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Sample records for amplification mlpa technique

  1. A novel study of Copy Number Variations in Hirschsprung disease using the Multiple Ligation-dependent Probe Amplification (MLPA technique

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    Antiñolo Guillermo

    2009-11-01

    Full Text Available Abstract Background Hirschsprung disease (HSCR is a congenital malformation of the hindgut produced by a disruption in neural crest cell migration during embryonic development. HSCR has a complex genetic etiology and mutations in several genes, mainly the RET proto-oncogene, have been related to the disease. There is a clear predominance of missense/nonsense mutations in these genes whereas copy number variations (CNVs have been seldom described, probably due to the limitations of conventional techniques usually employed for mutational analysis. Methods In this study we have aimed to analyze the presence of CNVs in some HSCR genes (RET, EDN3, GDNF and ZFHX1B using the Multiple Ligation-dependent Probe Amplification (MLPA approach. Results Two alterations in the MLPA profiles of RET and EDN3 were detected, but a detailed inspection showed that the decrease in the corresponding dosages were due to point mutations affecting the hybridization probes regions. Conclusion Our results indicate that CNVs of the gene coding regions analyzed here are not a common molecular cause of Hirschsprung disease. However, further studies are required to determine the presence of CNVs affecting non-coding regulatory regions, as well as other candidate genes.

  2. Detection of MDM2/CDK4 amplification in lipomatous soft tissue tumors from formalin-fixed, paraffin-embedded tissue: comparison of multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH).

    Science.gov (United States)

    Creytens, David; van Gorp, Joost; Ferdinande, Liesbeth; Speel, Ernst-Jan; Libbrecht, Louis

    2015-02-01

    In this study, the detection of MDM2 and CDK4 amplification was evaluated in lipomatous soft tissue tumors using multiplex ligation-dependent probe amplification (MLPA), a PCR-based technique, in comparison with fluorescence in situ hybridization (FISH). These 2 techniques were evaluated in a series of 77 formalin-fixed, paraffin-embedded lipomatous tumors (27 benign adipose tumors, 28 atypical lipomatous tumors/well-differentiated liposarcomas, 18 dedifferentiated liposarcomas, and 4 pleomorphic liposarcomas). Using MLPA, with a cut-off ratio of >2, 36/71 samples (22 atypical lipomatous tumors/well-differentiated liposarcomas, and 14 dedifferentiated liposarcomas) showed MDM2 and CDK4 amplification. Using FISH as gold standard, MLPA showed a sensitivity of 90% (36/40) and a specificity of 100% (31/31) in detecting amplification of MDM2 and CDK4 in lipomatous soft tissue tumors. In case of high-level amplification (MDM2-CDK4/CEP12 ratio >5), concordance was 100%. Four cases of atypical lipomatous tumor/well-differentiated liposarcoma (4/26, 15%) with a low MDM2 and CDK4 amplification level (MDM2-CDK4/CEP12 ratio ranging between 2 and 2.5) detected by FISH showed no amplification by MLPA, although gain of MDM2 and CDK4 (ratios ranging between 1.6 and 1.9) was seen with MLPA. No amplification was detected in benign lipomatous tumors and pleomorphic liposarcomas. Furthermore, there was a very high concordance between the ratios obtained by FISH and MLPA. In conclusion, MLPA proves to be an appropriate and straightforward technique for screening MDM2/CDK4 amplification in lipomatous tumors, especially when a correct cut-off value and reference samples are chosen, and could be considered a good alternative to FISH to determine MDM2 and CDK4 amplification in liposarcomas. Moreover, because MLPA, as a multiplex technique, allows simultaneous detection of multiple chromosomal changes of interest, it could be in the future a very reliable and fast molecular analysis on

  3. 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...

  4. Rapid identification and characterization of Penicillium marneffei using multiplex ligation-dependent probe amplification (MLPA) in paraffin-embedded tissue samples

    NARCIS (Netherlands)

    J.M. Zhang; J.F. Sun; P.Y. Feng; X.Q. Li; C.M. Lu; S. Lu; W.Y. Cai; L.Y. Xi; G.S. de Hoog

    2011-01-01

    Penicillium marneffei infection is a deadly disease and early diagnosis leads to prompt and appropriate antifungal therapy. To develop a sensitive method to diagnose P. marneffei infection, a multiplex ligation-dependent probe amplification (MLPA) assay was adapted. This method can rapidly and speci

  5. 多重连接依赖探针扩增技术检测胎儿非整倍体染色体异常%Fetal aneuploidy detected by multiplex ligation-dependent probe amplification (MLPA)

    Institute of Scientific and Technical Information of China (English)

    吴琦嫦; 王文博; 江雨; 孔辉; 钟晓玲; 于威威; 孙丽; 周裕林

    2010-01-01

    Objective To investigate the role of muhiplex ligation-dependent probe amplification(MLPA) in identifying fetal aneuploidy of chromosomes 13,18,21,X,and Y. Methods From June 2007 to December 2008,263 samples(prenatal diagnosis group),including amniotic or umbilical cord blood from pregnant women who required prenatal diagnosis,were processed in parallel by MLPA and conventional karyotype to detect fetal aneuploidy.Another 26 samples(fetal death group).ineluding retained abortion and fetal death,were also processed bv MLPA. Results Five cases of 21-trisomy,4 eases of 18-trisomy,1 case of 13-trisomy and 3 cases of 45,X were identified among the prenatal diagnosis group by MLPA,and the results were consistent with karyotype.Two cases of 45,X and 1 case of 18-trisomy were identified among the retained abortion and fetal death group. Conclusions MLPA is a rapid,efficient,simple,reliable and economical technique in detecting most common chromosomal aneuploidies and have important clinical value.%目的 探讨多重连接依赖探针扩增技术(multiplex ligation-dependent probe amplifiea-tion,MLPA)在检测胎儿非整倍体染色体异常中的作用. 方法 2007年6月至2008年12月对263例需进行产前诊断的孕妇(产前诊断组)取羊水或脐血进行MLPA检测,同时进行传统的染色体核型分析.对26例发生稽留流产或死胎的孕妇取胎儿组织提取DNA进行MLPA检测. 结果 产前诊断组检出5例21-三体,4例18-三体,1例13-三体和3例45,X,与细胞核型分析结果一致.稽留流产或死胎组检出2例45,x和1例18-三体. 结论 MLPA可用于检测胎儿最常见的13、18、21、X、Y染色体非整倍体异常,用于产前诊断,快速简单,准确经济,有一定的临床推广价值.

  6. Multiplex detection of GMO with ligation-dependent probes amplification(MLPA)%应用MLPA技术进行转基因多重检测研究

    Institute of Scientific and Technical Information of China (English)

    凌杏园; 向才玉; 章桂明; 康林; 陈洪俊; 陈枝楠

    2011-01-01

    多重连接探针扩增技术已广泛应用于医学基因点突变、基因缺失和基因甲基化等基因检测,具有高通量、特异性高和经济的特点.本文首次将这一技术应用于转基因检测,实现了高通量转基因检测的目的,提高了检测效率.%MLPA (multiplex ligation -dependent probes amplification), a multiplex, high -specificity and economical detection method, was reported in 2002 and widely used in the detection of gene mutation, gene deletion and DNA methylation. This paper introduces the detection of GMO with MLPA, with which the detection of GMO is high -throughput and high efficiency.

  7. Rapid screening for chromosomal aneuploidies using array-MLPA

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    van Beuningen Rinie

    2011-05-01

    Full Text Available Abstract Background Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening. Methods We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes. Results In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7% including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases. Conclusions Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18

  8. 多重连接探针扩增(MLPA)技术同时检测五种病毒的研究%Simultaneous Detection of Five Virues by Multiplex Ligation-dependent Probe Amplification(MLPA) Technology

    Institute of Scientific and Technical Information of China (English)

    史喜菊; 马贵平; 乔彩霞; 郭志红; 张伟; 刘全国; 李炎鑫; 李冰玲

    2013-01-01

    Current detection technologies for diagnosis of animal diseases is mostly targeted at single pathogen,but the prevalence of animal diseases is characterized by mixed infection with more than one pathogen.In order to resolve the trouble,here we describe the new multiparameter assay,which is based on multiplex ligation-dependent probe amplification(MLPA) technology with the advantages of specificity,sensitivity and high-throughput.Five pairs of specific probe targeted at Swine influenza virus(SIV),Pseudorabies virus(PRV),Foot and mouth disease virus (FMDV),Transmissible gastroenteritis virus (TGEV) and Porcine reproductive and respiratory syndrome virus (PRRSV),were designed,respectiviely.The mixture of five standard RNA/DNA was used as template,together with the mixture of these probes as probe and the PCR universal primer,one MLPA method for simultaneous detection of the five porcine viruses was developed.The result of specificity test showed that the designed probes had good specificity without mismatch between each virus-specific probe pair and other six viruses,and that the mixture of the five pairs of probe only amplified the corresponding one specific fragment from the eight virus templates,respectively,no amplification signal was produced among Porcine parvovirus(PPV),Classical swine fever virus(CSFV) and Porcine epidemic diarrhea virus(PEDV) with the same probe mixture.The result of sensitivity test showed that the concentration of nucleic acid of single virus in one MLPA reaction was up to 3 000~6 000 copies.All the results showed that the developed MLPA method in this article accomplished the simultaneous detection of five viruses in one reaction,which indicates MLPA technology may be an alternative to simultaneous detection of many pathogens in the future in the field of veterinary medicine.%现有的动物疫病诊断技术多是针对单一病原进行的,而动物疫病的流行却出现了多种病毒混合感染,现有诊断技术不能很好地

  9. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms.

    Science.gov (United States)

    Terefework, Zewdu; Pham, Chi L; Prosperi, Anja C; Entius, Mark M; Errami, Abdellatif; van Spanning, Rob J M; Zaura, Egija; Ten Cate, Jacob M; Crielaard, Wim

    2008-12-01

    A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.

  10. Utility of MLPA in mutation analysis and carrier detection for Duchenne muscular dystrophy

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    Prashant K Verma

    2012-01-01

    Full Text Available Context: Multiplex ligation probe amplification (MLPA is a new technique to identify deletions and duplications and can evaluate all 79 exons in dystrophin gene in patients with Duchenne muscular dystrophy (DMD. Being semi-quantitative, MLPA is also effective in detecting duplications and carrier testing of females; both of which cannot be done using multiplex PCR. It has found applications in diagnostics of many genetic disorders. Aim: To study the utility of MLPA in diagnosis and carrier detection for DMD. Materials and Methods: Mutation analysis and carrier detection was done by multiplex PCR and MLPA and the results were compared. Results and Conclusions: We present data showing utility of MLPA in identifying mutations in cases with DMD/BMD. In the present study using MLPA, we identified mutations in additional 5.6% cases of DMD in whom multiplex PCR was not able to detect intragenic deletions. In addition, MLPA also correctly confirmed carrier status of two obligate carriers and revealed carrier status in 6 of 8 mothers of sporadic cases.

  11. Detection of deletion mutations of FBN1 in two patients with Marfan syndrome using next generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) technique%NGS和MLPA技术检测2例马凡综合征患者FBN1基因缺失突变

    Institute of Scientific and Technical Information of China (English)

    卢鑫鑫; 黄肖利; 王韧; 陈喜军; 饶慧英; 吴文冰; 丘丽萍; 黄毅; 伍严安

    2015-01-01

    目的 对2例马凡综合征(Marfan's syndrome,MFS)患者的原纤维蛋白-1基因(FBN1)进行突变检测.方法 提取患者的外周血全基因组DNA,用第二代测序技术(NGS)和多重连接探针扩增技术(MLPA)对FBN1进行突变筛查,对这2种方法提示有拷贝数异常的外显子进行PCR和DNA Sanger测序以证实突变.结果 NGS和MLPA技术检测均显示1例患者有18号外显子缺失突变,另1例患者其56号外显子有缺失突变.经PCR和Sanger测序证实前者18号外显子及其两侧翼区有大片段缺失c.2114-2357_2167+747de13158bp,后者第56号外显子及其内含子有9 bp的缺失突变c.6864_c.6871+1delCTGTGTAGG.结论 NGS和MLPA技术有助于筛查基因组缺失突变,但仍需借助Sanger测序等方法验证.

  12. Gene changes in Duchenne muscular dystrophy: Comparison of multiplex PCR and multiplex ligation-dependent probe amplification techniques

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    Kohli Sudha

    2010-01-01

    Full Text Available Background: Duchenne muscular dystrophy (DMD is a common X-linked recessive neuromuscular disorder, affecting 1 in 3,500 live male births. About 65% of cases are caused by deletions; ~5% to 8%, by duplication; and the remaining, by point mutations of the dystrophin gene. The frequency of complex rearrangements (double-deletion and non-contiguous duplications is reported to be 4%. Aim: In this study, we examined the usefulness of multiplex ligation-dependent probe amplification (MLPA for screening of deletion and duplication mutations in a group of DMD/ BMD (Becker muscular dystrophy patients from India. Patients and Methods: We analyzed 180 patients referred from all over India, by both multiplex PCR technique (22 exons and MLPA (all 79 exons. Results and Conclusion: By multiplex PCR, deletions were detected in 90 (50% patients. MLPA studies in these cases detected 3 additional deletions, 16 (8.9% duplications and 2 point mutations. MLPA is useful to verify absence of deletions/ duplications in all 79 exons. This sets the stage to look for point mutations using RNA- or DNA-based tests because of the availability of the drug PTC124. Also, the extent of the deletions and duplications could be more accurately defined by MLPA. The delineation of the precise extent of deletion helps in deciding whether exon-skipping technique would be useful as therapy.

  13. Custom-designed MLPA using multiple short synthetic probes

    DEFF Research Database (Denmark)

    Serizawa, R.R.; Ralfkiaer, U.; Dahl, C.;

    2010-01-01

    Ligation of two oligonucleotide probes hybridized adjacently to a DNA template has been widely used for detection of genome alterations. The multiplex ligation-dependent probe amplification (MLPA) technique allows simultaneous screening of multiple target sequences in a single reaction by using......-stranded bacteriophage vector to introduce a sequence of defined length between the primer binding site and the specific target sequence. Here we demonstrate that differences in amplicon length can be achieved by using multiple short synthetic probes for each target sequence. When joined by a DNA ligase, these probes...

  14. MLPA method for PMP22 gene analysis:

    OpenAIRE

    Kokalj-Vokač, Nadja; Stangler Herodež, Špela; Zagradišnik, Boris

    2005-01-01

    DNA copy number alterations are responsible for several categories of human diseases and syndromes. These changes can be detected by cytogenetic studies when there is involvement of several kilobases or megabases of DNA. Examination of sub-microscopic changes is possible by using short probes flanked by the same primer pairs. Multiplex ligation-dependent probe amplification (MLPA) is a simple, high resolution method by which not sample nucleic acids but probes added to the samples are amplifi...

  15. Detección de un caso de síndrome de Williams-Beuren por MLPA Detection of a Williams Beuren syndrome case by MLPA

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    Sergio Laurito

    2013-02-01

    the family. Fluorescence in situ hybridization (FISH is considered the gold standard technique for detecting WBS. Multiplex ligation-dependent probe amplification (MLPA has been introduced into DNA diagnostic laboratories for the detection of copy number variations in several diseases including WBS. The objective of this study was to confirm, by MLPA, the clinical diagnosis of WBS in a pediatric patient. This technique allowed to detect the deletion of CYLN2, FZD9, STX1A, ELN, LIMK1 and RFC2 genes. In geographic regions were the detection by F ISH is not available for this disease, the MLPA methodology allowed to confirm the clinic diagnostic of WBS. To our knowledge this is the first report demonstrating the confirmation of WBS by MLPA in Argentina.

  16. Clinical utility of multiplex ligation-dependent probe amplification technique in identification of aetiology of unexplained mental retardation: A study in 203 Indian patients

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    Vijay R Boggula

    2014-01-01

    Full Text Available Background & objectives: Developmental delay (DD/mental retardation also described as intellectual disability (ID, is seen in 1-3 per cent of general population. Diagnosis continues to be a challenge at clinical level. With the advancement of new molecular cytogenetic techniques such as cytogenetic microarray (CMA, multiplex ligation-dependent probe amplification (MLPA techniques, many microdeletion/microduplication syndromes with DD/ID are now delineated. MLPA technique can probe 40-50 genomic regions in a single reaction and is being used for evaluation of cases with DD/ID. In this study we evaluated the clinical utility of MLPA techniques with different probe sets to identify the aetiology of unexplained mental retardation in patients with ID/DD. Methods: A total of 203 randomly selected DD/ID cases with/without malformations were studied. MLPA probe sets for subtelomeric regions (P070/P036 and common microdeletions/microduplications (P245-A2 and X-chromosome (P106 were used. Positive cases with MLPA technique were confirmed using either fluorescence in situ hybridization (FISH or follow up confirmatory MLPA probe sets. Results: The overall detection rate was found to be 9.3 per cent (19 out of 203. The detection rates were 6.9 and 7.4 per cent for common microdeletion/microduplication and subtelomeric probe sets, respectively. No abnormality was detected with probe set for X-linked ID. The subtelomeric abnormalities detected included deletions of 1p36.33, 4p, 5p, 9p, 9q, 13q telomeric regions and duplication of 9pter. The deletions/duplications detected in non telomeric regions include regions for Prader Willi/Angelman regions, Williams syndrome, Smith Magenis syndrome and Velocardiofacial syndrome. Interpretation & conclusions: Our results show that the use of P245-A2 and P070/P036-E1 probes gives good diagnostic yield. Though MLPA cannot probe the whole genome like cytogenetic microarray, due to its ease and relative low cost it is an

  17. Integrated multiplex ligation dependent probe amplification (MLPA) assays for the detection of alterations in the HEXB, GM2A and SMARCAL1 genes to support the diagnosis of Morbus Sandhoff, M. Tay-Sachs variant AB and Schimke immuno-osseous dysplasia in humans.

    Science.gov (United States)

    Sobek, Anna K U; Evers, Christina; Dekomien, Gabriele

    2013-02-01

    Multiplex ligation dependent probe amplification (MLPA) assays were designed for the genes HEXB (OMIM: 606873), GM2A (OMIM: 613109) and SMARCAL1 (OMIM: 606622) of humans. Two sets of synthetic MLPA probes for these coding exons were tested. Changes in copy numbers were detected as well as single nucleotide polymorphisms (SNPs) by complementary DNA sequence analyses. The MLPA method was shown to be reliable for mutation detection and identified five published and 12 new mutations. In all cases from a Morbus Sandhoff cohort of patients, exclusively one variation in copy number was observed and linked to a nucleotide alteration called c.1614-14C>A. This deletion comprised exons 1-5. One of these cases is described in detail. Deletions were neither detected in the GM2A nor the SMARCAL1 genes. The MLPA assays complement routine diagnostics for M. Sandhoff (OMIM: 268800), M. Tay-Sachs variant AB (OMIM: 272750) and Schimke immuno-osseous dysplasia (OMIM: 242900). PMID:23010210

  18. Application research of multiplex ligation- dependent probe amplification (MLPA) in rapid prenatal detection of aneuploid abnormalities%MLPA技术在快速检测胎儿染色体非整倍体异常中的应用

    Institute of Scientific and Technical Information of China (English)

    江雨; 王文博; 吴琦嫦; 周裕林

    2009-01-01

    目的:探讨多重探针连接依赖式扩增(multiplex ligation-dependent probe amplification,MLPA)在快速检测胎儿染色体非整倍体异常中的应用价值.方法:282例产前诊断标本(羊水179例、脐带血90例和绒毛13例)同时进行MLPA检测及核型分析,用计算机辅助数据分析方法得出MLPA检测结果.结果:MLPA分析在标本接收后24 h内即可得出结果,共检出染色体倍体异常产前诊断标本17例,包括唐氏综合征(Down Syndrome,47,+21)7例、爱德华氏综合征(Edwards Syndrome,47,+18)5例、特纳氏综合征(Turner Syndrome,45,X)3例、帕陶氏综合征(Patau Syndrome,47,+13)1例及XYY综合征(47,XYY)1例.MLPA检测24 h报告结果临床符合率为97.9%.结论:MLPA技术具有快速、准确性高、成本低等优点,可作为诊断常见染色体非整倍体异常的可靠方法.

