Sample records for helicase-dependent isothermal amplification

  1. Helicase-Dependent Isothermal Amplification of DNA and RNA by Using Self-Avoiding Molecular Recognition Systems.

    PubMed

    Yang, Zunyi; McLendon, Chris; Hutter, Daniel; Bradley, Kevin M; Hoshika, Shuichi; Frye, Carole B; Benner, Steven A

    2015-06-15

    Assays that detect DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low-resource environments, and requires equipment and power that might not be available in these environments. Isothermal procedures, which avoid thermal cycling, are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a "self avoiding molecular recognition system" (SAMRS) eliminates these artifacts and gives clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3'-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, difficult to achieve with HDA using standard primers. Thus, SAMRS-HDA is a more versatile approach than standard HDA, with a broader applicability for xNA-targeted diagnostics and research. PMID:25953623

  2. Detection of Group A Streptococcus in Pharyngeal Swab Specimens by Use of the AmpliVue GAS Isothermal Helicase-Dependent Amplification Assay.

    PubMed

    Faron, Matthew L; Ledeboer, Nathan A; Granato, Paul; Daly, Judy A; Pierce, Kristina; Pancholi, Preeti; Uphoff, Timothy S; Buchan, Blake W

    2015-07-01

    We evaluated the clinical performance (sensitivity and specificity) of the AmpliVue group A Streptococcus (GAS) isothermal helicase-dependent amplification assay using 1,192 pharyngeal swab specimens. AmpliVue GAS assay results were compared to the results of routine throat cultures on selective streptococcal blood agar plates. The sensitivity and specificity of the AmpliVue GAS assay were 98.3% (95% confidence interval [CI], 95 to 100%) and 93.2% (95% CI, 91 to 95%), respectively. PMID:25972419

  3. Rapid detection of Staphylococcus aureus in dairy and meat foods by combination of capture with silica-coated magnetic nanoparticles and thermophilic helicase-dependent isothermal amplification.

    PubMed

    Chen, Xingxing; Wu, Xiaoli; Gan, Min; Xu, Feng; He, Lihua; Yang, Dong; Xu, Hengyi; Shah, Nagendra P; Wei, Hua

    2015-03-01

    Staphylococcus aureus is one of the main pathogens in dairy and meat products; therefore, developing a highly sensitive and rapid method for its detection is necessary. In this study, a quantitative detection method for Staph. aureus was developed using silica-coated magnetic nanoparticles and thermophilic helicase-dependent isothermal amplification. First, genomic DNA was extracted from lysed bacteria using silica-coated magnetic nanoparticles and amplified using thermophilic helicase-dependent isothermal amplification. After adding the nucleic-acid dye SYBR Green I to the amplicons, the fluorescence intensity was observed using a UV lamp or recorded using a fluorescence spectrophotometer. This detection system had a detection limit of 5×10(0) cfu/mL in pure culture and milk-powder samples and 5×10(1) cfu/mL in pork samples using a UV light in less than 2h. In addition, a good linear relationship was obtained between fluorescence intensity and bacterial concentrations ranging from 10(2) to 10(4) cfu/mL under optimal conditions. Furthermore, the results from contaminated milk powder and pork samples suggested that the detection system could be used for the quantitative analysis of Staph. aureus and applied potentially to the food industry for the detection of this pathogen. PMID:25547304

  4. Miniaturized isothermal nucleic acid amplification, a review.

    PubMed

    Asiello, Peter J; Baeumner, Antje J

    2011-04-21

    Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented. PMID:21387067

  5. Isothermal amplification of insect DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The loop-mediated isothermal amplification of DNA (LAMP) method can amplify a target DNA sequence at a constant temperature in about 1 hour. LAMP has broad application in agriculture and medicine because of the need for rapid and inexpensive diagnoses. The power of LAMP is being used by researchers ...

  6. Diagnostic Devices for Isothermal Nucleic Acid Amplification

    PubMed Central

    Chang, Chia-Chen; Chen, Chien-Cheng; Wei, Shih-Chung; Lu, Hui-Hsin; Liang, Yang-Hung; Lin, Chii-Wann

    2012-01-01

    Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development. PMID:22969402

  7. Low Cost Extraction and Isothermal Amplification of DNA for Infectious Diarrhea Diagnosis

    PubMed Central

    Huang, Shichu; Do, Jaephil; Mahalanabis, Madhumita; Fan, Andy; Zhao, Lei; Jepeal, Lisa; Singh, Satish K.; Klapperich, Catherine M.

    2013-01-01

    In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10?2 pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health. PMID:23555883

  8. Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis.

    PubMed

    Huang, Shichu; Do, Jaephil; Mahalanabis, Madhumita; Fan, Andy; Zhao, Lei; Jepeal, Lisa; Singh, Satish K; Klapperich, Catherine M

    2013-01-01

    In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10(-2) pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health. PMID:23555883

  9. In-field diagnostics using loop-mediated isothermal amplification.

    PubMed

    Tomlinson, Jenny

    2013-01-01

    Loop-mediated isothermal amplification (LAMP) is a method for amplification and detection of target organisms which, unlike polymerase chain reaction, does not require thermal cycling. LAMP assays can be developed in the laboratory for subsequent deployment in the field, where the simplicity of isothermal amplification makes LAMP a suitable method for rapid detection of phytoplasmas with levels of sensitivity and specificity approaching those of more complex and time-consuming laboratory methods. PMID:22987425

  10. Loop-Mediated Isothermal Amplification for Detection of African Trypanosomes

    PubMed Central

    Kuboki, Noritaka; Inoue, Noboru; Sakurai, Tatsuya; Di Cello, Francescopaolo; Grab, Dennis J.; Suzuki, Hiroshi; Sugimoto, Chihiro; Igarashi, Ikuo

    2003-01-01

    While PCR is a method of choice for the detection of African trypanosomes in both humans and animals, the expense of this method negates its use as a diagnostic method for the detection of endemic trypanosomiasis in African countries. The loop-mediated isothermal amplification (LAMP) reaction is a method that amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions with only simple incubators. An added advantage of LAMP over PCR-based methods is that DNA amplification can be monitored spectrophotometrically and/or with the naked eye without the use of dyes. Here we report our conditions for a highly sensitive, specific, and easy diagnostic assay based on LAMP technology for the detection of parasites in the Trypanosoma brucei group (including T. brucei brucei, T. brucei gambiense, T. brucei rhodesiense, and T. evansi) and T. congolense. We show that the sensitivity of the LAMP-based method for detection of trypanosomes in vitro is up to 100 times higher than that of PCR-based methods. In vivo studies in mice infected with human-infective T. brucei gambiense further highlight the potential clinical importance of LAMP as a diagnostic tool for the identification of African trypanosomiasis. PMID:14662933

  11. Accelerated reaction by loop-mediated isothermal amplification using loop primers

    Microsoft Academic Search

    K. Nagamine; T. Hase; T. Notomi

    2002-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity. We have developed a method that accelerates the LAMP reaction by using additional primers, termed loop primers. Loop primers hybridize to

  12. Study on Loop-Mediated Isothermal Amplification Assay for Detection of Salmonella in Meat Products

    Microsoft Academic Search

    Wang Yu; Zhang Wei; Yuan Yaowu; Ma Xiaoyan; Zhang Huiyan; Su Xudong; Wang Zhenqiang; Ma Bo

    2009-01-01

    A novel nucleic acid amplification method, termed Loop-mediated Isothermal Amplification (LAMP), which amplifies DNA with high specificity, efficiency, andrapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity, may be a valuable tool for the rapid detection of infectious diseases. This study designed two pairs of gene-specific primers of conservative

  13. Rapid sexing of bovine preimplantation embryos using loop-mediated isothermal amplification

    Microsoft Academic Search

    Hiroki Hirayama; Soichi Kageyama; Satoru Moriyasu; Ken Sawai; Sadao Onoe; Yoshiyuki Takahashi; Seiji Katagiri; Keiko Toen; Keiko Watanabe; Tsugunori Notomi; Hidenari Yamashina; Sigenori Matsuzaki; Akira Minamihashi

    2004-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method that amplifies a target sequence specifically under isothermal conditions. The product of LAMP is detected by the turbidity of the reaction mixture without electrophoresis. The objective of this study was to develop a rapid sexing method for bovine preimplantation embryos using LAMP. The first experiment was conducted to optimize the

  14. Wolbachia detection in insects through LAMP: loop mediated isothermal amplification

    PubMed Central

    2014-01-01

    Background The bacterium Wolbachia is a promising agent for the biological control of vector-borne diseases as some strains have the ability to block the transmission of key human disease-causing pathogens. Fast, accurate and inexpensive methods of differentiating between infected and uninfected insects will be of critical importance as field-based trials of Wolbachia-based bio-control become increasingly common. Findings We have developed a specific and sensitive method of detecting Wolbachia based on the isothermal DNA amplification. This technique can be performed in an ordinary heat block without the need for gel-based visualisation, and is effective for a wide variety of insect hosts. Conclusion Here we present the development of a rapid, highly sensitive and inexpensive method to detect Wolbachia in a variety of insect hosts, including key mosquito disease vectors. PMID:24885509

  15. Brief review of monitoring methods for loop-mediated isothermal amplification (LAMP).

    PubMed

    Zhang, Xuzhi; Lowe, Stuart B; Gooding, John Justin

    2014-11-15

    The loop-mediated isothermal amplification (LAMP) technique has the potential to revolutionize molecular biology because it allows DNA amplification under isothermal conditions and is highly compatible with point-of-care analysis. To achieve efficient genetic analysis of samples, the method of real-time or endpoint determination selected to monitor the biochemical reaction is of great importance. In this paper we briefly review progress in the development of monitoring methods for LAMP. PMID:24949822

  16. Development of loop-mediated isothermal amplification (LAMP) method for diagnosis of equine piroplasmosis

    Microsoft Academic Search

    Andy Alhassan; Oriel M. M. Thekisoe; Naoaki Yokoyama; Noboru Inoue; Makhosazana Y. Motloang; Peter A. Mbati; Hong Yin; Yoshinari Katayama; Toru Anzai; Chihiro Sugimoto; Ikuo Igarashi

    2007-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid method whereby DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. In this study, we used LAMP primer sets designed from EMA-1 and Bc 48 genes for detection of Theileria equi and

  17. Detection of Loop-Mediated Isothermal Amplification Reaction by Turbidity Derived from Magnesium Pyrophosphate Formation

    Microsoft Academic Search

    Yasuyoshi Mori; Kentaro Nagamine; Norihiro Tomita; Tsugunori Notomi

    2001-01-01

    The loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method that uses only one type of enzyme. One of the characteristics of the LAMP method is its ability to synthesize extremely large amount of DNA. Accordingly, a large amount of by-product, pyrophosphate ion, is produced, yielding white precipitate of magnesium pyrophosphate in the reaction mixture. Judging the presence

  18. Two methods for increased specificity and sensitivity in loop-mediated isothermal amplification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The technique of loop-mediated isothermal amplification (LAMP) utilizes 4 (or 6) primers targeting 6 (or 8) regions within a fairly small segment of a genome for amplification, with concentration higher than that used in traditional PCR methods. The high concentrations of primers used leads to an in...

  19. LAMP (Loop-mediated isothermal amplification of DNA) - A technique for biotype discrimination in Bemisia tabaci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Loop-mediated isothermal amplification of DNA (LAMP) can amplify a target DNA sequence at a constant temperature in about 1 hour. LAMP technology has great potential for agricultural applications because of the need for rapid and inexpensive diagnoses. Assays based on LAMP technology are well suited...

  20. Rapid detection of porcine parvovirus DNA by sensitive loop-mediated isothermal amplification.

    PubMed

    Chen, Hao-tai; Zhang, Jie; Yang, Sheng-hai; Ma, Li-na; Ma, Yan-ping; Liu, Xiang-tao; Cai, Xue-peng; Zhang, Yong-guang; Liu, Yong-sheng

    2009-06-01

    A method of loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for porcine parvovirus (PPV) DNA. The amplification could be finished in 45 min under isothermal condition at 62 degrees C by employing a set of four primers targeting VP2 gene of PPV. LAMP assay showed higher sensitivity than PCR, with a detection limit of 5 copies of PPV genomic DNA per reaction. No cross reactivity was observed from the samples of other related viruses including canine parvovirus, parvovirus B19, porcine circovirus type 1, porcine circovirus type 2 and porcine peudorabies virus. The detection rate of PPV LAMP for 125 clinical samples was 97.6% and appeared higher than that of PCR method. The result indicated the potential usefulness of the technique as a simple, rapid procedure for the detection of PPV. PMID:19428576

  1. Specific and rapid detection of foodborne Salmonella by loop-mediated isothermal amplification method

    Microsoft Academic Search

    Li Wang; Lei Shi; M. J. Alam; Yuhuan Geng; Lin Li

    2008-01-01

    We developed and evaluated the specificity and sensitivity of a loop-mediated isothermal amplification (LAMP) method for rapid detection of the food-borne pathogen Salmonella. A pair of outer primers and a pair of inner primers was specially designed for recognizing six distinct sequences on the target invA gene. By the detection system, 241bp target DNA was amplified and visualized as ladder-like

  2. A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers

    PubMed Central

    Du, Yan; Hughes, Randall A.; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.; Li, Bingling

    2015-01-01

    Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20–100 copies/?l, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device. PMID:26050646

  3. A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers.

    PubMed

    Du, Yan; Hughes, Randall A; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D; Li, Bingling

    2015-01-01

    Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20-100 copies/?l, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device. PMID:26050646

  4. Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection

    PubMed Central

    Roskos, Kristina; Hickerson, Anna I.; Lu, Hsiang-Wei; Ferguson, Tanya M.; Shinde, Deepali N.; Klaue, Yvonne; Niemz, Angelika

    2013-01-01

    Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden. PMID:23922706

  5. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

    PubMed

    Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

    2015-01-01

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65?°C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique. PMID:26154567

  6. The Development of a Loop-Mediated Isothermal Amplification Method (LAMP) for Echinococcus granulosis Coprodetection

    PubMed Central

    Salant, Harold; Abbasi, Ibrahim; Hamburger, Joseph

    2012-01-01

    We have previously developed a polymerase chain reaction (PCR) assay for detection of Echinococcus granulosus infection, which proved very sensitive and specific for identification of infected dogs. We have now developed a loop-mediated isothermal amplification (LAMP) assay, which amplifies the same genomic repeated sequences of E. granulosus for coprodetection. This assay enabled detection of a single egg in fecal samples and showed high species specificity for E. granulosus with no cross-amplification of DNA from closely related helminths, including Echinococcus multilocularis. Because the method does not require thermocycling for DNA amplification, or electrophoresis for amplicon detection, it can potentially be used for premortem identification of E. granulosus-infected dogs to enable large-scale surveys in endemic countries where highly specialized equipment to undertake PCR analysis is rare. PMID:22987649

  7. Tuberculosis Biomarker Extraction and Isothermal Amplification in an Integrated Diagnostic Device

    PubMed Central

    Creecy, Amy; Russ, Patricia K.; Solinas, Francesca; Wright, David W.; Haselton, Frederick R.

    2015-01-01

    In this study, we integrated magnetic bead-based sample preparation and isothermal loop mediated amplification (LAMP) of TB in a single tube. Surrogate sputum samples produced by the Program for Appropriate Technology in Health containing inactivated TB bacteria were used to test the diagnostic. In order to test the sample preparation method, samples were lysed, and DNA was manually extracted and eluted into water in the tube. In a thermal cycler, LAMP amplified TB DNA from 103 TB cells/mL of sputum at 53.5 ± 3.3 minutes, 104 cells/mL at 46.3 ± 2.2 minutes, and 105 cells/mL at 41.6 ± 1.9 minutes. Negative control samples did not amplify. Next, sample preparation was combined with in-tubing isothermal LAMP amplification by replacing the water elution chamber with a LAMP reaction chamber. In this intermediate configuration, LAMP amplified 103 cells/mL at 74 ± 10 minutes, 104 cells/mL at 60 ± 9 minutes, and 105 TB cells/mL of sputum at 54 ± 9 minutes. Two of three negative controls did not amplify; one amplified at 100 minutes. In the semi-automated system, DNA was eluted directly into an isothermal reaction solution containing the faster OptiGene DNA polymerase. The low surrogate sputum concentration, 103 TB cells/mL, amplified at 52.8 ± 3.3 minutes, 104 cells/mL at 45.4 ± 11.3 minutes, and 105 cells/mL at 31.8 ± 2.9 minutes. TB negative samples amplified at 66.4 ± 7.4 minutes. This study demonstrated the feasibility of a single tube design for integrating sample preparation and isothermal amplification, which with further development could be useful for point-of-care applications, particularly in a low-resource setting. PMID:26132307

  8. GMO detection in food and feed through screening by visual loop-mediated isothermal amplification assays.

    PubMed

    Wang, Cong; Li, Rong; Quan, Sheng; Shen, Ping; Zhang, Dabing; Shi, Jianxin; Yang, Litao

    2015-06-01

    Isothermal DNA/RNA amplification techniques are the primary methodology for developing on-spot rapid nucleic acid amplification assays, and the loop-mediated isothermal amplification (LAMP) technique has been developed and applied in the detection of foodborne pathogens, plant/animal viruses, and genetically modified (GM) food/feed contents. In this study, one set of LAMP assays targeting on eight frequently used universal elements, marker genes, and exogenous target genes, such as CaMV35S promoter, FMV35S promoter, NOS, bar, cry1Ac, CP4 epsps, pat, and NptII, were developed for visual screening of GM contents in plant-derived food samples with high efficiency and accuracy. For these eight LAMP assays, their specificity was evaluated by testing commercial GM plant events and their limits of detection were also determined, which are 10 haploid genome equivalents (HGE) for FMV35S promoter, cry1Ac, and pat assays, as well as five HGE for CaMV35S promoter, bar, NOS terminator, CP4 epsps, and NptII assays. The screening applicability of these LAMP assays was further validated successfully using practical canola, soybean, and maize samples. The results suggested that the established visual LAMP assays are applicable and cost-effective for GM screening in plant-derived food samples. PMID:25822163

  9. Simultaneous detection of RNA and DNA targets based on multiplex isothermal amplification.

    PubMed

    Dobnik, David; Morisset, Dany; Lenar?i?, Rok; Ravnikar, Maja

    2014-04-01

    The detection of pathogenic microorganisms present in food, feed, plant, and other samples is important for providing safe food as well as for preventing the spread of microbes. The genome of pathogens is made of DNA or RNA, therefore a multiplex diagnostics tool would ideally be able to amplify and detect both RNA and DNA targets in parallel. With this goal we have developed an isothermal nucleic acid sequence based amplification [NASBA] implemented microarray analysis (NAIMA) procedure, suitable for the simultaneous multiplex amplification of RNA and DNA targets, coupled with the detection on ArrayTubes. The method is demonstrated to be very sensitive and specific for the detection of two economically important quarantine plant pathogens of potato, the potato spindle tuber viroid (RNA target) and Ralstonia solanacearum (DNA target). Because of its isothermal amplification and simple detection equipment, the method is also applicable for on-site analyses. NAIMA can be used in any domain where there is the need to detect RNA and DNA targets simultaneously. PMID:24625323

  10. Development of loop-mediated isothermal amplification test for the diagnosis of contagious agalactia in goats.

    PubMed

    Rekha, Valsala; Rana, Rajneesh; Thomas, Prasad; Viswas, Konasagara Nagaleekar; Singh, Vijendra Pal; Agarwal, Rajesh Kumar; Arun, Thachappully Remesh; Karthik, Kumaragurubaran; Sophia, Inbaraj

    2015-03-01

    Contagious agalactia is a highly infectious disease affecting sheep and goats, mainly caused by Mycoplasma agalactiae. Although various tests are available for diagnosis of contagious agalactia, none of them is credited with the capacity to provide rapid and cost-effective diagnosis. This article reports the development of loop-mediated isothermal amplification (LAMP) test targeting the p40 gene of M. agalactiae, for the diagnosis of classical contagious agalactia. Optimum amplification was obtained at 58 °C in 70 min. The developed test was found to be 100-fold more sensitive than PCR and detected up to 20-fg level of DNA. The test was also superior to conventional PCR in detecting from artificially contaminated milk, i.e. 10(4)-fold more sensitive. The developed LAMP test could detect up to 10 cfu/ml of artificially contaminated milk, indicating its potential for being developed as a field test for rapid and sensitive diagnosis. PMID:25616985

  11. Fluorescence aptameric sensor for isothermal circular strand-displacement polymerization amplification detection of adenosine triphosphate.

    PubMed

    Song, Weiling; Zhang, Qiao; Xie, Xuxu; Zhang, Shusheng

    2014-11-15

    In this work, isothermal circular strand-displacement polymerization amplification assay is developed for highly specific and sensitive detection of adenosine triphosphate (ATP). The amplification process consists of circular common target molecule-displacement polymerization (CCDP) and circular nucleic acid strand-displacement polymerization (CNDP). In the presence of ATP, the complementary strand was released from the aptamer by the target recognition of ATP, and catalyzed the subsequent cycle reaction. With the polymerase and primer, the displaced target triggers the process of CCDP. With the involvement of nicking endonuclease, the released complementary strand triggers the CNDP. Combined CCDP with CNDP, the exponentially produced fluorescence probes are obtained, achieving a detection limit of ATP as low as 2.6 × 10(-10)M. Moreover, the proposed strategy exhibits an excellent specificity and is successfully applied in real sample assay which demonstrates potential application in practical samples. PMID:24851721

  12. Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection.

    PubMed

    Mauk, Michael G; Liu, Changchun; Sadik, Mohamed; Bau, Haim H

    2015-01-01

    Molecular (nucleic acid)-based diagnostics tests have many advantages over immunoassays, particularly with regard to sensitivity and specificity. Most on-site diagnostic tests, however, are immunoassay-based because conventional nucleic acid-based tests (NATs) require extensive sample processing, trained operators, and specialized equipment. To make NATs more convenient, especially for point-of-care diagnostics and on-site testing, a simple plastic microfluidic cassette ("chip") has been developed for nucleic acid-based testing of blood, other clinical specimens, food, water, and environmental samples. The chip combines nucleic acid isolation by solid-phase extraction; isothermal enzymatic amplification such as LAMP (Loop-mediated AMPlification), NASBA (Nucleic Acid Sequence Based Amplification), and RPA (Recombinase Polymerase Amplification); and real-time optical detection of DNA or RNA analytes. The microfluidic cassette incorporates an embedded nucleic acid binding membrane in the amplification reaction chamber. Target nucleic acids extracted from a lysate are captured on the membrane and amplified at a constant incubation temperature. The amplification product, labeled with a fluorophore reporter, is excited with a LED light source and monitored in situ in real time with a photodiode or a CCD detector (such as available in a smartphone). For blood analysis, a companion filtration device that separates plasma from whole blood to provide cell-free samples for virus and bacterial lysis and nucleic acid testing in the microfluidic chip has also been developed. For HIV virus detection in blood, the microfluidic NAT chip achieves a sensitivity and specificity that are nearly comparable to conventional benchtop protocols using spin columns and thermal cyclers. PMID:25626529

  13. Loop-Mediated Isothermal Amplification (LAMP) for Detection of Phytoplasmas in the Field.

    PubMed

    Dickinson, Matt

    2015-01-01

    Loop-mediated isothermal amplification (LAMP) is a nucleic acid-based detection method with many applications. This chapter details its use for detection of phytoplasma diseases, combining a rapid 2-min DNA extraction method with real-time LAMP product detection such that the entire procedure can be undertaken and completed in the field within 40 min. Furthermore, the assays include an anneal curve validation step to guard against false positives and an assay for host plant DNA to guard against false negatives. PMID:25981249

  14. Monitoring the progression of loop-mediated isothermal amplification using conductivity.

    PubMed

    Zhang, Xuzhi; Liu, Wenwen; Lu, Xun; Justin Gooding, J; Li, Qiufen; Qu, Keming

    2014-12-01

    Loop-mediated isothermal amplification (LAMP) yields a large amount of DNA, as well as magnesium pyrophosphate precipitate, causing a decrease in ionic strength that can be measured with a conductivity meter. There is a clear relationship between the conductivity of the LAMP mixture solution and the duration of biochemical reaction. Moreover, there is also a clear relationship between the change in conductivity and the amount of initial template DNA over the range of 0.08 to 3.2 ng. These results demonstrate the feasibility not only for detecting the LAMP product qualitatively but also for real-time monitoring the biochemical reaction progression quantitatively using conductivity measurements. PMID:25168192

  15. Development of loop-mediated isothermal amplification assays for rapid and easy detection of Coxiella Burnetii.

    PubMed

    Chen, Hua-Wei; Ching, Wei-Mei

    2014-12-01

    Q fever is an important worldwide zoonosis that is caused by infection with Coxiella burnetii. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of the transposase gene insertion element IS1111a of C. burnetii. The sensitivity of this LAMP assay is very similar to quantitative PCR (qPCR) method with a detection limit at 25 copies of the gene, the equivalent of about one C. burnetii organism. Several methods for the detection of LAMP product were also performed to show the diverse way of detection which may be used in different settings depending on the user's infrastructure and resource. PMID:25449632

  16. Detection of mink enteritis virus by loop-mediated isothermal amplification (LAMP).

    PubMed

    Wang, Jianke; Cheng, Shipeng; Yi, Li; Cheng, Yuening; Yang, Shen; Xu, Hongli; Li, Zhenguang; Shi, Xinchuan; Wu, Hua; Yan, Xijun

    2013-02-01

    Loop-mediated isothermal amplification (LAMP) method was discovered in the last decade but only used for the first time in the diagnosis of mink enteritis virus (MEV) infection in this study. The amplification could be completed within 60 min, under isothermal condition at 65°C, by employing a set of four primers targeting the VP2 gene of MEV. The LAMP was more sensitive than the conventional PCR, with a detection limit of 10(-1) median tissue culture infective doses (TCID(50))/ml per reaction, compared with 10 TCID(50)/ml for PCR analysis. No cross reactivity was observed for other related viruses, including canine distemper virus (CDV) and Aleutian mink disease parvovirus (AMDV). Eighty four of 230 clinical samples were found to be positive for MEV, which is higher than that determined by using the conventional PCR method (68). The results indicate the LAMP can be potentially used to determine MEV as a simple, rapid procedure. This assay would be an available alternative to PCR analysis for the diagnosis of MEV infection in mink, particularly in less well-equipped laboratories and in rural settings where resources are limited. PMID:23183142

  17. Rapid and sensitive detection of Penaeus monodon nucleopolyhedrovirus by loop-mediated isothermal amplification.

    PubMed

    Chaivisuthangkura, Parin; Srisuk, Chutima; Rukpratanporn, Sombat; Longyant, Siwaporn; Sridulyakul, Pattarin; Sithigorngul, Paisarn

    2009-12-01

    Loop-mediated isothermal amplification (LAMP) is a novel, sensitive and rapid method for amplification of nucleic acids under isothermal conditions. In this report, a LAMP method was developed for detection of Penaeus monodon nucleopolyhedrovirus (PemoNPV), known previously as monodon baculovirus (MBV), using a set of six primers designed to specifically recognize the PemoNPV polyhedrin gene. The optimized time and temperature conditions for the LAMP assay were 60 min at 63 degrees C. The sensitivity of LAMP for PemoNPV detection was approximately 50 viral copies ng(-1) genomic DNA (equivalent to 150 viral copies per reaction). Using a DNA template extracted from PemoNPV-infected shrimp by a viral nucleic acid kit, the detection limit of LAMP was 0.7 fg while that of nested PCR was 70 fg; therefore, the LAMP assay was 100 times more sensitive than nested PCR. The LAMP method did not amplify a product using nucleic acid extracted from shrimp infected with other viruses including yellow head virus (YHV), Taura syndrome virus (TSV), white spot syndrome virus (WSSV), Penaeus stylirostris densovirus (PstDNV) known previously as infectious hypodermal and hematopoietic necrosis virus (IHHNV), and Penaeus monodon densovirus (PmDNV) known previously as hepatopancreatic parvovirus (HPV). PMID:19703492

  18. Loop-mediated isothermal amplification for rapid and convenient detection of Mycoplasma hyopneumoniae.

    PubMed

    Li, Jiahe; Minion, F Chris; Petersen, Andrew C; Jiang, Fei; Yang, Sheng; Guo, Panpan; Li, Jinxiang; Wu, Wenxue

    2013-04-01

    Loop-mediated isothermal amplification (LAMP), a novel method of gene amplification, was employed in this study for detecting Mycoplasma hyopneumoniae in the respiratory tract or lungs of swine. The pathogen can be detected in LAMP reactions containing as few as 10 fg purified target DNA (10 copies of M. hyopneumoniae genome) within 30 min, which was comparable to real-time PCR. After 30-min reaction at 63 °C, the addition of a certain amount of dye (SYBR Green I and hydroxyl naphthol blue at a proper ratio) into the LAMP reaction system makes the results easily determined as positive or negative by visual inspection. In addition, the LAMP was able to distinguish between M. hyopneumoniae and other closely-related mycoplasma strains, indicating a high degree of specificity. The LAMP assay was more simple and cheap, since the reaction could be completed under isothermal conditions and less laboratorial infrastructure are required. And, it was proven reliable for M. hyopneumoniae diagnosis of nasal swab and lung samples from the field. PMID:23184577

  19. Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification: A Novel Analytically Rapid, Sensitive, Multiplex Loop-Mediated Isothermal Amplification Detection Technique.

    PubMed

    Wang, Yi; Wang, Yan; Lan, Ruiting; Xu, Huaqing; Ma, Aijing; Li, Dongxun; Dai, Hang; Yuan, Xuejiao; Xu, Jianguo; Ye, Changyun

    2015-07-01

    Loop-mediated isothermal amplification (LAMP) is restricted to detecting a single target, limiting the usefulness of this method. To achieve multiplex LAMP-based detection, we developed a novel approach we called the multiple endonuclease restriction real-time-LAMP assay. In this system, the LAMP forward or backward inner primers contain 5' end short sequences that are recognized by the restriction endonuclease Nb.BsrDI, and the new forward or backward inner primers were modified at the 5' end with a fluorophore and in the middle with a dark quencher. Nb.BsrDI digests the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which releases the quenching, resulting in a gain of signal. The assay permitted real-time detection of single or multiple target sequences in a single tube, and the positive results can be obtained in as short as 12 minutes. The novel methodology is highly efficient and specific, detecting down to 250 fg of DNA per reaction of Listeria DNA tested, and was successful in evaluating raw meat samples. The multiple endonuclease restriction real-time-LAMP technology, which is an extension of LAMP to accommodate robust, target-specific, and multiplex detection, provides a molecular diagnostic tool with less detection time and high sensitivity and specificity compared with those of LAMP and quantitative real-time PCR. PMID:26094089

  20. Development of a rapid cyprinid herpesvirus 2 detection method by loop-mediated isothermal amplification.

    PubMed

    Liang, L-G; Xie, J; Luo, D

    2014-10-01

    Cyprinid herpesvirus 2 (CyHV2) is a pathogen that causes severe disease and high mortality in goldfish and Prussian carp. We developed a six primer loop-mediated isothermal amplification (LAMP) assay targeting the intercapsomeric triplex protein gene. CyHV-2 DNA was 10-fold serially diluted (10(8)-10(0) copies ?l(-1)) and was used as the template to determine primer sensitivity. LAMP assays were performed with DNA templates from other pathogens to determine specificity. The LAMP assay had an unequivocal detection limit of 10 copies ?l(-1), which was 100 times lower than that of the polymerase chain reaction. Other pathogen strains were not amplified by the LAMP primers, indicating good specificity. SYBR Green I was added to visually detect the amplification products. Assay applicability was evaluated in 120 samples of Carassius auratus gibelio, and a positive rate of 92·5% was obtained. In conclusion, a conventional LAMP assay has high convenience, rapidity, sensitivity and specificity for detecting CyHV-2 in infected aquatic organisms. Significance and impact of the study: Herpesviral haematopoietic necrosis, caused by cyprinid herpesvirus 2 (CyHV-2), is a severe disease of goldfish and Prussian carp associated with high mortality. We developed a loop-mediated isothermal amplification (LAMP) assay to detect CyHV-2 at relatively low plasmid DNA copy levels. The results show that the LAMP assay has a number of advantages (simple, sensitive, rapid and specific) over the conventional polymerase chain reaction and can be applied in the laboratory and field. Particularly, the method is highly applicable to facilitate surveillance and early diagnosis of CyHV-2. PMID:24935791

  1. Loop-mediated isothermal amplification (LAMP): methods for plant species identification in food.

    PubMed

    Focke, Felix; Haase, Ilka; Fischer, Markus

    2013-03-27

    Loop-mediated isothermal amplification (LAMP) is a DNA-based analytical method that can be used as an isothermal alternative to polymerase chain reaction (PCR). In comparison to PCR, the advantage of LAMP is the possibility to perform the isothermal reaction without any sophisticated technical equipment; only a water bath is needed, and naked eye detection is sufficient. Up to now, an application of LAMP methods for the detection of even closely related plant species in food or feed matrices has not been described, whereas a large number of PCR methods for that topic are cited in the literature. The aim of the study was the evaluation of LAMP-based methods for plant species identification with respect to method parameters such as R(2), LOD, and LOQ. An existing (real-time) PCR method (for the detection of spices) was used for comparison. It could be shown that the developed LAMP methods have potential as alternative strategies to PCR in DNA-based analysis. PMID:23432417

  2. Rapid detection of mud crab dicistrovirus-1 using loop-mediated isothermal amplification.

    PubMed

    Guo, Zhixun; Zhang, Di; Ma, Hongling; Su, Youlu; Feng, Juan; Xu, Liwen

    2014-11-01

    Mud crab dicistrovirus-1 (MCDV-1) was isolated from the mud crab (Scylla paramamosain), resulting in mass mortality and widespread economic loss in China. In this study, a detection method for MCDV-1 using loop-mediated isothermal amplification was developed. Two pairs of primers targeting the VP2 gene were designed. These primers were the outer primers F3 and B3, and the inner primers FIP and BIP. Optimal amplification was carried out using 0.2 ?mol/L F3/B3, 1.6 ?mol/L FIP/BIP, 6 mmol/L Mg(2+), 0.8 mmol/L dNTPs, and 0.8 mol/L betaine, and completed in 1h at 62°C. The products demonstrated a ladder pattern on agarose gel electrophoresis and could also be detected visually according to turbidity, or by adding SYBR Green I and observing a color change from orange to green. The proposed method could specifically amplify MCDV-1 gene fragments. Sensitivity assay revealed that six copies of the viral genome could be detected by this method, which was 1000-fold more sensitive than that of conventional PCR using constructed plasmid as amplification template. At clinical sample level, sensitivity of LAMP was 100-fold higher than that of conventional PCR. PMID:25172047

  3. Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies

    PubMed Central

    Mairinger, Fabian D; Walter, Robert FH; Vollbrecht, Claudia; Hager, Thomas; Worm, Karl; Ting, Saskia; Wohlschläger, Jeremias; Zarogoulidis, Paul; Zarogoulidis, Konstantinos; Schmid, Kurt W

    2014-01-01

    Background and methods Isothermal multiple displacement amplification (IMDA) can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. Results A total of 250 ?g DNA (concentration 5 ?g/?L) was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. Conclusion We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA. PMID:25152625

  4. Detection of the food allergen celery via loop-mediated isothermal amplification technique.

    PubMed

    Zahradnik, Celine; Martzy, Roland; Mach, Robert L; Krska, Rudolf; Farnleitner, Andreas H; Brunner, Kurt

    2014-11-01

    Since 2005, celery and celery products have to be labeled according to Directive 2003/89/EC due to their allergenic potential. In order to provide a DNA-based, rapid and simple detection method suitable for high-throughput analysis, a loop-mediated isothermal amplification (LAMP) assay for the detection of celery (Apium graveolens) was developed. The assay was tested for specificity for celery since closely related species also hold food relevance. The limit of detection (LOD) for spiked food samples was found to be as low as 7.8 mg of dry celery powder per kilogram. An evaluation of different amplification and detection platforms was performed to show reliable detection independent from the instrument used for amplification (thermal cycler or heating block) and detection mechanisms (real-time fluorescence detection, agarose gel electrophoresis or nucleic acid staining). The analysis of 10 commercial food samples representing diverse and complex food matrices, and a false-negative rate of 0% for approximately 24 target copies or 0.08 ng celery DNA for three selected food matrices show that LAMP has the potential to be used as an alternative strategy for the detection of allergenic celery. The performance of the developed LAMP assay turned out to be equal or superior to the best available PCR assay for the detection of celery in food products. PMID:24880868

  5. Development of an in situ loop-mediated isothermal amplification technique for chromosomal localization of DNA sequences

    NASA Astrophysics Data System (ADS)

    Meng, Qinglei; Wang, Shi; Zhang, Lingling; Huang, Xiaoting; Bao, Zhenmin

    2013-01-01

    In situ loop-mediated isothermal amplification (in situ LAMP) combines in situ hybridization and loop-mediated isothermal amplification (LAMP) techniques for chromosomal localization of DNA sequences. In situ LAMP is a method that is generally more specific and sensitive than conventional techniques such as fluorescence in situ hybridization (FISH), primed in situ labeling (PRINS), and cycling primed in situ labeling (C-PRINS). Here, we describe the development and application of in situ LAMP to identify the chromosomal localization of DNA sequences. To benchmark this technique, we successfully applied this technique to localize the major ribosomal RNA gene on the chromosomes of the Zhikong scallop ( Chlamys farreri).

  6. Development of loop-mediated isothermal amplification (LAMP) assay for rapid diagnosis of ovine theileriosis in China

    Microsoft Academic Search

    Zhijie Liu; Junlin Hou; Mohammed A. Bakheit; Diaeldin A. Salih; Jianxun Luo; Hong Yin; Jabbar S. Ahmed; Ulrike Seitzer

    2008-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid detection method in which the target deoxyribonucleic\\u000a acid (DNA) can be efficiently amplified with high specificity and sensitivity under isothermal conditions using a set of either\\u000a four or six specific primers. In this study, we have identified a conserved sequence for Theileria luwenshuni (UTRlu8) and for T. uilenbergi (UTRu6) suitable for

  7. Development and comparison of a rapid isothermal nucleic acid amplification test for typing of herpes simplex virus types 1 and 2 on a portable fluorescence detector.

    PubMed

    Tong, Yanhong; McCarthy, Kaitlin; Kong, Huimin; Lemieux, Bertrand

    2012-11-01

    We have developed a rapid and simple molecular test, the IsoGlow HSV Typing assay, for the detection and typing of herpes simplex virus (type 1 and 2) from genital or oral lesions. Clinical samples suspended in viral transport mediums are simply diluted and then added to a helicase-dependent amplification master mix. The amplification and detection were performed on a portable fluorescence detector called the FireFly instrument. Detection of amplification products is based on end-point analysis using cycling probe technology. An internal control nucleic acid was included in the amplification master mix to monitor the presence of amplification inhibitors in the samples. Because the device has only two fluorescence detection channels, two strategies were developed and compared to detect the internal control template: internal control detected by melting curve analysis using a dual-labeled probe, versus internal control detection using end-point fluorescence release by a CPT probe at a lower temperature. Both have a total turnaround time of about 1 hour. Clinical performance relative to herpes viral culture was evaluated using 176 clinical specimens. Both formats of the IsoGlow HSV typing assay had sensitivities comparable to that of the Food and Drug Administration-cleared IsoAmp HSV (BioHelix Corp., Beverly MA) test and specificity for the two types of HSV comparable to that of ELVIS HSV (Diagnostic Hybrids, Athens, OH). PMID:22951487

  8. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification.

    PubMed

    Borysiak, Mark D; Kimura, Kevin W; Posner, Jonathan D

    2015-04-01

    Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications. PMID:25666345

  9. A simple colorimetric DNA detection by target-induced hybridization chain reaction for isothermal signal amplification.

    PubMed

    Ma, Cuiping; Wang, Wenshuo; Mulchandani, Ashok; Shi, Chao

    2014-07-15

    A novel DNA detection method is presented based on a gold nanoparticle (AuNP) colorimetric assay and hybridization chain reaction (HCR). In this method, target DNA hybridized with probe DNA modified on AuNP, and triggered HCR. The resulting HCR products with a large number of negative charges significantly enhanced the stability of AuNPs, inhibiting aggregation of AuNPs at an elevated salt concentration. The approach was highly sensitive and selective. Using this enzyme-free and isothermal signal amplification method, we were able to detect target DNA at concentrations as low as 0.5 nM with the naked eye. Our method also has great potential for detecting other analytes, such as metal ions, proteins, and small molecules, if the target analytes could make HCR products attach to AuNPs. PMID:24780220

  10. Protein detection through different platforms of immuno-loop-mediated isothermal amplification

    NASA Astrophysics Data System (ADS)

    Pourhassan-Moghaddam, Mohammad; Rahmati-Yamchi, Mohammad; Akbarzadeh, Abolfazl; Daraee, Hadis; Nejati-Koshki, Kazem; Hanifehpour, Younes; Joo, Sang Woo

    2013-11-01

    Different immunoassay-based methods have been devised to detect protein targets. These methods have some challenges that make them inefficient for assaying ultra-low-amounted proteins. ELISA, iPCR, iRCA, and iNASBA are the common immunoassay-based methods of protein detection, each of which has specific and common technical challenges making it necessary to introduce a novel method in order to avoid their problems for detection of target proteins. Here we propose a new method nominated as `immuno-loop-mediated isothermal amplification' or `iLAMP'. This new method is free from the problems of the previous methods and has significant advantages over them. In this paper we also offer various configurations in order to improve the applicability of this method in real-world sample analyses. Important potential applications of this method are stated as well.

  11. Direct detection of Theileria annulata in bovine blood samples using standard and isothermal DNA amplification approaches.

    PubMed

    Gomes, Jacinto; Inácio, João

    2015-01-01

    Tropical theileriosis is a tick-borne disease responsible for important health problems in cattle, caused by the hemoprotozoan Theileria annulata. Traditionally, detection of Theileria pathogens in infected animals requires the microscopic examination of stained-blood smears and serological methods. Molecular diagnostic assays have been developed for the detection of Theileria parasites, including PCR-based and reverse line blotting approaches, but these methods usually demand qualified personnel, complex instrumentation, and expensive materials. Loop-mediated isothermal amplification (LAMP) can facilitate the design of molecular assays independent of the use of sophisticated equipment. In this chapter we describe the application of two molecular assays for the direct detection of T. annulata in bovine blood samples, based in real-time PCR and LAMP, both targeting the Tams1-encoding gene of this parasite. PMID:25399096

  12. Loop-mediated isothermal amplification (LAMP)-based method for rapid mushroom species identification.

    PubMed

    Vaagt, Franziska; Haase, Ilka; Fischer, Markus

    2013-02-27

    Toxic mushroom species, such as the death cap ( Amanita phalloides ), are responsible for most mushroom poisonings. In the present work, novel loop-mediated isothermal amplification (LAMP) assays were used for the differentiation of even closely related edible and toxic mushroom species. The applicability of these methods was tested by cross-reaction studies and analysis of spiked mushroom samples (raw and fried material). Contaminations at the level of 2% (w/w) could be detected in different mushroom blends. Three detection methods were used: agarose gel analysis, fluorimetric real-time detection, and visual detection by lateral flow dipsticks (LFD). The LAMP assay combined with LFD detection allows the identification of A. phalloides in about 2 h (including DNA extraction) at a very low level of technical equipment (micropestle, water bath, and mobile centrifuge), which makes this technique perfectly suited for on-site applications. PMID:23350919

  13. Development of Loop-Mediated Isothermal Amplification for Detection of Leifsonia xyli subsp. xyli in Sugarcane

    PubMed Central

    Liu, Jing; Guo, Jinlong; Chen, Rukai; Grisham, Michael Paul

    2013-01-01

    Ratoon stunt, caused by the xylem-limited coryneform bacterium Leifsonia xyli subsp. xyli (Lxx), is a deep bacteriosis and prevalent in most of sugarcane-producing countries. Based on loop-mediated isothermal amplification (LAMP), we developed a method for detecting Lxx. The major advantages of the LAMP method are visual judgment by color and time saving with only 60?min for identification of Lxx and without the need for costly PCR apparatus and gel scanner. In the present study, positive and negative samples detected by the LAMP method were clearly distinguishable. When total DNA extracted from internode juice was used as the template, the sensitivity of LAMP was 10 times higher than that of the conventional PCR detection. The LAMP assay is a highly specific, rapid, and sensitive method for the diagnosis of ratoon stunt caused by Lxx in sugarcane. This is the first report of LAMP-based assay for the detection of Lxx in sugarcane. PMID:23710444

  14. Rapid detection of Salmonella Typhi by loop-mediated isothermal amplification (LAMP) method

    PubMed Central

    Abdullah, J.; Saffie, N.; Sjasri, F.A.R.; Husin, A.; Abdul-Rahman, Z.; Ismail, A.; Aziah, I.; Mohamed, M.

    2014-01-01

    An in-house loop-mediated isothermal amplification (LAMP) reaction was established and evaluated for sensitivity and specificity in detecting the presence of Salmonella Typhi (S. Typhi) isolates from Kelantan, Malaysia. Three sets of primers consisting of two outer and 4 inner were designed based on locus STBHUCCB_38510 of chaperone PapD of S. Typhi genes. The reaction was optimised using genomic DNA of S. Typhi ATCC7251 as the template. The products were visualised directly by colour changes of the reaction. Positive results were indicated by green fluorescence and negative by orange colour. The test was further evaluated for specificity, sensitivity and application on field samples. The results were compared with those obtained by gold standard culture method and Polymerase Chain Reaction (PCR). This method was highly specific and -10 times more sensitive in detecting S. Typhi compared to the optimised conventional polymerase chain reaction (PCR) method. PMID:25763045

  15. Development of a loop-mediated isothermal amplification assay for detection of Trichomonas vaginalis.

    PubMed

    Reyes, John Carlo B; Solon, Juan Antonio A; Rivera, Windell L

    2014-07-01

    A loop-mediated isothermal amplification (LAMP) assay targeting the 2-kbp repeated DNA species-specific sequence was developed for detection of Trichomonas vaginalis, the causative agent of trichomoniasis. The analytical sensitivity and specificity of the LAMP assay were evaluated using pooled genital swab and urine specimens, respectively, spiked with T. vaginalis trophozoites. Genital secretion and urine did not inhibit the detection of the parasite. The sensitivity of the LAMP was 10-1000 times higher than the PCR performed. The detection limit of LAMP was 1 trichomonad for both spiked genital swab and urine specimens. Also, LAMP did not exhibit cross-reactivity with closely-related trichomonads, Trichomonas tenax and Pentatrichomonas hominis, and other enteric and urogenital microorganisms, Entamoeba histolytica, Candida albicans, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. This is the first report of a LAMP assay for the detection of T. vaginalis and has prospective application for rapid diagnosis and control of trichomoniasis. PMID:24792836

  16. A New Loop-Mediated Isothermal Amplification Method for Rapid, Simple, and Sensitive Detection of Leptospira spp. in Urine

    PubMed Central

    Nakajima, Chie; Harunari, Tsunehito; Tanikawa, Tsutomu; Tokiwa, Toshihiro; Uchimura, Eriko; Furuya, Tokujiro; Mingala, Claro Niegos; Villanueva, Marvin Ardeza; Ohnishi, Makoto; Suzuki, Yasuhiko

    2012-01-01

    We developed a new loop-mediated isothermal amplification (LAMP) method to detect rrs, a 16S rRNA gene of pathogenic Leptospira spp. in urine. The method enables detection of two leptospiral cells per reaction mixture following boiling of urine specimens. The sensitivity of this method is higher than that of culture or of flaB nested PCR. PMID:22422858

  17. SENSITIVE AND RAPID DETECTION OF FLAVOBACTERIUM COLUMNARE IN CHANNEL CATFISH ICTALURUS PUNCTATUS BY A LOOP-MEDIATED ISOTHERMAL AMPLIFICATION METHOD

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: To evaluate the loop-mediated isothermal amplification method (LAMP) for rapid detection of Flavobacterium columnare and determine the suitability of LAMP for rapid diagnosis of columnaris infection in channel catfish, Ictalurus punctatus. Methods and Results: A set of four primers, two outer ...

  18. Operational Feasibility of Using Loop-Mediated Isothermal Amplification for Diagnosis of Pulmonary Tuberculosis in Microscopy Centers of Developing Countries

    Microsoft Academic Search

    Catharina C. Boehme; Pamela Nabeta; German Henostroza; Rubhana Raqib; Zeaur Rahim; Martina Gerhardt; Erica Sanga; Michael Hoelscher; Tsugunori Notomi; Tetsu Hase; Mark D. Perkins

    The characteristics of loop-mediated isothermal amplification (LAMP) make it a promising platform for the molecular detection of tuberculosis (TB) in developing countries. Here, we report on the first clinical evaluation of LAMP for the detection of pulmonary TB in microscopy centers in Peru, Bangladesh, and Tanzania to determine its operational applicability in such settings. A prototype LAMP assay with simplified

  19. Endpoint Visual Detection of Three Genetically Modified Rice Events by Loop-Mediated Isothermal Amplification

    PubMed Central

    Chen, Xiaoyun; Wang, Xiaofu; Jin, Nuo; Zhou, Yu; Huang, Sainan; Miao, Qingmei; Zhu, Qing; Xu, Junfeng

    2012-01-01

    Genetically modified (GM) rice KMD1, TT51-1, and KF6 are three of the most well known transgenic Bt rice lines in China. A rapid and sensitive molecular assay for risk assessment of GM rice is needed. Polymerase chain reaction (PCR), currently the most common method for detecting genetically modified organisms, requires temperature cycling and relatively complex procedures. Here we developed a visual and rapid loop-mediated isothermal amplification (LAMP) method to amplify three GM rice event-specific junction sequences. Target DNA was amplified and visualized by two indicators (SYBR green or hydroxy naphthol blue [HNB]) within 60 min at an isothermal temperature of 63 °C. Different kinds of plants were selected to ensure the specificity of detection and the results of the non-target samples were negative, indicating that the primer sets for the three GM rice varieties had good levels of specificity. The sensitivity of LAMP, with detection limits at low concentration levels (0.01%–0.005% GM), was 10- to 100-fold greater than that of conventional PCR. Additionally, the LAMP assay coupled with an indicator (SYBR green or HNB) facilitated analysis. These findings revealed that the rapid detection method was suitable as a simple field-based test to determine the status of GM crops. PMID:23203072

  20. Detection of pathogen-specific antibodies by loop-mediated isothermal amplification.

    PubMed

    Burbulis, Ian E; Yamaguchi, Kumiko; Nikolskaia, Olga V; Prigge, Sean T; Magez, Stefan; Bisser, Sylvie; Reller, Megan E; Grab, Dennis J

    2015-04-01

    Loop-mediated isothermal amplification (LAMP) is a method for enzymatically replicating DNA that has great utility for clinical diagnosis at the point of care (POC), given its high sensitivity, specificity, speed, and technical requirements (isothermal conditions). Here, we adapted LAMP for measuring protein analytes by creating a protein-DNA fusion (referred to here as a "LAMPole") that attaches oligonucleotides (LAMP templates) to IgG antibodies. This fusion consists of a DNA element covalently bonded to an IgG-binding polypeptide (protein L/G domain). In our platform, LAMP is expected to provide the most suitable means for amplifying LAMPoles for clinical diagnosis at the POC, while quantitative PCR is more suitable for laboratory-based quantification of antigen-specific IgG abundance. As proof of concept, we measured serological responses to a protozoan parasite by quantifying changes in solution turbidity in real time. We observed a >6-log fold difference in signal between sera from vaccinated versus control mice and in a clinical patient sample versus a control. We assert that LAMPoles will be useful for increasing the sensitivity of measuring proteins, whether it be in a clinical laboratory or in a field setting, thereby improving acute diagnosis of a variety of infections. PMID:25651920

  1. Development of loop-mediated isothermal amplification (LAMP) method for diagnosis of equine piroplasmosis.

    PubMed

    Alhassan, Andy; Thekisoe, Oriel M M; Yokoyama, Naoaki; Inoue, Noboru; Motloang, Makhosazana Y; Mbati, Peter A; Yin, Hong; Katayama, Yoshinari; Anzai, Toru; Sugimoto, Chihiro; Igarashi, Ikuo

    2007-01-31

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid method whereby DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. In this study, we used LAMP primer sets designed from EMA-1 and Bc 48 genes for detection of Theileria equi and Babesia caballi infections, respectively. These primer sets specifically amplified DNA of the respective parasites. Both primer sets amplified T. equi and B. caballi up to 10(-6) dilution of 10-fold serially diluted samples. Furthermore, DNA extracted from blood collected from a horse experimentally infected with T. equi was amplified by a T. equi LAMP primer set from days 2 to 35 post-infection, demonstrating the high sensitivity of these primers. Of 55 samples collected from China, 81.8% and 56.3% were positively detected by LAMP for T. equi and B. caballi infections, respectively. In contrast, 91.8% and 45.9% of the 37 samples collected from South Africa were LAMP positive for T. equi and B. caballi, respectively. These results suggest that LAMP could be a potential diagnostic tool for epidemiological studies of equine piroplasmosis. PMID:16973284

  2. New closed tube loop mediated isothermal amplification assay for prevention of product cross-contamination

    PubMed Central

    Karthik, K.; Rathore, Rajesh; Thomas, Prasad; Arun, T.R.; Viswas, K.N.; Dhama, Kuldeep; Agarwal, R.K.

    2014-01-01

    Loop mediated isothermal amplification (LAMP) assay, a promising diagnostic test, has been developed for detection of different pathogens of human as well as animals. Various positive points support its use as a field level test but the major problem is product cross contamination leading to false positive results. Different methods were adopted by various researchers to control this false positive amplification due to cross contamination but all have their own advantages and disadvantages. A new closed tube LAMP assay based on agar dye capsule was developed in the present study and this technique has some advantages over the other closed tube technique.•Agar at the concentration of 1.5% was used to sandwich SYBR green dye I with the aid of intradermal syringe. This agar dye capsule was placed over the LAMP reaction mixture before it was amplified.•To eliminate the hazardous nature of Ultra Violet (UV) light during result visualization of LAMP products, the present study demonstrates the use of Light Emitting Diode (LED) lights for result visualization.•LAMP was carried out for Brucella species detection using this modified techniques yielding good results without any cross contamination and LED showed similar fluorescence compared to UV.

  3. Rapid detection of Opisthorchis viverrini copro-DNA using loop-mediated isothermal amplification (LAMP)

    PubMed Central

    Arimatsu, Yuji; Kaewkes, Sasithorn; Laha, Thewarach; Hong, Sung-Jong; Sripa, Banchob

    2014-01-01

    Opisthorchis viverrini and other foodborne trematode infections are major health problem in Thailand, the Lao People’s Democratic Republic, Vietnam and Cambodia. Differential diagnosis of O. viverrini based on the microscopic observation of parasite eggs is difficult in areas where Clonorchis sinensis and minute intestinal flukes coexist. We therefore established a rapid, sensitive and specific method for detecting O. viverrini infection from the stool samples using the loop-mediated isothermal amplification (LAMP) method. A total of five primers from seven regions were designed to target the internal transcribed spacer 1 (ITS1) in ribosomal DNA for specific amplification. Hydroxy naphthol blue (HNB) was more effective to detect the LAMP product compared to the Real-time LAMP and turbidity assay for its simple and distinct detection. The LAMP assay specifically amplified O. viverrini ITS1 but not C. sinensis and minute intestinal flukes with the limit of detection around 10?3 ng DNA/?L. The sensitivity of the LAMP was 100% compare to egg positive samples. While all microscopically positive samples were positive by LAMP, additionally 5 of 13 (38.5%) microscopically negative samples were also LAMP positive. The technique has great potential for differential diagnosis in endemic areas with mixed O. viverrini and intestinal fluke infections. As is is an easy and simple method, the LAMP is potentially applicable for point-of-care diagnosis. PMID:21871581

  4. Specific diagnosis of Opisthorchis viverrini using loop-mediated isothermal amplification (LAMP) targeting parasite microsatellites.

    PubMed

    Arimatsu, Yuji; Kaewkes, Sasithorn; Laha, Thewarach; Sripa, Banchob

    2015-01-01

    Opisthorchis viverrini and other food-borne trematode infections are major health problems in Thailand, the Lao People's Democratic Republic, Vietnam and Cambodia. Differential diagnosis of O. viverrini based on the microscopic observation of parasite eggs is difficult in areas where Clonorchis sinensis and minute intestinal flukes coexist. Recently, loop-mediated isothermal amplification (LAMP) has been widely used for detection and identification of trematode for its simple method that is useful in low-resource or field settings. We have reported ITS1-LAMP assay to detect O. viverrini infection from human feces. The sensitivity and specificity of the test was 100% and 61.5%. The sensitivity of the test appeared to be higher than microscopic egg examination; however non-specific amplification from other parasites could not be ruled out. We therefore targeted microsatellites of O. viverrini that is a species specific sequence. By using hydroxyl naphthol blue (HNB)-LAMP, O. viverrini microsatellite 6 (OVMS6) could specifically amplify DNA from O. viverrini genome, but not other parasites such as C. sinensis, Opisthorchis felineus, Centrocestus caninus, Haplorchis taichui, Fasciola gigantica and Haplorchoodes sp. The detection limit of the test is 1 ng genomic DNA, which was 1000 times lower than the ITS1-LAMP, but targeting microstellites showed more specific detection of O. viverrini. In addition, the colorimetric LAMP assay was simple and effective; this makes it potentially applicable for point-of-care diagnosis. PMID:25268466

  5. Detection of fish pathogens by loop-mediated isothermal amplification (LAMP) technique.

    PubMed

    Soliman, Hatem; Saleh, Mona; El-Matbouli, Mansour

    2015-01-01

    Rapid detection of fish pathogens is mandatory for applying the crucial preventive and control measures to reduce fish losses and, consequently, minimize the economic impact of diseases on the fish farm owners. The currently used molecular diagnostic tools of fish infectious agents, such as PCR and RT-PCR, are sensitive and specific but still have some drawbacks. These tools are usually time consuming and laborious, need skilled persons, and require sophisticated devices to be performed. Therefore, next-generation tools for rapid diagnosis of fish infectious diseases were developed to conquer these shortages. One of these novel tools is the loop-mediated isothermal amplification (LAMP) technique. LAMP is considered a more advantageous tool than PCR because it needs only a heating block or a thermostatically controlled water bath as a source of constant temperature. It is considered to be more specific than the PCR assay as it uses 4-6 primers, which may diminish the occurrence of false-positive results. The time required for the amplification process by LAMP is ranging from 30 min to 1 h comparing to 3-5 h in the case of PCR. The visual detection methods coupled with the LAMP assay eliminates the post-run processing for detection of the amplification products. Its sensitivity is either comparable with the PCR or better than it. A variety of LAMP assays were developed for simple and rapid detection of a diversity of fish pathogens. Herein, we describe how to perform a LAMP assay and troubleshoot any potential problem arising during the process. PMID:25399095

  6. Integrated centrifugal reverse transcriptase loop-mediated isothermal amplification microdevice for influenza A virus detection.

    PubMed

    Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Choi, Goro; Seo, Tae Seok

    2015-06-15

    An integrated reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) microdevice which consists of microbead-assisted RNA purification and RT-LAMP with real-time monitoring by a miniaturized optical detector was demonstrated. The integrated RT-LAMP microdevice includes four reservoirs for a viral RNA sample (purified influenza A viral RNA or lysates), a washing solution (70% ethanol), an elution solution (RNase-free water), and an RT-LAMP cocktail, and two chambers (a waste chamber and an RT-LAMP reaction chamber). The separate reservoirs for a washing solution, an elution solution, and an RT-LAMP cocktail were designed with capillary valves for stable storage. Three influenza A virus strains (A/H1N1, A/H3N2, and A/H5N1) were used for RNA templates, and RT-LAMP primer sets were designed to detect hemagglutinin (HA) and conserved M gene. Sequential sample flow to the microbeads for RNA purification was achieved by centrifugal force with optimization of capillary valves and a siphon channel. Furthermore, the purified RNA solution was successfully isolated from the waste solution by changing the rotational direction, and combined with the RT-LAMP cocktail in the RT-LAMP reaction chamber for target gene amplification. Total process from the sample injection to the result was completed in 47 min. Influenza A H1N1 virus was confirmed on the integrated RT-LAMP microdevice even with 10 copies of viral RNAs, which revealed 10-fold higher sensitivity than that of a conventional RT-PCR. Subtyping and specificity test of influenza A H1N1 viral lysates were also performed and clinical samples were successfully genotyped to confirm influenza A virus on our proposed integrated microdevice. PMID:25569879

  7. Ultrasensitive electrochemiluminescent aptasensor for ochratoxin A detection with the loop-mediated isothermal amplification.

