performed on hundreds of thousands of CD4+ T-cells in a single experiment. The scdPCR method was then applied to CD4+ T cells obtained from HIV-1-infected individuals on antiretroviral therapy. Overall, our results suggest that effects of LRAs on HIV-1 reactivation may be heterogeneous—increasing transcription from active cells in some cases and increasing the number of transcriptionally active cells in others. Genomic DNA and human mRNA isolated from HIV-1 reactivated cells could also be detected and quantified from individual cells. As a result, our assay has the potential to provide needed insight into various reservoir eradication strategies.

  18. Single-cell qPCR facilitates the optimization of hematopoietic differentiation in hPSCs/OP9 coculture system.

    Science.gov (United States)

    Chen, Haide; Jiang, Mengmeng; Xiao, Lei; Huang, He

    2018-03-15

    Human pluripotent stem cells (hPSCs)/OP9 coculture system is a widely used hematopoietic differentiation approach. The limited understanding of this process leads to its low efficiency. Thus, we used single-cell qPCR to reveal the gene expression profiles of individual CD34+ cells from different stages of differentiation. According to the dynamic gene expression of hematopoietic transcription factors, we overexpressed specific hematopoietic transcription factors (Gata2, Lmo2, Etv2, ERG, and SCL) at an early stage of hematopoietic differentiation. After overexpression, we generated more CD34+ cells with normal expression level of CD43 and CD31, which are used to define various hematopoietic progenitors. Furthermore, these CD34+ cells possessed normal differentiation potency in colony-forming unit assays and normal gene expression profiles. In this study, we demonstrated that single-cell qPCR can provide guidance for optimization of hematopoietic differentiation and transient overexpression of selected hematopoietic transcription factors can enhance hematopoietic differentiation.

  19. High-throughput Characterization of HIV-1 Reservoir Reactivation Using a Single-Cell-in-Droplet PCR Assay.

    Science.gov (United States)

    Yucha, Robert W; Hobbs, Kristen S; Hanhauser, Emily; Hogan, Louise E; Nieves, Wildaliz; Ozen, Mehmet O; Inci, Fatih; York, Vanessa; Gibson, Erica A; Thanh, Cassandra; Shafiee, Hadi; El Assal, Rami; Kiselinova, Maja; Robles, Yvonne P; Bae, Helen; Leadabrand, Kaitlyn S; Wang, ShuQi; Deeks, Steven G; Kuritzkes, Daniel R; Demirci, Utkan; Henrich, Timothy J

    2017-06-01

    Reactivation of latent viral reservoirs is on the forefront of HIV-1 eradication research. However, it is unknown if latency reversing agents (LRAs) increase the level of viral transcription from cells producing HIV RNA or harboring transcriptionally-inactive (latent) infection. We therefore developed a microfluidic single-cell-in-droplet (scd)PCR assay to directly measure the number of CD4 + T cells that produce unspliced (us)RNA and multiply spliced (ms)RNA following ex vivo latency reversal with either an histone deacetylase inhibitor (romidepsin) or T cell receptor (TCR) stimulation. Detection of HIV-1 transcriptional activity can also be performed on hundreds of thousands of CD4+ T-cells in a single experiment. The scdPCR method was then applied to CD4 + T cells obtained from HIV-1-infected individuals on antiretroviral therapy. Overall, our results suggest that effects of LRAs on HIV-1 reactivation may be heterogeneous-increasing transcription from active cells in some cases and increasing the number of transcriptionally active cells in others. Genomic DNA and human mRNA isolated from HIV-1 reactivated cells could also be detected and quantified from individual cells. As a result, our assay has the potential to provide needed insight into various reservoir eradication strategies. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Improvement of Barley yellow dwarf virus-PAV detection in single aphids using a fluorescent real time RT-PCR.

    Science.gov (United States)

    Fabre, Frédéric; Kervarrec, Christine; Mieuzet, Lucie; Riault, Gérard; Vialatte, Aude; Jacquot, Emmanuel

    2003-06-09

    One of the major factors determining the incidence of Barley yellow dwarf virus (BYDV) on autumn-sown cereals is the viruliferous state of immigrant winged aphids. This variable is assessed routinely using the enzyme-linked immunosorbant assay (ELISA). However, the threshold for virus detection by ELISA can lead to false negative results for aphids carrying less than 10(6) particles. Although molecular detection techniques enabling the detection of lower virus quantities in samples are available, the relatively laborious sample preparation and data analysis have restricted their use in routine applications. A gel-free real-time one-step reverse transcription polymerase chain reaction (RT-PCR) protocol is described for specific detection and quantitation of BYDV-PAV, the most widespread BYDV species in Western Europe. This new assay, based on TaqMan technology, detects and quantifies from 10(2) to 10(8) BYDV-PAV RNA copies. This test is 10 and 10(3) times more sensitive than the standard RT-PCR and ELISA assays published previously for BYDV-PAV detection and significantly improves virus detection in single aphids. Extraction of nucleic acids from aphids using either phenol/chloroform or chelatin resin-based protocols allow the use of pooled samples or of a small part (up to 1/1600th) of a single aphid extract for efficient BYDV-PAV detection.

  1. Pulmonary toxoplasmosis in immunocompromised patients with interstitial pneumonia: a single-centre prospective study assessing PCR-based diagnosis.

    Science.gov (United States)

    Desoubeaux, Guillaume; Cabanne, Églantine; Franck-Martel, Claire; Gombert, Martin; Gyan, Emmanuel; Lissandre, Séverine; Renaud, Marc; Monjanel, Hélène; Dartigeas, Caroline; Bailly, Éric; Van Langendonck, Nathalie; Chandenier, Jacques

    2016-08-01

    Pulmonary toxoplasmosis has become a very rare parasitic infection since the advent of highly active antiretroviral therapies. It is generally diagnosed by the direct microscopic observation of Toxoplasma gondii tachyzoites in bronchoalveolar lavage fluid (BALF). The aim of this study was to assess possible improvements in diagnostic performance associated with the use of real-time PCR. This prospective study was carried out on BALFs obtained from immunocompromised patients over a 2-year period. We systematically compared the results of conventional staining with those of molecular detection. Two cases of pulmonary toxoplasmosis were diagnosed for a total of 336 samples. PCR did not detect any additional cases and was more time-consuming than conventional staining. Conventional staining is a reliable technique and is probably the most appropriate method for experienced microbiology laboratories, whereas T. gondii-specific PCR may be useful for laboratories with less experience in parasitology. 2015_030, May 27th 2015. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  2. A Unique Primer with an Inosine Chain at the 5'-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method.

    Directory of Open Access Journals (Sweden)

    Hideki Shojo

    Full Text Available Polymerase chain reaction-amplified product length polymorphism (PCR-APLP is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3'-terminus of each primer. To use this method at least two allele-specific primers and one "counter-primer", which serves as a common forward or reverse primer of the allele-specific primers, are required. The allele-specific primers have SNP sites at the 3'-terminus, and another primer should have a few non-complementary flaps at the 5'-terminus to detect SNPs by determining the difference of amplicon length by PCR and subsequent electrophoresis. A major disadvantage of the addition of a non-complementary flap is the non-specific annealing of the primer with non-complementary flaps. However, a design principle for avoiding this undesired annealing has not been fully established, therefore, it is often difficult to design effective APLP primers. Here, we report allele-specific primers with an inosine chain at the 5'-terminus for PCR-APLP analysis. This unique design improves the competitiveness of allele-specific primers and the reliability of SNP analysis when using the PCR-APLP method.

  3. Rep-PCR typing of Staphylococcus spp. strains in meat paste production line and identification of their origin

    Directory of Open Access Journals (Sweden)

    Ivan Manga

    2015-05-01

    Full Text Available A meat paste production line and its microbial parameters have been evaluated in single Czech company. The raw meat paste samples before heat treatment were tested positively for the presence of three staphylococci species: Staphylococcus aureus, Staphylococcus haemolyticus and Staphylococcus epidermidis. Subsequent microbial analysis of meat paste components and ingredients (fresh meat, water, spices, equipment identified only the spices used as positive for S. aureus (coriander, cinnamon, badian, mustard – (10 - 40 cfu/g and S. haemolyticus strains (juniper, ginger. The collection of sixteen collected strains (S. aureus (n = 4, S. haemolyticus (n = 4, S. epidermidis (n = 8 has been typed with the rep-PCR method utilising (GTG5 primer. Analysis of the fingerprints using the unweighted pair-group method using arithmetic averages (UPGMA clustering method revealed presence of eleven strain clusters with similarity lower than 90%: two fingerprint clusters of S. aureus, three individual clusters characteristic for S. haemolyticus and six different S. epidermidis specific clusters. The S. aureus strains from different types of spice were identical, resp. very similar. Molecular tracking composed from the rep-PCR analysis of acquired isolates and comparison among all collected fingerprints confirmed the spices to be the source of both S. aureus and S. haemolyticus strains identified in raw meat paste. The additional rep-PCR analysis of the S. epidermidis collection confirmed usability and performance of this method. The antibiotic susceptibility to fourteen individual antibiotics has been examined among the collected staphylococci strains. The predominant erythromycin resistance (68.8% was followed with the resistance to amoxicillin/clavulanic acid (56.2%. Other resistances observed were less frequent (clindamycin – 12.5%, oxacillin – 6.3%, tetracycline – 6.3%, sulphamethoxazole-trimethoprim – 6.3%, chloramphenicol – 6.3%, novobiocin – 6

  4. Single reaction, real time RT-PCR detection of all known avian and human metapneumoviruses.

    Science.gov (United States)

    Lemaitre, E; Allée, C; Vabret, A; Eterradossi, N; Brown, P A

    2018-01-01

    Current molecular methods for the detection of avian and human metapneumovirus (AMPV, HMPV) are specifically targeted towards each virus species or individual subgroups of these. Here a broad range SYBR Green I real time RT-PCR was developed which amplified a highly conserved fragment of sequence in the N open reading frame. This method was sufficiently efficient and specific in detecting all MPVs. Its validation according to the NF U47-600 norm for the four AMPV subgroups estimated low limits of detection between 1000 and 10copies/μL, similar with detection levels described previously for real time RT-PCRs targeting specific subgroups. RNA viruses present a challenge for the design of durable molecular diagnostic test due to the rate of change in their genome sequences which can vary substantially in different areas and over time. The fact that the regions of sequence for primer hybridization in the described method have remained sufficiently conserved since the AMPV and HMPV diverged, should give the best chance of continued detection of current subgroups and of potential unknown or future emerging MPV strains. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Automated purification of Borrelia burgdorferi s.l. PCR products with KingFisherTM magnetic particle processor prior to genome sequencing

    International Nuclear Information System (INIS)

    Maekinen, Johanna; Marttila, Harri; Viljanen, Matti K.

    2001-01-01

    Borrelia burgdorferi sensu lato genospecies were differentiated by PCR-based sequencing of the borrelial flagellin gene. To evaluate the usefulness of KingFisher TM magnetic particle processor in PCR product purification, borrelia PCR products were purified with KingFisher TM magnetic particle processor prior to cycle sequencing and the quality of the sequence data received was analyzed. KingFisher was found to offer a rapid and reliable alternative for borrelial PCR product purification

  6. Automated purification of Borrelia burgdorferi s.l. PCR products with KingFisher{sup TM} magnetic particle processor prior to genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Maekinen, Johanna E-mail: johanna.makinen@utu.fi; Marttila, Harri; Viljanen, Matti K

    2001-07-01

    Borrelia burgdorferi sensu lato genospecies were differentiated by PCR-based sequencing of the borrelial flagellin gene. To evaluate the usefulness of KingFisher{sup TM} magnetic particle processor in PCR product purification, borrelia PCR products were purified with KingFisher{sup TM} magnetic particle processor prior to cycle sequencing and the quality of the sequence data received was analyzed. KingFisher was found to offer a rapid and reliable alternative for borrelial PCR product purification.

  7. In vivo recombineering of bacteriophage λ by PCR fragments and single-strand oligonucleotides

    International Nuclear Information System (INIS)

    Oppenheim, Amos B.; Rattray, Alison J.; Bubunenko, Mikhail; Thomason, Lynn C.; Court, Donald L.

    2004-01-01

    We demonstrate that the bacteriophage λ Red functions efficiently recombine linear DNA or single-strand oligonucleotides (ss-oligos) into bacteriophage λ to create specific changes in the viral genome. Point mutations, deletions, and gene replacements have been created. While recombineering with oligonucleotides, we encountered other mutations accompanying the desired point mutational change. DNA sequence analysis suggests that these unwanted mutations are mainly frameshift deletions introduced during oligonucleotide synthesis

  8. Single Top-Quark Production at CDF

    CERN Multimedia

    CERN. Geneva

    2008-01-01

    The main challenge of the single top-quark search at the Tevatron is the huge background from W+jets events and QCD events, which makes the use of advanced multivariate techniques essential. The recent single top analyses using either the matrix element method, neural networks, likelihood discriminants or boosted decision trees as well as the combination of the former three analyses will be presented...

  9. New Physics in Single-Top Production

    CERN Document Server

    Kind, OM; The ATLAS collaboration

    2013-01-01

    In this presentation for TOP 2013 the latest results on searches of physics beyond the Standard Model using single-top signatures from CDF, CMS, D0 and ATLAS are collected. This includes searches for unknown resonances like W' or b*, measurements of the W helicity fractions and top polarisation in single-top events, as well as tests for CP violation, FCNC or anomalous weak couplings.

  10. Development of a PCR assay suitable for Campylobacter spp. mass screening programs in broiler production

    DEFF Research Database (Denmark)

    Bang, Dang Duong; Pedersen, Karl; Madsen, Mogens

    2001-01-01

    culture techniques since 1998. However, using conventional culture methods is time consuming and laborious, and therefore a Polymerase Chain Reaction (PCR) Campylobacter detection assay suitable for mass screening of cloacal swab samples from broilers was developed. By comparing the PCR detection...... with conventional culture methods, significantly more samples were found positive for Campylobacter with the PCR method. The PCR method is rapid, sensitive and suitable for mass screening for Campylobacter in poultry. Using this PCR method Campylobacter can be detected within 15 h. Notably, the method can...... be applied to detect Campylobacter directly from chicken feces at the species level....

  11. CODEHOP PCR and CODEHOP PCR primer design.

    Science.gov (United States)

    Staheli, Jeannette P; Boyce, Richard; Kovarik, Dina; Rose, Timothy M

    2011-01-01

    While PCR primer design for the amplification of known sequences is usually quite straightforward, the design, and successful application of primers aimed at the detection of as yet unknown genes is often not. The search for genes that are presumed to be distantly related to a known gene sequence, such as homologous genes in different species, paralogs in the same genome, or novel pathogens in diverse hosts, often turns into the proverbial search for the needle in the haystack. PCR-based methods commonly used to address this issue involve the use of either consensus primers or degenerate primers, both of which have significant shortcomings regarding sensitivity and specificity. We have developed a novel primer design approach that diminishes these shortcomings and instead takes advantage of the strengths of both consensus and degenerate primer designs, by combining the two concepts into a Consensus-Degenerate Hybrid Oligonucleotide Primer (CODEHOP) approach. CODEHOP PCR primers contain a relatively short degenerate 3' core and a 5' nondegenerate clamp. The 3' degenerate core consists of a pool of primers containing all possible codons for a 3-4 aminoacid motif that is highly conserved in multiply aligned sequences from known members of a protein family. Each primer in the pool also contains a single 5' nondegenerate nucleotide sequence derived from a codon consensus across the aligned aminoacid sequences flanking the conserved motif. During the initial PCR amplification cycles, the degenerate core is responsible for specific binding to sequences encoding the conserved aminoacid motif. The longer consensus clamp region serves to stabilize the primer and allows the participation of all primers in the pool in the efficient amplification of products during later PCR cycles. We have developed an interactive web site and algorithm (iCODEHOP) for designing CODEHOP PCR primers from multiply aligned protein sequences, which is freely available online. Here, we describe the

  12. Novel single-round PCR and cloning of full-length envelope genes of HIV-1 may yield new insight into biomolecular antibacterial drug development.

    Science.gov (United States)

    McDonald, Richard; Burnett, Virginia

    2005-06-01

    Nested or semi-nested polymerase chain reaction (PCR) with a 'hot start' is the preferred amplification method for full-length, in-frame envelope genes (gp160) of the human immunodeficiency virus type 1 (HIV-1). This generally follows an extensive screening process. This paper describes an effective single-round PCR method and cloning process for HIV-1 gp160 from clinical samples, and cell and tissue cultures developed during the early stages of construction of a molecular HIV-1 vaccine. The amplification method and cloning process are adaptable to full-length HIV-1, HIV-2, and other viral production processes. Also described within, is one solution to the most-often extensive screening process for inserts containing full-length, in-frame gp160. Of note, was a perceived toxicity of gp160 to bacteria during the culturing and the scaling-up process that created the extensive screening process. The toxicity association was not found with the individual gp160 genes, the gp120 or the gp41 gene, with other viral regions similar or larger in molecular weight to gp160, or with other non-gp160 full-length genes of HIV-1 such as pol and gag genes. The HIV-1 gp160 toxicity issue may provide insight towards the development of the next generation of novel biomolecular drugs against bacterial infections.

  13. [Progress in digital PCR technology and application].

    Science.gov (United States)

    Lin, Jiaqi; Su, Guocheng; Su, Wenjin; Zhou, Changyi

    2017-02-25

    Digital PCR is an emerging analysis technology for absolute quantification after realtime-PCR. Through digital PCR, single DNA molecules are distributed into isolated reactions, and the product with fluorescence signal can be detected and analyzed after amplification. With the advantages of higher sensitivity and accuracy, digital PCR, independent of a standard curve, is developing rapidly and applied widely to the next generation sequencing and detection fields, such as gene mutation, copy number variation, microorganism, and genetically modified food. In this article, we reviewed the quantitative method and research progress of digital PCR technology in the main application fields.

  14. Restriction fragment length polymorphism (RFLP) analysis of PCR products amplified from 18S ribosomal RNA gene of Trypanosoma congolense

    International Nuclear Information System (INIS)

    Osanyo, A.; Majiwa, P.W.

    2006-01-01

    Oligonucleotide primers were designed from the conserved nucleotide sequences of 18S ribosomal RNA (18S rRNA) gene of protozoans: Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum. The primers were used in polymerace chain reaction (PCR) to generate PCR products of approximately 1 Kb using genomic DNA from T. brucei and the four genotypic groups of T. congolense as template. The five PCR products so produced were digested with several restriction enzymes and hybridized to a DNA probe made from T. brucei PCR product of the same 18S rRNA gene region. Most restriction enzyme digests revealed polymorphism with respect to the location of their recognition sites on the five PCR products. The restriction fragment length polymorphism (RFLP) pattern observed indicate that the 18S rRNA gene sequences of trypanosomes: T. brucei and the four genotypes of T.congolence group are heterogeneous. The results further demonstrate that the region that was amplified can be used in specific identification of trypanosomes species and subspecies.(author)

  15. Real-Time PCR Detection ofBurkholderia cepaciain Pharmaceutical Products Contaminated with Low Levels of Bacterial Contamination.

    Science.gov (United States)

    Jimenez, Luis; Jashari, Theranda; Vasquez, Jenifer; Zapata, Stephanie; Bochis, Joy; Kulko, Margarita; Ellman, Victoria; Gardner, Matthew; Choe, Tina

    2018-01-01

    A real-time polymerase chain reaction (RT-PCR) assay was developed to detect Burkholderia cepacia in pharmaceutical products contaminated with low levels of bacteria. Different pharmaceutical suspensions were artificially contaminated with B. cepacia , Escherichia coli , Staphylococcus aureus , and Bacillus megaterium After a 24 h incubation in trypticase soy broth with Tween 20, samples were streaked on mannitol salt, phenyl ethyl alcohol, eosin methylene blue, MacConkey, and pseudomonas isolation agar. Microbial DNA was extracted from each sample by using a Tris-EDTA, proteinase K, Tween 20 buffer. Regular PCR targeting the 1.5 kilobases 16S rRNA eubacterial gene and cloning showed the predominant DNA in the extracted mix belonged to E. coli Selective media isolation of bacterial contamination showed B. cepacia only detected on pseudomonas isolation while eosin methylene blue and MacConkey detected only E. coli RT-PCR using primers PSL1 and PSR1 amplified a 209 bp 16S rRNA fragment using a Roche LightCycler 96 ® system with SYBR green I, a common double-stranded binding dye. The cycle at which fluorescence from amplification exceeds the background fluorescence was referred to as quantification cycle. All samples were found to be positive by standard microbiological testing and RT-PCR. B. cepacia was detected within 30 h in all contaminated samples using RT-PCR. Based upon standard curve analysis of B. cepacia DNA, the minimum DNA concentration that could be detected was 10 fg/uL with a correlation value of 0.98. RT-PCR detection of B. cepacia allowed faster quality control analysis, corrective actions, and process optimization. LAY ABSTRACT: A real-time polymerase chain reaction (RT-PCR) assay was developed to detect Burkholderia cepacia in pharmaceutical products contaminated with low levels of bacteria. B. cepacia is the number one reason for microbial contamination recalls of non-sterile drug products in the USA. RT-PCR using primers PSL1 and PSR1 amplified a

  16. A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

    Science.gov (United States)

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-01-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

  17. Development of a simplified RT-PCR without RNA isolation for rapid detection of RNA viruses in a single small brown planthopper (Laodelphax striatellus Fallén).

    Science.gov (United States)

    Xu, Qiufang; Liu, Haoqiu; Yuan, Pingping; Zhang, Xiaoxia; Chen, Qingqing; Jiang, Xuanli; Zhou, Yijun

    2017-05-03

    The small brown planthopper (SBPH) is an important pest of cereal crops and acts as a transmission vector for multiple RNA viruses. Rapid diagnosis of virus in the vector is crucial for efficient forecast and control of viral disease. Reverse transcription polymerase chain reaction (RT-PCR) is a rapid, sensitive and reliable method for virus detection. The traditional RT-PCR contains a RNA isolation step and is widely used for virus detection in insect. However, using the traditional RT-PCR for detecting RNA virus in individual SBPHs becomes challenging because of the expensive reagents and laborious procedure associated with RNA isolation when processing a large number of samples. We established a simplified RT-PCR method without RNA isolation for RNA virus detection in a single SBPH. This method is achieved by grinding a single SBPH in sterile water and using the crude extract directly as the template for RT-PCR. The crude extract containing the virus RNA can be prepared in approximately two minutes. Rice stripe virus (RSV), rice black streaked dwarf virus (RBSDV) and Himetobi P virus (HiPV) were successfully detected using this simplified method. The detection results were validated by sequencing and dot immunobinding assay, indicating that this simplified method is reliable for detecting different viruses in insects. The evaluation of the sensitivity of this method showed that both RSV and HiPV can be detected when the cDNA from the crude extract was diluted up to 10 3 fold. Compared to the traditional RT-PCR with RNA isolation, the simplified RT-PCR method greatly reduces the sample processing time, decreases the detection cost, and improves the efficiency by avoiding RNA isolation. A simplified RT-PCR method is developed for rapid detection of RNA virus in a single SBPH without the laborious RNA isolation step. It offers a convenient alternative to the traditional RT-PCR method.

  18. Identification of new isolates of Bacillus thuringiensis using rep-PCR products and delta-endotoxin electron microscopy

    Directory of Open Access Journals (Sweden)

    A.S.G. Lima

    2002-01-01

    Full Text Available PCR has been used to analyze the distribution of REP (Repetitive Extragenic Palindromic and ERIC (Enterobacterial Repetitive Intergenic Consensus sequences (rep-PCR found within the genome of the bacterium Bacillus thuringiensis, with the purpose to analyze the genetic similarities among 56 subspecies samples and 95 field isolates. The PCR products were analyzed by EB-AGE (ethidium bromide-agarose electrophoresis and then submitted to banding comparisons, based on the Phyllip software algorithm. When the banding similarities were considered for comparison purposes among all the strains, the phylogenic tree patterns varied according to the rep-PCR primers considered, but, from a broader point of view, the ERIC sequences produced better results, which, together with electron microscopy analysis of the released parasporal bodies and colony morphology characteristics, allowed to detect two possible new subspecies of B. thuringiensis.

  19. Identification of new isolates of Bacillus thuringiensis using rep-PCR products and d-endotoxin electron microscopy

    Directory of Open Access Journals (Sweden)

    Lima A.S.G.

    2002-01-01

    Full Text Available PCR has been used to analyze the distribution of REP (Repetitive Extragenic Palindromic and ERIC (Enterobacterial Repetitive Intergenic Consensus sequences (rep-PCR found within the genome of the bacterium Bacillus thuringiensis, with the purpose to analyze the genetic similarities among 56 subspecies samples and 95 field isolates. The PCR products were analyzed by EB-AGE (ethidium bromide-agarose electrophoresis and then submitted to banding comparisons, based on the Phyllip software algorithm. When the banding similarities were considered for comparison purposes among all the strains, the phylogenic tree patterns varied according to the rep-PCR primers considered, but, from a broader point of view, the ERIC sequences produced better results, which, together with electron microscopy analysis of the released parasporal bodies and colony morphology characteristics, allowed to detect two possible new subspecies of B. thuringiensis.

  20. Analysis of Single Nucleotide Polymorphism (SNP rs22114085 Associated with Canine Atopic Dermatitis by PCR-RFLP Method

    Directory of Open Access Journals (Sweden)

    Martina Miluchová

    2012-05-01

    Full Text Available Canine atopic dermatitis (cAD is a common inflammatory skin disease that is considered to be a naturally occurring, spontaneous model of human atopic dermatitis (eczema. The aim of the paper was to identify of the SNP rs22114085 in different dog breeds. The material involved 52 dogs from 5 different breeds. Canine genomic DNA was isolated from saliva by modified method with using DNAzol® and linear polyacrylamide (LPA carrier and from blood by using commercial kit NucleospinBlood and used in order to estimate rs22114085 SNP genotypes by PCR-RFLP method. The PCR products were digested with DdeI restriction enzyme. The C allele was distributed in Czech Pointer, Chihuahua, German Wirehaired Pointer with an allele frequency ranging from 0.4545 to 1.00. In the population of Czech Pointer we detected all genotypes CC, CT and TT with frequency in male 0.25, 0.5833 and 0.1667, and in female 0.2728, 0.3636 and 0.3636, subsequently. In German Wirehaired Pointer was detected homozygote genotype CC in male and heterozygote genotype CT in female with frequency 1 and 1. In Chihuahua was observed homozygote genotype CC and heterozygote genotype CT with frequency 0.3333 and 0.6667, subsequently. In Golden retriever and Pincher we detected genotype TT with frequency 1.

  1. Analysis of single nucleotide polymorphism (SNP RS23472497 associated with canine atopic dermatitis by ACRS-PCR method

    Directory of Open Access Journals (Sweden)

    Martina Miluchová

    2014-05-01

    Full Text Available The aim of the paper was to identify of the SNP rs23472497 associated with canine atopic dermatitis (cAD. cAD is a common inflammatory skin disease that is considered to be a naturally occurring, spontaneous model of human atopic dermatitis (eczema. The material involved 60 dogs from 6 different breeds. Canine genomic DNA was isolated from saliva by modified method with using DNAzol® and linear polyacrylamide (LPA carrier and from blood by using commercial kit NucleospinBlood and used in order to estimate rs23472497 SNP genotypes by ACRS-PCR method. The PCR products were digested with NlaIII restriction enzyme. In the population of Czech Pointer and Slovak Wirehaired Pointer we detected all genotypes AA, AG and GG with frequency 0.0732, 0.5122 and 0.4146 for Czech Pointer and 0.1818, 0.5455 and 0.2727 for Slovak Wirehaired Pointer. In Border Collie was observed heterozygote genotype AG and homozygote genotype GG with frequency 0.6667 and 0.3333, subsequently. In German Wirehaired Pointer, Australian Shepherd dog and American Staffordshire terrier we detected only genotype AG with frequency 1. The A allele was distributed with an allele frequency ranging from 0.3293 to 0.5. The G allele was distributed with an allele frequency ranging from 0.5 to 0.6707.

  2. Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

    Science.gov (United States)

    Aravindran, S.; Sahilah, A. M.; Aminah, A.

    2014-09-01

    Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

  3. Purification and Concentration of PCR Products Leads to Increased Signal intensities with Fewer Allelic Drop-Outs and Artifacts

    DEFF Research Database (Denmark)

    Maria Irlund Pedersen, Line; Stangegaard, Michael; Mogensen, Helle Smidt

    2011-01-01

    and the quality of the DNA profiles without re-amplification of the sample. We have validated and implemented an automated method to purify and 2-fold concentrate PCR products resulting in allelic peaks with higher intensity (a median height across all loci from 130 to 404 RFU), fewer allelic dropouts......Capillary electrophoresis of amplified DNA isolated from trace evidence samples occasionally results in inadequate STR-profiles due to artifacts caused by e.g. primers and dNTPs. Removal of artifacts by purification and subsequent concentration of the PCR products may increase the sensitivity...

  4. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning.

    Science.gov (United States)

    Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva

    2017-01-01

    The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Quick and clean cloning: a ligation-independent cloning strategy for selective cloning of specific PCR products from non-specific mixes.

    Directory of Open Access Journals (Sweden)

    Frank Thieme

    Full Text Available We have developed an efficient strategy for cloning of PCR products that contain an unknown region flanked by a known sequence. As with ligation-independent cloning, the strategy is based on homology between sequences present in both the vector and the insert. However, in contrast to ligation-independent cloning, the cloning vector has homology with only one of the two primers used for amplification of the insert. The other side of the linearized cloning vector has homology with a sequence present in the insert, but nested and non-overlapping with the gene-specific primer used for amplification. Since only specific products contain this sequence, but none of the non-specific products, only specific products can be cloned. Cloning is performed using a one-step reaction that only requires incubation for 10 minutes at room temperature in the presence of T4 DNA polymerase to generate single-stranded extensions at the ends of the vector and insert. The reaction mix is then directly transformed into E. coli where the annealed vector-insert complex is repaired and ligated. We have tested this method, which we call quick and clean cloning (QC cloning, for cloning of the variable regions of immunoglobulins expressed in non-Hodgkin lymphoma tumor samples. This method can also be applied to identify the flanking sequence of DNA elements such as T-DNA or transposon insertions, or be used for cloning of any PCR product with high specificity.

  6. Evaluation of PCR and nested PCR for laboratory diagnosis of hepatitis C virus infection.

    Science.gov (United States)

    Aslanzadeh, J; Padilla, B B; Shanley, J D

    1996-06-01

    The detection of hepatitis C virus (HCV) RNA by nested polymerase chain reaction (PCR) is believed to be the most reliable method to diagnose HCV infections. A pitfall of nested PCR is that it is prone to contamination. Single step reverse transcription-PCR (RT-PCR) was performed, prospectively, on 80 sera from 59 patients with a set of primers that amplified a 273 bp sequence unique to the 5' noncoding (NC) region of the HCV genome. Nested PCR, was performed on all PCR negative specimens with a set of primers that amplified a 255 bp internal to the original primers. Single step RT-PCR was positive on 45 sera from 35 patients following gel electrophoresis and on two additional sera from two patients following Southern blot hybridization. Nested PCR was positive on two more sera following gel electrophoresis of the nested PCR products. These two patients were seropositive and subsequent serum from one patient was positive by single step PCR. Three additional sera were positive following Southern blot analysis of the nested PCR products. Two patients were seropositive and had elevated serum alanine aminotransferase (ALT) levels. The third patient was seronegative with normal ALT level and was considered a false positive. The remaining seronegative control specimens were PCR negative by both methods. The majority of PCR positive patients (82%) had elevated ALT levels, while the majority of PCR negative seropositive patients had normal ALT levels. We conclude that single step PCR is a sensitive test for the laboratory diagnoses of the majority of the HCV infections.

  7. [Detection of bacteria genus Campylobacter in poultry products by PCR method].

    Science.gov (United States)

    Bulakhov, A V; Efimochkina, N R; Sheveleva, S A

    2010-01-01

    Researches on method PCR adaptation for detection Campylobacter spp. in poultry meat with use of two devices and kits and its comparison with a bacteriological method under characteristics of specificity and the bottom limit of definition are carried out. Higher efficiency of detection of Campylobacters to PCR in real time, than a bacteriological method, and also suitability for the purposes of the foods control of the kits intended initially for clinical diagnostics is shown. It is specified on necessity of a stage of bacteria enrichment before PCR up to a level above 10(5) CFU/g.

  8. [Use of real-time PCR for quantitative assessment of lactic acid bacteria and bifidobacteria in dairy products].

    Science.gov (United States)

    Zelenaia, L B; Kovalenko, N K; Oblap, R V; Hovak, N B; Golubets, R A

    2012-01-01

    Composition of lactic acid bacteria and bifidobacteria in raw milk and home-made milk products has been analyzed using real-time PCR (quantitative PCR) with genus-specific primers to Enterococcus, Lactobacillus and Bifidobacteria. Bacteria belonging to these genera have been revealed in all samples analyzed (milk, sour cream, cottage cheese). It has been shown that the representatives of Enterococcus and Lactobacillus genera dominated in the samples analyzed (10(3)-10(7) genome equivalent/ml (mg)). The largest number of these microorganisms (10(7) genome equivalent/mg) has been detected in cottage cheese.

  9. Improvement of the sensitivity and resolution of PCR-SSCP analysis ...

    Indian Academy of Sciences (India)

    25-dihydroxyvitamin D3) re- ceptor (VDR) to ... C for 5 min. After amplifi- cation, PCR product was purified with low-melting agarose. Keywords. single-strand conformation polymorphism; mutation screening; primer; PCR. Journal of Genetics ...

  10. Comparison of phenotypic and PCR methods for detection of carbapenemases production by Enterobacteriaceae

    Directory of Open Access Journals (Sweden)

    Maryam AlTamimi

    2017-01-01

    Full Text Available Dissemination of carbapenem resistance via Enterobacteriaceae, particularly among Klebsiella pneumoniae and Escherichia coli, is a major public health concern. Rapid methods for determining antimicrobial susceptibility are important to ensure adequate and appropriate use of antimicrobial agents and to limit the spread of these bacteria. In the current study, we compared the rapidity, sensitivity and specificity of traditional methods and molecular-based Xpert Carba-R PCR assay to identify sixty isolates, (26 E. coli and 34 K. pneumoniae. The specificity of MicroScan was 100% while sensitivity to ertapenem (ERT, imipenem (IMI, and meropenem (MER was 93%, 68.9%, and 55.17%, respectively. For the modified Hodge test, the specificity was 96.77% and sensitivity was 89.65%. Although some results of phenotypic assays matched with the definite PCR identification, some results were misleading. Out of the 29 positive PCR samples, three samples of K. pneumoniae were negative for the MHT and one E. coli sample was MHT positive but negative for the PCR. Nine samples were positive for the PCR but were determined as carbapenem sensitive by MicroScan. While MicroScan and MHT requires several hours and multi-steps to obtain results, Xpert Carba-R PCR assay takes less than an hour. Therefore, we recommend using Gene xpert Carba-R assay for the optimal carbapenemnase detection with reducing material, manpower and cost. Also it is important to know the type of carbapenemase is present.

  11. Determination of cis/trans phase of variations in the MC1R gene with allele-specific PCR and single base extension

    DEFF Research Database (Denmark)

    Mengel-From, Jonas; Børsting, Claus; Sanchez, Juan J

    2008-01-01

    The MC1R gene encodes a protein with key regulatory functions in the melanin synthesis. A multiplex PCR and a multiplex single base extension protocol were established for genotyping six exonic MC1R variations highly penetrant for red hair (R), four exonic MC1R variations weakly penetrant for red...

  12. Estimating trematode prevalence in snail hosts using a single-step duplex PCR: how badly does cercarial shedding underestimate infection rates?

    Czech Academy of Sciences Publication Activity Database

    Born-Torrijos, A.; Poulin, R.; Raga, J. A.; Holzer, Astrid S.

    2014-01-01

    Roč. 7, MAY 2014 (2014), s. 243 ISSN 1756-3305 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : prevalence * detection * snail host * double infection * single-steo duplex PCR Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.430, year: 2014

  13. A SYBR Green real-time PCR assay to detect and quantify pork meat in processed poultry meat products.

    Science.gov (United States)

    Soares, Sónia; Amaral, Joana S; Oliveira, M Beatriz P P; Mafra, Isabel

    2013-05-01

    Species identification in meat products has grown in interest in recent years since these foodstuffs are susceptible targets for fraudulent labelling. In this work, a real-time PCR approach based on SYBR Green dye was proposed for the quantitative detection of pork meat in processed meat products. For the development of the method, binary meat mixtures containing known amounts of pork meat in poultry meat were used to obtain a normalised calibration model from 0.1 to 25% with high linear correlation and PCR efficiency. The method revealed high specificity by melting curve analysis, being successfully validated through its application to blind meat mixtures, which confirmed its adequacy for pork meat determination. The fully applicability of the method was further demonstrated in commercial meat products, allowing verification of labelling compliance and identification of meat species in processed foods. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Rapid genetically modified organism (GMO screening of various food products and animal feeds using multiplex polymerase chain reaction (PCR

    Directory of Open Access Journals (Sweden)

    Lisha, V.

    2017-01-01

    Full Text Available modified crops which brought up a controversy on the safety usage of genetically modified organisms (GMOs. It has been implemented globally that all GMO products and its derived ingredients should have regulations on the usage and labelling. Thus, it is necessary to develop methods that allow rapid screening of GMO products to comply with the regulations. This study employed a reliable and flexible multiplex polymerase chain reaction (PCR method for the rapid detection of transgenic elements in genetically modified soy and maize along with the soybean LECTIN gene and maize ZEIN gene respectively. The selected four common transgenic elements were 35S promoter (35S; Agrobacterium tumefaciens nopaline synthase terminator (NOS; 5-enolypyruvylshikimate-3-phosphate synthase (epsps gene; and Cry1Ab delta-endotoxin (cry1Ab gene. Optimization of the multiplex PCR methods were carried out by using 1% Roundup ReadyTM Soybean (RRS as the certified reference material for soybean that produced fourplex PCR method detecting 35S promoter, NOS terminator, epsps gene and soybean LECTIN gene and by using 1% MON810 as the certified reference material for maize that produced triplex PCR method detecting 35S promoter, cry1Ab gene and maize ZEIN gene prior to screening of the GMO traits in various food products and animal feeds. 1/9 (11.1% of the animal feed contained maize and 1/15 (6.7% of the soybean food products showed positive results for the detection of GMO transgenic gene. None of the maize food products showed positive results for GMO transgenic gene. In total, approximately 4% of the food products and animal feed were positive as GMO. This indicated GMOs have not widely entered the food chain. However, it is necessary to have an appropriate screening method due to GMOs’ unknown potential risk to humans and to animals. This rapid screening method will provide leverage in terms of being economically wise, time saving and reliable.

  15. Single pion production in neutrino-nucleon interactions

    Science.gov (United States)

    Kabirnezhad, M.

    2018-01-01

    This work represents an extension of the single pion production model proposed by Rein [Z. Phys. C 35, 43 (1987)., 10.1007/BF01561054]. The model consists of resonant pion production and nonresonant background contributions coming from three Born diagrams in the helicity basis. The new work includes lepton mass effects, and nonresonance interaction is described by five diagrams based on a nonlinear σ model. This work provides a full kinematic description of single pion production in the neutrino-nucleon interactions, including resonant and nonresonant interactions in the helicity basis, in order to study the interference effect.

  16. Genotyping Single Nucleotide Polymorphism C4685T in 14. Intron of Bovine CAPN1 Gene by Rapid Tetra-Primer ARMS-PCR Method

    Directory of Open Access Journals (Sweden)

    Michal Gábor

    2011-05-01

    Full Text Available Single nucleotide polymorphism (SNP C4685T located in 14. intron of bovine CAPN1 gene have shown significant association with a higher lean share in valuable cuts for mutant genotype TT. The work was oriented to developed a sensitive single tube tetra-primer amplification refractory mutation system PCR (ARMS-PCR method for detection of C4685T polymorphism in CAPNI gene and analysis of genotype structure in population of 130 animals of Slovak Pinzgau cattle. The genomic DNA was isolated from samples of blood and hairs of cattle. Design of primers for ARMS-PCR was realized by using program Tetra-Primer ARMS-PCR. The presence of wild allele C and mutant allele T on agarose gel was detected by one control 439 bp fragment for both alleles and one specific fragment for each allele C - 204 bp and T - 290 bp. For the checking of correct genotyping was used PCR-RFLP method with restriction endonuclease BseGI. In the population of Slovak Pinzgau cattle we detected all genotypes. There were detected homozygote genotype CC with frequency 0.3308, heterozygote genotype CT with frequency 0.4 and homozygote genotype TT with frequency 0.2692. Frequency of alleles C and T for SNP C4685T of gene CAPN1 were 0.5308 and 0.4692.

  17. Optimization of a multiplex PCR assay for detecting transgenic soybean components in feed products.

    Science.gov (United States)

    Tian, Fang; Wang, Xiumin; Teng, Da; Yang, Yalin; Guan, Qingfeng; Ao, Changjin; Wang, Jianhua

    2011-11-01

    A multiplex polymerase chain reaction (m-PCR) assay was developed for the simultaneous detection of multiple components of genetically modified (GM) soybean. It uses two sets of primers (I, lectin1/35S/CP4; II, lectin2/35S/CP4) specific for a soybean reference gene, the 35S promoter, and an event-specific gene. Amplified fragments of 118, 414, 195, and 320 bp were easily detected by agarose gel electrophoresis and were positively confirmed by sequencing. Primer set concentrations and annealing temperatures in the m-PCR were optimized. The optimized m-PCR conditions were obtained for primer set I at a ratio of 1:2:3 and a 59.2 °C annealing temperature and set II at the same ratio and 58.6 °C, 60.3 °C, and 61.2 °C annealing temperatures. The sensitivities of the two m-PCR primer sets (I and II) were 0.25% and 0.5%, respectively. The results showed that this m-PCR assay provides rapid, reliable, and effective identification of multiple components of GM soybean in feed.

  18. Development and Evaluation of a Single-Step Duplex PCR for Simultaneous Detection of Fasciola hepatica and Fasciola gigantica (Family Fasciolidae, Class Trematoda, Phylum Platyhelminthes)

    Science.gov (United States)

    Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

    2012-01-01

    A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap. PMID:22692744

  19. Development and evaluation of a single-step duplex PCR for simultaneous detection of Fasciola hepatica and Fasciola gigantica (family Fasciolidae, class Trematoda, phylum Platyhelminthes).

    Science.gov (United States)

    Le, Thanh Hoa; Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

    2012-08-01

    A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap.

  20. Reverse-Transcriptase PCR Detection of Leptospira: Absence of Agreement with Single-Specimen Microscopic Agglutination Testing.

    Science.gov (United States)

    Waggoner, Jesse J; Balassiano, Ilana; Mohamed-Hadley, Alisha; Vital-Brazil, Juliana Magalhães; Sahoo, Malaya K; Pinsky, Benjamin A

    2015-01-01

    Reference diagnostic tests for leptospirosis include nucleic acid amplification tests, bacterial culture, and microscopic agglutination testing (MAT) of acute and convalescent serum. However, clinical laboratories often do not receive paired specimens. In the current study, we tested serum samples using a highly sensitive real-time nucleic acid amplification test for Leptospira and compared results to MAT performed on the same specimens. 478 serum samples from suspected leptospirosis cases in Rio de Janeiro were tested using a real-time RT-PCR for the diagnosis of leptospirosis, malaria and dengue (the Lepto-MD assay). The Lepto-MD assay detects all species of Leptospira (saprophytic, intermediate, and pathogenic), and in the current study, we demonstrate that this assay amplifies both Leptospira RNA and DNA. Dengue virus RNA was identified in 10 patients, and no cases of malaria were detected. A total of 65 samples (13.6%) were positive for Leptospira: 35 samples (7.3%) in the Lepto-MD assay, 33 samples (6.9%) by MAT, and 3 samples tested positive by both (kappa statistic 0.02). Poor agreement between methods was consistent regardless of the titer used to define positive MAT results or the day of disease at sample collection. Leptospira nucleic acids were detected in the Lepto-MD assay as late as day 22, and cycle threshold values did not differ based on the day of disease. When Lepto-MD assay results were added to the MAT results for all patients in 2008 (n=818), the number of detected leptospirosis cases increased by 30.4%, from 102 (12.5%) to 133 (16.3%). This study demonstrates a lack of agreement between nucleic acid detection of Leptospira and single-specimen MAT, which may result from the clearance of bacteremia coinciding with the appearance of agglutinating antibodies. A combined testing strategy for acute leptospirosis, including molecular and serologic testing, appears necessary to maximize case detection.

  1. [Identification of Env-specific monoclonal antibodies from Chinese HIV-1 infected person by magnetic beads separating B cells and single cell RT-PCR cloning].

    Science.gov (United States)

    Huang, Xiang-Ying; Yu, Shuang-Qing; Cheng, Zhan; Ye, Jing-Rong; Xu, Ke; Feng, Xia; Zeng, Yi

    2013-04-01

    To establish a simple and practical method for screening of Env-specific monoclonal antibodies from HIV-1 infected individuals. Human B cells were purified by negative sorting from PBMCs and memory B cells were further enriched using anti-CD27 microbeads. Gp120 antigen labbled with biotin was incubated with memory B cells to specifically bind IgG on cells membrane. The memory B cells expressing the Env-specific antibody were harvested by magnetic beads separating, counted and diluted to the level of single cell in each PCR well that loading with catch buffer containing RNase inhibitor to get RNAs. The antibody genes were amplified by single cell RT-PCR and nested PCR, cloned into eukaryotic expression vectors and transfected into 293T cells. The binding activity of recombinant antibodies to Env were tested by ELISA. Three monocolonal Env-specific antibodies were isolated from one HIV-1 infected individual. We can obtain Env-specific antibody by biotin labbled antigen, magnetic beads separating technique coupled with single cell RT-PCR and expression cloning.

  2. Improved methodology for identification of protists and microalgae from plankton samples preserved in Lugol's iodine solution: combining microscopic analysis with single-cell PCR.

    Science.gov (United States)

    Auinger, Barbara M; Pfandl, Karin; Boenigk, Jens

    2008-04-01

    Here we introduce a method for quantitative analysis of planktonic protists and microalgae from preserved field samples combining morphological and small-subunit (SSU) rRNA gene sequence analysis. We linked a microscopic screening with PCR of single cells using field samples preserved with Lugol's iodine solution. Cells possessing a rigid cell wall were incubated with Viscozyme and subsequently with proteinase K for cell disruption; this was unnecessary for fragile cells. The addition of sodium thiosulfate to the PCR tube considerably decreased the inhibiting effect of the fixative (iodine) on the PCR and thus allowed for successful single-cell PCR even of long DNA fragments (up to as many as 3,000 base pairs). We further applied the protocol to investigate the dominant SSU rRNA genotypes in distinct flagellate morphospecies originating from different samples. We hypothesized that despite the morphological similarity, protist morphospecies in different habitats or sampled during different seasons are represented by different genotypes. Our results indicate species-specific differences: the two species Ochromonas sp. and Dinobryon divergens were represented by several different genotypes each, and for the latter species, the dominating genotype differed with habitat. In contrast, Dinobryon pediforme, Dinobryon bavaricum, and Synura sphagnicola were exclusively represented by a single genotype each, and the respective genotype was the same in different samples. In summary, our results highlight the significance of molecular variation within protist morphospecies.

  3. Effectiveness of various cleaning and disinfectant products on Clostridium difficile spores of PCR ribotypes 010, 014 and 027

    Directory of Open Access Journals (Sweden)

    N. Kenters

    2017-06-01

    Full Text Available Abstract Background In healthcare facilities, Clostridium difficile infections spread by transmission of bacterial spores. Appropriate sporicidal disinfectants are needed to prevent development of clusters and outbreaks. In this study different cleaning/disinfecting wipes and sprays were tested for their efficacy against spores of distinctive C. difficile PCR ribotypes. Methods Four different products were tested; 1 hydrogen peroxide 1.5%; 2 glucoprotamin 1.5%; 3 a mixture of ethanol, propane and N-alkyl amino propyl glycine; and 4 a mixture of didecyldimonium chloride, benzalkonium chloride, polyaminopropyl, biguanide and dimenthicone as active ingredients. Tiles were contaminated with a test solution containing a concentration of 5x106CFU/ml spores of C. difficile strains belonging to PCR ribotypes 010, 014 or 027. The tiles were left to dry for an hour and then wiped or sprayed with one of the sprays or wipes as intended by the manufacturers. When products neutralized after 5 min, microbiological cultures and ATP measures were performed. Results Irrespective of the disinfection method, the microbial count log10 reduction of C. difficile PCR ribotype 010 was highest, followed by the reduction of C. difficile 014 and C. difficile 027. Overall, the wipes performed better than the sprays with the same active ingredient. On average, although not significantly, a difference in relative light units (RLU reduction between the wipes and sprays was found. The wipes had a higher RLU log10 reduction, but no significant difference for RLU reduction was observed between the different C. difficile strains (p = 0.16. Conclusion C. difficile spores of PCR ribotypes 014 and 027 strains are more difficult to eradicate than non-toxigenic PCR ribotype 010. In general, impregnated cleaning/disinfection wipes performed better than ready-to-use sprays. Wipes with hydrogen peroxide (1.5% showed the highest bactericidal activity.

  4. Use of a restriction enzyme-digested PCR product as substrate for helicase assays.

    Science.gov (United States)

    Shin, Jae-Ho; Reeve, John N; Kelman, Zvi

    2005-01-13

    DNA helicases play essential roles in many cellular processes. The currently available techniques to generate substrates for helicase assays are fairly complicated and need some expertise not available in all laboratories. Here, a PCR-based method to generate a substrate for a helicase assay is described, and its application for several archaeal, bacterial and viral enzymes is demonstrated.

  5. Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay.

    Science.gov (United States)

    Lyu, Xiaodong; Wang, Xianwei; Zhang, Lina; Chen, Zhenzhu; Zhao, Yu; Hu, Jieying; Fan, Ruihua; Song, Yongping

    2017-07-25

    Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management. We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization. Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL). We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an

  6. Single top quark production in ATLAS at the LHC

    Directory of Open Access Journals (Sweden)

    Stillings Jan A.

    2013-11-01

    Full Text Available Measurements of the single top quark production cross-sections in proton collisions with the ATLAS detector at the Large Hadron Collider are presented. The single top-quark production in the t and Wt-channels and the determination of the CKM matrix element |Vtb| are discussed. A separate measurement of the top and antitop quark cross-sections and their ratio is shown. These measurements are sensitive to the parton distribution function in the proton. In addition, limits on exotic production in single top quark processes are outlined. This also includes the search for flavour-changing neutral currents and for additional W’ bosons in the s-channel.

  7. Novel touchdown-PCR method for the detection of putrescine producing gram-negative bacteria in food products.

    Science.gov (United States)

    Wunderlichová, Leona; Buňková, Leona; Koutný, Marek; Valenta, Tomáš; Buňka, František

    2013-06-01

    Formation of biogenic amines may occur in food due to metabolic activities of contaminating Gram-negative bacteria. Putrescine is assumed to be the major biogenic amine associated with microbial food spoilage. Gram-negative bacteria can form putrescine by three metabolic pathways that can include eight different enzymes. The objective of this study was to design new sets of primers able to detect all important enzymes involved in the production of putrescine by Gram-negative bacteria. Seven new sets of consensual primers based on gene sequences of different bacteria were designed and used for detection of the speA, adiA, adi, speB, aguA, speC, and speF genes. A newly developed touchdown polymerase chain reaction (PCR) method using these primers was successfully applied on several putrescine-producers. Selected PCR products were sequenced and high similarity of their sequences (99-91%) with known sequences of the corresponding genes confirmed high specificity of the developed sets of primers. Furthermore, all the investigated bacteria produced both putrescine and agmatine, an intermediate of putrescine production, which was confirmed by chemical analysis. The developed new touchdown PCR method could easily be used to detect potential foodborne Gram-negative producers of putrescine. The newly developed sets of primers could also be useful in further research on putrescine metabolism in contaminating microbiota. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Light axigluon and single top production at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Yue, Chong-Xing; Cao, Shi-Yue; Zeng, Qing-Guo [Department of Physics, Liaoning Normal University,Dalian 116029 (China)

    2014-04-28

    The light axigluon model can explain the Tevatron tt-macron forward-backward asymmetry and at the same time satisfy the constraints from the electroweak precision measurement and the ATLAS and CMS data, which induces the flavor changing (FC) couplings of axigluon with the SM and new quarks. We investigate the effects of these FC couplings on the s- and t-channel single top productions at the LHC and the FC decays Z→b-macrons+bs-macron, t→cγ and cg. Our numerical results show that the light axigluon can give significantly contributions to single top production and the rare top decays t→cγ and cg.

  9. Asymmetric PCR for good quality ssDNA generation towards DNA aptamer production

    Directory of Open Access Journals (Sweden)

    Junji Tominaga4

    2012-04-01

    Full Text Available Aptamers are ssDNA or RNA that binds to wide variety of target molecules with high affinity and specificity producedby systematic evolution of ligands by exponential enrichment (SELEX. Compared to RNA aptamer, DNA aptamer is muchmore stable, favourable to be used in many applications. The most critical step in DNA SELEX experiment is the conversion ofdsDNA to ssDNA. The purpose of this study was to develop an economic and efficient approach of generating ssDNA byusing asymmetric PCR. Our results showed that primer ratio (sense primer:antisense primer of 20:1 and sense primer amountof 10 to 100 pmol, up to 20 PCR cycles using 20 ng of initial template, in combination with polyacrylamide gel electrophoresis,were the optimal conditions for generating good quality and quantity of ssDNA. The generation of ssDNA via this approachcan greatly enhance the success rate of DNA aptamer generation.

  10. Next day Salmonella spp. detection method based on real-time PCR for meat, dairy and vegetable food products.

    Science.gov (United States)

    Rodriguez-Lazaro, David; Gonzalez-García, Patricia; Delibato, Elisabetta; De Medici, Dario; García-Gimeno, Rosa Maria; Valero, Antonio; Hernandez, Marta

    2014-08-01

    The microbiological standard for detection of Salmonella relies on several cultural steps and requires more than 5 days for final confirmation, and as consequence there is a need for an alternative rapid methodology for its detection. The aim of this study was to compare different detection strategies based on real-time PCR for a rapid and sensitive detection in an ample range of food products: raw pork and poultry meat, ready to eat lettuce salad and raw sheep milk cured cheese. Three main parameters were evaluated to reduce the time and cost for final results: the initial sample size (25 and 50 g), the incubation times (6, 10 and 18 h) and the bacterial DNA extraction (simple boiling of the culture after washing the bacterial pellet, the use of the Chelex resin, and a commercial silica column). The results obtained demonstrate that a combination of an incubation in buffered peptone water for 18 h of a 25 g-sample coupled to a DNA extraction by boiling and a real-time PCR assay detected down to 2-4 Salmonella spp.CFU per sample in less than 21 h in different types of food products. This RTi-PCR-based method is fully compatible with the ISO standard, providing results more rapidly and cost-effectively. The results were confirmed in a large number of naturally contaminated food samples with at least the same analytical performance as the reference method. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Hot topic: Bovine milk samples yielding negative or nonspecific results in bacterial culturing--the possible role of PCR-single strand conformation polymorphism in mastitis diagnosis.

    Science.gov (United States)

    Schwaiger, K; Wimmer, M; Huber-Schlenstedt, R; Fehlings, K; Hölzel, C S; Bauer, J

    2012-01-01

    A large proportion of mastitis milk samples yield negative or nonspecific results (i.e., no mastitis pathogen can be identified) in bacterial culturing. Therefore, the culture-independent PCR-single strand conformation polymorphism method was applied to the investigation of bovine mastitis milk samples. In addition to the known mastitis pathogens, the method was suitable for the detection of fastidious bacteria such as Mycoplasma spp., which are often missed by conventional culturing methods. The detection of Helcococcus ovis in 4 samples might indicate an involvement of this species in pathogenesis of bovine mastitis. In conclusion, PCR-single-strand conformation polymorphism is a promising tool for gaining new insights into the bacteriological etiology of mastitis. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. Detection of the free living amoeba Naegleria fowleri by using conventional and real-time PCR based on a single copy DNA sequence.

    Science.gov (United States)

    Régoudis, Estelle; Pélandakis, Michel

    2016-02-01

    The amoeba-flagellate Naegleria fowleri is a causative agent of primary amoebic meningoencephalitis (PAM). This thermophilic species occurs worldwide and tends to proliferate in warm aquatic environment. The PAM cases remain rare but this infection is mostly fatal. Here, we describe a single copy region which has been cloned and sequenced, and was used for both conventional and real-time PCR. Targeting a single-copy DNA sequence allows to directly quantify the N. fowleri cells. The real-time PCR results give a detection limit of 1 copy per reaction with high reproducibility without the need of a Taqman probe. This procedure is of interest as compared to other procedures which are mostly based on the detection of multi-copy DNA associated with a Taqman probe. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Search for anomalous Wtb couplings in single top quark production

    NARCIS (Netherlands)

    Abazov, V.M.; et al., [Unknown; de Jong, S.J.; Demarteau, M.; Houben, P.; van den Berg, P.J.

    2008-01-01

    In 0.9 fb(-1) of p(p)over-bar collisions, the D0 Collaboration presented evidence for single top quark production in events with an isolated lepton, missing transverse momentum, and two to four jets. We examine these data to study the Lorentz structure of the Wtb coupling. The standard model

  14. Extent of sensitivity of single photon production to parton distribution ...

    Indian Academy of Sciences (India)

    The single-prompt photon yield is expected to be sensitive to parton distribution function (PDF) in general and to gluon distribution in particular of the colliding hadron [2–9]. It is also considered an essential ingredient to quantify the nuclear modification of direct photon production in the relativistic nucleus–nucleus collisions ...

  15. Production of single cell proterin from brewery spent grains ...

    African Journals Online (AJOL)

    The production of single cell protein (SCP) by the propagation of the yeast, Saccharomyces cerevisae obtained from the Federal Institute of Industrial Research Oshtxli was studied by using the extract of spent grains obtained from the International Beer and Beverage Industries, Kacltuia, Nigeria as a substrate in a medium ...

  16. A single product perishing inventory model with demand interaction ...

    African Journals Online (AJOL)

    The paper describes a single perishing product inventory model in which items deteriorate in two phases and then perish. An independent demand takes place at constant rates for items in both phases. A demand for an item in Phase I not satisfied may be satisfied by an item in Phase II, based on a probability measure.

  17. Search for Single Top Quark Production at HERA

    CERN Document Server

    Aaron, F D; Alexa, C; Alimujiang, K; Andreev, V; Antunovic, B; Asmone, A; Backovic, S; Baghdasaryan, A; Barrelet, E; Bartel, W; Begzsuren, K; Belousov, A; Bizot, J C; Boudry, V; Bozovic-Jelisavcic, I; Bracinik, J; Brandt, G; Brinkmann, M; Brisson, V; Bruncko, D; Bunyatyan, A; Buschhorn, G; Bystritskaya, L; Campbell, A J; Cantun Avila, K B; Cassol-Brunner, F; Cerny, K; Cerny, V; Chekelian, V; Cholewa, A; Contreras, J G; Coughlan, J A; Cozzika, G; Cvach, J; Dainton, J B; Daum, K; Deak, M; de Boer, Y; Delcourt, B; Del Degan, M; Delvax, J; De Roeck, A; De Wolf, E A; Diaconu, C; Dodonov, V; Dossanov, A; Dubak, A; Eckerlin, G; Efremenko, V; Egli, S; Eliseev, A; Elsen, E; Falkiewicz, A; Favart, L; Fedotov, A; Felst, R; Feltesse, J; Ferencei, J; Fischer, D J; Fleischer, M; Fomenko, A; Gabathuler, E; Gayler, J; Ghazaryan, S; Glazov, A; Glushkov, I; Goerlich, L; Gogitidze, N; Gouzevitch, M; Grab, C; Greenshaw, T; Grell, B R; Grindhammer, G; Habib, S; Haidt, D; Helebrant, C; Henderson, R C W; Hennekemper, E; Henschel, H; Herbst, M; Herrera, G; Hildebrandt, M; Hiller, K H; Hoffmann, D; Horisberger, R; Hreus, T; Jacquet, M; Janssen, M E; Janssen, X; Jonsson, L; Jung, Andreas Werner; Jung, H; Kapichine, M; Katzy, J; Kenyon, I R; Kiesling, C; Klein, M; Kleinwort, C; Kluge, T; Knutsson, A; Kogler, R; Kostka, P; Kraemer, M; Krastev, K; Kretzschmar, J; Kropivnitskaya, A; Kruger, K; Kutak, K; Landon, M P J; Lange, W; Lastovicka-Medin, G; Laycock, P; Lebedev, A; Leibenguth, G; Lendermann, V; Levonian, S; Li, G; Lipka, K; Liptaj, A; List, B; List, J; Loktionova, N; Lopez-Fernandez, R; Lubimov, V; Lytkin, L; Makankine, A; Malinovski, E; Marage, P; Marti, Ll; Martyn, H U.; Maxfield, S J; Mehta, A; Meyer, A B; Meyer, H; Meyer, H; Meyer, J; Michels, V; Mikocki, S; Milcewicz-Mika, I; Moreau, F; Morozov, A; Morris, J V; Mozer, Matthias Ulrich; Mudrinic, M; Muller, K; Murin, P; Naumann, Th; Newman, P R; Niebuhr, C; Nikiforov, A; Nowak, G; Nowak, K; Nozicka, M; Olivier, B; Olsson, J E; Osman, S; Ozerov, D; Palichik, V; Panagoulias, I; Pandurovic, M; Papadopoulou, Th; Pascaud, C; Patel, G D; Pejchal, O; Perez, E; Petrukhin, A; Picuric, I; Piec, S; Pitzl, D; Placakyte, R; Pokorny, B; Polifka, R; Povh, B; Preda, T; Radescu, V; Rahmat, A J; Raicevic, N; Raspiareza, A; Ravdandorj, T; Reimer, P; Rizvi, E; Robmann, P; Roland, B; Roosen, R; Rostovtsev, A; Rotaru, M; Ruiz Tabasco, J E; Rurikova, Z; Rusakov, S; Salek, D; Sankey, D P C; Sauter, M; Sauvan, E; Schmitt, S; Schmitz, C; Schoeffel, L; Schoning, A; Schultz-Coulon, H C; Sefkow, F; Shaw-West, R N; Shtarkov, L N; Shushkevich, S; Sloan, T; Smiljanic, Ivan; Soloviev, Y; Sopicki, P; South, D; Spaskov, V; Specka, Arnd E; Staykova, Z; Steder, M; Stella, B; Stoicea, G; Straumann, U.; Sunar, D; Sykora, T; Tchoulakov, V; Thompson, G; Thompson, P D; Toll, T; Tomasz, F; Tran, T H; Traynor, D; Trinh, T N; Truol, P; Tsakov, I; Tseepeldorj, B; Turnau, J; Urban, K; Valkarova, A; Vallee, C; Van Mechelen, P; Vargas Trevino, A; Vazdik, Y; Vinokurova, S; Volchinski, V; von den Driesch, M; Wegener, D; Wissing, Ch; Wunsch, E; Zacek, J; Zalesak, J; Zhang, Z; Zhokin, A; Zimmermann, T; Zohrabyan, H; Zomer, F; Zus, R

    2009-01-01

    A search for single top quark production is performed in the full ep data sample collected by the H1 experiment at HERA, corresponding to an integrated luminosity of 474 pb^-1. Decays of top quarks into a b quark and a W boson with subsequent leptonic or hadronic decay of the W are investigated. A multivariate analysis is performed to discriminate top quark production from Standard Model background processes. An upper limit on the top quark production cross section via flavour changing neutral current processes sigma (ep -> etX) < 0.25 pb is established at 95% CL. Limits on the anomalous coupling kappa_{tu gamma} are derived.

  18. Top pair and single top production in ATLAS

    CERN Document Server

    Fabbri, Federica; The ATLAS collaboration

    2017-01-01

    Measurements of inclusive and differential top-quark production cross sections in proton-proton collisions at a center of mass energy of 8 TeV and 13 TeV at the Large Hadron Collider using the ATLAS detector are presented. The inclusive measurements of top quark pair and single top quark production are compared to the best available theoretical calculations. Differential measurements of the kinematic properties of top quark events are also discussed. These measurements, including results using boosted top quarks, probe our understanding of top quark production up to the TeV scale.

  19. Volume production of polarization controlled single-mode VCSELs

    Science.gov (United States)

    Grabherr, Martin; King, Roger; Jäger, Roland; Wiedenmann, Dieter; Gerlach, Philipp; Duckeck, Denise; Wimmer, Christian

    2008-02-01

    Over the past 3 years laser based tracking systems for optical PC mice have outnumbered the traditional VCSEL market datacom by far. Whereas VCSEL for datacom in the 850 nm regime emit in multipe transverse modes, all laser based tracking systems demand for single-mode operation which require advanced manufacturing technology. Next generation tracking systems even require single-polarization characteristics in order to avoid unwanted movement of the pointer due to polarization flips. High volume manufacturing and optimized production methods are crucial for achieving the addressed technical and commercial targets of this consumer market. The resulting ideal laser source which emits single-mode and single-polarization at low cost is also a promising platform for further applications like tuneable diode laser absorption spectroscopy (TDLAS) or miniature atomic clocks when adapted to the according wavelengths.