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

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    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

  20. Novel MLPA procedure using self-designed probes allows comprehensive analysis for CNVs of the genes involved in Hirschsprung disease

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    Antiñolo Guillermo

    2010-05-01

    Full Text Available Abstract Background Hirschsprung disease is characterized by the absence of intramural ganglion cells in the enteric plexuses, due to a fail during enteric nervous system formation. Hirschsprung has a complex genetic aetiology and mutations in several genes have been related to the disease. There is a clear predominance of missense/nonsense mutations in these genes whereas copy number variations (CNVs have been seldom described, probably due to the limitations of conventional techniques usually employed for mutational analysis. In this study, we have looked for CNVs in some of the genes related to Hirschsprung (EDNRB, GFRA1, NRTN and PHOX2B using the Multiple Ligation-dependent Probe Amplification (MLPA approach. Methods CNVs screening was performed in 208 HSCR patients using a self-designed set of MLPA probes, covering the coding region of those genes. Results A deletion comprising the first 4 exons in GFRA1 gene was detected in 2 sporadic HSCR patients and in silico approaches have shown that the critical translation initiation signal in the mutant gene was abolished. In this study, we have been able to validate the reliability of this technique for CNVs screening in HSCR. Conclusions The implemented MLPA based technique presented here allows CNV analysis of genes involved in HSCR that have not been not previously evaluated. Our results indicate that CNVs could be implicated in the pathogenesis of HSCR, although they seem to be an uncommon molecular cause of HSCR.

  1. Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach.

    Science.gov (United States)

    Sánchez, J L Acero; Henry, O Y F; Joda, H; Solnestam, B Werne; Kvastad, L; Johansson, E; Akan, P; Lundeberg, J; Lladach, N; Ramakrishnan, D; Riley, I; O'Sullivan, C K

    2016-08-15

    Asymmetric multiplex ligation-dependent probe amplification (MLPA) was developed for the amplification of seven breast cancer related mRNA markers and the MLPA products were electrochemically detected via hybridization. Seven breast cancer genetic markers were amplified by means of the MLPA reaction, which allows for multiplex amplification of multiple targets with a single primer pair. Novel synthetic MLPA probes were designed to include a unique barcode sequence in each amplified gene. Capture probes complementary to each of the barcode sequences were immobilized on each electrode of a low-cost electrode microarray manufactured on standard printed circuit board (PCB) substrates. The functionalised electrodes were exposed to the single-stranded MLPA products and following hybridization, a horseradish peroxidase (HRP)-labelled DNA secondary probe complementary to the amplified strand completed the genocomplex, which was electrochemically detected following substrate addition. The electrode arrays fabricated using PCB technology exhibited an excellent electrochemical performance, equivalent to planar photolithographically-fabricated gold electrodes, but at a vastly reduced cost (>50 times lower per array). The optimised system was demonstrated to be highly specific with negligible cross-reactivity allowing the simultaneous detection of the seven mRNA markers, with limits of detections as low as 25pM. This approach provides a novel strategy for the genetic profiling of tumour cells via integrated "amplification-to-detection". PMID:27085955

  2. BeeDoctor, a versatile MLPA-based diagnostic tool for screening bee viruses.

    Directory of Open Access Journals (Sweden)

    Lina De Smet

    Full Text Available The long-term decline of managed honeybee hives in the world has drawn significant attention to the scientific community and bee-keeping industry. A high pathogen load is believed to play a crucial role in this phenomenon, with the bee viruses being key players. Most of the currently characterized honeybee viruses (around twenty are positive stranded RNA viruses. Techniques based on RNA signatures are widely used to determine the viral load in honeybee colonies. High throughput screening for viral loads necessitates the development of a multiplex polymerase chain reaction approach in which different viruses can be targeted simultaneously. A new multiparameter assay, called "BeeDoctor", was developed based on multiplex-ligation probe dependent amplification (MLPA technology. This assay detects 10 honeybee viruses in one reaction. "BeeDoctor" is also able to screen selectively for either the positive strand of the targeted RNA bee viruses or the negative strand, which is indicative for active viral replication. Due to its sensitivity and specificity, the MLPA assay is a useful tool for rapid diagnosis, pathogen characterization, and epidemiology of viruses in honeybee populations. "BeeDoctor" was used for screening 363 samples from apiaries located throughout Flanders; the northern half of Belgium. Using the "BeeDoctor", virus infections were detected in almost eighty percent of the colonies, with deformed wing virus by far the most frequently detected virus and multiple virus infections were found in 26 percent of the colonies.

  3. BeeDoctor, a versatile MLPA-based diagnostic tool for screening bee viruses.

    Science.gov (United States)

    De Smet, Lina; Ravoet, Jorgen; de Miranda, Joachim R; Wenseleers, Tom; Mueller, Matthias Y; Moritz, Robin F A; de Graaf, Dirk C

    2012-01-01

    The long-term decline of managed honeybee hives in the world has drawn significant attention to the scientific community and bee-keeping industry. A high pathogen load is believed to play a crucial role in this phenomenon, with the bee viruses being key players. Most of the currently characterized honeybee viruses (around twenty) are positive stranded RNA viruses. Techniques based on RNA signatures are widely used to determine the viral load in honeybee colonies. High throughput screening for viral loads necessitates the development of a multiplex polymerase chain reaction approach in which different viruses can be targeted simultaneously. A new multiparameter assay, called "BeeDoctor", was developed based on multiplex-ligation probe dependent amplification (MLPA) technology. This assay detects 10 honeybee viruses in one reaction. "BeeDoctor" is also able to screen selectively for either the positive strand of the targeted RNA bee viruses or the negative strand, which is indicative for active viral replication. Due to its sensitivity and specificity, the MLPA assay is a useful tool for rapid diagnosis, pathogen characterization, and epidemiology of viruses in honeybee populations. "BeeDoctor" was used for screening 363 samples from apiaries located throughout Flanders; the northern half of Belgium. Using the "BeeDoctor", virus infections were detected in almost eighty percent of the colonies, with deformed wing virus by far the most frequently detected virus and multiple virus infections were found in 26 percent of the colonies. PMID:23144717

  4. 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

  5. Diagnostic yield by supplementing prenatal metaphase karyotyping with MLPA for microdeletion syndromes and subtelomere imbalances

    DEFF Research Database (Denmark)

    Kjaergaard, S; Sundberg, K; Jørgensen, F S;

    2010-01-01

    The aim of the study was to retrospectively assess the relevance of using multiplex ligation-dependent probe amplification (MLPA) for detection of selected microdeletion syndromes (22q11, Prader-Willi/Angelman, Miller-Dieker, Smith-Magenis, 1p-, Williams), the reciprocal microduplication syndromes...

  6. Diagnostic yield by supplementing prenatal metaphase karyotyping with MLPA for microdeletion syndromes and subtelomere imbalances

    DEFF Research Database (Denmark)

    Kjaergaard, S; Sundberg, K; Jørgensen, F S;

    2010-01-01

    The aim of the study was to retrospectively assess the relevance of using multiplex ligation-dependent probe amplification (MLPA) for detection of selected microdeletion syndromes (22q11, Prader-Willi/Angelman, Miller-Dieker, Smith-Magenis, 1p-, Williams), the reciprocal microduplication syndrome...

  7. Multiplex ligation-dependent probe amplification for the detection of chromosomal gains and losses in formalin-fixed tissue.

    NARCIS (Netherlands)

    Dijk, M.C.R.F. van; Rombout, P.D.M.; Sprenger, S.H.E.; Straatman, H.M.P.M.; Bernsen, M.R.; Ruiter, D.J.; Jeuken, J.W.M.

    2005-01-01

    Molecular analysis on formalin-fixed paraffin-embedded tissue is of increasing importance in diagnostic histopathology and tumor research. Multiplex ligation-dependent probe amplification (MLPA) is a technique that can be used for detection of copy number alterations of up to 45 different DNA sequen

  8. Colorimetric quantification of mRNA expression in rare tumour cells amplified by multiple ligation-dependent probe amplification.

    Science.gov (United States)

    Acero Sanchez, Josep L; Henry, Olivier Y F; Mairal, Teresa; Laddach, Nadja; Nygren, Anders; Hauch, Siegfried; Fetisch, Jasmin; O'Sullivan, Ciara K

    2010-07-01

    An enzyme-linked oligonucleotide assay (ELONA) for quantification of mRNA expression of five genes involved in breast cancer, extracted from isolated rare tumour cells and amplified by multiplex ligation-dependent probe amplification (MLPA) is presented. In MLPA, a multiplex oligonucleotide ligation assay is combined with a PCR reaction in which all ligation products are amplified by use of a single primer pair. Biotinylated probes complementary to each of the target sequences were immobilised on the surface of a streptavidin-coated microtitre plate and exposed to single-stranded MLPA products. A universal reporting probe sequence modified with horseradish peroxidase (URP-HRP) and complementary to a universal primer used during the MLPA step was further added to the surface-bound duplex as a reporter probe. Simultaneous addition of anchoring probe and target, followed by addition of reporter probe, rather than sequential addition, was achieved with no significant effect on sensitivity and limits of detection, but considerably reduced the required assay time. Detection limits as low as 20 pmol L(-1), with an overall assay time of 95 min could be achieved with negligible cross-reactivity between probes and non-specific targets present in the MLPA-PCR product. The same MLPA-PCR product was analysed using capillary electrophoresis, the technique typically used for analysis of MLPA products, and good correlation was observed. The assay presented is easy to carry out, relatively inexpensive, rapid, does not require sophisticated instrumentation, and enables quantitative analysis, making it very promising for the analysis of MLPA products. PMID:20526769

  9. 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.

  10. Custom-Designed MLPA Using Multiple Short Synthetic Probes Application to Methylation Analysis of Five Promoter CpG Islands in Tumor and Urine Specimens from Patients with Bladder Cancer

    DEFF Research Database (Denmark)

    Serizawa, R.R.; Ralfkiaer, U.; Dahl, C.;

    2010-01-01

    Ligation of two oligonucleotide probes hybridized adjacently to a DNA template has been widely used for detection of genome alterations. The multiplex ligation-dependent probe amplification (MLPA) technique allows simultaneous screening of multiple target sequences in a single reaction by using......-stranded bacteriophage vector to introduce a sequence of defined length between the primer binding site and the specific target sequence. Here we demonstrate that differences in amplicon length can be achieved by using multiple short synthetic probes for each target sequence. When joined by a DNA ligase, these probes...

  11. High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq.

    Science.gov (United States)

    Kondrashova, Olga; Love, Clare J; Lunke, Sebastian; Hsu, Arthur L; Waring, Paul M; Taylor, Graham R

    2015-01-01

    Whilst next generation sequencing can report point mutations in fixed tissue tumour samples reliably, the accurate determination of copy number is more challenging. The conventional Multiplex Ligation-dependent Probe Amplification (MLPA) assay is an effective tool for measurement of gene dosage, but is restricted to around 50 targets due to size resolution of the MLPA probes. By switching from a size-resolved format, to a sequence-resolved format we developed a scalable, high-throughput, quantitative assay. MLPA-seq is capable of detecting deletions, duplications, and amplifications in as little as 5ng of genomic DNA, including from formalin-fixed paraffin-embedded (FFPE) tumour samples. We show that this method can detect BRCA1, BRCA2, ERBB2 and CCNE1 copy number changes in DNA extracted from snap-frozen and FFPE tumour tissue, with 100% sensitivity and >99.5% specificity.

  12. PWS/AS MS-MLPA Confirms Maternal Origin of 15q11.2 Microduplication

    Directory of Open Access Journals (Sweden)

    Angelika J. Dawson

    2015-01-01

    Full Text Available The proximal region of the long arm of chromosome 15q11.2-q13 is associated with various neurodevelopmental disorders, including Prader-Willi (PWS and Angelman (AS syndromes, autism, and other developmental abnormalities resulting from deletions and duplications. In addition, this region encompasses imprinted genes that cause PWS or AS, depending on the parent-of-origin. This imprinting allows for diagnosis of PWS or AS based on methylation status using methylation sensitive (MS multiplex ligation dependent probe amplification (MLPA. Maternally derived microduplications at 15q11.2-q13 have been associated with autism and other neuropsychiatric disorders. Multiple methods have been used to determine the parent-of-origin for 15q11.2-q13 microdeletions and microduplications. In the present study, a four-year-old nondysmorphic female patient with developmental delay was found to have a de novo ~5 Mb duplication within 15q11.2 by oligonucleotide genomic array. In order to determine the significance of this microduplication to the clinical phenotype, the parent-of-origin needed to be identified. The PWS/AS MS-MLPA assay is generally used to distinguish between deletion and uniparental disomy (UPD of 15q11.2-q13, resulting in either PWS or AS. However, our study shows that PWS/AS MS-MLPA can also efficiently distinguish the parental origin of duplications of 15q11.2-q13.

  13. Detection of Genetically Modified Organisms in Foods by DNA Amplification Techniques

    OpenAIRE

    García-Cañas, Virginia; Cifuentes, Alejandro; González, Ramón

    2004-01-01

    In this article, the different DNA amplification techniques that are being used for detecting genetically modified organisms (GMOs) in foods are examined. This study intends to provide an updated overview (including works published till June 2002) on the principal applications of such techniques together with their main advantages and drawbacks in GMO detection in foods. Some relevant facts on sampling, DNA isolation, and DNA amplification methods are discussed. Moreover, these analytical pro...

  14. Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol, and application in a diagnostic centre

    Directory of Open Access Journals (Sweden)

    Hills Alison

    2007-03-01

    Full Text Available Abstract Background Commercial MLPA kits (MRC-Holland are available for detecting imbalance at the subtelomere regions of chromosomes; each kit consists of one probe for each subtelomere. Methods For validation of the kits, 208 patients were tested, of which 128 were known to be abnormal, corresponding to 8528 genomic regions overall. Validation samples included those with trisomy 13, 18 and 21, microscopically visible terminal deletions and duplications, sex chromosome abnormalities and submicroscopic abnormalities identified by multiprobe FISH. A robust and sensitive analysis system was developed to allow accurate interpretation of single probe results, which is essential as breakpoints may occur between MLPA probes. Results The validation results showed that MLPA is a highly efficient technique for medium-throughput screening for subtelomere imbalance, with 95% confidence intervals for positive and negative predictive accuracies of 0.951-0.996 and 0.9996-1 respectively. A diagnostic testing strategy was established for subtelomere MLPA and any subsequent follow-up tests that may be required. The efficacy of this approach was demonstrated during 15 months of diagnostic testing when 455 patients were tested and 27 (5.9% abnormal cases were detected. Conclusion The development of a robust, medium-throughput analysis system for the interpretation of results from subtelomere assays will be of benefit to other Centres wishing to implement such an MLPA-based service.

  15. Screening of congenital heart disease patients using multiplex ligation-dependent probe amplification

    DEFF Research Database (Denmark)

    Sørensen, Karina Meden; El-Segaier, Milad; Fernlund, Eva;

    2012-01-01

    with CHD for CNVs in specific genomic regions may lead to early diagnosis and awareness of extracardiac symptoms. We designed a multiplex ligation-dependent probe amplification (MLPA) assay specifically for screening of CHD patients. The MLPA assay allows for simultaneous analysis of CNVs in 25 genomic...

  16. Multiplex Ligation-Dependent Probe Amplification of Uveal Melanoma : Correlation with Metastatic Death

    NARCIS (Netherlands)

    Damato, Bertil; Dopierala, Justyna; Klaasen, Annelies; van Dijk, Marcory; Sibbring, Julie; Coupland, Sarah E.

    2009-01-01

    PURPOSE. To evaluate multiplex ligation-dependent probe amplification (MLPA) of uveal melanoma as a predictive tool for metastatic death. METHODS. Uveal melanoma specimens of 73 patients treated between 1998 and 2000 were included. DNA samples were analyzed with MLPA evaluating 31 loci on chromosome

  17. Identification of deletions and duplications in the Duchenne muscular dystrophy gene and female carrier status in western India using combined methods of multiplex polymerase chain reaction and multiplex ligation-dependent probe amplification

    Directory of Open Access Journals (Sweden)

    Rashna S Dastur

    2011-01-01

    Full Text Available Background: The technique of multiplex ligation-dependent probe amplification (MLPA assay is an advanced technique to identify deletions and duplications of all the 79 exons of DMD gene in patients with Duchenne/Becker muscular dystrophy (DMD/BMD and female carriers. Aim: To use MLPA assay to detect deletions which remained unidentified on multiplex polymerase chain reaction (mPCR analysis, scanning 32 exons of the "hot spot" region. Besides knowing the deletions and/or duplications, MLPA was also used to determine the carrier status of the females at risk. Materials and Methods: Twenty male patients showing no deletions on mPCR and 10 suspected carrier females were studied by MLPA assay using P-034 and P-035, probe sets (MRC Holland covering all the 79 exons followed by capillary electrophoresis on sequencing system. Results: On MLPA analysis, nine patients showed deletions of exons other than 32 exons screened by mPCR represented by absence of peak. Value of peak areas were double or more in four patients indicating duplications of exons. Carrier status was confirmed in 50% of females at risk. Conclusion: Combining the two techniques, mPCR followed by MLPA assay, has enabled more accurate detection and extent of deletions and duplications which otherwise would have remained unidentified, thereby increasing the mutation pick up rate. These findings have also allowed prediction of expected phenotype. Determining carrier status has a considerable significance in estimating the risk in future pregnancies and prenatal testing options to limit the birth of affected individuals.

  18. Expanding the mutation spectrum in 130 probands with ARPKD: identification of 62 novel PKHD1 mutations by sanger sequencing and MLPA analysis.

