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Sample records for acid sequence-based amplification

  1. Nucleic acid sequence-based amplification with oligochromatography for detection of Trypanosoma brucei in clinical samples

    NARCIS (Netherlands)

    C.M. Mugasa; T. Laurent; G.J. Schoone; P.A. Kager; G.W. Lubega; H.D.F.H. Schallig

    2009-01-01

    Molecular tools, such as real-time nucleic acid sequence-based amplification (NASBA) and PCR, have been developed to detect Trypanosoma brucei parasites in blood for the diagnosis of human African trypanosomiasis (HAT). Despite good sensitivity, these techniques are not implemented in HAT control pr

  2. Real-Time Nucleic Acid Sequence-Based Amplification Using Molecular Beacons for Detection of Enterovirus RNA in Clinical Specimens

    OpenAIRE

    Landry, Marie L.; Garner, Robin; Ferguson, David

    2005-01-01

    Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays w...

  3. Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

    OpenAIRE

    Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

    2005-01-01

    An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nu...

  4. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

    Directory of Open Access Journals (Sweden)

    Kager Piet A

    2006-10-01

    Full Text Available Abstract Background Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (Plasmodium antigen detection do often not allow for species discrimination as microscopy does, but also become insensitive at Methods This paper reports the development of a sensitive and specific real-time Quantitative Nucleic Acid Sequence Based Amplification (real-time QT-NASBA assays, based on the small-subunit 18S rRNA gene, to identify the four human Plasmodium species. Results The lower detection limit of the assay is 100 – 1000 molecules in vitro RNA for all species, which corresponds to 0.01 – 0.1 parasite per diagnostic sample (i.e. 50 μl of processed blood. The real-time QT-NASBA was further evaluated using 79 clinical samples from malaria patients: i.e. 11 Plasmodium. falciparum, 37 Plasmodium vivax, seven Plasmodium malariae, four Plasmodium ovale and 20 mixed infections. The initial diagnosis of 69 out of the 79 samples was confirmed with the developed real-time QT-NASBA. Re-analysis of seven available original slides resolved five mismatches. Three of those were initially identified as P. malariae mono-infection, but after re-reading the slides P. falciparum was found, confirming the real-time QT-NASBA result. The other two slides were of poor quality not allowing true species identification. The remaining five discordant results could not be explained by microscopy, but may be due to extreme low numbers of parasites present in the samples. In addition, 12 Plasmodium berghei isolates from mice and 20 blood samples from healthy donors did not show any reaction in the assay. Conclusion Real-time QT-NASBA is a very sensitive and specific technique with a detection limit of 0.1 Plasmodium parasite per diagnostic sample (50 μl of blood and can be used for the detection, identification and quantitative measurement of low parasitaemia of Plasmodium species, thus

  5. Establishment of the Nucleic Acid Sequence-based Amplification Method for Detecting Vibio Alginolyticus%溶藻弧菌的依赖于核酸序列恒温扩增检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    秦胜利; 王建广

    2012-01-01

    A new method, based on Nucleic Acid Sequence-based Amplification (NAS-BA) to detect Vibio alginolyticus of samples, was established. A highly specific set of primers was synthesized to target the hsp60 gene of Vibio alginolyticus so as to establish Nucleic Acid Sequence-based Amplification method. Specificity and sensitivity were tested. The results showed that the sensitivity of NASBA was 6. 9×102cfu ? mL-1 which was higher than the result of PCR method. Detecting Vibio alginolyticus with NASBA was more specific and sensitive than PCR method and has lower instrumental requirement. So,there is a broad prospect.%采用自行建立和优化的依赖于核酸序列恒温扩增(NASBA)检测体系,对溶藻弧菌进行检测.采用溶藻弧菌的hsp60基因为目的片段设计特异性引物,建成可快速检测溶藻弧菌的NASBA检测法,并进行了特异性和灵敏度试验.结果表明:所建立起的NASBA检测方法,灵敏度为6.9× 102 cfu·mL-1,高于普通PCR方法.溶藻弧菌的依赖于核酸序列恒温扩增检测方法具有较高灵敏度和和良好特异性,并且对仪器要求更低,用普通恒温设备即可进行反应,具有广阔的推广前景.

  6. The application of nucleic acid sequence?based amplification,real?time PCR and GM test in invasive aspergillosis diagnosis%核酸序列依赖性扩增、Real?time PCR及GM试验诊断侵袭性曲霉菌感染的临床应用评价

    Institute of Scientific and Technical Information of China (English)

    王立朋; 鲍翠霞; 于丽梅; 张晓录; 于威娟; 张霞; 李玮; 黄葆华; 李杰

    2015-01-01

    Objective To study the diagnostic performance of nucleic acid sequence?based amplification ( NASBA) assay,real?time PCR and GM test in detecting invasive aspergillosis for clinical diagnosis.Methods Blood samples from 80 patients at a high risk for IA were collected during from November 2013 to June 2014.These patients were categorized as 8 proven IA,26 probable IA, and 46 non?IA according to the 2008 revised definitions of EORTC/MSG.Blood samples were tested by NASBA,real?time PCR and GM test and their diagnostic parameters were calculated,respectively.Result The sensitivity of NASBA,real?time PCR and GM test was 76.47%,67.65% and 52.94%,while their specificity was 80.43%,89.13%,80.43%,respectively.The efficiency of various com?binations of tests was also evaluated.Perfect specificity (100%) and positive predictive value (100%) were achieved by combining NASBA and real?time PCR as a serial testing.A combination of NASBA and real?time PCR as a parallel testing was the most sensitive (94.12%).Conclusion The sensitivity and specificity of NASBA and real?time PCR were superior to GM test.Combination of these assays could be particularly useful in specific clinical situations.%目的 核酸序列依赖性扩增 ( nucleic acid sequence?based amplification,NASBA)、Real?time PCR及GM试验在侵袭性曲霉菌感染中的诊断价值. 方法 收集2013年11月~2014年6月临床上曲霉菌感染高危病患的血液标本80例,并根据EORTC/MSG诊断标准分为确诊组8例,拟诊组26例,非感染组46例,分别利用NASBA、real?time PCR及GM试验进行检测,计算3种方法的诊断指标并分析评价. 结果 NASBA、real?time PCR及GM试验3种方法的灵敏度分别为76.47%、67.65%、52.94%,特异度分别为80.43%、89.13%、80.43%. 联合诊断结果显示,NASBA与real?time PCR串联方案有最好的特异度 (100%)及阳性预测值(100%);NASBA与real?time PCR并联方案则最为灵敏(94.12%). 结论 NASBA用于诊断IA最为敏感,而real?time PCR

  7. A method for amplification of unknown flanking sequences based on touchdown PCR and suppression-PCR.

    Science.gov (United States)

    Gao, Song; He, Dan; Li, Guangquan; Zhang, Yanhua; Lv, Huiying; Wang, Li

    2016-09-15

    Thermal asymmetric staggered PCR is the most widely used technique to obtain the flanking sequences. However, it has some limitations, including a low rate of positivity, and complex operation. In this study, a improved method of it was made based on suppression-PCR and touchdown PCR. The PCR fragment obtained by the amplification was used directly for sequencing after gel purification. Using this improved method, the positive rate of amplified flanking sequences of the ATMT mutants reached 99%. In addition, the time from DNA extraction to flanking sequence analysis was shortened to 2 days with about 6 dollars each sample. PMID:27393656

  8. A method for amplification of unknown flanking sequences based on touchdown PCR and suppression-PCR.

    Science.gov (United States)

    Gao, Song; He, Dan; Li, Guangquan; Zhang, Yanhua; Lv, Huiying; Wang, Li

    2016-09-15

    Thermal asymmetric staggered PCR is the most widely used technique to obtain the flanking sequences. However, it has some limitations, including a low rate of positivity, and complex operation. In this study, a improved method of it was made based on suppression-PCR and touchdown PCR. The PCR fragment obtained by the amplification was used directly for sequencing after gel purification. Using this improved method, the positive rate of amplified flanking sequences of the ATMT mutants reached 99%. In addition, the time from DNA extraction to flanking sequence analysis was shortened to 2 days with about 6 dollars each sample.

  9. Non-instrumented nucleic acid amplification assay

    Science.gov (United States)

    Weigl, Bernhard H.; Domingo, Gonzalo; Gerlach, Jay; Tang, Dennis; Harvey, Darrel; Talwar, Nick; Fichtenholz, Alex; van Lew, Bill; LaBarre, Paul

    2008-02-01

    We have developed components of a diagnostic disposable platform that has the dual purpose of providing molecular diagnostics at the point of care (POC) as well as stabilizing specimens for further analysis via a centralized surveillance system. This diagnostic is targeted for use in low-resource settings by minimally trained health workers. The disposable device does not require any additional instrumentation and will be almost as rapid and simple to use as a lateral flow strip test - yet will offer the sensitivity and specificity of nucleic acid amplification tests (NAATs). The low-cost integrated device is composed of three functional components: (1) a sample-processing subunit that generates clean and stabilized DNA from raw samples containing nucleic acids, (2) a NA amplification subunit, and (3) visual amplicon detection sub-unit. The device integrates chemical exothermic heating, temperature stabilization using phase-change materials, and isothermal nucleic acid amplification. The aim of developing this system is to provide pathogen detection with NAAT-level sensitivity in low-resource settings where there is no access to instrumentation. If a disease occurs, patients would be tested with the disposable in the field. A nucleic acid sample would be preserved within the spent disposable which could be sent to a central laboratory facility for further analysis if needed.

  10. Detection of North American eastern and western equine encephalitis viruses by nucleic acid amplification assays.

    Science.gov (United States)

    Lambert, Amy J; Martin, Denise A; Lanciotti, Robert S

    2003-01-01

    We have developed nucleic acid sequence-based amplification (NASBA), standard reverse transcription PCR (RT-PCR), and TaqMan nucleic acid amplification assays for the rapid detection of North American eastern equine encephalitis (EEE) and western equine encephalitis (WEE) viral RNAs from samples collected in the field and clinical samples. The sensitivities of these assays have been compared to that of virus isolation. While all three types of nucleic acid amplification assays provide rapid detection of viral RNAs comparable to the isolation of viruses in Vero cells, the TaqMan assays for North American EEE and WEE viral RNAs are the most sensitive. We have shown these assays to be specific for North American EEE and WEE viral RNAs by testing geographically and temporally distinct strains of EEE and WEE viruses along with a battery of related and unrelated arthropodborne viruses. In addition, all three types of nucleic acid amplification assays have been used to detect North American EEE and WEE viral RNAs from mosquito and vertebrate tissue samples. The sensitivity, specificity, and rapidity of nucleic acid amplification demonstrate the usefulness of NASBA, standard RT-PCR, and TaqMan assays, in both research and diagnostic settings, to detect North American EEE and WEE viral RNAs. PMID:12517876

  11. One New Method of Nucleic Acid Amplification-Loop-mediated Isothermal Amplification of DNA

    Institute of Scientific and Technical Information of China (English)

    Xue-en FANG; Jian LI; Qin CHEN

    2008-01-01

    Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method, which amplifies DNA with high specificity, sensitivity, rapidity and efficiency under isothermal conditions using a set of four specially designed primers and a Bst DNA polymerase with strand displacement activity. The basic principle, characteristics, development of LAMP and its applications are summarized in this article.

  12. Repetitive sequence based polymerase chain reaction to differentiate close bacteria strains in acidic sites

    Institute of Scientific and Technical Information of China (English)

    XIE Ming; YIN Hua-qun; LIU Yi; LIU Jie; LIU Xue-duan

    2008-01-01

    To study the diversity of bacteria strains newly isolated from several acid mine drainage(AMD) sites in China,repetitive sequence based polymerase chain reaction (rep-PCR),a well established technology for diversity analysis of closely related bacteria strains,was conducted on 30 strains of bacteria Leptospirillum ferriphilium,8 strains of bacteria Acidithiobacillus ferrooxidans,as well as the Acidithiobacillus ferrooxidans type strain ATCC (American Type Culture Collection) 23270.The results showed that,using ERIC and BOX primer sets,rep-PCR produced highly discriminatory banding patterns.Phylogenetic analysis based on ERIC-PCR banding types was made and the results indicated that rep-PCR could be used as a rapid and highly discriminatory screening technique in studying bacterial diversity,especially in differentiating bacteria within one species in AMD.

  13. Comparison of Three Nucleic Acid Amplification Assays of Cerebrospinal Fluid for Diagnosis of Cytomegalovirus Encephalitis

    Science.gov (United States)

    Bestetti, Arabella; Pierotti, Chiara; Terreni, Mariarosa; Zappa, Alessandra; Vago, Luca; Lazzarin, Adriano; Cinque, Paola

    2001-01-01

    The diagnostic reliabilities of three cytomegalovirus (CMV) nucleic acid amplification assays of cerebrospinal fluid (CSF) were compared by using CSF samples from human immunodeficiency virus-infected patients with a postmortem histopathological diagnosis of CMV encephalitis (n = 15) or other central nervous system conditions (n = 16). By using a nested PCR assay, the quantitative COBAS AMPLICOR CMV MONITOR PCR, and the NucliSens CMV pp67 nucleic acid sequence-based amplification assay, sensitivities were 93.3, 86.6, and 93.3%, respectively, and specificities were 93.7, 93.7, and 87.5%, respectively. The COBAS AMPLICOR assay revealed significantly higher CMV DNA levels in patients with diffuse ventriculoencephalitis than in patients with focal periventricular lesions. PMID:11230445

  14. Prevalence of Plasmodium spp. in malaria asymptomatic African migrants assessed by nucleic acid sequence based amplification

    NARCIS (Netherlands)

    M. Marangi; R. Di Tullio; P.F. Mens; D. Martinelli; V. Fazio; G. Angarano; H.D.F.H. Schallig; A. Giangaspero; G. Scotto

    2009-01-01

    Background: Malaria is one of the most important infectious diseases in the world. Although most cases are found distributed in the tropical regions of Africa, Asia, Central and South Americas, there is in Europe a significant increase in the number of imported cases in non-endemic countries, in par

  15. Development and implementation of real-time nucleic acid amplification for the detection of enterovirus infections in comparison to rapid culture of various clinical specimens

    NARCIS (Netherlands)

    van Doornum, G J J; Schutten, M; Voermans, J; Guldemeester, G J J; Niesters, H G M

    2007-01-01

    Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the Magna

  16. Quantitation of viral load using real-time amplification techniques

    NARCIS (Netherlands)

    Niesters, H G

    2001-01-01

    Real-time PCR amplification techniques are currently used to determine the viral load in clinical samples for an increasing number of targets. Real-time PCR reduces the time necessary to generate results after amplification. In-house developed PCR and nucleic acid sequence-based amplification (NASBA

  17. The structural analysis of protein sequences based on the quasi-amino acids code

    Institute of Scientific and Technical Information of China (English)

    Zhu Ping; Tang Xu-Qing; Xu Zhen-Yuan

    2009-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑, +, *) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑,+, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, +, ×) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of 'the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3).

  18. Polyethersulfone improves isothermal nucleic acid amplification compared to current paper-based diagnostics.

    Science.gov (United States)

    Linnes, J C; Rodriguez, N M; Liu, L; Klapperich, C M

    2016-04-01

    Devices based on rapid, paper-based, isothermal nucleic acid amplification techniques have recently emerged with the potential to fill a growing need for highly sensitive point-of-care diagnostics throughout the world. As this field develops, such devices will require optimized materials that promote amplification and sample preparation. Herein, we systematically investigated isothermal nucleic acid amplification in materials currently used in rapid diagnostics (cellulose paper, glass fiber, and nitrocellulose) and two additional porous membranes with upstream sample preparation capabilities (polyethersulfone and polycarbonate). We compared amplification efficiency from four separate DNA and RNA targets (Bordetella pertussis, Chlamydia trachomatis, Neisseria gonorrhoeae, and Influenza A H1N1) within these materials using two different isothermal amplification schemes, helicase dependent amplification (tHDA) and loop-mediated isothermal amplification (LAMP), and traditional PCR. We found that the current paper-based diagnostic membranes inhibited nucleic acid amplification when compared to membrane-free controls; however, polyethersulfone allowed for efficient amplification in both LAMP and tHDA reactions. Further, observing the performance of traditional PCR amplification within these membranes was not predicative of their effects on in situ LAMP and tHDA. Polyethersulfone is a new material for paper-based nucleic acid amplification, yet provides an optimal support for rapid molecular diagnostics for point-of-care applications. PMID:26906904

  19. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2015-10-01

    Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  20. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    P.F. Mens; G.J. Schoone; P.A. Kager; H.D.F.H. Schallig

    2006-01-01

    Background: Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (< 20 parasites/mu l) the technique becomes less sensitive and time consuming. Rapid diagnostic tests based on Plasmodium antigen detection

  1. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    Science.gov (United States)

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use. PMID:26706801

  2. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    Science.gov (United States)

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use.

  3. A Simple, Low-Cost Platform for Real-Time Isothermal Nucleic Acid Amplification

    Directory of Open Access Journals (Sweden)

    Pascal Craw

    2015-09-01

    Full Text Available Advances in microfluidics and the introduction of isothermal nucleic acid amplification assays have resulted in a range of solutions for nucleic acid amplification tests suited for point of care and field use. However, miniaturisation of instrumentation for such assays has not seen such rapid advances and fluorescence based assays still depend on complex, bulky and expensive optics such as fluorescence microscopes, photomultiplier tubes and sensitive lens assemblies. In this work we demonstrate a robust, low cost platform for isothermal nucleic acid amplification on a microfluidic device. Using easily obtainable materials and commercial off-the-shelf components, we show real time fluorescence detection using a low cost photodiode and operational amplifier without need for lenses. Temperature regulation on the device is achieved using a heater fabricated with standard printed circuit board fabrication methods. These facile construction methods allow fabrications at a cost compatible with widespread deployment to resource poor settings.

  4. Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends

    OpenAIRE

    Zhang, Chunsun; Xing, Da

    2007-01-01

    The possibility of performing fast and small-volume nucleic acid amplification and analysis on a single chip has attracted great interest. Devices based on this idea, referred to as micro total analysis, microfluidic analysis, or simply ‘Lab on a chip’ systems, have witnessed steady advances over the last several years. Here, we summarize recent research on chip substrates, surface treatments, PCR reaction volume and speed, architecture, approaches to eliminating cross-contamination and contr...

  5. 核酸扩增技术在病原体检测中的应用%Application of nucleic acid amplification in pathogen detection

    Institute of Scientific and Technical Information of China (English)

    范吉云; 郭晓奎; 李擎天

    2009-01-01

    传统的病原体检测方法在检测敏感性、特异性、应用范围等方面存在许多不足.PCR技术已被用于感染早期的病原体检测,但在应用过程中也面临不少问题.近年来出现的新的核酸扩增技术可弥补普通PCR技术的缺点.此文就其中依赖核酸序列的扩增技术、PCR-胶体金免疫层析技术和多重荧光实时PcR技术进行综述.%The traditional pathogen detection mathods have many disadvantages in the sensitivity, specificity and application range. There are still some problems in PCB, which has been used for pathogen detection in the early stage of infection. New nucleic acid amplification technologies may make up the deficiency of PCR. In this review, three methods including nucleic acid sequence-based amplification (NASBA), PCR-immunochromatography test and multiplex fluorescent real-time PCR technology are described.

  6. Isothermal cycling and cascade signal amplification strategy for ultrasensitive colorimetric detection of nucleic acids

    International Nuclear Information System (INIS)

    We have designed a novel isothermal cascade signal-amplification strategy for ultrasensitive colorimetric determination of nucleic acids. It is based on double-cycling amplification with formation of DNAzyme via a polymerase-induced strand-displacement reaction and nicking endonuclease-assisted recycling. The assay makes use of a hairpin DNA, a short primer, KF-polymerase, and nicking endonuclease. The presence of a target DNA triggers the strand-displacement and polymerization reaction with the formation of numerous DNAzyme molecules. Upon addition of H2O2 to the resulting mixture, the H2O2 reacts with 2,2′-azino-bis (3-ethylbenzothiozoline)-6-sulfonate to form a colored product in the aid of DNAzyme, which is quantified by photometry at 415 nm. Under optimal conditions, the assay allows target DNA to be determined at concentration as low as 0.6 aM. (author)

  7. Nuclemeter: A Reaction-Diffusion Based Method for Quantifying Nucleic Acids Undergoing Enzymatic Amplification

    Science.gov (United States)

    Liu, Changchun; Sadik, Mohamed M.; Mauk, Michael G.; Edelstein, Paul H.; Bushman, Frederic D.; Gross, Robert; Bau, Haim H.

    2014-01-01

    Real-time amplification and quantification of specific nucleic acid sequences plays a major role in medical and biotechnological applications. In the case of infectious diseases, such as HIV, quantification of the pathogen-load in patient specimens is critical to assess disease progression and effectiveness of drug therapy. Typically, nucleic acid quantification requires expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low-resource settings. This paper describes a simple, low-cost, reaction-diffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. The method was tested for HIV viral load monitoring and performed on par with conventional benchtop methods. The proposed method is suitable for nucleic acid quantification at point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. PMID:25477046

  8. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  9. Real-time nucleic acid sequence-based amplification is more convenient than real-time PCR for quantification of Plasmodium falciparum.

    NARCIS (Netherlands)

    Schneider, P.; Wolters, L.R.; Schoone, G.; Schallig, H.; Sillekens, P.; Hermsen, R.; Sauerwein, R.W.

    2005-01-01

    Determination of the number of malaria parasites by routine or even expert microscopy is not always sufficiently sensitive for detailed quantitative studies on the population dynamics of Plasmodium falciparum, such as intervention or vaccine trials. To circumvent this problem, two more sensitive ass

  10. Real-time detection of noroviruses in surface water by use of a broadly reactive nucleic acid sequence-based amplification assay.

    NARCIS (Netherlands)

    Rutjes, Saskia A; Berg, Harold H J L van den; Lodder, Willemijn J; Roda Husman, Ana Maria de

    2006-01-01

    Noroviruses are the most common agents causing outbreaks of viral gastroenteritis. Outbreaks originating from contaminated drinking water and from recreational waters have been described. Due to a lack of cell culture systems, noroviruses are detected mostly by molecular methods. Molecular detection

  11. Amplification of RNA by NASBA allows direct detection of viable cells of Ralstonia solanacearum in potato

    NARCIS (Netherlands)

    Bentsink, L.; Leone, G.O.M.; Beckhoven, van J.R.C.M.; Schijndel, van H.B.; Gemen, van B.; Wolf, van der J.M.

    2002-01-01

    Aims: The objective of this study was to develop a Nucleic Acid Sequence Based Amplification (NASBA) assay, targeting 16S rRNA sequences, for direct detection of viable cells of Ralstonia solanacearum, the causal organism of bacterial wilt. The presence of intact 16S rRNA is considered to be a usefu

  12. Culture confirmation of gonococcal infection by recall of subjects found to be positive by nucleic acid amplification tests in general practice

    DEFF Research Database (Denmark)

    Møller, Jens Kjølseth

    2010-01-01

    To evaluate a routine notification of general practitioners to recall nucleic acid amplification test (NAAT)-positive subjects for culture of Neisseria gonorrhoeae to confirm gonococcal infection in the community.......To evaluate a routine notification of general practitioners to recall nucleic acid amplification test (NAAT)-positive subjects for culture of Neisseria gonorrhoeae to confirm gonococcal infection in the community....

  13. Immunocytochemistry versus nucleic acid amplification in fine needle aspirates and tissues of extrapulmonary tuberculosis

    Directory of Open Access Journals (Sweden)

    Madhu Mati Goel

    2012-01-01

    Full Text Available Background: Immunocytochemistry (ICC is an established routine diagnostic adjunct to cytology and histology for tumor diagnosis but has received little attention for diagnosis of tuberculosis. Aims: To have an objective method of direct visualization of mycobacteria or their products in clinical extrapulmonary tuberculosis (EPTB specimens, immunocytochemical localization of M. tuberculosis antigen by staining with species specific monoclonal antibody to 38-kDa antigen of Mycobacterium tuberculosis complex. Materials and Methods: Immunostaining with specific monoclonal antibody to 38-kDa antigen of Mycobacterium tuberculosis complex was done in fresh and archival fine needle aspirates and tissue granulomata of 302 cases of extrapulmonary tuberculosis and was compared with the molecular diagnostic i.e., nucleic amplification and conventional [Cytomorphology, Ziehl Neelsen (ZN staining and culture] tests and 386 controls. Results: Diagnostic indices by Bayesian analysis for all types of archival and fresh material varied from 64 to 76% in nucleic acid amplification (NAA and 96 to 98% in ICC. There was no significant difference in the diagnostic indices of ZN staining and/ or ICC in fresh or archival material whereas the sensitivity of NAA differed significantly in fresh versus archival material both in cytology (71.4% vs 52.1% and histology (51.1% vs 38.8%. ICC can be easily used on archival smears and formalin-fixed paraffin-embedded tissue sections with almost equal sensitivity and specificity as with fresh material, in contrast to NAA which showed significant difference in test results on archival and fresh material. Conclusions: Low detection sensitivity of MTB DNA in archival material from known tuberculous cases showed the limitation of in-house NAA-based molecular diagnosis. ICC was found to be sensitive, specific and a better technique than NAA and can be used as an adjunct to conventional morphology and ZN staining for the diagnosis of

  14. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids.

    Science.gov (United States)

    Lv, Yifan; Cui, Liang; Peng, Ruizi; Zhao, Zilong; Qiu, Liping; Chen, Huapei; Jin, Cheng; Zhang, Xiao-Bing; Tan, Weihong

    2015-12-01

    Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies.

  15. Reliability of nucleic acid amplification for detection of Mycobacterium tuberculosis: an international collaborative quality control study among 30 laboratories.

    Science.gov (United States)

    Noordhoek, G T; van Embden, J D; Kolk, A H

    1996-01-01

    Nucleic acid amplification to detect Mycobacterium tuberculosis in clinical specimens is increasingly used as a laboratory tool for the diagnosis of tuberculosis. However, the specificity and sensitivity of these tests may be questioned, and no standardized reagents for quality control assessment are available. To estimate the performance of amplification tests for routine diagnosis, we initiated an interlaboratory study involving 30 laboratories in 18 countries. We prepared blinded panels of 20 sputum samples containing no, 100, or 1,000 mycobacterial cells. Each laboratory was asked to detect M. tuberculosis by their routine method of nucleic acid amplification. Only five laboratories correctly identified the presence or absence of mycobacterial DNA in all 20 samples. Seven laboratories detected mycobacterial DNA in all positive samples, and 13 laboratories correctly reported the absence of DNA in the negative samples. Lack of specificity was more of a problem than lack of sensitivity. Reliability was not found to be associated with the use of any particular method. Reliable detection of M. tuberculosis in clinical samples by nucleic acid amplification techniques is possible, but many laboratories do not use adequate quality controls. This study underlines the need for good laboratory practice and reference reagents to monitor the performance of the whole assay, including pretreatment of clinical samples. PMID:8880513

  16. Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids

    Science.gov (United States)

    Li, Zhao; Liu, Yong; Wei, Qingquan; Liu, Yuanjie; Liu, Wenwen; Zhang, Xuelian; Yu, Yude

    2016-01-01

    Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm2 area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10-1 to 4 × 10-3 copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings. PMID:27074005

  17. Locked nucleic acid inhibits amplification of contaminating DNA in real-time PCR

    DEFF Research Database (Denmark)

    Hummelshoj, Lone; Ryder, Lars P; Madsen, Hans O;

    2005-01-01

    in intronic DNA, the aim was to inhibit the amplification of genomic DNA without affecting the amplification of reverse-transcribed spliced mRNA. LNA was designed to bind within intron 5 in the x-box binding protein 1 (XBP1) gene. An irrelevant LNA oligonucleotide served as a negative control. In both PCR...

  18. Automated nucleic acid amplification testing in blood banks: An additional layer of blood safety

    Directory of Open Access Journals (Sweden)

    Pragati Chigurupati

    2015-01-01

    Full Text Available Context: A total of 30 million blood components are transfused each year in India. Blood safety thus becomes a top priority, especially with a population of around 1.23 billion and a high prevalence rate of human immunodeficiency virus (HIV, hepatitis B virus (HBV and hepatitis C virus (HCV in general population. Nucleic acid amplification testing (NAT in blood donor screening has been implemented in many developed countries to reduce the risk of transfusion-transmitted viral infections (TTIs. NAT takes care of the dynamics of window period of viruses and offers the safest blood pack for donation. Aims: The aim of this study is to show the value of NAT in blood screening. Settings and Design: Dhanavantari Blood Bank, Rajahmundry, Andhra Pradesh, India. Subjects and Methods: Over a period of 1 year from January 2012 to December 2012, a total number of 15,000 blood donor samples were subjected to tests for HIV, HBV, and HCV by enzyme-linked immunosorbent assay (ELISA method and 8000 ELISA nonreactive samples were subjected for NAT using multiplex polymerase chain reaction technology. Results: Of the 15,000 donors tested, 525 were seroreactive. In 8000 ELISA negative blood samples subjected to NAT, 4 donor samples were reactive for HBV. The NAT yield was 1 in 2000. Conclusions: NAT could detect HIV, HBV, and HCV cases in blood donor samples those were undetected by serological tests. NAT could interdict 2500 infectious donations among our approximate 5 million annual blood donations.

  19. Establishment of the nucleic acid sequence-based amplificationmethod of detecting Vibrio parahaemolyticus%依赖于核酸序列恒温扩增技术快速检测副溶血性弧菌方法的建立

    Institute of Scientific and Technical Information of China (English)

    倪鑫; 王志聪; 雷质文; 梁成珠; 汪东风; 姜英辉; 王建广; 祝素贞

    2011-01-01

    为建立副溶血性弧菌的快速检测方法,本研究采用依赖于核酸序列恒温扩增(NASBA)技术,以副溶血性弧菌的tlh基因为扩增的靶基因设计特异性引物和探针,建立可快速扩增副溶血性弧菌的NASBA方法.特异性和灵敏度试验结果表明:该NASBA方法对副溶血性弧菌的最小检出量为5.1×102 cfu/mL,高于普通PCR方法,而且与其他种属的菌无任何交叉反应.此外,本研究将副溶血弧菌扩增产物采用通用型核酸扩增物快速检测板进行检测,实现了特异性强的快速副溶血弧菌的检测.该方法对仪器要求低,具有良好的应用前景.%In this study, we adopted a technology based on nucleic acid sequence-based amplification (NASBA), to establish a rapid test method of Vibrio parahaemolyticus. Specific primers and probes were designed for the tlh target gene of V. Parahaemolyticus and the detection method of NASBA was established. Its specificity and sensitivity were tested. The results showed that the sensitivity of the NASBA was 5.1 x 102 cfii/mL which was higher than that of PCR method and this method had no cross reaction with other species of bacteria. The amplification products of V. Pamhaemolyticus were rapidly detected by using the universal rapid detection board of nucleic acid amplification product. In conclusion, detecting V. Parahaemolyticus with NASBA method was more specific and sensitive than PCR method and has lower instrumental requirement and a broad application.

  20. Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification.

    Science.gov (United States)

    Lin, S Y; Hwang, S C; Yang, Y C; Wang, C F; Chen, Y H; Chen, T C; Lu, P L

    2016-06-01

    We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.

  1. Tissue donation and virus safety: more nucleic acid amplification testing is needed.

    Science.gov (United States)

    Pruss, A; Caspari, G; Krüger, D H; Blümel, J; Nübling, C M; Gürtler, L; Gerlich, W H

    2010-10-01

    In tissue and organ transplantation, it is of great importance to avoid the transmission of blood-borne viruses to the recipient. While serologic testing for anti-human immunodeficiency virus (HIV)-1 and -2, anti-hepatitis C virus (HCV), hepatitis B surface antigen (HBsAg), anti-hepatitis B core antigen (HBc), and Treponema pallidum infection is mandatory, there is until now in most countries no explicit demand for nucleic acid amplification testing (NAT) to detect HIV, hepatitis B virus (HBV), and HCV infection. After a review of reports in the literature on viral transmission events, tissue-specific issues, and manufacturing and inactivation procedures, we evaluated the significance of HIV, HCV, and HBV detection using NAT  in  donors of various types of tissues and compared our results with the experiences of blood banking organizations. There is a significant risk of HIV, HCV, and HBV transmission by musculoskeletal tissues because of their high blood content and the high donor-recipient ratio. If no effective virus inactivation procedure for musculoskeletal tissue is applied, donors should be screened using NAT  for  HIV, HCV, and HBV. Serologically screened cardiovascular tissue carries a very low risk of HIV, HCV, or HBV transmission. Nevertheless, because effective virus inactivation is impossible (retention of tissue morphology) and the donor-recipient ratio may be as high as 1:10, we concluded that NAT  should be performed for HIV, HCV, and HBV as an additional safety measure. Although cornea allografts carry the lowest risk of transmitting HIV, HCV, and HBV  owing to corneal physiology, morphology, and the epidemiology of corneal diseases, NAT  for  HCV should still be performed. If the NAT  screening of a donor for HIV, HCV, and HBV is negative, quarantine storage of the donor tissue seems dispensable. In view of numerous synergistic effects with transfusion medicine, it would be advantageous for tissue banks to cooperate with blood

  2. Detection of Salmonella invA by isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) in Zambia.

    Science.gov (United States)

    Isogai, Emiko; Makungu, Chitwambi; Yabe, John; Sinkala, Patson; Nambota, Andrew; Isogai, Hiroshi; Fukushi, Hideto; Silungwe, Manda; Mubita, Charles; Syakalima, Michelo; Hang'ombe, Bernard Mudenda; Kozaki, Shunji; Yasuda, Jun

    2005-01-01

    The isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) is a new isothermal DNA amplification method composed of exo Bca DNA polymerase, RNaseH and DNA-RNA chimeric primers. We detected invA of Salmonella from chicken carcasses, egg yolk and cattle fecal samples. Fifty-three of 59 isolates were invA-positive in ICAN-chromatostrip detection. The result was consistent with those obtained by standard PCR. Salmonella invA was detected in 12 of 14 carcass rinses by ICAN, while in 7 of 14 rinses by standard PCR. These results indicate that ICAN is an efficient, sensitive and simple system to detect invA of Salmonella species in developing countries such as Zambia.

  3. Improved sensitivity of nucleic acid amplification for rapid diagnosis of tuberculous meningitis

    DEFF Research Database (Denmark)

    Johansen, Isik Somuncu; Lundgren, Bettina; Tabak, Fehmi;

    2004-01-01

    Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method) for the detec......Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method...

  4. Nucleic acid amplification technology screening for hepatitis C virus and human immunodeficiency virus for blood donations

    International Nuclear Information System (INIS)

    To investigate the performance of the commercial Roche COBAS AmpliScreen assay, and demonstrate whether the COBAS AmpliScreen human immunodeficiency virus-1 (HIV-1) test, v1.5, and COBAS AmpliScreen hepatitis C virus (HCV) v 2.0 for screening for HIV-1 and HCV RNA in the donated blood units from which plasma mini pools were collected, by nucleic acid amplification technology (NAT), could detect the positive pools and reduce the risk of transmission of infections for those routinely tested by serological assays. The study was performed on 3288 plasma samples collected from blood donors in a period of 13 months, from August 2004 to August 2005, at Al-Hada Armed Forces Hospital, Molecular Pathology Laboratory, Taif, Kingdom of Saudi Arabia. The samples were tested by the reverse transcriptase polymerase chain reaction (RT-PCR) after RNA extraction (this represents the major method in NAT assays), in parallel with the routine serological testing to detect qualitatively for HIV-1 and HCV. The NAT assays that include an automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays, and the routine serological screening assays for the detection of the HIV-1 and HCV RNA in the plasma samples from the blood donors have shown to be a reliable combination that would meet our requirements. The collected data further confirms the results from the serological assays and enables us to decrease the residual risk of transmission to a minimum with the finding of no seronegative window period donation. The results demonstrate that out of 3288 samples, the percentages of RT-PCR (NAT) negative blood donations that were also confirmed as seronegative were 99% for HCV, and 99.1% for HIV-1. The modified combined systems (automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays) for NAT screening assays has allowed the release of all blood donations supplied in the

  5. Diagnostic value of nine nucleic acid amplification test systems for Mycobacterium tuberculosis complex

    Directory of Open Access Journals (Sweden)

    Gülnur Tarhan

    2015-09-01

    Full Text Available Objective: In this study, nine commercial Nucleic Acid Amplification Test Systems (NAATs were evaluated for diagnostic performance of Mycobacterium tuberculosis complex (MTBC from smear positive sputum species (SPss and smear negative sputum specimens (SNss. Methods: Sixty SPss and 55 SNss were examined icroscopically by Ehrlich Ziehl Neelsen (EZN staining method, and also inoculated on Löwenstein Jensen (LJ medium for culture. The sensitivity and specificity of nine NAATs were calculated according to LJ culture method accepted as gold standard. Results: When LJ culture results were taken as gold standard; the sensitivity rates of method COBAS Amplicor MTB (Method A, GenProbe MTD (Method B, Cobas TaqMan MTB PCR Method C, iCycler iQ RT PCR (Method D, TaqMan PCR AB 5700 (Method E, TaqMan PCR AB7700 (Method F, ightCycler® 480 RT PCR (Method G, Rotor Gene RT PCR (Method H and the AdvanSure TB/NTM RT PCR (Method I for SPss were 98.3 %, 93.3 %, 96.7 %, 100 %, 93.3 %, 100 %, 100 %, 100 % and 100 %, respectively. The sensitivity was 53.84% for the methods A, B, D, E, G and I; 38.46% for the method C and H; 61.5% for the method F for the method I in SNss. There were no statistical significant differences between the nine NAATs (p≥0.05. The specificity was 100% for all nine NAATs in SNss. The positivity rates of methods were 53.8% for methods A, B, D, E, G, I; 38.5% for methods C and H, and 61.5% for method F in SNss. These rates were 100% for D, F, G, H and I; 98.3% for method A; 96.7% for method C; 93,3% for methods B and E in SPss. Statistical analysis showed that there was no statistically significant differences among the nine NAATs (p≥0.05. Conclusion: It is concluded that the nine NAATs might be useful for detecting MTBC from SPss, but not effective for SNss. J Microbiol Infect Dis 2015;5(3: 103-109

  6. Development of an electrochemical DNA biosensor for detection of specific Mycobacterium tuberculosis sequence based on poly(L-glutamic acid) modified electrode

    Indian Academy of Sciences (India)

    MERVE YESIL; SONER DONMEZ; FATMA ARSLAN

    2016-11-01

    An electrochemical DNA biosensor was developed by avidin-biotin interaction of a biotinylated probe and avidin-attached, poly(L-glutamic) acid coated pencil graphite electrode (PGA/PGE) for detection of specific Mycobacterium tuberculosis DNA sequence. The discrimination of fully complementary hybridization and mismatch hybridization was carried out by electrochemical reduction current of Meldola’s Blue (MDB) in square wave voltammetry (SWV). The calibration graph of the DNA biosensor was linear between 1.5–12.5 nM and the detection limit was calculated as 1.3 nM. The proposed biosensor successfully discriminated short andlong oligonucleotides related to DNA sequence of Mycobacterium tuberculosis in optimal condition.

  7. Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms.

    Directory of Open Access Journals (Sweden)

    Kieran Cashin

    Full Text Available The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1 strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation

  8. Label-free electrochemical nucleic acid biosensing by tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme amplification.

    Science.gov (United States)

    Liu, Shufeng; Gong, Hongwei; Wang, Yanqun; Wang, Li

    2016-03-15

    Owing to the intrinsic importance of nucleic acid as bio-targets, the achievement of its simple and sensitive detection with high confidence is very essential for biological studies and diagnostic purposes. Herein, a label-free, isothermal, and ultrasensitive electrochemical detection of target DNA was developed by using a tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme releasing amplification strategy. Upon sensing of the nucleic acid analyte for the assembled hairpin-like probe DNA on the electrode, the DNA polymerase guided the target recycling and simultaneously triggered the lambda exonuclease cleavage, accompanied by the cascade recycling of the released new complementary strand and the amplified liberation of the G-rich sequence of the HRP-mimicking DNAzyme. The electrocatalytic reduction of H2O2 by the generated hemin/G-quadruplex DNAzyme was used for the signal readout and further amplification toward target response. Such tandem functional operation by DNA polymerase, lambda exonuclease and DNAzyme endows the developed biosensor with a high sensitivity and also a high confidence. A low detection limit of 5 fM with an excellent selectivity toward target DNA could be achieved. It also exhibits the distinct advantages of simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus may offer a promising avenue for the applications in disease diagnosis and clinical biomedicine. PMID:26513289

  9. Point-of-care multiplexed assays of nucleic acids using microcapillary-based loop-mediated isothermal amplification.

    Science.gov (United States)

    Zhang, Yi; Zhang, Lu; Sun, Jiashu; Liu, Yulei; Ma, Xingjie; Cui, Shangjin; Ma, Liying; Xi, Jianzhong Jeff; Jiang, Xingyu

    2014-07-15

    This report demonstrates a straightforward, robust, multiplexed and point-of-care microcapillary-based loop-mediated isothermal amplification (cLAMP) for assaying nucleic acids. This assay integrates capillaries (glass or plastic) to introduce and house sample/reagents, segments of water droplets to prevent contamination, pocket warmers to provide heat, and a hand-held flashlight for a visual readout of the fluorescent signal. The cLAMP system allows the simultaneous detection of two RNA targets of human immunodeficiency virus (HIV) from multiple plasma samples, and achieves a high sensitivity of two copies of standard plasmid. As few nucleic acid detection methods can be wholly independent of external power supply and equipment, our cLAMP holds great promise for point-of-care applications in resource-poor settings. PMID:24937125

  10. On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria.

    Science.gov (United States)

    Kunze, A; Dilcher, M; Abd El Wahed, A; Hufert, F; Niessner, R; Seidel, M

    2016-01-01

    This work presents an on-chip isothermal nucleic acid amplification test (iNAAT) for the multiplex amplification and detection of viral and bacterial DNA by a flow-based chemiluminescence microarray. In a principle study, on-chip recombinase polymerase amplification (RPA) on defined spots of a DNA microarray was used to spatially separate the amplification reaction of DNA from two viruses (Human adenovirus 41, Phi X 174) and the bacterium Enterococcus faecalis, which are relevant for water hygiene. By establishing the developed assay on the microarray analysis platform MCR 3, the automation of isothermal multiplex-amplification (39 °C, 40 min) and subsequent detection by chemiluminescence imaging was realized. Within 48 min, the microbes could be identified by the spot position on the microarray while the generated chemiluminescence signal correlated with the amount of applied microbe DNA. The limit of detection (LOD) determined for HAdV 41, Phi X 174, and E. faecalis was 35 GU/μL, 1 GU/μL, and 5 × 10(3) GU/μL (genomic units), which is comparable to the sensitivity reported for qPCR analysis, respectively. Moreover the simultaneous amplification and detection of DNA from all three microbes was possible. The presented assay shows that complex enzymatic reactions like an isothermal amplification can be performed in an easy-to-use experimental setup. Furthermore, iNAATs can be potent candidates for multipathogen detection in clinical, food, or environmental samples in routine or field monitoring approaches.

  11. Chip-based device for parallel sorting, amplification, detection, and identification of nucleic acid subsequences

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Colston, Jr, Billy W.

    2016-08-09

    An apparatus for chip-based sorting, amplification, detection, and identification of a sample having a planar substrate. The planar substrate is divided into cells. The cells are arranged on the planar substrate in rows and columns. Electrodes are located in the cells. A micro-reactor maker produces micro-reactors containing the sample. The micro-reactor maker is positioned to deliver the micro-reactors to the planar substrate. A microprocessor is connected to the electrodes for manipulating the micro-reactors on the planar substrate. A detector is positioned to interrogate the sample contained in the micro-reactors.

  12. Ultrasensitive detection of nucleic acids by template enhanced hybridization followed by rolling circle amplification and catalytic hairpin assembly.

    Science.gov (United States)

    Song, Weiling; Zhang, Qiao; Sun, Wenbo

    2015-02-11

    An ultrasensitive protocol for fluorescent detection of DNA is designed by combining the template enhanced hybridization process (TEHP) with Rolling Circle Amplification (RCA) and Catalytic Hairpin Assembly (CHA), showing a remarkable amplification efficiency.

  13. Reliability of nucleic acid amplification methods for detection of Chlamydia trachomatis in urine: results of the first international collaborative quality control study among 96 laboratories

    NARCIS (Netherlands)

    R.P.A.J. Verkooyen (Roel); G.T. Noordhoek; P.E. Klapper; J. Reid; J. Schirm; G.M. Cleator; M. Ieven; G. Hoddevik

    2003-01-01

    textabstractThe first European Quality Control Concerted Action study was organized to assess the ability of laboratories to detect Chlamydia trachomatis in a panel of urine samples by nucleic acid amplification tests (NATs). The panel consisted of lyophilized urine samples, includ

  14. Implementation of Oral and Rectal Gonococcal and Chlamydial Nucleic Acid Amplification-Based Testing as a Component of Local Health Department Activities.

    Science.gov (United States)

    Nall, Jennifer; Barr, Breona; McNeil, Candice J; Bachmann, Laura H

    2016-10-01

    From January 1, 2014, to May 31, 2015, 452 individuals received extragenital nucleic acid amplification-based Neisseria gonorrhoeae and Chlamydia trachomatis testing through public health venues. Seventy-four individuals (16%) tested positive for Neisseria gonorrhoeae and/or Chlamydia trachomatis at an extragenital site and 40 (54%) would not have been effectively diagnosed and treated in the absence of extragenital testing.

  15. Detection of Staphylococcus epidermidis by a Quartz Crystal Microbalance Nucleic Acid Biosensor Array Using Au Nanoparticle Signal Amplification

    Directory of Open Access Journals (Sweden)

    Weiling Fu

    2008-10-01

    Full Text Available Staphylococcus epidermidis is a critical pathogen of nosocomial blood infections, resulting in significant morbidity and mortality. A piezoelectric quartz crystal microbalance (QCM nucleic acid biosensor array using Au nanoparticle signal amplification was developed to rapidly detect S. epidermidis in clinical samples. The synthesized thiolated probes specific targeting S. epidermidis 16S rRNA gene were immobilized on the surface of QCM nucleic acid biosensor arrays. Hybridization was induced by exposing the immobilized probes to the PCR amplified fragments of S. epidermidis, resulting in a mass change and a consequent frequency shift of the QCM biosensor. To further enhance frequency shift results from above described hybridizations, streptavidin coated Au nanoparticles were conjugated to the PCR amplified fragments. The results showed that the lowest detection limit of current QCM system was 1.3×103 CFU/mL. A linear correlation was found when the concentration of S. epidermidis varied from 1.3×103 to 1.3×107 CFU/mL. In addition, 55 clinical samples were detected with both current QCM biosensor system and conventional clinical microbiological method, and the sensitivity and specificity of current QCM biosensor system were 97.14% and 100%, respectively. In conclusion, the current QCM system is a rapid, low-cost and sensitive method that can be used to identify infection of S. epidermidis in clinical samples.

  16. High Interlaboratory Reprocucibility of DNA Sequence-based Typing of Bacteria in a Multicenter Study

    DEFF Research Database (Denmark)

    Sousa, MA de; Boye, Kit; Lencastre, H de;

    2006-01-01

    Current DNA amplification-based typing methods for bacterial pathogens often lack interlaboratory reproducibility. In this international study, DNA sequence-based typing of the Staphylococcus aureus protein A gene (spa, 110 to 422 bp) showed 100% intra- and interlaboratory reproducibility without...

  17. An ultrasensitive electrochemical immunosensor platform with double signal amplification for indole-3-acetic acid determinations in plant seeds.

    Science.gov (United States)

    Yin, Huanshun; Xu, Zhenning; Zhou, Yunlei; Wang, Mo; Ai, Shiyun

    2013-03-21

    A label-free electrochemical immunosensor for ultra-sensitive detection of indole-3-acetic acid (IAA), a very important phytohormone, has been developed in this work. The detection strategy was mainly based on 4-aminophenylboronic acid, magnetic nanoparticles functionalized with horseradish peroxidase-conjugated goat anti-rat immunoglobulin G (HRP-IgG-Fe(3)O(4)) and rat monoclonal antibody against IAA-modified gold nanoparticles (anti-IAA-AuNPs). HRP-IgG-AuNPs was covalently assembled on the electrode surface through the specific chemical reaction between boronic acid and the vicinal diol in HRP-IgG. Then, anti-IAA-AuNPs was further assembled on the electrode via the interaction between IgG and antibody. Through the dual amplification of HRP-IgG-Fe(3)O(4) and anti-IAA-AuNPs, the trapping capacity of the immunosensor for IAA was significantly enhanced based on the promotion of the immunoreaction between antibody and antigen, which resulted in a large decrease of the electrochemical response of the redox probe, Fe(CN)(6)(3-), and an increase in sensitivity. The developed electrochemical immunosensor exhibited a wide linear range from 0.02 to 500 ng mL(-1) with a low detection limit of 0.018 ng mL(-1) (S/N = 3). Moreover, the proposed immunosensor showed acceptable selectivity, reproducibility, accuracy and stability. The IAA extracted from various seeds was successfully detected using the developed immunosensor. This assay method might provide an alternative strategy for the detection of various phytohormones. PMID:23377501

  18. Nucleic acid amplification tests (NAATs for gonorrhoea diagnosis in women: Experience of a tertiary care hospital in north India

    Directory of Open Access Journals (Sweden)

    Seema Sood

    2014-01-01

    Full Text Available Background & objectives: Gonorrhoea is among the most frequent of the estimated bacterial sexually transmitted infections (STIs and has significant health implications in women. The use of nucleic acid amplification tests (NAATs has been shown to provide enhanced diagnosis of gonorrhoea in female patients. However, it is recommended that an on-going assessment of the test assays should be performed to check for any probable sequence variation occurring in the targeted region. In this study, an in-house PCR targeting opa-gene of Neisseria gonorrhoeae was used in conjunction with 16S ribosomal PCR to determine the presence of gonorrhoea in female patients attending the tertiary care hospitals. Methods: Endocervical samples collected from 250 female patients with complaints of vaginal or cervical discharge or pain in lower abdomen were tested using opa and 16S ribosomal assay. The samples were also processed by conventional methods. Results: Of the 250 female patients included in the study, only one was positive by conventional methods (microscopy and culture whereas 17 patients were found to be positive based on PCR results. Interpretation & conclusions: The clinical sensitivity of conventional methods for the detection of N. gonorrhoeae in female patients was low. The gonococcal detection rates increased when molecular method was used giving 16 additional positives. Studies should be done to find out other gene targets that may be used in the screening assays to detect the presence of gonorrhoea.

  19. Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA).

    Science.gov (United States)

    Lutz, Sascha; Weber, Patrick; Focke, Max; Faltin, Bernd; Hoffmann, Jochen; Müller, Claas; Mark, Daniel; Roth, Günter; Munday, Peter; Armes, Niall; Piepenburg, Olaf; Zengerle, Roland; von Stetten, Felix

    2010-04-01

    For the first time we demonstrate a self-sufficient lab-on-a-foil system for the fully automated analysis of nucleic acids which is based on the recently available isothermal recombinase polymerase amplification (RPA). The system consists of a novel, foil-based centrifugal microfluidic cartridge including prestored liquid and dry reagents, and a commercially available centrifugal analyzer for incubation at 37 degrees C and real-time fluorescence detection. The system was characterized with an assay for the detection of the antibiotic resistance gene mecA of Staphylococcus aureus. The limit of detection was <10 copies and time-to-result was <20 min. Microfluidic unit operations comprise storage and release of liquid reagents, reconstitution of lyophilized reagents, aliquoting the sample into < or = 30 independent reaction cavities, and mixing of reagents with the DNA samples. The foil-based cartridge was produced by blow-molding and sealed with a self-adhesive tape. The demonstrated system excels existing PCR based lab-on-a-chip platforms in terms of energy efficiency and time-to-result. Applications are suggested in the field of mobile point-of-care analysis, B-detection, or in combination with continuous monitoring systems. PMID:20300675

  20. Prospective evaluation of the Alere i Influenza A&B nucleic acid amplification versus Xpert Flu/RSV.

    Science.gov (United States)

    Nguyen Van, J C; Caméléna, F; Dahoun, M; Pilmis, B; Mizrahi, A; Lourtet, J; Behillil, S; Enouf, V; Le Monnier, A

    2016-05-01

    The rapid and accurate detection of influenza virus in respiratory specimens is required for optimal management of patients with acute respiratory infections. Because of the variability of the symptoms and the numerous other causes of influenza-like illness, the diagnosis of influenza cannot be made on the basis of clinical criteria alone. Thus, rapid influenza diagnostic tests have been developed such as the Alere i Influenza A&B isothermal nucleic acid assay. We prospectively evaluated the performance of the Alere i Influenza A&B assay in comparison with our routine Xpert Flu/RSV assay. Positive samples were subtyped according to the protocol from the National Influenza Center (Paris, France). A total of 96 respiratory nasal swab samples were analyzed: with both methods, 38 were positive and 56 were negative. Samples were prospectively collected from January 20 to April 8, 2015, from patient (86 adult and 10 pediatric patients) presenting with an influenza-like illness through the French influenza season. In comparison with the Xpert Flu/RSV assay, the overall sensitivity and specificity of the Alere i Influenza A&B assay were 95% and 100%, respectively. Our results indicate that the Alere i Influenza A&B assay has a good overall analytical performance and a high degree of concordance with the PCR-based Xpert Flu/RSV assay. The Alere i Influenza A&B isothermal nucleic acid amplification test is a powerful tool for influenza detection due to its high sensitivity and specificity as well as its ability to generate results within 15min. PMID:26899154

  1. Detection of Chlamydia trachomatis by Nucleic Acid Amplification Testing: Our Evaluation Suggests that CDC-Recommended Approaches for Confirmatory Testing Are Ill-Advised

    OpenAIRE

    Schachter, Julius; Chow, Joan M.; Howard, Holly; Bolan, Gail; Moncada, Jeanne

    2006-01-01

    We evaluated three CDC-suggested approaches for confirming positive nucleic acid amplification tests (NAATs) for Chlamydia trachomatis: (i) repeat the original test on the original specimen, (ii) retest the original specimen with a different test, and (iii) perform a different test on a duplicate specimen. For approach 1, specimens (genital swabs or first-catch urine [FCU]) initially positive by the Abbott LCx Probe System Chlamydia trachomatis Assay (LCx; Abbott Laboratories), the APTIMA Com...

  2. Reliability of Nucleic Acid Amplification Methods for Detection of Chlamydia trachomatis in Urine: Results of the First International Collaborative Quality Control Study among 96 Laboratories

    OpenAIRE

    Verkooyen, Roel; Noordhoek, G T; Klapper, P.E.; Reid, J.; Schirm, J.; Cleator, G. M.; Ieven, M.; Hoddevik, G.

    2003-01-01

    textabstractThe first European Quality Control Concerted Action study was organized to assess the ability of laboratories to detect Chlamydia trachomatis in a panel of urine samples by nucleic acid amplification tests (NATs). The panel consisted of lyophilized urine samples, including three negative, two strongly positive, and five weakly positive samples. Ninety-six laboratories in 22 countries participated with a total of 102 data sets. Of 204 strongly positive samples 199 (97.5%) were corr...

  3. Clinical utility of a nested nucleic acid amplification format in comparison to viral culture for the diagnosis of mucosal herpes simplex infection in a genitourinary medicine setting

    OpenAIRE

    Wyatt Dorothy E; McCaughey Conall; O'Neill Hugh J; Coyle Peter V; McBride Michael O

    2001-01-01

    Abstract Background Nested nucleic acid amplification tests are often thought too sensitive or prone to generatingfalse positive results for routine use. The current study investigated the specificity and clinicalutility of a routine multiplex nested assay for mucosal herpetic infections. Methods Ninety patients, categorised into those clinically diagnosed to (a) have and (b) not haveherpetic infection, were enrolled. Swabs from oral and ano-genital sites were assayed by thenested assay and c...