  20. Agarose gel purification of PCR products for denaturing gradient gel electrophoresis results in GC-clamp deletion.

    Science.gov (United States)

    Sun, Guowei; Xiao, Jinzhou; Lu, Man; Wang, Hongming; Chen, Xiaobing; Yu, Yongxin; Pan, Yingjie; Wang, Yongjie

    2015-01-01

    The 16S ribosomal RNA (rRNA) gene of marine archaeal samples was amplified using a nested PCR approach, and the V3 region of 16S rRNA gene of crab gut microbiota (CGM) was amplified using the V3 universal primer pair with a guanine and cytosine (GC)-clamp. Unpurified PCR products (UPPs), products purified from reaction solution (PPFSs), and products purified from gel (PPFGs) of above two DNA samples were used for denaturing gradient gel electrophoresis (DGGE) analysis, respectively. In contrast to almost identical band patterns shared by both the UPP and PPFS, the PPFGs were barely observed on the DGGE gel for both the marine archaea and CGM samples. Both PPFS and PPFG of CGM V3 regions were subjected to cloning. A small amount of positive clones was obtained for PPFS, but no positive clones were observed for PPFG. The melt curve and direct sequencing analysis of PPFS and PPFG of E. coli V3 region indicated that the Tm value of PPFG (82.35 ± 0.19 °C) was less than that of PPFS (83.81 ± 0.11 °C), and the number of shorter GC-clamps was significant higher in PPFG than in PPFS. The ultraviolet exposure experiment indicated that the ultraviolet was not responsible for the deletion of the GC-clamps. We conclude that the gel purification method is not suitable for DGGE PCR products or even other GC-rich DNA samples.

  1. [Development and application of real-time PCR for identification and detection of horse meat in animal-origin products].

    Science.gov (United States)

    Li, Nan; Wang, Jiahui; Shen, Qing; Han, Chunhui; Zhang, Jing; Li, Fengqin; Xu, Jin; Jiang, Tao

    2013-11-01

    To develop a real-time PCR method for identification and detection of domestic horse meat (Equus caballus) in animal-origin products. The primer and TaqMan-probe was designed and synthesized according to the EU reference laboratory and 87 bp fragments was amplified for horse ingredients. The specificity and sensitivity was tested by artificially spiked horse meat into other domestic meat, such as cattle, sheep, pork, chicken, duck and rabbit. 122 samples of cattle and sheep products were random collected in Beijing market and the detection of horse meat was carried out. The real-time PCR in this study has high specificity and sensitivity for horse meat. No cross-reaction was observed between the horse and sheep, pork, chicken, duck and rabbit meat. There was little cross reaction between horse and cattle when the CT value reach 33. 81. The method can detect 0.1% of horse meat mixed with other domestic animal-origin products. No horse meat ingredients were detected in 122 samples in this survey. There was no horse meat mixed into cattle and sheep products in Beijing marked.

  2. A Fast and Reliable Real-Time PCR Method for Detection of Ten Animal Species in Meat Products.

    Science.gov (United States)

    Dalsecco, Lissandra Sousa; Palhares, Rafael Melo; Oliveira, Pollyana Carvalho; Teixeira, Lilian Viana; Drummond, Marcela Gonçalves; de Oliveira, Denise Aparecida Andrade

    2018-02-01

    Species substitution in meat products is a common problem reported worldwide. This type of food fraud is, typically, an intentional act for economic gain, using sources of low-priced meats in high-value meat products. Consequences include economic, health, and religious concerns. Highly sensitive and efficient techniques are thus required to detect meat species. This paper describes a method based on real-time PCR to detect 10 animal species (Bos taurus, Sus scrofa, Ovis aries, Capra hircus, Gallus gallus, Meleagris gallopavo, Bubalus bubalis, Equus caballus, Felis catus, and Canis familiaris) in meat product. The method combines species-specific and universal (used here as internal positive control) primers, and applies melt curve analysis for amplicon checking. Method accuracy was evaluated on 46 experimental meat mixtures and all species were correctly identified in all cases, at 1% test sensitivity. Analysis of 14 commercial meat products revealed that 6 of 14 samples had nondeclared bovine and/or chicken material. We performed an interlaboratory comparison using the reference meat mixtures and commercial samples, achieving 100% of reproducibility. The developed test proved to be effective and reliable for routine analysis of meat products. This paper describes a fast and reliable method for species detection in meat products based on real-time PCR. It can be applied for analysis of in natura or processed meat. The method proposed here can play an important role in controlling the origin of meat products, ensuring their quality and safety for the entire food industry-producers to consumers. © 2018 Institute of Food Technologists®.

  3. Rapid assembly of multiple DNA fragments through direct transformation of PCR products into E. coli and Lactobacillus.

    Science.gov (United States)

    Cao, Pinghua; Wang, Lei; Zhou, Guangxian; Wang, Yaoyue; Chen, Yulin

    2014-11-01

    This article describes a rapid, highly efficient and versatile method for seamlessly assembling multiple DNA fragments into a vector at any desired position. The inserted fragments and vector backbone were amplified by high-fidelity PCR containing 20 bp to 50 bp overlapping regions at 3' and/or 5' termini. These linearised fragments were equimolarly mixed, and then cyclised in a prolonged overlap extension PCR without adding primers. The resulting PCR products were DNA multimers that could be directly transformed into host strains, yielding the desired chimeric plasmid. The proposed method was illustrated by constructing an Escherichia coli co-expression vector. The feasibility of the method in Lactobacillus was further validated by assembling an E. coli-Lactobacillus shuttle vector. Results showed that three to four fragments could be simultaneously and precisely inserted in a vector in only 2-3 days using the proposed method. The acceptable transformation efficiency was determined through the tested host strains; more than 95% of the colonies were positive transformants. Therefore, the proposed method is sufficiently competent for high-efficiency insertion of multiple DNA fragments into a plasmid and has theoretically good application potential for gene cloning and protein expression because it is simple, easy to implement, flexible and yields highly positive clones. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Single-Tube Dodecaplex PCR Panel of Polymorphic Microsatellite Markers Closely Linked to theDMPKCTG Repeat for Preimplantation Genetic Diagnosis of Myotonic Dystrophy Type 1.

    Science.gov (United States)

    Lian, Mulias; Zhao, Mingjue; Lee, Caroline G; Chong, Samuel S

    2017-06-01

    Preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1) currently uses conventional PCR to detect nonexpanded dystrophia myotonica protein kinase ( DMPK ) alleles or triplet-primed PCR to detect the CTG-expanded alleles, coupled with analysis of linked microsatellite markers to increase diagnostic accuracy. We aimed to simplify the process of identification and selection of informative linked markers for application to DM1 PGD. An in silico search was performed to identify all markers within 1-1.5 Mb flanking the DMPK gene. Five previously known (D19S559, APOC2, D19S543, D19S112, and BV209569) and 7 novel (DM45050, DM45178, DM45209, DM45958, DM46513, DM46892, and DM47004.1) markers with potentially high heterozygosity values and polymorphism information content were selected and optimized in a single-tube multiplex PCR panel. Analysis of 184 DNA samples of Chinese and Caucasian individuals (91 from unrelated, anonymized cord blood of Chinese babies born at the National University Hospital, Singapore, and 93 Caucasian DNA samples from the Human Variation Panel HD100CAU) confirmed the high polymorphism indices of all markers (polymorphism information content >0.5), with observed heterozygosity values ranging from 0.62-0.93. All individuals were heterozygous for at least 6 markers, with 99.5% of individuals heterozygous for at least 2 markers on either side of the DMPK CTG repeat. The dodecaplex marker assay was successfully validated on 42 single cells and 12 whole genome amplified single cells. The DM1 multiplex PCR panel is suitable for use in DM1 PGD either as a standalone linkage-based assay or as a complement to DMPK CTG repeat expansion-mutation detection. © 2017 American Association for Clinical Chemistry.

  5. Detection of the single nucleotide polymorphism causing feline autosomal-dominant polycystic kidney disease in Persians from the UK using a novel real-time PCR assay.

    Science.gov (United States)

    Helps, Chris R; Tasker, Séverine; Barr, Frances J; Wills, Sheila J; Gruffydd-Jones, Timothy J

    2007-02-01

    Autosomal-dominant polycystic kidney disease (AD-PKD) is the most prevalent inherited genetic disease of cats, particularly affecting Persians. Until recently the condition has been diagnosed by renal ultrasound screening. With the identification of the genetic mutation responsible for AD-PKD it is now possible to use advanced molecular techniques to screen for the disease. We have developed a rapid, sensitive and specific real-time PCR genotyping assay that can detect the single nucleotide polymorphism responsible for AD-PKD. Of 72 UK Persian and Exotic Shorthair cats submitted for AD-PKD ultrasound screening, 29 were found to have the disease, 41 were negative and 2 were equivocal. The recently published PCR-RFLP method showed the AD-PKD mutation to be present in all 29 diseased cats and absent in the 41 negative and 2 equivocal cats. Our real-time PCR genotyping assay was in complete agreement with the PCR-RFLP results. Of 600 blood or buccal swabs analysed from April 2005 to January 2006, 165 were found to be AD-PKD positive and 435 were negative, giving a prevalence of 27.5%. All 194 cats with AD-PKD were found to be heterozygous for the mutation.

  6. Development of pork DNA detection in meat products by PCR technique

    Directory of Open Access Journals (Sweden)

    Intaraphad, U.

    2005-09-01

    Full Text Available The polymerase chain reaction (PCR was used to determine pig DNA fragment in meat mixture using specific oligonucleotide primer having 10-30 bp in size to amplify the DNA fragment. Firstly, the β-actin F and the β-actin R primers were used to identify DNA extraction process in beef, pork and chicken. The 284 bp DNA fragment was obtained from beef and chicken meat and 248 bp was amplified from pork. Secondly, pig F and pig R primers for pork were used as the PCR amplifier which resulted in 531 bp DNA fragment from pork; however, it gave negative results for beef and chicken meat. Finally, the obtained nucleotide sequence was compared with AF535163 in the GenBank database and homology was 98%. This work was also submitted to GenBank and obtained an accession number of AY621117.A comparison between the sensitivity of the commercial kit (QIAamp kit and the RSB lysis buffer for the DNA extraction process was carried out by mixing pork with chicken meat at ratios of 1:1, 1:5, 1:10, 1:50, 1:150 and 1:200. QIAamp kit gave the best results at the smallest ratio of 0.5% (1:200, while the RSB lysis buffer gave good results at the ratio of 2% (1:50. This indicated that the QIAamp kit had a higher sensitivity than the RSB lysis buffer. Lastly, a determination of pork DNA fragment from heated pork at 121ºC for 15 min. using the Pig F and Pig R primers for pork were done. The result was similar to that obtained from the fresh pork at 531 bp DNA fragment.

  7. Single top quark production and properties at hadron colliders

    CERN Document Server

    Skovpen, Kirill

    2016-01-01

    The results of cross section measurements for electroweak production of top quarks in t channel, s channel, and in association with W-boson are presented from LHC and Tevatron experiments. These measurements are used to place constraints on the CKM matrix element $V_{tb}$. Top quark polarization is studied in the measurement of the top quark spin asymmetry in single top events. Anomalous structure of top quark coupling is probed.

  8. Single Boson Production Cross Section Measurements in CMS

    CERN Document Server

    INSPIRE-00571407

    2017-01-01

    Measurements of single boson production cross sections are presented. They are based on proton-proton collision data at 8 and 13 TeV recorded with the CMS detector at the LHC. Inclusive and differential cross sections with respect to various observables are measured in various phase spaces.These measurements are compared to perturbative QCD predictions and generally show good agreement with the prediction.

  9. Simulating colonic survival of probiotics in single-strain products compared to multi-strain products.

    Science.gov (United States)

    Forssten, S D; Ouwehand, A C

    2017-01-01

    Background : Probiotic formulations can be single- or multi-strain. Commercially, multi-strain preparations have been suggested to have improved functionality over single-strain cultures. Probiotics are often tested as single-strain preparations but may subsequently be commercially formulated as multi-strain products. Objective : The aim of this study was to determine what happens at the site of action, the intestine, with probiotics as single- compared to multi-strain preparations. The human gastrointestinal tract contains a broad mixture of different microbes which may affect the survival of different probiotics in different ways. Design : The current study was performed to evaluate, in an in vitro colon simulation, whether probiotics influence each other's survival when they are taken as a combination of several strains (HOWARU Restore; Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium lactis Bl-04 and B. lactis Bi-07) compared to the strains as single preparations. Results : All strains could be detected after the colon simulations and there were no substantial differences in levels of the same strain when comparing single- and multi-strain products. Conclusions : It can be concluded that probiotics do not have an antagonistic effect on each other's survival when used in a multi-strain product compared to a single-strain product, at least within a microbiota in a simulated colonic environment.

  10. Uncovering the single top: observation of electroweak top quark production

    Energy Technology Data Exchange (ETDEWEB)

    Benitez, Jorge Armando [Michigan State Univ., East Lansing, MI (United States)

    2009-01-01

    The top quark is generally produced in quark and anti-quark pairs. However, the Standard Model also predicts the production of only one top quark which is mediated by the electroweak interaction, known as 'Single Top'. Single Top quark production is important because it provides a unique and direct way to measure the CKM matrix element Vtb, and can be used to explore physics possibilities beyond the Standard Model predictions. This dissertation presents the results of the observation of Single Top using 2.3 fb-1 of Data collected with the D0 detector at the Fermilab Tevatron collider. The analysis includes the Single Top muon+jets and electron+jets final states and employs Boosted Decision Tress as a method to separate the signal from the background. The resulting Single Top cross section measurement is: (1) σ(p$\\bar{p}$→ tb + X, tqb + X) = 3.74-0.74+0.95 pb, where the errors include both statistical and systematic uncertainties. The probability to measure a cross section at this value or higher in the absence of signal is p = 1.9 x 10-6. This corresponds to a standard deviation Gaussian equivalence of 4.6. When combining this result with two other analysis methods, the resulting cross section measurement is: (2) σ(p$\\bar{p}$ → tb + X, tqb + X) = 3.94 ± 0.88 pb, and the corresponding measurement significance is 5.0 standard deviations.

  11. Measurement of single top quark production with CMS

    CERN Document Server

    Andrea, Jeremy

    2018-01-01

    Several measurements of single top quark production in proton-proton collisions at the LHC at centre-of-mass energies of 7, 8 and 13 TeV, using data collected with the CMS experiment, are presented. The analyses investigate separately the productions of top via t-channel exchange, in association with a W boson (tW) or via the s-channel. Final states with at least one charged lepton and one b-jet are explored to measure inclusive production cross sections. Fiducial and differential cross section measurements in the t-channel are also reported. The measurements can be used to constrain directly the Vtb CKM matrix element by comparing with the most precise standard model theory predictions. Measurements of rare processes involving a top quark and a neutral EWK boson (Z or photon) are also discussed.

  12. Improvements in Production of Single-Walled Carbon Nanotubes

    Science.gov (United States)

    Balzano, Leandro; Resasco, Daniel E.

    2009-01-01

    A continuing program of research and development has been directed toward improvement of a prior batch process in which single-walled carbon nanotubes are formed by catalytic disproportionation of carbon monoxide in a fluidized-bed reactor. The overall effect of the improvements has been to make progress toward converting the process from a batch mode to a continuous mode and to scaling of production to larger quantities. Efforts have also been made to optimize associated purification and dispersion post processes to make them effective at large scales and to investigate means of incorporating the purified products into composite materials. The ultimate purpose of the program is to enable the production of high-quality single-walled carbon nanotubes in quantities large enough and at costs low enough to foster the further development of practical applications. The fluidized bed used in this process contains mixed-metal catalyst particles. The choice of the catalyst and the operating conditions is such that the yield of single-walled carbon nanotubes, relative to all forms of carbon (including carbon fibers, multi-walled carbon nanotubes, and graphite) produced in the disproportionation reaction is more than 90 weight percent. After the reaction, the nanotubes are dispersed in various solvents in preparation for end use, which typically involves blending into a plastic, ceramic, or other matrix to form a composite material. Notwithstanding the batch nature of the unmodified prior fluidized-bed process, the fluidized-bed reactor operates in a continuous mode during the process. The operation is almost entirely automated, utilizing mass flow controllers, a control computer running software specific to the process, and other equipment. Moreover, an important inherent advantage of fluidized- bed reactors in general is that solid particles can be added to and removed from fluidized beds during operation. For these reasons, the process and equipment were amenable to

  13. Chum-RNA allows preparation of a high-quality cDNA library from a single-cell quantity of mRNA without PCR amplification.

    Science.gov (United States)

    Tougan, Takahiro; Okuzaki, Daisuke; Nojima, Hiroshi

    2008-09-01

    Linear RNA amplification using T7 RNA polymerase is useful in genome-wide analysis of gene expression using DNA microarrays, but exponential amplification using polymerase chain reaction (PCR) is still required for cDNA library preparation from single-cell quantities of RNA. We have designed a small RNA molecule called chum-RNA that has enabled us to prepare a single-cell cDNA library after four rounds of T7-based linear amplification, without using PCR amplification. Chum-RNA drove cDNA synthesis from only 0.49 femtograms of mRNA (730 mRNA molecules) as a substrate, a quantity that corresponds to a minor population of mRNA molecules in a single mammalian cell. Analysis of the independent cDNA clone of this library (6.6 x 10(5) cfu) suggests that 30-fold RNA amplification occurred in each round of the amplification process. The size distribution and representation of mRNAs in the resulting one-cell cDNA library retained its similarity to that of the million-cell cDNA library. The use of chum-RNA might also facilitate reactions involving other DNA/RNA modifying enzymes whose Michaelis constant (K(m)) values are around 1 mM, allowing them to be activated in the presence of only small quantities of substrate.

  14. Highly Sensitive GMO Detection Using Real-Time PCR with a Large Amount of DNA Template: Single-Laboratory Validation.

    Science.gov (United States)

    Mano, Junichi; Hatano, Shuko; Nagatomi, Yasuaki; Futo, Satoshi; Takabatake, Reona; Kitta, Kazumi

    2018-03-01

    Current genetically modified organism (GMO) detection methods allow for sensitive detection. However, a further increase in sensitivity will enable more efficient testing for large grain samples and reliable testing for processed foods. In this study, we investigated real-time PCR-based GMO detection methods using a large amount of DNA template. We selected target sequences that are commonly introduced into many kinds of GM crops, i.e., 35S promoter and nopaline synthase (NOS) terminator. This makes the newly developed method applicable to a wide range of GMOs, including some unauthorized ones. The estimated LOD of the new method was 0.005% of GM maize events; to the best of our knowledge, this method is the most sensitive among the GM maize detection methods for which the LOD was evaluated in terms of GMO content. A 10-fold increase in the DNA amount as compared with the amount used under common testing conditions gave an approximately 10-fold reduction in the LOD without PCR inhibition. Our method is applicable to various analytical samples, including processed foods. The use of other primers and fluorescence probes would permit highly sensitive detection of various recombinant DNA sequences besides the 35S promoter and NOS terminator.

  15. Oil Reservoir Production Optimization using Single Shooting and ESDIRK Methods

    DEFF Research Database (Denmark)

    Capolei, Andrea; Völcker, Carsten; Frydendall, Jan

    2012-01-01

    the injections and oil production such that flow is uniform in a given geological structure. Even in the case of conventional water flooding, feedback based optimal control technologies may enable higher oil recovery than with conventional operational strategies. The optimal control problems that must be solved......Conventional recovery techniques enable recovery of 10-50% of the oil in an oil field. Advances in smart well technology and enhanced oil recovery techniques enable significant larger recovery. To realize this potential, feedback model-based optimal control technologies are needed to manipulate...... are large-scale problems and require specialized numerical algorithms. In this paper, we combine a single shooting optimization algorithm based on sequential quadratic programming (SQP) with explicit singly diagonally implicit Runge-Kutta (ESDIRK) integration methods and the a continuous adjoint method...

  16. A performance comparison of single product kanban control systems

    Directory of Open Access Journals (Sweden)

    Alvin Ang

    2015-01-01

    Full Text Available This paper presents a simulation experiment comparing the Single Stage, Single Product Base Stock (BS, Traditional Kanban Control System (TKCS and Extended Kanban Control System (EKCS. The results showed that BS incurs the highest cost in all scenarios; while EKCS is found to be effective only in a very niche scenario. TKCS is still a very powerful factory management system to date; and EKCS did not perform exceptionally well. The only time EKCS did outperform TKCS was during low demand arrival rates and low Backorder (Cb and Shortage costs (Cs. That is because during then, it holds no stock. The most important discovery made here is that EKCS becomes TKCS once it has base stock (or dispatched kanbans. The results have also evinced the strength of the pure kanban system, the TKCS over BS. Hence managers using BS should consider upgrading to TKCS to save cost.

  17. Single pion electro- and neutrino production on heavy targets

    International Nuclear Information System (INIS)

    Paschos, E. A.; Schienbein, I.; Yu, J.Y.

    2007-04-01

    We present a calculation of single pion electroproduction cross sections on heavy targets in the kinematic region of the Δ(1232) resonance. Final state interactions of the pions are taken into account using the pion multiple scattering model of Adler, Nussinov and Paschos (ANP model). For electroproduction and neutral current reactions we obtain results for carbon, oxygen, argon and iron targets and find a significant reduction of the W-spectra for π 0 as compared to the free nucleon case. On the other hand, the charged pion spectra are only little affected by final state interactions. Measurements of such cross sections with the CLAS detector at JLAB could help to improve our understanding of pion rescattering effects and serve as important/valuable input for calculations of single pion neutrino production on heavy targets relevant for current and future long baseline neutrino experiments. Two ratios, in Eq. (3.8) and (3.10), will test important properties of the model. (authors)

  18. Production strategies and applications of microbial single cell oils

    Directory of Open Access Journals (Sweden)

    Katrin Ochsenreither

    2016-10-01

    Full Text Available Polyunsaturated fatty acids (PUFAs of the -3 and -6 class (e.g. -linolenic acid, linoleic acid are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF or solid state fermentation (SSF. The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g. medium, pH-value, temperature, aeration, nitrogen source. From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids

  19. Production Strategies and Applications of Microbial Single Cell Oils.

    Science.gov (United States)

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  20. One-stop polymerase chain reaction (PCR): An improved PCR ...

    African Journals Online (AJOL)

    -cycling steps to visualize amplicons, decelerating PCR sample processing and result calling. “One-stop PCR” was developed by including both the loading buffer and nontoxic staining dye within a single PCR tube, allowing direct loading and ...

  1. Identification of Five Novel Salmonella Typhi-Specific Genes as Markers for Diagnosis of Typhoid Fever Using Single-Gene Target PCR Assays

    Directory of Open Access Journals (Sweden)

    Yuan Xin Goay

    2016-01-01

    Full Text Available Salmonella Typhi (S. Typhi causes typhoid fever which is a disease characterised by high mortality and morbidity worldwide. In order to curtail the transmission of this highly infectious disease, identification of new markers that can detect the pathogen is needed for development of sensitive and specific diagnostic tests. In this study, genomic comparison of S. Typhi with other enteric pathogens was performed, and 6 S. Typhi genes, that is, STY0201, STY0307, STY0322, STY0326, STY2020, and STY2021, were found to be specific in silico. Six PCR assays each targeting a unique gene were developed to test the specificity of these genes in vitro. The diagnostic sensitivities and specificities of each assay were determined using 39 S. Typhi, 62 non-Typhi Salmonella, and 10 non-Salmonella clinical isolates. The results showed that 5 of these genes, that is, STY0307, STY0322, STY0326, STY2020, and STY2021, demonstrated 100% sensitivity (39/39 and 100% specificity (0/72. The detection limit of the 5 PCR assays was 32 pg for STY0322, 6.4 pg for STY0326, STY2020, and STY2021, and 1.28 pg for STY0307. In conclusion, 5 PCR assays using STY0307, STY0322, STY0326, STY2020, and STY2021 were developed and found to be highly specific at single-gene target resolution for diagnosis of typhoid fever.

  2. By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX

    DEFF Research Database (Denmark)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recogniz...

  3. Hard single diffractive jet production at D0

    International Nuclear Information System (INIS)

    Abachi, S.; Abbott, B.; Abolins, M.

    1996-08-01

    Preliminary results from the D null experiment on jet production with forward rapidity gaps in p anti p collisions are presented. A class of dijet events with a forward rapidity gap is observed at center-of-mass energies √s = 1800 GeV and 630 GeV. The number of events with rapidity gaps at both center-of-mass energies is significantly greater than the expectation from multiplicity fluctuations and is consistent with a hard single diffractive process. A small class of events with two forward gaps and central dijets is also observed at 1800 GeV. This topology is consistent with hard double pomeron exchange

  4. Single and Double Top Quark Production at the Tevatron

    Energy Technology Data Exchange (ETDEWEB)

    Wicke, Daniel; CDF, for the; collaborations, D0

    2010-06-01

    The CDF and D0 experiments have measured single and double top quark production in ppbar collisions at the Tevatron at a centre-of-mass energy of 1.96TeV. The applied methods are used to constrain properties of the top quark and to search for new physics. Several methods of signal to background separation and of the estimation of the background contributions are discussed. Experimental results using an integraged luminosity up to 5.3fb{sup -1} are presented.

  5. A modified molecular beacons-based multiplex real-time PCR assay for simultaneous detection of eight foodborne pathogens in a single reaction and its application.

    Science.gov (United States)

    Hu, Qinghua; Lyu, Dongyue; Shi, Xiaolu; Jiang, Yixiang; Lin, Yiman; Li, Yinghui; Qiu, Yaqun; He, Lianhua; Zhang, Ran; Li, Qingge

    2014-03-01

    Foodborne disease outbreaks are often caused by one of the major pathogens. Early identification of the causal pathogen is crucial for disease control and prevention. We describe a real-time polymerase chain reaction (rtPCR) assay that can identify, in a single reaction, up to eight common foodborne bacterial pathogens, including Salmonella enterica subsp. enterica, Listeria monocytogenes, Escherichia coli O157, Vibrio parahaemolyticus, V. vulnificus, Campylobacter jejuni, Enterobacter sakazakii, and Shigella spp. This multiplex rtPCR assay takes advantage of modified molecular beacons and the multicolor combinational probe coding strategy to discriminate each pathogen and the homo-tag assisted non-dimer (HAND) system to prevent dimer formation. The detection limits of the assay ranged from 1.3×10(3) colony-forming units (CFU)/g stool (L. monocytogenes) to 1.6×10(4) CFU/g stool (Shigella spp.). The target genes were 100% specific as assessed on 986 reference strains covering 41 species since no cross-reactions were observed. The assay was applied to the detection of foodborne pathogens in 11,167 clinical samples and the results were compared with culture methods for further validation. The sensitivity and specificity of the rtPCR were 100% and 99%, respectively. When performed in a 96-well rtPCR system, more than 90 samples could be analyzed within 3 h. Given the high accuracy, sensitivity, specificity, and short turn-around time, the established assay could be used for the rapid and reliable identification of the causative pathogens responsible for a certain foodborne disease outbreak and rapid screening of these major foodborne pathogens in laboratory-based surveillance of outpatient clinical samples or even food samples.

  6. Construction of a System for the Strawberry Nursery Production towards Elimination of Latent Infection of Anthracnose Fungi by a Combination of PCR and Microtube Hybridization

    Directory of Open Access Journals (Sweden)

    Kazuyoshi Furuta

    2017-02-01

    Full Text Available One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge.

  7. Construction of a System for the Strawberry Nursery Production towards Elimination of Latent Infection of Anthracnose Fungi by a Combination of PCR and Microtube Hybridization.

    Science.gov (United States)

    Furuta, Kazuyoshi; Nagashima, Saki; Inukai, Tsuyoshi; Masuta, Chikara

    2017-02-01

    One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH) using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge.

  8. Study on sensitivity of southern blotting hybridization using a 32P-labeled probe of PCR products in detecting human cytomegalovirus

    International Nuclear Information System (INIS)

    Bu Hengfu; Chen Juan; Shen Rongsen; Ma Liren; Xu Yongqiang

    1996-01-01

    Southern blotting hybridization (SBH) using a 32 P-labeled probe is one of the most practical methods for genetic diagnosis of pathogen. On the basis of establishing PCR and nested PCR for detecting human cytomegalovirus (HCMV), a 32 P-labeled probe was prepared with the amplified products of 613 bp PCR outer primers and hybridized with 300 bp inner primer amplified product, resulting in increase in detecting sensitivity from 17 ng (in 1.2% agarose electrophoresis) before SBH to 500 pg (autoradiographed), in other words, increasing the sensitivity of detecting HCMV by 10 2 dilutions after using SBH. The method of PCR and SBH using a 32 P-labeled probe could detect less than 1 gene copy of HCMV, therefore, it is a rapid and reliable diagnosis method for detecting HCMV latent infection

  9. Real-time PCR with molecular beacons provides a highly accurate assay for detection of Tay-Sachs alleles in single cells.

    Science.gov (United States)

    Rice, John E; Sanchez, J Aquiles; Pierce, Kenneth E; Wangh, Lawrence J

    2002-12-01

    The results presented here provide the first single-cell genetic assay for Tay-Sachs disease based on real-time PCR. Individual lymphoblasts were lysed with an optimized lysis buffer and assayed using one pair of primers that amplifies both the wild type and 1278 + TATC Tay-Sachs alleles. The resulting amplicons were detected in real time with two molecular beacons each with a different colored fluorochrome. The kinetics of amplicon accumulation generate objective criteria by which to evaluate the validity of each reaction. The assay had an overall utility of 95%, based on the detection of at least one signal in 235 of the 248 attempted tests and an efficiency of 97%, as 7 of the 235 samples were excluded from further analysis for objective quantitative reasons. The accuracy of the assay was 99.1%, because 228 of 230 samples gave signals consistent with the genotype of the cells. Only two of the 135 heterozygous samples were allele drop-outs, a rate far lower than previously reported for single-cell Tay-Sachs assays using conventional methods of PCR. Copyright 2002 John Wiley & Sons, Ltd.

  10. Detection of Single-Nucleotide Polymorphisms in Plasmodium falciparum by PCR Primer Extension and Lateral Flow Immunoassay

    NARCIS (Netherlands)

    Moers, A. P. H. A.; Hallett, R. L.; Burrow, R.; Schallig, H. D. F. H.; Sutherland, C. J.; van Amerongen, A.

    2015-01-01

    The resistance of Plasmodium falciparum to some antimalarial drugs is linked to single-nucleotide polymorphisms (SNPs). Currently, there are no methods for the identification of resistant parasites that are sufficiently simple, cheap, and fast enough to be performed at point-of-care, i.e., in local

  11. FACS-based single-cell PCR data - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available data DOI 10.18908/lsdba.nbdc01108-001 Description of data contents Gene expression patterns at the single-n...expressed in the nervous system, the patterns of + indicate that these genes have different expression patte

  12. arXiv Single top-quark production with SHERPA

    CERN Document Server

    Bothmann, Enrico; Schönherr, Marek

    2018-03-15

    We present results at next-to-leading order accuracy in QCD for single top-quark production in the t, s and tW channels at the lhc at a centre-of-mass energy of 8TeV, obtained with the sherpa event generator. We find them in very good agreement with measured values and quantify their theory uncertainties. Uncertainties stemming from the choice between the four- and the five-flavour scheme are found to be typically of the order of 5–10% over large ranges of phase space. We discuss the impact of parton distribution functions, and in particular of the bottom PDF. We also show how different cuts on QCD radiation patterns improve the signal-to-background ratio in realistic fiducial volumes.

  13. Quantitative real-time PCR technique for the identification of E. coli residual DNA in streptokinase recombinant product.

    Science.gov (United States)

    Fazelahi, Mansoureh; Kia, Vahid; Kaghazian, Hooman; Paryan, Mahdi

    2017-11-26

    Recombinant streptokinase is a biopharmaceutical which is usually produced in E. coli. Residual DNA as a contamination and risk factor may remain in the product. It is necessary to control the production procedure to exclude any possible contamination. The aim of the present study was to develop a highly specific and sensitive quantitative real-time PCR-based method to determine the amount of E. coli DNA in recombinant streptokinase. A specific primers and a probe was designed to detect all strains of E. coli. To determine the specificity, in addition to using NCBI BLASTn, 28 samples including human, bacterial, and viral genomes were used. The results confirmed that the assay detects no genomic DNA but E. coli's and the specificity was determined to be 100%. To determine the sensitivity and limit of detection of the assay, a 10-fold serial dilution (10 1 to 10 7 copies/µL) was tested in triplicate. The sensitivity of the test was determined to be 101 copies/µL or 35 fg/µL. Inter-assay and intra-assay were determined to be 0.86 and 1.69%, respectively. Based on the results, this assay can be used as an accurate method to evaluate the contamination of recombinant streptokinase in E. coli.

  14. Application of Single Strand Conformational Polymorphism (PCR-SSCP) in Identification of Some Beta-Globin Gene Mutations in A Group of Egyptian Beta-Thalassemia Patients and Carriers

    International Nuclear Information System (INIS)

    Somaya, E.T.; Soliman, M.D

    2010-01-01

    The present study investigated whether the single-strand conformational polymorphism (SSCP) method could be employed to identify (rather than simply detect) four of the most common beta-globin gene mutations in the Egyptian population: IVS-I-110, IVS-I-6, the IVS-I-1, and Codon 39. Using DNA from 90 beta-thalassemia patients and carriers, by PCR the appropriate 238-bp region of the human beta-globin gene was amplified, the reaction products (Single-stranded DNA) were analyzed by none denaturing polyacrylamide gel electrophoresis, and the bands visualized by silver staining. Single-stranded DNA (ssDNA) fragments showed reproducible pattern of bands that were characteristic of the mutations present. With the use of control samples containing six of the 10 possible combinations of the four beta-globin gene mutations under study, we were able to predict the mutations present in 23 out of 90 (26.4%) of the patients studied. These predictions were confirmed independently by the amplification refractory mutation system (ARMS) method. It is concluded that this non-radioactive PCR-SSCP method can be used to reliably identify mutations in beta-thalassemia patients, provided that suitable controls are available. However, usefulness of this method for determining the genotype of beta-thalassaemic individuals is obviously limited by the great number of controls required. Moreover, the ability to detect mutations by SSCP is in general lower compared to other methods, ARMS, DGGE or DHPLC, which are reported to detect 49.5% to 73% of the mutations present. The SSCP method is nevertheless much easier to employ than other methods and is especially successful for beta-thalassemia carriers. This method would thus be particularly useful for an initial screening of target groups (prenatal diagnosis)

  15. Enumeration of Salmonellae in Table Eggs, Pasteurized Egg Products, and Egg-Containing Dishes by Using Quantitative Real-Time PCR

    DEFF Research Database (Denmark)

    Jakočiūnė, Džiuginta; Pasquali, Frédérique; da Silva, Cristiana Soares

    2014-01-01

    PCR) was employed for enumeration of salmonellae in different matrices: table eggs, pasteurized egg products, and egg-containing dishes. Salmonella enterica serovar Enteritidis and S. enterica serovar Tennessee were used to artificially contaminate these matrices. The results showed a linear regression between...... of salmonellae in two egg-containing dishes, long egg and tiramisu, at abused refrigeration temperatures, and results indicated the growth of bacteria over a 1-week period. In conclusion, enrichment qPCR was shown to be reliable for enumeration of salmonellae in different egg products....

  16. Resolving incomplete single nucleotide polymorphism tagging of HLA-DQ2.2 for coeliac disease genotyping using digital droplet PCR.

    Science.gov (United States)

    Hardy, M Y; Ontiveros, N; Varney, M D; Tye-Din, J A

    2018-04-01

    A hallmark of coeliac disease (CD) is the exceptionally strong genetic association with HLA-DQ2.5, DQ8, and DQ2.2. HLA typing provides information on CD risk important to both clinicians and researchers. A method that enables simple and fast detection of all CD risk genotypes is particularly desirable for the study of large populations. Single nucleotide polymorphism (SNP)-based HLA typing can detect the CD risk genotypes by detecting a combination of six SNPs but this approach can struggle to resolve HLA-DQ2.2, seen in 4% of European CD patients, because of the low resolution of one negatively predicting SNP. We sought to optimise SNP-based HLA typing by harnessing the additional resolution of digital droplet PCR to resolve HLA-DQ2.2. Here we test this two-step approach in an unselected sample of Mexican DNA and compare its accuracy to DNA typed using traditional exon detection. The addition of digital droplet PCR for samples requiring negative prediction of HLA-DQ2.2 enabled HLA-DQ2.2 to be accurately typed. This technique is a simple addition to a SNP-based typing strategy and enables comprehensive definition of all at-risk HLA genotypes in CD in a timely and cost-effective manner. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. Tentacle Probes: differentiation of difficult single-nucleotide polymorphisms and deletions by presence or absence of a signal in real-time PCR.

    Science.gov (United States)

    Satterfield, Brent C; Kulesh, David A; Norwood, David A; Wasieloski, Leonard P; Caplan, Michael R; West, Jay A A

    2007-12-01

    False-positive results are a common problem in real-time PCR identification of DNA sequences that differ from near neighbors by a single-nucleotide polymorphism (SNP) or deletion. Because of a lack of sufficient probe specificity, post-PCR analysis, such as a melting curve, is often required for mutation differentiation. Tentacle Probes, cooperative reagents with both a capture and a detection probe based on specific cell-targeting principles, were developed as a replacement for 2 chromosomal TaqMan-minor groove binder (MGB) assays previously developed for Yersinia pestis and Bacillus anthracis detection. We compared TaqMan-MGB probes to Tentacle Probes for SNP and deletion detection based on the presence or absence of a growth curve. With the TaqMan-MGB Y. pestis yp48 assays, false-positive results for Yersinia pseudotuberculosis occurred at every concentration tested, and with the TaqMan-MGB B. anthracis gyrA assays, false-positive results occurred in 21 of 29 boil preps of environmental samples of near neighbors. With Tentacle Probes no false-positive results occurred. The high specificity exhibited by Tentacle Probes may eliminate melting curve analysis for SNP and deletion mutation detection, allowing the diagnostic use of previously difficult targets.

  18. [Application of double created restriction site PCR-RFLP to identify MGMT gene polymorphisms].

    Science.gov (United States)

    Wang, Wei; Miao, Wenbin; Qiu, Yulan; Xia, Zhaolin

    2008-01-01

    To develop a proper assay for identifying single nucleotide polymorphisms( SNPs) of the MGMT gene. PCR primers were designed by create restriction site (CRS) method, then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was adopted to identify four SNPs in MGMT gene. By PCR, one primer pair yielded target products containing MGMT84 SNP site, and the other primer pair yielded target products containing MGMT143, 160, 178 SNP sites. Four restriction enzymes were adopted to identify the four SNPs, respectively. The effects of PCR and RFLP were good. The methods for four SNPs of MGMT determinated by CRS-PCR-RFLP theory could be facility, economy, and rapidness.

  19. Development of a novel approach for the production of dried genomic DNA for use as standards for qualitative PCR testing of food-borne pathogens

    DEFF Research Database (Denmark)

    Trapmann, S.; Catalani, P.; Hoorfar, Jeffrey

    2004-01-01

    As part of a multi-centre European project, FOOD-PCR, the feasibility of a novel approach for production of dried bacterial DNA that could be used as certified reference materials (CRM) was assessed. Selected strains of Salmonella typhimurium, Listeria monocytogenes, Escherichia coli O157...

  20. Single pi-zero production in neutrino interactions

    International Nuclear Information System (INIS)

    Chapin, T.J.

    1976-01-01

    Production of single π 0 particles in neutrino reactions was studied in an experiment at the Brookhaven National Laboratory Alternating Gradient Synchrotron. The neutral current reactions, νn → νnπ 0 and νp → νpπ 0 , and the charged current reaction, νn → μ - pπ 0 , were investigated. The neutrino detector was made up of optical spark chambers and liquid and solid scintillation counters. The π 0 is detected by observing showers from its decay into two gamma rays. Muons are distinguished from other particles by their long range without interaction. Time of flight measurement is used to discriminate against neutron background. The neutral and charged current events are discussed, and the ratio of neutral current events to charged current events is found to be 0.149 +- 0.048 after corrections. Nuclear charge exchange corrections to this result because the detector contains complex nuclei are also discussed. Kinematic distributions for the final state particles and the pπ 0 mass distribution are given

  1. Development of a multiplex PCR assay detecting 52 autosomal SNPs

    DEFF Research Database (Denmark)

    Sanchez Sanchez, Juan Jose; Phillips, C.; Børsting, Claus

    2006-01-01

    for amplifying 52 genomic DNA fragments, each containing one SNP, in a single tube, and accurately genotyping the PCR product mixture using two single base extension reactions. This multiplex approach reduces the cost of SNP genotyping and requires as little as 0.5 ng of genomic DNA to detect 52 SNPs. We used...

  2. Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

    Science.gov (United States)

    Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

    2017-08-04

    Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

  3. Quantification of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV-UG) in single and mixed infected Cassava (Manihot esculenta Crantz) using quantitative PCR.

    Science.gov (United States)

    Naseem, Saadia; Winter, Stephan

    2016-01-01

    The quantity of genomic DNA-A and DNA-B of African cassava mosaic virus (ACMV) and East African cassava mosaic virus Uganda (Uganda variant, EACMV-UG) was analysed using quantitative PCR to assess virus concentrations in plants from susceptible and tolerant cultivars. The concentrations of genome components in absolute and relative quantification experiments in single and mixed viral infections were determined. Virus concentration was much higher in symptomatic leaf tissues compared to non-symptomatic leaves and corresponded with the severity of disease symptoms. In general, higher titres were recorded for EACMV-UG Ca055 compared to ACMV DRC6. The quantitative assessment also showed that the distribution of both viruses in the moderately resistant cassava cv. TMS 30572 was not different from the highly susceptible cv. TME 117. Natural mixed infections with both viruses gave severe disease symptoms. Relative quantification of virus genomes in mixed infections showed higher concentrations of EACMV-UG DNA-A compared to ACMV DNA-A, but a marked reduction of EACMV-UG DNA-B. The higher concentrations of EACMV-UG DNA-B compared to EACMV DNA-A accumulation in single infections were consistent. Since DNA-B is implicated in virus cell-to-cell spread and systemic movement, the abundance of the EACMV-UG DNA-B may be an important factor driving cassava mosaic disease epidemic. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Development of SCAR markers and PCR assays for single or simultaneous species-specific detection of Phytophthora nicotianae and Pythium helicoides in ebb-and-flow irrigated kalanchoe.

    Science.gov (United States)

    Ahonsi, Monday O; Ling, Yin; Kageyama, Koji

    2010-11-01

    Phytophthora nicotianae and Pythium helicoides are important water-borne oomycete pathogens of irrigated ornamentals particularly ebb-and-flow irrigated kalanchoe in Japan. We developed novel PCR-based sequence characterized amplified region markers and assays for rapid identification and species-specific detection of both pathogens in separate PCR reactions or simultaneously in a duplex PCR.

  5. Development of a real-time PCR method coupled with a selective pre-enrichment step for quantification of Morganella morganii and Morganella psychrotolerans in fish products

    DEFF Research Database (Denmark)

    Podeur, Gaetan; Dalgaard, Paw; Leroi, Francoise

    2015-01-01

    purified DNA from 23 other histamine producing bacteria and 26 isolates with no or limited histamine production. The efficiency of the qPCR reactions on artificially contaminated fish samples were 100.8% and 96.3% respectively. The limit of quantification (LOQ) without enrichment was 4 log CFU......PCR) methods for quantification of M. morganii and M. psychrotolerans have been developed. Selective primers amplified a 110 bp region of the vasD gene for M. psychrotolerans and a 171 bp region of the galactokinase gene for M. morganii. These primer-sets showed high specificity as demonstrated by using...

  6. PCR-based analysis of disease in tomato singly or mixed inoculated with Fusarium oxysporum f. sp. lycopersici races 1 and 2

    Directory of Open Access Journals (Sweden)

    OLUSEGUN SAMUEL BALOGUN

    2008-07-01

    Full Text Available The pathogenic response of two tomato cultivars to races of Fusarium oxysporum f. sp.. lycopersici (cv. Momotaro, insensitive to race 1 of the pathogen, and cv. Ponderosa sensitive to race 1, was studied in greenhouse and laboratory experiments by inoculating the cultivars singly with race 1 or race 2, and in mixed inoculation with the two races of the pathogen. A pre-symptom PCR assay two weeks after inoculation showed that a fragment of the intergenic spacer region (IGS of ribosomal DNA was amplifi ed by DNA templates from leaf samples of cv. Momotaro tomato plants inoculated with only race 2, or with race 1+2, but in the cv. Ponderosa the fragment was amplifi ed only in plants inoculated with race 1+2. Race-specifi c analysis using the sp13 and sp23 primers confi rmed that the amplifi ed fragment was from race 2 in cv. Momotaro and from races 1+2 in cv. Ponderosa. Later wilt symptoms mirrored the pre-symptom and post-symptom molecular analytical results: cv. Momotaro plants inoculated with only race 1 remained symptomless, while the ‘Momotaro’ plants inoculated with both races (1+2 did not manifest more severe wilt symptoms than plants inoculated with race 2 alone; cv. Ponderosa plants that were mixed-inoculated with race 1+2 manifested more severe symptoms, and at an earlier date than plants inoculated with only race 2. Growth parameters such as number of leaves and plant height showed the race 1+2 infected cv. Ponderosa were significantly retarded in growth, suggesting that significant synergism between the fungal races in tomato pathosystem can occur only when the host cultivar is sensitive to both races. An additional important finding is that pre-symptom leaf sampling of apparently healthy plants is useful in PCR diagnostic analysis to predict impending fusarial wilt outbreaks in tomato especially in infested soil.

  7. The Pan-AC assay: a single-reaction real-time PCR test for quantitative detection of a broad range of Aspergillus and Candida species.

    Science.gov (United States)

    Basková, Lenka; Landlinger, Christine; Preuner, Sandra; Lion, Thomas

    2007-09-01

    In view of the growing incidence and the high mortality of invasive aspergillosis and candidiasis, adequate diagnostic techniques permitting timely onset of treatment are of paramount importance. More than 90 % of all invasive fungal infections in immunocompromised individuals can be attributed to Candida and Aspergillus species. To date, standardized techniques permitting rapid, sensitive and, no less importantly, economic screening for the clinically most relevant fungi are lacking. In the present report, a real-time quantitative PCR assay, developed for the detection of the most common pathogenic Candida and Aspergillus species, is described. The single-reaction PCR assay targets a judiciously selected region of the 28S subunit of the fungal rDNA gene. The unique design of the universal primer/probe system, including a pan-Aspergillus and pan-Candida (Pan-AC) hydrolysis probe, facilitates the detection of numerous Aspergillus species (e.g. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus versicolor and Aspergillus nidulans) and Candida species (e.g. Candida albicans, Candida glabrata, Candida krusei, Candida tropicalis, Candida parapsilosis, Candida kefyr, Candida guilliermondii, Candida lusitaniae and Candida dubliniensis). The assay permits highly reproducible detection of 10 fg fungal DNA, which corresponds to a fraction of a fungal genome, and facilitates accurate quantification of fungal load across a range of at least five logs. Upon standardization of the technique using cultured fungal strains, the applicability in the clinical setting was assessed by investigating a series of clinical specimens from patients with documented fungal infections (n=17). The Pan-AC assay provides an attractive and economic approach to the screening and monitoring of invasive aspergillosis and candidiasis, which is readily applicable to routine clinical diagnosis.

  8. TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations.

    Directory of Open Access Journals (Sweden)

    Dawn N Birdsell

    Full Text Available Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis, therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays

  9. Comparative, Collaborative, and On-Site Validation of a TaqMan PCR Method as a Tool for Certified Production of Fresh, Campylobacter-Free Chickens

    DEFF Research Database (Denmark)

    Krause, Michael; Josefsen, Mathilde Hartmann; Lund, Marianne

    2006-01-01

    Certified Campylobacter-free poultry products have been produced in Denmark since 2002, the first example of fresh (unprocessed and nonfrozen) chickens labeled "Campylobacter free." This success occurred partly through use of a 4-hour gel-based PCR testing scheme on fecal swabs. In this study......, a faster, real-time PCR approach was validated in comparative and collaborative trials, based on recommendations from the Nordic system for validation of alternative microbiological methods (NordVal). The comparative real-time PCR trial was performed in comparison to two reference culture protocols...... as positive. The comparative trial resulted in relative accuracy, sensitivity, and specificity of 98%, 95%, and 97%, respectively. The collaborative trial included nine laboratories testing neck skin, cloacal swab, and shoe cover samples, spiked with low, medium, and high concentrations of Campylobacter...

  10. Rapid and Efficient cDNA Library Screening by Self-Ligation ofInverse PCR Products (SLIP)

    Energy Technology Data Exchange (ETDEWEB)

    Hoskins, Roger A.; Stapleton, Mark; George, Reed A.; Yu, Charles; Wan, Kenneth H.; Carlson, Joseph W.; Celniker, Susan E.

    2005-04-22

    The production of comprehensive cDNA clone collections is an important goal of the human and model organism genome projects. cDNA sequences are used to determine the structures of transcripts, including splice junctions, polyadenylation sites, and 5' and 3' untranslated regions (UTRs). cDNA collections are also valuable resources for functional studies of genes and proteins. Expressed Sequence Tag (EST)sequencing is the method of choice for recovering cDNAs representing a majority of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a library at random, so it realizes diminishing returns as the project progresses. To drive cDNA collections toward completion new methods are needed to recover cDNAs representing specific genes and alternative transcripts, including transcripts with low expression levels. We describe a simple and effective inverse-PCR-based method for screening plasmid libraries to recover intact cDNAs for specific transcripts. We tested the method by screening libraries used in our Drosophila EST projects for 153 transcription factor genes that were not yet represented by full-length cDNAs. We recovered target-specific clones for 104 of the genes: 46 exactly match, 30 improve and 28partially match current gene annotations. Successful application of the screening method depends on cDNA library complexity and quality of the gene models. The approach should be effective for improving cDNA collections for other model organisms and the human. It also provides a simple and rapid method for isolating cDNAs of interest in any system for which plasmid cDNA libraries and complete or partial gene sequences are available.

  11. Detection and prevalence of pathogenic Yersinia enterocolitica in refrigerated and frozen dairy products by duplex PCR and dot hybridization targeting the virF and ail genes.

    Science.gov (United States)

    Ye, Y W; Ling, N; Han, Y J; Wu, Q P

    2014-11-01

    Pathogenic Yersinia enterocolitica is involved in yersiniosis through expression of chromosome-borne or plasmid-borne virulence factors. Yersinia enterocolitica is a cold-tolerant pathogen frequently isolated from refrigerated or frozen foods. However, little attention has been focused on the prevalence of pathogenic Y. enterocolitica in refrigerated or frozen dairy samples in China. In this study, we developed a new duplex PCR targeting the plasmid-borne virF gene and chromosome-borne ail gene for detection of pathogenic Y. enterocolitica isolates. We established a detection limit for the duplex PCR of 6.5 × 10(2)cfu/mL in artificially contaminated dairy samples. In addition, the duplex PCR could detect directly 4.5 to 5.7 cfu of Y. enterocolitica in 5 mL of brain heart infusion broth after 6 h of enrichment at 28 °C. A newly developed dot hybridization assay further confirmed specificity of the duplex PCR for detection of virulent Y. enterocolitica. Furthermore, 13 Y. enterocolitica and 5 pathogenic strains, from 88 commercial frozen or refrigerated dairy products, were detected successfully by the China National Standard method (GB/T4789.8-2008) and the duplex PCR, respectively. Finally, biotypes and serotypes of pathogenic Y. enterocolitica strains were further characterized. The duplex PCR developed here is reliable for large-scale screening, routine monitoring, and risk assessment of pathogenic Y. enterocolitica in refrigerated or frozen dairy products. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. 9 CFR 381.445 - Guidelines for voluntary nutrition labeling of single-ingredient, raw products.

    Science.gov (United States)

    2010-01-01

    ... INSPECTION REGULATIONS Nutrition Labeling § 381.445 Guidelines for voluntary nutrition labeling of single-ingredient, raw products. (a) Nutrition information on the cuts of single-ingredient, raw poultry products... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Guidelines for voluntary nutrition...

  13. 9 CFR 317.345 - Guidelines for voluntary nutrition labeling of single-ingredient, raw products.

    Science.gov (United States)

    2010-01-01

    ... DEVICES, AND CONTAINERS Nutrition Labeling § 317.345 Guidelines for voluntary nutrition labeling of single-ingredient, raw products. (a) Nutrition information on the cuts of single-ingredient, raw meat products... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Guidelines for voluntary nutrition...

  14. Monitoring transmission routes of Listeria spp. in smoked salmon production with repetitive element sequence-based PCR techniques.

    Science.gov (United States)

    Zunabovic, M; Domig, K J; Pichler, I; Kneifel, W

    2012-03-01

    Various techniques have been used for tracing the transmission routes of Listeria species and for the assessment of hygiene standards in food processing plants. The potential of repetitive element sequence-based PCR (Rep-PCR) methods (GTG₅ and REPI + II) for the typing of Listeria isolates (n = 116), including Listeria monocytogenes (n = 46), was evaluated in a particular situation arising from the relocation of a company producing cold-smoked salmon. Pulsed-field gel electrophoresis (PFGE) using three restriction enzymes (ApaI, AscI, and SmaI) was used for comparison. Identical transmission scenarios among two companies could be identified by cluster analysis of L. monocytogenes isolates that were indistinguishable by both Rep-PCR and PFGE. The calculated diversity index (DI) indicates that Rep-PCR subtyping of Listeria species with primer sets GTG₅ and REPI + II has a lower discrimination power than does PFGE. When concatenated Rep-PCR cluster analysis was used, the DI increased from 0.934 (REPI + II) and 0.923 (GTG₅) to 0.956. The discrimination power of this method was similar to that of PFGE typing based on restriction enzyme Apa I (DI = 0.955). Listeria welshimeri may be useful as an indicator for monitoring smoked salmon processing environments. Rep-PCR meets the expectations of a reasonable, fast, and low-cost molecular subtyping method for the routine monitoring of Listeria species. The discriminatory power as characterized by the DI sufficiently quantifies the probability of unrelated isolates being characterized as different subtypes. Therefore, Rep-PCR typing based on two primer systems (GTG₅ and REPI + II) may be a useful tool for monitoring industrial hygiene.

  15. 76 FR 76890 - Nutrition Labeling of Single-Ingredient Products and Ground or Chopped Meat and Poultry Products...

    Science.gov (United States)

    2011-12-09

    .... FSIS-2005-0018] Nutrition Labeling of Single-Ingredient Products and Ground or Chopped Meat and Poultry... (FSIS) is delaying the effective date of the final regulations that require nutrition labeling of the major cuts of single-ingredient, raw meat and poultry products and ground or chopped meat and poultry...

  16. Detection of the Single Nucleotide Polymorphism at Position rs2735940 in the Human Telomerase Reverse Transcriptase Gene by the Introduction of a New Restriction Enzyme Site for the PCR-RFLP Assay.

    Science.gov (United States)

    Wang, Sihua; Ding, Mingcui; Duan, Xiaoran; Wang, Tuanwei; Feng, Xiaolei; Wang, Pengpeng; Yao, Wu; Wu, Yongjun; Yan, Zhen; Feng, Feifei; Yu, Songcheng; Wang, Wei

    2017-09-01

    It has been shown that the single nucleotide polymorphism (SNP) of the rs2735940 site in the human telomerase reverse transcriptase ( hTERT ) gene is associated with increased cancer risk. The traditional method to detect SNP genotypes is polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). However, there is a limitation to utilizing PCR-RFLP due to a lack of proper restriction enzyme sites at many polymorphic loci. This study used an improved PCR-RFLP method with a mismatched base for detection of the SNP rs2735940. A new restriction enzyme cutting site was created by created restriction site PCR (CRS-PCR), and in addition, the restriction enzyme Msp I for CRS-PCR was cheaper than other enzymes. We used this novel assay to determine the allele frequencies in 552 healthy Chinese Han individuals, and found the allele frequencies to be 63% for allele C and 37% for allele T In summary, the modified PCR-RFLP can be used to detect the SNP of rs2735940 with low cost and high efficiency. © 2017 by the Association of Clinical Scientists, Inc.

  17. Treatment of PCR products with exonuclease I and heat-labile alkaline phosphatase improves the visibility of combined bisulfite restriction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Kousuke; Emoto, Noriko; Sunohara, Mitsuhiro; Kawakami, Masanori; Kage, Hidenori; Nagase, Takahide; Ohishi, Nobuya [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Takai, Daiya, E-mail: dtakai-ind@umin.ac.jp [Department of Clinical Laboratory, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan)

    2010-08-27

    Research highlights: {yields} Incubating PCR products at a high temperature causes smears in gel electrophoresis. {yields} Smears interfere with the interpretation of methylation analysis using COBRA. {yields} Treatment with exonuclease I and heat-labile alkaline phosphatase eliminates smears. {yields} The elimination of smears improves the visibility of COBRA. -- Abstract: DNA methylation plays a vital role in the regulation of gene expression. Abnormal promoter hypermethylation is an important mechanism of inactivating tumor suppressor genes in human cancers. Combined bisulfite restriction analysis (COBRA) is a widely used method for identifying the DNA methylation of specific CpG sites. Here, we report that exonuclease I and heat-labile alkaline phosphatase can be used for PCR purification for COBRA, improving the visibility of gel electrophoresis after restriction digestion. This improvement is observed when restriction digestion is performed at a high temperature, such as 60 {sup o}C or 65 {sup o}C, with BstUI and TaqI, respectively. This simple method can be applied instead of DNA purification using spin columns or phenol/chloroform extraction. It can also be applied to other situations when PCR products are digested by thermophile-derived restriction enzymes, such as PCR restriction fragment length polymorphism (RFLP) analysis.

  18. Return handling options and order quantities for single period products

    NARCIS (Netherlands)

    D. Vlachos (Dimitrios); R. Dekker (Rommert)

    2000-01-01

    textabstractProducts which are sold through E-commerce or mail sales catalogues tend to have a much higher return rate than traditional products. The returns are especially problematic for seasonal products. To support decision making in these situations we study various options, which may be

  19. Rapid Detection of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari in Fresh Chicken Meat and By-Products in Bangkok, Thailand, Using Modified Multiplex PCR.

    Science.gov (United States)

    Saiyudthong, S; Phusri, K; Buates, S

    2015-07-01

    A multiplex PCR assay for simultaneous detection and differentiation of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari was developed and validated to assess the occurrence of these bacteria in fresh chicken meat and by-products in Bangkok, Thailand, by using a new combination of four previously published PCR primers for C. jejuni, C. coli, C. lari, and a universal 16S rDNA gene as an internal control. The specificity was determined by using 13 strains of other bacteria. With pure culture DNA, the detection limit was 0.017 ng/PCR for C. jejuni and C. coli and was 0.016 ng/PCR for C. lari. It can detect 10 CFU of C. jejuni, C. coli, and C. lari in 2 g of chicken meat within a 16-h enrichment time. Our multiplex PCR assay was applied for identification of Campylobacter spp. in 122 supermarket samples and 108 fresh market samples. Of the 230 samples evaluated by multiplex PCR, 54.0, 3.3, and 10.7% of supermarket samples were positive for C. jejuni, C. coli, and mixed C. jejuni and C. coli, respectively, and 56.5 and 33.3% of fresh market samples were positive for C. jejuni and mixed C. jejuni and C. coli, respectively. No sample was positive for C. lari. Fresh market samples had significantly higher C. jejuni and C. coli contamination than those from supermarkets (relative risk: 1.3; P = 0.0001). Compared with the culture method (a gold standard), the sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of multiplex PCR were 97.7, 86.8, 96.1, 92.0, and 95.2%, respectively. No significant difference was observed between results from two methods (P = 0.55). Therefore, the established multiplex PCR was not only rapid and easy to perform but had a high sensitivity and specificity to distinguish between C. jejuni, C. coli, and C. lari, even in samples containing mixed contamination. Our study indicated that fresh chicken meat and by-products from fresh markets were significantly less hygienic than those

  20. Propidium monoazide combined with real-time quantitative PCR to quantify viable Alternaria spp. contamination in tomato products.

    Science.gov (United States)

    Crespo-Sempere, Ana; Estiarte, Núria; Marín, Sonia; Sanchis, Vicente; Ramos, Antonio J

    2013-08-01

    Alternaria is a common contaminating genus of fungi in fruits, grains, and vegetables that causes severe economic losses to farmers and the food industry. Furthermore, it is claimed that Alternaria spp. are able to produce phytotoxic metabolites, and mycotoxins that are unsafe for human and animal health. DNA amplification techniques are being increasingly applied to detect, identify, and quantify mycotoxigenic fungi in foodstuffs, but the inability of these methods to distinguish between viable and nonviable cells might lead to an overestimation of mycotoxin-producing living cells. A promising technique to overcome this problem is the pre-treatment of samples with nucleic acid intercalating dyes, such as propidium monoazide (PMA), prior to quantitative PCR (qPCR). PMA selectively penetrates cells with a damaged membrane inhibiting DNA amplification during qPCRs. In our study, a primer pair (Alt4-Alt5) to specifically amplify and quantify Alternaria spp. by qPCR was designed. Quantification data of qPCR achieved a detection limit of 10(2)conidia/g of tomato. Here, we have optimized for the first time a DNA amplification-based PMA sample pre-treatment protocol for detecting viable Alternaria spp. cells. Artificially inoculated tomato samples treated with 65μM of PMA, showed a reduction in the signal by almost 7cycles in qPCR between live and heat-killed Alternaria spp. conidia. The tomato matrix had a protective effect on the cells against PMA toxicity, reducing the efficiency to distinguish between viable and nonviable cells. The results reported here indicate that the PMA-qPCR method is a suitable tool for quantifying viable Alternaria cells, which could be useful for estimating potential risks of mycotoxin contamination. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Detection of alcohol-tolerant hiochi bacteria by PCR.

    OpenAIRE

    Nakagawa, T; Shimada, M; Mukai, H; Asada, K; Kato, I; Fujino, K; Sato, T

    1994-01-01

    We report a sensitive and rapid method for detection of hiochi bacteria by PCR. This method involves the electrophoresis of amplified DNA. Nucleotide sequences of the spacer region between 16S and 23S rRNA genes of 11 Lactobacillus strains were identified by analysis of PCR products. Five primers were designed by analysis of similarities among these sequences. A single cell of Lactobacillus casei subsp. casei could be detected when purified genomic DNA was used as the template. When various c...

  2. Single Top quark production cross section using ATLAS detector at the LHC

    CERN Document Server

    Estrada Pastor, Oscar; The ATLAS collaboration

    2018-01-01

    Measurements of single top-quark production in proton-proton collisions are presented based on the 8 TeV and 13 TeV ATLAS datasets. In the leading order process, a W boson is exchanged in the t-channel. The cross-section for the production of single top-quarks and single anti-top-quarks, their ratio, as well as differential cross-section measurements are also reported. These analyses include limits on anomalous contributions to the Wtb vertex and measurement of the top quark polarization. Measurements of the inclusive and differential cross-sections for the production of a single top quark in association with a W boson, the second largest single-top production mode, are also presented. Finally, evidence for s-channel single-top production in the 8 TeV ATLAS dataset is presented. All measurements are compared to state-of-the-art theoretical calculations.

  3. Return handling options and order quantities for single period products

    OpenAIRE

    Vlachos, D.; Dekker, R.

    2000-01-01

    textabstractProducts which are sold through E-commerce or mail sales catalogues tend to have a much higher return rate than traditional products. The returns are especially problematic for seasonal products. To support decision making in these situations we study various options, which may be considered as strategic decisions, on handling the increased return flow. Closed form analytic expressions for optimal order quantities are obtained by solving the models developed for each option. Decis...

  4. An Undergraduate Laboratory Experiment for Upper-Level Forensic Science, Biochemistry, or Molecular Biology Courses: Human DNA Amplification Using STR Single Locus Primers by Real-Time PCR with SYBR Green Detection

    Science.gov (United States)

    Elkins, Kelly M.; Kadunc, Raelynn E.

    2012-01-01

    In this laboratory experiment, real-time polymerase chain reaction (real-time PCR) was conducted using published human TPOX single-locus DNA primers for validation and various student-designed short tandem repeat (STR) primers for Combined DNA Index System (CODIS) loci. SYBR Green was used to detect the amplification of the expected amplicons. The…

  5. Design and Assessment of a Real Time Reverse Transcription-PCR Method to Genotype Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae).

    Science.gov (United States)

    A real-time, reverse transcription-PCR (RT-qPCR) assay was developed to differentiate the four genogroups of male-specific ssRNA coliphages (FRNA) (family Leviviridae). As FRNA display a trend of source-specificity (human sewage or animal waste) at the genogroup level, this assa...

  6. Customized Pull Systems for Single-Product Flow Lines

    NARCIS (Netherlands)

    Gaury, E.G.A.; Kleijnen, J.P.C.; Pierreval, H.

    1998-01-01

    Traditionally pull production systems are managed through classic control systems such as Kanban, Conwip, or Base stock, but this paper proposes ‘customized’ pull control. Customization means that a given production line is managed through a pull control system that in principle connects each stage

  7. Expression, production and renaturation of a functional single-chain ...

    African Journals Online (AJOL)

    The single-chain variable antibody fragment (scFv) against human intercellular adhesion molecule-1 (ICAM-1) was expressed at a high level in Escherichia coli as inclusion bodies. We attempted to refold the scFv by ion-exchange chromatography (IEC), dialysis and dilution. The results show that the column ...