    Science.gov (United States)

    Melchionda, Salvatore; Palladino, Teresa; Castellana, Stefano; Giordano, Mario; Benetti, Elisa; De Bonis, Patrizia; Zelante, Leopoldo; Bisceglia, Luigi

    2016-09-01

    Autosomal recessive polycystic kidney disease (ARPKD) is a rare severe genetic disorder arising in the perinatal period, although a late-onset presentation of the disease has been described. Pulmonary hypoplasia is the major cause of morbidity and mortality in the newborn period. ARPKD is caused by mutations in the PKHD1 (polycystic kidney and hepatic disease 1) gene that is among the largest human genes. To achieve a molecular diagnosis of the disease, a large series of Italian affected subjects were recruited. Exhaustive mutation analysis of PKHD1 gene was carried out by Sanger sequencing and multiple ligation probe amplification (MLPA) technique in 110 individuals. A total of 173 mutations resulting in a detection rate of 78.6% were identified. Additional 20 unrelated patients, in whom it was not possible to analyze the whole coding sequence, have been included in this study. Taking into account the total number (n=130) of this cohort of patients, 107 different types of mutations have been detected in 193 mutated alleles. Out of 107 mutations, 62 were novel: 11 nonsense, 6 frameshift, 7 splice site mutations, 2 in-frame deletions and 2 multiexon deletion detected by MLPA. Thirty-four were missense variants. In conclusion, our report expands the spectrum of PKHD1 mutations and confirms the heterogeneity of this disorder. The population under study represents the largest Italian ARPKD cohort reported to date. The estimated costs and the time invested for molecular screening of genes with large size and allelic heterogeneity such as PKHD1 demand the use of next-generation sequencing (NGS) technologies for a faster and cheaper screening of the affected subjects.

  19. Expanding the mutation spectrum in 130 probands with ARPKD: identification of 62 novel PKHD1 mutations by sanger sequencing and MLPA analysis.

    Science.gov (United States)

    Melchionda, Salvatore; Palladino, Teresa; Castellana, Stefano; Giordano, Mario; Benetti, Elisa; De Bonis, Patrizia; Zelante, Leopoldo; Bisceglia, Luigi

    2016-09-01

    Autosomal recessive polycystic kidney disease (ARPKD) is a rare severe genetic disorder arising in the perinatal period, although a late-onset presentation of the disease has been described. Pulmonary hypoplasia is the major cause of morbidity and mortality in the newborn period. ARPKD is caused by mutations in the PKHD1 (polycystic kidney and hepatic disease 1) gene that is among the largest human genes. To achieve a molecular diagnosis of the disease, a large series of Italian affected subjects were recruited. Exhaustive mutation analysis of PKHD1 gene was carried out by Sanger sequencing and multiple ligation probe amplification (MLPA) technique in 110 individuals. A total of 173 mutations resulting in a detection rate of 78.6% were identified. Additional 20 unrelated patients, in whom it was not possible to analyze the whole coding sequence, have been included in this study. Taking into account the total number (n=130) of this cohort of patients, 107 different types of mutations have been detected in 193 mutated alleles. Out of 107 mutations, 62 were novel: 11 nonsense, 6 frameshift, 7 splice site mutations, 2 in-frame deletions and 2 multiexon deletion detected by MLPA. Thirty-four were missense variants. In conclusion, our report expands the spectrum of PKHD1 mutations and confirms the heterogeneity of this disorder. The population under study represents the largest Italian ARPKD cohort reported to date. The estimated costs and the time invested for molecular screening of genes with large size and allelic heterogeneity such as PKHD1 demand the use of next-generation sequencing (NGS) technologies for a faster and cheaper screening of the affected subjects. PMID:27225849

  20. Genetic Diagnosis of Spinal Muscular Atrophy Using MLPA%运用MLPA进行脊肌萎缩症的基因诊断

    Institute of Scientific and Technical Information of China (English)

    陈红苓; 孟英韬; 舒剑波; 宋力

    2012-01-01

    Objective: To perform genetic diagnosis for 30 suspected patients with spinal muscular atrophy (SMA) using multiplex ligation dependent probe amplification (MLPA) and PCR-restriction fragment length polymorphism (PCR- RFLP), and compare the results of the two methods. Methods: The genomic DNA was isolated using salting-out method from peripheral blood of each subject from 30 families.Exon 7 and 8 of SMN genes were amplified by allele specific PCR. The PCR products were digested with Dral I and Dral I digested PCR products. Simultaneously, the DNA samples were analyzed by SALSA MLPA Kit P021. Results: Both PCR-RFLP and MLPA analysis showed the same that 22 patients with exon 7 and 8 homozygous deletion, and 2 patients with only exon 7 homozygous deletion of SMN1. The other 6 cases presented no homozygous deletion by PCR-RFLP, but one child and two mothers of them were detected heterozygous by MLPA. Also MLPA analysis found three "2+0"carriers from 3 families. The data also showed that the SMN2 copy numbers were mainly 4 or 5 in SMA patients, while the carriers and the normal individuals were 2 or 3 and 1 or 2 copies respectively. There was clear statistical significance in the group of patient -carrier and group of patient-normal individuals (P 0.05). Conclusion: Compared with PCR-RFLP, MLPA is more convenient, precise, high-effective, and it can accurately quantitative analysis of SMNl and SMN2. MLPA is a kind of technique of genetic diagnosis for common genetic disease.%目的:应用多重连接依赖式探针扩增法(MLPA)和聚合酶链式限制性片段长度多态性分析(PCR-RFLP)技术对30例临床疑似脊肌萎缩症(SMA)患者进行基因诊断,并对两种方法进行比较.方法:盐析方法提取30例家系成员外周血DNA,常规PCR方法扩增SMN7、8外显子,用DralⅠ和DralⅠ酶切PCR产物,琼脂糖凝胶电泳检测PCR及酶切产物.同时利用MLPA试剂盒P021方法进行验证比较.结果:经PCR-RFLP方法判断22例SMN1第7+8号外

  1. Increased nuchal translucency with normal karyotype: a follow-up study of 100 cases supplemented with CGH and MLPA analyses

    DEFF Research Database (Denmark)

    Schou, K V; Kirchhoff, M; Nygaard, U;

    2009-01-01

    OBJECTIVE: To evaluate whether high-resolution comparative genomic hybridization (HR-CGH) and subtelomeric and syndrome-specific multiplex ligation-dependent probe amplification (MLPA) would detect minor chromosomal aberrations in fetuses with increased nuchal translucency thickness (NT) and norm...... disease, which supports the current approach of repeated ultrasound examinations in these high-risk pregnancies....... and subtelomeric regions. Pregnancy outcome was followed up. RESULTS: Among 80 liveborn children who were followed up, three (4%) had syndromes involving mental retardation, including a case of Sotos syndrome caused by a de novo mutation. 15% of fetuses were lost during pregnancy due to abnormalities...

  2. EG-02CORRELATION OF MGMT PROMOTER METHYLATION STATUS ANALYSIS USING 6 MS-MLPA PROBES AND CLINICAL RESPONSE OF TEMOZOLOMIDE IN GLIOBLASTOMA PATIENTS

    Science.gov (United States)

    Fakkert, Michelle; de Leng, Wendy; de Weger, Roel; Willems, Stefan; Spliet, Wim; van Hecke, Wim; de Vos, Filip

    2014-01-01

    INTRODUCTION: For patients diagnosed with Glioblastoma Multiforme (GBM) O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation is an important predictive factor for treatment with temozolomide (TMZ). MGMT reverses the toxic effect of alkylating chemotherapies like TMZ, therefore absence of the MGMT protein, due to promoter hypermethylation, results in greater tumor response and prolonged survival. MGMT methylation status can be determined using Methylation Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA). Previous research has documented the predictive value of MGMT MS-MLPA probe mix ME011-A1 containing 3 MGMT probes, but no documentation is available for the current commercially available MS-MLPA probe mix ME011-B containing 6 MGMT probes. The aim of this study is to determine the predictive value of MGMT promoter methylation status for GBM patients using the ME011-B probe mix. METHODS: Patients were included if diagnosed with GBM and treated with TMZ. Retrospectively 102 patients were evaluated for MGMT promoter methylation using the MS-MLPA probe mix ME011-B. Methylation status was compared to clinical outcome to determine the predictive value of MS-MLPA promoter methylation status determined by ME011-B probes. Comparison of methylation status with clinical response was also used to determine which combination of probes provides the best prediction of the response to TMZ. RESULTS: Preliminary MS-MLPA results of 79 patients indicate that the number of patients with promoter hypermethylation in tumors ranges from 15%-67% depending on the probe using a cut-off value of >25%. However, when eliminating the lowest and highest probe and calculating the mean, 65% of the tumors show hypermethylation. CONCLUSION: MGMT promoter methylation status was determined using MS-MLPA probe mix ME011-B, results indicate that over half of the patients diagnosed with GBM might benefit from TMZ therapy. Obtaining clinical response of patients and further

  3. The effects of different maceration techniques on nuclear DNA amplification using human bone.

    Science.gov (United States)

    Lee, Esther J; Luedtke, Jennifer G; Allison, Jamie L; Arber, Carolyn E; Merriwether, D Andrew; Steadman, Dawnie Wolfe

    2010-07-01

    Forensic anthropologists routinely macerate human bone for the purposes of identity and trauma analysis, but the heat and chemical treatments used can destroy genetic evidence. As a follow-up to a previous study on nuclear DNA recovery that used pig ribs, this study utilizes human skeletal remains treated with various bone maceration techniques for nuclear DNA amplification using the standard Combined DNA Index System (CODIS) markers. DNA was extracted from 18 samples of human lower leg bones subjected to nine chemical and heat maceration techniques. Genotyping was carried out using the AmpFlSTR COfiler and AmpFlSTR Profiler Plus ID kits. Results showed that heat treatments via microwave or Biz/Na(2)CO(3) in sub-boiling water efficiently macerate bone and produce amplifiable nuclear DNA for genetic analysis. Long-term use of chemicals such as hydrogen peroxide is discouraged as it results in poor bone quality and has deleterious effects on DNA amplification.

  4. Signal Amplification Technique (SAT): an approach for improving resolution and reducing image noise in computed tomography

    International Nuclear Information System (INIS)

    Spatial resolution improvements in computed tomography (CT) have been limited by the large and unique error propagation properties of this technique. The desire to provide maximum image resolution has resulted in the use of reconstruction filter functions designed to produce tomographic images with resolution as close as possible to the intrinsic detector resolution. Thus, many CT systems produce images with excessive noise with the system resolution determined by the detector resolution rather than the reconstruction algorithm. CT is a rigorous mathematical technique which applies an increasing amplification to increasing spatial frequencies in the measured data. This mathematical approach to spatial frequency amplification cannot distinguish between signal and noise and therefore both are amplified equally. We report here a method in which tomographic resolution is improved by using very small detectors to selectively amplify the signal and not noise. Thus, this approach is referred to as the signal amplification technique (SAT). SAT can provide dramatic improvements in image resolution without increases in statistical noise or dose because increases in the cutoff frequency of the reconstruction algorithm are not required to improve image resolution. Alternatively, in cases where image counts are low, such as in rapid dynamic or receptor studies, statistical noise can be reduced by lowering the cutoff frequency while still maintaining the best possible image resolution. A possible system design for a positron CT system with SAT is described

  5. Signal Amplification Technique (SAT): an approach for improving resolution and reducing image noise in computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, M.E.; Huang, S.C.; Hoffman, E.J.; Plummer, D.; Carson, R.

    1981-01-01

    Spatial resolution improvements in computed tomography (CT) have been limited by the large and unique error propagation properties of this technique. The desire to provide maximum image resolution has resulted in the use of reconstruction filter functions designed to produce tomographic images with resolution as close as possible to the intrinsic detector resolution. Thus, many CT systems produce images with excessive noise with the system resolution determined by the detector resolution rather than the reconstruction algorithm. CT is a rigorous mathematical technique which applies an increasing amplification to increasing spatial frequencies in the measured data. This mathematical approach to spatial frequency amplification cannot distinguish between signal and noise and therefore both are amplified equally. We report here a method in which tomographic resolution is improved by using very small detectors to selectively amplify the signal and not noise. Thus, this approach is referred to as the signal amplification technique (SAT). SAT can provide dramatic improvements in image resolution without increases in statistical noise or dose because increases in the cutoff frequency of the reconstruction algorithm are not required to improve image resolution. Alternatively, in cases where image counts are low, such as in rapid dynamic or receptor studies, statistical noise can be reduced by lowering the cutoff frequency while still maintaining the best possible image resolution. A possible system design for a positron CT system with SAT is described.

  6. Clinical application of a ligation-independent pathway of multiplex ligation-dependent probe amplification for the determination of quinolone susceptibility of Streptococcus pneumoniae.

    Science.gov (United States)

    Uno, Naoki; Araki, Nobuko; Kaku, Norihito; Kosai, Kosuke; Hasegawa, Hiroo; Yanagihara, Katsunori

    2016-09-01

    We previously uncovered a ligation-independent pathway of multiplex ligation-dependent probe amplification (MLPA) through which products of MLPA could be amplified without both hybridization and ligation reactions. Here, we utilized this pathway to detect an antibiotic resistance mutation of quinolones in Streptococcus pneumoniae. PMID:27343683

  7. Etablierung der MLPA-Analyse für seltene genetische Erkrankungen (orphan diseases) : Morbus Sandhoff (HEXB), Morbus Tay-Sachs Typ AB (GM2A) und Morbus Schimke (SMARCAL1)

    OpenAIRE

    Sobek, Anna Kathrin Ulrike

    2014-01-01

    Für die Gene HEXB, GM2A und SMARCAL1, krankheitsursächlich für die rezessiv vererbten Erkrankungen M. Sandhoff, M. Tay-Sachs Variante AB und M. Schimke, wurde die multiplex ligation dependent probe amplification (MLPA)-Analyse entwickelt, verifiziert und validiert. Zudem wurde eine bereits vorhandene Patientenkohorte nachuntersucht. Im Rahmen der Arbeit wurde die MLPA-Analyse für die vier Exons des GM2-Gens, die 14 Exons des HEXB-Gens und die 18 Exons des SMARCAL1-Gens etabliert. ...

  8. [Female genital surgery, G-spot amplification techniques--state of the science].

    Science.gov (United States)

    Bachelet, J-T; Mojallal, A; Boucher, F

    2014-10-01

    The G-spot amplification is a process of "functional" intimate surgery consisting of a temporary physical increase of the size and sensitivity of the G-spot with a filler injected into the septum between the bladder and the vagina's anterior wall, in order to increase the frequency and importance of female orgasm during vaginal penetration. This surgical technique is based on the existence of an eponymous anatomical area described by Dr Gräfenberg in 1950, responsible upon stimulation of systematic orgasm different from the clitoral orgasm, referring to the vaginal orgasm as described by Freud in 1905. The purpose of this article is to review the scientific basis of the G-spot, whose very existence is currently a debated topic, and to discuss the role of G-spot amplification surgery.

  9. Detección de un caso de síndrome de Williams-Beuren por MLPA

    Directory of Open Access Journals (Sweden)

    Sergio Laurito

    2013-02-01

    Full Text Available El síndrome de Williams-Beuren (WBS es un trastorno del desarrollo neurológico que incluye diferentes manifestaciones clínicas como estenosis aórtica supravalvular, lesiones cerebrovasculares, retraso en el crecimiento, rasgos faciales "élficos" y retraso mental. Es causado por una microdeleción heterocigótica de genes contiguos en la banda cromosómica 7q11.23, generando un cambio en el número de copias (CNV de esta región crítica. Los pacientes presentan una amplia manifestación clínica y variada expresión fenotípica. La confirmación de la sospecha clínica es esencial para el seguimiento clínico del paciente y el asesoramiento genético de la familia. La técnica estándar para la detección de WBS es la hibridización fluorescente in situ. En los últimos años la metodología MLPA (Multiplex Ligation dependent Probe Amplification ha sido incorporada a los laboratorios diagnósticos para la detección de CNV relacionados con distintas enfermedades, incluyendo WBS. El objetivo de este trabajo fue confirmar el diagnóstico clínico de WBS en un niño, utilizando la técnica de MLPA. Los ensayos por MLPA permitieron detectar la deleción de los genes CYLN2, FZD9, STX1A, ELN, LIMK1y RFC2. En regiones geográficas donde la determinación por FISH (Fluorescence In Situ Hybridization no está disponible para esta enfermedad, la metodología MLPA ha permitido confirmar el diagnóstico clínico y detectar los genes involucrados en la alteración. Hasta nuestro conocimiento no hay otros casos publicados sobre síndrome de WB detectado por la técnica MLPA en la Argentina.

  10. Identification of a novel large CYP17A1 deletion by MLPA analysis in a family with classic 17α-hydroxylase deficiency.

    Science.gov (United States)

    Turkkahraman, Doga; Guran, Tulay; Ivison, Hannah; Griffin, Aliesha; Vijzelaar, Raymon; Krone, Nils

    2015-01-01

    Steroid 17α-hydroxylase deficiency (17OHD) is a rare form of congenital adrenal hyperplasia caused by mutations in the 17α-hydroxylase ( CYP17A1) gene. CYP17A1 is a key enzyme in the biosynthesis of adrenal and gonadal steroid hormones facilitating both 17α-hydroxylase and 17,20-lyase activities. We characterized a partial CYP17A1 deletion in a Kurdish family with 17OHD by multiplex ligation-dependent probe amplification (MLPA). The index patient presented with amenorrhea and lack of pubertal development. Investigations established the diagnosis of 46,XY disorder of sex development (DSD). She is the daughter of consanguineous parents and has 2 sisters with similar clinical presentation. All patients showed biochemical signs of primary adrenal and gonadal insufficiency. The molecular genetic analysis by PCR suggested a deletion spanning exons 1–6 of the CYP17A1 gene. MLPA analysis confirmed the large partial CYP17A1 deletion in patients and parents in homozygous and heterozygous state, respectively. This is the first report employing MLPA for mutation analysis to detect a deletion of CYP17A1 spanning multiple exons in 3 patients with classic 17OHD. Therefore, it is important to consider large partial CYP17A1 deletions in 17OHD in addition to point mutations in cases where no segregation analysis is possible to determine the correct genotype. PMID:25765894

  11. Challenging loop-mediated isothermal amplification(LAMP) technique for molecular detection of Toxoplasma gondii

    Institute of Scientific and Technical Information of China (English)

    Shirzad; Fallahi; Zahra; Arab; Mazar; Mehrdad; Ghasemian; Ali; Haghighi

    2015-01-01

    Objective:To compare analytical sensitivity and specificity of a newly described DNA amplification technique.LAMP and nested PCR assay targeting the RE and Bl genes for the detection of Toxoplasma gondii(T.gondii) DNA.Methods:The analytical sensitivity of LAMP and ncstcd-PCR was obtained against 10-fold serial dilutions of T.gondii DNA ranging from 1 ng to 0.01 fg.DNA samples of other parasites and human chromosomal DNA were used to determine the specificity of molecular assays.Results:After testing LAMP and nesled-PCR in duplicate,the detection limit of RE-LAMP.B1-LAMP,RE-nested PCR and B1-nested PCR assays was one fg.100 fg,1 pg and 10 pg of T.gondii DNA respectively.All the LAMP assays and nested PCRs were 100% specific.The RE-LAMP assay revealed the most sensitivity for the detection of T.gondii DNA.Conclusions:The obtained results demonstrate that the LAMP technique has a greater sensitivity for detection of T.gondii.Furthermore,these findings indicate that primers based on the RE are more suitable than those based on the B1 gene.However,the B1-LAMP assay has potential as a diagnostic tool for detection of T.gondii.