    PubMed

    Yuan, Yali; Wei, Shiqiang; Liu, Guangpeng; Xie, Shunbi; Chai, Yaqin; Yuan, Ruo

    2014-02-01

    In this study, we for the first time presented an efficient, accurate, rapid, simple and ultrasensitive detection system for small molecule ochratoxin A (OTA) by using the integration of loop-mediated isothermal amplification (LAMP) technique and subsequently direct readout of LAMP amplicons with a signal-on electrochemiluminescent (ECL) system. Firstly, the dsDNA composed by OTA aptamer and its capture DNA were immobilized on the electrode. After the target recognition, the OTA aptamer bond with target OTA and subsequently left off the electrode, which effectively decreased the immobilization amount of OTA aptamer on electrode. Then, the remaining OTA aptamers on the electrode served as inner primer to initiate the LAMP reaction. Interestingly, the LAMP amplification was detected by monitoring the intercalation of DNA-binding Ru(phen)3(2+) ECL indictors into newly formed amplicons with a set of integrated electrodes. The ECL indictor Ru(phen)3(2+) binding to amplicons caused the reduction of the ECL intensity due to the slow diffusion of Ru(phen)3(2+)-amplicons complex to the electrode surface. Therefore, the presence of more OTA was expected to lead to the release of more OTA aptamer, which meant less OTA aptamer remained on electrode for producing LAMP amplicons, resulting in less Ru(phen)3(2+) interlaced into the formed amplicons within a fixed Ru(phen)3(2+) amount with an obviously increased ECL signal input. As a result, a detection limit as low as 10 fM for OTA was achieved. The aptasensor also has good reproducibility and stability. PMID:24456596

  8. Sensitive and Rapid Detection of Giardia lamblia Infection in Pet Dogs using Loop-Mediated Isothermal Amplification

    PubMed Central

    Li, Jie; Wang, Peiyuan; Zhang, Aiguo; Zhang, Ping; Alsarakibi, Muhamd

    2013-01-01

    Giardia lamblia is recognized as one of the most prevalent parasites in dogs. The present study aimed to establish a loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of G. lamblia from dogs. The fecal samples were collected and prepared for microscopic analysis, and then the genomic DNA was extracted directly from purified cysts. The concentration of DNA samples of G. lamblia were diluted by 10-fold serially ranging from 10-1 to 10-5 ng/µl for LAMP and PCR assays. The LAMP assay allows the amplification to be finished within 60 min under isothermal conditions of 63? by employing 6 oligonucleotide primers designed based on G. lamblia elongation factor 1 alpha (EF1?) gene sequence. Our tests showed that the specific amplification products were obtained only with G. lamblia, while no amplification products were detected with DNA of other related protozoans. Sensitivity evaluation indicated that the LAMP assay was sensitive 10 times more than PCR. It is concluded that LAMP is a rapid, highly sensitive and specific DNA amplification technique for detection of G. lamblia, which has implications for effective control and prevention of giardiasis. PMID:23710094

  9. Detection of the Quarantine Species Thrips palmi by Loop-Mediated Isothermal Amplification

    PubMed Central

    Przybylska, Arnika; Fiedler, ?aneta; Kucharczyk, Halina; Obr?palska-St?plowska, Aleksandra

    2015-01-01

    Thrips palmi (from the order Thysanoptera) is a serious insect pest of various crops, including vegetables, fruits and ornamental plants, causing significant economic losses. Its presence constitutes a double threat; not only does T. palmi feed on the plants, it is also a vector for several plant viruses. T. palmi originated in Asia, but has spread to North and Central America, Africa, Oceania and the Caribbean in recent decades. This species has been sporadically noted in Europe and is under quarantine regulation in the European Union. For non-specialists its larval stages are indistinguishable morphologically from another widespread and serious insect pest Frankliniella occidentalis (a non-quarantine species in the European Union) as well as other frequently occurring thrips. In this study, we have developed a loop-mediated isothermal amplification protocol to amplify rDNA regions of T. palmi. The results were consistent whether isolated DNA or crushed insects were used as template, indicating that the DNA isolation step could be omitted. The described method is species-specific and sensitive and provides a rapid diagnostic tool to detect T. palmi in the field. PMID:25793743

  10. Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification.

    PubMed

    Kursa, Olimpia; Wo?niakowski, Grzegorz; Tomczyk, Grzegorz; Sawicka, Anna; Minta, Zenon

    2015-03-01

    Mycoplasma synoviae (MS) remains a serious concern in production of poultry and affects world production of chickens and turkeys. Loop-mediated isothermal amplification (LAMP) of DNA has been recently used for the identification of different economically important avian pathogens. The aim of this study was to develop LAMP for simple and inexpensive detection of MS strains in poultry using specifically designed primers targeting hemagglutin A (vlh) gene. The assay was conducted in a water bath for 1 h at 63 °C. The results were visualized after addition of SYBR Green(®) fluorescent dye. LAMP was specific exclusively for MS without cross-reactivity with other Mycoplasma species. The sensitivity of LAMP was determined as 10(-1) CFU/ml and was 1,000 times higher than MS-specific polymerase chain reaction. LAMP assay was conducted on 18 MS field strains to ensure its reliability and usefulness. This is the first report on LAMP development and application for the rapid detection of MS isolated from chickens. This simple method may be applied by diagnostic laboratories without access to expensive equipment. PMID:25413672

  11. Identification of pork in meat products using real-time loop-mediated isothermal amplification

    PubMed Central

    Yang, Lixia; Fu, Shujun; Peng, Xinkai; Li, Le; Song, Taoping; Li, Lin

    2014-01-01

    In this study, a one-step, real-time, loop-mediated isothermal amplification (RealAmp) assay was developed, for the highly specific detection of pork DNA. For the assay, the mtDNA of cytochrome b (cytb) gene was amplified at 63 °C using SYBR Green I for 45 min with a Real-Time Polymerase Chain Reaction (PCR) System that measured the fluorescent signal at one-minute intervals. As little as 1 pg of template DNA could be detected, without any cross-reactivity with non-target species. Meat mixtures, heat-treated at 100 °C for 15 min, prepared by mixing pork meat with beef at different ratios (0.01%–10%) were tested, and the RealAmp assays allowed the detection of as little as 0.01% pork in the meat mixtures. Thus, this work showed that RealAmp could be used for specific identification and sensitive quantification of meat species, even for heat-treated meat products. PMID:26019573

  12. Development of a loop-mediated isothermal amplification assay for the detection of porcine hokovirus.

    PubMed

    Li, Bin; Sun, Bing; Du, Lu-ping; Mao, Ai-hua; Wen, Li-bin; Ni, Yan-xiu; Zhang, Xue-han; He, Kong-wang

    2013-11-01

    Hokoviruses have recently been detected as pathogens belonging to the family Parvoviridae, which comprises porcine hokovirus (PHoV) and bovine hokovirus (BHoV). In this study, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid, specific and sensitive detection of PHoV. A set of four primers specific for six regions within the PHoV VP1/2 genes was designed using online software. The reaction temperature and time were optimized at 65°C and 60 min, respectively. LAMP products were detected by agarose gel electrophoresis or by visual inspection of a color change caused by a fluorescent dye. The method was highly specific for PHoV, and no cross-reaction was observed with porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), porcine bocavirus (PBoV), pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), classic swine fever virus (CSFV), or Japanese encephalitis virus (JEV). The detection limit was approximately 10 copies per reaction, which was 10 times more sensitive than conventional PCR. Furthermore, the efficiency of detection of PHoV in clinical samples was comparable to that of PCR and sequencing. These results show that the LAMP assay is a simple, rapid, sensitive and specific method for detecting PHoV. It does not require specialized equipment and can be used to detect PHoV both in the laboratory and in the field. PMID:23850717

  13. Rapid detection of the Klebsiella pneumoniae carbapenemase (KPC) gene by loop-mediated isothermal amplification (LAMP).

    PubMed

    Nakano, Ryuichi; Nakano, Akiyo; Ishii, Yoshikazu; Ubagai, Tsuneyuki; Kikuchi-Ueda, Takane; Kikuchi, Hirotoshi; Tansho-Nagakawa, Shigeru; Kamoshida, Go; Mu, Xiaoqin; Ono, Yasuo

    2015-03-01

    Klebsiella pneumoniae carbapenemases (KPC), which are associated with resistance to carbapenem, have recently spread worldwide and have become a global concern. It is necessary to detect KPC-producing organisms in clinical settings to be able to control the spread of this resistance. We have developed a loop-mediated isothermal amplification (LAMP) method for rapid detection of KPC producers. LAMP primer sets were designed to recognize the homologous regions of blaKPC-2 to blaKPC-17 and could amplify blaKPC rapidly. The specificity and sensitivity of the primers in the LAMP reactions for blaKPC detection were determined. This LAMP assay was able to specifically detect KPC producers at 68 °C, and no cross-reactivity was observed for other types of ?-lactamase (class A, B, C, or D) producers. The detection limit for this assay was found to be 10(0) CFU per tube, in 25 min, which was 10-fold more sensitive than a PCR assay for blaKPC detection. Then, the sensitivity of the LAMP reactions for blaKPC detection in human specimens (sputum samples, urine samples, fecal samples and blood samples) was analyzed; it was observed that the LAMP assay had almost the same sensitivity in these samples as when using purified DNA. The LAMP assay is easy to perform and rapid. It may therefore be routinely applied for detection of KPC producers in the clinical laboratory. PMID:25529001

  14. Elevated OPN, IP-10, and Neutrophilia in Loop-Mediated Isothermal Amplification Confirmed Tuberculosis Patients

    PubMed Central

    Leano, Susan; Nakajima, Chie; Niki, Toshiro; Ashino, Yugo; Suzuki, Yasuhiko; Telan, Elisabeth

    2014-01-01

    Tuberculosis (TB) is the second most common cause of death from infectious diseases and results in high socioeconomic losses to many countries. Proper diagnosis is the first step in TB eradication. To develop a rapid, simple, and accurate diagnostic TB test and to characterize the prevalence of Mycobacterium tuberculosis (MTB) genotypes and immune profiles of TB patients, a total of 37?TB patients and 30 healthy control (HC) from Metro Manila were enrolled. Loop-mediated isothermal amplification (LAMP) reliably detected MTB infection. Manila genotype was identified by spoligotyping method in all TB patients. Osteopontin (OPN), interferon-?-induced protein 10?kDa (IP-10), and neutrophil counts were found to reflect the acute stage of MTB infection. The sensitivity and specificity were 94.6% and 93.3%, respectively, for both OPN and IP-10, and they were 83.8% and 78.6%, respectively, for neutrophils. The combination of OPN, IP-10, neutrophil count, IL-6, IL-8, TNF-?, MCP-1, platelets, galectin-9, and leukocyte count correctly identifies all the HC and 96.3% of TB patients. LAMP method may serve as a rapid, supportive method in addition to time-consuming culture methods. OPN, IP-10, and neutrophil counts are useful in detecting MTB infection and may have utility in monitoring the course of the disease. PMID:25378811

  15. Development of a loop-mediated isothermal amplification method for rapid detection of pigeon circovirus.

    PubMed

    Tsai, Shinn Shyong; Chang, Yeng Ling; Huang, Yen Li; Liu, Hung Jen; Ke, Guan Ming; Chiou, Chwei Jang; Hsieh, Yao Ching; Chang, Tsung Chou; Cheng, Li Ting; Chuang, Kuo Pin

    2014-05-01

    There are no effective antiviral treatments for pigeon circovirus (PiCV); thus, rapid diagnosis is critical for effective control of the disease caused by this virus. The recent development of a novel LAMP technique that amplifies nucleic acids rapidly with high specificity and sensitivity under isothermal conditions has overcome some of the deficiencies of nucleic-acid-based diagnostic tests. We established a LAMP method for rapid detection of PiCV using two pairs of primers that were designed from PiCV and compared its sensitivity and specificity with that of PCR. Amplification by LAMP was optimal at 63 °C for 60 min. The detection limit was nearly 0.5 pg of PiCV DNA, making it ten times more sensitive than PCR. There was no cross-reaction with porcine circovirus type 2 (PCV2), pigeon Trichomonas gallinae, or pigeon herpesvirus (PHV) under the same conditions. The assay also successfully detected the pathogen DNA in the tissues of infected pigeons. This is the first report indicating that LAMP is a valuable, rapid method of detecting PiCV with high sensitivity and specificity. PMID:24193953

  16. Loop-mediated isothermal amplification: rapid detection of Angiostrongylus cantonensis infection in Pomacea canaliculata

    PubMed Central

    2011-01-01

    Background Angiostrongylus cantonensis is a zoonotic parasite that causes eosinophilic meningitis in humans. The most common source of infection with A. cantonensis is the consumption of raw or undercooked mollusks (e.g., snails and slugs) harbouring infectious third-stage larvae (L3). However, the parasite is difficult to identify in snails. The purpose of this study was to develop a quick, simple molecular method to survey for A. cantonensis in intermediate host snails. Findings We used a loop-mediated isothermal amplification (LAMP) assay, which was performed using Bst DNA polymerase. Reactions amplified the A. cantonensis 18S rRNA gene and demonstrated high sensitivity; as little as 1 fg of DNA was detected in the samples. Furthermore, no cross-reactivity was found with other parasites such as Toxoplasma gondii, Plasmodium falciparum, Schistosoma japonicum, Clonorchis sinensis, Paragonimus westermani and Anisakis. Pomacea canaliculata snails were exposed to A. cantonensis first-stage larvae (L1) in the laboratory, and L3 were observed in the snails thirty-five days after infection. All nine samples were positive as determined by the LAMP assay for A. cantonensis, which was identified as positive by using PCR and microscopy, this demonstrates that LAMP is sensitive and effective for diagnosis. Conclusions LAMP is an appropriate diagnostic method for the routine identification of A. cantonensis within its intermediate host snail P. canaliculata because of its simplicity, sensitivity, and specificity. It holds great promise as a useful monitoring tool for A. cantonensis in endemic regions. PMID:22023992

  17. Detection of canine parvovirus in fecal samples using loop-mediated isothermal amplification.

    PubMed

    Cho, Ho-Seong; Kang, Jong-Il; Park, Nam-Yong

    2006-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel, sensitive, and rapid technique for detection of genomic DNA. The end-product of the technique is a white precipitate of magnesium pyrophosphate that is visible without the use of gel electrophoresis. The LAMP method was applied to the detection of canine parvovirus (CPV) genomic DNA. A set of 4 primers, 2 outer and 2 inner, were designed from CPV genomic DNA targeting the VP2 gene. The optimal reaction time and temperature for LAMP were determined to be 60 minutes and 63 degrees C. On the basis of results for 50 canine fecal samples using polymerase chain reaction (PCR) analysis as the gold standard, the relative sensitivity of LAMP was 100% and the relative specificity was 76.9%. The detection limit of the LAMP method was 10(-1) median tissue culture infective doses (TCID50)/ml, compared with 10 TCID50/ml for PCR analysis. In addition to the advantage resulting from visual detection of the end product, the LAMP method is very rapid, requiring only 1 hour to complete. This assay would be a viable alterative to PCR analysis for diagnosis of CPV infection in dogs. The LAMP method holds promise for use as a diagnostic assay for CPV detection in a clinical setting. PMID:16566261

  18. A Reverse Transcription Loop-Mediated Isothermal Amplification Assay Optimized to Detect Multiple HIV Subtypes

    PubMed Central

    Ocwieja, Karen E.; Sherrill-Mix, Scott; Liu, Changchun; Song, Jinzhao; Bau, Haim; Bushman, Frederic D.

    2015-01-01

    Diagnostic methods for detecting and quantifying HIV RNA have been improving, but efficient methods for point-of-care analysis are still needed, particularly for applications in resource-limited settings. Detection based on reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is particularly useful for this, because when combined with fluorescence-based DNA detection, RT-LAMP can be implemented with minimal equipment and expense. Assays have been developed to detect HIV RNA with RT-LAMP, but existing methods detect only a limited subset of HIV subtypes. Here we report a bioinformatic study to develop optimized primers, followed by empirical testing of 44 new primer designs. One primer set (ACeIN-26), targeting the HIV integrase coding region, consistently detected subtypes A, B, C, D, and G. The assay was sensitive to at least 5000 copies per reaction for subtypes A, B, C, D, and G, with Z-factors of above 0.69 (detection of the minor subtype F was found to be unreliable). There are already rapid and efficient assays available for detecting HIV infection in a binary yes/no format, but the rapid RT-LAMP assay described here has additional uses, including 1) tracking response to medication by comparing longitudinal values for a subject, 2) detecting of infection in neonates unimpeded by the presence of maternal antibody, and 3) detecting infection prior to seroconversion. PMID:25675344

  19. Immunocapture and direct binding loop mediated isothermal amplification simplify molecular diagnosis of Cyprinid herpesvirus-3.

    PubMed

    Soliman, Hatem; El-Matbouli, Mansour

    2009-12-01

    Loop mediated isothermal amplification (LAMP) assay is used for rapid diagnosis of Cyprinid herpesvirus-3, formerly designated koi herpesvirus (KHV), with comparable sensitivity to PCR. To reduce the time required for the LAMP assay, an immunocapture (IC) and direct binding (DB) techniques were developed to exclude the DNA extraction step in molecular diagnostic procedures of the virus. Both techniques were evaluated by using PCR and CyHV-3-LAMP assays. The DB-LAMP/PCR assays were more sensitive (detecting 0.1 virus particles/ml) than the IC-LAMP/PCR assays (detecting 1 virus particle/ml). By using the SYBR Green I stain and the DB/LAMP assay the complete CyHV-3 diagnostic process can be achieved within 90 min compared to more than 5 h for the routine PCR assay. Both assays (IC/DB) could amplify successfully CyHV-3 from clinical samples which prove its application to diagnostic tests. The DB-LAMP assay is a simple, rapid, sensitive technique and applicable to the diagnosis of CyHV-3 in the field. PMID:19651160

  20. Direct detection of Marek's disease virus in poultry dust by loop-mediated isothermal amplification.

    PubMed

    Wo?niakowski, Grzegorz; Samorek-Salamonowicz, El?bieta

    2014-11-01

    Marek's disease virus (MDV) is a serious concern for poultry production and represents a unique herpesvirus model. MDV can be shed by doubly infected chickens despite vaccination. The fully infectious MDV particles are produced in the feather follicle epithelium (FFE), and MDV remains infectious for many months in fine skin particles and feather debris. Molecular biology methods including PCR and real-time PCR have been shown to be valuable for the detection of MDV DNA in farm dust. Recently, loop-mediated isothermal amplification (LAMP) was found to be useful in the detection of MDV in feathers and internal organs of infected chickens. LAMP is also less affected by the inhibitors present in DNA samples. Taking into account the advantages of LAMP, direct detection of MDV DNA in poultry dust has been conducted in this research. The detection of MDV DNA was possible in 11 out of the 12 examined dust samples without DNA extraction. The DNA was retrieved from dust samples by dilution and incubation at 95 °C for 5 min. The direct detection of MDV DNA in the dust was possible within 30 min using a water bath and UV light. The results were confirmed by electrophoresis and melting curve analysis of the LAMP products. Our results show that LAMP may be used to test for the presence of virulent MDV in poultry farm dust without DNA extraction. PMID:24986718

  1. Multicenter Clinical Evaluation of the Novel Alere i Strep A Isothermal Nucleic Acid Amplification Test.

    PubMed

    Cohen, Daniel M; Russo, Michael E; Jaggi, Preeti; Kline, Jennifer; Gluckman, William; Parekh, Amisha

    2015-07-01

    Rapid detection of group A beta-hemolytic streptococcus (GAS) is used routinely to help diagnose and treat pharyngitis. However, available rapid antigen detection tests for GAS have relatively low sensitivity, and backup testing is recommended in children. Newer assays are more sensitive yet require excessive time for practical point-of-care use as well as laboratory personnel. The Alere i strep A test is an isothermal nucleic acid amplification test designed to offer highly sensitive results at the point of care within 8 min when performed by nonlaboratory personnel. The performance of the Alere i strep A test was evaluated in a multicenter prospective trial in a Clinical Laboratory Improvement Amendments (CLIA)-waived setting in comparison to bacterial culture in 481 children and adults. Compared to culture, the Aleri i strep A test had 96.0% sensitivity and 94.6% specificity. Discrepant results were adjudicated by PCR and found the Alere i strep A test to have 98.7% sensitivity and 98.5% specificity. Overall, the Alere i strep A test could provide a one-step, rapid, point-of-care testing method for GAS pharyngitis and obviate backup testing on negative results. PMID:25972418

  2. Detection of foot-and-mouth disease virus rna by reverse transcription loop-mediated isothermal amplification

    PubMed Central

    2011-01-01

    A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for foot-and-mouth disease virus (FMDV) RNA. The amplification was able to finish in 45 min under isothermal condition at 64°C by employing a set of four primers targeting FMDV 2B. The assay showed higher sensitivity than RT-PCR. No cross reactivity was observed from other RNA viruses including classical swine fever virus, swine vesicular disease, porcine reproductive and respiratory syndrome virus, Japanese encephalitis virus. Furthermore, the assay correctly detected 84 FMDV positive samples but not 65 FMDV negative specimens. The result indicated the potential usefulness of the technique as a simple and rapid procedure for the detection of FMDV infection. PMID:22070774

  3. Rapid and Sensitive Detection of Mycobacterium ulcerans by Use of a Loop-Mediated Isothermal Amplification Test

    PubMed Central

    Yeboah-Manu, Dorothy; Stinear, Timothy P.; Fyfe, Janet A. M.

    2012-01-01

    This work reports the design and evaluation of a rapid loop-mediated isothermal amplification test for detecting Mycobacterium ulcerans DNA based on the multicopy insertion sequence IS2404. The test is robust and specific with a detection limit equivalent to 20 copies of the target sequence (0.01 to 0.1 genome). The test has potential for the diagnosis of Buruli ulcer under field conditions. PMID:22357495

  4. Rapid detection of peste des petits ruminants virus by a reverse transcription loop-mediated isothermal amplification assay

    Microsoft Academic Search

    Lin Li; Jingyue Bao; Xiaodong Wu; Zhiliang Wang; Junwei Wang; Mingxia Gong; Chunju Liu; Jinming Li

    2010-01-01

    Peste des petits ruminants virus (PPRV) is the causative agent of peste des petits ruminants (PPR), an economically important viral disease of small ruminants. In this report, a one-step, single-tube, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of PPRV. A set of six LAMP primers were designed based on the matrix gene sequence of PPRV

  5. Rapid detection of the most common high-risk human papillomaviruses by loop-mediated isothermal amplification

    Microsoft Academic Search

    Chitladda Saetiew; Temduang Limpaiboon; Patcharee Jearanaikoon; Sakda Daduang; Chamsai Pientong; Anusak Kerdsin; Jureerut Daduang

    2011-01-01

    Persistent infection with high-risk human papillomavirus (HPV) is a major risk factor for development of cervical cancer. At present, polymerase chain reaction (PCR)-based methods, the most widely molecular tools used for HPV detection, are time-consuming and require expensive instruments. In this study, loop-mediated isothermal amplification (LAMP) was established for detection of HPV types 16, 18, 45 and 58 which are

  6. Evaluation of a Loop-Mediated Isothermal Amplification Method Using Fecal Specimens for Differential Detection of Taenia Species from Humans? ‡

    PubMed Central

    Nkouawa, Agathe; Sako, Yasuhito; Li, Tiaoying; Chen, Xingwang; Wandra, Toni; Swastika, I. Kadek; Nakao, Minoru; Yanagida, Tetsuya; Nakaya, Kazuhiro; Qiu, Dongchuan; Ito, Akira

    2010-01-01

    We compared the performance of loop-mediated isothermal amplification (LAMP) with that of a multiplex PCR method for differential detection of human Taenia parasites in fecal specimens from taeniasis patients. The LAMP method, with no false positives, showed a higher sensitivity (88.4%) than the multiplex PCR (37.2%). Thus, it is expected that the LAMP method has a high value for molecular diagnosis of taeniasis. PMID:20631114

  7. Loop?mediated Isothermal Amplification assay (LAMP) based detection of Pasteurella multocida in cases of haemorrhagic septicaemia and fowl cholera.

    PubMed

    Bhimani, Mayurkumar; Bhanderi, Bharat; Roy, Ashish

    2015-06-30

    Twenty two isolates of Pasteurella multocida were obtained from different tissues of dead birds and animals (cattle, buffalo, sheep, and goat) suspected of fowl cholera and haemorrhagic septicaemia. The isolates were confirmed as P. multocida by various biochemical tests and PM PCR. An attempt was made to standardize Loop mediated isothermal amplification (LAMP) using newly designed primer sequences of KMT1 gene. Loop mediated isothermal amplification was conducted using 6 sets of primers at 65°C for 30 minutes and the result was confirmed by visual observation using SYBR green fluorescence dye as marker of positive reaction under UV transilluminator. On electrophoretic analysis of the products on 2% agarose gel, a ladder like pattern was observed, which suggested a positive amplification, whereas no amplification was observed in negative controls. Additionally, product of positive reaction yielded a green fluorescence following addition of SYBR green under UV transilluminator. It was observed that LAMP is a more sensitive test than polymerase chain reaction (PCR), as the former could detect DNA to lower limit of 22.8 pg/µl, while the latter could detect DNA to lower limit of 2.28 ng/ µl, thus LAMP could detect 100 times lesser concentration of DNA in comparison to PCR. Loop mediated isothermal amplification is a rather newer molecular technique, which can be used for rapid detection of infectious agent at field level and which does not require sophisticated instrument, i.e. thermal cycler. Furthermore, unlike the conventional PCR technique, LAMP requires lesser time to perform and result can be read visually. PMID:26129662

  8. Detection of phytoplasma by loop-mediated isothermal amplification of DNA (LAMP).

    PubMed

    Obura, E; Masiga, D; Wachira, F; Gurja, B; Khan, Z R

    2011-02-01

    Napier stunt phytoplasma (16SrXI and 16SrIII) in eastern Africa is a serious threat to the expansion of Napier grass (Pennisetum purpureum) farming in the region, where it is widely cultivated as fodder in zero grazing livestock systems. The grass has high potential for bio-fuel production, and has been adopted by farmers as a countermeasure to cereal stem borer Lepidoptera, since it attracts and traps the insect. Diagnosis of stunt phytoplasma have been largely by nested polymerase chain reaction (nPCR) targeting the 16S rRNA gene. However, the method is laborious, costly and technically demanding. This investigation has developed a simpler but effective phytoplasma diagnostic tool, called; loop-mediated isothermal amplification of DNA (LAMP). The assay was tested on 8 symptomatic and 8 asymptomatic plants, while its detection limit was compared to nested PCR using samples serially diluted from 3 ng/?l to 0.38 pg/?l. Molecular typing of LAMP products was determined by BsrI restriction digestion and Southern blot analysis. The assay sensitivity, positive and negative predictive values were estimated, while the specificity was tested on 11 phytoplasma groups. LAMP was specific to 5 phytoplasma groups: 16SrVI, X, XI and XVI. BsrI restriction digestion produced two predicted fragments, and there was specific binding of probe DNA to the LAMP amplicons in Southern blot analysis. The assay sensitivity was 100%, while the positive and negative predictive values were 63 and 100% respectively. LAMP was 20-fold more sensitive than nested PCR. This study validates LAMP for routine diagnosis of Napier stunt and other closely related phytoplasmas. PMID:21185882

  9. Rapid detection of active human cytomegalovirus infection in pregnancy using loop-mediated isothermal amplification.

    PubMed

    Wang, Xiaoli; Li, Xiaoyan; Hu, Shuhong; Qu, Hongmei; Zhang, Yinghong; Ni, Huijie; Wang, Xiaoliang

    2015-08-01

    Understanding the association between congenital human cytomegalovirus (HCMV) infection and active maternal HCMV infection during pregnancy is important for maternal and neonatal healthcare. In the present study, a loop?mediated isothermal amplification (LAMP) method was established for the detection of CMV DNA from whole blood or amniotic fluid samples, using reverse transcription?quantitative polymerase chain reaction. The results of the present study demonstrated that the CMV LAMP assay detection was specific for CMV DNA, whereas it did not detect viral DNA from herpes simplex type 1 (HSV?1), HSV?2, varicella zoster virus, HSV?6 or HSV?7. Sensitivity determination using serially?diluted CMV glycoprotein B?containing plasmids, demonstrated that >10 copies per tube were detectable using the CMV LAMP method. Furthermore, the detection results, using the LAMP method for 336 whole blood samples, demonstrated that at a threshold of 101?104 copies per tube, the sensitivity of this method was 86.96?100%, the specificity was 97.24?100%, the positive predictive value was 76.92?100% and the negative predictive value was 99.05?100%. The results for 11 amniotic fluid samples from pregnant women with whole blood CMV?positive and 15 control amniotic fluid samples, indicated that the CMV LAMP assay was sensitive and specific for CMV detection. In conclusion, in the present study, a CMV LAMP method was developed, which was shown to be sensitive, specific and efficient in the detection of HCMV infection. Furthermore, CMV LAMP is capable of detecting active CMV infection in pregnant women. Therefore, the current study provides novel insights into diagnostic approaches for active CMV infection in pregnant women. PMID:25847382

  10. Digital Isothermal Quantification of Nucleic Acids via Simultaneous Chemical Initiation of Recombinase Polymerase Amplification Reactions on SlipChip

    PubMed Central

    Shen, Feng; Davydova, Elena K.; Du, Wenbin; Kreutz, Jason E.; Piepenburg, Olaf; Ismagilov, Rustem F.

    2011-01-01

    In this paper, digital quantitative detection of nucleic acids was achieved at the single-molecule level by chemical initiation of over one thousand sequence-specific, nanoliter, isothermal amplification reactions in parallel. Digital polymerase chain reaction (digital PCR), a method used for quantification of nucleic acids, counts the presence or absence of amplification of individual molecules. However it still requires temperature cycling, which is undesirable under resource-limited conditions. This makes isothermal methods for nucleic acid amplification, such as recombinase polymerase amplification (RPA), more attractive. A microfluidic digital RPA SlipChip is described here for simultaneous initiation of over one thousand nL-scale RPA reactions by adding a chemical initiator to each reaction compartment with a simple slipping step after instrument-free pipette loading. Two designs of the SlipChip, two-step slipping and one-step slipping, were validated using digital RPA. By using the digital RPA SlipChip, false positive results from pre-initiation of the RPA amplification reaction before incubation were eliminated. End-point fluorescence readout was used for “yes or no” digital quantification. The performance of digital RPA in a SlipChip was validated by amplifying and counting single molecules of the target nucleic acid, Methicillin-resistant Staphylococcus aureus (MRSA) genomic DNA. The digital RPA on SlipChip was also tolerant to fluctuations of the incubation temperature (37–42 °C), and its performance was comparable to digital PCR on the same SlipChip design. The digital RPA SlipChip provides a simple method to quantify nucleic acids without requiring thermal cycling or kinetic measurements, with potential applications in diagnostics and environmental monitoring under resource-limited settings. The ability to initiate thousands of chemical reactions in parallel on the nanoliter scale using solvent-resistant glass devices is likely to be useful for a broader range of applications. PMID:21476587

  11. Detection of cucumber mosaic virus isolates from banana by one-step reverse transcription loop-mediated isothermal amplification.

    PubMed

    Peng, Jun; Shi, Minjing; Xia, Zihao; Huang, Junsheng; Fan, Zaifeng

    2012-11-01

    Cucumber mosaic virus (CMV) is one of the most devastating threats to the banana industry. A single-tube, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid detection of CMV-infected banana and plantain (Musa spp.). The reaction was performed in a single tube at 63 °C for 90 min using a real-time turbidimeter, with an improved closed-tube visual detection system in which fluorescent dye was added to the inside of the lid prior to amplification. This RT-LAMP assay is an alternative method for the rapid detection of CMV in banana plants and tissue culture materials. PMID:22782136

  12. A reverse transcription loop-mediated isothermal amplification assay to rapidly diagnose foot-and-mouth disease virus C

    PubMed Central

    Ding, Yao-zhong; Zhou, Jian-hua; Ma, Li-na; Qi, Yan-ni; Wei, Gang

    2014-01-01

    A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to rapidly detect foot-and-mouth disease virus serotype C (FMDV C). By testing 10-fold serial dilutions of FMDV C samples, sensitivity of the FMDV C RT-LAMP was found to be 10 times higher than that of conventional reverse transcription-PCR (RT-PCR). No cross-reactivity with A, Asia 1, or O FMDV or swine vesicular disease virus (SVDV) indicated that FMDV C RT-LAMP may be an exciting novel method for detecting FMDV C. PMID:24690607

  13. A reverse transcription loop-mediated isothermal amplification assay to rapidly diagnose foot-and-mouth disease virus C.

    PubMed

    Ding, Yao-Zhong; Zhou, Jian-Hua; Ma, Li-Na; Qi, Yan-Ni; Wei, Gang; Zhang, Jie; Zhang, Yong-Guang

    2014-01-01

    A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to rapidly detect foot-and-mouth disease virus serotype C (FMDV C). By testing 10-fold serial dilutions of FMDV C samples, sensitivity of the FMDV C RT-LAMP was found to be 10 times higher than that of conventional reverse transcription- PCR (RT-PCR). No cross-reactivity with A, Asia 1, or O FMDV or swine vesicular disease virus (SVDV) indicated that FMDV C RT-LAMP may be an exciting novel method for detecting FMDV C. PMID:24690607

  14. Evaluation of a Loop-Mediated Isothermal Amplification-Based Methodology To Detect Carbapenemase Carriage in Acinetobacter Clinical Isolates

    PubMed Central

    Vergara, Andrea; Zboromyrska, Yuliya; Mosqueda, Noraida; Morosini, María Isabel; García-Fernández, Sergio; Roca, Ignasi; Cantón, Rafael; Marco, Francesc

    2014-01-01

    Carbapenem-resistant Acinetobacter baumannii is a major source of nosocomial infections worldwide and is mainly associated with the acquisition of OXA-type carbapenemases and, to a lesser extent, metallo-?-lactamases (MBLs). In this study, 82 nonepidemiologically related Acinetobacter strains carrying different types of OXA or MBL enzymes were tested using the Eazyplex system, a loop-mediated isothermal amplification (LAMP)-based method to rapidly detect carbapenemase carriage. The presence/absence of carbapenem-hydrolyzing enzymes was correctly determined for all isolates in <30 min. PMID:25224010

  15. An integrated disposable device for DNA extraction and helicase dependent amplification

    E-print Network

    for world health applications, since the need for instrumentation to control flow rate and temperature. The possiblility of reducing or eliminating the requirement for accurate temperature control and cycling makes scheme with a pair of primers, reaction buffer, and enzyme mix similar to PCR. The reaction is unlike

  16. Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for Rapid Detection of Anaplasma ovis?

    PubMed Central

    Ma, Miling; Liu, Zhijie; Sun, Ming; Yang, Jifei; Guan, Guiquan; Li, Youquan; Luo, Jianxun; Yin, Hong

    2011-01-01

    Anaplasma ovis is an intraerythrocytic rickettsial pathogen of small ruminants. Loop-mediated isothermal amplification (LAMP) is a nucleic acid detection method in which the target DNA can be efficiently amplified with high specificity and sensitivity under isothermal conditions. In this study, a LAMP method was developed for the specific detection of A. ovis, using LAMP primers designed on the basis of the major surface protein 4 gene. LAMP was performed at 65°C for 30 min. Its specificity was confirmed by successful amplification of several A. ovis isolates and through EcoRI restriction analysis of LAMP products. No cross-reactivity with the A. marginale Lushi isolate, Mycoplasma mycoides subsp. capri, Chlamydophila psittaci, Theileria ovis, T. luwenshuni, T. uilenbergi, or the Babesia sp. Xinjiang isolate was observed. Detection using the LAMP method was compared with that using conventional PCR in 227 field samples; LAMP demonstrated a sensitivity of 95.45%. In summary, LAMP is a specific, sensitive, and rapid test for the diagnosis of A. ovis infection, with the potential to be standardized as a detection method for A. ovis in areas of endemicity. PMID:21471346

  17. Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification.

    PubMed

    Xie, Shunbi; Chai, Yaqin; Yuan, Yali; Bai, Lijuan; Yuan, Ruo

    2014-05-15

    Loop-mediated isothermal amplification (LAMP) is an outstanding DNA amplification procedure, in which the reaction can accumulate 10(9) copies from less than 10 copies of input template within an hour. While the amplification reaction is extremely powerful, the quantitative detection of LAMP products is still analytically difficult. Besides, the type of targets that LAMP can detect is also less, which to some extent limited the application of LAMP. In this study, we are reporting for the first time an efficient and accurate detection system which employs the integration of LAMP, aptamer and the electrochemical method for the sensitive detection of Ochratoxin A (OTA). Aptamers were designed as the forward outer primer to trigger the LAMP reaction, and then the LAMP amplification products were combined with a redox active molecule methylene blue (MB) and analyzed by an electrode using differential pulse voltammograms (DPV). As the reaction progresses, the MB intercalated into double-stranded regions of LAMP amplicons reduces the free MB concentration. Hence, the peak current of reaction mixture decreased with the amplification because of the slow diffusion of MB-amplified DNA complex to the electrode surface. The peak height of the current was related to the input amount of the aptamers, providing a ready means to detection the concentration of OTA. With such design, the proposed assay showed a good linear relationship within the range of 0.001-50 nM with a detection limit of 0.3 pM (defined as S/N = 3) for OTA. PMID:24412766

  18. A one-step reverse transcription loop-mediated isothermal amplification for detection and discrimination of infectious bursal disease virus

    PubMed Central

    2011-01-01

    Background Infectious bursal disease (IBD) is a highly contagious immunosuppressive disease in young chickens caused by infectious bursal disease virus (IBDV). It causes huge economic losses to the poultry industry. The objective of this study is to develop a loop-mediated isothermal amplification (LAMP) method for the detection and discrimination of IBDV. Results In this study, we applied reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect IBDV in one simple step and further identified the very virulent strain from non-vvIBDVs with a simply post-amplification restriction enzyme analysis. Based on sequence analysis, a set of two inner, two outer and two loop primers were designed to target the VP5 gene and they showed great specificity with no cross reaction to the other common avian pathogens. The detection limit determined by both color change inspection and agarose gel electrophoresis was 28 copies viral RNA, which was almost as sensitive as a real-time RT-PCR previous developed in our laboratory. We also identified a unique Tfi I restriction site located exclusively in non-vvIBDVs, so very virulent strain could be distinguished from current vaccine strains. By screening a panel of clinical specimens, results showed that this method is high feasible in clinical settings, and it obtained results 100% correlated with real-time RT-PCR. Conclusion RT-LAMP is a rapid, simple and sensitive assay. In combination with the Tfi I restriction analysis, this method holds great promises not only in laboratory detection and discrimination of IBDV but also in large scale field and clinical studies. PMID:21385415

  19. Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop loop-mediated isothermal...

  20. Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-

    E-print Network

    Cai, Long

    primer design. With these new tools, a high-precision and rapid DNA amplification technology becomes are causing a paradigm shift away from the standard protocol of medical care toward genotyped medicine. This new type of medicine is based on the accumulating knowledge of gene poly- morphisms (SNPs

  1. Evaluation of the rapid loop-mediated isothermal amplification assay Illumigene for diagnosis of Clostridium difficile in an outbreak situation.

    PubMed

    Norén, Torbjörn; Unemo, Magnus; Magnusson, Cecilia; Eiserman, Maud; Matussek, Andreas

    2014-02-01

    An outbreak of Clostridium difficile infection (CDI) at Höglandet Hospital Eksjö in southern Sweden in 2011 was mainly due to a multidrug-resistant PCR ribotype 046 (30% of all samples). Diagnostics used routinely was the Vidas CDAB assay, but to control the outbreak the rapid loop-mediated isothermal amplification (LAMP) assay Illumigene was introduced and both techniques were compared to Toxigenic culture (TC) prospectively. The LAMP assay had a superior sensitivity, that is, 98% compared to 79% for the Vidas CDAB assay. Most importantly, the mean turn-around-time from collecting sample to result was reduced from 59 h to 2 h enabling early isolation of patients and effective hygiene precautions. This may potentially decrease the morbidity and nosocomial transmissions of C. difficile. PMID:23758095

  2. Caprine arthritis encephalitis virus detection in blood by loop-mediated isothermal amplification (LAMP) assay targeting the proviral gag region.

    PubMed

    Balbin, Michelle M; Belotindos, Lawrence P; Abes, Nancy S; Mingala, Claro N

    2014-05-01

    Caprine arthritis encephalitis virus (CAEV), of the genus Lentivirus of the Retroviridae family, causes persistent disease, which is characterized by polyarthritis and mastitis in adult goats and progressive paresis (leukoencephalomyelitis) in kids. A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of CAEV in blood samples. Species-specific primers amplifying the gag gene region in the provirus were used for the detection of CAEV. The LAMP assay result was obtained 30 min after incubation on a constant temperature at 63 °C in a heat block. Resulting amplicons were visualized by addition of SYBR green dye after the reaction and checked by agarose gel electrophoresis. The sensitivity of LAMP assay was evaluated by comparing the result with the nested polymerase chain reaction. Based on the experiments, the result of the assay indicated a rapid and sensitive test for the detection of CAEV. PMID:24630755

  3. Rapid typing of foot-and-mouth disease serotype Asia 1 by reverse transcription loop-mediated isothermal amplification

    PubMed Central

    2011-01-01

    A reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay was rapidly used to detect serotype Asia 1 of foot-and-mouth disease virus (FMDV) within 45 min at 61°C. All FMDV serotype Asia 1 reference strains were positive by RT-LAMP, while other viruses such as FMDV serotypes O, C, A and classical swine fever virus, swine vesicular disease virus, porcine reproductive and respiratory syndrome virus and Japanese encephalitis virus remained negative. Furthermore, FMDV sreotype Asia 1 positive samples were able to detect by RT-LAMP assay. This RT-LAMP assay may be suitable particularly for diagnosis of FMDV serotype Asia 1 infection in field stations. PMID:22040459

  4. Comparison of Conventional PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Arcobacter Species

    PubMed Central

    Wang, Xiaoyu; Seo, Dong Joo; Lee, Min Hwa

    2014-01-01

    This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species. PMID:24478488

  5. Sensitive and Rapid Detection of the New Delhi Metallo-Beta-Lactamase Gene by Loop-Mediated Isothermal Amplification

    PubMed Central

    Liu, Wei; Zou, Dayang; Li, Yan; Wang, Xuesong; He, Xiang; Wei, Xiao; Shao, Changlin; Li, Xuelian; Shang, Wei; Yu, Kaitao; Liu, Dawei; Li, Yunmei; Guo, Jing; Yin, Zhitao

    2012-01-01

    New Delhi metallo-?-lactamase 1 (NDM-1), which is associated with resistance to carbapenem, was first reported in 2008. A sensitive and rapid molecular assay to detect the plasmid blaNDM-1 in clinical isolates is needed to control its spread. We describe a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of blaNDM-1 from pure culture and sputum, urine, and fecal samples. Eight sets of primers were designed to recognize six or eight distinct sequences on target blaNDM-1, and one set was selected as the most appropriate set of primers for its rapid detection. The specificity and sensitivity of the primers in the LAMP reactions for blaNDM-1 detection were determined. The sensitivity of the LAMP assay for blaNDM-1 detection in sputum, urine, and fecal samples was also tested. Two methods, namely, monitoring of turbidity and addition of calcein to the reaction tube, were used to determine negative and positive results. The results showed that target DNA was amplified and visualized by the two detection methods within 70 min at an isothermal temperature of 65°C. The sensitivity of LAMP, with a detection limit of 10.70 pg/?l DNA, was 100-fold greater than that of PCR. Thirteen infection bacterial strains without blaNDM-1 were selected for testing of specificity, and the results of the amplification were negative, which showed that the primers had good levels of specificity. The LAMP method reported here is demonstrated to be a potentially valuable means for the detection of blaNDM-1 and rapid clinical diagnosis, being fast, simple, and low in cost. PMID:22357496

  6. An Isothermal System that Couples Ligand-dependent Catalysis to Ligand-independent Exponential Amplification

    PubMed Central

    Lam, Bianca J.; Joyce, Gerald F.

    2011-01-01

    A system was devised that enables quantitative, ligand-dependent exponential amplification for various ligands that can be recognized by an RNA aptamer. The aptamer is linked to an RNA enzyme that catalyzes the joining of two oligonucleotide substrates. The product of this reaction is another RNA enzyme that undergoes self-sustained replication at constant temperature, increasing in copy number exponentially. The concentration of the ligand determines the amount of time required for the replication products to reach a threshold concentration. A standardized plot of time to threshold versus ligand concentration can be used to determine the concentration of ligand in an unknown sample. This system is analogous to quantitative PCR, linking rare recognition events to subsequent exponential amplification, but unlike PCR can be applied to the quantitative detection of non-nucleic-acid ligands. PMID:21322594

  7. An isothermal and sensitive nucleic acids assay by target sequence recycled rolling circle amplification.

    PubMed

    Long, Yi; Zhou, Xiaoming; Xing, Da

    2013-08-15

    Sequence-specific nucleic acid detection is playing a more and more important role in modern life sciences. Traditional rolling circle amplification (RCA) involves multiple distinct reaction steps and the experiment result is influenced by multiple factors. What's more, a main limitation of traditional RCA is that each target strand hybridizes with only one padlock probe, and this 1:1 hybridization ratio limits the sensitivity. Here we have proposed target sequence recycled rolling circle amplification (TR-RCA) to increase sensitivity by one step. We demonstrated that our method can not only make RCA occur, but also one target DNA can be reused and thus achieving self-recycle. In TR-RCA, the dumbbell probe recognizes the target DNA and hybridizes with it, and then the stem of the dumbbell probe is opened, after that the opened area anneals with the primer and triggers RCA. At the same time, after a target is displaced, it recognizes and hybridizes with another dumbbell probe, triggering the next cycle of RCA. This amplification method is achievable at a constant temperature simply by mixing dumbbell probes, target DNA, primers, and other chemical complexes together in one tube. Our method has significant advantages in ease of operation. And the results indicate that the target DNA can be detected at fM level with high specificity. PMID:23517825

  8. Development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of Sugarcane mosaic virus and Sorghum mosaic virus in sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in sugarcane. Six sets of four primers corresponding to the conserved coat protein gene were designed for each virus and their succ...

  9. A real-time reverse transcription loop-mediated isothermal amplification assay for the rapid detection of yellow fever virus.

    PubMed

    Kwallah, Allan ole; Inoue, Shingo; Muigai, Anne W T; Kubo, Toru; Sang, Rosemary; Morita, Kouichi; Mwau, Matilu

    2013-10-01

    Yellow fever, a mosquito-borne disease, is an important viral hemorrhagic fever in Africa and South America where it is endemic. Detection of yellow fever virus (YFV) in Africa remains a challenge due to a lack of highly specific tests. The aim of this study was to develop and optimize a rapid detection reverse transcription loop-mediated isothermal amplification (RT-LAMP) for YFV. The RT-LAMP was done isothermally at 62 °C using a real-time turbidimeter that allowed detection within 1h. Specificity of the RT-LAMP was determined using RNA from flaviviruses and other related viruses where only YFV RNA was detected: West Nile virus, dengue viruses, Japanese encephalitis virus, Rift Valley fever virus, and chikungunya virus. In addition, equal sensitivity was also observed when the RT-LAMP and the real-time RT-PCR were compared using YFV-spiked human serum samples with a detection limit of 0.29 PFU/ml. Two Kenyan YFV wild strains showed an equal detection limit as the vaccine strain 17D in this study. The RT-LAMP reduced the time of reaction from 3h to 1h and increased sensitivity tenfold compared to RT-PCR. Therefore, this test offers a simple, rapid and reliable diagnostic tool for yellow fever when there are outbreaks of acute hemorrhagic fever in Kenya and other African countries. PMID:23692685

  10. Development of reverse transcription loop-mediated isothermal amplification assays to detect Hantaan virus and Seoul virus.

    PubMed

    Hu, Dan; Hao, Lina; Zhang, Jinhai; Yao, Pingping; Zhang, Qi; Lv, Heng; Gong, Xiufang; Pan, Xiuzhen; Cao, Min; Zhu, Jin; Zhang, Yun; Feng, Youjun; Wang, Changjun

    2015-09-01

    We developed two assays based on one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) to identify Hantaan virus (HTNV) and Seoul virus (SEOV), members of the Hantavirus genus that cause hemorrhagic fever with renal syndrome (HFRS). Our results showed that these assays can be conducted within 30min under isothermal conditions. The detection limit for HTNV was around 10 copies per reaction, similar to detection levels for quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. The detection limit for SEOV was 100 copies per reaction, a sensitivity that was 10-fold lower than that for qRT-PCR assays but 10-fold higher than that for RT-PCR assays. The method we developed was specific for both HTNV and SEOV without any cross-reaction with other pathogens. We conclude that RT-LAMP assays could be useful for the rapid and direct detection of HTNV and SEOV clinically, and for the epidemiological investigation of HFRS. PMID:25920565

  11. Loop-Mediated Isothermal Amplification Procedure (LAMP) for Detection of the Potato Zebra Chip Pathogen "Candidatus Liberibacter solanacearum".

    PubMed

    Ravindran, Aravind; Lévy, Julien; Pierson, Elizabeth; Gross, Dennis C

    2015-01-01

    An efficient loop-mediated isothermal amplification procedure (LAMP) for the detection of "Candidatus Liberibacter solanacearum" (Lso), the bacterial causal agent of potato zebra chip (ZC) disease, is described in this chapter. Similar to the polymerase chain reaction (PCR), the LAMP employs a bacterial polymerase to amplify specific DNA sequences. However, the method differs from conventional PCR in that it uses six primers specific to the target region to generate a loop structure and autocycling strand displacement rather than thermocycling for sequence amplification. Moreover, unlike PCR that requires agarose gel electrophoresis for resolution, the positive LAMP results can be visualized directly as a precipitate within the reaction tubes. The 16S rDNA gene of "Ca. Liberibacter solanacearum" was used as the target for the design of the six LAMP primers. The LAMP technique is a reliable, rapid, and cost-effective method of detecting the "Ca. Liberibacter solanacearum" pathogen in the potato/tomato psyllid, Bactericera cockerelli, and in field-grown potato plants and tubers. PMID:25981248

  12. Development and evaluation of a novel and rapid detection assay for Botrytis cinerea based on loop-mediated isothermal amplification.

    PubMed

    Duan, Ya-Bing; Ge, Chang-Yan; Zhang, Xiao-Ke; Wang, Jian-Xin; Zhou, Ming-Guo

    2014-01-01

    Botrytis cinerea is a devastating plant pathogen that causes grey mould disease. In this study, we developed a visual detection method of B. cinerea based on the Bcos5 sequence using loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB). The LAMP reaction was optimal at 63 °C for 45 min. When HNB was added prior to amplification, samples with B. cinerea DNA developed a characteristic sky blue color after the reaction but those without DNA or with DNA of other plant pathogenic fungi did not. Results of HNB staining method were reconfirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for B. cinerea was 10(-3) ng µL(-1) of genomic DNA per reaction, which was 10-fold more sensitive than conventional PCR (10(-2) ng µL(-1)). Detection of the LAMP assay for inoculum of B. cinerea was possible in the inoculated tomato and strawberry petals. In the 191 diseased samples, 180 (94.2%) were confirmed as positive by LAMP, 172 (90.1%) positive by the tissue separation, while 147 (77.0%) positive by PCR. Because the LAMP assay performed well in aspects of sensitivity, specificity, repeatability, reliability, and visibility, it is suitable for rapid detection of B. cinerea in infected plant materials prior to storage and during transportation, such as cut flowers, fruits and vegetables. PMID:25329402

  13. Development and Evaluation of a Novel and Rapid Detection Assay for Botrytis cinerea Based on Loop-Mediated Isothermal Amplification

    PubMed Central

    Duan, Ya-Bing; Ge, Chang-Yan; Zhang, Xiao-Ke; Wang, Jian-Xin; Zhou, Ming-Guo

    2014-01-01

    Botrytis cinerea is a devastating plant pathogen that causes grey mould disease. In this study, we developed a visual detection method of B. cinerea based on the Bcos5 sequence using loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB). The LAMP reaction was optimal at 63°C for 45 min. When HNB was added prior to amplification, samples with B. cinerea DNA developed a characteristic sky blue color after the reaction but those without DNA or with DNA of other plant pathogenic fungi did not. Results of HNB staining method were reconfirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for B. cinerea was 10?3 ng µL?1 of genomic DNA per reaction, which was 10-fold more sensitive than conventional PCR (10?2 ng µL?1). Detection of the LAMP assay for inoculum of B. cinerea was possible in the inoculated tomato and strawberry petals. In the 191 diseased samples, 180 (94.2%) were confirmed as positive by LAMP, 172 (90.1%) positive by the tissue separation, while 147 (77.0%) positive by PCR. Because the LAMP assay performed well in aspects of sensitivity, specificity, repeatability, reliability, and visibility, it is suitable for rapid detection of B. cinerea in infected plant materials prior to storage and during transportation, such as cut flowers, fruits and vegetables. PMID:25329402

  14. Rapid and Sensitive Detection of Listeria ivanovii by Loop-Mediated Isothermal Amplification of the smcL Gene

    PubMed Central

    Wang, Yi; Wang, Yan; Xu, Huaqing; Dai, Hang; Meng, Shuang; Ye, Changyun

    2014-01-01

    A loop-mediated isothermal amplification (LAMP) assay for rapid and sensitive detection of the L. ivanovii strains had been developed and evaluated in this study. Oligonucleotide primers specific for L. ivanovii species were designed corresponding to smcL gene sequences. The primers set comprise six primers targeting eight regions on the species-specific gene smcL. The LAMP assay could be completed within 1 h at 64°C in a water bath. Amplification products were directly observed by the Loopamp Fluorescent Detection Reagent (FD) or detected by agarose gel electrophoresis. Moreover, the LAMP reactions were also detected by real-time measurement of turbidity. The exclusivity of 77 non-L. ivanovii and the inclusivity of 17 L. ivanovii were both 100% in the assay. Sensitivity of the LAMP assay was 250 fg DNA and 16 CFU per reaction for detection of L. ivanovii in pure cultures and simulated human stool. The LAMP assay was 10 and 100-fold more sensitive than quantitative PCR (qPCR) and conventional PCR assays,respectively. When applied to human stool samples spiked with low level (8 CFU/0.5 g) of L. ivanovii strains, the new LAMP assay described here achieved positive detection after 6 hours enrichment. In conclusion, the new LAMP assay in this study can be used as a valuable, rapid and sensitive detection tool for the detection of L. ivanovii in field, medical and veterinary laboratories. PMID:25549337

  15. Successful diagnosis of tuberculous lymphadenitis by loop-mediated isothermal amplification of cutaneous samples from an ulcerated surface lesion: a case report

    PubMed Central

    2014-01-01

    Introduction Tuberculous lymphadenitis is the most frequent form of extrapulmonary tuberculous. Although nucleic acid amplification assays such as polymerase chain reaction have recently become mainstream techniques for diagnosing tuberculous lymphadenitis, they are still not routinely performed in developing countries because of their high costs and complicated procedures. Case presentation We describe a case of tuberculous lymphadenitis in a 79-year-old Japanese man who had been on continuous hemodialysis for end-stage renal disease. We employed loop-mediated isothermal amplification and the procedure for ultrarapid extraction to develop a fast and easy-to-perform procedure for diagnosing tuberculous lymphadenitis. Conclusions The commercially available loop-mediated isothermal amplification assay kit and a rapid purification procedure enabled us to identify and amplify a Mycobacterium tuberculosis–specific gene within just 1.5 hours. PMID:25030753

  16. Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

    NASA Astrophysics Data System (ADS)

    Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

    2015-02-01

    A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/?l templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

  17. Development of mitochondrial loop-mediated isothermal amplification for detection of the small liver fluke Opisthorchis viverrini (Opisthorchiidae; Trematoda; Platyhelminthes).

    PubMed

    Le, Thanh Hoa; Nguyen, Nga Thi Bich; Truong, Nam Hai; De, Nguyen Van

    2012-04-01

    Mitochondrial DNA sequences offer major advantages over the more usual nuclear targets for loop-mediated isothermal amplification approaches (mito-LAMP) because multiple copies occur in every cell. Four LAMP primers [F3, FIP(F1c+F2), BIP(B1c+B2), and B3] were designed based on the mitochondrial nad1 sequence of Opisthorchis viverrini and used for a highly specific assay (mito-OvLAMP) to distinguish DNA of O. viverrini from that of another opisthorchiid (Clonorchis sinensis) and other trematodes (Haplorchis pumilio, Haplorchis taichui, Fasciola hepatica, and Fasciola gigantica). Conventional PCR was applied using F3/B3 primer pairs to verify the specificity of the primers for O. viverrini DNA templates. All LAMP-positive samples could be detected with the naked eye in sunlight, by gel electrophoresis (stained with ethidium bromide), and by addition of SYBR green I to the product in sunlight or under UV light. Only DNA from O. viverrini yielded amplification products by LAMP (and by PCR verification), and the LAMP limit of detection was as little as 100 fg (10(-4) ng DNA), indicating that this assay is 10 to 100 times more sensitive than PCR. Field testing was done using representative egg and metacercarial samples collected from localities where the fluke is endemic. With the advantages of simplicity, rapidity, sensitivity, and cost effectiveness, mito-OvLAMP is a good tool for molecular detection and epidemiology studies in regions or countries where O. viverrini is endemic, which can lead to more effective control of opisthorchiasis and trematodiasis. PMID:22322346

  18. Rapid detection of Vibrio parahaemolyticus in raw oysters using immunomagnetic separation combined with loop-mediated isothermal amplification.

    PubMed

    Zeng, Jing; Wei, Haiyan; Zhang, Lei; Liu, Xuefeng; Zhang, Haiyu; Cheng, Jinxia; Ma, Dan; Zhang, Ximeng; Fu, Pubo; Liu, Li

    2014-03-17

    The objective of this study was to develop a method that combined nanoparticle-based immunomagnetic separation (IMS) with real-time loop-mediated isothermal amplification (LAMP) for the rapid detection of Vibrio parahaemolyticus. Magnetic nanoparticles were functionalized with monoclonal antibodies that were produced against flagella from V. parahaemolyticus to capture and separate the target cells from raw oysters. After optimization, the immunomagnetic nanoparticles (IMNPs) presented a capture efficiency of 87.3% for 10(5) colony-forming unit (CFU)/mL of V. parahaemolyticus using 2.5?g of IMNPs within 30min. Although a very low level of non-specific binding was seen among 8 non-V. parahaemolyticus Vibrio spp. and 5 non-Vibrio strains, the IMS-LAMP method identified 133 V. parahaemolyticus strains correctly without the amplification from 54 other strains. The detection limit was about 1.4×10(2)CFU/mL in pure culture and was unaffected by the presence of 10(8)CFU/mL of competing microflora. When applied in spiked oysters, the sensitivity was found to be 1.9×10(3)CFU/g without enrichment. After enrichment for 6-8h, the limit of detectability could be improved to 1.9 to 0.19CFU/g. Hence, the IMS-LAMP assay provided a rapid, simple, and cost-effective method for total V. parahaemolyticus detection. This method will have important implications in the rapid detection of contaminated food in the early stage before distribution. PMID:24480190

  19. Rapid and sensitive detection of Candidatus Liberibacter asiaticus by loop mediated isothermal amplification combined with a lateral flow dipstick

    PubMed Central

    2014-01-01

    Background Citrus Huanglongbing (HLB) is the most devastating bacterial citrus disease worldwide. Three Candidatus Liberibacter species are associated with different forms of the disease: Candidatus Liberibacter asiaticus, Candidatus Liberibacter americanus and Candidatus Liberibacter africanus. Amongst them, Candidatus Liberibacter asiaticus is the most widespread and economically important. These Gram-negative bacterial plant pathogens are phloem-limited and vectored by citrus psyllids. The current management strategy of HLB is based on early and accurate detection of Candidatus Liberibacter asiaticus in both citrus plants and vector insects. Nowadays, real time PCR is the method of choice for this task, mainly because of its sensitivity and reliability. However, this methodology has several drawbacks, namely high equipment costs, the need for highly trained personnel, the time required to conduct the whole process, and the difficulty in carrying out the detection reactions in field conditions. Results A recent DNA amplification technique known as Loop Mediated Isothermal Amplification (LAMP) was adapted for the detection of Candidatus Liberibacter asiaticus. This methodology was combined with a Lateral Flow Dipstick (LFD) device for visual detection of the resulting amplicons, eliminating the need for gel electrophoresis. The assay was highly specific for the targeted bacterium. No cross-reaction was observed with DNA from any of the other phytopathogenic bacteria or fungi assayed. By serially diluting purified DNA from an infected plant, the sensitivity of the assay was found to be 10 picograms. This sensitivity level was proven to be similar to the values obtained running a real time PCR in parallel. This methodology was able to detect Candidatus Liberibacter asiaticus from different kinds of samples including infected citrus plants and psyllids. Conclusions Our results indicate that the methodology here reported constitutes a step forward in the development of new tools for the management, control and eradication of this destructive citrus disease. This system constitutes a potentially field-capable approach for the detection of the most relevant HLB-associated bacteria in plant material and psyllid vectors. PMID:24708539

  20. Rapid and simple detection of methicillin-resistance staphylococcus aureus by orfX loop-mediated isothermal amplification assay

    PubMed Central

    2014-01-01

    Background Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most prevalent pathogens responsible for nosocomial infections throughout the world. As clinical MRSA diagnosis is concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for MRSA detection. This study aimed at developing a simple loop-mediated isothermal amplification (LAMP) assay targeting on orfX for the rapid detection of methicillin-resistance Staphylococcus aureus (MRSA). Results The protocol was designed by targeting orfX, a highly conserved open reading frame in S. aureus. One hundred and sixteen reference strains, including 52 Gram-positive and 64 Gram-negative isolates, were included for evaluation and optimization of the orfX-LAMP assay. This assay had been further performed on 667 Staphylococcus (566 MRSA, 25 MSSA, 53 MRCNS and 23 MSCNS) strains and were comparatively validated by PCR assay using primers F3 and B3, with rapid template DNA processing, simple equipments (water bath) and direct result determination (both naked eye and under UV light) applied. The indispensability of each primer had been confirmed, and the optimal amplification was obtained under 65°C for 45 min. The 25 ?l reactant was found to be the most cost-efficient volume, and the detection limit was determined to be 10 DNA copies and 10 CFU/reaction. High specificity was observed when orfX-LAMP assay was subjected to 116 reference strains. For application, 557 (98.4%, 557/566) and 519 (91.7%, 519/566) tested strains had been detected positive by LAMP and PCR assays. The detection rate, positive predictive value (PPV) and negative predictive value (NPV) of orfX-LAMP were 98.4%, 100% and 92.7% respectively. Conclusions The established orfX-LAMP assay had been demonstrated to be a valid and rapid detection method on MRSA. PMID:24456841

  1. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants.