  8. Improvement of Torque Production in Single-Phase Induction Motors ...

    African Journals Online (AJOL)

    Existing single phase induction motors exhibit low starting torque. Moreover, during accelerating time and at steady state, they produce a significant level of torque pulsations which gives rise to noise and vibration in the machine. As part of efforts to mitigate these problems, a performance improvement strategy using a PWM ...

  9. Extent of sensitivity of single photon production to parton distribution ...

    Indian Academy of Sciences (India)

    The prompt photon cross-section is found to be described equally well by all the PDFs within the experimental errors at the RHIC and the LHC energies. The deviation in the single-prompt photon yield for different PDF sets is within ±20% when compared to CTEQ4M, indicating the upper bound of uncertainty in determining ...

  10. Single Assignment C (SAC): High Productivity meets High Performance

    NARCIS (Netherlands)

    Grelck, C.; Zsók, V.; Horváth, Z.; Plasmeijer, R.

    2012-01-01

    We present the ins and outs of the purely functional, data parallel programming language SaC (Single Assignment C). SaC defines state- and side-effect-free semantics on top of a syntax resembling that of imperative languages like C/C++/C# or Java: functional programming with curly brackets. In

  11. Production of a phage-displayed single chain variable fragment ...

    African Journals Online (AJOL)

    Purpose: To develop specific single chain variable fragments (scFv) against infectious bursal disease virus (IBDV) via phage display technology. Methods: Purified viruses were initially applied for iterative panning rounds of scFv phage display libraries. The binding ability of the selected scFv antibody fragments against the ...

  12. Multiplex PCR and minisequencing of SNPs--a model with 35 Y chromosome SNPs

    DEFF Research Database (Denmark)

    Sanchez, Juan J; Børsting, Claus; Hallenberg, Charlotte

    2003-01-01

    We have developed a robust single nucleotide polymorphism (SNPs) typing assay with co-amplification of 25 DNA-fragments and the detection of 35 human Y chromosome SNPs. The sizes of the PCR products ranged from 79 to 186 base pairs. PCR primers were designed to have a theoretical Tm of 60 +/- 5 d...

  13. Isolation and Identification of Campylobacter spp. from Poultry and Poultry By-Products in Tunisia by Conventional Culture Method and Multiplex Real-Time PCR.

    Science.gov (United States)

    Jribi, Hela; Sellami, Hanen; Mariam, Siala; Smaoui, Salma; Ghorbel, Asma; Hachicha, Salma; Benejat, Lucie; Messadi-Akrout, Feriel; Mégraud, Francis; Gdoura, Radhouane

    2017-10-01

    Thermophilic Campylobacter spp. are one of the primary causes of bacterial human diarrhea. The consumption of poultry meats, by-products, or both is suspected to be a major cause of human campylobacteriosis. The aims of this study were to determine the prevalence of thermophilic Campylobacter spp. in fresh poultry meat and poultry by-products by conventional culture methods and to confirm Campylobacter jejuni and Campylobacter coli isolates by using the multiplex PCR assay. Two hundred fifty fresh poultry samples were collected from a variety of supermarkets and slaughterhouses located in Sfax, Tunisia, including chicken (n =149) and turkey (n =101). The samples were analyzed using conventional microbiological examinations according to the 2006 International Organization for Standardization method (ISO 10272-1) for Campylobacter spp. Concurrently, a real-time PCR was used for identification of C. jejuni and C. coli . Of the 250 samples of poultry meat and poultry by-products, 25.6% (n = 64) were contaminated with Campylobacter spp. The highest prevalence of Campylobacter spp. was found in chicken meat (26.8%) followed by turkey meat (23.7%). Among the different products, poultry breasts showed the highest contamination (36.6%) followed by poultry by-products (30%), poultry wings (28%) and poultry legs (26%) showed the lowest contamination, and no contamination was found on neck skin. Of the 64 thermophilic Campylobacter isolates, C. jejuni (59.7%) was the most frequently isolated species and 10.9% of the isolates were identified as C. coli . All of the 64 Campylobacter isolates identified by the conventional culture methods were further confirmed by PCR. The seasonal peak of Campylobacter spp. contamination was in the warm seasons (spring and summer). The study concluded that high proportions of poultry meat and poultry by-products marketed in Tunisia are contaminated by Campylobacter spp. Furthermore, to ensure food safety, poultry meats must be properly cooked

  14. Search for anomalous Wtb couplings in single top quark production

    Czech Academy of Sciences Publication Activity Database

    Abazov, V. M.; Abbott, B.; Abolins, M.; Kupčo, Alexander; Lokajíček, Miloš

    2008-01-01

    Roč. 101, č. 22 (2008), 221801/1-221801/7 ISSN 0031-9007 R&D Projects: GA MŠk LA08047; GA MŠk 1P05LA257; GA MŠk LC527 Institutional research plan: CEZ:AV0Z10100502 Keywords : collisions * D0 * single top quark * Lorentz structure Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 7.180, year: 2008

  15. Production of single-walled carbon nanotube grids

    Science.gov (United States)

    Hauge, Robert H; Xu, Ya-Qiong; Pheasant, Sean

    2013-12-03

    A method of forming a nanotube grid includes placing a plurality of catalyst nanoparticles on a grid framework, contacting the catalyst nanoparticles with a gas mixture that includes hydrogen and a carbon source in a reaction chamber, forming an activated gas from the gas mixture, heating the grid framework and activated gas, and controlling a growth time to generate a single-wall carbon nanotube array radially about the grid framework. A filter membrane may be produced by this method.

  16. Sensitive and specific detection of pine nut (Pinus spp.) by real-time PCR in complex food products.

    Science.gov (United States)

    Garino, Cristiano; De Paolis, Angelo; Coïsson, Jean Daniel; Bianchi, Daniela Manila; Decastelli, Lucia; Arlorio, Marco

    2016-03-01

    Pine nuts are a known source of food allergens and several cases of adverse immunological reaction after ingestion have been reported. To protect allergic consumers, methods to unequivocally detect the presence of pine nuts in complex matrices must be developed. A Taqman-based real time PCR method for the detection of Pinus spp. was set up. A homemade pesto spiked at known concentration of pine nut powder was used as model food. Moreover, DNA was purified from commercial foods declaring or not the presence of pine nuts. The method displayed a very high efficiency and specificity for the genus Pinus. The intrinsic LOD was 1pg of DNA, while the practical LOD evaluated on model foods was 0.1ppm of pine nuts powder, the lowest ever registered for the detection of food allergens via real-time PCR. Finally, the declared presence/absence of pine nut in commercial foods was confirmed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis

    Science.gov (United States)

    Torriani, Sandra; Zapparoli, Giacomo; Dellaglio, Franco

    1999-01-01

    Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene of L. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp. delbrueckii LMG 6412T, which clustered with L. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains. PMID:10508059

  18. Detection of seven virulence and toxin genes of Campylobacter jejuni isolates from Danish turkeys by PCR and cytolethal distending toxin production of the isolates.

    Science.gov (United States)

    Bang, Dang Duong; Borck, Birgitte; Nielsen, Eva Møller; Scheutz, Flemming; Pedersen, Karl; Madsen, Mogens

    2004-10-01

    A total of 117 Campylobacter jejuni isolates from Danish turkeys were tested for the presence of seven virulence and toxin genes by PCR. One hundred seventeen (100%) isolates were positive for flaA, cadF, and ceuE gene primers. One hundred three (88%) isolates were positive for cdt gene cluster PCR detection (cdt gene cluster-PCR), whereas 101 (86.3%), 102 (87.2%), and 110 (94%) isolates were positive for cdtA-, cdtB-, and cdtC-PCR, respectively. Only 39 (33.3%) isolates were positive for virB11. Of 117 isolates, 114 (97.4%) produced cytolethal distending toxin (CDT) in Vero cell assays, 105 (89.7%) in Colon 205 assays, and 109 (93.2%) in chicken embryo cell assays. The CDT titers were determined in Vero cell assays. Of 117 isolates, 50 (42.7%) produced a CDT titer of 1:100, 29 (24.8%) of 1:50, and 27 (23%) of 1:5 to 1:10; 8 (6.8%) produced a CDT titer at undiluted supernatants and 3 (2.6%) produced no toxin. Twenty-nine C. jejuni isolates that were PCR negative for one or more individual cdt toxin genes also produced low or no CDT toxin. The high prevalence of the seven virulence and toxin genes demonstrates that these putative pathogenic determinants are widespread among Campylobacter isolates from turkeys and calls for further investigation for the elimination of Campylobacter infection in industrial turkey production and in industrial food chains.

  19. Scheduling a Single Mobile Robot Incorporated into Production Environment

    DEFF Research Database (Denmark)

    Dang, Vinh Quang; Nielsen, Izabela Ewa; Steger-Jensen, Kenn

    2013-01-01

    Eco-production and logistics with environmental consciousness are playing a larger role in manufacturing firms. They involve scheduling, planning, developing and implementing manufacturing processes and technologies that are required not only to keep productivity high but also to respond....... This chapter deals with the problem of finding optimal operating sequence in a manufacturing cell of a mobile robot with manipulation arm that feeds materials to feeders. The “Bartender Concept” is discussed to show the cooperation between the mobile robot and industrial environment. The performance criterion...... is to minimize total traveling time of the robot with the smallest consumed amount of battery energy in a given planning horizon. A mixed-integer programming (MIP) model is developed to find the optimal solutions for the problem. Two case studies are implemented at an impeller production line to demonstrate...

  20. Detection of coding genes for enterotoxins in Bacillus cereus by PCR and their products by BCET-RPLA and ELISA Assay

    Directory of Open Access Journals (Sweden)

    Marcela Vyletělová

    2010-01-01

    Full Text Available Determination of enterotoxin production, diarrhoeal and emetic gene identification was studied in 41 Bacillus cereus strains isolated from raw cows’ and raw goats’ milk, pasteurized milk, dairy products during technological processing and from dairy plant equipment. Presence of enterotoxins was detected by BCET-RPLA (HBL and ELISA immunoassay (NHE. Gene identification (nheA, nheB, nheC, hblA, hblC, hblD, bceT, cytK-1, cytK-2, entFM and ces was achieved by means of PCR. Enterotoxin HBL was detected in 32 strains, enterotoxin NHE in all 41 strains. Presence of all three genes nheA, nheB and nheC was confirmed in 40 strains and genes hblA, hblC and hblD in 29 strains. Comparison of used methods was as follow: 1 BCET-RPLA (which detects L2 component and PCR (positive or negative all three hblA, hblC and hblD gene detection were identical in 30 (73%; 2 ELISA (NheA and PCR (all three nheC, nheB and nheA gene expression were identical in 40 (98% cases isolated strains.

  1. Duplex real-time PCR method for the detection of sesame (Sesamum indicum) and flaxseed (Linum usitatissimum) DNA in processed food products.

    Science.gov (United States)

    López-Calleja, Inés María; de la Cruz, Silvia; Martín, Rosario; González, Isabel; García, Teresa

    2015-01-01

    The development of a duplex real-time polymerase chain reaction (PCR) method allowing the simultaneous detection of sesame and flaxseed DNA in commercial food products is described. This duplex real-time PCR technique is based in the design of sesame- and flaxseed-specific primers based on the ITS1 region and two TaqMan fluorescent probes. The method was positive for sesame and flaxseed, and showed no cross-reactivity for all other heterologous plant and animal species tested. Sesame and flaxseed could be detected in a series of model samples with defined raw and heat-treated sesame in flaxseed, and flaxseed in sesame, respectively, with detection limits of 1.3 mg kg(-1) for sesame and 1.4 mg kg(-1) for flaxseed. The applicability of the assay for determining sesame and flaxseed in different food matrices was investigated by analysing a total of 238 commercial foodstuffs. This PCR method is useful for highly selective and sensitive detection of traces of sesame and flaxseed in commercial food products.

  2. Single Top quark production cross section and properties using the ATLAS detector at the LHC

    CERN Document Server

    Pedraza Lopez, Sebastian; The ATLAS collaboration

    2015-01-01

    Measurements of single top-quark production in proton proton collisions at 7 and 8 TeV are presented. In the leading order process, a W boson is exchanged in the t-channel. The single top-quark and anti-top total production cross sections, their ratio, as well as a measurement of the inclusive production cross section is presented. In addition, a measurement of the production cross section of a single top quark in association with a W boson is presented. All measurements are compared to state-of-the-art theoretical calculations and the CKM matrix element |Vtb| is determined. In addition, the s-channel production is explored and limits on exotic production in single top quark processes are discussed. This includes the search for flavor changing neutral currents and the search for additional W’ bosons or a search for monotops.

  3. Quantitative (real-time) PCR

    International Nuclear Information System (INIS)

    Denman, S.E.; McSweeney, C.S.

    2005-01-01

    Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later

  4. 75 FR 82148 - Nutrition Labeling of Single-Ingredient Products and Ground or Chopped Meat and Poultry Products

    Science.gov (United States)

    2010-12-29

    ... poultry products inspection regulations to require nutrition labeling of the major cuts of single... cuts: This final rule requires nutrition labeling of the major cuts of single-ingredient, raw meat and... in the voluntary nutrition labeling program to provide nutrition labeling for the major cuts of...

  5. Evaluation of real-time PCR detection methods for detecting rice products contaminated by rice genetically modified with a CpTI-KDEL-T-nos transgenic construct.

    Science.gov (United States)

    Nakamura, Kosuke; Akiyama, Hiroshi; Kawano, Noriaki; Kobayashi, Tomoko; Yoshimatsu, Kayo; Mano, Junichi; Kitta, Kazumi; Ohmori, Kiyomi; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko

    2013-12-01

    Genetically modified (GM) rice (Oryza sativa) lines, such as insecticidal Kefeng and Kemingdao, have been developed and found unauthorised in processed rice products in many countries. Therefore, qualitative detection methods for the GM rice are required for the GM food regulation. A transgenic construct for expressing cowpea (Vigna unguiculata) trypsin inhibitor (CpTI) was detected in some imported processed rice products contaminated with Kemingdao. The 3' terminal sequence of the identified transgenic construct for expression of CpTI included an endoplasmic reticulum retention signal coding sequence (KDEL) and nopaline synthase terminator (T-nos). The sequence was identical to that in a report on Kefeng. A novel construct-specific real-time polymerase chain reaction (PCR) detection method for detecting the junction region sequence between the CpTI-KDEL and T-nos was developed. The imported processed rice products were evaluated for the contamination of the GM rice using the developed construct-specific real-time PCR methods, and detection frequency was compared with five event-specific detection methods. The construct-specific detection methods detected the GM rice at higher frequency than the event-specific detection methods. Therefore, we propose that the construct-specific detection method is a beneficial tool for screening the contamination of GM rice lines, such as Kefeng, in processed rice products for the GM food regulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Search for single photons from supersymmetric particle production

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, E.; Ford, W.T.; Qi, N.; Read A.L. Jr.; Smith, J.G.; Camporesi, T.; De Sangro, R.; Marini, A.; Peruzzi, I.; Piccolo, M.; Ronga, F.; Blume, H.T.; Hurst, R.B.; Venuti, J.P.; Wald, H.B.; Weinstein, R.; Band, H.R.; Gettner, M.W.; Goderre, G.P.; Meyer, O.A.; Moromisato, J.H.; Polvado, R.O.; Shambroom, W.D.; Sleeman, J.C.; von Goeler, E.; Ash, W.W.; Chadwick, G.B.; Clearwater, S.H.; Coombes, R.W.; Kaye, H.S.; Lau, K.H.; Leedy, R.E.; Lynch, H.L.; Messner, R.L.; Moss, L.J.; Muller, F.; Nelson, H.N.; Ritson, D.M.; Rosenberg, L.J.; Wiser, D.E.; Zdarko, R.W.; Groom, D.E.; Lee, H.Y.; Delfino, M.C.; Heltsley, B.K.; Johnson, J.R.; Lavine, T.L.; Maruyama, T.; Prepost, R.

    1985-03-18

    A search in e/sup +/e/sup -/ annihilation for final states which contain only a single energetic photon has been performed at ..sqrt..s = 29 GeV with the MAC detector at PEP. The upper limit on an anomalous signal has been interpreted in terms of mass limits for supersymmetric particles under the assumption of radiative pair paroduction of either supersymmetric photons or neutrinos. For the supersymmetric electron (e) this limit is m/sub e/>37 GeV/c/sup 2/ at the 90% confidence level if M/sub e//sub L/ = m/sub e//sub R/ and the supersymmetric photo (gamma-tilde) has m/sub gamma-tilde/ = 0.

  7. Evaluation of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis for the detection of the rpoB mutations associated with resistance to rifampicin in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Lee, H.; Cho, S.-N.; Bang, H.-E.; Kim, S.-C.; Victor, T.C.; Jordaan, A.; Suffys, P.N.; Gomes, H.M.; Singh, U.; Suresh, V.N.; Khan, B.K.

    2003-01-01

    Resistance of Mycobacterium tuberculosis to rifampicin (RIF) has been associated with mutations of the rpoB gene, which encodes for the RNA polymerase B subunit. Based on this information, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) has been suggested as a sensitive and rapid screening test for the detection of RIF-resistant M. tuberculosis from clinical isolates. PCR-SSCP analyses with radioisotopes and without radioisotopes were employed to detect mutations of the rpoB gene associated with resistance to RIF in four laboratories, and results were compared with those of sequence analysis and the conventional proportion method of drug susceptibility test between laboratories. Radioisotopic PCR-SSCP showed an excellent correlation with sequence analysis of the 157 bp region of the rpoB gene by identifying correctly all 32 isolates analyzed in this study, with a high resolution of the banding patterns obtained. In a separate study, non-radioisotopic PCR-SSCP also gave a good correlation with sequence analysis in 22 isolates, but two (9.1%) isolates were classified as resistant by PCR-SSCP despite wild type sequences. When PCR-SSCP was compared with the results obtained using the proportion method, sensitivity of 44% to 85% were obtained in the 4 laboratories that participated in this study. Possible reasons for discordant results are discussed. It has been concluded that despite discordant results, which were sometimes observed, depending on the experimental conditions, PCR-SSCP appears to be an effective and promising method for the rapid detection of RIF-resistant M. tuberculosis, a marker of multidrug resistant tuberculosis. (author)

  8. Advance Planning of Form Properties in the Written Production of Single and Multiple Words

    Science.gov (United States)

    Damian, Markus F.; Stadthagen-Gonzalez, Hans

    2009-01-01

    Three experiments investigated the scope of advance planning in written production. Experiment 1 manipulated phonological factors in single word written production, and Experiments 2 and 3 did the same in the production of adjective-noun utterances. In all three experiments, effects on latencies were found which mirrored those previously…

  9. Estimating sensitivity and specificity of a PCR for boot socks to detect Campylobacter in broiler primary production using Bayesian latent class analysis.

    Science.gov (United States)

    Matt, Monika; Nordentoft, Steen; Kopacka, Ian; Pölzler, Thomas; Lassnig, Heimo; Jelovcan, Sandra; Stüger, Hans Peter

    2016-06-01

    .85-0.98]). In our study, PCR detection on boot sock samples is more sensitive than conventional culture. In view of the advantage of rapid results before slaughter and low costs for sampling, especially in combination with existing Salmonella surveillance systems (just another pair of boot socks needed), this method-matrix combination could be a valuable surveillance tool in the broiler primary production. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Methane production from coal by a single methanogen

    Science.gov (United States)

    Sakata, S.; Mayumi, D.; Mochimaru, H.; Tamaki, H.; Yamamoto, K.; Yoshioka, H.; Suzuki, Y.; Kamagata, Y.

    2017-12-01

    Previous geochemical studies indicate that biogenic methane greatly contributes to the formation of coalbed methane (CBM). It is unclear, however, what part of coal is used for the methane production and what types of microbes mediate the process. Here we hypothesized that methylotrophic methanogens use methoxylated aromatic compounds (MACs) derived from lignin. We incubated 11 species of methanogens belonging to order Methanosarcinales with 7 types of MACs. Two strains of methanogens, i.e., Methermicoccus shengliensis AmaM and ZC-1, produced methane from the MACs. In fact, these methanogens used over 30 types of commercially available MACs in addition to methanol and methylamines. To date, it is widely believed that methanogens use very limited number of small compounds such as hydrogen plus carbon dioxide, acetate, and methanol, and only three methanogenic pathways are recognized accordingly. Here, in contrast, two Methermicoccus strains used many types of MACs. We therefore propose this "methoxydotrophic" process as the fourth methanogenic pathway. Incubation of AmaM with 2-methoxybenzoate resulted in methanogenesis associated with the stoichiometric production of 2-hydroxybenzoate. Incubation with 2-methoxy-[7-13C] benzoate and with [13C] bicarbonate indicated that two thirds of methane carbon derived from the methoxy group and one third from CO2. Furthermore, incubation with [2-13C] acetate resulted in significant increases of 13C in both methane and CO2. These results suggest the occurrence of O-demethylation, CO2 reduction and acetyl-CoA metabolism in the methoxydotrophic methanogenesis. Furthermore, incubation of AmaM with lignite, subbituminous or bituminous coals in the bicarbonate-buffered media revealed that AmaM produced methane directly from coals via the methoxydotrophic pathway. Although 4 types of MACs were detected in the coal media in addition to methanol and methylamines, their total concentrations were too low to account for the methane

  11. Application of a real-time qPCR method to measure the methanogen concentration during anaerobic digestion as an indicator of biogas production capacity.

    Science.gov (United States)

    Traversi, Deborah; Villa, Silvia; Lorenzi, Eugenio; Degan, Raffaella; Gilli, Giorgio

    2012-11-30

    Biogas is an energy source that is produced via the anaerobic digestion of various organic materials, including waste-water sludge and organic urban wastes. Among the microorganisms involved in digestion, methanogens are the major microbiological group responsible for methane production. To study the microbiological equilibrium in an anaerobic reactor, we detected the methanogen concentration during wet digestion processes fed with pre-treated urban organic waste and waste-water sludge. Two different pre-treatments were used in successive experimental digestions: pressure-extrusion and turbo-mixing. Chemical parameters were collected to describe the process and its production. The method used is based on real-time quantitative PCR (RT-qPCR) with the functional gene mcrA as target. First, we evaluated the validity of the analyses. Next, we applied this method to 50 digestate samples and then we performed a statistical analysis. A positive and significant correlation between the biogas production rate and methanogen abundance was observed (r = 0.579, p amount and also the higher methanogen presence (F = 41.190, p biogas/kg TVS (F = 7.053; p < 0.05). The applied method is suitable to describe microbiome into the anaerobic reactor, moreover methanogen concentration may have potential for use as a digestion optimisation tool. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Genotyping of the 19-bp insertion/deletion polymorphism in the 5' flank of beta-hydroxylase gene by dissociation analysis of allele-specific PCR products

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2005-01-01

    The 19-bp insertion/deletion polymorphism in the 5' flank of the dopamine beta-hydroxylase (DBH) gene has been associated with psychiatric disorders. We have developed a simple, reliable and inexpensive closed-tube assay for genotyping of this polymorphism based upon T(m) determination of amplified...... and a conventional approach based upon agarose gel electrophoresis of amplified fragments revealed complete concordance between the two procedures. The insights obtained in this study may be utilized to develop assays based upon dissociation analysis of PCR products for genotyping of other insertion...

  13. Analysis of Multiallelic CNVs by Emulsion Haplotype Fusion PCR.

    Science.gov (United States)

    Tyson, Jess; Armour, John A L

    2017-01-01

    Emulsion-fusion PCR recovers long-range sequence information by combining products in cis from individual genomic DNA molecules. Emulsion droplets act as very numerous small reaction chambers in which different PCR products from a single genomic DNA molecule are condensed into short joint products, to unite sequences in cis from widely separated genomic sites. These products can therefore provide information about the arrangement of sequences and variants at a larger scale than established long-read sequencing methods. The method has been useful in defining the phase of variants in haplotypes, the typing of inversions, and determining the configuration of sequence variants in multiallelic CNVs. In this description we outline the rationale for the application of emulsion-fusion PCR methods to the analysis of multiallelic CNVs, and give practical details for our own implementation of the method in that context.

  14. Cross section formulae on single W and Z boson productions in electron-positron collisions

    International Nuclear Information System (INIS)

    Katuya, Mituaki

    1987-01-01

    The formulae are given for the transverse momentum distributions and total cross sections for the single W boson and Z boson productions in electron-positron collisions by using the equivalent photon approximation. (author)

  15. Single transverse-spin asymmetry in high transverse momentum pion production in pp collisions

    DEFF Research Database (Denmark)

    Kouvaris, Christoforos; Qiu, Jian-Wei; Vogelsang, Werner

    2006-01-01

    We study the single-spin (left-right) asymmetry in single-inclusive pion production in hadronic scattering. This asymmetry is power-suppressed in the transverse momentum of the produced pion and can be analyzed in terms of twist-three parton correlation functions in the proton. We present new...

  16. Altering Reservoir Wettability to Improve Production from Single Wells

    Energy Technology Data Exchange (ETDEWEB)

    W. W. Weiss

    2006-09-30

    tests were conducted in an area of the field that has not met production expectations. The dataset on the 23 Phosphoria well surfactant soaks was updated. An analysis of the oil decline curves indicted that 4.5 lb of chemical produced a barrel of incremental oil. The AI analysis supports the adage 'good wells are the best candidates.' The generally better performance of surfactant in the high permeability core laboratory tests supports this observation. AI correlations were developed to predict the response to water-frac stimulations in a tight San Andres reservoir. The correlations maybe useful in the design of Cedar Creek Anticline surfactant soak treatments planned for next year. Nuclear Magnetic Resonance scans of dolomite cores to measure porosity and saturation during the high temperature laboratory work were acquired. The scans could not be correlated with physical measurement using either conventional or AI methods.

  17. Single top-quark production cross-section using the ATLAS detector at the LHC

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00395821; The ATLAS collaboration

    2017-01-01

    Measurements of single top-quark production in proton–proton collisions are presented based on the 8 TeV and 13 TeV ATLAS datasets. In the leading-order process, a $W$ boson is exchanged in the $t$-channel. The fiducial cross-sections measurements for the production of single top-quarks and single anti-top-quarks, as well as the total cross-sections and their ratios are presented. At 8 TeV, differential cross-section measurements of the $t$-channel process are also reported, these analyses include limits on anomalous contributions to the $Wtb$ vertex and measurement of the top quark polarization. A measurement of the production cross-section of a single top quark in association with a $W$ boson, the second largest single-top production mode, is also presented. Finally, evidence for $s$-channel single-top production in the 8 TeV ATLAS dataset is presented. All measurements are compared to state-of-the-art theoretical calculations.

  18. Forecasting demand for single-period products : A case study in the apparel industry

    NARCIS (Netherlands)

    Mostard, Julien; Teunter, Ruud; de Koster, Rene

    2011-01-01

    The problem considered is that of forecasting demand for single-period products before the period starts. We study this problem for the case of a mail order apparel company that needs to order its products pre-season. The lack of historical demand data implies that other sources of data are needed.

  19. PCR screening reveals considerable unexploited biosynthetic potential of ansamycins and a mysterious family of AHBA-containing natural products in actinomycetes.

    Science.gov (United States)

    Wang, H-X; Chen, Y-Y; Ge, L; Fang, T-T; Meng, J; Liu, Z; Fang, X-Y; Ni, S; Lin, C; Wu, Y-Y; Wang, M-L; Shi, N-N; He, H-G; Hong, K; Shen, Y-M

    2013-07-01

    Ansamycins are a family of macrolactams that are synthesized by type I polyketide synthase (PKS) using 3-amino-5-hydroxybenzoic acid (AHBA) as the starter unit. Most members of the family have strong antimicrobial, antifungal, anticancer and/or antiviral activities. We aimed to discover new ansamycins and/or other AHBA-containing natural products from actinobacteria. Through PCR screening of AHBA synthase gene, we identified 26 AHBA synthase gene-positive strains from 206 plant-associated actinomycetes (five positives) and 688 marine-derived actinomycetes (21 positives), representing a positive ratio of 2·4-3·1%. Twenty-five ansamycins, including eight new compounds, were isolated from six AHBA synthase gene-positive strains through TLC-guided fractionations followed by repeated column chromatography. To gain information about those potential ansamycin gene clusters whose products were unknown, seven strains with phylogenetically divergent AHBA synthase genes were subjected to fosmid library construction. Of the seven gene clusters we obtained, three show characteristics for typical ansamycin gene clusters, and other four, from Micromonospora spp., appear to lack the amide synthase gene, which is unusual for ansamycin biosynthesis. The gene composition of these four gene clusters suggests that they are involved in the biosynthesis of a new family of hybrid PK-NRP compounds containing AHBA substructure. PCR screening of AHBA synthase is an efficient approach to discover novel ansamycins and other AHBA-containing natural products. This work demonstrates that the AHBA-based screening method is a useful approach for discovering novel ansamycins and other AHBA-containing natural products from new microbial resources. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

  20. Search for single-top production in ep collisions at HERA

    CERN Document Server

    Abramowicz, H.

    2012-02-14

    A search for single-top production, $ep \\rightarrow etX$, has been performed with the ZEUS detector at HERA using data corresponding to an integrated luminosity of $0.37\\fbi$. No evidence for top production was found, consistent with the expectation from the Standard Model. Limits were computed for single-top production via flavour changing neutral current transitions. The result was combined with a previous ZEUS result yielding a total luminosity of 0.50fb-1. A 95% credibility level upper limit of 0.13 pb was obtained for the cross section at the centre-of-mass energy of $\\sqrt{s}=315\\gev$.

  1. Characterization of Newly BredCordyceps militarisStrains for Higher Production of Cordycepin through HPLC and URP-PCR Analysis.

    Science.gov (United States)

    Lee, Hyun-Hee; Kang, Naru; Park, Inmyoung; Park, Jungwook; Kim, Inyoung; Kim, Jieun; Kim, Namgyu; Lee, Jae-Yun; Seo, Young-Su

    2017-07-28

    Cordyceps militaris , a member of Ascomycota, a mushroom referred to as caterpillar Dongchung-ha-cho, is commercially valuable because of its high content of bioactive substances, including cordycepin, and its potential for artificial cultivation. Cordycepin (3'-deoxyadenosine) is highly associated with the pharmacological effects of C. militaris . C. militaris is heterothallic in that two mating-type loci, idiomorph MAT1-1 and MAT1-2 , exist discretely in two different spores. In this study, nine C. militaris strains were mated with each other to prepare newly bred strains that produced a larger amount of cordycepin than the parent strains. Nine strains of C. militaris were identified by comparing the internal transcribed spacer sequence, and a total of 12 single spores were isolated from the nine strains of C. militaris . After the MAT idiomorph was confirmed by PCR, 36 mating combinations were performed with six single spores with MAT1-1 and the others with MAT1-2 . Eight mating combinations were successfully mated, producing stroma with perithecia. Cordycepin content analysis of all strains by high-performance liquid chromatography revealed that the KASP4-bred strain produced the maximum cordycepin among all strains, regardless of the medium and stroma parts. Finally, universal rice primer-PCR was performed to demonstrate that the bred strains were genetically different from the parental strains and new C. militaris strains. These results may be related to the recombination of genes during mating. The newly produced strains can be used to meet the industrial demand for cordycepin. In addition, breeding through mating suggests the possibility of producing numerous cordycepin-producing C. militaris strains.

  2. Study of correlation of PDF uncertainty in single top and top pair production at the LHC

    CERN Document Server

    The ATLAS collaboration

    2015-01-01

    The incomplete knowledge of parton distribution functions is an important source of systematic uncertainty for top-quark measurements, including top-quark pair and single top-quark production cross sections, as well as for analyses that have a large background from these processes. The correlation of the parton-distribution-function uncertainty is studied for top-quark pair production and single top-quark production in association with a W boson, in final states with two reconstructed leptons. Four types of correlation are studied: between total production cross-sections, between cross-section and acceptance correction, between the two processes for common selection requirements, and between different jet multiplicity requirements. The uncertainty correlation is evaluated for several sets of parton distribution functions using simulated samples of top-quark pair and single top-quark events.

  3. Single top quark production cross-section and properties using the ATLAS detector at the LHC

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00358737; The ATLAS collaboration

    2015-01-01

    ATLAS measurements of single top-quark processes are summarized. Measurements using data at 7 and 8 TeV collisions from the LHC are presented. The measurements are performed using the semi-leptonic decay mode of the top-quark. Production cross-sections and the $\\left|V_{tb}\\right|$ CKM matrix element extraction are shown. All measurements are compared to theoretical calculations. In addition, the $s$-channel production mode is explored along with limits on exotic production modes.

  4. [Application of created restriction site PCR-RFLP to identify alcohol dehydrogenase 2 gene polymorphism].

    Science.gov (United States)

    Jiao, Jie; Wang, Wei; Liu, Jing; Xia, Zhaolin

    2009-01-01

    To develop a appropriate assay for identifying single nucleotide polymorphism (SNP) of alcohol dehydrogenase 2 (ADH2) gene. According to base substitution situation of one single base mutational site, we designed the present study primers. One of the primers was designed on the basis of neighbourhood sequence of the mutational site, that is, we made one mismatch base to let product a new enzyme site between the 3' end of the primer and the single base mutation type after the PCR amplification. Then PCR-RFLP was adopted to identify the SNP in ADH2 gene. One primer pair can get target products containing ADH2 SNP site by PCR, restriction enzymes Bsh1236I were adopted to identify the SNP site. The expected results were reached. It suggested that the method of detecting the SNP of ADH2 based on CRS-PCR-RFLP theory is facilitated, economic, and rapid.

  5. Real-Time PCR Detection of Paenibacillus spp. in Raw Milk To Predict Shelf Life Performance of Pasteurized Fluid Milk Products

    Science.gov (United States)

    Ranieri, Matthew L.; Ivy, Reid A.; Mitchell, W. Robert; Call, Emma; Masiello, Stephanie N.; Wiedmann, Martin

    2012-01-01

    Psychrotolerant sporeformers, specifically Paenibacillus spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While Paenibacillus spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of Paenibacillus spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect Paenibacillus spp. in fluid milk and to discriminate between Paenibacillus and other closely related spore-forming bacteria. Specificity was confirmed using 16 Paenibacillus and 17 Bacillus isolates. All 16 Paenibacillus isolates were detected with a mean cycle threshold (CT) of 19.14 ± 0.54. While 14/17 Bacillus isolates showed no signal (CT > 40), 3 Bacillus isolates showed very weak positive signals (CT = 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 × 101 CFU/ml using total genomic DNA extracted from raw milk samples inoculated with Paenibacillus. Application of the TaqMan PCR to colony lysates obtained from heat-treated and enriched raw milk provided fast and accurate detection of Paenibacillus. Heat-treated milk samples where Paenibacillus (≥1 CFU/ml) was detected by this colony TaqMan PCR showed high bacterial counts (>4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of Paenibacillus that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product. PMID:22685148

  6. Real-time PCR detection of Paenibacillus spp. in raw milk to predict shelf life performance of pasteurized fluid milk products.

    Science.gov (United States)

    Ranieri, Matthew L; Ivy, Reid A; Mitchell, W Robert; Call, Emma; Masiello, Stephanie N; Wiedmann, Martin; Boor, Kathryn J

    2012-08-01

    Psychrotolerant sporeformers, specifically Paenibacillus spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While Paenibacillus spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of Paenibacillus spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect Paenibacillus spp. in fluid milk and to discriminate between Paenibacillus and other closely related spore-forming bacteria. Specificity was confirmed using 16 Paenibacillus and 17 Bacillus isolates. All 16 Paenibacillus isolates were detected with a mean cycle threshold (C(T)) of 19.14 ± 0.54. While 14/17 Bacillus isolates showed no signal (C(T) > 40), 3 Bacillus isolates showed very weak positive signals (C(T) = 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 × 10(1) CFU/ml using total genomic DNA extracted from raw milk samples inoculated with Paenibacillus. Application of the TaqMan PCR to colony lysates obtained from heat-treated and enriched raw milk provided fast and accurate detection of Paenibacillus. Heat-treated milk samples where Paenibacillus (≥1 CFU/ml) was detected by this colony TaqMan PCR showed high bacterial counts (>4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of Paenibacillus that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product.

  7. Development, optimization, and single laboratory validation of an event-specific real-time PCR method for the detection and quantification of Golden Rice 2 using a novel taxon-specific assay.

    Science.gov (United States)

    Jacchia, Sara; Nardini, Elena; Savini, Christian; Petrillo, Mauro; Angers-Loustau, Alexandre; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

    2015-02-18

    In this study, we developed, optimized, and in-house validated a real-time PCR method for the event-specific detection and quantification of Golden Rice 2, a genetically modified rice with provitamin A in the grain. We optimized and evaluated the performance of the taxon (targeting rice Phospholipase D α2 gene)- and event (targeting the 3' insert-to-plant DNA junction)-specific assays that compose the method as independent modules, using haploid genome equivalents as unit of measurement. We verified the specificity of the two real-time PCR assays and determined their dynamic range, limit of quantification, limit of detection, and robustness. We also confirmed that the taxon-specific DNA sequence is present in single copy in the rice genome and verified its stability of amplification across 132 rice varieties. A relative quantification experiment evidenced the correct performance of the two assays when used in combination.

  8. Observation of prompt single muon production by 400 GeV protons

    International Nuclear Information System (INIS)

    Merritt, K.W.B.

    1981-01-01

    The observation of prompt single muon production from 400 GeV protons interacting in an iron target is reported. The experiment used a variable-density calorimeter made of iron plates and plastic scintillator as a target, followed by a large-acceptance muon identifier and an iron toroidal spectrometer. Single muon and dimuon events were separated with good efficiency using the muon identifier, and the rate of prompt single muons was measured by varying the density of the target-calorimeter, thereby changing the relative rate of prompt and non-prompt single muon production. Prompt single muon signals were observed in two different kinematic regions-p/sub μ/ 1 GeV/c and 10 GeV/c 0.5 GeV/c. Approximate equality was found between the prompt lμ - and prompt lμ - signal in the high p region (in the high p 1 region, only positive muons were accepted by the trigger). The observed cross section in both regions was approx. 70 nb/nucleon, assuming linear A dependence for the production of the prompt muons. Hadronic production of charmed particles was the most likely source of the prompt muons; other possible sources could not account for the large rates observed. Three different models for charm production-uncorrelated D production, correlated DD production, and diffractive production of Λ/sub c/ - D pairs-are compared to the data and used to calculate cross sections. Within the DD model, the range of kinematic parameters allowed by the data is determined and the corresponding range of cross sections is 20 to 70 μb/nucleon. The results of this experiment are compared with other experimental results and with theoretical predictions of charm production

  9. Isolation and Identification of Lactic Acid Bacteria from Traditional Dairy Products in Baotou and Bayannur of Midwestern Inner Mongolia and q-PCR Analysis of Predominant Species

    Science.gov (United States)

    2016-01-01

    In this study, traditional culture method and 16S rRNA gene analysis were applied to reveal the composition and diversity of lactic acid bacteria (LAB) of fermented cow milk, huruud and urum from Baotou and Bayannur of midwestern Inner Mongolia. Also, the quantitative results of dominant LAB species in three different types of dairy products from Baotou and Bayannur were gained by quantitative polymerase chain reaction (q-PCR) technology. Two hundred and two LAB strains isolated from sixty-six samples were identified and classified into four genera, namely Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, and twenty-one species and subspecies. From these isolates, Lactococcus lactis subsp. lactis (32.18%), Lactobacillus plantarum (12.38%) and Leuconosto mesenteroides (11.39%) were considered as the dominated LAB species under the condition of cultivating in MRS and M17 medium. And the q-PCR results revealed that the number of dominant species varied from samples to samples and from region to region. This study clearly shows the composition and diversity of LAB existing in fermented cow milk, huruud and urum, which could be considered as valuable resources for LAB isolation and further probiotic selection. PMID:27621691

  10. [Duplex real-time PCR assay for rapid detection of E. coli O157 and E. coli O104 in the legume plants and its products].

    Science.gov (United States)

    Zhao, Xiaomei; Zhao, Guiming; Wang, Ping; Chen, Ying; Jiao, Yanchao; Luo, Adong

    2016-03-01

    To establish a rapid assay to detect enterohemorrhagic Escherichia coli O157 (E. coli O157) and enterohemorrhagic Escherichia coli O104 (E. coli O104) in the legume plants and its products by using the duplex real-time PCR. Based on part fragments of E. coli O157 specific gene rfbE and E. coli O104 specific gene wzy, primers and Taq-Man probes were designed. Results DNA (Q157): DNA (O104) = 1 : 3, DNA 2 μL, Master Mix 12.5 μL, primers (10 μmol/L) 1 μL,Taq-Man probes( 10 μmol/L) 0.5 μL, ddH2O 25 μL. The two pathogens could be detected in one reaction system, the lowest limit of detection sensitivity was 10(2) CFU/mL(g). This method is rapid and convenient, with good specificity, high sensitivity. The duplex real-time PCR assay could provide a cost-effective and convenient method for detect foodborne pathogenic bacteria.

  11. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria

    DEFF Research Database (Denmark)

    Hammar, Petter; Angermayr, S. Andreas; Sjostrom, Staffan L.

    2015-01-01

    Background: Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.Results: We present a method for high-throughput, single......-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for L-lactate production, and sort strains with high productivity. We demonstrate the separation...... of low- and high-producing reference strains, as well as enrichment of a more productive L-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically...

  12. Quantitative Real-Time PCR Analysis of YKL-40 and Its Comparison with Mammalian Chitinase mRNAs in Normal Human Tissues Using a Single Standard DNA

    Directory of Open Access Journals (Sweden)

    Misa Ohno

    2015-04-01

    Full Text Available YKL-40 (YKL for the first three N-terminal residues of a 40 kDa protein belongs to a group of human chitinase-like proteins (CLPs, which are similar to chitinases but lack chitinolytic activity. YKL-40 mRNA and its protein levels have been reported elevated in multiple disorders including asthma, cystic fibrosis, rheumatoid arthritis and malignant tumors. Here, we quantified the YKL-40 mRNA levels and compared them with chitinases and housekeeping genes in normal human tissues. To establish the quantitative real-time PCR (qPCR system for evaluation of relative YKL-40 mRNA levels, we constructed a human standard DNA molecule by ligating cDNAs of YKL-40, two mammalian chitinases and two housekeeping genes in a one-to-one ratio. We generated cDNAs from various normal human tissues and analyzed the YKL-40 mRNA expression levels using a qPCR system with the standard DNA. We found that YKL-40 mRNA is present widely in human tissues while its expression patterns exhibit clear tissue specificity. Highest YKL-40 mRNA levels were detected in the liver, followed by kidney, trachea and lung. The levels of YKL-40 mRNA in the kidney and liver were more than 100-times higher than those of chitotriosidase mRNA. Our study provides for the first time a comprehensive analysis of the relative expression levels of YKL-40 mRNA versus mammalian chitinases in normal human tissues.

  13. Detection of gene copy number aberrations in mantle cell lymphoma by a single quantitative multiplex PCR assay: clinicopathological relevance and prognosis value.

    Science.gov (United States)

    Jardin, Fabrice; Picquenot, Jean-Michel; Parmentier, Françoise; Ruminy, Philippe; Cornic, Marie; Penther, Dominique; Bertrand, Philippe; Lanic, Hélène; Cassuto, Ophélie; Humbrecht, Catherine; Lemasle, Emilie; Wautier, Agathe; Bastard, Christian; Tilly, Hervé

    2009-09-01

    The t(11;14)(q13;q32) is the hallmark of mantle cell lymphoma (MCL). Additional genetic alterations occur in the majority of cases. This study aimed to design a polymerase chain reaction (PCR) assay to determine the incidence and relevance of recurrent gene copy number aberrations in this disease. Forty-two MCL cases with frozen- or paraffin-embedded (FFPE) tissues were selected. Three different quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF) assays were designed to simultaneously analyse eight genes (CDKN2A, RB1, ATM, CDK2, TP53, MYC, CDKN1B, MDM2), to analyse the 9p21 locus (CDKN2A/CDKN2B) and FFPE tissues. Gains of MYC, CDK2, CDKN1B, and MDM2 were observed in 10% of cases. Losses of RB1, CDKN2A, ATM or TP53 were observed in 38%, 31%, 24% and 10% of cases, respectively. Analysis of the 9p21 locus indicated that, in most cases, tumours displayed a complete inactivation of p14(ARF)/p15I(NK4B)/p16I(NK4A). CDKN2A and MYC aberrations were associated with a high MCL international prognostic index (MIPI). CDK2/MDM2 gains and CDKN2A/TP53 losses correlated with an unfavourable outcome. PCR experiments with frozen and FFPE-tissues indicated that our approach is valid in a routine diagnostic setting, providing a powerful tool that could be used for patient stratification in combination with MIPI in future clinical trials.

  14. An integrated multi−period planning of the production and transportation of multiple petroleum products in a single pipeline system

    Directory of Open Access Journals (Sweden)

    Alberto Herrán

    2011-01-01

    Full Text Available A multiproduct pipeline provides an economic way to transport large volumes of refined petroleum products over long distances. In such a pipeline, different products are pumped back−to−back without any separation device between them. The sequence and lengths of such pumping runs must be carefully selected in order to meet market demands while minimizing pipeline operational costs and satisfying several constraints. The production planning and scheduling of the products at the refinery must also be synchronized with the transportation in order to avoid the usage of the system at some peak−hour time intervals. In this paper, we propose a multi−period mixed integer nonlinear programming (MINLP model for an optimal planning and scheduling of the production and transportation of multiple petroleum products from a refinery plant connected to several depots through a single pipeline system. The objective of this work is to generalize the mixed integer linear programming (MILP formulation proposed by Cafaro and Cerdá (2004, Computers and Chemical Engineering where only a single planning period was considered and the production planning and scheduling was not part of the decision process. Numerical examples show how the use of a single period model for a given time period may lead to infeasible solutions when it is used for the upcoming periods. These examples also show how integrating production planning with the transportation and the use of a multi−period model may result in a cost saving compared to using a single−period model for each period, independently.

  15. Single Top-Quark Production Cross Section Using the ATLAS Detector at the LHC

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00239978; The ATLAS collaboration

    2016-01-01

    Recent measurements of the production of single top quarks in proton--proton collisions at centre-of-mass energies of $\\sqrt{s}=7\\,\\mathrm{TeV}$, $8\\,\\mathrm{TeV}$ and $13\\,\\mathrm{TeV}$ with the ATLAS detector at the LHC are presented. Four measurements of the production cross sections for single top quarks via the $s$- and $t$-channel exchange of a $W$ boson as well as in association with a \\Wboson{} are discussed. The results are compared to state-of-the-art theoretical calculations, and used to extract the value of the CKM matrix element $V_{tb}$. Recently found evidence for the production of single top quarks in the $s$-channel at $8\\,\\mathrm{TeV}$ is presented. Finally, the determination of anomalous couplings at the $W\\!-\\!t\\!-\\!b$ vertex from an analysis of top-quark decays is shown.

  16. Autonomy of image and use of single or multiple sense modalities in original verbal image production.

    Science.gov (United States)

    Khatena, J

    1978-06-01

    The use of a single or of multiple sense modalities in the production of original verbal images as related to autonomy of imagery was explored. 72 college adults were administered Onomatopoeia and Images and the Gordon Test of Visual Imagery Control. A modified scoring procedure for the Gordon scale differentiated imagers who were moderate or low in autonomy. The two groups produced original verbal images using multiple sense modalities more frequently than a single modality.

  17. Measurement of single top production in pp collisions at 7 TeV with ...

    Indian Academy of Sciences (India)

    2012-11-08

    Nov 8, 2012 ... 1223–1226. Measurement of single top production in pp collisions ... The measurement of t-channel single top cross-section in proton–proton collisions at ... channel μ. 2D,. 50.9. 50.9. ±. 104.1. -1. =7 TeV, L=35.9 pb s. CMS. Figure 1. Comparison of the cross-section measurements in all channels in the 2D-.

  18. Direct Production of High $p_T$ Single Photons at the CERN Intersecting Storage Rings

    CERN Document Server

    Diakonou, M; Resvanis, L.K.; Filippas, T.A.; Fokitis, E.; Trakkas, C.; Cnops, A.M.; Cobb, J.H.; Fowler, E.C.; Hood, D.M.; Iwata, S.; Palmer, R.B.; Rahm, D.C.; Rehak, P.; Stumer, I.; Fabjan, C.W.; Fields, T.; Lissauer, D.; Mannelli, I.; Molzon, W.; Mouzourakis, P.; Nakamura, K.; Nappi, A.; Willis, W.J.

    1979-01-01

    Single photon production in pp collisions at 30 < √ s < 62 GeV has been measured with liquid-argon-lead calorimeters at the CERN ISR. This process remains approximately constant with increasing √ s . For fixed √ s , the single photon to π 0 ratio increases strongly with increase in p T . The γ π 0 ratio is about 0.2 for p T above 4.5 GeV/c.

  19. Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection ofCylindrocladium scopariumon Eucalyptus.

    Science.gov (United States)

    Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

    2016-10-01

    Eucalyptus dieback disease, caused by Cylindrocladium scoparium , has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium . The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

  20. Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

    Directory of Open Access Journals (Sweden)

    Tian-Min Qiao

    2016-10-01

    Full Text Available Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP were developed for detection of C. scoparium based on factor 1-alpha (tef1 and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

  1. Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

    Science.gov (United States)

    Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

    2016-01-01

    Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products. PMID:27721691

  2. Single top measurements at the LHC: $s$-channel and $Wt$ production

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00214457; The ATLAS collaboration

    2016-01-01

    This paper summarises the latest experimental results on single top quark physics by the ATLAS and CMS collaborations using LHC proton--proton collisions at $\\sqrt{s}=8 \\rm \\ TeV$. Searches for single top-quark production in the $s$-channel and associated $Wt$ mode are presented and a determination of the CKM matrix element $|V_{tb}|$ is discussed. Evidence for $s$-channel production is reported by the ATLAS collaboration and the $Wt$ process has been observed at the LHC.

  3. Single-Event Transgene Product Levels Predict Levels in Genetically Modified Breeding Stacks.

    Science.gov (United States)

    Gampala, Satyalinga Srinivas; Fast, Brandon J; Richey, Kimberly A; Gao, Zhifang; Hill, Ryan; Wulfkuhle, Bryant; Shan, Guomin; Bradfisch, Greg A; Herman, Rod A

    2017-09-13

    The concentration of transgene products (proteins and double-stranded RNA) in genetically modified (GM) crop tissues is measured to support food, feed, and environmental risk assessments. Measurement of transgene product concentrations in breeding stacks of previously assessed and approved GM events is required by many regulatory authorities to evaluate unexpected transgene interactions that might affect expression. Research was conducted to determine how well concentrations of transgene products in single GM events predict levels in breeding stacks composed of these events. The concentrations of transgene products were compared between GM maize, soybean, and cotton breeding stacks (MON-87427 × MON-89034 × DAS-Ø15Ø7-1 × MON-87411 × DAS-59122-7 × DAS-40278-9 corn, DAS-81419-2 × DAS-44406-6 soybean, and DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 × MON-88913-8 × DAS-81910-7 cotton) and their component single events (MON-87427, MON-89034, DAS-Ø15Ø7-1, MON-87411, DAS-59122-7, and DAS-40278-9 corn, DAS-81419-2, and DAS-44406-6 soybean, and DAS-21023-5, DAS-24236-5, SYN-IR102-7, MON-88913-8, and DAS-81910-7 cotton). Comparisons were made within a crop and transgene product across plant tissue types and were also made across transgene products in each breeding stack for grain/seed. Scatter plots were generated comparing expression in the stacks to their component events, and the percent of variability accounted for by the line of identity (y = x) was calculated (coefficient of identity, I 2 ). Results support transgene concentrations in single events predicting similar concentrations in breeding stacks containing the single events. Therefore, food, feed, and environmental risk assessments based on concentrations of transgene products in single GM events are generally applicable to breeding stacks composed of these events.

  4. Single top quarks at the Tevatron and observation of the s-channel production mode

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    The presentation gives an overview of single-top-quark production at the Tevatron proton-antiproton collider. The talk covers measurements of the total s+t channel production cross section and the extraction of the CKM matrix element |V_tb|. Furthermore, separate analyses of the s-channel and t-channel production modes are discussed. The data correspond to total integrated luminosities of up to 9.7 fb-1 per experiment and represent in most cases the full Run-II dataset. Through a combination of the CDF and D0 measurements the first observation of single-top-quark production in the s-channel is claimed. This is particularly highlighted in the seminar.

  5. Probing the Higgs self coupling via single Higgs production at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Degrassi, G. [Dipartimento di Matematica e Fisica, Università di Roma Tre andINFN, sezione di Roma Tre,Via della Vasca Navale 84, I-00146 Rome (Italy); Giardino, P.P. [Physics Department, Brookhaven National Laboratory,20 Pennsylvania St., Upton NY 11742 (United States); Maltoni, F.; Pagani, D. [Centre for Cosmology, Particle Physics and Phenomenology (CP3),Université Catholique de Louvain,B-1348 Louvain-la-Neuve (Belgium)

    2016-12-16

    We propose a method to determine the trilinear Higgs self coupling that is alternative to the direct measurement of Higgs pair production total cross sections and differential distributions. The method relies on the effects that electroweak loops featuring an anomalous trilinear coupling would imprint on single Higgs production at the LHC. We first calculate these contributions to all the phenomenologically relevant Higgs production (ggF, VBF, WH, ZH, tt̄H) and decay (γγ, WW{sup ∗}/ZZ{sup ∗}→4f, bb̄, ττ) modes at the LHC and then estimate the sensitivity to the trilinear coupling via a one-parameter fit to the single Higgs measurements at the LHC 8 TeV. We find that the bounds on the self coupling are already competitive with those from Higgs pair production and will be further improved in the current and next LHC runs.

  6. A search for single electron production in electron positron annihilation at E = 29 GeV

    International Nuclear Information System (INIS)

    Steele, T.R.

    1989-09-01

    This thesis presents experimental results from the ASP detector which took data on e + e - interactions in the PEP storage ring at SLAC. Its design was particularly suitable for searching for production of supersymmetric particles. The motivations for and phenomenology of Supersymmetry are discussed. In particular, the production of a single supersymmetric electron (''selectron'', e) in combination with a supersymmetric photon (''photino'', γ) would result in events in which a single electron and no other particles are observed in the detector at an e + e - collider such as PEP, provided the masses of these particles are not too large. Such events would also result from the production of a single supersymmetric W-boson (''wino'', W) in combination with a supersymmetric neutrino (''sneutrino'', ν). These processes make it possible to search for electrons and winos with masses greater than the beam energy. Observation of these unusual events would distinctly indicate the production of new particles. The ASP detector was designed to be hermetic and to provide efficient event reconstruction for low multiplicity events. The detector is described and its performance is evaluated; it is found to be well-suited to this study. The data sample collected with the detector was thoroughly analyzed for evidence of single-electron events. The various possible background processes are considered and Monte Carlo calculations of the distributions from single selectron and single wino production are presented. Using this information an efficient off-line event selection process was developed, and it is described in detail. 82 refs., 41 figs., 4 tabs

  7. Dynamic optimization approach for integrated supplier selection and tracking control of single product inventory system with product discount

    Science.gov (United States)

    Sutrisno; Widowati; Heru Tjahjana, R.

    2017-01-01

    In this paper, we propose a mathematical model in the form of dynamic/multi-stage optimization to solve an integrated supplier selection problem and tracking control problem of single product inventory system with product discount. The product discount will be stated as a piece-wise linear function. We use dynamic programming to solve this proposed optimization to determine the optimal supplier and the optimal product volume that will be purchased from the optimal supplier for each time period so that the inventory level tracks a reference trajectory given by decision maker with minimal total cost. We give a numerical experiment to evaluate the proposed model. From the result, the optimal supplier was determined for each time period and the inventory level follows the given reference well.

  8. Principles and technical aspects of PCR amplification

    National Research Council Canada - National Science Library

    Pelt-Verkuil, Elizabeth van; Belkum, Alex van; Hays, John P

    2008-01-01

    ... to illustrate any particularly important concepts or comments. Indeed, all commercial PCR biotechnology companies offer information about their products on internet sites and in online technical manuals. These online resources will be invaluable for any readers requiring more detailed PCR protocols. The authors have provided references for many PCR co...

  9. Bio imaging of intracellular NO production in single bone cells after mechanical stimulation

    NARCIS (Netherlands)

    Vatsa, A.; Mizuno, D.; Smit, T.H.; Schmidt, C.; Mac Kintosh, F.C.; Klein-Nulend, J.

    2006-01-01

    We show the intracellular upregulation of NO production after mechanical stimulation, an essential chemical signal in bone remodeling. This is done in real time using the fluorescent chromophore DAR-4M AM. Differences in cellular response to mechanical stimulation of different regions of a single

  10. Economic Optimizing Control for Single-Cell Protein Production in a U-Loop Reactor

    DEFF Research Database (Denmark)

    Drejer, André; Ritschel, Tobias Kasper Skovborg; Jørgensen, Sten Bay

    2017-01-01

    The production of single-cell protein (SCP) in a U-loop reactor by a methanotroph is a cost efficient sustainable alternative to protein from fish meal obtained by over-fishing the oceans. SCP serves as animal feed. In this paper, we present a mathematical model that describes the dynamics of SCP...

  11. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria

    NARCIS (Netherlands)

    Hammar, P.; Angermayr, S.A.; Sjostrom, S.L.; van der Meer, J.; Hellingwerf, K.J.; Hudson, E.P.; Joensson, H.N.

    2015-01-01

    BACKGROUND: Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible. RESULTS: We present a method for high-throughput, single-cell

  12. QCD corrections to single top quark production in electron-photon interactions

    CERN Document Server

    Kühn, J H; Uwer, Peter

    2003-01-01

    Single top quark production in electron-photon interactions provides a clean environment for the measurement of the Cabibbo-Kobayashi-Maskawa matrix element V sub t sub b. Aiming at an experimental precision at the percent level the knowledge of radiative corrections is important. In this paper we present results for the radiative corrections in quantum chromodynamics. (orig.)

  13. The E. coli Single Protein Production (cSPP) System for Production and Structural Analysis of Membrane Proteins

    OpenAIRE

    Mao, Lili; Vaiphei, S. Thangminlal; Shimazu, Tsutomu; Schneider, William M.; Tang, Yuefeng; Mani, Rajeswari; Roth, Monica J.; Montelione, Gaetano T.; Inouye, Masayori

    2009-01-01

    At present, only 0.9% of PDB-deposited structures are of membrane proteins in spite of the fact that membrane proteins constitute approximately 30% of total proteins in most genomes from bacteria to humans. Here we address some of the major bottlenecks in the structural studies of membrane proteins and discuss the ability of the new technology, the Single-Protein Production (SPP) system, to help solve these bottlenecks.

  14. Quantitative photoacoustics to measure single cell melanin production and nanoparticle attachment

    Science.gov (United States)

    Bhattacharyya, Kiran; Eshein, Adam; Chandrasekhar, Anand; Viator, John A.

    2015-04-01

    Photoacoustics can be used as a label-free spectroscopic method of identifying pigmented proteins and characterizing their intracellular concentration over time in a single living cell. The authors use a microscopic laser irradiation system with a 5 ns, Q-switched laser focused onto single cells in order to collect photoacoustic responses of melanoma cells from the HS936 cell line and gold nanoparticle labeled breast cancer cells from the T47D cell line. The volume averaged intracellular concentration of melanin is found to range from 29-270 mM for single melanoma cells and the number of gold nanoparticles (AuNP) is shown to range from 850-5900 AuNPs/cell. Additionally, the melanin production response to UV-A light stimulus is measured in four melanoma cells to find a mass production rate of 5.7 pg of melanin every 15 min.

  15. Methods of forming single source precursors, methods of forming polymeric single source precursors, and single source precursors and intermediate products formed by such methods

    Science.gov (United States)

    Fox, Robert V.; Rodriguez, Rene G.; Pak, Joshua J.; Sun, Chivin; Margulieux, Kelsey R.; Holland, Andrew W.

    2012-12-04

    Methods of forming single source precursors (SSPs) include forming intermediate products having the empirical formula 1/2{L.sub.2N(.mu.-X).sub.2M'X.sub.2}.sub.2, and reacting MER with the intermediate products to form SSPs of the formula L.sub.2N(.mu.-ER).sub.2M'(ER).sub.2, wherein L is a Lewis base, M is a Group IA atom, N is a Group IB atom, M' is a Group IIIB atom, each E is a Group VIB atom, each X is a Group VIIA atom or a nitrate group, and each R group is an alkyl, aryl, vinyl, (per)fluoro alkyl, (per)fluoro aryl, silane, or carbamato group. Methods of forming polymeric or copolymeric SSPs include reacting at least one of HE.sup.1R.sup.1E.sup.1H and MER with one or more substances having the empirical formula L.sub.2N(.mu.-ER).sub.2M'(ER).sub.2 or L.sub.2N(.mu.-X).sub.2M'(X).sub.2 to form a polymeric or copolymeric SSP. New SSPs and intermediate products are formed by such methods.

  16. Production of single cell protein (SCP) from food and agricultural waste by using Saccharomyces cerevisiae.

    Science.gov (United States)

    Gervasi, Teresa; Pellizzeri, Vito; Calabrese, Giorgio; Di Bella, Giuseppa; Cicero, Nicola; Dugo, Giacomo

    2018-03-01

    Food waste is the single-largest component of the waste stream, in order to protect and safeguard the public health, useful and innovative recycling methods are investigated. The conversion of food wastes in value-added products is becoming a more economically viable and interesting practice. Food waste, collected in the distribution sector and citrus industries, was characterised for its potential as a raw material to use in fermentation processes. In this study, the production of single-cell protein (SCP) using food waste as a substrate was investigated. The purpose of this study has been to produce SCP from mixtures of food waste using Saccharomyces cerevisiae. The main fermentation test was carried out using a 25 l bioreactor. The utilisation of food waste can allow us to not only to reduce environmental pollution, but also to obtain value-added products such as protein supply for animal feed.

  17. Search for single-top production in ep collisions at HERA

    Energy Technology Data Exchange (ETDEWEB)

    Abramowicz, H. [Tel Aviv Univ. (Israel). School of Physics; Max Planck Institute for Physics, Munich (Germany); Abt, I. [Max Planck Institute for Physics, Munich (Germany); Adamczyk, L. [AGH-Univ. of Science and Technology, Krakow (PL). Faculty of Physics and Applied Computer Science] (and others)

    2011-11-15

    A search for single-top production, ep{yields}etX, has been performed with the ZEUS detector at HERA using data corresponding to an integrated luminosity of 0.37 fb{sup -1}. No evidence for top production was found, consistent with the expectation from the Standard Model. Limits were computed for single-top production via flavour changing neutral current transitions. The result was combined with a previous ZEUS result yielding a total luminosity of 0.50 fb{sup -1}. A 95% credibility level upper limit of 0.13 pb was obtained for the cross section at the centre-of-mass energy of {radical}(s)=315 GeV. (orig.)

  18. Single- and central-diffractive production of open charm and bottom mesons at the LHC

    CERN Document Server

    Łuszczak, Marta; Szczurek, Antoni

    2015-01-01

    We discuss diffractive production of open charm and bottom mesons at the LHC. The differential cross sections for single- and central-diffractive mechanisms for $c\\bar c$ and $b\\bar b$ pair production are calculated in the framework of the Ingelman-Schlein model corrected for absorption effects. The LO gluon-gluon fusion and quark-antiquark anihilation partonic subprocesses are taken into consideration, which are calculated within standard collinear approximation. The extra corrections from reggeon exchanges are taken into account. The hadronization of charm and bottom quarks is taken into account by means of fragmentation functions. Predictions for single- and central-diffractive production in the case of $D$ and $B$ mesons, as well as $D\\bar D$ pairs are presented, including detector acceptance of the ATLAS, CMS and LHCb Collaborations.