  4. A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections

    OpenAIRE

    Feeney Susan A; Mitchell Suzanne J; Mitchell Frederick; De Ornellas Dennis; McCaughey Conall; O'Neill Hugh J; Ong Grace M; Coyle Peter V; Wyatt Dorothy E; Forde Marian; Stockton Joanne

    2004-01-01

    Abstract Background Immunofluorescence and virus culture are the main methods used to diagnose acute respiratory virus infections. Diagnosing these infections using nucleic acid amplification presents technical challenges, one of which is facilitating the different optimal annealing temperatures needed for each virus. To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 c...

  5. A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings.

    Directory of Open Access Journals (Sweden)

    Paul LaBarre

    Full Text Available BACKGROUND: Molecular assays targeted to nucleic acid (NA markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR instrumentation (another is sample preparation. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented. CONCLUSIONS/SIGNIFICANCE: We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes.

  6. Comparison of nucleic acid hybridization and nucleic acid amplification using conserved sequences from the 5' noncoding region for detection of bovine viral diarrhea virus.

    OpenAIRE

    Ridpath, J F; Bolin, S R; Katz, J

    1993-01-01

    Primers and probes derived from conserved sequences located in the 5' noncoding region of pestiviruses were evaluated for detection of bovine viral diarrhea virus. With these reagents, hybridization and polymerase chain reaction tests detected 62 of 90 and 90 of 90 bovine viral diarrhea virus isolates, respectively. A quick lysis method for preparing RNA for use in polymerase chain reaction amplification also was evaluated.

  7. Detection of Vibrio cholerae by isothermal cross-priming amplification combined with nucleic acid detection strip analysis.

    Science.gov (United States)

    Zhang, Xia; Du, Xin-Jun; Guan, Chun; Li, Ping; Zheng, Wen-Jie; Wang, Shuo

    2015-08-01

    Vibrio cholerae is a water- and food-borne human pathogen, and V. cholerae serotypes O1 and O139 have attracted attention because of their severe pathogenesis. However, non-O1, non-O139 cholera vibrios (NCVs) were also recently recognized as having virulence properties. In this study, we developed a cross-priming amplification (CPA) method for the detection of all serotypes of V. cholerae. The specificity of the CPA method was tested using a panel of 60 different bacterial strains. All of the V. cholerae strains showed positive results, and 41 other types of bacteria gave negative results. The limit of detection of the CPA method was 79.28 fg of genomic DNA, 4.2 × 10(2) CFU/ml for bacteria in pure culture, and 5.6 CFU per 25 g of sample with pre-enrichment. This method showed a higher sensitivity than the loop-mediated isothermal amplification (LAMP) method did and was more convenient to perform. These results indicate that the CPA method can be used for the rapid preliminary screening of V. cholerae.

  8. Nucleic acid specific-based amplification and its application in inspection and quarantine%NASBA技术及其在检验检疫中的应用

    Institute of Scientific and Technical Information of China (English)

    王英超; 王宁宁; 吴兴海; 陈长法; 魏晓棠; 封立平; 张成标

    2014-01-01

    Nucleic acid specific-based amplification (NASBA) is a new technology to amplify RNA originated in PCR. As a new research means, NASBA has the characteristics of convenience, good accuracy, high sensitivity and short periods, especially applicable to RNA analysis. The nucleic acid analysis technology is an important means in entry-exit inspection and quarantine, which can be used to detect and identify pathogenic microorganism in food, pests and pathogen in animals and plants. The paper briefly introduced basic principle of NASBA, compared NASBA to RT-PCR, realtime RT-PCR and other isothermal amplification methods and revealed their differences and similarity. According to the usage characteristics of NASBA, the paper reviewed the application and prospect of NASBA in food safety detection and animal and plant quarantine in entry-exit inspection and quarantine.%序列特异性核酸体外扩增技术(nucleic acid specific-based amplification, NASBA)是在PCR基础上发展起来的一种扩增RNA的新技术,作为一种新型研究手段,具有便捷、准确性好、灵敏度高、周期短的特点,尤其适用于RNA的分析研究。核酸分析技术是出入境检验检疫工作的重要手段,可用于食品病原微生物、动植物产品中的有害生物、病原的分析及鉴定。本文简要介绍了NASBA技术的基本原理,在论证对比NASBA技术与普通PCR方法、荧光PCR方法及其他恒温扩增等核酸分析技术的差异及相似性后,根据其使用特点进一步对NASBA在进出境检验检疫的食品安全检测及动植物检疫的应用予以综述及展望。

  9. Nucleotide and Predicted Amino Acid Sequence-Based Analysis of the Avian Metapneumovirus Type C Cell Attachment Glycoprotein Gene: Phylogenetic Analysis and Molecular Epidemiology of U.S. Pneumoviruses

    Science.gov (United States)

    Alvarez, Rene; Lwamba, Humphrey M.; Kapczynski, Darrell R.; Njenga, M. Kariuki; Seal, Bruce S.

    2003-01-01

    A serologically distinct avian metapneumovirus (aMPV) was isolated in the United States after an outbreak of turkey rhinotracheitis (TRT) in February 1997. The newly recognized U.S. virus was subsequently demonstrated to be genetically distinct from European subtypes and was designated aMPV serotype C (aMPV/C). We have determined the nucleotide sequence of the gene encoding the cell attachment glycoprotein (G) of aMPV/C (Colorado strain and three Minnesota isolates) and predicted amino acid sequence by sequencing cloned cDNAs synthesized from intracellular RNA of aMPV/C-infected cells. The nucleotide sequence comprised 1,321 nucleotides with only one predicted open reading frame encoding a protein of 435 amino acids, with a predicted Mr of 48,840. The structural characteristics of the predicted G protein of aMPV/C were similar to those of the human respiratory syncytial virus (hRSV) attachment G protein, including two mucin-like regions (heparin-binding domains) flanking both sides of a CX3C chemokine motif present in a conserved hydrophobic pocket. Comparison of the deduced G-protein amino acid sequence of aMPV/C with those of aMPV serotypes A, B, and D, as well as hRSV revealed overall predicted amino acid sequence identities ranging from 4 to 16.5%, suggesting a distant relationship. However, G-protein sequence identities ranged from 72 to 97% when aMPV/C was compared to other members within the aMPV/C subtype or 21% for the recently identified human MPV (hMPV) G protein. Ratios of nonsynonymous to synonymous nucleotide changes were greater than one in the G gene when comparing the more recent Minnesota isolates to the original Colorado isolate. Epidemiologically, this indicates positive selection among U.S. isolates since the first outbreak of TRT in the United States. PMID:12682171

  10. Development of Chemiluminescent Lateral Flow Assay for the Detection of Nucleic Acids

    OpenAIRE

    Nugen, Sam R.; Catherine Fill; Yuhong Wang

    2012-01-01

    Rapid, sensitive detection methods are of utmost importance for the identification of pathogens related to health and safety. Herein we report the development of a nucleic acid sequence-based lateral flow assay which achieves a low limit of detection using chemiluminescence. On-membrane enzymatic signal amplification is used to reduce the limit of detection to the sub-femtomol level. To demonstrate this assay, we detected synthetic nucleic acid sequences representative of Trypanosoma mRNA, th...

  11. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment...... methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number...... of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often...

  12. SIMPLIFIED DIAGNOSIS OF MALARIA INFECTION: GFM/PCR/ELISA A SIMPLIFIED NUCLEIC ACID AMPLIFICATION TECHNIQUE BY PCR/ELISA

    Directory of Open Access Journals (Sweden)

    Ricardo Luiz Dantas MACHADO

    1998-09-01

    Full Text Available We report an adaptation of a technique for the blood sample collection (GFM as well as for the extraction and amplification of Plasmodium DNA for the diagnosis of malaria infection by the PCR/ELISA. The method of blood sample collection requires less expertise and saves both time and money, thus reducing the cost by more than half. The material is also suitable for genetic analysis in either fresh or stored specimens prepared by this method.Relatamos a adaptação de uma técnica para coleta de amostras (MFV e outra para extração, amplificação de DNA de parasitas da malária para diagnóstico por PCR/ELISA. O método de coleta de amostras requer menos habilidade e economisa tempo e dinheiro, assim reduzindo a mais da metade o custo. O material é também adequado para análise genética em especimens frescos ou estocados, preparados por este método.

  13. Comparison of an rRNA‐based and DNA‐based nucleic acid amplification test for the detection of Chlamydia trachomatis in trachoma

    Science.gov (United States)

    Yang, Jon L; Schachter, Julius; Moncada, Jeanne; Habte, Dereje; Zerihun, Mulat; House, Jenafir I; Zhou, Zhaoxia; Hong, Kevin C; Maxey, Kathryn; Gaynor, Bruce D; Lietman, Thomas M

    2007-01-01

    Background/Aim The World Health Organisation (WHO) hopes to achieve global elimination of trachoma, still the leading cause of preventable blindness worldwide, in part through mass antibiotic treatment. DNA‐based nucleic acid amplification tests (NAATs) are currently used to evaluate the success of treatment programmes by measuring the prevalence of C trachomatis infection. Some believe that newer ribosomal RNA (rRNA)‐based tests may be much more sensitive since bacterial rRNA is present in amounts up to 10 000 times that of genomic DNA. Others believe that rRNA‐based tests are instead less sensitive but more specific, due to the presence of dead or subviable organisms that the test may not detect. This study compares an rRNA‐based test to a DNA‐based test for the detection of ocular C trachomatis infection in children living in trachoma‐endemic villages. Methods An rRNA‐based amplification test and DNA‐based polymerase chain reaction (PCR) were performed on swab specimens taken from the right upper tarsal conjunctiva of 56 children aged 0–10 years living in two villages in Amhara, Ethiopia. Results The rRNA‐based test detected ocular C trachomatis infection in 35 (63%) subjects compared with 22 (39%) detected by PCR (McNemar's test, p = 0.0002). The rRNA‐based test gave positive results for all subjects that were positive by PCR, and also detected infection in 13 (23%) additional subjects. Conclusion The rRNA‐based test appears to have significantly greater sensitivity than PCR for the detection of ocular chlamydial infection in children in trachoma‐endemic villages. Using the rRNA‐based test, we may be able to detect infection that was previously missed with PCR. Past studies using DNA‐based tests to assess prevalence of infectious trachoma following antibiotic treatment may have underestimated the true prevalence of infection. PMID:17050583

  14. Isothermal DNA amplification in vitro: the helicase-dependent amplification system.

    Science.gov (United States)

    Jeong, Yong-Joo; Park, Kkothanahreum; Kim, Dong-Eun

    2009-10-01

    Since the development of polymerase chain reaction, amplification of nucleic acids has emerged as an elemental tool for molecular biology, genomics, and biotechnology. Amplification methods often use temperature cycling to exponentially amplify nucleic acids; however, isothermal amplification methods have also been developed, which do not require heating the double-stranded nucleic acid to dissociate the synthesized products from templates. Among the several methods used for isothermal DNA amplification, the helicase-dependent amplification (HDA) is discussed in this review with an emphasis on the reconstituted DNA replication system. Since DNA helicase can unwind the double-stranded DNA without the need for heating, the HDA system provides a very useful tool to amplify DNA in vitro under isothermal conditions with a simplified reaction scheme. This review describes components and detailed aspects of current HDA systems using Escherichia coli UvrD helicase and T7 bacteriophage gp4 helicase with consideration of the processivity and efficiency of DNA amplification. PMID:19629390

  15. Enzymatic electrochemical detection of epidemic-causing Vibrio cholerae with a disposable oligonucleotide-modified screen-printed bisensor coupled to a dry-reagent-based nucleic acid amplification assay.

    Science.gov (United States)

    Yu, Choo Yee; Ang, Geik Yong; Chan, Kok Gan; Banga Singh, Kirnpal Kaur; Chan, Yean Yean

    2015-08-15

    In this study, we developed a nucleic acid-sensing platform in which a simple, dry-reagent-based nucleic acid amplification assay is combined with a portable multiplex electrochemical genosensor. Preparation of an amplification reaction mix targeting multiple DNA regions of interest is greatly simplified because the lyophilized reagents need only be reconstituted with ultrapure water before the DNA sample is added. The presence of single or multiple target DNAs causes the corresponding single-stranded DNA (ssDNA) amplicons to be generated and tagged with a fluorescein label. The fluorescein-labeled ssDNA amplicons are then analyzed using capture probe-modified screen-printed gold electrode bisensors. Enzymatic amplification of the hybridization event is achieved through the catalytic production of electroactive α-naphthol by anti-fluorescein-conjugated alkaline phosphatase. The applicability of this platform as a diagnostic tool is demonstrated with the detection of toxigenic Vibrio cholerae serogroups O1 and O139, which are associated with cholera epidemics and pandemics. The platform showed excellent diagnostic sensitivity and specificity (100%) when challenged with 168 spiked stool samples. The limit of detection was low (10 colony-forming units/ml) for both toxigenic V. cholerae serogroups. A heat stability assay revealed that the dry-reagent amplification reaction mix was stable at temperatures of 4-56 °C, with an estimated shelf life of seven months. The findings of this study highlight the potential of combining a dry-reagent-based nucleic acid amplification assay with an electrochemical genosensor in a more convenient, sensitive, and sequence-specific detection strategy for multiple target nucleic acids.

  16. Hybrid Chirped Pulse Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Jovanovic, I; Barty, C P J

    2002-05-07

    We present a novel chirped pulse amplification method which combines optical parametric amplification and laser amplification. We have demonstrated this hybrid CPA concept with a combination of beta-barium borate and Ti:sapphire. High-efficiency, multi-terawatt compatible amplification is achieved without gain narrowing and without electro-optic modulators using a simple commercial pump laser.

  17. Selective Adsorption and Chiral Amplification of Amino Acids in Vermiculite Clay -Implications for the origin of biochirality

    CERN Document Server

    Fraser, Donald G; Jakschitz, Thomas; Rode, Bernd M

    2010-01-01

    Smectite clays are hydrated layer silicates that, like micas, occur naturally in abundance. Importantly, they have readily modifiable interlayer spaces that provide excellent sites for nanochemistry. Vermiculite is one such smectite clay and in the presence of small chain-length alkyl-NH3Cl ions, forms sensitive, 1-D ordered model clay systems with expandable nano-pore inter-layer regions. These inter-layers readily adsorb organic molecules. N-propyl NH3Cl vermiculite clay gels were used to determine the adsorption of alanine, lysine and histidine by chiral HPLC. The results show that during reaction with fresh vermiculite interlayers, significant chiral enrichment of either L- and D-enantiomers occurs depending on the amino acid. Chiral enrichment of the supernatant solutions is up to about 1% per pass. In contrast, addition to clay interlayers already reacted with amino acid solutions resulted in little or no change in D/L ratio during the time of the experiment. Adsorption of small amounts of amphiphilic o...

  18. Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

    Directory of Open Access Journals (Sweden)

    Anja Gulliksen

    2012-01-01

    Full Text Available The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n=28 from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection.

  19. Evaluation of three enzyme immunoassays and a nucleic acid amplification test for the diagnosis of Clostridium difficile-associated diarrhea at a university hospital in Brazil

    Directory of Open Access Journals (Sweden)

    Rodrigo Otávio Silveira Silva

    2014-07-01

    Full Text Available Introduction Despite the known importance of Clostridium difficile as a nosocomial pathogen, few studies regarding Clostridium difficile infection (CDI in Brazil have been conducted. To date, the diagnostic tests that are available on the Brazilian market for the diagnosis of CDI have not been evaluated. The aim of this study was to compare the performances of four commercial methods for the diagnosis of CDI in patients from a university hospital in Brazil. Methods Three enzyme immunoassays (EIAs and one nucleic acid amplification test (NAAT were evaluated against a cytotoxicity assay (CTA and toxigenic culture (TC. Stool samples from 92 patients with suspected CDI were used in this study. Results Twenty-five (27.2% of 92 samples were positive according to the CTA, and 23 (25% were positive according to the TC. All EIAs and the NAAT test demonstrated sensitivities between 59 and 68% and specificities greater than 91%. Conclusions All four methods exhibited low sensitivities for the diagnosis of CDI, which could lead to a large number of false-negative results, an increased risk of cross-infection to other patients, and overtreatment with empirical antibiotics.

  20. Selective adsorption and chiral amplification of amino acids in vermiculite clay-implications for the origin of biochirality.

    Science.gov (United States)

    Fraser, Donald G; Fitz, Daniel; Jakschitz, T; Rode, Bernd M

    2011-01-21

    Smectite clays are hydrated layer silicates that, like micas, occur naturally in abundance. Importantly, they have readily modifiable interlayer spaces that provide excellent sites for nanochemistry. Vermiculite is one such smectite clay and in the presence of small chain-length alkyl-NH(3)Cl ions forms sensitive, 1-D ordered model clay systems with expandable nano-pore inter-layer regions. These inter-layers readily adsorb organic molecules. n-Propyl NH(3)Cl vermiculite clay gels were used to determine the adsorption of alanine, lysine and histidine by chiral HPLC. The results show that during reaction with fresh vermiculite interlayers, significant chiral enrichment of either L- and D-enantiomers occurs depending on the amino acid. Chiral enrichment of the supernatant solutions is up to about 1% per pass. In contrast, addition to clay interlayers already reacted with amino acid solutions resulted in little or no change in D/L ratio during the time of the experiment. Adsorption of small amounts of amphiphilic organic molecules in clay inter-layers is known to produce Layer-by-Layer or Langmuir-Blodgett films. Moreover atomistic simulations show that self-organization of organic species in clay interlayers is important. These non-centrosymmetric, chirally active nanofilms may cause clays to act subsequently as chiral amplifiers, concentrating organic material from dilute solution and having different adsorption energetics for D- and L-enantiomers. The additional role of clays in RNA oligomerization already postulated by Ferris and others, together with the need for the organization of amphiphilic molecules and lipids noted by Szostak and others, suggests that such chiral separation by clays in lagoonal environments at normal biological temperatures might also have played a significant role in the origin of biochirality.

  1. Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15.

    Science.gov (United States)

    Huzly, Daniela; Korn, Klaus; Bierbaum, Sibylle; Eberle, Björn; Falcone, Valeria; Knöll, Antje; Steininger, Philipp; Panning, Marcus

    2016-09-01

    The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary. PMID:27316440

  2. Concordance study between one-step nucleic acid amplification and morphologic techniques to detect lymph node metastasis in papillary carcinoma of the thyroid.

    Science.gov (United States)

    del Carmen, Sofía; Gatius, Sonia; Franch-Arcas, Guzmán; Baena, José Antonio; Gonzalez, Oscar; Zafon, Carlos; Cuevas, Dolors; Valls, Joan; Pérez, Angustias; Martinez, Mercedes; Ros, Susana; Macías, Carmen García; Iglesias, Carmela; Matías-Guiu, Xavier; de Álava, Enrique

    2016-02-01

    Tumor resection in papillary thyroid carcinoma (PTC) is often accompanied by lymph node (LN) removal of the central and lateral cervical compartments. One-step nucleic acid amplification (OSNA) is a polymerase chain reaction-based technique that quantifies cytokeratin 19 (CK19) messenger RNA copies. Our aim is to assess the value of OSNA in detection of LN metastases in PTC, in comparison with imprints and microscopic analysis of formalin-fixed, paraffin-embedded (FFPE) tissue. A total of 387 LNs from 37 patients were studied. From each half LN, 2 imprints were taken and analyzed with hematoxylin and eosin (H&E) and CK19 immunostaining. One half of the LN was submitted to OSNA and one half to FFPE processing and H&E and CK19 staining. For concordance analysis, every single LN was considered as a case. A group of 11 cases with discordant results between OSNA and H&E/CK19 FFPE sections were subjected to additional FFPE serial sectioning and H&E and CK19 staining. We found a high degree of concordance between the assays used, with sensitivities ranging from 0.81 to 0.95, and specificities ranging from 0.87 and 0.98. OSNA allowed upstaging of patients from pN0 to pN1, in comparison with standard pathologic analysis. Identification of a metastatic LN with more than 15000 CK19 messenger RNA copies predicted the presence of a second LN with macrometastasis (<5000 copies). In summary, the study shows that OSNA application in sentinel or suspicious LN may be helpful in assessing nodal status in PTC patients.

  3. Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses.

    Directory of Open Access Journals (Sweden)

    Yi Liu

    Full Text Available In this study, a viral microarray based assay was developed to detect the human herpesviruses and enteroviruses associated with central nervous system infections, including herpes simplex virus type 1, type 2 (HSV1 and HSV2, Epstein-Barr virus (EBV, cytomegalovirus (CMV, enterovirus 71 (EV71, coxsackievirus A 16 (CA16 and B 5(CB5. The DNA polymerase gene of human herpesviruses and 5'-untranslated region of enteroviruses were selected as the targets to design primers and probes. Human herpesviruses DNA and enteroviruses RNA were extracted simultaneously by using a guanidinium thiocyanate acid buffer, and were subsequently amplified through a biotinylated asymmetry multiplex RT-PCR with the specific primer of enteroviruses. In total, 90 blood samples and 49 cerebrospinal fluids samples with suspected systemic or neurological virus infections were investigated. Out of 139 samples, 66 were identified as positive. The specificities of this multiplex RT-PCR microarray assay were over 96% but the sensitivities were various from 100% for HSV1, HSV2, EV71 and CB5, 95.83% for CMV, 80% for EBV to 71.43% for CA16 in comparison with reference standards of TaqMan qPCR/qRT-PCR. The high Kappa values (>0.90 from HSV1, HSV2, CMV, EV71 and CB5 were obtained, indicating almost perfect agreement in term of the 5 viruses detection. But lower Kappa values for EBV (0.63 and CA16 (0.74 displayed a moderate to substantial agreement. This study provides an innovation of simultaneous extraction, amplification, hybridization and detection of DNA viruses and RNA viruses with simplicity and specificity, and demonstrates a potential clinical utility for a variety of viruses' detection.

  4. Diagnosis of tuberculosis by using a nucleic acid amplification test in an urban population with high HIV prevalence in the United States.

    Directory of Open Access Journals (Sweden)

    Miwako Kobayashi

    Full Text Available BACKGROUND: Use of nucleic acid amplification tests (NAAT for the diagnosis of Mycobacterium tuberculosis (TB has been recommended on respiratory specimens submitted for acid-fast bacilli (AFB testing. It also helps distinguish between TB and non-tuberculous mycobacteria (NTM species in a setting where NTM rates are relatively high. The purposes of this study are to describe the trend and characteristics of all AFB smear-positive respiratory samples that underwent amplified Mycobacterium tuberculosis direct (MTD testing, a type of NAAT, and to evaluate the clinical utility and necessity of the test for diagnosis of TB in a population with high-HIV prevalence. METHODS: Prospective diagnostic testing and retrospective data analyses were conducted on all AFB smear-positive respiratory samples that underwent MTD testing from 2001 to 2011 at Grady Memorial Hospital (GMH, Atlanta, USA. The test performance was compared to culture. RESULTS: A total of 2,240 AFB smear-positive specimens from 1,412 patients were tested and analyzed in the study. The proportion of specimens that were culture-positive for TB was 28.5%. Sensitivity, specificity, positive predictive value, and negative predictive value of the MTD were 99.0%, 98.0%, 95.3% and 99.6%, respectively. A downward trend was observed in the yearly numbers as well as the proportions of MTD-positive specimens during the study period (p<0.01. There were 2,027 (90.5% specimens from patients with known HIV status, of which 70.6% was HIV positive and the majority of them (81.8% had CD4 counts of less than 200 cells/µL. HIV-positives were more likely to have NTM compared to HIV negatives (67.7% vs. 35.4%, p<0.01. CONCLUSION: Despite the decrease in the incidence of TB, NAAT continues to be an accurate and important diagnostic test in a population with high HIV prevalence, and it differentiates TB and NTM organisms.

  5. Microfluidic Digital Chip for Absolute Quantification of Nucleic Acid Amplification%一种可绝对定量核酸的数字PCR微流控芯片

    Institute of Scientific and Technical Information of China (English)

    朱强远; 杨文秀; 高一博; 于丙文; 邱琳; 周超; 金伟; 金钦汉; 牟颖

    2013-01-01

    构建了一种新型的可进行核酸单分子扩增和核酸绝对定量的数字聚合酶链式反应(数字PCR)微流控芯片.应用多层软光刻技术,以聚二甲基硅氧烷(PDMS)作为芯片材料,盖玻片作为基底制作了具有3层结构以及微阀控制功能的微流控芯片.芯片的大小与载玻片相当,可同时检测4个样品,每个样品通入芯片后平均分配到640个反应小室,每个小室的体积为6 nL.以从肺癌细胞A549中提取的18sRNA为样品检测了该芯片的可行性.将样品稀释数倍后通入芯片,核酸分子随机分布在640个小室中并扩增.核酸分子在芯片中的分布符合泊松分布原理,当样品中待测核酸分子平均拷贝数低于0.5个/小室时,则每个反应小室包含0个或1个分子.经过PCR扩增后,有模板分子的小室检测结果为阳性反应,而无模板分子的小室为阴性反应,最后通过计数阳性反应室的个数,可绝对定量原始待测样品中的目标DNA分子拷贝数.实验结果表明,该数字PCR芯片可实现DNA单分子反应和核酸绝对定量,具有成本低、灵敏度高、节省时间和试剂以及操作简单等优点,为数字PCR方法在普通实验室的应用提供了一种新途径,可用于癌症及感染性疾病的早期诊断、单细胞分析、产前诊断以及各种细菌病毒的核酸检验等研究.%A novel microfluidic digital polymerase chain reaction (PCR) chip for single molecule amplification and absolute quantification of nucleic acid was fabricated by multilayer soft lithography technique and composed of three layers with valves controlling liquid, the material of silicone elastomer polydimethylsiloxane (PDMS) and glass coverslip. The microfluidic chip is equal to a piece of glass coverslip in size, which contains 4 separate panels, and each panel contains 640 independent 6 nL-chambers; the chip is capable of detecting 4 samples simultaneously. Digital PCR on the microfluidic chip was tested

  6. Towards Engineered Processes for Sequencing-Based Analysis of Single Circulating Tumor Cells.

    Science.gov (United States)

    Adalsteinsson, Viktor A; Love, J Christopher

    2014-05-01

    Sequencing-based analysis of single circulating tumor cells (CTCs) has the potential to revolutionize our understanding of metastatic cancer and improve clinical care. Technologies exist to enrich, identify, recover, and sequence single cells, but to enable systematic routine analysis of single CTCs from a range of cancer patients, there is a need to establish processes that efficiently integrate these specific operations. Such engineered processes should address challenges associated with the yield and viability of enriched CTCs, the robust identification of candidate single CTCs with minimal degradation of DNA, the bias in whole-genome amplification, and the efficient handling of candidate single CTCs or their amplified DNA products. Advances in methods for single-cell analysis and nanoscale technologies suggest opportunities to overcome these challenges, and could create integrated platforms that perform several of the unit operations together. Ultimately, technologies should be selected or adapted for optimal performance and compatibility in an integrated process. PMID:24839591

  7. Terabit Nyquist PDM-32QAM signal transmission with training sequence based time domain channel estimation.

    Science.gov (United States)

    Zhang, Fan; Wang, Dan; Ding, Rui; Chen, Zhangyuan

    2014-09-22

    We propose a time domain structure of channel estimation for coherent optical communication systems, which employs training sequence based equalizer and is transparent to arbitrary quadrature amplitude modulation (QAM) formats. Enabled with this methodology, 1.02 Tb/s polarization division multiplexed 32 QAM Nyquist pulse shaping signal with a net spectral efficiency of 7.46 b/s/Hz is transmitted over standard single-mode fiber link with Erbium-doped fiber amplifier only amplification. After 1190 km transmission, the average bit-error rate is lower than the 20% hard-decision forward error correction threshold of 1.5 × 10(-2). The transmission distance can be extended to 1428 km by employing intra-subchannel nonlinear compensation with the digital back-propagation method.

  8. Cost analysis of a nucleic acid amplification test in the diagnosis of pulmonary tuberculosis at an urban hospital with a high prevalence of TB/HIV.

    Directory of Open Access Journals (Sweden)

    Max W Adelman

    Full Text Available INTRODUCTION: The Centers for Disease Control and Prevention has recommended using a nucleic acid amplification test (NAAT for diagnosing pulmonary tuberculosis (TB but there is a lack of data on NAAT cost-effectiveness. METHODS: We conducted a prospective cohort study that included all patients with an AFB smear-positive respiratory specimen at Grady Memorial Hospital in Atlanta, GA, USA between January 2002 and June 2008. We determined the sensitivity, specificity, and positive and negative predictive value of a commercially available and FDA-approved NAAT (amplified MTD, Gen-Probe compared to the gold standard of culture. A cost analysis was performed and included costs related to laboratory tests, hospital charges, anti-TB medications, and contact investigations. Average cost per patient was calculated under two conditions: (1 using a NAAT on all AFB smear-postive respiratory specimens and (2 not using a NAAT. One-way sensitivity analyses were conducted to determine sensitivity of cost difference to reasonable ranges of model inputs. RESULTS: During a 6 1/2 year study period, there were 1,009 patients with an AFB smear-positive respiratory specimen at our public urban hospital. We found the NAAT to be highly sensitive (99.6% and specific (99.1% on AFB smear-positive specimens compared to culture. Overall, the positive predictive value (PPV of an AFB smear-positive respiratory specimen for culture-confirmed TB was 27%. The PPV of an AFB smear-positive respiratory specimen for culture-confirmed TB was significantly higher for HIV-uninfected persons compared to those who were HIV-seropositive (152/271 [56%] vs. 85/445 [19%]; RR = 2.94, 95% CI 2.36-3.65, p<0.001. The cost savings of using the NAAT was $2,003 per AFB smear-positive case. CONCLUSIONS: Routine use of the NAAT on AFB smear-positive respiratory specimens was highly cost-saving in our setting at a U.S. urban public hospital with a high prevalence of TB and HIV because of the low

  9. Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals.

    Science.gov (United States)

    Grubaugh, Nathan D; Petz, Lawrence N; Melanson, Vanessa R; McMenamy, Scott S; Turell, Michael J; Long, Lewis S; Pisarcik, Sarah E; Kengluecha, Ampornpan; Jaichapor, Boonsong; O'Guinn, Monica L; Lee, John S

    2013-02-01

    Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiated between four mosquito genera and eight whole blood samples. The microarray platform was field evaluated in Thailand and successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differentiated between mosquito genera (Aedes, Armigeres, Culex, and Mansonia), and detected mammalian bloodmeals (human and dog). We showed that the microarray platform and amplification strategies described here can be used to discern specific information on a wide variety of viruses and their vectors.

  10. The Seneca Amplification Construction

    Directory of Open Access Journals (Sweden)

    Wallace Chafe

    2012-01-01

    Full Text Available The polysynthetic morphology of the Northern Iroquoian languages presents a challenge to studies of clause combining. The discussion here focuses on a Seneca construction that may appear within a single clause but may also straddle clause boundaries. It amplifies the information provided by a referent, here called the trigger, that is introduced by the pronominal prefix within a verb or occasionally in some other way. The particle neh signals that further information about that referent will follow. This construction is found at four levels of syntactic complexity. At the first level the trigger and its amplification occur within the same prosodic phrase and the amplification is a noun. At the second level the amplification occurs in a separate prosodic phrase but remains a noun. At the third level the amplification exhibits verb morphology but has been lexicalized with a nominal function. At the fourth level the amplification functions as a full clause and neh serves as a marker of clause combining. Several varieties of amplification are discussed, as are cases in which the speaker judges that no amplification is needed. It is suggested that the typologically similar Caddo language illustrates a situation in which this construction could never arise, simply because Caddo verbs lack the pronominal element that triggers the construction in Seneca.

  11. Speeding disease gene discovery by sequence based candidate prioritization

    Directory of Open Access Journals (Sweden)

    Porteous David J

    2005-03-01

    Full Text Available Abstract Background Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation to knowledge of the disease or phenotype in question. However, here we show that disease genes share patterns of sequence-based features that can provide a good basis for automatic prioritization of candidates by machine learning. Results We examined a variety of sequence-based features and found that for many of them there are significant differences between the sets of genes known to be involved in human hereditary disease and those not known to be involved in disease. We have created an automatic classifier called PROSPECTR based on those features using the alternating decision tree algorithm which ranks genes in the order of likelihood of involvement in disease. On average, PROSPECTR enriches lists for disease genes two-fold 77% of the time, five-fold 37% of the time and twenty-fold 11% of the time. Conclusion PROSPECTR is a simple and effective way to identify genes involved in Mendelian and oligogenic disorders. It performs markedly better than the single existing sequence-based classifier on novel data. PROSPECTR could save investigators looking at large regions of interest time and effort by prioritizing positional candidate genes for mutation detection and case-control association studies.

  12. Early amplification options.

    Science.gov (United States)

    Gabbard, Sandra Abbott; Schryer, Jennifer

    2003-01-01

    Children with permanent hearing loss have been remediated with hearing amplification devices for decades. The influx of young infants identified with hearing loss through successful newborn hearing screening programs has established a need for amplification resources for infants within the first six months of life. For the approximately two of every 1000 infants born who are identified with bilateral hearing loss [Mehl and Thomson, 1998, Pediatrics 101, p. e4], the use of amplification is commonly the first step in treating the sequella of their loss. The use of hearing aids, combined with early intervention, has been shown to significantly improve the speech and language skills of young children with hearing loss [Yoshinaga-Itano, 2000, Seminars in Hearing 21, p. 309]. Speech and language delays have contributed to compromised academic performance of school aged children with hearing loss [Johnson et al., 1997, Educational Audiology Handbook, Singular Publishing, San Diego]. Most hard-of-hearing and deaf children use hearing aids and other assistive listening devices every day throughout their lifetime and the life expectancy of a hearing aid is only five to eight years. The current challenge for pediatric audiologists is selecting and evaluating the available amplification to provide the best options for children and their families. Amplification technology has seen an explosion in growth the past few years and the options continue to expand rapidly. This article examines currently available amplification technology and reviews the selection criteria that may be used for infants and young children. Issues such as style, type, amplification features, signal processing strategies, and verification and validation tools are also discussed. PMID:14648816

  13. Quantum Feedback Amplification

    Science.gov (United States)

    Yamamoto, Naoki

    2016-04-01

    Quantum amplification is essential for various quantum technologies such as communication and weak-signal detection. However, its practical use is still limited due to inevitable device fragility that brings about distortion in the output signal or state. This paper presents a general theory that solves this critical issue. The key idea is simple and easy to implement: just a passive feedback of the amplifier's auxiliary mode, which is usually thrown away. In fact, this scheme makes the controlled amplifier significantly robust, and furthermore it realizes the minimum-noise amplification even under realistic imperfections. Hence, the presented theory enables the quantum amplification to be implemented at a practical level. Also, a nondegenerate parametric amplifier subjected to a special detuning is proposed to show that, additionally, it has a broadband nature.

  14. Isothermal nucleic acid amplification technology applied in detection of Salmonella%恒温扩增核酸法检测沙门菌属效果分析

    Institute of Scientific and Technical Information of China (English)

    肖征; 刘秀贞

    2012-01-01

    目的 观察核酸恒温扩增商品试剂盒对沙门菌属的检测效果.方法 对商品销售的两种恒温扩增检测试剂与普通PCR试剂盒进行检测灵敏度、特异性及操作简便性的比较.结果 常规PCR法A、恒温扩增试剂B及C检测沙门菌属的灵敏度分别为约4×103 CFU/ml、4×103 CFU/ml和约4×104 CFU/ml;对21株临床分离的沙门菌属的检测阳性率分别为76.2%、28.6%和100.0%;用11株非沙门肠道菌株直接检测的特异性均为100.0%;检测过程除常规的核酸提取外,核酸扩增常规法、试剂B、C的核酸检测和结果观察的时间约为2、2、2.5h,以常规法及试剂C的结果观察方式比较方便.结论 试剂C操作时间短、使用方便、检测敏感度及特异性比较好,是一种适用于对沙门菌属快速检测的恒温扩增试剂;对待商品试剂应做好试用工作,以选择好真正适用的产品.%OBJECTIVE To evaluate the efficacy of commercially available isothermal nucleic amplification technology reagents in detecting Salmonella spp. METHODS The routine PCR reagent (A) was compared with two commercially available isothermal nucleic amplification reagents (B and C) for their sensitivity, specificity and operation flexibility in detecting Salmonella spp. RESULTS Reagent A, B and C showed sensitivity of detecting 4 X103 CFU/ml, 4 X 103 CFU/ml and 4 X 104 CFU/ml of Salmonella spp, respectively. The positive rates of detection of clinically isolated Salmonella spp were 76. 2%, 28. 6% and 100. 0%, respectively; all reagents showed no reactions with 11 non-Salmonella enteric bacteria strains with the specificity of 100. 0%; the methods A,B and C took 2, 2 and 2. 5 hours respectively to complete the amplification and results reading after the common procedure of DNA extraction. It was more convenient to observe the results with reagents A and C than B. CONCLUSION Reagent C can be used in field test for Salmonella .spp detection. It is suggested that

  15. Amplification-Free Detection of Circulating microRNA Biomarkers from Body Fluids Based on Fluorogenic Oligonucleotide-Templated Reaction between Engineered Peptide Nucleic Acid Probes: Application to Prostate Cancer Diagnosis.

    Science.gov (United States)

    Metcalf, Gavin A D; Shibakawa, Akifumi; Patel, Hinesh; Sita-Lumsden, Ailsa; Zivi, Andrea; Rama, Nona; Bevan, Charlotte L; Ladame, Sylvain

    2016-08-16

    Highly abundant in cells, microRNAs (or miRs) play a key role as regulators of gene expression. A proportion of them are also detectable in biofluids making them ideal noninvasive biomarkers for pathologies in which miR levels are aberrantly expressed, such as cancer. Peptide nucleic acids (PNAs) are engineered uncharged oligonucleotide analogues capable of hybridizing to complementary nucleic acids with high affinity and high specificity. Herein, novel PNA-based fluorogenic biosensors have been designed and synthesized that target miR biomarkers for prostate cancer (PCa). The sensing strategy is based on oligonucleotide-templated reactions where the only miR of interest serves as a matrix to catalyze an otherwise highly unfavorable fluorogenic reaction. Validated in vitro using synthetic RNAs, these newly developed biosensors were then shown to detect endogenous concentrations of miR in human blood samples without the need for any amplification step and with minimal sample processing. This low-cost, quantitative, and versatile sensing technology has been technically validated using gold-standard RT-qPCR. Compared to RT-qPCR however, this enzyme-free, isothermal blood test is amenable to incorporation into low-cost portable devices and could therefore be suitable for widespread public screening. PMID:27498854

  16. Flux amplification in SSPX

    Science.gov (United States)

    Lodestro, Lynda; Hooper, E. B.; Jayakumar, R. J.; Pearlstein, L. D.; Wood, R. D.; McLean, H. S.

    2007-11-01

    Flux amplification---the ratio of poloidal flux enclosed between the magnetic and geometric axes to that between the separatrix and the geometric axis---is a key measure of efficiency for edge-current-driven spheromaks. With the new, modular capacitor bank, permitting flexible programming of the gun current, studies of flux amplification under various drive scenarios can be performed. Analysis of recent results of pulsed operation with the new bank finds an efficiency ˜ 0.2, in selected shots, of the conversion of gun energy to confined magnetic energy during the pulses, and suggests a route toward sustained efficiency at 0.2. Results of experiments, a model calculation of field build-up, and NIMROD simulations exploring this newly suggested scenario will be presented.

  17. Study on screening blood donors by nucleic acid amplification technique combined with Enzyme- linked immunosorbent assay%核酸扩增与酶联免疫法联合在血液筛查中的初步应用

    Institute of Scientific and Technical Information of China (English)

    杜勇; 杨亮; 蒋炜; 王佳维; 张哲

    2012-01-01

    Objective;The purpose of this study was to improve security level of clinical blood transfusion and e-valuate the necessity and practicability of the testing methodology based on nucleic acid amplification technique (NAT) in addition to the regular immunoassay test (EIA). Methods; The samples tested as negative by ELISA were screened by NAT with two work flow ( single detection or combined detection). The NAT - positive samples were further tested by Roche COBAS CAP_CTM system and eletro - cheniluminescence(ECL) system to evaluate the virus load and serological properties. Results; 28 NAT-positive samples were detected in the 20,925 ELISA negative donor samples. All samples were HBV DNA positive and 11 among the 28 samples were serology positive. The remaining risk of HBV infection was 0.13% under the routine EIA test. Conclusion; The risk of HBV infection still remain under the current blood donor screening method using repeated ELISA testing. The introduction of NAT test can help to reduce the risk of transfusion - transmitted disease which has a great value to increase the safety of blood.%目的:在酶联免疫法( enzyme immunoassay,EIA)检测的基础上,探讨HBV核酸扩增检测(nucleic acid amplification testing NAT)技术应用于血液筛查的意义.方法:分别使用两种模式(单检或混检)NAT与EIA两遍检测方式同时进行血液筛查,对NAT阳性标本作进一步做鉴别试验和病毒血清标志物.结果:20925份EIA(-)标本共发现28份核酸三项(HBV DNA、HCV RNA、HIV RNA)呈反应性,均为HBV- DNA,即EIA两遍检测合格后的HBV- DNA阳性率0.13%,检测其中11份血清,乙肝标志物均呈阳性.结论:EIA阴性献血者中仍有极少数的HBV感染者,核酸扩增检测和酶联免疫检测互补能够检测出EIA漏检的HBV携带者,对提高HBsAg阴性血液标本中HBV感染检出率具有重要价值.

  18. Evaluation of Three Automated Nucleic Acid Amplification Systems for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in First-Void Urine Specimens▿

    OpenAIRE

    Levett, P N; Brandt, K.; Olenius, K.; Brown, C.; Montgomery, K.; Horsman, G. B.

    2008-01-01

    A total of 500 first-void urine specimens were tested for the presence of Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acids using ProbeTec ET reagents on a Viper platform (BD Diagnostics, Mississauga, Ontario, Canada), Aptima Combo 2 reagents on a Tigris platform (Gen-Probe, Inc., San Diego, CA), and Abbott RealTime CT/NG reagents on an m2000 platform (Abbott Molecular Diagnostics, Des Plaines, IL). The performance of the three assays for detection of N. gonorrhoeae was comparable...

  19. Amplification of an MFS Transporter Encoding Gene penT Significantly Stimulates Penicillin Production and Enhances the Sensitivity of Penicillium chrysogenum to Phenylacetic Acid

    Institute of Scientific and Technical Information of China (English)

    Jing Yang; Xinxin Xu; Gang Liu

    2012-01-01

    Penicillin is historically important as the first discovered drug against bacterial infections in human.Although the penicillin biosynthetic pathway and regulatory mechanism have been well studied in Penicillium chrysogenum,the compartnentation and molecular transport of penicillin or its precursors are still poorly understood.In search of the genomic database,more than 830 open reading frames (ORFs) were found to encode transmembrane proteins of P.chrysogenum.In order to investigate their roles on penicillin production,one of them (penT) was selected and cloned.The deduced protein of penT belongs to the major facilitator superfamily (MFS) and contains 12transmembrane spanning domains (TMS).During fermentation,the transcription of penT was greatly induced by penicillin precursors phenylacetic acid (PAA) and phenoxyacetic acid (POA).Knock-down of penT resulted in significant decrease of penicillin production,while over-expression of penT under the promoter of trpC enhanced the penicillin production.Introduction of an additional penT in the wild-type strain of P.chrysogenum doubled the penicillin production and enhanced the sensitivity of P.chrysogenum to the penicillin precursors PAA or POA.These results indicate that penT stimulates penicillin production probably through enhancing the translocation of penicillin precursors across fungal cellular membrane.

  20. Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases.

    Science.gov (United States)

    Sahoo, Pravas Ranjan; Sethy, Kamadev; Mohapatra, Swagat; Panda, Debasis

    2016-05-01

    India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease. PMID:27284221

  1. Development of Sequence-Based Microsatellite Marker for Phalaenopsis Orchid

    Directory of Open Access Journals (Sweden)

    FATIMAH

    2011-06-01

    Full Text Available Phalaenopsis is one of the most interesting genera of orchids due to the members are often used as parents to produce hybrids. The establishment and development of highly reliable and discriminatory methods for identifying species and cultivars has become increasingly more important to plant breeders and members of the nursery industry. The aim of this research was to develop sequence-based microsatellite (eSSR markers for the Phalaenopsis orchid designed from the sequence of GenBank NCBI. Seventeen primers were designed and thirteen primers pairs could amplify the DNA giving the expected PCR product with polymorphism. A total of 51 alleles, with an average of 3 alleles per locus and polymorphism information content (PIC values at 0.674, were detected at the 16 SSR loci. Therefore, these markers could be used for identification of the Phalaenopsis orchid used in this study. Genetic similarity and principle coordinate analysis identified five major groups of Phalaenopsis sp. the first group consisted of P. amabilis, P. fuscata, P. javanica, and P. zebrine. The second group consisted of P. amabilis, P. amboinensis, P. bellina, P. floresens, and P. mannii. The third group consisted of P. bellina, P. cornucervi, P. cornucervi, P. violaceae sumatra, P. modesta. The forth group consisted of P. cornucervi and P. lueddemanniana, and the fifth group was P. amboinensis.

  2. Coherent white light amplification

    Science.gov (United States)

    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.

  3. Rapid Diagnosis of Human Herpesvirus 6 Infection by a Novel DNA Amplification Method, Loop-Mediated Isothermal Amplification

    OpenAIRE

    Ihira, Masaru; Yoshikawa, Tetsushi; Enomoto, Yoshihiko; Akimoto, Shiho; Ohashi, Masahiro; Suga, Sadao; Nishimura, Naoko; Ozaki, Takao; Nishiyama, Yukihiro; Notomi, Tsugunori; Ohta, Yoshinori; Asano, Yoshizo

    2004-01-01

    A novel nucleic acid amplification method, termed loop-mediated isothermal amplification (LAMP), which amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions, may be a valuable tool for the rapid detection of infectious agents. LAMP was developed for human herpesvirus 6 (HHV-6), and its reliability was evaluated in this study. Although LAMP products were detected in HHV-6 B and HHV-6 A DNA, they were not detected in HHV-7 and human cytomegalovirus DNA. The s...

  4. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  5. Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics.

    Science.gov (United States)

    Willmann, Matthias; El-Hadidi, Mohamed; Huson, Daniel H; Schütz, Monika; Weidenmaier, Christopher; Autenrieth, Ingo B; Peter, Silke

    2015-12-01

    The human gut forms a dynamic reservoir of antibiotic resistance genes (ARGs). Treatment with antimicrobial agents has a significant impact on the intestinal resistome and leads to enhanced horizontal transfer and selection of resistance. We have monitored the development of intestinal ARGs over a 6-day course of ciprofloxacin (Cp) treatment in two healthy individuals by using sequenced-based metagenomics and different ARG quantification methods. Fixed- and random-effect models were applied to determine the change in ARG abundance per defined daily dose of Cp as an expression of the respective selection pressure. Among various shifts in the composition of the intestinal resistome, we found in one individual a strong positive selection for class D beta-lactamases which were partly located on a mobile genetic element. Furthermore, a trend to a negative selection has been observed with class A beta-lactamases (-2.66 hits per million sample reads/defined daily dose; P = 0.06). By 4 weeks after the end of treatment, the composition of ARGs returned toward their initial state but to a different degree in both subjects. We present here a novel analysis algorithm for the determination of antibiotic selection pressure which can be applied in clinical settings to compare therapeutic regimens regarding their effect on the intestinal resistome. This information is of critical importance for clinicians to choose antimicrobial agents with a low selective force on their patients' intestinal ARGs, likely resulting in a diminished spread of resistance and a reduced burden of hospital-acquired infections with multidrug-resistant pathogens. PMID:26369961

  6. Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics.

    Science.gov (United States)

    Willmann, Matthias; El-Hadidi, Mohamed; Huson, Daniel H; Schütz, Monika; Weidenmaier, Christopher; Autenrieth, Ingo B; Peter, Silke

    2015-12-01

    The human gut forms a dynamic reservoir of antibiotic resistance genes (ARGs). Treatment with antimicrobial agents has a significant impact on the intestinal resistome and leads to enhanced horizontal transfer and selection of resistance. We have monitored the development of intestinal ARGs over a 6-day course of ciprofloxacin (Cp) treatment in two healthy individuals by using sequenced-based metagenomics and different ARG quantification methods. Fixed- and random-effect models were applied to determine the change in ARG abundance per defined daily dose of Cp as an expression of the respective selection pressure. Among various shifts in the composition of the intestinal resistome, we found in one individual a strong positive selection for class D beta-lactamases which were partly located on a mobile genetic element. Furthermore, a trend to a negative selection has been observed with class A beta-lactamases (-2.66 hits per million sample reads/defined daily dose; P = 0.06). By 4 weeks after the end of treatment, the composition of ARGs returned toward their initial state but to a different degree in both subjects. We present here a novel analysis algorithm for the determination of antibiotic selection pressure which can be applied in clinical settings to compare therapeutic regimens regarding their effect on the intestinal resistome. This information is of critical importance for clinicians to choose antimicrobial agents with a low selective force on their patients' intestinal ARGs, likely resulting in a diminished spread of resistance and a reduced burden of hospital-acquired infections with multidrug-resistant pathogens.

  7. Efficient Audio Power Amplification - Challenges

    DEFF Research Database (Denmark)

    Andersen, Michael Andreas E.

    2005-01-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where extens...

  8. Efficient audio power amplification - challenges

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Michael A.E.

    2005-07-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where extensive research and development are needed is covered. (au)

  9. Gene promoter hypermethylation is found in sentinel lymph nodes of breast cancer patients, in samples identified as positive by one-step nucleic acid amplification of cytokeratin 19 mRNA.

    Science.gov (United States)

    Martín-Sánchez, E; Pernaut-Leza, E; Mendaza, S; Cordoba, A; Vicente-Garcia, F; Monreal-Santesteban, I; Vizcaino, J Pérez; De Cerio, M J Díaz; Perez-Janices, N; Blanco-Luquin, I; Escors, D; Ulazia-Garmendia, A; Guerrero-Setas, D

    2016-07-01

    We analysed the promoter methylation status of five genes, involved in adhesion (EPB41L3, TSLC-1), apoptosis (RASSF1, RASSF2) or angiogenesis (TSP-1), in intraoperative sentinel lymph node (SLN) biopsy samples from patients with breast cancer, that had been processed by the one-step nucleic acid amplification (OSNA) technique. SLN resection is performed to estimate the risk of tumour cells in the clinically negative axilla, to avoid unnecessary axillary lymph node dissection. OSNA is currently one of the eligible molecular methods for detecting tumour cells in SLNs. It is based on the quantitative evaluation of cytokeratin 19 mRNA which allows distinguishing between macrometastasis, micrometastasis and isolated tumour cells, on the basis of the quantity of tumour cells present. There have been no prior studies on the question whether or not samples processed by OSNA can be used for further molecular studies, including epigenetic abnormalities which are some of the most important molecular alterations in breast cancer. Genomic DNA was extracted from samples obtained from 50 patients diagnosed with primary breast cancer. The content of tumour cells in SLNs was evaluated by OSNA, and the promoter methylation status of the selected genes was analysed by methylation-specific PCR. All were found to be hypermethylated to a variable degree, and RASSF1 hypermethylation was significantly associated with macrometastasis, micrometastasis and isolated tumour cells (p = 0.002). We show that samples used for OSNA are suitable for molecular studies, including gene promoter methylation. These samples provide a new source of material for the identification of additional biomarkers. PMID:27097811

  10. Next generation Chirped Pulse Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Nees, J.; Biswal, S.; Mourou, G. [Univ. Michigan, Center for Ultrafast Optical Science, Ann Arbor, MI (United States); Nishimura, Akihiko; Takuma, Hiroshi

    1998-03-01

    The limiting factors of Chirped Pulse Amplification (CPA) are discussed and experimental results of CPA in Yb:glass regenerative amplifier are given. Scaling of Yb:glass to the petawatt level is briefly discussed. (author)

  11. Development of Chemiluminescent Lateral Flow Assay for the Detection of Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Sam R. Nugen

    2012-01-01

    Full Text Available Rapid, sensitive detection methods are of utmost importance for the identification of pathogens related to health and safety. Herein we report the development of a nucleic acid sequence-based lateral flow assay which achieves a low limit of detection using chemiluminescence. On-membrane enzymatic signal amplification is used to reduce the limit of detection to the sub-femtomol level. To demonstrate this assay, we detected synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, with relevance in human and animal health in sub-Saharan Africa. The intensity of the chemiluminescent signal was evaluated by using a charge-coupled device as well as a microtiter plate reader. We demonstrated that our lateral flow chemiluminescent assay has a very low limit of detection and is easy to use. The limit of detection was determined to be 0.5 fmols of nucleic acid target.

  12. Combined use of real-time PCR and nested sequence-based typing in survey of human Legionella infection.

    Science.gov (United States)

    Qin, T; Zhou, H; Ren, H; Shi, W; Jin, H; Jiang, X; Xu, Y; Zhou, M; Li, J; Wang, J; Shao, Z; Xu, X

    2016-07-01

    Legionnaires' disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey of Legionella infection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospitals in Shanghai, China. A total of 265 bronchoalveolar lavage fluid (BALF) specimens were collected from hospital A between January 2012 and December 2013, and 359 sputum specimens were collected from hospital B throughout 2012. A total of 71 specimens were positive for Legionella according to real-time PCR focusing on the 5S rRNA gene. Seventy of these specimens were identified as Legionella pneumophila as a result of real-time PCR amplification of the dotA gene. Results of nested SBT revealed high genetic polymorphism in these L. pneumophila and ST1 was the predominant sequence type. These data revealed that the burden of LD in China is much greater than that recognized previously, and real-time PCR may be a suitable monitoring technology for LD in large sample surveys in regions lacking the economic and technical resources to perform other methods, such as urinary antigen tests and culture methods. PMID:26790498

  13. Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution

    Indian Academy of Sciences (India)

    S Balaji; N Srinivasan

    2007-01-01

    Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low.

  14. Complementarity of ELISA and nucleic acid amplification test in blood screening%血筛用酶联免疫吸附试验与核酸检测互补性探讨和研究

    Institute of Scientific and Technical Information of China (English)

    曾劲峰; 叶贤林; 马兰; 张红; 庄乃保; 李活

    2008-01-01

    目的 为了提高临床输血的安全性,探讨核酸检测(NAT)与酶联免疫吸附试验(ELISA)技术在血液筛查工作中的互补特性.方法 对2007年6月至2008年3月采集的无偿献血者标本共计45 022例用ELISA血清学检测方法对血液传染性指标HBsAg、抗-HCV、抗-HIV、梅毒螺旋体、丙氨酸氨基转移酶(ALT)进行检测,各项指标均正常的标本用NAT技术检测,以研究2种检测方法的互补性.结果 45 022例标本中血清学检测及ALT不合格人数共计803例,不合格率为1.98%.对各项检测指标合格的36 806例标本进行核酸检测,结果HBV-DNA呈阳性3例.HBV-RNA、HIV-RNA均未检出.结论 NAT与ELISA的血液筛查检测互补作用主要体现在3个方面:1)病理生理过程互补,检测窗口期的长短主要由检测对象的生理属性来决定,而非检测方法缺陷.2)检测方法学互补,由于检测方法学的不同使得NAT技术的检测灵敏度明显高于ELISA血清学检测方法.3)影响各自实验的错误发生各不相同.%Objective To investigate the complementarity of ELISA and nucleic acid amplification test(NAT)in blood screening,and to improve the security of clinieal blood transfusion.Methods A total of 45 022 blood samples from the blood donors without payment from June 2007to March 2008 were enrolled in the study.ELISA was applied to determining HBsAg,anti-HCV,anti-HIV,anti-treponema pallidum(anti-TP)and ALT,and then the normal samples for the above parameters(serologically negative for HBsAg.anti-HCV, anti-HIV,anti-TP and ALT)were detected with NAT.The complementarity of ELISA and NAT was analyzed.Results Totally 803 cases(1.98%)were unqualified(serologically positive)out of the 45 022 blood samples.The qualified 36 806samples were further detected with NAT.The results showed 3 cases were HBV-DNA positive,but none was positive for HBV-RNA and HIV-RNA.Conclusion The complementary action of ELISA and NAT is due to different window phase for detected

  15. A DNA nanomachine based on rolling circle amplification-bridged two-stage exonuclease III-assisted recycling strategy for label-free multi-amplified biosensing of nucleic acid.