  12. Detecting 22q11.2 deletions by use of multiplex ligation-dependent probe amplification on DNA from neonatal dried blood spot samples

    DEFF Research Database (Denmark)

    Sørensen, Karina M; Agergaard, Peter; Olesen, Charlotte;

    2010-01-01

    of 22q11.2 deletions among certain manifestations, eg, congenital heart disease, on selected Danes, a multiplex ligation-dependant probe amplification (MLPA) analysis was designed. The analysis was planned to be performed on DNA extracted from dried blood spot samples (DBSS) obtained from Guthrie cards...... collected during neonatal screening programs. However, the DNA concentration necessary for a standard MLPA analysis (20 ng) could not be attained from DBSS, and a novel MLPA design was developed to permit for analysis on limited amounts of DNA (2 ng). A pilot study is reported here that validates the new...... MLPA design using nine patients diagnosed with the 22q11.2 deletion and 101 controls. All deletions were identified using DNA extracted from DBSS, and no copy number variations were detected in the controls, resulting in a specificity and sensitivity of 100%. It is thereby concluded that the novel MLPA...

  13. Effectiveness of multiplex ligation-dependent probe amplification assay used for detecting deletion of Prader-Willi syndrome%应用多重连接探针扩增法简便高效检测Prader-Willi综合征的基因缺失

    Institute of Scientific and Technical Information of China (English)

    Hong SHAO; Va LIP; Bai-Lin WU

    2005-01-01

    Objective: Prader-Willi syndrome (PWS) is characterized by severe hypotonia and feeding difficulties in early infancy, followed by excessive eating and gradual development of morbid obesity in later infancy or early childhood. Patients with PWS are often too young to manifest sufficient features or have atypical findings, making genetic testing important to confirm the diagnosis of PWS. Approximately 99% of patients with PWS have a diagnostic abnormality in the parent-specific methylation imprint within the Prader-Willi critical region (PWCR) at chromosome 15q11.2-q12. Of them, 70% have a paternal deletion; 25% have a maternal uniparental disomy (UPD); and <5% have a mutation in the imprinting center. Methods: Current techniques can identify a diagnostic abnormality, such as paternal deletion or maternal UPD for most of patients with PWS, but they are labor-intensive and cost-expensive. Multiplex ligation-dependent probe amplification (MLPA) is a novel, simple, and cost-effective technique for analysis of relative quantification in a single assay, which has recently been applied for the detection of genomic deletions, duplications, and amplifications in a variety of genes. Results: Six out of 20 patients referred for genetic diagnosis of PWS were found to have a deletion by MLPA, confirmed by FISH and DNA methylation analysis with 100% concordance. Conclusion: MLPA's high sensitivity and specificity for deletion detection is the same as FISH or Southern blot based analysis. Additional collaborative effort for developing and validating the complete MLPA-PWS assay, for not only detecting deletion but also identifying methylation abnormality, is on going.

  14. Identification of deletions and duplications of the dystrophin gene in Duchenne muscular dystrophy patients from Henan by MLPA%河南省杜氏肌营养不良患者dystrophin基因突变的MLPA检测

    Institute of Scientific and Technical Information of China (English)

    王凤羽; 孙伟伟; 李聪敏; 常明秀; 丰慧根; 马林先

    2011-01-01

    目的:探讨多重连接依赖式探针扩增技术(MLPA)在杜氏肌营养不良(DMD)患者基因诊断中的应用价值,了解河南省DMD患者dystrophin基因突变热点.方法:采用MLPA检测48例河南省DMD患者及13例缺失型患者母亲dystrophin基因突变.结果:48例DMD患者中,有31例(64.6%)检测出dystrophin基因外显子缺失,4例(8.3%)检测出外显子重复.河南省DMD患者dystrophin基因缺失/重复热点区域为第46~53外显子和第8~18外显子.13例患者母亲有11人检测出杂合突变,突变类型与患者相同,余2人未检测出突变.河南省DMD患者基因外显子缺失、重复分布与北京相似(x2=0.256,P=0.880),但与香港和台湾地区有着较大差异(x2分别为11.470和11.303,P分别为0.003和0.004).结论:MLPA在DMD患者及携带者基因诊断中有很高的应用价值.河南省DMD患者dystrophin基因的突变热点与国内其他地区有差异.%Aim: To evaluate the efficacy of multiplex ligation-dependent probe amplification technique ( MLPA) in gene diagnosis of Duchenne muscular dystrophy(DMD) patients,and comprehend frequency of deletion and duplication of every exon in dystrophin gene in Henan DMD patients. Methods: Applying MLPA,deletions and duplications of dystrophin gene in 48 Henan DMD patients and 13 mothers of DMD patients with deletion were detected. Results:In 48 patients, exon deletion was detected in 31 patients(64. 6% ) and exon duplication was detected in 4 patients(8. 3% ) . The mutational hot spot regions of deletion and duplication was ejcons 46 ~S3 and exons 8 - 18 in dystrophin gene in the 48 Henan DMD patients. Heterozygous mutations which were similar to their children were detected in 11 out of 13 mothers. The frequency of deletion and duplication of dystrophin gene in Henan DMD patients was similar to those from Beijing (x2 = 0. 256, P - 0.880) , but different from those from Hong Kong and Taiwan(x2 =11.470 and 11. 303,P =0. 003 and 0. 004). Conclusion

  15. Noiseless phase quadrature amplification via an electro-optic feed-forward technique

    CERN Document Server

    Buchler, B C; Ralph, T C; Buchler, Ben C.; Huntington, Elanor H.; Ralph, Timothy C.

    1999-01-01

    Theoretical results are presented which show that noiseless phase quadrature amplification is possible, and limited experimentally only by the efficiency of the phase detection system. Experimental results obtained using a Nd:YAG laser show a signal gain of 10dB and a signal transfer ratio of T_s=0.9. This result easily exceeds the standard quantum limit for signal transfer. The results also explicitly demonstrate the phase sensitive nature of the amplification process.

  16. Detecting aneuploidies of fetus by multiplex ligation-dependent probe amplification%多重连接探针扩增技术检测胎儿非整倍体异常

    Institute of Scientific and Technical Information of China (English)

    王凤羽; 马林先; 李聪敏; 张华; 丰慧根

    2012-01-01

    目的:探讨多重连接探针扩增技术(MLPA)在常见染色体非整倍体异常及其在产前诊断中的应用价值.方法:选择200份羊水标本,提取标本DNA,采用MLPA技术对样本染色体进行分析,并与传统染色体核型分析结果进行比较.结果:在200例样本中,除1例因羊水污染应用传统染色体核型分析失败外,其余检测结果与传统染色体核型分析方法的结果一致(21三体4例,18三体3例,13三体1例,X单体1例,X三体1例,其余190例正常).结论:MLPA技术分析胎儿染色体非整倍体异常是一种简单、快速且有效的方法.%Aim: To investigate the application value of the multiplex ligation-dependent probe amplification technique ( MLPA ) in common aneuploidies and prenatal diagnosis. Methods: A total of 200 amniotic fluid samples were collected. The DNA extracted from amniotic fluid was detected by MLPA. The results of chromosomal G-banding and MLPA of amniotic fluid were compared. Results:Out of 200 samples, the results of 199 by MLPA were consistent with traditional karyotype analysis, including4 trisomy 21,3 trisomy 18 ,1 trisomy 13 ,1 monosomy X,l female with extra X and 190 normal karyotype. Only one case with contamination was failed to reach conclusion by karyotype analysis. Conclusion: MLPA is a simple, rapid and efficacy method for analyzing aneuploids in amniotic fluid.

  17. Neurofibromatosis tipo I: Mutación de splicing detectada por MLPA y secuenciación en la Argentina

    Directory of Open Access Journals (Sweden)

    Sergio Laurito

    2015-04-01

    Full Text Available La neurofibromatosis tipo 1 (NF1 es un desorden genético autosómico dominante, con una prevalencia de 1 en 2500-3000 nacidos vivos. La dificultad diagnóstica se debe al tamaño extenso del gen NF1 con pocos sitios hot-spot, la ausencia de una clara relación genotipo-fenotipo y rasgos clínicos con un espectro muy heterogéneo. Un caso sospechoso de NF1 procedente de la provincia de Jujuy fue analizado por MLPA (multiplex ligation-dependent probe amplification en nuestro laboratorio. Mujer, adolescente mestiza (Amerindia/Europea, con un osteoma maxilar, lordosis lumbar, neurofibromas cutáneos y manchas café con leche. Por MLPA se detectó una alteración en el exón 13 del gen NF1. Por secuenciación del exón 13 se identificó una mutación "missense" en la posición 1466 del ARNm (NM_000267.3:c.1466A>G que introduce un sitio de splicing aberrante. La patogenicidad de la mutación fue corroborada en la base de datos de variantes clínicas del National Center for Biotechnology Information. En nuestro conocimiento, este es el primer registro de una mutación NF1 en un paciente proveniente de poblaciones mestizas del Noroeste Argentino. La alteración ha sido reportada en individuos de otras poblaciones de origen muy disímil al del caso presentado, como la europea, sugiriendo que el sitio podría considerarse un sitio hot-spot del gen. Donde exista baja disponibilidad de diagnósticos moleculares, como en nuestro caso, se puede aplicar un algoritmo que comience por el estudio del gen NF1 por MLPA, metodología relativamente sencilla y de costo accesible. Con ella se evita enviar muestras al extranjero para análisis genéticos.

  18. Method for signal conditioning and data acquisition system, based on variable amplification and feedback technique

    Energy Technology Data Exchange (ETDEWEB)

    Conti, Livio, E-mail: livio.conti@uninettunouniversity.net [Facoltà di Ingegneria, Università Telematica Internazionale Uninettuno, Corso Vittorio Emanuele II 39, 00186 Rome, Italy INFN Sezione Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome (Italy); Sgrigna, Vittorio [Dipartimento di Matematica e Fisica, Università Roma Tre, 84 Via della Vasca Navale, I-00146 Rome (Italy); Zilpimiani, David [National Institute of Geophysics, Georgian Academy of Sciences, 1 M. Alexidze St., 009 Tbilisi, Georgia (United States); Assante, Dario [Facoltà di Ingegneria, Università Telematica Internazionale Uninettuno, Corso Vittorio Emanuele II 39, 00186 Rome, Italy INFN Sezione Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome (Italy)

    2014-08-21

    An original method of signal conditioning and adaptive amplification is proposed for data acquisition systems of analog signals, conceived to obtain a high resolution spectrum of any input signal. The procedure is based on a feedback scheme of the signal amplification with aim at maximizing the dynamic range and resolution of the data acquisition system. The paper describes the signal conditioning, digitization, and data processing procedures applied to an a priori unknown signal in order to enucleate its amplitude and frequency content for applications in different environments: on the ground, in space, or in the laboratory. An electronic board of the conditioning module has also been constructed and described. In the paper are also discussed the main fields of application and advantages of the method with respect to those known today.

  19. Carrier diagnosis of F9 gross deletion by multiple ligation-dependent probe amplification in hemophilia B%多重连接探针扩增技术在凝血因子Ⅸ基因大片段缺失的血友病B基因携带者诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    陈星; 梁燕; 闫梅; 刘敬忠

    2012-01-01

    Objective To investigate the application of multiplex ligation-dependent probe amplification (MLPA) in the gene diagnosis of hemophilia B (HB). Methods MLPA and linkage analysis of short tandem repeat (STR) were used for gene diagnoses of two HB families with gross deletions of F9 gene, which were negative by sequencing. Results The MLPA results indicated the loss of one or two exons in the two patients with the ratio lower than 0.10. Their mothers showed a ratio average of 0.50±0.05 for the corresponding probes, which revealed she was carrier of large deletions of the F9 gene. The ratios of three sisters of the HB patients were normal, which indicated they were non-carriers. Linkage analysis was consistent with MLPA, but sequencing was not conclusive. Conclusion This report illustrated that MLPA technique represented an efficient method to screen F9 gene gross deletions in sequencing undiagnosed carriers of hemophilia B.%目的 探讨多重连接探针扩增技术(MLPA)在血友病B(HB)基因诊断中的应用.方法 采用MLPA和短串联重复序列(STR)基因连锁分析对由于凝血因子Ⅸ(F9)基因大片段缺失导致测序失败的2个HB家系进行基因诊断.结果 MLPA检测结果显示,2例HB患者F9基因存在1或2个外显子的缺失,缺失位置Ratio值<0.10;患者母亲相应位置Ratio值为0.50±0.05,可判断为携带者;其他女性受检者Ratio值为0.71~1.30,可排除携带者.基因连锁分析与MLPA判断结论一致.结论 MLPA为HB的直接基因诊断提供了一种新的方法,可用于测序无法检出的F9基因大片段缺失的携带者诊断.

  20. MLPA在常染色体显性遗传多囊肾病基因诊断中的应用%Application of MLPA in gene diagnosis of autosomal dominant polycystic kidney disease

    Institute of Scientific and Technical Information of China (English)

    于国鹏; 齐隽; 龙飞; 黄驿晨; 钱小强; 陶炯; 陈建华

    2011-01-01

    目的 探讨多重连接探针扩增技术(MLPA)在常染色体显性遗传多囊肾病(ADPKD)基因诊断中的应用.方法 采用MLPA对20例ADPKD患者的PKD1基因和PKD2基因进行检测.MLPA检测结果显示单-外显子扩增或疑似扩增者采用RT-PCR检测验证;MLPA检测结果显示单一外显子缺失或疑似缺失者采用PCR检测验证,存在扩增产物者进行测序验证.结果 MLPA检测显示:1例患者单一外显子缺失(PKD1 Exon40),5例单一外显子疑似缺失(PKD1 Exon1、PKD1 Exon25、PKD2 Exon8、PKD2 Exon8、PKD1 Exon25),3例单一外显子疑似扩增(PKD1 Exon6、PKD1Exon7、PKD1 Exon7).经RT-PCR检测验证,1例患者单一外显子扩增(PKD1 Exon6);经PCR检测与测序验证,1例患者单一外显子错义突变(PKD1 Exon40),1例单一外显子缺失(PKD2 Exon8).结论 MLPA为ADPKD的基因诊断提供了一种新的方法.%Objective To investigate the application of multiplex ligation-dependent probe amplification ( MLPA) in the gene diagnosis of autosomal dominant poiycystic kidney disease (ADPKD). Methods MLPA was employed to detect the PKD1 gene and PKD2 gene in 20 patients with ADPKD. Verification with RT-PCR was performed for those with single exon duplication or suspected duplication detected by MLPA. Those with single exon deletion or suspected deletion detected by MLPA were verified with PCR, and sequencing analysis was conducted in those with amplification products. Results One patient with single exon deletion (PKD1 Exon40), 5 patients with single exon suspected deletion ( PKD1 Exonl, PKD1 Exon25, PKD2 ExonS, PKD2 ExonS and PKD1 Exon25) and 3 patients with single exon suspected duplication ( PKD1 Exon6, PKD1 Exon7 and PKD1 Exon7) were detected by MLPA. One patient with single exon duplication (PKD1 Exon6) was verified by RT-PCR, and one patient with single exon missense mutation (PKD1 Exon40) and one patient with single exon deletion (PKD2 Exon8) were verified by PCR and sequencing analysis. Conclusion

  1. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    International Nuclear Information System (INIS)

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author)

  2. Evaluation of multiplex ligation-dependent probe amplification analysis versus multiplex polymerase chain reaction assays in the detection of dystrophin gene rearrangements in an Iranian population subset

    Directory of Open Access Journals (Sweden)

    Nayereh Nouri

    2014-01-01

    Full Text Available Background: The Duchenne muscular dystrophy (DMD gene is located in the short arm of the X chromosome (Xp21. It spans 2.4 Mb of the human genomic DNA and is composed of 79 exons. Mutations in the Dystrophin gene result in DMD and Becker muscular dystrophy. In this study, the efficiency of multiplex ligation-dependent probe amplification (MLPA over multiplex polymerase chain reaction (PCR assays in an Iranian population was investigated. Materials and Methods: Multiplex PCR assays and MLPA analysis were carried out in 74 patients affected with DMD. Results: Multiplex PCR detected deletions in 51% of the patients with DMD. MLPA analysis could determine all the deletions detected by the multiplex PCR. Additionally, MLPA was able to identify one more deletion and duplication in patients without detectable mutations by multiplex PCR. Moreover, MLPA precisely determined the exact size of the deletions. Conclusion: Although MLPA analysis is more sensitive for detection of deletions and duplications in the dystrophin gene, multiplex PCR might be used for the initial analysis of the boys affected with DMD in the Iranian population as it was able to detect 95% of the rearrangements in patients with DMD.

  3. 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.

  4. 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.

  5. Rapid Detection of high-level oncogene amplifications in ultrasonic surgical aspirations of brain tumors

    Directory of Open Access Journals (Sweden)

    Truong Long N

    2012-06-01

    Full Text Available Abstract Background Genomic tumor information, such as identification of amplified oncogenes, can be used to plan treatment. The two sources of a brain tumor that are commonly available include formalin-fixed, paraffin-embedded (FFPE sections from the small diagnostic biopsy and the ultrasonic surgical aspiration that contains the bulk of the tumor. In research centers, frozen tissue of a brain tumor may also be available. This study compared ultrasonic surgical aspiration and FFPE specimens from the same brain tumors for retrieval of DNA and molecular assessment of amplified oncogenes. Methods Surgical aspirations were centrifuged to separate erythrocytes from the tumor cells that predominantly formed large, overlying buffy coats. These were sampled to harvest nuclear pellets for DNA purification. Four glioblastomas, 2 lung carcinoma metastases, and an ependymoma were tested. An inexpensive PCR technique, multiplex ligation-dependent probe amplification (MLPA, quantified 79 oncogenes using 3 kits. Copy number (CN results were normalized to DNA from non-neoplastic brain (NB in calculated ratios, [tumor DNA]/[NB DNA]. Bland-Altman and Spearman rank correlative comparisons were determined. Regression analysis identified outliers. Results Purification of DNA from ultrasonic surgical aspirations was rapid ( Conclusions Buffy coats of centrifuged ultrasonic aspirations contained abundant tumor cells whose DNA permitted rapid, multiplex detection of high-level oncogene amplifications that were confirmed in FFPE. Virtual slides http://www.diagnosticpathology.diagnomx.eu/vs/1883718801686466

  6. Multiplex ligation-dependent probe amplification for rapid detection of deletions and duplications in the dystrophin gene

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective:Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked disorders caused by mutations in the dystrophin gene. The majority of recognized mutations are copy number changes of individual exons. The objective of the present study was to assess the multiplex ligation-dependent probe amplification (MLPA) effects of detection of gene mutations. Methods: Samples of 20 control males and 80 males and their mothers referred to our diagnostic facility on the clinical suspicion of DMD or BMD were tested by MLPA and multiplex PCR. Results: The mean DQs for all peak of 20 control male samples was 1.02 (range from 0.83 to 1.21) by MLPA. Deletions or duplications were identified in 6 out of 31 families that had been previously tested as negative by multiplex PCR. One case of complex rearrangement involving a duplication of two regions: dupEX3-9 and dupEX 17-41 were found by MLPA. Conclusions: MLPA is a highly sensitive method and rapid alternative to multiplex PCR for detection of DMD and BMD.

  7. A comparative study of mPCR, MLPA, and muscle biopsy results in a cohort of children with Duchenne muscular dystrophy: A first study

    Directory of Open Access Journals (Sweden)

    M Manjunath

    2015-01-01

    Conclusions: This is the first study from India and possibly in English literature, comparing the sensitivity and pattern of mutations by both mPCR and MLPA in the same cohort of DMD. It further validates that 36.4% of MLPA-negative cases were confirmed to have DMD by IHC. The clinical accuracy has been very high in our cohort. MLPA-negative samples should be subjected for next-generation sequencing before contemplating a biopsy.