    PubMed

    Niessen, Ludwig; Luo, Jie; Denschlag, Carla; Vogel, Rudi F

    2013-12-01

    Bacterial pathogens and toxicants, parasites as well as mycotoxin producing fungi are the major biotic factors influencing the safety of food. Moreover, viral infections and prions may be present as quasi biotic challenging factors. A vast array of culture dependent analytical methods and protocols for food safety testing has been developed during the past decades. Presently, protocols involving molecular biological techniques such as PCR-based nucleic acid amplification and hybridization have become available for many of the known pathogens with their major advantages being rapidness, high sensitivity and specificity. However, this type of assays is still quite labor- and cost intensive and mostly cannot be operated directly in the field. Recently, loop-mediated isothermal amplification (LAMP) of DNA has emerged as an alternative to the use of PCR-based methods not only in food safety testing but also in a wide array of application. Its advantages over PCR-based techniques are even shorter reaction time, no need for specific equipment, high sensitivity and specificity as well as comparably low susceptibility to inhibitors present in sample materials which enables detection of the pathogens in sample materials even without time consuming sample preparation. The present article presents a critical review of the application of LAMP-based methods and their usefulness in detecting and identifying food borne bacterial pathogens and toxicants as well as mycotoxin producing food borne fungi as compared to other methods. Moreover does it elaborate on new developments in the design and automation of LAMP-based assays and their implications for the future developments of food testing. PMID:24010598

  2. Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    PubMed Central

    Fernández-Soto, Pedro; Mvoulouga, Prosper Obolo; Akue, Jean Paul; Abán, Julio López; Santiago, Belén Vicente; Sánchez, Miguel Cordero; Muro, Antonio

    2014-01-01

    The filarial parasite Loa loa, the causative agent of loiasis, is endemic in Central and Western Africa infecting 3–13 million people. L. loa has been associated with fatal encephalopathic reactions in high Loa-infected individuals receiving ivermectin during mass drug administration programs for the control of onchocerciasis and lymphatic filariasis. In endemic areas, the only diagnostic method routinely used is the microscopic examination of mid-day blood samples by thick blood film. Improved methods for detection of L. loa are needed in endemic regions with limited resources, where delayed diagnosis results in high mortality. We have investigated the use of a loop-mediated isothermal amplification (LAMP) assay to facilitate rapid, inexpensive, molecular diagnosis of loiasis. Primers for LAMP were designed from a species-specific repetitive DNA sequence from L. loa retrieved from GenBank. Genomic DNA of a L. loa adult worm was used to optimize the LAMP conditions using a thermocycler or a conventional heating block. Amplification of DNA in the LAMP mixture was visually inspected for turbidity as well as addition of fluorescent dye. LAMP specificity was evaluated using DNA from other parasites; sensitivity was evaluated using DNA from L. loa 10-fold serially diluted. Simulated human blood samples spiked with DNA from L. loa were also tested for sensitivity. Upon addition of fluorescent dye, all positive reactions turned green while the negative controls remained orange under ambient light. After electrophoresis on agarose gels, a ladder of multiple bands of different sizes could be observed in positive samples. The detection limit of the assay was found to be as little as 0.5 ag of L. loa genomic DNA when using a heating block. We have designed, for the first time, a highly sensitive LAMP assay for the detection of L. loa which is potentially adaptable for field diagnosis and disease surveillance in loiasis-endemic areas. PMID:24722638

  3. Detection of specific UL49 sequences of Marek's disease virus CVI988/Rispens strain using loop-mediated isothermal amplification.

    PubMed

    Wo?niakowski, Grzegorz; Niczyporuk, Jowita Samanta

    2015-09-01

    Marek's disease (MD) is a tumoral disease of chickens that can be controlled by vaccines based on non-pathogenic strains of turkey herpesvirus (HVT), SB-1 strain belonging to serotype 2, or the attenuated CVI988/Rispens strain belonging to serotype 1 of Marek's disease virus (MDV). Currently, the 'gold standard' in MD prophylaxis is the Rispens strain-based vaccine which protects against very virulent MDV and disease onset. Previous studies have shown that loop-mediated isothermal amplification (LAMP) is a rapid alternative to polymerase chain reaction (PCR) for detection and differentiation of HVT, SB-1 and virulent MDV strains. The aim of this study was to develop and evaluate a novel LAMP assay for the detection of the UL49 Rispens-specific region. This assay was validated using material from infected chicken embryo fibroblasts (CEFs) and tissue samples from vaccinated chickens. The analytical sensitivity of the assay was 10-times higher than PCR and reliably amplified 0.1 log10 TCID50/ml. The MDV Rispens was also detected at 18h after infection of CEFs. The results showed LAMP to be selective and a sensitive method to detect Rispens as early as 3 d.p.v. in all internal organs of chickens. Furthermore, the method was also capable to detect Rispens in 5 out of 26 chickens originating from different flocks. A mismatch amplification mutation assay (MAMA-PCR) confirmed the presence of Rispens strain in all LAMP-positive chickens. This is the first report of the specific visual detection of Rispens in vitro and in vivo using LAMP. The method may be useful for monitoring of successful chicken vaccination as well as in vitro studies in infected cell cultures. PMID:25920566

  4. A Portable Automatic Endpoint Detection System for Amplicons of Loop Mediated Isothermal Amplification on Microfluidic Compact Disk Platform

    PubMed Central

    Uddin, Shah Mukim; Ibrahim, Fatimah; Sayad, Abkar Ahmed; Thiha, Aung; Pei, Koh Xiu; Mohktar, Mas S.; Hashim, Uda; Cho, Jongman; Thong, Kwai Lin

    2015-01-01

    In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10?3 ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment. PMID:25751077

  5. Comparison of a loop-mediated isothermal amplification for orf virus with quantitative real-time PCR

    PubMed Central

    2013-01-01

    Background Orf virus (ORFV) causes orf (also known as contagious ecthyma or contagious papular dermatitis), a severe infectious skin disease in goats, sheep and other ruminants. Therefore, a rapid, highly specific and accurate method for the diagnosis of ORFV infections is essential to ensure that the appropriate treatments are administered and to reduce economic losses. Methods A loop-mediated isothermal amplification (LAMP) assay based on the identification of the F1L gene was developed for the specific detection of ORFV infections. The sensitivity and specificity of the LAMP assay were evaluated, and the effectiveness of this method was compared with that of real-time PCR. Results The sensitivity of this assay was determined to be 10 copies of a standard plasmid. Furthermore, no cross-reactivity was found with either capripox virus or FMDV. The LAMP and real-time PCR assays were both able to detect intracutaneous- and cohabitation-infection samples, with a concordance of 97.83%. LAMP demonstrated a sensitivity of 89.13%. Conclusion The LAMP assay is a highly efficient and practical method for detecting ORFV infection. This LAMP method shows great potential for monitoring the prevalence of orf, and it could prove to be a powerful supplemental tool for current diagnostic methods. PMID:23634981

  6. Loop-Mediated Isothermal Amplification of Specific Endoglucanase Gene Sequence for Detection of the Bacterial Wilt Pathogen Ralstonia solanacearum

    PubMed Central

    Pirc, Manca; Llop, Pablo; Ravnikar, Maja; Dreo, Tanja

    2014-01-01

    The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes. PMID:24763488

  7. Rapid and Sensitive Detection of Plesiomonas shigelloides by Loop-Mediated Isothermal Amplification of the hugA Gene

    PubMed Central

    Meng, Shuang; Xu, Jianguo; Xiong, Yanwen; Ye, Changyun

    2012-01-01

    Plesiomonas shigelloides is one of the causative agents of human gastroenteritis, with increasing number of reports describing such infections in recent years. In this study, the hugA gene was chosen as the target to design loop-mediated isothermal amplification (LAMP) assays for the rapid, specific, and sensitive detection of P. shigelloides. The performance of the assay with reference plasmids and spiked human stools as samples was evaluated and compared with those of quantitative PCR (qPCR). No false-positive results were observed for the 32 non-P. shigelloides strains used to evaluate assay specificity. The limit of detection for P. shigelloides was approximately 20 copies per reaction in reference plasmids and 5×103 CFU per gram in spiked human stool, which were more sensitive than the results of qPCR. When applied in human stool samples spiked with 2 low levels of P. shigelloides, the LAMP assays achieved accurate detection after 6-h enrichment. In conclusion, the LAMP assay developed in this study is a valuable method for rapid, cost-effective, and simple detection of P. shigelloides in basic clinical and field laboratories in the rural areas of China. PMID:23077478

  8. Rapid Detection of the Marek's Disease Viral Genome in Chicken Feathers by Loop-Mediated Isothermal Amplification

    PubMed Central

    Baskaran, Subasty; Gopal, Dhinakar Raj; Devarajan, Jeyanthi; Kathaperumal, Kumanan

    2012-01-01

    A loop-mediated isothermal amplification (LAMP) method for the rapid detection of serotype 1 Marek's disease virus (MDV) was developed. The method used a set of three pairs of primers to amplify the MEQ gene for detecting serotype 1 MDV. The MDV LAMP method did not cross-react with serotype 2 and serotype 3, nor did the LAMP primers have binding sites for the common avian DNA viruses (reticuloendotheliosis virus, chicken anemia virus, subgroup J of the avian leukosis virus). Additionally, the assay could detect up to 10 copies of the MEQ gene in the MD viral genome, and it had 10 times higher sensitivity than the traditional PCR methods. The LAMP master mix was stable for 90 days at ?20°C. Furthermore, the efficiency of LAMP for detection of serotype 1 MDV in clinical samples was comparable to those of PCR and viral isolation. The LAMP procedure is simple and does not rely on any special equipment. The detection of serotype 1 MDV by LAMP will be useful for detecting and controlling oncogenic Marek's disease. PMID:22170920

  9. Bacteria screening, viability, and confirmation assays using bacteriophage-impedimetric/loop-mediated isothermal amplification dual-response biosensors.

    PubMed

    Tlili, Chaker; Sokullu, Esen; Safavieh, Mohammadali; Tolba, Mona; Ahmed, Minhaz Uddin; Zourob, Mohammed

    2013-05-21

    Here, we integrate two complementary detection strategies for the identification and quantification of Escherichia coli based on bacteriophage T4 as a natural bioreceptor for living bacteria cells. The first approach involves screening and viability assays, employing bacteriophage as the recognition element in label-free electrochemical impedance spectroscopy. The complementary approach is a confirmation by loop-mediated isothermal amplification (LAMP) to amplify specifically the E. coli Tuf gene after lysis of the bound E. coli cells, followed by detection using linear sweep voltammetry. Bacteriphage T4 was cross-linked, in the presence of 1,4-phenylene diisothiocyanate, on a cysteamine-modified gold electrode. The impedimetric biosensor exhibits specific and reproducible detection with sensitivity over the concentration range of 10(3)-10(9) cfu/mL, while the linear response of the LAMP approach was determined to be 10(2)-10(7) cfu/mL. The limit of detection (LOD) of 8 × 10(2) cfu/mL in less than 15 min and 10(2) cfu/mL within a response time of 40 min were achieved for the impedimetric and LAMP method, respectively. This work provides evidence that integration of the T4-bacteriophage-modified biosensor and LAMP can achieve screening, viability, and confirmation in less than 1 h. PMID:23510137

  10. Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens.

    PubMed

    Barkway, Christopher P; Pocock, Rebecca L; Vrba, Vladimir; Blake, Damer P

    2015-01-01

    Eimeria species parasites, protozoa which cause the enteric disease coccidiosis, pose a serious threat to the production and welfare of chickens. In the absence of effective control clinical coccidiosis can be devastating. Resistance to the chemoprophylactics frequently used to control Eimeria is common and sub-clinical infection is widespread, influencing feed conversion ratios and susceptibility to other pathogens such as Clostridium perfringens. Despite the availability of polymerase chain reaction (PCR)-based tools, diagnosis of Eimeria infection still relies almost entirely on traditional approaches such as lesion scoring and oocyst morphology, but neither is straightforward. Limitations of the existing molecular tools include the requirement for specialist equipment and difficulties accessing DNA as template. In response a simple field DNA preparation protocol and a panel of species-specific loop-mediated isothermal amplification (LAMP) assays have been developed for the seven Eimeria recognised to infect the chicken. We now provide a detailed protocol describing the preparation of genomic DNA from intestinal tissue collected post-mortem, followed by setup and readout of the LAMP assays. Eimeria species-specific LAMP can be used to monitor parasite occurrence, assessing the efficacy of a farm's anticoccidial strategy, and to diagnose sub-clinical infection or clinical disease with particular value when expert surveillance is unavailable. PMID:25741643

  11. A portable automatic endpoint detection system for amplicons of loop mediated isothermal amplification on microfluidic compact disk platform.

    PubMed

    Uddin, Shah Mukim; Ibrahim, Fatimah; Sayad, Abkar Ahmed; Thiha, Aung; Pei, Koh Xiu; Mohktar, Mas S; Hashim, Uda; Cho, Jongman; Thong, Kwai Lin

    2015-01-01

    In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10(-3) ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment. PMID:25751077

  12. DNA Hydrogels: DhITACT: DNA Hydrogel Formation by Isothermal Amplification of Complementary Target in Fluidic Channels (Adv. Mater. 23/2015).

    PubMed

    Lee, Ho Yeon; Jeong, Hansaem; Jung, Il Young; Jang, Bora; Seo, Young Chang; Lee, Haeshin; Lee, Hyukjin

    2015-06-01

    H. Lee and co-workers demonstrate, on page 3513, the novel platform for rapid and accurate detection of infectious pathogens. "DNA hydrogel formation by isothermal amplification of complementary target in fluidic channels" (DhITACT) enables the naked-eye detection of ebola and Bacillus Anthracis using a microfluidic array chip by selective blockage of the matching channels through in situ hydrogel formation when target pathogen strands are present. PMID:26094756

  13. Rapid diagnosis of lymph node metastasis in lung cancer with loop-mediated isothermal amplification assay using carcinoembryonic antigen–mRNA

    Microsoft Academic Search

    Jun Maeda; Masayoshi Inoue; Kadzuki Nakabayashi; Yasuhiro Otomo; Yasushi Shintani; Mitsunori Ohta; Meinoshin Okumura; Nariaki Matsuura

    2009-01-01

    We investigated the clinical utility of our novel loop-mediated isothermal amplification (LAMP) assay developed as a rapid molecular diagnostic method, using carcinoembryonic antigen (CEA)–mRNA as a marker for detecting tumor cells in patients with non-small cell lung cancer (NSCLC). We evaluated the sensitivity of our LAMP technique using a known quantity of synthesized standard CEA–mRNA. On the basis of those

  14. A one-step reverse transcriptase loop-mediated isothermal amplification assay for simple and rapid detection of swine vesicular disease virus

    Microsoft Academic Search

    Anne-Lie Blomström; Mikhayil Hakhverdyan; Scott M. Reid; Juliet P. Dukes; Donald P. King; Sándor Belák; Mikael Berg

    2008-01-01

    This report describes the development of a one-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for the detection of swine vesicular disease virus (SVDV). The assay detects the virus rapidly, within 30–60min and the result is visualised either by gel-electrophoresis or by the naked eye through the addition of SybrGreen. A collection of 28 SVDV isolates were tested positive, while

  15. Evaluation of a real-time PCR and a loop-mediated isothermal amplification for detection of Xanthomonas arboricola pv. pruni in plant tissue samples.

    PubMed

    Palacio-Bielsa, Ana; López-Soriano, Pablo; Bühlmann, Andreas; van Doorn, Joop; Pham, Khanh; Cambra, Miguel A; Berruete, Isabel M; Pothier, Joël F; Duffy, Brion; Olmos, Antonio; López, María M

    2015-05-01

    Operational capacity of real-time PCR and loop-mediated isothermal amplification (LAMP) diagnostic assays for detection of Xanthomonas arboricola pv. pruni was established in a ring-test involving four laboratories. Symptomatic and healthy almond leaf samples with two methods of sample preparation were analyzed. Kappa coefficient, sensitivity, specificity, likelihood ratios and post-test probability of detection were estimated to manage the risk associated with the use of the two methods. PMID:25769438

  16. Real-time loop-mediated isothermal amplification assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder.

    PubMed

    Jain, Neha; Kumar, Jyoti S; Parida, M M; Merwyn, S; Rai, G P; Agarwal, G S

    2011-06-01

    Loop-mediated isothermal amplification (LAMP) assay is a powerful and innovative gene amplification technique that specifically amplifies the target gene under isothermal conditions with a high degree of sensitivity, rapidity and specificity. The major advantage of the LAMP assay is monitoring of amplified products without the requirement of any sophisticated equipment. In the present study a real time LAMP assay was employed for rapid and real time detection of Bacillus anthracis spores spiked in 0.1 g of soil and talcum powder ranging from 2 to 10(7) spores. DNA was isolated from spiked soil and talcum powder using PBS containing 1% Triton X-100, and heat treatment. Isolated DNA was used as template for LAMP and PCR. LAMP amplification was obtained in 60 min under isothermal condition at 63°C by employing a set of six primers targeting the pag gene of B. anthracis. The detection limit of LAMP assay in soil and talcum powder was found to be as low as 5 spores, compared to 10(3) spores and 10(4) spores by PCR in talcum powder and soil, respectively. The findings suggest that LAMP is a more rapid and sensitive assay than PCR for detecting anthrax spores, additionally the methodology to prepare DNA from spiked samples is simple, rapid and cost effective. PMID:25187140

  17. A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples.

    PubMed

    Sun, Yi; Quyen, Than Linh; Hung, Tran Quang; Chin, Wai Hoe; Wolff, Anders; Bang, Dang Duong

    2015-04-21

    Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics. PMID:25715949

  18. Development of simple, rapid and sensitive detection assay for grouper nervous necrosis virus using real-time loop-mediated isothermal amplification.

    PubMed

    Mekata, T; Satoh, J; Inada, M; Dinesh, S; Harsha, P; Itami, T; Sudhakaran, R

    2014-07-30

    A quantitative rapid detection method based on loop-mediated isothermal amplification has been developed for red-spotted grouper nervous necrosis virus (RGNNV). The nested polymerase chain reaction (PCR) assay is the mainstream inspection of the brooder in the hatchery. In this study, a real-time loop-mediated isothermal amplification (LAMP) method has been applied for RGNNV detection, known as a high-speed gene amplification procedure. Of the three temperatures (60 °C, 63 °C and 65 °C) attempted, it has been found that 63 °C is giving higher amplification from 11th minute onwards. Sensitivity analysis performed in comparison with real-time polymerase chain reaction, reverse transcriptase PCR and nested RT-PCR using various concentrations of template revealed that real-time LAMP method is efficient in terms of cost and time consumption. Specificity analysis revealed that the method developed is specific to RGNNV, whereas it has sequence cross-match with tiger puffer NNV giving advantage in detecting both the viruses. This method could be much efficient in analysing RGNNV in combination with TPNNV. PMID:25073724

  19. Development of loop-mediated isothermal amplification to detect Streptococcus suis and its application to retail pork meat in Japan.

    PubMed

    Arai, Sakura; Tohya, Mari; Yamada, Ryoko; Osawa, Ro; Nomoto, Ryohei; Kawamura, Yoshiaki; Sekizaki, Tsutomu

    2015-09-01

    We here developed a novel loop-mediated isothermal amplification (LAMP) method to detect Streptococcus suis in raw pork meat. This method, designated LAMPSS, targeted the recombination/repair protein (recN) gene of S. suis and detected all serotypes of S. suis, except those taxonomically removed from authentic S. suis, i.e., serotypes 20, 22, 26, 32, 33, and 34. The specificity of LAMPSS was confirmed and its detection limit was 5.4cfu/reaction. Among the 966 raw pork meat samples examined, including sliced pork, minced pork, and the liver, tongue, heart, and small intestine, 255 samples tested positive with LAMPSS. The rate of contamination was higher in the organs than in pork. No significant difference was observed in the total bacterial count between LAMPSS-positive and -negative samples. The number of shops that provided LAMPSS-positive pork was slightly higher in those that sold swine organs and pork than in those that sold only pork, suggesting that cross contamination occurred from the organs to pork. Among the 255 which tested positive for LAMPSS, only 47 samples tested positive for the previously described LAMP specific for S. suis serotype 2. Two isolates of S. suis serotype 2, belonging to sequence type 28, which is potentially hazardous to humans, as well as those of some other serotypes were obtained from 19 out of 47 samples by combining LAMP with a replica plating method. These results suggest that LAMPSS will be a useful tool for the surveillance of raw pork meat in the retail market. PMID:26043307

  20. Development of a loop-mediated isothermal amplification method for rapid detection of porcine boca-like virus.

    PubMed

    Li, Bin; Ma, Jun-jie; Xiao, Shao-bo; Zhang, Xue-han; Wen, Li-bin; Mao, Li; Ni, Yan-xiu; Guo, Rong-li; Zhou, Jun-ming; Lv, Li-xin; He, Kong-wang

    2012-02-01

    The porcine boca-like virus (Pbo-likeV) was recently discovered in Swedish pigs with post-weaning multisystemic wasting syndrome (PMWS). In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for rapid, specific and sensitive detection of Pbo-likeV. A set of four primers specific for six regions of Pbo-likeV VP1/2 genes was designed with the online software. The reaction temperature and time were optimized to 65 °C and 60 min, respectively. LAMP products were detected by agarose gel electrophoresis or by visual inspection of a color change due to addition of fluorescent dye. The developed method was highly specific for detection of Pbo-likeV, and no cross-reaction was observed with other swine viruses, such as porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), porcine parvovirus (PPV) and classic swine fever virus (CSFV) found commonly in China. The lower detection limit of the LAMP assay was approximately 10 copies per reaction, and it was 100 times more sensitive than that of conventional PCR. Furthermore, the efficiency of LAMP for detection Pbo-likeV in clinical samples was comparable to PCR and sequencing. These results showed that the LAMP assay is a simple, rapid, sensitive and specific technique for detection of Pbo-likeV, and the procedure of LAMP does not rely on any special equipment. It has capacity for the detection of Pbo-likeV both in the laboratory and on farms. PMID:22172971

  1. Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification

    PubMed Central

    Peng, Peichao; Cheng, Xiaoxing; Wang, Guoqing; Qian, Minping; Gao, Huafang; Han, Bei; Chen, Yusheng; Hu, Yinghui; Geng, Rong; Hu, Chengping; Zhang, Wei; Yang, Jingping; Wan, Huanying; Yu, Qin; Wei, Liping; Li, Jiashu; Tian, Guizhen; Wang, Qiuyue; Hu, Ke; Wang, Siqin; Wang, Ruiqin; Du, Juan; He, Bei; Ma, Jianjun; Zhong, Xiaoning; Mu, Lan; Cai, Shaoxi; Zhu, Xiangdong; Xing, Wanli; Yu, Jun; Deng, Minghua; Gao, Zhancheng

    2012-01-01

    Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship. Trial Registration ClinicalTrials.gov NCT00567827 PMID:22719933

  2. The development of loop-mediated isothermal amplification targeting alpha-tubulin DNA for the rapid detection of Plasmodium vivax

    PubMed Central

    2014-01-01

    Background Malaria that is caused by Plasmodium vivax is the most widely distributed human malaria. Its recent resurgence in many parts of the world, including the Republic of Korea (ROK), emphasizes the importance of improved access to the early and accurate detection of P. vivax to reduce disease burden. In this study, a rapid and efficient loop-mediated isothermal amplification (LAMP)-based method was developed and validated using blood samples from malaria-suspected patients. Method A LAMP assay targeting the ?-tubulin gene for the detection of P. vivax was developed with six primers that recognize different regions of the target gene. The diagnostic performance of the ?-tubulin LAMP assay was compared to three other tests: microscopic examinations, rapid diagnostic tests (RDTs), and nested polymerase chain reactions (PCRs) using 177 whole blood specimens obtained from ROK military personnel from May to December 2011. Results The ?-tubulin LAMP assay was highly sensitive with a detection limit of 100 copies of P. vivax ?-tubulin gene per reaction within 50 min. It specifically amplified the target gene only from P. vivax. Validation of the ?-tubulin LAMP assay showed that the assay had the highest sensitivity (P?

  3. Rapid, Simple, and Sensitive Detection of Anaplasma phagocytophilum by Loop-Mediated Isothermal Amplification of the msp2 Gene ?

    PubMed Central

    Pan, Lei; Zhang, Lijuan; Wang, Guiqiang; Liu, Qinghui; Yu, Yanyan; Wang, Shiwen; Yu, Huilan; He, Jing

    2011-01-01

    Anaplasma phagocytophilum is the causative agent of human granulocytic anaplasmosis, which is prevalent throughout China. In this study, we describe a rapid, simple, and sensitive loop-mediated isothermal amplification (LAMP) assay targeting the msp2 gene of A. phagocytophilum that is ideal for application in rural areas in China. This assay has the potential to detect A. phagocytophilum early in infection as an alternative to existing methods. A total of 42 suspected cases of infection with A. phagocytophilum, 15 serologically confirmed and 27 probable cases, were analyzed by the msp2 LAMP assay. To validate the accuracy of LAMP, previously established nested-PCR and real-time PCR assays were utilized. The sensitivity of LAMP was 25 copies per reaction (approximately 1,250 copies per ml blood) for A. phagocytophilum, and the assay did not detect false positives among 27 members of the order Rickettsiales and 17 common clinical pathogens. To evaluate the clinical applicability of the LAMP assay, a total of 42 clinical samples were examined. A positive LAMP result was obtained for 12 of the confirmed cases and for 14 of 27 suspected cases, while only 1 confirmed case and 3 cases (2 confirmed cases and 1 suspected case) were detected by nested PCR and real-time PCR, respectively. The LAMP assay described in this study demonstrated a high level of sensitivity comparable with that of nested PCR and real-time PCR for the detection of A. phagocytophilum. This LAMP assay is a valuable method for rapid, cost-effective, and simple detection of A. phagocytophilum in the rural areas of China. PMID:21976758

  4. Loop-Mediated Isothermal Amplification Assay for Rapid Diagnosis of Malaria Infections in an Area of Endemicity in Thailand

    PubMed Central

    Sattabongkot, Jetsumon; Tsuboi, Takafumi; Han, Eun-Taek; Bantuchai, Sirasate

    2014-01-01

    The loop-mediated isothermal amplification (LAMP) method, developed by our group for diagnosis of four human malaria parasites, was evaluated on a large scale at a remote clinic in Thailand where malaria is endemic. A total of 899 febrile patients were analyzed in this study. LAMP was first evaluated in 219 patients, and the result was compared to those of two histidine-rich protein (HRP)-2 rapid diagnostic tests (RDTs) and microscopy as a gold standard. LAMP DNA extraction was conducted by a simple boiling method, and the test results were assessed visually. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 95.7%, 100%, 100%, and 98%, respectively, for LAMP and 98.6%, 98%, 95.8%, and 99.3%, respectively, for RDTs. Since RDT-positive results were based on one out of two RDTs, the sensitivity of RDTs was slightly higher than that of LAMP. However, LAMP tended to be more specific than RDTs. LAMP next was evaluated in 680 patients, and the result was compared to that of microscopy as a gold standard. Sensitivity, specificity, PPV, NPV, and diagnostic accuracy of LAMP were 88.9%, 96.9%, 92.2%, 95.5%, and 94.6%, respectively. Nested PCR was used to confirm the discrepant results. Malaria LAMP in a remote clinic in Thailand achieved an acceptable result, indicating that LAMP malaria diagnosis is feasible in a field setting with limited technical resources. Additionally, the rapid boiling method for extracting DNA from dried blood spots proved to be simple, fast, and suitable for use in the field. PMID:24574279

  5. Development and application of loop-mediated isothermal amplification assays based on ITS-1 for rapid detection of Toxoplasma gondii in pork.

    PubMed

    Zhuo, Xunhui; Huang, Bin; Luo, Jiaqing; Yu, Haijie; Yan, Baolong; Yang, Yi; Du, Aifang

    2015-03-15

    The loop-mediated isothermal amplification (LAMP) assay is a novel method that rapidly amplifies DNA with high specificity and sensitivity under isothermal conditions. In this study, we established a LAMP assay with six primers targeting a highly conserved region of Toxoplasma gondii ITS-1 sequence. The amplification protocol completes within 30 min under isothermal condition in a 65°C water bath while specificity tests confirmed no cross-reactivity with DNA templates of Neospora caninum, Eimeria tenella, Cryptosporidium parvum, Listeria monocytogenes and Streptococcus suis. The detection limit of the LAMP assay was 0.9 fg T. gondii genomic DNA, a sensitivity that was 10-fold higher than that of a conventional PCR assay. Both LAMP assay and conventional PCR were applied to detect T. gondii genomic DNA in 118 diaphragm samples obtained from pig farms in Zhejiang Province, China. Our results showed that the LAMP assay is more sensitive than conventional PCR (13.56% and 9.32%). The LAMP assay established in this study provides a simple, specific, sensitive and rapid method of T. gondii genomic DNA detection, hence is expected to plays an important role in the monitoring of T. gondii contamination in various food products. PMID:25624074

  6. [Rapid detection of Macrobrachium rosenbergii nodavirus isolated in China by a reverse-transcription loop-mediated isothermal amplification assay combined with a lateral flow dipstick method].

    PubMed

    Lin, Feng; Liu, Li; Hao, Gui-Jie; Cao, Zheng; Sheng, Peng-Cheng; Wu, Ying-Lei; Shen, Jin-Yu

    2014-09-01

    White coloration of the muscle of the giant river prawn (Macrobrachium rosenbergii) is a serious problem in China. The Macrobrachium rosenbergii Nodavirus (MrNV) has been confirmed to be the pathogen that causes this disorder. To develop a rapid, sensitive and specific technology for the detection of Macrobrachium rosenbergii Nodavirus isolated from China (MrNV-China), a reverse-transcription loop- mediated isothermal amplification assay combined with a lateral flow dipstick (RT-LAMP-LFD) assay method is described. A set of four primers and a labeled probe were designed specifically to recognize six distinct regions of the MrNV RNA2 gene. Results showed the sensitivity of the RT-LAMP-LFD assay was ten-times higher than the reverse-transcription loop-mediated isothermal amplification assay (RT-LAMP) with agarose gel electrophoresis. The assay was conducted with one-step amplification at 61°C in a single tube within 45 min. No product was generated from shrimps infected with other viruses, including DNA viruses (infectious hypodermal and hematopoietic necrosis virus (IHHNV); white spot syndrome virus (WSSV)) and RNA viruses (Taura syndrome virus (TSV); infectious myonecrosis virus (IMNV); yellow head virus (YHV)). Results were visualized by the LFD method. Therefore, the described rapid and sensitive assay is potentially useful for MrNV detection. PMID:25562958

  7. Development of a Reverse Transcriptase Loop-Mediated Isothermal Amplification (LAMP) Assay for the Sensitive Detection of Leishmania Parasites in Clinical Samples

    PubMed Central

    Adams, Emily R.; Schoone, Gerard J.; Ageed, Al Farazdag; Safi, Sayda El; Schallig, Henk D. F. H.

    2010-01-01

    Here we describe a generic, reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) assay, for the identification of Leishmania species from clinical samples. LAMP is an isothermal reaction recently developed as a point-of-care diagnostic tool. Primers were designed in the conserved region of the 18S ribosomal RNA (rRNA) gene; amplification was visualized by the pre-amplification addition of fluorescent detection reagent (FDR) and a simple UV lamp. By using a reverse-transcriptase step, the system detected infections between 10 and 100 parasites per mL. The assay was tested on a range of nucleic acid extracts from Leishmania species, visceral leishmaniasis (VL) patients from Sudan, and cutaneous leishmaniasis (CL) patients from Suriname. The sensitivity of RT-LAMP from the blood of VL patients was 83% (N = 30) compared with microscopy of bone-marrow and lymph-node aspirates; for CL patients the observed sensitivity was 98% (N = 43). The potential to use LAMP as a diagnostic tool for leishmaniasis is discussed. PMID:20348505

  8. Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV).

    PubMed

    Bhadra, Sanchita; Jiang, Yu Sherry; Kumar, Mia R; Johnson, Reed F; Hensley, Lisa E; Ellington, Andrew D

    2015-01-01

    The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens. PMID:25856093

  9. A magnetic bead-based assay for the rapid detection of methicillin-resistant Staphylococcus aureus by using a microfluidic system with integrated loop-mediated isothermal amplification.

    PubMed

    Wang, Chih-Hung; Lien, Kang-Yi; Wu, Jiunn-Jong; Lee, Gwo-Bin

    2011-04-21

    This study reports a new diagnostic assay for the rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) by combing nucleic acid extraction and isothermal amplification of target nucleic acids in a magnetic bead-based microfluidic system. By using specific probe-conjugated magnetic beads, the target deoxyribonucleic acid (DNA) of the MRSA can be specifically recognized and hybridized onto the surface of the magnetic beads which are then mixed with clinical sample lysates. This is followed by purifying and concentrating the target DNA from the clinical sample lysates by applying a magnetic field. Nucleic acid amplification of the target genes can then be performed by the use of a loop-mediated isothermal amplification (LAMP) process via the incorporation of a built-in micro temperature control module, followed by analyzing the optical density (OD) of the LAMP amplicons using a spectrophotometer. Significantly, experimental results show that the limit of detection (LOD) for MRSA in the clinical samples is approximately 10 fg ?L(-1) by performing this diagnostic assay in the magnetic bead-based microfluidic system. In addition, the entire diagnostic protocol, from bio-sample pre-treatment to optical detection, can be automatically completed within 60 min. Consequently, this miniature diagnostic assay may become a powerful tool for the rapid purification and detection of MRSA and a potential point-of-care platform for detection of other types of infections. PMID:21399774

  10. Rapid, Simple and Sensitive Detection of Q Fever by Loop-Mediated Isothermal Amplification of the htpAB Gene

    PubMed Central

    Pan, Lei; Zhang, Lijuan

    2013-01-01

    Background Q fever is the most widespread zoonosis, and domestic animals are the most common sources of transmission. It is not only difficult to distinguish from other febrile diseases because of the lack of specific clinical manifestations in humans, but it is also difficult to identify the disease in C. burnetii-carrying animals because of the lack of identifiable features. Conventional serodiagnosis requires sera from the acute and convalescent stages of infection, which are unavailable at early diagnosis. Nested PCR and real-time PCR require equipment. In this study, we developed a Loop-Mediated Isothermal Amplification (LAMP) assay to identify C. burnetii rapidly and sensitively. Methods A universal LAMP primer set was designed to detect the repeated sequence IS1111a of the htpAB gene of C. burnetii using PrimerExplorer V4 software. The sensitivity of the LAMP assay was evaluated using known quantities of recombined reference plasmids containing the targeted genes. The specificity of the developed LAMP assay was determined using 26 members of order Rickettsiae and 18 other common pathogens. The utility of the LAMP assay was further compared with real time PCR by the examination 24 blood samples including 6 confirmed and 18 probable Q fever cases, which diagnosed by IFA serological assessment and real time PCR. In addition, 126 animal samples from 4 provinces including 97 goats, 7 cattle, 18 horses, 3 marmots and 1 deer were compared by these two methods. Results The limits of detection of the LAMP assay for the htpAB gene were 1 copy per reaction. The specificity of the LAMP assay was 100%, and no cross-reaction was observed among the bacteria used in the study. The positive rate of unknown febrile patients was 33.3%(95%CI 30.2%–36.4%) for the LAMP assay and 8.3%(95%CI 7.4%–9.2%) for the real time PCR(P<0.05). Similarly, the total positive rate of animals was 7.9%(95%CI 7.1%–8.7%) for the LAMP assay and 0.8%(95%CI 0.7%–0.9%)for the real time PCR(P<0.01). Using the developed LAMP assay, Q fever in the Yi Li area, Xinjiang Province, was confirmed. Conclusions The LAMP assay is a potential tool to support the diagnosis of Q fever in humans and domestic animals in the field, especially in the rural areas of China, because of its rapid and sensitive detection without the aid of sophisticated equipment or a complicated protocol. PMID:23696915

  11. Development and comparative evaluation of loop mediated isothermal amplification (LAMP) assay for simple visual detection of orf virus in sheep and goats.

    PubMed

    Venkatesan, G; Bhanuprakash, V; Balamurugan, V

    2015-06-01

    A loop-mediated isothermal amplification (LAMP) assay targeting DNA Pol gene was optimized and evaluated for the rapid detection of orf virus in clinical samples. The LAMP assay was found to be specific and sensitive. The detection rate of LAMP (89.3%) was better than PCR (67.9%) and comparable to real-time PCR (91.1%) in clinical samples by gel electrophoresis and visual detection methods. This LAMP assay is simple and does not rely upon any special equipment and could be employed in clinical diagnosis and epidemiological survey of orf infection. PMID:25828693

  12. Development of a Sensitive Loop-Mediated Isothermal Amplification Assay That Provides Specimen-to-Result Diagnosis of Respiratory Syncytial Virus Infection in 30 Minutes

    PubMed Central

    Chong, Sylvia; Bulir, David; Ruyter, Alexandra; Mwawasi, Ken; Waltho, Daniel

    2013-01-01

    Rapid isothermal amplification methods have recently been introduced, and some of these methods offer significant advantages over PCR. The objective of this study was to develop a rapid and sensitive multiplex loop-mediated isothermal amplification (M-LAMP) assay for the detection of respiratory syncytial virus subgroups A and B (RSV A and B). We designed six primers each for the matrix gene of RSV A and the polymerase gene of RSV B and developed an M-LAMP assay by using a commercially available master mix and a real-time fluorometer (Genie II; Optigene, United Kingdom) that displays real-time amplification, time to positivity, and amplicon annealing temperature (Tm). The M-LAMP was evaluated against PCR by testing 275 nasopharyngeal (NP) specimens. The final optimized M-LAMP assay had a mean amplification time of 14.2 min (compared with 90 to 120 min for PCR) and had an analytical sensitivity of 1 genome equivalent (ge) for both RSV A and B. Using PCR as a comparator, M-LAMP had a sensitivity of 100% (81/81) and specificity of 100% (194/194). We also evaluated a 3- to 10-min specimen processing method involving vortexing with glass beads and heating to 98°C in M-swab medium (Copan Italia, Brescia, Italy) and found that this rapid processing method allowed detection of 37/41 (90.2%) of positives when we used extracted nucleic acid. In summary, the M-LAMP assay had excellent sensitivity and specificity for detecting RSV A and B in NP specimens and, when coupled with a rapid specimen preparation method, could provide a specimen-to-result diagnosis time of 30 min. PMID:23761156

  13. A one-step reverse transcriptase loop-mediated isothermal amplification assay for simple and rapid detection of swine vesicular disease virus.

    PubMed

    Blomström, Anne-Lie; Hakhverdyan, Mikhayil; Reid, Scott M; Dukes, Juliet P; King, Donald P; Belák, Sándor; Berg, Mikael

    2008-01-01

    This report describes the development of a one-step reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for the detection of swine vesicular disease virus (SVDV). The assay detects the virus rapidly, within 30-60 min and the result is visualised either by gel-electrophoresis or by the naked eye through the addition of SybrGreen. A collection of 28 SVDV isolates were tested positive, while heterologous viruses such as foot-and-mouth disease virus and vesicular stomatitis virus remained negative. The performance of the RT-LAMP was compared directly with real-time PCR using RNA from clinical samples including nasal swabs, serum and faeces. For nasal swabs and serum the sensitivity of the RT-LAMP was shown to be at least equivalent to real-time PCR. Interestingly, for faecal samples the RT-LAMP assay was shown to be even more sensitive than real-time PCR, possibly because it is less sensitive to inhibitory substances. This RT-LAMP assay provides a number of benefits for the diagnosis of SVD, since the assay is sensitive and rapid, and the isothermal amplification strategy used is not reliant upon expensive equipment it is particularly suited for "front line" diagnosis of SVD in modestly equipped laboratories, in field stations or in mobile diagnostic units. PMID:17920701

  14. Rapid and sensitive detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawns by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick.

    PubMed

    Puthawibool, Teeranart; Senapin, Saengchan; Flegel, Timothy W; Kiatpathomchai, Wansika

    2010-10-01

    Loop-mediated isothermal amplification (LAMP) allows rapid amplification of nucleic acids under isothermal conditions. It can be combined with a chromatographic lateral flow dipstick (LFD) for much more efficient, field-friendly detection of MrNV. In this work, RT-LAMP was performed at 65 degrees C for 40 min, followed by 5 min for hybridization with an FITC-labeled DNA probe and 5 min for LFD resulted in visualization of DNA amplicons trapped at the LFD test line. Thus, total assay time, including 10 min for rapid RNA extraction was approximately 60 min. In addition to advantages of short assay time, confirmation of amplicon identity by hybridization and elimination of electrophoresis with carcinogenic ethidium bromide, the RT-LAMP-LFD was more sensitive than an existing RT-PCR method for detection of MrNV. The RT-LAMP-LFD method gave negative test results with nucleic acid extracts from normal shrimp and from shrimp infected with other viruses including DNA viruses [PstDNV (IHHNV), PemoNPV (MBV), PmDNV (HPV), WSSV] and RNA viruses (TSV, IMNV, YHV/GAV). PMID:20655379

  15. Development and evaluation of a reverse transcription loop-mediated isothermal amplification assay for rapid detection of a new SFTS bunyavirus.

    PubMed

    Yang, Guoliang; Li, Bing; Liu, Lanzheng; Huang, Weichu; Zhang, Wen; Liu, Yuandong

    2012-09-01

    The etiological agent of severe fever with thrombocytopenia syndrome (SFTS) is a bunyavirus that was first identified in China in 2009. We have developed and validated a one-step, single-tube, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SFTS bunyavirus (SFTSV). This assay demonstrated high specificity and sensitivity, with a detection limit of 10(1) TCID(50) ml(-1). When combined with the fluorescent detection reagent (FDR) method, results could be determined by observing a color change within 30 min. As an accurate, rapid, simple and low-cost diagnostic method, this RT-LAMP assay will be helpful for detecting and preventing further SFTSV infection in China. PMID:22643834

  16. Development of Primer Sets for Loop-Mediated Isothermal Amplification that Enables Rapid and Specific Detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae.

    PubMed

    Wang, Deguo; Liu, Yanhong

    2015-01-01

    Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as targets, four sets of LAMP primers were designed for identification and differentiation of S. dysgalactiae, S. uberis and S. agalactiae. The detection limit of all four LAMP primer sets were 0.1 pg DNA template per reaction, the LAMP method with 16S rRNA gene and 16S-23S rRNA intergenic spacers as the targets can differentiate the three pathogens, which is potentially useful in epidemiological studies. PMID:26016433

  17. Comparison of a TaqMan real-time polymerase chain reaction assay with a loop-mediated isothermal amplification assay for detection of Gallid herpesvirus 1.

    PubMed

    Ou, Shan-Chia; Giambrone, Joseph J; Macklin, Kenneth S

    2012-01-01

    A TaqMan real-time polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) assay were developed to detect Gallid herpesvirus 1 (GaHV-1, formerly Infectious laryngotracheitis virus). The standard curve of real-time PCR was established, and the sensitivity reached 10 copies/?l. In the current study, the conversion between viral titer and GaHV-1 genomic copy number was constructed. Six primers for LAMP assay amplified target gene at 65°C within 45 min, and the detection limit was 60 copies/?l. The 6 primers were highly specific, sensitive, and reproducible for detection of GaHV-1. Although the sensitivity of LAMP was lower than that of real-time PCR, LAMP was faster, less expensive, and did not require a thermocycler. The LAMP assay would be a viable alternative assay in diagnostic laboratories that do not employ real-time PCR technology. PMID:22362944

  18. Development of a loop-mediated isothermal amplification assay for rapid detection of Nocardia salmonicida, the causative agent of nocardiosis in fish.

    PubMed

    Xia, Liqun; Zhang, Honglian; Lu, Yishan; Cai, Jia; Wang, Bei; Jian, Jichang

    2015-03-01

    Nocardia salmonicida is one of the main pathogens of fish nocardiosis. The purpose of this study was to build a loop-mediated isothermal amplification (LAMP) method for the rapid and sensitive detection of N. salmonicida. A set of four primers were designed from the 16S-23S rRNA intergenic spacer region of N. salmonicida, and conditions for LAMP were optimized as incubating all the reagents for 60 min at 64°C. LAMP products were judged with agar gel electrophoresis as well as with the naked eye after the addition of SYBR Green I. Results showed the sensitivity of the LAMP assay was 1.68 × 10(3) CFU/ml (16.8 CFU per reaction) and 10-fold higher than that of PCR. The LAMP method was also effectively applied to detect N. salmonicida in diseased fish samples, and it may potentially facilitate the surveillance and early diagnosis of fish nocardiosis. PMID:25262681

  19. Development of Primer Sets for Loop-Mediated Isothermal Amplification that Enables Rapid and Specific Detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae

    PubMed Central

    Wang, Deguo; Liu, Yanhong

    2015-01-01

    Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as targets, four sets of LAMP primers were designed for identification and differentiation of S. dysgalactiae, S. uberis and S. agalactiae. The detection limit of all four LAMP primer sets were 0.1 pg DNA template per reaction, the LAMP method with 16S rRNA gene and 16S-23S rRNA intergenic spacers as the targets can differentiate the three pathogens, which is potentially useful in epidemiological studies. PMID:26016433

  20. Rapid Detection and Differentiation of Dengue Virus Serotypes by a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay

    PubMed Central

    Parida, Manmohan; Horioke, Kouhei; Ishida, Hiroyuki; Dash, Paban Kumar; Saxena, Parag; Jana, Asha Mukul; Islam, Mohammed Alimul; Inoue, Shingo; Hosaka, Norimitsu; Morita, Kouichi

    2005-01-01

    The development and validation of a one-step, real-time, and quantitative dengue virus serotype-specific reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the 3? noncoding region for the rapid detection and differentiation of dengue virus serotypes are reported. The RT-LAMP assay is very simple and rapid, wherein the amplification can be obtained in 30 min under isothermal conditions at 63°C by employing a set of four serotype-specific primer mixtures through real-time monitoring in an inexpensive turbidimeter. The evaluation of the RT-LAMP assay for use for clinical diagnosis with a limited number of patient serum samples, confirmed to be infected with each serotype, revealed a higher sensitivity by picking up 100% samples as positive, whereas 87% and 81% of the samples were positive by reverse transcription-PCR and virus isolation, respectively. The sensitivity and specificity of the RT-LAMP assay for the detection of viral RNA in patient serum samples with reference to virus isolation were 100% and 93%, respectively. The optimal assay conditions with zero background and no cross-reaction with other closely related members of the Flavivirus family (Japanese encephalitis, West Nile, and St. Louis encephalitis viruses) as well as within the four serotypes of dengue virus were established. None of the serum samples from healthy individuals screened in this study showed any cross-reaction with the four dengue virus serotype-specific RT-LAMP assay primers. These findings demonstrate that RT-LAMP assay has the potential clinical application for detection and differentiation of dengue virus serotypes, especially in developing countries. PMID:15956414

  1. Loop-Mediated Isothermal Amplification for Rapid Detection and Differentiation of Wild-Type Bovine Herpesvirus-1 and Glycoprotein E-Deleted Marker Vaccine Strain.

    PubMed

    Pawar, Sachin S; Meshram, Chetan D; Singh, Niraj K; Saini, Mohini; Mishra, B P; Gupta, Praveen K

    2015-10-01

    Bovine herpesvirus-1 (BoHV-1) is an important viral pathogen affecting cattle and causing numerous reproductive disorders leading to significant economic losses to the cattle industry. The control programs for BoHV-1 are widely based on the use of glycoprotein E-deleted marker vaccines, wherein detection and differentiation of wild-type and gE-deleted vaccine strains is of crucial importance for proper disease management. In this study, we report rapid and simple loop-mediated isothermal amplification (LAMP) assays for detection and differentiation of gE-deleted BoHV-1 from wild-type virus under isothermal conditions. The assays could be completed in 90 mintes, including viral DNA isolation, target amplification and visual interpretation of results with naked eye. The analytical sensitivity of the assays was 10 times higher than conventional PCR and could detect as little as 100 fg of viral DNA per reaction. The applicability of LAMP for detection of BoHV-1 in bovine semen was assessed by testing semen samples collected from breeding bulls and compared with TaqMan real-time PCR (as gold standard). The LAMP assays had diagnostic specificity of 100%. The diagnostic sensitivity was 88.2% and 83.3% for gB- and gE-LAMP, respectively, when compared with TaqMan real-time PCR. Our results have shown that the LAMP method developed in this study is a potential tool for rapid, sensitive, specific, cost-effective, and user-friendly detection and differentiation of wild type BoHV-1 from gE-deleted marker vaccine. PMID:26158457

  2. Specific Detection of Viable Salmonella Cells by an Ethidium Monoazide-Loop Mediated Isothermal Amplification (EMA-LAMP) Method

    Microsoft Academic Search

    Yuxia Lu; Weiqing Yang; Lei Shi; Lin Li; Muhammad Jahangir Alam; Siyuan Guo; Shin-ichi Miyoshi

    The persistence ofDNA after the cell deathcauses a major issue in aspects of medical or biological studies. The signal from viable bacterial cells can- not be distinguished from the dead cells in the con- ventional DNA-based detection methods. In the present study, the loop-mediated isothermal amplifi- cation (LAMP) method combined with the ethidium monoazide (EMA) treatment was applied for specific

  3. Isothermal detection of multiple point mutations by a surface plasmon resonance biosensor with Au nanoparticles enhanced surface-anchored rolling circle amplification.

    PubMed

    Xiang, Yang; Deng, Kun; Xia, Han; Yao, Chunyan; Chen, Qinghai; Zhang, Liqun; Liu, Zhiyong; Fu, Weiling

    2013-11-15

    In this study, we developed a surface plasmon resonance (SPR) DNA biosensor method using surface-anchored rolling circle amplification (RCA) and Au nanoparticles modified probes (AuNPs) to isothermally detect multiple point mutations associated with drug-resistance in multidrug-resistant Mycobacterium Tuberculosis (MDRTB). A set of probes contains an allele-specific padlock probe (PLP), a capture probe and an AuNPs. The linear PLPs, circularized by ligation upon the recognition of the point mutation on DNA targets, hybridize to the capture probes via the specific tag/anti-tag recognition. Upon recognition each point mutation is identified by locating into the corresponding channel on the chip. Then the immobilized primer (capture probe)-template (circular PLP) complex are amplified isothermally as RCA and further amplified by AuNPs. The RCA products immobilized on the chip surface cause great SPR angle changes consequently. The 5 pM synthetic oligonucleotides and 8.2 pg uL(-1) of genomic DNA from clinical samples can be detected by the method. The positive mutation detection is achieved with a wild-type to mutant ratio of 5000:1. The method was demonstrated by targeting five clinically meaningful mutations in MDRTB. Thirty clinical samples were identified and they were in good agreement with the results from sequencing. PMID:23811476

  4. Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP(®) using reverse transcription-recombinase polymerase amplification.

    PubMed

    Zhang, Shulu; Ravelonandro, Michel; Russell, Paul; McOwen, Nathan; Briard, Pascal; Bohannon, Seven; Vrient, Albert

    2014-10-01

    Plum pox virus (PPV) causes the most destructive viral disease known as plum pox or Sharka disease in stone fruit trees. As an important regulated pathogen, detection of PPV is thus of critical importance to quarantine and eradication of the spreading disease. In this study, the innovative development of two AmplifyRP(®) tests is reported for a rapid isothermal detection of PPV using reverse transcription-recombinase polymerase amplification. In an AmplifyRP(®) test, all specific recombination and amplification reactions occur at a constant temperature without thermal cycling and the test results are either recorded in real-time with a portable fluorescence reader or displayed using a lateral flow strip contained inside an amplicon detection chamber. The major improvement of this assay is that the entire test from sample preparation to result can be completed in as little as 20min and can be performed easily both in laboratories and in the field. The results from this study demonstrated the ability of the AmplifyRP(®) technique to detect all nine PPV strains (An, C, CR, D, EA, M, Rec, T, or W). Among the economic benefits to pathogen surveys is the higher sensitivity of the AmplifyRP(®) to detect PPV when compared to the conventional ELISA and ImmunoStrip(®) assays. This is the first report describing the use of such an innovative technique to detect rapidly plant viruses affecting perennial crops. PMID:25010790

  5. Development of a Reverse Transcription Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Subtype H7N9 Avian Influenza Virus

    PubMed Central

    Bao, Hongmei; Zhao, Yuhui; Wang, Yunhe; Xu, Xiaolong; Shi, Jianzhong; Zeng, Xianying; Wang, Xiurong; Chen, Hualan

    2014-01-01

    A novel influenza A (H7N9) virus has emerged in China. To rapidly detect this virus from clinical samples, we developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of the H7N9 virus. The minimum detection limit of the RT-LAMP assay was 0.01?PFU H7N9 virus, making this method 100-fold more sensitive to the detection of the H7N9 virus than conventional RT-PCR. The H7N9 virus RT-LAMP assays can efficiently detect different sources of H7N9 influenza virus RNA (from chickens, pigeons, the environment, and humans). No cross-reactive amplification with the RNA of other subtype influenza viruses or of other avian respiratory viruses was observed. The assays can effectively detect H7N9 influenza virus RNA in drinking water, soil, cloacal swab, and tracheal swab samples that were collected from live poultry markets, as well as human H7N9 virus, in less than 30?min. These results suggest that the H7N9 virus RT-LAMP assays were efficient, practical, and rapid diagnostic methods for the epidemiological surveillance and diagnosis of influenza A (H7N9) virus from different resource samples. PMID:24689044

  6. Detection of Cucurbit chlorotic yellows virus from Bemisia tabaci captured on sticky traps using reverse transcription loop-mediated isothermal amplification (RT-LAMP) and simple template preparation.

    PubMed

    Okuda, Mitsuru; Okuda, Shiori; Iwai, Hisashi

    2015-09-01

    Cucurbit chlorotic yellows virus (CCYV) of the genus Crinivirus within the family Closteroviridae is an emerging infectious agent of cucurbits leading to severe disease and significant economic losses. Effective detection and identification methods for this virus are urgently required. In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect CCYV from its vector Bemisia tabaci. LAMP primer sets to detect CCYV were evaluated for their sensitivity and specificity, and a primer set designed from the HSP70h gene with corresponding loop primers were selected. The RT-LAMP assay was applied to detect CCYV from viruliferous B. tabaci trapped on sticky traps. A simple extraction procedure using RNAsecure™ was developed for template preparation. CCYV was detected in all of the B. tabaci 0, 1, 7 and 14 days after they were trapped. Although the rise of turbidity was delayed in reactions using RNA from B. tabaci trapped for 7 and 14 days compared with those from 0 and 1 day, the DNA amplification was sufficient to detect CCYV in all of the samples. These findings therefore present a simple template preparation method and an effective RT-LAMP assay, which can be easily and rapidly performed to monitor CCYV-viruliferous B. tabaci in the field. PMID:25912723

  7. Loop-mediated isothermal amplification of vanA gene enables a rapid and naked-eye detection of vancomycin-resistant enterococci infection.

    PubMed

    Kim, Hye Jin; Kim, Yu Jin; Yong, Dong Eun; Lee, Kyungwon; Park, Jeon Han; Lee, Jae Myun; Yoon, Sang Sun

    2014-09-01

    Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infection at intensive care unit (ICU). A rapid and sensitive detection of VRE infection is in high demand for timely and suitable antibiotic treatment. Here, we optimized a distinct DNA-based diagnostic technique, loop-mediated isothermal amplification (LAMP) for a rapid detection of the presence of vanA gene, a critical component of the gene cluster required for vancomycin resistance. Amplification efficiency was optimal at 62°C and with 2mM MgSO4. The detection limit of the DNA template was 80pg and LAMP amplicons were detected within 40min; thereby suggesting a potential applicability of LAMP as a sensitive and urgent diagnostic method. Furthermore, positive LAMP reaction was directly detected with the naked-eye by monitoring the formation of a white precipitate or the color change induced by hydroxy naphthol blue (HNB) dye. Finally, 56 clinical isolates were successfully tested for the presence of vanA gene by LAMP, which was determined to be more sensitive than PCR. Together, our results clearly demonstrate the usefulness of LAMP for the diagnosis of VRE infection. PMID:24925601

  8. Development of a rapid, simple method for detecting Naegleria fowleri visually in water samples by loop-mediated isothermal amplification (LAMP).

    PubMed

    Mahittikorn, Aongart; Mori, Hirotake; Popruk, Supaluk; Roobthaisong, Amonrattana; Sutthikornchai, Chantira; Koompapong, Khuanchai; Siri, Sukhontha; Sukthana, Yaowalark; Nacapunchai, Duangporn

    2015-01-01

    Naegleria fowleri is the causative agent of the fatal disease primary amebic meningoencephalitis. Detection of N. fowleri using conventional culture and biochemical-based assays is time-consuming and laborious, while molecular techniques, such as PCR, require laboratory skills and expensive equipment. We developed and evaluated a novel loop-mediated isothermal amplification (LAMP) assay targeting the virulence-related gene for N. fowleri. Time to results is about 90 min and amplification products were easily detected visually using hydroxy naphthol blue. The LAMP was highly specific after testing against related microorganisms and able to detect one trophozoite, as determined with spiked water and cerebrospinal fluid samples. The assay was then evaluated with a set of 80 water samples collected during the flooding crisis in Thailand in 2011, and 30 natural water samples from border areas of northern, eastern, western, and southern Thailand. N. fowleri was detected in 13 and 10 samples using LAMP and PCR, respectively, with a Kappa coefficient of 0.855. To the best of our knowledge, this is the first report of a LAMP assay for N. fowleri. Due to its simplicity, speed, and high sensitivity, the LAMP method described here might be useful for quickly detecting and diagnosing N. fowleri in water and clinical samples, particularly in resource-poor settings. PMID:25822175

  9. Rapid and sensitive detection of Penaeus monodon nucleopolyhedrovirus (PemoNPV) by loop-mediated isothermal amplification combined with a lateral-flow dipstick.