    Science.gov (United States)

    Xue, Qingwang; Lv, Yanqin; Cui, Hui; Gu, Xiaohong; Zhang, Shuqiu; Liu, Jifeng

    2015-01-26

    An autonomous DNA nanomachine based on rolling circle amplification (RCA)-bridged two-stage exonuclease III (Exo III)-induced recycling amplification (Exo III-RCA-Exo III) was developed for label-free and highly sensitive homogeneous multi-amplified detection of DNA combined with sensitive fluorescence detection technique. According to the configuration, the analysis of DNA is accomplished by recognizing the target to a unlabeled molecular beacon (UMB) that integrates target-binding and signal transducer within one multifunctional design, followed by the target-binding of UMB in duplex DNA removed stepwise by Exo III accompanied by the releasing of target DNA for the successive hybridization and cleavage process and autonomous generation of the primer that initiate RCA process with a rational designed padlock DNA. The RCA products containing thousands of repeated catalytic sequences catalytically hybridize with a hairpin reporter probe that includes a "caged" inactive G-quadruplex sequence (HGP) and were then detected by Exo III-assisted recycling amplification, liberating the active G-quadruplex and generating remarkable ZnPPIX/G-quadruplex fluorescence signals with the help of zinc(II)-protoporphyrin IX (ZnPPIX). The proposed strategy showed a wide dynamic range over 7 orders of magnitude with a low limit of detection of 0.51 aM. In addition, this designed protocol can discriminate mismatched DNA from perfectly matched target DNA, and holds a great potential for early diagnosis in gene-related diseases.

  16. Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism.

    Science.gov (United States)

    Rozemuller, E H; Bouwens, A G; van Oort, E; Versluis, L F; Marsh, S G; Bodmer, J G; Tilanus, M G

    1995-01-01

    An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Strand Invasion Based Amplification (SIBA®: a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

    Directory of Open Access Journals (Sweden)

    Mark J Hoser

    Full Text Available Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA. SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

  18. Optical chirped beam amplification and propagation

    Science.gov (United States)

    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.

  19. Double regenerative amplification of picosecond pulses

    Science.gov (United States)

    Bai, Zhen-ao; Chen, Li-yuan; Bai, Zhen-xu; Chen, Meng; Li, Gang

    2012-04-01

    An double Nd:YAG regenerative amplification picosecond pulse laser is demonstrated under the semiconductor saturable absorption mirror(SESAM) mode-locking technology and regenerative amplification technology, using BBO crystal as PC electro-optic crystal. The laser obtained is 20.71ps pulse width at 10 KHz repetition rate, and the energy power is up to 4W which is much larger than the system without pre-amplification. This result will lay a foundation for the following amplification.

  20. Comprehensive human genome amplification using multiple displacement amplification

    OpenAIRE

    Dean, Frank B.; Hosono, Seiyu; Fang, Linhua; Wu, Xiaohong; Faruqi, A. Fawad; Bray-Ward, Patricia; Zhenyu SUN; Zong, Qiuling; Du, Yuefen; Du, Jing; Driscoll, Mark; Song, Wanmin; Kingsmore, Stephen F.; Egholm, Michael; Lasken, Roger S.

    2002-01-01

    Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multi...

  1. Hybrid chirped pulse amplification system

    Science.gov (United States)

    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.

  2. Evaluation of application of pooling nucleic acid amplification testing in men who have sex with men population in China%HIV集合核酸检测在男男性行为人群中的应用评价

    Institute of Scientific and Technical Information of China (English)

    江华洲; 沈圣; 裴丽健; 黄晓婕; 吴昊; 闫红梅; 潘品良; 蒋岩

    2011-01-01

    Objective To evaluate the application of pooling HIV nucleic acid amplification testing (NAAT) among men who had sex with men (MSM) population, and to investigate suitable HIV screening strategy and the feasibility of calculation of HIV incidence using pooling NAAT among MSM population in China.Methods Four thousand eight hundred and fifty-six samples were collected from MSM population from April 2008 to September 2009 among with 4 156 were in Heilongjiang province and 700 were in Beijing in China. After standard testing with an HIV ELISA and WB confirmation testing, HIV antibody-negative samples were pooled and screened for HIV using NAAT.A three-stage pooling strategy was adopted.The HIV positive rate estimated by the four HIV screening strategies was calculated.In addition, 4 156 HIV positive specimens from Heilongjiang province were screened with the BED capture enzyme immunoassay (BED-CEIA).The HIV-1 incidences were estimated by BED-CEIA assay and pooling NAAT individually.ResultsOne hundred and forty-three of 4 856 subjects were HIV infected.130 were 3rd and 4th generation ELISA positive; 13 were antibody-negative but acutely HIV infected.According to the evaluation of four HIV screening strategies, routine HIV screening test together with pooling NAAT was more effective than other strategies for screening out window period generation ELISA+WB+pooling NAAT' were 2.68%(95% confidence interval CI=2.22%-3.14%), 2.82%(95%CI=2.35%-3.29%), 2.94%(95%CI=2.46%-3.42%) and 2.94%(95%CI=2.46%-3.42%), respectively.The differences were not significant (χ2=0.854 3, P=0.836 4).Of the 88 HIV positive samples from Heilongjiang province, 44 participants were tested as recent HIV infections by BED-CEIA assay. The estimated HIV-1 incidence was 2.36% (95%CI=1.63%-3.08%) and 2.92% (95%CI=1.01%-4.83%) based on BED-CEIA assay and pooling NAAT,respectively.Conclusions Pooling NAAT is a effective screening test in HIV negative population to detect window period infection among MSM

  3. 核酸扩增技术在广州市献血员血液筛查中的应用价值%Evaluation of Nucleic Acid Amplification Screening for Blood Donors in Guangzhou

    Institute of Scientific and Technical Information of China (English)

    明凯华; 雷秀霞; 徐邦牢; 罗丽香; 胡洁洁

    2015-01-01

    【目的】评价核酸扩增技术(NAT)在广州市献血员血液筛查的应用价值。【方法】收集22139名无偿献血员血样,采用酶联免疫吸附试验(ELISA)检测乙型肝炎病毒(HBV)、丙型肝炎病毒(HCV)、梅毒螺旋体(TP)和人免疫缺陷病毒(HIV),并检测谷丙转氨酶(ALT)水平。对四项ELISA检测阴性和ALT≤40U/L者血样,用COBASs201系统进行HBVDNA、HCVRNA、HIVRNA检测。NAT反应性样本、HBV、HCV和HIVELISA检测阳性血样以COBASAmpliScreen试剂盒鉴定。【结果】22139名献血员中,21776例双试剂血清免疫学检测阴性,其中19例为NAT反应阳性,检出率0.087%(19/21776),后经NAT鉴定检测,HBV、HCV和HIV反应阳性检出率分别为0.051%(11/21776)、0.028%(6/21776)和0.009%(2/21776)。126例HBsAg阳性样本中,25例NAT阴性,其中15例HBsAg中和试验阳性,为低水平慢性感染携带者。50例anti‐HCV阳性血样,4例为NAT阴性,补充ELISA检测为anti‐HCV阴性。16例anti‐HIV阳性样本中,7例为NAT阴性,其单样品核酸检测(ID‐NAT)和补充ELISA检测均为anti‐HIV阴性。【结论】NAT血液筛查对HBV、HCV和HIV经ELISA检测阴性样本的检出率较高,在该地开展NAT血液筛查,对于降低输血残余危险有重大意义。少量HBsAg阳性的低水平感染慢性携带者,汇集核酸检测(MP‐NAT)阴性,HBsAg筛查依然是必不可少的筛查手段。%[Objective] To evaluate the application value of nucleic acid amplification technology (NAT) in screening of blood donors in Guangzhou .[Methods] Blood samples from 22 ,139 blood donors in Guangzhou were collected .Enzyme‐linked immunosorbent assay (ELISA) was used to detect the levels of hepatitis B sur‐face antigen (HBsAg ) ,anti‐hepatitis C virus (anti‐HCV ) ,anti‐human immunodeficiency virus (anti‐HIV ) and anti‐Treponemia pallid (anti‐TP) .And the

  4. Spheromak Impedance and Current Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Fowler, T K; Hua, D D; Stallard, B W

    2002-01-31

    It is shown that high current amplification can be achieved only by injecting helicity on the timescale for reconnection, {tau}{sub REC}, which determines the effective impedance of the spheromak. An approximate equation for current amplification is: dI{sub TOR}{sup 2}/dt {approx} I{sup 2}/{tau}{sub REC} - I{sub TOR}{sup 2}/{tau}{sub closed} where I is the gun current, I{sub TOR} is the spheromak toroidal current and {tau}{sub CLOSED} is the ohmic decay time of the spheromak. Achieving high current amplification, I{sub TOR} >> I, requires {tau}{sub REC} <<{tau}{sub CLOSED}. For resistive reconnection, this requires reconnection in a cold zone feeding helicity into a hot zone. Here we propose an impedance model based on these ideas in a form that can be implemented in the Corsica-based helicity transport code. The most important feature of the model is the possibility that {tau}{sub REC} actually increases as the spheromak temperature increases, perhaps accounting for the ''voltage sag'' observed in some experiments, and a tendency toward a constant ratio of field to current, B {proportional_to} I, or I{sub TOR} {approx} I. Program implications are discussed.

  5. Magnetism Teaching Sequences Based on an Inductive Approach for First-Year Thai University Science Students

    Science.gov (United States)

    Narjaikaew, Pattawan; Emarat, Narumon; Arayathanitkul, Kwan; Cowie, Bronwen

    2010-01-01

    The study investigated the impact on student motivation and understanding of magnetism of teaching sequences based on an inductive approach. The study was conducted in large lecture classes. A pre- and post-Conceptual Survey of Electricity and Magnetism was conducted with just fewer than 700 Thai undergraduate science students, before and after…

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

    OpenAIRE

    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...

  7. Simple system for isothermal DNA amplification coupled to lateral flow detection.

    Directory of Open Access Journals (Sweden)

    Kristina Roskos

    Full Text Available 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.

  8. Heralded amplification of photonic qubits.

    Science.gov (United States)

    Bruno, Natalia; Pini, Vittorio; Martin, Anthony; Verma, Varun B; Nam, Sae Woo; Mirin, Richard; Lita, Adriana; Marsili, Francesco; Korzh, Boris; Bussières, Félix; Sangouard, Nicolas; Zbinden, Hugo; Gisin, Nicolas; Thew, Rob

    2016-01-11

    We demonstrate postselection free heralded qubit amplification for Time-Bin qubits and single photon states in an all-fibre, telecom-wavelength, scheme that highlights the simplicity, stability and potential for fully integrated photonic solutions. Exploiting high-efficiency superconducting detectors, the gain, fidelity and the performance of the amplifier are studied as a function of loss. We also demonstrate the first heralded single photon amplifier with independent sources. This provides a significant advance towards demonstrating device-independent quantum key distribution as well as fundamental tests of quantum mechanics over extended distances. PMID:26832244

  9. Resonant primordial gravitational waves amplification

    Directory of Open Access Journals (Sweden)

    Chunshan Lin

    2016-01-01

    Full Text Available 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.

  10. Dynamics and Control of DNA Sequence Amplification

    CERN Document Server

    Marimuthu, Karthikeyan

    2014-01-01

    DNA amplification is the process of replication of a specified DNA sequence \\emph{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 (PCR) 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 tempe...

  11. Dynamics and control of DNA sequence amplification

    International Nuclear Information System (INIS)

    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

  12. Dynamics and control of DNA sequence amplification

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. State of the art and challenges in sequence based T-cell epitope prediction

    DEFF Research Database (Denmark)

    Lundegaard, Claus; Hoof, Ilka; Lund, Ole;

    2010-01-01

    field has evolved significantly. Methods have now been developed that produce highly accurate binding predictions for many alleles and integrate both proteasomal cleavage and transport events. Moreover have so-called pan-specific methods been developed, which allow for prediction of peptide binding to......Sequence based T-cell epitope predictions have improved immensely in the last decade. From predictions of peptide binding to major histocompatibility complex molecules with moderate accuracy, limited allele coverage, and no good estimates of the other events in the antigen-processing pathway, the...... MHC alleles characterized by limited or no peptide binding data. Most of the developed methods are publicly available, and have proven to be very useful as a shortcut in epitope discovery. Here, we will go through some of the history of sequence-based predictions of helper as well as cytotoxic T cell...

  14. Risk Perception and Social Amplification

    International Nuclear Information System (INIS)

    This paper seeks to consider social amplification as it applies to risk perception. Perceptions of the magnitude of a risk are conditioned by issues such as the degree of uncertainty in probability and consequences, the nature of the consequences and the relative weightings placed on probability and consequences. Risk perceptions are also influenced by factors such as confidence in the operator of an industrial process, trust in the regulator and the perceived fairness of regulatory decision-making. Different people may hold different views about these issues and there may also be difficulties in communication. The paper identifies and discusses self-reinforcing mechanisms, which will be labelled 'lock-in' here. They appear to apply in many situations where social amplification is observed. Historically, the term 'lock-in' has been applied mainly in the technological context but, in this paper, four types of lock-in are identified, namely scientific/technological, economic, social and institutional lock-in. One type of lock-in tends to lead to the next and all are buttressed by people's general acceptance of the familiar, fear of the unknown and resistance to change. The regulator seeks to make decisions which achieve the common good rather than supporting or perpetuating any set of vested interests. In this regard the locked-in positions of stakeholders, whether organisations, interest groups, or individual members of the public, are obstacles and challenges. Existing methods of consultation are unsatisfactory in terms of achieving a proper and productive level of dialogue with stakeholders

  15. Evaluation of Repetitive Element Sequence-Based PCR as a Molecular Typing Method for Clostridium difficile

    OpenAIRE

    Spigaglia, Patrizia; Mastrantonio, Paola

    2003-01-01

    Repetitive element sequence-based PCR (rep-PCR) is a typing method that enables the generation of DNA fingerprinting that discriminates bacterial strains. In this study, we evaluated the applicability of rep-PCR in typing Clostridium difficile clinical isolates. The results obtained by rep-PCR were compared with those obtained by pulsed-field gel electrophoresis (PFGE) and PCR ribotyping. A high correspondence between pattern differentiations produced by rep-PCR and PFGE was observed, whereas...

  16. AbCD: arbitrary coverage design for sequencing-based genetic studies

    OpenAIRE

    Kang, Jian; Huang, Kuan-Chieh; Xu, Zheng; Wang, Yunfei; Abecasis, Gonçalo R.; Li, Yun

    2013-01-01

    Summary: Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbi...

  17. Sequence-based characterization of five SLA loci in Asian wild boars.

    Science.gov (United States)

    Jung, W Y; Choi, N R; Seo, D W; Lim, H T; Ho, C S; Lee, J H

    2014-10-01

    Two swine leucocyte antigen (SLA) class I (SLA-1 and SLA-2) and three class II (DRB1, DQB1 and DQA) genes were investigated for their diversity in Asian wild boars using a sequence-based typing method. A total of 15 alleles were detected at these loci, with eleven being novel. The findings provide one of the first glimpses of the SLA allelic diversity and architecture in the wild boar populations.

  18. Sequence-based characterization of the eight SLA loci in Korean native pigs.

    Science.gov (United States)

    Lee, Y J; Cho, K H; Kim, M J; Smith, D M; Ho, C S; Jung, K C; Jin, D I; Park, C S; Jeon, J T; Lee, J H

    2008-08-01

    Eight swine leucocyte antigen (SLA) gene (SLA-1, SLA-2, SLA-3, SLA-6, DRA, DRB1, DQA, DQB1) alleles were identified using sequence-based typing method in three Korean native pigs used for breeding at the National Institute of Animal Science in Korea. Six new alleles in class I genes and three new alleles in class II genes have been identified in this breed and can give valuable information for xenotransplantation and disease resistance.

  19. Clostridium difficile testing algorithms using glutamate dehydrogenase antigen and C. difficile toxin enzyme immunoassays with C. difficile nucleic acid amplification testing increase diagnostic yield in a tertiary pediatric population.

    Science.gov (United States)

    Ota, Kaede V; McGowan, Karin L

    2012-04-01

    We evaluated the performance of the rapid C. diff Quik Chek Complete's glutamate dehydrogenase antigen (GDH) and toxin A/B (CDT) tests in two algorithmic approaches for a tertiary pediatric population: algorithm 1 entailed initial testing with GDH/CDT followed by loop-mediated isothermal amplification (LAMP), and algorithm 2 entailed GDH/CDT followed by cytotoxicity neutralization assay (CCNA) for adjudication of discrepant GDH-positive/CDT-negative results. A true positive (TP) was defined as positivity by CCNA or positivity by LAMP plus another test (GDH, CDT, or the Premier C. difficile toxin A and B enzyme immunoassay [P-EIA]). A total of 141 specimens from 141 patients yielded 27 TPs and 19% prevalence. Sensitivity, specificity, positive predictive value, and negative predictive value were 56%, 100%, 100%, and 90% for P-EIA and 81%, 100%, 100%, and 96% for both algorithm 1 and algorithm 2. In summary, GDH-based algorithms detected C. difficile infections with superior sensitivity compared to P-EIA. The algorithms allowed immediate reporting of half of all TPs, but LAMP or CCNA was required to confirm the presence or absence of toxigenic C. difficile in GDH-positive/CDT-negative specimens. PMID:22259201

  20. Clostridium difficile testing algorithms using glutamate dehydrogenase antigen and C. difficile toxin enzyme immunoassays with C. difficile nucleic acid amplification testing increase diagnostic yield in a tertiary pediatric population.

    Science.gov (United States)

    Ota, Kaede V; McGowan, Karin L

    2012-04-01

    We evaluated the performance of the rapid C. diff Quik Chek Complete's glutamate dehydrogenase antigen (GDH) and toxin A/B (CDT) tests in two algorithmic approaches for a tertiary pediatric population: algorithm 1 entailed initial testing with GDH/CDT followed by loop-mediated isothermal amplification (LAMP), and algorithm 2 entailed GDH/CDT followed by cytotoxicity neutralization assay (CCNA) for adjudication of discrepant GDH-positive/CDT-negative results. A true positive (TP) was defined as positivity by CCNA or positivity by LAMP plus another test (GDH, CDT, or the Premier C. difficile toxin A and B enzyme immunoassay [P-EIA]). A total of 141 specimens from 141 patients yielded 27 TPs and 19% prevalence. Sensitivity, specificity, positive predictive value, and negative predictive value were 56%, 100%, 100%, and 90% for P-EIA and 81%, 100%, 100%, and 96% for both algorithm 1 and algorithm 2. In summary, GDH-based algorithms detected C. difficile infections with superior sensitivity compared to P-EIA. The algorithms allowed immediate reporting of half of all TPs, but LAMP or CCNA was required to confirm the presence or absence of toxigenic C. difficile in GDH-positive/CDT-negative specimens.

  1. Identification and evaluation of a new nucleic acid amplification test target for specific detection of Mycobacterium tuberculosis complex%鉴别结核分枝杆菌复合群的新型核酸扩增检测靶标评价

    Institute of Scientific and Technical Information of China (English)

    高诗会; 赵英伟; 胡忠义; 王洁; 陆俊梅; 闫丽萍; 郭琪; 马慧; 秦莲花

    2012-01-01

    Objective To identify and evaluate a new nucleic acid amplification (NAA) test target for specific detection of Mycobacterium tuberculosis (MTB) complex (MTC).Methods MTC-specific fragment was obtained by ISSR genotyping technology.Primer pairs were designed based on the sequences of MTC-specific fragment and tested in 211 mycobacterial strains including 107 MTC strains and 104 nontuberculous mycobacteria (NTM) strains.IS6110 element (specific identification of MTC strains) and 16s rRNA gene (specific identification of Mycobacterium) amplification were used as a control to evaluate the efficacy of the NAA test target in the detection of MTC strains.Results One MTC-specific fragment with the length of 588 bp,located in 315947-316534 of the genome from MTB reference strain H37 Rv,were obtained,cloned and sequenced.MTC-specific primer pairs MTCF/R were designed based on these sequences.All 211 mycobacterial strains accurately produced the genus-specific 16s rRNA amplicon.All MTC strains were positive in the MTCF/R PCR amplification while 99% MTC strains (106/107) were positive in the amplification of IS6110 sequences.All NTM strains were negative in both IS6110 and MTCF/R PCR amplification.Conclusions The MTC-specific fragment developed in this study can be used as a new NAA test target to correctly distinguish MTC from NTM.%目的 寻找新的鉴别诊断MTB复合群(MTC)高特异度和敏感的核酸靶标.方法 利用简单序列重复区间(ISSR)分型技术平台筛选MTC的特征片段,克隆测序获得特征序列并进行序列同源性分析,以该序列为基础设计MTC特征引物,并对211株分枝杆菌菌株(其中MTC107株、非结核分枝杆菌104株)进行鉴别检测.利用分枝杆菌属特征序列16s rRNA和MTC特征序列IS6110的鉴别结果,对MTC特征引物检测结果进行评估.结果 通过ISSR分型获得588 bp的MTC特征片段,该序列为MTC菌株的特征序列,位于MTB标准株H37Rv基因组的315947 ~316534位,以该序

  2. Tsunami Amplification due to Focusing

    Science.gov (United States)

    Moore, C. W.; Kanoglu, U.; Titov, V. V.; Aydin, B.; Spillane, M. C.; Synolakis, C. E.

    2012-12-01

    Tsunami runup measurements over the periphery of the Pacific Ocean after the devastating Great Japan tsunami of 11 March 2011 showed considerable variation in far-field and near-field impact. This variation of tsunami impact have been attributed to either directivity of the source or by local topographic effects. Directivity arguments alone, however, cannot explain the complexity of the radiated patterns in oceans with trenches and seamounts. Berry (2007, Proc. R. Soc. Lond. A 463, 3055-3071) discovered how such underwater features may concentrate tsunamis into cusped caustics and thus cause large local amplifications at specific focal points. Here, we examine focusing and local amplification, not by considering the effects of underwater diffractive lenses, but by considering the details of the dipole nature of the initial profile, and propose that certain regions of coastline are more at-risk, not simply because of directivity but because typical tsunami deformations create focal regions where abnormal tsunami wave height can be registered (Marchuk and Titov, 1989, Proc. IUGG/IOC International Tsunami Symposium, Novosibirsk, USSR). In this work, we present a new general analytical solution of the linear shallow-water wave equation for the propagation of a finite-crest-length source over a constant depth without any restriction on the initial profile. Unlike the analytical solution of Carrier and Yeh (2005, Comp. Mod. Eng. & Sci. 10(2), 113-121) which was restricted to initial conditions with Gaussian profiles and involved approximation, our solution is not only exact, but also general and allows the use of realistic initial waveform such as N-waves as defined by Tadepalli and Synolakis (1994, Proc. R. Soc. Lond. A 445, 99-112). We then verify our analytical solution for several typical wave profiles, both with the NOAA tsunami forecast model MOST (Titov and Synolakis, 1998, J. Waterw. Port Coast. Ocean Eng. 124(4), 157-171) which is validated and verified through

  3. Multiscale image contrast amplification (MUSICA)

    Science.gov (United States)

    Vuylsteke, Pieter; Schoeters, Emile P.

    1994-05-01

    This article presents a novel approach to the problem of detail contrast enhancement, based on multiresolution representation of the original image. The image is decomposed into a weighted sum of smooth, localized, 2D basis functions at multiple scales. Each transform coefficient represents the amount of local detail at some specific scale and at a specific position in the image. Detail contrast is enhanced by non-linear amplification of the transform coefficients. An inverse transform is then applied to the modified coefficients. This yields a uniformly contrast- enhanced image without artefacts. The MUSICA-algorithm is being applied routinely to computed radiography images of chest, skull, spine, shoulder, pelvis, extremities, and abdomen examinations, with excellent acceptance. It is useful for a wide range of applications in the medical, graphical, and industrial area.

  4. Mechanisms of Metal-Induced Centrosome Amplification

    OpenAIRE

    Holmes, Amie L.; Wise, John Pierce

    2010-01-01

    Exposure to toxic and carcinogenic metals is widespread; however, their mechanisms of action remain largely unknown. One potential mechanism for metal-induced carcinogenicity and toxicity is centrosome amplification. Here, we review the mechanisms for metal-induced centrosome amplification, including arsenic, chromium, mercury and nano-titanium dioxide.

  5. Risk Perception and Social Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.E. [Environment Agency (United Kingdom)

    2001-07-01

    This paper seeks to consider social amplification as it applies to risk perception. Perceptions of the magnitude of a risk are conditioned by issues such as the degree of uncertainty in probability and consequences, the nature of the consequences and the relative weightings placed on probability and consequences. Risk perceptions are also influenced by factors such as confidence in the operator of an industrial process, trust in the regulator and the perceived fairness of regulatory decision-making. Different people may hold different views about these issues and there may also be difficulties in communication. The paper identifies and discusses self-reinforcing mechanisms, which will be labelled 'lock-in' here. They appear to apply in many situations where social amplification is observed. Historically, the term 'lock-in' has been applied mainly in the technological context but, in this paper, four types of lock-in are identified, namely scientific/technological, economic, social and institutional lock-in. One type of lock-in tends to lead to the next and all are buttressed by people's general acceptance of the familiar, fear of the unknown and resistance to change. The regulator seeks to make decisions which achieve the common good rather than supporting or perpetuating any set of vested interests. In this regard the locked-in positions of stakeholders, whether organisations, interest groups, or individual members of the public, are obstacles and challenges. Existing methods of consultation are unsatisfactory in terms of achieving a proper and productive level of dialogue with stakeholders.

  6. A Novel Low Temperature PCR Assured High-Fidelity DNA Amplification

    Directory of Open Access Journals (Sweden)

    Shaoxia Zhou

    2013-06-01

    Full Text Available As previously reported, a novel low temperature (LoTemp polymerase chain reaction (PCR catalyzed by a moderately heat-resistant (MHR DNA polymerase with a chemical-assisted denaturation temperature set at 85 °C instead of the conventional 94–96 °C can achieve high-fidelity DNA amplification of a target DNA, even after up to 120 PCR thermal cycles. Furthermore, such accurate amplification is not achievable with conventional PCR. Now, using a well-recognized L1 gene segment of the human papillomavirus (HPV type 52 (HPV-52 as the template for experiments, we demonstrate that the LoTemp high-fidelity DNA amplification is attributed to an unusually high processivity and stability of the MHR DNA polymerase whose high fidelity in template-directed DNA synthesis is independent of non-existent 3'–5' exonuclease activity. Further studies and understanding of the characteristics of the LoTemp PCR technology may facilitate implementation of DNA sequencing-based diagnostics at the point of care in community hospital laboratories.

  7. Linking Arctic amplification and local feedbacks

    Science.gov (United States)

    Balcerak, Ernie

    2011-11-01

    Climate simulations show that as the Earth warms, the Arctic warms more than the average global warming. However, models differ on how much more the Arctic warms, and although scientists have proposed a variety of mechanisms to explain the Arctic warming amplification, there is no consensus on the main reasons for it. To shed light on this issue, Hwang et al. investigated the relationship between Arctic amplification and poleward energy transport and local Arctic feedbacks, such as changes in cloud cover or ice loss, across a group of models. The researchers noted that differences in atmospheric energy transport did not explain the ranges of polar amplification; rather, models with more amplification showed less energy transport into high latitudes. The authors found that decreasing energy transport is due to a coupled relationship between Arctic amplification and energy transport: Arctic amplification reduces the equator-to-pole temperature gradient, which strongly decreases energy transport. They suggest that this coupled relationship should be taken into account in studies of Arctic amplification. (Geophysical Research Letters, doi:10.1029/2011GL048546, 2011)

  8. Quantum Amplitude Amplification and Estimation

    CERN Document Server

    Brassard, G; Mosca, M; Tapp, A; Brassard, Gilles; Hoyer, Peter; Mosca, Michele; Tapp, Alain

    2000-01-01

    Consider a Boolean function $\\chi: X \\to \\{0,1\\}$ that partitions set $X$ between its good and bad elements, where $x$ is good if $\\chi(x)=1$ and bad otherwise. Consider also a quantum algorithm $\\mathcal A$ such that $A \\ket{0} = \\sum_{x\\in X} \\alpha_x \\ket{x}$ is a quantum superposition of the elements of $X$, and let $a$ denote the probability that a good element is produced if $A \\ket{0}$ is measured. If we repeat the process of running $A$, measuring the output, and using $\\chi$ to check the validity of the result, we shall expect to repeat $1/a$ times on the average before a solution is found. *Amplitude amplification* is a process that allows to find a good $x$ after an expected number of applications of $A$ and its inverse which is proportional to $1/\\sqrt{a}$, assuming algorithm $A$ makes no measurements. This is a generalization of Grover's searching algorithm in which $A$ was restricted to producing an equal superposition of all members of $X$ and we had a promise that a single $x$ existed such tha...

  9. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

    Directory of Open Access Journals (Sweden)

    Francisco Alexandre P

    2012-05-01

    Full Text Available Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

  10. Study design requirements for RNA sequencing-based breast cancer diagnostics.

    Science.gov (United States)

    Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

    2016-01-01

    Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic. PMID:26830453

  11. Raman amplification in optical communication systems

    DEFF Research Database (Denmark)

    Kjær, Rasmus

    2008-01-01

    Fiber Raman amplifiers are investigated with the purpose of identifying new applications and limitations for their use in optical communication systems. Three main topics are investigated, namely: New applications of dispersion compensating Raman amplifiers, the use Raman amplification to increase...

  12. Can Anomalous Amplification be Attained without Postselection?

    Science.gov (United States)

    Martínez-Rincón, Julián; Liu, Wei-Tao; Viza, Gerardo I.; Howell, John C.

    2016-03-01

    We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without discarding of data, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected. A tunable phase controls the strength of the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. We show that in the presence of technical noise the effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique.

  13. Can Anomalous Amplification be Attained Without Postselection?

    CERN Document Server

    Martínez-Rincón, Julián; Viza, Gerardo I; Howell, John C

    2015-01-01

    We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without the need of postselection, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected, and a phase controls the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. The effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique...

  14. Rolling circle amplification of metazoan mitochondrialgenomes

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Lindberg, D.R.; Boore, J.L.

    2005-07-31

    Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

  15. Onshore seismic amplifications due to bathymetric features

    Science.gov (United States)

    Rodríguez-Castellanos, A.; Carbajal-Romero, M.; Flores-Guzmán, N.; Olivera-Villaseñor, E.; Kryvko, A.

    2016-08-01

    We perform numerical calculations for onshore seismic amplifications, taking into consideration the effect of bathymetric features on the propagation of seismic movements. To this end, the boundary element method is applied. Boundary elements are employed to irradiate waves and, consequently, force densities can be obtained for each boundary element. From this assumption, Huygens’ principle is applied, and since the diffracted waves are built at the boundary from which they are radiated, this idea is equivalent to Somigliana’s representation theorem. The application of boundary conditions leads to a linear system being obtained (Fredholm integral equations). Several numerical models are analyzed, with the first one being used to verify the proposed formulation, and the others being used to estimate onshore seismic amplifications due to the presence of bathymetric features. The results obtained show that compressional waves (P-waves) generate onshore seismic amplifications that can vary from 1.2 to 5.2 times the amplitude of the incident wave. On the other hand, the shear waves (S-waves) can cause seismic amplifications of up to 4.0 times the incident wave. Furthermore, an important result is that in most cases the highest seismic amplifications from an offshore earthquake are located on the shoreline and not offshore, despite the seafloor configuration. Moreover, the influence of the incident angle of seismic waves on the seismic amplifications is highlighted.

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

    DEFF Research Database (Denmark)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper;

    2014-01-01

    -recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments...

  17. Fast interactive segmentation algorithm of image sequences based on relative fuzzy connectedness

    Institute of Scientific and Technical Information of China (English)

    Tian Chunna; Gao Xinbo

    2005-01-01

    A fast interactive segmentation algorithm of image-sequences based on relative fuzzy connectedness is presented. In comparison with the original algorithm, the proposed one, with the same accuracy, accelerates the segmentation speed by three times for single image. Meanwhile, this fast segmentation algorithm is extended from single object to multiple objects and from single-image to image-sequences. Thus the segmentation of multiple objects from complex background and batch segmentation of image-sequences can be achieved. In addition, a post-processing scheme is incorporated in this algorithm, which extracts smooth edge with one-pixel-width for each segmented object. The experimental results illustrate that the proposed algorithm can obtain the object regions of interest from medical image or image-sequences as well as man-made images quickly and reliably with only a little interaction.

  18. Analyzing Plasmodium falciparum erythrocyte membrane protein 1 gene expression by a next generation sequencing based method

    DEFF Research Database (Denmark)

    Jespersen, Jakob S.; Petersen, Bent; Seguin-Orlando, Andaine;

    2013-01-01

    Plasmodium falciparum is responsible for most cases of severe malaria and causes >1 million deaths every year. The particular virulence of this Plasmodium species is highly associated with the expression of certain members of the Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) family......, encoded by ~60 highly variable 'var' genes per haploid genome. PfEMP1 is exported to the surface of infected erythrocytes and is thought to be fundamental to immune evasion by adhesion to host and parasite factors. The highly variable nature has constituted a roadblock in var expression studies aimed...... at identifying PfEMP1 features associated with high virulence. Here we present the first effective method for sequence analysis of var genes expressed in field samples: a sequential PCR and next generation sequencing based technique applied on expressed var sequence tags and subsequently on long range PCR...

  19. Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikos; Vinther, Jeppe

    2015-01-01

    time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data......RNA structure-probing data can improve the prediction of RNA secondary and tertiary structure and allow structural changes to be identified and investigated. In recent years, massive parallel sequencing has dramatically improved the throughput of RNA structure probing experiments, but at the same......, we have made a collection of tools, which allow raw sequencing reads to be converted to normalized probing values using different published strategies. In addition, we also provide tools for visualization of the probing data in the UCSC Genome Browser and for converting RNA coordinates to genomic...

  20. Study on multiple-hops performance of MOOC sequences-based optical labels for OPS networks

    Science.gov (United States)

    Zhang, Chongfu; Qiu, Kun; Ma, Chunli

    2009-11-01

    In this paper, we utilize a new study method that is under independent case of multiple optical orthogonal codes to derive the probability function of MOOCS-OPS networks, discuss the performance characteristics for a variety of parameters, and compare some characteristics of the system employed by single optical orthogonal code or multiple optical orthogonal codes sequences-based optical labels. The performance of the system is also calculated, and our results verify that the method is effective. Additionally it is found that performance of MOOCS-OPS networks would, negatively, be worsened, compared with single optical orthogonal code-based optical label for optical packet switching (SOOC-OPS); however, MOOCS-OPS networks can greatly enlarge the scalability of optical packet switching networks.

  1. Heat induces gene amplification in cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Bin, E-mail: yanbin@mercyhealth.com [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Mercy Cancer Center, Mercy Medical Center-North Iowa, Mason City, IA 50401 (United States); Ouyang, Ruoyun [Department of Respiratory Medicine, The Second Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410011 (China); Huang, Chenghui [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Department of Oncology, The Third Xiangya Hospital, Xinagya School of Medicine, Central South University, Changsha 410013 (China); Liu, Franklin [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States); Neill, Daniel [Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS 39213 (United States); Li, Chuanyuan [Dermatology, Duke University Medical Center, Durham, NC 27710 (United States); Dewhirst, Mark [Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710 (United States)

    2012-10-26

    Highlights: Black-Right-Pointing-Pointer This study discovered that heat exposure (hyperthermia) results in gene amplification in cancer cells. Black-Right-Pointing-Pointer Hyperthermia induces DNA double strand breaks. Black-Right-Pointing-Pointer DNA double strand breaks are considered to be required for the initiation of gene amplification. Black-Right-Pointing-Pointer The underlying mechanism of heat-induced gene amplification is generation of DNA double strand breaks. -- Abstract: Background: Hyperthermia plays an important role in cancer therapy. However, as with radiation, it can cause DNA damage and therefore genetic instability. We studied whether hyperthermia can induce gene amplification in cancer cells and explored potential underlying molecular mechanisms. Materials and methods: (1) Hyperthermia: HCT116 colon cancer cells received water-submerged heating treatment at 42 or 44 Degree-Sign C for 30 min; (2) gene amplification assay using N-(phosphoacetyl)-L-aspartate (PALA) selection of cabamyl-P-synthetase, aspartate transcarbarmylase, dihydro-orotase (cad) gene amplified cells; (3) southern blotting for confirmation of increased cad gene copies in PALA-resistant cells; (4) {gamma}H2AX immunostaining to detect {gamma}H2AX foci as an indication for DNA double strand breaks. Results: (1) Heat exposure at 42 or 44 Degree-Sign C for 30 min induces gene amplification. The frequency of cad gene amplification increased by 2.8 and 6.5 folds respectively; (2) heat exposure at both 42 and 44 Degree-Sign C for 30 min induces DNA double strand breaks in HCT116 cells as shown by {gamma}H2AX immunostaining. Conclusion: This study shows that heat exposure can induce gene amplification in cancer cells, likely through the generation of DNA double strand breaks, which are believed to be required for the initiation of gene amplification. This process may be promoted by heat when cellular proteins that are responsible for checkpoints, DNA replication, DNA repair and

  2. Heat induces gene amplification in cancer cells

    International Nuclear Information System (INIS)

    Highlights: ► This study discovered that heat exposure (hyperthermia) results in gene amplification in cancer cells. ► Hyperthermia induces DNA double strand breaks. ► DNA double strand breaks are considered to be required for the initiation of gene amplification. ► The underlying mechanism of heat-induced gene amplification is generation of DNA double strand breaks. -- Abstract: Background: Hyperthermia plays an important role in cancer therapy. However, as with radiation, it can cause DNA damage and therefore genetic instability. We studied whether hyperthermia can induce gene amplification in cancer cells and explored potential underlying molecular mechanisms. Materials and methods: (1) Hyperthermia: HCT116 colon cancer cells received water-submerged heating treatment at 42 or 44 °C for 30 min; (2) gene amplification assay using N-(phosphoacetyl)-L-aspartate (PALA) selection of cabamyl-P-synthetase, aspartate transcarbarmylase, dihydro-orotase (cad) gene amplified cells; (3) southern blotting for confirmation of increased cad gene copies in PALA-resistant cells; (4) γH2AX immunostaining to detect γH2AX foci as an indication for DNA double strand breaks. Results: (1) Heat exposure at 42 or 44 °C for 30 min induces gene amplification. The frequency of cad gene amplification increased by 2.8 and 6.5 folds respectively; (2) heat exposure at both 42 and 44 °C for 30 min induces DNA double strand breaks in HCT116 cells as shown by γH2AX immunostaining. Conclusion: This study shows that heat exposure can induce gene amplification in cancer cells, likely through the generation of DNA double strand breaks, which are believed to be required for the initiation of gene amplification. This process may be promoted by heat when cellular proteins that are responsible for checkpoints, DNA replication, DNA repair and telomere functions are denatured. To our knowledge, this is the first study to provide direct evidence of hyperthermia induced gene amplification.

  3. Ultrasensitive Visual Detection of HIV DNA Biomarkers via a Multi-amplification Nanoplatform

    OpenAIRE

    Yuyin Long; Cuisong Zhou; Congmin Wang; Honglian Cai; Cuiyun Yin; Qiufang Yang; Dan Xiao

    2016-01-01

    Methodologies to detect disease biomarkers at ultralow concentrations can potentially improve the standard of living. A facile and label-free multi-amplification strategy is proposed for the ultrasensitive visual detection of HIV DNA biomarkers in real physiological media. This multi-amplification strategy not only exhibits a signficantly low detection limit down to 4.8 pM but also provides a label-free, cost-effective and facile technique for visualizing a few molecules of nucleic acid analy...

  4. Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification.

    Directory of Open Access Journals (Sweden)

    David S Boyle

    Full Text Available 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 (IS1081were 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

  5. A mathematical approach to estimate the efficacy of individual-donation and minipool nucleic acid amplification test options in preventing transmission risk by window period and occult hepatitis B virus infections

    Science.gov (United States)

    Vermeulen, Marion; van Drimmelen, Harry; Coleman, Charl; Mitchel, Josephine; Reddy, Ravi; Lelie, Nico

    2016-01-01

    BACKGROUND Sensitivity data from a head-to-head comparison study in South Africa were used to compare the efficacy of the Ultrio Plus assay in individual-donation (ID) and minipool (MP)4 and MP8 formats with that of TaqScreen MP6 in preventing hepatitis B virus (HBV) transmission risk. STUDY DESIGN AND METHODS The replicate nucleic acid test (NAT) results on 106 HBV NAT (Ultrio)-yield samples and 29 HBV DNA (Ultrio)-negative, hepatitis B surface antigen (HBsAg)-positive samples were used to determine the viral load in copies/mL against the Eurohep HBV standard by probit analysis. Random viral load distributions were established in 32 pre-HBsAg window period (WP), 15 post-HBsAg WP, and 56 occult HBV infection (OBI) donations. Regression analysis of log viral load and Poisson distribution statistics of infectious HBV particles in blood components was used to predict infectivity and efficacy of NAT options in removing HBV transmission risk. RESULTS For red blood cell transfusions (20 mL of plasma), the modeling predicted an Ultrio Plus ID-NAT efficacy of 68 and 83% in removing WP and (antibody to hepatitis B surface antigen–negative) OBI transmission risk, respectively, compared to 52 and 49% by TaqScreen MP6. For 200 mL of fresh-frozen plasma the estimated efficacy levels by these ID- and MP6-NAT options reduced to 57 and 44% for WP and to 67 and 34% for OBI donations, respectively. CONCLUSION The efficacy of the currently available commercial NAT systems in reducing HBV transmission risk is mainly driven by the pool size and the transfusion plasma volume. The modeled OBI transmission risk and NAT efficacy levels were in line with those recently reported in three lookback studies and give more insight in the incremental safety provided by HBsAg and antibody to hepatitis B core antigen testing of ID-NAT screened blood. PMID:24749834

  6. Time varying arctic climate change amplification

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. ESTIMATION OF AMPLIFICATION FACTOR IN EARTHQUAKE ENGINEERING

    Directory of Open Access Journals (Sweden)

    Nazarov Yuriy Pavlovich

    2015-03-01

    Full Text Available The authors are the developers of Odyssey Software (Eurosoft Co. for the analysis of seismological data and computing of seismic loads and their parameters. While communicating with the users of the software, the authors have revealed some uncertainty about both understanding of the term "amplification factor (AF" and calculation of the amplification factor using various methods. In this article, a simple example shows that the determination of the amplification factor as the ratio of the acceleration’s spectrum to the maximal acceleration is derived from the classical definition of AF in the form of the ratio of maximal dynamic displacement to the displacement by the action of static load. Deterministic and probabilistic ap-proaches for the calculating of the AF were discussed. There was an example of AFs calculation and their envelopes for translational and rotational components of seismic impact by using Odyssey Software.

  8. Amplification, Redundancy, and Quantum Chernoff Information

    Science.gov (United States)

    Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

    2014-04-01

    Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the "collapse of the wave packet," and a way to avoid embarrassing problems exemplified by Schrödinger's cat. Such a bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen interpretation. Quantum Darwinism views amplification as replication, in many copies, of the information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. This leads to objective reality via the presence of robust and widely accessible records of selected quantum states. The resulting redundancy (the number of copies deposited in the environment) follows from the quantum Chernoff information that quantifies the information transmitted by a typical elementary subsystem of the environment.

  9. On Arbitrary Phases in Quantum Amplitude Amplification

    CERN Document Server

    Hoyer, P

    2000-01-01

    We consider the use of arbitrary phases in quantum amplitude amplification which is a generalization of quantum searching. We prove that the phase condition in amplitude amplification is given by $\\tan(\\phi/2)=\\tan(\\phi/2)(1-2a)$, where $\\phi$ and $\\phi$ are the phases used and where $a$ is the success probability of the given algorithm. Thus the choice of phases depends nontrivially and nonlinearly on the success probability. Utilizing this condition, we give methods for constructing quantum algorithms that succeed with certainty and for implementing arbitrary rotations. We also conclude that phase errors of order up to $\\frac{1}{\\sqrt{a}}$ can be tolerated in amplitude amplification.

  10. Ambiguous allele combinations in HLA Class I and Class II sequence-based typing: when precise nucleotide sequencing leads to imprecise allele identification

    Directory of Open Access Journals (Sweden)

    Larsen Paula

    2004-09-01

    Full Text Available Abstract Sequence-based typing (SBT is one of the most comprehensive methods utilized for HLA typing. However, one of the inherent problems with this typing method is the interpretation of ambiguous allele combinations which occur when two or more different allele combinations produce identical sequences. The purpose of this study is to investigate the probability of this occurrence. We performed HLA-A,-B SBT for Exons 2 and 3 on 676 donors. Samples were analyzed with a capillary sequencer. The racial distribution of the donors was as follows: 615-Caucasian, 13-Asian, 23-African American, 17-Hispanic and 8-Unknown. 672 donors were analyzed for HLA-A locus ambiguities and 666 donors were analyzed for HLA-B locus ambiguities. At the HLA-A locus a total of 548 total ambiguous allele combinations were identified (548/1344 = 41%. Most (278/548 = 51% of these ambiguities were due to the fact that Exon 4 analysis was not performed. At the HLA-B locus 322 total ambiguous allele combinations were found (322/1332 = 24%. The HLA-B*07/08/15/27/35/44 antigens, common in Caucasians, produced a large portion of the ambiguities (279/322 = 87%. A large portion of HLA-A and B ambiguous allele combinations can be addressed by utilizing a group-specific primary amplification approach to produce an unambiguous homozygous sequence. Therefore, although the prevalence of ambiguous allele combinations is high, if the resolution of these ambiguities is clinically warranted, methods exist to compensate for this problem.

  11. Continuous phase amplification with a Sagnac interferometer

    CERN Document Server

    Starling, David J; Williams, Nathan S; Jordan, Andrew N; Howell, John C

    2009-01-01

    We describe a weak value inspired phase amplification technique in a Sagnac interferometer. We monitor the relative phase between two paths of a slightly misaligned interferometer by measuring the average position of a split-Gaussian mode in the dark port. Although we monitor only the dark port, we show that the signal varies linearly with phase and that we can obtain similar sensitivity to balanced homodyne detection. We derive the source of the amplification both with classical wave optics and as an inverse weak value.

  12. Parametric Amplification For Detecting Weak Optical Signals

    Science.gov (United States)

    Hemmati, Hamid; Chen, Chien; Chakravarthi, Prakash

    1996-01-01

    Optical-communication receivers of proposed type implement high-sensitivity scheme of optical parametric amplification followed by direct detection for reception of extremely weak signals. Incorporates both optical parametric amplification and direct detection into optimized design enhancing effective signal-to-noise ratios during reception in photon-starved (photon-counting) regime. Eliminates need for complexity of heterodyne detection scheme and partly overcomes limitations imposed on older direct-detection schemes by noise generated in receivers and by limits on quantum efficiencies of photodetectors.

  13. A dual amplification fluorescent strategy for sensitive detection of DNA methyltransferase activity based on strand displacement amplification and DNAzyme amplification.

    Science.gov (United States)

    Cui, Wanling; Wang, Lei; Jiang, Wei

    2016-03-15

    DNA methyltransferase (MTase) plays a critical role in many biological processes and has been regarded as a predictive cancer biomarker and a therapeutic target in cancer treatment. Sensitive detection of DNA MTase activity is essential for early cancer diagnosis and therapeutics. Here, we developed a dual amplification fluorescent strategy for sensitive detection of DNA MTase activity based on strand displacement amplification (SDA) and DNAzyme amplification. A trifunctional double-stranded DNA (dsDNA) probe was designed including a methylation site for DNA MTase recognition, a complementary sequence of 8-17 DNAzyme for synthesizing DNAzyme, and a nicking site for nicking enzyme cleavage. Firstly, the trifunctional dsDNA probe was methylated by DNA MTase to form the methylated dsDNA. Subsequently, HpaII restriction endonuclease specifically cleaved the residue of unmethylated dsDNA. Next, under the action of polymerase and nicking enzyme, the methylared dsDNA initiated SDA, releasing numbers of 8-17 DNAzymes. Finally, the released 8-17 DNAzymes triggered DNAzyme amplification reaction to induce a significant fluorescence enhancement. This strategy could detect DNA MTase activity as low as 0.0082U/mL. Additionally, the strategy was successfully applied for evaluating the inhibitions of DNA MTase using two anticancer drugs, 5-azacytidine and 5-aza-2'-deoxycytidine. The results indicate the proposed strategy has a potential application in early cancer diagnosis and therapeutics.

  14. Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

    KAUST Repository

    Wang, Bing

    2013-05-09

    Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

  15. Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species.

    Science.gov (United States)

    Menkis, Audrius; Urbina, Hector; James, Timothy Y; Rosling, Anna

    2014-12-01

    The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600(T) (=CBS138755(ExT)) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described. PMID:25457942

  16. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  17. Sequence-Based Pronunciation Variation Modeling for Spontaneous ASR Using a Noisy Channel Approach

    Science.gov (United States)

    Hofmann, Hansjörg; Sakti, Sakriani; Hori, Chiori; Kashioka, Hideki; Nakamura, Satoshi; Minker, Wolfgang

    The performance of English automatic speech recognition systems decreases when recognizing spontaneous speech mainly due to multiple pronunciation variants in the utterances. Previous approaches address this problem by modeling the alteration of the pronunciation on a phoneme to phoneme level. However, the phonetic transformation effects induced by the pronunciation of the whole sentence have not yet been considered. In this article, the sequence-based pronunciation variation is modeled using a noisy channel approach where the spontaneous phoneme sequence is considered as a “noisy” string and the goal is to recover the “clean” string of the word sequence. Hereby, the whole word sequence and its effect on the alternation of the phonemes will be taken into consideration. Moreover, the system not only learns the phoneme transformation but also the mapping from the phoneme to the word directly. In this study, first the phonemes will be recognized with the present recognition system and afterwards the pronunciation variation model based on the noisy channel approach will map from the phoneme to the word level. Two well-known natural language processing approaches are adopted and derived from the noisy channel model theory: Joint-sequence models and statistical machine translation. Both of them are applied and various experiments are conducted using microphone and telephone of spontaneous speech.

  18. Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers

    Directory of Open Access Journals (Sweden)

    Dybowski J Nikolaj

    2011-11-01

    Full Text Available Abstract Background Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. Results We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. Conclusions Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.

  19. Loop-Mediated Amplification Accelerated by Stem Primers

    Directory of Open Access Journals (Sweden)

    Laurence Tisi

    2011-12-01

    Full Text Available Isothermal nucleic acid amplifications (iNAATs have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance equivalent to that of PCR, but its application has been limited by the challenging primer design. The design of six primers in LAMP requires a selection of eight priming sites with significant restrictions imposed on their respective positioning and orientation. In order to relieve primer design constraints we propose an alternative approach which uses Stem primers instead of Loop primers and demonstrate the application of STEM-LAMP in assaying for Clostridium difficile, Listeria monocytogenes and HIV. Stem primers used in LAMP in combination with loop-generating and displacement primers gave significant benefits in speed and sensitivity, similar to those offered by Loop primers, while offering additional options of forward and reverse orientations, multiplexing, use in conjunction with Loop primers or even omission of one or two displacement primers, where necessary. Stem primers represent a valuable alternative to Loop primers and an additional tool for IVD assay development by offering more choices for primer design at the same time increasing assay speed, sensitivity, and reproducibility.

  20. Method Of Signal Amplification In Multi-Chromophore Luminescence Sensors

    Energy Technology Data Exchange (ETDEWEB)

    Levitsky, Igor A. (Fall River, MA); Krivoshlykov, Sergei G. (Shrewsbury, MA)

    2004-02-03

    A fluorescence-based method for highly sensitive and selective detection of analyte molecules is proposed. The method employs the energy transfer between two or more fluorescent chromophores in a carefully selected polymer matrix. In one preferred embodiment, signal amplification has been achieved in the fluorescent sensing of dimethyl methylphosphonate (DMMP) using two dyes, 3-aminofluoranthene (AM) and Nile Red (NR), in a hydrogen bond acidic polymer matrix. The selected polymer matrix quenches the fluorescence of both dyes and shifts dye emission and absorption spectra relative to more inert matrices. Upon DMMP sorption, the AM fluorescence shifts to the red at the same time the NR absorption shifts to the blue, resulting in better band overlap and increased energy transfer between chromophores. In another preferred embodiment, the sensitive material is incorporated into an optical fiber system enabling efficient excitation of the dye and collecting the fluorescent signal form the sensitive material on the remote end of the system. The proposed method can be applied to multichromophore luminescence sensor systems incorporating N-chromophores leading to N-fold signal amplification and improved selectivity. The method can be used in all applications where highly sensitive detection of basic gases, such as dimethyl methylphosphonate (DMMP), Sarin, Soman and other chemical warfare agents having basic properties, is required, including environmental monitoring, chemical industry and medicine.

  1. DNA Extraction and Amplification from Contemporary Polynesian Bark-Cloth

    Science.gov (United States)

    Moncada, Ximena; Payacán, Claudia; Arriaza, Francisco; Lobos, Sergio; Seelenfreund, Daniela; Seelenfreund, Andrea

    2013-01-01

    Background Paper mulberry has been used for thousands of years in Asia and Oceania for making paper and bark-cloth, respectively. Museums around the world hold valuable collections of Polynesian bark-cloth. Genetic analysis of the plant fibers from which the textiles were made may answer a number of questions of interest related to provenance, authenticity or species used in the manufacture of these textiles. Recovery of nucleic acids from paper mulberry bark-cloth has not been reported before. Methodology We describe a simple method for the extraction of PCR-amplifiable DNA from small samples of contemporary Polynesian bark-cloth (tapa) using two types of nuclear markers. We report the amplification of about 300 bp sequences of the ITS1 region and of a microsatellite marker. Conclusions Sufficient DNA was retrieved from all bark-cloth samples to permit successful PCR amplification. This method shows a means of obtaining useful genetic information from modern bark-cloth samples and opens perspectives for the analyses of small fragments derived from ethnographic materials. PMID:23437166

  2. Desert Amplification in a Warming Climate

    Science.gov (United States)

    Zhou, Liming

    2016-08-01

    Here I analyze the observed and projected surface temperature anomalies over land between 50°S-50°N for the period 1950–2099 by large-scale ecoregion and find strongest warming consistently and persistently seen over driest ecoregions such as the Sahara desert and the Arabian Peninsula during various 30-year periods, pointing to desert amplification in a warming climate. This amplification enhances linearly with the global mean greenhouse gases(GHGs) radiative forcing and is attributable primarily to a stronger GHGs-enhanced downward longwave radiation forcing reaching the surface over drier ecoregions as a consequence of a warmer and thus moister atmosphere in response to increasing GHGs. These results indicate that desert amplification may represent a fundamental pattern of global warming associated with water vapor feedbacks over land in low- and mid- latitudes where surface warming rates depend inversely on ecosystem dryness. It is likely that desert amplification might involve two types of water vapor feedbacks that maximize respectively in the tropical upper troposphere and near the surface over deserts, with both being very dry and thus extremely sensitive to changes of water vapor.

  3. Optical Pattern Recognition With Self-Amplification

    Science.gov (United States)

    Liu, Hua-Kuang

    1994-01-01

    In optical pattern recognition system with self-amplification, no reference beam used in addressing mode. Polarization of laser beam and orientation of photorefractive crystal chosen to maximize photorefractive effect. Intensity of recognition signal is orders of magnitude greater than other optical correlators. Apparatus regarded as real-time or quasi-real-time optical pattern recognizer with memory and reprogrammability.