  8. 多重连接依赖探针扩增在假肥大型肌营养不良症家系基因诊断中的应用%Genetic diagnosis of Duchenne/Becker muscular dystrophy by MLPA

    Institute of Scientific and Technical Information of China (English)

    张媛媛; 刘晓亮; 何蓉; 麻宏伟; 赵彦艳

    2014-01-01

    Objective To assess the value of multiplex ligation-dependent probe amplification (MLPA) for the genetic and prenatal diagnosis of Duchenne/Becker muscular dystrophy (DMD/BMD).Methods Forty seven patients clinically diagnosed or suspected with DMD/BMD were recruited.Deletion or duplication of the 79 exons of the DMD gene were detected by MLPA.PCR and sequencing were used to detect single exon deletion.MLPA was also used for identifying carriers.For cases requesting prenatal diagnosis,short tandem repeat (STR) capillary electrophoresis,linkage analysis and MLPA were applied to determine fetal DMD gene.Results Among the 47 patients,deletions and duplications encompassing one or more exons were identified in 31 and 7 cases with MLPA,respectively.Seven patients had single exon deletions.However,one of which was actually a point mutation in the probe-conjugated region and was confirmed by PCR and sequencing.Of the 23 mothers with MLPA positive sons,13 were found to carry either deletions or duplications.Prenatal diagnosis has identified 2 male affected fetuses and 3 female carrier fetuses in the 13 cases examined,which was in conformity with linkage analysis.Conclusion Our data demonstrated that MLPA is a rapid,direct and reliable method for detecting deletions or duplications of the DMD gene.It can also indicate small changes within the sequences detected by the probe.Combing MLPA with PCR,sequencing and linkage analysis could make the genetic diagnosis of DMD/BMD more accurate.%目的 评估多重连接依赖探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术在假肥大型肌营养不良症(Duchenne/Becker muscular dystrophy,DMD/BMD)患者临床诊断、携带者筛查及产前诊断中的应用.方法 应用MLPA法检测DMD基因79个外显子的缺失或重复突变,DNA测序以及STR毛细管电泳与连锁分析方法进行验证及辅助诊断.结果 47例患儿中7例可见重复突变,31例可见缺失突变,其中7

  9. Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA).

    NARCIS (Netherlands)

    Koolen, D.A.; Nillesen, W.M.; Versteeg, M.H.; Merkx, G.F.M.; Knoers, N.V.A.M.; Kets, M.; Vermeer, S.; Ravenswaaij-Arts, C.M.A. van; Kovel, C.G.F. de; Brunner, H.G.; Smeets, D.F.C.M.; Vries, L.B.A. de; Sistermans, E.A.

    2004-01-01

    BACKGROUND: Subtelomeric rearrangements contribute to idiopathic mental retardation and human malformations, sometimes as distinct mental retardation syndromes. However, for most subtelomeric defects a characteristic clinical phenotype remains to be elucidated. OBJECTIVE: To screen for submicroscopi

  10. Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium vivax infection

    Directory of Open Access Journals (Sweden)

    Wang Wei-Ming

    2011-06-01

    Full Text Available Abstract Background Loop-mediated isothermal amplification (LAMP is a high performance method for detecting DNA and holds promise for use in the molecular detection of infectious pathogens, including Plasmodium spp. However, in most malaria-endemic areas, which are often resource-limited, current LAMP methods are not feasible for diagnosis due to difficulties in accurately interpreting results with problems of sensitive visualization of amplified products, and the risk of contamination resulting from the high quantity of amplified DNA produced. In this study, we establish a novel visualized LAMP method in a closed-tube system, and validate it for the diagnosis of malaria under simulated field conditions. Methods A visualized LAMP method was established by the addition of a microcrystalline wax-dye capsule containing the highly sensitive DNA fluorescence dye SYBR Green I to a normal LAMP reaction prior to the initiation of the reaction. A total of 89 blood samples were collected on filter paper and processed using a simple boiling method for DNA extraction, and then tested by the visualized LAMP method for Plasmodium vivax infection. Results The wax capsule remained intact during isothermal amplification, and released the DNA dye to the reaction mixture only when the temperature was raised to the melting point following amplification. Soon after cooling down, the solidified wax sealed the reaction mix at the bottom of the tube, thus minimizing the risk of aerosol contamination. Compared to microscopy, the sensitivity and specificity of LAMP were 98.3% (95% confidence interval (CI: 91.1-99.7% and 100% (95% CI: 88.3-100%, and were in close agreement with a nested polymerase chain reaction method. Conclusions This novel, cheap and quick visualized LAMP method is feasible for malaria diagnosis in resource-limited field settings.

  11. Validation of multiplex ligation-dependent probe amplification for confirmation of array comparative genomic hybridization.

    Science.gov (United States)

    Jennings, Lawrence J; Yu, Min; Fitzpatrick, Carrie; Smith, Frederick A

    2011-09-01

    The American College of Medical Genetics recommends that each laboratory should confirm abnormal or ambiguous results detected by array comparative genomic hybridization (aCGH). At present, the gold standard method for aCGH confirmation is fluorescent in situ hybridization (FISH). However, FISH is not well suited for small tandem duplications or very small deletions that are detectable by oligonucleotide arrays. Therefore, we developed and validated multiplex ligation-dependent probe amplification (MLPA) for aCGH confirmation. The method performance validation showed linearity through the expected analytical measurement range (0.05 to 2 genome equivalents). The interassay normalized coefficient of variation averaged 3.7% across 12 control and target probes. This low imprecision allowed detection of 20% mosaicism with exceptional confidence (Pcomparision with reference populations. We have successfully incorporated aCGH confirmation using custom-designed MLPA into our normal workflow, and used it for confirmation of all abnormal or ambiguous results. PMID:21817904

  12. C-MYC amplification and expression in stomach cancer samples in Iranian population using two techniques of CISH and IHC

    Directory of Open Access Journals (Sweden)

    Malihea Khaleghian

    2015-07-01

    Results: Our data revealed that both diffuse and intestinal types of gastric cancer occurred significantly in men more than women. Our results showed an indication of some correlation between grades and CISH results, although the difference was not significant. Our data also showed that CISH+ patients (43.1% were more frequent in comparison with IHC+ patients (14.7%. There was a correlation between CISH and IHC. This result revealed that there was a significant difference between grades and IHC. There was also no statistically significant difference between CISH amplification in diffuse and intestinal types. Conclusion: Our conclusion is that for the treatment, management of stomach cancer, and monitoring of progress and prognosis of the tumor that is almost important for patients and clinicians, CISH test is a better and feasible to IHC test, with regards to sensitivity and specificity.

  13. A low cost technique for synthesis of gold nanoparticles using microwave heating and its application in signal amplification for detecting Escherichia Coli O157:H7 bacteria

    Science.gov (United States)

    Thanh Ngo, Vo Ke; Giang Nguyen, Dang; Phat Huynh, Trong; Lam, Quang Vinh

    2016-09-01

    In the present work a low cost technique for preparation of gold nanoparticles (AuNPs) using microwave heating was developed. The effect of different elements (precursor reagents, irradiation time, and microwave radiation power) on the final morphology of AuNPs obtained through the microwave assisted technique has been investigated. The characterization of the samples has been carried out by transmission electron microscopy, UV-vis absorption spectroscopy, Fourier transform infrared spectroscopy, and powder x-ray diffraction. The results showed that to some extent the above-mentioned characterizations influenced the size of synthetized nanoparticles and application of microwave heating has many advantages such as low cost, rapid preparation and highly uniform particles. As an application in quartz crystal microbalance (QCM) immunosensor, AuNPs are conjugated with the Escherichia coli (E.coli) O157:H7 antibodies for signal amplification to detect E.coli O157:H7 bacteria residual in QCM system.

  14. A low cost technique for synthesis of gold nanoparticles using microwave heating and its application in signal amplification for detecting Escherichia Coli O157:H7 bacteria

    Science.gov (United States)

    Thanh Ngo, Vo Ke; Giang Nguyen, Dang; Phat Huynh, Trong; Lam, Quang Vinh

    2016-09-01

    In the present work a low cost technique for preparation of gold nanoparticles (AuNPs) using microwave heating was developed. The effect of different elements (precursor reagents, irradiation time, and microwave radiation power) on the final morphology of AuNPs obtained through the microwave assisted technique has been investigated. The characterization of the samples has been carried out by transmission electron microscopy, UV–vis absorption spectroscopy, Fourier transform infrared spectroscopy, and powder x-ray diffraction. The results showed that to some extent the above-mentioned characterizations influenced the size of synthetized nanoparticles and application of microwave heating has many advantages such as low cost, rapid preparation and highly uniform particles. As an application in quartz crystal microbalance (QCM) immunosensor, AuNPs are conjugated with the Escherichia coli (E.coli) O157:H7 antibodies for signal amplification to detect E.coli O157:H7 bacteria residual in QCM system.

  15. Analysis the Result of 105 Cases Spontaneously Abortion Detecting by MLPA%应用MLPA检测105例自然流产绒毛的结果分析

    Institute of Scientific and Technical Information of China (English)

    黄朋; 费冬梅; 刘天盛; 黄红倩; 郑陈光

    2013-01-01

    目的:应用多重探针扩增技术(multiplex ligation-dependent probe ampli-cation,MLPA)检测自然流产与21、18、13及性染色体数目异常的关系。方法对105例自然流产胎儿绒毛组织进行MLPA检测,PCR产物用3130基因分析仪进行信号收集,应用Cof alyzer对电泳结果进行片段分析。结果105例标本中有101例检测成功(97.1%),提示有43例为染色体核型异常,其中24例45,X,4例47,+21,2例47,+18,9例47,XXY,4例47,+13,总的异常检出率为42.6%。结论对101例流产标本的检测与分析,有42.6%的因素是由于21、18、13及性染色体异常引起的,其中性染色体异常占所有异常核型的76.7%,说明性染色体异常是流产的易感因子。%Objective: To analysis the relationship of spontaneously abortion and 21, 18, 13 and sex chromosome aneuploidy abnormality with the technology of multiple ligation-dependent probe amplification(MLPA). Methods:105 spontaneously abortion chorionic vil us was detected by MLPA using kit P095 and the results were obtained by using ABI3130 genetic analyzer; Analysis of copy number changes for chromosomes 13, 18, 21, X and Y was carried out with Cof alyzer. Results: MLPA test was successful in 101 cases (97.1%), indicated 48 cases were chromosome aneuploidy abnormal, including 24 cases 45X, 4 cases +21, 9 cases XXY, 4 cases +13; the abnormal rate was 42.6%. Conclusion:about 42.6%spontaneously aborted was caused by aneuploidy abnormal (13, 18, 21, X and Y), about 76.7% was sex chromosome abnormal, this indicated sex chromosome abnormal was an importance factor induced abortion.

  16. Performance of reversed transcription loop-mediated isothermal amplification technique detecting EV71: a systematic review with meta-analysis.

    Science.gov (United States)

    Lei, Xiaoying; Wen, Hongling; Zhao, Li; Yu, Xuejie

    2014-04-01

    Human enterovirus 71 (EV71) is the major etiological agent of hand, foot and mouth disease (HFMD), which is a common infectious disease in young children. Studies in the past have shown that reversed transcription loop-mediated isothermal amplification (RT-LAMP) was a rapid approach for the detection of EV71 in HFMD. This meta-analysis study is to evaluate the diagnostic role of RT-LAMP in detecting EV71 infection. A comprehensive literature research of PubMed, Embase, Wan Fang Data, and Chinese National Knowledge Infrastructure databases was conducted on articles aiming at the diagnostic performance of RT-LAMP in EV71 detection published before February 10, 2014. Data from selected studies were pooled to yield the summary sensitivity, specificity, positive and negative likelihood ratio (PLR, NLR), diagnostic odds ratio (DOR), and receiver operating characteristic (SROC) curve by using STATA VERSION 12.0 software. Ten studies including a total of 907 clinical samples were of high quality in this meta-analysis. Overall, the pooled sensitivity, specificity, PLR, NLR, DOR, and the area under the SROC curve was 0.99 (0.97, 1.00), 0.97 (0.94, 1.00), 5.90 (95% CI: 3.90-8.94), 0.20 (95% CI: 0.14-0.29), and 1.00 (95% CI: 0.99-1.00), respectively. The univariate analysis of potential variables showed some changes in the diagnostic performance, but none of the differences reached statistical significance. Despite inter-study variability, the test performance of RT-LAMP was consistent with real-time RT-PCR in detecting EV71. This meta-analysis suggests that RT-LAMP is a useful diagnostic tool with high sensitivity and specificity for detecting EV71. PMID:24815384

  17. Performance of reversed transcription loop-mediated isothermal amplification technique detecting EV71: a systematic review with meta-analysis.

    Science.gov (United States)

    Lei, Xiaoying; Wen, Hongling; Zhao, Li; Yu, Xuejie

    2014-04-01

    Human enterovirus 71 (EV71) is the major etiological agent of hand, foot and mouth disease (HFMD), which is a common infectious disease in young children. Studies in the past have shown that reversed transcription loop-mediated isothermal amplification (RT-LAMP) was a rapid approach for the detection of EV71 in HFMD. This meta-analysis study is to evaluate the diagnostic role of RT-LAMP in detecting EV71 infection. A comprehensive literature research of PubMed, Embase, Wan Fang Data, and Chinese National Knowledge Infrastructure databases was conducted on articles aiming at the diagnostic performance of RT-LAMP in EV71 detection published before February 10, 2014. Data from selected studies were pooled to yield the summary sensitivity, specificity, positive and negative likelihood ratio (PLR, NLR), diagnostic odds ratio (DOR), and receiver operating characteristic (SROC) curve by using STATA VERSION 12.0 software. Ten studies including a total of 907 clinical samples were of high quality in this meta-analysis. Overall, the pooled sensitivity, specificity, PLR, NLR, DOR, and the area under the SROC curve was 0.99 (0.97, 1.00), 0.97 (0.94, 1.00), 5.90 (95% CI: 3.90-8.94), 0.20 (95% CI: 0.14-0.29), and 1.00 (95% CI: 0.99-1.00), respectively. The univariate analysis of potential variables showed some changes in the diagnostic performance, but none of the differences reached statistical significance. Despite inter-study variability, the test performance of RT-LAMP was consistent with real-time RT-PCR in detecting EV71. This meta-analysis suggests that RT-LAMP is a useful diagnostic tool with high sensitivity and specificity for detecting EV71.

  18. Molecular diagnosis of spinal muscular atrophy by multiplex ligation-dependent probe amplification%MLPA方法在脊髓性肌肉萎缩症分子诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    曾健; 柯龙凤; 邓小军; 蔡美英; 涂向东; 兰风华

    2008-01-01

    目的 探讨多重连接依赖性探针扩增(MLPA)技术在脊髓性肌肉萎缩症(SMA)分子诊断中的应用.方法 从13例SMA患者、31名患者父母的外周血标本和10份胎儿羊水标本,以及50名正常人外周血标本中提取基因组DNA,应用MLPA技术进行分析,同时也行常规聚合酶链反应-限制性片段长度多态性(PCR-RFLP)和位点特异性PCR分析.结果 MLPA分析结果与常规PCR-RFLP和位点特异性PCR结果相符:13例患者的运动神经元存活基因(SMN)1基因均呈纯合缺失,SMN2基因拷贝数的增加与SMA表型的严重程度(从I型到Ⅲ型)存在显著性差异(P<0.05);31名患者父母SMN1基因1拷贝的人数为29(占93.5%),2拷贝的为2(占6.5%);50名正常健康成人SMN1基因1拷贝的人数为1(占2.0%),2拷贝的为48(占96.O%);SMA患者父母组和健康正常成人组之间的SMN1基因拷贝数存在显著件差异(P<0.01);10例胎儿中2例存在SMN1的纯合缺失.结论 MLPA是一种准确可靠的SMA分子诊断新方法.%Objective To investigate the effect of multiplex ligation-dependent probe amplification (MLPA)in molecular diagnosis of spinal muscular atrophy(SMA).Methods Peripheral blood samples were collected from 13 SMA patients.31 parents of SMA patients,50 healthy individuals without family history of SMA,and 10 specimens of amniotic fluid from these families were collected too.Genomic DNA was analyzed by MLPA,conventional PCR-RFLP,and allele-specific PCR.Results In complete agreement with the results of conventional PCR-RFLP and allele-specific PCR.MLPA analysis showed that all of the 13 patients had homozygous deletion of the Survival of motor neuron 1(SMN1)geBe,and there Wag significant difference between the SMA severity(type I to typeⅢ)and SMN2 copy humber(P<0.05).of the 31 parents 29(93.5%)had 1 copy of SMNI,2(6.5%)had 2 copies of SMN1.Of the 50 healthy individuals.1(2.0%)had 1 copy of SMN1,48(96.O%)had 2 copies of SMN1,and 1(2.0%)had 3 copies.The SMN1 copy humber

  19. MLPA analysis for a panel of syndromes with mental retardation reveals imbalances in 5.8% of patients with mental retardation and dysmorphic features, including duplications of the Sotos syndrome and Williams-Beuren syndrome regions

    DEFF Research Database (Denmark)

    Kirchhoff, Maria; Bisgaard, Anne-Marie; Bryndorf, Thue;

    2007-01-01

    -Beuren, Prader-Willi, Angelman, Miller-Dieker, Smith-Magenis, and 22q11-deletion syndromes). Patients were initially referred for HR-CGH analysis and MRS-MLPA was performed retrospectively. MRS-MLPA analysis revealed imbalances in 15/258 patients (5.8%). Ten deletions were identified, including deletions of 1p36...

  20. 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.

  1. Copy-number variations in Y-chromosomal azoospermia factor regions identified by multiplex ligation-dependent probe amplification.

    Science.gov (United States)

    Saito, Kazuki; Miyado, Mami; Kobori, Yoshitomo; Tanaka, Yoko; Ishikawa, Hiromichi; Yoshida, Atsumi; Katsumi, Momori; Saito, Hidekazu; Kubota, Toshiro; Okada, Hiroshi; Ogata, Tsutomu; Fukami, Maki

    2015-03-01

    Although copy-number variations (CNVs) in Y-chromosomal azoospermia factor (AZF) regions have been associated with the risk of spermatogenic failure (SF), the precise frequency, genomic basis and clinical consequences of these CNVs remain unclear. Here we performed multiplex ligation-dependent probe amplification (MLPA) analysis of 56 Japanese SF patients and 65 control individuals. We compared the results of MLPA with those of conventional sequence-tagged site PCR analyses. Eleven simple and complex CNVs, including three hitherto unreported variations, were identified by MLPA. Seven of the 11 CNVs were undetectable by conventional analyses. CNVs were widely distributed in AZF regions and shared by ~60% of the patients and ~40% of the controls. Most breakpoints resided within locus-specific repeats. The majority of CNVs, including the most common gr/gr deletion, were identified in the patient and control groups at similar frequencies, whereas simple duplications were observed exclusively in the patient group. The results imply that AZF-linked CNVs are more frequent and heterogeneous than previously reported. Non-allelic homologous recombination likely underlies these CNVs. Our data confirm the functional neutrality of the gr/gr deletion in the Japanese population. We also found a possible association between AZF-linked simple duplications and SF, which needs to be evaluated in future studies.