  19. Comparative study of shale-gas production using single- and dual-continuum approaches

    KAUST Repository

    El-Amin, Mohamed

    2017-07-06

    In this paper, we explore the possibility of specifying the ideal hypothetical positions of matrices blocks and fractures in fractured porous media as a single-continuum reservoir model in a way that mimics the dual-porosity dual-permeability (DPDP) configuration. In order to get an ideal mimic, we use the typical configuration and geometrical hypotheses of the DPDP model for the SDFM. Unlike the DPDP model which consists of two equations for the two-continuum coupled by a transfer term, the proposed single-domain fracture model (SDFM) model consists of a single equation for the single-continuum. Each one of the two models includes slippage effect, adsorption, Knudsen diffusion, geomechanics, and thermodynamics deviation factor. For the thermodynamics calculations, the cubic Peng-Robinson equation of state is employed. The diffusion model is verified by calculating the total mass flux through a nanopore by combination of slip flow and Knudsen diffusion and compared with experimental data. A semi-implicit scheme is used for the time discretization while the thermodynamics equations are updated explicitly. The spatial discretization is done using the cell-centered finite difference (CCFD) method. Finally, numerical experiments are performed under variations of the physical parameters. Several results are discussed such as pressure, production rate and cumulative production. We compare the results of the two models using the same dimensions and physical and computational parameters. We found that the DPDP and the SDFM models production rate and cumulative production behave similarly with approximately the same slope but with some differences in values. Moreover, we found that the poroelasticity effect reduces the production rate and consequently the cumulative production rate but in the SDFM model the reservoir takes more time to achieve depletion than the DPDP model. The normal fracture factor which appears in the transfer term of the DPDP model is adjusted against

  20. Multiprobe RNase protection assay with internally labeled radioactive probes, generated by RT-PCR and nested PCR.

    Science.gov (United States)

    von Wolff, M; Tabibzadeh, S

    1999-07-01

    RNase Protection Assay (RPAs) is a highly sensitive and reproducible method of quantitating the levels of specific mRNA transcripts. The introduction of the commercially available Multiprobe RPAs allow comparing and quantifying the expression of up to different mRNA species in a single sample of 1-20 micrograms of total RNA. To generate probes which are not commercially available, we prepared highly specific probes by RT-PCR and nested PCR. Then, after ligation of a T7 promoter, another PCR was performed with a primer set consisting of a specific sense primer and antisense T7 primer. Only the antisense strand of the double stranded PCR-product contained the T7-promoter sequence on its 5' end, allowing in vitro transcription and internal labeling with [alpha-32]UTP. Probe concentration was determined in a scintillation counter and equal counts were introduced in the assay. In vitro transcription of the PCR generated probes resulted in radioactive probes with a very high specific activity, allowing simultaneous analysis of 70 different RNA samples. RPA could be performed under the same conditions as recommended for the commercially available probe sets, avoiding time consuming optimization of reaction conditions. Negative controls consisted of yeast RNA and sense RNA probes. Positive controls were single stranded templates, generated by asymmetric PCR. Dilution series revealed a high reproducibility and the potential of this technique to semi-quantitate mRNA in different RNA samples. In conclusion, probes may be generated by RT-PCR and nested PCR that will work with the commercially available Multiprobe RPAs. The high probe yield allows analysis of a great number of samples using the same set of probes with a high reproducibility.

  1. A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model

    Science.gov (United States)

    Stojowska, Karolina; Krawczyk, Beata

    2014-01-01

    We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal “band-based” results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3′ recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5′ rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided. PMID:25522278

  2. A new double digestion ligation mediated suppression PCR method for simultaneous bacteria DNA-typing and confirmation of species: an Acinetobacter sp. model.

    Directory of Open Access Journals (Sweden)

    Karolina Stojowska

    Full Text Available We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s, while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR, whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR. The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal "band-based" results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3' recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5' rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided.

  3. Development of 23 individual TaqMan® real-time PCR assays for identifying common foodborne pathogens using a single set of amplification conditions.

    Science.gov (United States)

    Cremonesi, Paola; Pisani, Laura Francesca; Lecchi, Cristina; Ceciliani, Fabrizio; Martino, Pieranna; Bonastre, Armand Sanchez; Karus, Avo; Balzaretti, Claudia; Castiglioni, Bianca

    2014-10-01

    Most of the acute intestinal diseases are caused by foodborne pathogens with infants and elderly people being at major risk. The aim of this study was to develop a procedure to simultaneously detect 20 foodborne pathogens in complex alimentary matrices such as milk, cheese and meat. The list of targets include, among the others, Listeria spp., Salmonella spp., Shigella spp., Escherichia coli spp., Campylobacter spp., Clostridium spp. and Staphylococcus aureus. The accuracy of detection was determined by using ATCC strains as positive and negative controls. The achieved sensitivity of each of assays was 1 pg of genomic DNA, which was equivalent to ∼1 cfu. The working ranges of the TaqMan(®) Real-time PCR assays, when used quantitatively on cheese and meat samples inoculated with serial dilution of Listeria spp., Listeria monocytogenes, S. aureus, Salmonella enterica, Shigella boydii, E. coli O157:H7, Bacillus cereus, Campylobacter coli, Yersinia enterocolitica, Enterobacter sakazakii and Pseudomonas aeruginosa was 10(8) cfu/g to 10(4) cfu/g. No matrix interferences were observed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Production of Single W Bosons at LEP and Measurement of $WW\\gamma$ Gauge Coupling Parameters

    CERN Document Server

    Achard, P; Aguilar-Benítez, M; Alcaraz, J; Alemanni, G; Allaby, James V; Aloisio, A; Alviggi, M G; Anderhub, H; Andreev, V P; Anselmo, F; Arefev, A; Azemoon, T; Aziz, T; Bagnaia, P; Bajo, A; Baksay, G; Baksay, L; Baldew, S V; Banerjee, S; Banerjee, Sw; Barczyk, A; Barillère, R; Bartalini, P; Basile, M; Batalova, N; Battiston, R; Bay, A; Becattini, F; Becker, U; Behner, F; Bellucci, L; Berbeco, R; Berdugo, J; Berges, P; Bertucci, B; Betev, B L; Biasini, M; Biglietti, M; Biland, A; Blaising, J J; Blyth, S C; Bobbink, Gerjan J; Böhm, A; Boldizsar, L; Borgia, B; Bottai, S; Bourilkov, D; Bourquin, Maurice; Braccini, S; Branson, J G; Brochu, F; Burger, J D; Burger, W J; Cai, X D; Capell, M; Cara Romeo, G; Carlino, G; Cartacci, A M; Casaus, J; Cavallari, F; Cavallo, N; Cecchi, C; Cerrada, M; Chamizo-Llatas, M; Chang, Y H; Chemarin, M; Chen, A; Chen, G; Chen, G M; Chen, H F; Chen, H S; Chiefari, G; Cifarelli, Luisa; Cindolo, F; Clare, I; Clare, R; Coignet, G; Colino, N; Costantini, S; de la Cruz, B; Cucciarelli, S; van Dalen, J A; De Asmundis, R; Déglon, P L; Debreczeni, J; Degré, A; Dehmelt, K; Deiters, K; Della Volpe, D; Delmeire, E; Denes, P; De Notaristefani, F; De Salvo, A; Diemoz, M; Dierckxsens, M; Dionisi, C; Dittmar, Michael; Doria, A; Dova, M T; Duchesneau, D; Echenard, B; Eline, A; El-Mamouni, H; Engler, A; Eppling, F J; Ewers, A; Extermann, Pierre; Falagán, M A; Falciano, S; Favara, A; Fay, J; Fedin, O; Felcini, Marta; Ferguson, T; Fesefeldt, H S; Fiandrini, E; Field, J H; Filthaut, Frank; Fisher, P H; Fisher, W; Fisk, I; Forconi, G; Freudenreich, Klaus; Furetta, C; Galaktionov, Yu; Ganguli, S N; García-Abia, P; Gataullin, M; Gentile, S; Giagu, S; Gong, Z F; Grenier, G; Grimm, O; Grünewald, M W; Guida, M; van Gulik, R; Gupta, V K; Gurtu, A; Gutay, L J; Haas, D; Hakobyan, R S; Hatzifotiadou, D; Hebbeker, T; Hervé, A; Hirschfelder, J; Hofer, H; Hohlmann, M; Holzner, G; Hou, S R; Hu, Y; Jin, B N; Jones, L W; de Jong, P; Josa-Mutuberria, I; Käfer, D; Kaur, M; Kienzle-Focacci, M N; Kim, J K; Kirkby, Jasper; Kittel, E W; Klimentov, A; König, A C; Kopal, M; Koutsenko, V F; Kräber, M H; Krämer, R W; Krenz, W; Krüger, A; Kunin, A; Ladrón de Guevara, P; Laktineh, I; Landi, G; Lebeau, M; Lebedev, A; Lebrun, P; Lecomte, P; Lecoq, P; Le Coultre, P; Le Goff, J M; Leiste, R; Levtchenko, M; Levchenko, P M; Li, C; Likhoded, S A; Lin, C H; Lin, W T; Linde, Frank L; Lista, L; Liu, Z A; Lohmann, W; Longo, E; Lü, Y S; Lübelsmeyer, K; Luci, C; Luminari, L; Lustermann, W; Ma Wen Gan; Malgeri, L; Malinin, A; Maña, C; Mangeol, D J J; Mans, J; Martin, J P; Marzano, F; Mazumdar, K; McNeil, R R; Mele, S; Merola, L; Meschini, M; Metzger, W J; Mihul, A; Milcent, H; Mirabelli, G; Mnich, J; Mohanty, G B; Muanza, G S; Muijs, A J M; Musicar, B; Musy, M; Nagy, S; Natale, S; Napolitano, M; Nessi-Tedaldi, F; Newman, H; Niessen, T; Nisati, A; Nowak, H; Ofierzynski, R A; Organtini, G; Palomares, C; Pandoulas, D; Paolucci, P; Paramatti, R; Passaleva, G; Patricelli, S; Paul, T; Pauluzzi, M; Paus, C; Pauss, Felicitas; Pedace, M; Pensotti, S; Perret-Gallix, D; Petersen, B; Piccolo, D; Pierella, F; Pioppi, M; Piroué, P A; Pistolesi, E; Plyaskin, V; Pohl, M; Pozhidaev, V; Pothier, J; Prokofiev, D O; Prokofev, D; Quartieri, J; Rahal-Callot, G; Rahaman, M A; Raics, P; Raja, N; Ramelli, R; Rancoita, P G; Ranieri, R; Raspereza, A V; Razis, P A; Ren, D; Rescigno, M; Reucroft, S; Riemann, S; Riles, K; Roe, B P; Romero, L; Rosca, A; Rosier-Lees, S; Roth, S; Rosenbleck, C; Roux, B; Rubio, Juan Antonio; Ruggiero, G; Rykaczewski, H; Sakharov, A; Saremi, S; Sarkar, S; Salicio, J; Sánchez, E; Sanders, M P; Schäfer, C; Shchegelskii, V; Schmidt-Kärst, S; Schmitz, D; Schopper, Herwig Franz; Schotanus, D J; Schwering, G; Sciacca, C; Servoli, L; Shevchenko, S; Shivarov, N; Shoutko, V; Shumilov, E; Shvorob, A V; Siedenburg, T; Son, D; Souga, C; Spillantini, P; Steuer, M; Stickland, D P; Stoyanov, B; Strässner, A; Sudhakar, K; Sultanov, G G; Sun, L Z; Sushkov, S V; Suter, H; Swain, J D; Szillási, Z; Tang, X W; Tarjan, P; Tauscher, Ludwig; Taylor, L; Tellili, B; Teyssier, D; Timmermans, C; Ting, Samuel C C; Ting, S M; Tonwar, S C; Tóth, J; Tully, C; Tung, K L; Ulbricht, J; Valente, E; Van de Walle, R T; Vásquez, R P; Veszpremi, V; Vesztergombi, G; Vetlitskii, I; Vicinanza, D; Viertel, Gert M; Villa, S; Vivargent, M; Vlachos, S; Vodopyanov, I; Vogel, H; Vogt, H; Vorobev, I; Vorobyov, A A; Wadhwa, M; Wallraff, W; Wang, X L; Wang, Z M; Weber, M; Wienemann, P; Wilkens, H; Wynhoff, S; Xia, L; Xu, Z Z; Yamamoto, J; Yang, B Z; Yang, C G; Yang, H J; Yang, M; Yeh, S C; Zalite, A; Zalite, Yu; Zhang, Z P; Zhao, J; Zhu, G Y; Zhu, R Y; Zhuang, H L; Zichichi, A; Zimmermann, B; Zöller, M

    2002-01-01

    \\documentclass[12pt,a4paper,dvips]{article} \\begin{document} \\begin{center} {Production of Single W Bosons at LEP and \\\\ Measurement of \\boldmath$\\rm W W \\gamma$ Gauge Coupling Parameters} \\end{center} \\begin{abstract} Single W boson production in electron-positron collisions is studied with the L3 detector at centre-of-mass energies between $192\\mathrm{\\ Ge\\kern -0.1em V}$ and $209\\mathrm{\\ Ge\\kern -0.1em V}$. Events with two acoplanar hadronic jets or a single energetic lepton are selected, and the single W cross section is measured. Combining the results with measurements at lower centre-of-mass energies, the ratio of the measured cross section to the Standard Model expectation is found to be $1.12^{+0.11}_{-0.10}\\pm0.03$. From all single W data, the WW$\\gamma$ gauge coupling parameter $\\kappa_\\gamma$ is measured to be $1.116^{+0.082}_{-0.086}\\pm0.068$. \\end{abstract} \\end{document}

  5. Growth of optical-quality anthracene crystals doped with dibenzoterrylene for controlled single photon production

    Energy Technology Data Exchange (ETDEWEB)

    Major, Kyle D., E-mail: kyle.major11@imperial.ac.uk; Lien, Yu-Hung; Polisseni, Claudio; Grandi, Samuele; Kho, Kiang Wei; Clark, Alex S.; Hwang, J.; Hinds, E. A., E-mail: ed.hinds@imperial.ac.uk [Centre for Cold Matter, Department of Physics, Blackett Laboratory, Imperial College London, Prince Consort Road, London SW7 2AZ (United Kingdom)

    2015-08-15

    Dibenzoterrylene (DBT) molecules within a crystalline anthracene matrix show promise as quantum emitters for controlled, single photon production. We present the design and construction of a chamber in which we reproducibly grow doped anthracene crystals of optical quality that are several mm across and a few μm thick. We demonstrate control of the DBT concentration over the range 6–300 parts per trillion and show that these DBT molecules are stable single-photon emitters. We interpret our data with a simple model that provides some information on the vapour pressure of DBT.

  6. Optimization and validation of DNA extraction and real-time PCR assay for the quantitative measurement of residual host cell DNA in biopharmaceutical products.

    Science.gov (United States)

    Hu, B; Sellers, J; Kupec, J; Ngo, W; Fenton, S; Yang, T-Y; Grebanier, A

    2014-01-01

    Host cell DNA contamination occurs during the production of biopharmaceuticals and must be controlled and monitored for the purity and safety of the drug products. A sodium iodide-based DNA extraction and a subsequent real time PCR assay were developed and validated for the quantitative measurement of residual host cell DNA impurity in monoclonal antibody therapeutic products. A sodium iodide-based commercial kit was optimized for the removal of interfering matrices. Several incubation steps from the kit protocol were combined and a neutralization buffer was introduced to protein digestion step to eliminate any precipitation from the detergent. The elimination of the two washing steps significantly reduced assay variability from loss of DNA pellets. The optimized DNA extraction procedure can recover DNA close to 100% for DNA concentrations from 10 to 100,000pg/mL. Of the published sequences of repetitive interspersed nuclear elements, we identified a nucleotide mismatch from the published CHO probe. Correction of this nucleotide increased DNA amplification by a thousand fold. The optimized assay was further validated for the quantitation of residual CHO DNA according to ICH guidelines with preset assay acceptance criteria. The method met all assay acceptance criteria and was found linear, accurate and precise for the quantitation of residual CHO in the linear range of 10-100,000pg DNA/mL. LOQ was measured at 10pg DNA/mL and LOD at 1pg DNA/mL. No matrix interference to our validated assay was detected from bioreactor harvest, Protein A eluate or eluate from ion exchange columns. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Observation of Electroweak Single Top-Quark Production with the CDF II Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Lueck, Jan [Karlsruhe Inst. of Technology (Germany)

    2009-07-24

    The standard model of elementary particle physics (SM) predicts, besides the top-quark pair production via the strong interaction, also the electroweak production of single top-quarks [19]. Up to now, the Fermilab Tevatron proton-antiproton-collider is the only place to produce and study top quarks emerging from hadron-hadron-collisions. Top quarks were directly observed in 1995 during the Tevatron Run I at a center-of-mass energy of √s = 1.8 TeV simultaneously by the CDF and D0 Collaborations via the strong production of top-quark pairs. Run II of the Tevatron data taking period started 2001 at √s = 1.96 TeV after a five year upgrade of the Tevatron accelerator complex and of both experiments. One main component of its physics program is the determination of the properties of the top quark including its electroweak production. Even though Run II is still ongoing, the study of the top quark is already a successful endeavor, confirmed by dozens of publications from both Tevatron experiments. A comprehensive review of top-quark physics can be found in reference. The reasons for searching for single top-quark production are compelling. As the electroweak top-quark production proceeds via a Wtb vertex, it provides the unique opportunity of the direct measurement of the CKM matrix element |Vtb|, which is expected to be |Vtb| ~ 1 in the SM. Significant deviations from unity could be an indication of a fourth quark generation, a production mode via flavor-changing neutral currents, and other new phenomena, respectively. There are two dominating electroweak top-quark production modes at the Fermilab Tevatron: the t-channel exchange of a virtual W boson striking a b quark and the s-channel production of a timelike W boson via the fusion of two quarks. In proton-antiproton-collisions the third electroweak production mode, the associated Wt production of an on-shell W boson in conjunction with a top quark has a comparatively negligible small

  8. Detection of seven virulence and toxin genes of Campylobacter jejuni isolates from Danish turkeys by PCR and cytolethal distending toxin production of the isolates

    DEFF Research Database (Denmark)

    Bang, Dang Duong; Borck, Birgitte; Nielsen, Eva Møller

    2004-01-01

    A total of 117 Campylobacter jejuni isolates from Danish turkeys were tested for the presence of seven virulence and toxin genes by PCR. One hundred seventeen (100%) isolates were positive for flaA, cadF, and ceuE gene primers. One hundred three (88%) isolates were positive for cdt gene cluster PCR...

  9. Grammatical gender in the production of single words: some evidence from Greek.

    Science.gov (United States)

    Plemmenou, Evangelia; Bard, Ellen G; Branigan, Holly P

    2002-01-01

    The present study investigated the effect of prior grammatical gender information provided by the production of a bare noun on the production of a syntactically unrelated, gender-inflected color adjective. The target language was Greek. A lexical priming task involving picture naming was employed. Participants saw a series of pictures, some in color and some in black-and-white; they had to name a black-and-white picture with the single noun (prime) and a color picture with the appropriately inflected color adjective (target). Prior gender information was shown to affect subsequent production of gender-marked words. The effect was restricted to nouns of one gender class (masculine) only. The implications of these results for the representation and processing of gender in production are discussed. Copyright 2001 Elsevier Science (USA).

  10. cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR.

    Science.gov (United States)

    Hillmann, Andrew; Dunne, Eimear; Kenny, Dermot

    2009-01-01

    The comparison of two RNA populations that differ from the effects of a single-independent variable, such as a drug treatment or a specific genetic defect, can identify differences in the abundance of specific transcripts that vary in a population-dependent manner. There are a variety of methods for identifying differentially expressed genes, including microarray, SAGE, qRT-PCR, and DDGE. This protocol describes a potentially less sensitive yet relatively easy and cost-effective alternative that does not require prior knowledge of the transcriptomes under investigation and is particularly applicable when minimal levels of starting material, RNA, are available. RNA input can often be a limiting factor when analyzing RNA from, for example, rigorously purified blood cells. This protocol describes the use of SMART-PCR to amplify cDNA from sub-microgram levels of RNA. The amplified cDNA populations under comparison are then subjected to suppression subtractive hybridization (SSH-PCR), a technique that couples subtractive hybridization with suppression PCR to selectively amplify fragments of differentially expressed genes. The final products are cDNA populations enriched for significantly over-represented transcripts in either of the two input RNA preparations. These cDNA populations may then be cloned to make subtracted cDNA libraries and/or used as probes to screen subtracted cDNA, global cDNA, or genomic DNA libraries.

  11. Measurement of the top quark mass from single-top production events

    CERN Document Server

    CMS Collaboration

    2016-01-01

    We measure the mass of the top quark from events where a single top quark is produced. The analysis is performed on data from $\\mathrm{pp}$ collisions collected by the CMS detector at a center of mass energy of 8 TeV. The top quark is reconstructed from its decay $\\mathrm{t} \\rightarrow \\mathrm{W}^+ \\mathrm{b}$, with the $\\mathrm{W}$ boson decaying leptonically in the muon channel. Specific event topology and kinematic properties are used in order to enrich the sample in single-top-quark events in the t-channel, at the expense of top-quark pair production events. For the single-top quark component, a fit to the reconstructed top invariant mass distribution yields $m_{\\mathrm{t}}=172.60 \\pm 0.77~\\mathrm{(stat)}~^{+0.97}_{-0.93}~\\mathrm{(syst)}$ GeV.

  12. Comparison of INNO-LiPA HPV Genotyping v2 with PCR product subcloning and sequencing for identification of genital human papillomavirus genotypes in African women.

    Science.gov (United States)

    Didelot-Rousseau, Marie-Noëlle; Courgnaud, Valérie; Nagot, Nicolas; Ouedraogo, Abdoulaye; Konate, Issouf; Mayaud, Philippe; Weiss, Helen; Van de Perre, Philippe; Segondy, Michel

    2006-08-01

    The performance characteristics of the INNO-LiPA Genotyping v2 test for human papillomavirus (HPV) identification were assessed by comparing results with those obtained by PCR product sequencing after subcloning, in genital samples from 20 highly sexually exposed African women. The INNO-LiPA HPV Genotyping v2 test identified more HPV types than subcloning/sequencing (56 versus 37, respectively). Overall, 86.5% (32/37) of the HPV types identified by subcloning/sequencing were identified by the INNO-LiPA HPV Genotyping v2 test, whereas 57.1% (32/56) of the HPV types identified by the INNO-LiPA HPV Genotyping v2 test were identified by subcloning/sequencing. Of the 20 clinical samples tested, 7 had identical types detected under both methods and a further 11 had more types detected under INNO-LiPA HPV Genotyping v2 than subcloning/sequencing. Of the remaining two samples, the same number of types were detected under both methods, but different types were detected. INNO-LiPA HPV Genotyping v2 test appears as a valid method for identifying HPV subtypes in women with multiple HPV infection.

  13. Multivariate searches for single top quark production with the D0 detector

    Science.gov (United States)

    Abazov, V. M.; Abbott, B.; Abolins, M.; Acharya, B. S.; Adams, M.; Adams, T.; Agelou, M.; Agram, J.-L.; Ahn, S. H.; Ahsan, M.; Alexeev, G. D.; Alkhazov, G.; Alton, A.; Alverson, G.; Alves, G. A.; Anastasoaie, M.; Andeen, T.; Anderson, S.; Andrieu, B.; Anzelc, M. S.; Arnoud, Y.; Arov, M.; Askew, A.; Åsman, B.; Assis Jesus, A. C. S.; Atramentov, O.; Autermann, C.; Avila, C.; Ay, C.; Badaud, F.; Baden, A.; Bagby, L.; Baldin, B.; Bandurin, D. V.; Banerjee, P.; Banerjee, S.; Barberis, E.; Bargassa, P.; Baringer, P.; Barnes, C.; Barreto, J.; Bartlett, J. F.; Bassler, U.; Bauer, D.; Bean, A.; Begalli, M.; Begel, M.; Belanger-Champagne, C.; Bellavance, A.; Benitez, J. A.; Beri, S. B.; Bernardi, G.; Bernhard, R.; Berntzon, L.; Bertram, I.; Besançon, M.; Beuselinck, R.; Bezzubov, V. A.; Bhat, P. C.; Bhatnagar, V.; Binder, M.; Biscarat, C.; Black, K. M.; Blackler, I.; Blazey, G.; Blekman, F.; Blessing, S.; Bloch, D.; Bloom, K.; Blumenschein, U.; Boehnlein, A.; Boeriu, O.; Bolton, T. A.; Boos, E.; Borcherding, F.; Borissov, G.; Bos, K.; Bose, T.; Brandt, A.; Brock, R.; Brooijmans, G.; Bross, A.; Brown, D.; Buchanan, N. J.; Buchholz, D.; Buehler, M.; Buescher, V.; Bunichev, V.; Burdin, S.; Burke, S.; Burnett, T. H.; Busato, E.; Buszello, C. P.; Butler, J. M.; Calvet, S.; Cammin, J.; Caron, S.; Carvalho, W.; Casey, B. C. K.; Cason, N. M.; Castilla-Valdez, H.; Chakrabarti, S.; Chakraborty, D.; Chan, K. M.; Chandra, A.; Chapin, D.; Charles, F.; Cheu, E.; Chevallier, F.; Cho, D. K.; Choi, S.; Choudhary, B.; Christofek, L.; Claes, D.; Clément, B.; Clément, C.; Coadou, Y.; Cooke, M.; Cooper, W. E.; Coppage, D.; Corcoran, M.; Cousinou, M.-C.; Cox, B.; Crépé-Renaudin, S.; Cutts, D.; Ćwiok, M.; da Motta, H.; Das, A.; Das, M.; Davies, B.; Davies, G.; Davis, G. A.; de, K.; de Jong, P.; de Jong, S. J.; de La Cruz-Burelo, E.; de Oliveira Martins, C.; Degenhardt, J. D.; Déliot, F.; Demarteau, M.; Demina, R.; Demine, P.; Denisov, D.; Denisov, S. P.; Desai, S.; Diehl, H. T.; Diesburg, M.; Doidge, M.; Dominguez, A.; Dong, H.; Dudko, L. V.; Duflot, L.; Dugad, S. R.; Duperrin, A.; Dyer, J.; Dyshkant, A.; Eads, M.; Edmunds, D.; Edwards, T.; Ellison, J.; Elmsheuser, J.; Elvira, V. D.; Eno, S.; Ermolov, P.; Estrada, J.; Evans, H.; Evdokimov, A.; Evdokimov, V. N.; Fatakia, S. N.; Feligioni, L.; Ferapontov, A. V.; Ferbel, T.; Fiedler, F.; Filthaut, F.; Fisher, W.; Fisk, H. E.; Fleck, I.; Ford, M.; Fortner, M.; Fox, H.; Fu, S.; Fuess, S.; Gadfort, T.; Galea, C. F.; Gallas, E.; Galyaev, E.; Garcia, C.; Garcia-Bellido, A.; Gardner, J.; Gavrilov, V.; Gay, A.; Gay, P.; Gelé, D.; Gelhaus, R.; Gerber, C. E.; Gershtein, Y.; Gillberg, D.; Ginther, G.; Gollub, N.; Gómez, B.; Gounder, K.; Goussiou, A.; Grannis, P. D.; Greenlee, H.; Greenwood, Z. D.; Gregores, E. M.; Grenier, G.; Gris, Ph.; Grivaz, J.-F.; Grünendahl, S.; Grünewald, M. W.; Guo, F.; Guo, J.; Gutierrez, G.; Gutierrez, P.; Haas, A.; Hadley, N. J.; Haefner, P.; Hagopian, S.; Haley, J.; Hall, I.; Hall, R. E.; Han, L.; Hanagaki, K.; Harder, K.; Harel, A.; Harrington, R.; Hauptman, J. M.; Hauser, R.; Hays, J.; Hebbeker, T.; Hedin, D.; Hegeman, J. G.; Heinmiller, J. M.; Heinson, A. P.; Heintz, U.; Hensel, C.; Hesketh, G.; Hildreth, M. D.; Hirosky, R.; Hobbs, J. D.; Hoeneisen, B.; Hohlfeld, M.; Hong, S. J.; Hooper, R.; Houben, P.; Hu, Y.; Hynek, V.; Iashvili, I.; Illingworth, R.; Ito, A. S.; Jabeen, S.; Jaffré, M.; Jain, S.; Jakobs, K.; Jarvis, C.; Jenkins, A.; Jesik, R.; Johns, K.; Johnson, C.; Johnson, M.; Jonckheere, A.; Jonsson, P.; Juste, A.; Käfer, D.; Kahn, S.; Kajfasz, E.; Kalinin, A. M.; Kalk, J. M.; Kalk, J. R.; Kappler, S.; Karmanov, D.; Kasper, J.; Katsanos, I.; Kau, D.; Kaur, R.; Kehoe, R.; Kermiche, S.; Kesisoglou, S.; Khanov, A.; Kharchilava, A.; Kharzheev, Y. M.; Khatidze, D.; Kim, H.; Kim, T. J.; Kirby, M. H.; Klima, B.; Kohli, J. M.; Konrath, J.-P.; Kopal, M.; Korablev, V. M.; Kotcher, J.; Kothari, B.; Koubarovsky, A.; Kozelov, A. V.; Kozminski, J.; Kryemadhi, A.; Krzywdzinski, S.; Kuhl, T.; Kumar, A.; Kunori, S.; Kupco, A.; Kurča, T.; Kvita, J.; Lager, S.; Lammers, S.; Landsberg, G.; Lazoflores, J.; Le Bihan, A.-C.; Lebrun, P.; Lee, W. M.; Leflat, A.; Lehner, F.; Leonidopoulos, C.; Lesne, V.; Leveque, J.; Lewis, P.; Li, J.; Li, Q. Z.; Lima, J. G. R.; Lincoln, D.; Linnemann, J.; Lipaev, V. V.; Lipton, R.; Liu, Z.; Lobo, L.; Lobodenko, A.; Lokajicek, M.; Lounis, A.; Love, P.; Lubatti, H. J.; Lynker, M.; Lyon, A. L.; Maciel, A. K. A.; Madaras, R. J.; Mättig, P.; Magass, C.; Magerkurth, A.; Magnan, A.-M.; Makovec, N.; Mal, P. K.; Malbouisson, H. B.; Malik, S.; Malyshev, V. L.; Mao, H. S.; Maravin, Y.; Martens, M.; Mattingly, S. E. K.; McCarthy, R.; McCroskey, R.; Meder, D.; Melnitchouk, A.; Mendes, A.; Mendoza, L.; Merkin, M.; Merritt, K. W.; Meyer, A.; Meyer, J.; Michaut, M.

    2007-05-01

    We present a search for electroweak production of single top quarks in the s-channel (pp¯→tb¯+X) and t-channel (pp¯→tqb¯+X) modes. We have analyzed 230pb-1 of data collected with the D0 detector at the Fermilab Tevatron Collider at a center-of-mass energy of s=1.96TeV. No evidence for a single top quark signal is found. We set 95% confidence level upper limits on the production cross sections, based on binned likelihoods formed from a neural network output. The observed (expected) limits are 6.4 pb (4.5 pb) in the s-channel and 5.0 pb (5.8 pb) in the t-channel.

  14. High throughput production of single core double emulsions in a parallelized microfluidic device.

    Science.gov (United States)

    Romanowsky, Mark B; Abate, Adam R; Rotem, Assaf; Holtze, Christian; Weitz, David A

    2012-02-21

    Double emulsions are useful templates for microcapsules and complex particles, but no method yet exists for making double emulsions with both high uniformity and high throughput. We present a parallel numbering-up design for microfluidic double emulsion devices, which combines the excellent control of microfluidics with throughput suitable for mass production. We demonstrate the design with devices incorporating up to 15 dropmaker units in a two-dimensional or three-dimensional array, producing single-core double emulsion drops at rates over 1 kg day(-1) and with diameter variation less than 6%. This design provides a route to integrating hundreds of dropmakers or more in a single chip, facilitating industrial-scale production rates of many tons per year.

  15. Single-diffractive Drell-Yan pair production at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Ceccopieri, Federico Alberto [Universita degli Studi di Perugia, Dipartimento di Fisica e Geologia, Perugia (Italy); Universite de Liege, IFPA, Liege (Belgium); INFN, Sezione di Perugia (Italy)

    2017-01-15

    We present predictions for single-diffractive low-mass Drell-Yan pair production in pp collisions at the LHC at √(s) = 13 TeV. Predictions are obtained adopting a factorised form for the relevant cross sections and are based on a new set of diffractive parton distributions resulting from the QCD analysis of combined HERA leading proton data. We discuss a number of observables useful to characterise the expected factorisation breaking effects. (orig.)

  16. Search for single top quark production via contact interactions at LEP2

    CERN Document Server

    Abdallah, J; Adam, W; Adzic, P; Albrecht, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Amaldi, U; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W-D; Arnoud, Y; Ask, S; Asman, B; Augustin, J E; Augustinus, A; Baillon, P; Ballestrero, A; Bambade, P; Barbier, R; Bardin, D; Barker, G J; Baroncelli, A; Battaglia, M; Baubillier, M; Becks, K-H; Begalli, M; Behrmann, A; Ben-Haim, E; Benekos, N; Benvenuti, A; Berat, C; Berggren, M; Bertrand, D; Besancon, M; Besson, N; Bloch, D; Blom, M; Bluj, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Brenner, R; Brodet, E; Bruckman, P; Brunet, J M; Buschbeck, B; Buschmann, P; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F; Chapkin, M; Charpentier, Ph; Checchia, P; Chierici, R; Chliapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Crennell, D; Cuevas, J; D'Hondt, J; da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; De Boer, W; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; de Paula, L; Di Ciaccio, L; Di Simone, A; Doroba, K; Drees, J; Eigen, G; Ekelof, T; Ellert, M; Elsing, M; Espirito Santo, M C; Fanourakis, G; Fassouliotis, D; Feindt, M; Fernandez, J; Ferrer, A; Ferro, F; Flagmeyer, U; Foeth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J; Gandelman, M; Garcia, C; Gavillet, Ph; Gazis, E; Gokieli, R; Golob, B; Gomez-Ceballos, G; Goncalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Hoffman, J; Holmgren, S-O; Holt, P J; Houlden, M A; Jackson, J N; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Katsanevas, S; Katsoufis, E; Kernel, G; Kersevan, B P; Kerzel, U; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kouznetsov, O; Krumstein, Z; Kucharczyk, M; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; Lopez, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Marechal, B; Margoni, M; Marin, J-C; Mariotti, C; Markou, A; Martinez-Rivero, C; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; McNulty, R; Meroni, C; Migliore, E; Mitaroff, W; Mjoernmark, U; Moa, T; Moch, M; Moenig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Mueller, U; Muenich, K; Mulders, M; Mundim, L; Murray, W; Muryn, B; Myatt, G; Myklebust, T; Nassiakou, M; Navarria, F; Nawrocki, K; Nemecek, S; Nicolaidou, R; Nikolenko, M; Oblakowska-Mucha, A; Obraztsov, V; Oliveira, O; Olshevski, A; Onofre, A; Orava, R; Osterberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, Th D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Pozdniakov, V; Pukhaeva, N; Pullia, A; Radojicic, D; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P; Richard, F; Ridky, J; Rivero, M; Rodriguez, D; Romero, A; Ronchese, P; Roudeau, P; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovsky, A; Salmi, L; Salt, J; Sander, C; Savoy-Navarro, A; Schwickerath, U; Sekulin, R; Siebel, M; Sisakian, A; Smadja, G; Smirnova, O; Sokolov, A; Sopczak, A; Sosnowski, R; Spassov, T; Stanitzki, M; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Tabarelli, T; Tegenfeldt, F; Timmermans, J; Tkatchev, L; Tobin, M; Todorovova, S; Tome, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M-L; Tyapkin, I A; Tyapkin, P; Tzamarias, S; Uvarov, V; Valenti, G; Van Dam, P; Van Eldik, J; van Remortel, N; Van Vulpen, I; Vegni, G; Veloso, F; Venus, W; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weiser, C; Wicke, D; Wickens, J; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O; Zalewska, A; Zalewski, P; Zavrtanik, D; Zhuravlov, V; Zimin, N I; Zintchenko, A; Zupan, M

    2011-01-01

    Single top quark production via four-fermion contact interactions associated to flavour-changing neutral currents was searched for in data taken by the DELPHI detector at LEP2. The data were accumulated at centre-of-mass energies ranging from 189 to 209 GeV, with an integrated luminosity of 598.1 pb^-1. No evidence for a signal was found. Limits on the energy scale Lambda, were set for scalar-, vector- and tensor-like coupling scenarios.

  17. On the NNLO QCD corrections to single-top production at the LHC

    Directory of Open Access Journals (Sweden)

    Mathias Brucherseifer

    2014-09-01

    Full Text Available We present a fully-differential calculation of the NNLO QCD corrections to the t-channel mechanism for producing single top quarks at the LHC. We work in the structure function approximation, computing QCD corrections to the light- and heavy-quark lines separately and neglecting the dynamical cross-talk between the two. The neglected contribution, which appears at NNLO for the first time, is color-suppressed and is expected to be sub-dominant. Within this approximation, we find that, for the total cross section, NNLO QCD corrections are in the few percent range and, therefore, are comparable to NLO QCD corrections. We also find that the scale independence of the theoretical prediction for single-top production improves significantly once NNLO QCD corrections are included. Furthermore, we show how these results change if a cut on the transverse momentum of the top quark is applied and derive the NNLO QCD prediction for the ratio of single top and single anti-top production cross sections at the 8 TeV LHC.

  18. Detection method for genetically modified papaya using duplex PCR.

    Science.gov (United States)

    Yamaguchi, Akihiro; Shimizu, Kaori; Mishima, Takashi; Aoki, Nobutaro; Hattori, Hideki; Sato, Hidetaka; Ueda, Nobuo; Watanabe, Takahiro; Hino, Akihiro; Akiyama, Hiroshi; Maitani, Tamio

    2006-08-01

    A simple and rapid method for the identification of genetically modified (GM) papaya, derived from Line 55-1, was developed by modifying the Japanese official PCR method. Genomic DNA was directly extracted from the fresh fruit without the lyophilization step, using a commercial silica-based kit. To develop a duplex PCR method which simultaneously detects the GM papaya-specific gene and the intrinsic papain gene, the papain 2-5'/3' (amplicon size; 184 bp) primer pair for the detection of the papain gene was newly designed within the region of the products (211 bp) amplified using the papain 1-5'/-3' primer pair adopted in the Japanese official PCR method. To detect the GM papaya-specific gene, the primer pair Nos C-5'/CaM N-3' described in the Japanese official method was used. The DNA sequences of the GM papaya gene and the intrinsic papain gene were co-amplified using the PCR method in a single tube. The developed duplex PCR method allows the simultaneous detection of the products by means of agarose gel electrophoresis or microchip electrophoresis. The proposed method for GM papaya identification is simple and rapid.

  19. The casein genes in goat breeds from different Continents: analysis by Polymerase Chain Reaction – Single Strand Conformation Polymorphism (PCR-SSCP

    Directory of Open Access Journals (Sweden)

    A. Caroli

    2010-04-01

    Full Text Available A screening of casein gene variability was carried out by Polymerase Chain Reaction – Single Strand Conformation Polymorphism in 8 goat breeds from Sudan (Nubian goat, Turkey (Angora Goat Lalahan Tiftic, Angora Goat Yerkoy, Hair goat and India (Jammu, Maharashtra, Rajasthan, South Goat. A total of 16 different alleles or groups of alleles were found, showing conspicuous differences among breeds. The allele frequencies were submitted to cluster analysis in order to highlight differences between breeds, also including data from Red Sokoto, West African Dwarf Nigeria, West African Dwarf Cameroon, and Borno Goat. The tree obtained from the cluster analysis showed two main lineages. The West African goat clustered together, the Indian and Turkish breeds were in the other group. Nubian goat was found in an intermediate position.

  20. Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products.

    Science.gov (United States)

    van Asch, Barbara; Silva Santos, Liliana; Carneiro, Joao; Pereira, Filipe; Amorim, Antonio

    2011-07-13

    A genetic method to identify the breed of origin could serve as a useful tool for inspecting the authenticity of the increasing number of monobreed foodstuffs, such as those derived from small local European pig breeds. Mitochondrial DNA (mtDNA) is practically the only reliable genomic target for PCR in processed products, and its haploid nature and strict maternal inheritance greatly facilitate genetic analysis. As a result of strategies that sought to improve the production traits of European pigs, most industrial breeds presently show a high frequency of Asian alleles, while the absence or low frequency of such Asian alleles has been observed in small rustic breeds from which highly prized dry-cured and other traditional products are derived. Therefore, the detection of Asian ancestry would indicate nonconformity in Protected Denomination of Origin products. This study presents a single base extension assay based on 15 diagnostic mtDNA single nucleotide polymorphisms to discriminate between Asian and European Sus scrofa lineages. The test was robust, sensitive and accurate in a wide range of processed foodstuffs and allowed accurate detection of pig genetic material and identification of maternal ancestry. A market survey suggested that nonconformity of products derived from Portuguese breeds is an unusual event at present, but regular surveys both in the local populations and in commercial products would be advisible. Taking into consideration the limitations presented by other methodologies, this mtDNA-based test probably attains the highest resolution for the direct genetic test for population of origin in Sus scrofa food products.

  1. Determining stocks and flows of structural wood products in single family homes in the United States between 1950 and 2010

    DEFF Research Database (Denmark)

    Sianchuk, Robert A.; McFarlane, Paul N.; Ackom, Emmanuel

    2012-01-01

    The stocks and flows of six major structural wood products (SWPs)-lumber, plywood, oriented strand board [OSB], glue laminated timber, I-joists, and laminated veneer lumber (LVL)-in US single family homes were modeled from 1950 to 2010. The consumption of these products in US single family homes...

  2. The normally expressed kappa immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

    DEFF Research Database (Denmark)

    Juul, L; Hougs, L; Andersen, V

    1997-01-01

    . V genes from the Jkappa-proximal duplication unit of the kappa locus were almost exclusively used. A total of 65% of the sequences could be assigned to four or five genes: A27 (humkv325), L6 (Vg), L2 (humkv328), and A3 and/or A19. N additions and P nucleotides were quite common and found in 32......The expressed human kappa light chain gene repertoire utilized by healthy individuals was studied by two different single-sided specific PCR techniques to avoid bias for certain V genes. A total of 103 rearranged kappa sequences from peripheral blood mononuclear cells from healthy individuals were...... agreement with those of previous repertoire studies using potentially V-gene-biased techniques. Thus, it is clear that restricted V-gene usage, common N and P additions, and extended CDR3 regions are normal features and not, as has been claimed, characteristics of pathological autoantibodies....

  3. Measurement of the single π0 production rate in neutral current neutrino interactions on water

    Science.gov (United States)

    Abe, K.; Amey, J.; Andreopoulos, C.; Antonova, M.; Aoki, S.; Ariga, A.; Ashida, Y.; Assylbekov, S.; Autiero, D.; Ban, S.; Barbi, M.; Barker, G. J.; Barr, G.; Barry, C.; Bartet-Friburg, P.; Batkiewicz, M.; Berardi, V.; Berkman, S.; Bhadra, S.; Bienstock, S.; Blondel, A.; Bolognesi, S.; Bordoni, S.; Boyd, S. B.; Brailsford, D.; Bravar, A.; Bronner, C.; Buizza Avanzini, M.; Calland, R. G.; Campbell, T.; Cao, S.; Cartwright, S. L.; Castillo, R.; Catanesi, M. G.; Cervera, A.; Chappell, A.; Checchia, C.; Cherdack, D.; Chikuma, N.; Christodoulou, G.; Clifton, A.; Coleman, J.; Collazuol, G.; Coplowe, D.; Cremonesi, L.; Cudd, A.; Dabrowska, A.; De Rosa, G.; Dealtry, T.; Denner, P. F.; Dennis, S. R.; Densham, C.; Dewhurst, D.; Di Lodovico, F.; Di Luise, S.; Dolan, S.; Drapier, O.; Duffy, K. E.; Dumarchez, J.; Dunkman, M.; Dunne, P.; Dziewiecki, M.; Emery-Schrenk, S.; Ereditato, A.; Feusels, T.; Finch, A. J.; Fiorentini, G. A.; Friend, M.; Fujii, Y.; Fukuda, D.; Fukuda, Y.; Furmanski, A. P.; Galymov, V.; Garcia, A.; Giffin, S. G.; Giganti, C.; Gilje, K.; Gizzarelli, F.; Golan, T.; Gonin, M.; Grant, N.; Hadley, D. R.; Haegel, L.; Haigh, J. T.; Hamilton, P.; Hansen, D.; Harada, J.; Hara, T.; Hartz, M.; Hasegawa, T.; Hastings, N. C.; Hayashino, T.; Hayato, Y.; Helmer, R. L.; Hierholzer, M.; Hillairet, A.; Himmel, A.; Hiraki, T.; Hiramoto, A.; Hirota, S.; Hogan, M.; Holeczek, J.; Hosomi, F.; Huang, K.; Ichikawa, A. K.; Ieki, K.; Ikeda, M.; Imber, J.; Insler, J.; Intonti, R. A.; Irvine, T. J.; Ishida, T.; Ishii, T.; Iwai, E.; Iwamoto, K.; Izmaylov, A.; Jacob, A.; Jamieson, B.; Jiang, M.; Johnson, S.; Jo, J. H.; Jonsson, P.; Jung, C. K.; Kabirnezhad, M.; Kaboth, A. C.; Kajita, T.; Kakuno, H.; Kameda, J.; Karlen, D.; Karpikov, I.; Katori, T.; Kearns, E.; Khabibullin, M.; Khotjantsev, A.; Kielczewska, D.; Kikawa, T.; Kim, H.; Kim, J.; King, S.; Kisiel, J.; Knight, A.; Knox, A.; Kobayashi, T.; Koch, L.; Koga, T.; Koller, P. P.; Konaka, A.; Kondo, K.; Kopylov, A.; Kormos, L. L.; Korzenev, A.; Koshio, Y.; Kowalik, K.; Kropp, W.; Kudenko, Y.; Kurjata, R.; Kutter, T.; Lagoda, J.; Lamont, I.; Lamoureux, M.; Larkin, E.; Lasorak, P.; Laveder, M.; Lawe, M.; Lazos, M.; Licciardi, M.; Lindner, T.; Liptak, Z. J.; Litchfield, R. P.; Li, X.; Longhin, A.; Lopez, J. P.; Lou, T.; Ludovici, L.; Lu, X.; Magaletti, L.; Mahn, K.; Malek, M.; Manly, S.; Maret, L.; Marino, A. D.; Marteau, J.; Martin, J. F.; Martins, P.; Martynenko, S.; Maruyama, T.; Matveev, V.; Mavrokoridis, K.; Ma, W. Y.; Mazzucato, E.; McCarthy, M.; McCauley, N.; McFarland, K. S.; McGrew, C.; Mefodiev, A.; Metelko, C.; Mezzetto, M.; Mijakowski, P.; Minamino, A.; Mineev, O.; Mine, S.; Missert, A.; Miura, M.; Moriyama, S.; Morrison, J.; Mueller, Th. A.; Murphy, S.; Myslik, J.; Nakadaira, T.; Nakahata, M.; Nakamura, K. G.; Nakamura, K.; Nakamura, K. D.; Nakanishi, Y.; Nakayama, S.; Nakaya, T.; Nakayoshi, K.; Nantais, C.; Nielsen, C.; Nirkko, M.; Nishikawa, K.; Nishimura, Y.; Novella, P.; Nowak, J.; O'Keeffe, H. M.; Ohta, R.; Okumura, K.; Okusawa, T.; Oryszczak, W.; Oser, S. M.; Ovsyannikova, T.; Owen, R. A.; Oyama, Y.; Palladino, V.; Palomino, J. L.; Paolone, V.; Patel, N. D.; Paudyal, P.; Pavin, M.; Payne, D.; Perkin, J. D.; Petrov, Y.; Pickard, L.; Pickering, L.; Pinzon Guerra, E. S.; Pistillo, C.; Popov, B.; Posiadala-Zezula, M.; Poutissou, J.-M.; Poutissou, R.; Pritchard, A.; Przewlocki, P.; Quilain, B.; Radermacher, T.; Radicioni, E.; Ratoff, P. N.; Ravonel, M.; Rayner, M. A.; Redij, A.; Reinherz-Aronis, E.; Riccio, C.; Rojas, P.; Rondio, E.; Rossi, B.; Roth, S.; Rubbia, A.; Ruggeri, A. C.; Rychter, A.; Sacco, R.; Sakashita, K.; Sánchez, F.; Sato, F.; Scantamburlo, E.; Scholberg, K.; Schwehr, J.; Scott, M.; Seiya, Y.; Sekiguchi, T.; Sekiya, H.; Sgalaberna, D.; Shah, R.; Shaikhiev, A.; Shaker, F.; Shaw, D.; Shiozawa, M.; Shirahige, T.; Short, S.; Smy, M.; Sobczyk, J. T.; Sobel, H.; Sorel, M.; Southwell, L.; Stamoulis, P.; Steinmann, J.; Stewart, T.; Stowell, P.; Suda, Y.; Suvorov, S.; Suzuki, A.; Suzuki, K.; Suzuki, S. Y.; Suzuki, Y.; Tacik, R.; Tada, M.; Takahashi, S.; Takeda, A.; Takeuchi, Y.; Tamura, R.; Tanaka, H. K.; Tanaka, H. A.; Terhorst, D.; Terri, R.; Thakore, T.; Thompson, L. F.; Tobayama, S.; Toki, W.; Tomura, T.; Touramanis, C.; Tsukamoto, T.; Tzanov, M.; Uchida, Y.; Vacheret, A.; Vagins, M.; Vallari, Z.; Vasseur, G.; Vilela, C.; Vladisavljevic, T.; Wachala, T.; Wakamatsu, K.; Walter, C. W.; Wark, D.; Warzycha, W.; Wascko, M. O.; Weber, A.; Wendell, R.; Wilkes, R. J.; Wilking, M. J.; Wilkinson, C.; Wilson, J. R.; Wilson, R. J.; Wret, C.; Yamada, Y.; Yamamoto, K.; Yamamoto, M.; Yanagisawa, C.; Yano, T.; Yen, S.; Yershov, N.; Yokoyama, M.; Yoo, J.; Yoshida, K.; Yuan, T.; Yu, M.; Zalewska, A.; Zalipska, J.; Zambelli, L.; Zaremba, K.; Ziembicki, M.; Zimmerman, E. D.; Zito, M.; Żmuda, J.; T2K Collaboration

    2018-02-01

    The single π0 production rate in neutral current neutrino interactions on water in a neutrino beam with a peak neutrino energy of 0.6 GeV has been measured using the PØD, one of the subdetectors of the T2K near detector. The production rate was measured for data taking periods when the PØD contained water (2.64 ×1020 protons-on-target) and also periods without water (3.49 ×1020 protons-on-target). A measurement of the neutral current single π0 production rate on water is made using appropriate subtraction of the production rate with water in from the rate with water out of the target region. The subtraction analysis yields 106 ±41 ±69 signal events where the uncertainties are statistical (stat.) and systematic (sys.) respectively. This is consistent with the prediction of 157 events from the nominal simulation. The measured to expected ratio is 0.68 ±0.26 (stat ) ±0.44 (sys ) ±0.12 (flux ) . The nominal simulation uses a flux integrated cross section of 7.63 ×10-39 cm2 per nucleon with an average neutrino interaction energy of 1.3 GeV.

  4. Measurement of Single-top t-channel Production Using ATLAS Data

    CERN Document Server

    Holzbauer, Jenny; Schwienhorst, R; Repko, W; Lapidus, L; Pratt, S

    2012-01-01

    This document reports the measurement of the single-top t-channel cross-section using data from the ATLAS detector, located at the Large Hadron Collider on the border of France and Switzerland. The data used were collected during the first half of 2011, from proton-proton collisions with a 7 TeV center-of-mass collision energy. Single-top is electroweak top-quark production and t-channel is one of the standard model production modes. To isolate this production, selections are applied to find events with a similar final state. A cut-based analysis is used to further isolate the signal using a series of selections in several orthogonal kinematic regions. Finally, a statistical analysis is performed to determine the measured cross-section and the CKM matrix element |Vtb|. The cross-section for top and anti-top production is considered separately and the resulting cross-sections are σ t+ = 59 +18 -16 pb for the positive charge channel and σ t- = 33 +13 -12 pb for the negative charge chan...

  5. The Impact of Single Amino Acids on Growth and Volatile Aroma Production by Saccharomyces cerevisiae Strains

    Directory of Open Access Journals (Sweden)

    Samantha Fairbairn

    2017-12-01

    Full Text Available Nitrogen availability and utilization by Saccharomyces cerevisiae significantly influence fermentation kinetics and the production of volatile compounds important for wine aroma. Amino acids are the most important nitrogen source and have been classified based on how well they support growth. This study evaluated the effect of single amino acids on growth kinetics and major volatile production of two phenotypically different commercial wine yeast strains in synthetic grape must. Four growth parameters, lag phase, maximum growth rate, total biomass formation and time to complete fermentation were evaluated. In contrast with previous findings, in fermentative conditions, phenylalanine and valine supported growth well and asparagine supported it poorly. The four parameters showed good correlations for most amino acid treatments, with some notable exceptions. Single amino acid treatments resulted in the predictable production of aromatic compounds, with a linear correlation between amino acid concentration and the concentration of aromatic compounds that are directly derived from these amino acids. With the increased complexity of nitrogen sources, linear correlations were lost and aroma production became unpredictable. However, even in complex medium minor changes in amino acid concentration continued to directly impact the formation of aromatic compounds, suggesting that the relative concentration of individual amino acids remains a predictor of aromatic outputs, independently of the complexity of metabolic interactions between carbon and nitrogen metabolism and between amino acid degradation and utilization pathways.

  6. Higgs production in association with a single top quark at the LHC.

    Science.gov (United States)

    Demartin, Federico; Maltoni, Fabio; Mawatari, Kentarou; Zaro, Marco

    We present a detailed study of Higgs boson production in association with a single top quark at the LHC, at next-to-leading order accuracy in QCD. We consider total and differential cross sections, at the parton level as well as by matching short distance events to parton showers, for both t -channel and s -channel production. We provide predictions relevant for the LHC at 13 TeV together with a thorough evaluation of the residual uncertainties coming from scale variation, parton distributions, strong coupling constant and heavy quark masses. In addition, for t -channel production, we compare results as obtained in the 4-flavour and 5-flavour schemes, pinning down the most relevant differences between them. Finally, we study the sensitivity to a non-standard-model relative phase between the Higgs couplings to the top quark and to the weak bosons.

  7. Estimating sensitivity and specificity of a PCR for boot socks to detect Campylobacter in broiler primary production using Bayesian latent class analysis

    DEFF Research Database (Denmark)

    Matt, Monika; Nordentoft, Steen; Ian, Kopacka

    2016-01-01

    The present study compares three different assays for sample collection and detection of Campylobacter spp. in broiler flocks, based on (i) the collection of faecal samples from intestinal organs (caecum), (ii) individual faecal droppings collected from the bedding and (iii) faecal material...... collected by socks placed on the outside of a pair of boots (boot socks) and used for walking around in the flock. The two first methods are examined for Campylobacter using a culture method (ISO-10272-2:2006), while the boot socks are tested using PCR. The PCR-assay is a genus specific multiplex PCR...... samples were collected at slaughter.The results were evaluated in the absence of a gold standard using a Bayesian latent class model. Austrian results showed higher sensitivity for PCR detection in sock samples (0.98; Bayesian credible interval (BCI) [0.93-1]) than for culture of faecal droppings (0...

  8. Measurement of single top quark production at D0 using a matrix element method

    Energy Technology Data Exchange (ETDEWEB)

    Mitrevski, Jovan Pavle [Columbia Univ., New York, NY (United States)

    2007-01-01

    Until now, the top quark has only been observed produced in pairs, by the strong force. According to the standard model, it can also be produced singly, via an electroweak interaction. Top quarks produced this way provide powerful ways to test the charged-current electroweak interactions of the top quark, to measure |Vtb|, and to search for physics beyond the standard model. This thesis describes the application of the matrix element analysis technique to the search for single top quark production with the D0 detector using 0.9 fb-1 of Run II data. From a comparison of the matrix element discriminants between data and the background model, assuming a Standard Model s-channel to t-channel cross section ratio of σst = 0.44, we measure the single top quark production cross section: σ(p$\\bar{p}$ → tb + X, tqb + X) = 4.8$-1.4\\atop{+1.6}$ pb. This result has a p-value of 0.08%, corresponding to a 3.2 standard deviation Gaussian equivalent significance.

  9. Single top quark production cross-section measurements using the ATLAS and CMS detectors at the LHC

    CERN Document Server

    Finelli, Kevin Daniel; The ATLAS collaboration

    2015-01-01

    Measurements of single top quark production in proton--proton collisions at 7 and 8 TeV using the ATLAS and CMS detectors at the LHC are presented. In the leading order process, a $W$ boson is exchanged in the $t$-channel. The single top quark and anti-top total production cross-sections ratio, as well as a measurement of the inclusive and fiducial production cross-sections are presented. In addition, a measurement of the production cross-section of a single top quark in association with a $W$ boson is presented. All measurements are compared to state-of-the-art theoretical calculations and the CKM matrix element $|V_{tb}|$ is determined. The $s$-channel production is also explored and limits on exotic production in single top quark processes are discussed. This includes the search for additional $W’$ bosons and a search for monotops.

  10. Detection of undeclared animal by-products in commercial canine canned foods: Comparative analyses by ELISA and PCR-RFLP coupled with slab gel electrophoresis or capillary gel electrophoresis.

    Science.gov (United States)

    Hsieh, Ming-Kun; Shih, Pei-Yin; Wei, Chia-Fong; Vickroy, Thomas W; Chou, Chi-Chung

    2016-03-30

    The potential presence of undeclared animal by-products in pet foods is not subject to routine examination. Previously published methods for species-based identification of animal by-products have not been used routinely owing to inconsistent results. The present study evaluated the utility of several approaches for accurate identification of animal by-products in 11 commercial brands of canine canned foods. Canine canned foods from several countries were analysed by ELISA, PCR-RFLP coupled with slab-gel electrophoresis (SGE) and capillary gel electrophoresis (CGE) to test for evidence of by-products derived from cattle, chicken, sheep or pig. While CGE-based analysis detected all (24) animal-derived by-products that were reported for the 11 test samples, SGE and ELISA detected only 22/24 (92%) and 14/24 (58%) of labelled by-products, respectively. In addition, undeclared animal by-products were found using all three analytical approaches with CGE detecting more positives (19) than SGE (17) or ELISA (5). Significant disparities were evident between the labelled contents and the detected content of animal by-products. CGE-based testing for PCR products appears to provide greater sensitivity and accuracy than either SGE or ELISA-based methods. As testing of commercial products becomes more reliable and mainstream, manufacturers will need to develop more thorough and accurate labelling protocols. © 2015 Society of Chemical Industry.

  11. A conceptual framework for economic optimization of single hazard surveillance in livestock production chains.

    Science.gov (United States)

    Guo, Xuezhen; Claassen, G D H; Oude Lansink, A G J M; Saatkamp, H W

    2014-06-01

    Economic analysis of hazard surveillance in livestock production chains is essential for surveillance organizations (such as food safety authorities) when making scientifically based decisions on optimization of resource allocation. To enable this, quantitative decision support tools are required at two levels of analysis: (1) single-hazard surveillance system and (2) surveillance portfolio. This paper addresses the first level by presenting a conceptual approach for the economic analysis of single-hazard surveillance systems. The concept includes objective and subjective aspects of single-hazard surveillance system analysis: (1) a simulation part to derive an efficient set of surveillance setups based on the technical surveillance performance parameters (TSPPs) and the corresponding surveillance costs, i.e., objective analysis, and (2) a multi-criteria decision making model to evaluate the impacts of the hazard surveillance, i.e., subjective analysis. The conceptual approach was checked for (1) conceptual validity and (2) data validity. Issues regarding the practical use of the approach, particularly the data requirement, were discussed. We concluded that the conceptual approach is scientifically credible for economic analysis of single-hazard surveillance systems and that the practicability of the approach depends on data availability. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. A study of wrong-sign single muon production in νμ-nucleon interaction

    International Nuclear Information System (INIS)

    Mishra, S.R.; Auchincloss, P.S.; Blair, R.; Haber, C.; Ruiz, M.; Oltman, E.; Sciulli, F.J.; Shaevitz, M.H.; Smith, W.H.; Merritt, F.S.; Oreglia, M.; Reutens, P.; Coleman, R.; Fisk, H.E.; Lamm, M.J.; Levinthal, D.; Yovanovitch, D.D.; Marsh, W.; Rapidis, P.A.; White, H.B.; Bodek, A.; Borcherding, F.; Giokaris, N.; Lang, K.; Stockdale, I.E.

    1989-01-01

    We report on a search for ν μ -induced events where the single emerging muon carries lepton number opposite that of the incident neutrino. The rate and kinematic quantities of the candidate events are compared with known backgrounds from anti ν μ -induced charged current interactions and ν-induced interactions that produce dileptons. We derive an upper limit on the rate of wrong-sign single muon production relative to the rate of ν μ charged current interactions to be 1.6x10 -4 for y -4 for y>0.5 (90% CL). These upper limits enable us to constrain exotic sources of wrong-sign muons such as the charm component of the nucleon sea, flavor changing neutral currents and lepton number violating processes. Finally, the rate and kinematic properties of these events are compared with those of the neutrino-induced opposite-sign dimuon events. (orig.)

  13. Measurement of top quark polarisation in $t$-channel single top quark production

    CERN Document Server

    Khachatryan, Vardan; Tumasyan, Armen; Adam, Wolfgang; Aşılar, Ece; Bergauer, Thomas; Brandstetter, Johannes; Brondolin, Erica; Dragicevic, Marko; Erö, Janos; Flechl, Martin; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Hartl, Christian; Hörmann, Natascha; Hrubec, Josef; Jeitler, Manfred; Knünz, Valentin; König, Axel; Krammer, Manfred; Krätschmer, Ilse; Liko, Dietrich; Matsushita, Takashi; Mikulec, Ivan; Rabady, Dinyar; Rahbaran, Babak; Rohringer, Herbert; Schieck, Jochen; Schöfbeck, Robert; Strauss, Josef; Treberer-Treberspurg, Wolfgang; Waltenberger, Wolfgang; Wulz, Claudia-Elisabeth; Mossolov, Vladimir; Shumeiko, Nikolai; Suarez Gonzalez, Juan; Alderweireldt, Sara; Cornelis, Tom; De Wolf, Eddi A; Janssen, Xavier; Knutsson, Albert; Lauwers, Jasper; Luyckx, Sten; Van De Klundert, Merijn; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Van Spilbeeck, Alex; Abu Zeid, Shimaa; Blekman, Freya; D'Hondt, Jorgen; Daci, Nadir; De Bruyn, Isabelle; Deroover, Kevin; Heracleous, Natalie; Keaveney, James; Lowette, Steven; Moreels, Lieselotte; Olbrechts, Annik; Python, Quentin; Strom, Derek; Tavernier, Stefaan; Van Doninck, Walter; Van Mulders, Petra; Van Onsem, Gerrit Patrick; Van Parijs, Isis; Barria, Patrizia; Brun, Hugues; Caillol, Cécile; Clerbaux, Barbara; De Lentdecker, Gilles; Fasanella, Giuseppe; Favart, Laurent; Grebenyuk, Anastasia; Karapostoli, Georgia; Lenzi, Thomas; Léonard, Alexandre; Maerschalk, Thierry; Marinov, Andrey; Perniè, Luca; Randle-conde, Aidan; Seva, Tomislav; Vander Velde, Catherine; Vanlaer, Pascal; Yonamine, Ryo; Zenoni, Florian; Zhang, Fengwangdong; Beernaert, Kelly; Benucci, Leonardo; Cimmino, Anna; Crucy, Shannon; Dobur, Didar; Fagot, Alexis; Garcia, Guillaume; Gul, Muhammad; Mccartin, Joseph; Ocampo Rios, Alberto Andres; Poyraz, Deniz; Ryckbosch, Dirk; Salva Diblen, Sinem; Sigamani, Michael; Tytgat, Michael; Van Driessche, Ward; Yazgan, Efe; Zaganidis, Nicolas; Basegmez, Suzan; Beluffi, Camille; Bondu, Olivier; Brochet, Sébastien; Bruno, Giacomo; Caudron, Adrien; Ceard, Ludivine; Da Silveira, Gustavo Gil; Delaere, Christophe; Favart, Denis; Forthomme, Laurent; Giammanco, Andrea; Hollar, Jonathan; Jafari, Abideh; Jez, Pavel; Komm, Matthias; Lemaitre, Vincent; Mertens, Alexandre; Musich, Marco; Nuttens, Claude; Perrini, Lucia; Pin, Arnaud; Piotrzkowski, Krzysztof; Popov, Andrey; Quertenmont, Loic; Selvaggi, Michele; Vidal Marono, Miguel; Beliy, Nikita; Hammad, Gregory Habib; Aldá Júnior, Walter Luiz; Alves, Fábio Lúcio; Alves, Gilvan; Brito, Lucas; Correa Martins Junior, Marcos; Hamer, Matthias; Hensel, Carsten; Mora Herrera, Clemencia; Moraes, Arthur; Pol, Maria Elena; Rebello Teles, Patricia; Belchior Batista Das Chagas, Ewerton; Carvalho, Wagner; Chinellato, Jose; Custódio, Analu; Melo Da Costa, Eliza; De Jesus Damiao, Dilson; De Oliveira Martins, Carley; Fonseca De Souza, Sandro; Huertas Guativa, Lina Milena; Malbouisson, Helena; Matos Figueiredo, Diego; Mundim, Luiz; Nogima, Helio; Prado Da Silva, Wanda Lucia; Santoro, Alberto; Sznajder, Andre; Tonelli Manganote, Edmilson José; Vilela Pereira, Antonio; Ahuja, Sudha; Bernardes, Cesar Augusto; De Souza Santos, Angelo; Dogra, Sunil; Tomei, Thiago; De Moraes Gregores, Eduardo; Mercadante, Pedro G; Moon, Chang-Seong; Novaes, Sergio F; Padula, Sandra; Romero Abad, David; Ruiz Vargas, José Cupertino; Aleksandrov, Aleksandar; Hadjiiska, Roumyana; Iaydjiev, Plamen; Rodozov, Mircho; Stoykova, Stefka; Sultanov, Georgi; Vutova, Mariana; Dimitrov, Anton; Glushkov, Ivan; Litov, Leander; Pavlov, Borislav; Petkov, Peicho; Ahmad, Muhammad; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Chen, Mingshui; Cheng, Tongguang; Du, Ran; Jiang, Chun-Hua; Plestina, Roko; Romeo, Francesco; Shaheen, Sarmad Masood; Spiezia, Aniello; Tao, Junquan; Wang, Chunjie; Wang, Zheng; Zhang, Huaqiao; Asawatangtrakuldee, Chayanit; Ban, Yong; Li, Qiang; Liu, Shuai; Mao, Yajun; Qian, Si-Jin; Wang, Dayong; Xu, Zijun; Avila, Carlos; Cabrera, Andrés; Chaparro Sierra, Luisa Fernanda; Florez, Carlos; Gomez, Juan Pablo; Gomez Moreno, Bernardo; Sanabria, Juan Carlos; Godinovic, Nikola; Lelas, Damir; Puljak, Ivica; Ribeiro Cipriano, Pedro M; Antunovic, Zeljko; Kovac, Marko; Brigljevic, Vuko; Kadija, Kreso; Luetic, Jelena; Micanovic, Sasa; Sudic, Lucija; Attikis, Alexandros; Mavromanolakis, Georgios; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Rykaczewski, Hans; Bodlak, Martin; Finger, Miroslav; Finger Jr, Michael; Abdelalim, Ahmed Ali; Awad, Adel; El Sawy, Mai; Mahrous, Ayman; Radi, Amr; Calpas, Betty

    2016-04-13

    A first measurement of the top quark spin asymmetry, sensitive to the top quark polarisation, in $t$-channel single top quark production is presented. It is based on a sample of pp collisions at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 19.7 fb$^{-1}$. A high-purity sample of $t$-channel single top quark events with an isolated muon is selected. Signal and background components are estimated using a fit to data. A differential cross section measurement, corrected for detector effects, of an angular observable sensitive to the top quark polarisation is performed. The differential distribution is used to extract a top quark spin asymmetry of 0.26 $\\pm$ 0.03 (stat) $\\pm$ 0.10 (syst), which is compatible with a $p$-value of 4.6% with the standard model prediction of 0.44.