  4. Social amplification of risk: a conceptual framework

    International Nuclear Information System (INIS)

    One of the most perplexing problems in risk analysis is why some relatively minor risks or risk events, as assessed by technical experts, often elicit strong public concerns and result in substantial impacts upon society and economy. This article sets forth a conceptual framework that seeks to link systematically the technical assessment of risk with psychological, sociological, and cultural perspectives of risk perception and risk-related behavior. The main thesis is that hazards interact with psychological, social, institutional, and cultural processes in ways that may amplify or attenuate public responses to the risk or risk event. A structural description of the social amplification of risk is now possible. Amplification occurs at two stages: in the transfer of information about the risk, and in the response mechanisms of society. Signals about risk are processed by individual and social amplification stations, including the scientist who communicates the risk assessment, the news media, cultural groups, interpersonal networks, and others. Key steps of amplifications can be identified at each stage. The amplified risk leads to behavioral responses, which, in turn, result in secondary impacts. Models are presented that portray the elements and linkages in the proposed conceptual framework

  5. Desert Amplification in a Warming Climate

    Science.gov (United States)

    Zhou, Liming

    2016-01-01

    Here I analyze the observed and projected surface temperature anomalies over land between 50°S-50°N for the period 1950–2099 by large-scale ecoregion and find strongest warming consistently and persistently seen over driest ecoregions such as the Sahara desert and the Arabian Peninsula during various 30-year periods, pointing to desert amplification in a warming climate. This amplification enhances linearly with the global mean greenhouse gases(GHGs) radiative forcing and is attributable primarily to a stronger GHGs-enhanced downward longwave radiation forcing reaching the surface over drier ecoregions as a consequence of a warmer and thus moister atmosphere in response to increasing GHGs. These results indicate that desert amplification may represent a fundamental pattern of global warming associated with water vapor feedbacks over land in low- and mid- latitudes where surface warming rates depend inversely on ecosystem dryness. It is likely that desert amplification might involve two types of water vapor feedbacks that maximize respectively in the tropical upper troposphere and near the surface over deserts, with both being very dry and thus extremely sensitive to changes of water vapor. PMID:27538725

  6. Desert Amplification in a Warming Climate.

    Science.gov (United States)

    Zhou, Liming

    2016-01-01

    Here I analyze the observed and projected surface temperature anomalies over land between 50°S-50°N for the period 1950-2099 by large-scale ecoregion and find strongest warming consistently and persistently seen over driest ecoregions such as the Sahara desert and the Arabian Peninsula during various 30-year periods, pointing to desert amplification in a warming climate. This amplification enhances linearly with the global mean greenhouse gases(GHGs) radiative forcing and is attributable primarily to a stronger GHGs-enhanced downward longwave radiation forcing reaching the surface over drier ecoregions as a consequence of a warmer and thus moister atmosphere in response to increasing GHGs. These results indicate that desert amplification may represent a fundamental pattern of global warming associated with water vapor feedbacks over land in low- and mid- latitudes where surface warming rates depend inversely on ecosystem dryness. It is likely that desert amplification might involve two types of water vapor feedbacks that maximize respectively in the tropical upper troposphere and near the surface over deserts, with both being very dry and thus extremely sensitive to changes of water vapor. PMID:27538725

  7. Electromagnetic waves amplification in a coaxial triode with virtual cathode

    Energy Technology Data Exchange (ETDEWEB)

    Grigoryev, V.P.; Antoshkin, M.Y.; Koval, T.V.; Kuryakov, A.M. [Tomsk Politechnical Univ. (Russian Federation)

    1995-11-01

    The present paper presents the results of analytical and numerical investigations on the amplification of microwaves in the vircator triode of coaxial making. The range of a parameters of the greatest amplification was define for TH and TE-modes.

  8. Rapid microfluidic thermal cycler for nucleic acid amplification

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Vafai, Kambiz

    2015-10-27

    A system for thermal cycling a material to be thermal cycled including a microfluidic heat exchanger; a porous medium in the microfluidic heat exchanger; a microfluidic thermal cycling chamber containing the material to be thermal cycled, the microfluidic thermal cycling chamber operatively connected to the microfluidic heat exchanger; a working fluid at first temperature; a first system for transmitting the working fluid at first temperature to the microfluidic heat exchanger; a working fluid at a second temperature, a second system for transmitting the working fluid at second temperature to the microfluidic heat exchanger; a pump for flowing the working fluid at the first temperature from the first system to the microfluidic heat exchanger and through the porous medium; and flowing the working fluid at the second temperature from the second system to the heat exchanger and through the porous medium.

  9. HLA polymorphisms in Cabo Verde and Guiné-Bissau inferred from sequence-based typing.

    Science.gov (United States)

    Spínola, Hélder; Bruges-Armas, Jácome; Middleton, Derek; Brehm, António

    2005-10-01

    Human leukocyte antigen (HLA)-A, -B, and -DRB1 polymorphisms were examined in the Cabo Verde and Guiné-Bissau populations. The data were obtained at high-resolution level, using sequence-based typing. The most frequent alleles in each locus was: A*020101 (16.7% in Guiné-Bissau and 13.5% in Cabo Verde), B*350101 (14.4% in Guiné-Bissau and 13.2% in Cabo Verde), DRB1*1304 (19.6% in Guiné-Bissau), and DRB1*1101 (10.1% in Cabo Verde). The predominant three loci haplotype in Guiné-Bissau was A*2301-B*1503-DRB1*1101 (4.6%) and in Cabo Verde was A*3002-B*350101-DRB1*1001 (2.8%), exclusive to northwestern islands (5.6%) and absent in Guiné-Bissau. The present study corroborates historic sources and other genetic studies that say Cabo Verde were populated not only by Africans but also by Europeans. Haplotypes and dendrogram analysis shows a Caucasian genetic influence in today's gene pool of Cabo Verdeans. Haplotypes and allele frequencies present a differential distribution between southeastern and northwestern Cabo Verde islands, which could be the result of different genetic influences, founder effect, or bottlenecks. Dendrograms and principal coordinates analysis show that Guineans are more similar to North Africans than other HLA-studied sub-Saharans, probably from ancient and recent genetic contacts with other peoples, namely East Africans. PMID:16386651

  10. MICA polymorphism in a population from north Morocco, Metalsa Berbers, using sequence-based typing.

    Science.gov (United States)

    Piancatelli, Daniela; Del Beato, Tiziana; Oumhani, Khadija; El Aouad, Rajae; Adorno, Domenico

    2005-08-01

    The MICA gene encodes a family of nonclassical major histocompatibility complex class I molecules. Data on MICA polymorphism in different populations are still limited. In the present study, MICA allele frequencies (af) were assessed in 82 unrelated healthy individuals from a Moroccan Berber population named Metalsa (ME) by means of sequence-based typing of exons 2, 3, 4, and 5. In consideration of the linkage disequilibrium existing between MICA and human leukocyte antigen (HLA) class I alleles, MICA/HLA-B, MICA/HLA-Cw, and MICA/HLA-A haplotype frequencies (hf) were estimated. A wide allelic distribution including 16 different MICA alleles was found in ME. The most common MICA alleles were MICA*00801 (af = 0.268), *004 (0.232), *00902 (0.140), *00901 (0.085), and *00901 (0.073). The most common MICA/HLA-B haplotypes were MICA*004-B*4403 and MICA*009-B*50 (hf = 0.113 for both these haplotypes). Some known MICA and HLA-B associations were confirmed in this population. Noteworthy was the high frequency of MICA*009 (af = 0.226); the high frequency of B*50 found in ME (af = 0.114) permitted us to evidence the associations of MICA*00902 with B*5001 (hf = 0.068) or *5002 (hf = 0.045), whereas MICA*00901 was mainly associated with B*5101 (hf = 0.038), which corresponds to the previously described association MICA*009/A6-HLA-B*51. This study extends the previous knowledge on MICA polymorphism to a North African white population and may have implications for disease associations and transplantation.

  11. A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones.

    Science.gov (United States)

    Martins, Natacha; Picão, Renata Cristina; Cerqueira-Alves, Morgana; Uehara, Aline; Barbosa, Lívia Carvalho; Riley, Lee W; Moreira, Beatriz Meurer

    2016-08-01

    A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings.

  12. Comparison of two multilocus sequence based genotyping schemes for Leptospira species.

    Directory of Open Access Journals (Sweden)

    Ahmed Ahmed

    2011-11-01

    Full Text Available BACKGROUND: Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results. METHODS AND FINDINGS: A total of 48 isolates consisting of L. interrogans (n = 40 and L. kirschneri (n = 8 were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively. Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5-96.5 vs. 93.5 (95% CI 88.6-98.4. The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L. CONCLUSIONS: This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages.

  13. SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations.

    Science.gov (United States)

    Zhan, Xiaowei; Liu, Dajiang J

    2015-12-01

    Next-generation sequencing has enabled the study of a comprehensive catalogue of genetic variants for their impact on various complex diseases. Numerous consortia studies of complex traits have publically released their summary association statistics, which have become an invaluable resource for learning the underlying biology, understanding the genetic architecture, and guiding clinical translations. There is great interest in the field in developing novel statistical methods for analyzing and interpreting results from these genotype-phenotype association studies. One popular platform for method development and data analysis is R. In order to enable these analyses in R, it is necessary to develop packages that can efficiently query files of summary association statistics, explore the linkage disequilibrium structure between variants, and integrate various bioinformatics databases. The complexity and scale of sequence datasets and databases pose significant computational challenges for method developers. To address these challenges and facilitate method development, we developed the R package SEQMINER for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases. SEQMINER provides an infrastructure where novel methods can be distributed and applied to analyzing sequence datasets in practice. We illustrate the performance of SEQMINER using datasets from the 1000 Genomes Project. We show that SEQMINER is highly efficient and easy to use. It will greatly accelerate the process of applying statistical innovations to analyze and interpret sequence-based associations. The R package, its source code and documentations are available from http://cran.r-project.org/web/packages/seqminer and http://seqminer.genomic.codes/.

  14. A new evolutionary theory deduced mathematically from entropy amplification

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A new evolutionary theory which is able to unite the present evolutionary debates is deduced mathematically from the principle of entropy amplification.It suggests that the extensive evolution is driven by the amplification of entropy,or microscopic diversity,and the biological evolution is driven by the amplification of biodiversity.Forming high hierarchies is the most important way for the amplification and brings out spontaneously three kinds of selection.This theory has some positive cultural meanings.

  15. Parametric Amplification of Vacuum Fluctuations in a Spinor Condensate

    DEFF Research Database (Denmark)

    Klempt, C.; Topic, O.; Gebreyesus, G.;

    2010-01-01

    Parametric amplification of vacuum fluctuations is crucial in modern quantum optics, enabling the creation of squeezing and entanglement. We demonstrate the parametric amplification of vacuum fluctuations for matter waves using a spinor F=2 87Rb condensate. Interatomic interactions lead to correl......Parametric amplification of vacuum fluctuations is crucial in modern quantum optics, enabling the creation of squeezing and entanglement. We demonstrate the parametric amplification of vacuum fluctuations for matter waves using a spinor F=2 87Rb condensate. Interatomic interactions lead...

  16. Plasmonic Terahertz Amplification in Graphene-Based Asymmetric Hyperbolic Metamaterial

    Directory of Open Access Journals (Sweden)

    Igor Nefedov

    2015-05-01

    Full Text Available We propose and theoretically explore terahertz amplification, based on stimulated generation of plasmons in graphene asymmetric hyperbolic metamaterials (AHMM, strongly coupled to terahertz radiation. In contrast to the terahertz amplification in resonant nanocavities, AHMM provides a wide-band THz amplification without any reflection in optically thin graphene multilayers.

  17. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

  18. RNA amplification for successful gene profiling analysis

    Directory of Open Access Journals (Sweden)

    Wang Ena

    2005-07-01

    Full Text Available Abstract The study of clinical samples is often limited by the amount of material available to study. While proteins cannot be multiplied in their natural form, DNA and RNA can be amplified from small specimens and used for high-throughput analyses. Therefore, genetic studies offer the best opportunity to screen for novel insights of human pathology when little material is available. Precise estimates of DNA copy numbers in a given specimen are necessary. However, most studies investigate static variables such as the genetic background of patients or mutations within pathological specimens without a need to assess proportionality of expression among different genes throughout the genome. Comparative genomic hybridization of DNA samples represents a crude exception to this rule since genomic amplification or deletion is compared among different specimens directly. For gene expression analysis, however, it is critical to accurately estimate the proportional expression of distinct RNA transcripts since such proportions directly govern cell function by modulating protein expression. Furthermore, comparative estimates of relative RNA expression at different time points portray the response of cells to environmental stimuli, indirectly informing about broader biological events affecting a particular tissue in physiological or pathological conditions. This cognitive reaction of cells is similar to the detection of electroencephalographic patterns which inform about the status of the brain in response to external stimuli. As our need to understand human pathophysiology at the global level increases, the development and refinement of technologies for high fidelity messenger RNA amplification have become the focus of increasing interest during the past decade. The need to increase the abundance of RNA has been met not only for gene specific amplification, but, most importantly for global transcriptome wide, unbiased amplification. Now gene

  19. A sequence-based approach to identify reference genes for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Chari Raj

    2010-08-01

    Full Text Available Abstract Background An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer may not be suitable in another (e.g. breast cancer. Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate. Methods Serial analysis of gene expression (SAGE profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR, and their impact on differential expression analysis of microarray data was evaluated. Results We show that (i conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii reference genes identified for lung cancer do not perform well for other cancer types (breast and brain, (iii reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung

  20. Sequencing-based variant detection in the polyploid crop oilseed rape

    Science.gov (United States)

    2013-01-01

    Background The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products. Results A protocol was developed to tag PCR products with 5’ 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2.b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively. Conclusions The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs. PMID:23915099

  1. Amplification of postwildfire peak flow by debris

    Science.gov (United States)

    Kean, J. W.; McGuire, L. A.; Rengers, F. K.; Smith, J. B.; Staley, D. M.

    2016-08-01

    In burned steeplands, the peak depth and discharge of postwildfire runoff can substantially increase from the addition of debris. Yet methods to estimate the increase over water flow are lacking. We quantified the potential amplification of peak stage and discharge using video observations of postwildfire runoff, compiled data on postwildfire peak flow (Qp), and a physically based model. Comparison of flood and debris flow data with similar distributions in drainage area (A) and rainfall intensity (I) showed that the median runoff coefficient (C = Qp/AI) of debris flows is 50 times greater than that of floods. The striking increase in Qp can be explained using a fully predictive model that describes the additional flow resistance caused by the emergence of coarse-grained surge fronts. The model provides estimates of the amplification of peak depth, discharge, and shear stress needed for assessing postwildfire hazards and constraining models of bedrock incision.

  2. Gravito-magnetic amplification in cosmology

    CERN Document Server

    Tsagas, Christos G

    2009-01-01

    Magnetic fields interact with gravitational waves in various ways. We consider the coupling between the Weyl and the Maxwell fields in cosmology and study the effects of the former on the latter. The approach is fully analytical and the results are gauge-invariant. We show that the nature and the outcome of the gravito-magnetic interaction depends on the electric properties of the cosmic medium. When the conductivity is high, gravitational waves reduce the standard (adiabatic) decay rate of the B-field, leading to its superadiabatic amplification. In poorly conductive environments, on the other hand, Weyl-curvature distortions can result into the resonant amplification of large-scale cosmological magnetic fields. Driven by the gravitational waves, these B-fields oscillate with an amplitude that is found to diverge when the wavelengths of the two sources coincide. We present technical and physical aspects of the gravito-magnetic interaction and discuss its potential implications.

  3. Diffusive shock acceleration and magnetic field amplification

    CERN Document Server

    Schure, K M; Drury, L O'C; Bykov, A M

    2012-01-01

    Diffusive shock acceleration is the theory of particle acceleration through multiple shock crossings. In order for this process to proceed at a rate that can be reconciled with observations of high-energy electrons in the vicinity of the shock, and for cosmic rays protons to be accelerated to energies up to observed galactic values, significant magnetic field amplification is required. In this review we will discuss various theories on how magnetic field amplification can proceed in the presence of a cosmic ray population. On both short and long scales, cosmic ray streaming can induce instabilities that act to amplify the magnetic field. Developments in this area that have occurred over the past decade are the main focus of this paper.

  4. Parametric nanomechanical amplification at very high frequency.

    Science.gov (United States)

    Karabalin, R B; Feng, X L; Roukes, M L

    2009-09-01

    Parametric resonance and amplification are important in both fundamental physics and technological applications. Here we report very high frequency (VHF) parametric resonators and mechanical-domain amplifiers based on nanoelectromechanical systems (NEMS). Compound mechanical nanostructures patterned by multilayer, top-down nanofabrication are read out by a novel scheme that parametrically modulates longitudinal stress in doubly clamped beam NEMS resonators. Parametric pumping and signal amplification are demonstrated for VHF resonators up to approximately 130 MHz and provide useful enhancement of both resonance signal amplitude and quality factor. We find that Joule heating and reduced thermal conductance in these nanostructures ultimately impose an upper limit to device performance. We develop a theoretical model to account for both the parametric response and nonequilibrium thermal transport in these composite nanostructures. The results closely conform to our experimental observations, elucidate the frequency and threshold-voltage scaling in parametric VHF NEMS resonators and sensors, and establish the ultimate sensitivity limits of this approach.

  5. Introduction to Quantum Noise, Measurement and Amplification

    OpenAIRE

    Clerk, A. A.; Devoret, M. H.; Girvin, S. M.; Marquardt, F.; Schoelkopf, R. J.

    2008-01-01

    The topic of quantum noise has become extremely timely due to the rise of quantum information physics and the resulting interchange of ideas between the condensed matter and AMO/quantum optics communities. This review gives a pedagogical introduction to the physics of quantum noise and its connections to quantum measurement and quantum amplification. After introducing quantum noise spectra and methods for their detection, we describe the basics of weak continuous measurements. Particular atte...

  6. Single genome amplification and direct amplicon sequencing of Plasmodium spp. DNA from ape fecal specimens

    OpenAIRE

    Liu, Weimin; Li, Yingying; Peeters, Martine; Rayner, Julian; Sharp, Paul; Shaw, George; Hahn, Beatrice

    2010-01-01

    Conventional PCR followed by molecular cloning and sequencing of amplified products is commonly used to test clinical specimens for target sequences of interest, such as viral, bacterial or parasite nucleic acids. However, this approach has serious limitations when used to analyze mixtures of genetically divergent templates1–9. This is because Taq polymerase is prone to switch templates during the amplification process, thereby generating recombinants that do not exist in vivo4. When amplicon...

  7. Single genome amplification and direct amplicon sequencing of Plasmodium spp. DNA from ape fecal specimens

    OpenAIRE

    sprotocols

    2015-01-01

    Conventional PCR followed by molecular cloning and sequencing of amplified products is commonly used to test clinical specimens for target sequences of interest, such as viral, bacterial or parasite nucleic acids. However, this approach has serious limitations when used to analyze mixtures of genetically divergent templates (1-9). This is because Taq polymerase is prone to switch templates during the amplification process, thereby generating recombinants that do not exist in vivo (4). When am...

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

    Science.gov (United States)

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

    2015-06-01

    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/μl, 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.

  9. All Three Rows of Outer Hair Cells Are Required for Cochlear Amplification

    Directory of Open Access Journals (Sweden)

    Michio Murakoshi

    2015-01-01

    Full Text Available In the mammalian auditory system, the three rows of outer hair cells (OHCs located in the cochlea are thought to increase the displacement amplitude of the organ of Corti. This cochlear amplification is thought to contribute to the high sensitivity, wide dynamic range, and sharp frequency selectivity of the hearing system. Recent studies have shown that traumatic stimuli, such as noise exposure and ototoxic acid, cause functional loss of OHCs in one, two, or all three rows. However, the degree of decrease in cochlear amplification caused by such functional losses remains unclear. In the present study, a finite element model of a cross section of the gerbil cochlea was constructed. Then, to determine effects of the functional losses of OHCs on the cochlear amplification, changes in the displacement amplitude of the basilar membrane (BM due to the functional losses of OHCs were calculated. Results showed that the displacement amplitude of the BM decreases significantly when a single row of OHCs lost its function, suggesting that all three rows of OHCs are required for cochlear amplification.

  10. Ultrasensitive DNA detection based on two-step quantitative amplification on magnetic nanoparticles

    Science.gov (United States)

    Jin, Mingliang; Liu, Xia; van den Berg, Albert; Zhou, Guofu; Shui, Lingling

    2016-08-01

    Sensitive detection of a specific deoxyribo nucleic acid (DNA) sequence is important for biomedical applications. In this report, a two-step amplification strategy is developed based on magnetic nanoparticles (MNPs) to achieve ultrasensitive DNA fluorescence detection. The first level amplification is obtained from multiple binding sites on MNPs to achieve thousands of probe DNA molecules on one nanoparticle surface. The second level amplification is gained by enzymatic reaction to achieve fluorescence signal enhancement. MNPs functionalized by probe DNA (DNAp) are bound to target DNA (t-DNA) molecules with a ratio of 1:1 on a substrate with capture DNA (DNAc). After the MNPs with DNAp are released from the substrate, alkaline phosphatase (AP) is labelled to MNPs via hybridization reaction between DNAp on MNPs and detection DNAs (DNAd) with AP. The AP on MNPs catalyses non-fluorescent 4-methylumbelliferyl phosphate (4-MUP) to fluorescent 4-methylumbelliferone (4-MU) with high intensity. Finally, fluorescence intensity of the 4-MU is detected by a conventional fluorescence spectrophotometer. With this two-step amplification strategy, the limit of detection (LOD) of 2.8 × 10‑18 mol l‑1 for t-DNA has been achieved.

  11. Ultrasensitive Visual Detection of HIV DNA Biomarkers via a Multi-amplification Nanoplatform.

    Science.gov (United States)

    Long, Yuyin; Zhou, Cuisong; Wang, Congmin; Cai, Honglian; Yin, Cuiyun; Yang, Qiufang; Xiao, Dan

    2016-01-01

    Methodologies to detect disease biomarkers at ultralow concentrations can potentially improve the standard of living. A facile and label-free multi-amplification strategy is proposed for the ultrasensitive visual detection of HIV DNA biomarkers in real physiological media. This multi-amplification strategy not only exhibits a signficantly low detection limit down to 4.8 pM but also provides a label-free, cost-effective and facile technique for visualizing a few molecules of nucleic acid analyte with the naked eye. Importantly, the biosensor is capable of discriminating single-based mismatch lower than 5.0 nM in human serum samples. Moreover, the visual sensing platform exhibits excellent specificity, acceptable reusability and a long-term stability. All these advantages could be attributed to the nanofibrous sensing platform that 1) has a high surface-area-to-volume provided by electrospun nanofibrous membrane, and 2) combines glucose oxidase (GOx) biocatalysis, DNAzyme-catalyzed colorimetric reaction and catalytic hairpin assembly (CHA) recycling amplification together. This multi-amplification nanoplatform promises label-free and visual single-based mismatch DNA monitoring with high sensitivity and specificity, suggesting wide applications that range from virus detection to genetic disease diagnosis. PMID:27032385

  12. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection.

    Directory of Open Access Journals (Sweden)

    Ahmed Abd El Wahed

    Full Text Available Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF. Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR are the standard method for molecular detection of the dengue virus (DENV. Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA assays were developed to detect DENV1-4.Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4 to 241 (DENV1-3 RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal and in Bangkok (Thailand. In Kedougou, the RT-RPA was operated at an ambient temperature of 38 °C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31 and 100% (n=23, respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90 and 100%(n=41, respectively.During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations.

  13. Host suppression and bioinformatics for sequence-based characterization of unknown pathogens.

    Energy Technology Data Exchange (ETDEWEB)

    Branda, Steven S.; Lane, Todd W.; Misra, Milind; Meagher, Robert J.; Patel, Kamlesh D.; Kaiser, Julia N.

    2009-11-01

    Bioweapons and emerging infectious diseases pose formidable and growing threats to our national security. Rapid advances in biotechnology and the increasing efficiency of global transportation networks virtually guarantee that the United States will face potentially devastating infectious disease outbreaks caused by novel ('unknown') pathogens either intentionally or accidentally introduced into the population. Unfortunately, our nation's biodefense and public health infrastructure is primarily designed to handle previously characterized ('known') pathogens. While modern DNA assays can identify known pathogens quickly, identifying unknown pathogens currently depends upon slow, classical microbiological methods of isolation and culture that can take weeks to produce actionable information. In many scenarios that delay would be costly, in terms of casualties and economic damage; indeed, it can mean the difference between a manageable public health incident and a full-blown epidemic. To close this gap in our nation's biodefense capability, we will develop, validate, and optimize a system to extract nucleic acids from unknown pathogens present in clinical samples drawn from infected patients. This system will extract nucleic acids from a clinical sample, amplify pathogen and specific host response nucleic acid sequences. These sequences will then be suitable for ultra-high-throughput sequencing (UHTS) carried out by a third party. The data generated from UHTS will then be processed through a new data assimilation and Bioinformatic analysis pipeline that will allow us to characterize an unknown pathogen in hours to days instead of weeks to months. Our methods will require no a priori knowledge of the pathogen, and no isolation or culturing; therefore it will circumvent many of the major roadblocks confronting a clinical microbiologist or virologist when presented with an unknown or engineered pathogen.

  14. Parametric Amplification of Gravitational Fluctuations during Reheating

    International Nuclear Information System (INIS)

    Cosmological perturbations can undergo amplification by parametric resonance during preheating even on scales larger than the Hubble radius, without violating causality. A unified description of gravitational and matter fluctuations is crucial to determine the strength of the instability. To extract specific signatures of the oscillating inflaton field during reheating, it is essential to focus on a variable describing metric fluctuations which is constant in the standard analyses of inflation. For a massive inflaton without self-coupling, we find no additional growth of superhorizon modes during reheating beyond the usual predictions. For a massless self-coupled inflaton, there is a sub-Hubble scale resonance. copyright 1999 The American Physical Society

  15. Amplification Effects and Unconventional Monetary Policies

    Directory of Open Access Journals (Sweden)

    Cécile BASTIDON GILLES

    2012-02-01

    Full Text Available Global financial crises trigger off amplification effects, which allow relatively small shocks to propagate through the whole financial system. For this reason, the range of Central banks policies is now widening beyond conventional monetary policies and lending of last resort. The aim of this paper is to establish a rule for this practice. The model is based on the formalization of funding conditions in various types of markets. We conduct a comprehensive analysis of the “unconventional monetary policies”, and especially quantify government bonds purchases by the Central bank.

  16. Intramolecular derivatization of 2'-amino-pyrimidine modified RNA with functional groups that is compatible with re-amplification.

    OpenAIRE

    Kujau, M J; Wölfl, S

    1998-01-01

    To expand the scope of nucleic acid aptamers as a tool for precise molecular recognition, functional groups that are not naturally present in nucleic acid molecules are desired. For in vitro selection these new functional groups must be compatible with the selection process. The present method allows the introduction of succinimide activated side chains at internal amino groups of 2'-amino-pyrimidine-RNA in a combinatorial fashion that is compatible with enzymatic re-amplification.

  17. Amplification of fluorescence using collinear picosecond optical parametric amplification at degeneracy

    Institute of Scientific and Technical Information of China (English)

    Zhang Jing; Zhang Qiu-Lin; Jiang Man; Zhang Dong-Xiang; Feng Bao-Hua; Zhang Jing-Yuan

    2012-01-01

    We demonstrate the output characteristic of broadband parametric amplification of incoherent light pulses in a 355-nm pumped degenerate picosecond optical parametric amplification with either saturated or unsaturated amplification.The optical parametric amplifier is seeded by the fluorescence generated in a solution of pyridine-1 dye in ethanol.With the saturated amplification,we can obtain high energy incoherent light pulses,whose full widtth at half maximum bandwidth varies from 16 nm to 53 nm for the different phase matching angles near degeneracy.Moreover,the unsaturated bandwidth of the amplified pulses fits well to the calculated result at degeneracy.Selecting s-polarized fluorescence with a Glan-Taylor prism,the maximum bandwidth of the amplified fluorescence is found to be 59 nm for a purely s-polarized seed.The maximum output energy is 0.67 mJ for the optical parametric amplifier.By using an optical filter and compressor,the generated high energy incoherent light has great potential as the incoherent pump,signal or idler wave of a parametric down-conversion process,so that a wave with a high degree of coherence can be generated from an incoherent pump light.

  18. Multiplex allele-specific target amplification based on PCR suppression

    OpenAIRE

    Broude, Natalia E.; Zhang, Lingang; Woodward, Karen; Englert, David; Cantor, Charles R.

    2001-01-01

    We have developed a strategy for multiplex PCR based on PCR suppression. PCR suppression allows DNA target amplification with only one sequence-specific primer per target and a second primer that is common for all targets. Therefore, an n-plex PCR would require only n + 1 primers. We have demonstrated uniform, efficient amplification of targeted sequences in 14-plex PCR. The high specificity of suppression PCR also provides multiplexed amplification with allele specifi...

  19. Loss of KLF14 triggers centrosome amplification and tumorigenesis

    OpenAIRE

    Fan, Guangjian; Sun, Lianhui; Shan, Peipei; Zhang, Xianying; Huan, Jinliang; Li, Dali; Wang, Tingting; Wei, Tingting; Zhang, Xiaohong; Gu, Xiaoyang; Yao, Liangfang; Xuan, Yang; Hou, Zhaoyuan; Cui, Yongping; Cao, Liu

    2015-01-01

    Centrosome amplification is frequent in cancer, but the underlying mechanisms remain unclear. Here we report that disruption of the Kruppel-like factor 14 (KLF14) gene in mice causes centrosome amplification, aneuploidy and spontaneous tumorigenesis. Molecularly, KLF14 functions as a transcriptional repressor of Plk4, a polo-like kinase whose overexpression induces centrosome overduplication. Transient knockdown of KLF14 is sufficient to induce Plk4-directed centrosome amplification. Clinical...

  20. Comparison of sensor structures for the signal amplification of surface plasmon resonance immunoassay using enzyme precipitation

    Science.gov (United States)

    Yang, Chih-Tsung; Thierry, Benjamin

    2015-12-01

    Surface plasmon resonance (SPR) biosensing has been successfully applied for the label-free detection of a broad range of bioanalytes ranging from bacteria, cell, exosome, protein and nucleic acids. When it comes to the detection of small molecules or analytes found at low concentration, amplification schemes are desirable to enhance binding signals and in turn increase sensitivity. A number of SPR signal amplification schemes have been developed and validated; however, little effort has been devoted to understanding the effect of the SPR sensor structures on the amplification of binding signals and therefore on the overall sensing performance. The physical phenomenon of long-range SPR (LRSPR) relies on the propagation of coupled surface plasmonic waves on the opposite sides of a nanoscale-thick noble metal film suspended between two dielectrics with similar refractive indices. Importantly, as compared with commonly used conventional SPR (cSPR), LRSPR is not only characterized by a longer penetration depth of the plasmonic waves in the analyzed medium but also by a greater sensitivity to bulk refractive index changes. In this work, an immunoassay signal amplification platform based on horseradish peroxidase (HRP) catalyzed precipitation was utilized to investigate the sensing performance with regards to cSPR and LRSPR. The enzymatic precipitation of 3, 3'-diaminobenzidine tetrahydrochloride (DAB)/H2O2 was used to amplify SPR signals. The structure-function relationship of cSPR and LRSPR sensors is presented for both standard refractometric measurements and the enzymatic precipitation scheme. Experimental data shows that despite its inherent higher sensitivity to bulk refractive index changes and higher figure of merit, LRSPR was characterized by a lower angular sensitivity in the model enzymatic amplification scheme used here.

  1. Adaptation of Shift Sequence Based Method for High Number in Shifts Rostering Problem for Health Care Workers

    Directory of Open Access Journals (Sweden)

    Mindaugas Liogys

    2013-08-01

    Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts.Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases.Design/methodology/approach—Usually rostering problems are highly constrained. Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1.Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration.During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering problem

  2. Adaptation of Shift Sequence Based Method for High Number in Shifts Rostering Problem for Health Care Workers

    Directory of Open Access Journals (Sweden)

    Mindaugas Liogys

    2011-08-01

    Full Text Available Purpose—is to investigate a shift sequence-based approach efficiency then problem consisting of a high number of shifts. Research objectives:• Solve health care workers rostering problem using a shift sequence based method.• Measure its efficiency then number of shifts increases. Design/methodology/approach—Usually rostering problems are highly constrained.Constraints are classified to soft and hard constraints. Soft and hard constraints of the problem are additionally classified to: sequence constraints, schedule constraints and roster constraints. Sequence constraints are considered when constructing shift sequences. Schedule constraints are considered when constructing a schedule. Roster constraints are applied, then constructing overall solution, i.e. combining all schedules.Shift sequence based approach consists of two stages:• Shift sequences construction,• The construction of schedules.In the shift sequences construction stage, the shift sequences are constructed for each set of health care workers of different skill, considering sequence constraints. Shifts sequences are ranked by their penalties for easier retrieval in later stage.In schedules construction stage, schedules for each health care worker are constructed iteratively, using the shift sequences produced in stage 1. Shift sequence based method is an adaptive iterative method where health care workers who received the highest schedule penalties in the last iteration are scheduled first at the current iteration. During the roster construction, and after a schedule has been generated for the current health care worker, an improvement method based on an efficient greedy local search is carried out on the partial roster. It simply swaps any pair of shifts between two health care workers in the (partial roster, as long as the swaps satisfy hard constraints and decrease the roster penalty.Findings—Using shift sequence method for solving health care workers rostering

  3. Experimental noiseless linear amplification using weak measurements

    Science.gov (United States)

    Ho, Joseph; Boston, Allen; Palsson, Matthew; Pryde, Geoff

    2016-09-01

    The viability of quantum communication schemes rely on sending quantum states of light over long distances. However, transmission loss can degrade the signal strength, adding noise. Heralded noiseless amplification of a quantum signal can provide a solution by enabling longer direct transmission distances and by enabling entanglement distillation. The central idea of heralded noiseless amplification—a conditional modification of the probability distribution over photon number of an optical quantum state—is suggestive of a parallel with weak measurement: in a weak measurement, learning partial information about an observable leads to a conditional back-action of a commensurate size. Here we experimentally investigate the application of weak, or variable-strength, measurements to the task of heralded amplification, by using a quantum logic gate to weakly couple a small single-optical-mode quantum state (the signal) to an ancilla photon (the meter). The weak measurement is carried out by choosing the measurement basis of the meter photon and, by conditioning on the meter outcomes, the signal is amplified. We characterise the gain of the amplifier as a function of the measurement strength, and use interferometric methods to show that the operation preserves the coherence of the signal.

  4. Space Optical Communications Using Laser Beam Amplification

    Science.gov (United States)

    Agrawal, Govind

    2015-01-01

    The Space Optical Communications Using Laser Beam Amplification (SOCLBA) project will provide a capability to amplify a laser beam that is received in a modulating retro-reflector (MRR) located in a satellite in low Earth orbit. It will also improve the pointing procedure between Earth and spacecraft terminals. The technology uses laser arrays to strengthen the reflected laser beam from the spacecraft. The results of first year's work (2014) show amplification factors of 60 times the power of the signal beam. MMRs are mirrors that reflect light beams back to the source. In space optical communications, a high-powered laser interrogator beam is directed from the ground to a satellite. Within the satellite, the beam is redirected back to ground using the MMR. In the MMR, the beam passes through modulators, which encode a data signal onto the returning beam. MMRs can be used in small spacecraft for optical communications. The SOCLBA project is significant to NASA and small spacecraft due to its application to CubeSats for optical data transmission to ground stations, as well as possible application to spacecraft for optical data transmission.

  5. Optimization of noncollinear optical parametric amplification

    Science.gov (United States)

    Schimpf, D. N.; Rothardt, J.; Limpert, J.; Tünnermann, A.

    2007-02-01

    Noncollinearly phase-matched optical parametric amplifiers (NOPAs) - pumped with the green light of a frequency doubled Yb-doped fiber-amplifier system 1, 2 - permit convenient generation of ultrashort pulses in the visible (VIS) and near infrared (NIR) 3. The broad bandwidth of the parametric gain via the noncollinear pump configuration allows amplification of few-cycle optical pulses when seeded with a spectrally flat, re-compressible signal. The short pulses tunable over a wide region in the visible permit transcend of frontiers in physics and lifescience. For instance, the resulting high temporal resolution is of significance for many spectroscopic techniques. Furthermore, the high magnitudes of the peak-powers of the produced pulses allow research in high-field physics. To understand the demands of noncollinear optical parametric amplification using a fiber pump source, it is important to investigate this configuration in detail 4. An analysis provides not only insight into the parametric process but also determines an optimal choice of experimental parameters for the objective. Here, the intention is to design a configuration which yields the shortest possible temporal pulse. As a consequence of this analysis, the experimental setup could be optimized. A number of aspects of optical parametric amplifier performance have been treated analytically and computationally 5, but these do not fully cover the situation under consideration here.

  6. Magnetic Field Amplification in Young Galaxies

    CERN Document Server

    Schober, Jennifer; Klessen, Ralf S

    2013-01-01

    The Universe at present is highly magnetized, with fields of the order of a few 10^-5 G and coherence lengths larger than 10 kpc in typical galaxies like the Milky Way. We propose that the magnetic field was amplified to this values already during the formation and the early evolution of the galaxies. Turbulence in young galaxies is driven by accretion as well as by supernova (SN) explosions of the first generation of stars. The small-scale dynamo can convert the turbulent kinetic energy into magnetic energy and amplify very weak primordial magnetic seed fields on short timescales. The amplification takes place in two phases: in the kinematic phase the magnetic field grows exponentially, with the largest growth on the smallest non-resistive scale. In the following non-linear phase the magnetic energy is shifted towards larger scales until the dynamo saturates on the turbulent forcing scale. To describe the amplification of the magnetic field quantitatively we model the microphysics in the interstellar medium ...

  7. Compared the New Molecular Method for Rapid Detection of Avian Leukemia Virus by Using Denaturing High Performance Liquid Chromatography Combined with Nucleic Acid Amplification and Real-time PCR%PCR结合变性高效液相色谱法与荧光定量PCR法在检测禽白血病中的比较与应用

    Institute of Scientific and Technical Information of China (English)

    孙涛; 张太翔; 徐彪; 梁成珠; 朱来华; 岳志芹

    2011-01-01

    Compared the new molecular method for rapid detection of avian leukemia virus by using denaturing high performance liquid chromatography(DHPLC) combined with nucleic acid amplification and Real-time PCR in this study. According to the sequence of pol gene of ALV, one pair of primers and the TaqMan probe were designed by using Primer Premier 5. 0. The PCR fragment which was amplified by the primers were analysised by DHPLC and the results of Real-time PCR by the primers and the TaqMan probe. They all compared to normal chicken embryo allantoic fluid, duck plague virus(DPV),infectious bronchitis virus(IBV) ,goose parvovirus(GPV) ,avian influenza virus(H5Nl AIV),Newcastle disease virus(NDV), infectious bursal disease virus (IBDV) ,EDSV. There were tested to confirm the specificity of the PCR-DHPLC assay and no positive absorption peaks occurred. The detection limit of ALV AV228 by PCR-DHPLC was 3 pg,10 fold iower than the ordinary Realtime PCR. The results of detcting organ samples from the chickens were tested by PCR-DHPLC and Real-time PCR,showing 100% agreement.%本研究旨在比较PCR结合变性高效液相色谱技术(PCR-DHPLC)与荧光定量PCR (Real-time PCR)两种方法在检测禽白血病中的应用.根据禽白血病pol基因序列,设计1对引物和1条探针,利用引物进行禽白血病模板的RT-PCR扩增,产物经变性高效液相色谱上样处理;利用引物及探针进行荧光定量PCR扩增,结果与PCR-DHPLC进行比对.两种方法同时用正常鸡胚尿囊液、鸭瘟病毒、传染性支气管炎病毒、鹅细小病毒、H5N1亚型禽流感病毒、新城疫病毒、传染性法氏囊病毒、减蛋综合症病毒做特异性检测;以稀释成不同梯度的AV228毒株核酸做敏感性检测.试验结果表明PCR-DHPLC方法只对禽白血病病原有阳性扩增的吸收峰,Real-time PCR也只对禽白血病病原有阳性扩增,两法均对其他禽源病毒核酸无特异性扩增;PCR-DHPLC与Real-time PCR法

  8. Seismic Wave Amplification in 3D Alluvial Basins: 3D/1D Amplification Ratios from Fast Multipole BEM Simulations

    CERN Document Server

    Fajardo, Kristel C Meza; Chaillat, Stéphanie; Lenti, Luca

    2016-01-01

    In this work, we study seismic wave amplification in alluvial basins having 3D standard geometries through the Fast Multipole Boundary Element Method in the frequency domain. We investigate how much 3D amplification differs from the 1D (horizontal layering) case. Considering incident fields of plane harmonic waves, we examine the relationships between the amplification level and the most relevant physical parameters of the problem (impedance contrast, 3D aspect ratio, vertical and oblique incidence of plane waves). The FMBEM results show that the most important parameters for wave amplification are the impedance contrast and the so-called equivalent shape ratio. Using these two parameters, we derive simple rules to compute the fundamental frequency for various 3D basin shapes and the corresponding 3D/1D amplification factor for 5% damping. Effects on amplification due to 3D basin asymmetry are also studied and incorporated in the derived rules.

  9. HLA-B27 detection – comparison of genetic sequence-based method and flow cytometry assay

    OpenAIRE

    Skalska, Urszula; Kozakiewicz, Anna; Maśliński, Włodzimierz; Jurkowska, Monika

    2015-01-01

    Objectives The presence of human leukocyte antigen B27 (HLA-B27) is strongly associated with ankylosing spondylitis. HLA-B27 testing is routinely applied in the diagnosis of this disease. The aim of the present study was to compare two methods of HLA-B27 detection – a genetic sequence-based method and a flow cytometry assay. Material and methods Peripheral blood was obtained from 300 individuals with suspected spondyloarthropathy. Expression of HLA-B27 on the T cell surface was analysed by fl...

  10. Optofluidic analysis system for amplification-free, direct detection of Ebola infection

    Science.gov (United States)

    Cai, H.; Parks, J. W.; Wall, T. A.; Stott, M. A.; Stambaugh, A.; Alfson, K.; Griffiths, A.; Mathies, R. A.; Carrion, R.; Patterson, J. L.; Hawkins, A. R.; Schmidt, H.

    2015-09-01

    The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

  11. Amplification of Chirality through Self-Replication of Micellar Aggregates in Water

    KAUST Repository

    Bukhryakov, Konstantin V.

    2015-03-17

    We describe a system in which the self-replication of micellar aggregates results in a spontaneous amplification of chirality in the reaction products. In this system, amphiphiles are synthesized from two "clickable" fragments: a water-soluble "head" and a hydrophobic "tail". Under biphasic conditions, the reaction is autocatalytic, as aggregates facilitate the transfer of hydrophobic molecules to the aqueous phase. When chiral, partially enantioenriched surfactant heads are used, a strong nonlinear induction of chirality in the reaction products is observed. Preseeding the reaction mixture with an amphiphile of one chirality results in the amplification of this product and therefore information transfer between generations of self-replicating aggregates. Because our amphiphiles are capable of catalysis, information transfer, and self-assembly into bounded structures, they present a plausible model for prenucleic acid "lipid world" entities. © 2015 American Chemical Society.

  12. Signal Amplification of Bioassay Using Zinc Nanomaterials

    Science.gov (United States)

    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

  13. Broadening and Amplification of an Infrared Femtosecond Pulse for Optical Parametric Chirped-Pulse Amplification

    Institute of Scientific and Technical Information of China (English)

    WANG He-Lin; YANG Ai-Jun; LENG Yu-Xin

    2011-01-01

    A high-average-power diode-pumped narrowband regenerative chirped pulse amplifier is developed using the thin-rod Nd:YAG laser architecture for optical parametric chirped-pulse amplification (OPCPA).The effect of the etalons on the amplified pulse in the regenerative cavity is studied experimentally and theoretically.By inserting glass etalons of thickness 1 mm and 5 mm into the regenerative cavity,the pre-stretching pulse from an (O)ffner stretcher is further broadened to above 200ps,which matches the amplification windows of the signal pulses in OPCPA and is suitable for use as a pump source in the OPCPA system.The bandwidth of the amplified pulse is 1.5 nm,and an output energy of 2mJ is achieved at a repetition rate of 10 Hz.Optical parametric chirped pulse amplification (OPCPA)[1-4] has attracted a great deal of attention as the most promising technique for generating ultrashort ultrahigh-peak-power laser pulses because of its very broad gain bandwidth,negligible thermal load on the nonlinear crystal,and extremely high singlepass gain as compared to amplifiers based on laser gain media.For efficient amplification and high fidelity of dispersion compensation in OPCPA,a femtosecond seed pulse is first stretched to several tens of picoseconds with a bulk grating stretcher or a fiber stretcher.%A high-average-power diode-pumped narrowband regenerative chirped pulse amplifier is developed using the thin-rod Nd:YAG laser architecture for optical parametric chirped-pulse amplification (OPCPA). The effect of the etalons on the amplified pulse in the regenerative cavity is studied experimentally and theoretically. By inserting glass etalons of thickness 1 mm and 5 mm into the regenerative cavity, the pre-stretching pulse from an (O)finer stretcher is further broadened to above 200 ps, which matches the amplification windows of the signal pulses in OPCPA and is suitable for use as a pump source in the OPCPA system. The bandwidth of the amplified pulse is 1.5 nm, and an

  14. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  15. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

    Science.gov (United States)

    Littlejohn, Mathew D.; Tiplady, Kathryn; Fink, Tania A.; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G.; Harland, Chad; Scott, Andrew; Snell, Russell G.; Davis, Stephen R.; Spelman, Richard J.

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  16. Deep sequencing-based identification of small regulatory RNAs in Synechocystis sp. PCC 6803.

    Directory of Open Access Journals (Sweden)

    Wen Xu

    Full Text Available Synechocystis sp. PCC 6803 is a genetically tractable model organism for photosynthesis research. The genome of Synechocystis sp. PCC 6803 consists of a circular chromosome and seven plasmids. The importance of small regulatory RNAs (sRNAs as mediators of a number of cellular processes in bacteria has begun to be recognized. However, little is known regarding sRNAs in Synechocystis sp. PCC 6803. To provide a comprehensive overview of sRNAs in this model organism, the sRNAs of Synechocystis sp. PCC 6803 were analyzed using deep sequencing, and 7,951,189 reads were obtained. High quality mapping reads (6,127,890 were mapped onto the genome and assembled into 16,192 transcribed regions (clusters based on read overlap. A total number of 5211 putative sRNAs were revealed from the genome and the 4 megaplasmids, and 27 of these molecules, including four from plasmids, were confirmed by RT-PCR. In addition, possible target genes regulated by all of the putative sRNAs identified in this study were predicted by IntaRNA and analyzed for functional categorization and biological pathways, which provided evidence that sRNAs are indeed involved in many different metabolic pathways, including basic metabolic pathways, such as glycolysis/gluconeogenesis, the citrate cycle, fatty acid metabolism and adaptations to environmentally stress-induced changes. The information from this study provides a valuable reservoir for understanding the sRNA-mediated regulation of the complex physiology and metabolic processes of cyanobacteria.

  17. Magnetic field amplification in turbulent astrophysical plasmas

    CERN Document Server

    Federrath, Christoph

    2016-01-01

    Magnetic fields play an important role in astrophysical accretion discs, and in the interstellar and intergalactic medium. They drive jets, suppress fragmentation in star-forming clouds and can have a significant impact on the accretion rate of stars. However, the exact amplification mechanisms of cosmic magnetic fields remain relatively poorly understood. Here I start by reviewing recent advances in the numerical and theoretical modelling of the 'turbulent dynamo', which may explain the origin of galactic and inter-galactic magnetic fields. While dynamo action was previously investigated in great detail for incompressible plasmas, I here place particular emphasis on highly compressible astrophysical plasmas, which are characterised by strong density fluctuations and shocks, such as the interstellar medium. I find that dynamo action works not only in subsonic plasmas, but also in highly supersonic, compressible plasmas, as well as for low and high magnetic Prandtl numbers. I further present new numerical simu...

  18. Anisotropic metamaterials with simultaneous attenuation and amplification

    CERN Document Server

    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.

  19. Amplification sans bruit d'images optiques

    Science.gov (United States)

    Gigan, S.; Delaubert, V.; Lopez, L.; Treps, N.; Maitre, A.; Fabre, C.

    2004-11-01

    Nous utilisons un Oscillateur Paramétrique Optique (OPO) pompé sous le seuil dans le but d'amplifier une image multimode transverse sans dégradation du rapport signal à bruit. Le dispositif expérimental met en œuvre un OPO de type II triplement résonant et semi-confocal pour le faisceau amplifié. L'existence d'effets quantiques lors de l'amplification multimode dans un tel dispositif a été montrée expérimentalement. Plus généralement, ceci nous a amené à étudier les propriétés quantiques transverses des faisceaux lumineux amplifiés. Une telle étude peut trouver des applications non seulement en imagerie, mais également dans le traitement quantique de l'information.

  20. Strengthening weak value amplification with recycled photons

    CERN Document Server

    Dressel, Justin; Jordan, Andrew N; Graham, Trent M; Kwiat, Paul G

    2013-01-01

    We consider the use of cyclic weak measurements to improve the sensitivity of weak-value amplification precision measurement schemes. Previous weak-value experiments have used only a small fraction of events, while discarding the rest through the process of "post-selection". We extend this idea by considering recycling of events which are typically unused in a weak measurement. Here we treat a sequence of polarized laser pulses effectively trapped inside an interferometer using a Pockels cell and polarization optics. In principle, all photons can be post-selected, which will improve the measurement sensitivity. We first provide a qualitative argument for the expected improvements from recycling photons, followed by the exact result for the recycling of collimated beam pulses, and numerical calculations for diverging beams. We show that beam degradation effects can be mitigated via profile flipping or Zeno reshaping. The main advantage of such a recycling scheme is an effective power increase, while maintainin...

  1. Dispersion compensation in chirped pulse amplification systems

    Science.gov (United States)

    Bayramian, Andrew James; Molander, William A.

    2014-07-15

    A chirped pulse amplification system includes a laser source providing an input laser pulse along an optical path. The input laser pulse is characterized by a first temporal duration. The system also includes a multi-pass pulse stretcher disposed along the optical path. The multi-pass pulse stretcher includes a first set of mirrors operable to receive input light in a first plane and output light in a second plane parallel to the first plane and a first diffraction grating. The pulse stretcher also includes a second set of mirrors operable to receive light diffracted from the first diffraction grating and a second diffraction grating. The pulse stretcher further includes a reflective element operable to reflect light diffracted from the second diffraction grating. The system further includes an amplifier, a pulse compressor, and a passive dispersion compensator disposed along the optical path.

  2. Beyond the diffraction limit via optical amplification

    CERN Document Server

    Kellerer, Aglae N

    2016-01-01

    In a previous article we suggested a method to overcome the diffraction limit behind a telescope. We refer to theory and recent numerical simulations, and test whether it is indeed possible to use photon amplification to enhance the angular resolution of a telescope or a microscope beyond the diffraction limit. An essential addition is the proposal to select events with above-average ratio of stimulated to spontaneous photons. We find that the diffraction limit of a telescope is surpassed by a factor ten for an amplifier gain of 200, if the analysis is restricted to a tenth of the incoming astronomical photons. A gain of 70 is sufficient with a hundredth of the photons.

  3. Short-Pulse Amplification by Strongly-Coupled Brillouin Scattering

    CERN Document Server

    Edwards, Matthew R; Mikhailova, Julia M; Fisch, Nathaniel J

    2016-01-01

    We examine the feasibility of strongly-coupled stimulated Brillouin scattering as a mechanism for the plasma-based amplification of sub-picosecond pulses. In particular, we use fluid theory and particle-in-cell simulations to compare the relative advantages of Raman and Brillouin amplification over a broad range of achievable parameters.

  4. A Theoretical Evaluation of Optical Parametric Amplification in BBO Crystal

    Institute of Scientific and Technical Information of China (English)

    邵敏; 薛绍林; 林尊琪

    2005-01-01

    The noncollinear optical parametric amplification in BBO crystal is theoretically investigated. The phase matching angle, gain bandwidth, optimal noncollinear angle and conversion efficiency for both type-Ⅰ and type-Ⅱ BBO are simulated. The numerical simulation results are important to the practical optical parametric amplification experiments with BBO crystal.

  5. The Quantum Theory of Optical Parametric Amplification

    Science.gov (United States)

    Hussain, N. A.

    Available from UMI in association with The British Library. Requires signed TDF. The aim of this thesis is to investigate the effect of parametric amplification on various forms of light. In particular we shall consider number and coherent states, but many of the calculations hold for those states whose operators satisfy the properties, = = ==0 e.g. chaotic light. The first chapter lays down the fundamental preliminaries necessary for our calculations and reviews linear amplifier theory. We consider the phase sensitive and insensitive forms of amplifiers modelling the former on the degenerate parametric amplifier and the latter on the non-degenerate and inverted population amplifiers. Chapter 2 deals with balanced homodyne detection of a narrow band coherent state before and after degenerate parametric amplification. In chapter 3 we consider a continuous mode number state produced by atomic emission and parametrically amplified using the formalism of Collett and Gardiner. We give general results for the output flux intensity and also consider the simpler case where the atomic decay rate is much smaller than the parametric cavity decay rate. Also we consider the degree of second order coherence using this simplified theory. Chapters 4 and 5 consider the double amplifier interferometer, using single and continuous mode theories, and enable us to determine the form of amplifier which produces the best visibility and hence lowest noise figures. The travelling-wave parametric amplifier is discussed in chapter 6 and is contrasted with the cavity parametric amplifier discussed in chapters 1 and 2. Finally we consider the much contemplated idea of using amplifiers to boost signals in fibre optic transmission lines using our model of the parametric amplifier and examining the degradation of the signal-to-noise ratio. We consider both coherent and squeezed inputs and our results hold for both cavity and travelling -wave amplifiers.

  6. CLUSS: Clustering of protein sequences based on a new similarity measure

    Directory of Open Access Journals (Sweden)

    Brzezinski Ryszard

    2007-08-01

    Full Text Available Abstract Background The rapid burgeoning of available protein data makes the use of clustering within families of proteins increasingly important. The challenge is to identify subfamilies of evolutionarily related sequences. This identification reveals phylogenetic relationships, which provide prior knowledge to help researchers understand biological phenomena. A good evolutionary model is essential to achieve a clustering that reflects the biological reality, and an accurate estimate of protein sequence similarity is crucial to the building of such a model. Most existing algorithms estimate this similarity using techniques that are not necessarily biologically plausible, especially for hard-to-align sequences such as proteins with different domain structures, which cause many difficulties for the alignment-dependent algorithms. In this paper, we propose a novel similarity measure based on matching amino acid subsequences. This measure, named SMS for Substitution Matching Similarity, is especially designed for application to non-aligned protein sequences. It allows us to develop a new alignment-free algorithm, named CLUSS, for clustering protein families. To the best of our knowledge, this is the first alignment-free algorithm for clustering protein sequences. Unlike other clustering algorithms, CLUSS is effective on both alignable and non-alignable protein families. In the rest of the paper, we use the term "phylogenetic" in the sense of "relatedness of biological functions". Results To show the effectiveness of CLUSS, we performed an extensive clustering on COG database. To demonstrate its ability to deal with hard-to-align sequences, we tested it on the GH2 family. In addition, we carried out experimental comparisons of CLUSS with a variety of mainstream algorithms. These comparisons were made on hard-to-align and easy-to-align protein sequences. The results of these experiments show the superiority of CLUSS in yielding clusters of proteins

  7. A conversational system for the computer analysis of nucleic acid sequences.

    OpenAIRE

    Sege, R; Söll, D.; Ruddle, F H; Queen, C

    1981-01-01

    We present a conversational system for the computer analysis of nucleic acid and protein sequences based on the well-known Queen and Korn program (1). The system can be used by persons with only minimal knowledge of computers.