  2. GENOMIC PROFILING BY MULTIPLEX LIGATION - DEPENDENT PROBE AMPLIFICATION IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS

    Directory of Open Access Journals (Sweden)

    Georgiana-Emilia Grigore

    2013-11-01

    Full Text Available The clinical management of severe pathological conditions, such as B-cell chronic lymphocytic leukemia (B-CLL, is subject to continuous optimization and re-evaluation. Patients may fully benefit from rapid, standardized laboratory tools designed to facilitate their early stratification according to disease risk, stage and prognosis. Such technologies may also aid the clinician in selecting the therapeutic option with the greatest chances of success. The presence of specific genetic abnormalities are frequently associated with the clinical outcome of oncologic patients in general, and B-CLL patients in particular. In the current study, a group of 58 B-CLL patients were evaluated for the detection of gene copy number alterations (deletions or duplication/ amplifications within 45 distinct genetic targets, by means of a novel molecular methodology, Multiplex Ligation - Dependent Probe Amplification (MLPA. Simple or complex genetic defects were identified in 67% of cases, and the most common aberrations observed were: deletion of the short arm of chromosome 13 in 33% of cases, deletion of the long arm of chromosome 11 in 16% of cases, trisomy 12 in 16% of cases, and deletion of the short arm of chromosome 17 in 7% of cases. The main conclusion of the study presented here points towards MLPA as a potential key step of clinical management protocols in B-CLL, providing that it will be fully standardised for routine diagnosis.

  3. 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.

  4. 应用多重连接依赖探针扩增技术快速检测胎儿染色体非整倍体异常%Application of multiplex ligation-dependent probe amplification for rapid detection of aneuploidies in prenatal diagnosis

    Institute of Scientific and Technical Information of China (English)

    马定远; 许争峰; 胡平; 张菁菁; 易龙; 季修庆; 杨驰; 成建; 李璃; 林颖

    2011-01-01

    Objective To determine the applicability of multiplex ligation-dependent probe amplification (MLPA) for rapid detection of aneuploidies in prenatal diagnosis.Methods A total of 561 prenatal samples were analyzed in parallel by MLPA and traditional karyotyping. Another 20 clinical samples with known common chromosome abnormalities were also determined by MLPA to evaluate the accuracy and reliability of MLPA. The results obtained from MLPA were compared with that from traditional karyotyping.Results The results were available within 48 h.A total of 38 aneuploidies were identified by MLPA,including 20 cases of trisomy 21,10 cases of trisomy 18,1 case of trisomy 13,4 cases of Turner syndrome,1 case of Klinefelter syndrome,1 case of 47,XYY trisomy and 1 case of 48,XYY,+18.MLPA was able to detect all the expected aneuploidies with 100% accuracy.The results obtained from MLPA agreed with traditional karyotyping.Among 561 prenatal samples,the results of 550 samples were concordant with those of karyotyping,and the coincidence rate of MLPA was 98.04%.Conclusion MLPA is a rapid,simple and reliable method for detection of the most common chromosome aneuploidies in prenatal diagnosis.MLPA is a valuable tool in prenatal clinical practice.%目的 探讨多重连接依赖探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术在常见染色体非整倍体异常检测及其在产前诊断中的应用价值.方法 应用MLPA技术检测561份产前诊断样本和20例已知染色体异倍体标本,所有样本均进行常规染色体核型分析,比较MLPA结果和染色体核型分析结果,评价MLPA技术的临床符合率.结果 MLPA技术能够在48 h内出具检测结果,共检测出38例染色体异倍体,包括20例21-三体,10例18-三体,1例13-三体,4例Turner综合征,1例Klinefelter综合征,1例超雄综合征,1例48,XYY,+18双三体综合征.MLPA结果与染色体核型结果一致,检测结果100%准确.在561份产前诊断样本中,有550

  5. Multiplex Ligation-Dependent Probe Amplification Analysis of GATA4 Gene Copy Number Variations in Patients with Isolated Congenital Heart Disease

    Directory of Open Access Journals (Sweden)

    Valentina Guida

    2010-01-01

    Full Text Available GATA4 mutations are found in patients with different isolated congenital heart defects (CHDs, mostly cardiac septal defects and tetralogy of Fallot. In addition, GATA4 is supposed to be the responsible gene for the CHDs in the chromosomal 8p23 deletion syndrome, which is recognized as a malformation syndrome with clinical symptoms of facial anomalies, microcephaly, mental retardation, and congenital heart defects. Thus far, no study has been carried out to investigate the role of GATA4 copy number variations (CNVs in non-syndromic CHDs. To explore the possible occurrence of GATA4 gene CNVs in isolated CHDs, we analyzed by multiplex ligation-dependent probe amplification (MLPA a cohort of 161 non-syndromic patients with cardiac anomalies previously associated with GATA4 gene mutations. The patients were mutation-negative for GATA4, NKX2.5, and FOG2 genes after screening with denaturing high performance liquid chromatography. MLPA analysis revealed that normalized MLPA signals were all found within the normal range values for all exons in all patients, excluding a major contribution of GATA4 gene CNVs in CHD pathogenesis.

  6. Genetic imbalances detected by multiplex ligation-dependent probe amplification in a cohort of patients with oral squamous cell carcinoma-the first step towards clinical personalized medicine.

    Science.gov (United States)

    Ribeiro, Ilda Patrícia; Marques, Francisco; Caramelo, Francisco; Ferrão, José; Prazeres, Hugo; Julião, Maria José; Rifi, Widad; Savola, Suvi; de Melo, Joana Barbosa; Baptista, Isabel Poiares; Carreira, Isabel Marques

    2014-05-01

    Oral tumors are a growing health problem worldwide; thus, it is mandatory to establish genetic markers in order to improve diagnosis and early detection of tumors, control relapses and, ultimately, delineate individualized therapies. This study was the first to evaluate and discuss the clinical applicability of a multiplex ligation-dependent probe amplification (MLPA) probe panel directed to head and neck cancer. Thirty primary oral squamous cell tumors were analyzed using the P428 MLPA probe panel. We detected genetic imbalances in 26 patients and observed a consistent pattern of distribution of genetic alterations in terms of losses and gains for some chromosomes, particularly for chromosomes 3, 8, and 11. Regarding the latter, some specific genes were highlighted due to frequent losses of genetic material--RARB, FHIT, CSMD1, GATA4, and MTUS1--and others due to gains--MCCC1, MYC, WISP1, PTK2, CCND1, FGF4, FADD, and CTTN. We also verified that the gains of MYC and WISP1 genes seem to suggest higher propensity of tumors localized in the floor of the mouth. This study proved the value of this MLPA probe panel for a first-tier analysis of oral tumors. The probemix was developed to include target regions that have been already shown to be of diagnostic/prognostic relevance for oral tumors. Furthermore, this study emphasized several of those specific genetic targets, suggesting its importance to oral tumor development, to predict patients' outcomes, and also to guide the development of novel molecular therapies.

  7. Partial protoporphyrinogen oxidase (PPOX gene deletions, due to different Alu-mediated mechanisms, identified by MLPA analysis in patients with variegate porphyria

    Directory of Open Access Journals (Sweden)

    Barbaro Michela

    2013-01-01

    Full Text Available Abstract Variegate porphyria (VP is an autosomal dominantly inherited hepatic porphyria. The genetic defect in the PPOX gene leads to a partial defect of protoporphyrinogen oxidase, the penultimate enzyme of heme biosynthesis. Affected individuals can develop cutaneous symptoms in sun-exposed areas of the skin and/or neuropsychiatric acute attacks. The identification of the genetic defect in VP families is of crucial importance to detect the carrier status which allows counseling to prevent potentially life threatening neurovisceral attacks, usually triggered by factors such as certain drugs, alcohol or fasting. In a total of 31 Swedish VP families sequence analysis had identified a genetic defect in 26. In the remaining five families an extended genetic investigation was necessary. After the development of a synthetic probe set, MLPA analysis to screen for single exon deletions/duplications was performed. We describe here, for the first time, two partial deletions within the PPOX gene detected by MLPA analysis. One deletion affects exon 5 and 6 (c.339-197_616+320del1099 and has been identified in four families, most probably after a founder effect. The other extends from exon 5 to exon 9 (c.339-350_987+229del2609 and was found in one family. We show that both deletions are mediated by Alu repeats. Our findings emphasize the usefulness of MLPA analysis as a complement to PPOX gene sequencing analysis for comprehensive genetic diagnostics in patients with VP.

  8. 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.

  9. 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...

  10. Double-labelling immunohistochemistry for MGMT and a “cocktail” of non-tumourous elements is a reliable, quick and easy technique for inferring methylation status in glioblastomas and other primary brain tumours

    Science.gov (United States)

    2013-01-01

    Background Our aim was to develop a new protocol for MGMT immunohistochemistry with good agreement between observers and good correlation with molecular genetic tests of tumour methylation. We examined 40 primary brain tumours (30 glioblastomas and 10 oligodendroglial tumours) with our new technique, namely double-labelling immunohistochemistry for MGMT and a "cocktail" of non-tumour antigens (CD34, CD45 and CD68). We compared the results with single-labelling immunohistochemistry for MGMT and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA, a recognised molecular genetic technique which we applied as the gold-standard for the methylation status). Results Double-labelling immunohistochemistry for MGMT produced a visual separation of tumourous and non-tumourous elements on the same histological slide, making it quick and easy to determine whether tumour cell nuclei were MGMT-positive or MGMT-negative (and thereby infer the methylation status of the tumour). We found good agreement between observers (kappa 0.76) and within observer (kappa 0.84). Furthermore, double-labelling showed good specificity (80%), sensitivity (73.33%), positive predictive value (PPV, 83.33%) and negative predictive value (NPV, 68.75%) compared to MS-MLPA. Double-labelling was quicker and easier to assess than single-labelling and it outperformed quantitative computerised image analysis of MGMT single-labelling in terms of sensitivity, specificity, PPV and NPV. Conclusions Double-labelling immunohistochemistry for MGMT and a cocktail of non-tumourous elements provides a "one look" method for determining whether tumour cell nuclei are MGMT-positive or MGMT-negative. This can be used to infer the methylation status of the tumour. There is good observer agreement and good specificity, sensitivity, PPV and NPV compared to a molecular gold-standard. PMID:24252243

  11. MLPA技术用于假性肥大型肌营养不良症产前基因诊断的价值%Clinical value of MLPA in the prenatal gene diagnosis of Duchenne muscular dystrophy

    Institute of Scientific and Technical Information of China (English)

    黎青; 李少英; 张慧敏; 何文智; 马晓燕; 王晓蔓; 冼嘉嘉; 孙筱放; 陈敦金

    2013-01-01

    目的 探讨多重连接探针扩增(MLPA)技术用于假性肥大型肌营养不良症(DMD)先证者家系中高风险孕妇产前DMD基因诊断的价值.方法 收集2005年至2012年广州医学院第三附属医院、南方医科大学南方医院等4家医院的155例有DMD先证者家系的高风险孕妇,其中7例孕早期孕妇取绒毛标本,148例孕中期孕妇取羊水样本,对绒毛标本和血性羊水标本排除母体DNA污染后,采用MLPA技术对绒毛和羊水样本行胎儿DMD基因检测;计算155个家系中DMD基因外显子突变发生次数.结果 (1)155例孕妇中共检出DMD胎儿27例、胎儿DMD基因携带者28例、正常胎儿100例.155例胎儿中,男胎72例,其中27例为DMD胎儿(38%);女胎83例,其中28例胎儿为DMD基因携带者(34%).(2)27例DMD胎儿中,DMD外显子缺失突变22例(14.2%,22/155);外显子重复突变5例,(3.2%,5/155);28例DMD基因携带者中,DMD外显子杂合缺失突变25例(16.1%,25/155),外显子杂合重复突变3例(1.9%,3/155).155个家系中,DMD基因突变的发生主要分布在外显子45 ~ 52之间,其中外显子49突变发生次数最高,共22次.(3)7例早孕期孕妇的绒毛组织DMD基因诊断结果中,有两例胎儿DMD基因型分别与先证者、孕妇的DMD基因型一致,其中1例为患儿、1例为DMD基因携带者,分别给予终止妊娠和继续妊娠的处理.结论 MLPA技术用于DMD产前基因诊断,能准确区分DMD基因突变是属于缺失型、重复型突变还是杂合性缺失等,对DMD先证者家系的高危孕妇有较高的产前诊断价值,临床结果可靠;绒毛膜活检可用于产前DMD早期基因诊断.%Objective To investigate the clinical value of multiplex ligation-dependent probe amplification (MLPA) in the prenatal gene diagnosis of high risk pregnant women from Duchenne muscular dystrophy (DMD) families.Methods The 155 high risk pregnant women from DMD families were recruited from 2005 to 2012 in 4 hospitals in

  12. Rapid and Sensitive Detection of Shigella spp. and Salmonella spp. by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Luo, Lijuan; Liu, Dongxin; Luo, Xia; Xu, Yanmei; Hu, Shoukui; Niu, Lina; Xu, Jianguo; Ye, Changyun

    2015-01-01

    Shigella and Salmonella are frequently isolated from various food samples and can cause human gastroenteritis. Here, a novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully established and validated for simultaneous detection of Shigella strains and Salmonella strains in only a single reaction. Two sets of MERT-LAMP primers for 2 kinds of pathogens were designed from ipaH gene of Shigella spp. and invA gene of Salmonella spp., respectively. Under the constant condition at 63°C, the positive results were yielded in as short as 12 min with the genomic DNA extracted from the 19 Shigella strains and 14 Salmonella strains, and the target pathogens present in a sample could be simultaneously identified based on distinct fluorescence curves in real-time format. Accordingly, the multiplex detection assay significantly reduced effort, materials and reagents used, and amplification and differentiation were conducted at the same time, obviating the use of postdetection procedures. The analytical sensitivity of MERT-LAMP was found to be 62.5 and 125 fg DNA/reaction with genomic templates of Shigella strains and Salmonella strains, which was consist with normal LAMP assay, and at least 10- and 100-fold more sensitive than that of qPCR and conventional PCR approaches. The limit of detection of MERT-LAMP for Shigella strains and Salmonella strains detection in artificially contaminated milk samples was 5.8 and 6.4 CFU per vessel. In conclusion, the MERT-LAMP methodology described here demonstrated a potential and valuable means for simultaneous screening of Shigella and Salmonella in a wide variety of samples. PMID:26697000

  13. Rapid and sensitive detection of Shigella spp. and Salmonella spp. by multiple endonuclease restriction real-time loop-mediated isothermal amplification technique

    Directory of Open Access Journals (Sweden)

    Yi eWang

    2015-12-01

    Full Text Available Shigella and Salmonella are frequently isolated from various food samples and can cause human gastroenteritis. Here, a novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP were successfully established and validated for simultaneous detection of Shigella strains and Salmonella strains in only a single reaction. Two sets of MERT-LAMP primers for 2 kinds of pathogens were designed from ipaH gene of Shigella spp. and invA gene of Salmonella spp., respectively. Under the constant condition at 63˚C, the positive results were yielded in as short as 12 minutes with the genomic DNA extracted from the 19 Shigella strains and 14 Salmonella strains, and the target pathogens present in a sample could be simultaneously identified based on distinct fluorescence curves in real-time format. Accordingly, the multiplex detection assay significantly reduced effort, materials and reagents used, and amplification and differentiation were conducted at the same time, obviating the use of postdetection procedures. The analytical sensitivity of MERT-LAMP was found to be 62.5 fg and 125 fg DNA/reaction with genomic templates of Shigella strains and Salmonella strains, which was consist with normal LAMP assay, and at least 10- and 100-fold more sensitive than that of qPCR and conventional PCR approaches. The limit of detection of MERT-LAMP for Shigella strains and Salmonella strains detection in artificially contaminated milk samples was 5.8 CFU and 6.4 CFU per vessel. In conclusion, the MERT-LAMP methodology described here demonstrated a potential and valuable means for simultaneous screening of Shigella and Salmonella in a wide variety of samples.

  14. BeeDoctor, a versatile MLPA-based diagnostic tool for screening bee viruses

    OpenAIRE

    Lina De Smet; Jorgen Ravoet; de Miranda, Joachim R.; Tom Wenseleers; Mueller, Matthias Y.; Moritz, Robin F.A.; Dirk C de Graaf

    2012-01-01

    The long-term decline of managed honeybee hives in the world has drawn significant attention to the scientific community and bee-keeping industry. A high pathogen load is believed to play a crucial role in this phenomenon, with the bee viruses being key players. Most of the currently characterized honeybee viruses (around twenty) are positive stranded RNA viruses. Techniques based on RNA signatures are widely used to determine the viral load in honeybee colonies. High throughput screening for...

  15. 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.

  16. Combining approach with multiplex PCR and MLPA to detect deletion and duplication in DMD patients,carriers, and prenatal diagnosis%应用多重PCR和MLPA技术检测DMD患者和携带者的基因突变及产前诊断

    Institute of Scientific and Technical Information of China (English)

    李红; 丁洁; 王玮; 陈瑛; 陆伟; 邵红; 吴柏林

    2009-01-01

    Objective Applying multiplex PCR and multiplex ligation-dependent probe amplification (MLPA) in a clinical setting to detect deletions and duplications in the Duchenne/Becker muscular dystrophy (DMD/BMD) gene not only for patients, but also for identification of possible carriers and prenatal diagnosis. Methods Multiplex PCR was used first in patients clinically diagnosed with DMD/BMD to examine 26 exons for a large deletion in the two hot regions of the dystrophin gene. For patients without a deletion detected in the aforementioned regions, MLPA was used to further examine all 79 exons to determine whether a deletion in the remaining non-hot regions or any duplication was present. A similar approach was applied to suspected carriers. In requested prenatal diagnosis cases, specific PCR was used to detect deletions, while MLPA was applied to detect duplications. Results Multiplex PCR was used to examine 26 exons within the two hot regions in the Dystrophin gene for 22 patients with DMD;13 (13/22) had multi-exon deletions. For the 9 patients without deletions in the 26 exons, MLPA was used to examine 79 exons. 3 patients had duplications, 1 patient had a single deletion in exon 18, and no deletions or duplications could be detected in the remaining 5 patients. Of the 16 carriers, 2 out of the 3 that had family history had deletions, while the other 13 carriers were mothers of affected children who were sporadic patients without family history. Of them, 8 mothers were carriers for either deletions or duplications. For prenatal diagnosis, 9 fetuses were examined (one case was twins). Of them, 2 fetuses had familial deletions or duplications detected. These results were verified after induced abortion. In 7 fetuses, no deletions or duplications were detected and all developed into children. Conclusion Multiplex PCR can detect 92.86% of deletions and is useful for prenatal diagnosis of deletions because it is simple, reliable and inexpensive. It can be the first choice

  17. Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT

    Directory of Open Access Journals (Sweden)

    Reichert Jennifer G

    2008-10-01

    Full Text Available Abstract Background It has previously been shown that specific microdeletions and microduplications, many of which also associated with cognitive impairment (CI, can present with autism spectrum disorders (ASDs. Multiplex ligation-dependent probe amplification (MLPA represents an efficient method to screen for such recurrent microdeletions and microduplications. Methods In the current study, a total of 279 unrelated subjects ascertained for ASDs were screened for genomic disorders associated with CI using MLPA. Fluorescence in situ hybridization (FISH, quantitative polymerase chain reaction (Q-PCR and/or direct DNA sequencing were used to validate potential microdeletions and microduplications. Methylation-sensitive MLPA was used to characterize individuals with duplications in the Prader-Willi/Angelman (PWA region. Results MLPA showed two subjects with typical ASD-associated interstitial duplications of the 15q11-q13 PWA region of maternal origin. Two additional subjects showed smaller, de novo duplications of the PWA region that had not been previously characterized. Genes in these two novel duplications include GABRB3 and ATP10A in one case, and MKRN3, MAGEL2 and NDN in the other. In addition, two subjects showed duplications of the 22q11/DiGeorge syndrome region. One individual was found to carry a 12 kb deletion in one copy of the ASPA gene on 17p13, which when mutated in both alleles leads to Canavan disease. Two subjects showed partial duplication of the TM4SF2 gene on Xp11.4, previously implicated in X-linked non-specific mental retardation, but in our subsequent analyses such variants were also found in controls. A partial duplication in the ASMT gene, located in the pseudoautosomal region 1 (PAR1 of the sex chromosomes and previously suggested to be involved in ASD susceptibility, was observed in 6–7% of the cases but in only 2% of controls (P = 0.003. Conclusion MLPA proves to be an efficient method to screen for chromosomal

  18. 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.