  14. Single- and repeated-dose toxicities of aloe fermentation products in rats

    Science.gov (United States)

    Kim, Hyun-Kyoung; Baik, Soon-Ok; Choi, Soo-Young; Lee, Jae-Young

    2011-01-01

    In this study, aloe fermentation products were derived from mycelia from 3 mushrooms: Ganoderma lucidum (AG), Hericium erinaceum (AH), and Phellinus linteus (AP). Levels of aloin A and B increased with fermentation time. The highest levels were measured on the fifth day of fermentation. β-Glucan levels decreased with fermentation time. The safety of aloe fermentation products were examined in male and female Sprague-Dawley rats. Rats were orally administered the three aloe fermentation products at dose levels of 1, 2 or 5 g/kg for single-dose toxicity test and 0.5, 1, or 2 g/kg for repeated-dose toxicity test. There were no significant differences in body weight gain between vehicle control and AG-, AH- or AP-treated rats. Also, significant changes in daily feed intake and water consumption were not observed. In hematological analysis, none of the parameters were affected by aloe fermentation products with mushroom mycelia. This suggests that there are no negative effects on homeostasis and immunity. In blood biochemistry analysis, none of the markers were affected by feeding rats with AG, AH or AP. Similarly, there were no significant effects on markers for liver, kidney, skeletal and heart muscle functions. No remarkable lesions were observed in these organs at histopathology. Since there were no adverse effects of AG, AH and AP in single- or repeated-dose toxicity tests, even at higher doses than normal, we conclude that the aloe fermentation products with mushroom mycelia possess long-term safety and could be candidates as multifunctional nutrients for the improvement of intestinal function and immunity. PMID:21998613

  15. Application of Multiplex PCR for Detection and Differentiation of Entamoeba histolytica, Entamoeba dispar and Entamoeba moshkovskii.

    Directory of Open Access Journals (Sweden)

    Nozhat Zebardast

    2014-12-01

    Full Text Available Entamoeba moshkovskii and E. dispar are impossible to differentiate microscopically from the pathogenic species E. histolytica. Multiplex polymerase chain reaction (Multiplex PCR is a widespread molecular biology technique for amplification of multiple targets in a single PCR experiment.For detection and differentiation of the three-microscopy indistinguishable Entamoeba species in human, multiplex PCR assay using different DNA extraction methods was studied. A conserved forward primer was derived from the middle of the small-subunit rRNA gene, and reverse primers were designed from signature sequences specific to each of these three Entamoeba species.A 166-bp PCR product with E. histolytica DNA, a 580-bp product with E. moshkovskii DNA and a 752-bp product with E. dispar DNA were generated in a single-round and multiplex PCR reaction.We recommend this PCR assay as an accurate, rapid, and effective diagnostic method for the detection and discrimination of these three Entamoeba species in both routine diagnosis of amoebiasis and epidemiological surveys.

  16. Application of Created Restriction Site PCR-RFLP to Identify POT1 Gene Polymorphism.

    Science.gov (United States)

    Wang, Tuanwei; Wang, Sihua; Duan, Xiaoran; Feng, Xiaolei; Wang, Pengpeng; Yao, Wu; Wu, Yongjun; Feng, Feifei; Yu, Songcheng; Wu, Yiming; Wang, Wei

    2016-06-01

    Protection of telomeres protein 1 (POT1) plays pivotal roles in protection of chromosome ends and regulation of telomere length with other telomere binding proteins; its genetic polymorphisms are associated with many diseases. In this study, we explored a novel PCR-RFLP method for typing the single nucleotide polymorphism (SNP) rs1034794 of the human POT1 gene. A new restriction enzyme site was introduced into a POT1 gene amplification product by created restriction site PCR (CRS-PCR). One primer was designed based on changed sequence; after PCR amplification, a new restriction enzyme site for AluI was introduced into the PCR products. One hundred and seventy eight samples from Han Chinese individuals were tested to evaluate this new method. The 3'-end of the forward primer was next to the polymorphic site, and the third base from the 3'-end was the mismatched base A. The final PCR product contained the AGCT sequence (AluI recognition site) when the ancestral POT1 alleles were amplified. The data obtained with the new method perfectly matched those obtained with the sequencing method. Thus, CRS-PCR is a new low-cost and high-efficiency alternative for rs1034794 typing.

  17. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

    DEFF Research Database (Denmark)

    Kalle, Elena; Gulevich, Alexander; Rensing, Christopher Günther T

    2013-01-01

    . The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products.......In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur...... in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory...

  18. Electron reconstruction and calibration with single Z and W production in CMS at the LHC

    CERN Document Server

    Rovelli, Chiara

    2006-01-01

    The CMS experiment at the LHC is building an electromagnetic calorimeter with high performance. Preserving high reconstruction efficiency and best four momentum measurements for electrons is a necessity for optimal discovery prospects in the ZZ(*) and WW(*) Higgs boson decay channels. This is challenging in view of the material budget in front of ECAL and of the presence of a strong magnetic field. A new reconstruction strategy for electrons in CMS is described. The usage of electrons from single Z and W production for the ECAL calibration strategy is also discussed.

  19. High P{sub T} leptons and single W boson production at HERA

    Energy Technology Data Exchange (ETDEWEB)

    Korcsak-Gorzo, Katherine

    2010-12-15

    A search for isolated electrons and muons with high transverse momentum in events with large missing transverse momentum has been conducted. The results have been found to be compatible with the Standard Model expectations. The cross section for single W production has been measured and the total cross section in electron-proton collisions at HERA has been found to be {sigma}(ep {yields} eWX) = 0.93{sub -0.23}{sup +0.26}(stat.){+-}0.08(syst.) pb. The measurements are based on the complete available ZEUS data sets from the HERA I and II running periods taken between 1994-2007. (orig.)

  20. Threshold and jet radius joint resummation for single-inclusive jet production

    International Nuclear Information System (INIS)

    Liu, Xiaohui; Moch, Sven-Olaf; Ringer, Felix

    2017-08-01

    We present the first threshold and jet radius jointly resummed cross section for single-inclusive hadronic jet production. We work at next-to-leading logarithmic accuracy and our framework allows for a systematic extension beyond the currently achieved precision. Longstanding numerical issues are overcome by performing the resummation directly in momentum space within Soft Collinear Effective Theory. We present the first numerical results for the LHC and observe an improved description of the available data. Our results are of immediate relevance for LHC precision phenomenology including the extraction of parton distribution functions and the QCD strong coupling constant.

  1. Polymerase chain reaction methods (PCR in agrobiotechnology

    Directory of Open Access Journals (Sweden)

    Taški-Ajduković Ksenija

    2006-01-01

    Full Text Available The agricultural biotechnology applies polymerase chain reaction (PCR technology at numerous steps throughout product development. The major uses of PCR technology during product development include gene discovery and cloning, vector construction, transformant identification, screening and characterization as well as seed quality control. Commodity and food companies as well as testing laboratories rely on PCR technology to verify the presence or absence of genetically modification (GM in a product or to quantify the amount of GM material present in the product. This article describes the fundamental elements of PCR analysis and its application to the testing of grains and highlights some of areas to which attention must be paid in order to produce reliable test results. The article also discuses issues related to the analysis of different matrixes and the effect they may have on the accuracy of the PCR analytical results.

  2. Effective and Durable Co Single Atomic Cocatalysts for Photocatalytic Hydrogen Production.

    Science.gov (United States)

    Zhao, Qi; Yao, Weifeng; Huang, Cunping; Wu, Qiang; Xu, Qunjie

    2017-12-13

    This research reports for the first time that single cobalt atoms anchored in nitrogen-doped graphene (Co-NG) can serve as a highly effective and durable cocatalyst for visible light photocatalytic hydrogen production from water. Results show that, under identical conditions, the hydrogen production rate (1382 μmol/h) for 0.25 wt % Co-NG-loaded CdS photocatalyst (0.25 wt % Co-NG/CdS) is 3.42 times greater than that of nitrogen-doped graphene (NG) loaded CdS photocatalyst (NG/CdS) and about 1.3 times greater than the greatest hydrogen production rate (1077 μmol/h) for 1.5 wt % Pt nanoparticle loaded CdS photocatalyst (1.5 wt % Pt-NPs/CdS). At 420 nm irradiation, the quantum efficiency of the 0.25 wt % Co-NG/CdS photocatalyst is 50.5%, the highest efficiency among those literature-reported non-noble metal cocatalysts. The Co-NG/CdS nanocomposite-based photocatalyst also has an extended durability. No activity decline was detected during three cyclic photocatalytic life span tests. The very low cocatalyst loading, along with the facile preparation technology for this non-noble metal cocatalyst, will significantly reduce the hydrogen production costs and finally lead to the commercialization of the solar catalytic hydrogen production process. Based on experimental results, we conclude that Co-NG can successfully replace noble metal cocatalysts as a highly effective and durable cocatalyst for renewable solar hydrogen production. This finding will point to a new way for the development of highly effective, long life span, non-noble metal-based cocatalysts for renewable and cost-effective hydrogen production.

  3. Blockade of leukotriene production by a single oral dose of MK-0591 in active ulcerative colitis

    DEFF Research Database (Denmark)

    Hillingsø, Jens; Kjeldsen, J; Laursen, L S

    1995-01-01

    -ethyl)thio)-5(quinolin+ ++-2ylmethyl-oxy)-1H-indol-2yl)-2,2-dimethyl-propanoate) exerts its effect by binding to the 5-lipoxygenase activating protein, thereby inhibiting the translocation and activation of 5-lipoxygenase. METHODS: Concentrations of leukotriene B4 (LTB4) and prostaglandin E2 (PGE2) in rectal...... that a single oral 250 mg dose of MK-0591 results in nearly complete blockade of systemic leukotriene production and LTB4 formation in the target tissue of inflammation (the rectum). Controlled multiple-dose trials to assess the clinical efficacy of this novel 5-lipoxygenase-activating protein inhibitor seem......BACKGROUND: 5-Lipoxygenase products of arachidonic acid metabolism are thought to play a central role in the secondary amplification of the inflammatory response in a number of human inflammatory diseases, such as ulcerative colitis. MK-0591 (3-(1((4-chlorophenyl)methyl)-3((1,1-dimethyl...

  4. Charge-odd and single-spin effects in two pion production in ep bar collisions

    International Nuclear Information System (INIS)

    Galynskij, M.V.; Kuraev, E.A.; Shajkhatdenov, B.G.; Ratcliffe, P.G.

    2000-01-01

    We consider two-photon and Bremsstrahlung mechanisms for the production of two charged pions in high-energy electron (proton) scattering off a transversely polarised proton. Interference between the relevant amplitudes generates a charge-odd contribution to the cross section for the process. In a kinematics with a jet moving along electron spin-independent part may be used for determination of phase differences for pion-pion scattering in the states with orbital momentum 0 or 2 and 1 whereas in a kinematics with a jet moving along proton spin-dependent part may be used to explain the experimental data for single-spin correlations in the production of negatively charged pions. We also discuss the backgrounds and estimate the accuracy of the results at less than 10% level. In addition simplified formulae derived for specific kinematics, with small total transverse pion momentum, are given

  5. An analysis on single and central diffractive heavy flavour production at hadron colliders

    Energy Technology Data Exchange (ETDEWEB)

    Machado, M.V.T. [Universidade Federal do Pampa, Bage, RS (Brazil). Centro de Ciencias Exatas e Tecnologicas

    2008-09-15

    In this contribution results from a phenomenological analysis for the diffractive hadroproduction of heavy flavors at high energies are reported. Diffractive production of charm, bottom and top are calculated using the Regge factorization, taking into account recent experimental determination of the diffractive parton density functions in Pomeron by the H1 Collaboration at DESY-HERA. In addition, multiple-Pomeron corrections are considered through the rapidity gap survival probability factor. We give numerical predictions for single diffractive as well as double Pomeron exchange (DPE) cross sections, which agree with the available data for diffractive production of charm and beauty. We make estimates which could be compared to future measurements at the LHC. (author)

  6. Simulation, Control and Optimization of Single Cell Protein Production in a U-Loop Reactor

    DEFF Research Database (Denmark)

    Engoulevent, Franck Guillaume; Jørgensen, John Bagterp

    2012-01-01

    In 2011, the world population passed 7 billions inhabitants. While this number witnesses the success of humankind on earth, it also rises among other things questions about food supply. Declining live stock in the wild, rising price of energy combined with climatic change give a new economic...... potential for alternative sources of protein production. Single cell protein (SCP) is protein produced by growth of micro organisms. Among these micro organisms, Methylococcus Capsulatus is particular interesting as it can grow on either methane or methanol and contains 70% protein. The U-Loop reactor...... report simulation results. In addition we design and compare dierent regulatory control systems for regulation of SCP production in the U-Loop reactor. The purpose of the regulatory control systems is to keep the process at a steady state and to reject disturbances. We design and implement such control...

  7. Evidence for s-channel single top quark production at D0

    CERN Multimedia

    CERN. Geneva

    2013-01-01

    We present the measurements of the cross sections for the two main production modes of single top quarks at the Tevatron with 9.7/fb of data collected by the D0 detector. The analysis employs three different multivariate techniques which are combined to extract the small signal from the large backgrounds in the W+jets final state. We measure independently the t-channel (tqb) and the s-channel (tb), and obtain a lower limit on the CKM matrix element |Vtb|>0.92 at 95% CL. The results are compared with physics beyond the SM. The presence of the s-channel production is established in the D0 data with a significance of more than 3 standard deviations for the first time.

  8. Measurement of muon neutrino and antineutrino induced single neutral pion production cross sections

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Colin E. [Yale Univ., New Haven, CT (United States)

    2011-05-01

    Elucidating the nature of neutrino oscillation continues to be a goal in the vanguard of the efforts of physics experiment. As neutrino oscillation searches seek an increasingly elusive signal, a thorough understanding of the possible backgrounds becomes ever more important. Measurements of neutrino-nucleus interaction cross sections are key to this understanding. Searches for νμ → νe oscillation - a channel that may yield insight into the vanishingly small mixing parameter θ13, CP violation, and the neutrino mass hierarchy - are particularly susceptible to contamination from neutral current single π0 (NC 1π0) production. Unfortunately, the available data concerning NC 1π0 production are limited in scope and statistics. Without satisfactory constraints, theoretical models of NC 1π0 production yield substantially differing predictions in the critical Eν ~ 1 GeV regime. Additional investigation of this interaction can ameliorate the current deficiencies. The Mini Booster Neutrino Experiment (MiniBooNE) is a short-baseline neutrino oscillation search operating at the Fermi National Accelerator Laboratory (Fermilab). While the oscillation search is the principal charge of the MiniBooNE collaboration, the extensive data (~ 106 neutrino events) offer a rich resource with which to conduct neutrino cross section measurements. This work concerns the measurement of both neutrino and antineutrino NC 1π0 production cross sections at MiniBooNE. The size of the event samples used in the analysis exceeds that of all other similar experiments combined by an order of magnitude. We present the first measurements of the absolute NC 1π0 cross section as well as the first differential cross sections in both neutrino and antineutrino mode. Specifically, we measure single differential cross sections with respect to pion momentum and pion angle. We find the

  9. A one-step, triplex, real-time RT-PCR assay for the simultaneous detection of enterovirus 71, coxsackie A16 and pan-enterovirus in a single tube.

    Science.gov (United States)

    Zhang, Shiyin; Wang, Jin; Yan, Qiang; He, Shuizhen; Zhou, Wenbin; Ge, Shengxiang; Xia, Ningshao

    2014-01-01

    The recent, ongoing epidemic of hand, foot, and mouth disease (HFMD), which is caused by enterovirus infection, has affected millions of children and resulted in thousands of deaths in China. Enterovirus 71 (EV71) and coxsackie A16 (CA16) are the two major distinct pathogens for HFMD. However, EV71 is more commonly associated with neurologic complications and even fatalities. Therefore, simultaneously detecting and differentiating EV71 and CA16 specifically from other enteroviruses for diagnosing HFMD is important. Here, we developed a one-step, triplex, real-time RT-PCR assay for the simultaneous detection of EV71, CA16, and pan-enterovirus (EVs) in a single tube with an internal amplification control. The detection results for the serially diluted viruses indicate that the lower limit of detection for this assay is 0.001-0.04 TCID50/ml, 0.02 TCID50/ml, and 0.001 TCID50/ml for EVs, EV71, and CA16, respectively. After evaluating known HFMD virus stocks of 17 strains of 16 different serotypes, this assay showed a favorable detection spectrum and no obvious cross-reactivity. The results for 141 clinical throat swabs from HFMD-suspected patients demonstrated sensitivities of 98.4%, 98.7%, and 100% for EVs, EV71, and CA16, respectively, and 100% specificity for each virus. The application of this one-step, triplex, real-time RT-PCR assay in clinical units will contribute to HFMD surveillance and help to identify causative pathogen in patients with suspected HFMD.

  10. A one-step, triplex, real-time RT-PCR assay for the simultaneous detection of enterovirus 71, coxsackie A16 and pan-enterovirus in a single tube.

    Directory of Open Access Journals (Sweden)

    Shiyin Zhang

    Full Text Available The recent, ongoing epidemic of hand, foot, and mouth disease (HFMD, which is caused by enterovirus infection, has affected millions of children and resulted in thousands of deaths in China. Enterovirus 71 (EV71 and coxsackie A16 (CA16 are the two major distinct pathogens for HFMD. However, EV71 is more commonly associated with neurologic complications and even fatalities. Therefore, simultaneously detecting and differentiating EV71 and CA16 specifically from other enteroviruses for diagnosing HFMD is important. Here, we developed a one-step, triplex, real-time RT-PCR assay for the simultaneous detection of EV71, CA16, and pan-enterovirus (EVs in a single tube with an internal amplification control. The detection results for the serially diluted viruses indicate that the lower limit of detection for this assay is 0.001-0.04 TCID50/ml, 0.02 TCID50/ml, and 0.001 TCID50/ml for EVs, EV71, and CA16, respectively. After evaluating known HFMD virus stocks of 17 strains of 16 different serotypes, this assay showed a favorable detection spectrum and no obvious cross-reactivity. The results for 141 clinical throat swabs from HFMD-suspected patients demonstrated sensitivities of 98.4%, 98.7%, and 100% for EVs, EV71, and CA16, respectively, and 100% specificity for each virus. The application of this one-step, triplex, real-time RT-PCR assay in clinical units will contribute to HFMD surveillance and help to identify causative pathogen in patients with suspected HFMD.

  11. PCR-RFLP

    African Journals Online (AJOL)

    2012-03-30

    Mar 30, 2012 ... The. cpDNA PCR-RFLP based genetic distance (GD) among 30 tea accessions ranged from 0 to 0.071, with the mean of 0.049. This study suggests that the optimization system was suitable for PCR-RFLP analysis of. cpDNA in tea. Key words: Camellia sinensis, PCR-RFLP, chloroplast DNA, establishment.

  12. Quantification of ochratoxin A-producing molds in food products by SYBR Green and TaqMan real-time PCR methods

    DEFF Research Database (Denmark)

    Rodríguez, Alicia; Rodríguez, Mar; Luque, M. Isabel

    2011-01-01

    Ochratoxin A (OTA) is a mycotoxin synthesized by a variety of different fungi, most of them from the genera Penicillium and Aspergillus. Early detection and quantification of OTA producing species is crucial to improve food safety. In the present work, two protocols of real-time qPCR based on SYBR...... 1 and 10 conidia/g for SYBR Green assay and TaqMan. No significant differences were found between the Ct values obtained from pure mold DNA and pure mold DNA mixed with food DNA. The ability of the designed qPCR methods to quantify two known conidial suspensions inoculated on several foods...... was evaluated. The amount of conidia assessed by both qPCR methods was close to the inoculated amount for most foods and indicates that the described procedure holds potential for use for the detection and quantification of OTA producing molds in foods....

  13. COMPARATIVE PRODUCTION OF SINGLE CELL PROTEIN FROM FISH PROTEIN ISOLATE WASTAGE AND ULTRA FILTERED CHEESE WHEY

    Directory of Open Access Journals (Sweden)

    Soroush Haghighi-Manesh

    2013-02-01

    Full Text Available Fish protein isolate wastage and ultra filtered cheese whey were used as substrates for fermentation by Kluyveromyces marxianus to produce single cell protein, under batch and aerobic condition in which pH and temperature were adjusted to 4.5 and 35°C. The produced biomass was analyzed for protein content in different periods of time during fermentation. About 82% and 75% of total protein was produced in the first 18 h of 96 h fermentation of ultra filtered cheese whey and protein isolate wastage respectively, which can be an indication of the exponential phase of the yeast growth. The results of biomass yield measurements during 96 h process also confirm this finding. Moreover, since ultra filtered cheese whey was higher in single cell protein yield, solubility, water holding capacity, water absorption and power of biological and chemical oxygen demand reduction, and also was lower in foam overrun and stability than fish protein isolate wastage, it was selected as the suitable substrate for single cell protein production.

  14. Single cell protein production of Chlorella sp. using food processing waste as a cultivation medium

    Science.gov (United States)

    Putri, D.; Ulhidayati, A.; Musthofa, I. A.; Wardani, A. K.

    2018-03-01

    The aim of this study was to investigate the effect of various food processing wastes on the production of single cell protein by Chlorella sp. Three various food processing wastes i.e. tofu waste, tempeh waste and cheese whey waste were used as cultivation medium for Chlorella sp. growth. Sea water was used as a control of cultivation medium. The addition of waste into cultivation medium was 10%, 20%, 30%, 40%, and 50%. The result showed that the highest yield of cell mass and protein content was found in 50% tofu waste cultivation medium was 47.8 × 106 cell/ml with protein content was 52.24%. The 50% tofu waste medium showed improved cell yield as nearly as 30% than tempeh waste medium. The yield of biomass and protein content when 30% tempeh waste was used as cultivation medium was 37.1 × 106 cell/ml and 52%, respectively. Thus, food processing waste especially tofu waste would be a promising candidate for cultivation medium for single cell production from Chlorella sp. Moreover, the utilization of waste can reduce environmental pollution and increase protein supply for food supplement or animal feed.

  15. Indirect Regulation of Endogenous Glucose Production by Insulin: The Single Gateway Hypothesis Revisited.

    Science.gov (United States)

    Bergman, Richard N; Iyer, Malini S

    2017-07-01

    On the basis of studies that investigated the intraportal versus systemic insulin infusion and transendothelial transport of insulin, we proposed the "single gateway hypothesis," which supposes an indirect regulation of hepatic glucose production by insulin; the rate-limiting transport of insulin across the adipose tissue capillaries is responsible for the slow suppression of free fatty acids (FFAs), which in turn is responsible for delayed suppression of hepatic endogenous glucose production (EGP) during insulin infusion. Preventing the fall in plasma FFAs during insulin infusion either by administering intralipids or by inhibiting adipose tissue lipolysis led to failure in EGP suppression, thus supporting our hypothesis. More recently, mice lacking hepatic Foxo1 in addition to Akt1 and Akt2 (L-AktFoxo1TKO), all required for insulin signaling, surprisingly showed normal glycemia. Inhibiting the fall of plasma FFAs in these mice prevented the suppression of EGP during a clamp, reaffirming that the site of insulin action to control EGP is extrahepatic. Measuring whole-body turnover rates of glucose and FFAs in L-AktFoxo1TKO mice also confirmed that hepatic EGP was regulated by insulin-mediated control of FFAs. The knockout mouse model in combination with sophisticated molecular techniques confirmed our physiological findings and the single gateway hypothesis. © 2017 by the American Diabetes Association.

  16. Single-Particle Tracking of Human Immunodeficiency Virus Type 1 Productive Entry into Human Primary Macrophages.

    Science.gov (United States)

    Li, Qin; Li, Wei; Yin, Wen; Guo, Jia; Zhang, Zhi-Ping; Zeng, Dejun; Zhang, Xiaowei; Wu, Yuntao; Zhang, Xian-En; Cui, Zongqiang

    2017-04-25

    Macrophages are one of the major targets of human immunodeficiency virus (HIV-1), but the viral entry pathway remains poorly understood in these cells. Noninvasive virus labeling and single-virus tracking are effective tools for studying virus entry. Here, we constructed a quantum dot (QD)-encapsulated infectious HIV-1 particle to track viral entry at a single-particle level in live human primary macrophages. QDs were encapsulated in HIV-1 virions by incorporating viral accessory protein Vpr-conjugated QDs during virus assembly. With the HIV-1 particles encapsulating QDs, we monitored the early phase of viral infection in real time and observed that, during infection, HIV-1 was endocytosed in a clathrin-mediated manner; the particles were translocated into Rab5A-positive endosomes, and the core was released into the cytoplasm by viral envelope-mediated endosomal fusion. Drug inhibition assays verified that endosome fusion contributes to HIV-1 productive infection in primary macrophages. Additionally, we observed that a dynamic actin cytoskeleton is critical for HIV-1 entry and intracellular migration in primary macrophages. HIV-1 dynamics and infection could be blocked by multiple different actin inhibitors. Our study revealed a productive entry pathway in macrophages that requires both endosomal function and actin dynamics, which may assist in the development of inhibitors to block the HIV entry in macrophages.

  17. Comparison of single-word and adjective-noun phrase production using event-related brain potentials

    DEFF Research Database (Denmark)

    Lange, Violaine Michel

    2015-01-01

    in a time-window extending beyond early visual analysis. In a second experiment, different participants were asked to produce either single noun or adjective-noun dual-word phrases to black-and-white and coloured line drawings, respectively. Adjective-noun phrase production (2W) resulted in naming latencies...... stimuli varying in complexity -black and white line drawings, coloured line drawings, and arrays of drawings-in participants producing single nouns. Whilst naming latencies were similar for single noun production between visual stimuli conditions, ERPs differed between drawing arrays and single drawings...... 53 msec longer than single noun (1W) production. Waveform amplitude and topographic analyses carried out on stimulus- and response-aligned ERPs indicated that the two conditions differed in a late time-window, with a topographic pattern for 2W lasting from 300 to 480 msec after picture presentation...

  18. A Ribeiroia spp. (Class: Trematoda) - Specific PCR-based diagnostic

    Science.gov (United States)

    Reinitz, David M.; Yoshino, T.P.; Cole, Rebecca A.

    2007-01-01

    Increased reporting of amphibian malformations in North America has been noted with concern in light of reports that amphibian numbers and species are declining worldwide. Ribeiroia ondatrae has been shown to cause a variety of types of malformations in amphibians. However, little is known about the prevalence of R. ondatrae in North America. To aid in conducting field studies of Ribeiroia spp., we have developed a polymerase chain reaction (PCR)-based diagnostic. Herein, we describe the development of an accurate, rapid, simple, and cost-effective diagnostic for detection of Ribeiroia spp. infection in snails (Planorbella trivolvis). Candidate oligonucleotide primers for PCR were designed via DNA sequence analyses of multiple ribosomal internal transcribed spacer-2 regions from Ribeiroia spp. and Echinostoma spp. Comparison of consensus sequences determined from both genera identified areas of sequence potentially unique to Ribeiroia spp. The PCR reliably produced a diagnostic 290-base pair (bp) product in the presence of a wide concentration range of snail or frog DNA. Sensitivity was examined with DNA extracted from single R. ondatrae cercaria. The single-tube PCR could routinely detect less than 1 cercariae equivalent, because DNA isolated from a single cercaria could be diluted at least 1:50 and still yield a positive result via gel electrophoresis. An even more sensitive nested PCR also was developed that routinely detected 100 fg of the 290-bp fragment. The assay did not detect furcocercous cercariae of certain Schistosomatidae, Echinostoma sp., or Sphaeridiotrema globulus nor adults of Clinostomum sp. or Cyathocotyle bushiensis. Field testing of 137 P. trivolvis identified 3 positives with no overt environmental cross-reactivity, and results concurred with microscopic examinations in all cases. ?? American Society of Parasitologists 2007.

  19. Determining stocks and flows of structural wood products in single family homes in the United States between 1950 and 2010

    DEFF Research Database (Denmark)

    Sianchuk, Robert A.; McFarlane, Paul N.; Ackom, Emmanuel

    2012-01-01

    The stocks and flows of six major structural wood products (SWPs)-lumber, plywood, oriented strand board [OSB], glue laminated timber, I-joists, and laminated veneer lumber (LVL)-in US single family homes were modeled from 1950 to 2010. The consumption of these products in US single family homes......, modern SWPs, such as I-joists, LVL, and OSB, have replaced lumber and plywood products. The needs of the US single family housing industry have been met by a smaller mass of SWPs per unit area constructed. The mass of SWP present in construction wastes was influenced strongly by building cycles....... Production of construction waste peaked in 2005, when 3.31 million tonnes of SWPs were produced by 1.72 million single family housing starts. It diminished to 0.874 million tonnes of SWPs as the housing starts fell to 445,000 in 2009. In contrast, the mass of demolition wastes produced was affected...

  20. Single top-quark production cross-section and properties using the ATLAS detector at the LHC

    Directory of Open Access Journals (Sweden)

    Chegwidden Andrew M.

    2016-01-01

    Full Text Available ATLAS measurements of single top-quark processes are summarised. Measurements using data recorded at the LHC proton-proton collider at centre-of-mass energies of √s=7 TeV and 8 TeV are presented. The measurements are performed using the semi-leptonic decay mode of the top quark. Production cross-sections for the t-channel and Wt modes of single top-quark production and the extraction of the CKM matrix element |Vtb| are shown. All measurements are compared to theoretical calculations. In addition, the s-channel production mode is explored along with limits on exotic production modes.

  1. Development of a novel approach for the production of dried genomic DNA for use as standards for qualitative PCR testing of food-borne pathogens

    DEFF Research Database (Denmark)

    Trapmann, S.; Catalani, P.; Hoorfar, Jeffrey

    2004-01-01

    , Campylobacter jejuni and Yersinia enterocolitica were used to produce genomic DNA (gDNA). These preparations gave support to method development for qualitative polymerase chain reaction (PCR) detection methods for food-borne pathogens. Purified gDNA was transformed into stable and dry gDNA by using...

  2. Low-cost, real-time, continuous flow PCR system for pathogen detection.

    Science.gov (United States)

    Fernández-Carballo, B Leticia; McGuiness, Ian; McBeth, Christine; Kalashnikov, Maxim; Borrós, Salvador; Sharon, Andre; Sauer-Budge, Alexis F

    2016-04-01

    In this paper, we present a portable and low cost point-of-care (POC) PCR system for quantitative detection of pathogens. Our system is based on continuous flow PCR which maintains fixed temperatures zones and pushes the PCR solution between two heated areas allowing for faster heat transfer and as a result, a faster PCR. The PCR system is built around a 46.0 mm × 30.9 mm × 0.4 mm disposable thermoplastic chip. In order to make the single-use chip economically viable, it was manufactured by hot embossing and was designed to be compatible with roll-to-roll embossing for large scale production. The prototype instrumentation surrounding the chip includes two heaters, thermal sensors, and an optical system. The optical system allows for pathogen detection via real time fluorescence measurements. FAM probes were used as fluorescent reporters of the amplicons generated during the PCR. To demonstrate the function of the chip, two infectious bacteria targets were selected: Chlamydia trachomatis and Escherichia coli O157:H7. For both bacteria, the limit of detection of the system was determined, PCR efficiencies were calculated, and different flow velocities were tested. We have demonstrated successful detection for these two bacterial pathogens highlighting the versatility and broad utility of our portable, low-cost, and rapid PCR diagnostic device.

  3. Chirality-Controlled Growth of Single-Wall Carbon Nanotubes Using Vapor Phase Epitaxy: Mechanistic Understanding and Scalable Production

    Science.gov (United States)

    2016-09-15

    AFRL-AFOSR-VA-TR-2016-0319 Chirality-Controlled Growth of Single -Wall Carbon Nanotubes Using Vapor Phase Epitaxy: Mechanistic Understanding and...controlled growth of single -wall carbon nanotubes using vapor phase epitaxy: mechanistic understanding and scalable production FA9550-14-1-0115 Zhou...controlled synthesis of single -wall carbon nanotubes. Firstly, we have successfully demonstrated a vapor-phase-epitaxy-analogous general strategy for

  4. Observation of the production of a W boson in association with a single charm quark.

    Science.gov (United States)

    Aaltonen, T; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Appel, J A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Auerbach, B; Aurisano, A; Azfar, F; Badgett, W; Bae, T; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauce, M; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Bland, K R; Blumenfeld, B; Bocci, A; Bodek, A; Bortoletto, D; Boudreau, J; Boveia, A; Brigliadori, L; Bromberg, C; Brucken, E; Budagov, J; Burkett, K; Busetto, G; Bussey, P; Butti, P; Buzatu, A; Calamba, A; Camarda, S; Campanelli, M; Canelli, F; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Cho, K; Chou, J P; Chokheli, D; Clark, A; Clarke, C; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Cremonesi, M; Cuevas, J; Culbertson, R; d'Ascenzo, N; Datta, M; Demortier, L; Deninno, M; Devoto, F; d'Errico, M; Di Canto, A; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dorigo, M; Driutti, A; Ebina, K; Edgar, R; Elagin, A; Erbacher, R; Errede, S; Esham, B; Eusebi, R; Farrington, S; Fernández Ramos, J P; Field, R; Flanagan, G; Forrest, R; Franklin, M; Freeman, J C; Funakoshi, Y; Garfinkel, A F; Garosi, P; Gerberich, H; Gerchtein, E; Giagu, S; Giakoumopoulou, V; Gibson, K; Ginsburg, C M; Giokaris, N; Giromini, P; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldin, D; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González López, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gramellini, E; Grinstein, S; Grosso-Pilcher, C; Group, R C; Guimaraes da Costa, J; Hahn, S R; Han, J Y; Happacher, F; Hara, K; Hare, M; Harr, R F; Harrington-Taber, T; Hatakeyama, K; Hays, C; Heinrich, J; Herndon, M; Hocker, A; Hopkins, W; Hou, S; Hughes, R E; Hurwitz, M; Husemann, U; Huston, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Junk, T R; Kambeitz, M; Kamon, T; Karchin, P E; Kasmi, A; Kato, Y; Ketchum, W; Keung, J; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kim, Y J; Kimura, N; Kirby, M; Klimenko, S; Knoepfel, K; Kondo, K; Kong, D J; Konigsberg, J; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Kruse, M; Kuhr, T; Kurata, M; Kwang, S; Laasanen, A T; Lammel, S; Lancaster, M; Lannon, K; Latino, G; Lee, H S; Lee, J S; Leone, S; Lewis, J D; Limosani, A; Lipeles, E; Liu, H; Liu, Q; Liu, T; Lockwitz, S; Loginov, A; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; Madrak, R; Maestro, P; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Martínez, M; Matera, K; Mattson, M E; Mazzacane, A; Mazzanti, P; McNulty, R; Mehta, A; Mehtala, P; Mesropian, C; Miao, T; Mietlicki, D; Mitra, A; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M J; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakano, I; Napier, A; Nett, J; Neu, C; Nigmanov, T; Nodulman, L; Noh, S Y; Norniella, O; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Ortolan, L; Pagliarone, C; Palencia, E; Palni, P; Papadimitriou, V; Parker, W; Pauletta, G; Paulini, M; Paus, C; Phillips, T J; Piacentino, G; Pianori, E; Pilot, J; Pitts, K; Plager, C; Pondrom, L; Poprocki, S; Potamianos, K; Prokoshin, F; Pranko, A; Ptohos, F; Punzi, G; Ranjan, N; Redondo Fernández, I; Renton, P; Rescigno, M; Riddick, T; Rimondi, F; Ristori, L; Robson, A; Rodriguez, T; Rolli, S; Ronzani, M; Roser, R; Rosner, J L; Ruffini, F; Ruiz, A; Russ, J; Rusu, V; Safonov, A; Sakumoto, W K; Sakurai, Y; Santi, L; Sato, K; Saveliev, V; Savoy-Navarro, A; Schlabach, P; Schmidt, E E; Schwarz, T; Scodellaro, L; Seidel, S; Seiya, Y; Semenov, A; Sforza, F; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shochet, M; Shreyber-Tecker, I; Simonenko, A; Sinervo, P; Sliwa, K; Smith, J R; Snider, F D; Sorin, V; Song, H; Stancari, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Sudo, Y; Sukhanov, A; Suslov, I; Takemasa, K; Takeuchi, Y; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thomson, E; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Trovato, M; Ukegawa, F; Uozumi, S; Vázquez, F; Velev, G; Vellidis, C; Vernieri, C; Vidal, M; Vilar, R; Vizán, J; Vogel, M; Volpi, G; Wagner, P; Wallny, R; Wang, S M; Warburton, A; Waters, D; Wester, W C; Whiteson, D; Wicklund, A B; Wilbur, S; Williams, H H; Wilson, J S; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, H; Wright, T; Wu, X; Wu, Z; Yamamoto, K; Yamato, D; Yang, T; Yang, U K; Yang, Y C; Yao, W-M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Zanetti, A M; Zeng, Y; Zhou, C; Zucchelli, S

    2013-02-15

    The first observation of the production of a W boson with a single charm quark (c) jet in pp[over ¯] collisions at √s=1.96  TeV is reported. The analysis uses data corresponding to 4.3  fb(-1), recorded with the CDF II detector at the Fermilab Tevatron. Charm quark candidates are selected through the identification of an electron or muon from charm-hadron semileptonic decay within a hadronic jet, and a Wc signal is observed with a significance of 5.7 standard deviations. The production cross section σ(Wc)(p(Tc)>20  GeV/c,|η(c)|quark-mixing matrix element V(cs) is derived, |V(cs)|=1.08±0.16 along with a lower limit of |V(cs)|>0.71 at the 95% confidence level, assuming that the Wc production through c to s quark coupling is dominant.

  5. Search for Single Top Quark Production in ep Collisions at HERA

    CERN Document Server

    Aktas, A.; Anthonis, T.; Asmone, A.; Babaev, A.; Backovic, S.; Bahr, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Baumgartner, S.; Becker, J.; Beckingham, M.; Behnke, O.; Behrendt, O.; Belousov, A.; Berger, C.; Berndt, T.; Bizot, J.C.; Bohme, J.; Boenig, M.O.; Boudry, V.; Bracinik, J.; Braunschweig, W.; Brisson, V.; Broker, H.B.; Brown, D.P.; Bruncko, D.; Busser, F.W.; Bunyatyan, A.; Buschhorn, G.; Bystritskaya, L.; Campbell, A.J.; Caron, S.; Cassol-Brunner, F.; Chekelian, V.; Clarke, D.; Collard, C.; Contreras, J.G.; Coppens, Y.R.; Coughlan, J.A.; Cousinou, M.C.; Cox, B.E.; Cozzika, G.; Cvach, J.; Dainton, J.B.; Dau, W.D.; Daum, K.; Delcourt, B.; Delerue, N.; Demirchyan, R.; De Roeck, A.; De Wolf, E.A.; Diaconu, C.; Dingfelder, J.; Dodonov, V.; Dowell, J.D.; Dubak, A.; Duprel, C.; Eckerlin, Guenter; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Ellerbrock, M.; Elsen, E.; Erdmann, M.; Erdmann, W.; Faulkner, P.J.W.; Favart, L.; Fedotov, A.; Felst, R.; Ferencei, J.; Fleischer, M.; Fleischmann, P.; Fleming, Y.H.; Flucke, G.; Flugge, G.; Fomenko, A.; Foresti, I.; Formanek, J.; Franke, G.; Frising, G.; Gabathuler, E.; Gabathuler, K.; Garvey, J.; Gassner, J.; Gayler, Joerg; Gerhards, R.; Gerlich, C.; Ghazaryan, Samvel; Goerlich, L.; Gogitidze, N.; Gorbounov, S.; Grab, C.; Grabski, V.; Grassler, H.; Greenshaw, T.; Gregori, M.; Grindhammer, Guenter; Haidt, D.; Hajduk, L.; Haller, J.; Heinzelmann, G.; Henderson, R.C.W.; Henschel, H.; Henshaw, O.; Heremans, R.; Herrera, G.; Herynek, I.; Hildebrandt, M.; Hiller, K.H.; Hladky, J.; Hoting, P.; Hoffmann, D.; Horisberger, R.; Hovhannisyan, A.; Ibbotson, M.; Jacquet, M.; Janauschek, L.; Janssen, X.; Jemanov, V.; Jonsson, L.; Johnson, C.; Johnson, D.P.; Jung, H.; Kant, D.; Kapichine, M.; Karlsson, M.; Katzy, J.; Keil, F.; Keller, N.; Kennedy, J.; Kenyon, I.R.; Kiesling, Christian M.; Klein, M.; Kleinwort, C.; Kluge, T.; Knies, G.; Koblitz, B.; Kolya, S.D.; Korbel, V.; Kostka, P.; Koutouev, R.; Kropivnitskaya, A.; Kroseberg, J.; Kueckens, J.; Kuhr, T.; Landon, M.P.J.; Lange, W.; Lastovicka, T.; Laycock, P.; Lebedev, A.; Leissner, B.; Lemrani, R.; Lendermann, V.; Levonian, S.; List, B.; Lobodzinska, E.; Loktionova, N.; Lopez-Fernandez, R.; Lubimov, V.; Lueders, H.; Luders, S.; Luke, D.; Lytkin, L.; Makankine, A.; Malden, N.; Malinovski, E.; Mangano, S.; Marage, P.; Marks, J.; Marshall, R.; Martyn, H.U.; Martyniak, J.; Maxfield, S.J.; Meer, D.; Mehta, A.; Meier, K.; Meyer, A.B.; Meyer, H.; Meyer, J.; Michine, S.; Mikocki, S.; Milstead, D.; Moreau, F.; Morozov, A.; Morozov, I.; Morris, J.V.; Muller, K.; Murin, P.; Nagovizin, V.; Naroska, B.; Naumann, J.; Naumann, T.; Newman, Paul R.; Niebergall, F.; Niebuhr, C.; Nikitin, D.; Nowak, G.; Nozicka, M.; Olivier, B.; Olsson, J.E.; Ossoskov, G.; Ozerov, D.; Pascaud, C.; Patel, G.D.; Peez, M.; Perez, E.; Petrukhin, A.; Pitzl, D.; Poschl, R.; Povh, B.; Raicevic, N.; Rauschenberger, J.; Reimer, P.; Reisert, B.; Risler, C.; Rizvi, E.; Robmann, P.; Roosen, R.; Rostovtsev, A.; Rusakov, S.; Rybicki, K.; Sankey, D.P.C.; Sauvan, E.; Schatzel, S.; Scheins, J.; Schilling, F.P.; Schleper, P.; Schmidt, S.; Schmitt, S.; Schneider, M.; Schoeffel, L.; Schoning, A.; Schroder, V.; Schultz-Coulon, H.C.; Schwanenberger, C.; Sedlak, K.; Sefkow, F.; Sheviakov, I.; Shtarkov, L.N.; Sirois, Y.; Sloan, T.; Smirnov, P.; Soloviev, Y.; South, D.; Spaskov, V.; Specka, Arnd E.; Spitzer, H.; Stamen, R.; Stella, B.; Stiewe, J.; Strauch, I.; Straumann, U.; Thompson, Graham; Thompson, P.D.; Tomasz, F.; Traynor, D.; Truoel, Peter; Tsipolitis, G.; Tsurin, I.; Turnau, J.; Turney, J.E.; Tzamariudaki, E.; Uraev, A.; Urban, Marcel; Usik, A.; Valkar, S.; Valkarova, A.; Vallee, C.; Van Mechelen, P.; Vargas Trevino, A.; Vassiliev, S.; Vazdik, Y.; Veelken, C.; Vest, A.; Vichnevski, A.; Vinokurova, S.; Volchinski, V.; Wacker, K.; Wagner, J.; Waugh, B.; Weber, G.; Weber, R.; Wegener, D.; Werner, C.; Werner, N.; Wessels, M.; Wessling, B.; Winde, M.; Winter, G.G.; Wissing, C.; Woehrling, E.E.; Wunsch, E.; Zacek, J.; Zalesak, J.; Zhang, Z.; Zhokin, A.; Zomer, F.; zur Nedden, M.

    2004-01-01

    A search for single top quark production is performed in e^\\pm p collisions at HERA. The search exploits data corresponding to an integrated luminosity of 118.3 pb^-1. A model for the anomalous production of top quarks in a flavour changing neutral current process involving a t-u-gamma coupling is investigated. Decays of top quarks into a b quark and a W boson are considered in the leptonic and the hadronic decay channels of the W. Both a cut-based analysis and a multivariate likelihood analysis are performed to discriminate anomalous top quark production from Standard Model background processes. In the leptonic channel, 5 events are found while 1.31 \\pm 0.22 events are expected from the Standard Model background. In the hadronic channel, no excess above the expectation for Standard Model processes is found. These observations lead to a cross section \\sigma (ep -> e t X) = 0.29 +0.15 -0.14 pb at \\sqrt{s} = 319 GeV. Alternatively, assuming that the observed events are due to a statistical fluctuation, upper li...

  6. (PCR) for direct cloning of blunt-end DNA fragments

    African Journals Online (AJOL)

    Administrator

    2011-09-19

    Sep 19, 2011 ... interest by PCR using proof reading DNA polymerase, such as Pfu, KOD and Primerstar, is preferred since the. PCR products with a higher degree of fidelity are required in many investigations. However, traditional blunt-end cloning method for direct cloning of blunt-end PCR products is not efficient since ...

  7. Detection of SEA-type α-thalassemia in embryo biopsies by digital PCR.

    Science.gov (United States)

    Lee, Ta-Hsien; Hsu, Ya-Chiung; Chang, Chia Lin

    2017-08-01

    Accurate and efficient pre-implantation genetic diagnosis (PGD) based on the analysis of single or oligo-cells is needed for timely identification of embryos that are affected by deleterious genetic traits in in vitro fertilization (IVF) clinics. Polymerase chain reaction (PCR) is the backbone of modern genetic diagnoses, and a spectrum of PCR-based techniques have been used to detect various thalassemia mutations in prenatal diagnosis (PND) and PGD. Among thalassemias, SEA-type α-thalassemia is the most common variety found in Asia, and can lead to Bart's hydrops fetalis and serious maternal complications. To formulate an efficient digital PCR for clinical diagnosis of SEA-type α-thalassemia in cultured embryos, we conducted a pilot study to detect the α-globin and SEA-type deletion alleles in blastomere biopsies with a highly sensitive microfluidics-based digital PCR method. Genomic DNA from embryo biopsy samples were extracted, and crude DNA extracts were first amplified by a conventional PCR procedure followed by a nested PCR reaction with primers and probes that are designed for digital PCR amplification. Analysis of microfluidics-based PCR reactions showed that robust signals for normal α-globin and SEA-type deletion alleles, together with an internal control gene, can be routinely generated using crude embryo biopsies after a 10 6 -fold dilution of primary PCR products. The SEA-type deletion in cultured embryos can be sensitively diagnosed with the digital PCR procedure in clinics. The adoption of this robust PGD method could prevent the implantation of IVF embryos that are destined to develop Bart's hydrops fetalis in a timely manner. The results also help inform future development of a standard digital PCR procedure for cost-effective PGD of α-thalassemia in a standard IVF clinic. Copyright © 2017. Published by Elsevier B.V.

  8. Contaminations Occurring in Fungal PCR Assays

    Science.gov (United States)

    Loeffler, Juergen; Hebart, Holger; Bialek, Ralf; Hagmeyer, Lars; Schmidt, Diethard; Serey, Francois-Prâseth; Hartmann, Matthias; Eucker, Jan; Einsele, Hermann

    1999-01-01

    Successful in vitro amplification of fungal DNA in clinical specimens has been reported recently. In a collaboration among five European centers, the frequency and risk of contamination due to airborne spore inoculation or carryover contamination in fungal PCR were analyzed. The identities of all contaminants were specified by cycle sequencing and GenBank analysis. Twelve of 150 PCR assays that together included over 2,800 samples were found to be contaminated (3.3% of the negative controls were contaminated during the DNA extraction, and 4.7% of the PCR mixtures were contaminated during the amplification process). Contaminants were specified as Aspergillus fumigatus, Saccharomyces cerevisiae, and Acremonium spp. Further analysis showed that commercially available products like zymolyase powder or 10× PCR buffer may contain fungal DNA. In conclusion, the risk of contamination is not higher in fungal PCR assays than in other diagnostic PCR-based assays if general precautions are taken. PMID:10074553

  9. Rapid diagnosis of aneuploidy using segmental duplication quantitative fluorescent PCR.

    Directory of Open Access Journals (Sweden)

    Xiangdong Kong

    Full Text Available The aim of this study was use a simple and rapid procedure, called segmental duplication quantitative fluorescent polymerase chain reaction (SD-QF-PCR, for the prenatal diagnosis of fetal chromosomal aneuploidies. This method is based on the co-amplification of segmental duplications located on two different chromosomes using a single pair of fluorescent primers. The PCR products of different sizes were subsequently analyzed through capillary electrophoresis, and the aneuploidies were determined based on the relative dosage between the two chromosomes. Each primer set, containing five pairs of primers, was designed to simultaneously detect aneuploidies located on chromosomes 21, 18, 13, X and Y in a single reaction. We applied these two primer sets to DNA samples isolated from individuals with trisomy 21 (n = 36; trisomy 18 (n = 6; trisomy 13 (n = 4; 45, X (n = 5; 47, XXX (n = 3; 48, XXYY (n = 2; and unaffected controls (n = 40. We evaluated the performance of this method using the karyotyping results. A correct and unambiguous diagnosis with 100% sensitivity and 100% specificity, was achieved for clinical samples examined. Thus, the present study demonstrates that SD-QF-PCR is a robust, rapid and sensitive method for the diagnosis of common aneuploidies, and these analyses can be performed in less than 4 hours for a single sample, providing a competitive alternative for routine use.

  10. Off-shell single-top production at NLO matched to parton showers

    Energy Technology Data Exchange (ETDEWEB)

    Frederix, R. [Physik Department T31, Technische Universität München,James-Franck-Str. 1, D-85748 Garching (Germany); Frixione, S. [INFN - Sezione di Genova,Via Dodecaneso 33, I-16146, Genoa (Italy); Papanastasiou, A.S. [Cavendish Laboratory, University of Cambridge,J.J. Thomson Avenue, CB3 0HE, Cambridge (United Kingdom); Prestel, S. [SLAC National Accelerator Laboratory,2575 Sand Hill Road, Menlo Park, CA 94025-7090 (United States); Torrielli, P. [Dipartimento di Fisica, Università di Torino and INFN - Sezione di Torino,Via P. Giuria 1, I-10125, Turin (Italy)

    2016-06-06

    We study the hadroproduction of a Wb pair in association with a light jet, focusing on the dominant t-channel contribution and including exactly at the matrix-element level all non-resonant and off-shell effects induced by the finite top-quark width. Our simulations are accurate to the next-to-leading order in QCD, and are matched to the HERWIG6 and PYTHIA8 parton showers through the MC@NLO method. We present phenomenological results relevant to the 8 TeV LHC, and carry out a thorough comparison to the case of on-shell t-channel single-top production. We formulate our approach so that it can be applied to the general case of matrix elements that feature coloured intermediate resonances and are matched to parton showers.

  11. Evidence for production of single top quarks and first direct measurement of |Vtb|

    Energy Technology Data Exchange (ETDEWEB)

    Abazov, V.M.; Abbott, B.; Abolins, M.; Acharya, B.S.; Adams, M.; Adams, T.; Aguilo, E.; Ahn, S.H.; Ahsan, M.; Alexeev, G.D.; Alkhazov, G.; /Buenos Aires U. /Rio de

    2006-12-01

    The D0 Collaboration presents first evidence for the production of single top quarks at the Fermilab Tevatron p{bar p} collider. Using a 0.9 fb{sup -1} dataset, we apply a multivariate analysis to separate signal from background and measure {sigma}(p{bar p} {yields} tb + X, tqb + X) = 4.9 {+-} 1.4 pb. The probability to measure a cross section at this value or higher in the absence of signal is 0.035%, corresponding to a 3.4 standard deviation significance. We use the cross section measurement to directly determine the CKM matrix element that describes the W tb coupling and find 0.68 < |V{sub tb}| {le} 1 at 95% C.L.

  12. Search for s-channel single top-quark production in pp collisions

    CERN Document Server

    Merola, Mario

    2015-01-01

    A search for single top-quark production in the s channel in proton-proton collisions at a centre-of-mass energy of 8 TeV by the CMS detector at the LHC is presented. Leptonic decay modes of the top quark with an electron or muon in the final state are considered. The signal is extracted by performing a maximum-likelihood fit to the distribution of a multivariate discriminant defined using Boosted Decision Trees to separate the expected signal contribution from the background processes. Data collected in 2012, corresponding to an integrated luminosity of 19.3 / fb, lead to an upper limit on the cross section times branching ratio of 11.5 pb at 95pct confidence level.

  13. Measuring the WWγ vertex in single W production at ep colliders

    International Nuclear Information System (INIS)

    Baur, U.; Zeppenfeld, D.

    1989-01-01

    A detailed analysis of single W production in ep collisions via ep→eW ± X is presented by using helicity amplitudes for general WWγ couplings. Analytic expressions are given for the γq→W ± q' helicity amplitudes which describe ep→eWX in the Weizsaecker-Williams approximation and provide a semiquantitative understanding of the results obtained with the full matrix elements. Possibilities to test the gauge theory structure of the WWγ vertex at HERA (√s=314 GeV) and at an ep collider in the LEP tunnel (√s≅1.4 TeV) are explored. It is found that at HERA the WWγ vertex can be measured with 30-50% accuracy after a few years of running. (orig.)

  14. Study of KS0 pair production in single-tag two-photon collisions

    Science.gov (United States)

    Masuda, M.; Uehara, S.; Watanabe, Y.; Adachi, I.; Ahn, J. K.; Aihara, H.; Al Said, S.; Asner, D. M.; Atmacan, H.; Aulchenko, V.; Aushev, T.; Ayad, R.; Babu, V.; Badhrees, I.; Bansal, V.; Behera, P.; Berger, M.; Bhardwaj, V.; Bhuyan, B.; Biswal, J.; Bondar, A.; Bonvicini, G.; Bozek, A.; Bračko, M.; Červenkov, D.; Chen, A.; Cheon, B. G.; Chilikin, K.; Cho, K.; Choi, Y.; Choudhury, S.; Cinabro, D.; Czank, T.; Dash, N.; Di Carlo, S.; Doležal, Z.; Drásal, Z.; Dutta, D.; Eidelman, S.; Epifanov, D.; Fast, J. E.; Ferber, T.; Fulsom, B. G.; Garg, R.; Gaur, V.; Gabyshev, N.; Garmash, A.; Gelb, M.; Giri, A.; Goldenzweig, P.; Guido, E.; Haba, J.; Hayasaka, K.; Hayashii, H.; Hedges, M. T.; Hou, W.-S.; Iijima, T.; Inami, K.; Inguglia, G.; Ishikawa, A.; Itoh, R.; Iwasaki, M.; Iwasaki, Y.; Jacobs, W. W.; Jaegle, I.; Jin, Y.; Joo, K. K.; Julius, T.; Kang, K. H.; Karyan, G.; Kawasaki, T.; Kichimi, H.; Kiesling, C.; Kim, D. Y.; Kim, H. J.; Kim, J. B.; Kim, K. T.; Kim, S. H.; Kodyš, P.; Kotchetkov, D.; Križan, P.; Kroeger, R.; Krokovny, P.; Kulasiri, R.; Kuzmin, A.; Kwon, Y.-J.; Lee, I. S.; Lee, S. C.; Li, L. K.; Li, Y.; Li Gioi, L.; Libby, J.; Liventsev, D.; Lubej, M.; Luo, T.; Matsuda, T.; Matvienko, D.; Merola, M.; Miyabayashi, K.; Miyata, H.; Mizuk, R.; Mohanty, G. B.; Moon, H. K.; Mori, T.; Mussa, R.; Nakao, M.; Nakazawa, H.; Nanut, T.; Nath, K. J.; Natkaniec, Z.; Nayak, M.; Niiyama, M.; Nisar, N. K.; Nishida, S.; Ogawa, S.; Okuno, S.; Ono, H.; Onuki, Y.; Pakhlov, P.; Pakhlova, G.; Pal, B.; Park, H.; Paul, S.; Pedlar, T. K.; Pestotnik, R.; Piilonen, L. E.; Ritter, M.; Rostomyan, A.; Russo, G.; Sakai, Y.; Salehi, M.; Sandilya, S.; Santelj, L.; Sanuki, T.; Savinov, V.; Schneider, O.; Schnell, G.; Schwanda, C.; Seidl, R.; Seino, Y.; Senyo, K.; Seon, O.; Sevior, M. E.; Shebalin, V.; Shen, C. P.; Shibata, T.-A.; Shimizu, N.; Shiu, J.-G.; Shwartz, B.; Sokolov, A.; Solovieva, E.; Starič, M.; Strube, J. F.; Sumihama, M.; Sumiyoshi, T.; Takizawa, M.; Tamponi, U.; Tanida, K.; Tenchini, F.; Teramoto, Y.; Uchida, M.; Uglov, T.; Unno, Y.; Uno, S.; Urquijo, P.; Van Hulse, C.; Varner, G.; Vinokurova, A.; Vorobyev, V.; Vossen, A.; Wang, B.; Wang, C. H.; Wang, M.-Z.; Wang, P.; Wang, X. L.; Watanabe, M.; Widmann, E.; Won, E.; Ye, H.; Yuan, C. Z.; Yusa, Y.; Zakharov, S.; Zhang, Z. P.; Zhilich, V.; Zhukova, V.; Zhulanov, V.; Zupanc, A.; Belle Collaboration

    2018-03-01

    We report a measurement of the cross section for KS0 pair production in single-tag two-photon collisions, γ*γ →KS0KS0, for Q2 up to 30 GeV2 , where Q2 is the negative of the invariant mass squared of the tagged photon. The measurement covers the kinematic range 1.0 GeV total energy and kaon scattering angle, respectively, in the γ*γ center-of-mass system. These results are based on a data sample of 759 fb-1 collected with the Belle detector at the KEKB asymmetric-energy e+e- collider. For the first time, the transition form factor of the f2'(1525 ) meson is measured separately for the helicity-0, -1, and -2 components and also compared with theoretical calculations. We have derived the cross section for the process for W total.

  15. Production of multi-, oligo- and single-pore membranes using a continuous ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Apel, P.Yu., E-mail: apel@nrmail.jinr.ru [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Dubna International University, Universitetskaya Str. 19, 141980 Dubna (Russian Federation); Ivanov, O.M.; Lizunov, N.E.; Mamonova, T.I.; Nechaev, A.N. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Olejniczak, K. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation); Faculty of Chemistry, Nicolaus Copernicus University, Gagarina Str. 7, 87-100 Torun (Poland); Vacik, J. [Nuclear Physics Institute, ASCR, v.v.i., 25068 Řež (Czech Republic); Dmitriev, S.N. [Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 141980 Dubna (Russian Federation)

    2015-12-15

    Ion track membranes (ITM) have attracted significant interest over the past two decades due to their numerous applications in physical, biological, chemical, biochemical and medical experimental works. A particular feature of ITM technology is the possibility to fabricate samples with a predetermined number of pores, including single-pore membranes. The present report describes a procedure that allowed for the production of multi-, oligo- and single-pore membranes using a continuous ion beam from an IC-100 cyclotron. The beam was scanned over a set of small diaphragms, from 17 to ∼1000 μm in diameter. Ions passed through the apertures and impinged two sandwiched polymer foils, with the total thickness close to the ion range in the polymer. The foils were pulled across the ion beam at a constant speed. The ratio between the transport speed and the scanning frequency determined the distance between irradiation spots. The beam intensity and the aperture diameters were adjusted such that either several, one or no ions passed through the diaphragms during one half-period of scanning. After irradiation, the lower foil was separated from the upper foil and was etched to obtain pores 6–8 μm in diameter. The pores were found using a color chemical reaction between two reagents placed on opposite sides of the foil. The located pores were further confirmed using SEM and optical microscopy. The numbers of tracks in the irradiation spots were consistent with the Poisson statistics. Samples with single or few tracks obtained in this way were employed to study fine phenomena in ion track nanopores.

  16. Detection of seven virulence and toxin genes of Campylobacter jejuni isolates from Danish turkeys by PCR and cytolethal distending toxin production of the isolates

    DEFF Research Database (Denmark)

    Bang, Dang Duong; Borck, Birgitte; Nielsen, Eva Møller

    2004-01-01

    A total of 117 Campylobacter jejuni isolates from Danish turkeys were tested for the presence of seven virulence and toxin genes by PCR. One hundred seventeen (100%) isolates were positive for flaA, cadF, and ceuE gene primers. One hundred three (88%) isolates were positive for cdt gene cluster PCR.......7%) in Colon 205 assays, and 109 (93.2%) in chicken embryo cell assays. The CDT titers were determined in Vero cell assays. Of 117 isolates, 50 (42.7%) produced a CDT titer of 1:100, 29 (24.8%) of 1:50, and 27 (23%) of 1:5 to 1:10; 8 (6.8%) produced a CDT titer at undiluted supernatants and 3 (2.6%) produced...

  17. Real-Time PCR Detection of Paenibacillus spp. in Raw Milk To Predict Shelf Life Performance of Pasteurized Fluid Milk Products

    OpenAIRE

    Ranieri, Matthew L.; Ivy, Reid A.; Mitchell, W. Robert; Call, Emma; Masiello, Stephanie N.; Wiedmann, Martin; Boor, Kathryn J.

    2012-01-01

    Psychrotolerant sporeformers, specifically Paenibacillus spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While Paenibacillus spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of Paenibacillus spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect...

  18. An expanded nuclear phylogenomic PCR toolkit for Sapindales1

    Science.gov (United States)

    Collins, Elizabeth S.; Gostel, Morgan R.; Weeks, Andrea

    2016-01-01

    Premise of the study: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Methods and Results: Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16–90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Conclusions: Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation. PMID:28101434

  19. An expanded nuclear phylogenomic PCR toolkit for Sapindales.

    Science.gov (United States)

    Collins, Elizabeth S; Gostel, Morgan R; Weeks, Andrea

    2016-12-01

    We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba . On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16-90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation.

  20. External PCR, ASN's decision

    International Nuclear Information System (INIS)

    Anon.

    2012-01-01

    The French law imposes in some situations the presence of a person skilled in radiation protection (PCR). This article describes the cases when this person must belong to the staff of the enterprise or when this person may be sub-contracted. For instance in most nuclear facilities the PCR must be on the payroll, for enterprises dedicated to nuclear transport the PCR's job can be sub-contracted. A decision given by the ASN (French Nuclear Safety Authority) sets the minimal requests (in terms of training, job contract, activities) of the sub-contracted PCR. (A.C.)

  1. Single Top quark production via W-gluon fusion at LHC.Simulation with PYTHIA 5.7 Event Generator

    CERN Document Server

    Ahmedov, A; Kukhtin, V V; Mehdiyev, R; Metreveli, Z V; Salihagic, D

    1999-01-01

    The electroweak production of single top quarks via so-called W-gluon fusion in proton-proton interactions at sqrt(s)=14 TeV has been studied. Single Top quark production cross sections have been calculated. Simulations of the top quark production in W-gluon fusion process with further decay to Wb -> l nu b final state and of the corresponding backgrounds have been performed. The use of several kinematical distributions allowed to suppress backgrounds and to perform the reconstruction of the mass of the e - nu - jet system.