    PubMed

    Nimitphak, Tongchai; Meemetta, Watcharachai; Arunrut, Narong; Senapin, Saengchan; Kiatpathomchai, Wansika

    2010-02-01

    Several methods such as traditional PCR or nested-PCR, immuno assay and histopathology have been developed for detection of Penaeus monodon nucleopolyhedrovirus (PemoNPV) formerly called monodon baculovirus (MBV). However, these methods have various disadvantages including low sensitivity, long assay time, use of toxic substances or unsuitability for field diagnosis. Loop-mediated isothermal amplification of target nucleotide sequences under isothermal conditions, combined with amplicon detection by chromatographic lateral-flow dipsticks allows for more efficient, field friendly detection within 75 min (not including DNA preparation time). In this study, the LAMP amplicon was biotinylated via an inner LAMP primer designed from a BamHI fragment B, a hypothetical protein gene of PemoNPV under isothermal condition at 63 degrees C for 1 h. Next, the LAMP product was hybridized at 63 degrees C for 5 min with an optimal FITC-labeled probe that was designed specifically for the LAMP amplicons. The FITC-labeled biotinylated LAMP product picked up gold-labeled, anti-FITC near the LFD origin and the whole, triple-labeled complex was captured by an immobilized biotin-binding protein to yield a red nano-gold stripe at the LFD test line. With a DNA template extracted from PemoNPV-infected shrimp, the LAMP-LFD detection limit was 0.1 pg, whereas one-step PCR and nested-PCR followed with gel electrophoresis was 1 pg. The LAMP-LFD method gave negative test results with buffer and DNA from shrimp infected with other common shrimp DNA viruses including, Penaeus monodon densovirus (PmDNV) formerly called hepatopancreatic parvovirus (HPV), white spot syndrome virus (WSSV) and Penaeus stylirostris densovirus (PstDNV) formerly called infectious hypodermal and hematopoietic necrosis virus (IHHNV). The test platform can be adapted easily for rapid detection of other shrimp viruses, since the LAMP-LFD combination system was a highly sensitive, specific, convenient, and does not require sophisticated instruments. PMID:19818396

  10. Highly sensitive fluorescence assay of DNA methyltransferase activity by methylation-sensitive cleavage-based primer generation exponential isothermal amplification-induced G-quadruplex formation.

    PubMed

    Xue, Qingwang; Lv, Yanqin; Xu, Shuling; Zhang, Yuanfu; Wang, Lei; Li, Rui; Yue, Qiaoli; Li, Haibo; Gu, Xiaohong; Zhang, Shuqiu; Liu, Jifeng

    2015-04-15

    Site-specific identification of DNA methylation and assay of MTase activity are imperative for determining specific cancer types, provide insights into the mechanism of gene repression, and develop novel drugs to treat methylation-related diseases. Herein, we developed a highly sensitive fluorescence assay of DNA methyltransferase by methylation-sensitive cleavage-based primer generation exponential isothermal amplification (PG-EXPA) coupled with supramolecular fluorescent Zinc(II)-protoporphyrin IX (ZnPPIX)/G-quadruplex. In the presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease Dpn I. The cleaved hairpin probe then functions as a signal primer to initiate the exponential isothermal amplification reaction (EXPAR) by hybridizing with a unimolecular DNA containing three functional domains as the amplification template, producing a large number of G-quadruplex nanostructures by utilizing polymerases and nicking enzymes as mechanical activators. The G-quadruplex nanostructures act as host for ZnPPIX that lead to supramolecular complexes ZnPPIX/G-quadruplex, which provides optical labels for amplified fluorescence detection of Dam MTase. While in the absence of Dam MTase, neither methylation/cleavage nor PG-EXPA reaction can be initiated and no fluorescence signal is observed. The proposed method exhibits a wide dynamic range from 0.0002 to 20U/mL and an extremely low detection limit of 8.6×10(-5)U/mL, which is superior to most conventional approaches for the MTase assay. Owing to the specific site recognition of MTase toward its substrate, the proposed sensing system was able to readily discriminate Dam MTase from other MTase such as M.SssI and even detect the target in a complex biological matrix. Furthermore, the application of the proposed sensing strategy for screening Dam MTase inhibitors was also demonstrated with satisfactory results. This novel method not only provides a promising platform for monitoring activity and inhibition of DNA MTases, but also shows great potentials in biological process researches, drugs discovery and clinical diagnostics. PMID:25506903

  11. Target-regulated proximity hybridization with three-way DNA junction for in situ enhanced electronic detection of marine biotoxin based on isothermal cycling signal amplification strategy.

    PubMed

    Liu, Bingqian; Chen, Jinfeng; Wei, Qiaohua; Zhang, Bing; Zhang, Lan; Tang, Dianping

    2015-07-15

    A new signal amplification strategy based on target-regulated DNA proximity hybridization (TRPH) reaction accompanying formation of three-way DNA junction was designed for electronic detection of Microcystin-LR (MC-LR used in this case), coupling with junction-induced isothermal cycling signal amplification. Initially, a sandwiched-type immunoreaction was carried out in a low-cost PCR tube between anti-MC-LR mAb1 antibody-labeled DNA1 (mAb1-DNA1) and anti-MC-LR mAb2-labeled DNA2 (mAb2-DNA2) in the presence of target to form a three-way DNA junction. Then, the junction could undergo an unbiased strand displacement reaction on an h-like DNA nanostructure-modified electrode (labeled with methylene blue redox tag on the short DNA strand), thereby resulting in the dissociation of methylene blue-labeled signal DNA from the electrode. The newly formed double-stranded DNA could be cleaved again by exonuclease III, and the released three-way DNA junction retriggered the strand-displacement reaction with h-like DNA nanostructures for junction recycling. During the strand-displacement reaction, numerous methylene blue-labeled DNA strands were far away from the electrode, thus decreasing the detectable electrochemical signal within the applied potentials. Under optimal conditions, the TRPH-based immunosensing system exhibited good electrochemical responses for detecting target MC-LR at a concentration as low as 1.0ngkg(-1) (1.0ppt). Additionally, the precision, reproducibility, specificity and method accuracy were also investigated with acceptable results. PMID:25747510

  12. A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model

    PubMed Central

    Fernández-Soto, Pedro; Gandasegui Arahuetes, Javier; Sánchez Hernández, Alicia; López Abán, Julio; Vicente Santiago, Belén; Muro, Antonio

    2014-01-01

    Background Human schistosomiasis, mainly due to Schistosoma mansoni species, is one of the most prevalent parasitic diseases worldwide. To overcome the drawbacks of classical parasitological and serological methods in detecting S. mansoni infections, especially in acute stage of the disease, development of cost-effective, simple and rapid molecular methods is still needed for the diagnosis of schistosomiasis. A promising approach is the loop-mediated isothermal amplification (LAMP) technology. Compared to PCR-based assays, LAMP has the advantages of reaction simplicity, rapidity, specificity, cost-effectiveness and higher amplification efficiency. Additionally, as results can be inspected by the naked eye, the technique has great potential for use in low-income countries. Methodology/Principal findings A sequence corresponding to a mitochondrial S. mansoni minisatellite DNA region was selected as a target for designing a LAMP-based method to detect S. mansoni DNA in stool samples. We used a S. mansoni murine model to obtain well defined stool and sera samples from infected mice with S. mansoni cercariae. Samples were taken weekly from week 0 to 8 post-infection and the Kato-Katz and ELISA techniques were used for monitoring the infection. Primer set designed were tested using a commercial reaction mixture for LAMP assay and an in house mixture to compare results. Specificity of LAMP was tested using 16 DNA samples from different parasites, including several Schistosoma species, and no cross-reactions were found. The detection limit of our LAMP assay (SmMIT-LAMP) was 1 fg of S. mansoni DNA. When testing stool samples from infected mice the SmMIT-LAMP detected S. mansoni DNA as soon as 1 week post-infection. Conclusions/Significance We have developed, for the first time, a cost-effective, easy to perform, specific and sensitive LAMP assay for early detection of S. mansoni in stool samples. The method is potentially and readily adaptable for field diagnosis and disease surveillance in schistosomiasis-endemic areas. PMID:25187956

  13. Ag(I)-coordinated hairpin DNA for homogenous electronic monitoring of hepatitis C virus accompanying isothermal cycling signal amplification strategy.

    PubMed

    Lu, Minghua; Xu, Linfang; Zhang, Xiaona; Xiao, Rui; Wang, Youmei

    2015-11-15

    This work designs a new homogenous electronic monitoring platform for sensitive detection of hepatitis C virus (HCV) on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay consists of target-induced Ag(+) dissociation from hairpin DNA and an isothermal circular strand-displacement polymerization (ICSDP) reaction. Upon target analyte introduction, HCV DNA initially hybridizes with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion, then the newly formed DNA duplex induces the ICSDP reaction with the aid of primer and polymerase, and then the displaced target DNA retriggers Ag(I)-coordinated hairpin DNA with target recycling, thereby resulting in formation of numerous free Ag(+) ions in the detection cell. The released Ag(+) ions can be readily captured by the negatively charged screen-printed carbon electrode, and subsequent anodic-stripping voltammetric detection of the captured Ag(+) ions are conducted to form the anodic current for the production of the electrochemical signal within the applied potential. Under optimal conditions, the ICSDP-based homogenous sensing system can be utilized for the detection of HCV DNA at a concentration as low as 2.3pM. Intra- and inter-assay coefficients of variation with identical batches are below 9.5% and 10.5%, respectively. The analysis in 5 clinical serum specimens shows good accordance between results obtained by the developed method and commercial Cobas® Amplicor HCV Test Analyzer. PMID:26071691

  14. Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification

    PubMed Central

    2013-01-01

    Background Tick-borne encephalitis virus (TBEV) is a causative agent of acute central nervous system disease in humans. It has three subtypes, far eastern (FE), Siberian (Sib) and European (Eu) subtypes, which are distributed over a wide area of Europe and Asia. The objective of this study was to develop a simple and rapid assay for the detection of TBEV RNA by using reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) method that can differentiate the three subtypes of TBEV and can be used for clinical diagnosis and epidemiological study. Methods Primers for TBEV-specific and subtype-specific RT-LAMP assay were designed to target the consensus sequence in NS1 of all subtypes and the consensus sequence in the E gene of each subtype, respectiveluy. In vitro transcribed RNA of Oshima strain that belongs to FE subtype was serially diluted and used to examine the sensitivity of the assay. Cross-reactivity of subtype-specific RT-LAMP assay was tested by using the RNA of Oshima and Sofjin (FE), IR-99 (Sib) and Hochosterwitz (Eu) strains. RNA extracted from the mixtures of TBEV and ticks, and of TBEV and human blood, and the mouse tissues infected with TBEV, were evaluated in the assay. Positive amplification was observed by real-time monitoring of turbidity and by visual detection of color change. Results The sensitivity of TBEV-specific RT-LAMP assay was 102 copies of target RNA per reaction volume. FE-specific RT-LAMP assay amplified viral genes of Oshima and Sofjin strains but not of IR-99 and Hochosterwitz strains, and of Japanese encephalitis virus. RT-LAMP assay for Sib and for Eu specifically amplified viral genes of IR-99 and Hochosterwitz strains, respectively. We also showed that tick or human blood extract did not inhibit the amplification of viral gene during the assay. Furthermore, we confirmed that the TBEV RT-LAMP could detect virus RNA from peripheral and central nervous system tissues of laboratory mice infected with TBEV. Conclusion TBEV RT-LAMP assay offers a sensitive, specific, rapid and easy-to-handle method for the detection of TBEV RNA in tick samples and this may be applied in the clinical samples collected from TBE-suspected patients. PMID:23452322

  15. Rapid detection of blaNDM, blaKPC, blaIMP, and blaVIM carbapenemase genes in bacteria by loop-mediated isothermal amplification.

    PubMed

    Cheng, Cancan; Zheng, Fen; Rui, Yongyu

    2014-12-01

    A loop-mediated isothermal amplification (LAMP) assay was developed and evaluated for rapid detection of blaKPC, blaNDM, blaIMP, and blaVIM carbapenemase genes. Six oligonucleotides, including outer, inner, and loop primers, were designed for eight distinct regions in each target gene. Two qualitative criteria were used to evaluate LAMP reactions: visual inspection of color change and real-time detection of fluorescence change. The lower detection limit was 10 colony forming units (CFU) per reaction for real-time detection and 100 CFU per reaction for visual inspection for each gene. Two hundred twenty-two carbapenem-resistant clinical isolates (including 100 Pseudomonas aeruginosa, 100 Acinetobacter sp., and 22 Enterobacteriaceae) were tested by LAMP assay. At the same time, these isolates were confirmed by conventional polymerase chain reaction (PCR) and sequencing analysis. In these clinical isolates, the results of 11 strains with blaNDM, 11 strains with blaKPC, 11 strains with blaVIM, and 2 strains with blaIMP obtained using LAMP assays were concordant with conventional PCR. The LAMP method reported here may be a useful and powerful tool for rapid detection of blaNDM, blaKPC, blaIMP, and blaVIM carbapenemase genes in bacteria. PMID:25000338

  16. Establishment of a novel one-step reverse transcription loop-mediated isothermal amplification assay for rapid identification of RNA from the severe fever with thrombocytopenia syndrome virus.

    PubMed

    Xu, Haihong; Zhang, Lei; Shen, Guangqiang; Feng, Cen; Wang, Xinying; Yan, Jie; Zhang, Yanjun

    2013-12-01

    As an emerging infectious disease, severe fever with thrombocytopenia syndrome virus (SFTSV) infection has been found in many areas of China. Suitable laboratory diagnostic method is urgently needed in clinical detections and epidemiological investigations. In this study, a modified, low-cost and rapid visualized one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of RNA from the SFTSV has been established. In order to avoid the risk of aerosol contamination and facilitate the naked eye to observe, a microcrystalline wax-dye capsule wrapping the highly sensitive DNA fluorescence dye SYBR Green I was added to the RT-LAMP reaction tube before the initiation of the assay. The detection limit of the established RT-LAMP assay was 10 fg template RNA per reaction mixture. The RT-LAMP assay was confirmed to be high specific to SFTSV, and no cross-reaction was found with the detection of the Chikungunya fever virus, Hemorrhagic Fever with Renal Syndrome virus (HFRSV), and Dengue fever virus. The assay was then applied for the detection of SFTSV RNA in 32 clinical serum samples and showed 94.4% consistence with the detection results of the real-time RT-PCR. The whole process, from sample preparation to result reporting, can be completed within 2h. This adapted, cost efficient and quick visualized RT-LAMP method is feasible for SFTSV field diagnosis in resource-limited field settings. PMID:23911296

  17. Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: tomato necrotic stunt virus.

    PubMed

    Li, Rugang; Ling, Kai-Shu

    2014-05-01

    Tomato necrotic stunt virus (ToNStV) is an emerging potyvirus that causes severe stunting to infected tomato plants. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for sensitive detection of ToNStV. The sensitivity of RT-LAMP was comparable to that of conventional RT-PCR, with detection of ToNStV in a reaction containing only 8 pg of total tomato RNA or with 1:20,000 dilution of crude tissue extract. This assay was able to detect ToNStV in a broad range of solanaceous plant species. The RT-LAMP for ToNStV was specific with no cross-reactivity to other potyviruses (i.e. Potato virus Y and Tobacco etch virus), as well as several other common tomato viruses. RT-LAMP should complement RT-PCR and real-time RT-PCR assays reported previously, with a potential to provide a simple, rapid, and sensitive field diagnostic method for ToNStV. PMID:24503040

  18. Highly Sensitive Detection of Malaria Parasitemia in a Malaria-Endemic Setting: Performance of a New Loop-Mediated Isothermal Amplification Kit in a Remote Clinic in Uganda

    PubMed Central

    Hopkins, Heidi; González, Iveth J.; Polley, Spencer D.; Angutoko, Patrick; Ategeka, John; Asiimwe, Caroline; Agaba, Bosco; Kyabayinze, Daniel J.; Sutherland, Colin J.; Perkins, Mark D.; Bell, David

    2013-01-01

    Background.?Current malaria diagnostic tests, including microscopy and antigen-detecting rapid tests, cannot reliably detect low-density infections. Molecular methods such as polymerase chain reaction (PCR) are highly sensitive but remain too complex for field deployment. A new commercial molecular assay based on loop-mediated isothermal amplification (LAMP) was assessed for field use. Methods.?Malaria LAMP (Eiken Chemical, Japan) was evaluated for samples from 272 outpatients at a rural Ugandan clinic and compared with expert microscopy, nested PCR, and quantitative PCR (qPCR). Two technicians performed the assay after 3 days of training, using 2 alternative blood sample–preparation methods and visual interpretation of results by fluorescence assay. Results.?Compared with 3-well nested PCR, the sensitivity of both LAMP and single-well nested PCR was 90%; the microscopy sensitivity was 51%. For samples with a Plasmodium falciparum qPCR titer of ?2 parasites/µL, LAMP sensitivity was 97.8% (95% confidence interval, 93.7%–99.5%). Most false-negative LAMP results involved samples with parasitemia levels detectable by 3-well nested PCR but very low or undetectable by qPCR. Conclusions.?Malaria LAMP in a remote Ugandan clinic achieved sensitivity similar to that of single-well nested PCR in a United Kingdom reference laboratory. LAMP dramatically lowers the detection threshold achievable in malaria-endemic settings, providing a new tool for diagnosis, surveillance, and screening in elimination strategies. PMID:23633405

  19. Rapid and simple detection of Japanese encephalitis virus by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick.

    PubMed

    Deng, Jieru; Pei, Jingjing; Gou, Hongchao; Ye, Zuodong; Liu, Cuicui; Chen, Jinding

    2015-03-01

    Japanese encephalitis virus (JEV) is a major cause of viral encephalitis in geographical areas, such as Asia and Western Pacific, where it is a threat to human and animal health. To control this disease, it is necessary to develop a rapid, simple, accurate method for diagnosis. In this study, a method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) coupled with a lateral flow dipstick (LFD) has been developed to detect JEV (JEV RT-LAMP-LFD). The entire assay can be completed within 70 min, and in this study, no false positive results were observed when other pathogens were tested, indicating that the assay is a highly specific method for the detection of JEV. Additionally, the sensitivity of the RT-LAMP-LFD assay for SA14-14-2 strain was 50 pg of RNA, which was similar to that of RT-PCR and RT-LAMP combined with gel electrophoresis, and was 10-fold more sensitive than RT-LAMP combined with calcein. The limit of detection for this assay was 5 pg of RNA. In addition, no false positive results were obtained with 14 serum samples. Our results indicate that this RT-LAMP-LFD assay will be of great value for JEV infection testing due to its rapid and highly specific and sensitive properties. PMID:25512133

  20. Detection and differentiation of Japanese encephalitis virus genotype I and genotype III by reverse transcription loop-mediated isothermal amplification combined with restriction fragment length polymorphism.

    PubMed

    Zhang, Liang; Cao, Sanjie; Wu, Rui; Zhu, Shuquan; Liu, Hanyang; Yuan, Lei; Shi, Shuangyan; Zhang, Dan; Huang, Xiaobo; Wen, Xintian; Wen, Yiping; Yan, Qigui; Huang, Yong; Ma, Xiaoping

    2015-04-01

    Japanese encephalitis (JE), which is a mosquito-borne arboviral infection, is the leading cause of viral encephalitis in Asian countries. The causative agent of JE is Japanese encephalitis virus (JEV), in which the predominant genotype has changed from genotype III (G III) to genotype I (G I). However, a method for the rapid differentiation between JEV G I and G III remains unavailable. This study aimed to establish a rapid JEV genotyping method using reverse transcription loop-mediated isothermal amplification (RT-LAMP). An Spe I site, which was located in the target sequence (C gene) of JEV G III strains but not in JEV G I strains, was selected as the RT-LAMP target. After testing 64 specimens, results showed that RT-LAMP can detect and differentiate JEV G I and G III specifically. Thus, a novel RT-LAMP system for the rapid detection and differentiation of JEV G I and G III was developed successfully. PMID:25537950

  1. Development and evaluation of a real-time reverse transcription-loop-mediated isothermal amplification assay for rapid detection of Rift Valley fever virus in clinical specimens.

    PubMed

    Le Roux, C A; Kubo, T; Grobbelaar, A A; van Vuren, P Jansen; Weyer, J; Nel, L H; Swanepoel, R; Morita, K; Paweska, J T

    2009-03-01

    This paper reports on the development and validation of a real-time reverse transcription-loop-mediated isothermal amplification assay (RT-LAMP) targeting the genomic large RNA segment of Rift Valley fever virus (RVFV). The set of six designed RT-LAMP primers identified strains of RVFV isolated in geographically distinct areas over a period of 50 years; there was no cross-reactivity with other genetically related and unrelated arboviruses. When testing serial sera and plasma from sheep experimentally infected with wild-type RVFV, there was 100% agreement between results of the RT-LAMP, a TaqMan-based real-time PCR, and virus isolation. Similarly, the assay had very high levels of diagnostic sensitivity and specificity when testing various clinical specimens from humans and animals naturally infected with the virus during recent outbreaks of the disease in Africa. The detection of specific viral genome targets in positive clinical specimens was achieved in less than 30 min. As a highly accurate, rapid, and very simple nucleic acid detection format, the RT-LAMP has the potential to be used in less-well-equipped laboratories in Africa and as a portable device during RVF outbreaks in remote areas, and it can be a valuable tool for the differential diagnosis of viral hemorrhagic fevers. PMID:19109471

  2. Development and Evaluation of a Real-Time Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Rift Valley Fever Virus in Clinical Specimens?

    PubMed Central

    Le Roux, C. A.; Kubo, T.; Grobbelaar, A. A.; van Vuren, P. Jansen; Weyer, J.; Nel, L. H.; Swanepoel, R.; Morita, K.; Paweska, J. T.

    2009-01-01

    This paper reports on the development and validation of a real-time reverse transcription-loop-mediated isothermal amplification assay (RT-LAMP) targeting the genomic large RNA segment of Rift Valley fever virus (RVFV). The set of six designed RT-LAMP primers identified strains of RVFV isolated in geographically distinct areas over a period of 50 years; there was no cross-reactivity with other genetically related and unrelated arboviruses. When testing serial sera and plasma from sheep experimentally infected with wild-type RVFV, there was 100% agreement between results of the RT-LAMP, a TaqMan-based real-time PCR, and virus isolation. Similarly, the assay had very high levels of diagnostic sensitivity and specificity when testing various clinical specimens from humans and animals naturally infected with the virus during recent outbreaks of the disease in Africa. The detection of specific viral genome targets in positive clinical specimens was achieved in less than 30 min. As a highly accurate, rapid, and very simple nucleic acid detection format, the RT-LAMP has the potential to be used in less-well-equipped laboratories in Africa and as a portable device during RVF outbreaks in remote areas, and it can be a valuable tool for the differential diagnosis of viral hemorrhagic fevers. PMID:19109471

  3. Development and evaluation of a loop-mediated isothermal amplification assay for the rapid detection of porcine cytomegalovirus under field conditions

    PubMed Central

    2012-01-01

    Background Porcine cytomegalovirus (PCMV) induces silent infection in adult pigs but more frequently causes fatal, generalized infection in newborn piglets. This study aimed to develop a new loop-mediated isothermal amplification (LAMP) method for the sensitive, rapid, and inexpensive detection of PCMV under field conditions. Methods Tissue obtained from nine-week-old PCMV-free Landrace pigs or pig samples from postmortem examinations were analyzed. The samples were found to have clinical signs and lesions consistent with inclusion body rhinitis. Six specific primers were designed by targeting the PCMV DNA polymerase (DPOL) DNA. The LAMP reaction was optimized in a water bath. The sensitivity and specificity of LAMP and polymerase chain reaction (PCR) were compared. Results PCMV DNA was amplified at 65°C, and the result could be detected as early as 30 min into the reaction. Positive reactions could be visualized by the naked eye as a color change brought on by the addition of SYBR Green. The sensitivity and specificity of LAMP were found to be similar to those of the PCR. Conclusions LAMP is a high-throughput technique for the detection of PCMV and has a high specificity, sensitivity and simplicity; these factors make it suitable for detection of PCMV under field conditions. PMID:23272902

  4. Visual Detection of Canine Parvovirus Based on Loop-Mediated Isothermal Amplification Combined with Enzyme-Linked Immunosorbent Assay and with Lateral Flow Dipstick

    PubMed Central

    SUN, Yu-Ling; YEN, Chon-Ho; TU, Ching-Fu

    2013-01-01

    ABSTRACT Loop-mediated isothermal amplification (LAMP) combined with enzyme-linked immunosorbent assay (LAMP–ELISA) and with lateral flow dipstick (LAMP–LFD) are rapid, sensitive and specific methods for the visual detection of clinical pathogens. In this study, LAMP–ELISA and LAMP–LFD were developed for the visual detection of canine parvovirus (CPV). For LAMP, a set of four primers (biotin-labeled forward inner primers) was designed to specifically amplify a region of the VP2 gene of CPV. The optimum time and temperature for LAMP were 60 min and 65°C, respectively. The specific capture oligonucleotide probes, biotin-labeled CPV probe for LAMP–ELISA and fluorescein isothiocyanate-labeled CPV probe for LAMP–LFD were also designed for hybridization with LAMP amplicons on streptavidin-coated wells and LFD strips, respectively. For the comparison of detection sensitivity, conventional PCR and LAMP for CPV detection were also performed. The CPV detection limits by PCR, PCR–ELISA, LAMP, LAMP–ELISA and LAMP–LFD were 102, 102, 10?1, 10?1 and 10?1 TCID50/ml, respectively. In tests using artificially contaminated dog fecal samples, the samples with CPV inoculation levels of ?1 TCID50/ml gave positive results by both LAMP–ELISA and LAMP–LFD. Our data indicated that both LAMP–ELISA and LAMP–LFD are promising as rapid, sensitive and specific methods for an efficient diagnosis of CPV infection. PMID:24334855

  5. A Loop-Mediated Isothermal Amplification (LAMP) Assay for Strongyloides stercoralis in Stool That Uses a Visual Detection Method with SYTO-82 Fluorescent Dye

    PubMed Central

    Watts, Matthew R.; James, Gregory; Sultana, Yasmin; Ginn, Andrew N.; Outhred, Alexander C.; Kong, Fanrong; Verweij, Jaco J.; Iredell, Jonathan R.; Chen, Sharon C-A.; Lee, Rogan

    2014-01-01

    An assay to detect Strongyloides stercoralis in stool specimens was developed using the loop-mediated isothermal amplification (LAMP) method. Primers were based on the 28S ribosomal subunit gene. The reaction conditions were optimized and SYTO-82 fluorescent dye was used to allow real-time and visual detection of the product. The product identity was confirmed with restriction enzyme digestion, cloning, and sequence analysis. The assay was specific when tested against DNA from bacteria, fungi and parasites, and 30 normal stool samples. Analytical sensitivity was to < 10 copies of target sequence in a plasmid and up to a 10-2 dilution of DNA extracted from a Strongyloides ratti larva spiked into stool. Sensitivity was increased when further dilutions were made in water, indicative of reduced reaction inhibition. Twenty-seven of 28 stool samples microscopy and polymerase chain reaction positive for S. stercoralis were positive with the LAMP method. On the basis of these findings, the assay warrants further clinical validation. PMID:24323513

  6. An Optimized Protocol for DNA Extraction from Wheat Seeds and Loop-Mediated Isothermal Amplification (LAMP) to Detect Fusarium graminearum Contamination of Wheat Grain

    PubMed Central

    Abd-Elsalam, Kamel; Bahkali, Ali; Moslem, Mohamed; Amin, Osama E.; Niessen, Ludwig

    2011-01-01

    A simple, rapid, and efficient method for isolating genomic DNA from germinated seeds of wheat that is free from polysaccharides and polyphenols is reported. DNA was extracted, treated with RNase, measured and tested for completeness using agarose gel electrophoresis. DNA purification from wheat grains yielded abundant, amplifiable DNA with yields typically between 100 and 200 ng DNA/mg. The effectiveness and reliability of the method was tested by assessing quantity and quality of the isolated DNA using three PCR-based markers. Inter-simple sequence repeats (ISSRs) were used to assess the genetic diversity between different wheat varieties. Specific PCR primer pair Tox5-1/Tox5-2 and a loop-mediated isothermal amplification (LAMP) procedure were used to detect genomic DNA of Fusarium graminearum in contaminated wheat seeds. In this method there is no need to use liquid nitrogen for crushing germinated seedlings. The protocol takes approximately one hour to prepare high quality DNA. In combination with the LAMP assay it is a fast and cost-effective alternative to traditional diagnostic methods for the early detection of toxigenic fusaria in cereals. PMID:21747688

  7. Visual Detection and Evaluation of Latent and Lytic Gene Expression during Epstein-Barr Virus Infection Using One-Step Reverse Transcription Loop-Mediated Isothermal Amplification

    PubMed Central

    Liu, Xiaoying; Tang, Jingfeng; Wang, Man; Ma, Qiang; Wang, Yefu

    2013-01-01

    Epstein-Barr virus (EBV)-associated disease exhibits distinct gene expression patterns characterized by the transcription of EBV nuclear antigen (EBNA) 1, EBNA2, latent membrane protein (LMP) 1, LMP2A, and BZLF1 (Zebra). A series of visual reverse transcript loop-mediated isothermal amplification (RT-LAMP) assays were performed to examine the expression of EBNA1, EBNA2, LMP1, LMP2A and BZLF1. The sensitivity of RT-LAMP for these transcripts was approximately equivalent to real-time RT-PCR (RT-qPCR), which was developed to quantify relative levels of EBV transcripts, and 10 to 100-fold more sensitive than conventional RT-PCR. Cross-reactions to other viruses were not observed upon examination of cell lines infected with herpes simplex viruses-1 and -2 (HSV-1 and -2), varicella zoster virus (VZV), human cytomegalovirus (HCMV) or Kaposi’s sarcoma-associated herpesvirus. When applied to 146 specimens, RT-LAMP exhibited high clinical sensitivity and specificity, with an excellent agreement (? > 0.92) compared to RT-qPCR. These assays are convenient for rapid early diagnosis and for surveillance of EBV-infected individuals by evaluating the EBV transcriptional profile, because the results can be visualized with the naked eye. These assays may be employed in further investigations because they can aid the design of improved therapeutic regimens and can be used specifically in resource-poor settings. PMID:24351866

  8. Visual detection of canine parvovirus based on loop-mediated isothermal amplification combined with enzyme-linked immunosorbent assay and with lateral flow dipstick.

    PubMed

    Sun, Yu-Ling; Yen, Chon-Ho; Tu, Ching-Fu

    2014-04-01

    Loop-mediated isothermal amplification (LAMP) combined with enzyme-linked immunosorbent assay (LAMP-ELISA) and with lateral flow dipstick (LAMP-LFD) are rapid, sensitive and specific methods for the visual detection of clinical pathogens. In this study, LAMP-ELISA and LAMP-LFD were developed for the visual detection of canine parvovirus (CPV). For LAMP, a set of four primers (biotin-labeled forward inner primers) was designed to specifically amplify a region of the VP2 gene of CPV. The optimum time and temperature for LAMP were 60 min and 65°C, respectively. The specific capture oligonucleotide probes, biotin-labeled CPV probe for LAMP-ELISA and fluorescein isothiocyanate-labeled CPV probe for LAMP-LFD were also designed for hybridization with LAMP amplicons on streptavidin-coated wells and LFD strips, respectively. For the comparison of detection sensitivity, conventional PCR and LAMP for CPV detection were also performed. The CPV detection limits by PCR, PCR-ELISA, LAMP, LAMP-ELISA and LAMP-LFD were 10(2), 10(2), 10(-1), 10(-1) and 10(-1) TCID50/ml, respectively. In tests using artificially contaminated dog fecal samples, the samples with CPV inoculation levels of ?1 TCID50/ml gave positive results by both LAMP-ELISA and LAMP-LFD. Our data indicated that both LAMP-ELISA and LAMP-LFD are promising as rapid, sensitive and specific methods for an efficient diagnosis of CPV infection. PMID:24334855

  9. Development of loop-mediated isothermal amplification and SYBR green real-time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species.

    PubMed

    Anthony Johnson, A M; Dasgupta, I; Sai Gopal, D V R

    2014-07-01

    Citrus yellow mosaic badnavirus (CMBV) is an important pathogen in southern India spread by infected citrus propagules. One of the measures to arrest the spread of CMBV is to develop methods to screen and certify citrus propagules as CMBV-free. The methods loop-mediated isothermal amplification (LAMP) and SYBR green real-time PCR (SGRTPCR) have been developed for the efficient detection of CMBV in citrus propagules. This paper compares the sensitivities of LAMP and SGRTPCR with polymerase chain reaction (PCR) for the detection of CMBV. Whereas PCR and LAMP were able to detect CMBV from a minimum of 10 ng of total DNA of infected leaf samples, SGRTPCR could detect the same from 1 ng of total DNA. Using SGRTPCR, the viral titres were estimated to be the highest in rough lemon and lowest in Nagpur Mandarin of the five naturally infected citrus species tested. The results will help in designing suitable strategies for the sensitive detection of CMBV from citrus propagules. PMID:24675064

  10. A loop-mediated isothermal amplification (LAMP) assay for Strongyloides stercoralis in stool that uses a visual detection method with SYTO-82 fluorescent dye.

    PubMed

    Watts, Matthew R; James, Gregory; Sultana, Yasmin; Ginn, Andrew N; Outhred, Alexander C; Kong, Fanrong; Verweij, Jaco J; Iredell, Jonathan R; Chen, Sharon C-A; Lee, Rogan

    2014-02-01

    An assay to detect Strongyloides stercoralis in stool specimens was developed using the loop-mediated isothermal amplification (LAMP) method. Primers were based on the 28S ribosomal subunit gene. The reaction conditions were optimized and SYTO-82 fluorescent dye was used to allow real-time and visual detection of the product. The product identity was confirmed with restriction enzyme digestion, cloning, and sequence analysis. The assay was specific when tested against DNA from bacteria, fungi and parasites, and 30 normal stool samples. Analytical sensitivity was to < 10 copies of target sequence in a plasmid and up to a 10(-2) dilution of DNA extracted from a Strongyloides ratti larva spiked into stool. Sensitivity was increased when further dilutions were made in water, indicative of reduced reaction inhibition. Twenty-seven of 28 stool samples microscopy and polymerase chain reaction positive for S. stercoralis were positive with the LAMP method. On the basis of these findings, the assay warrants further clinical validation. PMID:24323513

  11. Identification of human DNA in forensic evidence by loop-mediated isothermal amplification combined with a colorimetric gold nanoparticle hybridization probe.

    PubMed

    Watthanapanpituck, Khanistha; Kiatpathomchai, Wansika; Chu, Eric; Panvisavas, Nathinee

    2014-11-01

    A DNA test based on loop-mediated isothermal amplification (LAMP) and colorimetric gold nanoparticle (AuNP) hybridization probe to detect the presence of human DNA in forensic evidence was developed. The LAMP primer set targeted eight regions of the human cytochrome b, and its specificity was verified against the DNA of 11 animal species, which included animals closely related to humans, such as chimpanzee and orangutan. By using the AuNP probe, sequence-specific LAMP product could be detected and the test result could be visualized through the change in color. The limit of detection was demonstrated with reproducibility to be as low as 718 fg of genomic DNA, which is equivalent to approximately 100 plasmid DNA copies containing the cytochrome b DNA target region. A simple DNA extraction method for the commonly found forensic biological samples was also devised to streamline the test process. This LAMP-AuNP human DNA test showed to be a robust, specific, and cost-effective tool for the forensic identification of human specimens without requiring sophisticated laboratory instruments. PMID:24827529

  12. The Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Salmonella enterica serovar Typhi

    PubMed Central

    Fan, Fenxia; Du, Pengcheng; Kan, Biao; Yan, Meiying

    2015-01-01

    Typhoid fever remains a public health threat in many countries. A positive result in traditional culture is a gold-standard for typhoid diagnosis, but this method is time consuming and not sensitive enough for detection of samples containing a low copy number of the target organism. The availability of the loop-mediated isothermal amplification (LAMP) assay, which offers high speed and simplicity in detection of specific targets, has vastly improved the diagnosis of numerous infectious diseases. However, little research efforts have been made on utilizing this approach for diagnosis of Salmonella enterica serovar Typhi by targeting a single and specific gene. In this study, a LAMP assay for rapid detection of S. Typhi based on a novel marker gene, termed STY2879-LAMP, was established and evaluated with real-time PCR (RT-PCR). The specificity tests showed that STY2879 could be amplified in all S. Typhi strains isolated in different years and regions in China, whereas no amplification was observable in non-typhoidal strains covering 34 Salmonella serotypes and other pathogens causing febrile illness. The detection limit of STY2879-LAMP for S. Typhi was 15 copies/reaction in reference plasmids, 200 CFU/g with simple heat-treatment of DNA extracted from simulated stool samples and 20 CFU/ml with DNA extracted from simulated blood samples, which was 10 fold more sensitive than the parallel RT-PCR control experiment. Furthermore, the sensitivity of STY2879-LAMP and RT-PCR combining the traditional culture enrichment method for simulated stool and blood spiked with lower S. Typhi count during the 10 h enrichment time was also determined. In comparison with LAMP, the positive reaction time for RT-PCR required additional 2-3 h enrichment time for either simulated stool or blood specimens. Therefore, STY2879-LAMP is of practical value in the clinical settings and has a good potential for application in developing regions due to its easy-to-use protocol. PMID:25910059

  13. The Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Salmonella enterica serovar Typhi.

    PubMed

    Fan, Fenxia; Du, Pengcheng; Kan, Biao; Yan, Meiying

    2015-01-01

    Typhoid fever remains a public health threat in many countries. A positive result in traditional culture is a gold-standard for typhoid diagnosis, but this method is time consuming and not sensitive enough for detection of samples containing a low copy number of the target organism. The availability of the loop-mediated isothermal amplification (LAMP) assay, which offers high speed and simplicity in detection of specific targets, has vastly improved the diagnosis of numerous infectious diseases. However, little research efforts have been made on utilizing this approach for diagnosis of Salmonella enterica serovar Typhi by targeting a single and specific gene. In this study, a LAMP assay for rapid detection of S. Typhi based on a novel marker gene, termed STY2879-LAMP, was established and evaluated with real-time PCR (RT-PCR). The specificity tests showed that STY2879 could be amplified in all S. Typhi strains isolated in different years and regions in China, whereas no amplification was observable in non-typhoidal strains covering 34 Salmonella serotypes and other pathogens causing febrile illness. The detection limit of STY2879-LAMP for S. Typhi was 15 copies/reaction in reference plasmids, 200 CFU/g with simple heat-treatment of DNA extracted from simulated stool samples and 20 CFU/ml with DNA extracted from simulated blood samples, which was 10 fold more sensitive than the parallel RT-PCR control experiment. Furthermore, the sensitivity of STY2879-LAMP and RT-PCR combining the traditional culture enrichment method for simulated stool and blood spiked with lower S. Typhi count during the 10 h enrichment time was also determined. In comparison with LAMP, the positive reaction time for RT-PCR required additional 2-3 h enrichment time for either simulated stool or blood specimens. Therefore, STY2879-LAMP is of practical value in the clinical settings and has a good potential for application in developing regions due to its easy-to-use protocol. PMID:25910059

  14. Rapid, simple, and sensitive detection of the ompB gene of spotted fever group rickettsiae by loop-mediated isothermal amplification

    PubMed Central

    2012-01-01

    Background Spotted fever caused spotted fever group rickettsiae (SFGR) is prevalent throughout China. In this study, we describe a rapid, simple, and sensitive loop-mediated isothermal amplification (LAMP) assay targeting the ompB gene of spotted fever group rickettsiae ideal for application in China. The LAMP assay has the potential to detect spotted fever group rickettsiae early in infection and could therefore serve as an alternative to existing methods. Methods A set of universal primers which are specific 7 common species of spotted fever group rickettsiae in China were designed using PrimerExplorer V4 software based on conserved sequences of ompB gene. The sensitivity, specificity and reproducibility of the LAMP were evaluated. The LAMP assay for detecting SFGR was compared with conventional PCR assays for sensitivity and specificity in early phase blood samples obtained from 11 infected human subjects. Results The sensitivity of the LAMP assay was five copies per reaction (25 ?L total volume), and the assay did not detect false-positive amplification across 42 strains of 27 members of the order Rickettsiales and 17 common clinical pathogens. The LAMP assay was negative to typhus group rickettsiae including R. prowazekii and R. typhi for no available conserved sequences of ompB was obtained for designing primers. To evaluate the clinical applicability of the LAMP assay, a total of 11 clinical samples, 10 samples confirmed serologically (3 cases), ecologically (1 case), by real-time polymerase chain reaction (PCR; 2 cases), ecologically and by real-time PCR (1 case), and serologically and by real-time PCR (3 cases) were analyzed by the ompB LAMP assay. Data were validated using a previously established nested PCR protocol and real-time PCR. A positive LAMP result was obtained for 8 of the 10 confirmed cases (sensitivity, 73%; specificity, 100%), while none of these samples were positive by nested PCR (sensitivity, 0%; specificity, 100%). Conclusions The LAMP assay described here is the most reliable among the three methods tested and would be an ideal choice for development as a rapid and cost-effective means of detecting SFGR in China. PMID:23057497

  15. Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification.

    PubMed

    Zhang, Jinhai; Feng, Youjun; Hu, Dan; Lv, Heng; Zhu, Jing; Cao, Min; Zheng, Feng; Zhu, Jin; Gong, Xiufang; Hao, Lina; Srinivas, Swaminath; Ren, Hao; Qi, Zhongtian; Li, Bingjun; Wang, Changjun

    2013-11-01

    An epidemic of human H7N9 influenza virus infection recently emerged in China whose clinical features include high mortality and which has also resulted in serious economic loss. The novel reassortant avian-origin influenza A (H7N9) virus which was the causative agent of this epidemic raised the possibility of triggering a large-scale influenza pandemic worldwide. It seemed likely that fast molecular detection assays specific for this virus would be in great demand. Here, we report a one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of the hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 virus, the minimum detection limit of which was evaluated using in vitro RNA transcription templates. In total, 135 samples from clinical specimens (from either patients or poultry) were tested using this method in comparison with the real-time PCR recommended by the World Health Organization (WHO). Our results showed that (i) RT-LAMP-based trials can be completed in approximately 12 to 23 min and (ii) the detection limit for the H7 gene is around 10 copies per reaction, similar to that of the real-time PCR, whereas the detection limit for its counterpart the N9 gene is 5 copies per reaction, a 100-fold-higher sensitivity than the WHO-recommended method. Indeed, this excellent performance of our method was also validated by the results for a series of clinical specimens. Therefore, we believe that the simple, fast, and sensitive method of RT-LAMP might be widely applied for detection of H7N9 infections and may play a role in prevention of an influenza pandemic. PMID:24006004

  16. Validation of an apicoplast genome target for the detection of Plasmodium species using polymerase chain reaction and loop mediated isothermal amplification.

    PubMed

    Oriero, C E; van Geertruyden, J-P; Jacobs, J; D'Alessandro, U; Nwakanma, D

    2015-07-01

    The genome of the Plasmodium apicoplast, which has a higher copy number compared with current targets for molecular diagnosis of malaria, appears to be a suitable target for detection of submicroscopic infections that are capable of sustaining transmission. Novel primers targeting a conserved segment of the apicoplast (PFC10_AP|0010:rRNA) were designed and used in a number of different high throughput platforms such as single-step PCR (ssPCR), nested PCR (nPCR) and loop-mediated isothermal amplification (LAMP) for parasite detection. Replicates of ten-fold serial dilutions of Plasmodium falciparum 3D7 DNA, with equivalent parasite density ranges of 200 000 to 0.2 parasites/?L, were used to determine the limit of detection and repeatability of each assay. A panel of 184 archived DNA samples extracted from either EDTA whole blood or dried blood spots, from across West Africa and South East Asia was used to determine the diagnostic performance of the assays. All assays amplified the 2 parasites/?L dilution except the ssPCR, which amplified two of the three replicates. Using an 18S rRNA PCR as reference, the sensitivity was 98% (95% CI 93-100%) for the LAMP assay, 87% (95% CI 79-93%) for ssPCR and 100% (95% CI 97-100%) for nPCR. Specificity was 91% (95% CI 83-96%) for LAMP, 82% (95% CI 72-90%) for ssPCR and 66% (95% CI 54-76%) for nPCR. The apicoplast genome-based nPCR detected more positive samples overall than the reference method. Discrepant samples were confirmed as true positives using a probe-based real-time quantitative PCR assay. The results show that the apicoplast genome is a suitable target for molecular diagnosis of malaria. PMID:25747504

  17. Improvement of the quantitation method for the tdh (+) Vibrio parahaemolyticus in molluscan shellfish based on most-probable- number, immunomagnetic separation, and loop-mediated isothermal amplification.

    PubMed

    Escalante-Maldonado, Oscar; Kayali, Ahmad Y; Yamazaki, Wataru; Vuddhakul, Varaporn; Nakaguchi, Yoshitsugu; Nishibuchi, Mitsuaki

    2015-01-01

    Vibrio parahaemolyticus is a marine microorganism that can cause seafood-borne gastroenteritis in humans. The infection can be spread and has become a pandemic through the international trade of contaminated seafood. Strains carrying the tdh gene encoding the thermostable direct hemolysin (TDH) and/or the trh gene encoding the TDH-related hemolysin (TRH) are considered to be pathogenic with the former gene being the most frequently found in clinical strains. However, their distribution frequency in environmental isolates is below 1%. Thus, very sensitive methods are required for detection and quantitation of tdh (+) strains in seafood. We previously reported a method to detect and quantify tdh (+) V. parahaemolyticus in seafood. This method consists of three components: the most-probable-number (MPN), the immunomagnetic separation (IMS) targeting all established K antigens, and the loop-mediated isothermal amplification (LAMP) targeting the tdh gene. However, this method faces regional issues in tropical zones of the world. Technicians have difficulties in securing dependable reagents in high-temperature climates where we found MPN underestimation in samples having tdh (+) strains as well as other microorganisms present at high concentrations. In the present study, we solved the underestimation problem associated with the salt polymyxin broth enrichment for the MPN component and with the immunomagnetic bead-target association for the IMS component. We also improved the supply and maintenance of the dependable reagents by introducing a dried reagent system to the LAMP component. The modified method is specific, sensitive, quick and easy and applicable regardless of the concentrations of tdh (+) V. parahaemolyticus. Therefore, we conclude this modified method is useful in world tropical, sub-tropical, and temperate zones. PMID:25914681

  18. Loop-Mediated Isothermal Amplification for Rickettsia typhi (the Causal Agent of Murine Typhus): Problems with Diagnosis at the Limit of Detection

    PubMed Central

    Dittrich, Sabine; Castonguay-Vanier, Josée; Moore, Catrin E.; Thongyoo, Narongchai; Newton, Paul N.

    2014-01-01

    Murine typhus is a flea-borne disease of worldwide distribution caused by Rickettsia typhi. Although treatment with tetracycline antibiotics is effective, treatment is often misguided or delayed due to diagnostic difficulties. As the gold standard immunofluorescence assay is imperfect, we aimed to develop and evaluate a loop-mediated isothermal amplification (LAMP) assay. LAMP assays have the potential to fulfill the WHO ASSURED criteria (affordable, sensitive, specific, user friendly, robust and rapid, equipment free, deliverable to those who need them) for diagnostic methodologies, as they can detect pathogen-derived nucleic acid with low technical expenditure. The LAMP assay was developed using samples of bacterial isolates (n = 41), buffy coat specimens from R. typhi PCR-positive Lao patients (n = 42), and diverse negative controls (n = 47). The method was then evaluated prospectively using consecutive patients with suspected scrub typhus or murine typhus (n = 266). The limit of detection was ?40 DNA copies/LAMP reaction, with an analytical sensitivity of <10 DNA copies/reaction based on isolate dilutions. Despite these low cutoffs, the clinical sensitivity was disappointing, with 48% (95% confidence interval [95% CI], 32.5 to 62.7%) (specificity, 100% [95% CI, 100 to 100%]) in the developmental phase and 33% (95% CI, 9.2 to 56.8%) (specificity, 98.5% [95% CI, 97.0% to 100%]) in the prospective study. This low diagnostic accuracy was attributed to low patient R. typhi bacterial loads (median, 210 DNA copies/ml blood; interquartile range, 130 to 500). PCR-positive but LAMP-negative samples demonstrated significantly lower bacterial loads than LAMP-positive samples. Our findings highlight the diagnostic challenges for diseases with low pathogen burdens and emphasize the need to integrate pathogen biology with improved template production for assay development strategies. PMID:24371248

  19. Simple and rapid method for the detection of Filobasidiella neoformans in a probiotic dairy product by using loop-mediated isothermal amplification.

    PubMed

    Ishikawa, Hiroshi; Kasahara, Kohei; Sato, Sumie; Shimakawa, Yasuhisa; Watanabe, Koichi

    2014-05-16

    Yeast contamination is a serious problem in the food industry and a major cause of food spoilage. Several yeasts, such as Filobasidiella neoformans, which cause cryptococcosis in humans, are also opportunistic pathogens, so a simple and rapid method for monitoring yeast contamination in food is essential. Here, we developed a simple and rapid method that utilizes loop-mediated isothermal amplification (LAMP) for the detection of F. neoformans. A set of five specific LAMP primers was designed that targeted the 5.8S-26S rDNA internal transcribed spacer 2 region of F. neoformans, and the primer set's specificity was confirmed. In a pure culture of F. neoformans, the LAMP assay had a lower sensitivity threshold of 10(2)cells/mL at a runtime of 60min. In a probiotic dairy product artificially contaminated with F. neoformans, the LAMP assay also had a lower sensitivity threshold of 10(2)cells/mL, which was comparable to the sensitivity of a quantitative PCR (qPCR) assay. We also developed a simple two-step method for the extraction of DNA from a probiotic dairy product that can be performed within 15min. This method involves initial protease treatment of the test sample at 45°C for 3min followed by boiling at 100°C for 5min under alkaline conditions. In a probiotic dairy product artificially contaminated with F. neoformans, analysis by means of our novel DNA extraction method followed by LAMP with our specific primer set had a lower sensitivity threshold of 10(3)cells/mL at a runtime of 60min. In contrast, use of our novel method of DNA extraction followed by qPCR assay had a lower sensitivity threshold of only 10(5)cells/mL at a runtime of 3 to 4h. Therefore, unlike the PCR assay, our LAMP assay can be used to quickly evaluate yeast contamination and is sensitive even for crude samples containing bacteria or background impurities. Our study provides a powerful tool for the primary screening of large numbers of food samples for yeast contamination. PMID:24685682

  20. Novel multifunction-integrated molecular beacon for the amplification detection of DNA hybridization based on primer/template-free isothermal polymerization.

    PubMed

    Dong, Haiyan; Wu, Zai-Sheng; Xu, Jianguo; Ma, Ji; Zhang, Huijuan; Wang, Jie; Shen, Weiyu; Xie, Jingjing; Jia, Lee

    2015-10-15

    Molecular beacon (MB) is widely explored as a signaling probe in powerful biosensing systems, for example, enzyme-assisted strand displacement amplification (SDA)-based system. The existing polymerization-based amplification system is often composed of recognition element, primer, template and fluorescence reporter. To develop a new MB sensing system and simply the signal amplification design, we herein attempted to propose a multifunctional integrated MB (MI-MB) for the polymerization amplification detection of target DNA via introducing a G-rich fragment into the loop of MB without using any exogenous auxiliary oligonucleotide probe. Utilizing only one MI-MB probe, the p53 target gene could trigger the cycles of hybridization/polymerization/displacement, resulting in amplification of the target hybridization event. Thus, the p53 gene can be detected down to 5×10(-10)M with the linear response range from 5×10(-10)M to 4×10(-7)M. Using the MI-MB, we could readily discriminate the point mutation-contained p53 from the wild-type one. As a proof-of-concept study, owing to its simplicity and multifunction, including recognition, replication, amplification and signaling, the MI-MB exhibits the great potential for the development of different biosensors for various biomedical applications, especially, for early cancer diagnosis. PMID:25982726

  1. Development and Evaluation of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid and Real-Time Detection of the Swine-Origin Influenza A H1N1 Virus

    PubMed Central

    Parida, Manmohan; Shukla, Jyoti; Sharma, Shashi; Ranghia Santhosh, Sanna; Ravi, Vasanthapuram; Mani, Reeta; Thomas, Maria; Khare, Shashi; Rai, Arvind; Kant Ratho, Radha; Pujari, Sujit; Mishra, Bijayanti; Lakshmana Rao, Putcha Venkata; Vijayaraghavan, Rajagopalan

    2011-01-01

    The recent emergence of the swine-origin influenza A H1N1 virus (S-OIV) poses a serious global health threat. Rapid detection and differentiation of S-OIV from seasonal influenza is crucial for patient management and control of the epidemics. A one-step, single-tube accelerated and quantitative S-OIV-specific H1 reverse transcription loop-mediated isothermal amplification (RTLAMP) assay for clinical diagnosis of S-OIV by targeting the H1 gene is reported in this article. A comparative evaluation of the H1-specific RTLAMP assay vis-à-vis the World Health Organization-approved real-time polymerase chain reaction (RTPCR), involving 239 acute-phase throat swab samples, demonstrated exceptionally higher sensitivity by picking up all of the 116 H1N1-positive cases and 36 additional positive cases among the negatives that were sequence-confirmed as S-OIV H1N1. None of the real-time RTPCR-positive samples were missed by the RTLAMP system. The comparative analysis revealed that S-OIV RTLAMP was up to tenfold more sensitive than the World Health Organization real-time RTPCR; it had a detection limit of 0.1 tissue culture infectious dosage of 50/ml. One of the most attractive features of this isothermal gene amplification assay is that it seems to have an advantage in monitoring gene amplification by means of SYBR Green I dye-mediated naked-eye visualization within 30 minutes compared to 2 to 3 hours for a real-time reverse transcription polymerase chain reaction. This suggests that the RTLAMP assay is a valuable tool for rapid, real-time detection and quantification of S-OIV in acute-phase throat swab samples without requiring sophisticated equipment. PMID:21227400

  2. Comparison of loop-mediated isothermal amplification (LAMP) and nested-PCR assay targeting the RE and B1 gene for detection of Toxoplasma gondii in blood samples of children with leukaemia.

    PubMed

    Fallahi, Shirzad; Seyyed Tabaei, Seyyed Javad; Pournia, Yadollah; Zebardast, Nozhat; Kazemi, Bahram

    2014-07-01

    Toxoplasmosis diagnosis constitutes an important measure for disease prevention and control. In this paper, a newly described DNA amplification technique, loop-mediated isothermal amplification (LAMP), and nested-PCR targeting the repeated element (RE) and B1 gene, were compared to each other for the detection of Toxoplasma gondii DNA in blood samples of children with leukaemia. One hundred ten blood samples from these patients were analyzed by LAMP and nested-PCR. Out of 50 seropositive samples (IgM+, IgG+), positive results were obtained with 92% and 86% on RE, B1-LAMP and 82% and 68% on RE, B1-nested PCR analyses, respectively. Of the 50 seronegative samples, three, two and one samples were detected positive by RE-LAMP, B1-LAMP and RE-nested PCR assays, respectively, while none were detected positive by B1-nested PCR. None of the 10 IgM-, IgG+ samples was detected positive after testing LAMP and nested-PCR assays in duplicate. This is the first report of a study in which the LAMP method was applied with high sensitivity and efficacy for the diagnosis of T. gonii in blood samples of children with leukaemia. PMID:24792838

  3. Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. cubense tropical race 4 in soil.

    PubMed

    Zhang, Xin; Zhang, He; Pu, Jinji; Qi, Yanxiang; Yu, Qunfang; Xie, Yixian; Peng, Jun

    2013-01-01

    Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt (Panama disease), is one of the most devastating diseases of banana (Musa spp.). The Foc tropical race 4 (TR4) is currently known as a major concern in global banana production. No effective resistance is known in Musa to Foc, and no effective measures for controlling Foc once banana plants have been infected in place. Early and accurate detection of Foc TR4 is essential to protect banana industry and guide banana planting. A real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) was developed for the rapid and quantitative detection of Foc TR4 in soil. The detection limit of the RealAmp assay was approximately 0.4 pg/µl plasmid DNA when mixed with extracted soil DNA or 10(3) spores/g of artificial infested soil, and no cross-reaction with other relative pathogens were observed. The RealAmp assay for quantifying genomic DNA of TR4 was confirmed by testing both artificially and naturally infested samples. Quantification of the soil-borne pathogen DNA of Foc TR4 in naturally infested samples was no significant difference compared to classic real-time PCR (P>0.05). Additionally, RealAmp assay was visual with an improved closed-tube visual detection system by adding SYBR Green I fluorescent dye to the inside of the lid prior to amplification, which avoided the inhibitory effects of the stain on DNA amplification and makes the assay more convenient in the field and could thus become a simple, rapid and effective technique that has potential as an alternative tool for the detection and monitoring of Foc TR4 in field, which would be a routine DNA-based testing service for the soil-borne pathogen in South China. PMID:24376590

  4. Ultrasensitive fluorescence detection of nucleic acids using exonuclease III-induced cascade two-stage isothermal amplification-mediated zinc (II)-protoporphyrin IX/G-quadruplex supramolecular fluorescent nanotags.

    PubMed

    Xue, Qingwang; Lv, Yanqin; Zhang, Yuanfu; Xu, Shulin; Li, Rui; Yue, Qiaoli; Li, Haibo; Wang, Lei; Gu, Xiaohong; Zhang, Shuqiu; Liu, Jifeng

    2014-11-15

    A cascadic sensing system was developed for detection of DNA target at ultralow concentration by a combination of magnetic nanoparticles (MNPs) and exonuclease III (Exo III)-induced cascade two-stage isothermal amplification in the study. An ingeniously designed capture hairpin probe (CHP) that integrates target-binding and signal transduction sequences within one multifunctional design was assembled on MNPs. Upon sensing of the analyte nucleic acid, the hairpin probe on MNPs could be opened and stepwise removed by Exo III accompanied by the releasing of target DNA for the successive hybridization and cleavage process and the generation of bare signal transduction sequences of CHP as a new trigger for next circular reaction. The new DNA triggers initiate hybridizing with hairpin DNA probe that contains a partially "caged" G-quadruplex sequence (GHP), forming a duplex structure and liberating the active G-quadruplex structure. Then, Exo III digests the resulting duplex domain, leading to the recycling of new DNA trigger and simultaneously generating numerous ZnPPIX/G-quadruplex supramolecular complexes with the help of the zinc (II)-protoporphyrin IX (ZnPPIX), as an optical label for amplified fluorescence sensing event. Finally, numerous liberated cascade ZnPPIX/G-quadruplex supramolecular complexes give a remarkable fluorescence response. Because of two-stage autocatalytic recycling amplification and the specifically catalyzed formation of ZnPPIX/G-quadruplex supramolecular complexes, this newly designed protocol provides a high sensitivity with a detection limit of 0.75 fM, can discriminate mismatched DNA from perfectly matched target DNA, and gives low matrix effect due to using MNPs as the separation and amplification elements in the real samples. Therefore, it holds great potential for early diagnosis in gene-related diseases. PMID:24912035

  5. Comparison of Real-Time PCR, Reverse Transcriptase Real-Time PCR, Loop-Mediated Isothermal Amplification, and the FDA Conventional Microbiological Method for the Detection of Salmonella spp. in Produce ? †

    PubMed Central

    Zhang, Guodong; Brown, Eric W.; González-Escalona, Narjol

    2011-01-01

    Contamination of foods, especially produce, with Salmonella spp. is a major concern for public health. Several methods are available for the detection of Salmonella in produce, but their relative efficiency for detecting Salmonella in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of Salmonella in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with Salmonella serovars at two different levels (105 and <101 CFU/25 g of produce). The inoculated produce was assayed by the FDA Salmonella culture method (Bacteriological Analytical Manual) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of Salmonella cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live Salmonella cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of Salmonella spp. in six high-risk produce commodities. PMID:21803916

  6. Preliminary Validation of Direct Detection of Foot-And-Mouth Disease Virus within Clinical Samples Using Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Simple Lateral Flow Device for Detection

    PubMed Central

    Waters, Ryan A.; Fowler, Veronica L.; Armson, Bryony; Nelson, Noel; Gloster, John; Paton, David J.; King, Donald P.

    2014-01-01

    Rapid, field-based diagnostic assays are desirable tools for the control of foot-and-mouth disease (FMD). Current approaches involve either; 1) Detection of FMD virus (FMDV) with immuochromatographic antigen lateral flow devices (LFD), which have relatively low analytical sensitivity, or 2) portable RT-qPCR that has high analytical sensitivity but is expensive. Loop-mediated isothermal amplification (LAMP) may provide a platform upon which to develop field based assays without these drawbacks. The objective of this study was to modify an FMDV-specific reverse transcription–LAMP (RT-LAMP) assay to enable detection of dual-labelled LAMP products with an LFD, and to evaluate simple sample processing protocols without nucleic acid extraction. The limit of detection of this assay was demonstrated to be equivalent to that of a laboratory based real-time RT-qPCR assay and to have a 10,000 fold higher analytical sensitivity than the FMDV-specific antigen LFD currently used in the field. Importantly, this study demonstrated that FMDV RNA could be detected from epithelial suspensions without the need for prior RNA extraction, utilising a rudimentary heat source for amplification. Once optimised, this RT-LAMP-LFD protocol was able to detect multiple serotypes from field epithelial samples, in addition to detecting FMDV in the air surrounding infected cattle, pigs and sheep, including pre-clinical detection. This study describes the development and evaluation of an assay format, which may be used as a future basis for rapid and low cost detection of FMDV. In addition it provides providing “proof of concept” for the future use of LAMP assays to tackle other challenging diagnostic scenarios encompassing veterinary and human health. PMID:25165973

  7. The development of an accelerated reverse-transcription loop mediated isothermal amplification for the serotype specific detection of bluetongue virus 8 in clinical samples.