  8. Optimization of dynamic economic dispatch with valve-point effect using chaotic sequence based differential evolution algorithms

    International Nuclear Information System (INIS)

    A chaotic sequence based differential evolution (DE) approach for solving the dynamic economic dispatch problem (DEDP) with valve-point effect is presented in this paper. The proposed method combines the DE algorithm with the local search technique to improve the performance of the algorithm. DE is the main optimizer, while an approximated model for local search is applied to fine tune in the solution of the DE run. To accelerate convergence of DE, a series of constraints handling rules are adopted. An initial population obtained by using chaotic sequence exerts optimal performance of the proposed algorithm. The combined algorithm is validated for two test systems consisting of 10 and 13 thermal units whose incremental fuel cost function takes into account the valve-point loading effects. The proposed combined method outperforms other algorithms reported in literatures for DEDP considering valve-point effects.

  9. Rapid detection of Brucella spp. using loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Chen, Shouyi; Li, Xunde; Li, Juntao; Atwill, Edward R

    2013-01-01

    Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Livestock that are most vulnerable to brucellosis include cattle, goats, and pigs. Brucella spp. cause serious health problems to humans and animals and economic losses to the livestock industry. Traditional methods for detection of Brucella spp. take 48-72 h (Kumar et al., J Commun Dis 29:131-137, 1997; Barrouin-Melo et al., Res Vet Sci 83:340-346, 2007) that do not meet the food industry's need of rapid detection. Therefore, there is an urgent need of fast, specific, sensitive, and inexpensive method for diagnosing of Brucella spp. Loop-mediated isothermal amplification (LAMP) is a method to amplify nucleic acid at constant temperatures. Amplification can be detected by visual detection, fluorescent stain, turbidity, and electrophoresis. We targeted at the Brucella-specific gene omp25 and designed LAMP primers for detection of Brucella spp. Amplification of DNA with Bst DNA polymerase can be completed at 65 °C in 60 min. Amplified products can be detected by SYBR Green I stain and 2.0% agarose gel electrophoresis. The LAMP method is feasible for detection of Brucella spp. from blood and milk samples.

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

    Science.gov (United States)

    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.

  11. Development of a Loop-Mediated Isothermal Amplification Assay for Porcine Circovirus Type 2

    Institute of Scientific and Technical Information of China (English)

    Ye-bing Liu; Lei Zhang; Qin-hong Xue; Yi-bao Ning; Zhi-gang Zhang

    2011-01-01

    In this study,the loop-mediated isothermal amplification(LAMP)method was used to develop a rapid and simple detection system for porcine circovirus type 2(PCV2).According to the PCV2 sequences published in GenBank,multiple LAMP primers were designed targeting conserved sequences of PCV2.Using the DNA extracted from PCV2 isolates HUN-09 and SD-09 as the template,LAMP reactions in a PCV2 LAMP system was performed,the amplification products were detected by adding SYBR Green I and could be observed directly by the naked eye.The results showed highly-efficient and specific amplification in 30 min at 63℃ with a LAMP real-time turbidimeter.Furthermore,PCV2 DNA templates,with a detection limit of 5.5×10-5ng of nucleic acid,indicated that this assay was highly sensitive.The results obtained with the naked eye after SYBR Green I staining were consistent with those detected by the real-time turbidimeter,showing the potential simplicity of interpretation of the assay results.The LAMP assay appeared to have greater accuracy than PCR and virus isolation for the analysis of 18 clinical samples.In addition it offers higher specificity and sensitivity,shorter reaction times and simpler procedures than the currently available methods of PCV2 detection.It is therefore a promising tool for the effective and efficient detection of PCV2.

  12. Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

    Directory of Open Access Journals (Sweden)

    Shelly Sehgal

    2015-01-01

    Full Text Available The present investigation was aimed at understanding the molecular mechanism of gene amplification. Interplay of fragile sites in promoting gene amplification was also elucidated. The amplification promoting sequences were chosen from the Saccharomyces cerevisiae ARS, 5S rRNA regions of Plantago ovata and P. lagopus, proposed sites of replication pausing at Ste20 gene locus of S. cerevisiae, and the bend DNA sequences within fragile site FRA11A in humans. The gene amplification assays showed that plasmid bearing APS from yeast and human beings led to enhanced protein concentration as compared to the wild type. Both the in silico and in vitro analyses were pointed out at the strong bending potential of these APS. In addition, high mitotic stability and presence of TTTT repeats and SAR amongst these sequences encourage gene amplification. Phylogenetic analysis of S. cerevisiae ARS was also conducted. The combinatorial power of different aspects of APS analyzed in the present investigation was harnessed to reach a consensus about the factors which stimulate gene expression, in presence of these sequences. It was concluded that the mechanism of gene amplification was that AT rich tracts present in fragile sites of yeast serve as binding sites for MAR/SAR and DNA unwinding elements. The DNA protein interactions necessary for ORC activation are facilitated by DNA bending. These specific bindings at ORC promote repeated rounds of DNA replication leading to gene amplification.

  13. A novel modification of real-time AS-qPCR by using locked nucleic acid-modified oligonucleotide probe as wild type allele amplification blockers for quantitative detection of the JAK2 V617F mutation%评价AS-LNA-qPCR法检测JAK2 V617F突变率的临床应用价值

    Institute of Scientific and Technical Information of China (English)

    邵冬华; 梁国威; 何美琳; 曹清芸

    2013-01-01

    Objective To develop a novel real-time PCR for sensitively quantitative detection of JAK2 V617F allele burden in peripheral blood.Methods Based on the real-time allele-specific PCR (AS-qPCR),the locked nucleic acid (LNA)-modified oligonucleotide probe was used for selectively blocking amplification of wild-type alleles in AS-qPCR,and then a novel AS-LNA-qPCR method was established.The percentages of sample JAK2 V617F alleles were directly calculated by its threshold cycle (Ct) values according to the standard curve which generated by JAK2 V617F alleles with its Ct values.We validated intra-and inter-assay variability for quantifying JAK2 V617F.We also assayed 623 apparent healthy donors by our method to validate its clinical application value.Results The quantitative lower limit of this method for JAK2 V617F was 0.01%,and the intra-and inter-assay average variability for quantifying percentage of JAK2 V617F in total DNA was 6.3% and 8.6%,respectively.Nineteen JAK2 V617F-positive individuals were identified using AS-LNA-qPCR in blood of 623 apparently healthy donors,and the range of percentages of JAK2 V617F alleles were 0.01%-5.49%.Conclusion The AS-LNA-qPCR with highly sensitive and reproducible quantification of JAK2 V617F mutant burden can be used clinically for diagnosis as well as evaluation of disease prognosis and efficacy of therapy in patients with myeloproliferative neoplasms.%目的 建立一种定量检测外周血细胞酪氨酸激酶2(JAK2)基因V617F突变率的等位基因特异性实时荧光定量PCR(AS-qPCR)方法.方法 在AS-qPCR基础上,引入1条锁核酸(LNA)修饰的寡核苷酸探针,用以选择性抑制AS-qPCR中突变引物对野生等位基因的非特异性扩增,定量检测JAK2 V617F突变率,称之为AS-LNA-qPCR法.通过AS-LNA-qPCR法测定样本的循环阈值(Ct值),根据AS-LNA-qPCR法检测不同JAK2 V617F突变率标准品的Ct值,绘制标准曲线,根据标准曲线直接获得检测样本中JAK2 V617F突变率.

  14. 一步核酸扩增仪术中诊断乳腺癌前哨淋巴结转移的前瞻性、多中心临床观察%Prospective multi-center study of one-step nucleic acid amplification assay for the detection of sentinel lymph nodes metastases in breast cancer patients

    Institute of Scientific and Technical Information of China (English)

    王永胜; 欧阳涛; 吴炅; 刘艳辉; 曹旭晨; 孙晓; 付丽; 廖宁; 杨文涛

    2013-01-01

    Objective To evaluate the roles of Sysmex RD100i one-step nucleic acid amplification (OSNA) assay in the intraoperative assessments of breast cancer sentinel lymph nodes (SLNs).Methods A total of 552 consecutive prospective patients were enrolled from five centers nationwide from February to December 2010.And SLNs were sliced into alternating 2 mm blocks.The odd blocks were tested by the OSNA assay intraoperatively and the even ones assessed by postoperative histology.In addition,intraoperative histological assessments were performed on the even blocks of 211 patients by frozen section and all blocks by touch imprint cytology.Results A total of 1188 SLNs were removed.The mean turnaround time of the assay was 37.3 min.Thcrc was no significant difference of turnaround time at each center (P =0.074).As compared to postoperative histology,the overall performance of the assay had an accuracy of 91.4% (1086/1188),a sensitivity of 83.7% (159/190) and a specificity of 92.9% (927/998).The sensitivity of the assay was higher than frozen section (77.6% (59/76) vs 69.7% (53/76),P =0.286) and was significantly higher than touch imprint cytology (83.6% (158/189) vs 76.2% (144/189),P =0.044).For nodes with micro-metastases,the sensitivity of the assay was higher than frozen section (8/17 vs 4/17,P =0.289) and was significantly higher than touch imprint cytology (62.5% (30/48) vs 35.4% (17/48),P = 0.007).Conclusion As an accurate and rapid intraoperative assay for assessing breast SLNs,the OSNA assay may replace frozen section and touch imprint cytology for clinical applications.%目的 评估应用一步核酸扩增(OSNA)技术进行乳腺癌前哨淋巴结(SLN)术中检测诊断的价值.方法 共入组2010年2至12月全国5个乳腺病中心的552例原发性乳腺癌患者,术中将SLN根据其质量及短轴长度进行切分后,行OSNA检测和印片细胞学检测,术后行逐层切片病理检测.另外,211例患者术中同时行快速冰

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

    Directory of Open Access Journals (Sweden)

    Kuntal Mukherjee

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

  16. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    Science.gov (United States)

    Cary, Robert E.

    2015-12-08

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Shichu Huang

    Full Text Available 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.

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

    Science.gov (United States)

    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

  20. Complementary weak-value amplification with concatenated postselections

    CERN Document Server

    Viza, Gerardo I; Liu, Wei-Tao; Howell, John C

    2016-01-01

    We measure a transverse momentum kick in a Sagnac interferometer using weak-value amplification with two postselections. The first postselection is controlled by a polarization dependent phase mismatch between both paths of a Sagnac interferometer and the second postselection is controlled by a polarizer at the exit port. By monitoring the darkport of the interferometer, we study the complementary amplification of the concatenated postselections, where the polarization extinction ratio is greater than the contrast of the spatial interference. In this case, we find an improvement in the amplification of the signal of interest by introducing a second postselection to the system.

  1. Amplification of Spin Waves by Thermal Spin-Transfer Torque

    Science.gov (United States)

    Padrón-Hernández, E.; Azevedo, A.; Rezende, S. M.

    2011-11-01

    We observe amplification of spin-wave packets propagating along a film of single-crystal yttrium iron garnet subject to a transverse temperature gradient. The spin waves are excited and detected with standard techniques used in magnetostatic microwave delay lines in the 1-2 GHz frequency range. The amplification is attributed to the action of a thermal spin-transfer torque acting on the magnetization that opposes the relaxation and which is created by spin currents generated through the spin-Seebeck effect. The experimental data are interpreted with a spin-wave model that gives an amplification gain in very good agreement with the data.

  2. Amplification and chromosomal dispersion of human endogenous retroviral sequences

    International Nuclear Information System (INIS)

    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

  3. PCR amplification on microarrays of gel immobilized oligonucleotides

    Science.gov (United States)

    Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

    2003-11-04

    The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

  4. Thermal amplification of field-correlation harvesting

    CERN Document Server

    Brown, Eric G

    2013-01-01

    We study the harvesting of quantum and classical correlations from a hot scalar field in a periodic cavity by a pair of spatially separated oscillator-detectors. Specifically, we utilize non-perturbative and exact (non-numerical) techniques to solve for the evolution of the detectors-field system and then we examine how the entanglement, Gaussian quantum discord, and mutual information obtained by the detectors change with the temperature of the field. While (as expected) the harvested entanglement rapidly decays to zero as temperature is increased, we find remarkably that both the mutual information and the discord can actually be increased by multiple orders of magnitude via increasing the temperature. We go on to explain this phenomenon by taking advantage of the translational invariance of the field and use this to make accurate predictions of the behavior of thermal amplification; by this we also introduce a new perspective on field-correlation harvesting that we feel is worthy of consideration in its ow...

  5. Small Sample Whole-Genome Amplification

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. Local Runup Amplification By Resonant Wave Interactions

    CERN Document Server

    Stefanakis, Themistoklis; Dutykh, Denys

    2011-01-01

    Until now the analysis of long wave runup on a plane beach has been focused on finding its maximum value, failing to capture the existence of resonant regimes. One-dimensional numerical simulations in the framework of the Nonlinear Shallow Water Equations (NSWE) are used to investigate the Boundary Value Problem (BVP) for plane and non-trivial beaches. Monochromatic waves, as well as virtual wave-gage recordings from real tsunami simulations, are used as forcing conditions to the BVP. Resonant phenomena between the incident wavelength and the beach slope are found to occur, which result in enhanced runup of non-leading waves. The evolution of energy reveals the existence of a quasi-periodic state for the case of sinusoidal waves, the energy level of which, as well as the time required to reach that state, depend on the incident wavelength for a given beach slope. Dispersion is found to slightly reduce the value of maximum runup, but not to change the overall picture. Runup amplification occurs for both leadin...

  7. AGAPE Andromeda Gravitational Amplification Pixel Experiment

    CERN Document Server

    Ansari, R; Baillon, Paul; Bouquet, A; Coupinot, G; Coutures, C; Ghesquière, C; Giraud-Héraud, Yannick; Gondolo, P; Hecquet, J; Kaplan, J; Le Du, Y; Melchior, A L; Moniez, M; Picat, J P; Soucail, G

    1999-01-01

    The aim of the AGAPE (Andromeda Gravitational Amplification Pixel Experiment), experiment which has been first proposed in June 1992 is to examine the distribution of massive astrophysical compact halo objects ((MACHO's) which possibly are in the galactic haloes and which could account for the missing dark matter. Those objects have a mass which is a fraction of solar mass and could be detected by gravitational microlensing: the light of a star is amplified when a MACHO is crossing its line of sight from the earth. This technique has been proposed by Paczy\\'nski in 1986. The AGAPE collaboration applies this technique in an original way by using, as target stars, the stars of another galaxy without resolving them. The recent progresses in photometry with CCD allow now to see tiny variations of the surface brightness of a galaxy like M~31. Those tiny variations can be the result of a single microlensing event on the background stars contributing to the surface brightness. The AGAPE collaboration has now cumulat...

  8. A PCR amplification method without DNA extraction.

    Science.gov (United States)

    Li, Hongwei; Xu, Haiyue; Zhao, Chunjiang; Sulaiman, Yiming; Wu, Changxin

    2011-02-01

    To develop a simple and inexpensive method for direct PCR amplification of animal DNA from tissues, we optimized different components and their concentration in lysis buffer systems. Finally, we acquired the optimized buffer system composed of 10 mmol tris(hydroxymethyl)aminomethane (Tris)-Cl (pH 8.0), 2 mmol ethylene diamine tetraacetic (EDTA) (pH 8.0), 0.2 mol NaCl and 200 μg/mL Proteinase K. Interestingly, the optimized buffer is also very effective when working with common human sample types, including blood, buccal cells and hair. The direct PCR method requires fewer reagents (Tris-Cl, EDTA, Protease K and NaCl) and less incubation time (only 35 min). The cost of treating every sample is less than $0.02, and all steps can be completed on a thermal cycler in a 96-well format. So, the proposed method will significantly improve high-throughput PCR-based molecular assays in animal systems and in common human sample types.

  9. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones.

    Science.gov (United States)

    Rodriguez-Manzano, Jesus; Karymov, Mikhail A; Begolo, Stefano; Selck, David A; Zhukov, Dmitriy V; Jue, Erik; Ismagilov, Rustem F

    2016-03-22

    Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests. PMID:26900709

  10. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones.

    Science.gov (United States)

    Rodriguez-Manzano, Jesus; Karymov, Mikhail A; Begolo, Stefano; Selck, David A; Zhukov, Dmitriy V; Jue, Erik; Ismagilov, Rustem F

    2016-03-22

    Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests.

  11. Targeting helicase-dependent amplification products with an electrochemical genosensor for reliable and sensitive screening of genetically modified organisms.

    Science.gov (United States)

    Moura-Melo, Suely; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Dos Santos Junior, J Ribeiro; da Silva Fonseca, Rosana A; Lobo-Castañón, Maria Jesús

    2015-08-18

    Cultivation of genetically modified organisms (GMOs) and their use in food and feed is constantly expanding; thus, the question of informing consumers about their presence in food has proven of significant interest. The development of sensitive, rapid, robust, and reliable methods for the detection of GMOs is crucial for proper food labeling. In response, we have experimentally characterized the helicase-dependent isothermal amplification (HDA) and sequence-specific detection of a transgene from the Cauliflower Mosaic Virus 35S Promoter (CaMV35S), inserted into most transgenic plants. HDA is one of the simplest approaches for DNA amplification, emulating the bacterial replication machinery, and resembling PCR but under isothermal conditions. However, it usually suffers from a lack of selectivity, which is due to the accumulation of spurious amplification products. To improve the selectivity of HDA, which makes the detection of amplification products more reliable, we have developed an electrochemical platform targeting the central sequence of HDA copies of the transgene. A binary monolayer architecture is built onto a thin gold film where, upon the formation of perfect nucleic acid duplexes with the amplification products, these are enzyme-labeled and electrochemically transduced. The resulting combined system increases genosensor detectability up to 10(6)-fold, allowing Yes/No detection of GMOs with a limit of detection of ∼30 copies of the CaMV35S genomic DNA. A set of general utility rules in the design of genosensors for detection of HDA amplicons, which may assist in the development of point-of-care tests, is also included. The method provides a versatile tool for detecting nucleic acids with extremely low abundance not only for food safety control but also in the diagnostics and environmental control areas.

  12. Generation of recombinant pestiviruses using a full genome amplification strategy

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse;

    Aim Complete genome amplification of viral RNA provides a new tool for generation of modified pestiviruses. We have recently reported a full genome amplification strategy for direct recovery of infectious pestivirus (Rasmussen et al., 2008). This comprised rescue of BDV strain “Gifhorn” from a full......-length RT-PCR amplicon demonstrating that long RT-PCR can be used for direct generation of an infectious pestivirus. The strategy is not limited to amplification of BDV “Gifhorn”, but can be further utilized for amplification of a diverse selection of pestivirus strains and for the generation of modified...... of an existing infectious clone. The long RT-PCR strategy significantly simplifies and streamlines the workflow and facilitates generation of new modified pestiviruses and also allows direct full-length sequence analysis. References Rasmussen et al., J. Virol. Methods 149(2), 330 (2008)....

  13. Nonlinear Zel'dovich effect: Parametric amplification from medium rotation

    CERN Document Server

    Faccio, Daniele

    2016-01-01

    The interaction of light with rotating media has attracted recent interest for both fundamental and applied studies including rotational Doppler shift measurements. It is also possible to obtain amplification through the scattering of light with orbital angular momentum from a rotating and absorbing cylinder, as proposed by Zel'dovich more than 40 years ago. This amplification mechanism has never been observed experimentally yet has connections to other fields such as Penrose superradiance in rotating black holes. Here we propose a nonlinear optics system whereby incident light carrying orbital angular momentum drives parametric interaction in a rotating medium. The crystal rotation is shown to take the phase-mismatched parametric interaction with negligible energy exchange at zero rotation to amplification for sufficiently large rotation rates. The amplification is shown to result from breaking of anti-PT symmetry induced by the medium rotation.

  14. Isothermal DNA amplification strategies for duplex microorganism detection.

    Science.gov (United States)

    Santiago-Felipe, Sara; Tortajada-Genaro, Luis Antonio; Morais, Sergi; Puchades, Rosa; Maquieira, Ángel

    2015-05-01

    A valid solution for micro-analytical systems is the selection of a compatible amplification reaction with a simple, highly-integrated efficient design that allows the detection of multiple genomic targets. Two approaches under isothermal conditions are presented: recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA). Both methods were applied to a duplex assay specific for Salmonella spp. and Cronobacter spp., with excellent amplification yields (0.2-8.6 · 10(8) fold). The proposed approaches were successfully compared to conventional PCR and tested for the milk sample analysis as a microarray format on a compact disc (support and driver). Satisfactory results were obtained in terms of resistance to inhibition, selectivity, sensitivity (10(1)-10(2)CFU/mL) and reproducibility (below 12.5%). The methods studied are efficient and cost-effective, with a high potential to automate microorganisms detection by integrated analytical systems working at a constant low temperature.

  15. Ultrabroadband noncollinear optical parametric amplification with LBO crystal.

    Science.gov (United States)

    Zhao, Baozhen; Jiang, Yongliang; Sueda, Keiich; Miyanaga, Noriaki; Kobayashi, Takayoshi

    2008-11-10

    Ultrabroadband visible noncollinear optical parametric amplification (NOPA) was achieved in an LBO crystal, with a continuum seed pulse generated from a sapphire plate. The spectral bandwidth of the amplified visible pulse was about 200 nm, which can support sub-5 fs pulse amplification. An amplified output of 0.21 microJ with an average gain of about 210 was achieved. This provides, to the best of our knowledge, the first-time demonstration of such broadband amplification with a biaxial nonlinear optical crystal. Both the simulation and experimental results indicate that the LBO has a great potential as nonlinear medium in power amplifier for TW to PW noncollinear optical parametric chirped pulse amplification (NOPCPA) systems. PMID:19581976

  16. Pulse Distortion in Saturated Fiber Optical Parametric Chirped Pulse Amplification

    OpenAIRE

    Lali-Dastjerdi, Zohreh; Da Ros, Francesco; Rottwitt, Karsten; Galili, Michael; Peucheret, Christophe

    2012-01-01

    Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation.

  17. Structural Determinants of the Capacity of Heparin to Inhibit the Formation of the Human Amplification C3 Convertase

    OpenAIRE

    Kazatchkine, Michel D.; Fearon, Douglas T.; Metcalfe, Dean D.; Rosenberg, Robert D.; Austen, K. Frank

    1981-01-01

    The ability of heparin glycosaminoglycan to prevent formation of the properdin-stabilized amplification C3 convertase is independent of antithrombin binding activity and requires substitution of the amino sugar and a degree of oxygen (O)-sulfation which could be on the uronic acid or the amino sugar. Preparations of heparin glycosaminoglycan isolated by different techniques from different species (rat, human, and porcine) exhibited an equivalent capacity to inhibit generation of the amplifica...

  18. Fingerprinting Internet DNS Amplification DDoS Activities

    OpenAIRE

    Fachkha, Claude; Bou-Harb, Elias; Debbabi, Mourad

    2013-01-01

    This work proposes a novel approach to infer and characterize Internet-scale DNS amplification DDoS attacks by leveraging the darknet space. Complementary to the pioneer work on inferring Distributed Denial of Service (DDoS) activities using darknet, this work shows that we can extract DDoS activities without relying on backscattered analysis. The aim of this work is to extract cyber security intelligence related to DNS Amplification DDoS activities such as detection period, attack duration, ...

  19. Measurement-Based Noiseless Linear Amplification for Quantum Communication

    OpenAIRE

    Chrzanowski, Helen M.; Walk, Nathan; Assad, Syed M.; Janousek, Jiri; Hosseini, Sara; Ralph, Timothy C.; Symul, Thomas; Lam, Ping Koy

    2014-01-01

    Entanglement distillation is an indispensable ingredient in extended quantum communication networks. Distillation protocols are necessarily non-deterministic and require advanced experimental techniques such as noiseless amplification. Recently it was shown that the benefits of noiseless amplification could be extracted by performing a post-selective filtering of the measurement record to improve the performance of quantum key distribution. We apply this protocol to entanglement degraded by t...

  20. On the amplification of acoustic phonons in carbon nanotube

    OpenAIRE

    Dompreh, K. A.; Mensah, N. G.; Sakyi-Arthur, D.; Mensah, S. Y.

    2016-01-01

    We present a theoretical study of acoustic phonons amplification in Carbon Nanotubes (CNT). The phenomenon is via Cerenkov emission (CE) of acoustic phonons using intraband transitions proposed by Mensah et. al.,~\\cite{1} in Semiconductor Superlattices (SSL) and confirmed in ~\\cite{2}. From this, an asymmetric graph of $\\Gamma^{CNT}$ on $\\frac{V_d}{V_s}$ and $\\Omega\\tau$ were obtained where amplification ($\\Gamma_{amp}^{CNT}$) $>>$ absorption ($\\Gamma_{abs}^{CNT}$). The ratio, $\\frac{\\vert \\G...

  1. Engineering targeted chromosomal amplifications in human breast epithelial cells.

    Science.gov (United States)

    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.

  2. Aerosol Lidar for the Relative Backscatter Amplification Measurements

    Science.gov (United States)

    Razenkov, Igor A.; Banakh, Victor A.; Nadeev, Alexander I.

    2016-06-01

    Backscatter amplification presents only in a turbulent atmosphere, when the laser beam is propagates twice through the same inhomogeneities. We proposed technical solution to detect backscatter amplification. An aerosol micro pulse lidar with a beam expansion via receiving telescope was built to study this effect. Our system allows simultaneous detection of two returns from the same scattering volume: exactly on the axis of the laser beam and off the axis.

  3. Methods for microbial DNA extraction from soil for PCR amplification

    OpenAIRE

    Yeates C; Gillings, MR; Davison AD; Altavilla N; Veal DA

    1998-01-01

    Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol pr...

  4. Aerosol Lidar for the Relative Backscatter Amplification Measurements

    Directory of Open Access Journals (Sweden)

    Razenkov Igor A.

    2016-01-01

    Full Text Available Backscatter amplification presents only in a turbulent atmosphere, when the laser beam is propagates twice through the same inhomogeneities. We proposed technical solution to detect backscatter amplification. An aerosol micro pulse lidar with a beam expansion via receiving telescope was built to study this effect. Our system allows simultaneous detection of two returns from the same scattering volume: exactly on the axis of the laser beam and off the axis.

  5. Pulse Distortion in Saturated Fiber Optical Parametric Chirped Pulse Amplification

    DEFF Research Database (Denmark)

    Lali-Dastjerdi, Zohreh; Da Ros, Francesco; Rottwitt, Karsten;

    2012-01-01

    Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation.......Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation....

  6. Controllable Amplification of Entanglement for Two Qutrits under Decoherence

    Institute of Scientific and Technical Information of China (English)

    ZHENG Qiang; XIE Xiao-Yao; ZHI Qi-Jun; REN Zhong-Zhou

    2011-01-01

    Entanglement dynamics of a two-qutrit Heisenberg spin chain with the external magnetic fields and DM interaction under the intrinsic decoherence is investigated. Depending on whether there is inhomogeneous magnetic field,the entanglement amplification, i.e. the phenomenon that the finally stable entanglement is bigger than that of the initial one, is found for one kind of initial states. The reasons for the controllable entanglement amplification are discussed.

  7. Problems encountered when defining Arctic amplification as a ratio.

    Science.gov (United States)

    Hind, Alistair; Zhang, Qiong; Brattström, Gudrun

    2016-01-01

    In climate change science the term 'Arctic amplification' has become synonymous with an estimation of the ratio of a change in Arctic temperatures compared with a broader reference change under the same period, usually in global temperatures. Here, it is shown that this definition of Arctic amplification comes with a suite of difficulties related to the statistical properties of the ratio estimator itself. Most problematic is the complexity of categorizing uncertainty in Arctic amplification when the global, or reference, change in temperature is close to 0 over a period of interest, in which case it may be impossible to set bounds on this uncertainty. An important conceptual distinction is made between the 'Ratio of Means' and 'Mean Ratio' approaches to defining a ratio estimate of Arctic amplification, as they do not only possess different uncertainty properties regarding the amplification factor, but are also demonstrated to ask different scientific questions. Uncertainty in the estimated range of the Arctic amplification factor using the latest global climate models and climate forcing scenarios is expanded upon and shown to be greater than previously demonstrated for future climate projections, particularly using forcing scenarios with lower concentrations of greenhouse gases. PMID:27461918

  8. Targeting MET Amplification as a New Oncogenic Driver

    Energy Technology Data Exchange (ETDEWEB)

    Kawakami, Hisato [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Okamoto, Isamu, E-mail: okamotoi@kokyu.med.kyushu-u.ac.jp [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Center for Clinical and Translational Research, Kyushu University Hospital, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582 (Japan); Okamoto, Wataru [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Division of Transrlational Research, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577 (Japan); Tanizaki, Junko [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, HIM223, 450 Brookline Avenue, Boston, MA 02215 (United States); Nakagawa, Kazuhiko [Department of Medical Oncology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan); Nishio, Kazuto [Department of Genome Biology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511 (Japan)

    2014-07-22

    Certain genetically defined cancers are dependent on a single overactive oncogene for their proliferation and survival, a phenomenon known as “oncogene addiction”. A new generation of drugs that selectively target such “driver oncogenes” manifests a clinical efficacy greater than that of conventional chemotherapy in appropriate genetically defined patients. MET is a proto-oncogene that encodes a receptor tyrosine kinase, and aberrant activation of MET signaling occurs in a subset of advanced cancers as result of various genetic alterations including gene amplification, polysomy, and gene mutation. Our preclinical studies have shown that inhibition of MET signaling either with the small-molecule MET inhibitor crizotinib or by RNA interference targeted to MET mRNA resulted in marked antitumor effects in cancer cell lines with MET amplification both in vitro and in vivo. Furthermore, patients with non-small cell lung cancer or gastric cancer positive for MET amplification have shown a pronounced clinical response to crizotinib. Accumulating preclinical and clinical evidence thus suggests that MET amplification is an “oncogenic driver” and therefore a valid target for treatment. However, the prevalence of MET amplification has not been fully determined, possibly in part because of the difficulty in evaluating gene amplification. In this review, we provide a rationale for targeting this genetic alteration in cancer therapy.

  9. Targeting MET Amplification as a New Oncogenic Driver

    Directory of Open Access Journals (Sweden)

    Hisato Kawakami

    2014-07-01

    Full Text Available Certain genetically defined cancers are dependent on a single overactive oncogene for their proliferation and survival, a phenomenon known as “oncogene addiction”. A new generation of drugs that selectively target such “driver oncogenes” manifests a clinical efficacy greater than that of conventional chemotherapy in appropriate genetically defined patients. MET is a proto-oncogene that encodes a receptor tyrosine kinase, and aberrant activation of MET signaling occurs in a subset of advanced cancers as result of various genetic alterations including gene amplification, polysomy, and gene mutation. Our preclinical studies have shown that inhibition of MET signaling either with the small-molecule MET inhibitor crizotinib or by RNA interference targeted to MET mRNA resulted in marked antitumor effects in cancer cell lines with MET amplification both in vitro and in vivo. Furthermore, patients with non-small cell lung cancer or gastric cancer positive for MET amplification have shown a pronounced clinical response to crizotinib. Accumulating preclinical and clinical evidence thus suggests that MET amplification is an “oncogenic driver” and therefore a valid target for treatment. However, the prevalence of MET amplification has not been fully determined, possibly in part because of the difficulty in evaluating gene amplification. In this review, we provide a rationale for targeting this genetic alteration in cancer therapy.

  10. Gold nanoparticle-based lateral flow biosensor for rapid visual detection of Leishmania-specific DNA amplification products.

    Science.gov (United States)

    Toubanaki, Dimitra K; Athanasiou, Evita; Karagouni, Evdokia

    2016-08-01

    Leishmaniasis is a disease, caused by Leishmania parasites, which infect humans and animals, posing a major social and economic burden worldwide. The need for accurate and sensitive disease diagnosis led to the widespread adoption of PCR amplification. Detection of the amplification products (i.e. gel electrophoresis) require time-consuming protocols performed by trained personnel, with high cost. Aim of the present study was the simplification of PCR product detection, using a nucleic acid lateral flow, combined with functionalized gold nanoparticles. Amplification reactions targeting kinetoplastid DNA of Leishmania spp were performed on canine blood samples and a positive signal was formed as a red test zone. The visual detection was completed in 20min. Extensive optimization enabled the detection of 100fmol of target DNA. Clinical samples of infected dog blood were analyzed with high specificity. Overall, the proposed lateral flow biosensor can be considered an appealing alternative platform for Leishmania-specific amplification products detection with low cost and attractive simplicity. PMID:27255490

  11. 16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria

    Science.gov (United States)

    Subedi, Shradha; Kong, Fanrong; Jelfs, Peter; Gray, Timothy J.; Xiao, Meng; Sintchenko, Vitali; Chen, Sharon C-A

    2016-01-01

    Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included. Identification was compared with that achieved by high performance liquid chromatography (HPLC), in-house PCR and 16S/ITS sequencing. Isolates of all species yielded a SCGE profile comprising a single fragment length (or peak) except for M. scrofulaceum (two peaks). SCGE peaks of ATCC strains were distinct except for peak overlap between Mycobacterium kansasii and M. marinum. Of clinical/environmental strains, unique peaks were seen for 7/17 (41%) species (M. haemophilum, M. kubicae, M. lentiflavum, M. terrae, M. kansasii, M. asiaticum and M. triplex); 3/17 (18%) species were identified by HPLC. There were five SCGE fragment length types (I–V) each of M. avium, M. intracellulare and M. gordonae. Overlap of fragment lengths was seen between M. marinum and M. ulcerans; for M. gordonae SCGE type III and M. paragordonae; M. avium SCGE types III and IV, and M. intracellulare SCGE type I; M. chimaera, M. parascrofulaceum and M. intracellulare SCGE types III and IV; M. branderi and M. avium type V; and M. vulneris and M. intracellulare type V. The ITS-SCGE method was able to provide the first line rapid and reproducible species identification/screening of SG-NTM and was more discriminatory than HPLC. PMID:27749897

  12. [Homologous Analysis Using Repetitive-sequence-based PCR Typing of Exfoliative Toxin-producing Staphylococcus aureus Isolated from Our Hospital].

    Science.gov (United States)

    Miyamoto, Hitoshi; Murakami, Shinobu; Nishimiya, Tatsuya; Suemori, Koichiro; Tauchi, Hisamichi

    2015-05-01

    We examined staphylococcal coagulase types and homologous analysis using the DiversiLab repetitive-sequence-based PCR system in exfoliative toxin (ET)-producing Staphylococcus aureus. Twenty-two isolates (17 methicillin-sensitive Staphylococcus aureus (MSSA) and 5 methicillin-resistant Staphylococcus aureus (MRSA) isolates) obtained in our hospital from January 2012 and December 2013 were used. Three groups were classified according to the coagulase types and serotypes of ET. The first group (4 MSSA) showed coagulase type I and ET-A, and the second group (3 MSSA and 2 MRSA) showed coagulase type I and ET-B. The third group (10 MSSA and 3 MRSA) showed coagulase type V and ET-B. An analysis by DiversiLab demonstrated that homology was high in both the first and second groups. The homogenousness was high among the third group isolates except for the ocular isolates. In our hospital, three important groups were present according to a coagulase type and an ET type, and the homology of ocular isolates could be different from other materials isolates.

  13. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

    Science.gov (United States)

    Eisenhaber, Birgit; Kuchibhatla, Durga; Sherman, Westley; Sirota, Fernanda L; Berezovsky, Igor N; Wong, Wing-Cheong; Eisenhaber, Frank

    2016-01-01

    As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction. PMID:27115649

  14. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

    Science.gov (United States)

    Eisenhaber, Birgit; Kuchibhatla, Durga; Sherman, Westley; Sirota, Fernanda L; Berezovsky, Igor N; Wong, Wing-Cheong; Eisenhaber, Frank

    2016-01-01

    As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction.

  15. Sequence-based Methods in Human Microbial Ecology: A The 2nd HumanGenome Comes of Age

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-06-01

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  16. Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification

    Science.gov (United States)

    Yan, Yurong; Ding, Shijia; Zhao, Dan; Yuan, Rui; Zhang, Yuhong; Cheng, Wei

    2016-01-01

    Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.

  17. Amplification of thermostable lipase genes fragment from thermogenic phase of domestic waste composting process

    Science.gov (United States)

    Nurhasanah, Nurbaiti, Santi; Madayanti, Fida; Akhmaloka

    2015-09-01

    Lipases are lipolytic enzymes, catalyze the hydrolysis of fatty acid ester bonds of triglycerides to produce free fatty acids and glycerol. The enzyme is widely used in various fields of biotechnological industry. Hence, lipases with unique properties (e.g.thermostable lipase) are still being explored by variation methods. One of the strategy is by using metagenomic approach to amplify the gene directly from environmental sample. This research was focused on amplification of lipase gene fragment directly from the thermogenic phase of domestic waste composting in aerated trenches. We used domestic waste compost from waste treatment at SABUGA, ITB for the sample. Total chromosomal DNA were directly extracted from several stages at thermogenic phase of compost. The DNA was then directly used as a template for amplification of thermostable lipase gene fragments using a set of internal primers namely Flip-1a and Rlip-1a that has been affixed with a GC clamp in reverse primer. The results showed that the primers amplified the gene from four stages of thermogenic phase with the size of lipase gene fragment of approximately 570 base pairs (bp). These results were further used for Denaturing Gradient Gel Electrophoresis (DGGE) analysis to determine diversity of thermostable lipase gene fragments.

  18. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  19. Regulation of ribosomal DNA amplification by the TOR pathway.

    Science.gov (United States)

    Jack, Carmen V; Cruz, Cristina; Hull, Ryan M; Keller, Markus A; Ralser, Markus; Houseley, Jonathan

    2015-08-01

    Repeated regions are widespread in eukaryotic genomes, and key functional elements such as the ribosomal DNA tend to be formed of high copy repeated sequences organized in tandem arrays. In general, high copy repeats are remarkably stable, but a number of organisms display rapid ribosomal DNA amplification at specific times or under specific conditions. Here we demonstrate that target of rapamycin (TOR) signaling stimulates ribosomal DNA amplification in budding yeast, linking external nutrient availability to ribosomal DNA copy number. We show that ribosomal DNA amplification is regulated by three histone deacetylases: Sir2, Hst3, and Hst4. These enzymes control homologous recombination-dependent and nonhomologous recombination-dependent amplification pathways that act in concert to mediate rapid, directional ribosomal DNA copy number change. Amplification is completely repressed by rapamycin, an inhibitor of the nutrient-responsive TOR pathway; this effect is separable from growth rate and is mediated directly through Sir2, Hst3, and Hst4. Caloric restriction is known to up-regulate expression of nicotinamidase Pnc1, an enzyme that enhances Sir2, Hst3, and Hst4 activity. In contrast, normal glucose concentrations stretch the ribosome synthesis capacity of cells with low ribosomal DNA copy number, and we find that these cells show a previously unrecognized transcriptional response to caloric excess by reducing PNC1 expression. PNC1 down-regulation forms a key element in the control of ribosomal DNA amplification as overexpression of PNC1 substantially reduces ribosomal DNA amplification rate. Our results reveal how a signaling pathway can orchestrate specific genome changes and demonstrate that the copy number of repetitive DNA can be altered to suit environmental conditions.

  20. Optical Parametric Amplification for High Peak and Average Power

    Energy Technology Data Exchange (ETDEWEB)

    Jovanovic, I

    2001-11-26

    Optical parametric amplification is an established broadband amplification technology based on a second-order nonlinear process of difference-frequency generation (DFG). When used in chirped pulse amplification (CPA), the technology has been termed optical parametric chirped pulse amplification (OPCPA). OPCPA holds a potential for producing unprecedented levels of peak and average power in optical pulses through its scalable ultrashort pulse amplification capability and the absence of quantum defect, respectively. The theory of three-wave parametric interactions is presented, followed by a description of the numerical model developed for nanosecond pulses. Spectral, temperature and angular characteristics of OPCPA are calculated, with an estimate of pulse contrast. An OPCPA system centered at 1054 nm, based on a commercial tabletop Q-switched pump laser, was developed as the front end for a large Nd-glass petawatt-class short-pulse laser. The system does not utilize electro-optic modulators or multi-pass amplification. The obtained overall 6% efficiency is the highest to date in OPCPA that uses a tabletop commercial pump laser. The first compression of pulses amplified in highly nondegenerate OPCPA is reported, with the obtained pulse width of 60 fs. This represents the shortest pulse to date produced in OPCPA. Optical parametric amplification in {beta}-barium borate was combined with laser amplification in Ti:sapphire to produce the first hybrid CPA system, with an overall conversion efficiency of 15%. Hybrid CPA combines the benefits of high gain in OPCPA with high conversion efficiency in Ti:sapphire to allow significant simplification of future tabletop multi-terawatt sources. Preliminary modeling of average power limits in OPCPA and pump laser design are presented, and an approach based on cascaded DFG is proposed to increase the average power beyond the single-crystal limit. Angular and beam quality effects in optical parametric amplification are modeled

  1. Problems encountered when defining Arctic amplification as a ratio

    Science.gov (United States)

    Hind, Alistair; Zhang, Qiong; Brattström, Gudrun

    2016-07-01

    In climate change science the term ‘Arctic amplification’ has become synonymous with an estimation of the ratio of a change in Arctic temperatures compared with a broader reference change under the same period, usually in global temperatures. Here, it is shown that this definition of Arctic amplification comes with a suite of difficulties related to the statistical properties of the ratio estimator itself. Most problematic is the complexity of categorizing uncertainty in Arctic amplification when the global, or reference, change in temperature is close to 0 over a period of interest, in which case it may be impossible to set bounds on this uncertainty. An important conceptual distinction is made between the ‘Ratio of Means’ and ‘Mean Ratio’ approaches to defining a ratio estimate of Arctic amplification, as they do not only possess different uncertainty properties regarding the amplification factor, but are also demonstrated to ask different scientific questions. Uncertainty in the estimated range of the Arctic amplification factor using the latest global climate models and climate forcing scenarios is expanded upon and shown to be greater than previously demonstrated for future climate projections, particularly using forcing scenarios with lower concentrations of greenhouse gases.

  2. Magnetic Amplification by Magnetized Cosmic Rays in SNR Shocks

    CERN Document Server

    Riquelme, Mario A

    2009-01-01

    (Abridged) X-ray observations of synchrotron rims in supernova remnant (SNR) shocks show evidence of strong magnetic field amplification (a factor of ~100 between the upstream and downstream medium). This amplification may be due to plasma instabilities driven by shock-accelerated cosmic rays (CRs). One candidate is the cosmic ray current-driven (CRCD) instability (Bell 2004), caused by the electric current of large Larmor radii CRs propagating parallel to the upstream magnetic field. Particle-in-cell (PIC) simulations have shown that the back-reaction of the amplified field on CRs would limit the amplification factor of this instability to less than ~10 in galactic SNRs. In this paper, we study the possibility of further amplification driven near shocks by "magnetized" CRs, whose Larmor radii are smaller than the length scale of the field that was previously amplified by the CRCD instability. We find that additional amplification can occur due to a new instability, driven by the CR current perpendicular to t...

  3. Adaptive base-isolation of civil structures using variable amplification

    Institute of Scientific and Technical Information of China (English)

    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 study, a new semi-active damping system using variable amplification will be investigated for adaptive baseisolation. It uses a novel variable amplification device (VAD) connected in series with a passive damper. The VAD is capable of producing multiple amplification factors, each corresponding to a different amplification state. Forces from the damper are amplified to the structure according to the current amplification state, which is selected via a semi-active control algorithm specifically tailored to the system's unique damping characteristics. To demonstrate the effectiveness of the VAD-damper system for adaptive base-isolation, numerical simulations are conducted for three and seven-story base-isolated buildings subject to both far and near-field ground motions. The results indicate that the system can achieve significant reductions in response compared to the base-isolated buildings with no damper. The proposed system is also found to perform well compared to a typical semi-active damper.

  4. High-temperature ultrafast polariton parametric amplification in semiconductor microcavities

    Science.gov (United States)

    Saba, M.; Ciuti, C.; Bloch, J.; Thierry-Mieg, V.; André, R.; Dang, Le Si; Kundermann, S.; Mura, A.; Bongiovanni, G.; Staehli, J. L.; Deveaud, B.

    2001-12-01

    Cavity polaritons, the elementary optical excitations of semiconductor microcavities, may be understood as a superposition of excitons and cavity photons. Owing to their composite nature, these bosonic particles have a distinct optical response, at the same time very fast and highly nonlinear. Very efficient light amplification due to polariton-polariton parametric scattering has recently been reported in semiconductor microcavities at liquid-helium temperatures. Here we demonstrate polariton parametric amplification up to 120K in GaAlAs-based microcavities and up to 220K in CdTe-based microcavities. We show that the cut-off temperature for the amplification is ultimately determined by the binding energy of the exciton. A 5-µm-thick planar microcavity can amplify a weak light pulse more than 5,000 times. The effective gain coefficient of an equivalent homogeneous medium would be 107cm-1. The subpicosecond duration and high efficiency of the amplification could be exploited for high-repetition all-optical microscopic switches and amplifiers. 105 polaritons occupy the same quantum state during the amplification, realizing a dynamical condensate of strongly interacting bosons which can be studied at high temperature.

  5. Amplification of Information by Photons and the Quantum Chernoff Bound

    Science.gov (United States)

    Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

    2014-03-01

    Amplification was regarded, since the early days of quantum theory, as a mysterious ingredient that endows quantum microstates with macroscopic consequences, key to the ``collapse of the wavepacket,'' and a way to avoid embarrassing problems exemplified by Schrödinger's cat. This bridge between the quantum microworld and the classical world of our experience was postulated ad hoc in the Copenhagen Interpretation. Quantum Darwinism views amplification as replication, in many copies, of information about quantum states. We show that such amplification is a natural consequence of a broad class of models of decoherence, including the photon environment we use to obtain most of our information. The resultant amplification is huge, proportional to # ξQCB . Here, #  is the environment size and ξQCB is the ``typical'' Quantum Chernoff Information, which quantifies the efficiency of the amplification. The information communicated though the environment is imprinted in the states of individual environment subsystems, e.g., in single photons, which document the transfer of information into the environment and result in the emergence of the classical world. See, http://mike.zwolak.org

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

    Science.gov (United States)

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

    2012-03-01

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

  7. HLA-A Gene Polymorphism Defined by High-Resolution Sequence Based Typing in 161 Northern Chinese Han People

    Institute of Scientific and Technical Information of China (English)

    Chunxia Yan; Haiyan Sun; Xiuqing Zhang; Jian Wang; Huanming Yang; Shengbin Li; Ruilin Wang; Jingxiang Li; Yajun Deng; Dongying Wu; Hongbo Zhang; Hongxing Zhang; Lidong Wang; Chunrong Zhang

    2003-01-01

    Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods--sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590),and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205,A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.

  8. Modeling Loss Amplification After Devastating Disasters

    Science.gov (United States)

    Boissonnade, A. C.; Muir Wood, R.

    2008-05-01

    With the catastrophic events that occurred in 2004 and 2005 came the realization that Catastrophic (Cat) loss models were not properly modeling insured losses and their associated uncertainty. One reason was that major catastrophes were generally characterized by losses caused by the primary initiating events. Such approaches are not adequate when losses can result from the compounded impacts of scenarios of secondary cascading events (physical, economic, social and political) that can have much larger impacts than those due to the primary events themselves. Situations where more and more cascading events can occur will result in different outcomes, some leading to extreme loss events, generally referred as Super Cats. These situations occurred in December 2004 with the Sumatra earthquake and tsunami and in August 2005 with hurricane Katrina and resulting New Orleans flooding. A review of historical events shows that these events are not exceptions. Modeling such scenarios adds new levels of complexity and different perspectives in the understanding of characterizing and assessing impacts of catastrophic events. Modeling economic consequences of extreme events can be improved by developing scenarios of cascades of secondary events triggered by the primary event(s). The likelihood of each scenario should be modeled, along with the hazards of primary and secondary events and resulting losses with their impacts to the different stakeholders. In addition, it is also important to model the impacts of the hazards on the infrastructure and the resulting disruption to the residents and the local economy because these can result in additional losses. This paper describes current work with the goals of better modeling the full economic impacts from catastrophic events, and of a more comprehensive treatment of uncertainty. We will present approaches for modeling loss amplification that account for all the ways in which the cost incurred for a certain level of damage due to a

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

    Science.gov (United States)

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

    2012-12-01

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

  10. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.

    Science.gov (United States)

    Zhan, Aibin; Bailey, Sarah A; Heath, Daniel D; Macisaac, Hugh J

    2014-09-01

    Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification.

  11. Measurement-based noiseless linear amplification for quantum communication

    Science.gov (United States)

    Chrzanowski, H. M.; Walk, N.; Haw, J. Y.; Thearle, O.; Assad, S. M.; Janousek, J.; Hosseini, S.; Ralph, T. C.; Symul, T.; Lam, P. K.

    2014-11-01

    Entanglement distillation is an indispensable ingredient in extended quantum communication networks. Distillation protocols are necessarily non-deterministic and require non-trivial experimental techniques such as noiseless amplification. We show that noiseless amplification could be achieved by performing a post-selective filtering of measurement outcomes. We termed this protocol measurement-based noiseless linear amplification (MBNLA). We apply this protocol to entanglement that suffers transmission loss of up to the equivalent of 100km of optical fibre and show that it is capable of distilling entanglement to a level stronger than that achievable by transmitting a maximally entangled state through the same channel. We also provide a proof-of-principle demonstration of secret key extraction from an otherwise insecure regime via MBNLA. Compared to its physical counterpart, MBNLA not only is easier in term of implementation, but also allows one to achieve near optimal probability of success.

  12. Amplification of spin waves by the spin Seebeck effect

    Science.gov (United States)

    Padrón-Hernández, E.; Azevedo, A.; Rezende, S. M.

    2012-04-01

    We observe amplification of spin-wave packets propagating along a film of single-crystal yttrium iron garnet (YIG) subject to a transverse temperature gradient. The spin waves are excited and detected with standard techniques used to study volume or surface magnetostatic waves in the 1-2 GHz frequency range. Amplification gains larger than 20 are observed in a YIG film heated by a current of 20 mA in a Pt layer in a simple YIG/Pt bilayer. The amplification is attributed to the action of a spin-transfer thermal torque acting on the magnetization that opposes the relaxation and which is created by spin currents generated through the spin Seebeck effect. The experimental data are interpreted with a spin-wave model.

  13. Identification of genetic elements associated with EPSPs gene amplification.

    Directory of Open Access Journals (Sweden)

    Todd A Gaines

    Full Text Available Weed populations can have high genetic plasticity and rapid responses to environmental selection pressures. For example, 100-fold amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS gene evolved in the weed species Amaranthus palmeri to confer resistance to glyphosate, the world's most important herbicide. However, the gene amplification mechanism is unknown. We sequenced the EPSPS gene and genomic regions flanking EPSPS loci in A. palmeri, and searched for mobile genetic elements or repetitive sequences. The EPSPS gene was 10,229 bp, containing 8 exons and 7 introns. The gene amplification likely proceeded through a DNA-mediated mechanism, as introns exist in the amplified gene copies and the entire amplified sequence is at least 30 kb in length. Our data support the presence of two EPSPS loci in susceptible (S A. palmeri, and that only one of these was amplified in glyphosate-resistant (R A. palmeri. The EPSPS gene amplification event likely occurred recently, as no sequence polymorphisms were found within introns of amplified EPSPS copies from R individuals. Sequences with homology to miniature inverted-repeat transposable elements (MITEs were identified next to EPSPS gene copies only in R individuals. Additionally, a putative Activator (Ac transposase and a repetitive sequence region were associated with amplified EPSPS genes. The mechanism controlling this DNA-mediated amplification remains unknown. Further investigation is necessary to determine if the gene amplification may have proceeded via DNA transposon-mediated replication, and/or unequal recombination between different genomic regions resulting in replication of the EPSPS gene.

  14. The Efficiency of Magnetic Field Amplification at Shocks by Turbulence

    Science.gov (United States)

    Ji(), Suoqing; Oh, S. Peng; Ruszkowski, M.; Markevitch, M.

    2016-09-01

    Turbulent dynamo field amplification has often been invoked to explain the strong field strengths in thin rims in supernova shocks (˜100 μG) and in radio relics in galaxy clusters (˜μG). We present high resolution MHD simulations of the interaction between pre-shock turbulence, clumping and shocks, to quantify the conditions under which turbulent dynamo amplification can be significant. We demonstrate numerically converged field amplification which scales with Alfvén Mach number, B/B_0 ∝ M_A, up to M_A ˜ 150. This implies that the post-shock field strength is relatively independent of the seed field. Amplification is dominated by compression at low M_A, and stretching (turbulent amplification) at high M_A. For high M_A, the B-field grows exponentially and saturates at equipartition with turbulence, while the vorticity jumps sharply at the shock and subsequently decays; the resulting field is orientated predominately along the shock normal (an effect only apparent in 3D and not 2D). This agrees with the radial field bias seen in supernova remnants. By contrast, for low M_A, field amplification is mostly compressional, relatively modest, and results in a predominantly perpendicular field. The latter is consistent with the polarization seen in radio relics. Our results are relatively robust to the assumed level of gas clumping. Our results imply that the turbulent dynamo may be important for supernovae, but is only consistent with the field strength, and not geometry, for cluster radio relics. For the latter, this implies strong pre-existing B-fields in the ambient cluster outskirts.

  15. The emergence of surface-based Arctic amplification

    Directory of Open Access Journals (Sweden)

    M. C. Serreze

    2009-02-01

    Full Text Available Rises in surface and lower troposphere air temperatures through the 21st century are projected to be especially pronounced over the Arctic Ocean during the cold season. This Arctic amplification is largely driven by loss of the sea ice cover, allowing for strong heat transfers from the ocean to the atmosphere. Consistent with observed reductions in sea ice extent, fields from both the NCEP/NCAR and JRA-25 reanalyses point to emergence of surface-based Arctic amplification in the last decade.

  16. Influence of environmental noise on the weak value amplification

    Science.gov (United States)

    Zhu, Xuannmin; Zhang, Yu-Xiang

    2016-05-01

    Quantum systems are always disturbed by environmental noise. We have investigated the influence of the environmental noise on the amplification in weak measurements. Three typical quantum noise processes are discussed in this article. The maximum expectation values of the observables of the measuring device decrease sharply with the strength of the depolarizing and phase damping channels, while the amplification effect of weak measurement is immune to the amplitude damping noise. To obtain significantly amplified signals, we must ensure that the preselection quantum systems are kept away from the depolarizing and phase damping processes.

  17. Nanoscale field effect transistor for biomolecular signal amplification

    CERN Document Server

    Chen, Yu; Hong, Mi K; Erramilli, Shyamsunder; Rosenberg, Carol; Mohanty, Pritiraj

    2008-01-01

    We report amplification of biomolecular recognition signal in lithographically defined silicon nanochannel devices. The devices are configured as field effect transistors (FET) in the reversed source-drain bias region. The measurement of the differential conductance of the nanowire channels in the FET allows sensitive detection of changes in the surface potential due to biomolecular binding. Narrower silicon channels demonstrate higher sensitivity to binding due to increased surface-to-volume ratio. The operation of the device in the negative source-drain region demonstrates signal amplification. The equivalence between protein binding and change in the surface potential is described.

  18. Ultra-broad bandwidth parametric amplification at degeneracy.

    Science.gov (United States)

    Limpert, J; Aguergaray, C; Montant, S; Manek-Hönninger, I; Petit, S; Descamps, D; Cormier, E; Salin, F

    2005-09-19

    We report on a novel approach of ultra-broad bandwidth parametric amplification around degeneracy. A bandwidth of up to 400 nm centered around 800 nm is amplified in a BBO crystal by using chirped pump pulses with a bandwitdth as broad as 10 nm. A supercontinuum signal is generated in a microstructured fiber, having to first order a quadratic chirp, which is necessary to ensure temporal overlap of the interacting waves over this broad bandwidth. Furthermore, we discuss the potential of this approach for an octave-spanning parametric amplification.

  19. Methods for microbial DNA extraction from soil for PCR amplification

    Directory of Open Access Journals (Sweden)

    Yeates C

    1998-01-01

    Full Text Available Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1. DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.