  19. 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

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. Rapid high-throughput analysis of DNaseI hypersensitive sites using a modified Multiplex Ligation-dependent Probe Amplification approach

    Directory of Open Access Journals (Sweden)

    Sinclair Andrew H

    2009-09-01

    Full Text Available Abstract Background Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbers of cells. We aimed to develop a quick and straightforward method for the analysis of DNaseI hypersensitive sites that overcomes these problems. Results We have developed a modified Multiplex Ligation-dependent Probe Amplification (MLPA approach for the identification and analysis of genomic regulatory regions. The utility of this approach was demonstrated by simultaneously analysing 20 loci from the ENCODE project for DNaseI hypersensitivity in a range of different cell lines. We were able to obtain reproducible results with as little as 5 × 104 cells per DNaseI treatment. Our results broadly matched those previously reported by the ENCODE project, and both technical and biological replicates showed high correlations, indicating the sensitivity and reproducibility of this method. Conclusion This new method will considerably facilitate the identification and analysis of DNaseI hypersensitive sites. Due to the multiplexing potential of MLPA (up to 50 loci can be examined it is possible to analyse dozens of DNaseI hypersensitive sites in a single reaction. Furthermore, the high sensitivity of MLPA means that fewer than 105 cells per DNaseI treatment can be used, allowing the discovery and analysis of tissue specific regulatory regions without the need for pooling. This method is quick and easy and results can be obtained within 48 hours after harvesting of cells or tissues. As no special equipment is required, this method can be applied by any laboratory interested in the analysis of DNaseI hypersensitive regions.

  5. Detection of major genetic causation of Congenital Heart Defect in fetuses by multiplex ligation-dependent probe amplification:a cost-effective method in developing countries.%多重连接依赖的探针扩增技术在检测胎儿先天性心脏病遗传学病因中的应用

    Institute of Scientific and Technical Information of China (English)

    朱湘玉; 茹彤; 朱海燕; 胡娅莉

    2012-01-01

    Objective; To determine the efficiency of multiplex ligation dependent probe amplification (MLPA) in the detection of the major genetic causes of congenital heart defect (CHD). Methods; 34 cord blood were collected from fetuses, who were affected with CHD, detected by ultrasonograph. Karyotyping and MLPA analysis were performed after DNA extraction. Another 32 cases of DNAs which had been tested previously were also analyzed with the present MLPA kit. Among these 32 cases, trisomy - 13, 16, 18, 21, and trisomy - 21 with microduplication 22ql 1, microdeletion and microduplication of 22ql 1 were included. Results; Of all the 66 cases, all the trisomies of chromosome 13 (3 cases) , 18 (7 cases) and 21 ( 10 cases of trisomy -21 and 1 case of trisomy -21 with microduplication 22ql 1) were detected by the present MLPA kit. Results: Of the five cases of known 22ql 1 deletion (3 megabases) were anastomotic in the size of deletion. In the 34 new cases, two additional cases of 22ql 1 deletion (3 megabases) were detected and proved by MLPA - P250 kit subsequently. Five case of trisomy - 16 and one case of 69, XXX and one case of balanced translocation were suggested as normal by MLPA. Conclusion; MLPA could detect common trisomies and microdeletion or microduplication that may cause CHD.%目的 探讨多重连接依赖的探针扩增技术(MLPA)用于检测胎儿先天性心脏病遗传学病因的可行性.方法 2006年11月至2009年12月间,共收集34例超声发现为先天性心脏病胎儿的脐血进行染色体核型分析,同时提取脐血淋巴细胞DNA后进行MLPA检测.选取先前已进行核型分析及MLPA确诊的32例标本作为对照,其中包括13-三体、16-三体、18-三体、21-三体、21-三体合并22q11微扩增以及不同范围的22q11微扩增或微缺失.结果 66例标本中,本实验所用的MLPA探针共检出3例13-三体、7例18-三体、10例21-三体、1例21-三体合并22q11微扩增.5例22q11微缺失的缺失

  6. 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.

  7. 核酸检测中HIV病毒载量对内质控扩增的影响%Effects of HIV viral load on internal control amplification by using NAT technique

    Institute of Scientific and Technical Information of China (English)

    余谨; 毕昊; 陆华新; 王先广; 赵磊; 沈钢

    2012-01-01

    目的 评估酶联免疫法的窗口期HIV血样.方法 将酶联免疫法阴性标本采用六混样用2种试剂进行平行核酸检测,在检测出阳性标本后,亦用2种试剂对其拆分进行单管核酸检测.结果 10个月内共筛查16769例酶联免疫阴性标本中,核酸检测出1例HIV阳性标本,罗氏一代试剂由于该标本病毒载量浓度过高体现出抑制作用,罗氏二代试剂未显示出抑制作用.结论 目前现行开展的检测技术仍有安全隐患,为进一步保证临床用血的安全,开展核酸检测可以提高临床用血质量,为临床安全用血提供强有力的保障.%Objective To determine the prevalence of viral infections (HBV.HCV and HIV) in serological window period in blood donors screened with nucleic acid testing (NAT) . Methods All blood donors were tested with serological tests( Ag-HBVs,Anti-HCV and Anti-HIV)and molecular testing with NAT by PP6 and rPPl for HBV.HCV and HIV. The window period was defined with the positive NAT and negative serological test. Results During ten months, we evaluated 16 769 blood donors. One subject was identified with HIV in serological window period. HIV viral load has the effect on internal control amplification by using NAT technique. Conclusion Unsafe blood in the performance of viral infections due to HIV in serological window period in donors by using NAT technique.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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)

  13. Low frequency of MLL-partial tandem duplications in paediatric acute myeloid leukaemia using MLPA as a novel DNA screenings technique.

    NARCIS (Netherlands)

    Balgobind, B.V.; Hollink, I.H.; Reinhardt, D.; Wering, E.R. van; Graaf, S.S.N. de; Baruchel, A.; Stary, J.; Beverloo, H.B.; Greef, G.E. de; Pieters, R.; Zwaan, C.M.; Heuvel-Eibrink, M.M. van den

    2010-01-01

    Mixed-lineage leukaemia (MLL)-partial tandem duplications (PTDs) are found in 3-5% of adult acute myeloid leukaemia (AML), and are associated with poor prognosis. In adult AML, MLL-PTD is only detected in patients with trisomy 11 or internal tandem duplications of FLT3 (FLT3-ITD). To date, studies i

  14. 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

  15. 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)

  16. Amplification of the Insulin-Like Growth Factor 1 Receptor Gene Is a Rare Event in Adrenocortical Adenocarcinomas: Searching for Potential Mechanisms of Overexpression

    Directory of Open Access Journals (Sweden)

    Tamaya Castro Ribeiro

    2014-01-01

    Full Text Available Context. IGF1R overexpression appears to be a prognostic biomarker of metastatic pediatric adrenocortical tumors. However, the molecular mechanisms that are implicated in its upregulation remain unknown. Aim. To investigate the potential mechanisms involved in IGF1R overexpression. Patients and Methods. We studied 64 adrenocortical tumors. IGF1R copy number variation was determined in all patients using MLPA and confirmed using real time PCR. In a subgroup of 32 patients, automatic sequencing was used to identify IGF1R allelic variants and the expression of microRNAs involved in IGF1R regulation by real time PCR. Results. IGF1R amplification was detected in an adrenocortical carcinoma that was diagnosed in a 46-year-old woman with Cushing’s syndrome and virilization. IGF1R overexpression was demonstrated in this case. In addition, gene amplification of other loci was identified in this adrenocortical malignant tumor, but no IGF1R copy number variation was evidenced in the remaining cases. Automatic sequencing revealed three known polymorphisms but they did not correlate with its expression. Expression of miR-100, miR-145, miR-375, and miR-126 did not correlate with IGF1R expression. Conclusion. We demonstrated amplification and overexpression of IGF1R gene in only one adrenocortical carcinoma, suggesting that these combined events are uncommon. In addition, IGF1R polymorphisms and abnormal microRNA expression did not correlate with IGF1R upregulation in adrenocortical tumors.

  17. 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

  18. ELECTRON AMPLIFICATION IN DIAMOND.

    Energy Technology Data Exchange (ETDEWEB)

    SMEDLEY, J.; BEN-ZVI, I.; BURRILL, A.; CHANG, X.; GRIMES, J.; RAO, T.; SEGALOV, Z.; WU, Q.

    2006-07-10

    We report on recent progress toward development of secondary emission ''amplifiers'' for photocathodes. Secondary emission gain of over 300 has been achieved in transmission mode and emission mode for a variety of diamond samples. Techniques of sample preparation, including hydrogenation to achieve negative electron affinity (NEA), have been adapted to this application.

  19. 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....

  20. 多重连接依赖式探针扩增技术在α地中海贫血基因诊断与产前诊断中的应用%The application of multiplex ligation-dependent probe amplification technology in diagnosis and prenatal diagnosis of α-thalassemia

    Institute of Scientific and Technical Information of China (English)

    陈亚军; 杨学煌; 曾宪琪; 乔伶俐

    2013-01-01

    Objective To investigate the multiplex ligation-dependent probe amplification (MLPA) technology in the detection of gene deletion and prenatal diagnosis of α-thalassaemia.Methods Phenotypes were analyzed by whole blood cell counting and hemoglobin component detection of peripheral blood samples from the subjects.The gene deletions and point mutations of α-thalassaemia were detected with regular gap-PCR and reverse dot blot (RDB) method.At last,the MLPA method was applied for detection of α-globin gene deletion.All the prenatal diagnosis samples were detected with both gap-PCR and MLPA method.Results α-thalassaemia phenotype was found in 75 samples from 1256 (628 couples) peripheral blood samples for pre-pregnancy or prenatal thalassemia gene screening.Among them,71 samples carrying α-gene mutations and consistent with phenotypes were detected by routine methods.Inthe other 3 samples with no α-gene mutations detected and 1 sample with HbH phenotype but genotype of-α42/αα were analyzed by MLPA and found each one samples of whole α-globin gene cluster deletion,respectively.Seventeen high risk couples were screened.Among the 17 prenatal diagnosis samples,2 villus samples contaminated by exogenous DNA were confirmed by MLPA method.Conclusions MLPA is an effective complement for α-thalassaemia gene deletion detection.The molecular diagnosis strategy and process of gap-PCR combined with MLPA for α-thalassaemia gene deletion detection can prevent the missing of gene deletion,and false-positive or false-negative misdiagnosis of α-thalassaemia in prenatal diagnosis.%目的 探讨多重连接依赖式探针扩增(M LPA)技术在α地中海贫血(地贫)基因缺失检测及产前诊断中的应用.方法 采用全血细胞计数和血红蛋白成分检测对受检者外周血标本进行表型分析,采用常规跨越裂点PCR(gap-PCR)技术及反向斑点杂交(RDB)法检测α地贫基因缺失及点突变,采用MLPA技术检测α珠蛋白基因缺失;产前

  1. Paternally originated Wolf-Hirschhorn syndrome detected by multiplex ligation-dependent probe amplification and microarray comparative genomic hybridization%运用多重连接探针扩增和微阵列-比较基因杂交芯片技术诊断父源性Wolf-Hirschhorn 综合征一家系

    Institute of Scientific and Technical Information of China (English)

    朱春江; 黄志云; 吴维青; 赵芹; 蒋海艳; 谢建生

    2012-01-01

    Objective To confirm the diagnosis of a Wolf-Hirschhorn syndrome by family study using both cytogenetic and molecular genetic techniques.Method G-band karyotyping was performed for all the 6 members in the family.Multiplex ligation-dependent probe amplification ( MLPA ) was used to detect the chromosome abnormality for the proband,his father and brother.Microarray comparative genomic hybridization (Array-CGH) was carried out to map the exact chromosomal breakpoints for the proband.Result The proband presented with a typical face,delayed growth and hypotonia in Wolf-Hirschhorn syndrome.His G-band karyotype was 46,XY,der(4) t(4;8) ( p16.2 ; p23.1 )pat.MLPA showed 4pter loss and 8pter gain.Array-CGH revealed an XY male with a 3.781 Mb deletion of 4p16.3-p16.2 and a 6.760 Mb duplication of 8p23.3-p23.1.The proband's brother has mental retardation and skeletal abnormalities.His G-band karyotype was 46,XY,der ( 8 ) t ( 4 ; 8 ) ( p 16.2 ; p23.1 ) pat.M LPA showed 4pter gain and 8 pter loss.The proband's father had normal phenotype with a balanced translocation of 46,XY,t (4;8) (p16.2; p23.1 )pat.MLPA showed a normal result.The proband's grandfather showed a normal phenotype with a balanced translocation 46,XY,t ( 4 ; 8 ) ( p16.2 ; p23.1 ).The other members in the family showed normal phenotypes with normal karyotypes.Conclusion The proband has features of Wolf-Hirschhorn sypdrome with partial monosomy 4p and partial trisomy 8p.The proband's brother has a partial trisomy 4p and partial monosomy 8p.The derived chromosomes are inherited from paternal balanced translocation t(4 ;8)( p16.2;p23.1).%目的 对怀疑为Wolf-Hirschhorn综合征患儿的1个家系进行细胞遗传学和分子遗传学诊断.方法 对该家系6人全部进行外周血淋巴细胞培养、G显带分析染色体核型,先证者及其父亲、哥哥行多重连接探针扩增( MLPA)检测进一步确定核型,先证者同时进行微阵列-比较基因组杂交(array-CGH)检测获得其染色体结

  2. Interactive Effects of Growth Regulators, Carbon Sources, pH on Plant Regeneration and Assessment of Genetic Fidelity Using Single Primer Amplification Reaction (SPARS) Techniques in Withania somnifera L.

    Science.gov (United States)

    Fatima, Nigar; Ahmad, Naseem; Ahmad, Iqbal; Anis, Mohammad

    2015-09-01

    An improved and methodical in vitro shoot morphogenic approach through axillary bud multiplication was established in a drug yielding plant, Withania somnifera L. Effects of plant growth regulators [6-benzyladenine (BA), kinetin (Kin), 2-isopentenyladenine (2iP), and thidiazuron (TDZ)] either singly or in combination with α-napthalene acetic acid (NAA), indole-3-butyric acid (IBA), and indole-3-acetic acid (IAA) in Murashige and Skoog (MS) medium were tested. The highest regeneration frequency (90 %) with optimum number of shoots (32 ± 0.00)/explant were obtained on MS medium fortified with 2.5 μM 6-benzyladenine (BA) and 0.5 μM NAA and 30 g/l sucrose at pH 5.8. Among the tried TDZ concentrations, 0.5 μM resulted in maximum number of shoots (20.4 ± 0.40)/explant after 4 weeks of exposure. The proliferating shoot cultures established by repeated subculturing of the mother explants on the hormone-free medium produced the highest shoot number (29.4 ± 0.40) with shoot length (6.80 ± 0.12 cm)/explant at fourth subculture passage, which a decline in shoot proliferation was recorded. Different concentrations of NAA were tested for ex vitro rooting of microshoots. The maximum percentage of rooting 100 % with maximum roots (18.3 ± 0.1) was achieved in soilrite when basal portion of the microshoots were treated with 200 μM (NAA) for 15 min per shoot. The plantlets went through hardening phase in a growth chamber, prior to ex vitro transfer. The PCR-based single primer amplification reaction (SPAR) methods which include random amplified polymorphic DNA (RAPD) and direct amplification of minisatellite DNA (DAMD) markers has been used for assessment of genetic stability of micropropagated plantlets. No variation was observed in DNA fingerprinting patterns among the micropropagated and the donor plants illustrating their genetic uniformity. PMID:26152820

  3. Interactive Effects of Growth Regulators, Carbon Sources, pH on Plant Regeneration and Assessment of Genetic Fidelity Using Single Primer Amplification Reaction (SPARS) Techniques in Withania somnifera L.

    Science.gov (United States)

    Fatima, Nigar; Ahmad, Naseem; Ahmad, Iqbal; Anis, Mohammad

    2015-09-01

    An improved and methodical in vitro shoot morphogenic approach through axillary bud multiplication was established in a drug yielding plant, Withania somnifera L. Effects of plant growth regulators [6-benzyladenine (BA), kinetin (Kin), 2-isopentenyladenine (2iP), and thidiazuron (TDZ)] either singly or in combination with α-napthalene acetic acid (NAA), indole-3-butyric acid (IBA), and indole-3-acetic acid (IAA) in Murashige and Skoog (MS) medium were tested. The highest regeneration frequency (90 %) with optimum number of shoots (32 ± 0.00)/explant were obtained on MS medium fortified with 2.5 μM 6-benzyladenine (BA) and 0.5 μM NAA and 30 g/l sucrose at pH 5.8. Among the tried TDZ concentrations, 0.5 μM resulted in maximum number of shoots (20.4 ± 0.40)/explant after 4 weeks of exposure. The proliferating shoot cultures established by repeated subculturing of the mother explants on the hormone-free medium produced the highest shoot number (29.4 ± 0.40) with shoot length (6.80 ± 0.12 cm)/explant at fourth subculture passage, which a decline in shoot proliferation was recorded. Different concentrations of NAA were tested for ex vitro rooting of microshoots. The maximum percentage of rooting 100 % with maximum roots (18.3 ± 0.1) was achieved in soilrite when basal portion of the microshoots were treated with 200 μM (NAA) for 15 min per shoot. The plantlets went through hardening phase in a growth chamber, prior to ex vitro transfer. The PCR-based single primer amplification reaction (SPAR) methods which include random amplified polymorphic DNA (RAPD) and direct amplification of minisatellite DNA (DAMD) markers has been used for assessment of genetic stability of micropropagated plantlets. No variation was observed in DNA fingerprinting patterns among the micropropagated and the donor plants illustrating their genetic uniformity.