  2. Sensitivity evaluation of a single-step PCR assay using Ehrlichia canis p28 gene as a target and its application in diagnosis of canine ehrlichiosis Avaliação da sensibilidade da PCR em uma etapa com base no gene p28 de Ehrlichia canis e sua aplicação no diagnóstico da erliquiose canina

    Directory of Open Access Journals (Sweden)

    Andrea Cristina Higa Nakaghi

    2010-06-01

    Full Text Available The aim of this study was to optimize a PCR assay that amplifies an 843 pb fragment from the p28 gene of Ehrlichia canis and compare it with two other PCR methods used to amplify portions of the 16S rRNA and dsb genes of Ehrlichia. Blood samples were collected from dogs suspected of having a positive diagnosis for canine ehrlichiosis. Amplification of the p28 gene by PCR produced an 843-bp fragment and this assay could detect DNA from one gene copy among 1 billion cells. All positive samples detected by the p28-based PCR were also positive by the 16S rRNA nested-PCR and also by the dsb-based PCR. Among the p28-based PCR negative samples, 55.3% were co-negatives, but 27.6% were positive in 16S rRNA and dsb based PCR assays. The p28-based PCR seems to be a useful test for the molecular detection of E. canis, however improvements in this PCR sensitivity are desired, so that it can become an important alternative in the diagnosis of canine ehrlichiosis.O objetivo deste estudo foi aperfeiçoar um ensaio de PCR que amplificasse um fragmento de 843 pares de bases do gene p28 da Ehrlichia canis e compará-lo com outros dois métodos de PCR utilizados para amplificar partes do gene 16S rRNA e dsb do gênero Ehrlichia. Amostras sanguíneas foram colhidas de cães com diagnóstico clínico de erliquiose. A amplificação do gene p28 pela PCR produziu um fragmento de 843pb e esse ensaio permitiu a detecção do DNA de um parasita dentre 1 bilhão de células. Todas as amostras positivas detectadas pela PCR baseada no gene p28 foram também positivas pela nested PCR para detecção do gene 16S rRNA e também pela PCR dsb. Dentre as amostras negativas para a PCR p28, 55,3% foram co-negativas, mas 27,6% foram positivas pela PCR baseada nos genes 16S rRNA e dsb. A PCR p28 parece ser um teste útil para detecção molecular de E. canis, entretanto otimizações na sensibilidade nesta PCR são necessárias, para que esta técnica se torne uma importante

  3. Experimental study on productivity of modified single-basin solar still with a flat plate absorber

    Science.gov (United States)

    Ramanathan, V.; Kanimozhi, B.; Bhojwani, V. K.

    2017-05-01

    Solar still is an apparatus which uses solar energyto producedistilled water from saline water. This can be used in remote areas effectively wherein electricity is not available. The output from a conventional single basin solar still is found to be very low. Hence research is required to increase the productivity of the conventional solar still. This work is an attempt to increase the productivity of solar still. A flat mica plate is embedded in the conventional solar still to augment evaporation of the water from the input saline water. The flat plate absorber is placed in such a way that it is parallel to the glass cover of the solar still so as to maximize the absorption of solar radiations. By this modification, the maximum temperature of the absorber plate achieved was 95°C in comparison to 67°C of the conventional solar still. Experimental results of modified solar still were compared with conventional solar still. It was found that distillate output increased by 25% with a flat plate absorber when compared to conventional still.

  4. Single-pion production in pp collisions at 0.95 GeV/c (II)

    International Nuclear Information System (INIS)

    Abd El-Samad, S.; Bilger, R.; Clement, H.; Dietrich, M.; Doroshkevich, E.; Ehrhardt, K.; Erhardt, A.; Kress, J.; Meier, R.; Wagner, G.J.; Weidlich, U.; Zhang, G.; Brinkmann, K.T.; Freiesleben, H.; Jaekel, R.; Jakob, B.; Karsch, L.; Kuhlmann, E.; Schulte-Wissermann, M.; Sun, G.Y.; Dshemuchadse, S.; Eyrich, W.; Hauffe, J.; Schroeder, W.; Stinzing, F.; Waechter, J.; Wagner, M.; Wirth, S.; Filippi, A.; Marcello, S.; Fritsch, M.; Geyer, R.; Gillitzer, A.; Hesselbarth, D.; Kilian, K.; Marwinski, S.; Morsch, H.P.; Ritman, J.; Roderburg, E.; Moeller, K.; Naumann, L.; Schoenmeier, P.; Wilms, A.

    2009-01-01

    The single-pion production reactions pp→dπ + , pp→npπ + and pp→ppπ 0 were measured at a beam momentum of 0.95GeV/c (T p ∼400 MeV) using the short version of the COSY-TOF spectrometer. The central calorimeter provided particle identification, energy determination and neutron detection in addition to time-of-flight and angle measurements from other detector parts. Thus all pion production channels were recorded with 1-4 overconstraints. The main emphasis is put on the presentation and discussion of the npπ + channel, since the results on the other channels have already been published previously. The total and differential cross-sections obtained are compared to theoretical calculations. In contrast to the ppπ 0 channel we observe in the npπ + channel a strong influence of the Δ excitation. In particular, the pion angular distribution exhibits a (3 cos 2 Θ+1)-dependence, typical for a pure s-channel Δ excitation and identical to that observed in the dπ + channel. Since the latter is understood by a s-channel resonance in the 1 D 2 pn partial wave, we discuss an analogous scenario for the pnπ + channel. (orig.)

  5. Four-jet production in single- and double-parton scattering within high-energy factorization

    Energy Technology Data Exchange (ETDEWEB)

    Kutak, Krzysztof; Maciula, Rafal; Serino, Mirko [The H. Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences,Radzikowskiego 152, 31-342 Kraków (Poland); Szczurek, Antoni [The H. Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences,Radzikowskiego 152, 31-342 Kraków (Poland); Faculty of Mathematics and Natural Sciences, University of Rzeszów,ul. Pigonia 1, 35-310 Rzeszów (Poland); Hameren, Andreas van [The H. Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences,Radzikowskiego 152, 31-342 Kraków (Poland)

    2016-04-28

    We perform a first study of 4-jet production in a complete high-energy factorization (HEF) framework. We include and discuss contributions from both single-parton scattering (SPS) and double-parton scattering (DPS). The calculations are performed for kinematical situations relevant for two experimental measurements (ATLAS and CMS) at the LHC. We compare our results to those reported by the ATLAS and CMS collaborations for different sets of kinematical cuts. The results of the HEF approach are compared with their counterparts for collinear factorization. For symmetric cuts the DPS HEF result is considerably smaller than the one obtained with collinear factorization. The mechanism leading to this difference is of kinematical nature. We conclude that an analysis of inclusive 4-jet production with asymmetric p{sub T}-cuts below 50 GeV would be useful to enhance the DPS contribution relative to the SPS contribution. In contrast to the collinear approach, the HEF approach nicely describes the distribution of the ΔS variable, which involves all four jets and their angular correlations.

  6. Enhancement of in vitro interleukin-2 production in normal subjects following a single spinal manipulative treatment

    Directory of Open Access Journals (Sweden)

    Harris Glen M

    2008-05-01

    Full Text Available Abstract Background Increasing evidence supports somato-visceral effects of manual therapies. We have previously demonstrated that a single spinal manipulative treatment (SMT accompanied by audible release has an inhibitory effect on the production of proinflammatory cytokines in asymptomatic subjects. The purpose of this study is to report on SMT-related changes in the production of the immunoregulatory cytokine interleukin 2 (IL-2 and to investigate whether such changes might differ with respect to the treatment approach related to the presence or absence of an audible release (joint cavitation. Methods Of 76 asymptomatic subjects, 29 received SMT with cavitation (SMT-C, 23 were treated with SMT without cavitation (SMT-NC and 24 comprised the venipuncture control (VC group. The SMT-C and SMT-NC subjects received a single, similar force high velocity low amplitude manipulation, in the upper thoracic spine. However, in SMT-NC subjects, positioning and line of drive were not conducive to cavitation. Blood and serum samples were obtained before and then at 20 and 120 min post-intervention. The production of IL-2 in peripheral blood mononuclear cell cultures was induced by activation for 48 hr with Staphylococcal protein A (SPA and, in parallel preparations, with the combination of phorbol ester (TPA and calcium ionophore. The levels of IL-2 in culture supernatants and serum were assessed by specific immunoassays. Results Compared with VC and their respective baselines, SPA-induced secretion of IL-2 increased significantly in cultures established from both SMT-C and SMT-NC subjects at 20 min post-intervention. At 2 hr post-treatment, significant elevation of IL-2 synthesis was still apparent in preparations from SMT-treated groups though it became somewhat attenuated in SMT-NC subjects. Conversely, IL-2 synthesis induced by TPA and calcium ionophore was unaltered by either type of SMT and was comparable to that in VC group at all time points. No

  7. High-resolution melting PCR assay, applicable for diagnostics and screening studies, allowing detection and differentiation of several Babesia spp. infecting humans and animals

    OpenAIRE

    Rozej-Bielicka, Wioletta; Masny, Aleksander; Golab, Elzbieta

    2017-01-01

    The goal of the study was to design a single tube PCR test for detection and differentiation of Babesia species in DNA samples obtained from diverse biological materials. A multiplex, single tube PCR test was designed for amplification of approximately 400 bp region of the Babesia 18S rRNA gene. Universal primers were designed to match DNA of multiple Babesia spp. and to have low levels of similarity to DNA sequences of other intracellular protozoa and Babesia hosts. The PCR products amplifie...

  8. Towards the production of reliable quantitative microbiological data for risk assessment: Direct quantification of Campylobacter in naturally infected chicken fecal samples using selective culture and real-time PCR

    DEFF Research Database (Denmark)

    Garcia Clavero, Ana Belén; Vigre, Håkan; Josefsen, Mathilde Hasseldam

    2015-01-01

    Poultry has been identified as a significant source for human campylobacteriosis which constitutes an important zoonosis and public health problem in many areas of the world. Rapid, direct and accurate quantification of Campylobacter in poultry is essential for the assessment of public health risks...... and for the evaluation of control strategies implemented in poultry production. The aim of this study was to compare estimates of the numbers of Campylobacter spp. in naturally infected chicken fecal samples obtained using direct quantification by selective culture and by real-time PCR. Absolute quantification...... of Campylobacter by real-time PCR was performed using standard curves designed for two different DNA extraction methods: Easy-DNA™ Kit from Invitrogen (Easy-DNA) and NucliSENS® MiniMAG® from bioMérieux (MiniMAG). Results indicated that the estimation of the numbers of Campylobacter present in chicken fecal samples...

  9. Carboplatin enhances the production and persistence of radiation-induced DNA single-strand breaks

    International Nuclear Information System (INIS)

    Yang, L.; Douple, E.B.; O'Hara, J.A.; Wang, H.J.

    1995-01-01

    Fluorometric analysis of DNA unwinding and alkaline elution were used to investigate the production and persistence of DNA single-strand breaks (SSBs) in Chinese hamster V79 and xrs-5 cells treated with the chemotherapeutic agent carboplatin in combination with radiation. Carboplatin was administered to cells before irradiation in hypoxic conditions, or the drug was added immediately after irradiation during the postirradiation recovery period in air. The results of DNA unwinding studies suggest that carboplatin enhances the production of radiation-induced SSBs in hypoxic V79 cells and xrs-5 cells by a factor of 1.86 and 1.83, respectively, when combined with radiation compared to the SSBs produced by irradiation alone. Carboplatin alone did not produce a measureable number of SSBs. Alkaline elution profiles also indicated that the rate of elution of SSBs was higher in cells treated with the carboplatin is present after irradiation and during the postirradiation recovery period, the rejoining of radiation-induced SSBs by a factor of 1.46 in V79 cells with 20 Gy irradiation and by a factor of 2.02 in xrs-5 cells with 20 Gy irradiation. When carboplatin is present after irradiation and during the postirradiation recovery period, the rejoining of radiation-induced SSBs is inhibited during this postirradiation incubation period (radiopotentiation) with a relative inhibition factor at 1 h postirradiation of 1.25 in V79 cells and 1.15 in xrs-5 cells. An increased production and persistence of SSBs resulting from the interaction of carboplatin with radiation may be an important step in the mechanism responsible for the potentiated cell killing previously from studies in animal tumors and in cultured cells. 31 refs., 7 figs

  10. Measurement of Muon Neutrino Charged Current Single $\\pi^0$ Production on Hydrocarbon using MINERvA

    Energy Technology Data Exchange (ETDEWEB)

    Altinok, Ozgur [Tufts Univ., Medford, MA (United States)

    2017-01-01

    A sample of charged-current single pion production events for the semi- exclusive channel νµ + CH → µ-π0 + nucleon(s) has been obtained using neutrino exposures of the MINERvA detector. Differential cross sections for muon momentum, muon production angle, pion momentum, pion production angle, and four-momentum transfer square Q2 are reported and are compared to a GENIE-based simulation. The cross section versus neutrino energy is also re- ported. The effects of pion final-state interactions on these cross sections are investigated. The effect of baryon resonance suppression at low Q2 is examined and an event re-weight used by two previous experiments is shown to improve the data versus simulation agreement. The differential cross sections for Q2 for Eν < 4.0 GeV and Eν ≥ 4.0 GeV are examined and the shapes of these distributions are compared to those from the experiment’s $\\bar{v}$µ-CC (π0) measurement. The polarization of the pπ0 system is measured and compared to the simulation predictions. The hadronic invariant mass W distribution is examined for evidence of resonance content, and a search is reported for evidence of a two-particle two-hole (2p2h) contribution. All of the differential cross-section measurements of this Thesis are compared with published MINERvA measurements for νµ-CC (π+) and \\bar{v}$µ-CC (π0) processes.

  11. Species-specific detection and quantification of common barnacle larvae from the Japanese coast using quantitative real-time PCR.

    Science.gov (United States)

    Endo, Noriyuki; Sato, Kana; Matsumura, Kiyotaka; Yoshimura, Erina; Odaka, Yukiko; Nogata, Yasuyuki

    2010-11-01

    Species-specific detection and quantification methods for barnacle larvae using quantitative real-time polymerase chain reaction (qPCR) were developed. Species-specific primers for qPCR were designed for 13 barnacle species in the mitochondrial 12S ribosomal RNA gene region. Primer specificity was examined by PCR using template DNA extracted from each of the 13 barnacle species, other unidentified barnacle species, and field collected zooplankton samples. The resulting PCR products comprised single bands following agarose gel electrophoresis when the templates corresponded to primers. The amplifications were highly species-specific even for the field plankton samples. The field plankton samples were subjected to qPCR assay. The calculated DNA contents for each barnacle species were closely correlated with the number of larvae measured by microscopic examination. The method could be applied to quantify barnacle larvae in natural plankton samples.

  12. Screening for human papillomavirus in basaloid squamous carcinoma: utility of p16(INK4a), CISH, and PCR.

    Science.gov (United States)

    Winters, Ryan; Trotman, Winifred; Adamson, Christine S C; Rajendran, Vanitha; Tang, Alice; Elhosseiny, Abdelmonem; Evans, Mark F

    2011-06-01

    This study compares p16( INK4a) immunohistochemistry (IHC), HPV chromogenic in situ hybridization (ISH), and HPV polymerase chain reaction (PCR) genotyping for detection of HPV infection in basaloid squamous carcinoma (BSCC). A retrospective histopathological analysis of 40 BSCC from a single institution was carried out. p16 IHC, HPV DNA extraction and ISH, and HPV PCR genotyping were performed, and there was excellent agreement between all 3 methods of HPV detection. Analysis of variance yielded no significant differences between the results of the 3 tests ( P = .354) and Pearson product-moment correlation coefficients calculated for each pair of tests demonstrated direct correlation (r = .61 for PCR and IHC, r = .61 for PCR and ISH, and r = 1.00 for ISH and IHC). This supports the use of p16(INK4a) IHC as an initial screening tool for HPV infection in BSCC, while definitive evidence of HPV DNA can be sought subsequently with PCR or CISH.

  13. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence ...

  14. Interleukin 2-regulated in vitro antibody production following a single spinal manipulative treatment in normal subjects

    Directory of Open Access Journals (Sweden)

    Teodorczyk-Injeyan Julita A

    2010-09-01

    Full Text Available Abstract Background Our recent investigations have demonstrated that cell cultures from subjects, who received a single spinal manipulative treatment in the upper thoracic spine, show increased capacity for the production of the key immunoregulatory cytokine, interleukin-2. However, it has not been determined if such changes influence the response of the immune effector cells. Thus, the purpose of the present study was to determine whether, in the same subjects, spinal manipulation-related augmentation of the in vitro interleukin-2 synthesis is associated with the modulation of interleukin 2-dependent and/or interleukin-2-induced humoral immune response (antibody synthesis. Methods A total of seventy-four age and sex-matched healthy asymptomatic subjects were studied. The subjects were assigned randomly to: venipuncture control (n = 22, spinal manipulative treatment without cavitation (n = 25 or spinal manipulative treatment associated with cavitation (n = 27 groups. Heparinized blood samples were obtained from the subjects before (baseline and then at 20 minutes and 2 hours post-treatment. Immunoglobulin (antibody synthesis was induced in cultures of peripheral blood mononuclear cells by stimulation with conventional pokeweed mitogen or by application of human recombinant interleukin-2. Determinations of the levels of immunoglobulin G and immunoglobulin M production in culture supernatants were performed by specific immunoassays. Results The baseline levels of immunoglobulin synthesis induced by pokeweed mitogen or human recombinant interleukin-2 stimulation were comparable in all groups. No significant changes in the production of pokeweed mitogen-induced immunoglobulins were observed during the post-treatment period in any of the study groups. In contrast, the production of interleukin-2 -induced immunoglobulin G and immunoglobulin M was significantly increased in cultures from subjects treated with spinal manipulation. At 20 min post

  15. Comparison between digital PCR and real-time PCR in detection of Salmonella typhimurium in milk.

    Science.gov (United States)

    Wang, Meng; Yang, Junjie; Gai, Zhongtao; Huo, Shengnan; Zhu, Jianhua; Li, Jun; Wang, Ranran; Xing, Sheng; Shi, Guosheng; Shi, Feng; Zhang, Lei

    2018-02-02

    As a kind of zero-tolerance foodborne pathogens, Salmonella typhimurium poses a great threat to quality of food products and public health. Hence, rapid and efficient approaches to identify Salmonella typhimurium are urgently needed. Combined with PCR and fluorescence technique, real-time PCR (qPCR) and digital PCR (ddPCR) are regarded as suitable tools for detecting foodborne pathogens. To compare the effect between qPCR and ddPCR in detecting Salmonella typhimurium, a series of nucleic acid, pure strain culture and spiking milk samples were applied and the resistance to inhibitors referred in this article as well. Compared with qPCR, ddPCR exhibited more sensitive (10 -4 ng/μl or 10 2 cfu/ml) and less pre-culturing time (saving 2h). Moreover, ddPCR had stronger resistance to inhibitors than qPCR, yet absolute quantification hardly performed when target's concentration over 1ng/μl or 10 6 cfu/ml. This study provides an alternative strategy in detecting foodborne Salmonella typhimurium. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Observation of s-Channel Single Top Quark Production at the Tevatron

    Energy Technology Data Exchange (ETDEWEB)

    Cremonesi, Matteo [Univ. of Oxford (United Kingdom)

    2014-01-01

    Testing the Standard Model (SM) and looking for new phenomena have been the focus of generations of particle physicists in the last decades. Following this spirit, this thesis presents two searches. The first is the search for single top quark production from the exchange of an s-channel virtual W boson using events with an imbalance in the total transverse energy, b-tagged jets, and no identified leptons. Assuming the electroweak production of top quarks of mass 172.5 GeV/c2 in the s-channel, a cross section of 1.12+0.61 -0.57 (stat+syst) pb, with a significance of 1.9 standard deviations, is measured. This measurement is combined with the result obtained from events with an imbalance in total transverse momentum, b-tagged jets, and exactly one identified lepton, yielding a cross section of 1.36+0.37 -0.322 (stat+syst) pb, with a significance of 4.2 standard deviations. The first observation of single-top-quark production in the s channel through the combination of the CDF and D0 measurements is also reported. The measured cross section is σs = 1.29+0.26 -0.244 pb. The probability of observing a statistical fluctuation of the background to a cross section of the observed size or larger is 1.8 10-10, corresponding to a significance of 6.3 standard deviation. The second is the search for W'-like resonances decaying to tb. No significant excess above the SM prediction is found. Using a benchmark W' → tb left-right symmetric model, 95% C.L. mass-dependent upper limits are placed on the W0 boson production cross section times branching ratio to tb. Assuming a W' boson with SM-like couplings and allowed (forbidden) decay to leptons, W' → tb is excluded with 95% C.L. for W' boson masses below 860 (880) GeV/c2. Relaxing the hypothesis on SM-like couplings, we exclude W' boson coupling strength values as a function of the W' boson mass

  17. Market analysis of food products for detection of allergenic walnut (Juglans regia) and pecan (Carya illinoinensis) by real-time PCR.

    Science.gov (United States)

    López-Calleja, Inés María; de la Cruz, Silvia; González, Isabel; García, Teresa; Martín, Rosario

    2015-06-15

    Two real-time polymerase chain reaction (PCR)-based assays for detection of walnut (Juglans regia) and pecan (Carya illinoinensis) traces in a wide range of processed foods are described here. The method consists on a real-time PCR assay targeting the ITS1 region, using a nuclease (TaqMan) probe labeled with FAM and BBQ. The method was positive for walnut and pecan respectively, and negative for all other heterologous plants and animals tested. Using a series of model samples with defined raw walnut in wheat flour and heat-treated walnut in wheat flour with a range of concentrations of 0.1-100,000 mg kg(-1), a practical detection limit of 0.1 mg kg(-1) of walnut content was estimated. Identical binary mixtures were done for pecan, reaching the same limit of detection of 0.1 mg kg(-1). The assay was successfully trialed on a total of 232 commercial foodstuffs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Probing the top-Yukawa coupling in associated Higgs production with a single top quark

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Jung [Department of Physics, National Tsing Hua University,Hsinchu 300, Taiwan (China); Cheung, Kingman [Department of Physics, National Tsing Hua University,Hsinchu 300, Taiwan (China); Division of Quantum Phases and Devices, School of Physics, Konkuk University,Seoul 143-701 (Korea, Republic of); Lee, Jae Sik [Department of Physics, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju, 500-757 (Korea, Republic of); Lu, Chih-Ting [Department of Physics, National Tsing Hua University,Hsinchu 300, Taiwan (China)

    2014-05-15

    Associated production of the Higgs boson with a single top quark proceeds through Feynman diagrams, which are either proportional to the hWW, top-Yukawa, or the bottom-Yukawa couplings. It was shown in literature that the interference between the top-Yukawa and the gauge-Higgs diagrams can be significant, and thus the measurement of the cross sections can help pin down the sign and the size of the top-Yukawa coupling. Here we perform a detailed study with full detector simulations of such a possibility at the LHC-14 within the current allowed range of hWW and top-Yukawa couplings, using h→bb-macron, γγ, τ{sup +}τ{sup −}, ZZ{sup ∗}→4ℓ modes. We found that the LHC-14 has the potential to distinguish the size and the sign of the top-Yukawa coupling. Among the channels the h→bb-macron mode provides the best chance to probe the signal, followed by the h→γγ mode, which has the advantage of a narrow reconstructed mass peak. We also pointed out that the spatial separation among the final-state particles has the potential in differentiating among various values of the top-Yukawa coupling.

  19. Complete digital workflow for the production of implant-supported single-unit monolithic crowns.

    Science.gov (United States)

    Joda, Tim; Brägger, Urs

    2014-11-01

    The aim of this case series was to introduce a complete digital workflow for the production of monolithic implant crowns. Six patients were treated with implant-supported crowns made of resin nano ceramic (RNC). Starting with an intraoral optical scan (IOS), and following a CAD/CAM process, the monolithic crowns were bonded either to a novel prefabricated titanium abutment base (group A) or to a CAD/CAM-generated individualized titanium abutment (group B) in premolar or molar sites on a soft tissue level dental implant. Economic analyses included clinical and laboratory steps. An esthetic evaluation was performed to compare the two abutment-crown combinations. None of the digitally constructed RNC crowns required any clinical adaptation. Overall mean work time calculations revealed obvious differences for group A (65.3 min) compared with group B (86.5 min). Esthetic analysis demonstrated a more favorable outcome for the prefabricated bonding bases. Prefabricated or individualized abutments on monolithic RNC crowns using CAD/CAM technology in a model-free workflow seem to provide a feasible and streamlined treatment approach for single-edentulous space rehabilitation in the posterior region. However, RNC as full-contour material has to be considered experimental, and further large-scale clinical investigations with long-term follow-up observation are necessary. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Isoscalar single-pion production in the region of Roper and d⁎(2380 resonances

    Directory of Open Access Journals (Sweden)

    P. Adlarson

    2017-11-01

    Full Text Available Exclusive measurements of the quasi-free pn→ppπ− and pp→ppπ0 reactions have been performed by means of pd collisions at Tp=1.2 GeV using the WASA detector setup at COSY. Total and differential cross sections have been obtained covering the energy region Tp=0.95–1.3 GeV (s=2.3–2.46 GeV, which includes the regions of Δ(1232, N⁎(1440 and d⁎(2380 resonance excitations. From these measurements the isoscalar single-pion production has been extracted, for which data existed so far only below Tp=1 GeV. We observe a substantial increase of this cross section around 1 GeV, which can be related to the Roper resonance N⁎(1440, the strength of which shows up isolated from the Δ resonance in the isoscalar (NπI=0 invariant-mass spectrum. No evidence for a decay of the dibaryon resonance d⁎(2380 into the isoscalar (NNπI=0 channel is found. An upper limit of 180 μb (90% C.L. corresponding to a branching ratio of 9% has been deduced.

  1. Determination of Ethanol in Kombucha Products: Single-Laboratory Validation, First Action 2016.12.

    Science.gov (United States)

    Ebersole, Blake; Liu, Ying; Schmidt, Rich; Eckert, Matt; Brown, Paula N

    2017-05-01

    Kombucha is a fermented nonalcoholic beverage that has drawn government attention due to the possible presence of excess ethanol (≥0.5% alcohol by volume; ABV). A validated method that provides better precision and accuracy for measuring ethanol levels in kombucha is urgently needed by the kombucha industry. The current study validated a method for determining ethanol content in commercial kombucha products. The ethanol content in kombucha was measured using headspace GC with flame ionization detection. An ethanol standard curve ranging from 0.05 to 5.09% ABV was used, with correlation coefficients greater than 99.9%. The method detection limit was 0.003% ABV and the LOQ was 0.01% ABV. The RSDr ranged from 1.62 to 2.21% and the Horwitz ratio ranged from 0.4 to 0.6. The average accuracy of the method was 98.2%. This method was validated following the guidelines for single-laboratory validation by AOAC INTERNATIONAL and meets the requirements set by AOAC SMPR 2016.001, "Standard Method Performance Requirements for Determination of Ethanol in Kombucha."

  2. Lifting degeneracies in Higgs couplings using single top production in association with a Higgs boson

    CERN Document Server

    Farina, Marco; Maltoni, Fabio; Salvioni, Ennio; Thamm, Andrea

    2013-01-01

    Current Higgs data show an ambiguity in the value of the Yukawa couplings to quarks and leptons. Not so much because of still large uncertainties in the measurements but as the result of several almost degenerate minima in the coupling profile likelihood function. To break these degeneracies, it is important to identify and measure processes where the Higgs coupling to fermions interferes with other coupling(s). The most prominent example, the decay of $h \\to \\gamma \\gamma$, is not sufficient to give a definitive answer. In this Letter, we argue that $t$-channel single top production in association with a Higgs boson, with $h\\to b\\bar b$, can provide the necessary information to lift the remaining degeneracy in the top Yukawa. Within the Standard Model, the total rate is highly reduced due to an almost perfect destructive interference in the hard process, $W b \\rightarrow t h$. We first show that for non-standard couplings the cross section can be reliably computed without worrying about corrections from phys...

  3. Cross-section measurement of single-top t-channel production at ATLAS

    CERN Document Server

    Herrberg-Schubert, Ruth

    2014-06-02

    This study presents the cross-section measurement of electroweak single-top quark production in the t-channel with a semi-leptonically decaying top quark. The study is based on 4.7 fb^{-1} of proton-proton collision data recorded with the ATLAS detector at the Large Hadron Collider in the year 2011. Selected events contain two highly energetic jets, one of which is identified as originating from a beauty quark, as well as a highly energetic electron or muon and transverse missing energy. The case of three and four jets is also considered but eventually discarded since their inclusion degrades the precision of the result. The event reconstruction is done with a chi-square-based kinematic fit using W boson and top quark mass constraints. The chi-square value in each event serves to classify the event as a signal-like or background-like process. The cross-section is extracted by performing a template-based maximum likelihood fit to the distribution that displays the best discriminatory power: This distribution i...

  4. Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment.

    Directory of Open Access Journals (Sweden)

    Zhenming Yu

    Full Text Available Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.

  5. PCR-mediated recombination between Cryptosporidium spp. of lizards and snakes.

    Science.gov (United States)

    Zhou, Ling; Yang, Chunfu; Xiao, Lihua

    2003-01-01

    The presence or absence of genetic recombination has often been used as one of the criteria for Cryptosporidium species designation and population structure delineation. During a recent study of cryptosporidiosis in reptiles that were housed in the same room, 4 lizards were found to have concurrent infections of C. serpentis (a gastric parasite) and C. saurophilum (an intestinal parasite), and 6 snakes were concurrently infected with C. serpentis, C. saurophilum and a new Cryptosporidium as indicated by PCR-RFLP analysis of the SSU rRNA gene. DNA sequence analysis of cloned PCR products confirmed the diagnosis of mixed infections. Surprisingly, it appeared that 11 of the 22 clones (8 and 14 clones from a lizard and a snake, respectively) had chimeric sequences of two Cryptosporidium spp. BootScan analysis indicated the existence of recombinants among the cloned sequences and detection of the informative sites confirmed the BootScan results. Because the probability for genetic recombination between gastric and intestinal parasites is small, these hybrid sequences were likely results of PCR artifacts due to the presence of multiple templates. This was confirmed by PCR-sequencing analysis of single-copy templates using diluted DNA samples. Direct sequencing of 69 PCR products from 100- to 1,000-fold diluted DNAs from the same snake and lizard produced only sequences of C. serpentis, C. saurophilum and the unnamed Cryptosporidium sp. Thus, care should be taken to eliminate PCR artifacts when determining the presence of genetic recombination or interpreting results of population genetic studies.

  6. Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses.

    Science.gov (United States)

    Wan, Jingjing; Jing, Yuhang; Rao, Yue; Zhang, Shicheng; Luo, Gang

    2018-03-15

    Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste-activated sludge (WAS) was investigated. The TM process was also compared to a process with mesophilic alkaline fermentation followed by a mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 ml H 2 /g volatile solids [VS]) and methane yield (150.7 ml CH 4 /g VS) in the TM process were higher than those (6.7 ml H 2 /g VS and 127.8 ml CH 4 /g VS, respectively) in the MM process. The lowest methane yield (101.2 ml CH 4 /g VS) was obtained with the M process. Taxonomic results obtained from metagenomic analysis showed that different microbial community compositions were established in the hydrogen reactors of the TM and MM processes, which also significantly changed the microbial community compositions in the following methane reactors compared to that with the M process. The dynamics of bacterial pathogens were also evaluated. For the TM process, the reduced diversity and total abundance of bacterial pathogens in WAS were observed in the hydrogen reactor and were further reduced in the methane reactor, as revealed by metagenomic analysis. The results also showed not all bacterial pathogens were reduced in the reactors. For example, Collinsella aerofaciens was enriched in the hydrogen reactor, which was also confirmed by quantitative PCR (qPCR) analysis. The study further showed that qPCR was more sensitive for detecting bacterial pathogens than metagenomic analysis. Although there were some differences in the relative abundances of bacterial pathogens calculated by metagenomic and qPCR approaches, both approaches demonstrated that the TM process was more efficient for the removal of bacterial pathogens than the MM and M processes. IMPORTANCE This study developed an efficient process for bioenergy (H 2 and CH 4 ) production from WAS and elucidates the

  7. Rapid method for controlling the correct labeling of products containing common octopus (Octopus vulgaris) and main substitute species (Eledone cirrhosa and Dosidicus gigas) by fast real-time PCR.

    Science.gov (United States)

    Espiñeira, Montserrat; Vieites, Juan M

    2012-12-15

    The TaqMan real-time PCR has the highest potential for automation, therefore representing the currently most suitable method for screening, allowing the detection of fraudulent or unintentional mislabeling of species. This work describes the development of a real-time polymerase chain reaction (RT-PCR) system for the detection and identification of common octopus (Octopus vulgaris) and main substitute species (Eledone cirrhosa and Dosidicus gigas). This technique is notable for the combination of simplicity, speed, sensitivity and specificity in an homogeneous assay. The method can be applied to all kinds of products; fresh, frozen and processed, including those undergoing intensive processes of transformation. This methodology was validated to check how the degree of food processing affects the method and the detection of each species. Moreover, it was applied to 34 commercial samples to evaluate the labeling of products made from them. The methodology herein developed is useful to check the fulfillment of labeling regulations for seafood products and to verify traceability in commercial trade and for fisheries control. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Estrogen receptors alpha and beta in rat placenta: detection by RT-PCR, real time PCR and Western blotting

    Directory of Open Access Journals (Sweden)

    Al-Bader Maie D

    2006-03-01

    Full Text Available Abstract Background High levels of estrogens during pregnancy not only retard placental and fetal growth but can lead to reproductive tract abnormalities in male progeny. Estrogens act through estrogen receptors (ER to modulate the transcription of target genes. These ER exist in two isoforms, ER alpha and ER beta and recently several variants of these isoforms have been identified. Methods The expressions of ER isoforms and variants have been studied in rat placenta at 16, 19 and 21 days gestation (dg. Gene expression was assessed using RT-PCR and real time PCR while protein expression was studied using Western blotting followed by immunodetection. Placental homogenates were probed with: a monoclonal antibody raised against the steroid binding domain of the ER alpha (ER alpha -S, a monoclonal antibody raised against the hinge region of ER alpha (ER alpha -H and a polyclonal antibody raised against the amino terminus of ER beta. Results ER alpha and ER beta mRNA and protein were detected from as early as 16 dg. Two PCR products were detected for ER alpha, one for the wild type ER alpha, and a smaller variant. Real time PCR results suggested the presence of a single product for ER beta. The antibodies used for detection of ER alpha protein both identified a single 67 kDa isoform; however a second 54 kDa band, which may be an ER alpha variant, was identified when using the ER alpha -H antibody. The abundance of both ER alpha bands decreased significantly between 16 and 19 dg. As for ER beta, four bands (76, 59, 54 and 41 kDa were detected. The abundance of the 59 and 54 kDa bands decreased significantly between 16 and 19 dg. Conclusion This study shows that both ER protein isoforms and their variants are present in rat placenta. The decrease in their expression near parturition suggests that the placenta may be relatively unresponsive to estrogens at this stage.

  9. Cross-section measurement of single-top t-channel production at ATLAS

    International Nuclear Information System (INIS)

    Herrberg-Schubert, Ruth Hedwig Margarete

    2014-01-01

    This study presents the cross-section measurement of electroweak single-top quark production in the t-channel with a semi-leptonically decaying top quark. The study is based on 4.7 fb -1 of proton-proton collision data recorded with the ATLAS detector at the Large Hadron Collider in the year 2011. Selected events contain two highly energetic jets, one of which is identified as originating from a beauty quark, as well as a highly energetic electron or muon and transverse missing energy. The case of three and four jets is also considered but eventually discarded since their inclusion degrades the precision of the result. The event reconstruction is done with a chi-square-based kinematic fit using W boson and top quark mass constraints. The chi-square value in each event serves to classify the event as a signal-like or background-like process. The cross-section is extracted by performing a template-based maximum likelihood fit to the distribution that displays the best discriminatory power: This distribution is chosen such that the shape differences between signal and background with respect to the typical forward light jet kinematics of the t-channel are exploited. An observation of the single-top t-channel process with a significance of 5.7 σ is obtained, and the cross-section is measured to be 111 +29 -28 pb. Assuming vertical stroke V tb vertical stroke 2 >> vertical stroke V td vertical stroke 2 + vertical stroke V ts vertical stroke 2 as well as a (V-A), CP-conserving interaction, and allowing for the presence of anomalous couplings at the W-t-b vertex, the associated value of the CKM matrix element times an anomalous form factor is determined as vertical stroke V tb f L 1 vertical stroke =1.30 +0.13 -0.16 . The corresponding lower limit in the standard model scenario 0≤ vertical stroke V tb vertical stroke ≤1 amounts to 0.77 tb vertical stroke at 95% confidence level.

  10. MDE heteroduplex analysis of PCR products spanning each exon of the fibrillin (FBN1) gene greatly increases the efficiency of mutation detection in the Marfan syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Nijbroek, G.; Dietz, H.C. [Johns Hopkins Univ. School of Med., Baltimore, MD (United States); Pereira, L.; Ramirz, F. [Mount Sinai School of Med., New York, NY (United States)

    1994-09-01

    Defects in fibrillin (FNB1) cause the Marfan syndrome (MFS). Classic Marfan phenotype cosegregates with intragenic and/or flanking marker alleles in all families tested and a significant number of FBN1 mutations have been identified in affected individuals. Using a standard method of mutation detection, SSCP analysis of overlapping RT-PCR amplimers that span the entire coding sequence, the general experience has been a low yield of identifiable mutations, ranging from 10-20%. Possible explanations included low sensitivity of mutation screening procedures, under-representation of mutant transcript in patient samples either due to deletions or mutant alleles containing premature termination codons, clustering of mutations in yet uncharacterized regions of the gene, including regulatory elements, or genetic heterogeneity. In order to compensate for a potential reduced mutant transcript stability, we have devised a method to screen directly from genomic DNA. The intronic boundaries flanking each of the 65 FBN1 exons were characterized and primer pairs were fashioned such that all splice junctions would be included in the resultant amplimers. The entire gene was screened for a panel of 9 probands with classic Marfan syndrome using mutation detection enhancement (MDE) gel heteroduplex analysis. A mutation was identified in 5/9 (55%) of patient samples. All were either missense mutations involving a cysteine residue or small deletions that did not create a frame shift. In addition, 10 novel polymorphisms were found. We conclude that the majority of mutations causing Marfan syndrome reside in the FBN1 gene and that mutations creating premature termination codons are not the predominant cause of inefficient mutation detection using RT-PCR. We are currently modifying screening methods to increase sensitivity and targeting putative FBN1 gene promoter sequences for study.

  11. High-resolution phenotypic profiling of natural products-induced effects on the single-cell level

    KAUST Repository

    Kremb, Stephan Georg

    2017-03-15

    Natural products (NPs) are highly evolved molecules making them a valuable resource for new therapeutics. Here we demonstrate the usefulness of broad-spectrum phenotypic profiling of NP-induced perturbations on single cells with imaging-based High-Content Screening to inform on physiology, mechanisms-of-actions, and multi-level toxicity. Our technology platform aims at broad applicability using a comprehensive marker panel with standardized settings streamlined towards an easy implementation in laboratories dedicated to natural products research.

  12. Search for FCNC single top-quark production at sqrt{s} = 7 TeV with the ATLAS detector

    Czech Academy of Sciences Publication Activity Database

    Aad, G.; Abbott, B.; Abdallah, J.; Chudoba, Jiří; Gallus, Petr; Gunther, Jaroslav; Hruška, I.; Juránek, Vojtěch; Kepka, Oldřich; Kupčo, Alexander; Kůs, Vlastimil; Lipinský, L.; Lokajíček, Miloš; Marčišovský, Michal; Mikeštíková, Marcela; Myška, Miroslav; Němeček, Stanislav; Panušková, M.; Růžička, Pavel; Schovancová, Jaroslava; Šícho, Petr; Staroba, Pavel; Svatoš, Michal; Taševský, Marek; Tic, Tomáš; Valenta, J.; Vrba, Václav; Zeman, Martin

    2012-01-01

    Roč. 712, 4-5 (2012), s. 351-369 ISSN 0370-2693 R&D Projects: GA MŠk LA08032 Institutional research plan: CEZ:AV0Z10100502 Keywords : ATLAS * LHC * top physics * heavy quark production * FCNC * top single production * coupling constant Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 4.569, year: 2012 http://arxiv.org/abs/arXiv:1203.0529

  13. Molecular diagnostic PCR handbook

    International Nuclear Information System (INIS)

    Viljoen, G.J.; Crowther, J.R.; Nel, L.H.

    2005-01-01

    The uses of nucleic acid-directed methods have increased significantly in the past five years and have made important contributions to disease control country programmes for improving national and international trade. These developments include the more routine use of PCR as a diagnostic tool in veterinary diagnostic laboratories. However, there are many problems associated with the transfer and particularly, the application of this technology. These include lack of consideration of: the establishment of quality-assured procedures, the required set-up of the laboratory and the proper training of staff. This can lead to a situation where results are not assured. This book gives a comprehensive account of the practical aspects of PCR and strong consideration is given to ensure its optimal use in a laboratory environment. This includes the setting-up of a PCR laboratory; Good Laboratory Practice and standardised PCR protocols to detect animal disease pathogens. Examples of Standard Operating Procedures as used in individual specialist laboratories and an outline of training materials necessary for PCR technology transfer are presented. The difficulties, advantages and disadvantages in PCR applications are explained and placed in context with other test systems. Emphasis is placed on the use of PCR for detection of pathogens, with a particular focus on diagnosticians and scientists from the developing world. It is hoped that this book will enable readers from various disciplines and levels of expertise to better judge the merits of PCR and to increase their skills and knowledge in order to assist in a more logical, efficient and assured use of this technology

  14. Control of the Diameter and Chiral Angle Distributions during Production of Single-Wall Carbon Nanotubes

    Science.gov (United States)

    Nikolaev, Pavel

    2009-01-01

    Many applications of single wall carbon nanotubes (SWCNT), especially in microelectronics, will benefit from use of certain (n,m) nanotube types (metallic, small gap semiconductor, etc.) Especially fascinating is the possibility of quantum conductors that require metallic armchair nanotubes. However, as produced SWCNT samples are polydisperse, with many (n,m) types present and typical approx.1:2 metal/semiconductor ratio. Nanotube nucleation models predict that armchair nuclei are energetically preferential due to formation of partial triple bonds along the armchair edge. However, nuclei can not reach any meaningful thermal equilibrium in a rapidly expanding and cooling plume of carbon clusters, leading to polydispersity. In the present work, SWCNTs were produced by a pulsed laser vaporization (PLV) technique. The carbon vapor plume cooling rate was either increased by change in the oven temperature (expansion into colder gas), or decreased via "warm-up" with a laser pulse at the moment of nucleation. The effect of oven temperature and "warm-up" on nanotube type population was studied via photoluminescence, UV-Vis-NIR absorption and Raman spectroscopy. It was found that reduced temperatures leads to smaller average diameters, progressively narrower diameter distributions, and some preference toward armchair structures. "Warm-up" shifts nanotube population towards arm-chair structures as well, but the effect is small. Possible improvement of the "warm-up" approach to produce armchair SWCNTs will be discussed. These results demonstrate that PLV production technique can provide at least partial control over the nanotube (n,m) population. In addition, these results have implications for the understanding the nanotube nucleation mechanism in the laser oven.

  15. Single-step production of a recyclable nanobiocatalyst for organophosphate pesticides biodegradation using functionalized bacterial magnetosomes.

    Directory of Open Access Journals (Sweden)

    Nicolas Ginet

    Full Text Available Enzymes are versatile catalysts in laboratories and on an industrial scale; improving their immobilization would be beneficial to broadening their applicability and ensuring their (reuse. Lipid-coated nano-magnets produced by magnetotactic bacteria are suitable for a universally applicable single-step method of enzyme immobilization. By genetically functionalizing the membrane surrounding these magnetite particles with a phosphohydrolase, we engineered an easy-to-purify, robust and recyclable biocatalyst to degrade ethyl-paraoxon, a commonly used pesticide. For this, we genetically fused the opd gene from Flavobacterium sp. ATCC 27551 encoding a paraoxonase to mamC, an abundant protein of the magnetosome membrane in Magnetospirillum magneticum AMB-1. The MamC protein acts as an anchor for the paraoxonase to the magnetosome surface, thus producing magnetic nanoparticles displaying phosphohydrolase activity. Magnetosomes functionalized with Opd were easily recovered from genetically modified AMB-1 cells: after cellular disruption with a French press, the magnetic nanoparticles are purified using a commercially available magnetic separation system. The catalytic properties of the immobilized Opd were measured on ethyl-paraoxon hydrolysis: they are comparable with the purified enzyme, with K(m (and k(cat values of 58 µM (and 178 s(-1 and 43 µM (and 314 s(-1 for the immobilized and purified enzyme respectively. The Opd, a metalloenzyme requiring a zinc cofactor, is thus properly matured in AMB-1. The recycling of the functionalized magnetosomes was investigated and their catalytic activity proved to be stable over repeated use for pesticide degradation. In this study, we demonstrate the easy production of functionalized magnetic nanoparticles with suitably genetically modified magnetotactic bacteria that are efficient as a reusable nanobiocatalyst for pesticides bioremediation in contaminated effluents.

  16. Energy production from distillery wastewater using single and double-phase upflow anaerobic sludge blanket (UASB) reactor

    Energy Technology Data Exchange (ETDEWEB)

    Muyodi, F.J.; Rubindamayugi, M.S.T. [Univ. of Dar es Salaam, Applied Microbiology Unit (Tanzania, United Republic of)

    1997-12-31

    A Single-phase (SP) and Double-phase (DP) Upflow Anaerobic Sludge Blanket (UASB) reactors treating distillery wastewater were operated in parallel. The DP UASB reactor showed better performance than the SP UASB reactor in terms of maximum methane production rate, methane content and Chemical Oxygen Demand (COD) removal efficiency. (au) 20 refs.

  17. Search for anomalous production of single photons at $\\sqrt{s}$ = 130 and 136 GeV

    CERN Document Server

    Adam, W; Agasi, E; Ajinenko, I; Aleksan, Roy; Alekseev, G D; Alemany, R; Allport, P P; Almehed, S; Amaldi, Ugo; Amato, S; Andreazza, A; Andrieux, M L; Antilogus, P; Apel, W D; Arnoud, Y; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Bambade, P; Barão, F; Barate, R; Barbi, M S; Barbiellini, Guido; Bardin, Dimitri Yuri; Baroncelli, A; Bärring, O; Barrio, J A; Bartl, Walter; Bates, M J; Battaglia, Marco; Baubillier, M; Baudot, J; Becks, K H; Begalli, M; Beillière, P; Belokopytov, Yu A; Belous, K S; Benvenuti, Alberto C; Berggren, M; Bertini, D; Bertrand, D; Bianchi, F; Bigi, M; Bilenky, S M; Billoir, P; Bloch, D; Blume, M; Bolognese, T; Bonesini, M; Bonivento, W; Booth, P S L; Bosio, C; Botner, O; Boudinov, E; Bouquet, B; Bourdarios, C; Bowcock, T J V; Bozzo, M; Branchini, P; Brand, K D; Brenke, T; Brenner, R A; Bricman, C; Brown, R C A; Brückman, P; Brunet, J M; Bugge, L; Buran, T; Burgsmüller, T; Buschmann, P; Buys, A; Cabrera, S; Caccia, M; Calvi, M; Camacho-Rozas, A J; Camporesi, T; Canale, V; Canepa, M; Cankocak, K; Cao, F; Carena, F; Carroll, L; Caso, Carlo; Castillo-Gimenez, M V; Cattai, A; Cavallo, F R; Chabaud, V; Charpentier, P; Chaussard, L; Chauveau, J; Checchia, P; Chelkov, G A; Chen, M; Chierici, R; Chliapnikov, P V; Chochula, P; Chorowicz, V; Cindro, V; Collins, P; Contreras, J L; Contri, R; Cortina, E; Cosme, G; Cossutti, F; Crawley, H B; Crennell, D J; Crosetti, G; Cuevas-Maestro, J; Czellar, S; Dahl-Jensen, Erik; Dahm, J; D'Almagne, B; Dam, M; Damgaard, G; Dauncey, P D; Davenport, Martyn; Da Silva, W; Defoix, C; Deghorain, A; Della Ricca, G; Delpierre, P A; Demaria, N; De Angelis, A; de Boer, Wim; De Brabandere, S; De Clercq, C; La Vaissière, C de; De Lotto, B; De Min, A; De Paula, L S; De Saint-Jean, C; Dijkstra, H; Di Ciaccio, Lucia; Djama, F; Dolbeau, J; Dönszelmann, M; Doroba, K; Dracos, M; Drees, J; Drees, K A; Dris, M; Durand, J D; Edsall, D M; Ehret, R; Eigen, G; Ekelöf, T J C; Ekspong, Gösta; Elsing, M; Engel, J P; Erzen, B; Espirito-Santo, M C; Falk, E; Fassouliotis, D; Feindt, Michael; Fenyuk, A; Ferrer, A; Fichet, S; Filippas-Tassos, A; Firestone, A; Fischer, P A; Föth, H; Fokitis, E; Fontanelli, F; Formenti, F; Franek, B J; Frenkiel, P; Fries, D E C; Frodesen, A G; Frühwirth, R; Fulda-Quenzer, F; Fuster, J A; Galloni, A; Gamba, D; Gandelman, M; García, C; García, J; Gaspar, C; Gasparini, U; Gavillet, P; Gazis, E N; Gelé, D; Gerber, J P; Gibbs, M; Gokieli, R; Golob, B; Gopal, Gian P; Gorn, L; Górski, M; Guz, Yu; Gracco, Valerio; Graziani, E; Grosdidier, G; Grzelak, K; Gumenyuk, S A; Gunnarsson, P; Günther, M; Guy, J; Hahn, F; Hahn, S; Hajduk, Z; Hallgren, A; Hamacher, K; Hao, W; Harris, F J; Hedberg, V; Henriques, R P; Hernández, J J; Herquet, P; Herr, H; Hessing, T L; Higón, E; Hilke, Hans Jürgen; Hill, T S; Holmgren, S O; Holt, P J; Holthuizen, D J; Hoorelbeke, S; Houlden, M A; Hrubec, Josef; Huet, K; Hultqvist, K; Jackson, J N; Jacobsson, R; Jalocha, P; Janik, R; Jarlskog, C; Jarlskog, G; Jarry, P; Jean-Marie, B; Johansson, E K; Jönsson, L B; Jönsson, P E; Joram, Christian; Juillot, P; Kaiser, M; Kapusta, F; Karafasoulis, K; Karlsson, M; Karvelas, E; Katsanevas, S; Katsoufis, E C; Keränen, R; Khokhlov, Yu A; Khomenko, B A; Khovanskii, N N; King, B J; Kjaer, N J; Klein, H; Klovning, A; Kluit, P M; Köne, B; Kokkinias, P; Koratzinos, M; Korcyl, K; Kostyukhin, V; Kourkoumelis, C; Kuznetsov, O; Kramer, P H; Krammer, Manfred; Kreuter, C; Kronkvist, I J; Krumshtein, Z; Krupinski, W; Kubinec, P; Kucewicz, W; Kurvinen, K L; Lacasta, C; Laktineh, I; Lamblot, S; Lamsa, J; Lanceri, L; Lane, D W; Langefeld, P; Lapin, V; Last, I; Laugier, J P; Lauhakangas, R; Leser, G; Ledroit, F; Lefébure, V; Legan, C K; Leitner, R; Lemoigne, Y; Lemonne, J; Lenzen, Georg; Lepeltier, V; Lesiak, T; Libby, J; Liko, D; Lindner, R; Lipniacka, A; Lippi, I; Lörstad, B; Loken, J G; López, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J N; Maehlum, G; Maio, A; Malychev, V; Marco, J; Marco, R P; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Maron, T; Martínez-Rivero, C; Martínez-Vidal, F; Martí i García, S; Matorras, F; Matteuzzi, C; Matthiae, Giorgio; Mazzucato, M; McCubbin, M L; McKay, R; McNulty, R; Medbo, J; Merk, M; Meroni, C; Meyer, S; Meyer, W T; Myagkov, A; Michelotto, M; Migliore, E; Mirabito, L; Mitaroff, Winfried A; Mjörnmark, U; Moa, T; Møller, R; Mönig, K; Monge, M R; Morettini, P; Müller, H; Mundim, L M; Murray, W J; Muryn, B; Myatt, Gerald; Naraghi, F; Navarria, Francesco Luigi; Navas, S; Nawrocki, K; Negri, P; Némécek, S; Neumann, W; Neumeister, N; Nicolaidou, R; Nielsen, B S; Nieuwenhuizen, M; Nikolaenko, V; Niss, P; Nomerotski, A; Normand, Ainsley; Novák, M; Oberschulte-Beckmann, W; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, Risto; Österberg, K; Ouraou, A; Paganini, P; Paganoni, M; Pagès, P; Palka, H; Papadopoulou, T D; Papageorgiou, K; Pape, L; Parkes, C; Parodi, F; Passeri, A; Pegoraro, M; Peralta, L; Pernegger, H; Pernicka, Manfred; Perrotta, A; Petridou, C; Petrolini, A; Petrovykh, M; Phillips, H T; Piana, G; Pierre, F; Pimenta, M; Pindo, M; Plaszczynski, S; Podobrin, O; Pol, M E; Polok, G; Poropat, P; Pozdnyakov, V; Prest, M; Privitera, P; Pukhaeva, N; Pullia, Antonio; Radojicic, D; Ragazzi, S; Rahmani, H; Rames, J; Ratoff, P N; Read, A L; Reale, M; Rebecchi, P; Redaelli, N G; Regler, Meinhard; Reid, D; Renton, P B; Resvanis, L K; Richard, F; Richardson, J; Rídky, J; Rinaudo, G; Ripp, I; Romero, A; Roncagliolo, I; Ronchese, P; Roos, L; Rosenberg, E I; Rosso, E; Roudeau, Patrick; Rovelli, T; Rückstuhl, W; Ruhlmann-Kleider, V; Ruiz, A; Rybicki, K; Saarikko, H; Sacquin, Yu; Sadovskii, A; Sahr, O; Sajot, G; Salt, J; Sánchez, J; Sannino, M; Schimmelpfennig, M; Schneider, H; Schwickerath, U; Schyns, M A E; Sciolla, G; Scuri, F; Seager, P; Sedykh, Yu; Segar, A M; Seitz, A; Sekulin, R L; Serbelloni, L; Shellard, R C; Siccama, I; Siegrist, P; Simonetti, S; Simonetto, F; Sissakian, A N; Sitár, B; Skaali, T B; Smadja, G; Smirnov, N; Smirnova, O G; Smith, G R; Sosnowski, R; Souza-Santos, D; Spassoff, Tz; Spiriti, E; Sponholz, P; Squarcia, S; Stanescu, C; Stapnes, Steinar; Stavitski, I; Stevenson, K; Stichelbaut, F; Stocchi, A; Strauss, J; Strub, R; Stugu, B; Szczekowski, M; Szeptycka, M; Tabarelli de Fatis, T; Tavernet, J P; Chikilev, O G; Thomas, J; Tilquin, A; Timmermans, J; Tkatchev, L G; Todorov, T; Todorova, S; Toet, D Z; Tomaradze, A G; Tomé, B; Tonazzo, A; Tortora, L; Tranströmer, G; Treille, D; Trischuk, W; Tristram, G; Trombini, A; Troncon, C; Tsirou, A L; Turluer, M L; Tyapkin, I A; Tyndel, M; Tzamarias, S; Überschär, B; Ullaland, O; Uvarov, V; Valenti, G; Vallazza, E; van Apeldoorn, G W; van Dam, P; Van Doninck, W K; Van Eldik, J; Vassilopoulos, N; Vegni, G; Ventura, L; Venus, W A; Verbeure, F; Verlato, M; Vertogradov, L S; Vilanova, D; Vincent, P; Vitale, L; Vlasov, E; Vodopyanov, A S; Vrba, V; Wahlen, H; Walck, C; Weierstall, M; Weilhammer, Peter; Weiser, C; Wetherell, Alan M; Wicke, D; Wickens, J H; Wielers, M; Wilkinson, G R; Williams, W S C; Winter, M; Witek, M; Woschnagg, K; Yip, K; Yushchenko, O P; Zach, F; Zaitsev, A; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zevgolatakos, E; Zimin, N I; Zito, M; Zontar, D; Zucchelli, G C; Zumerle, G; Wiele

    1996-01-01

    This letter reports the results of the measurement of single photon production in the reaction $e^+e^- \\rightarrow \\gamma +$ invisible particles at centre-of-mass energies $\\sqrt{s}=$~130 and 136 GeV and an integrated luminosity of 5.83~pb$

  18. Single-tube hydroponics as a novel idea for small-scale production of crop seed in a plant incubator.

    Science.gov (United States)

    Kuroda, Masaharu; Ikenaga, Sachiko

    2015-01-01

    We present a novel protocol for small-scale production of crop seed in a plant incubator termed "Single-tube hydroponics." Our protocol minimizes the materials and methods for cultivation whereby a large number of independent plants can be cultured in a limited space. This study may aid in the improvement of crop seed components, especially in the cultivation of transgenic plants.

  19. Measurement of the Single Top Quark Production Cross Section at $\\sqrt {s} = 1.96$ TeV

    Energy Technology Data Exchange (ETDEWEB)

    Padilla, Mark Anthony [Univ. of California, Riverside, CA (United States)

    2011-01-01

    Within the standard model top quarks are predicted to be most often produced in pairs via the strong interaction. However they can also be produced singly through the weak interation. This is a rarer process with many experimental challenges. It is interesting because it provides a new window to search for evidence of physics beyond the standard model picture, such as a fourth generation of quarks or to search for insight into the Higgs Mechanism. Single top production also provides a direct way to calculate the CKM matrix element Vtb. This thesis presents new measurements for single top quark production in the s+t, s and t channels using 5.4 fb-1 of data collected at the DØ detector at Fermilab in Batavia, IL. The analysis was performed using Boosted decision trees to separate signal from background and Bayesian statistcs to calculate all the cross sections.

  20. Measurement of the associated production of a single top quark and a W boson in single-lepton events with the ATLAS detector

    International Nuclear Information System (INIS)

    Mergelmeyer, Sebastian

    2016-06-01

    The production of a single top quark in association with a W boson (Wt) is measured with the ATLAS detector using proton-proton collision events with one lepton, three jets and missing transverse energy at √(s)=8 TeV. Signal events are identified using an artificial neural network in an unconventional manner, addressing the large uncertainties due to the major background, which has an about 10 times larger cross section and a very similar signature compared with the Wt signal. State-of-the-art statistical methods are used to validate the modelling of the signal and the background, and to extract the cross section for Wt production. The cross section is found to be consistent with related measurements as well as the Standard Model prediction. In addition, a direct measurement of the CKM matrix element V tb is performed.

  1. Molecular Subtyping of Salmonella Typhimurium with Multiplex Oligonucleotide Ligation-PCR (MOL-PCR).

    Science.gov (United States)

    Wuyts, Véronique; Mattheus, Wesley; Roosens, Nancy H C; Marchal, Kathleen; Bertrand, Sophie; De Keersmaecker, Sigrid C J

    2017-01-01

    A multiplex oligonucleotide ligation-PCR (MOL-PCR) assay is a valuable high-throughput technique for the detection of bacteria and viruses, for characterization of pathogens and for diagnosis of genetic diseases, as it allows one to combine different types of molecular markers in a high-throughput multiplex assay. A MOL-PCR assay starts with a multiplex oligonucleotide ligation reaction for detection of the molecular marker, followed by a singleplex PCR for signal amplification and analysis of the MOL-PCR products on a Luminex platform. This last step occurs through a liquid bead suspension array in which the MOL-PCR products are hybridized to MagPlex-TAG beads.In this chapter, we describe the complete procedure for a MOL-PCR assay for subtyping of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant S. 1,4[5],12:i:- from DNA isolation through heat lysis up to data interpretation through a Gödel Prime Product. The subtyping assay consists of 50 discriminative molecular markers and two internal positive control markers divided over three MOL-PCR assays.

  2. Single Point Incremental Forming to increase material knowledge and production flexibility

    Science.gov (United States)

    Habraken, A. M.

    2016-08-01

    Nowadays, manufactured pieces can be divided into two groups: mass production and production of low volume number of parts. Within the second group (prototyping or small batch production), an emerging solution relies on Incremental Sheet Forming or ISF. ISF refers to processes where the plastic deformation occurs by repeated contact with a relatively small tool. More specifically, many publications over the past decade investigate Single Point Incremental Forming (SPIF) where the final shape is determined only by the tool movement. This manufacturing process is characterized by the forming of sheets by means of a CNC controlled generic tool stylus, with the sheets clamped by means of a non-workpiece-specific clamping system and in absence of a partial or a full die. The advantage is no tooling requirements and often enhanced formability, however it poses a challenge in term of process control and accuracy assurance. Note that the most commonly used materials in incremental forming are aluminum and steel alloys however other alloys are also used especially for medical industry applications, such as cobalt and chromium alloys, stainless steel and titanium alloys. Some scientists have applied incremental forming on PVC plates and other on sandwich panels composed of propylene with mild steel and aluminum metallic foams with aluminum sheet metal. Micro incremental forming of thin foils has also been developed. Starting from the scattering of the results of Finite Element (FE) simulations, when one tries to predict the tool force (see SPIF benchmark of 2014 Numisheet conference), we will see how SPIF and even micro SPIF (process applied on thin metallic sheet with a few grains within the thickness) allow investigating the material behavior. This lecture will focus on the identification of constitutive laws, on the SPIF forming mechanisms and formability as well as the failure mechanism. Different hypotheses have been proposed to explain SPIF formability, they will be

  3. A fully sealed plastic chip for multiplex PCR and its application in bacteria identification.

    Science.gov (United States)

    Xu, Youchun; Yan, He; Zhang, Yan; Jiang, Kewei; Lu, Ying; Ren, Yonghong; Wang, Hui; Wang, Shan; Xing, Wanli

    2015-07-07

    Multiplex PCR is an effective tool for simultaneous multiple target detection but is limited by the intrinsic interference and competition among primer pairs when it is performed in one reaction tube. Dividing a multiplex PCR into many single PCRs is a simple strategy to overcome this issue. Here, we constructed a plastic, easy-to-use, fully sealed multiplex PCR chip based on reversible centrifugation for the simultaneous detection of 63 target DNA sequences. The structure of the chip is quite simple, which contains sine-shaped infusing channels and a number of reaction chambers connecting to one side of these channels. Primer pairs for multiplex PCR were sequentially preloaded in the different reaction chambers, and the chip was enclosed with PCR-compatible adhesive tape. For usage, the PCR master mix containing a DNA template is pipetted into the infusing channels and centrifuged into the reaction chambers, leaving the infusing channels filled with air to avoid cross-contamination of the different chambers. Then, the chip is sealed and placed on a flat thermal cycler for PCR. Finally, amplification products can be detected in situ using a fluorescence scanner or recovered by reverse centrifugation for further analyses. Therefore, our chip possesses two functions: 1) it can be used for multi-target detection based on end-point in situ fluorescence detection; and 2) it can work as a sample preparation unit for analyses that need multiplex PCR such as hybridization and target sequencing. The performance of this chip was carefully examined and further illustrated in the identification of 8 pathogenic bacterial genomic DNA samples and 13 drug-resistance genes. Due to simplicity of its structure and operation, accuracy and generality, high-throughput capacity, and versatile functions (i.e., for in situ detection and sample preparation), our multiplex PCR chip has great potential in clinical diagnostics and nucleic acid-based point-of-care testing.

  4. [Multiplex PCR assay for the detection of Angiostrongylus cantonensis larvae in Pomacea canaliculata].

    Science.gov (United States)

    Wei, Fu-Rong; Liu, He-Xiang; Lv, Shan; Hu, Ling; Zhang, Yi

    2010-10-30

    To establish a multiplex PCR assay for detecting Angiostrongylus cantonensis larvae in Pomacea canaliculata. A pair of specific primers was designed based on the sequences of the small subunit rDNA of A. cantonensis (GenBank jAY295804), in combination with 16s rDNA specific primers of P. canaliculata, a multiplex PCR was developed. The PCR was performed on positive and negative snails, and the amplified products were analyzed by agarose gel electrophoresis and DNA sequencing. DNA template of 200 III stage larvae of A. cantonensis was diluted by negative snail DNA (1200 ng/microl, 120 ng/microl, 12 ng/microl, 1200 pg/microl, 120 pg/microl and 12 pg/microl), to find the minimum detectable level. Single blind method was used to evaluate the accuracy. After being detected by lung microscopy, 172 snails from field were tested by the multiplex PCR to assess the sensitivity and specificity. Agarose gel electrophoresis and DNA sequencing analysis indicated that the target sequences were efficiently amplified by the PCR assay (550 bp for P. canaliculata, 405 bp for A. cantonensis). The minimum detectable level was 120 pg/microl. The coincidence between the two methods stood for 84.3% (145/172), including 45 positives and 100 negatives. 24 snails were PCR positive and microscopy negative, 3 snails were PCR negative and microscopy positive. The sensitivity and specificity of multiplex PCR was 93.8% and 80.6%, respectively. Its positive rate (40.1%, 69/172) was significant higher than that of lung-microscopy (27.9%, 48/172)(chi2 = 14.8, P < 0.01). A multiplex PCR method has been developed for the detection of A. cantonensis larvae in P. canaliculata.

  5. Properties, production and applications of camelid single-domain antibody fragments

    NARCIS (Netherlands)

    Harmsen, M.M.; Haard, de H.J.