  20. Theory of light amplification in active fishnet metamaterials

    CERN Document Server

    Hamm, Joachim M; Tsakmakidis, Kosmas L; Hess, Ortwin

    2011-01-01

    We establish a theory that traces light amplification in an active double-fishnet metamaterial back to its microscopic origins. Based on ab initio calculations of the light/plasmon fields we extract energy rates and conversion efficiencies associated with gain/loss channels directly from Poynting's theorem. We find that for the negative refactive index mode both radiative loss and gain outweigh resistive loss by more than a factor of two, opening a broad window of steady-state amplification (free of instabilities) accessible even when a gain reduction close to the metal is taken into account.

  1. Raman amplification in the broken-wave regime

    CERN Document Server

    Farmer, John P

    2015-01-01

    In regimes far beyond the wavebreaking theshold of Raman amplification, we show that significant amplifcation can occur after the onset of wavebreaking, before phase mixing destroys the coupling between pump and probe. The amplification efficiency in this regime is therefore strongly dependent on the energy-transfer rate when wavebreaking occurs, and is, as such, sensitive to both the probe amplitude and profile. In order to access the higher-efficiency broken-wave regime, a short, intense probe is required. Parameter scans show the marked difference in behaviour compared to below wavebreaking, where longer, more energetic pulses lead to improved efficiencies.

  2. Femtosecond pulse amplification in cladding-pumped fibers

    OpenAIRE

    Minelly, J. D.; Galvanauskas, A.; Fermann, M. E.; Harter, D.; Caplen, J.E.; Chen, Z.J.; Payne, D. N.

    1995-01-01

    Femtosecond pulse amplification in a cladding-pumped fiber amplifier is demonstrated for the first time to our knowledge. Using a cladding-pumped erbium-doped fiber power amplifier and a passively mode-locked fiber seed oscillator in conjunction with an all-fiber chirped-pulse amplification system, we obtain 380-fs near-bandwidth-limited pulses with an average power of 260 mW. The pulse repetition rate is varied between 5 and 50 MHz, and pulse energies as high as 20 nJ are generated.

  3. Divided-pulse amplification to the joule level.

    Science.gov (United States)

    Webb, Benjamin; Azim, Ahmad; Bodnar, Nathan; Chini, Michael; Shah, Lawrence; Richardson, Martin

    2016-07-01

    Divided-pulse amplification (DPA) has proven to be a valuable tool in scaling the peak power of diode-pumped ytterbium-doped amplifiers to beyond the single-pulse threshold for parasitic nonlinear effects. DPA enables the amplification of picosecond pulses in solid-state amplifiers with limited bandwidth beyond the single-pulse damage threshold. In this Letter, we demonstrate DPA of picosecond pulses in a flashlamp-pumped Nd:YAG amplifier for the first time, to the best of our knowledge, yielding a combined pulse energy of 167 mJ. PMID:27367113

  4. Influence of environmental noise on the weak value amplification

    Science.gov (United States)

    Zhu, Xuannmin; Zhang, Yu-Xiang

    2016-08-01

    Quantum systems are always disturbed by environmental noise. We have investigated the influence of the environmental noise on the amplification in weak measurements. Three typical quantum noise processes are discussed in this article. The maximum expectation values of the observables of the measuring device decrease sharply with the strength of the depolarizing and phase damping channels, while the amplification effect of weak measurement is immune to the amplitude damping noise. To obtain significantly amplified signals, we must ensure that the preselection quantum systems are kept away from the depolarizing and phase damping processes.

  5. Amplification of Short Pulse High Power UV Laser

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    At recent year, with the development of CPA and other amplification technology, laser intensity achieves great increase and laser power can be high to PW(105) now, this ultrashort pulse lasers offer scientists a route to investigate laser-matter interaction in an absolute new regime.So far the researches on ultrashort pulse laser-matter interaction concentrated on infrared regime, yet ultraviolet laser has the advantage in intense field physics and ICF researches for its short wavelength and less nonlinear effects. KrF excimer is the best medium in UV ultrashort pulse amplification for its small saturation energy and high contrast ratio accessible.

  6. Ultra-broad bandwidth parametric amplification at degeneracy.

    Science.gov (United States)

    Limpert, J; Aguergaray, C; Montant, S; Manek-Hönninger, I; Petit, S; Descamps, D; Cormier, E; Salin, F

    2005-09-19

    We report on a novel approach of ultra-broad bandwidth parametric amplification around degeneracy. A bandwidth of up to 400 nm centered around 800 nm is amplified in a BBO crystal by using chirped pump pulses with a bandwitdth as broad as 10 nm. A supercontinuum signal is generated in a microstructured fiber, having to first order a quadratic chirp, which is necessary to ensure temporal overlap of the interacting waves over this broad bandwidth. Furthermore, we discuss the potential of this approach for an octave-spanning parametric amplification. PMID:19498762

  7. 三个新HLA等位基因A*24:224,A*24:225和A*24:257的测序鉴定%Identification of 3 novel HLA-A alleles A * 24: 224, A * 24 : 225 and A * 24: 257 by sequence-based typing

    Institute of Scientific and Technical Information of China (English)

    朱传福; 张红卫; 张毅; 聂向民

    2015-01-01

    目的 鉴定3个在中国汉族人群中发现的人类白细胞抗原(human leukocyte antigen,HLA)A位点新等位基因A* 24:224、A* 24:225和A* 24:257.方法 应用双链直接测序分型技术进行中华骨髓库志愿者常规HLA分型,对其中HLA-A位点无完全匹配结果者,采用等位基因特异性扩增测序分型方法进行新等位基因序列鉴定.结果 3例先证者在HLA-A位点分别有一个未知的新碱基序列,3个新序列均与HLA-A* 24:02:01:01最为相近,但在第2外显子分别出现了1或2个的碱基取代,并导致相应的密码子及其编码的氨基酸的改变.结论 3个新碱基序列均确认为HLA-A新等位基因,分别于2012年11月和2013年11月被世界卫生组织HLA因子命名委员会正式命名为HLA-A* 24:224、HLA-A*24:225和HLA-A* 24:257.%Objective To verify 3 novel HLA-A alleles A * 24:224,A * 24:225 and A * 24:257 identified in Chinese Han individuals.Methods No full matched results were obtained at HLA-A locus in HLA typing for China Marrow Donor Program (CMDP) using bi-allelic Sequence-Based Typing (SBT).The novel HLA alleles were identified with allele-specific amplification SBT.Results All of the three probands had a novel nucleotide sequence at HLA-A locus.All of the 3 new sequences are most close to HLA-A* 24:02:01:01 except for 1 or 2 nucleotide substitution in exon 2,which resulted in different changes in corresponding codons and encoded amino acids.Conclusion Three novel HLA-A alleles were confirmed and officially named as HLA-A * 24:224,HLA-A * 24:225 and HLA-A * 24:257 under the GenBank accession numbers JQ899198,JQ924283 and HG003642 by the WHO Nomenclature Committee for Factors of the HLA System in November 2012 and November 2013,respectively.

  8. Use of ramification amplification assay for detection of Escherichia coli O157:H7 and other E. coli Shiga toxin-producing strains.

    Science.gov (United States)

    Li, Fan; Zhao, Chunyan; Zhang, Wandi; Cui, Shenghui; Meng, Jianghong; Wu, Josephine; Zhang, David Y

    2005-12-01

    Escherichia coli O157:H7 and other Shiga toxin-producing E. coli (STEC) strains are important human pathogens that are mainly transmitted through the food chain. These pathogens have a low infectious dose and may cause life-threatening illnesses. However, detection of this microorganism in contaminated food or a patient's stool specimens presents a diagnostic challenge because of the low copy number in the sample. Often, a more sensitive nucleic acid amplification method, such as PCR, is required for rapid detection of this microorganism. Ramification amplification (RAM) is a recently introduced isothermal DNA amplification technique that utilizes a circular probe for target detection and achieves exponential amplification through the mechanism of primer extension, strand displacement, and ramification. In this study, we synthesized a circular probe specific for the Shiga toxin 2 gene (stx(2)). Our results showed that as few as 10 copies of stx(2) could be detected, indicating that the RAM assay was as sensitive as conventional PCR. We further tested 33 isolates of E coli O157:H7, STEC, Shigella dysenteriae, and nonpathogenic E. coli by RAM assay. Results showed that all 27 STEC isolates containing the stx(2) gene were identified by RAM assay, while S. dysenteriae and nonpathogenic E. coli isolates were undetected. The RAM results were 100% in concordance with those of PCR. Because of its simplicity and isothermal amplification, the RAM assay could be a useful method for detecting STEC in food and human specimens.

  9. Functional continuity: did field-induced oriented aperiodic constraints at Life's origin aid its sequence-based evolution?

    Science.gov (United States)

    Mitra-Delmotte, G.; Mitra, A. N.

    2014-04-01

    A non-biological analog undergoing Darwinian-like evolution could have enhanced the probability of many crucial independent bottom-up emergent steps, engendered within its premises, and smoothen the inanimate-animate transition. Now, the higher-level environment-mutable DNA sequences influence the lower-level pattern of oriented templates (enzymes, lipid membranes, RNA) in the organized cell matrix and hence their associated substrate-dynamics; note how templates are akin to local fields, kinetically constraining reactant orientations. Since the lowerlevel is likely the more primitive of the two (rather than Cairns-Smith's "readily available" rigid clay crystal sequence-based replicators as a memory-like basis for slowly mutating predecessor-patterns enroute to complex RNA-based Darwinian evolution), a gradual thermodynamic-to-kinetic transition in an isotropic medium, is proposed as driven by some order-parameter --via "available" field-responsive dipolar colloid networks, as apart from bio-organics, mineral colloids also can display liquid crystal (LC) phases (see [1]). An access to solid-like orientational order in a fluid matrix suggests how aperiodic patterns can be influenced and sustained (a la homeostasis) via external inhomogeneous fields (e.g. magnetic rocks); this renders these cooperative networks with potential as confining host-media, whose environment-sensitivity can not only influence their sterically-coupled guest-substrates but also their network properties (the latter can enable 'functions' like spontaneous transport under non-equilibrium suggesting a natural basis for their selection by the environment). In turn LC systems could have been preceded by even simpler anisotropic fluid hosts, viz., external field-induced mineral magnetic nanoparticle (MNP) aggregates. Indeed, the capacity of an MNP to couple its magnetic and rotational d.o.f.s suggests how an environment-sensitive field-influenced network of interacting dipolar colloids close to

  10. Highly efficient amplification of chronic wasting disease agent by protein misfolding cyclic amplification with beads (PMCAb.

    Directory of Open Access Journals (Sweden)

    Chad J Johnson

    Full Text Available Protein misfolding cyclic amplification (PMCA has emerged as an important technique for detecting low levels of pathogenic prion protein in biological samples. The method exploits the ability of the pathogenic prion protein to convert the normal prion protein to a proteinase K-resistant conformation. Inclusion of Teflon® beads in the PMCA reaction (PMCAb has been previously shown to increase the sensitivity and robustness of detection for the 263 K and SSLOW strains of hamster-adapted prions. Here, we demonstrate that PMCAb with saponin dramatically increases the sensitivity of detection for chronic wasting disease (CWD agent without compromising the specificity of the assay (i.e., no false positive results. Addition of Teflon® beads increased the robustness of the PMCA reaction, resulting in a decrease in the variability of PMCA results. Three rounds of serial PMCAb allowed detection of CWD agent from a 6.7 × 10(-13 dilution of 10% brain homogenate (1.3 fg of source brain. Titration of the same brain homogenate in transgenic mice expressing cervid prion protein (Tg(CerPrP1536(+/- mice allowed detection of CWD agent from the 10(-6 dilution of 10% brain homogenate. PMCAb is, thus, more sensitive than bioassay in transgenic mice by a factor exceeding 10(5. Additionally, we are able to amplify CWD agent from brain tissue and lymph nodes of CWD-positive white-tailed deer having Prnp alleles associated with reduced disease susceptibility.

  11. Highly efficient amplification of chronic wasting disease agent by protein misfolding cyclical amplification with beads (PMCAb)

    Science.gov (United States)

    Johnson, Chad J.; Aiken, Judd M.; McKenzie, Debbie; Samuel, Michael D.; Pedersen, Joel A.

    2012-01-01

    Protein misfolding cyclic amplification (PMCA) has emerged as an important technique for detecting low levels of pathogenic prion protein in biological samples. The method exploits the ability of the pathogenic prion protein to convert the normal prion protein to a proteinase K-resistant conformation. Inclusion of Teflon® beads in the PMCA reaction (PMCAb) has been previously shown to increase the sensitivity and robustness of detection for the 263 K and SSLOW strains of hamster-adapted prions. Here, we demonstrate that PMCAb with saponin dramatically increases the sensitivity of detection for chronic wasting disease (CWD) agent without compromising the specificity of the assay (i.e., no false positive results). Addition of Teflon® beads increased the robustness of the PMCA reaction, resulting in a decrease in the variability of PMCA results. Three rounds of serial PMCAb allowed detection of CWD agent from a 6.7×10−13 dilution of 10% brain homogenate (1.3 fg of source brain). Titration of the same brain homogenate in transgenic mice expressing cervid prion protein (Tg(CerPrP)1536+/−mice) allowed detection of CWD agent from the 10−6 dilution of 10% brain homogenate. PMCAb is, thus, more sensitive than bioassay in transgenic mice by a factor exceeding 105. Additionally, we are able to amplify CWD agent from brain tissue and lymph nodes of CWD-positive white-tailed deer having Prnp alleles associated with reduced disease susceptibility.

  12. Electrochemical biosensor for detection of DNA hydroxymethylation based on glycosylation and alkaline phosphatase catalytic signal amplification

    International Nuclear Information System (INIS)

    Highlights: • DNA Hydroxymethylation was detected by electrochemical method. • 5-Hydroxymethylation cytosine in target DNA was chemically modified with glucose group. • Alkaline phosphatase catalytic signal amplification strategy was used. • The developed method also showed excellent reproducibility and stability. - Abstract: DNA hydroxymethylation (5-hydroxymethylcytosine, 5hmC) is a kind of new epigenetic modification, which plays key roles in nuclear reprogramming, regulates the gene activity, and initiates the DNA demethylation in mammals. For further understanding the functions of 5hmC and the correlation with tumour, it is essential to develop sensitive and selective methods for detecting and sequencing 5hmC. Herein, a kind of electrochemical biosensor was fabricated for 5hmC detection based on the glycosylation modification of 5hmC and enzymatic signal amplification. Under the catalytic effect of T4 β-glucosyltransferase, the 5hmC in target DNA was chemically modified with glucose. Then with the bridge connection of 1,4-phenyldiboronic acid, alkaline phosphatase was further captured on the electrode surface to catalyze the hydrolysis of p-nitrophenyl phosphate disodium salt to produce p-nitrophenol. Based on the relationship between the electrochemical oxidation signal of p-nitrophenol and the concentration of target DNA, the 5hmC level can be detected with high sensitivity and selectivity. The developed method also showed excellent reproducibility and stability

  13. Whole genome amplification and its impact on CGH array profiles

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff

    2008-07-01

    Full Text Available Abstract Background Some array comparative genomic hybridisation (array CGH platforms require a minimum of micrograms of DNA for the generation of reliable and reproducible data. For studies where there are limited amounts of genetic material, whole genome amplification (WGA is an attractive method for generating sufficient quantities of genomic material from miniscule amounts of starting material. A range of WGA methods are available and the multiple displacement amplification (MDA approach has been shown to be highly accurate, although amplification bias has been reported. In the current study, WGA was used to amplify DNA extracted from whole blood. In total, six array CGH experiments were performed to investigate whether the use of whole genome amplified DNA (wgaDNA produces reliable and reproducible results. Four experiments were conducted on amplified DNA compared to unamplified DNA and two experiments on unamplified DNA compared to unamplified DNA. Findings All the experiments involving wgaDNA resulted in a high proportion of losses and gains of genomic material. Previously, amplification bias has been overcome by using amplified DNA in both the test and reference DNA. Our data suggests that this approach may not be effective, as the gains and losses introduced by WGA appears to be random and are not reproducible between different experiments using the same DNA. Conclusion In light of these findings, the use of both amplified test and reference DNA on CGH arrays may not provide an accurate representation of copy number variation in the DNA.

  14. Direct Extraction and Amplification of DNA from Soil.

    Science.gov (United States)

    Trevors, Jack T.; Leung, K.

    1998-01-01

    Presents an exercise that describes the direct extraction and purification of DNA from a small soil sample. Also discusses the subsequent amplification of a 343-bp Tn7 transposate A gene fragment (tnsA) from a strain of Pseudomonas aureofaciens 3732RNL11. Contains 21 references. (DDR)

  15. Soft x-ray amplification in an ablative capillary discharge

    International Nuclear Information System (INIS)

    Soft x-ray amplification in CVI 18.2 nm line is observed in an ablative UHMW-PE capillary discharge. The gain coefficient is measured to be 1.9 cm-1. The electron density is about 2 x 1019 cm-3. This indicates that capillary discharge pumping device can be a source for a compact soft x-ray laser. (author)

  16. Controlling the amplification of chirality in hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Mateos-Timoneda, Miguel A.; Crego-Calama, Mercedes; Reinhoudt, David N.

    2005-01-01

    The amplification of chirality (a high enantiomeric or diastereomeric excess induced by a small initial amount of chiral bias) on hydrogen-bonded assemblies has been studied using “sergeants-and-soldiers” experiments under thermodynamically controlled conditions. Here it is shown that different subs

  17. Reversible Gating of Plasmonic Coupling for Optical Signal Amplification.

    Science.gov (United States)

    Khoury, Christopher G; Fales, Andrew M; Vo-Dinh, Tuan

    2016-07-20

    Amplification of optical signals is useful for a wide variety of applications, ranging from data signal transmission to chemical sensing and biomedical diagnostics. One such application in chemical sensing is surface-enhanced Raman scattering (SERS), an important technique for increasing the Raman signal using the plasmonic effect of enhanced electromagnetic fields associated with metallic nanostructures. One of the most important limitations of SERS-based amplification is the difficulty to reproducibly control the SERS signal. Here, we describe the design and implementation of a unique hybrid system capable of producing reversible gating of plasmonic coupling for Raman signal amplification. The hybrid system is composed of two subsystems: (1) colloidal magneto-plasmonic nanoparticles for SERS enhancement and (2) a micromagnet substrate with an externally applied magnetic field to modulate the colloidal nanoparticles. For this proof of concept demonstration, the nanoparticles were labeled with a Raman-active dye, and it was shown that the detected SERS signal could be reproducibly modulated by controlling the externally applied magnetic field. The developed system provides a simple, robust, inexpensive, and reusable device for SERS signal modulation. These properties will open up new possibilities for optical signal amplification and gating as well for high-throughput, reproducible SERS detection.

  18. Ultrafast double-pulse parametric amplification for precision Ramsey metrology

    NARCIS (Netherlands)

    Kandula, D.Z.; Renault, A.A.L.; Gohle, C.; Wolf, A.L.; Witte, S.; Hogervorst, W.; Ubachs, W.M.G.; Eikema, K.S.E.

    2008-01-01

    We demonstrate phase stable, mJ-level parametric amplification of pulse pairs originating from a Ti: Sapphire frequency comb laser. The amplifier-induced phase shift between the pulses has been determined interferometrically with an accuracy of approximate to 10 mrad. Typical phase shifts are on the

  19. Resonant amplification of quantum fluctuations in a spinor gas

    DEFF Research Database (Denmark)

    Topic, O.; Scherer, M.; Gebreyesus, G.;

    2010-01-01

    Bose-Einstein condensates of atoms with non-zero spin are known to constitute an ideal system to investigate fundamental properties of magnetic superfluids. More recently it was realized that they also provide the fascinating opportunity to investigate the macroscopic amplification of quantum and...

  20. Transient amplification limits noise suppression in biochemical networks

    Science.gov (United States)

    Dixon, John; Lindemann, Anika; McCoy, Jonathan H.

    2016-01-01

    Cell physiology is orchestrated, on a molecular level, through complex networks of biochemical reactions. The propagation of random fluctuations through these networks can significantly impact cell behavior, raising challenging questions about how network design shapes the cell's ability to suppress or exploit these fluctuations. Here, drawing on insights from statistical physics, fluid dynamics, and systems biology, we explore how transient amplification phenomena arising from network connectivity naturally limit a biochemical system's ability to suppress small fluctuations around steady-state behaviors. We find that even a simple system consisting of two variables linked by a single interaction is capable of amplifying small fluctuations orders of magnitude beyond the levels predicted by linear stability theory. We also find that adding additional interactions can promote further amplification, even when these interactions implement classic design strategies known to suppress fluctuations. These results establish that transient amplification is an essential factor determining baseline noise levels in stable intracellular networks. Significantly, our analysis is not bound to specific systems or interaction mechanisms: we find that noise amplification is an emergent phenomenon found near steady states in any network containing sufficiently strong interactions, regardless of its form or function.

  1. Loss of KLF14 triggers centrosome amplification and tumorigenesis.

    Science.gov (United States)

    Fan, Guangjian; Sun, Lianhui; Shan, Peipei; Zhang, Xianying; Huan, Jinliang; Zhang, Xiaohong; Li, Dali; Wang, Tingting; Wei, Tingting; Zhang, Xiaohong; Gu, Xiaoyang; Yao, Liangfang; Xuan, Yang; Hou, Zhaoyuan; Cui, Yongping; Cao, Liu; Li, Xiaotao; Zhang, Shengping; Wang, Chuangui

    2015-01-01

    Centrosome amplification is frequent in cancer, but the underlying mechanisms remain unclear. Here we report that disruption of the Kruppel-like factor 14 (KLF14) gene in mice causes centrosome amplification, aneuploidy and spontaneous tumorigenesis. Molecularly, KLF14 functions as a transcriptional repressor of Plk4, a polo-like kinase whose overexpression induces centrosome overduplication. Transient knockdown of KLF14 is sufficient to induce Plk4-directed centrosome amplification. Clinically, KLF14 transcription is significantly downregulated, whereas Plk4 transcription is upregulated in multiple types of cancers, and there exists an inverse correlation between KLF14 and Plk4 protein expression in human breast and colon cancers. Moreover, KLF14 depletion promotes AOM/DSS-induced colon tumorigenesis. Our findings reveal that KLF14 reduction serves as a mechanism leading to centrosome amplification and tumorigenesis. On the other hand, forced expression of KLF14 leads to mitotic catastrophe. Collectively, our findings identify KLF14 as a tumour suppressor and highlight its potential as biomarker and therapeutic target for cancer. PMID:26439168

  2. Reversible Gating of Plasmonic Coupling for Optical Signal Amplification.

    Science.gov (United States)

    Khoury, Christopher G; Fales, Andrew M; Vo-Dinh, Tuan

    2016-07-20

    Amplification of optical signals is useful for a wide variety of applications, ranging from data signal transmission to chemical sensing and biomedical diagnostics. One such application in chemical sensing is surface-enhanced Raman scattering (SERS), an important technique for increasing the Raman signal using the plasmonic effect of enhanced electromagnetic fields associated with metallic nanostructures. One of the most important limitations of SERS-based amplification is the difficulty to reproducibly control the SERS signal. Here, we describe the design and implementation of a unique hybrid system capable of producing reversible gating of plasmonic coupling for Raman signal amplification. The hybrid system is composed of two subsystems: (1) colloidal magneto-plasmonic nanoparticles for SERS enhancement and (2) a micromagnet substrate with an externally applied magnetic field to modulate the colloidal nanoparticles. For this proof of concept demonstration, the nanoparticles were labeled with a Raman-active dye, and it was shown that the detected SERS signal could be reproducibly modulated by controlling the externally applied magnetic field. The developed system provides a simple, robust, inexpensive, and reusable device for SERS signal modulation. These properties will open up new possibilities for optical signal amplification and gating as well for high-throughput, reproducible SERS detection. PMID:27347606

  3. Loop-mediated isothermal amplification of single pollen grains

    Institute of Scientific and Technical Information of China (English)

    Ali Bektaş; Ignacio Chapela

    2014-01-01

    The polymerase chain reaction (PCR) has been a reliable and fruitful method for many applications in ecology. Nevertheless, unavoidable technical and instrumental require-ments of PCR have limited its widespread application in field situations. The recent development of isothermal DNA amplifica-tion methods provides an alternative to PCR, which circumvents key limitations of PCR for direct amplification in the field. Being able to analyze DNA in the pol en cloud of an ecosystem would provide very useful ecological information, yet would require a field-enabled, high-throughput method for this potential to be realized. Here, we demonstrate the applicability of the loop-mediated DNA amplification method (LAMP), an isothermal DNA amplification technique, to be used in pol en analysis. We demonstrate that LAMP can provide a reliable method to identify species from the pol en cloud, and that it can amplify successful y with sensitivity down to single pol en grains, thus opening the possibility of field-based, high-throughput analysis.

  4. Four-quadrant flyback converter for direct audio power amplification

    DEFF Research Database (Denmark)

    Ljusev, Petar; Andersen, Michael Andreas E.

    2005-01-01

    This paper presents a bidirectional, four-quadrant flyback converter for use in direct audio power amplification. When compared to the standard Class-D switching audio power amplifier with a separate power supply, the proposed four-quadrant flyback converter provides simple solution with better...

  5. Soil amplification with a strong impedance contrast: Boston, Massachusetts

    Science.gov (United States)

    Baise, Laurie G.; Kaklamanos, James; Berry, Bradford M; Thompson, Eric

    2016-01-01

    In this study, we evaluate the effect of strong sediment/bedrock impedance contrasts on soil amplification in Boston, Massachusetts, for typical sites along the Charles and Mystic Rivers. These sites can be characterized by artificial fill overlying marine sediments overlying glacial till and bedrock, where the depth to bedrock ranges from 20 to 80 m. The marine sediments generally consist of organic silts, sand, and Boston Blue Clay. We chose these sites because they represent typical foundation conditions in the city of Boston, and the soil conditions are similar to other high impedance contrast environments. The sediment/bedrock interface in this region results in an impedance ratio on the order of ten, which in turn results in a significant amplification of the ground motion. Using stratigraphic information derived from numerous boreholes across the region paired with geologic and geomorphologic constraints, we develop a depth-to-bedrock model for the greater Boston region. Using shear-wave velocity profiles from 30 locations, we develop average velocity profiles for sites mapped as artificial fill, glaciofluvial deposits, and bedrock. By pairing the depth-to-bedrock model with the surficial geology and the average shear-wave velocity profiles, we can predict soil amplification in Boston. We compare linear and equivalent-linear site response predictions for a soil layer of varying thickness over bedrock, and assess the effects of varying the bedrock shear-wave velocity (VSb) and quality factor (Q). In a moderate seismicity region like Boston, many earthquakes will result in ground motions that can be modeled with linear site response methods. We also assess the effect of bedrock depth on soil amplification for a generic soil profile in artificial fill, using both linear and equivalent-linear site response models. Finally, we assess the accuracy of the model results by comparing the predicted (linear site response) and observed site response at the Northeastern

  6. Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

    Science.gov (United States)

    Cox, Christopher R.; Voorhees, Kent J.

    Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

  7. Geometric Effects on the Amplification of First Mode Instability Waves

    Science.gov (United States)

    Kirk, Lindsay C.; Candler, Graham V.

    2013-01-01

    The effects of geometric changes on the amplification of first mode instability waves in an external supersonic boundary layer were investigated using numerical techniques. Boundary layer stability was analyzed at Mach 6 conditions similar to freestream conditions obtained in quiet ground test facilities so that results obtained in this study may be applied to future test article design to measure first mode instability waves. The DAKOTA optimization software package was used to optimize an axisymmetric geometry to maximize the amplification of the waves at first mode frequencies as computed by the 2D STABL hypersonic boundary layer stability analysis tool. First, geometric parameters such as nose radius, cone half angle, vehicle length, and surface curvature were examined separately to determine the individual effects on the first mode amplification. Finally, all geometric parameters were allowed to vary to produce a shape optimized to maximize the amplification of first mode instability waves while minimizing the amplification of second mode instability waves. Since first mode waves are known to be most unstable in the form of oblique wave, the geometries were optimized using a broad range of wave frequencies as well as a wide range of oblique wave angles to determine the geometry that most amplifies the first mode waves. Since first mode waves are seen most often in flows with low Mach numbers at the edge of the boundary layer, the edge Mach number for each geometry was recorded to determine any relationship between edge Mach number and the stability of first mode waves. Results indicate that an axisymmetric cone with a sharp nose and a slight flare at the aft end under the Mach 6 freestream conditions used here will lower the Mach number at the edge of the boundary layer to less than 4, and the corresponding stability analysis showed maximum first mode N factors of 3.

  8. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification

    NARCIS (Netherlands)

    S.O.L. Direito; E. Zaura; M. Little; P. Ehrenfreund; W.F.M. Röling

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement amplific

  9. New perspectives on microbial community distortion after whole-genome amplification

    Science.gov (United States)

    Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the e...

  10. Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens

    International Nuclear Information System (INIS)

    We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. (author)

  11. Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples

    OpenAIRE

    Minsoung Rhee; Yooli K Light; Meagher, Robert J.; Anup K. Singh

    2016-01-01

    Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template D...

  12. Nucleic acid detection system and method for detecting influenza

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  13. Fiber-Optical Parametric Amplification of Sub-Picosecond Pulses for High-Speed Optical Communications

    DEFF Research Database (Denmark)

    Lali-Dastjerdi, Zohreh; Cristofori, Valentina; Rottwitt, Karsten;

    2015-01-01

    This article reviews recent results of amplification of short optical pulses using fiber-optical parametric amplifiers. This includes chirped-pulse amplification of 400 fs pulses, error-free amplification of a 640-Gbit/s optical time-division multiplexed signal with less than a 1-dB power penalty...

  14. The separability of two-mode Gaussian state under amplification and symmetric damping

    Institute of Scientific and Technical Information of China (English)

    Chen Xiao-Yu; Jiang Li-Zhen; Wu Liang-Neng

    2007-01-01

    The performances of a two-mode Gaussian state under parametric amplification, symmetric amplitude damping and thermal noise are studied. The time-dependent complex correlation matrix of the state in evolution is given. The separability of the final two-mode Gaussian state is examined under symmetric amplification and asymmetric amplification separately.

  15. Sensitive and rapid detection of Paragonimus westermani infection in humans and animals by loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Chen, M X; Ai, L; Zhang, R L; Xia, J J; Wang, K; Chen, S H; Zhang, Y N; Xu, M J; Li, X; Zhu, X Q; Chen, J X

    2011-05-01

    In the present study, a loop-mediated isothermal amplification (LAMP) assay was developed and validated for the detection of Paragonimus westermani adults, metacercariae, and eggs in human and animal samples. The LAMP amplification can be finished in 45 min under isothermal condition at 60°C by employing a set of four species-specific primer mixtures and the results can be checked by naked-eye visualization. No amplification products were detected with deoxyribunucleic acid (DNA) of related trematode species including Fasciola hepatica, Fasciola gigantica, Clonorchis sinensis, Opisthorchis viverrini, Schistosoma mansoni, and Schistosoma japonicum. The method was further validated by examining P. westermani DNA in intermediate hosts including freshwater crabs and crayfish, as well as in sputum and pleural fluid samples from patients of paragonimiasis. These results indicated that the LAMP assay was highly specific, sensitive, and rapid, and it was approximately 100 times more sensitive than conventional specific PCR. The LAMP assay established in this study provides a rapid and sensitive tool for the detection of P. westermani DNA in freshwater crabs, crayfish, sputum, and pleural fluid samples, which has important implications for effective control of human paragonimiasis.

  16. Ultrasensitive electrochemical DNAzyme sensor for lead ion based on cleavage-induced template-independent polymerization and alkaline phosphatase amplification.

    Science.gov (United States)

    Liu, Shufeng; Wei, Wenji; Sun, Xinya; Wang, Li

    2016-09-15

    In this article, a simple, highly sensitive and selective electrochemical DNAzyme sensor for Pb(2+) was developed on the basis of a 8-17 DNAzyme cleavage-induced template-independent polymerization and alkaline phosphatase amplification strategy. The hairpin-like substrate strand (HP DNA) of 8-17 DNAzyme was firstly immobilized onto the electrode. In the presence of Pb(2+) and the catalytic strand of 8-17 DNAzyme, the HP DNA could be cleaved to expose the free 3'-OH terminal, which could be then utilized for the cascade operation by terminal deoxynucleotidyl transferase (TdTase) for the base extension to incorporate biotinylated dUTP (dUTP-biotin). The further conjugated streptavidin-labeled alkaline phosphatase (SA-ALP) then catalyzed conversion of electrochemically inactive 1-naphthyl phosphate (1-NP) for the generation of electrochemical response signal. The currently fabricated Pb(2+) sensor effectively combines triply cascade amplification effects including cyclic Pb(2+)-dependent DNAzyme cleavage, TdTase-mediated base extension and enzymatic catalysis of ALP. An impressive detection limit of 0.043nM toward Pb(2+) with an excellent selectivity could be ultimately obtained, which was superior than most of the electrochemical methods. Thus, the developed amplification strategy opens a promising avenue for the detection of metal ions and may extend for the detection of other nucleic acid-related analytes. PMID:27093488

  17. Loop-mediated isothermal amplification assay for the detection of Ehrlichia canis DNA in blood samples from dogs

    Directory of Open Access Journals (Sweden)

    SA Faggion

    2013-01-01

    Full Text Available The rickettsial bacterium Ehrlichia canis is the etiological agent of canine monocytic ehrlichiosis, one of the most important canine tick-borne diseases in the world. In this study, a loop-mediated isothermal amplification (LAMP assay was developed for detection of E. canis DNA using LAMP primers targeting the groESL operon. Reactions were performed at 60°C for 60 min and the results were visualized by gel electrophoresis. Successful amplification was obtained using plasmid DNA containing a fragment of the groESL operon and DNA extracted from blood samples that tested positive for E. canis by real-time PCR. The specificity of amplification was confirmed by EcoRI restriction of internal sites in the LAMP primers and no cross-reactivity with blood samples positive for Babesia spp., another common tick-borne pathogen, was observed. The high cost of nucleic acid tests (NAT is one of the disadvantages for their large-scale use as routine diagnostic tests. The E. canis LAMP assay developed here is an interesting alternative to PCR since it does not require a thermocycler, thus reducing costs for the veterinary clinical laboratory.

  18. Amplification of target-specific, ligation-dependent circular probe.

    Science.gov (United States)

    Zhang, D Y; Brandwein, M; Hsuih, T C; Li, H

    1998-05-12

    We describe a novel polymerase chain reaction (PCR)-based gene amplification method utilizing a circularizable oligodeoxyribonucleotide probe (C-probe). The C-probe contains two target complementary regions located at each terminus and an interposed generic PCR primer binding region. The hybridization of C-probe to a target brings two termini in direct apposition as the complementary regions of C-probe wind around the target to form a double helix. Subsequent ligation of the two termini results in a covalently linked C-probe that becomes 'locked on to' the target. The circular nature of the C-probe allows for the generation of a multimeric single-stranded DNA (ssDNA) via extension of the antisense primer by Taq DNA polymerase along the C-probe and displacement of downstream strand, analogous to 'rolling circle' replication of bacteriophage in vivo. This multimeric ssDNA then serves as a template for multiple sense primers to hybridize, extend, and displace downstream DNA, generating a large ramified (branching) DNA complex. Subsequent thermocycling denatures the dsDNA and initiates the next round of primer extension and ramification. This model results in significantly improved amplification kinetics (super-exponential) as compared to conventional PCR. Our results show that the C-probe was 1000 times more sensitive than the corresponding linear hemiprobes for detecting Epstein-Barr virus early RNA. The C-probe not only increases the power of amplification but also offers a means for decontaminating carryover amplicons. As the ligated C-probes possess no free termini, they are resistant to exonuclease digestion, whereas contaminated linear amplicons are susceptible to digestion. Treatment of the ligation reaction mixture with exonuclease prior to amplification eliminated the amplicon contaminant, which could also have been co-amplified with the same PCR primers; only the ligated C-probes were amplified. The combined advantages of the C-probe and thermocycling have a

  19. [Detection of the Zaire Subtype of the Ebola Virus by Isothermal Multiple Self-matching Initiated Amplification].

    Science.gov (United States)

    Li, Xinna; Nie, Kai; Wang, Ji; Zhang, Dan; Guan, Li; Liu, Jun; Ke, Yuehua; Zhou, Hangyu; Ma, Xuejun

    2016-01-01

    Given the Ebola outbreak in West Africa and the risks of spread to other regions, a rapid, sensitive and simple method for the detection of the Ebola virus (EBOV) is of great significance for the prevention and control of Ebola. We developed a simple colorimetric isothermal multiple self-matching initiated amplification (IMSA) for rapid detection of the Zaire subtype of the Ebola virus (EBOV-Z). This method employed six primers that recognized seven sites of the EBOV-Z nucleoprotein gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 1 h. Amplification products were detected through visual inspection of color change by pre-addition of hydroxyl naphthol blue dye. Relative sensitivity was validated by detection of serial tenfold dilutions of virus-like particles containing the partial EBOV-Z nucleoprotein gene and mock clinical sample. Specificity of IMSA was validated by detection of the plasma of 30 healthy volunteers, the dengue virus, and Japanese encephalitis virus. IMSA had comparable sensitivity to Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and cross-reaction with human plasma or other viruses was not observed. Reverse transcription-isothermal multiple self-matching initiated amplification (RT-IMSA) was also evaluated and compared in parallel with the commercial RT-qPCR kit for detection of EBOV-suspected samples of human blood in Sierra Leone. Sensitivity and specificity of the RT-IMSA was 91.4% and 100%, respectively. These data suggest that RT-IMSA is a valuable tool for the detection of the EBOV with the distinct advantages of simplicity and low cost compared with RT-qPCR. PMID:27295876

  20. [Detection of the Zaire Subtype of the Ebola Virus by Isothermal Multiple Self-matching Initiated Amplification].

    Science.gov (United States)

    Li, Xinna; Nie, Kai; Wang, Ji; Zhang, Dan; Guan, Li; Liu, Jun; Ke, Yuehua; Zhou, Hangyu; Ma, Xuejun

    2016-01-01

    Given the Ebola outbreak in West Africa and the risks of spread to other regions, a rapid, sensitive and simple method for the detection of the Ebola virus (EBOV) is of great significance for the prevention and control of Ebola. We developed a simple colorimetric isothermal multiple self-matching initiated amplification (IMSA) for rapid detection of the Zaire subtype of the Ebola virus (EBOV-Z). This method employed six primers that recognized seven sites of the EBOV-Z nucleoprotein gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 1 h. Amplification products were detected through visual inspection of color change by pre-addition of hydroxyl naphthol blue dye. Relative sensitivity was validated by detection of serial tenfold dilutions of virus-like particles containing the partial EBOV-Z nucleoprotein gene and mock clinical sample. Specificity of IMSA was validated by detection of the plasma of 30 healthy volunteers, the dengue virus, and Japanese encephalitis virus. IMSA had comparable sensitivity to Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and cross-reaction with human plasma or other viruses was not observed. Reverse transcription-isothermal multiple self-matching initiated amplification (RT-IMSA) was also evaluated and compared in parallel with the commercial RT-qPCR kit for detection of EBOV-suspected samples of human blood in Sierra Leone. Sensitivity and specificity of the RT-IMSA was 91.4% and 100%, respectively. These data suggest that RT-IMSA is a valuable tool for the detection of the EBOV with the distinct advantages of simplicity and low cost compared with RT-qPCR.

  1. Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid

    Directory of Open Access Journals (Sweden)

    Johnson Sandra

    2010-10-01

    Full Text Available Abstract Background Detection of bacterial nucleic acids in synovial fluid following total joint arthroplasty with suspected infection can be difficult; among other technical challenges, inhibitors in the specimens require extensive sample preparation and can diminish assay sensitivity even using polymerase chain reaction (PCR-based methods. To address this problem a simple protocol for prior use of multiple displacement amplification (MDA as an adjunct to PCR was established and tested on both purified S. aureus DNA as well as on clinical samples known to contain S. aureus nucleic acids. Findings A single round of MDA on purified nucleic acids resulted in a > 300 thousand-fold increase in template DNA on subsequent quantitative PCR (qPCR analysis. MDA use on clinical samples resulted in at least a 100-fold increase in sensitivity on subsequent qPCR and required no sample preparation other than a simple alkali/heat lysis step. Mixed samples of S. aureus DNA with a 103 - 104-fold excess of human genomic DNA still allowed for MDA amplification of the minor bacterial component to the threshold of detectability. Conclusion MDA is a promising technique that may serve to significantly enhance the sensitivity of molecular assays in cases of suspected joint infection while simultaneously reducing the specimen handling required.

  2. Spin noise amplification and giant noise in optical microcavity

    Energy Technology Data Exchange (ETDEWEB)

    Ryzhov, I. I.; Poltavtsev, S. V.; Kozlov, G. G.; Zapasskii, V. S. [Spin-Optics Laboratory, St. Petersburg State University, 198504 St. Petersburg (Russian Federation); Kavokin, A. V. [Department of Physics and Astronomy, University of Southampton, Southampton SO17 1BJ (United Kingdom); Spin-Optics Laboratory, St. Petersburg State University, 198504 St. Petersburg (Russian Federation); Lagoudakis, P. V. [Department of Physics and Astronomy, University of Southampton, Southampton SO17 1BJ (United Kingdom)

    2015-06-14

    When studying the spin-noise-induced fluctuations of Kerr rotation in a quantum-well microcavity, we have found a dramatic increase of the noise signal (by more than two orders of magnitude) in the vicinity of anti-crossing of the polariton branches. The effect is explained by nonlinear optical instability of the microcavity giving rise to the light-power-controlled amplification of the polarization noise signal. In the framework of the developed model of built-in amplifier, we also interpret the nontrivial spectral and intensity-related properties of the observed noise signal below the region of anti-crossing of polariton branches. The discovered effect of optically controllable amplification of broadband polarization signals in microcavities in the regime of optical instability may be of interest for detecting weak oscillations of optical anisotropy in fundamental research and for other applications in optical information processing.

  3. Signal amplification in a qubit-resonator system

    International Nuclear Information System (INIS)

    We study the dynamics of a qubit-resonator system, when the resonator is driven by two signals. The interaction of the qubit with the high-amplitude driving we consider in terms of the qubit dressed states. Interaction of the dressed qubit with the second probing signal can essentially change the amplitude of this signal. We calculate the transmission amplitude of the probe signal through the resonator as a function of the qubit energy and the driving frequency detuning. The regions of increase and attenuation of the transmitted signal are calculated and demonstrated graphically. We present the influence of the signal parameters on the value of the amplification, and discuss the values of the qubit-resonator system parameters for an optimal amplification and attenuation of the weak probe signal.

  4. Narrow band amplification of light carrying orbital angular momentum

    CERN Document Server

    Borba, G C; Pruvost, L; Felinto, D; Tabosa, J W R

    2016-01-01

    We report on the amplification of an optical vortex beam carrying orbital angular momentum via induced narrow Raman gain in an ensemble of cold cesium atoms. A 20\\% single-pass Raman gain of a weak vortex signal field is observed with a spectral width of order of 1 MHz, much smaller than the natural width, demonstrating that the amplification process preserves the phase structure of the vortex beam. The gain is observed in the degenerated two-level system associated with the hyperfine transition $6S_{1/2}(F=3)\\leftrightarrow 6P_{3/2}(F^{\\prime}=2)$ of cesium. Our experimental observations are explained with a simple theoretical model based on a three-level $\\Lambda$ system interacting coherently with the weak Laguerre-Gauss field and a strong coupling field, including an incoherent pumping rate between the two degenerate ground-states.

  5. Whole genome amplification - Review of applications and advances

    Energy Technology Data Exchange (ETDEWEB)

    Hawkins, Trevor L.; Detter, J.C.; Richardson, Paul

    2001-11-15

    The concept of Whole Genome Amplification is something that has arisen in the past few years as modifications to the polymerase chain reaction (PCR) have been adapted to replicate regions of genomes which are of biological interest. The applications here are many--forensics, embryonic disease diagnosis, bio terrorism genome detection, ''imoralization'' of clinical samples, microbial diversity, and genotyping. The key question is if DNA can be replicated a genome at a time without bias or non random distribution of the target. Several papers published in the last year and currently in preparation may lead to the conclusion that whole genome amplification may indeed be possible and therefore open up a new avenue to molecular biology.

  6. DC-driven thermoelectric Peltier device for precise DNA amplification

    Science.gov (United States)

    Yamaguchi, Shigeo; Suzuki, Tadzunu; Inoue, Kazuhito; Azumi, Yoshitaka

    2015-05-01

    Using a DC-driven Peltier device, we fabricated a DNA amplification system [polymerase chain reaction (PCR) system] with the aim of increasing its speed and precision. The Peltier device had a well block sandwiched by Bi2Se0.37Te2.36 as an N-type thermoelectric material and Bi0.59Sb1.30Te3 as a P-type material. The well block was directly controlled by the electric current, leading to a high thermal response. Using the Peltier device with the well block, we performed thermal cycles of a PCR, and we demonstrated that our PCR system produces a smaller amount of nonspecific products for the genome DNA (gDNA) of Arabidopsis thaliana, leading to a more precise DNA amplification system.

  7. Resonant Amplification of Turbulence by the Blast Wawes

    CERN Document Server

    Zankovich, A M

    2016-01-01

    We discuss an idea whether spherical blast waves can amplify by a non-local resonant hydrodynamic mechanism inhomogeneities formed by turbulence or phase segregation in the interstellar medium. We consider the problem of a blast-wave-turbulence interaction in the Linear Interaction Approximation. Mathematically, this is an eigenvalue problem for finding the structure and amplitude of eigenfunctions describing the response of the shock-wave flow to forced oscillations by external perturbations in the ambient interstellar medium. Linear analysis shows that the blast wave can amplify density and vorticity perturbations for a wide range of length scales with amplification coefficients of up to 20, with amplification the greater, the larger the length. There also exist resonant harmonics for which the gain becomes formally infinite in the linear approximation. Their orbital wavenumbers are within the range of macro- ($l \\sim 1$), meso- ($l \\sim 20$) and microscopic ($l > 200$) scales. Since the resonance width is ...

  8. Assessing Linearity of the Parasite Varroa destructor DNA Amplification

    Directory of Open Access Journals (Sweden)

    ODAGIU Antonia

    2009-12-01

    Full Text Available The importance of honeybee products make of disease prevention and control in honeybees one of the mainconcerns of beekeepers in the world. The PCR – RT reaction represents an alternative for amplification performed inorder to realize the Varroa destructor O. genotypization, very important stage in haoneybee resistance to parasitedescription and also in management of the treatments. The linearity data is a very important parameter and very usefulin determination of the amplification of the parasite DNA and success of the genotypization process. The amplificationefficiency was very satisfactory, fact revealed by the value of the regression line y = - 2.3103 * 26.552 together withcoefficient of determination equal (r2 = 0.9691, meaning that more than 96% of the reaction efficiency may beexplained by the process liniarity. The implementation of the RT-PCR method was successful and it represents apremise for validation process evolution.

  9. Quantum Privacy Amplification for a Sequence of Single Qubits

    Institute of Scientific and Technical Information of China (English)

    DENG Fu-Guo; LONG Gui-Lu

    2006-01-01

    We present a scheme for quantum privacy amplification (QPA) for a sequence of single qubits. The QPA procedure uses a unitary operation with two controlled-not gates and a Hadamard gate. Every two qubits are performed with the unitary gate operation, and a measurement is made on one photon and the other one is retained.The retained qubit carries the state information of the discarded one. In this way, the information leakage is reduced.The procedure can be performed repeatedly so that the information leakage is reduced to any arbitrarily low level. With this QPA scheme, the quantum secure direct communication with single qubits can be implemented with arbitrarily high security. We also exploit this scheme to do privacy amplification on the single qubits in quantum information sharing for long-distance communication with quantum repeaters.

  10. Phase Sensitive Amplification using Parametric Processes in Optical Fibers

    DEFF Research Database (Denmark)

    Kang, Ning

    Phase sensitive amplification using the parametric processes in fiber has the potential of delivering high gain and broadband operation with ultralow noise. It is able to regenerate both amplitude and phase modulated signals, simultaneously, with the appropriate design. This thesis concerns......, in specific, the design and optimization of such phase sensitive amplifiers (PSAs). For phase sensitive amplification in highly nonlinear fibers, optima points of operation have been identified for both the standard and the novel high stimulated Brillouin scattering (SBS) threshold highly nonlinear fiber....... Further, phase sensitive parametric processes in a nano-engineered silicon waveguide have been measured experimentally for the first time. Numerical optimizations show that with reduced waveguide propagation loss and reduced carrier life time, larger signal phase sensitive extinction ratio is achievable...

  11. Optical parametric chirped pulse amplification based on photonic crystal fibre

    Institute of Scientific and Technical Information of China (English)

    Wang He-Lin; Yang Ai-Jun; Leng Yu-Xin; Wang Cheng; Xu Zhi-Zhan; Hou Lan-Tian

    2011-01-01

    A compact two-stage optical parametric chirped pulse amplifier based on photonic crystal fibre is demonstrated.A 1064-nm soliton pulse is obtained in a home-made photonic crystal fibre(PCF)with femtosecond pulse pumping and then amplified to 2 mJ in an Nd:YAG regenerative amplifier.After the amplified pulses pass through the LBO crystal,the 532-nm double-frequency light with an energy of 0.8 mJ and a duration of over 100 ps at 10-Hz repetition rate is generated as a pump source in the following two-stage optical parametric amplification(OPA).The 850-am chirped signal light gain from the stretcher is 1.5×104in the first-stage OPA while it is 120 in the second-stage OPA.The total signal gain of optical parametric chirped pulse amplification(OPCPA)can reach 1.8×106.

  12. Analytical model of signal amplification in silicon waveguides

    Science.gov (United States)

    Meng, Fan; Yu, Chong-Xiu; Yuan, Jin-Hui

    2012-07-01

    In this paper, an analytical model to investigate the parametric amplification (PA) and the PA + stimulated Raman scattering (SRS) in silicon waveguides is put forward. When two pump signals are employed, the PA bandwidth of the probe signal is so large that the Raman contribution has to be considered. When Raman contribution fraction f is set to be 0, only the PA occurs to amplify the probe signal, and when f is set to be 0.043, the PA and the SRS amplify the probe signal at the same time. The signal amplifications of both single and dual pump schemes are investigated by using this model. With this model, three main affecting factors, i.e., zero dispersion wavelength (ZDWL), third-order dispersion (TOD), and fourth-order dispersion (FOD), are discussed in detail.

  13. Amplification, Decoherence, and the Acquisition of Information by Spin Environments

    Science.gov (United States)

    Zwolak, Michael; Riedel, C. Jess; Zurek, Wojciech H.

    2016-05-01

    Quantum Darwinism recognizes the role of the environment as a communication channel: Decoherence can selectively amplify information about the pointer states of a system of interest (preventing access to complementary information about their superpositions) and can make records of this information accessible to many observers. This redundancy explains the emergence of objective, classical reality in our quantum Universe. Here, we demonstrate that the amplification of information in realistic spin environments can be quantified by the quantum Chernoff information, which characterizes the distinguishability of partial records in individual environment subsystems. We show that, except for a set of initial states of measure zero, the environment always acquires redundant information. Moreover, the Chernoff information captures the rich behavior of amplification in both finite and infinite spin environments, from quadratic growth of the redundancy to oscillatory behavior. These results will considerably simplify experimental testing of quantum Darwinism, e.g., using nitrogen vacancies in diamond.

  14. Separate TRP channels mediate amplification and transduction in drosophila

    Science.gov (United States)

    Lehnert, Brendan P.; Baker, Allison E.; Wilson, Rachel I.

    2015-12-01

    Auditory receptor cells rely on mechanically-gated channels to transform sound stimuli into neural activity. Several TRP channels have been implicated in Drosophila auditory transduction, but mechanistic studies have been hampered by the inability to record subthreshold signals from receptor neurons. We developed a non-invasive method for measuring these signals by recording from a central neuron that is electrically coupled to a genetically-defined population of auditory receptors. We find that the TRPN family member NompC, which is necessary for the active amplification of motion by the auditory organ, is not required for transduction. Instead, NompC sensitizes the transduction complex to movement and precisely regulates the static forces on the complex. In contrast, the TRPV channels Nanchung and Inactive are required for responses to sound, suggesting they are components of the transduction complex. Thus, transduction and active amplification are genetically separable processes in Drosophila hearing.

  15. Retrieval and Amplification of DNA from Unstained Histopathological Sections

    Institute of Scientific and Technical Information of China (English)

    DonnaC.MONTAGUE; BeverlyD.LYN-COOK; 等

    1993-01-01

    Testing of compounds for carcinogenic potential in vivo involves various experimental designs.A few of these techniques are directed to demonstrate the genotoxicity and mutagenicity of the compound by histopathology.These changes shown by histochemical means include monoclonal antibody directed cellular markers.Development of the polymerase chain reaction technique(PCR)for amplification of DNA has facilitated the investigation of molecular events related to the formation of malignant neoplasms.We describe here a method for screening tissues for mutations of the H-ras gene using monoclonal antibodies directed toward normal and mutant p21 proteins.Formalin-fixed,paraffinembedded tissue sections are used to subsequently confirm the gene mutation by PCR amplification of the H-ras gene.The results indicated a successful application of this technique to demonstrate the presence of p21 oncoprotein in the tissues tested.

  16. Weak value amplification is suboptimal for estimation and detection.

    Science.gov (United States)

    Ferrie, Christopher; Combes, Joshua

    2014-01-31

    We show by using statistically rigorous arguments that the technique of weak value amplification does not perform better than standard statistical techniques for the tasks of single parameter estimation and signal detection. Specifically, we prove that postselection, a necessary ingredient for weak value amplification, decreases estimation accuracy and, moreover, arranging for anomalously large weak values is a suboptimal strategy. In doing so, we explicitly provide the optimal estimator, which in turn allows us to identify the optimal experimental arrangement to be the one in which all outcomes have equal weak values (all as small as possible) and the initial state of the meter is the maximal eigenvalue of the square of the system observable. Finally, we give precise quantitative conditions for when weak measurement (measurements without postselection or anomalously large weak values) can mitigate the effect of uncharacterized technical noise in estimation.

  17. Optical Amplification and Photosensitivity in Sol-Gel Based Waveguides

    OpenAIRE

    Selvarajan, A; T. Srinivas

    2001-01-01

    The sol-gel process has emerged as an effective route for the fabrication of optical waveguides and guided wave devices and circuits. In particular, it is possible to incorporate active dopants like neodymium, erbium, and cesium for integrated optical active devices and circuits. In this paper, a review of recent research on active devices and circuits based on sol-gel process is made. Specific studies undertaken in our laboratory on optical amplification and photosensitivity characteristi...

  18. Purely nonlinear disorder-induced localizations and their parametric amplification

    CERN Document Server

    Folli, Viola; Conti, Claudio

    2013-01-01

    We investigate spatial localization in a quadratic nonlinear medium in the presence of randomness. By means of numerical simulations and theoretical analyses we show that, in the down conversion regime, the transverse random modulation of the nonlinear susceptibility generates localizations of the fundamental wave that grow exponentially in propagation. The localization length is optically controlled by the pump intensity which determines the amplification rate. The results also apply to cubic nonlinearities.

  19. Hyper dispersion pulse compressor for chirped pulse amplification systems

    Energy Technology Data Exchange (ETDEWEB)

    Barty, Christopher P. J. (Hayward, CA)

    2011-11-29

    A grating pulse compressor configuration is introduced for increasing the optical dispersion for a given footprint and to make practical the application for chirped pulse amplification (CPA) to quasi-narrow bandwidth materials, such as Nd:YAG. The grating configurations often use cascaded pairs of gratings to increase angular dispersion an order of magnitude or more. Increased angular dispersion allows for decreased grating separation and a smaller compressor footprint.