    PubMed

    Mulholland, Catherine; Hoffmann, Bernd; McMenamy, Michael J; Korthase, Christian; Earley, Bernadette; Markey, Bryan; Cassidy, Joseph P; McKillen, John; Allan, Gordon; Welsh, Michael D

    2014-06-01

    In 2006 bluetongue virus serotype 8 (BTV 8) was identified for the first time in the Netherlands causing a major epidemic in sheep and cattle that quickly spread to neighbouring Belgium, Germany and beyond to France and the UK. This resulted in severe animal health and welfare problems as well as substantial economic losses to the agrifood industries of these countries. Given that the early diagnosis of BTV infection 'in-the-field' is extremely useful to its subsequent management and control, this study was established to design a novel, sensitive and rapid nucleic acid diagnostic test for the serotype-specific detection of BTV 8, which could be used without the use of advanced laboratory support and equipment. Primers for the detection of BTV 8 were based on genome segment 2 of the virus, the VP2 gene. The assay was assessed using a full panel of BTV reference strains and clinical samples. Positive amplification was observed using a fluorescent detection reagent. The sensitivity of the RT-LAMP assay was 102 copies of RNA. The assay did not amplify the closely related orbivirus EHDV. This novel RT-LAMP offers a sensitive, specific and rapid method of detecting BTV 8. The approach is inexpensive and easy to use and could potentially be used in a 'pen-side' setting 'in the field' or by smaller less well-equipped laboratories in developing countries. PMID:24642243

  8. Development of an allele-specific, loop-mediated, isothermal amplification method (AS-LAMP) to detect the L1014F kdr-w mutation in Anopheles gambiae s. l.

    PubMed Central

    2012-01-01

    Background Malaria control relies heavily on treated bed nets and indoor residual spraying with pyrethroid insecticides. Unfortunately, the resistance to pyrethroid insecticides, mainly due to the kdr mutation, is spreading in the main malaria vector Anopheles gambiae s.l., decreasing the insecticides’ efficacy. To manage the insecticide resistance rapidly and flexibly, simple and effective tools for the early detection of resistant mosquitoes are needed. This study aimed to develop an allele-specific, loop-mediated, isothermal amplification (AS-LAMP) method to detect the West African-type kdr mutation (kdr-w; L1014F) in field-collected mosquitoes. Methods DNA fragments of the wild-type and the mutated kdr gene were used to select the primers and develop the method. The primers were designed with the mutation at the 5’ end of the backward inner primer (BIP). The AS-LAMP method was compared to the AS-PCR method using the genomic DNA of 120 field-collected mosquitoes. Results The AS-LAMP method could discriminate between the wild-type homozygote, the heterozygote, and the kdr-w homozygote within 75?min. The AS-LAMP method has the advantage of being faster and at least as sensitive and specific as the AS-PCR method. Conclusions The AS-LAMP method can be used to detect the kdr mutation for quick decision-making, even in less well-equipped laboratories. PMID:22770418

  9. Evaluation of commercial kit based on loop-mediated isothermal amplification for rapid detection of low levels of uninjured and injured salmonella on duck meat, bean sprouts, and fishballs in singapore.

    PubMed

    Lim, Hazel Sin Yue; Zheng, Qianwang; Miks-Krajnik, Marta; Turner, Matthew; Yuk, Hyun-Gyun

    2015-06-01

    The objective of this study was to evaluate performance of the commercial kit based on loop-mediated isothermal amplification (LAMP) in comparison with the International Organization for Standardization method for detecting uninjured and sublethally injured Salmonella cells artificially inoculated at levels of 10(0) and 10(1) CFU/25 g on raw duck wing, raw mung bean sprouts, and processed fishballs. Injured cells were prepared by a heat treatment for duck wings and fishball samples and a chlorine treatment for bean sprout samples. Additionally, a validation study was performed on naturally contaminated food samples sold in Singapore. A total of 110 samples of each commodity were analyzed in this study. Regardless of inoculum levels, the detection by the commercial LAMP kit showed 100% sensitivity and specificity for both inoculated and uninoculated samples compared with the International Organization for Standardization method, with the exception of bean sprout samples. Only 20% of bean sprout samples inoculated with 10(0) CFU/25 g injured Salmonella cells were positive by using the commercial LAMP-based kit. However, all negative samples became positive following a secondary enrichment in Rappaport-Vassiliadis medium with soy broth or after concentration by centrifugation. These results suggest that secondary enrichment or centrifugation should be considered as an additional step to increase the sensitivity of the commercial LAMP-based kit with low numbers of injured target cells in samples with high background microflora (such as mung bean sprouts). The validation study also showed that the commercial LAMP-based kit provided 91% sensitivity and 95% specificity for naturally contaminated samples. Thus, this study demonstrates that the commercial LAMP-based kit might be a cost-effective method, as this system could provide rapid, accurate detection of both uninjured and injured Salmonella cells on raw duck wings, raw mung bean sprouts, and processed fishballs in less than 26 h. PMID:26038914

  10. Comparison of conventional RT-PCR, reverse-transcription loop-mediated isothermal amplification, and SYBR green I-based real-time RT-PCR in the rapid detection of bovine viral diarrhea virus nucleotide in contaminated commercial bovine sera batches.

    PubMed

    Zhang, Shu-Qin; Tan, Bin; Li, Peng; Wang, Feng-Xue; Guo, Li; Yang, Yong; Sun, Na; Zhu, Hong-Wei; Wen, Yong-Jun; Cheng, Shi-Peng

    2014-10-01

    Bovine viral diarrhea virus (BVDV) can contaminate biological products produced in bovine or porcine cells or manufactured using bovine sera. A rapid, specific, sensitive, and practical method of detecting BVDV in bio-products is needed. The purpose of this study was to compare three assays with respect to their ability to accurately detect BVDV in biological samples, namely reverse-transcription loop-mediated isothermal amplification (RT-LAMP), SYBR green I-based real-time RT-PCR, and conventional RT-PCR. All assays detected BVDV nucleotide and differentiated between BVDV-free and -contaminated bovine sera successfully. In addition, the results were specific to BVDV: the amplification of samples containing the closely related classical swine fever virus or other pathogenic bovine viruses yielded negative results. The lowest detection threshold, 10(1) copies, was displayed by the SYBR green I-based real-time RT-PCR and RT-LAMP assay. This assay was also the most effective in the detection of BVDV contamination in a set of commercially available bovine sera. The field conditions suggest that RT-LAMP is specific and sensitive to detecting BVDV in biological samples and may be used for quality control of biomaterials. PMID:25019170

  11. General purpose adsorption isotherms

    Microsoft Academic Search

    David G. Kinniburgh

    1986-01-01

    The fitting of adsorption isotherm equations to experimental data is often an important aspect of data analysis. If the Langmuir and Freundlich isotherms are used, then consideration must be given to the proper weighting of the observations. Preferably nonlinear regression (nonlinear least squares) should be used since this enables these isotherms to be fitted directly and also enables other isotherms

  12. ORIGINAL ARTICLE Comparative genomics-guided loop-mediated isothermal

    E-print Network

    Hsiang, Tom

    ORIGINAL ARTICLE Comparative genomics-guided loop-mediated isothermal amplification sequencing and analytical techniques, genomic sequence data of prok- aryotes are accumulating at a very rapid pace. As of October 2008, there are 873 complete and pub- lished genome sequences, as well as 2025

  13. Nucleic acid amplification: Alternative methods of polymerase chain reaction

    PubMed Central

    Fakruddin, Md; Mannan, Khanjada Shahnewaj Bin; Chowdhury, Abhijit; Mazumdar, Reaz Mohammad; Hossain, Md. Nur; Islam, Sumaiya; Chowdhury, Md. Alimuddin

    2013-01-01

    Nucleic acid amplification is a valuable molecular tool not only in basic research but also in application oriented fields, such as clinical medicine development, infectious diseases diagnosis, gene cloning and industrial quality control. A comperehensive review of the literature on the principles, applications, challenges and prospects of different alternative methods of polymerase chain reaction (PCR) was performed. PCR was the first nucleic acid amplification method. With the advancement of research, a no of alternative nucleic acid amplification methods has been developed such as loop mediated isothermal amplification, nucleic acid sequence based amplification, strand displacement amplification, multiple displacement amplification. Most of the alternative methods are isothermal obviating the need for thermal cyclers. Though principles of most of the alternate methods are relatively complex than that of PCR, they offer better applicability and sensitivity in cases where PCR has limitations. Most of the alternate methods still have to prove themselves through extensive validation studies and are not available in commercial form; they pose the potentiality to be used as replacements of PCR. Continuous research is going on in different parts of the world to make these methods viable technically and economically. PMID:24302831

  14. CENTRIFUGAL LABTUBE FOR FULLY AUTOMATED DNA EXTRACTION & LAMP AMPLIFICATION BASED ON AN INTEGRATED, LOW-COST HEATING SYSTEM

    E-print Network

    Hoehl, Melanie Margarete

    In this paper, we introduce a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA-extraction platform (LabTube). We demonstrate fully automated, ...

  15. Relativistic Singular Isothermal Toroids

    NASA Astrophysics Data System (ADS)

    Cai, Mike J.; Shu, Frank H.

    2003-01-01

    We construct self-similar, axisymmetric, time-independent solutions to Einstein's field equations for an isothermal gas with a flat rotation curve in the equatorial plane. The metric scales as ds2-->?2ds2 under the transformation r-->?r and t-->?1-nt, where n is a dimensionless measure of the strength of the gravitational field. The solution space forms a two-parameter family characterized by the ratios of the isothermal sound speed and the equatorial rotation speed to the speed of light. The isodensity surfaces are toroids, empty of matter along the rotation axis. Unlike the Newtonian case, the velocity field is not constant on a cylindrical radius because of frame dragging. As the configuration rotates faster, an ergoregion develops in the form of the exterior of a cone centered about the rotation axis. The sequence of solutions terminates when frame dragging becomes infinite and the ergocone closes onto the axis. The fluid velocity of the last solution has a modest value in the midplane but reaches the speed of light on the axis.

  16. Generalized privacy amplification

    Microsoft Academic Search

    Charles H. Bennett; Gilles Brassard; Claude Crépeau; Ueli M. Maurer

    1995-01-01

    This paper provides a general treatment of pri- vacy amplification by public discussion, a concept introduced by Bennett, Brassard, and Robert for a special scenario. Privacy amplification is a process that allows two parties to distill a secret key from a common random variable about which an eavesdropper has partial information. The two parties generally know nothing about the eavesdropper's

  17. NASBA: A detection and amplification system uniquely suited for RNA

    SciTech Connect

    Sooknanan, R.; Malek, L.T. [Cangen, Ontario (Canada)] [Cangen, Ontario (Canada)

    1995-06-01

    The invention of PCR (polymerase chain reaction) has revolutionized our ability to amplify and manipulate a nucleic acid sequence in vitro. The commercial rewards of this revolution have driven the development of other nuclei acid amplification and detection methodologies. This has created an alphabet soup of technologies that use different amplification methods, including NASBA (nucleic acid sequence-based amplification), LCR (ligase chain reaction), SDA (strand displacement amplification), QBR (Q-beta replicase), CPR (cycling probe reaction), and bDNA (branched DNA). Despite the differences in their processes, these amplification systems can be separated into two broad categories based on how they achieve their goal: sequence-based amplification systems, such as PCR, NASBA, and SDA, amplify a target nucleic acid sequence. Signal-based amplification systems, such as LCR, QBR, CPR and bDNA, amplify or alter a signal from a detection reaction that is target-dependent. While the various methods have relative strengths and weaknesses, only NASBA offers the unique ability to homogeneously amplify an RNA analyte in the presence of homologous genomic DNA under isothermal conditions. Since the detection of RNA sequences almost invariably measures biological activity, it is an excellent prognostic indicator of activities as diverse as virus production, gene expression, and cell viability. The isothermal nature of the reaction makes NASBA especially suitable for large-scale manual screening. These features extend NASBA`s application range from research to commercial diagnostic applications. Field test kits are presently under development for human diagnostics as well as the burgeoning fields of food and environmental diagnostic testing. These developments suggest future integration of NASBA into robotic workstations for high-throughput screening as well. 17 refs., 1 tab.

  18. Cavity optoelectromechanical regenerative amplification

    E-print Network

    Taylor, Michael A; Knittel, Joachim; Lee, Kwan H; McRae, Terry G; Bowen, Warwick P

    2011-01-01

    Regenerative amplification is demonstrated in a cavity optoelectromechanical system using electrical gradient forces and optomechanical transduction. Mechanical linewidth narrowing to $6.6 \\pm 1.4$ mHz was observed at a frequency of 27.3 MHz, corresponding to an effective mechanical quality factor of $4 \\times 10^9$. A theoretical model of the system was formulated, showing that the delay in electrical feedback allows additional linewidth narrowing compared to purely optomechanical regenerative amplification. The linewidth was confirmed experimentally to scale inversely with the mechanical energy as predicted by the model.

  19. Limits to Amplification

    Microsoft Academic Search

    J. B. Johnson; F. B. Llewellyn

    1934-01-01

    The amplification obtainable in a vacuum tube amplifier is limited by the noise in the circuit. Of the various sources of noise the most fundamental and inevitable is thermal agitation of electricity. Other sources are the influence of ions and of shot effect and flicker effect on the current in vacuum tubes, poor contacts, mechanical vibration, and hum from a-c

  20. Isothermal-Gas-Transfer Program

    NASA Technical Reports Server (NTRS)

    Levine, Don I.

    1989-01-01

    Isothermal Gas Transfer program (GASXFER) solves variety of problems in which gas or gas mixture transferred between two containers. Special features of program include ease of entering data and ease of obtaining output. Program displays, prints, or graphs complete pressure history of each gas as function of time. Written in Lotus Symphony macrolanguage.

  1. Moisture adsorption isotherms for mushroom

    Microsoft Academic Search

    S Arora; J Ahmed; G. S. V Raghavan

    2004-01-01

    The moisture adsorption isotherms of Agaricus bisporus and Pleurotus florida mushrooms were determined at temperatures (30–70°C) typically found in drying and storage. The samples were equilibrated above saturated salt solutions. Equilibrium moisture content of mushroom decreased with an increase in temperature at constant water activity. The data was adjusted to 11 sorption models to ascertain the best fit. Comparisons were

  2. An isothermal micro-calorimeter

    Microsoft Academic Search

    J B Stott

    1956-01-01

    A calorimeter is described which, although nearly isothermal and independent of the specific heats of the materials employed, can still be used over a wide range of temperatures and makes use of a bank of thermocouples to measure the heat evolved. An attempt is made to obtain the maximum theoretical sensitivity by making most of the heat produced pass down

  3. Cavity optoelectromechanical regenerative amplification

    E-print Network

    Michael A. Taylor; Alex Szorkovszky; Joachim Knittel; Kwan H. Lee; Terry G. McRae; Warwick P. Bowen

    2012-06-29

    Cavity optoelectromechanical regenerative amplification is demonstrated. An optical cavity enhances mechanical transduction, allowing sensitive measurement even for heavy oscillators. A 27.3 MHz mechanical mode of a microtoroid was linewidth narrowed to 6.6\\pm1.4 mHz, 30 times smaller than previously achieved with radiation pressure driving in such a system. These results may have applications in areas such as ultrasensitive optomechanical mass spectroscopy.

  4. Stochastic amplification in epidemics.

    PubMed

    Alonso, David; McKane, Alan J; Pascual, Mercedes

    2007-06-22

    The role of stochasticity and its interplay with nonlinearity are central current issues in studies of the complex population patterns observed in nature, including the pronounced oscillations of wildlife and infectious diseases. The dynamics of childhood diseases have provided influential case studies to develop and test mathematical models with practical application to epidemiology, but are also of general relevance to the central question of whether simple nonlinear systems can explain and predict the complex temporal and spatial patterns observed in nature outside laboratory conditions. Here, we present a stochastic theory for the major dynamical transitions in epidemics from regular to irregular cycles, which relies on the discrete nature of disease transmission and low spatial coupling. The full spectrum of stochastic fluctuations is derived analytically to show how the amplification of noise varies across these transitions. The changes in noise amplification and coherence appear robust to seasonal forcing, questioning the role of seasonality and its interplay with deterministic components of epidemiological models. Childhood diseases are shown to fall into regions of parameter space of high noise amplification. This type of "endogenous" stochastic resonance may be relevant to population oscillations in nonlinear ecological systems in general. PMID:17251128

  5. Venus: an isothermal lower atmosphere?

    PubMed

    Gale, W; Liwshitz, M; Sinclair, A C

    1969-05-30

    Use of Earth-based microwave data in extrapolating the atmospheric profile of Venus below the region probed by Mariner V and Venera 4 reveals an isothermal layer at 670 degrees +/- 20 degrees K that extends to an altitude of 7 +/- 2 kilometers. This model gives a value of 6054.8 kilometers for the radius of Venus, and agreement with brightness spectrum, radar cross sections, and results of microwave interferometry. PMID:17796610

  6. Isotherms of cadmium sorption density

    SciTech Connect

    Schulte, A. [Mulawarman Univ., East Kalimantan (Indonesia); Beese, F. [Institut fuer Bodenoekologie/GSF, OberschleiBheim (Germany)

    1994-07-01

    To study Cd sorption, 16 soil samples of different chemical soil reactions were taken and analyzed for their physical and chemical properties. Adsorption of ethylene glycol monoethyl ether (EGME) and N{sub 2} were determined to establish the specific surface area of the soils. The sorption of Cd was modeled on a per-mass basis using the Langmuir and Freundlich equations as well as per-surface area basis. Traditional sorption isotherms reveal the relation between the amount of Cd sorbed and the Cd concentration in the soil solution only for the soil under study and can therefore not be applied, or can be applied only with restrictions, to other soils. To meet the aim of modeling Cd sorption and mobility for other soils or locations differing greatly in their properties, we attempted to establish a generalizing sorption isotherm for soils of entirely different composition of the solid phase. On the basis of characteristic values the 16 soil samples taken were grouped into three different reaction types (aluminum-hydroxide, silicate, and carbonate-buffer range). The generalizing Cd sorption density isotherms for these different soil groups introduced in the following provide a useful mathematical model for the quantity-intensity relation of Cd in soils that differ greatly in their specific surface area and their composition. 16 refs., 7 figs., 5 tabs.

  7. Coherent white light amplification

    DOEpatents

    Jovanovic, Igor; Barty, Christopher P.

    2004-05-25

    A system for coherent simultaneous amplification of a broad spectral range of light that includes an optical parametric amplifier and a source of a seed pulse is described. A first angular dispersive element is operatively connected to the source of a seed pulse. A first imaging telescope is operatively connected to the first angular dispersive element and operatively connected to the optical parametric amplifier. A source of a pump pulse is operatively connected to the optical parametric amplifier. A second imaging telescope is operatively connected to the optical parametric amplifier and a second angular dispersive element is operatively connected to the second imaging telescope.

  8. Highly sensitive detection of gene expression of an intronless gene: amplification of mRNA, but not genomic DNA by nucleic acid sequence based amplification (NASBA)

    Microsoft Academic Search

    Albert Heim; Isabella Maria Grumbach; Stefanie Zeuke; Bert Top

    1998-01-01

    NASBA is an isothermal nucleic acid amplification reaction that amplifies mRNA in a dsDNA background. Although similar to the sensitive reverse transcription\\/ polymerase chain reaction (RT-PCR) in mRNA detection, NASBA is not prone to give false positive results caused by genomic dsDNA. Therefore, NASBA is unique for sensitive detection of transcription of intronless genes, which preclude strategies such as intron

  9. Protein Amplification and Simple Purification

    E-print Network

    Lebendiker, Mario

    18-1142-75 Edition AA Protein Amplification and Simple Purification The Recombinant Protein Handbook #12;Antibody Purification Handbook 18-1037-46 The Recombinant Protein Handbook Protein Amplification and Simple Purification 18-1142-75 Protein Purification Handbook 18-1132-29 Ion Exchange

  10. Detection of Nucleic Acid Targets Using Ramified Rolling Circle DNA Amplification: A Single Nucleotide Polymorphism Assay Model

    PubMed Central

    Smith, James H.; Beals, Thomas P.

    2013-01-01

    Background Isothermal amplification methods provide alternatives to PCR that may be preferable for some nucleic acid target detection tasks. Among current isothermal target detection methods, ramified rolling circle amplification (RAM) of single-stranded DNA circles that are formed by ligation of linear DNA probes (C-probes or padlock probes) offers a unique target detection system by linked primers and a simple amplification system that is unconstrained by the target’s sequence context. Earlier implementations of RAM-based target detection were reported to be limited by background noise, due in part to unligated C-probe in the amplification reaction. We show here that a target-detection system using a biotinylated target-capture probe together with automated bead-handling reduces or eliminates background amplification noise. We demonstrate the system’s performance by detection of a single-nucleotide polymorphism in human genomic DNA. Methodology Target detection by RAM entails hybridization and ligation of a C-probe, followed by amplification and RAM signal detection. We evaluated RAM target detection in genomic DNA using recognition of a human Factor V gene single nucleotide polymorphism (G1691A) as a model. Locus-specific C-probes were annealed and ligated to genomic DNAs that represent the 3 possible genotypes at this locus, then ligated C-probes were amplified by real time RAM. The majority of the steps in the assay were performed with a magnetic bead-based chemistry on an automated platform. We show that the specificity of C-probe ligation permits accurate genotyping of this polymorphism. The assay as described here eliminates some of the background noise previously described for C-probe ligation, RAM amplification assays. Conclusion The methods and results presented here show that a combination of C-probe detection, automated sample processing, and isothermal RAM amplification provide a practical approach for detecting DNA targets in complex mixtures. PMID:23724122

  11. Quantitative characterization of adsorption isotherms using isothermal microcalorimetry.

    PubMed

    Pudipeddi, M; Sokoloski, T D; Duddu, S P; Carstensen, J T

    1996-04-01

    The integral heat of adsorption of water vapor on sodium benzoate samples was determined at various partial vapor pressures using a heat conduction microcalorimeter. An equation is presented to describe the calorimetric integral heat response (mJ/g of solid) as a function of relative humidity. This equation, although similar in principle to the well-known BET equation, relates the heat evolved (rather than volume or mass of gas adsorbed) upon adsorption to the partial pressure of the gas. It qualitatively describes the shape of the calorimetric isotherm and quantitatively allows the calculation of "monolayer capacity" or the apparent surface area with water as the adsorbate. The modified BET equation was applied to the calorimetric adsorption data available in the literature. The surface area or the monolayer coverage values of the solid samples used in these studies were calculated from data-fitted parameter estimates. Good agreement was found between Vm or surface area values obtained by the application of the model to the calorimetric data and those reported by the authors using conventional gravimetric or volumetric measurement of adsorption. The model satisfactorily described the experimental calorimetric data of water vapor adsorption on sodium benzoate. The model equation and the use of isothermal microcalorimetry provide a means to obtain the water adsorption surface area of solid materials. The method may also be useful in comparing the surface properties of drugs and excipients obtained by different methods or from different sources. The microcalorimetric method to characterize adsorption is more sensitive and convenient in comparison with some of the conventional techniques. PMID:8901073

  12. Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

    PubMed

    Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

    2015-02-01

    Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells. PMID:25579461

  13. Rapid identification of black grain eumycetoma causative agents using rolling circle amplification.

    PubMed

    Ahmed, Sarah A; van den Ende, Bert H G Gerrits; Fahal, Ahmed H; van de Sande, Wendy W J; de Hoog, G S

    2014-12-01

    Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling Circle Amplification (RCA) uses species-specific padlock probes and isothermal DNA amplification. The tests were based on ITS sequences and developed for Falciformispora senegalensis, F. tompkinsii, Madurella fahalii, M. mycetomatis, M. pseudomycetomatis, M. tropicana, Medicopsis romeroi, and Trematosphaeria grisea. With the isothermal RCA assay, 62 isolates were successfully identified with 100% specificity and no cross reactivity or false results. The main advantage of this technique is the low-cost, high specificity, and simplicity. In addition, it is highly reproducible and can be performed within a single day. PMID:25474355

  14. CARBON ADSORPTION ISOTHERMS FOR TOXIC ORGANICS

    EPA Science Inventory

    An experimental protocol for measuring the activated carbon adsorption isotherm was developed and applied to a wide range of organic compounds. Methods for treatment of the isotherm data and a standard format for presentation of results are shown. In the early phase of the study ...

  15. Isothermal Circumstellar Dust Shell Model for Teaching

    ERIC Educational Resources Information Center

    Robinson, G.; Towers, I. N.; Jovanoski, Z.

    2009-01-01

    We introduce a model of radiative transfer in circumstellar dust shells. By assuming that the shell is both isothermal and its thickness is small compared to its radius, the model is simple enough for students to grasp and yet still provides a quantitative description of the relevant physical features. The isothermal model can be used in a…

  16. Isothermal transitions of a thermosetting system

    NASA Technical Reports Server (NTRS)

    Gillham, J. K.; Benci, J. A.; Noshay, A.

    1974-01-01

    A study of the curing reactions of a cycloaliphatic epoxy resin/anhydride system by torsional braid analysis showed the existence of two critical isothermal temperatures - namely, the maximum glass transition temperature of the thermoset system and the glass transition temperature of the material at its gel point. Two rheologically active kinetic transitions occur during isothermal cure which correspond to gelation and vitrification. Three types of isothermal behavior occur. Methods for determining the time to gel and the time to vitrify, and also the two above-mentioned critical isothermal temperatures, have been developed. The time to gel obeyed the Arrhenius relationship, whereas the time to vitrify passed through a minimum. Application of these results to thermosetting systems in general is discussed in terms of the influence of molecular structure on the values of the critical isothermal temperatures.

  17. Characterization of Norovirus RNA replicase for in vitro amplification of RNA

    PubMed Central

    2013-01-01

    Background The isothermal amplification of RNA in vitro has been used for the study of in vitro evolution of RNA. Although Q? replicase has been traditionally used as an enzyme for this purpose, we planned to use norovirus replicase (NV3Dpol) due to its structural simplicity in the scope of in vitro autonomous evolution of the protein. Characteristics of the enzyme NV3Dpolin vitro were re-evaluated in this context. Results NV3Dpol, synthesized by using a cell-free translation system, represented the activities which were reported in the previous several studies and the reports were not fully consistent each other. The efficiency of the initiation of replication was dependent on the 3’-terminal structure of single-stranded RNA template, and especially, NV3Dpol preferred a self-priming small stem-loop. In the non-self-priming and primer-independent replication reaction, the presence of -CCC residues at the 3’-terminus increased the initiation efficiency and we demonstrated the one-pot isothermal RNA (even dsRNA) amplification by 16-fold. NV3Dpol also showed a weak activity of elongation-reaction from a long primer. Based on these results, we present a scheme of the primer-independent isothermal amplification of RNA with NV3Dpolin vitro. Conclusions NV3Dpol can be used as an RNA replicase in in vitro RNA?+?protein evolution with the RNA of special terminal sequences. PMID:24106810

  18. The Isothermal Dendritic Growth Experiment

    NASA Technical Reports Server (NTRS)

    Glicksman, M. E.; Koss, M. B.; Malarik, D. C.

    1998-01-01

    The growth of dendrites is one of the commonly observed forms of solidification encountered when metals and alloys freeze under low thermal gradients, as occurs in most casting and welding processes. In engineering alloys, the details of the dendritic morphology directly relates to important material responses and properties. Of more generic interest, dendritic growth is also an archetypical problem in morphogenesis, where a complex pattern evolves from simple starting conditions. Thus, the physical understanding and mathematical description of how dendritic patterns emerge during the growth process are of interest to both scientists and engineers. The Isothermal Dendritic Growth Experiment (IDGE) is a basic science experiment designed to measure, for a fundamental test of theory, the kinetics and morphology of dendritic growth without complications induced by gravity-driven convection. The IDGE, a collaboration between Rensselaer Polytechnic Institute, in Troy NY, and NASA's Lewis Research Center (LeRC) was developed over a ten year period from a ground-based research program into a space flight experiment. Important to the success of this flight experiment was provision of in situ near-real-time teleoperations during the spaceflight experiment.

  19. ISOFIT - A PROGRAM FOR FITTING SORPTION ISOTHERMS TO EXPERIMENTAL DATA

    EPA Science Inventory

    Isotherm expressions are important for describing the partitioning of contaminants in environmental systems. ISOFIT (ISOtherm FItting Tool) is a software program that fits isotherm parameters to experimental data via the minimization of a weighted sum of squared error (WSSE) obje...

  20. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for diagnosis of dengue

    PubMed Central

    Sahni, Ajay Kumar; Grover, Naveen; Sharma, Ajay; Khan, Inam Danish; Kishore, Jugal

    2012-01-01

    Background Dengue is an emerging public health problem causing serious morbidity and mortality in tropical developing countries. Early, sensitive and specific diagnosis is paramount for clinical decision making. Currently available diagnostic tests are limited in scope and utility. This study highlights applicability of RT-LAMP in dengue diagnosis. Methods 100 dengue confirmed cases, 100 dengue negative cases and 79 healthy negative controls from dengue epidemic between Sep 2009 to Jul 2011 were included. Dengue cases were profiled using WHO guidelines 2006, haematological and biochemical parameters evaluated and diagnosed using NS1 antigen, IgM and IgG enzyme immunoassay, RT-PCR and RT-LAMP. Positive cases were serotyped, genotyped and various tests were compared. Results Mean haematocrit, PT, PTT, platelet count, activated lymphocytes, serum fibrinogen, transaminases, bilirubin, lactate dehydrogenase, protein and sodium were significantly elevated in DHF/DSS as compared to DF. NS1 antigen, RT-PCR and RT-LAMP were sensitive during 1–3 days while ?-capture IgM EIA was specific after 5–7 days of initial infection. DEN-1 genotype III was predominant. Conclusion Deranged haematocrit and liver function tests are indicators of the severity of the disease. RT-LAMP is rapid, cost effective, highly sensitive and specific qualitative and quantitative technique which can detect dengue infection in both early and intermediary stages when NS1 antigen titres are not in the detectable range and the IgM antibody titres have just started to rise. Its superiority over existing techniques, amenability for automation and promising utility in low resource healthcare setups and field conditions raise it as the new gold standard for dengue diagnosis. PMID:24600118

  1. Development of Phage Immuno-Loop-Mediated Isothermal Amplification Assays for Organophosphorus Pesticides in Agro-

    E-print Network

    Hammock, Bruce D.

    Pesticides in Agro- products Xiude Hua,, Wei Yin,, Haiyan Shi,, Ming Li,, Yanru Wang,§ Hong Wang, Yonghao Ye of Plant Protection (State & Local Joint Engineering Research Center of Green Pesticide Invention-peptide phage library. One assay was used to screen eight organophosphorus (OP) pesticides with limits

  2. Rapid detection of porcine kobuvirus in feces by reverse transcription loop-mediated isothermal amplification

    PubMed Central

    2014-01-01

    Background PKV is a new emerging pathogen detected in diarrhea pigs. At present, no more detection methods were reported except RT-PCR method. this study was to develop a fast diagnostic method based on the LAMP reaction for rapid detection of PKV nucleic acid in fecal samples. Findings Two pairs of primers were designed to amplify the conservative 3D gene of PKV genome. The PKV RT-LAMP method possessed well specificity and had 100 times higher sensitivity than common reverse transcription PCR (RT-PCR), which could detect up to 10 RNA copies of the target gene. Conclusions The results showed that the optimal reaction condition for RT-LAMP was achieved at 64°C for 50 min. Furthermore, the RT-LAMP procedure does not demand special equipment and is time-saving. PMID:24755372

  3. Gibbs Adsorption Isotherm for Concentration as Variable

    NASA Astrophysics Data System (ADS)

    Zhang, Shimin

    Gibbs adsorption isotherm of the multicomponent system for concentration instead of chemical potential as independent variables is deduced and explained in a simple way. For the multicomponent system composed of ? and ? phases with plane interface, if the ? phase is a dilute solution, and component k is solvent as well as ck? << ck? , ci? << ci? , Gibbs adsorption isotherm of component i can be expressed as ? i(k) = -(ci? /RT)(? ? /? ci? )T,p,c_j^? (the dividing surface is placed where the adsorption of component k is zero). The adsorption of some components on the vapor-liquid interface of dilute solution with moderate or low pressure can meet the application condition of this adsorption isotherm. The adsorption of various components on the solid-liquid and liquid-liquid interface of dilute solution can also meet the application condition of this adsorption isotherm if various components of one phase are virtually insoluble in another phase.

  4. Isothermal compressibility in binary platinum based melts

    Microsoft Academic Search

    I G Kosnureva; M A Spiridonov; M M Mitko; V P Chentsov

    2008-01-01

    The method based on concentration dependences of density and formation heat values for determination of fluctuation structure factors and isothermal compressibility has been used for binary Pt-Si and Pt-Sn melts.

  5. Adsorption Isotherms and Surface Reaction Kinetics

    ERIC Educational Resources Information Center

    Lobo, L. S.; Bernardo, C. A.

    1974-01-01

    Explains an error that occurs in calculating the conditions for a maximum value of a rate expression for a bimolecular reaction. The rate expression is derived using the Langmuir adsorption isotherm to relate gas pressures and corresponding surface coverages. (GS)

  6. Rapid Detection of Mycobacterium tuberculosis by Recombinase Polymerase Amplification

    PubMed Central

    Teng Low, Hwee; Leader, Brandon Troy; Pérez-Osorio, Ailyn C.; Meyer, Jessica C.; O'Sullivan, Denise M.; Brooks, David G.; Piepenburg, Olaf; Forrest, Matthew S.

    2014-01-01

    Improved access to effective tests for diagnosing tuberculosis (TB) has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA) is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC) DNA in <20 minutes at 39°C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110) and 20 fg (IS1081)were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9) and 86.1% (95%CI: 78.1, 94.1) respectively (n?=?71). Specificities were 100% and 88.6% (95% CI: 80.8, 96.1) respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2) and 70.8% (95%CI: 62.9, 78.7) were obtained (n?=?90). Specificities were 95.4 (95% CI: 92.3,98.1) and 88% (95% CI: 83.6, 92.4) respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB assays could be of use for integration into a point-of-care test for use in resource constrained settings. PMID:25118698

  7. Optical chirped beam amplification and propagation

    DOEpatents

    Barty, Christopher P.

    2004-10-12

    A short pulse laser system uses dispersive optics in a chirped-beam amplification architecture to produce high peak power pulses and high peak intensities without the potential for intensity dependent damage to downstream optical components after amplification.

  8. Detection of piscine nodaviruses by real-time nucleic acid sequence based amplification (NASBA).

    PubMed

    Starkey, William G; Millar, Rose Mary; Jenkins, Mary E; Ireland, Jacqueline H; Muir, K Fiona; Richards, Randolph H

    2004-05-01

    Nucleic acid sequence based amplification (NASBA) is an isothermal nucleic acid amplification procedure based on target-specific primers and probes, and the co-ordinated activity of 3 enzymes: AMV reverse transcriptase, RNase H, and T7 RNA polymerase. We have developed a real-time NASBA procedure for detection of piscine nodaviruses, which have emerged as major pathogens of marine fish. Viral RNA was isolated by guanidine thiocyanate lysis followed by purification on silica particles. Primers were designed to target sequences in the nodavirus capsid protein gene, yielding an amplification product of 120 nucleotides. Amplification products were detected in real-time with a molecular beacon (FAM labelled/methyl-red quenched) that recognised an internal region of the target amplicon. Amplification and detection were performed at 41 degrees C for 90 min in a Corbett Research Rotorgene. Based on the detection of cell culture-derived nodavirus, and a synthetic RNA target, the real-time NASBA procedure was approximately 100-fold more sensitive than single-tube RT-PCR. When used to test a panel of 37 clinical samples (negative, n = 18; positive, n = 19), the real-time NASBA assay correctly identified all 18 negative and 19 positive samples. In comparison, the RT-PCR procedure identified all 18 negative samples, but only 16 of the positive samples. These results suggest that real-time NASBA may represent a sensitive and specific diagnostic procedure for piscine nodaviruses. PMID:15212274

  9. Modeling isothermal and non-isothermal flows in porous media

    NASA Astrophysics Data System (ADS)

    Mohseni Languri, Ehsan

    2011-12-01

    A complete understanding of the physics of flow and heat transfer phenomena in porous media is vital for accurate simulation of flow processes in industrial applications. In one such application pertaining to liquid composite molding (LCM) for manufacturing polymer composites, the fiber preforms used in LCM as reinforcements are limited not only to the single-scale porous media in the form of random fiber-mats, but also include dual-scale porous media in the form of woven or stitched fiber-mats. The conventional flow physics is not able to model the resin filling process in LCM involving the dual-scale porous media. In this study, the flow in dual-scale porous media is studied in order to predict the permeability of these fiber mats. The effect of aspect ratio of the fiber preform on the accuracy and flow during permeability estimation in single- and dual-scale porous media is analyzed experimentally and numerically. Flow of liquid in a free channel bounded on one side by porous medium is studied next, and two well-known boundary conditions of stress continuity and stress jump at the interface of the two regions are evaluated numerically. A point-wise solution for Stokes flow through periodic and non periodic porous media (made of cylindrical particles) adjacent to the free channel is presented using the Imite element based CFD software COMSOL. The efficacy of the two interfacial conditions is evaluated after volume averaging the point-wise velocity using a long averaging volume, also called the representative elementary volume or REV, and then comparing such a volume-averaged velocity profile with the available analytical solution. The investigation is carried out for five different porosities at three different Reynolds numbers to cover a wide range of applications. The presence of randomly-placed cylinders during the creation of non-periodic porous media damps out spatial fluctuations in the averaged velocity observed in periodic porous media. The analytical solutions obtained after applying the stress-continuity and stress-jump boundary conditions are found to work well at low porosities, which is in contradiction with the results achieved earlier by other researchers. The traditional approach of using averaged equations in the regions of sharp gradients in porous media to describe flow and transport is theoretically untenable and perhaps inaccurate. A novel ensemble averaging method is being proposed to test the accuracy of the volume averaged or smoothed description of flows in porous media in the regions of sharp gradients. In the new method, the flow in a certain arrangement of particles (called a realization) is averaged using a small unit cell, much smaller than the REV. Then such an averaged flow variable is further averaged over a whole gamut of randomly-generated particle realizations. First the accuracy of the ensemble averaging method was tested by comparing the permeability of an artificially generated porous medium obtained by the proposed method against the permeability predicted by some established theoretical models of permeability. The proposed method was found to be quite accurate. Later the ensemble average method was applied to the open-channel porous-medium interface region characterized by a sharp gradient in the flow velocities. It was discovered that the volume averaged description of such flows, characterized by the use of the Brinkman equation along with the stress-continuity and stress-jump conditions, is quite accurate for a range of Reynolds numbers. The non-isothermal transport during flow in porous media is examined next. The main focus in this area of research is the thermal dispersion term found in the heat transfer equation for single- and dual-scale porous media. Most of the previous efforts on modeling the heat transfer phenomena in porous media were devoted to isotropic porous media. However, for the anisotropic porous media widely in many industrial applications, not much research on the dispersion tensor is available. A new combined experimental/numerical approach to estimating

  10. Invited Commentary: Understanding Bias Amplification

    E-print Network

    California at Los Angeles, University of

    Invited Commentary: Understanding Bias Amplification Judea Pearl Cognitive Systems Laboratory the benefit of reducing con- founding bias carried by those covariates against the risk of amplify- ing residual bias carried by unmeasured confounders. The latter is characteristic of covariates that act like

  11. Isothermal and non-isothermal torrefaction characteristics and kinetics of microalga Scenedesmus obliquus CNW-N.

    PubMed

    Chen, Wei-Hsin; Wu, Zih-Ying; Chang, Jo-Shu

    2014-03-01

    Isothermal and non-isothermal torrefaction characteristics and kinetics of microalga Scenedesmus obliquus (S. obliquus) CNW-N are studied using thermogravimetric analysis. The pyrolysis of S. obliquus CNW-N with increasing temperature is characterized by four-stage decomposition. Depending on the torrefaction temperature, light, mild, and severe torrefaction from the weight loss and the maximum decomposition rate of the microalga can be classified. Under the same average temperature and torrefaction duration, non-isothermal torrefaction gives more severe pretreatment than the isothermal one. Increasing the heating rate of non-isothermal torrefaction also intensifies the pretreatment severity. Therefore, microalgae can be torrefied via non-isothermal torrefaction in a shorter time under the same pretreatment extent. The atomic H/C ratio in the microalga decreases with increasing torrefaction severity, whereas the atomic O/C ratio rises. The analysis suggests that the activation energy of isothermal torrefaction is 57.52×10(3)Jmol(-1), while it is between 40.14×10(3) and 88.41×10(3)Jmol(-1) for non-isothermal torrefaction. PMID:24457308

  12. High resolution argon adsorption isotherms for various zeolites

    Microsoft Academic Search

    K. Nakai; J. Sonoda; M. Yoshida; M. Hakuman; H. Naono

    2007-01-01

    Ar isotherms (87.3 K) and N2 isotherms (77.4 K) were measured for two silicas with different silanol content and two MFI zeolites with different alumina (proton) content. Silanols or protons give the significant effect on 2 isotherms, but has little influence on Ar isotherms. Ar isotherms for seven zeolites of various micropore size were measured in the pressure range of

  13. Isothermal solidification in a binary alloy melt

    NASA Technical Reports Server (NTRS)

    Laxmanan, V.

    1988-01-01

    A space shuttle experiment employing the General Purpose (Rocket) Furnace (GPF) in its isothermal mode of operation is manifested on MSL-3, circa 1989. The central aim of this experiment is to investigate the effect of reduced gravity levels on the segregation behavior in a slowly, and isothermally, cooled sample of a binary Pb-15 wt percent Sn alloy. This experiment would thus be able to simulate, in a small laboratory sample, about 20 mm dia 60 mm high and weighing about 150 grams, some aspects of the segregation phenomena occurring in large industrial ingots. Ground-based experiments conducted in the single-cavity simulator of the GPF, located at Marshall Space Flight Center (MSFC), in support of the microgravity experiment are described in detail. The results of the MSFC experiments are compared with other related experiments conducted at Case Western Reserve University (CWRU), wherein the isothermal constraints were relaxed.

  14. Linear nicking endonuclease-mediated strand displacement DNA amplification

    PubMed Central

    Joneja, Aric; Huang, Xiaohua

    2011-01-01

    We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

  15. Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

    PubMed Central

    Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

    2012-01-01

    A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer efficiency. Addition of thermostable RNase H resulted in the cleavage of the RNA loop which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9x above background), resulting in a ~2–2.8 fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time PCR reactions by measuring enhancement of donor fluorescence upon R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods. PMID:23000602

  16. Can adsorption isotherms predict sediment bioavailability?

    PubMed

    Lawrence, M A; Davies, N A; Edwards, P A; Taylor, M G; Simkiss, K

    2000-10-01

    The adsorption and desorption of 2,4-dichlorophenol (DCP) and pentachlorophenol (PCP) were studied for a range of synthetic particles, a dimethylditallowammonium exchanged clay and a natural sediment. The synthetic particles were Dowex 1X8400, Toyopearl Phenyl 650M and Toyopearl SP 650M. The bioaccumulation of the DCP and PCP from these particles was then studied using the oligochaete, Lumbriculus variegatus. There is a correlation between contaminant-particle interactions, as determined from adsorption and desorption isotherms, and bioaccumulation. Bioaccumulation by L. variegatus was found to be highest from the systems where differences in the classification of adsorption and desorption isotherms were observed. PMID:10879828

  17. Self-assembled DNA nanostructures prepared by rolling circle amplification for the delivery of siRNA conjugates.

    PubMed

    Hong, Cheol Am; Jang, Bora; Jeong, Eun Hye; Jeong, Hansaem; Lee, Hyukjin

    2014-11-01

    Inspired by the isothermal enzymatic process of rolling circle amplification (RCA) of DNA strands, we have developed a system to achieve more than a 200-fold increase in the synthesis of DNA nanostructures using a single-stranded circular DNA template. The amplified DNA nanostructures have shown efficient delivery of folic acid (FA) conjugated siRNAs into KB cells with a dose dependent gene silencing. PMID:24967959

  18. Frequency domain optical parametric amplification

    PubMed Central

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-01-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43?mJ two-cycle pulses at 1.8??m wavelength. PMID:24805968

  19. Hybrid chirped pulse amplification system

    DOEpatents

    Barty, Christopher P.; Jovanovic, Igor

    2005-03-29

    A hybrid chirped pulse amplification system wherein a short-pulse oscillator generates an oscillator pulse. The oscillator pulse is stretched to produce a stretched oscillator seed pulse. A pump laser generates a pump laser pulse. The stretched oscillator seed pulse and the pump laser pulse are directed into an optical parametric amplifier producing an optical parametric amplifier output amplified signal pulse and an optical parametric amplifier output unconverted pump pulse. The optical parametric amplifier output amplified signal pulse and the optical parametric amplifier output laser pulse are directed into a laser amplifier producing a laser amplifier output pulse. The laser amplifier output pulse is compressed to produce a recompressed hybrid chirped pulse amplification pulse.

  20. Apparatus to Measure Adiabatic and Isothermal Processes.

    ERIC Educational Resources Information Center

    Lamb, D. W.; White, G. M.

    1996-01-01

    Describes a simple manual apparatus designed to serve as an effective demonstration of the differences between isothermal and adiabatic processes for the general or elementary physics student. Enables students to verify Boyle's law for slow processes and identify the departure from this law for rapid processes and can also be used to give a clear…

  1. Perturbations of noise: Origins of isothermal flows

    Microsoft Academic Search

    Piotr Garbaczewski; M. Borna

    1999-01-01

    We perform a detailed analysis of both the phenomenological and analytic backgrounds for the ``Brownian recoil principle'' hypothesis [Phys. Rev. A 46, 4634 (1992)]. A corresponding theory of the isothermal Brownian motion of particle ensembles (Smoluchowski diffusion process approximation) takes into account the environmental recoil effects due to locally induced tiny heat flows. By means of local expectation values we

  2. Applications of Loop-Mediated Isothermal Amplificaton Methods (LAMP) for Identification and Diagnosis of Mycotic Diseases: Paracoccidioidomycosis and Ochroconis gallopava infection

    Microsoft Academic Search

    Ayako Sano; Eiko Nakagawa Itano

    \\u000a Loop-mediated isothermal amplification (LAMP) methods are now useful for the detection of a specific gene in infectious diseases,\\u000a genetic diseases, and\\/or genetic disorders in the large number of medical fields, and it was recently introduced to fungal\\u000a investigation. It is characterized by the use of four different primers specifically designed to recognize six distinct regions\\u000a of the target gene, and

  3. Rapid screening for human-pathogenic Mucorales using rolling circle amplification.

    PubMed

    Dolatabadi, S; Najafzadeh, M J; de Hoog, G S

    2014-12-01

    Mucormycosis has emerged as a relatively common severe mycosis in patients with haematological and allogeneic stem cell transplantation. Source of transmission is from unidentified sources in the environment. Early diagnosis of infection and its source of contamination are paramount for rapid and appropriate therapy. In this study, rolling circle amplification (RCA) is introduced as a sensitive, specific and reproducible isothermal DNA amplification technique for rapid molecular identification of six of the most virulent species (Rhizopus microsporus, R. arrhizus var. arrhizus, R. arrhizus var. delemar, Mucor irregularis, Mucor circinelloides, Lichtheimia ramosa, Lichtheimia corymbifera). DNAs of target species were successfully amplified, with no cross reactivity between species. RCA can be considered as a rapid detection method with high specificity and sensitivity, suitable for large screening. PMID:25187214

  4. Integrated microcapillary for sample-to-answer nucleic acid pretreatment, amplification, and detection.

    PubMed

    Zhang, Lu; Zhang, Yi; Wang, Chunyan; Feng, Qiang; Fan, Fei; Zhang, Guojun; Kang, Xixiong; Qin, Xuzhen; Sun, Jiashu; Li, Yinghui; Jiang, Xingyu

    2014-10-21

    This work develops an integrated microcapillary-based loop-mediated isothermal amplification (icLAMP) containing preloaded reagents and DNA extraction card, allowing for sample-to-answer screening of single nucleotide polymorphisms (SNPs) typing of the CYP2C19 gene from untreated blood samples with minimal user operation. With all reagents and the DNA extraction card preloaded inside the capillary, this icLAMP system can achieve on-site pretreatment, extraction, amplification, and detection of nucleic acids within 150 min, without the requirement for advanced instruments. As icLAMP technology carries many advantages such as disposability, easy operation, low cost, and reduced cross contamination and biohazard risks, we expect this system to have a great impact on point-of-care (POC) nucleic acid detection. PMID:25242282

  5. Development of a quantitative recombinase polymerase amplification assay with an internal positive control.

    PubMed

    Crannell, Zachary A; Rohrman, Brittany; Richards-Kortum, Rebecca

    2015-01-01

    It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest. PMID:25867513

  6. Adsorption-induced auto-amplification of enantiomeric excess on an achiral surface

    NASA Astrophysics Data System (ADS)

    Yun, Yongju; Gellman, Andrew J.

    2015-06-01

    The homochirality of biomolecules is a signature of life on Earth and has significant implications in, for example, the production of pharmaceutical compounds. It has been suggested that biomolecular homochirality may have arisen from the amplification of a spontaneously formed small enantiomeric excess (e.e.). Many minerals exhibit naturally chiral surfaces and so adsorption has been proposed as one possible mechanism for such an amplification of e.e. Here we show that when gas-phase mixtures of D- and L-aspartic acid are exposed to an achiral Cu(111) surface, a small e.e. in the gas phase, e.e.g, leads to an amplification of the e.e. on the surface, e.e.s, under equilibrium conditions. Adsorption-induced amplification of e.e. does not require a chiral surface. The dependence of e.e.s on e.e.g has been modelled successfully using a Langmuir-like adsorption isotherm that incorporates the formation of homochiral adsorbate clusters on the surface.

  7. Adsorption-induced auto-amplification of enantiomeric excess on an achiral surface.

    PubMed

    Yun, Yongju; Gellman, Andrew J

    2015-06-01

    The homochirality of biomolecules is a signature of life on Earth and has significant implications in, for example, the production of pharmaceutical compounds. It has been suggested that biomolecular homochirality may have arisen from the amplification of a spontaneously formed small enantiomeric excess (e.e.). Many minerals exhibit naturally chiral surfaces and so adsorption has been proposed as one possible mechanism for such an amplification of e.e. Here we show that when gas-phase mixtures of D- and L-aspartic acid are exposed to an achiral Cu(111) surface, a small e.e. in the gas phase, e.e.g, leads to an amplification of the e.e. on the surface, e.e.s, under equilibrium conditions. Adsorption-induced amplification of e.e. does not require a chiral surface. The dependence of e.e.s on e.e.g has been modelled successfully using a Langmuir-like adsorption isotherm that incorporates the formation of homochiral adsorbate clusters on the surface. PMID:25991532

  8. Self-lensing of a Singular Isothermal Sphere

    E-print Network

    Yun Wang

    2000-03-06

    Many astrophysical systems can be approximated as isothermal spheres. In an isothermal sphere, the ``foreground'' objects can act as lenses on ``background'' objects in the same distribution. We study gravitational lensing by a singular isothermal sphere analytically. Our results may have interesting applications.

  9. An evaluation of direct PCR amplification

    PubMed Central

    Hall, Daniel E.; Roy, Reena

    2014-01-01

    Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

  10. Dynamics and control of DNA sequence amplification

    SciTech Connect

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-10-28

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  11. Resonant Primordial Gravitational Waves Amplification

    E-print Network

    Lin, Chunshan

    2015-01-01

    We propose a mechanism to evade the Lyth bound in models of inflation. We minimally extend the conventional single-field inflation model in general relativity (GR) to a theory with non-vanishing graviton mass in the very early universe. The modification primarily affects the tensor perturbation, while the scalar and vector perturbations are the same as the ones in GR with a single scalar field at least at the level of linear perturbation theory. During the reheating stage, the graviton mass oscillates coherently and leads to resonant amplification of the primordial tensor perturbation. After reheating the graviton mass vanishes and we recover GR.

  12. Isothermal Equations of State of LLM-105

    NASA Astrophysics Data System (ADS)

    Gump, Jared C.; Stoltz, Chad A.; Freedman, Benjamin G.; Peiris, Suhithi M.

    2009-12-01

    2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is an energetic ingredient that has an impact sensitivity close to that of TATB, yet a calculated energy content close to HMX. Reported tests of formulated LLM-105 reveal that it is a good candidate for a new insensitive high-performance explosive. As use of LLM-105 increases, thermodynamic parameters and phase stability will need to be determined for accurate modeling. In order to accomplish this goal, isothermal equations of state of LLM-105 at static high-pressure and temperature were investigated using synchrotron angle-dispersive x-ray diffraction experiments. The samples were compressed and heated using diamond anvil cells. Pressure—volume data for LLM-105 at ambient temperature and 100° C were fit to the Birch-Murnaghan formalism to obtain isothermal equations of state. Temperature—volume data at ambient pressure were fit to obtain the volume thermal expansion coefficient.

  13. Isothermally heatsunk diffusion cloud chamber refrigerator

    SciTech Connect

    Menocal, S.G.

    1987-05-05

    This patent describes a diffusion cloud chamber isothermally heatsunk refrigerator which comprises: a heatsink consisting of two phases of a saturated substance existing in thermodynamic equilibrium at constant pressure and therefore at constant temperature, contained in a reservoir; a means of pressure damping to maintain constant pressure, as the ratio of the two phases present changes and introduces volumetric changes in the substance; a cooling member which transfer heat from vapor in contact with the cooling member surface to the ''cold side'' of a Peltier thermoelectric element with which the cooling member is in thermal contact; a Peltier thermoelectric element which removes the heat supplied by the cooling member from its ''cold side'' and pumps it to the ''hot side'' when driven by an electric current; and a means of transferring heat from the ''hot side'' of the Peltier thermoelectric element to the two-phase isothermal substance in the reservoir.

  14. Autocatalytic cure kinetics from isothermal DSC measurements

    SciTech Connect

    Keenan, M.R.

    1986-06-01

    Isothermal differential scanning calorimetry (DSC) can be used to characterize the cure kinetics of thermosetting polymers. Expressions relating autocatalytic rate law parameters to characteristic features of the DSC cure exotherm are developed. The simultaneous solution of these equations provides a simple method for estimating the rate law from isothermal DSC measurements. This technique does not require nonlinear least squares fitting, but rather, relies solely upon characteristics of the exotherm such as the peak reaction rate, time to the peak and extent of cure at the peak. The method is illustrated by obtaining the cure kinetics of an epoxy film adhesive (American Cyanamid FM 123-5) and a silicone encapsulating resin (Dow Corning Sylgard 184). The resulting rate laws are shown to describe the DSC exotherms in their entirety. The predictive ability of the rate law is also examined for the epoxy system and found to be good.

  15. On the Isothermality of Solar Plasmas

    NASA Technical Reports Server (NTRS)

    Landi, E.; Klimchuk, J. A.

    2010-01-01

    Recent measurements have shown that the quiet unstructured solar corona observed at the solar limb is close to isothermal, at a temperature that does not appear to change over wide areas or with time. Some in dividual active loop structures have also been found to be nearly iso thermal both along their axis and across their cross-section. Even a complex active region observed at the solar limb has been found to be composed of three distinct isothermal plasmas. If confirmed, these r esults would pose formidable challenges to the current theoretical understanding of the thermal structure and heating of the solar corona. For example, no current theoretical model can explain the excess dens ities and lifetimes of many observed loops if the loops are in fact i sothermal. All of these measurements are based on the so-called emiss ion measure (EM) diagnostic technique that is applied to a set of opt ically thin lines under the assumption of isothermal plasma. It provi des simultaneous measurement of both the temperature and EM. However, no study has ever been carried out to quantify the uncertainties in the technique and to rigorously assess its ability to discriminate bet ween isothermal and multithermal plasmas. Such a study is the topic o f the present work. We define a formal measure of the uncertainty in the EM diagnostic technique that can easily be applied to real data. We here apply it to synthetic data based on a variety of assumed plas ma thermal distributions, and develop a method to quantitatively asse ss the degree of multithermality of a plasma.

  16. On the nature of the origin of the isothermal and non-isothermal current released from dielectric materials

    Microsoft Academic Search

    Eugen R. Neagu; Rodica M. Neagu

    2001-01-01

    The mechanism of the isothermal and the non-isothermal current released from a polarized\\/charged dielectric material is analyzed and a model is presented to account for the experimental results, including the polarity reversal of the current. Isothermal discharging current and isothermal final discharging current experiments, for samples polarized\\/charged at constant current or constant voltage, have been carried out. At the same

  17. Trophic amplification of climate warming

    PubMed Central

    Kirby, Richard R.; Beaugrand, Gregory

    2009-01-01

    Ecosystems can alternate suddenly between contrasting persistent states due to internal processes or external drivers. It is important to understand the mechanisms by which these shifts occur, especially in exploited ecosystems. There have been several abrupt marine ecosystem shifts attributed either to fishing, recent climate change or a combination of these two drivers. We show that temperature has been an important driver of the trophodynamics of the North Sea, a heavily fished marine ecosystem, for nearly 50 years and that a recent pronounced change in temperature established a new ecosystem dynamic regime through a series of internal mechanisms. Using an end-to-end ecosystem approach that included primary producers, primary, secondary and tertiary consumers, and detritivores, we found that temperature modified the relationships among species through nonlinearities in the ecosystem involving ecological thresholds and trophic amplifications. Trophic amplification provides an alternative mechanism to positive feedback to drive an ecosystem towards a new dynamic regime, which in this case favours jellyfish in the plankton and decapods and detritivores in the benthos. Although overfishing is often held responsible for marine ecosystem degeneration, temperature can clearly bring about similar effects. Our results are relevant to ecosystem-based fisheries management (EBFM), seen as the way forward to manage exploited marine ecosystems. PMID:19740882

  18. Laser amplification of incoherent radiation

    NASA Technical Reports Server (NTRS)

    Menegozzi, L. N.; Lamb, W. E., Jr.

    1978-01-01

    The amplification of noise in a laser amplifier is treated theoretically. The model for the active medium and its description using density-matrix techniques, are taken from the theory of laser operation. The spectral behavior of the radiation in the nonlinear regime is studied and the formalism is written from the onset in the frequency domain. The statistics of the light are gradually modified by the nonlinear amplification process, and expressions are derived for the rate of change of fluctuations in intensity as a measure of statistical changes. In addition, the range of validity of Litvak's Gaussian-statistics approximation is discussed. In the homogeneous-broadening case, the evolution of initially broadband Gaussian radiation toward quasimonochromatic oscillations with laserlike statistics is explored in several numerical examples. The connections of this study with the time-domain work on self-pulsing in a ring-laser configuration, are established. Finally, spectral-narrowing and -rebroadening effects in Doppler-broadened media are discussed both analytically and with numerical examples. These examples show the distinct contribution of pulsations in the population ('Raman-type terms'), and saturation phenomena.

  19. Predicting anthocyanins' isothermal and non-isothermal degradation with the endpoints method.

    PubMed

    Peleg, Micha; Kim, Amy D; Normand, Mark D

    2015-11-15

    The thermal degradation of anthocyanins in a variety of media and over a large temperature range is known to follow first-order kinetics, and the temperature-dependence of the exponential rate constant a two-parameter model. These parameters can be estimated from the initial and final concentrations of only two isothermal or non-isothermal heat treatments by numerically solving a pair of simultaneous equations of which they are the two unknowns. Once calculated they can be used to reconstruct the entire degradation curves and predict those of other heat treatments in a pertinent temperature range. Commercial mathematical software can do the calculations, as demonstrated with computer simulations and published data on the isothermal and non-isothermal degradation of anthocyanins. The endpoints method's predictions were confirmed by comparison to the reported experimentally determined final concentrations. Where applicable, the method will eliminate the need to record sets of whole isothermal degradation curves in studies of the kinetics of anthocyanins' degradation. PMID:25977061

  20. fM to aM nucleic acid amplification for molecular diagnostics in a non-stick-coated metal microfluidic bioreactor.