    2007-01-01

    Camelids produce functional antibodies devoid of light chains of which the single N-terminal domain is fully capable of antigen binding. These single-domain antibody fragments (VHHs or Nanobodies®) have several advantages for biotechnological applications. They are well expressed in microorganisms

  6. Diagnosis of Trichomonas vaginalis infection by PCR using vaginal swab samples.

    Science.gov (United States)

    Madico, G; Quinn, T C; Rompalo, A; McKee, K T; Gaydos, C A

    1998-11-01

    Trichomonas vaginalis infection is the most prevalent nonviral sexually transmitted disease (STD) in the world. A PCR test using vaginal swab samples for the detection of T. vaginalis was developed to add T. vaginalis infection to the growing list of STDs that can be detected by DNA amplification techniques. A primer set, BTUB 9/2, was designed to target a well-conserved region in the beta-tubulin genes of T. vaginalis. All strains (15 of 15) of T. vaginalis tested were successfully detected by PCR giving a single predicted product of 112 bp in gel electrophoresis. No such targeted product was amplified with DNA from Trichomonas tenax, Trichomonas gallinae, Chlamydia trachomatis, Neisseria gonorrhoeae, Giardia lamblia, Chilomastix sulcatus, Dientamoeba fragilis, and Entamoeba histolytica. An optimal analytical sensitivity of one T. vaginalis organism per PCR was achieved. Culture, performed with the Inpouch TV culture system, was examined daily with a light microscope to identify T. vaginalis. Twenty-three of 350 (6.6%) vaginal swab samples from women attending an army medical clinic were culture positive for T. vaginalis. Of these culture positive specimens, PCR detected 22 of 23 (96%) with primer set BTUB 9/2, and wet preparation detected only 12 of 23 (52%). Seventeen specimens were BTUB 9/2-PCR positive and culture negative. Ten of these discordant specimens were determined to be as true positive by PCR using primer sets TVA 5-1/6 and/or AP65 A/B, which target different regions in the T. vaginalis genome, and seven were determined to be false positive. The sensitivity of BTUB 9/2-PCR was 97% and the specificity was 98%. The sensitivities of culture and wet preparation were 70 and 36%, respectively. The diagnosis of T. vaginalis infection by PCR is a sensitive and specific method that could be incorporated into a joint strategy for the screening of multiple STDs by using molecular amplification methods.

  7. Search for R-Parity Violating Production of Single Sneutrinos in $e^{+}e^{-}$ Collisions at $\\sqrt{s}$ = 189-209 GeV

    CERN Document Server

    Heister, A.; Barate, R.; Bruneliere, R.; De Bonis, I.; Decamp, D.; Goy, C.; Jezequel, S.; Lees, J.P.; Martin, F.; Merle, E.; Minard, M.N.; Pietrzyk, B.; Trocme, B.; Boix, G.; Bravo, S.; Casado, M.P.; Chmeissani, M.; Crespo, J.M.; Fernandez, E.; Fernandez-Bosman, M.; Garrido, L.; Grauges, E.; Lopez, J.; Martinez, M.; Merino, G.; Miquel, R.; Mir, L.M.; Pacheco, A.; Paneque, D.; Ruiz, H.; Colaleo, A.; Creanza, D.; De Filippis, N.; de Palma, M.; Iaselli, G.; Maggi, G.; Maggi, M.; Nuzzo, S.; Ranieri, A.; Raso, G.; Ruggieri, F.; Selvaggi, G.; Silvestris, L.; Tempesta, P.; Tricomi, A.; Zito, G.; Huang, X.; Lin, J.; Ouyang, Q.; Wang, T.; Xie, Y.; Xu, R.; Xue, S.; Zhang, J.; Zhang, L.; Zhao, W.; Abbaneo, D.; Azzurri, P.; Barklow, T.; Buchmuller, O.; Cattaneo, M.; Cerutti, F.; Clerbaux, B.; Drevermann, H.; Forty, R.W.; Frank, M.; Gianotti, F.; Greening, T.C.; Hansen, J.B.; Harvey, J.; Hutchcroft, D.E.; Janot, P.; Jost, B.; Kado, M.; Maley, P.; Mato, P.; Moutoussi, A.; Ranjard, F.; Rolandi, Gigi; Schlatter, D.; Sguazzoni, G.; Tejessy, W.; Teubert, F.; Valassi, A.; Videau, I.; Ward, J.J.; Badaud, F.; Dessagne, S.; Falvard, A.; Fayolle, D.; Gay, P.; Jousset, J.; Michel, B.; Monteil, S.; Pallin, D.; Pascolo, J.M.; Perret, P.; Hansen, J.D.; Hansen, J.R.; Hansen, P.H.; Nilsson, B.S.; Waananen, A.; Kyriakis, A.; Markou, C.; Simopoulou, E.; Vayaki, A.; Zachariadou, K.; Blondel, A.; Brient, J.C.; Machefert, F.; Rouge, A.; Swynghedauw, M.; Tanaka, R.; Videau, H.; Ciulli, V.; Focardi, E.; Parrini, G.; Antonelli, A.; Antonelli, M.; Bencivenni, G.; Bologna, G.; Bossi, F.; Campana, P.; Capon, G.; Chiarella, V.; Laurelli, P.; Mannocchi, G.; Murtas, F.; Murtas, G.P.; Passalacqua, L.; Pepe-Altarelli, M.; Spagnolo, P.; Kennedy, J.; Lynch, J.G.; Negus, P.; O'Shea, V.; Smith, D.; Thompson, A.S.; Wasserbaech, S.; Cavanaugh, R.; Dhamotharan, S.; Geweniger, C.; Hanke, P.; Hepp, V.; Kluge, E.E.; Leibenguth, G.; Putzer, A.; Stenzel, H.; Tittel, K.; Werner, S.; Wunsch, M.; Beuselinck, R.; Binnie, D.M.; Cameron, W.; Davies, G.; Dornan, P.J.; Girone, M.; Hill, R.D.; Marinelli, N.; Nowell, J.; Przysiezniak, H.; Rutherford, S.A.; Sedgbeer, J.K.; Thompson, J.C.; White, R.; Ghete, V.M.; Girtler, P.; Kneringer, E.; Kuhn, D.; Rudolph, G.; Bouhova-Thacker, E.; Bowdery, C.K.; Clarke, D.P.; Ellis, G.; Finch, A.J.; Foster, F.; Hughes, G.; Jones, R.W.L.; Pearson, M.R.; Robertson, N.A.; Smizanska, M.; Lemaitre, V.; Blumenschein, U.; Holldorfer, F.; Jakobs, K.; Kayser, F.; Kleinknecgt, K.; Muller, A.S.; Quast, G.; Renk, B.; Sander, H.G.; Schmeling, S.; Wachsmuth, H.; Zeitnitz, C.; Ziegler, T.; Bonissent, A.; Carr, J.; Coyle, P.; Curtil, C.; Ealet, A.; Fouchez, D.; Leroy, O.; Kachelhoffer, T.; Payre, P.; Rousseau, D.; Tilquin, A.; Ragusa, F.; David, A.; Dietl, H.; Ganis, G.; Huttmann, K.; Lutjens, G.; Mannert, C.; Manner, W.; Moser, H.-G.; Settles, R.; Wolf, G.; Boucrot, J.; Callot, O.; Davier, M.; Duflot, L.; Grivaz, J.F.; Heusse, P.; Jacholkowska, A.; Loomis, C.; Serin, L.; Veillet, J.J.; de Vivie de Regie, J.B.; Yuan, C.; Bagliesi, Giuseppe; Boccali, T.; Foa, L.; Giammanco, A.; Giassi, A.; Ligabue, F.; Messineo, A.; Palla, F.; Sanguinetti, G.; Sciaba, A.; Tenchini, R.; Venturi, A.; Verdini, P.G.; Awunor, O.; Blair, G.A.; Coles, J.; Cowan, G.; Garcia-Bellido, A.; Green, M.G.; Jones, L.T.; Medcalf, T.; Misiejuk, A.; Strong, J.A.; Teixeira-Dias, P.; Clifft, R.W.; Edgecock, T.R.; Norton, P.R.; Tomalin, I.R.; Bloch-Devaux, Brigitte; Boumediene, D.; Colas, P.; Fabbro, B.; Lancon, E.; Lemaire, M.C.; Locci, E.; Perez, P.; Rander, J.; Renardy, J.-F.; Rosowsky, A.; Seager, P.; Trabelsi, A.; Tuchming, B.; Vallage, B.; Konstantinidis, N.; Litke, A.M.; Taylor, G.; Booth, C.N.; Cartwright, S.; Combley, F.; Hodgson, P.N.; Lehto, M.; Thompson, L.F.; Affholderbach, K.; Boehrer, Armin; Brandt, S.; Grupen, C.; Hess, J.; Ngac, A.; Prange, G.; Sieler, U.; Borean, C.; Giannini, G.; He, H.; Putz, J.; Rothberg, J.; Armstrong, S.R.; Berkelman, Karl; Cranmer, K.; Ferguson, D.P.S.; Gao, Y.; Gonzalez, S.; Hayes, O.J.; Hu, H.; Jin, S.; Kile, J.; McNamara, P.A., III; Nielsen, J.; Pan, Y.B.; von Wimmersperg-Toeller, J.H.; Wiedenmann, W.; Wu, J.; Wu, Sau Lan; Wu, X.; Zobernig, G.; Dissertori, G.

    2002-01-01

    A search for single sneutrino production under the assumption that $R$-parity is violated via a single dominant $LL\\bar{E}$ coupling is presented. This search considers the process ${\\rm e} \\gamma \\;{\\smash{\\mathop{\\rightarrow}}}\\;\\tilde{\

  8. PCR-Based Diagnosis of Neoscytalidium dimidiatum Infection Using Internal Transcribed Spacer 1 Region of Ribosomal DNA Primers

    Directory of Open Access Journals (Sweden)

    Charussri Leeyaphan, M.D.

    2018-01-01

    Full Text Available Objective: To develop N. dimidiatum-specific single PCR-based identification with DNA sequences of nuclear ribosomal internal transcribed spacer (ITS 1 region primers to facilitate the rapid and accurate detection of N. dimidiatum. Methods: N. dimidiatum-specific PCR primers were designed based on the sequence of the internal transcribed spacer 1 region, which is located between 18S and 5.8S nuclear rDNA. Fungal DNA extracted from common causative species for superficial fungal infection including: 2 strains of N. dimidiatum, 9 species of dermatophyte (DMP and 25 species of non-dermatophyte (NDM colonies grown on culture plates were used for PCR analysis. Also, 30 clinical specimens collected from 30 patients clinically diagnosed with fungal nail and feet infection who attended Dermatology clinic Siriraj Hospital during October 2015 to November 2015 were used for PCR assay. Results: Using N. dimidiatum-specific PCR primers, the PCR product was amplified from two standard strains of N. dimidiatum, and there was no amplification from other DMP or NDM species. Regarding sensitivity as lower limit of detection, this PCR method was able to detect 10 pg of N. dimidiatum DNA with ethidium bromide staining and could detect N. dimidiatum in clinical samples. Conclusion: This newly developed N. dimidiatum-specific PCR identification system is rapid, sensitive, and specific. This diagnostic method will facilitate early and accurate diagnosis and accelerate appropriate treatment in patients with N. dimidiatum infection.

  9. Simultaneous Detection of Four Foodborne Viruses in Food Samples Using a One-Step Multiplex Reverse Transcription PCR.

    Science.gov (United States)

    Lee, Shin-Young; Kim, Mi-Ju; Kim, Hyun-Joong; Jeong, KwangCheol Casey; Kim, Hae-Yeong

    2018-02-28

    A one-step multiplex reverse transcription PCR (RT-PCR) method comprising six primer sets (for the detection of norovirus GI and GII, hepatitis A virus, rotavirus, and astrovirus) was developed to simultaneously detect four kinds of pathogenic viruses. The size of the PCR products for norovirus GI and GII, hepatitis A virus (VP3/VP1 and P2A regions), rotavirus, and astrovirus were 330, 164, 244, 198, 629, and 449 bp, respectively. The RT-PCR with the six primer sets showed specificity for the pathogenic viruses. The detection limit of the developed multiplex RT-PCR, as evaluated using serially diluted viral RNAs, was comparable to that of one-step single RT-PCR. Moreover, this multiplex RT-PCR was evaluated using food samples such as water, oysters, lettuce, and vegetable product. These food samples were artificially spiked with the four kinds of viruses in diverse combinations, and the spiked viruses in all food samples were detected successfully.

  10. Search for Electroweak Single Top Quark Production in 1.96 TeV Proton-Antiproton Collisions

    Energy Technology Data Exchange (ETDEWEB)

    Stelzer, Bernd [Univ. of Toronto, ON (Canada). Dept. of Physics

    2005-01-01

    This thesis describes the first search for electroweak single top quark production in proton-antiproton collisions at a center of mass energy of 1.96 TeV. The data sample used for this analysis corresponds to 162 pb-1 recorded by the upgraded Collider Detector at Fermilab. The search is performed by doing a classic maximum likelihood fit to the HT distribution in data. The kinematic variable HT is the scalar sum of transverse energies of all final state particles in the event. This variable has the advantage that its distribution looks very similar for both contributing (s-channel and t-channel) single top processes, but is different for background processes. The combination of both channels to one signal improves the sensitivity of the search. No significant evidence for electroweak single top quark production is found and we set an upper limit at the 95% confidence level on the combined single top quark production cross section of 17.8 pb.

  11. Measurement of single photon production in e[sup +]e[sup -] collisions near the Z[sup 0] resonance

    Energy Technology Data Exchange (ETDEWEB)

    Akers, R. (Manchester Univ. (United Kingdom). Dept. of Physics); Alexander, G.; Allison, J.; Anderson, K.J.; Arcelli, S.; Asai, S.; Astbury, A.; Axen, D.; Azuelos, G.; Ball, A.H.; Barberio, E.; Barlow, R.J.; Bartoldus, R.; Batley, J.R.; Beaudoin, G.; Beck, A.; Beck, G.A.; Becker, J.; Beeston, C.; Behnke, T.; Bell, K.W.; Bella, G.; Bentkowski, P.; Bentvelsen, S.; Berlich, P.; Bethke, S.; Biebel, O.; Bloodworth, I.J.; Bock, P.; Bosch, H.M.; Boutemeur, M.; Braibant, S.; Bright-Thomas, P.; Brown, R.M.; Buijs, A.; Burckhart, H.J.; Burgard, C.; Capiluppi, P.; Carnegie, R.K.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlesworth, C.; Charlton, D.G.; Chu, S.L.; Clarke, P.E.L.; Clayton, J.C.; Clowes, S.G.; Cohen, I.; Conboy, J.E.; Coupland, M.; Cuffiani, M.; Dado, S.; Dallapiccola, C.; Darling, C.; Dallavalle, G.M.; Jong, S. de; Deng, H.; Dittmar, M.; Dixit, M.S.; Couto e Silva, E. do; Duchovni, E.; Duboscq, J.E.; Duckeck, G.; Duerdoth, I.P.; Dunwoody, U.C.; Elcombe, P.A.; Estabrooks, P.G.; Et; OPAL Collaboration

    1995-01-01

    A measurement of the single photon production cross-section is presented based on a data-sample of 40.5 pb[sup -1] collected with the OPAL detector at centre-of-mass energies within 3 GeV of the Z[sup 0] mass. Single photon events arise from initial state radiation and the production of an ''invisible'' final state consisting of neutrinos or possibly particles such as sneutrinos or photinos. The single photon topology is also sensitive to new Z[sup 0] decays such as Z[sup 0] [yields] anti [nu][nu][sup *] [yields] anti [nu][nu][gamma] or Z[sup 0] [yields] [gamma]X, X [yields] invisible particles. A total of 447 single photon candidates were observed with energy exceeding 1.75 GeV in the polar angle region vertical stroke cos [theta]vertical stroke < 0.7. The estimated background from processes with visible reaction products, mainly e[sup +]e[sup -] [yields] e[sup +]e[sup -][gamma], is 37 [+-] 6 events. Interpreting the cross-sections as being solely due to Z[sup 0] decay to invisible particles and the expected W-contributions, the Z[sup 0] invisible width is determined to be 539 [+-] 26 [+-] 17 MeV corresponding to N[sub [nu

  12. IpO: plasmids and methods for simplified, PCR-based DNA transplant in yeast.

    Science.gov (United States)

    Horecka, Joe; Chu, Angela M; Davis, Ronald W

    2014-05-01

    Many yeast experiments require strains modified by recombinant DNA methods. Some experiments require precise insertion of a DNA segment into the genome without a selectable marker remaining. For these applications, we developed a new PCR-based method for marker-free DNA transplant. The current PCR-based method requires the labour-intensive construction of a PCR template plasmid with repeats of the DNA segment flanking URA3. The design of a new vector, IpO, reduces the work in cloning a single copy of the DNA segment between overlapping URA3 fragments present in the vector. Two PCRs are performed that capture the DNA segment and one or the other URA3 fragment. When the PCR products are co-transformed into yeast, recombination between the overlapping URA3 fragments restores URA3 and transposes the cloned DNA segment inside out, creating a repeat-URA3-repeat cassette. Sequences designed into the PCR primers target integration of the cassette into the genome. Subsequent selection with 5-fluoro-orotic acid yields strains that have 'popped out' URA3 via recombination between the DNA repeats, with the result being the precise insertion of the DNA segment minus the selectable marker. An additional advantage of the IpO method is that it eliminates PCR artifacts that can plague the current method's repeat-containing templates. Copyright © 2014 John Wiley & Sons, Ltd.

  13. A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

    Science.gov (United States)

    Huang, Kunlun; Zhang, Nan; Yuan, Yanfang; Shang, Ying; Luo, Yunbo

    2012-01-01

    In this study, a novel universal primer-multiplex-PCR (UP-M-PCR) method adding a universal primer (UP) in the multiplex PCR reaction system was described. A universal adapter was designed in the 5′-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP). PCR products were analyzed on sequencing gel electrophoresis (SGE) which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM) crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on. PMID:22272223

  14. Associated Production of ttbar and single top + Vector Bosons in Atlas

    CERN Document Server

    Protopopescu, Serban; The ATLAS collaboration

    2018-01-01

    Measurements of inclusive and differential cross sections of single top and t tbar pairs associated with vector bosons produced in pp collisions at 8 and 13 TeV center of mass collected with the Atlas detector are presented.

  15. Measurements of Pair Production Under Channelling Conditions by 70-180 GeV Photons Incident on Single Crystals

    CERN Multimedia

    2002-01-01

    This experiment will use the WA69 set-up to deliver a tagged photon beam in the energy range from 15~GeV to 150~GeV with a total angular spread of about @M~0.5~mrad. The incident photon direction is known to about 35~@mrad through the direction of the emitting electron. The photon beam is incident on an about 1~mm thick Ge single crystal in order to investigate pair production in single crystals. Above a certain energy threshold photons incident along crystal axis will show strongly increased pair production yi - the so-called .us Channelling Pair Production (ChPP). The produced pairs are analyzed in the @W-spectrometer. The large spread in incident photon angles offers an excellent opportunity to investigate in one single experiment the pair production in an angular region around a crystal axes and thereby compare ChPP with coherent (CPP) and incoherent (ICPP) processes. The very abrupt onset of ChPP (around threshold) will be measured and give a crucial test of the theoretical calculations. The differential...

  16. Search for single production of vector-like quarks decaying to a b quark and a Higgs boson

    CERN Document Server

    Sirunyan, Albert M; CMS Collaboration; Adam, Wolfgang; Ambrogi, Federico; Asilar, Ece; Bergauer, Thomas; Brandstetter, Johannes; Brondolin, Erica; Dragicevic, Marko; Erö, Janos; Escalante Del Valle, Alberto; Flechl, Martin; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Grossmann, Johannes; Hrubec, Josef; Jeitler, Manfred; König, Axel; Krammer, Natascha; Krätschmer, Ilse; Liko, Dietrich; Madlener, Thomas; Mikulec, Ivan; Pree, Elias; Rad, Navid; Rohringer, Herbert; Schieck, Jochen; Schöfbeck, Robert; Spanring, Markus; Spitzbart, Daniel; Taurok, Anton; Waltenberger, Wolfgang; Wittmann, Johannes; Wulz, Claudia-Elisabeth; Zarucki, Mateusz; Chekhovsky, Vladimir; Mossolov, Vladimir; Suarez Gonzalez, Juan; De Wolf, Eddi A; Di Croce, Davide; Janssen, Xavier; Lauwers, Jasper; Van De Klundert, Merijn; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Abu Zeid, Shimaa; Blekman, Freya; D'Hondt, Jorgen; De Bruyn, Isabelle; De Clercq, Jarne; Deroover, Kevin; Flouris, Giannis; Lontkovskyi, Denys; Lowette, Steven; Marchesini, Ivan; Moortgat, Seth; Moreels, Lieselotte; Python, Quentin; Skovpen, Kirill; Tavernier, Stefaan; Van Doninck, Walter; Van Mulders, Petra; Van Parijs, Isis; Beghin, Diego; Bilin, Bugra; Brun, Hugues; Clerbaux, Barbara; De Lentdecker, Gilles; Delannoy, Hugo; Dorney, Brian; Fasanella, Giuseppe; Favart, Laurent; Goldouzian, Reza; Grebenyuk, Anastasia; Kalsi, Amandeep Kaur; Lenzi, Thomas; Luetic, Jelena; Maerschalk, Thierry; Marinov, Andrey; Seva, Tomislav; Starling, Elizabeth; Vander Velde, Catherine; Vanlaer, Pascal; Vannerom, David; Yonamine, Ryo; Zenoni, Florian; Cornelis, Tom; Dobur, Didar; Fagot, Alexis; Gul, Muhammad; Khvastunov, Illia; Poyraz, Deniz; Roskas, Christos; Salva Diblen, Sinem; Trocino, Daniele; Tytgat, Michael; Verbeke, Willem; Vit, Martina; Zaganidis, Nicolas; Bakhshiansohi, Hamed; Bondu, Olivier; Brochet, Sébastien; Bruno, Giacomo; Caputo, Claudio; Caudron, Adrien; David, Pieter; De Visscher, Simon; Delaere, Christophe; Delcourt, Martin; Francois, Brieuc; Giammanco, Andrea; Komm, Matthias; Krintiras, Georgios; Lemaitre, Vincent; Magitteri, Alessio; Mertens, Alexandre; Musich, Marco; Piotrzkowski, Krzysztof; Quertenmont, Loic; Saggio, Alessia; Vidal Marono, Miguel; Wertz, Sébastien; Zobec, Joze; Aldá Júnior, Walter Luiz; Alves, Fábio Lúcio; Alves, Gilvan; Brito, Lucas; Correia Silva, Gilson; Hensel, Carsten; Moraes, Arthur; Pol, Maria Elena; Rebello Teles, Patricia; Belchior Batista Das Chagas, Ewerton; Carvalho, Wagner; Chinellato, Jose; Coelho, Eduardo; Melo Da Costa, Eliza; Da Silveira, Gustavo Gil; De Jesus Damiao, Dilson; Fonseca De Souza, Sandro; Huertas Guativa, Lina Milena; Malbouisson, Helena; Melo De Almeida, Miqueias; Mora Herrera, Clemencia; Mundim, Luiz; Nogima, Helio; Sanchez Rosas, Luis Junior; Santoro, Alberto; Sznajder, Andre; Thiel, Mauricio; Tonelli Manganote, Edmilson José; Torres Da Silva De Araujo, Felipe; Vilela Pereira, Antonio; Ahuja, Sudha; Bernardes, Cesar Augusto; Tomei, Thiago; De Moraes Gregores, Eduardo; Mercadante, Pedro G; Novaes, Sergio F; Padula, Sandra; Romero Abad, David; Ruiz Vargas, José Cupertino; Aleksandrov, Aleksandar; Hadjiiska, Roumyana; Iaydjiev, Plamen; Misheva, Milena; Rodozov, Mircho; Shopova, Mariana; Sultanov, Georgi; Dimitrov, Anton; Litov, Leander; Pavlov, Borislav; Petkov, Peicho; Fang, Wenxing; Gao, Xuyang; Yuan, Li; Ahmad, Muhammad; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Chen, Mingshui; Chen, Ye; Jiang, Chun-Hua; Leggat, Duncan; Liao, Hongbo; Liu, Zhenan; Romeo, Francesco; Shaheen, Sarmad Masood; Spiezia, Aniello; Tao, Junquan; Wang, Chunjie; Wang, Zheng; Yazgan, Efe; Zhang, Huaqiao; Zhao, Jingzhou; Ban, Yong; Chen, Geng; Li, Jing; Li, Qiang; Liu, Shuai; Mao, Yajun; Qian, Si-Jin; Wang, Dayong; Xu, Zijun; Zhang, Fengwangdong; Wang, Yi; Avila, Carlos; Cabrera, Andrés; Carrillo Montoya, Camilo Andres; Chaparro Sierra, Luisa Fernanda; Florez, Carlos; González Hernández, Carlos Felipe; Ruiz Alvarez, José David; Segura Delgado, Manuel Alejandro; Courbon, Benoit; Godinovic, Nikola; Lelas, Damir; Puljak, Ivica; Ribeiro Cipriano, Pedro M; Sculac, Toni; Antunovic, Zeljko; Kovac, Marko; Brigljevic, Vuko; Ferencek, Dinko; Kadija, Kreso; Mesic, Benjamin; Starodumov, Andrei; Susa, Tatjana; Ather, Mohsan Waseem; Attikis, Alexandros; Mavromanolakis, Georgios; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Rykaczewski, Hans; Finger, Miroslav; Finger Jr, Michael; Carrera Jarrin, Edgar; Abdalla, Hassan; Assran, Yasser; El-khateeb, Esraa; Bhowmik, Sandeep; Dewanjee, Ram Krishna; Kadastik, Mario; Perrini, Lucia; Raidal, Martti; Veelken, Christian; Eerola, Paula; Kirschenmann, Henning; Pekkanen, Juska; Voutilainen, Mikko; Havukainen, Joona; Heikkilä, Jaana Kristiina; Jarvinen, Terhi; Karimäki, Veikko; Kinnunen, Ritva; Lampén, Tapio; Lassila-Perini, Kati; Laurila, Santeri; Lehti, Sami; Lindén, Tomas; Luukka, Panja-Riina; Mäenpää, Teppo; Siikonen, Hannu; Tuominen, Eija; Tuominiemi, Jorma; Tuuva, Tuure; Besancon, Marc; Couderc, Fabrice; Dejardin, Marc; Denegri, Daniel; Faure, Jean-Louis; Ferri, Federico; Ganjour, Serguei; Ghosh, Saranya; Givernaud, Alain; Gras, Philippe; Hamel de Monchenault, Gautier; Jarry, Patrick; Leloup, Clément; Locci, Elizabeth; Machet, Martina; Malcles, Julie; Negro, Giulia; Rander, John; Rosowsky, André; Sahin, Mehmet Özgür; Titov, Maksym; Abdulsalam, Abdulla; Amendola, Chiara; Antropov, Iurii; Baffioni, Stephanie; Beaudette, Florian; Busson, Philippe; Cadamuro, Luca; Charlot, Claude; Granier de Cassagnac, Raphael; Jo, Mihee; Kucher, Inna; Lisniak, Stanislav; Lobanov, Artur; Martin Blanco, Javier; Nguyen, Matthew; Ochando, Christophe; Ortona, Giacomo; Paganini, Pascal; Pigard, Philipp; Salerno, Roberto; Sauvan, Jean-Baptiste; Sirois, Yves; Stahl Leiton, Andre Govinda; Strebler, Thomas; Yilmaz, Yetkin; Zabi, Alexandre; Zghiche, Amina; Agram, Jean-Laurent; Andrea, Jeremy; Bloch, Daniel; Brom, Jean-Marie; Buttignol, Michael; Chabert, Eric Christian; Collard, Caroline; Conte, Eric; Coubez, Xavier; Drouhin, Frédéric; Fontaine, Jean-Charles; Gelé, Denis; Goerlach, Ulrich; Jansová, Markéta; Juillot, Pierre; Le Bihan, Anne-Catherine; Tonon, Nicolas; Van Hove, Pierre; Gadrat, Sébastien; Beauceron, Stephanie; Bernet, Colin; Boudoul, Gaelle; Chanon, Nicolas; Chierici, Roberto; Contardo, Didier; Depasse, Pierre; El Mamouni, Houmani; Fay, Jean; Finco, Linda; Gascon, Susan; Gouzevitch, Maxime; Grenier, Gérald; Ille, Bernard; Lagarde, Francois; Laktineh, Imad Baptiste; Lethuillier, Morgan; Mirabito, Laurent; Pequegnot, Anne-Laure; Perries, Stephane; Popov, Andrey; Sordini, Viola; Vander Donckt, Muriel; Viret, Sébastien; Zhang, Sijing; Toriashvili, Tengizi; Tsamalaidze, Zviad; Autermann, Christian; Feld, Lutz; Kiesel, Maximilian Knut; Klein, Katja; Lipinski, Martin; Preuten, Marius; Schomakers, Christian; Schulz, Johannes; Teroerde, Marius; Wittmer, Bruno; Zhukov, Valery; Albert, Andreas; Duchardt, Deborah; Endres, Matthias; Erdmann, Martin; Erdweg, Sören; Esch, Thomas; Fischer, Robert; Güth, Andreas; Hebbeker, Thomas; Heidemann, Carsten; Hoepfner, Kerstin; Knutzen, Simon; Merschmeyer, Markus; Meyer, Arnd; Millet, Philipp; Mukherjee, Swagata; Pook, Tobias; Radziej, Markus; Reithler, Hans; Rieger, Marcel; Scheuch, Florian; Teyssier, Daniel; Thüer, Sebastian; Flügge, Günter; Kargoll, Bastian; Kress, Thomas; Künsken, Andreas; Müller, Thomas; Nehrkorn, Alexander; Nowack, Andreas; Pistone, Claudia; Pooth, Oliver; Stahl, Achim; Aldaya Martin, Maria; Arndt, Till; Asawatangtrakuldee, Chayanit; Beernaert, Kelly; Behnke, Olaf; Behrens, Ulf; Bermúdez Martínez, Armando; Bin Anuar, Afiq Aizuddin; Borras, Kerstin; Botta, Valeria; Campbell, Alan; Connor, Patrick; Contreras-Campana, Christian; Costanza, Francesco; Diez Pardos, Carmen; Eckerlin, Guenter; Eckstein, Doris; Eichhorn, Thomas; Eren, Engin; Gallo, Elisabetta; Garay Garcia, Jasone; Geiser, Achim; Grados Luyando, Juan Manuel; Grohsjean, Alexander; Gunnellini, Paolo; Guthoff, Moritz; Harb, Ali; Hauk, Johannes; Hempel, Maria; Jung, Hannes; Kasemann, Matthias; Keaveney, James; Kleinwort, Claus; Korol, Ievgen; Krücker, Dirk; Lange, Wolfgang; Lelek, Aleksandra; Lenz, Teresa; Lipka, Katerina; Lohmann, Wolfgang; Mankel, Rainer; Melzer-Pellmann, Isabell-Alissandra; Meyer, Andreas Bernhard; Missiroli, Marino; Mittag, Gregor; Mnich, Joachim; Mussgiller, Andreas; Ntomari, Eleni; Pitzl, Daniel; Raspereza, Alexei; Savitskyi, Mykola; Saxena, Pooja; Shevchenko, Rostyslav; Stefaniuk, Nazar; Van Onsem, Gerrit Patrick; Walsh, Roberval; Wen, Yiwen; Wichmann, Katarzyna; Wissing, Christoph; Zenaiev, Oleksandr; Aggleton, Robin; Bein, Samuel; Blobel, Volker; Centis Vignali, Matteo; Dreyer, Torben; Garutti, Erika; Gonzalez, Daniel; Haller, Johannes; Hinzmann, Andreas; Hoffmann, Malte; Karavdina, Anastasia; Klanner, Robert; Kogler, Roman; Kovalchuk, Nataliia; Kurz, Simon; Marconi, Daniele; Meyer, Mareike; Niedziela, Marek; Nowatschin, Dominik; Pantaleo, Felice; Peiffer, Thomas; Perieanu, Adrian; Scharf, Christian; Schleper, Peter; Schmidt, Alexander; Schumann, Svenja; Schwandt, Joern; Sonneveld, Jory; Stadie, Hartmut; Steinbrück, Georg; Stober, Fred-Markus Helmut; Stöver, Marc; Tholen, Heiner; Troendle, Daniel; Usai, Emanuele; Vanhoefer, Annika; Vormwald, Benedikt; Akbiyik, Melike; Barth, Christian; Baselga, Marta; Baur, Sebastian; Butz, Erik; Caspart, René; Chwalek, Thorsten; Colombo, Fabio; De Boer, Wim; Dierlamm, Alexander; Faltermann, Nils; Freund, Benedikt; Friese, Raphael; Giffels, Manuel; Harrendorf, Marco Alexander; Hartmann, Frank; Heindl, Stefan Michael; Husemann, Ulrich; Kassel, Florian; Kudella, Simon; Mildner, Hannes; Mozer, Matthias Ulrich; Müller, Thomas; Plagge, Michael; Quast, Gunter; Rabbertz, Klaus; Schröder, Matthias; Shvetsov, Ivan; Sieber, Georg; Simonis, Hans-Jürgen; Ulrich, Ralf; Wayand, Stefan; Weber, Marc; Weiler, Thomas; Williamson, Shawn; Wöhrmann, Clemens; Wolf, Roger; Anagnostou, Georgios; Daskalakis, Georgios; Geralis, Theodoros; Kyriakis, Aristotelis; Loukas, Demetrios; Topsis-Giotis, Iasonas; Karathanasis, George; Kesisoglou, Stilianos; Panagiotou, Apostolos; Saoulidou, Niki; Tziaferi, Eirini; Kousouris, Konstantinos; Evangelou, Ioannis; Foudas, Costas; Gianneios, Paraskevas; Katsoulis, Panagiotis; Kokkas, Panagiotis; Mallios, Stavros; Manthos, Nikolaos; Papadopoulos, Ioannis; Paradas, Evangelos; Strologas, John; Triantis, Frixos A; Tsitsonis, Dimitrios; Csanad, Mate; Filipovic, Nicolas; Pasztor, Gabriella; Surányi, Olivér; Veres, Gabor Istvan; Bencze, Gyorgy; Hajdu, Csaba; Horvath, Dezso; Hunyadi, Ádám; Sikler, Ferenc; Veszpremi, Viktor; Vesztergombi, Gyorgy; Beni, Noemi; Czellar, Sandor; Karancsi, János; Makovec, Alajos; Molnar, Jozsef; Szillasi, Zoltan; Bartók, Márton; Raics, Peter; Trocsanyi, Zoltan Laszlo; Ujvari, Balazs; Choudhury, Somnath; Komaragiri, Jyothsna Rani; Bahinipati, Seema; Mal, Prolay; Mandal, Koushik; Nayak, Aruna; Sahoo, Deepak Kumar; Sahoo, Niladribihari; Swain, Sanjay Kumar; Bansal, Sunil; Beri, Suman Bala; Bhatnagar, Vipin; Chawla, Ridhi; Dhingra, Nitish; Kaur, Anterpreet; Kaur, Manjit; Kaur, Sandeep; Kumar, Ramandeep; Kumari, Priyanka; Mehta, Ankita; Singh, Jasbir; Walia, Genius; Kumar, Ashok; Shah, Aashaq; Bhardwaj, Ashutosh; Chauhan, Sushil; Choudhary, Brajesh C; Garg, Rocky Bala; Keshri, Sumit; Kumar, Ajay; Malhotra, Shivali; Naimuddin, Md; Ranjan, Kirti; Sharma, Ramkrishna; Bhardwaj, Rishika; Bhattacharya, Rajarshi; Bhattacharya, Satyaki; Bhawandeep, Bhawandeep; Bhowmik, Debabrata; Dey, Sourav; Dutt, Suneel; Dutta, Suchandra; Ghosh, Shamik; Majumdar, Nayana; Modak, Atanu; Mondal, Kuntal; Mukhopadhyay, Supratik; Nandan, Saswati; Purohit, Arnab; Rout, Prasant Kumar; Roy, Ashim; Roy Chowdhury, Suvankar; Sarkar, Subir; Sharan, Manoj; Singh, Bipen; Thakur, Shalini; Behera, Prafulla Kumar; Chudasama, Ruchi; Dutta, Dipanwita; Jha, Vishwajeet; Kumar, Vineet; Mohanty, Ajit Kumar; Netrakanti, Pawan Kumar; Pant, Lalit Mohan; Shukla, Prashant; Topkar, Anita; Aziz, Tariq; Dugad, Shashikant; Mahakud, Bibhuprasad; Mitra, Soureek; Mohanty, Gagan Bihari; Sur, Nairit; Sutar, Bajrang; Banerjee, Sudeshna; Bhattacharya, Soham; Chatterjee, Suman; Das, Pallabi; Guchait, Monoranjan; Jain, Sandhya; Kumar, Sanjeev; Maity, Manas; Majumder, Gobinda; Mazumdar, Kajari; Sarkar, Tanmay; Wickramage, Nadeesha; Chauhan, Shubhanshu; Dube, Sourabh; Hegde, Vinay; Kapoor, Anshul; Kothekar, Kunal; Pandey, Shubham; Rane, Aditee; Sharma, Seema; Chenarani, Shirin; Eskandari Tadavani, Esmaeel; Etesami, Seyed Mohsen; Khakzad, Mohsen; Mohammadi Najafabadi, Mojtaba; Naseri, Mohsen; Paktinat Mehdiabadi, Saeid; Rezaei Hosseinabadi, Ferdos; Safarzadeh, Batool; Zeinali, Maryam; Felcini, Marta; Grunewald, Martin; Abbrescia, Marcello; Calabria, Cesare; Colaleo, Anna; Creanza, Donato; Cristella, Leonardo; De Filippis, Nicola; De Palma, Mauro; Errico, Filippo; Fiore, Luigi; Iaselli, Giuseppe; Lezki, Samet; Maggi, Giorgio; Maggi, Marcello; Miniello, Giorgia; My, Salvatore; Nuzzo, Salvatore; Pompili, Alexis; Pugliese, Gabriella; Radogna, Raffaella; Ranieri, Antonio; Selvaggi, Giovanna; Sharma, Archana; Silvestris, Lucia; Venditti, Rosamaria; Verwilligen, Piet; Abbiendi, Giovanni; Battilana, Carlo; Bonacorsi, Daniele; Borgonovi, Lisa; Braibant-Giacomelli, Sylvie; Campanini, Renato; Capiluppi, Paolo; Castro, Andrea; Cavallo, Francesca Romana; Chhibra, Simranjit Singh; Codispoti, Giuseppe; Cuffiani, Marco; Dallavalle, Gaetano-Marco; Fabbri, Fabrizio; Fanfani, Alessandra; Fasanella, Daniele; Giacomelli, Paolo; Grandi, Claudio; Guiducci, Luigi; Iemmi, Fabio; Marcellini, Stefano; Masetti, Gianni; Montanari, Alessandro; Navarria, Francesco; Perrotta, Andrea; Rossi, Antonio; Rovelli, Tiziano; Siroli, Gian Piero; Tosi, Nicolò; Albergo, Sebastiano; Costa, Salvatore; Di Mattia, Alessandro; Giordano, Ferdinando; Potenza, Renato; Tricomi, Alessia; Tuve, Cristina; Barbagli, Giuseppe; Chatterjee, Kalyanmoy; Ciulli, Vitaliano; Civinini, Carlo; D'Alessandro, Raffaello; Focardi, Ettore; Lenzi, Piergiulio; Meschini, Marco; Paoletti, Simone; Russo, Lorenzo; Sguazzoni, Giacomo; Strom, Derek; Viliani, Lorenzo; Benussi, Luigi; Bianco, Stefano; Fabbri, Franco; Piccolo, Davide; Primavera, Federica; Calvelli, Valerio; Ferro, Fabrizio; Panizzi, Luca; Ravera, Fabio; Robutti, Enrico; Tosi, Silvano; Benaglia, Andrea; Beschi, Andrea; Brianza, Luca; Brivio, Francesco; Ciriolo, Vincenzo; Dinardo, Mauro Emanuele; Fiorendi, Sara; Gennai, Simone; Ghezzi, Alessio; Govoni, Pietro; Malberti, Martina; Malvezzi, Sandra; Manzoni, Riccardo Andrea; Menasce, Dario; Moroni, Luigi; Paganoni, Marco; Pauwels, Kristof; Pedrini, Daniele; Pigazzini, Simone; Ragazzi, Stefano; Tabarelli de Fatis, Tommaso; Buontempo, Salvatore; Cavallo, Nicola; Di Guida, Salvatore; Fabozzi, Francesco; Fienga, Francesco; Iorio, Alberto Orso Maria; Khan, Wajid Ali; Lista, Luca; Meola, Sabino; Paolucci, Pierluigi; Sciacca, Crisostomo; Thyssen, Filip; Azzi, Patrizia; Bacchetta, Nicola; Benato, Lisa; Boletti, Alessio; Carlin, Roberto; Carvalho Antunes De Oliveira, Alexandra; Checchia, Paolo; Dall'Osso, Martino; De Castro Manzano, Pablo; Dorigo, Tommaso; Dosselli, Umberto; Gasparini, Fabrizio; Gasparini, Ugo; Gozzelino, Andrea; Lacaprara, Stefano; Lujan, Paul; Margoni, Martino; Meneguzzo, Anna Teresa; Pozzobon, Nicola; Ronchese, Paolo; Rossin, Roberto; Simonetto, Franco; Tiko, Andres; Torassa, Ezio; Zanetti, Marco; Zotto, Pierluigi; Zumerle, Gianni; Braghieri, Alessandro; Magnani, Alice; Montagna, Paolo; Ratti, Sergio P; Re, Valerio; Ressegotti, Martina; Riccardi, Cristina; Salvini, Paola; Vai, Ilaria; Vitulo, Paolo; Alunni Solestizi, Luisa; Biasini, Maurizio; Bilei, Gian Mario; Cecchi, Claudia; Ciangottini, Diego; Fanò, Livio; Lariccia, Paolo; Leonardi, Roberto; Manoni, Elisa; Mantovani, Giancarlo; Mariani, Valentina; Menichelli, Mauro; Rossi, Alessandro; Santocchia, Attilio; Spiga, Daniele; Androsov, Konstantin; Azzurri, Paolo; Bagliesi, Giuseppe; Bianchini, Lorenzo; Boccali, Tommaso; Borrello, Laura; Castaldi, Rino; Ciocci, Maria Agnese; Dell'Orso, Roberto; Fedi, Giacomo; Giannini, Leonardo; Giassi, Alessandro; Grippo, Maria Teresa; Ligabue, Franco; Lomtadze, Teimuraz; Manca, Elisabetta; Mandorli, Giulio; Messineo, Alberto; Palla, Fabrizio; Rizzi, Andrea; Spagnolo, Paolo; Tenchini, Roberto; Tonelli, Guido; Venturi, Andrea; Verdini, Piero Giorgio; Barone, Luciano; Cavallari, Francesca; Cipriani, Marco; Daci, Nadir; Del Re, Daniele; Di Marco, Emanuele; Diemoz, Marcella; Gelli, Simone; Longo, Egidio; Margaroli, Fabrizio; Marzocchi, Badder; Meridiani, Paolo; Organtini, Giovanni; Paramatti, Riccardo; Preiato, Federico; Rahatlou, Shahram; Rovelli, Chiara; Santanastasio, Francesco; Amapane, Nicola; Arcidiacono, Roberta; Argiro, Stefano; Arneodo, Michele; Bartosik, Nazar; Bellan, Riccardo; Biino, Cristina; Cartiglia, Nicolo; Cenna, Francesca; Costa, Marco; Covarelli, Roberto; Degano, Alessandro; Demaria, Natale; Kiani, Bilal; Mariotti, Chiara; Maselli, Silvia; Migliore, Ernesto; Monaco, Vincenzo; Monteil, Ennio; Monteno, Marco; Obertino, Maria Margherita; Pacher, Luca; Pastrone, Nadia; Pelliccioni, Mario; Pinna Angioni, Gian Luca; Romero, Alessandra; Ruspa, Marta; Sacchi, Roberto; Shchelina, Ksenia; Sola, Valentina; Solano, Ada; Staiano, Amedeo; Traczyk, Piotr; Belforte, Stefano; Casarsa, Massimo; Cossutti, Fabio; Della Ricca, Giuseppe; Zanetti, Anna; Kim, Dong Hee; Kim, Gui Nyun; Kim, Min Suk; Lee, Jeongeun; Lee, Sangeun; Lee, Seh Wook; Moon, Chang-Seong; Oh, Young Do; Sekmen, Sezen; Son, Dong-Chul; Yang, Yu Chul; Kim, Hyunchul; Moon, Dong Ho; Oh, Geonhee; Brochero Cifuentes, Javier Andres; Goh, Junghwan; Kim, Tae Jeong; Cho, Sungwoong; Choi, Suyong; Go, Yeonju; Gyun, Dooyeon; Ha, Seungkyu; Hong, Byung-Sik; Jo, Youngkwon; Kim, Yongsun; Lee, Kisoo; Lee, Kyong Sei; Lee, Songkyo; Lim, Jaehoon; Park, Sung Keun; Roh, Youn; Almond, John; Kim, Junho; Kim, Jae Sung; Lee, Haneol; Lee, Kyeongpil; Nam, Kyungwook; Oh, Sung Bin; Radburn-Smith, Benjamin Charles; Seo, Seon-hee; Yang, Unki; Yoo, Hwi Dong; Yu, Geum Bong; Kim, Hyunyong; Kim, Ji Hyun; Lee, Jason Sang Hun; Park, Inkyu; Choi, Young-Il; Hwang, Chanwook; Lee, Jongseok; Yu, Intae; Dudenas, Vytautas; Juodagalvis, Andrius; Vaitkus, Juozas; Ahmed, Ijaz; Ibrahim, Zainol Abidin; Md Ali, Mohd Adli Bin; Mohamad Idris, Faridah; Wan Abdullah, Wan Ahmad Tajuddin; Yusli, Mohd Nizam; Zolkapli, Zukhaimira; Reyes-Almanza, Rogelio; Ramirez-Sanchez, Gabriel; Duran-Osuna, Cecilia; Castilla-Valdez, Heriberto; De La Cruz-Burelo, Eduard; Heredia-De La Cruz, Ivan; Rabadán-Trejo, Raúl Iraq; Lopez-Fernandez, Ricardo; Mejia Guisao, Jhovanny; Sánchez Hernández, Alberto; Carrillo Moreno, Salvador; Oropeza Barrera, Cristina; Vazquez Valencia, Fabiola; Eysermans, Jan; Pedraza, Isabel; Salazar Ibarguen, Humberto Antonio; Uribe Estrada, Cecilia; Morelos Pineda, Antonio; Krofcheck, David; Butler, Philip H; Ahmad, Ashfaq; Ahmad, Muhammad; Hassan, Qamar; Hoorani, Hafeez R; Saddique, Asif; Shah, Mehar Ali; Shoaib, Muhammad; Waqas, Muhammad; Bialkowska, Helena; Bluj, Michal; Boimska, Bozena; Frueboes, Tomasz; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Szleper, Michal; Zalewski, Piotr; Bunkowski, Karol; Byszuk, Adrian; Doroba, Krzysztof; Kalinowski, Artur; Konecki, Marcin; Krolikowski, Jan; Misiura, Maciej; Olszewski, Michal; Pyskir, Andrzej; Walczak, Marek; Bargassa, Pedrame; Beirão Da Cruz E Silva, Cristóvão; Di Francesco, Agostino; Faccioli, Pietro; Galinhas, Bruno; Gallinaro, Michele; Hollar, Jonathan; Leonardo, Nuno; Lloret Iglesias, Lara; Nemallapudi, Mythra Varun; Seixas, Joao; Strong, Giles; Toldaiev, Oleksii; Vadruccio, Daniele; Varela, Joao; Afanasiev, Serguei; Alexakhin, Vadim; Golunov, Alexander; Golutvin, Igor; Gorbounov, Nikolai; Gorbunov, Ilya; Kamenev, Alexey; Karjavin, Vladimir; Lanev, Alexander; Malakhov, Alexander; Matveev, Viktor; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Shulha, Siarhei; Skatchkov, Nikolai; Smirnov, Vitaly; Zarubin, Anatoli; Ivanov, Yury; Kim, Victor; Kuznetsova, Ekaterina; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sosnov, Dmitry; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Karneyeu, Anton; Kirsanov, Mikhail; Krasnikov, Nikolai; Pashenkov, Anatoli; Tlisov, Danila; Toropin, Alexander; Epshteyn, Vladimir; Gavrilov, Vladimir; Lychkovskaya, Natalia; Popov, Vladimir; Pozdnyakov, Ivan; Safronov, Grigory; Spiridonov, Alexander; Stepennov, Anton; Stolin, Viatcheslav; Toms, Maria; Vlasov, Evgueni; Zhokin, Alexander; Aushev, Tagir; Bylinkin, Alexander; Chistov, Ruslan; Danilov, Mikhail; Parygin, Pavel; Philippov, Dmitry; Polikarpov, Sergey; Tarkovskii, Evgenii; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Rusakov, Sergey V; Terkulov, Adel; Baskakov, Alexey; Belyaev, Andrey; Boos, Edouard; Bunichev, Viacheslav; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Klyukhin, Vyacheslav; Kodolova, Olga; Lokhtin, Igor; Miagkov, Igor; Obraztsov, Stepan; Perfilov, Maxim; Petrushanko, Sergey; Savrin, Viktor; Blinov, Vladimir; Shtol, Dmitry; Skovpen, Yuri; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Elumakhov, Dmitry; Godizov, Anton; Kachanov, Vassili; Kalinin, Alexey; Konstantinov, Dmitri; Mandrik, Petr; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Babaev, Anton; Adzic, Petar; Cirkovic, Predrag; Devetak, Damir; Dordevic, Milos; Milosevic, Jovan; Alcaraz Maestre, Juan; Bachiller, Irene; Barrio Luna, Mar; Cerrada, Marcos; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Flix, Jose; Fouz, Maria Cruz; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Moran, Dermot; Pérez-Calero Yzquierdo, Antonio María; Puerta Pelayo, Jesus; Redondo, Ignacio; Romero, Luciano; Senghi Soares, Mara; Triossi, Andrea; Álvarez Fernández, Adrian; Albajar, Carmen; de Trocóniz, Jorge F; Cuevas, Javier; Erice, Carlos; Fernandez Menendez, Javier; Gonzalez Caballero, Isidro; González Fernández, Juan Rodrigo; Palencia Cortezon, Enrique; Sanchez Cruz, Sergio; Vischia, Pietro; Vizan Garcia, Jesus Manuel; Cabrillo, Iban Jose; Calderon, Alicia; Chazin Quero, Barbara; Duarte Campderros, Jordi; Fernandez, Marcos; Fernández Manteca, Pedro José; Garcia-Ferrero, Juan; García Alonso, Andrea; Gomez, Gervasio; Lopez Virto, Amparo; Marco, Jesus; Martinez Rivero, Celso; Martinez Ruiz del Arbol, Pablo; Matorras, Francisco; Piedra Gomez, Jonatan; Prieels, Cédric; Rodrigo, Teresa; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Trevisani, Nicolò; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Akgun, Bora; Auffray, Etiennette; Baillon, Paul; Ball, Austin; Barney, David; Bendavid, Joshua; Bianco, Michele; Bocci, Andrea; Botta, Cristina; Camporesi, Tiziano; Castello, Roberto; Cepeda, Maria; Cerminara, Gianluca; Chapon, Emilien; Chen, Yi; D'Enterria, David; Dabrowski, Anne; Daponte, Vincenzo; David Tinoco Mendes, Andre; De Gruttola, Michele; De Roeck, Albert; Deelen, Nikkie; Dobson, Marc; Du Pree, Tristan; Dünser, Marc; Dupont, Niels; Elliott-Peisert, Anna; Everaerts, Pieter; Fallavollita, Francesco; Franzoni, Giovanni; Fulcher, Jonathan; Funk, Wolfgang; Gigi, Dominique; Gilbert, Andrew; Gill, Karl; Glege, Frank; Gulhan, Doga; Hegeman, Jeroen; Innocente, Vincenzo; Jafari, Abideh; Janot, Patrick; Karacheban, Olena; Kieseler, Jan; Knünz, Valentin; Kornmayer, Andreas; Kortelainen, Matti J; Krammer, Manfred; Lange, Clemens; Lecoq, Paul; Lourenco, Carlos; Lucchini, Marco Toliman; Malgeri, Luca; Mannelli, Marcello; Martelli, Arabella; Meijers, Frans; Merlin, Jeremie Alexandre; Mersi, Stefano; Meschi, Emilio; Milenovic, Predrag; Moortgat, Filip; Mulders, Martijn; Neugebauer, Hannes; Ngadiuba, Jennifer; Orfanelli, Styliani; Orsini, Luciano; Pape, Luc; Perez, Emmanuel; Peruzzi, Marco; Petrilli, Achille; Petrucciani, Giovanni; Pfeiffer, Andreas; Pierini, Maurizio; Pitters, Florian Michael; Rabady, Dinyar; Racz, Attila; Reis, Thomas; Rolandi, Gigi; Rovere, Marco; Sakulin, Hannes; Schäfer, Christoph; Schwick, Christoph; Seidel, Markus; Selvaggi, Michele; Sharma, Archana; Silva, Pedro; Sphicas, Paraskevas; Stakia, Anna; Steggemann, Jan; Stoye, Markus; Tosi, Mia; Treille, Daniel; Tsirou, Andromachi; Veckalns, Viesturs; Verweij, Marta; Zeuner, Wolfram Dietrich; Bertl, Willi; Caminada, Lea; Deiters, Konrad; Erdmann, Wolfram; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; Kotlinski, Danek; Langenegger, Urs; Rohe, Tilman; Wiederkehr, Stephan Albert; Backhaus, Malte; Bäni, Lukas; Berger, Pirmin; Casal, Bruno; Dissertori, Günther; Dittmar, Michael; Donegà, Mauro; Dorfer, Christian; Grab, Christoph; Heidegger, Constantin; Hits, Dmitry; Hoss, Jan; Kasieczka, Gregor; Klijnsma, Thomas; Lustermann, Werner; Mangano, Boris; Marionneau, Matthieu; Meinhard, Maren Tabea; Meister, Daniel; Micheli, Francesco; Musella, Pasquale; Nessi-Tedaldi, Francesca; Pandolfi, Francesco; Pata, Joosep; Pauss, Felicitas; Perrin, Gaël; Perrozzi, Luca; Quittnat, Milena; Reichmann, Michael; Sanz Becerra, Diego Alejandro; Schönenberger, Myriam; Shchutska, Lesya; Tavolaro, Vittorio Raoul; Theofilatos, Konstantinos; Vesterbacka Olsson, Minna Leonora; Wallny, Rainer; Zhu, De Hua; Aarrestad, Thea Klaeboe; Amsler, Claude; Canelli, Maria Florencia; De Cosa, Annapaola; Del Burgo, Riccardo; Donato, Silvio; Galloni, Camilla; Hreus, Tomas; Kilminster, Benjamin; Pinna, Deborah; Rauco, Giorgia; Robmann, Peter; Salerno, Daniel; Schweiger, Korbinian; Seitz, Claudia; Takahashi, Yuta; Zucchetta, Alberto; Candelise, Vieri; Chang, Yu-Hsiang; Cheng, Kai-yu; Doan, Thi Hien; Jain, Shilpi; Khurana, Raman; Kuo, Chia-Ming; Lin, Willis; Pozdnyakov, Andrey; Yu, Shin-Shan; Kumar, Arun; Chang, Paoti; Chao, Yuan; Chen, Kai-Feng; Chen, Po-Hsun; Fiori, Francesco; Hou, George Wei-Shu; Hsiung, Yee; Liu, Yueh-Feng; Lu, Rong-Shyang; Paganis, Efstathios; Psallidas, Andreas; Steen, Arnaud; Tsai, Jui-fa; Asavapibhop, Burin; Kovitanggoon, Kittikul; Singh, Gurpreet; Srimanobhas, Norraphat; Bat, Ayse; Boran, Fatma; Cerci, Salim; Damarseckin, Serdal; Demiroglu, Zuhal Seyma; Dozen, Candan; Dumanoglu, Isa; Girgis, Semiray; Gokbulut, Gul; Guler, Yalcin; Hos, Ilknur; Kangal, Evrim Ersin; Kara, Ozgun; Kayis Topaksu, Aysel; Kiminsu, Ugur; Oglakci, Mehmet; Onengut, Gulsen; Ozdemir, Kadri; Sunar Cerci, Deniz; Tok, Ufuk Guney; Topakli, Huseyin; Turkcapar, Semra; Zorbakir, Ibrahim Soner; Zorbilmez, Caglar; Karapinar, Guler; Ocalan, Kadir; Yalvac, Metin; Zeyrek, Mehmet; Gülmez, Erhan; Kaya, Mithat; Kaya, Ozlem; Tekten, Sevgi; Yetkin, Elif Asli; Agaras, Merve Nazlim; Atay, Serhat; Cakir, Altan; Cankocak, Kerem; Komurcu, Yildiray; Grynyov, Boris; Levchuk, Leonid; Ball, Fionn; Beck, Lana; Brooke, James John; Burns, Douglas; Clement, Emyr; Cussans, David; Davignon, Olivier; Flacher, Henning; Goldstein, Joel; Heath, Greg P; Heath, Helen F; Kreczko, Lukasz; Newbold, Dave M; Paramesvaran, Sudarshan; Sakuma, Tai; Seif El Nasr-storey, Sarah; Smith, Dominic; Smith, Vincent J; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Calligaris, Luigi; Cieri, Davide; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Linacre, Jacob; Olaiya, Emmanuel; Petyt, David; Shepherd-Themistocleous, Claire; Thea, Alessandro; Tomalin, Ian R; Williams, Thomas; Womersley, William John; Auzinger, Georg; Bainbridge, Robert; Bloch, Philippe; Borg, Johan; Breeze, Shane; Buchmuller, Oliver; Bundock, Aaron; Casasso, Stefano; Citron, Matthew; Colling, David; Corpe, Louie; Dauncey, Paul; Davies, Gavin; Della Negra, Michel; Di Maria, Riccardo; Haddad, Yacine; Hall, Geoffrey; Iles, Gregory; James, Thomas; Lane, Rebecca; Laner, Christian; Lyons, Louis; Magnan, Anne-Marie; Malik, Sarah; Mastrolorenzo, Luca; Matsushita, Takashi; Nash, Jordan; Nikitenko, Alexander; Palladino, Vito; Pesaresi, Mark; Raymond, David Mark; Richards, Alexander; Rose, Andrew; Scott, Edward; Seez, Christopher; Shtipliyski, Antoni; Summers, Sioni; Tapper, Alexander; Uchida, Kirika; Vazquez Acosta, Monica; Virdee, Tejinder; Wardle, Nicholas; Winterbottom, Daniel; Wright, Jack; Zenz, Seth Conrad; Cole, Joanne; Hobson, Peter R; Khan, Akram; Kyberd, Paul; Morton, Alexander; Reid, Ivan; Teodorescu, Liliana; Zahid, Sema; Borzou, Ahmad; Call, Kenneth; Dittmann, Jay; Hatakeyama, Kenichi; Liu, Hongxuan; Pastika, Nathaniel; Smith, Caleb; Bartek, Rachel; Dominguez, Aaron; Buccilli, Andrew; Cooper, Seth; Henderson, Conor; Rumerio, Paolo; West, Christopher; Arcaro, Daniel; Avetisyan, Aram; Bose, Tulika; Gastler, Daniel; Rankin, Dylan; Richardson, Clint; Rohlf, James; Sulak, Lawrence; Zou, David; Benelli, Gabriele; Cutts, David; Hadley, Mary; Hakala, John; Heintz, Ulrich; Hogan, Julie Managan; Kwok, Ka Hei Martin; Laird, Edward; Landsberg, Greg; Lee, Jangbae; Mao, Zaixing; Narain, Meenakshi; Pazzini, Jacopo; Piperov, Stefan; Sagir, Sinan; Syarif, Rizki; Yu, David; Band, Reyer; Brainerd, Christopher; Breedon, Richard; Burns, Dustin; Calderon De La Barca Sanchez, Manuel; Chertok, Maxwell; Conway, John; Conway, Rylan; Cox, Peter Timothy; Erbacher, Robin; Flores, Chad; Funk, Garrett; Ko, Winston; Lander, Richard; Mclean, Christine; Mulhearn, Michael; Pellett, Dave; Pilot, Justin; Shalhout, Shalhout; Shi, Mengyao; Smith, John; Stolp, Dustin; Taylor, Devin; Tos, Kyle; Tripathi, Mani; Wang, Zhangqier; Bachtis, Michail; Bravo, Cameron; Cousins, Robert; Dasgupta, Abhigyan; Florent, Alice; Hauser, Jay; Ignatenko, Mikhail; Mccoll, Nickolas; Regnard, Simon; Saltzberg, David; Schnaible, Christian; Valuev, Vyacheslav; Bouvier, Elvire; Burt, Kira; Clare, Robert; Ellison, John Anthony; Gary, J William; Ghiasi Shirazi, Seyyed Mohammad Amin; Hanson, Gail; Karapostoli, Georgia; Kennedy, Elizabeth; Lacroix, Florent; Long, Owen Rosser; Olmedo Negrete, Manuel; Paneva, Mirena Ivova; Si, Weinan; Wang, Long; Wei, Hua; Wimpenny, Stephen; Yates, Brent; Branson, James G; Cittolin, Sergio; Derdzinski, Mark; Gerosa, Raffaele; Gilbert, Dylan; Hashemi, Bobak; Holzner, André; Klein, Daniel; Kole, Gouranga; Krutelyov, Vyacheslav; Letts, James; Masciovecchio, Mario; Olivito, Dominick; Padhi, Sanjay; Pieri, Marco; Sani, Matteo; Sharma, Vivek; Simon, Sean; Tadel, Matevz; Vartak, Adish; Wasserbaech, Steven; Wood, John; Würthwein, Frank; Yagil, Avraham; Zevi Della Porta, Giovanni; Amin, Nick; Bhandari, Rohan; Bradmiller-Feld, John; Campagnari, Claudio; Dishaw, Adam; Dutta, Valentina; Franco Sevilla, Manuel; Gouskos, Loukas; Heller, Ryan; Incandela, Joe; Ovcharova, Ana; Qu, Huilin; Richman, Jeffrey; Stuart, David; Suarez, Indara; Yoo, Jaehyeok; Anderson, Dustin; Bornheim, Adolf; Bunn, Julian; Dutta, Irene; Lawhorn, Jay Mathew; Newman, Harvey B; Nguyen, Thong; Pena, Cristian; Spiropulu, Maria; Vlimant, Jean-Roch; Wilkinson, Richard; Xie, Si; Zhang, Zhicai; Zhu, Ren-Yuan; Andrews, Michael Benjamin; Ferguson, Thomas; Mudholkar, Tanmay; Paulini, Manfred; Russ, James; Sun, Menglei; Vogel, Helmut; Vorobiev, Igor; Weinberg, Marc; Cumalat, John Perry; Ford, William T; Jensen, Frank; Johnson, Andrew; Krohn, Michael; Leontsinis, Stefanos; MacDonald, Emily; Mulholland, Troy; Stenson, Kevin; Wagner, Stephen Robert; Alexander, James; Chaves, Jorge; Cheng, Yangyang; Chu, Jennifer; Dittmer, Susan; Mcdermott, Kevin; Mirman, Nathan; Patterson, Juliet Ritchie; Quach, Dan; Rinkevicius, Aurelijus; Ryd, Anders; Skinnari, Louise; Soffi, Livia; Tan, Shao Min; Tao, Zhengcheng; Thom, Julia; Tucker, Jordan; Wittich, Peter; Zientek, Margaret; Abdullin, Salavat; Albrow, Michael; Alyari, Maral; Apollinari, Giorgio; Apresyan, Artur; Apyan, Aram; Banerjee, Sunanda; Bauerdick, Lothar AT; Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Bolla, Gino; Burkett, Kevin; Butler, Joel Nathan; Canepa, Anadi; Cerati, Giuseppe Benedetto; Cheung, Harry; Chlebana, Frank; Cremonesi, Matteo; Duarte, Javier; Elvira, Victor Daniel; Freeman, Jim; Gecse, Zoltan; Gottschalk, Erik; Gray, Lindsey; Green, Dan; Grünendahl, Stefan; Gutsche, Oliver; Hanlon, Jim; Harris, Robert M; Hasegawa, Satoshi; Hirschauer, James; Hu, Zhen; Jayatilaka, Bodhitha; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Klima, Boaz; Kreis, Benjamin; Lammel, Stephan; Lincoln, Don; Lipton, Ron; Liu, Miaoyuan; Liu, Tiehui; Lopes De Sá, Rafael; Lykken, Joseph; Maeshima, Kaori; Magini, Nicolo; Marraffino, John Michael; Mason, David; McBride, Patricia; Merkel, Petra; Mrenna, Stephen; Nahn, Steve; O'Dell, Vivian; Pedro, Kevin; Prokofyev, Oleg; Rakness, Gregory; Ristori, Luciano; Savoy-Navarro, Aurore; Schneider, Basil; Sexton-Kennedy, Elizabeth; Soha, Aron; Spalding, William J; Spiegel, Leonard; Stoynev, Stoyan; Strait, James; Strobbe, Nadja; Taylor, Lucas; Tkaczyk, Slawek; Tran, Nhan Viet; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vernieri, Caterina; Verzocchi, Marco; Vidal, Richard; Wang, Michael; Weber, Hannsjoerg Artur; Whitbeck, Andrew; Wu, Weimin; Acosta, Darin; Avery, Paul; Bortignon, Pierluigi; Bourilkov, Dimitri; Brinkerhoff, Andrew; Carnes, Andrew; Carver, Matthew; Curry, David; Field, Richard D; Furic, Ivan-Kresimir; Gleyzer, Sergei V; Joshi, Bhargav Madhusudan; Konigsberg, Jacobo; Korytov, Andrey; Kotov, Khristian; Ma, Peisen; Matchev, Konstantin; Mei, Hualin; Mitselmakher, Guenakh; Shi, Kun; Sperka, David; Terentyev, Nikolay; Thomas, Laurent; Wang, Jian; Wang, Sean-Jiun; Yelton, John; Joshi, Yagya Raj; Linn, Stephan; Markowitz, Pete; Rodriguez, Jorge Luis; Ackert, Andrew; Adams, Todd; Askew, Andrew; Hagopian, Sharon; Hagopian, Vasken; Johnson, Kurtis F; Kolberg, Ted; Martinez, German; Perry, Thomas; Prosper, Harrison; Saha, Anirban; Santra, Arka; Sharma, Varun; Yohay, Rachel; Baarmand, Marc M; Bhopatkar, Vallary; Colafranceschi, Stefano; Hohlmann, Marcus; Noonan, Daniel; Roy, Titas; Yumiceva, Francisco; Adams, Mark Raymond; Apanasevich, Leonard; Berry, Douglas; Betts, Russell Richard; Cavanaugh, Richard; Chen, Xuan; Evdokimov, Olga; Gerber, Cecilia Elena; Hangal, Dhanush Anil; Hofman, David Jonathan; Jung, Kurt; Kamin, Jason; Sandoval Gonzalez, Irving Daniel; Tonjes, Marguerite; Trauger, Hallie; Varelas, Nikos; Wang, Hui; Wu, Zhenbin; Zhang, Jingyu; Bilki, Burak; Clarida, Warren; Dilsiz, Kamuran; Durgut, Süleyman; Gandrajula, Reddy Pratap; Haytmyradov, Maksat; Khristenko, Viktor; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Ogul, Hasan; Onel, Yasar; Ozok, Ferhat; Penzo, Aldo; Snyder, Christina; Tiras, Emrah; Wetzel, James; Yi, Kai; Blumenfeld, Barry; Cocoros, Alice; Eminizer, Nicholas; Fehling, David; Feng, Lei; Gritsan, Andrei; Maksimovic, Petar; Roskes, Jeffrey; Sarica, Ulascan; Swartz, Morris; Xiao, Meng; You, Can; Al-bataineh, Ayman; Baringer, Philip; Bean, Alice; Boren, Samuel; Bowen, James; Castle, James; Khalil, Sadia; Kropivnitskaya, Anna; Majumder, Devdatta; Mcbrayer, William; Murray, Michael; Rogan, Christopher; Royon, Christophe; Sanders, Stephen; Schmitz, Erich; Tapia Takaki, Daniel; Wang, Quan; Ivanov, Andrew; Kaadze, Ketino; Maravin, Yurii; Mohammadi, Abdollah; Saini, Lovedeep Kaur; Skhirtladze, Nikoloz; Rebassoo, Finn; Wright, Douglas; Baden, Drew; Baron, Owen; Belloni, Alberto; Eno, Sarah Catherine; Feng, Yongbin; Ferraioli, Charles; Hadley, Nicholas John; Jabeen, Shabnam; Jeng, Geng-Yuan; Kellogg, Richard G; Kunkle, Joshua; Mignerey, Alice; Ricci-Tam, Francesca; Shin, Young Ho; Skuja, Andris; Tonwar, Suresh C; Abercrombie, Daniel; Allen, Brandon; Azzolini, Virginia; Barbieri, Richard; Baty, Austin; Bauer, Gerry; Bi, Ran; Brandt, Stephanie; Busza, Wit; Cali, Ivan Amos; D'Alfonso, Mariarosaria; Demiragli, Zeynep; Gomez Ceballos, Guillelmo; Goncharov, Maxim; Harris, Philip; Hsu, Dylan; Hu, Miao; Iiyama, Yutaro; Innocenti, Gian Michele; Klute, Markus; Kovalskyi, Dmytro; Lee, Yen-Jie; Levin, Andrew; Luckey, Paul David; Maier, Benedikt; Marini, Andrea Carlo; Mcginn, Christopher; Mironov, Camelia; Narayanan, Siddharth; Niu, Xinmei; Paus, Christoph; Roland, Christof; Roland, Gunther; Salfeld-Nebgen, Jakob; Stephans, George; Sumorok, Konstanty; Tatar, Kaya; Velicanu, Dragos; Wang, Jing; Wang, Ta-Wei; Wyslouch, Bolek; Benvenuti, Alberto; Chatterjee, Rajdeep Mohan; Evans, Andrew; Hansen, Peter; Hiltbrand, Joshua; Kalafut, Sean; Kubota, Yuichi; Lesko, Zachary; Mans, Jeremy; Nourbakhsh, Shervin; Ruckstuhl, Nicole; Rusack, Roger; Turkewitz, Jared; Wadud, Mohammad Abrar; Acosta, John Gabriel; Oliveros, Sandra; Avdeeva, Ekaterina; Bloom, Kenneth; Claes, Daniel R; Fangmeier, Caleb; Golf, Frank; Gonzalez Suarez, Rebeca; Kamalieddin, Rami; Kravchenko, Ilya; Monroy, Jose; Siado, Joaquin Emilo; Snow, Gregory R; Stieger, Benjamin; Dolen, James; Godshalk, Andrew; Harrington, Charles; Iashvili, Ia; Nguyen, Duong; Parker, Ashley; Rappoccio, Salvatore; Roozbahani, Bahareh; Alverson, George; Barberis, Emanuela; Freer, Chad; Hortiangtham, Apichart; Massironi, Andrea; Morse, David Michael; Orimoto, Toyoko; Teixeira De Lima, Rafael; Wamorkar, Tanvi; Wang, Bingran; Wisecarver, Andrew; Wood, Darien; Bhattacharya, Saptaparna; Charaf, Otman; Hahn, Kristan Allan; Mucia, Nicholas; Odell, Nathaniel; Schmitt, Michael Henry; Sung, Kevin; Trovato, Marco; Velasco, Mayda; Bucci, Rachael; Dev, Nabarun; Hildreth, Michael; Hurtado Anampa, Kenyi; Jessop, Colin; Karmgard, Daniel John; Kellams, Nathan; Lannon, Kevin; Li, Wenzhao; Loukas, Nikitas; Marinelli, Nancy; Meng, Fanbo; Mueller, Charles; Musienko, Yuri; Planer, Michael; Reinsvold, Allison; Ruchti, Randy; Siddireddy, Prasanna; Smith, Geoffrey; Taroni, Silvia; Wayne, Mitchell; Wightman, Andrew; Wolf, Matthias; Woodard, Anna; Alimena, Juliette; Antonelli, Louis; Bylsma, Ben; Durkin, Lloyd Stanley; Flowers, Sean; Francis, Brian; Hart, Andrew; Hill, Christopher; Ji, Weifeng; Ling, Ta-Yung; Liu, Bingxuan; Luo, Wuming; Winer, Brian L; Wulsin, Howard Wells; Cooperstein, Stephane; Driga, Olga; Elmer, Peter; Hardenbrook, Joshua; Hebda, Philip; Higginbotham, Samuel; Kalogeropoulos, Alexis; Lange, David; Luo, Jingyu; Marlow, Daniel; Mei, Kelvin; Ojalvo, Isabel; Olsen, James; Palmer, Christopher; Piroué, Pierre; Stickland, David; Tully, Christopher; Malik, Sudhir; Norberg, Scarlet; Barker, Anthony; Barnes, Virgil E; Das, Souvik; Folgueras, Santiago; Gutay, Laszlo; Jones, Matthew; Jung, Andreas Werner; Khatiwada, Ajeeta; Miller, David Harry; Neumeister, Norbert; Peng, Cheng-Chieh; Qiu, Hao; Schulte, Jan-Frederik; Sun, Jian; Wang, Fuqiang; Xiao, Rui; Xie, Wei; Cheng, Tongguang; Parashar, Neeti; Stupak, John; Chen, Zhenyu; Ecklund, Karl Matthew; Freed, Sarah; Geurts, Frank JM; Guilbaud, Maxime; Kilpatrick, Matthew; Li, Wei; Michlin, Benjamin; Padley, Brian Paul; Roberts, Jay; Rorie, Jamal; Shi, Wei; Tu, Zhoudunming; Zabel, James; Zhang, Aobo; Bodek, Arie; de Barbaro, Pawel; Demina, Regina; Duh, Yi-ting; Ferbel, Thomas; Galanti, Mario; Garcia-Bellido, Aran; Han, Jiyeon; Hindrichs, Otto; Khukhunaishvili, Aleko; Lo, Kin Ho; Tan, Ping; Verzetti, Mauro; Ciesielski, Robert; Goulianos, Konstantin; Mesropian, Christina; Agapitos, Antonis; Chou, John Paul; Gershtein, Yuri; Gómez Espinosa, Tirso Alejandro; Halkiadakis, Eva; Heindl, Maximilian; Hughes, Elliot; Kaplan, Steven; Kunnawalkam Elayavalli, Raghav; Kyriacou, Savvas; Lath, Amitabh; Montalvo, Roy; Nash, Kevin; Osherson, Marc; Saka, Halil; Salur, Sevil; Schnetzer, Steve; Sheffield, David; Somalwar, Sunil; Stone, Robert; Thomas, Scott; Thomassen, Peter; Walker, Matthew; Delannoy, Andrés G; Heideman, Joseph; Riley, Grant; Rose, Keith; Spanier, Stefan; Thapa, Krishna; Bouhali, Othmane; Castaneda Hernandez, Alfredo; Celik, Ali; Dalchenko, Mykhailo; De Mattia, Marco; Delgado, Andrea; Dildick, Sven; Eusebi, Ricardo; Gilmore, Jason; Huang, Tao; Kamon, Teruki; Mueller, Ryan; Pakhotin, Yuriy; Patel, Rishi; Perloff, Alexx; Perniè, Luca; Rathjens, Denis; Safonov, Alexei; Tatarinov, Aysen; Ulmer, Keith; Akchurin, Nural; Damgov, Jordan; De Guio, Federico; Dudero, Phillip Russell; Faulkner, James; Gurpinar, Emine; Kunori, Shuichi; Lamichhane, Kamal; Lee, Sung Won; Mengke, Tielige; Muthumuni, Samila; Peltola, Timo; Undleeb, Sonaina; Volobouev, Igor; Wang, Zhixing; Greene, Senta; Gurrola, Alfredo; Janjam, Ravi; Johns, Willard; Maguire, Charles; Melo, Andrew; Ni, Hong; Padeken, Klaas; Sheldon, Paul; Tuo, Shengquan; Velkovska, Julia; Xu, Qiao; Arenton, Michael Wayne; Barria, Patrizia; Cox, Bradley; Hirosky, Robert; Joyce, Matthew; Ledovskoy, Alexander; Li, Hengne; Neu, Christopher; Sinthuprasith, Tutanon; Wang, Yanchu; Wolfe, Evan; Xia, Fan; Harr, Robert; Karchin, Paul Edmund; Poudyal, Nabin; Sturdy, Jared; Thapa, Prakash; Zaleski, Shawn; Brodski, Michael; Buchanan, James; Caillol, Cécile; Carlsmith, Duncan; Dasu, Sridhara; Dodd, Laura; Duric, Senka; Gomber, Bhawna; Grothe, Monika; Herndon, Matthew; Hervé, Alain; Hussain, Usama; Klabbers, Pamela; Lanaro, Armando; Levine, Aaron; Long, Kenneth; Loveless, Richard; Rekovic, Vladimir; Ruggles, Tyler; Savin, Alexander; Smith, Nicholas; Smith, Wesley H; Woods, Nathaniel