  20. Uncertainty of site amplification derived from ground response analysis

    OpenAIRE

    Afshari, K; Stewart, JP

    2015-01-01

    Site-specific geotechnical ground response analyses (GRAs) are typically performed to evaluate stress and strain demands within soil profiles and/or to improve the estimation of site response relative to generic site terms from empirical prediction equations. Implementation of GRA results in probabilistic seismic hazard analysis (PSHA) requires knowledge of the mean and standard deviation of site amplification from GRA. We provide expressions for evaluating within-event standard deviations of...

  1. Risk communication and the social amplification of risk

    OpenAIRE

    Renn, Ortwin

    1991-01-01

    Risk communication is a novel concept in the scientific pursuit to understand and analyze risk related decisions and behavior in modem society. But the new term has only changed the focus of attention from a static description of what risk means for different communities to a dynamic analysis on how these communities exchange information about risk and adjust their behavior.The concept of social amplification of risk provides a framework for the analysis of communication as well as other soci...

  2. Whole genome amplification of DNA for genotyping pharmacogenetics candidate genes.

    Directory of Open Access Journals (Sweden)

    Santosh ePhilips

    2012-03-01

    Full Text Available Whole genome amplification (WGA technologies can be used to amplify genomic DNA when only small amounts of DNA are available. The Multiple Displacement Amplification Phi polymerase based amplification has been shown to accurately amplify DNA for a variety of genotyping assays; however, it has not been tested for genotyping many of the clinically relevant genes important for pharmacogenetic studies, such as the cytochrome P450 genes, that are typically difficult to genotype due to multiple pseudogenes, copy number variations, and high similarity to other related genes. We evaluated whole genome amplified samples for Taqman™ genotyping of SNPs in a variety of pharmacogenetic genes. In 24 DNA samples from the Coriell human diversity panel, the call rates and concordance between amplified (~200-fold amplification and unamplified samples was 100% for two SNPs in CYP2D6 and one in ESR1. In samples from a breast cancer clinical trial (Trial 1, we compared the genotyping results in samples before and after WGA for four SNPs in CYP2D6, one SNP in CYP2C19, one SNP in CYP19A1, two SNPs in ESR1, and two SNPs in ESR2. The concordance rates were all >97%. Finally, we compared the allele frequencies of 143 SNPs determined in Trial 1 (whole genome amplified DNA to the allele frequencies determined in unamplified DNA samples from a separate trial (Trial 2 that enrolled a similar population. The call rates and allele frequencies between the two trials were 98% and 99.7%, respectively. We conclude that the whole genome amplified DNA is suitable for Taqman™ genotyping for a wide variety of pharmacogenetically relevant SNPs.

  3. Amplification of acoustic waves in laminated piezoelectric semiconductor plates

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J.S.; Yang, X.M.; Turner, J.A. [University of Nebraska, Department of Engineering Mechanics, Lincoln, NE (United States)

    2004-12-01

    Two-dimensional equations for coupled extensional, flexural and thickness-shear motions of laminated plates of piezoelectric semiconductors are obtained systematically from the three-dimensional equations by retaining lower order terms in power series expansions in the plate thickness coordinate. The equations are used to analyze extensional waves in a composite plate of piezoelectric ceramics and semiconductors. Dispersion and dissipation due to semiconduction as well as wave amplification by a dc electric field are discussed. (orig.)

  4. Rapid Diagnosis of Extrapulmonary Tuberculosis by Ligase Chain Reaction Amplification

    OpenAIRE

    Gamboa, Fredy; Dominguez, José; Padilla, Eduardo; Manterola, José M.; Gazapo, Elena; Lonca, Joan; Matas, Lurdes; Hernandez, Agueda; Cardona, Pere Joan; Ausina, Vicente

    1998-01-01

    A rapid amplification-based test for the diagnosis of extrapulmonary tuberculosis, the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, was evaluated. Results from the LCx M. tuberculosis Assay were compared with those from culture and the final clinical diagnosis for each patient. A total of 526 nonrespiratory specimens from 492 patients were tested. The specimens included urine; feces; lymph node exudates; pleural, cerebrospinal, articular, and ascitic fluids; tissue biopsies;...

  5. Invertible Clipping for Increasing the Power Efficiency of OFDM Amplification

    OpenAIRE

    Ragusa, Salvatore; Palicot, Jacques; Louët, Yves; Lereau, Christian

    2006-01-01

    International audience Large fluctuations of OFDM signal amplitude represent an important problem for power amplification in mobile communication systems. In this paper, we propose a new Peak-to-Average Power Ratio (PAPR) reduction method based on the well known clipping and filtering one. Called "invertible clipping", it is performed thanks to a "soft clipping function". Since this soft clipping can be inverted in reception side, degradations are compensated. The derived method benefits f...

  6. Swing amplification and global modes reciprocity in models with cusps

    CERN Document Server

    Polyachenko, Evgeny

    2016-01-01

    Using 3D N-body simulations we analyse an onset of the bar in cuspy models, and argue that role of swing amplification is twofold. Amplified shot noise due to disc discreteness hampers bar formation, while induced resonance perturbations allow bar amplitude to overcome shots. A bar pattern speed and a growth rate obtained in N-body simulations agree well with global mode analysis.

  7. MYC Amplification in Angiosarcoma Arising from an Arteriovenous Graft Site

    Directory of Open Access Journals (Sweden)

    Kristen M. Paral

    2015-01-01

    Full Text Available Angiosarcoma arising in association with an arteriovenous graft (AVG or fistula is a unique clinicopathologic scenario that appears to be gaining recognition in the literature. Among reported cases, none has described high-level MYC gene amplification, a genetic aberration that is increasingly unifying the various clinicopathologic subdivisions of angiosarcoma. We therefore report the MYC gene status in a case of angiosarcoma arising at an AVG site.

  8. Topographic amplification from recorded earthquake data and numerical simulations

    OpenAIRE

    Cauzzi, Carlo; Swiss Seismological Service (SED-ETHZ), Zürich, Switzerland; Fäh, Donat; Swiss Seismological Service (SED-ETHZ), Zürich, Switzerland; Pessina, Vera; Istituto Nazionale di Geofisica e Vulcanologia, Sezione Milano-Pavia, Milano, Italia; Faccioli, Ezio; Department of Structural Engineering, Politecnico di Milano, Italy; Smerzini, Chiara; Department of Structural Engineering, Politecnico di Milano, Italy

    2012-01-01

    With the aim of contributing to the refinement of the next generation of tools for seismic hazard analyses, we present here an attempt at including topographic amplification factors in GMPEs, thus broadening the traditional options for site effects. With a view to critically discuss and complement with new data the approach of Cauzzi et al. (2010) and Paolucci (2002), information from additional numerical models including crustal layering are taken into account. The indications obtained from ...

  9. Enhanced sequencing coverage with digital droplet multiple displacement amplification.

    Science.gov (United States)

    Sidore, Angus M; Lan, Freeman; Lim, Shaun W; Abate, Adam R

    2016-04-20

    Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing.

  10. EGFR Amplification and Glioblastoma Stem-Like Cells

    Directory of Open Access Journals (Sweden)

    Katrin Liffers

    2015-01-01

    Full Text Available Glioblastoma (GBM, the most common malignant brain tumor in adults, contains a subpopulation of cells with a stem-like phenotype (GS-cells. GS-cells can be maintained in vitro using serum-free medium supplemented with epidermal growth factor, basic fibroblast growth factor-2, and heparin. However, this method does not conserve amplification of the Epidermal Growth Factor Receptor (EGFR gene, which is present in over 50% of all newly diagnosed GBM cases. GS-cells with retained EGFR amplification could overcome the limitations of current in vitro model systems and contribute significantly to preclinical research on EGFR-targeted therapy. This review recapitulates recent methodological approaches to expand stem-like cells from GBM with different EGFR status in order to maintain EGFR-dependent intratumoral heterogeneity in vitro. Further, it will summarize the current knowledge about the impact of EGFR amplification and overexpression on the stem-like phenotype of GBM-derived GS-cells and different approaches to target the EGFR-dependent GS-cell compartment of GBM.

  11. Diagnosis of brugian filariasis by loop-mediated isothermal amplification.

    Directory of Open Access Journals (Sweden)

    Catherine B Poole

    Full Text Available In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis.

  12. Diagnosis of brugian filariasis by loop-mediated isothermal amplification.

    Science.gov (United States)

    Poole, Catherine B; Tanner, Nathan A; Zhang, Yinhua; Evans, Thomas C; Carlow, Clotilde K S

    2012-01-01

    In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis.

  13. Mechanism of seasonal Arctic sea ice evolution and Arctic amplification

    Science.gov (United States)

    Kim, Kwang-Yul; Hamlington, Benjamin D.; Na, Hanna; Kim, Jinju

    2016-09-01

    Sea ice loss is proposed as a primary reason for the Arctic amplification, although the physical mechanism of the Arctic amplification and its connection with sea ice melting is still in debate. In the present study, monthly ERA-Interim reanalysis data are analyzed via cyclostationary empirical orthogonal function analysis to understand the seasonal mechanism of sea ice loss in the Arctic Ocean and the Arctic amplification. While sea ice loss is widespread over much of the perimeter of the Arctic Ocean in summer, sea ice remains thin in winter only in the Barents-Kara seas. Excessive turbulent heat flux through the sea surface exposed to air due to sea ice reduction warms the atmospheric column. Warmer air increases the downward longwave radiation and subsequently surface air temperature, which facilitates sea surface remains to be free of ice. This positive feedback mechanism is not clearly observed in the Laptev, East Siberian, Chukchi, and Beaufort seas, since sea ice refreezes in late fall (November) before excessive turbulent heat flux is available for warming the atmospheric column in winter. A detailed seasonal heat budget is presented in order to understand specific differences between the Barents-Kara seas and Laptev, East Siberian, Chukchi, and Beaufort seas.

  14. Raman amplification in plasma: thermal effects and damping

    Science.gov (United States)

    Farmer, J. P.; Ersfeld, B.; Raj, G.; Jaroszynski, D. A.

    2009-05-01

    The role of thermal effects on Raman amplification are investigated. The direct effects of damping on the process are found to be limited, leading only to a decrease from the peak output intensity predicted by cold plasma models. However, the shift in plasma resonance due to the Bohm-Gross shift can have a much larger influence, changing the required detuning between pump and probe and introducing an effective chirp through heating of the plasma by the pump pulse. This "thermal chirp" can both reduce the efficiency of the interaction and alter the evolution of the amplified probe, avoiding the increase in length observed in the linear regime without significant pump depletion. The influence of this chirp can be reduced by using a smaller ratio of laser frequency to plasma frequency, which simultaneously increases the growth rate of the probe and decreases the shift in plasma resonance. As such, thermal effects only serve to suppress the amplification of noise at low growth rates. The use of a chirped pump pulse can be used to suppress noise for higher growth rates, and has a smaller impact on the peak output intensity for seeded amplification. For the parameter ranges considered, Landau damping was found to be negligible, as Landau damping rates are typically small, and the low collisionality of the plasma causes the process to saturate quickly.

  15. Practical optimization of amplification mechanisms for piezoelectric actuators

    Science.gov (United States)

    Loveday, Philip W.

    2003-08-01

    A method for designing practical displacement amplification mechanisms for piezoelectric stack actuators was developed. The amplification mechanisms and the piezoelectric stack actuators were modeled using plane-strain finite elements. Optimal sizing and topology optimization were performed simultaneously to maximize the first natural frequency while satisfying free stroke and stress constraints. Optimal sizing variables were selected to control the kinematic behavior of the mechanism while a restricted variable thickness sheet topology optimization method was used to remove unnecessary material from stiff regions of the structure. Calculation of sensitivities was very efficient for the topology optimization variables but required the major portion of computational time for the optimal sizing variables. The method was applied to beam-type lever amplification mechanisms and two devices that included pre-stressing of the piezoelectric ceramics and pure translation of the output point were optimized, manufactured and tested. The results demonstrate that the method presented can be used to design amplified piezoelectric actuators that can be manufactured without interpretation by the designer.

  16. Three-dimensional topographic amplification of seismic motion: Engineering Applications

    Science.gov (United States)

    Assimaki, D.; Mohammadi, K.

    2012-12-01

    Topography effects are associated with the presence of strong topographic relief; documented observations during strong seismic events have shown that structures on the tops of hills, ridges, and canyons had suffered greater damage than similar structures at the hill bases or on level ground. While there is qualitative agreement between theory and observations on topography effects, there is clear quantitative discrepancy: numerical predictions of crest-to-base amplification factors rarely exceed the value of 2, while amplification values observed in the field are as high as 10. We here investigate the focusing and scattering of seismic waves in 3D features by means of a systematic parametric study of the seismic response of idealized geometries on the surface of homogeneous elastic half space using finite differences, to quantify the role of geometry, material properties and ground motion characteristics in the predicted ground surface response. We specifically focus on pyramid (convex) geometries and elastic homogeneous material behavior, and use Ricker wavelets as vertical and oblique incident pulses on ground surface. Results are compared to analytical solutions and thereafter extended to account for soil layering, nonlinear response and broadband incident motion characteristics. We then develop geometry, material and ground motion dependent dimensionless amplification factors that can multiply flat ground surface response spectra and account for topography effects as part of engineering design code provisions.omparison of the scattered wavefield complexity emanating at the vertex and toe of a 45deg single slope upon incidence of a vertical, a forward and a backward oblique wave.

  17. Diagnosis of brugian filariasis by loop-mediated isothermal amplification.

    Science.gov (United States)

    Poole, Catherine B; Tanner, Nathan A; Zhang, Yinhua; Evans, Thomas C; Carlow, Clotilde K S

    2012-01-01

    In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis. PMID:23272258

  18. Amplification of seismic ground motion in the Tunis basin: Numerical BEM simulations vs experimental evidences

    CERN Document Server

    Kham, Marc; Bouden-Romdhane, Nejla

    2013-01-01

    This paper aims at the analysis of seismic wave amplification in a deep alluvial basin in the city of Tunis in Tunisia. This sedimentary basin is 3000m wide and 350m deep. Since the seismic hazard is significant in this area, the depth of the basin and the strong impedance ratio raise the need for an accurate estimation of seismic motion amplification. Various experimental investigations were performed in previous studies to characterize site effects. The Boundary Element Method is considered herein to assess the parameter sensitivity of the amplification process and analyse the prevailing phenomena. The various frequencies of maximum amplification are correctly estimated by the BEM simulations. The maximum amplification level observed in the field is also well retrieved by the numerical simulations but, due to the sensitivity of the location of maximum amplification in space, the overall maximum amplification has to be considered. The influence of the wave-field incidence and material damping is also discuss...

  19. Use of Ramification Amplification Assay for Detection of Escherichia coli O157:H7 and Other E. coli Shiga Toxin-Producing Strains

    OpenAIRE

    Li, Fan; Zhao, Chunyan; Zhang, Wandi; Cui, Shenghui; Meng, Jianghong; Wu, Josephine; Zhang, David Y.

    2005-01-01

    Escherichia coli O157:H7 and other Shiga toxin-producing E. coli (STEC) strains are important human pathogens that are mainly transmitted through the food chain. These pathogens have a low infectious dose and may cause life-threatening illnesses. However, detection of this microorganism in contaminated food or a patient's stool specimens presents a diagnostic challenge because of the low copy number in the sample. Often, a more sensitive nucleic acid amplification method, such as PCR, is requ...

  20. Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification

    OpenAIRE

    Dean, Frank B.; Nelson, John R.; Giesler, Theresa L.; Lasken, Roger S.

    2001-01-01

    We describe a simple method of using rolling circle amplification to amplify vector DNA such as M13 or plasmid DNA from single colonies or plaques. Using random primers and φ29 DNA polymerase, circular DNA templates can be amplified 10,000-fold in a few hours. This procedure removes the need for lengthy growth periods and traditional DNA isolation methods. Reaction products can be used directly for DNA sequencing after phosphatase treatment to inactivate unincorporated nucleotides. Amplified ...

  1. Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification.

    Science.gov (United States)

    Itonaga, Masahiro; Matsuzaki, Ibu; Warigaya, Kenji; Tamura, Takaaki; Shimizu, Yuki; Fujimoto, Masakazu; Kojima, Fumiyoshi; Ichinose, Masao; Murata, Shin-Ichi

    2016-01-01

    Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP), for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. PNA-LNA mediated LAMP was applied for cDNA from 4 kinds of pancreatic carcinoma cell lines with or without KRAS point mutation. The amplified DNA products were verified by naked-eye as well as a real-time PCR equipment. By PNA-LNA mediated LAMP, amplification of wild type KRAS DNA was blocked by clamping PNA probe, whereas, mutant type KRAS DNA was significantly amplified within 50 min. Mutant alleles could be detected in samples which diluted until 0.1% of mutant-to-wild type ratio. On the other hand, mutant alleles could be reproducibly with a mutant-to-wild type ratio of 30% by direct sequencing and of 1% by PNA-clamping PCR. The limit of detection (LOD) of PNA-LNA mediated LAMP was much lower than the other conventional methods. Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V) of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. PNA-LNA mediated LAMP is a simple, rapid, specific and sensitive methodology for the detection of KRAS mutation. PMID:26999437

  2. Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification.

    Directory of Open Access Journals (Sweden)

    Masahiro Itonaga

    Full Text Available Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP, for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. PNA-LNA mediated LAMP was applied for cDNA from 4 kinds of pancreatic carcinoma cell lines with or without KRAS point mutation. The amplified DNA products were verified by naked-eye as well as a real-time PCR equipment. By PNA-LNA mediated LAMP, amplification of wild type KRAS DNA was blocked by clamping PNA probe, whereas, mutant type KRAS DNA was significantly amplified within 50 min. Mutant alleles could be detected in samples which diluted until 0.1% of mutant-to-wild type ratio. On the other hand, mutant alleles could be reproducibly with a mutant-to-wild type ratio of 30% by direct sequencing and of 1% by PNA-clamping PCR. The limit of detection (LOD of PNA-LNA mediated LAMP was much lower than the other conventional methods. Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. PNA-LNA mediated LAMP is a simple, rapid, specific and sensitive methodology for the detection of KRAS mutation.

  3. Application of Isothermal Amplification Technology in Molecular Diagnosis%恒温扩增技术在分子诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    李昕

    2011-01-01

    聚合酶链反应(PCR)技术是近年来广泛应用于科学研究和临床检验的一项技术.目前传统的PCR技术中核酸的扩增存在效率不高且需要专用的仪器设备等缺陷,而恒温扩增技术由于引物种类多样,检测方法多变,从而克服了传统PCR核酸扩增技术的缺点,使其越来越多地被应用于分子诊断中.经国内外学者的研究证实,恒温扩增技术有着广泛的应用前景,现着重对恒温扩增技术予以综述.%Polymerase chain reaction( PCR ) is a technology which is widely applied in scientific research and Clinical examination. At present, the conventional PCR employed by nucleic acid amplification has some shortcomings , surh as low efficiency , needing of special instrument ,etc. On the contrary, . the isothermal amplification methods have overcome these disadvantages by utilizing a rich variety of primers and testing methods. It is confirmed by domestic and oversea scholars that a wide range of medical applications of isothermal amplification technology is expected. Here is to provide an overview of isothermal amplification technology.

  4. PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular Localization

    Institute of Scientific and Technical Information of China (English)

    Evangelia I. Petsalaki; Pantelis G. Bagos; Zoi I. Litou; Stavros J. Hamodrakas

    2006-01-01

    The ability to predict the subcellular localization of a protein from its sequence is of great importance, as it provides information about the protein's function.We present a computational tool, PredSL, which utilizes neural networks, Markov chains, profile hidden Markov models, and scoring matrices for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence. It aims to classify proteins into five groups: chloroplast,thylakoid, mitochondrion, secretory pathway, and "other". When tested in a fivefold cross-validation procedure, PredSL demonstrates 86.7% and 87.1% overall accuracy for the plant and non-plant datasets, respectively. Compared with TargetP, which is the most widely used method to date, and LumenP, the results of PredSL are comparable in most cases. When tested on the experimentally verified proteins of the Saccharomyces cerevisiae genome, PredSL performs comparably if not better than any available algorithm for the same task. Furthermore, PredSL is the only method capable for the prediction of these subcellular localizations that is available as a stand-alone application through the URL:http://bioinformatics.biol.uoa.gr/PredSL/.

  5. Identification of family determining residues in Jumonji-C lysine demethylases: A sequence-based, family wide classification.

    Science.gov (United States)

    Slama, Patrick

    2016-03-01

    Histone post-translational modifications play a critical role in the regulation of gene expression. Methylation of lysines at N-terminal tails of histones has been shown to be involved in such regulation. While this modification was long considered to be irreversible, two different classes of enzymes capable of carrying out the demethylation of histone lysines were recently identified: the oxidases, such as LSD1, and the oxygenases (JmjC-containing). Here, a family-wide analysis of the second of these classes is proposed, with over 300 proteins studied at the sequence level. We show that a correlated evolution analysis yields some position/residue pairs which are critical at comparing JmjC sequences and enables the classification of JmjC domains into five families. A few positions appear more frequently among conditions, such as positions 23 (directly C-terminal to the second iron ligand), 24, 252 and 253 (directly N-terminal to a conserved Asn). Implications of family conditions are studied in detail on PHF2, revealing the meaningfulness of the sequence-derived conditions at the structural level. These results should help obtain insights on the diversity of JmjC-containing proteins solely by considering some of the amino acids present in their JmjC domain. PMID:26757344

  6. KRAS and MAPK1 Gene Amplification in Type II Ovarian Carcinomas

    Directory of Open Access Journals (Sweden)

    Noriyuki Ishikawa

    2013-07-01

    Full Text Available In this study, we examined the clinical significance of KRAS and MAPK1 amplification and assessed whether these amplified genes were potential therapeutic targets in type II ovarian carcinoma. Using fluorescence in situ hybridization, immunohistochemistry, and retrospectively collected clinical data, KRAS and MAPK1 amplifications were identified in 9 (13.2% and 5 (7.4% of 68 type II ovarian carcinoma tissue samples, respectively. Interestingly, co-amplification of KRAS and MAPK1 seemed to be absent in the type II ovarian carcinomas tested, except one case. Active phospho-ERK1/2 was identified in 26 (38.2% out of 68 type II ovarian carcinomas and did not correlate with KRAS or MAPK1 amplification. There was no significant relationship between KRAS amplification and overall or progression-free survival in patients with type II ovarian carcinoma. However, patients with MAPK1 amplification had significantly poorer progression-free survival than patients without MAPK1 amplification. Moreover, type II ovarian carcinoma cells with concomitant KRAS amplification and mutation exhibited dramatic growth reduction following treatment with the MEK inhibitor PD0325901. These findings indicate that KRAS/MAPK1 amplification is critical for the growth of a subset of type II ovarian carcinomas. Additionally, RAS/RAF/MEK/ERK pathway-targeted therapy may benefit selected patients with type II ovarian carcinoma harboring KRAS/MAPK1 amplifications.

  7. New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes for radiation molecular cytogenetics

    Directory of Open Access Journals (Sweden)

    Repin Mikhail V

    2009-06-01

    Full Text Available Abstract Background The objective of this work is to obtain the correct relative DNA contents of chromosomes in the normal male and female human diploid genomes for the use at FISH analysis of radiation-induced chromosome aberrations. Results The relative DNA contents of chromosomes in the male and female human diploid genomes have been calculated from the publicly available international Human Genome Project data. New sequence-based data on the relative DNA contents of human chromosomes were compared with the data recommended by the International Atomic Energy Agency in 2001. The differences in the values of the relative DNA contents of chromosomes obtained by using different approaches for 15 human chromosomes, mainly for large chromosomes, were below 2%. For the chromosomes 13, 17, 20 and 22 the differences were above 5%. Conclusion New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes were obtained. This approach, based on the genome sequence, can be recommended for the use in radiation molecular cytogenetics.

  8. Full Genome Sequence-Based Comparative Study of Wild-Type and Vaccine Strains of Infectious Laryngotracheitis Virus from Italy.

    Directory of Open Access Journals (Sweden)

    Alessandra Piccirillo

    Full Text Available Infectious laryngotracheitis (ILT is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV. Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980, 2007 and 2011, and two commercial chicken embryo origin (CEO vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and may be involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains.

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

    Science.gov (United States)

    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

  10. Weak value amplification via second-order correlated technique

    CERN Document Server

    Cui, Ting; Liu, Xiang; Zeng, Gui-Hua

    2015-01-01

    We propose a new framework combining weak measurement and second-order correlated technique. The theoretical analysis shows that WVA experiment can also be implemented by a second-order correlated system. We then build two-dimensional second-order correlated function patterns for achieving higher amplification factor and discuss the signal-to-noise ratio influence. Several advantages can be obtained by our proposal. For instance, detectors with high resolution are not necessary. Moreover, detectors with low saturation intensity are available in WVA setup. Finally, type-one technical noise can be effectively suppressed.

  11. Limits of Femtosecond Fiber Amplification by Parabolic Pre-Shaping

    CERN Document Server

    Fu, Walter; McComb, Timothy S; Lowder, Tyson L; Wise, Frank W

    2016-01-01

    We explore parabolic pre-shaping as a means of generating and amplifying ultrashort pulses. We develop a theoretical framework for modeling the technique and use its conclusions to design a femtosecond fiber amplifier. Starting from 9 ps pulses, we obtain 4.3 $\\mu$J, nearly transform-limited pulses 275 fs in duration, simultaneously achieving over 40 dB gain and 33-fold compression. Finally, we show that this amplification scheme is limited by Raman scattering, and outline a method by which the pulse duration and energy may be further improved and tailored for a given application.

  12. High power amplification of a tailored-pulse fiber laser

    Science.gov (United States)

    Saby, Julien; Sangla, Damien; Caplette, Stéphane; Boula-Picard, Reynald; Drolet, Mathieu; Reid, Benoit; Salin, François

    2013-02-01

    We demonstrate the amplification of a 1064nm pulse-programmable fiber laser with Large Pitch Rod-Type Fibers of various Mode field diameters from 50 to 70 μm. We have developed a high power fiber amplifier at 1064nm delivering up to 100W/1mJ at 15ns pulses and 30W/300μJ at 2ns with linearly polarized and diffraction limited output beam (M²LBO crystals leading to 50W at 532nm and 25W at 355nm with a diffraction limited output. Similar experiments performed at 1032nm are also reported.

  13. Genomic Amplifications Cause False Positives in CRISPR Screens.

    Science.gov (United States)

    Sheel, Ankur; Xue, Wen

    2016-08-01

    In CRISPR-based screens for essential genes, Munoz and colleagues and Aguirre and colleagues show that gene-independent targeting of genomic amplifications in human cancer cell lines reduces proliferation or survival. The correlation between CRISPR target site copy number and lethality demonstrates the need for scrutiny and complementary approaches to rule out off-target effects and false positives in CRISPR screens. Cancer Discov; 6(8); 824-6. ©2016 AACR.See related article by Munoz et al., p. 900See related article by Aguirre et al., p. 914. PMID:27485003

  14. Clinical performance of automated real-time nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance assay in diagnosis of pulmonary tuberculosis in 214 cases%利福平耐药结核分枝杆菌实时荧光定量核酸扩增检测技术在214例诊断肺结核患者中的临床应用评价

    Institute of Scientific and Technical Information of China (English)

    何贵清; 李涛; 施伎蝉; 宁洪叶; 吴祥兵; 蔡明明; 吴正兴; 胡陈婵; 蒋贤高

    2016-01-01

    目的:评估利福平耐药结核分枝杆菌实时荧光定量核酸扩增检测技术(Xpert M TB/RIF)在温州地区诊断肺结核及利福平耐药的临床应用价值。方法纳入可疑肺结核、临床诊断肺结核和可疑耐药肺结核患者214例,采集痰标本同时送检抗酸染色涂片、液体培养和 Xpert M TB/RIF 检测。以临床最终诊断结果为金标准,比较三种方法检测结核分枝杆菌的敏感度、特异度。以液体药物敏感试验结果为金标准,Xpert M TB/RIF 检测利福平耐药的敏感度和特异度。率的比较采取卡方检验。结果以临床最终诊断结果作为金标准,Xpert M TB/RIF 检测结核分枝杆菌的敏感度高于抗酸染色涂片(69.5%比44.1%,χ2=23.31,P <0.01),而与液体培养比较敏感度差异无统计学意义(69.5%比62.1%,χ2=2.15,P>0.05);Xpert M TB/RIF 在痰涂片阳性与阴性的标本中检测结核分枝杆菌的敏感度分别为97.4%和47.5%,在痰涂片阳性与阴性的标本中检测结核分枝杆菌的特异度均为100.0%。以液体药物敏感试验结果为金标准,Xpert M TB/RIF 检测痰标本利福平耐药的敏感度和特异度分别为92.9%和98.8%。结论 Xpert M TB/RIF 能够快速、准确地检测结核分枝杆菌及其利福平耐药性,且敏感度较高,具有很好的应用价值。%Objective To evaluate the clinical application of the automated nucleic acid amplification technology for rapid and simultaneous detection of tuberculosis and rifampicin resistance (Xpert M TB/RIF) in diagnosis of pulmonary tuberculosis in Wenzhou .Methods A total of 214 patients with suspected pulmonary tuberculosis , clinical diagnosed tuberculosis or suspected drug‐resistant tuberculosis were enrolled in this study .The patients′ sputum specimens were collected for acid‐fast smear ,liquid culture and Xpert M TB/RIF assay .The sensitivity

  15. Recovery of community genomes to assess subsurface metabolic potential: exploiting the capacity of next generation sequencing-based metagenomics

    Science.gov (United States)

    Wrighton, K. C.; Thomas, B.; Miller, C. S.; Sharon, I.; Wilkins, M. J.; VerBerkmoes, N. C.; Handley, K. M.; Lipton, M. S.; Hettich, R. L.; Williams, K. H.; Long, P. E.; Banfield, J. F.

    2011-12-01

    , the capacity to oxidize complex organic carbon, as well as lack of membrane bound electron transport chains and an incomplete citric acid cycle. We propose that these organisms grow cryptically on residual biomass from previous biostimulation experiments and thus demonstrate that resource utilization and turnover in the aquifer can be decoupled from existing acetate amendment and external terminal electron accepting processes. In addition to the first recovery of multiple genomes from these novel candidate divisions, our community genomic approach uncovered viral diversity not yet observed at the site, with the reconstruction of six phage genomes and the presence of CRISPR loci detected in bacterial genomes from diverse lineages. These findings have implications for predictive ecosystem modeling, highlighting the importance of integrating the response, adaptation, as well as biological and geochemical feedback mechanisms existing within complex subsurface communities to long term organic carbon amendment.

  16. On the amplification of magnetic fields in cosmic filaments and galaxy clusters

    CERN Document Server

    Vazza, F; Gheller, C; Wang, P

    2014-01-01

    The amplification of primordial magnetic fields via a small-scale turbulent dynamo during structure formation might be able to explain the observed magnetic fields in galaxy clusters. The magnetisation of more tenuous large-scale structures such as cosmic filaments is more uncertain, as it is challenging for numerical simulations to achieve the required dynamical range. In this work, we present magneto-hydrodynamical cosmological simulations on large uniform grids to study the amplification of primordial seed fields in the intracluster medium (ICM) and in the warm-hot-intergalactic medium (WHIM). In the ICM, we confirm that turbulence caused by structure formation can produce a significant dynamo amplification, even if the amplification is smaller than what is reported in other papers. In the WHIM inside filaments, we do not observe significant dynamo amplification, even though we achieve Reynolds numbers of $R_{\\rm e} \\sim 200-300$. The maximal amplification for large filaments is of the order of $\\sim 100$ ...

  17. A robust method for the amplification of RNA in the sense orientation

    OpenAIRE

    Quackenbush John; Marko Nicholas F; Frank Bryan; Lee Norman H

    2005-01-01

    Abstract Background Small quantities of RNA (1–4 μg total RNA) available from biological samples frequently require a single round of amplification prior to analysis, but current amplification strategies have limitations that may restrict their usefulness in downstream genomic applications. The Eberwine amplification method has been extensively validated but is limited by its ability to produce only antisense RNA. Alternatives lack extensive validation and are often confounded by problems wit...

  18. Fiber-Optical Parametric Amplification of Sub-Picosecond Pulses for High-Speed Optical Communications

    Science.gov (United States)

    Lali-Dastjerdi, Zohreh; Cristofori, Valentina; Rottwitt, Karsten; Galili, Michael; Peucheret, Christophe

    2015-03-01

    This article reviews recent results of amplification of short optical pulses using fiber-optical parametric amplifiers. This includes chirped-pulse amplification of 400 fs pulses, error-free amplification of a 640-Gbit/s optical time-division multiplexed signal with less than a 1-dB power penalty, and all-optical phase-preserving amplitude regeneration of a 640-Gbit/s return-to-zero differential phase-shift keying optical time-division multiplexed signal.

  19. Amplification of realistic Schrödinger-cat-state-like states by homodyne heralding

    DEFF Research Database (Denmark)

    Laghaout, Amine; Neergaard-Nielsen, Jonas S.; Rigas, Ioannes;

    2013-01-01

    We present a scheme for the amplification of Schrödinger cat states that collapses two smaller states onto their constructive interference via a homodyne projection. We analyze the performance of the amplification in terms of fidelity and success rate when the input consists of either exact coher...... coherent state superpositions or of photon-subtracted squeezed vacua. The impact of imprecise homodyne detection and of impure squeezing is quantified. We also assess the scalability of iterated amplifications....

  20. STUDY OF SOIL AMPLIFICATION BASED ON MICROTREMOR AND SEISMIC RECORDS IN LIMA PERU

    Science.gov (United States)

    Calderon, Diana; Sekiguchi, Toru; Nakai, Shoichi; Aguilar, Zenon; Lazares, Fernando

    The dynamic characteristics of the ground in Lima, capital of Peru, specifically the amplification are investigated. By using the small and large microtremor array measurements we estimated the soil velocity profiles with depths to the bedrock in many cases. These profiles were used to estimate the amplification factors. Important results are the large amplification factors at EMO, VSV, CAL and CMA (La Molina, Villa El Salvador, El Callao and Bellavista district, respectively).

  1. Amplification of stimulated Brillouin scattering of two collinear pulsed laser beams with orthogonal polarizations.

    Science.gov (United States)

    Shi, Jinwei; Chen, Xudong; Ouyang, Min; Liu, Juan; Liu, Dahe

    2009-06-10

    A polarization-controlling device was developed based on the fact that there can be a time delay between the seeder and the pumping beams during the amplification of a stimulated Brillouin scattering signal. The device causes two coaxially transmitted pulsed beams with orthogonal polarizations to have the same polarization in order to implement amplification by the pumping effect. An experiment showed that good pumping amplification can be achieved by using this technique. PMID:19516374

  2. A cascade amplification strategy based on rolling circle amplification and hydroxylamine amplified gold nanoparticles enables chemiluminescence detection of adenosine triphosphate.

    Science.gov (United States)

    Wang, Ping; Zhang, Tonghuan; Yang, Taoyi; Jin, Nan; Zhao, Yanjun; Fan, Aiping

    2014-08-01

    A highly sensitive and selective chemiluminescent (CL) biosensor for adenosine triphosphate (ATP) was developed by taking advantage of the ATP-dependent enzymatic reaction (ATP-DER), the powerful signal amplification capability of rolling circle amplification (RCA), and hydroxylamine-amplified gold nanoparticles (Au NPs). The strategy relies on the ability of ATP, a cofactor of T4 DNA ligase, to trigger the ligation-RCA reaction. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction between the two ends of the padlock probe, producing a closed circular DNA template that initiates the RCA reaction with phi29 DNA polymerase and dNTP. Therein, many complementary copies of the circular template can be generated. The ATP-DER is eventually converted into a detectable CL signal after a series of processes, including gold probe hybridization, hydroxylamine amplification, and oxidative gold metal dissolution coupled with a simple and sensitive luminol CL reaction. The CL signal is directly proportional to the ATP level. The results showed that the detection limit of the assay is 100 pM of ATP, which compares favorably with those of other ATP detection techniques. In addition, by taking advantage of ATP-DER, the proposed CL sensing system exhibits extraordinary specificity towards ATP and could distinguish the target molecule ATP from its analogues. The proposed method provides a new and versatile platform for the design of novel DNA ligation reaction-based CL sensing systems for other cofactors. This novel ATP-DER based CL sensing system may find wide applications in clinical diagnosis as well as in environmental and biomedical fields.

  3. Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

    Directory of Open Access Journals (Sweden)

    Eskandari Sepehr

    2007-10-01

    Full Text Available Abstract Background Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. ConSequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS family is an ideal model system to assess the quality of our predictions. Results The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores. A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further

  4. CDK4 amplification predicts recurrence of well-differentiated liposarcoma of the abdomen.

    Directory of Open Access Journals (Sweden)

    Sanghoon Lee

    Full Text Available The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD and dedifferentiated (DD liposarcomas.From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR.There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05. Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7% and MDM2 amplification in 46 cases (95.8%. WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041. High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54 was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012 and multivariate analyses (P = 0.020.Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection.

  5. Social amplification of risk in the Internet environment.

    Science.gov (United States)

    Chung, Ik Jae

    2011-12-01

    This article analyzes the dynamic process of risk amplification in the Internet environment with special emphasis on public concern for environmental risks from a high-speed railway tunnel construction project in South Korea. Environmental organizations and activists serving as social stations collected information about the project and its ecological impact, and communicated this with the general public, social groups, and institutions. The Internet provides social stations and the public with an efficient means for interactive communication and an open space for active information sharing and public participation. For example, while the website of an organization such as an environmental activist group can initially trigger local interest, the Internet allows this information to be disseminated to a much wider audience in a manner unavailable to the traditional media. Interaction among social stations demonstrates an amplifying process of public attention to the risk. Analyses of the volume of readers' comments to online newspaper articles and public opinions posted on message board of public and nonprofit organizations show the ripple effects of the amplification process as measured along temporal, geographical, and sectoral dimensions. Public attention is also influenced by the symbolic connotations of risk information. Interpretations of risk in religious, political, or legal terms intensify public concern for the environmental risk. PMID:21539590

  6. Extended amplification of acoustic signals by amphibian burrows.

    Science.gov (United States)

    Muñoz, Matías I; Penna, Mario

    2016-07-01

    Animals relying on acoustic signals for communication must cope with the constraints imposed by the environment for sound propagation. A resource to improve signal broadcast is the use of structures that favor the emission or the reception of sounds. We conducted playback experiments to assess the effect of the burrows occupied by the frogs Eupsophus emiliopugini and E. calcaratus on the amplitude of outgoing vocalizations. In addition, we evaluated the influence of these cavities on the reception of externally generated sounds potentially interfering with conspecific communication, namely, the vocalizations emitted by four syntopic species of anurans (E. emiliopugini, E. calcaratus, Batrachyla antartandica, and Pleurodema thaul) and the nocturnal owls Strix rufipes and Glaucidium nanum. Eupsophus advertisement calls emitted from within the burrows experienced average amplitude gains of 3-6 dB at 100 cm from the burrow openings. Likewise, the incoming vocalizations of amphibians and birds were amplified on average above 6 dB inside the cavities. The amplification of internally broadcast Eupsophus vocalizations favors signal detection by nearby conspecifics. Reciprocally, the amplification of incoming conspecific and heterospecific signals facilitates the detection of neighboring males and the monitoring of the levels of potentially interfering biotic noise by resident frogs, respectively. PMID:27209276

  7. Radiopolymerization of β(-)pinene: A case of chiral amplification

    International Nuclear Information System (INIS)

    β(-)Pinene was treated with γ radiation at three dose levels: 150, 300 and 600 kGy. The expected effect of radiation at these high doses was the partial racemization of the substrate as already observed in the case of other terpene monomers. Unexpectedly β(-)pinene underwent a radiopolymerization reaction into a solid resin and into a dimer. The structure of the products was studied by FT-IR spectroscopy also in comparison to a reference β(-)pinene resin prepared by cationic polymerization. A highly ordered structure was found in the case of the radiopolymer in comparison to the resin from cationic polymerization. Polarimetric measurements have shown astonishing enhancement in the optical activity of the radiopolymer and radiodimer in comparison to the starting optical activity of the β(-)pinene monomer. The results have been discussed in terms of amplification of chirality caused by γ radiation and the implications of this fact on the mechanism of chiral amplification on prebiotic molecules

  8. The national protocol for paediatric amplification in Australia.

    Science.gov (United States)

    King, Alison M

    2010-01-01

    This document describes the national protocol for the selection, fitting, verification, and evaluation of amplification for hearing-impaired children in Australia. It also outlines the approach to management of children who have auditory neuropathy spectrum disorder, children who have mild and unilateral hearing loss, and children who require cochlear implantation. Audiological management of all Australian citizens and permanent residents under twenty-one years of age who have a hearing loss is carried out by the national hearing service provider, Australian Hearing. It is funded by the Australian Government's Hearing Services Program to provide fully subsidised hearing aids, frequency modulated (FM) systems and ongoing audiological management. All hearing aids for children are multi-channel devices that offer wide dynamic range compression, directional microphone technology and feedback cancellation as well as access to multiple listening programs, telecoil and audio-input facilities. Hearing aid gain, frequency response and maximum power output are derived according to the NAL-NL1 prescription procedure and verified using real ear measurements. Amplification benefit is evaluated using a range of speech perception tests and functional assessment questionnaires. PMID:19919326

  9. Radiopolymerization of {beta}(-)pinene: A case of chiral amplification

    Energy Technology Data Exchange (ETDEWEB)

    Cataldo, Franco [Soc. Lupi Chemical Research, Via Casilina 1626/A, 00133 Rome (Italy)]. E-mail: cdcata@flashnet.it; Keheyan, Yeghis [CNR, Istituto per lo studio dei Materiali Nanostrutturati, Department of Chemistry, University ' La Sapienza' , P.le Aldo Moro 1, Rome (Italy)

    2006-05-15

    {beta}(-)Pinene was treated with {gamma} radiation at three dose levels: 150, 300 and 600 kGy. The expected effect of radiation at these high doses was the partial racemization of the substrate as already observed in the case of other terpene monomers. Unexpectedly {beta}(-)pinene underwent a radiopolymerization reaction into a solid resin and into a dimer. The structure of the products was studied by FT-IR spectroscopy also in comparison to a reference {beta}(-)pinene resin prepared by cationic polymerization. A highly ordered structure was found in the case of the radiopolymer in comparison to the resin from cationic polymerization. Polarimetric measurements have shown astonishing enhancement in the optical activity of the radiopolymer and radiodimer in comparison to the starting optical activity of the {beta}(-)pinene monomer. The results have been discussed in terms of amplification of chirality caused by {gamma} radiation and the implications of this fact on the mechanism of chiral amplification on prebiotic molecules.

  10. Advanced unrepeatered systems using novel Raman amplification schemes

    Science.gov (United States)

    Chang, Do-il; Pelouch, Wayne; Burtsev, Sergey; Perrier, Philippe; Fevrier, Herve

    2015-01-01

    Unrepeatered transmission systems provide a cost-effective solution to transmit high capacity channels in submarine networks to communicate between coastal population centers or in terrestrial networks to connect remote areas where service access is difficult. The main goal of unrepeatered systems has traditionally been to achieve the longest reach, however, increasing traffic demands now require unrepeatered systems to support both longer reach and higher transport capacity. As a result, transmission rate of unrepeatered systems has quickly moved from 10 Gb/s to 40 Gb/s or 100 Gb/s. This paper reviews the key basic technologies, with a specific focus on Raman amplification, required for long-reach, high-capacity unrepeatered optical transmission systems. We will discuss novel Raman amplification schemes, enhanced remote optically pumped amplifiers (ROPA), ultra-low loss / large effective area fibers, and coherent transmission with advanced modulation format and high FEC coding gain. We will also report recent experimental demonstrations that show how these technologies have been combined to achieve industry's leading capacity and reach transmission.

  11. Development and Application of Surface Plasmon Polaritons on Optical Amplification

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    2014-01-01

    Full Text Available Propagation of surface plasmon polaritons (SPPs along the interface between a metal and a dielectric has attracted significant attention due to its unique optical properties, which has inspired a plethora of fascinating applications in photonics and optoelectronics. However, SPPs suffer from large attenuation because of the ohmic losses in the metal layer. It has become the main bottom-neck problem for the development of high performance plasmonic devices. This limitation can be overcome by providing the material adjacent to the metal with optical gain. In this paper, a review of gain compensation to SPPs is presented. We focus on the spontaneous radiation amplification and simulated radiation amplification. The ohmic loss of metal was greatly improved by introducing optical gain. Then we introduce several gain mediums of dye doped, quantum dots, erbium ion, and semiconductor to compensate optical loss of SPPs. Using gain medium mentioned above can compensate losses and achieve many potential applications, for example, laser, amplifier, and LRSPP discussed.

  12. Resonant Amplification of Turbulence by the Blast Waves

    Science.gov (United States)

    Zankovich, A. M.; Kovalenko, I. G.

    2015-02-01

    We discuss the idea of whether spherical blast waves can amplify by a nonlocal resonant hydrodynamic mechanism inhomogeneities formed by turbulence or phase segregation in the interstellar medium. We consider the problem of a blast-wave-turbulence interaction in the Linear Interaction Approximation. Mathematically, this is an eigenvalue problem for finding the structure and amplitude of eigenfunctions describing the response of the shock-wave flow to forced oscillations by external perturbations in the ambient interstellar medium. Linear analysis shows that the blast wave can amplify density and vorticity perturbations for a wide range of length scales with amplification coefficients of up to 20, with increasing amplification the larger the length. There also exist resonant harmonics for which the gain becomes formally infinite in the linear approximation. Their orbital wavenumbers are within the range of macro- (l ~ 1), meso- (l ~ 20), and microscopic (l > 200) scales. Since the resonance width is narrow (typically, Δl < 1), resonance should select and amplify discrete isolated harmonics. We speculate on a possible explanation of an observed regular filamentary structure of regularly shaped round supernova remnants such as SNR 1572, 1006, or 0509-67.5. Resonant mesoscales found (l ≈ 18) are surprisingly close to the observed scales (l ≈ 15) of ripples in the shell's surface of SNR 0509-67.5.

  13. RESONANT AMPLIFICATION OF TURBULENCE BY THE BLAST WAVES

    Energy Technology Data Exchange (ETDEWEB)

    Zankovich, A. M.; Kovalenko, I. G., E-mail: ilya.g.kovalenko@gmail.com [Physicotechnical Institute, Volgograd State University, Volgograd 400062 (Russian Federation)

    2015-02-10

    We discuss the idea of whether spherical blast waves can amplify by a nonlocal resonant hydrodynamic mechanism inhomogeneities formed by turbulence or phase segregation in the interstellar medium. We consider the problem of a blast-wave-turbulence interaction in the Linear Interaction Approximation. Mathematically, this is an eigenvalue problem for finding the structure and amplitude of eigenfunctions describing the response of the shock-wave flow to forced oscillations by external perturbations in the ambient interstellar medium. Linear analysis shows that the blast wave can amplify density and vorticity perturbations for a wide range of length scales with amplification coefficients of up to 20, with increasing amplification the larger the length. There also exist resonant harmonics for which the gain becomes formally infinite in the linear approximation. Their orbital wavenumbers are within the range of macro- (l ∼ 1), meso- (l ∼ 20), and microscopic (l > 200) scales. Since the resonance width is narrow (typically, Δl < 1), resonance should select and amplify discrete isolated harmonics. We speculate on a possible explanation of an observed regular filamentary structure of regularly shaped round supernova remnants such as SNR 1572, 1006, or 0509-67.5. Resonant mesoscales found (l ≈ 18) are surprisingly close to the observed scales (l ≈ 15) of ripples in the shell's surface of SNR 0509-67.5.

  14. RESONANT AMPLIFICATION OF TURBULENCE BY THE BLAST WAVES

    International Nuclear Information System (INIS)

    We discuss the idea of whether spherical blast waves can amplify by a nonlocal resonant hydrodynamic mechanism inhomogeneities formed by turbulence or phase segregation in the interstellar medium. We consider the problem of a blast-wave-turbulence interaction in the Linear Interaction Approximation. Mathematically, this is an eigenvalue problem for finding the structure and amplitude of eigenfunctions describing the response of the shock-wave flow to forced oscillations by external perturbations in the ambient interstellar medium. Linear analysis shows that the blast wave can amplify density and vorticity perturbations for a wide range of length scales with amplification coefficients of up to 20, with increasing amplification the larger the length. There also exist resonant harmonics for which the gain becomes formally infinite in the linear approximation. Their orbital wavenumbers are within the range of macro- (l ∼ 1), meso- (l ∼ 20), and microscopic (l > 200) scales. Since the resonance width is narrow (typically, Δl < 1), resonance should select and amplify discrete isolated harmonics. We speculate on a possible explanation of an observed regular filamentary structure of regularly shaped round supernova remnants such as SNR 1572, 1006, or 0509-67.5. Resonant mesoscales found (l ≈ 18) are surprisingly close to the observed scales (l ≈ 15) of ripples in the shell's surface of SNR 0509-67.5

  15. Principle and Application of Loop-mediated Isothermal Amplification%环介导等温扩增反应的原理及应用

    Institute of Scientific and Technical Information of China (English)

    黄思佳; 解庭波; 严家新

    2011-01-01

    环介导等温扩增反应(Loop-mediated isothermal amplification,LAMP)是日本学者Notomi于2000年在NucleicAcids Res杂志上公开的一种新的基因诊断技术,该法操作简便,扩增效率及灵敏度高,已广泛应用于食品、临床、农业等领域,有望成为主流的基因诊断方法.本文对LAMP的反应特征及原理、优缺点、临床应用作一综述.%Loop-mediated isothermal amplification (LAMP) is a novel technique for genetic diagnosis, which was published on Nucleic Acids Res in 2000 by Notomi, a Japanese scientist. It is a simple, efficient and sensitive DNA amplification method which has been widely used in various fields including food, clinic and agriculture, and might be a mainstream method for genetic diagnosis. This paper reviews the reaction characters, principle, advantage, disadvantage as well as clinical application of LAMP.

  16. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  17. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets.

    Science.gov (United States)

    Sedlazeck, Fritz Joachim; Talloji, Prabhavathi; von Haeseler, Arndt; Bachmair, Andreas

    2013-03-01

    Identification of single nucleotide polymorphisms (SNPs) is a key element in sequence-based genetic analysis. Next generation sequencing offers a cost-effective basis to generate the necessary, large sequence data sets, and bioinformatic methods are being developed to process sequencing machine readouts. We were interested in detection of SNPs in a 350 kb region of an EMS-mutagenized Arabidopsis chromosome 3. The region was selectively analyzed using PCR-generated, overlapping fragments for Solexa sequencing. The ensuing reads provided a high coverage and were processed bioinformatically. In order to assess the SNP candidates obtained with a frequently used alignment program and SNP caller, we developed an additional method that allows the identification of high confidence SNP loci. The method can easily be applied to complete genome sequence data of sufficient coverage.

  18. Utility of a next-generation sequencing-based gene panel investigation in German patients with genetically unclassified limb-girdle muscular dystrophy.

    Science.gov (United States)

    Kuhn, Marius; Gläser, Dieter; Joshi, Pushpa Raj; Zierz, Stephan; Wenninger, Stephan; Schoser, Benedikt; Deschauer, Marcus

    2016-04-01

    Limb-girdle muscular dystrophies (LGMDs) are genetically heterogeneous and the diagnostic work-up including conventional genetic testing using Sanger sequencing remains complex and often unsatisfactory. We performed targeted sequencing of 23 LGMD-related genes and 15 genes in which alterations result in a similar phenotype in 58 patients with genetically unclassified LGMDs. A genetic diagnosis was possible in 19 of 58 patients (33 %). LGMD2A was the most common form, followed by LGMD2L and LGMD2I. In two patients, pathogenic mutations were identified in genes that are not classified as LGMD genes (glycogen branching enzyme and valosin-containing protein). Thus, a focused next-generation sequencing-based gene panel is a rather satisfactory tool for the diagnosis in unclassified LGMDs. PMID:26886200

  19. An assessment on DNA microarray and sequence-based methods for the characterization of methicillin-susceptible Staphylococcus aureus from Nigeria

    Directory of Open Access Journals (Sweden)

    Adebayo Osagie Shittu

    2015-10-01

    Full Text Available Staphylococcus aureus is an important human pathogen causing nosocomial and community-acquired infections worldwide. In the characterization of this opportunistic pathogen, DNA microarray hybridization technique is used as an alternative to sequence based genotyping to obtain a comprehensive assessment on the virulence, resistance determinants, and population structure. The objective of this study was to characterize a defined collection of S. aureus isolates from Nigeria using the microarray technique, and to assess the extent that it correlates with sequence-based genotyping methods. The clonal diversity and genomic content of 52 methicillin-susceptible Staphylococcus aureus (MSSA were investigated by spa typing, MLST and DNA microarray hybridization. More than half (55.8% of these isolates were associated with clonal complexes typically associated with methicillin-resistant S. aureus (MRSA clones i.e. CC1, CC5, CC8, CC30 and CC45. Certain genes linked with virulence (hlgA and clfA and adherence (ebpS, fnbA, sspA, sspB and sspP were detected in all isolates. A number of genes or gene clusters were associated with distinct clonal types. The enterotoxin gene cluster (egc was linked with CC5, CC25, CC30, CC45 and CC121, enterotoxin H gene (seh with CC1, exfoliative toxin D gene (etd with CC25 and CC80, and the epidermal cell differentiation inhibitor B gene (edinB with CC25, CC80 and CC152. The excellent agreement between data from DNA microarray and MLST in the delineation of Nigerian MSSA isolates indicates that the microarray technique is a useful tool to provide information on antibiotic resistance, clonal diversity and virulence factors associated with infection and disease.

  20. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  1. GMO detection using a bioluminescent real time reporter (BART of loop mediated isothermal amplification (LAMP suitable for field use

    Directory of Open Access Journals (Sweden)

    Kiddle Guy

    2012-04-01

    Full Text Available Abstract Background There is an increasing need for quantitative technologies suitable for molecular detection in a variety of settings for applications including food traceability and monitoring of genetically modified (GM crops and their products through the food processing chain. Conventional molecular diagnostics utilising real-time polymerase chain reaction (RT-PCR and fluorescence-based determination of amplification require temperature cycling and relatively complex optics. In contrast, isothermal amplification coupled to a bioluminescent output produced in real-time (BART occurs at a constant temperature and only requires a simple light detection and integration device. Results Loop mediated isothermal amplification (LAMP shows robustness to sample-derived inhibitors. Here we show the applicability of coupled LAMP and BART reactions (LAMP-BART for determination of genetically modified (GM maize target DNA at low levels of contamination (0.1-5.0% GM using certified reference material, and compare this to RT-PCR. Results show that conventional DNA extraction methods developed for PCR may not be optimal for LAMP-BART quantification. Additionally, we demonstrate that LAMP is more tolerant to plant sample-derived inhibitors, and show this can be exploited to develop rapid extraction techniques suitable for simple field-based qualitative tests for GM status determination. We also assess the effect of total DNA assay load on LAMP-BART quantitation. Conclusions LAMP-BART is an effective and sensitive technique for GM detection with significant potential for quantification even at low levels of contamination and in samples derived from crops such as maize with a large genome size. The resilience of LAMP-BART to acidic polysaccharides makes it well suited to rapid sample preparation techniques and hence to both high throughput laboratory settings and to portable GM detection applications. The impact of the plant sample matrix and genome loading

  2. Trigeminal ganglion neurons of mice show intracellular chloride accumulation and chloride-dependent amplification of capsaicin-induced responses.