    PubMed

    Huang, Guoliang; Huang, Qin; Ma, Li; Luo, Xianbo; Pang, Biao; Zhang, Zhixin; Wang, Ruliang; Zhang, Junqi; Li, Qi; Fu, Rongxin; Ye, Jiancheng

    2014-01-01

    A sensitive DNA isothermal amplification method for the detection of DNA at fM to aM concentrations for pathogen identification was developed using a non-stick-coated metal microfluidic bioreactor. A portable confocal optical detector was utilized to monitor the DNA amplification in micro- to nanoliter reaction assays in real-time, with fluorescence collection near the optical diffraction limit. The non-stick-coated metal microfluidic bioreactor, with a surface contact angle of 103°, was largely inert to bio-molecules, and DNA amplification could be performed in a minimum reaction volume of 40 nL. The isothermal nucleic acid amplification for Mycoplasma pneumoniae identification in the non-stick-coated microfluidic bioreactor could be performed at a minimum DNA template concentration of 1.3 aM, and a detection limit of three copies of genomic DNA was obtained. This microfluidic bioreactor offers a promising clinically relevant pathogen molecular diagnostic method via the amplification of targets from only a few copies of genomic DNA from a single bacterium. PMID:25475544

  1. Third Sound Amplification and Detailed Balance

    SciTech Connect

    Eddinger, J. D.; Ellis, F. M. [Department of Physics, Wesleyan University, Middletown, CT 06459 (United States)

    2006-09-07

    Condensation of atoms from the vapor into a third sound resonance is expected to be capable of acoustic amplification. This results from normal to superfluid conversion that coherently accommodates atoms into the third sound velocity field. Consideration of third sound in light of the equilibrium detailed balance between vapor particles and the superfluid film provides further evidence that acoustic amplification is attainable.

  2. Amplification, Technology, and Cochlear Implants for Infants.

    ERIC Educational Resources Information Center

    Adam, Arlie J.

    1993-01-01

    Early amplification is crucial to efficient habilitation and development of oral communication skills in hearing-impaired infants. Initial evaluation and fitting of amplification is a joint effort by the audiologist, therapist, and parents, whether the child uses traditional hearing aids or cochlear implants, and should be supplemented by a…

  3. Generalized Privacy Amplification Charles H. Bennett

    E-print Network

    Crépeau, Claude

    Generalized Privacy Amplification Charles H. Bennett IBM T. J. Watson Research Laboratory, Yorktown of privacy amplification by public discussion, a con­ cept introduced by Bennett, Brassard and Robert [1 g : f0; 1g n ! f0; 1g r such that Eve, de­ spite her partial knowledge about W and complete

  4. Generalized Privacy Amplification \\Lambda Charles H. Bennett

    E-print Network

    Crépeau, Claude

    Generalized Privacy Amplification \\Lambda Charles H. Bennett IBM Research y Gilles Brassard z of privacy amplification by public discussion, a concept introduced by Bennett, Brassard and Robert, Privacy am­ plification, Wire­tap channel, Secrecy capacity, R'enyi entropy, Universal hashing, Quantum

  5. The equivalence of isothermal and non-isothermal power law distributions with temperature duality

    NASA Astrophysics Data System (ADS)

    Zheng, Yahui; Du, Jiulin

    2015-06-01

    The concept of temperature duality states that the physical temperature and Lagrange temperature both have physical sense in the nonextensive system. By use of this concept, the isothermal power law distribution and the non-isothermal power law distribution are equivalent to each other when the detailed balance is satisfied. Also, the polytropic equation in stellar system and self-gravitating gaseous system can be deduced from both of these two distributions. This indicates that the polytropic system exhibits some 'equilibrium' configuration which, in the stellar system, is probably the result of so called 'violent relaxation'.

  6. Real-time duplex applications of loop-mediated AMPlification (LAMP) by assimilating probes.

    PubMed

    Kubota, Ryo; Jenkins, Daniel M

    2015-01-01

    Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for ?-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field. PMID:25741765

  7. Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP) by Assimilating Probes

    PubMed Central

    Kubota, Ryo; Jenkins, Daniel M.

    2015-01-01

    Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for ?-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field. PMID:25741765

  8. Isothermal adsorption kinetics on heterogeneous surfaces

    NASA Astrophysics Data System (ADS)

    Xia, Xinyu; Naumann d'Alnoncourt, Raoul; Strunk, Jennifer; Litvinov, Sergey; Muhler, Martin

    2007-04-01

    Adsorption kinetics on energetically heterogeneous surfaces under isothermal conditions is analyzed using the uniform energy distribution model. Considering the quasi-equilibrium of surface diffusion between the adsorption sites with different energy, the kinetic equations d?/dt=(kp-AK)(1-?) for first-order adsorption and d?/dt=kp(-AK?(1-?) for dissociative adsorption are obtained, where K is a coefficient describing the surface diffusion equilibrium, which depends on the coverage and the energy distribution. Under isochoric conditions with p decreasing due to adsorption, surface diffusion accelerates the rate towards equilibrium significantly, as observed in static calorimetric adsorption experiments. An approximate solution in Lagergren form is derived for this condition.

  9. Isothermal and non-isothermal viscoelastic flow of PTT fluid in lid-driven polar cavity

    NASA Astrophysics Data System (ADS)

    Mercan, Hatice; Atal?k, Kunt

    2012-12-01

    The isothermal and non-isothermal viscoelastic flow of Phan-Thien-Tanner (PTT) fluids is considered in liddriven polar cavity geometry, using a numerical solution method with parameter continuation technique. Thermoelastic effects, in terms of elastic/elongational effects and viscous dissipation, are demonstrated by the changes in vortical structure, temperature/stress distributions and heat transfer characteristics in the curved cavity. Central vortex/maximum temperature location shifts are observed under elastic and elongational (strain hardening and strain softening/shear thinning) effects for isothermal and non-isothermal conditions. The growth in size and strength of a secondary vortex is denoted in the downstream stationary corner of the cavity for the viscoelastic fluid under strain hardening, which also introduces an increase in stress gradients. Viscous heating is observed with elongational effects near the central vortex in the cavity. Stress components and their gradients decrease under viscous dissipation. The changes in temperature field and heat transfer properties in the cavity are revealed.

  10. Pressure-composition-isotherms of palladium alloys

    SciTech Connect

    Flanagan, T.B.

    1996-11-01

    About one year ago a summary report was submitted covering the previous three years of the contract. This earlier report should be consulted as a useful survey and evaluation of the research carried out by the authors. Because of difficulties during the current contract period arising from the anomalous nature of the melt-spun alloys received from LANL, it is not possible to contribute much beyond that given in last year's summary with regard to the overall picture of the behavior of Pd-rich alloys towards hydrogen and its isotopes. In this contract year deuterium was employed instead of hydrogen and instead of using cycled alloys, the alloys employed for each isotherm measurement were in their virgin condition. Because of the anomalous behavior of the melt-spun alloys, it was not feasible or worthwhile in some cases, e.g., when the alloy behaved anomalously, to carry out all of the originally proposed work. Nonetheless considering these obstacles, some useful data were obtained. For example, the obtaining of deuterium isotherms for the Pd-Rh alloys down to {minus}40 C using internally oxidized melt-spun alloys may prove to be useful.

  11. Development of Real-Time Multiplex Nucleic Acid Sequence-Based Amplification for Detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella spp. in Respiratory Specimens

    Microsoft Academic Search

    K. Loens; T. Beck; D. Ursi; M. Overdijk; P. Sillekens; H. Goossens; M. Ieven

    2008-01-01

    Received 27 February 2007\\/Returned for modification 21 June 2007\\/Accepted 5 November 2007 Real-time multiplex isothermal nucleic acid sequence-based amplification (NASBA) was developed to detect Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella spp. in respiratory specimens using the NucliSens Basic Kit (bioMerieux, Boxtel, The Netherlands). Oligonucleotide primers were derived from the M. pneumoniae, C. pneumoniae, and Legionella pneumophila 16S rRNA. For real-time

  12. A netlike rolling circle nucleic acid amplification technique.

    PubMed

    Zhu, Xiaoli; Feng, Chang; Zhang, Bin; Tong, Hui; Gao, Tao; Li, Genxi

    2015-01-01

    A nucleic acid amplification technique termed as netlike rolling circle amplification is proposed by introducing a nicking enzyme into the existing hyperbranched rolling circle amplification system. Surprisingly dense and uniform network morphology is observed; and cubic amplification is achieved for the sensitive detection of a sequence from HIV. PMID:25407326

  13. Circle-to-circle amplification on a digital microfluidic chip for amplified single molecule detection.

    PubMed

    Kühnemund, Malte; Witters, Daan; Nilsson, Mats; Lammertyn, Jeroen

    2014-08-21

    We demonstrate a novel digital microfluidic nucleic acid amplification concept which is based on padlock probe mediated DNA detection and isothermal circle-to-circle amplification (C2CA). This assay platform combines two digital approaches. First, digital microfluidic manipulation of droplets which serve as micro-reaction chambers and shuttling magnetic particles between these droplets facilitates the integration of complex solid phase multistep assays. We demonstrate an optimized novel particle extraction and transfer protocol for superparamagnetic particles on a digital microfluidic chip that allows for nearly 100% extraction efficiencies securing high assay performance. Second, the compartmentalization required for digital single molecule detection is solved by simple molecular biological means, circumventing the need for complex microfabrication procedures necessary for most, if not all, other digital nucleic acid detection methods. For that purpose, padlock probes are circularized in a strictly target dependent ligation reaction and amplified through two rounds of rolling circle amplification, including an intermediate digestion step. The reaction results in hundreds of 500 nm sized individually countable DNA nanospheres per detected target molecule. We demonstrate that integrated miniaturized digital microfluidic C2CA results in equally high numbers of C2CA products ?L(-1) as off-chip tube control experiments indicating high assay performance without signal loss. As low as 1 aM synthetic Pseudomonas aeruginosa DNA was detected with a linear dynamic range over 4 orders of magnitude up to 10 fM proving excellent suitability for infectious disease diagnostics. PMID:24934991

  14. The spatial pattern of cochlear amplification.

    PubMed

    Fisher, Jonathan A N; Nin, Fumiaki; Reichenbach, Tobias; Uthaiah, Revathy C; Hudspeth, A J

    2012-12-01

    Sensorineural hearing loss, which stems primarily from the failure of mechanosensory hair cells, changes the traveling waves that transmit acoustic signals along the cochlea. However, the connection between cochlear mechanics and the amplificatory function of hair cells remains unclear. Using an optical technique that permits the targeted inactivation of prestin, a protein of outer hair cells that generates forces on the basilar membrane, we demonstrate that these forces interact locally with cochlear traveling waves to achieve enormous mechanical amplification. By perturbing amplification in narrow segments of the basilar membrane, we further show that a cochlear traveling wave accumulates gain as it approaches its peak. Analysis of these results indicates that cochlear amplification produces negative damping that counters the viscous drag impeding traveling waves; targeted photoinactivation locally interrupts this compensation. These results reveal the locus of amplification in cochlear traveling waves and connect the characteristics of normal hearing to molecular forces. PMID:23217746

  15. Preferential Amplification of Pathogenic Sequences.

    PubMed

    Ge, Fang; Parker, Jayme; Chul Choi, Sang; Layer, Mark; Ross, Katherine; Jilly, Bernard; Chen, Jack

    2015-01-01

    The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called "Preferential Amplification of Pathogenic Sequences (PATHseq)" that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9-, and 10-mer oligonucleotides called "non-human primers" that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens. PMID:26067233

  16. Preferential Amplification of Pathogenic Sequences

    PubMed Central

    Ge, Fang; Parker, Jayme; Chul Choi, Sang; Layer, Mark; Ross, Katherine; Jilly, Bernard; Chen, Jack

    2015-01-01

    The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called “Preferential Amplification of Pathogenic Sequences (PATHseq)” that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9-, and 10-mer oligonucleotides called “non-human primers” that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens. PMID:26067233

  17. Advanced backward Raman amplification seeding

    NASA Astrophysics Data System (ADS)

    Malkin, Vladimir; Fisch, Nathaniel

    2010-11-01

    Next generations of ultrapowerful laser pulses, reaching exawatt and zetawatt powers within reasonably compact facilities, might be based on the backward Raman amplification (BRA) in plasmas. Amplified pulse intensities hundreds times higher than the pump intensity are already observed experimentally. More advanced BRA stages should produce even higher intensities. The largest nonfocused intensity, limited primarily by instabilities associated with the relativistic electron nonlinearity of the amplified laser pulse, is, roughly speaking, 0.1 of the fully relativistic value. It corresponds to the amplified pulse final (and shortest) duration be about the electron plasma wave period. The needed seed pulse should be at least that short then to stay ahead of the amplified pulse, rather than be shadowed by it (which would much reduce the seeding efficiency). However, at earlier BRA stages, when the amplified pulse is longer, the optimal duration of the seed pulse is also longer. This work proposes the use of self-contracting seed pulses for further optimizing the advanced BRA.

  18. Fluorescence Signal Amplification for Ultrasensitive DNA Detection

    Microsoft Academic Search

    Kim Doré; Mario Leclerc; Denis Boudreau

    \\u000a Ultrasensitive and reliable DNA detection tools are currently needed for the diagnostic of infectious and genetic diseases.\\u000a To achieve the required sensitivity, one can amplify either the target DNA or the signal generated by each target molecule\\u000a detected. Since enzymatic amplification of DNA is prone to contamination or inhibition, sensors that can benefit from signal\\u000a amplification are usually more robust.

  19. Notch3 Gene Amplification in Ovarian Cancer

    Microsoft Academic Search

    Joon T. Park; Kentaro Nakayama; Tsui-Lien Mao; Ben Davidson; Zhen Zhang; Robert J. Kurman; Charles G. Eberhart; Tian-Li Wang

    2006-01-01

    Gene amplification is one of the common mechanisms that activate oncogenes. In this study, we used single nucleotide polymorphism array to analyze genome-wide DNA copy number alterations in 31high-grade ovarian serous carcino- mas, the most lethal gynecologic neoplastic disease in women. We identified an amplicon at 19p13.12 in 6 of 31 (19.5%) ovarian high-grade serous carcinomas. This amplification was validated

  20. Ultrashort pulse amplification in Ti:sapphire

    SciTech Connect

    Huang, C.P.; Zhou, J.; Kapteyn, H.C.; Murnane, M.M. [Washington State Univ., Pullman, WA (United States). Dept. of Physics

    1994-12-31

    Using chirped-pulse amplification in it:sapphire, the authors have generated pulses of 21 fs duration at an energy of 0.5 mJ. They have also demonstrated further amplification of chirped pulses to 45 mJ with a bandwidth capable of supporting 25 fs pulses. The amplifier design minimizes material path-length, spectral distortion and clipping, and compensates for high-order dispersion by using a combination of prisms and diffraction gratings.

  1. Isothermal Decomposition of Hydrogen Peroxide Dihydrate

    NASA Technical Reports Server (NTRS)

    Loeffler, M. J.; Baragiola, R. A.

    2011-01-01

    We present a new method of growing pure solid hydrogen peroxide in an ultra high vacuum environment and apply it to determine thermal stability of the dihydrate compound that forms when water and hydrogen peroxide are mixed at low temperatures. Using infrared spectroscopy and thermogravimetric analysis, we quantified the isothermal decomposition of the metastable dihydrate at 151.6 K. This decomposition occurs by fractional distillation through the preferential sublimation of water, which leads to the formation of pure hydrogen peroxide. The results imply that in an astronomical environment where condensed mixtures of H2O2 and H2O are shielded from radiolytic decomposition and warmed to temperatures where sublimation is significant, highly concentrated or even pure hydrogen peroxide may form.

  2. Isothermal dendritic growth: A low gravity experiment

    NASA Technical Reports Server (NTRS)

    Glicksman, M. E.; Hahn, R. C.; Lograsso, T. A.; Rubinstein, E. R.; Selleck, M. E.; Winsa, E.

    1988-01-01

    The Isothermal Dendritic Growth Experiment is an active crystal growth experiment designed to test dendritic growth theory at low undercoolings where convection prohibits such studies at 1 g. The experiment will be essentially autonomous, though limited in-flight interaction through a computer interface is planned. One of the key components of the apparatus will be a crystal growth chamber capable of achieving oriented single crystal dendritic growth. Recent work indicates that seeding the chamber with a crystal of the proper orientation will not, in and of itself, be sufficient to meet this requirement. Additional flight hardware and software required for the STS flight experiment are currently being developed at NASA Lewis Research Center and at Rensselaer Polytechnic Institute.

  3. Isothermal Dendritic Growth Experiment - SCN Dendrites

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The Isothermal Dendritic Growth Experiment (IDGE), flown on three Space Shuttle missions, is yielding new insights into virtually all industrially relevant metal and alloy forming operations. IDGE used transparent organic liquids that form dendrites (treelike structures) similar to the crystals that form inside metal alloys. Comparing Earth-based and space-based dentrite growth velocity, tip size and shape provid a better understanding of the fundamentals of dentritic growth, including gravity's effects. These shadowgraphic images show succinonitrile (SCN) dentrites growing in a melt (liquid). The space-grown crystals also have cleaner, better defined sidebranches. IDGE was developed by Rensselaer Polytechnic Institude (RPI) and NASA/ Glenn Research Center(GRC). Advanced follow-on experiments are being developed for flight on the International Space Station. Photo gredit: NASA/Glenn Research Center

  4. Perturbations of noise: Origins of isothermal flows

    NASA Astrophysics Data System (ADS)

    Garbaczewski, Piotr

    1999-02-01

    We perform a detailed analysis of both the phenomenological and analytic backgrounds for the ``Brownian recoil principle'' hypothesis [Phys. Rev. A 46, 4634 (1992)]. A corresponding theory of the isothermal Brownian motion of particle ensembles (Smoluchowski diffusion process approximation) takes into account the environmental recoil effects due to locally induced tiny heat flows. By means of local expectation values we elevate the individually negligible phenomena to a non-negligible (accumulated) recoil effect on the ensemble average. The main technical input is a consequent exploitation of the Hamilton-Jacobi equation as a natural substitute for the local momentum conservation law. Together with the continuity equation (alternatively, Fokker-Planck), it forms a closed system of partial differential equations that uniquely determines an associated Markovian diffusion process. The third Newton law in the mean is utilized to generate diffusion-type processes that are either anomalous (enhanced) or generically nondispersive.

  5. Amplification uncertainty relation for probabilistic amplifiers

    E-print Network

    Ryo Namiki

    2015-02-17

    Traditionally, quantum amplification limit refers to the property of inevitable noise addition on canonical variables when the field amplitude of an unknown state is linearly transformed through a quantum channel. Recent theoretical studies have determined amplification limits for cases of probabilistic quantum channels or general quantum operations by specifying a set of input states or a state ensemble. However, it remains open how much excess noises on canonical variables are unavoidable and whether there exists a fundamental trade-off relations between the canonical pair in a general amplification process. In this paper we present an uncertainty-product form of amplification limits for general quantum operations by assuming an input ensemble of Gaussian distributed coherent states. It is simply derived from canonical uncertainty relations and retrieves basic properties of the traditional amplification limit. In addition, our amplification limit turns out to give a physical limitation on probabilistic reduction of an Einstein-Podolsky-Rosen uncertainty. In this regard, we find a condition that probabilistic amplifiers can be regarded as local filtering operations to distill entanglement. It establishes a clear benchmark to verify an advantage of non-Gaussian operations beyond Gaussian operations with a feasible input set of coherent states and standard homodyne measurements.

  6. Analytical Solutions of Singular Isothermal Quadrupole Lens

    NASA Astrophysics Data System (ADS)

    Chu, Zhe; Lin, W. P.; Yang, Xiaofeng

    2013-06-01

    Using an analytical method, we study the singular isothermal quadrupole (SIQ) lens system, which is the simplest lens model that can produce four images. In this case, the radial mass distribution is in accord with the profile of the singular isothermal sphere lens, and the tangential distribution is given by adding a quadrupole on the monopole component. The basic properties of the SIQ lens have been studied in this Letter, including the deflection potential, deflection angle, magnification, critical curve, caustic, pseudo-caustic, and transition locus. Analytical solutions of the image positions and magnifications for the source on axes are derived. We find that naked cusps will appear when the relative intensity k of quadrupole to monopole is larger than 0.6. According to the magnification invariant theory of the SIQ lens, the sum of the signed magnifications of the four images should be equal to unity, as found by Dalal. However, if a source lies in the naked cusp, the summed magnification of the left three images is smaller than the invariant 1. With this simple lens system, we study the situations where a point source infinitely approaches a cusp or a fold. The sum of the magnifications of the cusp image triplet is usually not equal to 0, and it is usually positive for major cusps while negative for minor cusps. Similarly, the sum of magnifications of the fold image pair is usually not equal to 0 either. Nevertheless, the cusp and fold relations are still equal to 0 in that the sum values are divided by infinite absolute magnifications by definition.

  7. Adsorption isotherms of microporous-mesoporous solids revisited

    Microsoft Academic Search

    Petr Schneider

    1995-01-01

    By application of the modified BET isotherm on adsorption data, for adsorption isotherms which are neither purely of the I or IV IUPAC type, it is possible to determine simultaneously the net micropore volume, the monolayer capacity and the BET parameterC. Specific surface obtained from the monolayer capacity represents the mesopore surface area and is not overestimated as in the

  8. Modeling of non-isothermal polymer jets in melt electrospinning

    Microsoft Academic Search

    Eduard Zhmayev; Huajun Zhou; Yong Lak Joo

    2008-01-01

    We have developed a model for non-isothermal, free surface flows of electrically charged viscoelastic fluids in the stable jet region of the melt electrospinning process. The model is based on thin filament approximation applied to fully coupled momentum, continuity, and energy equations, Gauss’ law, and the non-isothermal Giesekus constitutive model. The asymptotic jet thinning relationship widely used in previous electrospinning

  9. Calculation of elastic constants using isothermal molecular dynamics

    Microsoft Academic Search

    John R. Ray; Michael C. Moody; Aneesur Rahman

    1986-01-01

    A new form of molecular dynamics has been developed whose trajectories generate the isothermal or canonical ensemble of classical statistical physics. We have performed molecular-dynamics calculations of the elastic constants using this new ensemble. We find that the elastic constants, as well as other thermodynamic quantities, may be calculated just as efficiently in the isothermal form of molecular dynamics as

  10. TRANSCENDENTAL HARMONIC MAPPINGS AND GRAVITATIONAL LENSING BY ISOTHERMAL

    E-print Network

    Khavinson, Dmitry

    TRANSCENDENTAL HARMONIC MAPPINGS AND GRAVITATIONAL LENSING BY ISOTHERMAL GALAXIES DMITRY KHAVINSON harmonic mapping. We use complex dynamics to give an upper bound on the total number of such zeros. 1 passes near an isothermal, ellipsoidal galaxy. Indeed, using the complex formulation of the thin

  11. Isothermal reactivating Whiplash PCR for locally programmable molecular computation

    E-print Network

    Reif, John H.

    ds-DNA Double stranded deoxyribo nucleic acid PNA Peptide nucleic acid IR-WPCR Isothermal-specific peptide nucleic acid 1 Introduction 1.1 Need for an autocatalytic and isothermal WPCR protocol A primary Abbreviations PCR Polymerase chain reaction WPCR Whiplash polymerase chain reaction DNA Deoxyribo nucleic acid

  12. Highly Efficient Amplification of Chronic Wasting Disease Agent by Protein Misfolding Cyclic Amplification with

    E-print Network

    Highly Efficient Amplification of Chronic Wasting Disease Agent by Protein Misfolding Cyclic of Chronic Wasting Disease Agent by Protein Misfolding Cyclic Amplification with Beads (PMCAb). PLoS ONE 7 wasting disease (CWD) in deer, elk and moose, and Creutzfeldt-Jakob disease in humans. The etiological

  13. Isothermal densification and metamorphism of new snow

    NASA Astrophysics Data System (ADS)

    Schleef, S.; Loewe, H.; Schneebeli, M.

    2012-12-01

    The interplay between overburden stress and surface energy induced growth and coarsening is relevant for the densification of snow and porous ice at all densities. The densification of new snow is amenable to high precision experiments on short time scales. To this end we investigate the coupling of densification and metamorphism of new snow via time-lapse tomography experiments in the laboratory. We compare the evolution of density, strain, and specific surface area to previous long-time metamorphism experiments of snow and creep of polycrystalline ice. Experimental conditions are tailored to the requirements of time-lapse tomography and the measurements are conducted under nearly isothermal conditions at -20°C with a duration of two days. Images were taken with temporal resolution of a few hours which reveal precise details of the microstructure evolution due to sintering and compaction. We used different crystal shapes of natural new snow and snow samples obtained by sieving crystals grown in a snowmaker in the laboratory. To simulate the effect of overburden stress due to an overlying snowpack additional weights were applied to the sample. As expected we find an influence of the densification rate on initial density and overburden stress. We calculated strain rates and identified a transient creep behavior with a similar power law for all crystal types which substantially differs from the Andrade creep of polycrystalline ice. As a main result we found that the evolution of the specific surface area is independent of the density and follows a unique decay form for all measurements of each crystal type. The accuracy of the measurements allows to obtain a decay exponent for the SSA which is the same as previously obtained from the long-time regime during isothermal metamorphism after several months. Our preliminary results for all available types of new snow suggest a correlation between the initial density and SSA. We also find snow samples which coincide in initial density and SSA but differ in SSA decay rate. This indicates that these parameters are insufficient to describe SSA evolution and the crystal shape has also to be considered.

  14. Material Compatibility with Isothermal Pb-Li

    SciTech Connect

    Pint, Bruce A [ORNL; Walker, Larry R [ORNL; Unocic, Kinga A [ORNL

    2012-01-01

    Eutectic Pb-Li is a leading candidate for current fusion blanket concepts as a coolant. However, there is very little data about the compatibility of most materials with Pb-Li above 500 C where the dissolution rate of many conventional alloys increases rapidly. Current work is beginning to assess Pb-Li compatibility from 500 to 800 C using isothermal capsule experiments. Aluminide coatings hold some promise in protecting conventional Fe-base alloys at 600-700 C. However, there is a significant initial Al loss that has not been clearly explained. Furthermore, the reaction product with coated materials is LiAlO{sub 2} rather than Al{sub 2}O{sub 3} at 600 and 700 C. Even when pre-oxidized to form {alpha}-Al{sub 2}O{sub 3}, an alumina layer on FeCrAl transformed to LiAlO{sub 2} at 700 and 800 C. At 500 C, the preformed oxide partially transformed from alumina and some Li was detected in the oxide layer.

  15. Adsorption isotherm special study. Final report

    SciTech Connect

    NONE

    1993-05-01

    The study was designed to identify methods to determine adsorption applicable to Uranium Mill Tailings Remedial Action (UMTRA) Project sites, and to determine how changes in aquifer conditions affect metal adsorption, resulting retardation factors, and estimated contaminant migration rates. EPA and ASTM procedures were used to estimate sediment sorption of U, As, and Mo under varying groundwater geochemical conditions. Aquifer matrix materials from three distinct locations at the DOE UMTRA Project site in Rifle, CO, were used as the adsorbents under different pH conditions; these conditions stimulated geochemical environments under the tailings, near the tailings, and downgradient from the tailings. Grain size, total surface area, bulk and clay mineralogy, and petrography of the sediments were characterized. U and Mo yielded linear isotherms, while As had nonlinear ones. U and Mo were adsorbed strongly on sediments acidified to levels similar to tailings leachate. Changes in pH had much less effect on As adsorption. Mo was adsorbed very little at pH 7-7.3, U was weakly sorbed, and As was moderately sorbed. Velocities were estimated for metal transport at different pHs. Results show that the aquifer materials must be characterized to estimate metal transport velocities in aquifers and to develop groundwater restoration strategies for the UMTRA project.

  16. Isothermal thermogravimetric data acquisition analysis system

    NASA Technical Reports Server (NTRS)

    Cooper, Kenneth, Jr.

    1991-01-01

    The description of an Isothermal Thermogravimetric Analysis (TGA) Data Acquisition System is presented. The system consists of software and hardware to perform a wide variety of TGA experiments. The software is written in ANSI C using Borland's Turbo C++. The hardware consists of a 486/25 MHz machine with a Capital Equipment Corp. IEEE488 interface card. The interface is to a Hewlett Packard 3497A data acquisition system using two analog input cards and a digital actuator card. The system provides for 16 TGA rigs with weight and temperature measurements from each rig. Data collection is conducted in three phases. Acquisition is done at a rapid rate during initial startup, at a slower rate during extended data collection periods, and finally at a fast rate during shutdown. Parameters controlling the rate and duration of each phase are user programmable. Furnace control (raising and lowering) is also programmable. Provision is made for automatic restart in the event of power failure or other abnormal terminations. Initial trial runs were conducted to show system stability.

  17. An Experimental Investigation of Isothermal Swirling Flows

    NASA Astrophysics Data System (ADS)

    Johansson, T. Gunnar

    2001-11-01

    3D LDA measurements have been performed in a scaled-up generic model of a combustion chamber. The flow rig is designed to accommodate two different types of inlet conditions. In one of them the flow enters the axisymmetric chamber through a single annulus. The degree of swirl as well as the axial speed of the inlet air can be varied. In the other type of inlet there are two concentric inlet annuli. The degree of swirl as well as the flow rate can be varied individually in the two annuli. The flow rig is designed to also permit different temperatures of the two air streams, thus simulating the conditions in real combustion situations. So far only isothermal flows have been investigated. Measurements were carried out for the two types of inlet conditions. In both cases all three mean velocity components and all Reynolds stress components have been measured, thus mapping the global flow patterns. Although the two cases showed different flow patterns, especially near the inlet, both cases showed vortex breakdown and recirculating zones close to the inlet. Details of the experimental results will be presented.

  18. ISOTHERMAL AIR-INGRESS VALIDATION EXPERIMENTS

    SciTech Connect

    Chang H. Oh; Eung S. Kim

    2013-01-01

    Idaho National Laboratory has conducted airingress experiments as part of a campaign to validate computational fluid dynamics (CFD) calculations for very high-temperature gas-cooled reactor (VHTR) analysis. An isothermal test loop was designed to recreate exchange or stratified flow that occurs in the lower plenum of VHTR after a break in the primary loop allows helium to leak out and reactor building air to enter the reactor core. The experiment was designed to measure stratified flow in the inlet pipe connecting to the lower plenum of the General Atomics gas turbine–modular helium reactor (GT-MHR). Instead of helium and air, brine and sucrose were used as heavy fluids, and water was used as the lighter fluid to create, using scaling laws, the appropriate flow characteristics of the lower plenum immediately after depressurization. These results clearly indicate that stratified flow is established even for very small density differences. Corresponding CFD results were validated with the experimental data. A grid sensitivity study on CFD models was also performed using the Richardson extrapolation and the grid convergence index method for the numerical accuracy of CFD calculations. The calculated current speed showed very good agreement with the experimental data, indicating that current CFD methods are suitable for simulating density gradient stratified flow phenomena in an air-ingress accident.

  19. Isothermal Dendritic Growth Experiment - PVA Dendrites

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The Isothermal Dendritic Growth Experiment (IDGE), flown on three Space Shuttle missions, is yielding new insights into virtually all industrially relevant metal and alloy forming operations. IDGE used transparent organic liquids that form dendrites (treelike structures) similar to those inside metal alloys. Comparing Earth-based and space-based dendrite growth velocity, tip size and shape provides a better understanding of the fundamentals of dentritic growth, including gravity's effects. Shalowgraphic images of pivalic acid (PVA) dendrites forming from the melt show the subtle but distinct effects of gravity-driven heat convection on dentritic growth. In orbit, the dendrite grows as its latent heat is liberated by heat conduction. This yields a blunt dendrite tip. On Earth, heat is carried away by both conduction and gravity-driven convection. This yields a sharper dendrite tip. In addition, under terrestrial conditions, the sidebranches growing in the direction of gravity are augmented as gravity helps carry heat out of the way of the growing sidebranches as opposed to microgravity conditions where no augmentation takes place. IDGE was developed by Rensselaer Polytechnic Institute and NASA/Glenn Research Center. Advanced follow-on experiments are being developed for flight on the International Space Station. Photo Credit: NASA/Glenn Research Center

  20. USE OF LOOP-MEDIATED ISOTHERMAL AMPLIFICATION METHOD FOR RAPID DETECTION OF EDWARDSIELLA ICTALURI AND FLAVOBACTERIUM COLUMNARE IN CHANNEL CATFISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    After two decades of fast growth, aquaculture will continue to be a crucial food-producing industry worldwide. Infectious diseases are a critical limiting factor in aquaculture. Traditionally, isolation and a series of biochemical tests are required for pathogen identification. However, these pro...

  1. Rapid and Real-Time Detection of Chikungunya Virus by Reverse Transcription Loop-Mediated Isothermal Amplification Assay

    Microsoft Academic Search

    M. M. Parida; S. R. Santhosh; P. K. Dash; N. K. Tripathi; V. Lakshmi; N. Mamidi; A. Shrivastva; N. Gupta; P. Saxena; J. Pradeep Babu; P. V. Lakshmana Rao; Kouichi Morita

    2007-01-01

    template and time of positivity value over a range of 2 108 to 2 102 copies was obtained. The feasibility of CHIKV RT-LAMP for clinical diagnosis was validated with patient serum samples from an ongoing epidemic in Southern India. Optimal assay conditions with zero background were established for the detection of low levels of CHIKV in acute-phase patient serum samples.

  2. Loop-mediated isothermal amplification applied to filarial parasites detection in the mosquito vectors: Dirofilaria immitis as a study model

    Microsoft Academic Search

    Hiroka Aonuma; Aya Yoshimura; Namal Perera; Naoaki Shinzawa; Hironori Bando; Sugao Oshiro; Bryce Nelson; Shinya Fukumoto; Hirotaka Kanuka

    2009-01-01

    BACKGROUND: Despite recent advances in our understanding of the basic biology behind transmission of zoonotic infectious diseases harbored by arthropod vectors these diseases remain threatening public health concerns. For effective control of vector and treatment, precise sampling indicating the prevalence of such diseases is essential. With an aim to develop a quick and simple method to survey zoonotic pathogen-transmitting vectors,

  3. Privacy Amplification in the Isolated Qubits Model

    E-print Network

    Yi-Kai Liu

    2015-02-11

    Isolated qubits are a special class of quantum devices, which can be used to implement tamper-resistant cryptographic hardware such as one-time memories (OTM's). Unfortunately, these OTM constructions leak some information, and standard methods for privacy amplification cannot be applied here, because the adversary has advance knowledge of the hash function that the honest parties will use. In this paper we show a stronger form of privacy amplification that solves this problem, using a fixed hash function that is secure against all possible adversaries in the isolated qubits model. This allows us to construct single-bit OTM's which only leak an exponentially small amount of information. We then study a natural generalization of the isolated qubits model, where the adversary is allowed to perform a polynomially-bounded number of entangling gates, in addition to unbounded local operations and classical communication (LOCC). We show that our technique for privacy amplification is also secure in this setting.

  4. Time varying arctic climate change amplification

    SciTech Connect

    Chylek, Petr [Los Alamos National Laboratory; Dubey, Manvendra K [Los Alamos National Laboratory; Lesins, Glen [DALLHOUSIE U; Wang, Muyin [NOAA/JISAO

    2009-01-01

    During the past 130 years the global mean surface air temperature has risen by about 0.75 K. Due to feedbacks -- including the snow/ice albedo feedback -- the warming in the Arctic is expected to proceed at a faster rate than the global average. Climate model simulations suggest that this Arctic amplification produces warming that is two to three times larger than the global mean. Understanding the Arctic amplification is essential for projections of future Arctic climate including sea ice extent and melting of the Greenland ice sheet. We use the temperature records from the Arctic stations to show that (a) the Arctic amplification is larger at latitudes above 700 N compared to those within 64-70oN belt, and that, surprisingly; (b) the ratio of the Arctic to global rate of temperature change is not constant but varies on the decadal timescale. This time dependence will affect future projections of climate changes in the Arctic.

  5. On the isothermal geometry of corrugated graphene sheets

    E-print Network

    Andrzej Trzesowski

    2014-12-22

    Variational geometries describing corrugated graphene sheets are proposed. The isothermal thermomechanical properties of these sheets are described by a 2-dimensional Weyl space. The equation that couples the Weyl geometry with isothermal distributions of the temperature of graphene sheets, is formulated. This material space is observed in a 3-dimensional orthogonal configurational point space as regular surfaces which are endowed with a thermal state vector field fulfilling the isothermal thermal state equation. It enables to introduce a non-topological dimensionless thermal shape parameter of non-developable graphene sheets. The properties of the congruence of lines generated by the thermal state vector field are discussed.

  6. Isothermal moisture properties of wood-cementitious composites

    SciTech Connect

    Bouguerra, A. [Univ. de Rennes 1 (France)] [Univ. de Rennes 1 (France); Sallee, H. [CSTB de Grenoble, St. Martin d`Heres (France)] [CSTB de Grenoble, St. Martin d`Heres (France); Barquin, F. de [Centre Scientifique et Technique de la Construction, Limelette (Belgium). Div. Materiaux] [Centre Scientifique et Technique de la Construction, Limelette (Belgium). Div. Materiaux; Dheilly, R.M.; Queneudec, M. [Univ. de Picardie Jules Verne, Amiens (France). Lab. Batiment] [Univ. de Picardie Jules Verne, Amiens (France). Lab. Batiment

    1999-03-01

    This article describes a study undertaken to examine the moisture properties of lightweight concrete prepared from clay, cement, and wood aggregates at isothermal conditions. The sorption-desorption isotherm curves of different mixtures show a strong hysteresis. The effect of wood aggregates on the water absorption of composite has been investigated by gamma ray absorption spectrometer. It is found that the sorptivity of the composite is very affected by the presence of wood aggregates in clay-cement matrix. Test results have been confirmed both qualitatively, using magnetic resonance imaging method, and quantitatively, from capillary suction curve calculated from sorption isotherm and pore size distribution.

  7. Signal amplification by unidirectional coupling of oscillators

    NASA Astrophysics Data System (ADS)

    Rajamani, S.; Rajasekar, S.

    2013-07-01

    We report our investigation on the input signal amplification in unidirectionally coupled monostable Duffing oscillators in one- and two dimensions with first oscillator alone driven by a weak periodic signal. Applying a perturbation theory, we obtain a set of nonlinear equations for the response amplitude of the coupled oscillators. We identify the conditions for undamped signal propagation with enhanced amplitude through the coupled oscillators. When the number of oscillators increases the response amplitude approaches a limiting value. We determine this limiting value. Also, we analyse the signal amplification in the coupled oscillators in two dimensions with a fraction of oscillators chosen randomly for coupling and forcing.

  8. Assessing sequential oncogene amplification in human breast cancer

    SciTech Connect

    Janocko, L.E.; Lucke, J.F.; Groft, D.W.; Brown, K.A. [Allegheny-Singer Research Inst., Pittsburgh, PA (United States)] [and others

    1995-09-01

    Studies of amplification and/or overexpression of c-myc, HER-2/neu, and H-ras in breast cancer have shown that each is associated with a poor prognosis. The purpose of this study was to explore the possibility that there is a preferred sequence of amplification of these oncogenes in breast cancer. The frequencies of amplification and patterns of co-amplification of c-myc, HER-2/neu, and H-ras were studied in a group of 84 breast cancers. The data suggested a preferred sequence of amplification that consisted of c-myc amplification-HER-2/neu amplification-H-ras amplification. This model was supported by loglinear analysis. In addition, the levels of amplification of JC-A, a DNA fragment newly isolated from a patient with advanced breast cancer, were studied in 61 of these cases. The data suggested that JC-A amplification occurred early. Loglinear analysis supported a model in which JC-A amplification occurred either before or after c-myc amplification but was unrelated to Her-2/neu or ras amplification. 35 refs., 1 tab.

  9. The Statistics of Supersonic Isothermal Turbulence

    E-print Network

    Alexei G. Kritsuk; Michael L. Norman; Paolo Padoan; Rick Wagner

    2007-06-28

    We present results of large-scale three-dimensional simulations of supersonic Euler turbulence with the piecewise parabolic method and multiple grid resolutions up to 2048^3 points. Our numerical experiments describe non-magnetized driven turbulent flows with an isothermal equation of state and an rms Mach number of 6. We discuss numerical resolution issues and demonstrate convergence, in a statistical sense, of the inertial range dynamics in simulations on grids larger than 512^3 points. The simulations allowed us to measure the absolute velocity scaling exponents for the first time. The inertial range velocity scaling in this strongly compressible regime deviates substantially from the incompressible Kolmogorov laws. The slope of the velocity power spectrum, for instance, is -1.95 compared to -5/3 in the incompressible case. The exponent of the third-order velocity structure function is 1.28, while in incompressible turbulence it is known to be unity. We propose a natural extension of Kolmogorov's phenomenology that takes into account compressibility by mixing the velocity and density statistics and preserves the Kolmogorov scaling of the power spectrum and structure functions of the density-weighted velocity v=\\rho^{1/3}u. The low-order statistics of v appear to be invariant with respect to changes in the Mach number. For instance, at Mach 6 the slope of the power spectrum of v is -1.69, and the exponent of the third-order structure function of v is unity. We also directly measure the mass dimension of the "fractal" density distribution in the inertial subrange, D_m = 2.4, which is similar to the observed fractal dimension of molecular clouds and agrees well with the cascade phenomenology.

  10. Isothermal titration calorimetry in drug discovery.

    PubMed

    Ward, W H; Holdgate, G A

    2001-01-01

    Isothermal titration calorimetry (ITC) follows the heat change when a test compound binds to a target protein. It allows precise measurement of affinity. The method is direct, making interpretation facile, because there is no requirement for competing molecules. Titration in the presence of other ligands rapidly provides information on the mechanism of action of the test compound, identifying the intermolecular complexes that are relevant for structure-based design. Calorimetry allows measurement of stoichiometry and so evaluation of the proportion of the sample that is functional. ITC can characterize protein fragments and catalytically inactive mutant enzymes. It is the only technique which directly measures the enthalpy of binding (delta H degree). Interpretation of delta H degree and its temperature dependence (delta Cp) is usually qualitative, not quantitative. This is because of complicated contributions from linked equilibria and a single change in structure giving modification of several physicochemical properties. Measured delta H degree values allow characterization of proton movement linked to the association of protein and ligand, giving information on the ionization of groups involved in binding. Biochemical systems characteristically exhibit enthalpy-entropy compensation where increased bonding is offset by an entropic penalty, reducing the magnitude of change in affinity. This also causes a lack of correlation between the free energy of binding (delta G degree) and delta H degree. When characterizing structure-activity relationships (SAR), most groups involved in binding can be detected as contributing to delta H degree, but not to affinity. Large enthalpy changes may reflect a modified binding mode, or protein conformation changes. Thus, delta H degree values may highlight a potential discontinuity in SAR, so that experimental structural data are likely to be particularly valuable in molecular design. PMID:11774798

  11. Comparison of multifractal parameters form adsorption isotherms, desorption isotherms and mercury intrusion curves

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, Jorge; Mon, Rodolfo; Vidal Vázquez, Eva

    2013-04-01

    The soil pore space is composed of a continuum of pores extremely variable in size, which range from equivalent diameter sizes smaller than nanometers to an upper limit of the order of centimeters. So, it is quite typical for soil pore space to display a size range of more than a factor of 106 in scale. Nitrogen sorption and mercury injection provide pores size distributions in the range from about 0.1 to 0.001 ?m and 150 to 0.005 ?m, respectively. The aims of this study were to evaluate the scaling properties of nitrogen adsorption isotherms (NAI), nitrogen desorption isotherms (NDI) and mercury intrusion porosimetry (MIP) curves of agricultural soils from "La Pampa húmeda", in the north of Buenos Aires and south of Santa Fé provinces, Argentina. Both NAIs, NDIs and MIPs exhibited multifractal behavior but its scaling properties were different so that the multifractality index, assessed by the width of the generalized dimension and the singularity spectra ranked as follows: NAI > NDI > MIP. Also, parameterization by the Hurst exponent indicates NAIs were less persistent than NDIs and in turn, these were less persistent than MIPs. The multfractal approach was useful to characterize the heterogeneity of various domains of the soil nano- micro- and mesopore system at the scale of small aggregates.

  12. Isothermal model of ICF burn with finite alpha range treatment

    E-print Network

    Galloway, Conner Daniel (Conner Daniel Cross)

    2009-01-01

    A simple model for simulating deuterium tritium burn in inertial confinement fusion capsules is developed. The model, called the Isothermal Rarefaction Model, is zero dimensional (represented as ordinary differential ...

  13. Non-isothermal Crystallization Behaviors of HDPE/MWCNT Nanocomposites

    NASA Astrophysics Data System (ADS)

    Kim, Jihun; Seo, Youngwook P.; Seo, Yongsok; Hong, Soon Man

    2011-05-01

    Thermal properties and non-isothermal crystallization kinetics of polyolefin nanocomposites (high-density polyethylene/multi-walled carbon nanotubes) were characterized by differential scanning calorimetry and thermogravimetric analysis. In situ metallocence polymerization was used to prepare nanocomposites of multi-walled carbon nanotubes (MWCNTs) and high-density polyethylene (HDPE). This polymerization method consists of attaching a metallocene catalyst complex onto the surface of the MWCNTs followed by surface-initiated polymerization to generate polymer brushes on the surface. A kinetic equation for the non-isothermal crystallization was employed to analyze the crystallization characteristics of the nanocomposites. The Avramic exponent, n, can be reasonably well determined from the non-isothermal crystallization exotherm. The polarized optical microscopy showed that neat polyethylene possessed a well developed spherulite morphology: whereas, the nanocomposites displayed elongated entities that subsequently developed as bundle-like entities. Non-isothermal analysis implicitly provides clues about the morphological development history and HDPE molecular ordering around the carbon nanotubes.

  14. The Calculation of Adsorption Isotherms from Chromatographic Peak Shapes

    ERIC Educational Resources Information Center

    Neumann, M. G.

    1976-01-01

    Discusses the relationship between adsorption isotherms and elution peak shapes in gas chromatography, and describes a laboratory experiment which involves the adsorption of hexane, cyclohexane, and benzene on alumina at different temperatures. (MLH)

  15. Aptamer-conjugated bio-bar-code Au-Fe3O4 nanoparticles as amplification station for electrochemiluminescence detection of tumor cells.

    PubMed

    Chen, Min; Bi, Sai; Jia, Xiaoqiang; He, Peng

    2014-07-21

    An electrochemiluminescence (ECL) assay has been developed for highly sensitive and selective detection of tumor cells based on cell-SELEX aptamer-target cell interactions through a cascaded amplification process by using bio-bar-code Au-Fe3O4 as amplification station. Firstly, bio-bar-code toehold-aptamer/DNA primer/Au-Fe3O4 (TA/DP/Au-Fe3O4) nanoconjugates are fabricated with a ratio of 1:10 to efficiently avoid cross-linking reaction and recognize target cells, which are immobilized on the substrate by hybridizing aptamer to capture probe with 18-mer. Through strand displacement reaction (SDR), the TA/DP/Au-Fe3O4 composites further act as the amplification station to initiate rolling circle amplification (RCA). As a result, on the surface of TA/DP/Au-Fe3O4, a large number of Ru(bpy)2(dcbpy)NHS-labeled probes hybridize to RCA products, which are easily trapped by magnetic electrode to perform the magnetic particle-based ECL platform. Under isothermal conditions, this powerful amplification strategy permits detection of Ramos cells as low as 16 cells with an excellent selectivity. Moreover, analysis of Ramos cells in complex samples and whole blood samples further show the great potential of this ultrasensitive approach in clinical application involving cancer cells-related biological processes. PMID:25000857

  16. Isothermal Gas-liquid Flow Using the Lattice Boltzmann Method

    E-print Network

    Kim, Donghoon

    2012-10-19

    ISOTHERMAL GAS-LIQUID FLOW USING THE LATTICE BOLTZMANN METHOD A Thesis by DONGHOON KIM Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree... of MASTER OF SCIENCE August 2011 Major Subject: Nuclear Engineering ISOTHERMAL GAS-LIQUID FLOW USING THE LATTICE BOLTZMANN METHOD A Thesis by DONGHOON KIM Submitted to the Office of Graduate Studies of Texas A&M University...

  17. Linearization of adsorption isotherms for high-pressure applications

    Microsoft Academic Search

    Li Zhou; Yaping Zhou

    1998-01-01

    The adsorption data in the range of 77–298K and 0–7MPa for supercritical hydrogen were linearized by adopting the coordinates of lnln(n) vs 1\\/lnP. Compared to conventional isotherm equations, the proposed model for linear isotherms avoids the use of any fictitious physical quantity and thus does not display such abnormal behaviors as have been observed previously. Use of the linearization strategy

  18. Adsorption of nitrophenol onto activated carbon: isotherms and breakthrough curves

    Microsoft Academic Search

    Jia-Ming Chern; Yi-Wen Chien

    2002-01-01

    The adsorption isotherm of p-nitrophenol onto granular activated carbon in 25°C aqueous solution was experimentally determined by batch tests. Both the Freundlich and the Redlich-Peterson models were found to fit the adsorption isotherm data well. A series of column tests were performed to determine the breakthrough curves with varying bed depths (3–6cm) and water flow rates (21.6–86.4cm3\\/h). Explicit equations for

  19. Sorption isotherms and heat of sorption of pineapple

    Microsoft Academic Search

    M. D Hossain; B. K Bala; M. A Hossain; M. R. A Mondol

    2001-01-01

    Sorption isotherms of pineapple were determined at 20°C, 30°C, 40°C and 50°C temperatures by using dynamic method. Six two-parameter and one three-parameter isotherm models were selected to fit the observed data, and the modified BET model was found to be the best-fitted model for pineapple. The heat of sorption of pineapple decreased with an increase in moisture content and the

  20. Water Adsorption Isotherms of Chia ( Salvia hispanica L.) Seeds

    Microsoft Academic Search

    Ramón Moreira; Francisco Chenlo; Diego M. Prieto; María D. Torres

    The adsorption isotherms of chia seed (CS), black chia seed (BCS), white chia seed (WCS), and chia seed flour (CSF) were determined\\u000a at different temperatures (20, 35, 50, and 65 °C) using gravimetric method. Several saturated salt solutions were selected\\u000a to obtain different water activities in the range of 0.07 to 0.91. Adsorption isotherms were of type II, according to Brunauer’s

  1. High pressure sorption isotherms via differential pressure measurements

    Microsoft Academic Search

    John M. Zielinski; Charles G. Coe; Randy J. Nickel; Anthony M. Romeo; Alan C. Cooper; Guido P. Pez

    2007-01-01

    A differential pressure adsorption unit (DPAU) has been constructed which is capable of accurately measuring isotherm data\\u000a up to 2000 psia with as little as 100 mg of sample. This non-traditional adsorption\\/desorption method has been benchmarked\\u000a by comparing hydrogen and methane isotherms measured with standard volumetric and gravimetric instruments on a NaA (4A) zeolite\\u000a and an activated carbon at near

  2. Amplification of coupling for Yukawa potentials

    E-print Network

    S. De Leo; P. Rotelli

    2004-11-09

    It is well known that Yukawa potentials permit bound states in the Schrodinger equation only if the ratio of the exchanged mass to bound mass is below a critical multiple of the coupling constant. However, arguments suggested by the Darwin term imply a more complex situation. By numerically studying the Dirac equation with a Yukawa potential we investigate this amplification effect.

  3. Inhibition and Facilitation of Nucleic Acid Amplification

    Microsoft Academic Search

    IAN G. WILSON

    1997-01-01

    Factors that inhibit the amplification of nucleic acids by PCR are present with target DNAs from many sources. The inhib- itors generally act at one or more of three essential points in the reaction in the following ways: they interfere with the cell lysis necessary for extraction of DNA, they interfere by nucleic acid degradation or capture, and they inhibit

  4. Triggered amplification by hybridization chain reaction

    E-print Network

    Pierce, Niles A.

    Triggered amplification by hybridization chain reaction Robert M. Dirks and Niles A. Pierce chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment termed hybridization chain reaction (HCR). This class of mech- anisms suggests the possibility

  5. Privacy Amplification Secure Against Active Adversaries ?

    E-print Network

    Maurer, Ueli

    secret string S 0 . Bennett, Brassard, Cr'epeau, and Maurer showed that the length of S 0 can be almost equal to the con­ ditional R'enyi entropy of S given an opponent Eve's knowledge. All pre­ vious results amplification introduced by Bennett et. al. [2] is a technique for trans­ forming a string that is only

  6. Optical amplifier-powered quantum optical amplification

    SciTech Connect

    Jeffers, John [Department of Physics, Scottish Universities Physics Alliance, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG (United Kingdom)

    2011-05-15

    I show that an optical amplifier, when combined with photon subtraction, can be used for quantum state amplification, adding noise at a level below the standard minimum. The device could be used to significantly decrease the probability of incorrectly identifying coherent states chosen from a finite set.

  7. Phase-sensitive amplification in a fiber

    Microsoft Academic Search

    C. J. McKinstrie; S. Radic

    2004-01-01

    Phase-sensitive amplification (PSA) has the potential to improve significantly the performance of optical communication systems. PSA is known to occur in chi(2) devices, and in a fiber interferometer, which is an example of a chi(3) device. In this report some four-wave mixing processes are described, which produce PSA directly in fibers.

  8. Comparing Experimental and Simulated Pressure-Area Isotherms for DPPC

    PubMed Central

    Duncan, Susan L.; Larson, Ronald G.

    2008-01-01

    Although pressure-area isotherms are commonly measured for lipid monolayers, it is not always appreciated how much they can vary depending on experimental factors. Here, we compare experimental and simulated pressure-area isotherms for dipalmitoylphosphatidylcholine (DPPC) at temperatures ranging between 293.15 K and 323.15 K, and explore possible factors influencing the shape and position of the isotherms. Molecular dynamics simulations of DPPC monolayers using both coarse-grained (CG) and atomistic models yield results that are in rough agreement with some of the experimental isotherms, but with a steeper slope in the liquid-condensed region than seen experimentally and shifted to larger areas. The CG lipid model gives predictions that are very close to those of atomistic simulations, while greatly improving computational efficiency. There is much more variation among experimental isotherms than between isotherms obtained from CG simulations and from the most refined simulation available. Both atomistic and CG simulations yield liquid-condensed and liquid-expanded phase area compressibility moduli that are significantly larger than those typically measured experimentally, but compare well with some experimental values obtained under rapid compression. PMID:18199666

  9. AMPLIFICATION OF LOLIUM SSP. MICROSATELLITES IN POA SSP.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species amplification of forty-seven Lolium ssp. microsatellite primers were evaluated across eight Poa species or sub-species. Of these, eighteen Lolium SSR primer pairs generated one or more amplification products in one or more Poa ssp. Sequence evaluation of the amplification products in...

  10. Observationally based assessment of polar amplification of global warming

    E-print Network

    Bhatt, Uma

    Observationally based assessment of polar amplification of global warming Igor V. Polyakov,1) are similar, and do not support the predicted polar amplification of global warming. The possible moderating amplification of global warming. Intrinsic arctic variability obscures long-term changes, limiting our ability

  11. Multiresponsive rolling circle amplification for DNA logic gates mediated by endonuclease.

    PubMed

    Xu, Weidong; Deng, Ruijie; Wang, Lida; Li, Jinghong

    2014-08-01

    Rolling circle amplification (RCA), an efficient isothermal amplification method allowing the polymerase-mediated generation of long single-stranded DNA molecules made of tandem repeats, has been widely used in biomedical and nanotechnology fields due to structural and compositional versatility of its components. In this work, we confer multiresponsiveness to RCA reactions by designing dumbbell-shaped DNA templates and hairpin probes containing different endonuclease cleavage sites. Endonucleases trigger the release of RCA primers or the cleavage of DNA templates, which controls subsequent RCA reactions. A set of one-input and two-input DNA logic gates, which use endonucleases or hairpin probes as inputs, including YES, NOT, AND, OR, NOR, and INHIBIT, are constructed on the basis of our proposed multiresponsive RCA reactions. We demonstrate flexibility and scalability of these logic gates by integrating them to fabricate more complex three-input logic circuits (AND-OR and NOR-AND circuits). Moreover, our strategy is used to construct an assay system for endonuclease activity. Our proposed method might be applicable in the multichannel detection of endonucleases, nucleic acids, and other biomolecules. PMID:25014610

  12. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine.

    PubMed

    Ali, M Monsur; Li, Feng; Zhang, Zhiqing; Zhang, Kaixiang; Kang, Dong-Ku; Ankrum, James A; Le, X Chris; Zhao, Weian

    2014-05-21

    Rolling circle amplification (RCA) is an isothermal enzymatic process where a short DNA or RNA primer is amplified to form a long single stranded DNA or RNA using a circular DNA template and special DNA or RNA polymerases. The RCA product is a concatemer containing tens to hundreds of tandem repeats that are complementary to the circular template. The power, simplicity, and versatility of the DNA amplification technique have made it an attractive tool for biomedical research and nanobiotechnology. Traditionally, RCA has been used to develop sensitive diagnostic methods for a variety of targets including nucleic acids (DNA, RNA), small molecules, proteins, and cells. RCA has also attracted significant attention in the field of nanotechnology and nanobiotechnology. The RCA-produced long, single-stranded DNA with repeating units has been used as template for the periodic assembly of nanospecies. Moreover, since RCA products can be tailor-designed by manipulating the circular template, RCA has been employed to generate complex DNA nanostructures such as DNA origami, nanotubes, nanoribbons and DNA based metamaterials. These functional RCA based nanotechnologies have been utilized for biodetection, drug delivery, designing bioelectronic circuits and bioseparation. In this review, we introduce the fundamental engineering principles used to design RCA nanotechnologies, discuss recently developed RCA-based diagnostics and bioanalytical tools, and summarize the use of RCA to construct multivalent molecular scaffolds and nanostructures for applications in biology, diagnostics and therapeutics. PMID:24643375

  13. A Paper and Plastic Device for Performing Recombinase Polymerase Amplification of HIV DNA

    PubMed Central

    Rohrman, Brittany A.; Richards-Kortum, Rebecca R.

    2013-01-01

    Despite the importance of early diagnosis and treatment of HIV, only a small fraction of HIV-exposed infants in low- and middle-income countries are tested for the disease. The gold standard for early infant diagnosis, DNA PCR, requires resources that are unavailable in poor settings, and no point-of-care HIV DNA test is currently available. We have developed a device constructed of layers of paper, glass fiber, and plastic that is capable of performing isothermal, enzymatic amplification of HIV DNA. The device is inexpensive, small, light-weight, and easy to assemble. The device stores lyophilized enzymes, facilitates mixing of reaction components, and supports recombinase polymerase amplification in five steps of operation. Using commercially available lateral flow strips as a detection method, we demonstrate the ability of our device to amplify 10 copies of HIV DNA to detectable levels in 15 minutes. Our results suggest that our device, which is designed to be used after DNA extraction from dried-blood spots, may serve in conjunction with lateral flow strips as part of a point-of-care HIV DNA test to be used in low resource settings. PMID:22733333

  14. Comparison of protein adsorption isotherms and uptake rates in preparative cation-exchange materials

    Microsoft Academic Search

    Calendula Chang; Abraham M. Lenhoff

    1998-01-01

    Adsorption isotherms and effective diffusivities of lysozyme in a set of six preparative cation-exchange stationary phases were determined from batch uptake data in a stirred vessel. Both a pore diffusion and a homogeneous diffusion model were used in estimating diffusivities, with the isotherms fitted to a non-Langmuirian analytical isotherm equation. The capacities inferred from the isotherms are found to be

  15. Early detection of dengue virus by use of reverse transcription-recombinase polymerase amplification.

    PubMed

    Teoh, Boon-Teong; Sam, Sing-Sin; Tan, Kim-Kee; Danlami, Mohammed Bashar; Shu, Meng-Hooi; Johari, Jefree; Hooi, Poh-Sim; Brooks, David; Piepenburg, Olaf; Nentwich, Oliver; Wilder-Smith, Annelies; Franco, Leticia; Tenorio, Antonio; AbuBakar, Sazaly

    2015-03-01

    A method for the rapid diagnosis of early dengue virus (DENV) infection is highly needed. Here, a prototype reverse transcription-recombinase polymerase amplification (RT-RPA) assay was developed. The assay detected DENV RNA in <20 min without the need for thermocycling amplification. The assay enabled the detection of as few as 10 copies of DENV RNA. The designed RT-RPA primers and exo probe detected the DENV genome of at least 12 genotypes of DENV circulating globally without cross-reacting with other arboviruses. We assessed the diagnostic performance of the RT-RPA assay for the detection of DENV RNA in 203 serum samples of patients with clinically suspected dengue. The sera were simultaneously tested for DENV using a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay, quantitative RT-PCR (qRT-PCR), and IgM- and IgG-capture enzyme-linked immunosorbent assays (ELISA). Acute DENV infection was confirmed in 130 samples and 61 of the samples (46.9%) were classified as viremic with qRT-PCR. The RT-RPA assay showed good concordance (? of ?0.723) with the RT-LAMP and qRT-PCR assays in detecting the dengue viremic samples. When used in combination with ELISA, both the RT-RPA and RT-LAMP assays increased the detection of acute DENV infection to ?95.7% (?45/47) in samples obtained within 5 days of illness. The results from the study suggest that the RT-RPA assay is the most rapid molecular diagnostic tool available for the detection of DENV. Hence, it is possible to use the RT-RPA assay in a laboratory to complement routine serology testing for dengue. PMID:25568438

  16. Early Detection of Dengue Virus by Use of Reverse Transcription-Recombinase Polymerase Amplification

    PubMed Central

    Teoh, Boon-Teong; Sam, Sing-Sin; Tan, Kim-Kee; Danlami, Mohammed Bashar; Shu, Meng-Hooi; Johari, Jefree; Hooi, Poh-Sim; Brooks, David; Piepenburg, Olaf; Nentwich, Oliver; Wilder-Smith, Annelies; Franco, Leticia; Tenorio, Antonio

    2015-01-01

    A method for the rapid diagnosis of early dengue virus (DENV) infection is highly needed. Here, a prototype reverse transcription-recombinase polymerase amplification (RT-RPA) assay was developed. The assay detected DENV RNA in <20 min without the need for thermocycling amplification. The assay enabled the detection of as few as 10 copies of DENV RNA. The designed RT-RPA primers and exo probe detected the DENV genome of at least 12 genotypes of DENV circulating globally without cross-reacting with other arboviruses. We assessed the diagnostic performance of the RT-RPA assay for the detection of DENV RNA in 203 serum samples of patients with clinically suspected dengue. The sera were simultaneously tested for DENV using a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay, quantitative RT-PCR (qRT-PCR), and IgM- and IgG-capture enzyme-linked immunosorbent assays (ELISA). Acute DENV infection was confirmed in 130 samples and 61 of the samples (46.9%) were classified as viremic with qRT-PCR. The RT-RPA assay showed good concordance (? of ?0.723) with the RT-LAMP and qRT-PCR assays in detecting the dengue viremic samples. When used in combination with ELISA, both the RT-RPA and RT-LAMP assays increased the detection of acute DENV infection to ?95.7% (?45/47) in samples obtained within 5 days of illness. The results from the study suggest that the RT-RPA assay is the most rapid molecular diagnostic tool available for the detection of DENV. Hence, it is possible to use the RT-RPA assay in a laboratory to complement routine serology testing for dengue. PMID:25568438

  17. Gene-amplification model of carcinogenesis.

    PubMed Central

    Pall, M L

    1981-01-01

    A two-stage model of carcinogenesis is proposed based on recent evidence for the occurrence of proto-oncogenes in the vertebrate genome, evidence for gene amplification during carcinogenesis, and studies of the action of tumor promoters. The model is baed on the view that an increase in the level of gene product from such proto-oncogenes is sufficient to induce neoplastic transformation. It proposes that the initial step in carcinogenesis (initiation) is a mutation producing a tandem duplication of a proto-oncogene. Gene amplification can then occur by successive unequal sister chromatid crossing-over events in several cell cycles until sufficient gene product is produced to transform the cell. PMID:6941303

  18. Amplification effects in optomechanics via weak measurements

    NASA Astrophysics Data System (ADS)

    Li, Gang; Wang, Tao; Song, He-Shan

    2014-07-01

    We revisit the scheme of single-photon weak-coupling optomechanics using postselection, proposed by Pepper, Ghobadi, Jeffrey, Simon, and Bouwmeester [Phys. Rev. Lett. 109, 023601 (2012), 10.1103/PhysRevLett.109.023601], by analyzing the exact solution of the dynamical evolution. Positive and negative amplification effects of the displacement of the mirror's position can be generated when the Kerr phase is considered. This effect occurs when the postselected state of the photon is orthogonal to the initial state, which cannot be explained by the usual weak measurement results. The amplification effect can be further modulated by a phase shifter, and the maximal displacement state can appear within a short evolution time.