    2018-01-01

    A search is presented for single production of heavy vector-like quarks (B) that decay to a Higgs boson and a b quark, with the Higgs boson decaying to a highly boosted $ \\mathrm{b\\bar{b}} $ pair reconstructed as a single collimated jet. The analysis is based on data collected by the CMS experiment in proton-proton collisions at $\\sqrt{s} = $ 13 TeV, corresponding to an integrated luminosity of 35.9 fb$^{-1}$. The data are consistent with background expectations, and upper limits at 95% confidence level on the product of the B quark cross section and the branching fraction are obtained in the range 1.28-0.07 pb, for a narrow B quark with a mass between 700 and 1800 GeV. The production of B quarks with widths of 10, 20 and 30% of the resonance mass is also considered, and the sensitivities obtained are similar to those achieved in the narrow width case. This is the first search at the CERN LHC for the single production of a B quark through its fully hadronic decay channel, and the first study considering finit...

  17. Search for single production of vector-like quarks decaying to a b quark and a Higgs boson

    Energy Technology Data Exchange (ETDEWEB)

    Sirunyan, Albert M; et al.

    2018-02-05

    A search is presented for single production of heavy vector-like quarks (B) that decay to a Higgs boson and a b quark, with the Higgs boson decaying to a highly boosted $\\mathrm{b\\overline{b}}$ pair reconstructed as a single collimated jet. The analysis is based on data collected by the CMS experiment in proton-proton collisions at $\\sqrt{s} =$ 13 TeV, corresponding to an integrated luminosity of 35.9 fb$^{-1}$. The data are consistent with background expectations, and upper limits at 95% confidence level on the product of the B quark cross section and the branching fraction are obtained in the range 1.28-0.07 pb, for a narrow B quark with a mass between 700 and 1800 GeV. The production of B quarks with widths of 10, 20 and 30% of the resonance mass is also considered, and the sensitivities obtained are similar to those achieved in the narrow width case. This is the first search at the CERN LHC for the single production of a B quark through its fully hadronic decay channel, and the first study considering finite resonance widths of the B quark.

  18. Probing the importance of clonality: Single cell subcloning of clonally derived CHO cell lines yields widely diverse clones differing in growth, productivity, and product quality.

    Science.gov (United States)

    Ko, Peggy; Misaghi, Shahram; Hu, Zhilan; Zhan, Dejin; Tsukuda, Joni; Yim, Mandy; Sanford, Mark; Shaw, David; Shiratori, Masaru; Snedecor, Brad; Laird, Michael; Shen, Amy

    2017-12-11

    In the past few decades, a large variety of therapeutic antibodies and proteins have been expressed in Chinese hamster ovary (CHO) cells. This mammalian expression system is robust, scalable, relatively inexpensive, and importantly allows for post-translational modifications that are important for some therapeutic proteins. Historically, CHO cell lines were derived from colonies of cells grown in semi-solid or liquid plates using either serum-containing or serum-free media. Current advancements in cell sorting and imaging technologies have allowed for isolating and imaging single cell progenitors at the seeding step, significantly increasing the probability of isolating clonally derived cell lines. However, it is debatable how much population heterogeneity can be eliminated when clonally derived cell lines, originated from a single cell progenitor, are scaled up. To further investigate this phenomenon, we subcloned two different clonally derived (day 0 imaged and visually inspected) cell lines expressing antibody-X. The results showed that when six randomly chosen subclones of each line were evaluated in a production assay, these subclones displayed a range of variation in titer, specific productivity, growth, and product quality attributes. Some subclones displayed variations in transgene copy numbers. Additionally, clonal derivation did not assure stability of the derived cell lines. Our findings show that cell heterogeneity exists in a population even when derived from a single cell progenitor. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 2017. © 2017 American Institute of Chemical Engineers.

  19. Fast and non-invasive PCR sexing of primates: apes, Old World monkeys, New World monkeys and Strepsirrhines

    DEFF Research Database (Denmark)

    Villesen, Palle; Fredsted, Tina

    2006-01-01

    is described using a triple primer PCR reaction and agarose gel electrophoresis of the sex-chromosomal isoforms of the ubiquitously transcribed tetratricopeptide repeat protein gene (UTX/UTY). By comparing genomic data from several mammals we identified the UTX/UTY locus as the best candidate for a universal...... primate sexing marker. Using data from several species we identified a XY-conserved region, a Y conserved region and an X conserved region. This enabled the design of a triple primer PCR setup that amplifies X and Y products of different length in a single PCR reaction. Conclusion This simple PCR...... amplification of X and Y fragments is useful for sexing DNA samples from all species of primates. Furthermore, since the amplified fragments are very short the method can be applied to fragmented DNA extracted from non-invasive samples....

  20. Development of simple multiplex real-time PCR assays for foodborne pathogens detection and identification on LightCycler

    Directory of Open Access Journals (Sweden)

    Avo Karus1

    2017-03-01

    Full Text Available Most acute intestinal diseases are caused by food-borne pathogens. A fast and simple real-time PCR-based procedure for simultaneous detection of food contamination by any of the five food-borne pathogens: Campylobacter jejuni, Mycobacterium bovis, Enterobacter sakazaki, Shigella boydii, Clostridium perfrigens using multiplex EvaGreen real-time PCR for LightCycler was developed and evaluated. Real-time qPCR showed excellent sensitivity. Tm calling and Melting Curve Genotyping (MCG were used for analysis of PCR product melting curves. The Melting Curve Genotyping option showed good performance for discrimination of positive samples containing DNA of single pathogen or pathogen mixtures from negative samples.

  1. Development of a temperature-switch PCR-based SNP typing method for Mycobacterium ulcerans.

    Directory of Open Access Journals (Sweden)

    Katharina Röltgen

    Full Text Available Mycobacterium ulcerans (M. ulcerans, the causative agent of the devastating skin disease Buruli ulcer (BU, is characterized by an extremely low level of genetic diversity. Recently, we have reported the first discrimination of closely related M. ulcerans variants in the BU endemic Densu River Valley of Ghana. In the study real-time PCR-based single nucleotide polymorphism (SNP typing at 89 predefined loci revealed the presence of ten M. ulcerans haplotypes circulating in the BU endemic region. Here we describe the development of temperature-switch PCR (TSP assays that allow distinguishing these haplotypes by conventional agarose gel-based analysis of the PCR products. After validation of the accuracy of typing results, the TSP assays were successfully established in a reference laboratory in Ghana. Development of the cost-effective and rapid TSP-based genetic fingerprinting method will thus allow investigating the spread of M. ulcerans clones by regular genetic monitoring in BU endemic countries.

  2. Measurement of electroweak single top quark production in proton-antiproton collisions at 1.96 TeV

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Peter Joseph [Univ. of California, Los Angeles, CA (United States)

    2008-01-01

    The top quark is an extremely massive fundamental particle that is predominantly produced in pairs at particle collider experiments. The Standard Model of particle physics predicts that top quarks can also be produced singly by the electroweak force; however, this process is more difficult to detect because it occurs at a smaller rate and is more difficult to distinguish from background processes. The cross section of this process is related to the Cabbibo-Kobayashi-Maskawa matrix element |V tb|, and measurement of the single top quark production cross section is currently the only method to directly measure this quantity without assuming the number of generations of fermions. This thesis describes a measurement of the cross section of electroweak single top quark production in proton-antiproton collisions at a center-of-mass energy of 1.96 TeV. This analysis uses 2.2 fb-1 of integrated luminosity recorded by the Collider Detector at Fermilab. The search is performed using a matrix element method which calculates the differential cross section for each event for several signal and background hypotheses. These numbers are combined into a single discriminant and used to construct templates from Monte Carlo simulation. A maximum likelihood fit to the data distribution gives a measurement of the cross section. This analysis measures a value of 2.2$+0.8\\atop{-0.7}$ pb, which corresponds to a value of |V tb| = 0.88$+0.16\\atop{-0.14}$experimental±0.7(theoretical). The probability that this result originates from a background fluctuation in the absence of single top production (p-value) is 0.0003, which is equivalent to 3.4 standard deviations in Gaussian statistics. The expected (median) p-value as estimated from pseudo-experiments for this analysis is 0.000003, which corresponds to 4.5 standard deviations in Gaussian statistics.

  3. Search for the Single Production of Doubly-Charged Higgs Bosons and Constraints on their Couplings from Bhabha Scattering

    CERN Document Server

    Abbiendi, G; Akesson, P.F.; Alexander, G.; Allison, John; Amaral, P.; Anagnostou, G.; Anderson, K.J.; Arcelli, S.; Asai, S.; Axen, D.; Azuelos, G.; Bailey, I.; Barberio, E.; Barlow, R.J.; Batley, R.J.; Bechtle, P.; Behnke, T.; Bell, Kenneth Watson; Bell, P.J.; Bella, G.; Bellerive, A.; Benelli, G.; Bethke, S.; Biebel, O.; Boeriu, O.; Bock, P.; Boutemeur, M.; Braibant, S.; Brigliadori, L.; Brown, Robert M.; Buesser, K.; Burckhart, H.J.; Campana, S.; Carnegie, R.K.; Caron, B.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, David G.; Csilling, A.; Cuffiani, M.; Dado, S.; De Roeck, A.; De Wolf, E.A.; Desch, K.; Dienes, B.; Donkers, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Etzion, E.; Fabbri, F.; Feld, L.; Ferrari, P.; Fiedler, F.; Fleck, I.; Ford, M.; Frey, A.; Furtjes, A.; Gagnon, P.; Gary, John William; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Giunta, Marina; Goldberg, J.; Groll, M.; Gross, E.; Grunhaus, J.; Gruwe, M.; Gunther, P.O.; Gupta, A.; Hajdu, C.; Hamann, M.; Hanson, G.G.; Harder, K.; Harel, A.; Harin-Dirac, M.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Hensel, C.; Herten, G.; Heuer, R.D.; Hill, J.C.; Hoffman, Kara Dion; Horvath, D.; Igo-Kemenes, P.; Ishii, K.; Jeremie, H.; Jovanovic, P.; Junk, T.R.; Kanaya, N.; Kanzaki, J.; Karapetian, G.; Karlen, D.; Kawagoe, K.; Kawamoto, T.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Kim, D.H.; Klein, K.; Klier, A.; Kluth, S.; Kobayashi, T.; Kobel, M.; Komamiya, S.; Kormos, Laura L.; Kramer, T.; Krieger, P.; von Krogh, J.; Kruger, K.; Kuhl, T.; Kupper, M.; Lafferty, G.D.; Landsman, H.; Lanske, D.; Layter, J.G.; Leins, A.; Lellouch, D.; Lettso, J.; Levinson, L.; Lillich, J.; Lloyd, S.L.; Loebinger, F.K.; Lu, J.; Ludwig, J.; Macpherson, A.; Mader, W.; Marcellini, S.; Martin, A.J.; Masetti, G.; Mashimo, T.; Mattig, Peter; McDonald, W.J.; McKenna, J.; McMahon, T.J.; McPherson, R.A.; Meijers, F.; Menges, W.; Merritt, F.S.; Mes, H.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Moed, S.; Mohr, W.; Mori, T.; Mutter, A.; Nagai, K.; Nakamura, I.; Nanjo, H.; Neal, H.A.; Nisius, R.; O'Neale, S.W.; Oh, A.; Okpara, A.; Oreglia, M.J.; Orito, S.; Pahl, C.; Pasztor, G.; Pater, J.R.; Patrick, G.N.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poli, B.; Polok, J.; Pooth, O.; Przybycien, M.; Quadt, A.; Rabbertz, K.; Rembser, C.; Renkel, P.; Roney, J.M.; Rosati, S.; Rozen, Y.; Runge, K.; Sachs, K.; Saeki, T.; Sarkisyan, E.K.G.; Schaile, A.D.; Schaile, O.; Scharff-Hansen, P.; Schieck, J.; Schoerner-Sadenius, Thomas; Schroder, Matthias; Schumacher, M.; Schwick, C.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Sherwood, P.; Siroli, G.; Skuja, A.; Smith, A.M.; Sobie, R.; Soldner-Rembold, S.; Spano, F.; Stahl, A.; Stephens, K.; Strom, David M.; Strohmer, R.; Tarem, S.; Tasevsky, M.; Taylor, R.J.; Teuscher, R.; Thomson, M.A.; Torrence, E.; Toya, D.; Tran, P.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turner-Watson, M.F.; Ueda, I.; Ujvari, B.; Vollmer, C.F.; Vannerem, P.; Vertesi, R.; Verzocchi, M.; Voss, H.; Vossebeld, J.; Waller, D.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wengler, T.; Wermes, N.; Wetterling, G.W.; Wilson, D.; Wilson, J.A.; Wolf, G.; Wyatt, T.R.; Yamashita, S.; Zer-Zion, D.; Zivkovic, Lidija

    2003-01-01

    A search for single production of doubly-charged Higgs bosons has been performed using 600.7 pb^-1 of e+e- collision data with sqrt(s)=189--209GeV collected by the OPAL detector at LEP. No evidence for the existence of H++/-- is observed. Upper limits on the Yukawa coupling of the H++/-- to like-signed electron pairs are derived. Additionally, indirect constraints on the Yukawa coupling from Bhabha scattering, where the H++/-- would contribute via t-channel exchange, are derived for M(H++/--) < 2TeV. These are the first results for both a single production search and constraints from Bhabha scattering reported from LEP.

  4. Single production of the top partner in the T → tZ channel at the LHeC

    Science.gov (United States)

    Zhang, Yan-Ju; Han, Lin; Liu, Yao-Bei

    2017-05-01

    In this paper, we study the possibility of detecting the heavy vector-like top partner T in a simplified model with the decay channel T → tZ at the Large Hadron Electron Collider (LHeC). We first investigate the single top partner production process including the intergenerational mixing and the results show that the mixing between the top partner with the first generation can largely enhance the production cross section. We further study the observability of the single top partner through the process e+ p → T (→ tZ)νbare → t (→ bjj‧) Z (→ℓ+ℓ-)νbare at the LHeC with the proposed 140 GeV electron beam and 7 TeV proton beam. For some typical heavy T quark masses, the 3σ exclusion limits as well as the 5σ discovery region are respectively presented in terms of parameter space regions.

  5. Single production of the top partner in the T→tZ channel at the LHeC

    Directory of Open Access Journals (Sweden)

    Yan-Ju Zhang

    2017-05-01

    Full Text Available In this paper, we study the possibility of detecting the heavy vector-like top partner T in a simplified model with the decay channel T→tZ at the Large Hadron Electron Collider (LHeC. We first investigate the single top partner production process including the intergenerational mixing and the results show that the mixing between the top partner with the first generation can largely enhance the production cross section. We further study the observability of the single top partner through the process e+p→T(→tZν¯e→t(→bjj′Z(→ℓ+ℓ−ν¯e at the LHeC with the proposed 140 GeV electron beam and 7 TeV proton beam. For some typical heavy T quark masses, the 3σ exclusion limits as well as the 5σ discovery region are respectively presented in terms of parameter space regions.

  6. Search for Single Top Production in $e^{+}e^{-}$ Collisions at $\\sqrt{s}$ = 189 - 202 GeV

    CERN Document Server

    Barate, R; Ghez, P; Goy, C; Jézéquel, S; Lees, J P; Martin, F; Merle, E; Minard, M N; Pietrzyk, B; Alemany, R; Bravo, S; Casado, M P; Chmeissani, M; Crespo, J M; Fernández, E; Fernández-Bosman, M; Garrido, L; Graugès-Pous, E; Juste, A; Martínez, M; Merino, G; Miquel, R; Mir, L M; Morawitz, P; Pacheco, A; Riu, I; Ruiz, H; Colaleo, A; Creanza, D; De Palma, M; Iaselli, Giuseppe; Maggi, G; Maggi, M; Nuzzo, S; Ranieri, A; Raso, G; Ruggieri, F; Selvaggi, G; Silvestris, L; Tempesta, P; Tricomi, A; Zito, G; Huang, X; Lin, J; Ouyang, Q; Wang, T; Xie, Y; Xu, R; Xue, S; Zhang, J; Zhang, L; Zhao, W; Abbaneo, D; Boix, G; Buchmüller, O L; Cattaneo, M; Cerutti, F; Ciulli, V; Davies, G; Dissertori, G; Drevermann, H; Forty, Roger W; Frank, M; Gianotti, F; Greening, T C; Halley, A W; Hansen, J B; Harvey, J; Janot, P; Jost, B; Kado, M; Leroy, O; Maley, P; Mato, P; Minten, Adolf G; Moutoussi, A; Ranjard, F; Rolandi, Luigi; Schlatter, W D; Schmitt, M; Schneider, O; Spagnolo, P; Tejessy, W; Teubert, F; Tournefier, E; Valassi, Andrea; Wright, A E; Ajaltouni, Ziad J; Badaud, F; Chazelle, G; Deschamps, O; Dessagne, S; Falvard, A; Ferdi, C; Gay, P; Guicheney, C; Henrard, P; Jousset, J; Michel, B; Monteil, S; Montret, J C; Pallin, D; Pascolo, J M; Perret, P; Podlyski, F; Hansen, J D; Hansen, J R; Hansen, P H; Nilsson, B S; Rensch, B; Wäänänen, A; Daskalakis, G; Kyriakis, A; Markou, C; Simopoulou, Errietta; Vayaki, Anna; Blondel, A; Brient, J C; Machefert, F P; Rougé, A; Swynghedauw, M; Tanaka, R; Videau, H L; Focardi, E; Parrini, G; Zachariadou, K; Corden, M; Georgiopoulos, C H; Antonelli, A; Bencivenni, G; Bologna, G; Bossi, F; Campana, P; Capon, G; Chiarella, V; Laurelli, P; Mannocchi, G; Murtas, F; Murtas, G P; Passalacqua, L; Pepé-Altarelli, M; Chalmers, M; Kennedy, J; Lynch, J G; Negus, P; O'Shea, V; Räven, B; Smith, D; Teixeira-Dias, P; Thompson, A S; Ward, J J; Cavanaugh, R J; Dhamotharan, S; Geweniger, C; Hanke, P; Hepp, V; Kluge, E E; Leibenguth, G; Putzer, A; Tittel, K; Werner, S; Wunsch, M; Beuselinck, R; Binnie, David M; Cameron, W; Dornan, Peter J; Girone, M; Goodsir, S M; Marinelli, N; Martin, E B; Nash, J; Nowell, J; Przysiezniak, H; Sciabà, A; Sedgbeer, J K; Thompson, J C; Thomson, E; Williams, M D; Ghete, V M; Girtler, P; Kneringer, E; Kuhn, D; Rudolph, G; Bowdery, C K; Buck, P G; Ellis, G; Finch, A J; Foster, F; Hughes, G; Jones, R W L; Robertson, N A; Smizanska, M; Williams, M I; Giehl, I; Hölldorfer, F; Jakobs, K; Kleinknecht, K; Kröcker, M; Müller, A S; Nürnberger, H A; Quast, G; Renk, B; Rohne, E; Sander, H G; Schmeling, S; Wachsmuth, H W; Zeitnitz, C; Ziegler, T; Bonissent, A; Carr, J; Coyle, P; Ealet, A; Fouchez, D; Payre, P; Rousseau, D; Tilquin, A; Aleppo, M; Antonelli, M; Gilardoni, S S; Ragusa, F; Büscher, V; Dietl, H; Ganis, G; Hüttmann, K; Lütjens, G; Mannert, C; Männer, W; Moser, H G; Schael, S; Settles, Ronald; Seywerd, H C J; Stenzel, H; Wiedenmann, W; Wolf, G; Azzurri, P; Boucrot, J; Callot, O; Chen, S; Davier, M; Duflot, L; Grivaz, J F; Heusse, P; Jacholkowska, A; Lefrançois, J; Serin, L; Veillet, J J; Videau, I; De Vivie de Régie, J B; Zerwas, D; Bagliesi, G; Boccali, T; Bozzi, C; Calderini, G; Dell'Orso, R; Ferrante, I; Giassi, A; Gregorio, A; Ligabue, F; Marrocchesi, P S; Messineo, A; Palla, Fabrizio; Rizzo, G; Sanguinetti, G; Sguazzoni, G; Tenchini, Roberto; Venturi, A; Verdini, P G; Blair, G A; Coles, J; Cowan, G D; Green, M G; Hutchcroft, D E; Jones, L T; Medcalf, T; Strong, J A; Botterill, David R; Clifft, R W; Edgecock, T R; Norton, P R; Tomalin, I R; Bloch-Devaux, B; Colas, P; Fabbro, B; Faïf, G; Lançon, E; Lemaire, M C; Locci, E; Pérez, P; Rander, J; Renardy, J F; Rosowsky, A; Seager, P; Trabelsi, A; Tuchming, B; Vallage, B; Black, S N; Dann, J H; Loomis, C; Kim, H Y; Konstantinidis, N P; Litke, A M; McNeil, M A; Taylor, G; Booth, C N; Cartwright, S L; Combley, F; Hodgson, P N; Lehto, M H; Thompson, L F; Affholderbach, K; Böhrer, A; Brandt, S; Grupen, Claus; Hess, J; Misiejuk, A; Prange, G; Sieler, U; Borean, C; Giannini, G; Gobbo, B; Pütz, J; Rothberg, J E; Wasserbaech, S R; Williams, R W; Armstrong, S R; Elmer, P; Ferguson, D P S; Gao, Y; González, S; Hayes, O J; Hu, H; Jin, S; Kile, J; McNamara, P A; Nielsen, J; Orejudos, W; Pan, Y B; Saadi, Y; Scott, I J; Walsh, J; Von Wimmersperg-Töller, J H; Wu Sau Lan; Wu, X; Zobernig, G

    2000-01-01

    The single top production via flavour changing neutral currents in the reactions ee -> t c/u is searched for in approximately 411 pb-1 of data collected by ALEPH at centre-of-mass energies in the range between 189 and 202 GeV. In total, 58 events are selected in the data to be compared with 50.3 expected from Standard Model backgrounds. No deviation from the Standard Model expectation is observed. A 95\\%~CL upper limit of 0.72 pb on the single top production cross section at 202 GeV is derived assuming a top mass of 174 GeV/c^2 and a 100% branching ratio of the top decay into bW. A model dependent limit on the flavour-changing couplings kZ and kg is obtained by combining all centre-of-mass energies.

  7. Incidence of Listeria spp. and Listeria monocytogenes in a poultry processing environment and in poultry products and their rapid confirmation by multiplex PCR.

    OpenAIRE

    Lawrence, L M; Gilmour, A

    1994-01-01

    The incidence of Listeria spp. and Listeria monocytogenes in a poultry processing plant and in raw and cooked poultry products was determined over a 6-month period. Within the raw and cooked poultry processing environments, 46% (36 of 79) and 29% (51 of 173) of the samples contained Listeria spp. while 26% (21 of 79) and 15% (27 of 173) contained L. monocytogenes, respectively. Various sites within the processing environment were found to be consistently positive for L. monocytogenes througho...

  8. Effect of Single Bacterial Starter Culture on Odour Reduction During Controlled Fermentation of Cassava Tubers for Foofoo Production

    OpenAIRE

    Henshaw, E. E.; Ikpoh, I. S

    2010-01-01

    Effects of single bacterial starter culture on odour reduction during controlled fermentation of cassava tubers for foofoo production were investigated. Pure cultures were used to ferment cassava tubers in water for 96 h. The cultures used include Bacillus subtilis, Klebsiela sp., Lactobacillus plantarum and Leuconostoc mesenteroides. L. plantarum exhibited the highest acid producing ability, decreasing the pH of the Cassava tubers from 6.2 to 3.68 with a corresponding increase in total titra...

  9. Inclusive single-particle production in two-photon collisions at LEP II with the DELPHI detector

    CERN Document Server

    Abdallah, J.; Adam, W.; Adzic, P.; Albrecht, T.; Alemany-Fernandez, R.; Allmendinger, T.; Allport, P.P.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.D.; Arnoud, Y.; Ask, S.; Asman, B.; Augustin, J.E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barbier, R.; Bardin, D.; Barker, G.J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.H.; Begalli, M.; Behrmann, A.; Ben-Haim, E.; Benekos, N.; Benvenuti, A.; Berat, C.; Berggren, M.; Bertrand, D.; Besancon, M.; Besson, N.; Bloch, D.; Blom, M.; Bluj, M.; Bonesini, M.; Boonekamp, M.; Booth, P.S.L.; Borisov, G.; Botner, O.; Bouquet, B.; Bowcock, T.J.V.; Boyko, I.; Bracko, M.; Brenner, R.; Brodet, E.; Bruckman, P.; Brunet, J.M.; Buschbeck, B.; Buschmann, P.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Castro, N.; Cavallo, F.; Chapkin, M.; Charpentier, Ph.; Checchia, P.; Chierici, R.; Chliapnikov, P.; Chudoba, J.; Chung, S.U.; Cieslik, K.; Collins, P.; Contri, R.; Cosme, G.; Cossutti, F.; Costa, M.J.; Crennell, D.; Cuevas, J.; D'Hondt, J.; da Silva, T.; Da Silva, W.; Della Ricca, G.; De Angelis, A.; De Boer, W.; De Clercq, C.; De Lotto, B.; De Maria, N.; De Min, A.; de Paula, L.; Di Ciaccio, L.; Di Simone, A.; Doroba, K.; Drees, J.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Espirito Santo, M.C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferro, F.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fulda-Quenzer, F.; Fuster, J.; Gandelman, M.; Garcia, C.; Gavillet, Ph.; Gazis, E.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Goncalves, P.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hallgren, A.; Hamacher, K.; Hamilton, K.; Haug, S.; Hauler, F.; Hedberg, V.; Hennecke, M.; Hoffman, J.; Holmgren, S.O.; Holt, P.J.; Houlden, M.A.; Jackson, J.N.; Jarlskog, G.; Jarry, P.; Jeans, D.; Johansson, E.K.; Jonsson, P.; Joram, C.; Jungermann, L.; Kapusta, F.; Katsanevas, S.; Katsoufis, E.; Kernel, G.; Kersevan, B.P.; Kerzel, U.; King, B.T.; Kjaer, N.J.; Kluit, P.; Kokkinias, P.; Kourkoumelis, C.; Kouznetsov, O.; Krumstein, Z.; Kucharczyk, M.; Lamsa, J.; Leder, G.; Ledroit, F.; Leinonen, L.; Leitner, R.; Lemonne, J.; Lepeltier, V.; Lesiak, T.; Liebig, W.; Liko, D.; Lipniacka, A.; Lopes, J.H.; Lopez, J.M.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Malek, A.; Maltezos, S.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Mazzucato, F.; Mazzucato, M.; Mc Nulty, R.; Meroni, C.; Migliore, E.; Mitaroff, W.; Mjoernmark, U.; Moa, T.; Moch, M.; Moenig, K.; Monge, R.; Montenegro, J.; Moraes, D.; Moreno, S.; Morettini, P.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.; Murray, W.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.; Nawrocki, K.; Nemecek, S.; Nicolaidou, R.; Nikolenko, M.; Oblakowska-Mucha, A.; Obraztsov, V.; Olshevski, A.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Palacios, J.P.; Palka, H.; Papadopoulou, Th.D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Peralta, L.; Perepelitsa, V.; Perrotta, A.; Petrolini, A.; Piedra, J.; Pieri, L.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M.E.; Polok, G.; Pozdniakov, V.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Rebecchi, P.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.; Richard, F.; Ridky, J.; Rivero, M.; Rodriguez, D.; Romero, A.; Ronchese, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ryabtchikov, D.; Sadovsky, A.; Salmi, L.; Salt, J.; Sander, C.; Savoy-Navarro, A.; Schwickerath, U.; Sekulin, R.; Siebel, M.; Sisakian, A.; Smadja, G.; Smirnova, O.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Stanitzki, M.; Stocchi, A.; Strauss, J.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Szumlak, T.; Tabarelli, T.; Tegenfeldt, F.; Timmermans, J.; Tkatchev, L.; Tobin, M.; Todorovova, S.; Tome, B.; Tonazzo, A.; Tortosa, P.; Travnicek, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.L.; Tyapkin, I.A.; Tyapkin, P.; Tzamarias, S.; Uvarov, V.; Valenti, G.; Van Dam, P.; Van Eldik, J.; van Remortel, N.; Van Vulpen, I.; Vegni, G.; Veloso, F.; Venus, W.; Verdier, P.; Verzi, V.; Vilanova, D.; Vitale, L.; Vrba, V.; Wahlen, H.; Washbrook, A.J.; Weiser, C.; Wicke, D.; Wickens, J.; Wilkinson, G.; Winter, M.; Witek, M.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zhuravlov, V.; Zimine, N.I.; Zintchenko, A.; Zupan, M.

    2009-01-01

    A study of the inclusive charged hadron production in two-photon collisions is described. The data were collected with the DELPHI detector at LEP II. Results on the inclusive single-particle p_T distribution and the differential charged hadrons dsigma/dp_T cross-section are presented and compared to the predictions of perturbative NLO QCD calculations and to published results.

  10. Single intermediate vector boson production in $e^{+}e^{-}$ collisions at $\\sqrt{s}$ = 183 - 209 GeV

    CERN Document Server

    Abdallah, J; Adam, W; Adzic, P; Albrecht, T; Alderweireld, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Amaldi, Ugo; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W D; Arnoud, Y; Ask, S; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Ballestrero, A; Bambade, P; Barbier, R; Bardin, D; Barker, G J; Baroncelli, A; Battaglia, M; Baubillier, M; Becks, K H; Begalli, M; Behrmann, A; Ben-Haim, E; Benekos, N; Benvenuti, A C; Bérat, C; Berggren, M; Berntzon, L; Bertrand, D; Besançon, M; Besson, N; Bloch, D; Blom, M; Bluj, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Brenner, R; Brodet, E; Brückman, P; Brunet, J M; Buschmann, P; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F; Chapkin, M; Charpentier, P; Checchia, P; Chierici, R; Shlyapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Crennell, D J; Cuevas-Maestro, J; D'Hondt, J; Dalmau, J; Da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; de Boer, Wim; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; De Paula, L; Di Ciaccio, L; Di Simone, A; Doroba, K; Drees, J; Eigen, G; Ekelöf, T J C; Ellert, M; Elsing, M; Espirito-Santo, M C; Fanourakis, G K; Fassouliotis, D; Feindt, M; Fernández, J; Ferrer, A; Ferro, F; Flagmeyer, U; Föth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J; Gandelman, M; García, C; Gavillet, P; Gazis, E; Gokieli, R; Golob, B; Gómez-Ceballos, G; Gonçalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Herr, H; Hoffman, J; Holmgren, S O; Holt, P J; Houlden, M A; Hultqvist, K; Jackson, J N; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Johansson, P D; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Katsanevas, S; Katsoufis, E C; Kernel, G; Kersevan, B P; Kerzel, U; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kuznetsov, O; Krumshtein, Z; Kucharczyk, M; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; López, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Martínez-Rivero, C; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; McNulty, R; Meroni, C; Migliore, E; Mitaroff, W A; Mjörnmark, U; Moa, T; Moch, M; Mönig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Müller, U; Münich, K; Mulders, M; Mundim, L; Murray, W; Muryn, B; Myatt, G; Myklebust, T; Nassiakou, M; Navarria, Francesco Luigi; Nawrocki, K; Nicolaidou, R; Nikolenko, M; Oblakowska-Mucha, A; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, R; Österberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V F; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Pozdnyakov, V; Pukhaeva, N; Pullia, A; Rames, J; Read, A; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P B; Richard, F; Rídky, J; Rivero, M; Rodríguez, D; Romero, A; Ronchese, P; Roudeau, P; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovskii, A; Salmi, L; Salt, J; Sander, C; Savoy-Navarro, A; Schwickerath, U; Segar, A; Sekulin, R L; Siebel, M; Sisakian, A; Smadja, G; Smirnova, O; Sokolov, A; Sopczak, A; Sosnowski, R; Spassoff, Tz; Stanitzki, M; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Tabarelli de Fatis, T; Taffard, A C; Tegenfeldt, F; Timmermans, J; Tkatchev, L G; Tobin, M; Todorovova, S; Tomé, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M L; Tyapkin, I A; Tyapkin, P; Tzamarias, S; Uvarov, V; Valenti, G; van Dam, P; Van Eldik, J; Van Remortel, N; Van Vulpen, I; Vegni, G; Veloso, F; Venus, W; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weiser, C; Wicke, D; Wickens, J; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O P; Zalewska-Bak, A; Zalewski, P; Zavrtanik, D; Zhuravlov, V; Zimin, N I; Zintchenko, A; Zupan, M

    2006-01-01

    The production of single charged and neutral intermediate vector bosons in e+e- collisions has been studied in the data collected by the DELPHI experiment at LEP at centre-of-mass energies between 183 and 209 GeV, corresponding to an integrated luminosity of about 640 pb^{-1}. The measured cross-sections for the reactions, determined in limited kinematic regions, are in agreement with the Standard Model predictions.

  11. Single Intermediate Vector Boson Production in $e^+ e^-$ collisions at $\\sqrt{s}$ = 183 and 189 GeV

    CERN Document Server

    Abreu, P.; Adye, T.; Adzic, P.; Ajinenko, I.; Albrecht, Z.; Alderweireld, T.; Alekseev, G.D.; Alemany, R.; Allmendinger, T.; Allport, P.P.; Almehed, S.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Anassontzis, E.G.; Andersson, P.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.D.; Arnoud, Y.; Asman, B.; Augustin, J.E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barao, F.; Barbiellini, G.; Barbier, R.; Bardin, Dmitri Yu.; Barker, G.J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.H.; Begalli, M.; Behrmann, A.; Bellunato, T.; Belokopytov, Yu.; Benekos, N.C.; Benvenuti, A.C.; Berat, C.; Berggren, M.; Berntzon, L.; Bertrand, D.; Besancon, M.; Besson, N.; Bilenky, Mikhail S.; Bloch, D.; Blom, H.M.; Bol, L.; Bonesini, M.; Boonekamp, M.; Booth, P.S.L.; Borisov, G.; Bosio, C.; Botner, O.; Boudinov, E.; Bouquet, B.; Bowcock, T.J.V.; Boyko, I.; Bozovic, I.; Bozzo, M.; Bracko, M.; Branchini, P.; Brenner, R.A.; Bruckman, P.; Brunet, J.M.; Bugge, L.; Buschmann, P.; Caccia, M.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Carroll, L.; Caso, C.; Castillo Gimenez, M.V.; Cattai, A.; Cavallo, F.R.; Chapkin, M.; Charpentier, P.; Checchia, P.; Chelkov, G.A.; Chierici, R.; Chliapnikov, P.; Chochula, P.; Chorowicz, V.; Chudoba, J.; Cieslik, K.; Collins, P.; Contri, R.; Cortina, E.; Cosme, G.; Cossutti, F.; Costa, M.; Crawley, H.B.; Crennell, D.; Croix, J.; Crosetti, G.; Cuevas Maestro, J.; Czellar, S.; D'Hondt, J.; Dalmau, J.; Davenport, M.; Da Silva, W.; Della Ricca, G.; Delpierre, P.; Demaria, N.; De Angelis, A.; De Boer, W.; De Clercq, C.; De Lotto, B.; De Min, A.; De Paula, L.; Dijkstra, H.; Di Ciaccio, L.; Doroba, K.; Dracos, M.; Drees, J.; Dris, M.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Engel, J.P.; Espirito Santo, M.C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferrer-Ribas, E.; Ferro, F.; Firestone, A.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fontanelli, F.; Franek, B.; Frodesen, A.G.; Fruhwirth, R.; Fulda-Quenzer, F.; Fuster, J.; Galloni, A.; Gamba, D.; Gamblin, S.; Gandelman, M.; Garcia, C.; Gaspar, C.; Gaspar, M.; Gasparini, U.; Gavillet, P.; Gazis, Evangelos; Gele, D.; Geralis, T.; Ghodbane, N.; Gil Botella, Ines; Glege, F.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Goncalves, P.; Gonzalez Caballero, I.; Gopal, G.; Gorn, L.; Gouz, Yu.; Gracco, V.; Grahl, J.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hahn, F.; Hahn, S.; Haider, S.; Hallgren, A.; Hamacher, K.; Hansen, J.; Harris, F.J.; Haug, S.; Hauler, F.; Hedberg, V.; Heising, S.; Hernandez, J.J.; Herquet, P.; Herr, H.; Hertz, O.; Higon, E.; Holmgren, S.O.; Holt, P.J.; Hoorelbeke, S.; Houlden, M.; Hrubec, J.; Hughes, G.J.; Hultqvist, K.; Jackson, John Neil; Jacobsson, R.; Jalocha, P.; Jarlskog, C.; Jarlskog, G.; Jarry, P.; Jean-Marie, B.; Jeans, D.; Johansson, Erik Karl; Jonsson, P.; Joram, C.; Juillot, P.; Jungermann, L.; Kapusta, Frederic; Karafasoulis, K.; Katsanevas, S.; Katsoufis, E.C.; Keranen, R.; Kernel, G.; Kersevan, B.P.; Khokhlov, Yu.A.; Khomenko, B.A.; Khovanski, N.N.; Kiiskinen, A.; King, B.; Kinvig, A.; Kjaer, N.J.; Klapp, O.; Kluit, P.; Kokkinias, P.; Kostioukhine, V.; Kourkoumelis, C.; Kouznetsov, O.; Krammer, M.; Kriznic, E.; Krumstein, Z.; Kubinec, P.; Kucharczyk, M.; Kurowska, J.; Lamsa, J.W.; Laugier, J.P.; Leder, G.; Ledroit, Fabienne; Leinonen, L.; Leisos, A.; Leitner, R.; Lenzen, G.; Lepeltier, V.; Lesiak, T.; Lethuillier, M.; Libby, J.; Liebig, W.; Liko, D.; Lipniacka, A.; Lippi, I.; Loken, J.G.; Lopes, J.H.; Lopez, J.M.; Lopez-Fernandez, R.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Mahon, J.R.; Maio, A.; Malek, A.; Maltezos, S.; Malychev, V.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Marti i Garcia, S.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Matthiae, G.; Mazzucato, F.; Mazzucato, M.; McCubbin, M.; McKay, R.; McNulty, R.; McPherson, G.; Merle, E.; Meroni, C.; Meyer, W.T.; Miagkov, A.; Migliore, E.; Mirabito, L.; Mitaroff, W.A.; Mjoernmark, U.; Moa, T.; Moch, M.; Monig, Klaus; Monge, M.R.; Montenegro, J.; Moraes, D.; Morettini, P.; Morton, G.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.M.; Murray, W.J.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.L.; Nawrocki, K.; Negri, P.; Nemecek, S.; Neufeld, N.; Nicolaidou, R.; Niezurawski, P.; Nikolenko, M.; Nomokonov, V.; Nygren, A.; Obraztsov, V.; Olshevski, A.G.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Pain, R.; Paiva, R.; Palacios, J.; Palka, H.; Papadopoulou, T.D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Pavel, T.; Pegoraro, M.; Peralta, L.; Perepelitsa, V.; Pernicka, M.; Perrotta, A.; Petridou, C.; Petrolini, A.; Phillips, H.T.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M.E.; Polok, G.; Poropat, P.; Pozdniakov, V.; Privitera, P.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Ragazzi, S.; Rahmani, H.; Ratoff, P.N.; Read, Alexander L.; Rebecchi, P.; Redaelli, Nicola Giuseppe; Regler, M.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.B.; Resvanis, L.K.; Richard, F.; Ridky, J.; Rinaudo, G.; Ripp-Baudot, Isabelle; Romero, A.; Ronchese, P.; Rosenberg, E.I.; Rosinsky, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ruiz, A.; Saarikko, H.; Sacquin, Y.; Sadovsky, A.; Sajot, G.; Salmi, L.; Salt, J.; Sampsonidis, D.; Sannino, M.; Savoy-Navarro, A.; Schwanda, C.; Schwemling, P.; Schwering, B.; Schwickerath, U.; Scuri, Fabrizio; Seager, P.; Sedykh, Y.; Segar, A.M.; Sekulin, R.; Sette, G.; Shellard, R.C.; Siebel, M.; Simard, L.; Simonetto, F.; Sisakian, A.N.; Smadja, G.; Smirnov, N.; Smirnova, O.; Smith, G.R.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Spiriti, E.; Stanescu, C.; Stanitzki, M.; Stevenson, K.; Stocchi, A.; Strauss, J.; Strub, R.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Tabarelli, T.; Taffard, A.; Tegenfeldt, F.; Terranova, F.; Timmermans, Jan; Tinti, N.; Tkatchev, L.G.; Tobin, M.; Todorova, S.; Tome, B.; Tonazzo, A.; Tortora, L.; Tortosa, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.L.; Tyapkin, I.A.; Tyapkin, P.; Tzamarias, S.; Ullaland, O.; Uvarov, V.; Valenti, G.; Vallazza, E.; Van Dam, Piet; Van den Boeck, W.; Van Eldik, J.; Van Lysebetten, A.; Van Remortel, N.; Van Vulpen, I.; Vegni, G.; Ventura, L.; Venus, W.; Verbeure, F.; Verdier, P.; Verlato, M.; Vertogradov, L.S.; Verzi, V.; Vilanova, D.; Vitale, L.; Vlasov, E.; Vodopianov, A.S.; Voulgaris, G.; Vrba, V.; Wahlen, H.; Washbrook, A.J.; Weiser, C.; Wicke, D.; Wickens, J.H.; Wilkinson, G.R.; Winter, M.; Witek, M.; Wolf, G.; Yi, J.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zevgolatakos, E.; Zimine, N.I.; Zintchenko, A.; Zoller, P.; Zumerle, G.; Zupan, M.; Krammer, Manfred

    2001-01-01

    The cross-sections for the production of single charged and neutral intermediate vector bosons were measured using integrated luminosities of 52~pb$^{-1}$ and 154~pb$^{-1}$ collected by the DELPHI experiment at centre-of-mass energies of 182.6~GeV and 188.6~GeV, respectively. The cross-sections for the reactions were determined in limited kinematic regions. The results found are in agreement with the Standard Model predictions for these channels.

  12. Search for single top production via FCNC at LEP at $\\sqrt{s}$ = 189-208 GeV

    CERN Document Server

    Abdallah, J; Adam, W; Adzic, P; Albrecht, T; Alderweireld, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Amaldi, Ugo; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W D; Arnoud, Y; Ask, S; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Ballestrero, A; Bambade, P; Barbier, R; Bardin, Dimitri Yuri; Barker, G; Baroncelli, A; Battaglia, Marco; Baubillier, M; Becks, K H; Begalli, M; Behrmann, A; Ben-Haim, E; Benekos, N C; Benvenuti, Alberto C; Bérat, C; Berggren, M; Berntzon, L; Bertrand, D; Besançon, M; Besson, N; Bloch, D; Blom, M; Bluj, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Brenner, R; Brodet, E; Brückman, P; Brunet, J M; Bugge, L; Buschmann, P; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F R; Chapkin, M M; Charpentier, P; Checchia, P; Chierici, R; Shlyapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Crawley, B; Crennell, D J; Cuevas-Maestro, J; D'Hondt, J; Dalmau, J; Da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; de Boer, Wim; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; De Paula, L S; Di Ciaccio, Lucia; Di Simone, A; Doroba, K; Drees, J; Dris, M; Eigen, G; Ekelöf, T J C; Ellert, M; Elsing, M; Espirito-Santo, M C; Fanourakis, G K; Fassouliotis, D; Feindt, M; Fernández, J; Ferrer, A; Ferro, F; Flagmeyer, U; Föth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J A; Gandelman, M; García, C; Gavillet, P; Gazis, E N; Gokieli, R; Golob, B; Gómez-Ceballos, G; Gonçalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Herr, H; Hoffman, J; Holmgren, S O; Holt, P J; Houlden, M A; Hultqvist, K; Jackson, J N; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Johansson, P D; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Katsanevas, S; Katsoufis, E C; Kernel, G; Kersevan, Borut P; Kerzel, U; Kiiskinen, A P; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kuznetsov, O; Krumshtein, Z; Kucharczyk, M; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; López, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Martínez-Rivero, C; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; McNulty, R; Meroni, C; Meyer, W T; Migliore, E; Mitaroff, W A; Mjörnmark, U; Moa, T; Moch, M; Mönig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Müller, U; Münich, K; Mulders, M; Mundim, L M; Murray, W; Muryn, B; Myatt, G; Myklebust, T; Nassiakou, M; Navarria, Francesco Luigi; Nawrocki, K; Nicolaidou, R; Nikolenko, M; Oblakowska-Mucha, A; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, R; Österberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V F; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Pozdnyakov, V; Pukhaeva, N; Pullia, Antonio; Rames, J; Ramler, L; Read, A; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P B; Richard, F; Rídky, J; Rivero, M; Rodríguez, D; Romero, A; Ronchese, P; Rosenberg, E I; Roudeau, Patrick; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovskii, A; Salmi, L; Salt, J; Savoy-Navarro, A; Schwickerath, U; Segar, A; Sekulin, R L; Siebel, M; Sissakian, A N; Smadja, G; Smirnova, O G; Sokolov, A; Sopczak, A; Sosnowski, R; Spassoff, Tz; Stanitzki, M; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Tabarelli de Fatis, T; Taffard, A C; Tegenfeldt, F; Timmermans, J; Tkatchev, L G; Tobin, M; Todorovova, S; Tomé, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M L; Tyapkin, I A; Tyapkin, P; Tzamarias, S; Uvarov, V; Valenti, G; van Dam, P; Van Eldik, J; Van Lysebetten, A; Van Remortel, N; Van Vulpen, I B; Vegni, G; Veloso, F; Venus, W A; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weiser, C; Wicke, D; Wickens, J H; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O P; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zhuravlov, V; Zimin, N I; Zinchenko, A I; Zupan, M

    2004-01-01

    A search for single top production (e+e- -> t cbar) via Flavour Changing Neutral Currents (FCNC) was performed using the data taken by the DELPHI detector at LEP2. The data analysed have been accumulated at centre-of-mass energies ranging from 189 to 208 GeV. Limits at 95% confidence level were obtained on the anomalous coupling parameters kappa_gamma and kappa_Z.

  13. Measurement of single top production in pp collisions at 7 TeV with the CMS detector

    CERN Document Server

    Iorio, Alberto Orso Maria

    2011-01-01

    We report on the first measurement of the single top t-channel production cross section in proton-proton collisions at center of mass energy $\\sqrt{s}$ = 7 TeV with the Compact Muon Solenoid (CMS) detector at the Large Hadron Collider (LHC), performed with an integrated luminosity of 36 $pb^{-1}$ . Final states where the top decays leptonically through the chains $t \\rightarrow Wb \\rightarrow lb \

  14. Large-sub(pT) production of single and double photons in proton-proton and pion-proton collisions

    International Nuclear Information System (INIS)

    Berger, E.L.; Argonne National Lab., IL; Braaten, E.; Field, R.D.

    1984-01-01

    Quantum chromodynamic (QCD) predictions are made for the large transverse momentum production of single and double photons in proton-proton, proton-antiproton, and pion-proton collisions. In π - p collisions at center-of-mass energy W=27.4 GeV and psub(T)=4.0 GeV, it is estimated that about 0.3% of the 90 0 single photon triggers will be balanced on the 'away-side' by a single photon with roughly the same transverse momentum. In π + p collisions this fraction drops to about 0.09%. These fractions increase with psub(T). In addition to the pure QED annihilation term qanti q -> γγ, it is found that the QCD-induced subprocess gg -> γγ provides an important source of double photons. Photon bremsstrahlung contributions are also examined. Experimental study of the systematics of single and double photon production in hadron-hadron collisions will provide information on the size of the strong interaction coupling constant, αsub(s)(Q), and on the charges of the quarks. Knowledge of the gluon distributions within hadrons and of the effective transverse momentum of partons in hadrons can also be gained. (orig.)

  15. Leptoquark Single and Pair production at LHC with CalcHEP/CompHEP in the complete model

    CERN Document Server

    Belyaev, A; Mehdiyev, R; Pukhov, A E

    2005-01-01

    We study combined leptoquark (LQ) single and pair production at LHC at the level of detector simulation. A set of kinematical cuts to maximize significance for combined signal events has been worked out. It was shown that combination of signatures from LQ single and pair production not only significantly increases the LHC reach, but also allows us to give the correct signal interpretation. In particular, it was found that the LHC has potential to discover LQ with a mass up to 1.2 TeV and 1.5 TeV for the case of scalar and vector LQ, respectively, and LQ single production contributes about 30-50% to the total signal rate for LQ-l-q coupling, taken equal to the electromagnetic coupling. This work is based on the implementation of the most general form of scalar and vector LQ interactions with quarks and gluons into CalcHEP/CompHEP packages. This implementation, which authors made publicly available, was one the most important aspects of the study.

  16. Production Variability and Single Word Intelligibility in Aphasia and Apraxia of Speech

    Science.gov (United States)

    Haley, Katarina L.; Martin, Gwenyth

    2011-01-01

    This study was designed to estimate test-retest reliability of orthographic speech intelligibility testing in speakers with aphasia and AOS and to examine its relationship to the consistency of speaker and listener responses. Monosyllabic single word speech samples were recorded from 13 speakers with coexisting aphasia and AOS. These words were…

  17. Production of vertical arrays of small diameter single-walled carbon nanotubes

    Science.gov (United States)

    Hauge, Robert H; Xu, Ya-Qiong

    2013-08-13

    A hot filament chemical vapor deposition method has been developed to grow at least one vertical single-walled carbon nanotube (SWNT). In general, various embodiments of the present invention disclose novel processes for growing and/or producing enhanced nanotube carpets with decreased diameters as compared to the prior art.

  18. The Heteronuclear Single-Quantum Correlation (HSQC) Experiment: Vectors versus Product Operators

    Science.gov (United States)

    de la Vega-Herna´ndez, Karen; Antuch, Manuel

    2015-01-01

    A vectorial representation of the full sequence of events occurring during the 2D-NMR heteronuclear single-quantum correlation (HSQC) experiment is presented. The proposed vectorial representation conveys an understanding of the magnetization evolution during the HSQC pulse sequence for those who have little or no quantum mechanical background.…

  19. Production of multi-, oligo- and single-pore membranes using a continuous ion beam

    Czech Academy of Sciences Publication Activity Database

    Apel, P. Yu.; Ivanov, O.; Lizunov, N. E.; Mamonova, T. I.; Nechaev, A. N.; Olejniczak, K.; Vacík, Jiří; Dmitriev, S. N.

    2015-01-01

    Roč. 365, DEC (2015), s. 641-645 ISSN 0168-583X R&D Projects: GA MŠk LG14004 Institutional support: RVO:61389005 Keywords : ion beam * irradiation * ion track * etching * single nanopore Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.389, year: 2015

  20. A Study of Charged Current Single Charged Pion Productions on Carbon in a Few-GeV Neutrino Beam

    Energy Technology Data Exchange (ETDEWEB)

    Hiraide, Katsuki [Kyoto Univ. (Japan)

    2009-01-01

    Understanding single charged pion production via neutrino-nucleus charged current interaction in the neutrino energy region of a few GeV is essential for future neutrino oscillation experiments since this process is a dominant background for vμ → vx oscillation measurements. There are two contributions to this process: single pion production via baryonic resonance (vμN → μ-+) and coherent pion production interacting with the entire nucleus (vμA → μ-+), where N is nucleon in the nucleus and A is the nucleus. The purpose of the study presented in this thesis is a precise measurement of charged current single charged pion productions, resonant and coherent pion productions, with a good final state separation in the neutrino energy region of a few GeV. In this thesis, we focus on the study of charged current coherent pion production from muon neutrinos scattering on carbon, vμ 12C → μ-12+, in the SciBooNE experiment. This is motivated by the fact that without measuring this component first, the precise determination of resonant pion production cross section can not be achieved since the contribution of coherent pion production in the region of small muon scattering angle is not small. Furthermore, the coherent process is particularly interesting because it is deeply rooted in fundamental physics via Adler's partially conserved axial-vector current theorem. We took data from June 2007 until August 2008, in both the neutrino and antineutrino beam. In total, 2.52 x 1020 protons on target were collected. We have performed a search for charged current coherent pion production by using SciBooNE's full neutrino data set, corresponding to 0.99 x 1020 protons on target. No evidence for coherent pion production is observed. We set 90% confidence level upper limits on the cross section ratio

  1. A novel multimodal chromatography based single step purification process for efficient manufacturing of an E. coli based biotherapeutic protein product.

    Science.gov (United States)

    Bhambure, Rahul; Gupta, Darpan; Rathore, Anurag S

    2013-11-01

    Methionine oxidized, reduced and fMet forms of a native recombinant protein product are often the critical product variants which are associated with proteins expressed as bacterial inclusion bodies in E. coli. Such product variants differ from native protein in their structural and functional aspects, and may lead to loss of biological activity and immunogenic response in patients. This investigation focuses on evaluation of multimodal chromatography for selective removal of these product variants using recombinant human granulocyte colony stimulating factor (GCSF) as the model protein. Unique selectivity in separation of closely related product variants was obtained using combined pH and salt based elution gradients in hydrophobic charge induction chromatography. Simultaneous removal of process related impurities was also achieved in flow-through leading to single step purification process for the GCSF. Results indicate that the product recovery of up to 90.0% can be obtained with purity levels of greater than 99.0%. Binding the target protein at pHproduct variants using the combined pH and salt based elution gradient and removal of the host cell impurities in flow-through are the key novel features of the developed multimodal chromatographic purification step. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Productivity Improvement for the SHX--SEN's Single-Wafer High-Current Ion Implanter