    Directory of Open Access Journals (Sweden)

    Nicole Schöbel

    Full Text Available Intracellular Cl(- concentrations ([Cl(-](i of sensory neurons regulate signal transmission and signal amplification. In dorsal root ganglion (DRG and olfactory sensory neurons (OSNs, Cl(- is accumulated by the Na(+-K(+-2Cl(- cotransporter 1 (NKCC1, resulting in a [Cl(-](i above electrochemical equilibrium and a depolarizing Cl(- efflux upon Cl(- channel opening. Here, we investigate the [Cl(-](i and function of Cl(- in primary sensory neurons of trigeminal ganglia (TG of wild type (WT and NKCC1(-/- mice using pharmacological and imaging approaches, patch-clamping, as well as behavioral testing. The [Cl(-](i of WT TG neurons indicated active NKCC1-dependent Cl(- accumulation. Gamma-aminobutyric acid (GABA(A receptor activation induced a reduction of [Cl(-](i as well as Ca(2+ transients in a corresponding fraction of TG neurons. Ca(2+ transients were sensitive to inhibition of NKCC1 and voltage-gated Ca(2+ channels (VGCCs. Ca(2+ responses induced by capsaicin, a prototypical stimulus of transient receptor potential vanilloid subfamily member-1 (TRPV1 were diminished in NKCC1(-/- TG neurons, but elevated under conditions of a lowered [Cl(-](o suggesting a Cl(--dependent amplification of capsaicin-induced responses. Using next generation sequencing (NGS, we found expression of different Ca(2+-activated Cl(- channels (CaCCs in TGs of mice. Pharmacological inhibition of CaCCs reduced the amplitude of capsaicin-induced responses of TG neurons in Ca(2+ imaging and electrophysiological recordings. In a behavioral paradigm, NKCC1(-/- mice showed less avoidance of the aversive stimulus capsaicin. In summary, our results strongly argue for a Ca(2+-activated Cl(--dependent signal amplification mechanism in TG neurons that requires intracellular Cl(- accumulation by NKCC1 and the activation of CaCCs.

  3. Efficient amplification of self-gelling polypod-like structured DNA by rolling circle amplification and enzymatic digestion.

    Science.gov (United States)

    Yata, Tomoya; Takahashi, Yuki; Tan, Mengmeng; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki; Takakura, Yoshinobu; Nishikawa, Makiya

    2015-01-01

    The application of DNA as a functional material such as DNA hydrogel has attracted much attention. Despite an increasing interest, the high cost of DNA synthesis is a limiting factor for its utilization. To reduce the cost, we report here a highly efficient amplification technique for polypod-like structured DNA (polypodna) with adhesive ends that spontaneously forms DNA hydrogel. Two types of polypodna with three (tripodna) and four (tetrapodna) pods were selected, and a template oligodeoxynucleotide, containing a tandem sequence of a looped tripodna or tetrapodna, respectively, along with restriction enzyme (TspRI) sites, was designed. The template was circularized using T4 DNA ligase, and amplified by rolling circle amplification (RCA). The RCA product was highly viscous and resistant to restriction digestion. Observation under an electron microscope revealed microflower-like structures. These structures were composed of long DNA and magnesium pyrophosphate, and their treatment with EDTA followed by restriction digestion with TspRI resulted in numerous copies of polypodna with adhesive ends, which formed a DNA hydrogel. Thus, we believe this technique provides a new approach to produce DNA nanostructures, and helps in expanding their practical applications. PMID:26462616

  4. Clinical characteristics and outcome of patients with neuroblastoma presenting genomic amplification of loci other than MYCN.

    Directory of Open Access Journals (Sweden)

    Anne Guimier

    Full Text Available BACKGROUND: Somatically acquired genomic alterations with MYCN amplification (MNA are key features of neuroblastoma (NB, the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s distinct from MYCN. METHODS: Genomic profiles of 1100 NBs from French centres studied by array-CGH were re-examined specifically to identify regional amplifications. Patients were included if amplifications distinct from the MYCN locus were seen. A subset of NBs treated at Institut Curie and harbouring MNA as determined by array-CGH without other amplification was also studied. Clinical and histology data were retrospectively collected. RESULTS: In total, 56 patients were included and categorised into 3 groups. Group 1 (n = 8 presented regional amplification(s without MNA. Locus 12q13-14 was a recurrent amplified region (4/8 cases. This group was heterogeneous in terms of INSS stages, primary localisations and histology, with atypical clinical features. Group 2 (n = 26 had MNA as well as other regional amplifications. These patients shared clinical features of those of a group of NBs MYCN amplified (Group 3, n = 22. Overall survival for group 1 was better than that of groups 2 and 3 (5 year OS: 87.5%±11% vs 34.9%±7%, log-rank p<0.05. CONCLUSION: NBs harbouring regional amplification(s without MNA are rare and seem to show atypical features in clinical presentation and genomic profile. Further high resolution genetic explorations are justified in this heterogeneous group, especially when considering these alterations as predictive markers for targeted therapy.

  5. System for portable nucleic acid testing in low resource settings

    Science.gov (United States)

    Lu, Hsiang-Wei; Roskos, Kristina; Hickerson, Anna I.; Carey, Thomas; Niemz, Angelika

    2013-03-01

    Our overall goal is to enable timely diagnosis of infectious diseases through nucleic acid testing at the point-of-care and in low resource settings, via a compact system that integrates nucleic acid sample preparation, isothermal DNA amplification, and nucleic acid lateral flow (NALF) detection. We herein present an interim milestone, the design of the amplification and detection subsystem, and the characterization of thermal and fluidic control and assay execution within this system. Using an earlier prototype of the amplification and detection unit, comprised of a disposable cartridge containing flexible pouches, passive valves, and electrolysis-driven pumps, in conjunction with a small heater, we have demonstrated successful execution of an established and clinically validated isothermal loop-mediated amplification (LAMP) reaction targeting Mycobacterium tuberculosis (M.tb) DNA, coupled to NALF detection. The refined design presented herein incorporates miniaturized and integrated electrolytic pumps, novel passive valves, overall design changes to facilitate integration with an upstream sample preparation unit, and a refined instrument design that automates pumping, heating, and timing. Nucleic acid amplification occurs in a two-layer pouch that facilitates fluid handling and appropriate thermal control. The disposable cartridge is manufactured using low-cost and scalable techniques and forms a closed system to prevent workplace contamination by amplicons. In a parallel effort, we are developing a sample preparation unit based on similar design principles, which performs mechanical lysis of mycobacteria and DNA extraction from liquefied and disinfected sputum. Our next step is to combine sample preparation, amplification, and detection in a final integrated cartridge and device, to enable fully automated sample-in to answer-out diagnosis of active tuberculosis in primary care facilities of low-resource and high-burden countries.

  6. Induction and Amplification of Non-Newtonian Gravitational Fields

    CERN Document Server

    Tajmar, M

    2001-01-01

    One obtains a Maxwell-like structure of gravitation by applying the weak-field approximation to the well accepted theory of general relativity or by extending Newton's laws to time-dependent systems. This splits gravity in two parts, namely a gravitoelectric and gravitomagnetic (or cogravitational) one. Due to the obtained similar structure between gravitation and electromagnetism, one can express one field by the other one using a coupling constant depending on the mass to charge ratio of the field source. Calculations of induced gravitational fields using state-of-the-art fusion plasmas reach only accelerator threshold values for laboratory testing. Possible amplification mechanisms are mentioned in the literature and need to be explored. The possibility of using the principle of equivalence in the weak field approximation to induce non-Newtonian gravitational fields and the influence of electric charge on the free fall of bodies are also investigated, leading to some additional experimental recommendations...

  7. Self-Amplification of Solid Friction in Interleaved Assemblies

    Science.gov (United States)

    Alarcón, Héctor; Salez, Thomas; Poulard, Christophe; Bloch, Jean-Francis; Raphaël, Élie; Dalnoki-Veress, Kari; Restagno, Frédéric

    2016-01-01

    It is nearly impossible to separate two interleaved phone books when held by their spines. A full understanding of this astonishing demonstration of solid friction in complex assemblies remains elusive. In this Letter, we report on experiments with controlled booklets and show that the force required increases sharply with the number of sheets. A model captures the effect of the number of sheets, their thickness, and the overlapping distance. Furthermore, the data collapse onto a self-similar master curve with one dimensionless amplification parameter. In addition to solving a long-standing familiar enigma, this model system provides a framework with which one can accurately measure friction forces and coefficients at low loads, and that has relevance to complex assemblies from the macro- to the nanoscale.

  8. "Social Laser": Action Amplification by Stimulated Emission of Social Energy

    CERN Document Server

    Khrennikov, Andrei

    2015-01-01

    The problem of the "explanation" of recent social explosions, especially in the Middle East, but also in Southern Europe and the USA, have been debated actively in the social and political literature. We can mention the contributions of P. Mason, F. Fukuyama, E. Schmidt and J. Cohen, I. Krastev to this debate. We point out that the diversity of opinions and conclusions is really amazing. At the moment, there is no consistent and commonly acceptable theory of these phenomena. We present a model of social explosions based on a novel approach for the description of social processes, namely, the quantum-like approach. Here quantum theory is treated simply as an operational formalism - without any direct relation to physics. We explore the quantum-like laser model to describe the possibility of Action Amplification by Stimulated Emission of Social Energy (ASE).

  9. Multiplex amplification of large sets of human exons.

    Science.gov (United States)

    Porreca, Gregory J; Zhang, Kun; Li, Jin Billy; Xie, Bin; Austin, Derek; Vassallo, Sara L; LeProust, Emily M; Peck, Bill J; Emig, Christopher J; Dahl, Fredrik; Gao, Yuan; Church, George M; Shendure, Jay

    2007-11-01

    A new generation of technologies is poised to reduce DNA sequencing costs by several orders of magnitude. But our ability to fully leverage the power of these technologies is crippled by the absence of suitable 'front-end' methods for isolating complex subsets of a mammalian genome at a scale that matches the throughput at which these platforms will routinely operate. We show that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify approximately 10,000 human exons in a single multiplex reaction. Additionally, we show integration of this protocol with ultra-high-throughput sequencing for targeted variation discovery. Although the multiplex capture reaction is highly specific, we found that nonuniform capture is a key issue that will need to be resolved by additional optimization. We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing.

  10. Rapid PCR amplification of DNA utilizing Coriolis effects.

    Science.gov (United States)

    Mårtensson, Gustaf; Skote, Martin; Malmqvist, Mats; Falk, Mats; Asp, Allan; Svanvik, Nicke; Johansson, Arne

    2006-08-01

    A novel polymerase chain reaction (PCR) method is presented that utilizes Coriolis and centrifugal effects, produced by rotation of the sample disc, in order to increase internal circulatory rates, and with them temperature homogenization and mixing speeds. A proof of concept has been presented by testing a rapid 45-cycle PCR DNA amplification protocol. During the repeated heating and cooling that constitutes a PCR process, the 100 microL samples were rotated at a speed equivalent to an effective acceleration of gravity of 7,000 g. A cycle time of 20.5 s gave a total process time of 15 min to complete the 45 cycles. A theoretical and numerical analysis of the resulting flow, which describes the increased mixing and temperature homogenization, is presented. The device gives excellent reaction speed efficiency, which is beneficial for rapid PCR.

  11. Optimisation of geometrical ratchets for spin-current amplification

    Energy Technology Data Exchange (ETDEWEB)

    Abdullah, Ranjdar M. [Department of Electronics, University of York, Heslington, York YO10 5DD (United Kingdom); Vick, Andrew J. [Department of Electronics, University of York, Heslington, York YO10 5DD (United Kingdom); Department of Physics, University of York, York YO10 5DD (United Kingdom); Murphy, Benedict A. [Department of Physics, University of York, York YO10 5DD (United Kingdom); Hirohata, Atsufumi, E-mail: atsufumi.hirohata@york.ac.uk [Department of Electronics, University of York, Heslington, York YO10 5DD (United Kingdom); PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012 (Japan)

    2015-05-07

    A two-dimensional model is used to study the geometrical effects of a nonmagnetic (NM) nanowire upon a spin-polarised electron current in a lateral spin-valve structure. We found that the implemented ratchet shapes at the centre of the NM have a crucial effect on the diffusive rate for up- and down-spin electrons along the wire, which leads to the amplification of non-local spin-current signals. By using our simple model, the geometries have been optimised. The calculated spin-current signals are in good qualitative agreement with our recent experimental results [Abdullah et al., J. Phys. D: Appl. Phys. 47, 482001(FTC) (2014)]. Our model may be very useful to evaluate such a geometrical effect on spin-polarised electron transport.

  12. Shock induced porous barrier flows, with underlying wall pressure amplification

    Science.gov (United States)

    Skews, B. W.; Bugarin, S.

    The flow field resulting from the impact of a shock wave on a variety of sheets of permeable material is studied. Earlier studies examined the flow through stationary sheets. It has, however, been found that if the sheet is placed a short distance in front of a surface, and can move under the shock loading, the pressure on the surface is amplified following shock impact, compared to the pressures that would be experienced with no covering. An important application to consider is the effect that textile clothing may have on a persons body when exposed to a blast environment. Single and multiple layers of a range of textiles have been tested. It was established that the heavier, more impermeable textiles such as Kevlar can amplify the shock wave pressure by as much as 400%. Experiments were also done with the textiles placed at an angle to the incoming shock wave and the mechanism for the amplification established through schlieren photography and pressure measurements.

  13. SERS Amplification from Self-Organized Arrays of Plasmonic Nanocrescents.

    Science.gov (United States)

    Giordano, Maria Caterina; Foti, Antonino; Messina, Elena; Gucciardi, Pietro Giuseppe; Comoretto, Davide; Buatier de Mongeot, Francesco

    2016-03-01

    We report on the surface-enhanced Raman scattering (SERS) efficiency of self-organized arrays of Au nanocrescents confined on monolayers of polystyrene nanospheres. A dichroic SERS emission in the visible spectrum is observed due to the selective excitation of a localized surface plasmon (LSP) resonance along the "short axis" of the Au nanocrescents. Under these conditions SERS signal amplifications in the range of 10(3) have been observed with respect to a flat reference Au film. The far field and near field plasmonic response of Au nanocrescent arrays have been investigated as a function of the metal dose deposited onto the polymeric spheres. In this way, we show the possibility of simply tailoring the SERS emission by engineering the morphology of the plasmonic nanocrescents. We highlight the SERS activity of chains of satellite nanoclusters that decorate the border of each connected crescent and sustain isotropic high energy LSP resonances in the visible spectrum. PMID:26824254

  14. Cascaded Parametric Amplification for Highly Efficient Terahertz Generation

    CERN Document Server

    Ravi, Koustuban; Cirmi, Giovanni; Reichert, Fabian; Schimpf, Damian N; Muecke, Oliver D; Kaertner, Franz X

    2016-01-01

    A highly efficient, practical approach to high-energy terahertz (THz) generation based on spectrally cascaded optical parametric amplification (THz-COPA) is introduced. The THz wave initially generated by difference frequency generation between a strong narrowband optical pump and optical seed (0.1-10% of pump energy) kick-starts a repeated or cascaded energy down-conversion of pump photons. This helps to greatly surpass the quantum-defect efficiency and results in exponential growth of THz energy over crystal length. In cryogenically cooled periodically poled lithium niobate, energy conversion efficiencies >8% for 100 ps pulses are predicted. The calculations account for cascading effects, absorption, dispersion and laser-induced damage. Due to the coupled nonlinear interaction of multiple triplets of waves, THz-COPA exhibits physics distinct from conventional three-wave mixing parametric amplifiers. This in turn governs optimal phase-matching conditions, evolution of optical spectra as well as limitations o...

  15. Copy number change: evolving views on gene amplification.

    Science.gov (United States)

    Elliott, Kathryn T; Cuff, Laura E; Neidle, Ellen L

    2013-07-01

    The rapid pace of genomic sequence analysis is increasing the awareness of intrinsically dynamic genetic landscapes. Gene duplication and amplification (GDA) contribute to adaptation and evolution by allowing DNA regions to expand and contract in an accordion-like fashion. This process affects diverse aspects of bacterial infection, including antibiotic resistance and host-pathogen interactions. In this review, microbial GDA is discussed, primarily using recent bacterial examples that demonstrate medical and evolutionary consequences. Interplay between GDA and horizontal gene transfer further impact evolutionary trajectories. Complementing the discovery of gene duplication in clinical and environmental settings, experimental evolution provides a powerful method to document genetic change over time. New methods for GDA detection highlight both its importance and its potential application for genetic engineering, synthetic biology and biotechnology.

  16. Vortical field amplification and particle acceleration at rippled shocks

    CERN Document Server

    Fraschetti, F

    2013-01-01

    Supernova Remnants (SNRs) shocks are believed to accelerate charged particles and to generate strong turbulence in the post-shock flow. From high-energy observations in the past decade, a magnetic field at SNR shocks largely exceeding the shock-compressed interstellar field has been inferred. We outline how such a field amplification results from a small-scale dynamo process downstream of the shock, providing an explicit expression for the turbulence back-reaction to the fluid whirling. The spatial scale of the $X-$ray rims and the short time-variability can be obtained by using reasonable parameters for the interstellar turbulence. We show that such a vortical field saturation is faster than the acceleration time of the synchrotron emitting energetic electrons.

  17. Diffusive shock acceleration with magnetic field amplification and Alfvenic drift

    CERN Document Server

    Kang, Hyesung

    2012-01-01

    We explore how wave-particle interactions affect diffusive shock acceleration (DSA) at astrophysical shocks by performing time-dependent kinetic simulations, in which phenomenological models for magnetic field amplification (MFA), Alfvenic drift, thermal leakage injection, Bohm-like diffusion, and a free escape boundary are implemented. If the injection fraction of cosmic-ray (CR) particles is greater than 2x10^{-4}, for the shock parameters relevant for young supernova remnants, DSA is efficient enough to develop a significant shock precursor due to CR feedback, and magnetic field can be amplified up to a factor of 20 via CR streaming instability in the upstream region. If scattering centers drift with Alfven speed in the amplified magnetic field, the CR energy spectrum can be steepened significantly and the acceleration efficiency is reduced. Nonlinear DSA with self-consistent MFA and Alfvenic drift predicts that the postshock CR pressure saturates roughly at 10 % of the shock ram pressure for strong shocks...

  18. Microchameleons: nonlinear chemical microsystems for amplification and sensing.

    Science.gov (United States)

    Bishop, K J M; Gray, T P; Fialkowski, M; Grzybowski, B A

    2006-09-01

    In biological systems, the coupling of nonlinear biochemical kinetics and molecular transport enables functional sensing and "signal" amplification across many length scales. Drawing on biological inspiration, we describe how artificial reaction-diffusion (RD) microsystems can provide a basis for sensing applications, capable of amplifying micro- and nanoscopic events into macroscopic visual readouts. The RD applications reviewed here are based on a novel experimental technique, WETS for Wet Stamping, which offers unprecedented control over RD processes in microscopic and complex geometries. It is discussed how RD can be used to sense subtle differences in the thickness and/or absorptivity of thin absorptive films, amplify macromolecular phase transitions, detect the presence and quality of self-assembled monolayers, and provide dynamic spatiotemporal readouts of chemical "metabolites." PMID:17014236

  19. Detection of Entamoeba histolytica by Recombinase Polymerase Amplification.

    Science.gov (United States)

    Nair, Gayatri; Rebolledo, Mauricio; White, A Clinton; Crannell, Zachary; Richards-Kortum, R Rebecca; Pinilla, A Elizabeth; Ramírez, Juan David; López, M Consuelo; Castellanos-Gonzalez, Alejandro

    2015-09-01

    Amebiasis is an important cause of diarrheal disease worldwide and has been associated with childhood malnutrition. Traditional microscopy approaches are neither sensitive nor specific for Entamoeba histolytica. Antigen assays are more specific, but many cases are missed unless tested by molecular methods. Although polymerase chain reaction (PCR) is effective, the need for sophisticated, expensive equipment, infrastructure, and trained personnel limits its usefulness, especially in the resource-limited, endemic areas. Here, we report development of a recombinase polymerase amplification (RPA) method to detect E. histolytica specifically. Using visual detection by lateral flow (LF), the test was highly sensitive and specific and could be performed without additional equipment. The availability of this inexpensive, sensitive, and field-applicable diagnostic test could facilitate rapid diagnosis and treatment of amebiasis in endemic regions.

  20. On Magnetic Field Amplification in Gamma-Ray Burst Sources

    CERN Document Server

    Blackman, E G

    2002-01-01

    Magnetic fields play a dual role in gamma-ray bursts (GRBs). First, GRB and afterglow spectra (the latter interpreted as emission from external shocks) imply synchrotron radiation in a magnetic field that is a significant fraction of equipartition with the particle energy density. Second, magnetized rotators with $\\sim 10^{15}$ Gauss field may power GRB by transporting Poynting flux to large distances where it dissipates and also drives an external shock. The field amplification at external shocks and in the engine involve separate processes. External shock fields are likely either seeded by a pre-GRB wind, or are amplified by two-stream plasma instabilities with MHD turbulence playing a subsequent role. In the engine, the large scale fields are likely produced by MHD helical dynamos, since flux accretion cannot easily compete with turbulent diffusion, and because structures must be large enough to rise to coronae before diffusing. Why helical dynamos are feasible, and their relation to the magnetorotational ...

  1. No fitness cost of glyphosate resistance endowed by massive EPSPS gene amplification in Amaranthus palmeri.

    Science.gov (United States)

    Vila-Aiub, Martin M; Goh, Sou S; Gaines, Todd A; Han, Heping; Busi, Roberto; Yu, Qin; Powles, Stephen B

    2014-04-01

    Amplification of the EPSPS gene has been previously identified as the glyphosate resistance mechanism in many populations of Amaranthus palmeri, a major weed pest in US agriculture. Here, we evaluate the effects of EPSPS gene amplification on both the level of glyphosate resistance and fitness cost of resistance. A. palmeri individuals resistant to glyphosate by expressing a wide range of EPSPS gene copy numbers were evaluated under competitive conditions in the presence or absence of glyphosate. Survival rates to glyphosate and fitness traits of plants under intra-specific competition were assessed. Plants with higher amplification of the EPSPS gene (53-fold) showed high levels of glyphosate resistance, whereas less amplification of the EPSPS gene (21-fold) endowed a lower level of glyphosate resistance. Without glyphosate but under competitive conditions, plants exhibiting up to 76-fold EPSPS gene amplification exhibited similar height, and biomass allocation to vegetative and reproductive organs, compared to glyphosate susceptible A. palmeri plants with no amplification of the EPSPS gene. Both the additive effects of EPSPS gene amplification on the level of glyphosate resistance and the lack of associated fitness costs are key factors contributing to EPSPS gene amplification as a widespread and important glyphosate resistance mechanism likely to become much more evident in weed plant species.

  2. Quantification of HER2 autoantibodies in the amplification phenomenon of HER2 in breast cancer

    DEFF Research Database (Denmark)

    Lauterlein, Jens-Jacob L; Petersen, Eva R B; Olsen, Dorte Aa;

    2011-01-01

    Gene amplification of HER2 (human epidermal growth factor receptor 2) is a well-known phenomenon in various cancers. However, little is known about the mechanism of the gene amplification phenomenon itself. Autoantibodies to cellular receptors have been described in several cancer types. We hypot...

  3. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian;

    2015-01-01

    BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleoti...

  4. A robust method for the amplification of RNA in the sense orientation

    Directory of Open Access Journals (Sweden)

    Quackenbush John

    2005-03-01

    Full Text Available Abstract Background Small quantities of RNA (1–4 μg total RNA available from biological samples frequently require a single round of amplification prior to analysis, but current amplification strategies have limitations that may restrict their usefulness in downstream genomic applications. The Eberwine amplification method has been extensively validated but is limited by its ability to produce only antisense RNA. Alternatives lack extensive validation and are often confounded by problems with bias or yield attributable to their greater biological and technical complexity. Results To overcome these limitations, we have developed a straightforward and robust protocol for amplification of RNA in the sense orientation. This protocol is based upon Eberwine's method but incorporates elements of more recent amplification techniques while avoiding their complexities. Our technique yields greater than 100-fold amplification, generates long transcript, and produces mRNA that is well suited for use with microarray applications. Microarrays performed with RNA amplified using this protocol demonstrate minimal amplification bias and high reproducibility. Conclusion The protocol we describe here is readily adaptable for the production of sense or antisense, labeled or unlabeled RNA from intact or partially-degraded prokaryotic or eukaryotic total RNA. The method outperforms several commercial RNA amplification kits and can be used in conjunction with a variety of microarray platforms, such as cDNA arrays, oligonucleotide arrays, and Affymetrix GeneChip™ arrays.

  5. Dihydrofolate reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells

    DEFF Research Database (Denmark)

    Morales Torres, Christina; García, Maria J; Ribas, Maria;

    2009-01-01

    have analyzed the structure and dynamics of dihydrofolate reductase (DHFR) gene amplification in HT29 cells treated with methotrexate (MTX). Analysis of the DHFR gene amplification process shows that the amplicon exhibits a complex structure that is consistently reproduced in independent treatments...

  6. Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

    NARCIS (Netherlands)

    Baratti, M.; Alberti, A.; Groenen, M.A.M.; Veenendaal, T.; Fulgheri, F.D.

    2001-01-01

    Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (2

  7. Parametric amplification of matter waves in dipolar spinor Bose-Einstein condensates

    DEFF Research Database (Denmark)

    Deuretzbacher, F.; Gebreyesus, G.; Topic, O.;

    2010-01-01

    Spin-changing collisions may lead under proper conditions to the parametric amplification of matter waves in spinor Bose-Einstein condensates. Magnetic dipole-dipole interactions, although typically very weak in alkali-metal atoms, are shown to play a very relevant role in the amplification process...

  8. [Amplification and cloning of dahlia mosaic virus and carnation etched ring virus promoters].

    Science.gov (United States)

    Kuluev, B R; Chemeris, A V

    2007-12-01

    Amplification and cloning of dahlia mosaic virus promoter were carried out for the first time. Sequence analysis showed homology between this promoter and the promoters of other caulimoviruses. In addition, amplification and cloning of the carnation etched ring virus promoter was performed. PMID:18592695

  9. Pulse train amplification and regeneration based on semiconductor quantum dots waveguide

    DEFF Research Database (Denmark)

    Chen, Yaohui; Öhman, Filip; Mørk, Jesper

    2008-01-01

    We numerical analyze pulse train amplification up to 200 Gbit/s in quantum dot amplifiers and present regeneration properties with saturable absorber based on semiconductor quantum dot waveguides.......We numerical analyze pulse train amplification up to 200 Gbit/s in quantum dot amplifiers and present regeneration properties with saturable absorber based on semiconductor quantum dot waveguides....

  10. Simulation of Redox-Cycling Phenomena at Interdigitated Array (IDA) Electrodes: Amplification and Selectivity

    NARCIS (Netherlands)

    Odijk, M.; Olthuis, W.; Dam, T.V.A.; Berg, van den A.

    2008-01-01

    We present Finite Element Method (FEM) simulations of interdigitated array (IDA) electrode geometries to study and verify redox selectivity and redox cycling amplification factor. The simulations provide an adequate explanation of an earlier found, but poorly understood, high amplification factor (6

  11. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer

    DEFF Research Database (Denmark)

    Bechmann, Troels; Andersen, Rikke Fredslund; Pallisgaard, Niels;

    2013-01-01

    Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification...... in cfDNA during neoadjuvant chemotherapy....

  12. MYEOV : A candidate gene for DNA amplification events occurring centromeric to CCNDI in breast cancer

    NARCIS (Netherlands)

    Janssen, JWG; Cuny, M; Orsetti, B; Rodriguez, C; Valles, H; Bartram, CR; Schuuring, E; Theillet, C

    2002-01-01

    Rearrangements of chromosome 11q13 are frequently observed in human cancer. The 11q13 region harbors several chromosomal breakpoint clusters found in hematologic malignancies and exhibits frequent DNA amplification in carcinomas. DNA amplification patterns in breast tumors are consistent with the ex

  13. The Media and Genetically Modified Foods : Evidence in Support of Social Amplification of Risk

    NARCIS (Netherlands)

    Frewer, L.J.; Miles, S.; Marsh, R.

    2002-01-01

    Empirical examinations of the "social amplification of risk" framework are rare, partly because of the difficulties in predicting when conditions likely to result in amplification effects will occur. This means that it is difficult to examine changes in risk perception that are contemporaneous with

  14. Amplification and Suppression of Round-Off Error in Runge-Kutta Methods

    Science.gov (United States)

    Prentice, J. S. C.

    2011-01-01

    A simple nonstiff linear initial-value problem is used to demonstrate the amplification of round-off error in the course of using a second-order Runge-Kutta method. This amplification is understood in terms of an appropriate expression for the global error. An implicit method is then used to show how the roundoff error may actually be suppressed.…

  15. Evaluation of ribonucleic acid amplification protocols for human oocyte transcriptome analysis

    NARCIS (Netherlands)

    E. Mantikou; O. Bruning; S. Mastenbroek; S. Repping; T.M. Breit; M. de Jong

    2015-01-01

    OBJECTIVE: To develop a reliable, reproducible, and sensitive method for investigating gene-expression profiles from individual human oocytes. DESIGN: Five commercially available protocols were investigated for their efficiency to amplify messenger RNA (mRNA) from 54 single human oocytes. Protocols

  16. Multicenter evaluation of the Quidel Lyra Direct C. difficile nucleic acid amplification assay.

    Science.gov (United States)

    Beck, Eric T; Buchan, Blake W; Riebe, Katherine M; Alkins, Brenda R; Pancholi, Preeti; Granato, Paul A; Ledeboer, Nathan A

    2014-06-01

    Clostridium difficile is a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routine C. difficile testing. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well to C. difficile culture methods. PMID:24671790

  17. Multicenter evaluation of the Quidel Lyra Direct C. difficile nucleic acid amplification assay.

    Science.gov (United States)

    Beck, Eric T; Buchan, Blake W; Riebe, Katherine M; Alkins, Brenda R; Pancholi, Preeti; Granato, Paul A; Ledeboer, Nathan A

    2014-06-01

    Clostridium difficile is a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routine C. difficile testing. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well to C. difficile culture methods.

  18. External Quality Assessment Program for Chlamydia trachomatis Diagnostic Testing by Nucleic Acid Amplification Assays

    OpenAIRE

    Land, Sally; Tabrizi, Sepehr; Gust, Anthony; Johnson, Elizabeth; Garland, Susan; Dax, Elizabeth M.

    2002-01-01

    We report the results from 57 Australian diagnostic laboratories testing two external quality assessment panels using either the Roche Amplicor Chlamydia trachomatis test (R-PCR) or the Abbott LCx Chlamydia trachomatis assay (A-ligase chain reaction [LCR]). Panel samples were either normal urine spiked with Chlamydia trachomatis antigen or clinical urine specimens. There was no significant difference between laboratories or between assays in detection of C. trachomatis-positive clinical sampl...

  19. Mycoplasma pneumoniae: Current knowledge on nucleic acid amplification techniques and serological diagnostics

    Directory of Open Access Journals (Sweden)

    Katherine eLoens

    2016-03-01

    Full Text Available Mycoplasma pneumoniae (M. pneumoniae belongs to the class Mollicutes and has been recognized as a common cause of respiratory tract infections (RTIs, including community-acquired pneumonia (CAP, that occur worldwide and in all age groups. In addition, M. pneumoniae can simultaneously or sequentially lead to damage in the nervous system and has been associated with a wide variety of other acute and chronic diseases. During the past 10 years, the proportion of LRTI in children and adults, associated with M. pneumoniae infection has ranged from 0% to more than 50%. This variation is due to the age and the geographic location of the population examined but also due to the diagnostic methods used. The true role of M. pneumoniae in RTIs remains a challenge given the many limitations and lack of standardization of the applied diagnostic tool in most cases, with resultant wide variations in data from different studies.Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. Several recent reviews have summarized current methods for the detection and identification of M. pneumoniae. This review will therefore provide a look at the general principles, advantages, diagnostic value, and limitations of the most currently used detection techniques for the etiological diagnosis of a M. pneumoniae infection as they evolve from research to daily practice.

  20. Towards the use of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection

    Science.gov (United States)

    Tran, Quang Huy; Mai, Anh Tuan; Thuy Nguyen, Thanh; Chung Pham, Van; Hanh Nguyen, Thi Hong

    2012-06-01

    In this paper we represent a study on the potential use of protein A-tagged gold nanoparticles applied for signal amplification of electrochemical immunosensors. Gold nanoparticles (GNPs) were synthesized by the chemical reduction of tetrachloroauric (III) acid trihydrate using sodium ascorbate, and then tagged with protein A (PrA) via ultracentrifugation. UV-Vis spectroscopy and transmission electron microscopy were used to verify the characteristics of formed GNPs/PrA complex. The analyzed results indicate that GNPs were found spherically, homogeneously, and with an average diameter of about 10 nm. Immunoelectron microscopy was then used to investigate the bioactivity of the GNPs/PrA complex in solution by the effective binding of GNPs to viral particles. Scanning electron and fluorescence microscopies were also used to investigate the distribution and the bioactivity of the GNPs/PrA complex on the surface of the interdigitated sensor. Consequently, this study provided some assumptions of the potential application of protein A-tagged gold nanoparticles for signal amplification of electrochemical immunosensors in virus detection from clinical samples.

  1. Optimization of loop-mediated isothermal amplification (LAMP) assays for the detection of Leishmania DNA in human blood samples.

    Science.gov (United States)

    Abbasi, Ibrahim; Kirstein, Oscar D; Hailu, Asrat; Warburg, Alon

    2016-10-01

    Visceral leishmaniasis (VL), one of the most important neglected tropical diseases, is caused by Leishmania donovani eukaryotic protozoan parasite of the genus Leishmania, the disease is prevalent mainly in the Indian sub-continent, East Africa and Brazil. VL can be diagnosed by PCR amplifying ITS1 and/or kDNA genes. The current study involved the optimization of Loop-mediated isothermal amplification (LAMP) for the detection of Leishmania DNA in human blood or tissue samples. Three LAMP systems were developed; in two of those the primers were designed based on shared regions of the ITS1 gene among different Leishmania species, while the primers for the third LAMP system were derived from a newly identified repeated region in the Leishmania genome. The LAMP tests were shown to be sufficiently sensitive to detect 0.1pg of DNA from most Leishmania species. The green nucleic acid stain SYTO16, was used here for the first time to allow real-time monitoring of LAMP amplification. The advantage of real time-LAMP using SYTO 16 over end-point LAMP product detection is discussed. The efficacy of the real time-LAMP tests for detecting Leishmania DNA in dried blood samples from volunteers living in endemic areas, was compared with that of qRT-kDNA PCR. PMID:27288706

  2. Robust and efficient direct multiplex amplification method for large-scale DNA detection of blood samples on FTA cards

    International Nuclear Information System (INIS)

    Deoxyribonucleic acid (DNA) damage arising from radiations widely occurred along with the development of nuclear weapons and clinically wide application of computed tomography (CT) scan and nuclear medicine. All ionizing radiations (X-rays, γ-rays, alpha particles, etc.) and ultraviolet (UV) radiation lead to the DNA damage. Polymerase chain reaction (PCR) is one of the most wildly used techniques for detecting DNA damage as the amplification stops at the site of the damage. Improvements to enhance the efficiency of PCR are always required and remain a great challenge. Here we establish a multiplex PCR assay system (MPAS) that is served as a robust and efficient method for direct detection of target DNA sequences in genomic DNA. The establishment of the system is performed by adding a combination of PCR enhancers to standard PCR buffer, The performance of MPAS was demonstrated by carrying out the direct PCR amplification on l.2 mm human blood punch using commercially available primer sets which include multiple primer pairs. The optimized PCR system resulted in high quality genotyping results without any inhibitory effect indicated and led to a full-profile success rate of 98.13%. Our studies demonstrate that the MPAS provides an efficient and robust method for obtaining sensitive, reliable and reproducible PCR results from human blood samples. (authors)

  3. Development of a rapid and specific loop-mediated isothermal amplification detection method that targets Marek's disease virus meq gene.

    Science.gov (United States)

    Wei, Xiuying; Shi, Xingming; Zhao, Yan; Zhang, Jing; Wang, Mei; Liu, Changjun; Cui, Hongyu; Hu, Shunlei; Quan, Yanming; Chen, Hongyan; Wang, Yunfeng

    2012-08-01

    A rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) method was developed and evaluated for the detection of Marek's disease virus (MDV) by amplification of conserved MDV meq gene sequences. LAMP is an innovative technique that allows the rapid detection of targeted nucleic acid sequences under isothermal conditions without the need for complex instrumentation. In this study, meq gene sequences were amplified successfully from different MDV strains by LAMP within 60min and no cross-reactivity was observed in a panel of related viruses that were associated with diseases of chickens. The detection limit of LAMP was 3.2 copies/million cells compared with 320 copies/million cells required for conventional PCR. Positive detection rates were assessed using either LAMP or PCR by examination of feather follicles that were collected from chickens infected experimentally with either strain J-1 (n=20) or strain Md5 (n=17), In addition to these samples, three isolates that were suspected to have been infected in the clinic were also tested. Results showed that the positive detection rate for LAMP was 95% (38/40), compared with 87.5% (35/40) and 90% (38/40) for strains J-1 and Md5 by PCR, respectively. These results indicated that the LAMP assay was more sensitive, rapid and specific than conventional PCR for the detection of MDV. This easy-to-perform technique will be useful for the detection of MDV and will aid in the establishment of disease control protocols.

  4. Topics in free radical-mediated DNA damage: purines and damage amplification - superoxic reactions - bleomycin, the incomplete radiomimetic

    International Nuclear Information System (INIS)

    Only a small percentage of the DNA damage set by ionizing radiation in the living cell manifests itself as lethal. It is now increasingly accepted that clustered lesions may constitute the kind of damage that the repair enzymes cannot adequately deal with. The question is raised as to whether damage amplification reactions (radical transfer reactions) may contribute to these clustered lesions, and examples of such damage amplification reactions are given. In one example a purine is involved. With 2'-deoxy adenosine and 2'-deoxy guanosine it is shown that these purine nucleosides undergo unexpected radical reactions. Evidence for the radical transfer from the purine to the sugar moiety is provided by the formation of the 5'-aldehydes. These products have been assayed with 2-thiobarbituric acid (TBA), a reagent commonly applied to the detection of malonaldehyde. TBA-reactive material has also been assayed in γ-irradiated DNA, about one-third of this is free malonaldehyde, while the major part of the TBA-reactive material remains bound to the DNA. In contrast, bleomycin-treated DNA yields practically no free malonaldehyde, and the major TBA-reactive products are identified as the thymine and adenine base propenals. (Author)

  5. Microfluidic bead-based multienzyme-nanoparticle amplification for detection of circulating tumor cells in the blood using quantum dots labels.

    Science.gov (United States)

    Zhang, He; Fu, Xin; Hu, Jiayi; Zhu, Zhenjun

    2013-05-24

    This study reports the development of a microfluidic bead-based nucleic acid sensor for sensitive detection of circulating tumor cells in blood samples using multienzyme-nanoparticle amplification and quantum dot labels. In this method, the microbeads functionalized with the capture probes and modified electron rich proteins were arrayed within a microfluidic channel as sensing elements, and the gold nanoparticles (AuNPs) functionalized with the horseradish peroxidases (HRP) and DNA probes were used as labels. Hence, two signal amplification approaches are integrated for enhancing the detection sensitivity of circulating tumor cells. First, the large surface area of Au nanoparticle carrier allows several binding events of HRP on each nanosphere. Second, enhanced mass transport capability inherent from microfluidics leads to higher capture efficiency of targets because continuous flow within micro-channel delivers fresh analyte solution to the reaction site which maintains a high concentration gradient differential to enhance mass transport. Based on the dual signal amplification strategy, the developed microfluidic bead-based nucleic acid sensor could discriminate as low as 5 fM (signal-to-noise (S/N)3) of synthesized carcinoembryonic antigen (CEA) gene fragments and showed a 1000-fold increase in detection limit compared to the off-chip test. In addition, using spiked colorectal cancer cell lines (HT29) in the blood as a model system, the detection limit of this chip-based approach was found to be as low as 1 HT29 in 1 mL blood sample. This microfluidic bead-based nucleic acid sensor is a promising platform for disease-related nucleic acid molecules at the lowest level at their earliest incidence. PMID:23663673

  6. Millijoule pulse energy picosecond fiber chirped-pulse amplification system

    Institute of Scientific and Technical Information of China (English)

    Zhi Yang; Xiaohong Hu; Yishan Wang; Wei Zhang; Wei Zhao

    2011-01-01

    @@ The efficient generation of a 1.17-mJ laser pul8e with 360 ps duration using an ytterbium (Yb)-doped fiber amplifier chain seeded by a homemade mode-locked fiber laser is demonstrated experimentally.A specially designed figure-of-eight fiber laser acts as the seed source of a chirped-pulse amplification (CPA) system and generates mode-locked pulse8 with hundreds of picosecond widths.Two kinds of large-mode-area (LMA) double-clad Yb-doped fibers are employed to construct the pre-amplifier and main amplifier, All of the adopted instruments help avoid severe nonlinearity in fibers to raise sub-nanosecond pulse energy with acceptable signal-to-noise ratio (SNR).The output spectrum of this fiber-based CPA system shows that amplified spontaneous emission (ASE) is suppressed to better than 30 dB, and the onset of stimulated Raman scattering is excluded.%The efficient generation of a 1.17-mJ laser pulse with 360 ps duration using an ytterbium (Yb)-doped fiber amplifier chain seeded by a homemade mode-locked fiber laser is demonstrated experimentally. A specially designed figure-of-eight fiber laser acts as the seed source of a chirped-pulse amplification (CPA) system and generates mode-locked pulses with hundreds of picosecond widths. Two kinds of large-mode-area (LMA) double-clad Yb-doped fibers are employed to construct the pre-amplifier and main amplifier. All of the adopted instruments help avoid severe nonlinearity in fibers to raise sub-nanosecond pulse energy with acceptable signal-to-noise ratio (SNR). The output spectrum of this fiber-based CPA system shows that amplified spontaneous emission (ASE) is suppressed to better than 30 dB, and the onset of stimulated Raman scattering is excluded.

  7. Multiplexed Recombinase Polymerase Amplification Assay To Detect Intestinal Protozoa.

    Science.gov (United States)

    Crannell, Zachary; Castellanos-Gonzalez, Alejandro; Nair, Gayatri; Mejia, Rojelio; White, A Clinton; Richards-Kortum, Rebecca

    2016-02-01

    This work describes a proof-of-concept multiplex recombinase polymerase amplification (RPA) assay with lateral flow readout that is capable of simultaneously detecting and differentiating DNA from any of the diarrhea-causing protozoa Giardia, Cryptosporidium, and Entamoeba. Together, these parasites contribute significantly to the global burden of diarrheal illness. Differential diagnosis of these parasites is traditionally accomplished via stool microscopy. However, microscopy is insensitive and can miss up to half of all cases. DNA-based diagnostics such as polymerase chain reaction (PCR) are far more sensitive; however, they rely on expensive thermal cycling equipment, limiting their availability to centralized reference laboratories. Isothermal DNA amplification platforms, such as the RPA platform used in this study, alleviate the need for thermal cycling equipment and have the potential to broaden access to more sensitive diagnostics. Until now, multiplex RPA assays have not been developed that are capable of simultaneously detecting and differentiating infections caused by different pathogens. We developed a multiplex RPA assay to detect the presence of DNA from Giardia, Cryptosporidium, and Entamoeba. The multiplex assay was characterized using synthetic DNA, where the limits-of-detection were calculated to be 403, 425, and 368 gene copies per reaction of the synthetic Giardia, Cryptosporidium, and Entamoeba targets, respectively (roughly 1.5 orders of magnitude higher than for the same targets in a singleplex RPA assay). The multiplex assay was also characterized using DNA extracted from live parasites spiked into stool samples where the limits-of-detection were calculated to be 444, 6, and 9 parasites per reaction for Giardia, Cryptosporidium, and Entamoeba parasites, respectively. This proof-of-concept assay may be reconfigured to detect a wide variety of targets by re-designing the primer and probe sequences.

  8. Multivalent bifunctional chelator scaffolds for gallium-68 based positron emission tomography imaging probe design: signal amplification via multivalency.

    Science.gov (United States)

    Singh, Ajay N; Liu, Wei; Hao, Guiyang; Kumar, Amit; Gupta, Anjali; Öz, Orhan K; Hsieh, Jer-Tsong; Sun, Xiankai

    2011-08-17

    The role of the multivalent effect has been well recognized in the design of molecular imaging probes toward the desired imaging signal amplification. Recently, we reported a bifunctional chelator (BFC) scaffold design, which provides a simple and versatile approach to impart multivalency to radiometal based nuclear imaging probes. In this work, we report a series of BFC scaffolds ((t)Bu(3)-1-COOH, (t)Bu(3)-2-(COOH)(2), and (t)Bu(3)-3-(COOH)(3)) constructed on the framework of 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) for (68)Ga-based PET probe design and signal amplification via the multivalent effect. For proof of principle, a known integrin α(v)β(3) specific ligand (c(RGDyK)) was used to build the corresponding NOTA conjugates (H(3)1, H(3)2, and H(3)3), which present 1-3 copies of c(RGDyK) peptide, respectively, in a systematic manner. Using the integrin α(v)β(3) binding affinities (IC(50) values), enhanced specific binding was observed for multivalent conjugates (H(3)2: 43.9 ± 16.1 nM; H(3)3: 14.7 ± 5.0 nM) as compared to their monovalent counterpart (H(3)1: 171 ± 60 nM) and the intact c(RGDyK) peptide (204 ± 76 nM). The obtained conjugates were efficiently labeled with (68)Ga(3+) within 30 min at room temperature in high radiochemical yields (>95%). The in vivo evaluation of the labeled conjugates, (68)Ga-1, (68)Ga-2, and (68)Ga-3, was performed using male severe combined immunodeficiency (SCID) mice bearing integrin α(v)β(3) positive PC-3 tumor xenografts (n = 3). All (68)Ga-labeled conjugates showed high in vivo stability with no detectable metabolites found by radio-HPLC within 2 h postinjection (p.i.). The PET signal amplification in PC-3 tumor by the multivalent effect was clearly displayed by the tumor uptake of the (68)Ga-labeled conjugates ((68)Ga-3: 2.55 ± 0.50%ID/g; (68)Ga-2: 1.90 ± 0.10%ID/g; (68)Ga-1: 1.66 ± 0.15%ID/g) at 2 h p.i. In summary, we have designed and synthesized a series of NOTA-based BFC scaffolds with signal

  9. Novel real-time simultaneous amplification and testing method to accurately and rapidly detect Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Cui, Zhenling; Wang, Yongzhong; Fang, Liang; Zheng, Ruijuan; Huang, Xiaochen; Liu, Xiaoqin; Zhang, Gang; Rui, Dongmei; Ju, Jinliang; Hu, Zhongyi

    2012-03-01

    The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the Mycobacterium tuberculosis complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp M. tuberculosis 16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein-4-[4-(dimethylamino)phenylazo] benzoic acid N-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of M. tuberculosis H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of M. tuberculosis infection in clinical microbiology laboratories.

  10. PCR amplification of repetitive sequences as a possible approach in relative species quantification

    DEFF Research Database (Denmark)

    Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

    2012-01-01

    Abstract Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification...... of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species...... in binary mixtures. PCR LUX primers were designed that amplify repetitive and single copy sequences to establish the species dependent number (constants) (SDC) of amplified repetitive sequences per genome. The SDCs and data from amplification of repetitive sequences were tested for their applicability...

  11. Novel applications of locked nucleic acids.

    Science.gov (United States)

    Veedu, Rakesh N; Vester, Birte; Wengel, Jesper

    2007-01-01

    Locked Nucleic Acid (LNA) nucleoside triphosphates were prepared and their substrate properties for different polymerases during primer extension and PCR experiments investigated. Phusion High Fidelity DNA polymerase and 9( degrees )Nm(TM) DNA polymerase readily accept LNA nucleoside 5'-triphosphates as substrates in primer extension assays. However, in PCR assays, However, in PCR assays, DNA 9oN(m) polymerase proved to be the best for amplification employing the LNA-A nucleotide. PMID:18029570

  12. Development of double loop-mediated isothermal amplification to detect Listeria monocytogenes in food.

    Science.gov (United States)

    Wu, Rina; Liu, Xiang; Guo, Bangcheng; Chen, Fusheng; Wang, Xiaohong

    2014-12-01

    In this study, a double loop-mediated isothermal amplification (dLAMP) based on two target genes hlyA and iap was developed for the rapid detection of Listeria monocytogenes in food. The results revealed that the detection time and temperature of our dLAMP assay for L. monocytogenes were 15 min and 63 °C respectively, with a sensitivity of 10 fg DNA of L. monocytogenes per tube. While normal LAMP (nLAMP) of hlyA or iap was 100 fg DNA of L. monocytogenes per tube for 45 min and 63 °C. Furthermore, mineral oil and GoldViewII nucleic acid stain were chosen as the basic materials to develop a simple visualized identification of the positive samples. A total of 450 food samples were tested for L. monocytogenes using the dLAMP protocol developed in this study. The results showed that the accuracy of the dLAMP and the "gold standard" culture-biotechnical method were 100 % identical, suggesting that the modified dLAMP assay would provide a potential for detection of L. monocytogenes in food products. PMID:25086581

  13. Quantification of Fewer than Ten Copies of a DNA Biomarker without Amplification or Labeling.

    Science.gov (United States)

    Lee, Yoonhee; Kim, Youngkyu; Lee, Donggyu; Roy, Dhruvajyoti; Park, Joon Won

    2016-06-01

    Polymerase chain reaction (PCR) is a highly sensitive diagnosis technique for detection of nucleic acids and for monitoring residual disease; however, PCR can be unreliable for samples containing very few target molecules. Here, we describe a quantification method, using force-distance (FD) curve based atomic force microscopy (AFM) to detect a target DNA bound to small (1.4-1.9 μm diameter) probe DNA spots, allowing mapping of entire spots to nanometer resolution. Using a synthetic BCR-ABL fusion gene sequence target, we examined samples containing between one and 10 target copies. A high degree of correlation (r(2) = 0.994) between numbers of target copies and detected probe clusters was observed, and the approach could detect the BCR-ABL biomarker when only a single copy was present, although multiple screens were required. Our results clearly demonstrate that FD curve-based imaging is suitable for quantitative analysis of fewer than 10 copies of DNA biomarkers without amplification, modification, or labeling. PMID:27175474

  14. Isothermal rolling circle amplification of virus genomes for rapid antigen detection and typing.

    Science.gov (United States)

    Brasino, Michael D; Cha, Jennifer N

    2015-08-01

    In this work, isothermal rolling circle amplification (RCA) of the multi-kilobase genome of engineered filamentous bacteriophage is used to report the presence and identification of specific protein analytes in solution. First, bacteriophages were chosen as sensing platforms because peptides or antibodies that bind medically relevant targets can be isolated through phage display or expressed as fusions to their p3 and p8 coat proteins. Second, the circular, single-stranded genome contained within the phage serves as a natural large DNA template for a RCA reaction to rapidly generate exponential amounts of double stranded DNA in a single isothermal step that can be easily detected using low-cost fluorescent nucleic acid stains. Amplifying the entire phage genome also provides high detection sensitivities. Furthermore, since the sequence of the viral DNA can be easily modified with multiple restriction enzyme sites, a simple DNA digest can be applied to detect and identify multiple antigens simultaneously. The methods developed here will lead to protein sensors that are highly scalable to produce, can be run without complex biological equipment and do not require the use of multiple antibodies or high-cost fluorescent DNA probes or nucleotides.

  15. A novel electrochemical sensor for lead ion based on cascade DNA and quantum dots amplification

    International Nuclear Information System (INIS)

    A new enzyme-free and ultrasensitive electrochemical Pb2+ biosensor was developed. By coupling the DNA-assisted cascade of hybridization reaction with the quantum dots (QDs) for signal amplification, a detection limit as low as 6.1 pM can be obtained for Pb2+. In this study, the “8-17” DNAzyme was used for specific recognition of Pb2+. In the presence of Pb2+, the DNAzyme was activated and cleaved the substrate strand. And then, the hybridization between the linker probe and signal probe was initiated, which resulted in formation of a long cascade DNA structure as well as assemble of numerous QDs at last. By the use of magnetic beads, the free signal probe can be easily removed by external magnetic field. After acid lysis, a great amount of redox cations can be released from the QDs and eventually result in significantly amplified electrochemical signals. This method is highly sensitive, selective and simple without the participation of any protein based enzyme (nuclease), thereby holds great potential for real sample analysis

  16. Fingerprinting of cell lines by directed amplification of minisatellite-region DNA (DAMD

    Directory of Open Access Journals (Sweden)

    Silva L.M.

    2001-01-01

    Full Text Available The development of in vitro propagation of cells has been an extraordinary technical advance for several biological studies. The correct identification of the cell line used, however, is crucial, as a mistaken identity or the presence of another contaminating cell may lead to invalid and/or erroneous conclusions. We report here the application of a DNA fingerprinting procedure (directed amplification of minisatellite-region DNA, developed by Heath et al. [Nucleic Acids Research (1993 21: 5782-5785], to the characterization of cell lines. Genomic DNA of cells in culture was extracted and amplified by PCR in the presence of VNTR core sequences, and the amplicons were separated by agarose gel electrophoresis. After image capture with a digital camera, the banding profiles obtained were analyzed using a software (AnaGel specially developed for the storage and analysis of electrophoretic fingerprints. The fingerprints are useful for construction of a data base for identification of cell lines by comparison to reference profiles as well as comparison of similar lines from different sources and periodic follow-up of cells in culture.

  17. Amplification and Compression of Ultrashort Fundamental Solitons in An Erbium-Doped Nonlinear Amplifying Fiber Loop Mirror

    Institute of Scientific and Technical Information of China (English)

    P.; K.; A.; Wai

    2003-01-01

    A nonlinear amplifying loop mirror constructed from erbium-doped fiber is proposed for simultaneous amplification and compression of ultrashort fundamental solitons. Numerical simulations show that, the proposed device performs efficient high-quality amplification and compression of solitons.

  18. Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community.

    Science.gov (United States)

    Tanabe, Akifumi S; Nagai, Satoshi; Hida, Kohsuke; Yasuike, Motoshige; Fujiwara, Atushi; Nakamura, Yoji; Takano, Yoshihito; Katakura, Seiji

    2016-03-01

    The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1-3, V4-5 and V7-9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys in the Sea of Okhotsk, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4-5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1-3 region, followed by the V7-9 region, and the lowest variability in the V4-5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1-3 and V7-9 regions than in the V4-5 region, but no significant difference was detected between the V1-3 and V7-9 regions. We therefore conclude that the V1-3 region will be the most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.

  19. Procedures for DNA extraction and amplification from quills of crested porcupine (Hystrix cristata

    Directory of Open Access Journals (Sweden)

    Domenico Fulgione

    2000-09-01

    Full Text Available Abstract Genetic analysis in mammalian populations are useful for any conservation management. This kind of analysis utilised tissue of specimens studied involving a damages to the populations, only recently many study are indicated alternative procedure based on scales, hairs or feathers. The porcupine (Histrix cristata is an elusive species with localised populations. In this work I propose one procedure of genetic analysis starting by DNA quill in order to help studies about this species, without damage the population examined. The quills are easy to find because the porcupine loss them constantly. Nucleic acids extraction was done utilising synthetic resin (chelex and then ipervariable region of mitochondrial DNA was amplified through PCR with specific primers. The advantages of this selective amplification is the selective increase of interest DNA in spite of possible organic contamination. At this point two different procedure could be utilised to characterise of population: restriction fragment analysis or sequence analysis.

  20. Multiplex Ligation-Dependent Probe Amplification Technique for Copy Number Analysis on Small Amounts of DNA Material

    DEFF Research Database (Denmark)

    Sørensen, Karina; Andersen, Paal; Larsen, Lars;

    2008-01-01

    The multiplex ligation-dependent probe amplification (MLPA) technique is a sensitive technique for relative quantification of up to 50 different nucleic acid sequences in a single reaction, and the technique is routinely used for copy number analysis in various syndromes and diseases. The aim...... of the study was to exploit the potential of MLPA when the DNA material is limited. The DNA concentration required in standard MLPA analysis is not attainable from dried blood spot samples (DBSS) often used in neonatal screening programs. A novel design of MLPA probes has been developed to permit for MLPA...... analysis on small amounts of DNA. Six patients with congenital adrenal hyperplasia (CAH) were used in this study. DNA was extracted from both whole blood and DBSS and subjected to MLPA analysis using normal and modified probes. Results were analyzed using GeneMarker and manual Excel analysis. A total...