  19. Free randomness amplification using bipartite chain correlations

    NASA Astrophysics Data System (ADS)

    Grudka, Andrzej; Horodecki, Karol; Horodecki, Micha?; Horodecki, Pawe?; Paw?owski, Marcin; Ramanathan, Ravishankar

    2014-09-01

    A direct analysis of the task of randomness amplification from Santha-Vazirani sources using the violation of the chained Bell inequality is performed in terms of the convex combination of no-signaling boxes required to simulate quantum violation of the inequality. This analysis is used to find the exact threshold value of the initial randomness parameter from which perfect randomness can be extracted in the asymptotic limit of a large number of measurement settings. As a byproduct, we provide a tool for the analysis of randomness amplification protocols, namely a general characterization of the probability distributions of bits generated by Santha-Vazirani sources, which are shown to be mixtures of specific permutations of Bernoulli distributions with a parameter defined by the source.

  20. Amplification of trace amounts of nucleic acids

    DOEpatents

    Church, George M. (Brookline, MA); Zhang, Kun (Brighton, MA)

    2008-06-17

    Methods of reducing background during amplification of small amounts of nucleic acids employ careful analysis of sources of low level contamination. Ultraviolet light can be used to reduce nucleic acid contaminants in reagents and equipment. "Primer-dimer" background can be reduced by judicious design of primers. We have shown clean signal-to-noise with as little as starting material as one single human cell (.about.6 picogram), E. coli cell (.about.5 femtogram) or Prochlorococcus cell (.about.3 femtogram).

  1. Host range, amplification and arboviral disease emergence

    Microsoft Academic Search

    S. C. Weaver

    Etiologic agents of arboviral diseases are primarily zoonotic pathogens that are maintained in nature in cycles involving\\u000a arthropod transmission among a variety of susceptible reservoir hosts. In the simplest form of human exposure, spillover occurs\\u000a from the enzootic cycle when humans enter zoonotic foci and\\/or enzootic amplification increases circulation near humans. Examples\\u000a include Eastern (EEEV) and Western equine encephalitis viruses

  2. Host range, amplification and arboviral disease emergence.

    PubMed

    Weaver, S C

    2005-01-01

    Etiologic agents of arboviral diseases are primarily zoonotic pathogens that are maintained in nature in cycles involving arthropod transmission among a variety of susceptible reservoir hosts. In the simplest form of human exposure, spillover occurs from the enzootic cycle when humans enter zoonotic foci and/or enzootic amplification increases circulation near humans. Examples include Eastern (EEEV) and Western equine encephalitis viruses (WEEV), as well as West Nile (WNV), St. Louis encephalitis (SLEV) and Yellow fever viruses. Spillover can involve direct transmission to humans by primary enzootic vectors (e.g. WNV, SLEV and WEEV) and/or bridge vectors with more catholic feeding preferences that include humans (e.g. EEEV). Some viruses, such as Rift Valley fever, Japanese encephalitis and Venezuelan equine encephalitis viruses (VEEV) undergo secondary amplification involving replication in livestock animals, resulting in greater levels of spillover to humans in rural settings. In the case of VEEV, secondary amplification involves equines and requires adaptive mutations in enzootic strains that allow for efficient viremia production. Two of the most important human arboviral pathogens, Yellow fever and dengue viruses (DENV), have gone one step further and adopted humans as their amplification hosts, allowing for urban disease. The ancestral forms of DENV, sylvatic viruses transmitted among nonhuman primate reservoir hosts by arboreal mosquitoes, adapted to efficiently infect the urban mosquito vectors Aedes aegypti and Ae. albopictus during the past few thousand years as civilizations arose. Comparative studies of the sylvatic and urban forms of DENV may elucidate the evolution of arboviral virulence and the prospects for DENV eradication should effective vaccines be implemented. PMID:16358422

  3. Amplification of hofmeister effect by alcohols.

    PubMed

    Xu, Yun; Liu, Guangming

    2014-07-01

    We have demonstrated that Hofmeister effect can be amplified by adding alcohols to aqueous solutions. The lower critical solution temperature behavior of poly(N-isopropylacrylamide) has been employed as the model system to study the amplification of Hofmeister effect. The alcohols can more effectively amplify the Hofmeister effect following the series methanol < ethanol < 1-propanol < 2-propanol for the monohydric alcohols and following the series d-sorbitol ? xylitol ? meso-erythritol < glycerol < ethylene glycol < methanol for the polyhydric alcohols. Our study reveals that the relative extent of amplification of Hofmeister effect is determined by the stability of the water/alcohol complex, which is strongly dependent on the chemical structure of alcohols. The more stable solvent complex formed via stronger hydrogen bonds can more effectively differentiate the anions through the anion-solvent complex interactions, resulting in a stronger amplification of Hofmeister effect. This study provides an alternative method to tune the relative strength of Hofmeister effect besides salt concentration. PMID:24921669

  4. $beta$ $Yields$ $alpha$ Isothermal Transformation in Pure and Weakly Alloyed Uranium; TRANSFORMATION ISOTHERME $beta$ $Yields$ $alpha$ DANS L'URANIUM PUR ET FAIBLEMENT ALLIE

    Microsoft Academic Search

    H. Aubert; C. Lelong

    1966-01-01

    The TTT diagrams describing the β â α isothermal transformation have been made by isothermal dilatometry for pure uranium and 21 alloys based on chromium, silicon, molybdenum, iron, aluminium, zirconium. The thermal cycle preceding the isothermal step influences the decomposition kinetics at temperature corresponding to the eutectoid and martensitic mechanisms, but not in the range where the bainitic transformation occurs.

  5. Isothermal decomposition of gamma-irradiated palladium acetate

    NASA Astrophysics Data System (ADS)

    Mahfouz, R. M.; Alshehri, S. M.; Monshi, M. A. S.; Abd El-Salam, N. M.

    2004-06-01

    The isothermal decomposition of un-irradiated (pristine) and pre-gamma-irradiated palladium acetate was studied in the temperature range (498-508 K) and in air using the isothermal thermogravimetric technique. The data were analysed using various solid state reaction models. The results showed that the kinetics of isothermal decomposition of palladium acetate was governed by random nucleation reaction (Erofe'ev equation A(3)). The activation energies of the main decomposition process for un-irradiated and pre-gamma-irradiated samples were calculated. The change in texture and crystal structure of the investigated palladium acetate by gamma-irradiation was studied using electron microscopy and X-ray diffraction techniques.

  6. Critical dynamics of an isothermal compressible nonideal fluid.

    PubMed

    Gross, Markus; Varnik, Fathollah

    2012-12-01

    A pure fluid at its critical point shows a dramatic slow-down in its dynamics, due to a divergence of the order-parameter susceptibility and the coefficient of heat transport. Under isothermal conditions, however, sound waves provide the only possible relaxation mechanism for order-parameter fluctuations. Here we study the critical dynamics of an isothermal, compressible nonideal fluid via scaling arguments and computer simulations of the corresponding fluctuating hydrodynamics equations. We show that, below a critical dimension of 4, the order-parameter dynamics of an isothermal fluid effectively reduces to "model A," characterized by overdamped sound waves and a divergent bulk viscosity. In contrast, the shear viscosity remains finite above two dimensions. Possible applications of the model are discussed. PMID:23367905

  7. Moisture adsorption isotherms and glass transition temperature of pectin.

    PubMed

    Basu, Santanu; Shivhare, U S; Muley, S

    2013-06-01

    The moisture adsorption isotherms of low methoxyl pectin were determined at 30-70°C and water activity ranging from 0.11 to 0.94. The moisture adsorption isotherms revealed that the equilibrium moisture content increased with water activity. Increase in temperature, in general, resulted in decreased equilibrium moisture content. However in some cases, equilibrium moisture content values increased with temperature at higher water activities. Selected sorption models (GAB, Halsey, Henderson, Oswin, modified Oswin) were tested for describing the adsorption isotherms. Parameters of each sorption models were determined by nonlinear regression analysis. Oswin model gave the best fit for pectin sorption behaviour. Isosteric heat of sorption decreased with increase in moisture content and varied between 14.607 and 0.552 kJ/mol. Glass transition temperature decreased with increase in moisture content of pectin. PMID:24425957

  8. Detection of Hepatitis A Virus by the Nucleic Acid Sequence-Based Amplification Technique and Comparison with Reverse Transcription-PCR

    PubMed Central

    Jean, Julie; Blais, Burton; Darveau, André; Fliss, Ismaïl

    2001-01-01

    A nucleic acid sequence-based amplification (NASBA) technique for the detection of hepatitis A virus (HAV) in foods was developed and compared to the traditional reverse transcription (RT)-PCR technique. Oligonucleotide primers targeting the VP1 and VP2 genes encoding the major HAV capsid proteins were used for the amplification of viral RNA in an isothermal process resulting in the accumulation of RNA amplicons. Amplicons were detected by hybridization with a digoxigenin-labeled oligonucleotide probe in a dot blot assay format. Using the NASBA, as little as 0.4 ng of target RNA/ml was detected per comparison to 4 ng/ml for RT-PCR. When crude HAV viral lysate was used, a detection limit of 2 PFU (4 × 102 PFU/ml) was obtained with NASBA, compared to 50 PFU (1 × 104 PFU/ml) obtained with RT-PCR. No interference was encountered in the amplification of HAV RNA in the presence of excess nontarget RNA or DNA. The NASBA system successfully detected HAV recovered from experimentally inoculated samples of waste water, lettuce, and blueberries. Compared to RT-PCR and other amplification techniques, the NASBA system offers several advantages in terms of sensitivity, rapidity, and simplicity. This technique should be readily adaptable for detection of other RNA viruses in both foods and clinical samples. PMID:11722911

  9. Asymmetric parametric amplification in nonlinear left-handed transmission lines

    E-print Network

    Powell, David A; Kivshar, Yuri S

    2008-01-01

    We study parametric amplification in nonlinear left-handed transmission lines, which serve as model systems for nonlinear negative index metamaterials. We experimentally demonstrate amplification of a weak pump signal in three regimes: with the signal in the left-handed band, with the signal in the stop band, and with the signal at a defect frequency. In particular, we demonstrate the amplification of the incident wave by up to 15dB in the left-handed regime.

  10. Adaptive base-isolation of civil structures using variable amplification

    Microsoft Academic Search

    Kenneth K. Walsh; Makola M. Abdullah

    2006-01-01

    Semi-active dampers are used in base-isolation to reduce the seismic response of civil engineering structures. In the present\\u000a study, a new semi-active damping system using variable amplification will be investigated for adaptive base-isolation. It\\u000a uses a novel variable amplification device (VAD) connected in series with a passive damper. The VAD is capable of producing\\u000a multiple amplification factors, each corresponding to

  11. Direct measurement of protein binding energetics by isothermal titration calorimetry

    Microsoft Academic Search

    Stephanie Leavitt; Ernesto Freire

    2001-01-01

    Of all the techniques that are currently available to measure binding, isothermal titration calorimetry is the only one capable of measuring not only the magnitude of the binding affinity but also the magnitude of the two thermodynamic terms that define the binding affinity: the enthalpy (?H) and entropy (?S) changes. Recent advances in instrumentation have facilitated the development of experimental

  12. Experimental determination of single solute and competitive adsorption isotherms

    Microsoft Academic Search

    Andreas Seidel-Morgenstern

    2004-01-01

    In order to design and to optimise preparative liquid chromatography, the knowledge of the underlying thermodynamic functions, i.e. the adsorption isotherms, is of large importance. Usually these functions can not be predicted and various techniques have been suggested to determine them experimentally. In this paper, several important methods to measure adsorption equilibrium data are discussed and evaluated. The main focus

  13. Characterization of nanoporous materials from adsorption and desorption isotherms

    Microsoft Academic Search

    Peter I. Ravikovitch; Alexander V. Neimark

    2001-01-01

    We present a consistent method for calculation of pore size distributions in nanoporous materials from adsorption and desorption isotherms, which form the hysteresis loop H1 by the IUPAC classification. The method is based on the nonlocal density functional theory (NLDFT) of capillary condensation hysteresis in cylindrical pores. It is implemented for the nitrogen and argon sorption at their boiling temperatures.

  14. Surface Temperature: Contouring Isotherms (title provided or enhanced by cataloger)

    NSDL National Science Digital Library

    This interactive feature shows how an isothermal map of surface temperature is drawn. Students can select an individual contour value and watch as a virtual 'pencil' correctly places the line with respect to temperature values on the map. The animation also permits the user to color the spaces between the contour lines on the map.

  15. Gas adsorption isotherm equation based on vacancy solution theory

    Microsoft Academic Search

    Solot Suwanayuen; Ronald P. Danner

    1980-01-01

    Pennsylvania State University's new isotherm equation for pure gas adsorption treats the adsorption equilbrium as an osmotic equilibrium between two ''vacancy'' solutions having different compositions. One solution represents the gas phase and the other the adsorbed phase. The vacancy solution is composed of adsorbates and vacancies (imaginary entities defined as the vacuum space that acts as the solvent for the

  16. Isothermal spherical perfect fluid model: Uniqueness and Conformal mapping

    E-print Network

    Naresh Dadhich

    1996-05-01

    We prove the theorem: The necessary and sufficient condition for a spherically symmetric spacetime to represent an isothermal perfect fluid (barotropic equation of state with density falling off as inverse square of the curvature radius) distribution without boundary is that it is conformal to the ``minimally'' curved (gravitation only manifesting in tidal acceleration and being absent in particle trajectory) spacetime.

  17. Sorption Isotherms of Vaccum-Fried Carrot Chips

    Microsoft Academic Search

    Fan Liu-Ping; Zhang Min; Tao Qian; Xiao Gong-Nian

    2005-01-01

    The moisture sorption isotherms for carrot chips after vacuum frying were determined using a gravimetric technique at 10, 25, and 40°C and fitted with BET, GAB, Smith, Halsey, Henderson, and Peleg models. A nonlinear least-squares regression program was used to determine the models constants. The Peleg, Halsey, and GAB models were found to best represent the experimental data throughout the

  18. Material behavior changes in underfill encapsulants exposed to isothermal aging

    Microsoft Academic Search

    Chang Lin; Saiful Islam; Jeffrey C. Suhling; Pradeep Lall

    2006-01-01

    Silica filled epoxy encapsulants used for microelectronic packaging are known to exhibit evolving properties that change significantly with environmental exposures such as isothermal aging and thermal cycling. Most aging effects are typically exacerbated at higher temperatures at or above the glass transition temperature (Tg) of the encapsulant. Such extremes are often used during the high temperature dwells present in thermal

  19. The radiation of an isothermal sphere with consideration of scattering

    Microsoft Academic Search

    Yu. A. Popov

    1968-01-01

    We have solved the problem of the radiation from an isothermal sphere with a spherical scattering indicatrix. We demonstrate that the emissivity of the sphere and of the plane layer, with consideration of scattering, can be approximately presented by a single function of the product resulting from the multiplication of the attenuation factor by the geometric characteristic of the radiating

  20. Properties of Multivariate Binding Isotherms in Capillary Electrophoresis

    E-print Network

    Chen, David D.Y.

    Properties of Multivariate Binding Isotherms in Capillary Electrophoresis Michael T. Bowser, Andrea, BC, Canada V6T 1Z1 When more than one complexation additive is used in capillary electrophoresis (CE in capillary electrophoresis (CE) has increased dramati- cally in recent years. Terabe et al. were the first

  1. Finite Mass Isothermal Spheres and the Structure of Globular Clusters

    E-print Network

    Jes Madsen

    1996-01-23

    Utilizing a recently derived extension of the Maxwell-Boltzmann distribution to low occupation numbers (Simons 1994) this investigation discusses the structure of stellar dynamical isothermal spheres. The resulting models, which resemble King models, constitute a new sequence of physically well-motivated spherical equilibrium configurations of finite mass, and give nice fits to pre-core collapse globular cluster data.

  2. Desorption isotherm and heat pump drying kinetics of peas

    Microsoft Academic Search

    M. Shafiur Rahman; Conrad O. Perera; Caroline Thebaud

    1997-01-01

    Moisture desorption isotherms and thin layer drying kinetices of peas in a laboratory pilot heat pump dryer were measured and modeled. A mesh bottom tray was used and air flow was parallel to the two faces of the thin layer. Air drying temperature, and relative humidity were varied from 25 to 65 °C and 0.20 to 0.60, respectively. The air

  3. Isothermic surfaces: conformal geometry, Clifford algebras and integrable systems

    Microsoft Academic Search

    F. E. Burstall

    2000-01-01

    We give an account of the classical and integrable geometry of isothermic surfaces in arbitrary co-dimension. We show that the classical transformation theory of Darboux, Bianchi and Calapso goes through unchanged in arbitrary co-dimension as does the connection with the \\

  4. Isothermic surfaces: conformal geometry, Clifford algebras and integrable systems

    Microsoft Academic Search

    F. E. Burstall

    2000-01-01

    We give an account of the classical and integrable geometry of isothermic\\u000asurfaces in arbitrary co-dimension. We show that the classical transformation\\u000atheory of Darboux, Bianchi and Calapso goes through unchanged in arbitrary\\u000aco-dimension as does the connection with the \\

  5. Derivation of the Freundlich Adsorption Isotherm from Kinetics

    ERIC Educational Resources Information Center

    Skopp, Joseph

    2009-01-01

    The Freundlich adsorption isotherm is a useful description of adsorption phenomena. It is frequently presented as an empirical equation with little theoretical basis. In fact, a variety of derivations exist. Here a new derivation is presented using the concepts of fractal reaction kinetics. This derivation provides an alternative basis for…

  6. Stonecutter Mills, Inc., Isothermal Community College. PLATO Evaluation Series.

    ERIC Educational Resources Information Center

    Sherman, Greg

    Stonecutter Mills, Inc., is a textile manufacturing company with a major production facility in Spindale, North Carolina. In the past few years, Stonecutter Mills employees have been given an opportunity to spend up to 2 hours a week on company time to participate in PLATO-supported learning at Isothermal Community College. Employees could choose…

  7. Bifurcation and stability analysis of laminar isothermal counterflowing jets

    Microsoft Academic Search

    A. G. S ALINGER; J. N. S HADID; T. J. M OUNTZIARIS

    2006-01-01

    We present a numerical study of the structure and stability of laminar isothermal flows formed by two counterflowing jets of an incompressible Newtonian fluid. We demonstrate that symmetric counterflowing jets with identical mass flow rates exhibit multiple steady states and, in certain cases, time-dependent (periodic) steady states. Two geometric configurations were studied based on the inlet jet shapes: planar and

  8. Isothermal reactivating Whiplash PCR for locally programmable molecular computation

    E-print Network

    Reif, John H.

    chain reaction DNA Deoxyribo nucleic acid ds-DNA Double stranded deoxyribo nucleic acid PNA Peptide resonance energy transfer bis-PNA Bi-specific peptide nucleic acid 1 Introduction 1.1 Need nucleic acid IR-WPCR Isothermal reactivating Whiplash polymerase chain reaction FRET Fluorescence

  9. Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites

    E-print Network

    Bhatia, Sangeeta

    Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites Justin H" population of gold nanorods induces localized unveiling of cryptic collagen epitopes, which are in turn

  10. Mechanical entanglement via detuned parametric amplification

    NASA Astrophysics Data System (ADS)

    Szorkovszky, A.; Clerk, A. A.; Doherty, A. C.; Bowen, W. P.

    2014-06-01

    We propose two schemes to generate entanglement between a pair of mechanical oscillators using parametric amplification. In contrast to existing parametric drive-based protocols, both schemes operate in the steady-state. Using a detuned parametric drive to maintain equilibrium and to couple orthogonal quadratures, our approach can be viewed as a two-mode extension of previous proposals for parametric squeezing. We find that robust steady-state entanglement is possible for matched oscillators with well-controlled coupling. In addition, one of the proposed schemes is robust to differences in the damping rates of the two oscillators.

  11. Amplification of Signaling Events in Bacteria

    NSDL National Science Digital Library

    Frederick W. Dahlquist (University of Oregon; Knight Professor and Head, Department of Chemistry, Member, Institute of Molecular Biology REV)

    2002-05-14

    Bacteria respond to extremely shallow chemical gradients by modifying their motility in a process called chemotaxis. This chemotactic response is characterized by high sensitivity to small concentration differences, which extends over a large range of concentrations. This combination of high signal gain and large dynamic range results from both a memory of past events and the ability to amplify small differences in signal between the memory and the current environment. Dahlquist describes the signaling mechanism used by bacteria to regulate the flagellar motor and the places in this pathway where signal amplification may occur.

  12. Free electron laser designs for laser amplification

    DOEpatents

    Prosnitz, Donald (Walnut Creek, CA); Szoke, Abraham (Fremont, CA)

    1985-01-01

    Method for laser beam amplification by means of free electron laser techniques. With wiggler magnetic field strength B.sub.w and wavelength .lambda..sub.w =2.pi./k.sub.w regarded as variable parameters, the method(s) impose conditions such as substantial constancy of B.sub.w /k.sub.w or k.sub.w or B.sub.w and k.sub.w (alternating), coupled with a choice of either constant resonant phase angle or programmed phase space "bucket" area.

  13. Boosting riboswitch efficiency by RNA amplification

    PubMed Central

    Emadpour, Masoumeh; Karcher, Daniel; Bock, Ralph

    2015-01-01

    Riboswitches are RNA sensors that regulate gene expression in response to binding of small molecules. Although they conceptually represent simple on/off switches and, therefore, hold great promise for biotechnology and future synthetic biology applications, the induction of gene expression by natural riboswitches after ligand addition or removal is often only moderate and, consequently, the achievable expression levels are not very high. Here, we have designed an RNA amplification-based system that strongly improves the efficiency of riboswitches. We have successfully implemented the method in a biological system for which currently no efficient endogenous tools for inducible (trans)gene expression are available: the chloroplasts of higher plants. We further show that an HIV antigen whose constitutive expression from the chloroplast genome is deleterious to the plant can be inducibly expressed under the control of the RNA amplification-enhanced riboswitch (RAmpER) without causing a mutant phenotype, demonstrating the potential of the method for the production of proteins and metabolites that are toxic to the host cell. PMID:25824954

  14. Induction of gene amplification in Plasmodium falciparum

    SciTech Connect

    Rogers, P.L.

    1985-01-01

    Human erythrocytic in vitro cultures of Honduras I strain of the malaria parasite Plasmodium falciparum have been stressed stepwise with increasing concentrations of methotrexate (MTX), a folate antagonist. This selection has produced a strain that is 450 times more resistant to the drug than the original culture. Uptake of sublethal doses of radiolabeled MTX by infected red blood cells was 6-36 times greater in the resistant cultures than in the nonresistant controls. DNA isolated from all of the parasites was probed by hybridization with /sup 35/S-labeled DNA derived from a clone of the yeast thymidylate synthetase (TS) gene. This showed 50 to 100 times more increased hybridization of the TS probe to the DNA from the resistant parasites is direct evidence of gene amplification because DHFR and TS are actually one and the same bifunctional enzyme in P. falciparum. Hence, the evidence presented indicates that induced resistance of the malaria parasite to MTX in this case is due to overproduction of DHFR resulting from amplification of the DHFR-TS gene.

  15. Dynamical amplification of Arctic and global warming

    NASA Astrophysics Data System (ADS)

    Alekseev, Genrikh; Ivanov, Nikolai; Kharlanenkova, Natalia; Kuzmina, Svetlana; Bobylev, Leonid; Gnatiuk, Natalia; Urazgildeeva, Aleksandra

    2015-04-01

    The Arctic is coupled with global climate system by the atmosphere and ocean circulation that provides a major contribution to the Arctic energy budget. Therefore increase of meridional heat transport under global warming can impact on its Arctic amplification. Contribution of heat transport to the recent warming in the Arctic, Northern Hemisphere and the globe are estimated on base of reanalysis data, global climate model data and proposed special index. It is shown that significant part of linear trend during last four decades in average surface air temperature in these areas can be attributed to dynamical amplification. This attribution keeps until 400 mb height with progressive decreasing. The Arctic warming is amplified also due to an increase of humidity and cloudiness in the Arctic atmosphere that follow meridional transport gain. From October to January the Arctic warming trends are amplified as a result of ice edge retreat from the Siberian and Alaska coast and the heating of expanded volume of sea water. This investigation is supported with RFBR project 15-05-03512.

  16. Desert Amplification of Greenhouse Gas Warming

    NASA Astrophysics Data System (ADS)

    Cook, K. H.

    2013-12-01

    Surface temperatures over the Sahara and Arabian Deserts are increasing at a rate that is 3.5 times that of the global mean. These regions have warmed by 1.4 K between 1980 and 2012. In the tropical (and global) mean, added energy incident at the surface due to increased concentrations of greenhouse gases is used partly to increase the surface temperature, and partly to evaporate water. The resulting atmospheric water vapor anomaly is effectively mixed vertically and horizontally throughout the tropics on annual time scales, and amplifies the greenhouse effect (increased longwave back radiation to the surface) everywhere, including over the deserts. But, on the desert surface, evaporative cooling is disabled and the enhanced longwave energy incident on the surface serves only to increase surface temperature. Despite the fact that this desert amplification mechanism should operate over any dry surface, the other deserts of the world are not exhibiting accelerated warming. Each of these deserts is smaller than the Sahara/Arabian Desert area, and various regional processes dominate over the desert amplification mechanism.

  17. Power amplification in the mammalian cochlea.

    PubMed

    Lukashkin, Andrei N; Walling, Mark N; Russell, Ian J

    2007-08-01

    It was first suggested by Gold in 1948 [1] that the exquisite sensitivity and frequency selectivity of the mammalian cochlea is due to an active process referred to as the cochlear amplifier. It is thought that this process works by pumping energy to augment the otherwise damped sound-induced vibrations of the basilar membrane [2-4], a mechanism known as negative damping. The existence of the cochlear amplifier has been inferred from comparing responses of sensitive and compromised cochleae [5] and observations of acoustic emissions [6, 7] and through mathematical modeling [8, 9]. However, power amplification has yet to be demonstrated directly. Here, we prove that energy is indeed produced in the cochlea on a cycle-by-cycle basis. By using laser interferometry [10], we show that the nonlinear component of basilar-membrane responses to sound stimulation leads the forces acting on the membrane. This is possible only in active systems with negative damping [11]. Our finding provides the first direct evidence for power amplification in the mammalian cochlea. The finding also makes redundant current hypotheses of cochlear frequency sharpening and sensitization that are not based on negative damping. PMID:17658260

  18. A PARAMETER STUDY FOR BAROCLINIC VORTEX AMPLIFICATION

    SciTech Connect

    Raettig, Natalie; Klahr, Hubert [Max-Planck-Institut fuer Astronomie, Koenigstuhl 17, D-69117 Heidelberg (Germany); Lyra, Wladimir, E-mail: raettig@mpia.de, E-mail: klahr@mpia.de, E-mail: Wladimir.Lyra@jpl.nasa.gov [Department of Astrophysics, American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024 (United States)

    2013-03-10

    Recent studies have shown that baroclinic vortex amplification is strongly dependent on certain factors, namely, the global entropy gradient, the efficiency of thermal diffusion and/or relaxation as well as numerical resolution. We conduct a comprehensive study of a broad range and combination of various entropy gradients, thermal diffusion and thermal relaxation timescales via local shearing sheet simulations covering the parameter space relevant for protoplanetary disks. We measure the Reynolds stresses as a function of our control parameters and see that there is angular momentum transport even for entropy gradients as low as {beta} = -dln s/dln r = 1/2. Values we expect in protoplanetary disks are between {beta} = 0.5-2.0 The amplification-rate of the perturbations, {Gamma}, appears to be proportional to {beta}{sup 2} and thus proportional to the square of the Brunt-Vaeisaelae frequency ({Gamma}{proportional_to}{beta}{sup 2}{proportional_to}N {sup 2}). The saturation level of Reynolds stresses, on the other hand, seems to be proportional to {beta}{sup 1/2}. This highlights the importance of baroclinic effects even for the low entropy gradients expected in protoplanetary disks.

  19. Oxide-Dependent Adsorption of a Model Membrane Phospholipid, Dipalmitoylphosphatidylcholine: Bulk Adsorption Isotherms

    E-print Network

    Sahai, Nita

    Adsorption Isotherms Timothy A. Oleson*, and Nita Sahai,,§ Department of Geology & Geophysics, 1215 West the dominant controlling forces. We obtained bulk adsorption isotherms at 55 °COxide-Dependent Adsorption of a Model Membrane Phospholipid, Dipalmitoylphosphatidylcholine: Bulk

  20. 78 FR 66940 - Regulatory Requirements for Hearing Aid Devices and Personal Sound Amplification Products; Draft...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-07

    ...FDA-2013-D-1295] Regulatory Requirements for Hearing Aid Devices and Personal Sound Amplification...Regulatory Requirements for Hearing Aid Devices and Personal Sound Amplification...clarifies the distinction between hearing aids and personal sound amplification...

  1. Optimum sorption isotherm by linear and non-linear methods for malachite green onto lemon peel

    Microsoft Academic Search

    K. Vasanth Kumar

    2007-01-01

    Equilibrium studies were carried out at 305K for the sorption of malachite green onto lemon peel. The equilibrium data were fitted to the Freundlich, Langmuir and Redlich–Peterson isotherms by linear and non-linear methods. Non-linear method is a better way to obtain the isotherm parameters. The best fitting isotherm was found to be the Langmuir and Redlich–Peterson isotherm. Redlich Peterson is

  2. Asymmetric parametric amplification in nonlinear left-handed transmission lines

    E-print Network

    Asymmetric parametric amplification in nonlinear left-handed transmission lines David A. Powell amplification in nonlinear left-handed transmission lines, which serve as model systems for nonlinear negative-handed propagation in an asymmetric nonlinear left- handed transmission line due to the existence of multiple dynamic

  3. Correlations in single photon amplification : stimulated versus spontaneous processes

    E-print Network

    Boyer, Edmond

    873 Correlations in single photon amplification : stimulated versus spontaneous processes A of a single photon. It is shown that this amplifier thus appears not at all as a « photon cloner » but rather recently, it has been pointed out that novel questions arise when single photon optical amplification

  4. Multiple replication origins are used during Drosophila chorion gene amplification

    Microsoft Academic Search

    Margarete M. S. Heck; Allan C. Spradling

    1990-01-01

    DNA from Drosophila egg chambers under- going chorion gene amplification was analyzed using the two-dimensional gel technique of Brewer and Fangman. At stage 10, 34% of DNA molecules from the maximally amplified region of the third chromo- some chorion gene cluster contained replication forks or bubbles. These nonlinear forms were intermediates in the process of amplification; they were confined to

  5. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    ERIC Educational Resources Information Center

    Esernio-Jenssen, Debra; Barnes, Marilyn

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this…

  6. Generalized Privacy Amplification Charles H. Bennett Gilles Brassard

    E-print Network

    Crépeau, Claude

    Generalized Privacy Amplification Charles H. Bennett provides a general treatmentas the R'enyi entropy of or* *der two, is defined as the negative of privacy amplification by public discussion,laocon-garithm of its collision p* *robability: cept introduced by Bennett

  7. Explanatory Model for Sound Amplification in a Stethoscope

    ERIC Educational Resources Information Center

    Eshach, H.; Volfson, A.

    2015-01-01

    In the present paper we suggest an original physical explanatory model that explains the mechanism of the sound amplification process in a stethoscope. We discuss the amplification of a single pulse, a continuous wave of certain frequency, and finally we address the resonant frequencies. It is our belief that this model may provide students with…

  8. Clinical implication of centrosome amplification in plasma cell neoplasm

    Microsoft Academic Search

    Wee J. Chng; Greg J. Ahmann; Kim Henderson; Rafael Santana-Davila; Philip R. Greipp; Morie A. Gertz; Martha Q. Lacy; Angela Dispenzieri; Shaji Kumar; S. Vincent Rajkumar; John A. Lust; Robert A. Kyle; Steven R. Zeldenrust; Suzanne R. Hayman; Rafael Fonseca

    2006-01-01

    The mechanisms underlying aneuploidy in multiple myeloma (MM) are unclear. Centrosome amplification has been impli- cated as the cause of chromosomal insta- bility in a variety of tumors and is a potential mechanism causing aneuploidy in MM. Using immunofluorescent (IF) staining, centrosome amplification was detected in 67% of monoclonal gammopa- thies, including monoclonal gammopathy of undetermined significance (MGUS). We also

  9. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    Microsoft Academic Search

    Debra Esernio-Jenssen; Marilyn Barnes

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this may provide an efficacious alternative for children suspected of being sexually abused.

  10. Application of isothermal current deep level transient spectroscopy to solar cells

    SciTech Connect

    Rancour, D.P.; Pierret, R.F.; Lundstrom, M.S.; Melloch, M.R.

    1989-03-01

    The utility of isothermal current deep level transient spectroscopy (DLTS) techniques in directly probing solar cells is described and illustrated. A modified approach to processing the isothermal DLTS data is also presented. Specifically, it is pointed out that properly normalized isothermal data, whether derived from a current or capacitance transient, should conform to a single, temperature-independent curve.

  11. Understanding Inflections and Steps in Carbon Dioxide Adsorption Isotherms in Metal-Organic Frameworks

    E-print Network

    Yaghi, Omar M.

    Understanding Inflections and Steps in Carbon Dioxide Adsorption Isotherms in Metal-type mechanism"3c or a "gate effect."3a These unusual isotherm shapes are not found for CO2 adsorption in other experimental adsorption isotherms for CO2 in IRMOF-1 (MOF-5) over a wide range of temperatures. With decreasing

  12. Adsorption of dissolved organic carbon to mineral soils: A comparison of four isotherm approaches

    E-print Network

    Moore, Tim

    Adsorption of dissolved organic carbon to mineral soils: A comparison of four isotherm approaches D Langmuir Xi and Xf isotherms hold the advantage of estimating the maximum adsorption capacity, yet the Xf isotherm is a better reflection of adsorption processes. © 2008 Elsevier B.V. All rights reserved. 1

  13. Adsorption isotherms and thermal fluctuations K. R. Mecke* and J. Krim

    E-print Network

    Krim, Jacqueline

    Adsorption isotherms and thermal fluctuations K. R. Mecke* and J. Krim Physics Department fluctuations on adsorption isotherms is calculated within the context of a self- consistent mean-field theory the form of an adsorption isotherm, particularly in the thin-film regime ( 0 5 nm which is most commonly

  14. A modified Langmuir-Freundlich isotherm model for simulating pH-dependent adsorption effects

    E-print Network

    Clement, Prabhakar

    A modified Langmuir-Freundlich isotherm model for simulating pH-dependent adsorption effects equations such as Langmuir and Freundlich isotherms are widely used for modeling adsorption data. However as the modified Langmuir-Freundlich (MLF) isotherm, which can be used to simulate pH-dependent adsorption. The MLF

  15. Topographical and geological amplification: case studies and engineering implications

    USGS Publications Warehouse

    Celebi, M.

    1991-01-01

    Topographical and geological amplification that occurred during past earthquakes are quantified using spectral ratios of recorded motions. Several cases are presented from the 1985 Chilean and Mexican earthquakes as well as the 1983 Coalinga (California) and 1987 Supersition Hills (California) earthquake. The strong motions recorded in Mexico City during the 1985 Michoacan earthquake are supplemented by ambient motions recorded within Mexico City to quantify the now well known resonating frequencies of the Mexico City lakebed. Topographical amplification in Canal Beagle (Chile), Coalinga and Superstition Hills (California) are quantified using the ratios derived from the aftershocks following the earthquakes. A special dense array was deployed to record the aftershocks in each case. The implications of both geological and topographical amplification are discussed in light of current code provisions. The observed geological amplifications has already influenced the code provisions. Suggestions are made to the effect that the codes should include further provisions to take the amplification due to topography into account. ?? 1991.

  16. Signal Amplification of Bioassay Using Zinc Nanomaterials

    NASA Astrophysics Data System (ADS)

    Cowles, Chad L.

    An emerging trend in the analytical detection sciences is the employment of nanomaterials for bioassay signal transduction to identify analytes critical to public health. These nanomaterials have been specifically investigated for applications which require identification of trace levels of cells, proteins, or other molecules that can have broad ranging impacts to human health in fields such as clinical diagnostics, environmental monitoring, food and drink control, and the prevention of bioterrorism. Oftentimes these nanoparticle-based signal transduction or amplification approaches offer distinct advantages over conventional methods such as increased sensitivity, rapidity, or stability. The biological application of nanoparticles however, does suffer from drawbacks that have limited more widespread adoption of these techniques. Some of these drawbacks are, high cost and toxicity, arduous synthesis methods, functionalization and bioconjugation challenges, and laboratory disposal and environmental hazard issues, all of which have impeded the progression of this technology in some way or another. This work aims at developing novel techniques that offer solutions to a number of these hurdles through the development of new nanoparticle-based signal transduction approaches and the description of a previously undescribed nanomaterial. Zinc-based nanomaterials offer the opportunity to overcome some of the limitations that are encountered when other nanomaterials are employed for bioassay signal transduction. On the other hand, the biological application of zinc nanomaterials has been difficult because in general their fluorescence is in the blue range and the reported quantum yields are usually too low for highly sensitive applications. The advantages of using zinc nanomaterials for biological applications, such as reduced toxicity, simple synthesis, low cost, and straightforward functionalization strategies contribute to the research interest in their application as bioassay signal tranducers. To overcome the limitations associated with zinc-based nanomaterials, a novel signal transduction approach was developed that relies on zinc ion release from nanoparticle labels during an immunoassay. The development of an innovative method for zinc ion detection and the description of a previously undescribed zinc-based nanomaterial are also described in this work. There are three major contributions to science in this work: (1) The development of an original and innovative signal transduction approach for immunoassays that adopts fluorescence detection of zinc ions released from ZnS nanoparticle labels; (2) The discovery and development of dual signal amplification for immunoassay signal transduction using ion release and subsequent activation of a zinc dependent metallozyme; (3) The synthesis and characterization of a novel zinc-based nanomaterial and its biosensing application using both single and dual signal amplification strategies.

  17. Simulated Water Adsorption Isotherms in Hydrophilic and Hydrophobic Cylinderical Nanopores

    SciTech Connect

    StrioloDr., A [Vanderbilt University; Naicker, P. K. [Vanderbilt University; Chialvo, Ariel A [ORNL; Cummings, Peter T [ORNL; Gubbins, Dr. K. E. [North Carolina State University

    2005-01-01

    Grand canonical Monte Carlo simulations are performed to study the adsorption of water in single-walled carbon nanotubes (SWCNs). At room temperature the resulting adsorption isotherms in (10:10) and wider SWCNs are characterized by negligible amount of water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption/desorption hysteresis loops. The width of these loops decreases as pore diameter narrows. Adsorption/desorption hysteresis loops are not observed for water adsorption in (6:6) SWCNs. When the nanotubes are doped with small amounts of oxygenated sites it is possible to obtain adsorption isotherms in which the water uptake increases gradually as the pressure increases. Simulated X-ray diffraction patterns for confined water are also reported.

  18. A Conformal Mapping and Isothermal Perfect Fluid Model

    E-print Network

    Naresh Dadhich

    1996-05-01

    Instead of conformal to flat spacetime, we take the metric conformal to a spacetime which can be thought of as ``minimally'' curved in the sense that free particles experience no gravitational force yet it has non-zero curvature. The base spacetime can be written in the Kerr-Schild form in spherical polar coordinates. The conformal metric then admits the unique three parameter family of perfect fluid solution which is static and inhomogeneous. The density and pressure fall off in the curvature radial coordinates as $R^{-2}, $ for unbounded cosmological model with a barotropic equation of state. This is the characteristic of isothermal fluid. We thus have an ansatz for isothermal perfect fluid model. The solution can also represent bounded fluid spheres.

  19. LES of droplet-laden non-isothermal channel flow

    NASA Astrophysics Data System (ADS)

    Micha?ek, W. R.; Liew, R.; Kuerten, J. G. M.; Zeegers, J. C. H.

    2011-12-01

    In this paper subgrid models for LES of droplet-laden non-isothermal channel flow are tested and improved for three Reynolds numbers based on friction velocity, Re? of 150, 395, and 950 with the aim to develop a simulation method for LES of a droplet-laden Ranque-Hilsch vortex tube. A new subgrid model combining the beneficial properties of the dynamic eddy-viscosity model and the approximate deconvolution model is proposed. Furthermore, the subgrid model in the droplet equations based on approximate deconvolution is found to perform well also in non-isothermal channel flow. At the highest Reynolds number in the test the dynamic model yields results with a similar accuracy as the approximate deconvolution model.

  20. Multifractal characteristics of Nitrogen adsorption isotherms from tropical soils

    NASA Astrophysics Data System (ADS)

    Vidal Vázquez, Eva; Paz Ferreiro, Jorge

    2010-05-01

    One of the primary methods used to characterize a wide range of porous materials, including soils, are gas adsorption isotherms. An adsorption isotherm is a function relating the amount of adsorbed gas or vapour to the respective equilibrium pressure, during pressure increase at constant temperature. Adsorption data allow easily estimates of specific surface area and also can provide a characterization of pore surface heterogeneity. Most of the properties and the reactivity of soil colloids are influenced by their specific surface area and by parameters describing the surface heterogeneity. For a restricted scale range, linearity between applied pressure and volume of adsorbate holds, which is the basis for current estimations of specific surface area. However, adsorption isotherms contain also non-linear segments of pressure versus volume so that evidence of multifractal scale has been demonstrated. The aim of this study was to analyze the multifractal behaviour of nitrogen adsorption isotherms from a set of tropical soils. Samples were collected form 54 horizons belonging to 19 soil profiles in the state of Minas Gerais, Brazil. The most frequent soil type was Oxisol, according to the Soil Survey Staff, equivalent to Latossolo in the Brazilian soil classification system. Nitrogen adsorption isotherms at standard 77 K were measured using a Thermo Finnigan Sorptomatic 1990 gas sorption analyzer (Thermo Scientific, Waltham, MA). From the raw data a distributions of mass along a support was obtained to perform multifractal analysis. The probability distribution was constructed by dividing the values of the measure in a given segment by the sum of the measure in the whole scale range. The box-counting method was employed to perform multifractal analysis. All the analyzed N2 adsorption isotherms behave like a multifractal system. The singularity spectra, f(?), showed asymmetric concave down parabolic shapes, with a greater tendency toward the left side, where moments q >0. The width of the f(?) spectra ranged from 1.167 to 2.741 for individual isotherms. Therefore, shape and width of the singularity spectra suggest a high heterogeneity in the local scaling indices of the measure. The mass exponent function, ?(q), and the generalized dimension, Dq, also corroborate this pattern. The capacity dimension, D0, was not significantly different from 1.000, but the entropy dimension, D1, showed a wide range of values, from 0.317 to 0.749, as did the correlation dimension, D2, which oscillates between 0.157 and 0.675. In accordance with this parameter (D0- D2) ranged from 0.325 to 0.843. The value of D1 is also a good index of the degree of heterogeneity of a measure. The closer the D1 value to the capacity dimension, the more homogeneous is the distribution of the measure, whereas a D1 value close to zero is associated to clustering , so that most of the measure concentrates in a small size domain of the study scale. Because of the wide range of values obtained for D1, D2 and (D0 - D2), these multifractal parameters provide a good characterization of N2 adsorption isotherms and they appear to be appropriate to discriminate different soil types and soil horizons. Acknowledgement: This work was supported by Spanish Ministry of Education (Project PHB2009-0094-PC) and Spanish Ministry of Science and Innovation (Project CGL2009-13700-C02).

  1. Adsorption Isotherms of Hydrogen: The Role of Thermal Fluctuations

    NASA Astrophysics Data System (ADS)

    Vorberg, Jens; Herminghaus, Stephan; Mecke, Klaus

    2001-11-01

    It is shown that experimentally obtained isotherms of adsorption on solid substrates may be completely reconciled with Lifshitz theory when thermal fluctuations of the free film surface are taken into account. This is demonstrated for hydrogen adsorbed on gold as a model system. Analysis of the fluctuation contributions allows one to determine the surface tension of the free hydrogen film as a function of film thickness. It is found to decrease sharply for film thicknesses below seven atomic layers.

  2. Non-isothermal buckling behavior of viscoplastic shell structures

    NASA Technical Reports Server (NTRS)

    Riff, Richard; Simitses, G. J.

    1988-01-01

    Described are the mathematical model and solution methodologies for analyzing the structural response of thin, metallic elasto-viscoplastic shell structures under large thermomechanical loads and their non-isothermal buckling behavior. Among the system responses associated with these loads and conditions are snap-through, buckling, thermal buckling, and creep buckling. This geometric and material nonlinearities (of high order) can be anticipated and are considered in the model and the numerical treatment.

  3. Adsorption isotherms of phenols from water onto macroreticular resins

    Microsoft Academic Search

    Ruey-Shin Juang; Jia-Yun Shiau

    1999-01-01

    The amounts of equilibrium adsorption of phenol and 4-chlorophenol from water on non-ionic macroreticular resins were measured in the temperature range 288–318 K. It was shown that the isotherm data could not be fit by any conventional two- or three-parameter equation including the Langmuir, Freundlich, BET, and Redlich–Peterson equations over the entire range of concentration (1–32 mol m?3). They were

  4. Modelling of Non-Isothermal Non-Newtonian Viscoelastic Flows

    Microsoft Academic Search

    X. K. Li; X. H. Han; Q. L. Duan

    An adaptive coupled finite element (FE) and meshfree (MF) method in ALE description for numerical simulation of injection\\u000a molding processes is proposed. In combination with the proposed method, an iterative stabilized fractional step algorithm\\u000a using Characteristic Based Split procedure for numerical simulation of incompressible non-isothermal non-Newtonian fluid flows\\u000a is developed. The pressure stabilization is further enhanced with introduction of the

  5. Moisture sorption isotherms and thermodynamic properties of walnut kernels

    Microsoft Academic Search

    Hasan To?rul; Nurhan Arslan

    2007-01-01

    The moisture sorption isotherm data of walnut kernels stored in a chamber, the relative humidity (r.h.) of which is regulated by atomizing humidifier, were determined at three different temperatures (25, 35 and 45°C) and r.h. ranging from 10% to 90%. Eight models, namely the GAB, BET, Henderson, Iglesias and Chirife, Oswin, Peleg, Smith and Caurie equations, were fitted to the

  6. Isothermal Phase Diagrams of Binary Alloys and Two Oxidants

    Microsoft Academic Search

    S. WangC; C. S. Ni; F. Gesmundo; Y. Niu

    2010-01-01

    An example of an isothermal thermodynamic phase diagram of a quaternary system composed of a binary alloy and two oxidants\\u000a has been calculated under appropriate values of the stability of the corresponding compounds, assuming that each metal forms\\u000a only one compound with each oxidant. Initially, two-dimensional sections of the complete three-dimensional diagram made along\\u000a planes corresponding to constant values of

  7. Equilibrium sorption isotherm for metal ions on tree fern

    Microsoft Academic Search

    Y. S. Ho; C. T. Huang; H. W. Huang

    2002-01-01

    A new sorbent system for removing heavy metal ions, such as Zn(II), Cu(II) and Pb(II), from aqueous solutions has been investigated. This new sorbent is tree fern, an agriculture product. Variables of the system include solution temperature and sorbent particle size. The experimental results were fitted to the Langmuir, Freundlich and Redlich–Peterson isotherms to obtain the characteristic parameters of each

  8. Parameter identification in non-isothermal nucleation and growth processes

    NASA Astrophysics Data System (ADS)

    Hömberg, Dietmar; Lu, Shuai; Sakamoto, Kenichi; Yamamoto, Masahiro

    2014-03-01

    We study non-isothermal nucleation and growth phase transformations, which are described by a generalized Avrami model for the phase transition coupled with an energy balance to account for recalescence effects. The main novelty of our work is the identification of temperature dependent nucleation rates. We prove that such rates can be uniquely identified from measurements in a subdomain and apply an optimal control approach to develop a numerical strategy for its computation.

  9. Calorimetric studies of isothermal curing of phase separating epoxy networks

    Microsoft Academic Search

    W. Jenninger; J. E. K. Schawe; I. Alig

    2000-01-01

    To get a better understanding of the curing process of multi-component thermosets differential scanning calorimetric (DSC) and temperature modulated DSC (TMDSC) measurements were performed during isothermal curing of semi-interpenetrating polymer networks (semi-IPNs) with amounts of 10 or 20wt.% of linear polymer and of the corresponding pure networks at temperatures between 333 and 393K. The network component consists of diglycidylether of

  10. Isothermal diffusion in uranium-plutonium-zirconium alloys

    Microsoft Academic Search

    M. C. Petri; M. A. Dayananda

    1997-01-01

    Isothermal diffusion couple experiments were performed at 1023 K to investigate diffusion phenomena in body-centered cubic U?Pu?Zr alloys. The U?Pu?Zr alloys covered the uranium-rich corner of the ternary phase diagram with plutonium concentrations up to 27 at.% and zirconium concentrations up to 20 at.%. Ternary interdiffusion coefficients were calculated at the common composition between two couples with intersecting diffusion paths.

  11. [Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

    PubMed

    Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

    2006-01-01

    Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory. PMID:17027192

  12. Application of cross-priming amplification (CPA) for detection of fowl adenovirus (FAdV) strains.

    PubMed

    Niczyporuk, Jowita Samanta; Wo?niakowski, Grzegorz; Samorek-Salamonowicz, El?bieta

    2015-04-01

    Fowl adenoviruses (FAdVs) are widely distributed among chickens. Detection of FAdVs is mainly accomplished by virus isolation, serological assays, various polymerase chain reaction (PCR) assays, and loop-mediated isothermal amplification (LAMP). To increase the diagnostic capacity of currently applied techniques, cross-priming amplification (CPA) for the detection of the FAdV hexon gene was developed. The single CPA assay was optimised to detect all serotypes 1-8a-8b-11 representing the species Fowl aviadenovirus A-E. The optimal temperature and incubation time were determined to be 68 °C for 2 h. Using different incubation temperatures, it was possible to differentiate some FAdV serotypes. The results were recorded after addition of SYBR Green I(®) dye, which produced a greenish fluorescence under UV light. The CPA products separated by gel electrophoresis showed different "ladder-like" patterns for the different serotypes. The assay was specific for all serotypes of FAdV, and no cross-reactivity was observed with members of the genus Atadenovirus, duck atadenovirus A (egg drop syndrome virus EDS-76 [EDSV]) or control samples containing Marek's disease virus (MDV), infectious laryngotracheitis virus (ILTV) or chicken anaemia virus (CAV). The results of the newly developed FAdV-CPA were compared with those of real-time PCR. The sensitivity of CPA was equal to that of real-time PCR and reached 10(-2.0) TCID50, but the CPA method was more rapid and cheaper than the PCR systems. CPA is a highly specific, sensitive, efficient, and rapid tool for detection of all FAdV serotypes. This is the first report on the application of CPA for detection of FAdV strains. PMID:25655263

  13. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology

    PubMed Central

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10?3 for bcr1 and bcr3 and 10?2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL. PMID:25815362

  14. Coronal Diagnostic Spectrometer Observations of Isothermal and Multithermal Coronal Loops

    NASA Astrophysics Data System (ADS)

    Schmelz, J. T.; Nasraoui, K.; Del Zanna, G.; Cirtain, J. W.; DeLuca, E. E.; Mason, H. E.

    2007-04-01

    A data set obtained on 2003 January 17 with the Coronal Diagnostic Spectrometer (CDS) shows two loops sitting side by side on the solar disk. These loops are oriented along the CDS slit, so all pixels in each loop were observed simultaneously. So, although the instrument has a relatively slow time cadence, changes as a function of time that may occur during the CDS raster buildup will not affect the loop temperature results. Differential emission measure (DEM) analysis using a forward-folding technique shows different results for the two loops. For the first loop, the intensities of the lines that remain after background subtraction are well fit with a DEM curve that collapses to a single spike. In other words, the loop plasma at this location is isothermal. This analysis is confirmed with an emission measure loci method and agrees with the results obtained recently by other authors that show that the moderate spatial resolution of CDS can detect isothermal structures. For the second loop, the background-subtracted line intensities require a broad DEM, not consistent with isothermal plasma. This conclusion is confirmed with an automatic-inversion DEM method. In this Letter, we specifically address some of the concerns raised about CDS temperature analysis: the slow CDS temporal resolution, the moderate CDS spatial resolution, the inherent smoothing associated with DEM inversion, and line-of-sight effects on the DEM distribution.

  15. Anisotropic metamaterials with simultaneous attenuation and amplification

    E-print Network

    Mackay, Tom G

    2015-01-01

    Anisotropic metamaterials that are neither wholly dissipative nor wholly active at a specific frequency are permitted by classical electromagnetic theory. Well-established formalisms for the homogenization of particulate composite materials indicate that such a metamaterial may be conceptualized quite simply as a random mixture of electrically small spheroidal particles of at least two different isotropic dielectric materials, one of which must be dissipative but the other active. The realization of this metametarial is influenced by the volume fraction, spatial distribution, particle shape and size, and the relative permittivities of the component materials. Metamaterials displaying both dissipation and amplification at the same frequency with more complicated linear as well as nonlinear constitutive properties are possible.

  16. Superparamagnetic Nanoparticle Capture of Prions for Amplification?

    PubMed Central

    Miller, Michael B.; Supattapone, Surachai

    2011-01-01

    Prion diseases are associated with the presence of PrPSc, a disease-associated misfolded conformer of the prion protein. We report that superparamagnetic nanoparticles bind PrPSc molecules efficiently and specifically, permitting magnetic separation of prions from a sample mixture. Captured PrPSc molecules retain the activity to seed protein misfolding cyclic amplification (PMCA) reactions, enabling the rapid concentration of dilute prions to improve detection. Furthermore, superparamagnetic nanoparticles clear contaminated solutions of PrPSc. Our findings suggest that coupling magnetic nanoparticle capture with PMCA could accelerate and improve prion detection. Magnetic nanoparticles may also be useful for developing a nontoxic prion decontamination method for biologically derived products. PMID:21228242

  17. Optimizing biased semiconductor superlattices for terahertz amplification

    SciTech Connect

    Lei, Xiaoli [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049 (China); Xi'an University of Post and Telecommunications, Xi'an 710061 (China); Wang, Dawei [Electronic Materials Research Laboratory–Key Laboratory of the Ministry of Education and International Center for Dielectric Research, Xi'an Jiaotong University, Xi'an 710049 (China); Wu, Zhaoxin, E-mail: zhaoxinwu@mail.xjtu.edu.cn [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an 710049 (China); Dignam, M. M. [Department of Physics, Engineering Physics and Astronomy, Queen's University, Kingston, Ontario K7L 3N6 (Canada)

    2014-08-11

    Over the past 15 yr or more, researchers have been trying to achieve gain for electromagnetic fields in the terahertz frequency region using biased semiconductor superlattices, but with little success. In this work, we employ our model of the excitonic states in biased GaAs/Al{sub 0.3}Ga{sub 0.7}As semiconductor superlattices to find the optimal structures for amplification of terahertz radiation. In particular, we determine the optimum well width, barrier width, and bias field for terahertz fields with frequencies ranging from 1 to 4 terahertz. We find that gain coefficients on the order of 40?cm{sup ?1} should be achievable over most of this frequency range.

  18. Amplification of electromagnetic signals by ion channels.

    PubMed Central

    Galvanovskis, J; Sandblom, J

    1997-01-01

    Cells may respond to the exposure of low-frequency electromagnetic fields with changes in cell division, ion influx, chemical reaction rates, etc. The chain of events leading to such responses is difficult to study, mainly because of extremely small energies associated with low-frequency fields, usually much smaller than the thermal noise level. However, the presence of stochastic systems (for instance, ion channels) provides a basis for signal amplification, and could therefore, despite the low signal-to-noise ratio of the primary response, lead to the transmission of weak signals along the signaling pathways of cells. We have explored this possibility for an ion channel model, and we present a theory, based on the formalism of stochastically driven processes, that relates the time averages of the ion channel currents to the amplitude and frequency of the applied signal. It is concluded from this theory that the signal-to-noise ratio increases with the number of channels, the magnitude of the rate constants, and the frequency response of the intracellular sensing system (for instance, a calcium oscillator). The amplification properties of the stochastic system are further deduced from numerical simulations carried out on the model, which consists of multiple identical two-state channels, and the behavior for different parameters is examined. Numerical estimates of the parameters show that under optimum conditions, even very weak low-frequency electromagnetic signals (<100 Hz and down to 100 microT) may be detected in a cellular system with a large number of ion channels. PMID:9414219

  19. Cascade DNA nanomachine and exponential amplification biosensing.

    PubMed

    Xu, Jianguo; Wu, Zai-Sheng; Shen, Weiyu; Xu, Huo; Li, Hongling; Jia, Lee

    2015-11-15

    DNA is a versatile scaffold for the assembly of multifunctional nanostructures, and potential applications of various DNA nanodevices have been recently demonstrated for disease diagnosis and treatment. In the current study, a powerful cascade DNA nanomachine was developed that can execute the exponential amplification of p53 tumor suppressor gene. During the operation of the newly-proposed DNA nanomachine, dual-cyclical nucleic acid strand-displacement polymerization (dual-CNDP) was ingeniously introduced, where the target trigger is repeatedly used as the fuel molecule and the nicked fragments are dramatically accumulated. Moreover, each displaced nicked fragment is able to activate the another type of cyclical strand-displacement amplification, increasing exponentially the value of fluorescence intensity. Essentially, one target binding event can induce considerable number of subsequent reactions, and the nanodevice was called cascade DNA nanomachine. It can implement several functions, including recognition element, signaling probe, polymerization primer and template. Using the developed autonomous operation of DNA nanomachine, the p53 gene can be quantified in the wide concentration range from 0.05 to 150nM with the detection limit of 50pM. If taking into account the final volume of mixture, the detection limit is calculated as lower as 6.2pM, achieving an desirable assay ability. More strikingly, the mutant gene can be easily distinguished from the wild-type one. The proof-of-concept demonstrations reported herein is expected to promote the development and application of DNA nanomachine, showing great potential value in basic biology and medical diagnosis. PMID:26042874

  20. Mutualism Breakdown by Amplification of Wolbachia Genes

    PubMed Central

    Chrostek, Ewa; Teixeira, Luis

    2015-01-01

    Most insect species are associated with vertically transmitted endosymbionts. Because of the mode of transmission, the fitness of these symbionts is dependent on the fitness of the hosts. Therefore, these endosymbionts need to control their proliferation in order to minimize their cost for the host. The genetic bases and mechanisms of this regulation remain largely undetermined. The maternally inherited bacteria of the genus Wolbachia are the most common endosymbionts of insects, providing some of them with fitness benefits. In Drosophila melanogaster, Wolbachia wMelPop is a unique virulent variant that proliferates massively in the hosts and shortens their lifespan. The genetic bases of wMelPop virulence are unknown, and their identification would allow a better understanding of how Wolbachia levels are regulated. Here we show that amplification of a region containing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. Using Drosophila lines selected for carrying Wolbachia with different Octomom copy numbers, we demonstrate that the number of Octomom copies determines Wolbachia titers and the strength of the lethal phenotype. Octomom amplification is unstable, and reversion of copy number to one reverts all the phenotypes. Our results provide a link between genotype and phenotype in Wolbachia and identify a genomic region regulating Wolbachia proliferation. We also prove that these bacteria can evolve rapidly. Rapid evolution by changes in gene copy number may be common in endosymbionts with a high number of mobile elements and other repeated regions. Understanding wMelPop pathogenicity and variability also allows researchers to better control and predict the outcome of releasing mosquitoes transinfected with this variant to block human vector-borne diseases. Our results show that transition from a mutualist to a pathogen may occur because of a single genomic change in the endosymbiont. This implies that there must be constant selection on endosymbionts to control their densities. PMID:25668031

  1. Mutualism breakdown by amplification of Wolbachia genes.

    PubMed

    Chrostek, Ewa; Teixeira, Luis

    2015-02-01

    Most insect species are associated with vertically transmitted endosymbionts. Because of the mode of transmission, the fitness of these symbionts is dependent on the fitness of the hosts. Therefore, these endosymbionts need to control their proliferation in order to minimize their cost for the host. The genetic bases and mechanisms of this regulation remain largely undetermined. The maternally inherited bacteria of the genus Wolbachia are the most common endosymbionts of insects, providing some of them with fitness benefits. In Drosophila melanogaster, Wolbachia wMelPop is a unique virulent variant that proliferates massively in the hosts and shortens their lifespan. The genetic bases of wMelPop virulence are unknown, and their identification would allow a better understanding of how Wolbachia levels are regulated. Here we show that amplification of a region containing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. Using Drosophila lines selected for carrying Wolbachia with different Octomom copy numbers, we demonstrate that the number of Octomom copies determines Wolbachia titers and the strength of the lethal phenotype. Octomom amplification is unstable, and reversion of copy number to one reverts all the phenotypes. Our results provide a link between genotype and phenotype in Wolbachia and identify a genomic region regulating Wolbachia proliferation. We also prove that these bacteria can evolve rapidly. Rapid evolution by changes in gene copy number may be common in endosymbionts with a high number of mobile elements and other repeated regions. Understanding wMelPop pathogenicity and variability also allows researchers to better control and predict the outcome of releasing mosquitoes transinfected with this variant to block human vector-borne diseases. Our results show that transition from a mutualist to a pathogen may occur because of a single genomic change in the endosymbiont. This implies that there must be constant selection on endosymbionts to control their densities. PMID:25668031

  2. Clinical implication of centrosome amplification in plasma cell neoplasm.

    PubMed

    Chng, Wee J; Ahmann, Greg J; Henderson, Kim; Santana-Davila, Rafael; Greipp, Philip R; Gertz, Morie A; Lacy, Martha Q; Dispenzieri, Angela; Kumar, Shaji; Rajkumar, S Vincent; Lust, John A; Kyle, Robert A; Zeldenrust, Steven R; Hayman, Suzanne R; Fonseca, Rafael

    2006-05-01

    The mechanisms underlying aneuploidy in multiple myeloma (MM) are unclear. Centrosome amplification has been implicated as the cause of chromosomal instability in a variety of tumors and is a potential mechanism causing aneuploidy in MM. Using immunofluorescent (IF) staining, centrosome amplification was detected in 67% of monoclonal gammopathies, including monoclonal gammopathy of undetermined significance (MGUS). We also investigated the gene expression of centrosome proteins. Overall, gene expression data correlated well with IF-detected centrosome amplification, allowing us to derive a gene expression-based centrosome index (CI) as a surrogate for centrosome amplification. Clinically, MM patients with high CI (> 4) are associated with poor prognostic genetic and clinical subtypes (chromosome 13 deletion, t(4; 14), t(14;16), and PCLI > 1%, P < .05) and are shown here to have short survival (11.1 months versus 39.1 months, P < .001). On multivariate regression, a high CI is an independent prognostic factor. Given that centrosome amplification is already observed in MGUS and probably integral to early chromosomal instability and myeloma genesis, and patients with more extensive centrosome amplification have shorter survival, the mechanisms leading to centrosome amplification should be investigated because these may offer new avenues for therapeutic intervention. PMID:16373658

  3. Loop-mediated amplification of the Clavibacter michiganensis subsp. michiganensis micA gene is highly specific.

    PubMed

    Yasuhara-Bell, Jarred; Kubota, Ryo; Jenkins, Daniel M; Alvarez, Anne M

    2013-12-01

    Loop-mediated amplification (LAMP) was used to specifically identify Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial canker of tomato. LAMP primers were developed to detect micA, a chromosomally stable gene that encodes a type II lantibiotic, michiganin A, which inhibits growth of other C. michiganensis subspecies. In all, 409 bacterial strains (351 C. michiganensis subsp. michiganensis and 58 non-C. michiganensis subsp. michiganensis) from a worldwide collection were tested with LAMP to determine its specificity. LAMP results were compared with genetic profiles established using polymerase chain reaction (PCR) amplification of seven genes (dnaA, ppaJ, pat-1, chpC, tomA, ppaA, and ppaC). C. michiganensis subsp. michiganensis strains produced eight distinct profiles. The LAMP reaction identified all C. michiganensis subsp. michiganensis strains and discriminated them from other C. michiganensis subspecies and non-Clavibacter bacteria. LAMP has advantages over immunodiagnostic and other molecular detection methods because of its specificity and isothermal nature, which allows for easy field application. The LAMP reaction is also not affected by as many inhibitors as PCR. This diagnostic tool has potential to provide an easy, one-step test for rapid identification of C. michiganensis subsp. michiganensis. PMID:23802869

  4. A simple smart amplification assay for the rapid detection of human cytomegalovirus in the urine of neonates.

    PubMed

    Kohda, Chikara; Chiba, Nao; Shimokoba, Kengo; Mizuno, Katsumi; Negoro, Takaharu; Nakano, Yasuko; Tanaka, Kazuo

    2014-11-01

    Human cytomegalovirus (CMV) is the most common cause of infection-related congenital abnormalities in neonates and the leading cause of non-hereditary sensorineural hearing loss in childhood. In addition, the number of low-birth-weight infants has recently increased, especially in Japan, in association with an increasing frequency of postnatal CMV infections transferred through raw breast milk. The increase in the number of congenital CMV and postnatal CMV infections in low-birth-weight infants requires rapid detection at the bedside in order to ensure a correct diagnosis and provide early anti-viral therapy. In this report, a simplified smart amplification (SMAP) method was developed to detect CMV in the urine of neonates. This method does not require DNA extraction, and the DNA amplification procedure is performed under isothermal conditions. Therefore, it takes only 60 min to detect CMV in a urine sample, and CMV DNA was rapidly detectable in symptomatic infants. In brief, this SMAP-based assay provides a simple, rapid and efficient method for detecting human CMV at the bedside. PMID:25110117

  5. A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification.

    PubMed

    Wu, Wei; Zhao, Shiming; Mao, Yiping; Fang, Zhiyuan; Lu, Xuewen; Zeng, Lingwen

    2015-02-25

    Foodborne diseases caused by pathogens are one of the major problems in food safety. Convenient and sensitive point-of-care rapid diagnostic tests for food-borne pathogens have been a long-felt need of clinicians. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. These methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive aptamer based biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). In this assay, two different aptamers specific for the outmembrane of E. coli O157:H7 were used. One of the aptamers was used for magnetic bead enrichment, and the other was used as a signal reporter for this pathogen, which was amplified by isothermal strand displacement amplification (SDA) and further detected by a lateral flow biosensor. Only the captured aptamers on cell membrane were amplified, limitations of conventional DNA amplification based method such as false-positive can be largely reduced. The generated signals (red bands on the test zone of a lateral flow strip) can be unambiguously read out by the naked eye. As low as 10 colony forming units (CFU) of E. coli O157:H7 were detected in this study. Without DNA extraction, the reduced handling and simpler equipment requirement render this assay a simple and rapid alternative to conventional methods. PMID:25702275

  6. Colorimetric monitoring of rolling circle amplification for detection of H5N1 influenza virus using metal indicator.

    PubMed

    Hamidi, Seyed Vahid; Ghourchian, Hedayatollah

    2015-10-15

    A new colorimetric method for monitoring of rolling circle amplification was developed. At first H5N1 target hybrids with padlock probe (PLP) and then PLP is circularized upon the action of T4 ligase enzyme. Subsequently, the circular probe is served as a template for hyperbranched rolling circle amplification (HRCA) by utilizing Bst DNA polymerase enzyme. By improving the reaction, pyrophosphate is produced via DNA polymerization and chelates the Mg(2+) in the buffer solution. This causes change in solution color in the presence of hydroxy naphthol blue (HNB) as a metal indicator. By using pH shock instead of heat shock and isothermal RCA reaction not only the procedure becomes easier, but also application of HNB for colorimetric detection of RCA reaction further simplifies the assay. The responses of the biosensor toward H5N1 were linear in the concentration range from 0.16 to 1.20pM with a detection limit of 28 fM. PMID:25974174

  7. Amplification and chromosomal dispersion of human endogenous retroviral sequences

    SciTech Connect

    Steele, P.E.; Martin, M.A.; Rabson, A.B.; Bryan, T.; O'Brien, S.J.

    1986-09-01

    Endogenous retroviral sequences have undergone amplification events involving both viral and flanking cellular sequences. The authors cloned members of an amplified family of full-length endogenous retroviral sequences. Genomic blotting, employing a flanking cellular DNA probe derived from a member of this family, revealed a similar array of reactive bands in both humans and chimpanzees, indicating that an amplification event involving retroviral and associated cellular DNA sequences occurred before the evolutionary separation of these two primates. Southern analyses of restricted somatic cell hybrid DNA preparations suggested that endogenous retroviral segments are widely dispersed in the human genome and that amplification and dispersion events may be linked.

  8. Recyclable amplification protocol for the single-photon entangled state

    NASA Astrophysics Data System (ADS)

    Zhou, Lan; Sheng, Yu-Bo

    2015-04-01

    Photon loss is one of the main obstacles in long-distance quantum communication. In this letter, we put forward a highly efficient recyclable amplification protocol for protecting the single-photon entangled state. Different from all of the existing amplification protocols, by repeating the protocol, the discarded items can be reused to increase the success probability and the distilled new mixed state can be further amplified in a next round to increase its fidelity. In particular, this protocol is quite useful under high photon loss conditions. These features make our amplification protocol useful in future long-distance quantum communications.

  9. Preparation of DNA-containing extract for PCR amplification

    DOEpatents

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

  10. Sensitive colorimetric detection of protein by gold nanoparticles and rolling circle amplification.

    PubMed

    Chen, Chaohui; Luo, Ming; Ye, Tai; Li, Ningxing; Ji, Xinghu; He, Zhike

    2015-06-15

    An ultrasensitive method for the detection of protein is critically important in fundamental research and practical applications due to the low abundance of disease markers in body fluids or tissues. To detect the trace levels of disease markers with high sensitivity and specificity, a sensitive colorimetric biosensor for protein assay was developed using gold nanoparticles (AuNPs) and rolling circle amplification (RCA). After binding the biotinylated primer/circular template to the streptavidin-conjugated sandwich ELISA immunocomplex, the biotinylated primer was isothermally extended to generate single-stranded DNA (ssDNA). Sequentially, the padlock DNA was added and hybridized with the RCA products. The aggregation of the additional AuNPs in the supernatant containing the surplus padlock DNA and a certain concentration of salt could then be observed. The established sensor allowed for the specific detection of ?-fetoprotein (AFP) with a detection limit of 33.45 pg mL(-1). It was also demonstrated that this method could distinguish 500 pg mL(-1) AFP with the naked eye. In addition, this biosensor could be applied to complex sample analysis and could be further used as a universal method for any protein or virus determination by changing the corresponding antibodies. PMID:25988199

  11. Gap formation and stability in non-isothermal protoplanetary discs

    NASA Astrophysics Data System (ADS)

    Les, Robert; Lin, Min-Kai

    2015-06-01

    Several observations of transition discs show lopsided dust distributions. A potential explanation is the formation of a large-scale vortex acting as a dust-trap at the edge of a gap opened by a giant planet. Numerical models of gap-edge vortices have so far employed locally isothermal discs in which the temperature profile is held fixed, but the theory of this vortex-forming or `Rossby wave' instability was originally developed for adiabatic discs. We generalize the study of planetary gap stability to non-isothermal discs using customized numerical simulations of disc-planet systems where the planet opens an unstable gap. We include in the energy equation a simple cooling function with cooling time-scale t_c=? ? _k^{-1}, where ?k is the Keplerian frequency, and examine the effect of ? on the stability of gap edges and vortex lifetimes. We find increasing ? lowers the growth rate of non-axisymmetric perturbations, and the dominant azimuthal wavenumber m decreases. We find a quasi-steady state consisting of one large-scale, overdense vortex circulating the outer gap edge, typically lasting O(103) orbits. We find vortex lifetimes generally increase with the cooling time-scale tc up to an optimal value of tc ˜ 10 orbits, beyond which vortex lifetimes decrease. This non-monotonic dependence is qualitatively consistent with recent studies using strictly isothermal discs that vary the disc aspect ratio. The lifetime and observability of gap-edge vortices in protoplanetary discs is therefore dependent on disc thermodynamics.

  12. Centrifugal LabTube platform for fully automated DNA purification and LAMP amplification based on an integrated, low-cost heating system.

    PubMed

    Hoehl, Melanie M; Weißert, Michael; Dannenberg, Arne; Nesch, Thomas; Paust, Nils; von Stetten, Felix; Zengerle, Roland; Slocum, Alexander H; Steigert, Juergen

    2014-06-01

    This paper introduces a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA purification platform (LabTube). We demonstrate LabTube-based fully automated DNA purification of as low as 100 cell-equivalents of verotoxin-producing Escherichia coli (VTEC) in water, milk and apple juice in a laboratory centrifuge, followed by integrated and automated LAMP amplification with a reduction of hands-on time from 45 to 1 min. The heating system consists of two parallel SMD thick film resistors and a NTC as heating and temperature sensing elements. They are driven by a 3 V battery and controlled by a microcontroller. The LAMP reagents are stored in the elution chamber and the amplification starts immediately after the eluate is purged into the chamber. The LabTube, including a microcontroller-based heating system, demonstrates contamination-free and automated sample-to-answer nucleic acid testing within a laboratory centrifuge. The heating system can be easily parallelized within one LabTube and it is deployable for a variety of heating and electrical applications. PMID:24562605

  13. Easy-to-use rapid gene amplification method for direct detection of RNA and DNA viruses in sera and feces from various animals.

    PubMed

    Segawa, Takao; Kobayashi, Yuki; Sase, Yukina; Itou, Takuya; Suzuki, Miwa; Endoh, Tomoko; Nakanishi, Teruyuki; Sakai, Takeo

    2014-06-01

    The development of rapid and simple gene amplification tests is required for detection of pathogens to prevent transmission of infectious diseases between animals or from animals to humans. An easy-to-use rapid gene amplification method that can directly detect RNA and DNA viruses in clinical samples was developed. This method is based on combining loop-mediated isothermal amplification (LAMP) or reverse transcription-LAMP (RT-LAMP) and RNA GEM Tissue, a thermophilic enzyme that extracts nucleic acid by quickly digesting proteins and ribonucleases. The authors named these methods GEM LAMP and GEM RT-LAMP. These methods were able to detect viral DNA and RNA within 70 min in a single tube using only a water bath. The detection capacities were 10-100-fold more sensitive than those of previously established LAMP and RT-LAMP methods. The GEM LAMP and GEM RT-LAMP methods were used to detect macroscopically the presence of DNA and RNA viruses in sera or fecal samples from cattle, pigs, horses, dolphins, penguins, and sea lions using SYBR green I. The GEM LAMP and GEM RT-LAMP methods thus have considerable versatility as tools for detecting pathogens and are applicable to basic human and veterinary medicine, environmental hygiene, and point-of-care-testing. PMID:24560780

  14. Phenomenological Kinetics of Real Gas-Adsorption-Systems: Isothermal Adsorption

    NASA Astrophysics Data System (ADS)

    Rudzinski, W.; Panczyk, T.

    2002-06-01

    Since Langmuir published the derivation of his famous adsorption isotherm equation in 1918, hundreds of papers on the kinetics of gas adsorption on solid surfaces have appeared in the world literature. Until the early fifties of the 20th century, these were mainly papers reporting on experimental studies of the kinetics of adsorption in various adsorption systems. Surprisingly, although the Langmuir isotherm described the adsorption equilibria fairly well, the related kinetic expressions generally failed to describe the adsorption kinetics. So, beginning in the early fifties, vigorous attempts were made to improve that kinetic approach based on ideas of the Absolute Rate Theory (ART). Since then, one has been able to see more progress on the theoretical side than in the related experimental studies. However, the vast majority of these papers treated hypothetical adsorption kinetics in virtual adsorption systems with well-defined surfaces. This was especially true in the case of the theoretical studies of isothermal adsorption kinetics. Certain progress was made in theoretical studies of the kinetics of thermodesorption, where the energetic heterogeneity of the real solid surfaces was demonstrated in an impressive way. Here, almost all the attempts to take energetic surface heterogeneity into account were based on a further generalization of the ART approach. In the early eighties a new family of fundamental approaches appeared, linking the rate of adsorption/desorption processes to the chemical potentials of the bulk and the adsorbed molecules. Among them the so-called Statistical Rate Theory (SRT) has received the most advanced theoretical attention. The new SRT approach has been generalized during recent years for the case of energetically heterogeneous surfaces. This has been done for both the isothermal kinetics and the kinetics of thermodesorption. So we have only two fundamental approaches which have been generalized for consideration of the kinetics of gas adsorption in the real systems, i.e. the ART and the SRT approaches. The purpose of the present review is to discuss the features of the adsorption kinetics in real adsorption systems, where the solid surface energetic heterogeneity is the main factor determining these features. For that purpose we will thoroughly analyze existing and possible future generalizations of both the ART and SRT approaches, taking this crucial physical factor into account. Next, we will apply the obtained theoretical expressions to quantitatively simulate the observed adsorption kinetics in real adsorption systems. Our study does not refer to the special case of the kinetics of sorption by porous media where the exchange of mass between the gas and the adsorbed phase may not be assumed as the only possible rate-controlling step.

  15. Adsorption Isotherms of Hydrogen: The Role of Thermal Fluctuations

    E-print Network

    Jens Vorberg; Stephan Herminghaus; Klaus Mecke

    2001-05-28

    It is shown that experimentally obtained isotherms of adsorption on solid substrates may be completely reconciled with Lifshitz theory when thermal fluctuations are taken into account. This is achieved within the framework of a solid-on-solid model which is solved numerically. Analysis of the fluctuation contributions observed for hydrogen adsorption onto gold substrates allows to determine the surface tension of the free hydrogen film as a function of film thickness. It is found to decrease sharply for film thicknesses below seven atomic layers.

  16. Mesoscopic modeling of non-isothermal fluid systems

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Tang, Yuhang; Caswell, Bruce; Karniadakis, George Em

    2013-11-01

    The dynamical properties of fluid, including diffusivity and viscosity, are temperature-dependent and can significantly influence the flow dynamics in non-isothermal systems. To capture the correct temperature-dependence of a fluid, an energy conserving dissipative particle dynamics (eDPD) model is developed by expressing the weighting functions of the dissipative force and the random force as functions of temperature. The diffusivity and viscosity of liquid water at various temperatures ranging from 273 K to 373 K are used as examples for verifying the proposed model. For non-isothermal fluid systems, the present model can predict the diffusivity and viscosity consistent with available experimental data of water at various temperatures. Moreover, an analytical formula for determining the mesoscopic heat friction is proposed. The validation of the formula is confirmed by reproducing the experimental data in Prandtl number of liquid water at various temperatures. The proposed method is demonstrated in water but it can be readily extended to other liquids. The dynamical properties of fluid, including diffusivity and viscosity, are temperature-dependent and can significantly influence the flow dynamics in non-isothermal systems. To capture the correct temperature-dependence of a fluid, an energy conserving dissipative particle dynamics (eDPD) model is developed by expressing the weighting functions of the dissipative force and the random force as functions of temperature. The diffusivity and viscosity of liquid water at various temperatures ranging from 273 K to 373 K are used as examples for verifying the proposed model. For non-isothermal fluid systems, the present model can predict the diffusivity and viscosity consistent with available experimental data of water at various temperatures. Moreover, an analytical formula for determining the mesoscopic heat friction is proposed. The validation of the formula is confirmed by reproducing the experimental data in Prandtl number of liquid water at various temperatures. The proposed method is demonstrated in water but it can be readily extended to other liquids. Supported by the new DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.

  17. Galax2d: 2D isothermal Euler equations solver

    NASA Astrophysics Data System (ADS)

    Mulder, Wim

    2015-03-01

    Galax2d computes the 2D stationary solution of the isothermal Euler equations of gas dynamics in a rotating galaxy with a weak bar. The gravitational potential represents a weak bar and controls the flow. A damped Newton method solves the second-order upwind discretization of the equations for a steady-state solution, using a consistent linearization and a direct solver. The code can be applied as a tool for generating flow models if used on not too fine meshes, up to 256 by 256 cells for half a disk in polar coordinates.

  18. Wave Properties of Isothermal Magneto-Rotational Fluids

    E-print Network

    M. Sharif; Umber Sheikh

    2009-08-28

    In this paper, the isothermal plasma wave properties in the neighborhood of the pair production region for the Kerr black hole magnetosphere are discussed. We have considered the Fourier analyzed form of the perturbed general relativistic magnetohydrodynamical equations whose determinant leads to a dispersion relation. For the special scenario, the $x$-component of the complex wave vectors are numerically calculated. Respective components of the propagation vector, attenuation vector, phase and group velocities are shown in graphs. We have particularly investigated the existence of a Veselago medium and wave behavior (modes of waves dispersion

  19. Ageing effects during isothermal crystallization of polypropylene blended with elastomers

    NASA Astrophysics Data System (ADS)

    Wenig, W.

    1994-09-01

    The secondary crystallization of isotactic polypropylene in its blend with the elastomers ethylene-propylene-diene-terpolymer (EPDM) and trans-polyoctenylene (TOR), which occurs during isothermal crystallization, has been measured by time-dependent recording of X-ray wide-angle scattering. From the results, Avrami exponents were determined, which show that secondary crystallization takes place primarily within the already formed spherulites. Avrami exponents of the primary crystallization have been determined by the same method and also by observation of the spherulitic growth in the polarization microscope. It was found that both elastomers have different effects on the crystallization behaviour of the polypropylene.

  20. Batch removal of malachite green from aqueous solutions by adsorption on oil palm trunk fibre: Equilibrium isotherms and kinetic studies

    Microsoft Academic Search

    B. H. Hameed; M. I. El-Khaiary

    2008-01-01

    Oil palm trunk fibre (OPTF) – an agricultural solid waste – was used as low-cost adsorbent to remove malachite green (MG) from aqueous solutions. The operating variables studied were contact time, initial dye concentration, and solution pH. Equilibrium adsorption data were analyzed by three isotherms, namely the Freundlich isotherm, the Langmuir isotherm, and the multilayer adsorption isotherm. The best fit

  1. Optical pulse synthesis using brillouin selective sideband amplification

    NASA Technical Reports Server (NTRS)

    Yao, X. Steve (Inventor)

    2002-01-01

    Techniques for producing optical pulses based on Brillouin selective sideband amplification by using a common modulation control signal to modulate both a signal beam to produce multiple sideband signals and a single pump beam to produce multiple pump beams.

  2. Drag amplification and fatigue damage in vortex-induced vibrations

    E-print Network

    Jhingran, Vikas Gopal

    2008-01-01

    Fatigue damage and drag force amplification due to Vortex-Induced-Vibrations (VIV) continue to cause significant problems in the design of structures which operate in ocean current environments. These problems are magnified ...

  3. DNA amplification is rare in normal human cells

    SciTech Connect

    Wright, J.A.; Watt, F.M.; Hudson, D.L.; Stark, G.R. (Imperial Cancer Research Fund Labs., London (England)); Smith, H.S.; Hancock, M.C. (Peralta Cancer Research Institute, Oakland, CA (USA))

    1990-03-01

    Three types of normal human cells were selected in tissue culture with three drugs without observing a single amplification event from a total of 5 x 10{sup 8} cells. No drug-resistant colonies were observed when normal foreskin keratinocytes were selected with N-(phosphonacetyl)-L-aspartate or with hydroxyurea or when normal mammary epithelial cells were selected with methotrexate. Some slightly resistant colonies with limited potential for growth were obtained when normal diploid fibroblast cells derived from fetal lung were selected with methotrexate or hydroxyurea but careful copy-number analysis of the dihydrofolate reductase and ribonucleotide reductase genes revealed no evidence of amplification. The rarity of DNA amplification in normal human cells contrasts strongly with the situation in tumors and in established cell lines, where amplification of onogenes and of genes mediating drug resistance is frequent. The results suggest that tumors and cell lines have acquired the abnormal ability to amplify DNA with high frequency.

  4. Active cochlear amplification is dependent on supporting cell gap junctions.

    PubMed

    Zhu, Yan; Liang, Chun; Chen, Jin; Zong, Liang; Chen, Guang-Di; Zhao, Hong-Bo

    2013-01-01

    Mammalian hearing relies upon active cochlear mechanics, which arises from outer hair cell electromotility and hair bundle movement, to amplify acoustic stimulations increasing hearing sensitivity and frequency selectivity. Here we describe the novel finding that gap junctions between cochlear supporting cells also have a critical role in active cochlear amplification in vivo. We find that targeted-deletion of connexin 26 in Deiters cells and outer pillar cells, which constrain outer hair cells standing on the basilar membrane, causes a leftward shift in outer hair cell electromotility towards hyperpolarization, and reduces active cochlear amplification with hearing loss. Coincident with large reduction in distortion product otoacoustic emission and severe hearing loss at high frequencies, the shift is larger in shorter outer hair cells. Our study demonstrates that active cochlear amplification in vivo is dependent on supporting cell gap junctions. These new findings also show that connexin 26 deficiency can reduce active cochlear amplification to induce hearing loss. PMID:23653198

  5. Backward Raman amplification in the gas of rubidium dimers

    Microsoft Academic Search

    Hui Chen; Zoe-Elizabeth Sariyanni; Vladimir A. Sautenkov; Yuri V. Rostovtsev; Marlan O. Scully

    2006-01-01

    We experimentally and theoretically study Raman scattering in rubidium (Rb) dimers. We observe the optical lines resulting from Raman scattering and demonstrate Raman amplification in the backward direction. A theoretical model has been developed to explain experimental the results.

  6. Nonlinearity management in fiber transmission systems with hybrid amplification

    NASA Astrophysics Data System (ADS)

    Ania-Castañón, J. D.; Nasieva, I. O.; Kurukitkoson, N.; Turitsyn, S. K.; Borsier, C.; Pincemin, E.

    2004-04-01

    Nonlinearity management in transmission lines with periodic dispersion compensation and hybrid Raman-Erbium doped fiber amplification is studied both analytically and numerically. Different transmission/compensating fiber pairs are considered, with particular focus on the SMF/DCF case.

  7. Linear amplification of marginally neutral baroclinic waves

    NASA Astrophysics Data System (ADS)

    de Vries, Hylke; Ehrendorfer, Martin

    2008-10-01

    Baroclinic wave development is investigated for unstable parallel shear flows in the limit of vanishing normal-mode growth rate. This development is described in terms of the propagation and interaction mechanisms of two coherent structures, called counter-propagating Rossby waves (CRWs). It is shown that, in this limit of vanishing normal-mode growth rate, arbitrary initial conditions produce sustained linear amplification of the marginally neutral normal mode (mNM). This linear excitation of the mNM is subsequently interpreted in terms of a resonance phenomenon. Moreover, while the mathematical character of the normal-mode problem changes abruptly as the bifurcation point in the dispersion diagram is encountered and crossed, it is shown that from an initial-value (CRW) viewpoint, this transition is smooth. Consequently, the resonance interpretation remains relevant (albeit for a finite time) for wavenumbers slightly different from the ones defining cut-off points. The results are further applied to a two-layer version of the classic Eady model in which the upper rigid lid has been replaced by a simple stratosphere.

  8. Small Sample Whole-Genome Amplification

    SciTech Connect

    Hara, C A; Nguyen, C P; Wheeler, E K; Sorensen, K J; Arroyo, E S; Vrankovich, G P; Christian, A T

    2005-09-20

    Many challenges arise when trying to amplify and analyze human samples collected in the field due to limitations in sample quantity, and contamination of the starting material. Tests such as DNA fingerprinting and mitochondrial typing require a certain sample size and are carried out in large volume reactions; in cases where insufficient sample is present whole genome amplification (WGA) can be used. WGA allows very small quantities of DNA to be amplified in a way that enables subsequent DNA-based tests to be performed. A limiting step to WGA is sample preparation. To minimize the necessary sample size, we have developed two modifications of WGA: the first allows for an increase in amplified product from small, nanoscale, purified samples with the use of carrier DNA while the second is a single-step method for cleaning and amplifying samples all in one column. Conventional DNA cleanup involves binding the DNA to silica, washing away impurities, and then releasing the DNA for subsequent testing. We have eliminated losses associated with incomplete sample release, thereby decreasing the required amount of starting template for DNA testing. Both techniques address the limitations of sample size by providing ample copies of genomic samples. Carrier DNA, included in our WGA reactions, can be used when amplifying samples with the standard purification method, or can be used in conjunction with our single-step DNA purification technique to potentially further decrease the amount of starting sample necessary for future forensic DNA-based assays.

  9. Weak value amplification of atomic cat states

    E-print Network

    Sumei Huang; Girish S. Agarwal

    2015-05-02

    We show the utility of the weak value measurement to observe the quantum interference between two close lying atomic coherent states in a post-selected atomic cat state, produced in a system of $N$ identical two-level atoms weakly interacting with a single photon field. Through the observation of the negative parts of the Wigner distribution of the post-selected atomic cat state, we find that the post-selected atomic cat state becomes more nonclassical when the post-selected polarization state of the single photon field tends toward becoming orthogonal to its pre-selected state. We show that the small phase shift in the post-selected atomic cat state can be amplified via measuring the peak shift of its phase distribution when the post-selected state of the single photon field is nearly orthogonal to its pre-selected state. We find that the amplification factor of of 15 [5] can be obtained for a sample of 10 [100] atoms. This effectively provides us with a method to discriminate two close lying states on the Bloch sphere. We discuss possible experimental implementation of the scheme, and conclude with a discussion of the Fisher information.

  10. Condition of supralinear amplification in pairing action potentials with EPSPS

    Microsoft Academic Search

    Hidetoshi Urakubo; Masataka Watanabe

    2002-01-01

    We simulate pairing backpropagating action potentials (APs) with excitatory postsynaptic potentials (EPSPs) in a hippocampal CA1 model neuron, and make clear the synaptic-site dependence of the supralinear amplification, which is considered as the origin of LTP in spike-timing dependent plasticity (STDP). Pairing APs with EPSPs at randomly determined synaptic sites reveals that the supralinear amplification needs modest APs with strong

  11. Polar amplification in a coupled climate model with locked albedo

    Microsoft Academic Search

    Rune Grand Graversen; Minghuai Wang

    2009-01-01

    In recent years, a substantial reduction of the sea ice in the Arctic has been observed. At the same time, the near-surface\\u000a air in this region is warming at a rate almost twice as large as the global average—this phenomenon is known as the Arctic\\u000a amplification. The role of the ice-albedo feedback for the Arctic amplification is still a matter

  12. Quantum amplitude amplification algorithm: an explanation of availability bias

    E-print Network

    Franco, Riccardo

    2008-01-01

    In this article, I show that a recent family of quantum algorithms, based on the quantum amplitude amplification algorithm, can be used to describe a cognitive heuristic called availability bias. The amplitude amplification algorithm is used to define quantitatively the ease of a memory task, while the quantum amplitude estimation and the quantum counting algorithms to describe cognitive tasks such as estimating probability or approximate counting.

  13. Quantum amplitude amplification algorithm: an explanation of availability bias

    E-print Network

    Riccardo Franco

    2008-10-06

    In this article, I show that a recent family of quantum algorithms, based on the quantum amplitude amplification algorithm, can be used to describe a cognitive heuristic called availability bias. The amplitude amplification algorithm is used to define quantitatively the ease of a memory task, while the quantum amplitude estimation and the quantum counting algorithms to describe cognitive tasks such as estimating probability or approximate counting.

  14. The amplification of weak measurements under quantum noise

    E-print Network

    Xuanmin Zhu; Yu-Xiang Zhang

    2015-05-08

    The influence of outside quantum noises on the amplification of weak measurements is investigated. Three typical quantum noises are discussed. The maximum values of the pointer's shifts decrease sharply with the strength of the depolarizing channel and phase damping. In order to obtain significant amplified signals, the preselection quantum systems must be kept away from the two quantum noises. Interestingly, the amplification effect is immune to the amplitude damping noise.

  15. Engineering targeted chromosomal amplifications in human breast epithelial cells.

    PubMed

    Springer, Simeon; Yi, Kyung H; Park, Jeenah; Rajpurohit, Anandita; Price, Amanda J; Lauring, Josh

    2015-07-01

    Chromosomal amplifications are among the most common genetic alterations found in human cancers. However, experimental systems to study the processes that lead to specific, recurrent amplification events in human cancers are lacking. Moreover, some common amplifications, such as that at 8p11-12 in breast cancer, harbor multiple driver oncogenes, which are poorly modeled by conventional overexpression approaches. We sought to develop an experimental system to model recurrent chromosomal amplification events in human cell lines. Our strategy is to use homologous-recombination-mediated gene targeting to deliver a dominantly selectable, amplifiable marker to a specified chromosomal location. We used adeno-associated virus vectors to target human MCF-7 breast cancer cells at the ZNF703 locus, in the recurrent 8p11-12 amplicon, using the E. coli inosine monophosphate dehydrogenase (IMPDH) enzyme as a marker. We applied selective pressure using IMPDH inhibitors. Surviving clones were found to have increased copy number of ZNF703 (average 2.5-fold increase) by droplet digital PCR and FISH. Genome-wide array comparative genomic hybridization confirmed that amplifications had occurred on the short arm of chromosome 8, without changes on 8q or other chromosomes. Patterns of amplification were variable and similar to those seen in primary human breast cancers, including "sawtooth" patterns, distal copy number loss, and large continuous regions of copy number gain. This system will allow study of the cis- and trans-acting factors that are permissive for chromosomal amplification and provide a model to analyze oncogene cooperativity in amplifications harboring multiple candidate driver genes. PMID:26099605

  16. Microwave amplification in a GaAs bulk semiconductor

    Microsoft Academic Search

    H. W. Thim; M. R. Barber

    1966-01-01

    Continuous linear microwave amplification has been obtained usingn-type GaAs at room temperature. Amplification of signals in the 2 to 10 Gc\\/s range occurred when a dc field applied across semiconductor wafers mounted in a conventional reflection type amplifier circuit exceeded about 3100 volts\\/cm. Ohmic contacts were applied to wafers 125 µ square and 40 to 120 µ thick. The resistivity

  17. Low-noise preamplifier for multistage photorefractive image amplification

    NASA Astrophysics Data System (ADS)

    Breugnot, S.; Rajbenbach, H.; Defour, M.; Huignard, J.-P.

    1995-07-01

    We present a two-beam coupling configuration in photorefractive BaTiO3 that provides a low-noise amplification of the signal to be detected. A two-wave mixing gain of 100 is reached, in conjunction with very low beam fanning background in the signal direction. The extensions of this configuration to photorefractive heterodyne detection and to multistage image amplification are theoretically and experimentally studied.

  18. Methods for microbial DNA extraction from soil for PCR amplification

    Microsoft Academic Search

    C. Yeates; M. R. Gillings; A. D. Davison; N. Altavilla; D. A. Veal

    1998-01-01

    Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction\\u000a method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable\\u000a for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and\\u000a SDS followed by

  19. Oncogene-like induction of cellular invasion from centrosome amplification

    PubMed Central

    Godinho, Susana A.; Picone, Remigio; Burute, Mithila; Dagher, Regina; Su, Ying; Leung, Cheuk T.; Polyak, Kornelia; Brugge, Joan S.; Thery, Manuel; Pellman, David

    2014-01-01

    Centrosome amplification has long been recognized as a feature of human tumors, however its role in tumorigenesis remains unclear1. Centrosome amplification is poorly tolerated by non-transformed cells, and, in the absence of selection, extra centrosomes are spontaneously lost2. Thus, the high frequency of centrosome amplification, particularly in more aggressive tumors3, raises the possibility that extra centrosomes could, in some contexts, confer advantageous characteristics that promote tumor progression. Using a three-dimensional model system and other approaches to culture human mammary epithelial cells, we find that centrosome amplification triggers cell invasion. This invasive behavior is similar to that induced by overexpression of the breast cancer oncogene ErbB24 and indeed enhances invasiveness triggered by ErbB2. We show that, through increased centrosomal microtubule nucleation, centrosome amplification increases Rac1 activity, which disrupts normal cell-cell adhesion and promotes invasion. These findings demonstrate that centrosome amplification, a structural alteration of the cytoskeleton, can promote features of malignant transformation. PMID:24739973

  20. Empirical evidence for acceleration-dependent amplification factors

    USGS Publications Warehouse

    Borcherdt, R.D.

    2002-01-01

    Site-specific amplification factors, Fa and Fv, used in current U.S. building codes decrease with increasing base acceleration level as implied by the Loma Prieta earthquake at 0.1g and extrapolated using numerical models and laboratory results. The Northridge earthquake recordings of 17 January 1994 and subsequent geotechnical data permit empirical estimates of amplification at base acceleration levels up to 0.5g. Distance measures and normalization procedures used to infer amplification ratios from soil-rock pairs in predetermined azimuth-distance bins significantly influence the dependence of amplification estimates on base acceleration. Factors inferred using a hypocentral distance norm do not show a statistically significant dependence on base acceleration. Factors inferred using norms implied by the attenuation functions of Abrahamson and Silva show a statistically significant decrease with increasing base acceleration. The decrease is statistically more significant for stiff clay and sandy soil (site class D) sites than for stiffer sites underlain by gravely soils and soft rock (site class C). The decrease in amplification with increasing base acceleration is more pronounced for the short-period amplification factor, Fa, than for the midperiod factor, Fv.

  1. MYCN gene amplification in patients with neuroblastic tumors.

    PubMed

    Estiar, M A; Fazilaty, H; Aslanabadi, S; Seifi, M; Varghaei, P; Rezamand, A

    2014-01-01

    Although neuroblastic tumors are the most prevalent solid tumors, little is known about the genetic basis underlying their progression. The prognostic role for the MYCN gene in neuroblastic tumors is irrefutable. The aim of this study is to identify the frequency of MYCN gene amplification and its relationship with clinicopathological and prognostic factors in 40 patients with neuroblastic tumors by using real-time quantitative PCR. There was significant association between the age of older than 18 months and the high number of metastasis. 83.3% of metastatic neuroblastic tumors in patients aged more than 18 months were in stage 4, while it was about 12.5% in patients aged less than 18 months. We found an amplification of MYCN in 19 out of 40 patients. Also, we found MYCN gene amplification in 64% of neuroblastoma (NB) and 8% of gangelioneuroblastoma (GNB) cases. There was a significant association between the histological type of samples with MYCN gene amplification. Neuroblastic tumors have a varied range of MYCN gene amplification depend on histopathology types. No significant associations have been found between MYCN gene amplification and tumor evaluation, CNS involvement, metastasis, stage of disease and patients outcome. PMID:25231001

  2. Argon and Krypton Adsorption Isotherms on Single Carbon Nanotube Devices

    NASA Astrophysics Data System (ADS)

    Wang, Zenghui; Morse, Peter; Wei, Jiang; Vilches, Oscar; Cobden, David

    2009-03-01

    We have fabricated mass balances each consisting of an individual single-walled carbon nanotube suspended across a micron-sized trench in an oxidized Si wafer. The vibrational resonance frequency of a nanotube, which is in the range 50-500 MHz, is determined by monitoring the current through it while applying an electrostatic driving signal. By tracking changes in the resonance frequency we have measured isotherms of adsorbed mass vs vapor pressure for Ar ot Kr at liquid nitrogen temperatures. The sensitivity of the balances corresponds to just a few atoms. We have compared the monolayer mass shifts due to Ar and Kr, and measured a family of isotherms of Ar below 77 K. From the latter we calculated the isosteric heat of adsorption on the nanotube surface, which is found to be lower than that of Ar on basal plane graphite and only slightly larger than the latent heat of sublimation of bulk Ar at these temperatures. In one device we observed a phase transition in the adsorbed Ar near monolayer completion. In another device, which probably consists of two nanotubes joined in parallel, we observed enhanced adsorption at lower coverages which may be in the groove between the two nanotubes. This work is supported by the NSF, grant number 0606078.

  3. Analysis of moisture desorption isotherms of eggplant (Solanum melongena).

    PubMed

    Moreira, R; Chenlo, F; Torres, M D; Vallejo, N

    2010-10-01

    Sorption isotherms of eggplant were determined employing, as experimental technique, a static gravimetric method, using saturated salt solutions to achieve the equilibrium. The experiments were carried out at different temperatures (20, 35, 50 and 65 °C). The sorption isotherms can be classified, according to Brunauer's classification, as type II or III depending on temperature. Equilibrium moisture content data were correlated by two models usually applied to foodstuffs (Brunauer--Emmet--Teller (BET) and Halsey). BET model was employed to determine monolayer moisture content (0.121 kg/kg d.b.). Halsey model was selected by the goodness of fitting. Experimental data were analyzed by a thermodynamic approach to obtain some properties as net isosteric heat, equilibrium heat and differential and net integral entropy. The differential enthalpy and entropy decreased with increasing moisture content and satisfied the compensation theory. The net integral enthalpy and entropy showed maximum values (?31 kJ/mol and ?88 J/mol.K) at 0.093 (kg/kg d.b.) of moisture content. PMID:21339160

  4. ISOTHERMAL AND MULTITHERMAL ANALYSIS OF CORONAL LOOPS OBSERVED WITH AIA

    SciTech Connect

    Schmelz, J. T.; Jenkins, B. S.; Worley, B. T.; Anderson, D. J.; Pathak, S.; Kimble, J. A., E-mail: jschmelz@memphis.edu [Physics Department, University of Memphis, Memphis, TN 38152 (United States)

    2011-04-10

    The coronal filters in the Atmospheric Imaging Assembly (AIA) aboard the Solar Dynamics Observatory peak at different temperatures; the series covers the entire active region temperature range, making AIA ideal for multithermal analysis. Here, we analyze coronal loops from several active regions that have been observed by AIA. We have specifically targeted cool loops (or at least loops with a cool component) that were chosen in the 171 A channel of AIA, which has a peak response temperature of log T = 5.8. We wanted to determine if the loops could be described as isothermal or multithermal. We find that several of our 12 loops have narrow temperature distributions, which may be consistent with isothermal plasma; these can be modeled with a single flux tube. Other loops have intermediate-width temperature distributions, appear well-constrained, and should be multi-stranded. The remaining loops, however, have unrealistically broad differential emission measures. We find that this problem is the result of missing low-temperature lines in the AIA 131 A channel. If we repeat the analysis without the 131 A data, these loops also appear to be well-constrained and multi-stranded.

  5. Kinetics of tungsten carbidization under non-isothermal conditions

    SciTech Connect

    Kharatyan, S.L. [Department of Chemical Physics, Yerevan State University, Yerevan (Armenia); A.B. Nalbandyan Institute of Chemical Physics NAS RA, Yerevan (Armenia); Chatilyan, H.A. [A.B. Nalbandyan Institute of Chemical Physics NAS RA, Yerevan (Armenia)], E-mail: hakob@ichph.sci.am; Arakelyan, L.H. [Department of Chemical Physics, Yerevan State University, Yerevan (Armenia)

    2008-04-01

    Kinetic laws of high-temperature interaction between tungsten and methane are studied under non-isothermal conditions in the temperature interval 1273-2873 K. Computer Assisted Electrothermography was applied during which thin metallic wires 100 {mu}m in diameter were directly heated up by electric current in the carbon-containing atmosphere. Experimental data on weight gain, carbide layer growth, and microstructure of phases are obtained in the linear heating regime at heating rates from 10 to 1500 K/s. We established that the interaction between tungsten and methane in a wide interval of pressure and heating rates may proceed with simultaneous or consecutive formation of W{sub 2}C and WC carbide phases. Experimental data on weight gain and carbide layer growth were processed using calculation schemes deduced within the framework of a reaction diffusion model with the first type boundary conditions under non-isothermal conditions. Kinetic and diffusion constants are determined for tungsten carbidization with formation of the W{sub 2}C phase.

  6. Sorption isotherms and isosteric heats of sorption of Malaysian paddy.

    PubMed

    Mousa, Wael; Ghazali, Farinazleen Mohamad; Jinap, S; Ghazali, Hasanah Mohd; Radu, Son

    2014-10-01

    Understanding the water sorption characteristics of cereal is extremely essential for optimizing the drying process and ensuring storage stability. Water relation of rough rice was studied at 20, 30, 40 and 50 °C over relative humidity (RH.) between 0.113 and 0.976 using the gravimetric technique. The isotherms displayed the general sigmoid, Type II pattern and exhibited the phenomenon of hysteresis where it was more pronounced at lower temperatures. The sorption characteristics were temperature dependence where the sorption capacity of the paddy increased as the temperature was decreased at fixed (RH). Among the models assessed for their ability to fit the sorption data, Oswin equation was the best followed by the third order polynomial, GAB, Smith, Chung-Pfost, and Henderson models. The monolayer moisture content was higher for desorption than adsorption and tend to decrease with the increase in temperature. Given the temperature dependence of the sorption isotherms the isosteric heats of sorption were calculated using Claussius-Clapeyron equation. The net isosteric heats decreased as the moisture content was increased and heats of desorption were greater than that of adsorption. PMID:25328208

  7. Estimating Uranium Partition Coefficients from Laboratory Adsorption Isotherms

    SciTech Connect

    Hull, L.C. (INEEL); Grossman, C.; Fjeld, R.A.; Coates, J.T.; Elzerman, A.W. (Clemson University)

    2002-05-10

    An estimated 330 metric tons of uranium have been buried in the radioactive waste Subsurface Disposal Area (SDA) at the Idaho National Engineering and Environmental Laboratory (INEEL). An assessment of uranium transport parameters is being performed to decrease the uncertainty in risk and dose predictions derived from computer simulations of uranium fate and transport to the underlying Snake River Plain Aquifer. Uranium adsorption isotherms have been measured in the laboratory and fit with a Freundlich isotherm. The Freundlich n parameter was statistically identical for 14 sediment samples. The Freundlich Kf for seven samples, where material properties have been measured, is correlated to sediment surface area. Based on these empirical observations, a model has been derived for adsorption of uranium on INEEL sedimentary materials using surface complexation theory. The model was then used to predict the range of adsorption conditions to be expected at the SDA. Adsorption in the deep vadose zone is predicted to be stronger than in near-surface sediments because the total dissolved carbonate decreases with depth.

  8. Estimating Uranium Partition Coefficients from Laboratory Adsorption Isotherms

    SciTech Connect

    Hull, Laurence Charles; Grossman, Christopher; Fjeld, R. A.; Coates, C.J.; Elzerman, A.

    2002-08-01

    An estimated 330 metric tons of uranium have been buried in the radioactive waste Subsurface Disposal Area (SDA) at the Idaho National Engineering and Environmental Laboratory (INEEL). An assessment of uranium transport parameters is being performed to decrease the uncertainty in risk and dose predictions derived from computer simulations of uranium fate and transport to the underlying Snake River Plain Aquifer. Uranium adsorption isotherms have been measured in the laboratory and fit with a Freundlich isotherm. The Freundlich n parameter was statistically identical for 14 sediment samples. The Freundlich Kf for seven samples, where material properties have been measured, is correlated to sediment surface area. Based on these empirical observations, a model has been derived for adsorption of uranium on INEEL sedimentary materials using surface complexation theory. The model was then used to predict the range of adsorption conditions to be expected at the SDA. Adsorption in the deep vadose zone is predicted to be stronger than in near-surface sediments because the total dissolved carbonate decreases with depth.

  9. Unstable and stable CAD gene amplification: importance of flanking sequences and nuclear environment in gene amplification.

    PubMed Central

    Meinkoth, J; Killary, A M; Fournier, R E; Wahl, G M

    1987-01-01

    We analyzed the amplification of the CAD gene in independently isolated N-(phosphonacetyl)-L-aspartate-resistant clones derived from single parental clones in two mouse cell lines. We report for the first time that the CAD gene is amplified unstably in mouse cells, that the degree of instability varies greatly between clones, and that minute chromosomes and highly unstable chromosomelike structures contain the amplified sequences. These data are most consistent with the idea that the amplified unit in each clone consists of different flanking DNA and that such differences engender amplified sequences with unequal stability. We also introduced the mouse chromosome containing the CAD gene into hamster cells by microcell-mediated chromosome transfer to determine whether the propensity for unstable extrachromosomal amplification of the mouse CAD gene would prevail in the hamster cell nuclear environment. We report that the mouse CAD gene was amplified stably in expanded chromosomal regions in each of seven hybrids that were analyzed. This observation is consistent with the idea that the nuclear environment influences whether mutants containing intra- or extrachromosomally amplified sequences will be isolated. Images PMID:3600632

  10. In vitro aflatoxin adsorption by means of a montmorillonite silicate. A study of adsorption isotherms

    Microsoft Academic Search

    A. J. Ramos; E. Hernández

    1996-01-01

    To evaluate the affinity and capacity of a feedstuff additive, a montmorillonite silicate, to adsorb the four major naturally occurring aflatoxins, a study of the Langmuir and Freundlich adsorption isotherms was carried out. The Freundlich isotherm fits the data better than the Langmuir isotherm. The data reveal adsorptions of about 1000 ?g aflatoxin B1 g?1 montmorillonite, 425–450 ?g aflatoxin G1

  11. High-temperature behaviour of IN 738 LC under isothermal and thermo-mechanical cyclic loading

    Microsoft Academic Search

    H. Frenz; J. Meersmann; J. Ziebs; H.-J. Kühn; R. Sievert; J. Olschewski

    1997-01-01

    The temperature dependence of the cyclic behavior of IN 738 LC was studied. Cyclic iso- and non-isothermal tests were performed with proportional and non-proportional tension\\/torsion strain paths. It was shown that maximum and minimum stress values measured in isothermal strain controlled tests correspond quite well with results of non-isothermal tests. Thermal-mechanical constitutive equations based on the viscoplastic Chaboche model were

  12. Thermodynamic analysis of quantum light amplification

    SciTech Connect

    Boukobza, E.; Tannor, D. J. [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel)

    2006-12-15

    Thermodynamics of a three-level maser was studied in the pioneering work of Scovil and Schulz-DuBois [Phys. Rev. Lett. 2, 262 (1959)]. In this work we consider the same three-level model, but treat both the matter and the light quantum mechanically. Specifically, we analyze an extended (three-level) dissipative (ED) Jaynes-Cummings model (JCM) within the framework of a quantum heat engine, using formulas for heat flux and power in bipartite systems introduced in our previous work [E. Boukobza and D. J. Tannor Phys. Rev. A 74, 063823 (2006)] Amplification of the selected cavity mode occurs even in this simple model, as seen by a positive steady state power. However, initial field coherence is lost, as seen by the decaying off-diagonal field density matrix elements, and by the Husimi-Kano Q function. We show that after an initial transient time the field's entropy rises linearly during the operation of the engine, which we attribute to the dissipative nature of the evolution and not to matter-field entanglement. We show that the second law of thermodynamics is satisfied in two formulations (Clausius, Carnot) and that the efficiency of the ED JCM heat engine agrees with that defined intuitively by Scovil and Schulz-DuBois. Finally, we compare the steady state heat flux and power of the fully quantum model with the semiclassical counterpart of the ED JCM, and derive the engine efficiency formula of Scovil and Schulz-DuBois analytically from fundamental thermodynamic fluxes.

  13. Alternative Chemical Amplification Methods for Peroxy Radical Detection

    NASA Astrophysics Data System (ADS)

    Wood, E. C. D.

    2014-12-01

    Peroxy radicals (HO2, CH3O2, etc.) are commonly detected by the chemical amplification technique, in which ambient air is mixed with high concentrations of CO and NO, initiating a chain reaction that produces 30 - 200 NO2 molecules per sampled peroxy radical. The NO2 is then measured by one of several techniques. With the exception of CIMS-based techniques, the chemical amplification method has undergone only incremental improvements since it was first introduced in 1982. The disadvantages of the technique include the need to use high concentrations of CO and the greatly reduced sensitivity of the amplification chain length in the presence of water vapor. We present a new chemical amplification scheme in which either ethane or acetaldehyde is used in place of CO, with the NO2 product detected using Cavity Attenuated Phase Shift spectroscopy (CAPS). Under dry conditions, the amplification factor of the alternative amplifiers are approximately six times lower than the CO-based amplifier. The relative humidity "penalty" is not as severe, however, such that at typical ambient relative humidity (RH) values the amplification factor is within a factor of three of the CO-based amplifier. Combined with the NO2 sensitivity of CAPS and a dual-channel design, the detection limit of the ethane amplifier is less than 2 ppt (1 minute average, signal-to-noise ratio 2). The advantages of these alternative chemical amplification schemes are improved safety, a reduced RH correction, and increased sensitivity to organic peroxy radicals relative to HO2.

  14. Isothermal elastohydrodynamic lubrication of point contacts. 2: Ellipticity parameter results

    NASA Technical Reports Server (NTRS)

    Hamrock, B. J.; Dowson, D.

    1976-01-01

    A numerical solution of the isothermal elastohydrodynamic problem for point contacts is presented which reproduces all the essential features of experimental observations based upon optical interferometry. In particular, the two side lobes, in which minimum film thickness regions occur, emerge in the theoretical solutions. The influence of the ellipticity parameter on solutions to the point contact problem is explored. The ellipticity parameter k was varied from 1 (a ball on a plate) to 8 (a configuration approaching line contact). It is shown that the minimum film thickness can be related to the well known line contact solutions by a remarkably simple expression involving either k or the effective radius of curvature ratio R sub y/R sub x.

  15. Isothermal Analysis of CAN Type Combustor Using Five Hole Probe

    NASA Astrophysics Data System (ADS)

    Shah, R. D.; Banerjee, J.

    2012-10-01

    A five hole probe is developed and calibrated to carry out the isothermal flow analysis of a CAN type combustor. The axial, radial and tangential velocity distribution at different axial and radial locations of the combustor are measured using the five hole probe. The experimentally measured values of velocity distribution are then compared with the numerical results obtained using a ?-? turbulence model. The experimental results predict that the swirler vane angles do not have significant effect on the axial and radial velocity profiles at the primary axis and secondary axis. Peak values of the tangential velocity increases at the primary axis for the higher values of the swirler vane angles due to increase in tangential momentum.

  16. Isothermal decomposition of gamma-irradiated dysprosium acetate

    NASA Astrophysics Data System (ADS)

    Mahfouz, R. M.; Al-Shehri, S. M.; Monshi, M. A. S.; Abd El-Salam, N. M.

    Isothermal decomposition of un-irradiated and pre-gamma-irradiated dysprosium acetate [Dy(CH3COO)(3)] has been investigated at different temperatures between 603-623 K. Irradiation was observed to enhance the rate of decomposition without modifying the mechanism of the thermal decomposition. Thermal decomposition of dysposium acetate is shown to proceed by a nucleation and growth mechanism (Avarmi-Erofe'ev equation) both for un-irradiated and pre-gamma-irradiated samples. The enhancement of the decomposition was found to increase with an increase in the gamma-ray dose applied to the sample and may be attributed to an increase in point defects and formation of additional nucleation centers generated in the host lattice. Thermodynamic values of the main decomposition process were calculated and evaluated.

  17. Characterization of Isothermally Heat-Treated High Carbon Nanobainitic Steels

    NASA Astrophysics Data System (ADS)

    Sidhu, G.; Bhole, S. D.; Essadiqi, E.; Chen, D. L.

    2013-10-01

    Isothermal heat treatment close to the martensite-start temperature at various transformation times, followed by hardness and compression tests, has been performed for three new high carbon experimental nanobainitic steels. Microstructural characterization clearly revealed the formation of lower bainitic structures with plate thickness in the range of nanometers. Analysis of the volume fraction of the bainitic phase via x-ray diffraction indicates that the presence of Co and Al accelerates the transformation resulting in almost complete transformation within 24 h. The effect of transformation and the resulting microstructure on the mechanical properties are also presented. Finally, the data collected from the compression tests have been used to develop an enhanced correlation between the yield strength and hardness in steels. Comparison of the improved correlation with three other frequently used correlations from the literature reveals a good performance of the proposed correlation.

  18. Dust ion acoustic solitary structures in presence of isothermal positrons

    E-print Network

    Paul, Ashesh; Bandyopadhyay, Anup

    2015-01-01

    The Sagdeev potential technique has been employed to study the dust ion acoustic solitary waves and double layers in an unmagnetized collisionless dusty plasma consisting of negatively charged static dust grains, adiabatic warm ions, and isothermally distributed electrons and positrons. A computational scheme has been developed to draw the qualitatively different compositional parameter spaces or solution spaces showing the nature of existence of different solitary structures with respect to any parameter of the present plasma system. The qualitatively distinct solution spaces give the overall scenario regarding the existence of different solitary structures. The present system supports both positive and negative potential double layers. The negative potential double layer always restricts the occurrence of negative potential solitary waves, i.e., any sequence of negative potential solitary waves having monotonically increasing amplitude converges to a negative potential double layer. However, there exists a ...

  19. Optimal smoothing of site-energy distributions from adsorption isotherms

    SciTech Connect

    Brown, L.F.; Travis, B.J.

    1983-01-01

    The equation for the adsorption isotherm on a heterogeneous surface is a Fredholm integral equation. In solving it for the site-energy distribution (SED), some sort of smoothing must be carried out. The optimal amount of smoothing will give the most information that is possible without introducing nonexistent structure into the SED. Recently, Butler, Reeds, and Dawson proposed a criterion (the BRD criterion) for choosing the optimal smoothing parameter when using regularization to solve Fredholm equations. The BRD criterion is tested for its suitability in obtaining optimal SED's. This criterion is found to be too conservative. While using it never introduces nonexistent structure into the SED, significant information is often lost. At present, no simple criterion for choosing the optimal smoothing parameter exists, and a modeling approach is recommended.

  20. Perturbations of Noise: The origins of Isothermal Flows

    E-print Network

    Piotr Garbaczewski

    1998-09-22

    We make a detailed analysis of both phenomenological and analytic background for the "Brownian recoil principle" hypothesis (Phys. Rev. A 46, (1992), 4634). A corresponding theory of the isothermal Brownian motion of particle ensembles (Smoluchowski diffusion process approximation), gives account of the environmental recoil effects due to locally induced tiny heat flows. By means of local expectation values we elevate the individually negligible phenomena to a non-negligible (accumulated) recoil effect on the ensemble average. The main technical input is a consequent exploitation of the Hamilton-Jacobi equation as a natural substitute for the local momentum conservation law. Together with the continuity equation (alternatively, Fokker-Planck), it forms a closed system of partial differential equations which uniquely determines an associated Markovian diffusion process. The third Newton law in the mean is utilised to generate diffusion-type processes which are either anomalous (enhanced), or generically non-dispersive.