  4. 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

  5. 应用多重连接依赖探针扩增技术快速检测胎儿染色体非整倍体与结构异常%Application of multiplex ligation-dependent probe amplification for rapid detection of aneuploidies and structural chromosomal abnormalities in prenatal diagnosis

    Institute of Scientific and Technical Information of China (English)

    张菁菁; 胡平; 罗春玉; 季修庆; 周静; 刘安; 马定远; 许争峰

    2014-01-01

    目的 探讨多重连接依赖探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术在羊水细胞染色体非整倍体及染色体结构异常检测中的应用.方法 应用MLPA技术对286份羊水样本进行检测,并与常规染色体核型分析进行对比,对于检测到的染色体结构异常应用微阵列比较基因组杂交技术(array comparative genomic hybridization,aCGH)进行验证.结果 在286份羊水中,共检测到10例21-三体,2例18三体,1例13三体,1例嵌合21-三体,1例X单体,1例X染色体短臂大片段缺失,1例18号染色体短臂部分三体,1例18号染色体长臂和短臂大片段缺失.所有MLPA结果与染色体核型分析均一致.对于检测到的染色体结构异常均应用aCGH技术验证,检测结果符合率100%.结论 MLPA可快速检出常见染色体非整倍体以及染色体结构异常包括大片段缺失与重复,为临床产前诊断提供有价值的信息.%Objective To explore the value of multiplex ligation-dependent probe amplification (MLPA) for rapid detection of aneuploidies and structural chromosomal abnormalities during prenatal diagnosis.Methods Two hundred and eight six amniotic fluid samples were analyzed with both MLPA and conventional karyotyping.Structural abnormalities were verified with array comparative genomic hybridization.Results Ten cases of trisomy 21,2 cases of trisomy 18,1 case of trisomy 13,1 case of mosaic trisomy 21,1 case of 45,X,1 case of large deletion of Xp,1 case of trisomy 18p and 1 case of large deletion of 18p and 18q were identified.The same results were derived by both MLPA and conventional karyotyping.Structural abnormalities were verified by array comparative genomic hybridization (aCGH)with 100% accuracy.Conclusion In addition to aneuploidies,MLPA can rapidly identify large deletions and duplications of chromosomes 21,18,13,X and Y.MLPA is supplementary to conventional karyotyping for identification of such chromosomal abnormalities

  6. Rapid amplification of 3'cDNA ends of dioscin-glycosidase by 3'RACE technique%RACE技术对薯蓣皂苷糖苷酶基因cDNA 3'末端的快速扩增

    Institute of Scientific and Technical Information of China (English)

    骆宁; 金凤燮; 鱼红闪

    2010-01-01

    对微生物Absidia sp.G3d产薯蓣皂苷糖苷酶基因cDNA 3'末端的序列进行了调取.根据薯蓣皂苷糖苷酶基因的CDS区已知序列设计特异性引物,应用3'RACE(Rapid-Amplification of eDNA 3'Ends)技术,快速扩增得到cDNA 3'端未知序列片段,将PCR产物切胶回收,直接测序得到长度为258 bp的产物序列,经比对其中编码区长度为122 bp,非编码区长度为136 bp,Poly A部分长度为28 bp.这对其他类中草药高活性皂苷糖基水解酶基因cDNA3'末端的序列的调取提供了参考.

  7. 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.

  8. 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.

  9. 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.

  10. Detection of homozygous and heterozygous SMN deletions of spinal muscular atrophy in a single assay with multiplex ligation-dependent probe amplification%SMN基因缺失多重连接探针扩增法检测和识别脊柱肌肉萎缩症的纯合型或杂合型SMN基因缺失

    Institute of Scientific and Technical Information of China (English)

    Keith TOMASZEWICZ; Peter KANG; Bai-Lin WU

    2005-01-01

    Objective: Spinal muscular atrophy(SMA), an autosomal recessive neuromuscular degeneration of the anterior horn cells of the spinal cord and brain stem, results in one of the most common diseases with muscle fatigue and atrophy. Most SMA cases including all the types are due to the homozygous deletion of at least exon 7 within the survival motor neuron 1 (SMN-1) gene. Although a "golden standard" assay (PCR with mismatch primer followed by enzyme digestion) is very reliable for the identification of homozygous SMN-1 deletion, the carrier detection of heterozygous SMN-1 deletion remains a challenge. Methods: Some PCR-based gene dosage assays or multiplex PCR allow for the determination of the copy number of SMN-1 gene to identify heterozygous deletion, but these procedures are often time consuming and available on a limited clinical basis. Recently developed MLPA (multiplex ligation-dependent probe amplification) is an efficient procedure that can accurately analyze relative quantification to establish the copy number of the SMN gene. We performed a validation for simultaneous detection of homozygous SMN-1 deletions of SMA patients and heterozygous SMN-1 deletions of SMA carriers in a simple assay using a MLPA-SMA assay specific reagent. Results: Six out of 20 patients with SMA were found to have homozygous SMN-1 deletion, confirmed by the PCR/digestion assay. All 4 parents of the children with SMA had heterozygous SMN-1 deletion, confirmed by an independent relative quantitative analysis. Conclusion: MLPA provides a simple, rapid and accurate method of simultaneously detecting homozygous deletions and heterozygous deletions in a single assay for both SMN-1 and SMN-2 genes.

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  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. Detecting My cobacterium Tuberculosis in Sputum Specimens by Technique of Loop-mediated Isothermal Amplification%环介导等温扩增技术检测痰标本中结核分枝杆菌的研究

    Institute of Scientific and Technical Information of China (English)

    易海华; 丁永健; 钱志娟; 房超; 吴萍兰; 房婷

    2008-01-01

    [目的]寻找1种快速的,且敏感度高,特异性强的结核分枝杆菌的检测方法.[方法]环介导等温扩增基因检测(Loop-mediated isothermal amplification LAMP)是一种便捷、灵敏度高而又特异性强的核酸基因扩增检测技术.本课题组根据结核分枝杆菌gyrB特征性序列设计3对特征性引物对痰液中和培养基中的结核分枝杆菌进行检测.其中1对环状引物结合于特征性序列中环状结构部分,可极大地加快LAMP反应速度,且不干扰内引物在LAMP反应中作用.[结果]实验结果表明:使用环状引物的LAMP反应可在0.5h内完成,总共分析时间不超过1h.LAMP检测技术的灵敏度比经典PCR技术高100倍左右,LAMP检测技术具有与实时PCR(Real-time PCR)技术相同的特异度.另外,由于LAMP检测技术是在恒温的情况下进行,不需要特别昂贵的仪器设备,检测方法简单,结果判定直接.[结论]该方法的特点和优势可以使之在基层实验室及现场监测方面广泛使用,在快速检测方面具有一定的开发潜力.

  17. 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.

  18. 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.

  19. 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

  20. MS-MLPA方法在Prader-Willi综合征及Angelman综合征基因诊断中的应用%Methylation-specific multiplex ligation-dependent probe amplification in diagnosis of Prader-Willi syndrome and Angelman syndrome

    Institute of Scientific and Technical Information of China (English)

    李美蓉; 吴希如; 潘虹; 王小竹; 刘晓燕; 杨艳玲; 包新华; 张月华; 熊晖; 钟南; 秦炯

    2008-01-01

    目的 检测甲基化特异性的多莆连接依赖的探针扩增(MS-MLPA)方法的敏感性和可靠性,以寻求一种简单、重复性好、精确度高的用于Prader-Willi综合征(PWS)和Angeiman综合征(As)的基因诊断方法.方法 DNA提取试剂盒提取基因组DNA,然后,用DNA纯化试剂盒进行纯化.用MS-MLPA试剂盒Me028对临床诊断的2例PWS和4例AS患儿进行基因检测分析.扩增的PCR产物用测序仪ABI 310进行基因型分析,最终所得数据用GeneMarker软件进行分析.MS-MLPA的检测结果用甲基化特异性聚合酶链反应进行验证.结果 4例AS中3例源于母源染色体15q11~q13缺失,1例源于父源染色体15q11~q13单亲二倍体或印记中心缺陷;2例PWS中1例源于父源染色体15q11-q13缺失,1例尚不能明确原因.结论 MS-MLPA是一种简单、高效、准确、可靠的基因检测方法.%Objective To verify the sensitivity and reliability of methylation-specific multiplex ligation-dependent probe amplification(MS-MLPA)and to develop a simple,accurate,reliability method of genetic diagnosis for AS and PWS.Methods Pefipherai blood samples were collected from 4 suspected AS patients,2 suspected PWS patients,2 normal persons,and 2 molecular biologically proven positive controls (1 AS patient and l PWS patient).DNA was extracted and purified.MS-MLPA wag used to detect the methylation of the CpG dinucleotide and the copy number in the 15q.q13 region.The results of MS-MLPA were confirmed by MSP.Results Three cages with matemal deletion on 15q11-q13 region and one case with paternal uniparental disomy(UPD)or imprinting center defect in 15q11-q13 region were found in the 4 suspected AS patients.One PWS cage was found to be with paternal deletion in 15q11-q13 region and the other with paternal deletion in 15q11-q13 region or UPD or imprinting center defect in 15q11-q13 region.Conclusion MS-MLPA is a simple.rapid,accurate, and reliable method of genetic test.

  1. 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.

  2. 应用多重连接依赖式探针扩增技术快速高通量诊断胎儿染色体非整倍体异常%Rapid and high-throughput multiplex ligation-dependent probe amplification for diagnosis of chromosome aneuploidy

    Institute of Scientific and Technical Information of China (English)

    唐少华; 毛义建; 陈向南; 徐雪琴; 谢番妮; 吴昊; 李焕铮; 吕建新

    2011-01-01

    目的 评价多重连接依赖式探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)在染色体非整倍体诊断中的应用价值,为我国羊水染色体诊断提供一种快速、特异、高通量的分子诊断手段.方法 应用MLPA技术检测了500份羊水标本,所有标本均进行荧光原位杂交(fluorescence in situ hybridization,FISH)技术检测和常规染色体核型分析,应用RH-MLPA-v511数据分析软件获得MLPA结果,比较MLPA技术与FISH和染色体核型分析结果的准确性,总结MLPA技术临床应用过程中的关键要点.结果 在500份羊水标本中,MLPA检测成功率97%.3个工作日完成结果的为92%,需重复检测的为5%,失败为3%.对染色体非整倍体异常检测敏感性和准确性100%.证实38例非整倍体病例探针信号比值>正常二倍体4s,2例疑似三体结果>2s.分析了21号染色体8条探针的杂交效率,21三体患者8条探针中平均4条探针比值>1.3.结论 MLPA技术具有快速、特异、敏感、高通量、成本低等特点,可用于产前染色体非整倍体数目的快速检测,是传统染色体培养方法的补充,临床应用价值较高.%Objective To assess the diagnostic value of multiplex ligation-dependent probe amplification (MLPA) for detection of common chromosome aneuploidy in amniotic fluid (AF) cells in order to obtain an accurate, rapid, cost-effective and high-throughput method in routine prenatal clinical practice.Methods The MLPA test was performed on 500 AF samples by using kit P095 and the results were obtained by using analysis software RH-MLPA-v511. The results were compared with that from fluorescence in situ hybridization (FISH) and traditional karyotyping (TK). The technical critical issues were analyzed in routine diagnostic application. Results The absolute specificity and sensitivity of the MLPA test to detect the aneuploidy were 100%. For the 500 AF samples, the success rate of the MLPA tests was 97%. Among

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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...

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

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available 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 DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  10. Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

    Directory of Open Access Journals (Sweden)

    Scott A. Tomlins

    2006-02-01

    Full Text Available Expression profiling of clinically obtainable tumor specimens has been hindered by the need for microgram quantities of RNA. In vitro transcription (IVT-based amplifications are most commonly used to amplify small quantities of RNA for microarray analysis. However, significant drawbacks exist with IVT-based amplification, and the need for alternative amplification methods remains. Herein, we validate whole transcriptome amplification (WTA, an exponential amplification technique that produces cDNA libraries and amplified target in 3 to 4 hours from nanogram quantities of total RNA using a combination of cDNA microarrays and quantitative polymerase chain reaction (PCR. We demonstrate that WTA material can serve as a “molecular archive” because a WTA cDNA library can be faithfully amplified through multiple rounds of PCR amplification, allowing it to serve as a bankable and distributable resource. To demonstrate applicability, WTA was combined with laser capture microdissection to profile frozen prostate tissues. Unlike most IVT-based and exponential amplification techniques, WTA does not depend on the presence of a poly-A tail. Thus, we demonstrate that WTA is compatible with artificially degraded RNA and RNA isolated from formalin-fixed paraffin-embedded tissues. Taken together, WTA represents a versatile approach to profile and archive cDNA from minute tumor samples and is compatible with partially degraded RNA.

  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. 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

  14. 90 mJ parametric chirped pulse amplification of 10 fs pulses.

    Science.gov (United States)

    Tavella, Franz; Marcinkevicius, Andrius; Krausz, Ferenc

    2006-12-25

    We demonstrate the amplification of broadband pulses from a Ti:Sapphire oscillator by non-collinear optical parametric chirped-pulse amplification technique in a type-I BBO crystal to energies of 90 mJ. Partial compression of the amplified pulses is demonstrated down to a 10 fs duration. These parameters come in combination with good spatial quality and focusability of the amplified beam.

  15. Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences

    OpenAIRE

    La Mura Maurizio; Lee David; Allnutt Theo R; Powell Wayne

    2009-01-01

    Abstract Background The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR). Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. Results We have tested the specificity and sensitivity of the technique for use in GMO studies. Res...

  16. 90 mJ parametric chirped pulse amplification of 10 fs pulses.

    Science.gov (United States)

    Tavella, Franz; Marcinkevicius, Andrius; Krausz, Ferenc

    2006-12-25

    We demonstrate the amplification of broadband pulses from a Ti:Sapphire oscillator by non-collinear optical parametric chirped-pulse amplification technique in a type-I BBO crystal to energies of 90 mJ. Partial compression of the amplified pulses is demonstrated down to a 10 fs duration. These parameters come in combination with good spatial quality and focusability of the amplified beam. PMID:19532173

  17. 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.

  18. 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...

  19. Efficiency of multiplex ligation-dependent probe amplification combined with short tandem repeat linkage analysis for the prenatal diagnosis for Duchenne muscular dystrophy%MLPA联合遗传连锁分析在假肥大型肌营养不良症产前诊断中的价值

    Institute of Scientific and Technical Information of China (English)

    李涛; 吴东; 侯巧芳; 王莉; 郭谦楠; 康冰; 刘红彦; 杨科; 丁雪冰

    2013-01-01

    Objective To investigate the efficiency of multiplex ligation-dependent probe amplification (MLPA) combined with short tandem repeat (STR) linkage analysis for the prenatal diagnosis for Duchenne muscular dystrophy (DMD).Methods Gender of the fetus was first determined by the presence of Y chromosome sex-determining gene (SRY).Subsequently,combined MLPA and STR linkage analysis were applied for the probands,pregnant women and fetuses in 45 affected families.Results Among the 45 families,31 SRY-positive fetuses were identified,among whom six were diagnosed with DMD.For 14 SRY-negative fetuses,four were diagnosed as carriers.The remainders were normal.Conclusion MLPA can detect mutations in the exons of dystrophin gene,whilst STR linkage analysis can determine whether the fetus has inherited the maternal X chromosome bearing the mutant gene.As the result,the method can therefore detect affected fetuses in which no exonic mutations are detected with MLPA.By combining the two methods,the diagnostic rate for DMD can be greatly improved.%目的 探讨多重连接依赖探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)联合短串联重复序列(short tandem repeat,STR)基因连锁分析用于Duchenne型假肥大型肌营养不良症(Duchenne muscular dystrophy,DMD)产前诊断的价值.方法 通过检测Y染色体性别决定基因(Y chromosome sex-determining gene,SR Y)判断胎儿性别;MLPA检测45个DMD家系中先证者、孕妇以及胎儿Dystrophin基因突变情况,并对家系成员和胎儿进行第45、49、50内含子以及5′和3 ′端STR的连锁分析.结果 45个进行产前诊断的家系中,SRY阳性31例,其中6例为DMD患病胎儿;阴性14例,其中4例为携带者,余未见异常.结论 MLPA能检测胎儿Dystrophin基因外显子突变情况,STR连锁能分析胎儿是否继承母源性风险X染色体,因此,STR连锁分析能发现MLPA技术检测不到的外显子突变胎儿.将两种方法结合起来

  20. 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.

  1. 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.

  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. Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations

    Directory of Open Access Journals (Sweden)

    Ivell Richard

    2003-11-01

    Full Text Available Abstract Background The amplification of RNA with the T7-System is a widely used technique for obtaining increased amounts of RNA starting from limited material. The amplified RNA (aRNA can subsequently be used for microarray hybridizations, warranting sufficient signal for image analysis. We describe here an amplification-time dependent degradation of aRNA in prolonged standard T7 amplification protocols, that results in lower average size aRNA and decreased yields. Results A time-dependent degradation of amplified RNA (aRNA could be observed when using the classical "Eberwine" T7-Amplification method. When the amplification was conducted for more than 4 hours, the resulting aRNA showed a significantly smaller size distribution on gel electrophoresis and a concomitant reduction of aRNA yield. The degradation of aRNA could be correlated to the presence of the T7 RNA Polymerase in the amplification cocktail. The aRNA degradation resulted in a strong bias in microarray hybridizations with a high coefficient of variation and a significant reduction of signals of certain transcripts, that seem to be susceptible to this RNA degrading activity. The time-dependent degradation of these transcripts was verified by a real-time PCR approach. Conclusions It is important to perform amplifications not longer than 4 hours as there is a characteristic 'quality vs. yield' situation for longer amplification times. When conducting microarray hybridizations it is important not to compare results obtained with aRNA from different amplification times.

  7. 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...

  8. 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)

  9. 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...

  10. 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

  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. 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...

  13. 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.

  14. 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.

  15. 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.

  16. 应用多重连接依赖性探针扩增定量技术检测假肥大型肌营养不良重复突变及携带状态%Detection of duplication mutation and carriers of Duchenne/Becker muscular dystrophy by multiplex ligation-dependent probe amplification quantitative

    Institute of Scientific and Technical Information of China (English)

    林齐防; 陈万金; 王柠; 吴志英; 林珉婷; 慕容慎行

    2011-01-01

    Objective To analyze the dystrophin gene in patients with Duchenne/Becker muscular dystrophy (DMD/BMD) and their family members by multiplex ligation-dependent probe amplification (MLPA) method and to evaluate the application of this method in the mutations detection. Methods The whole dystrophin gene (79 exons) was analyzed by MLPA in 355 patients with DMD/BMD, the mothers of 46 patients with deletion mutation and the mothers of 8 patients with duplication mutation. The results were verified by PCR and sequencing when single exon deletion was found. Results One hundred and ninety cases were found to have deletion of one or more dystrophin exons, and 34 patients were identified to have duplication mutations. In 46 mothers of patients with deletion mutations, 28 were identified the mutations;and of 8 mothers of patients with duplication mutations, 6 were identified the mutations. There was no statistical significance between the carrier incidences in the 2 groups. A 23 bp deletion of "AGGGAACAGATCCTGGTAAAGCA" fragment in exon 17 was found in a patient. Conclusions Comparing with the traditional quantitative methods, MLPA can detect the deletion and duplication mutation in all the 79 exons of dystrophin gene in DMD/BMD patients, and can identify the carrier status in their family members. Furthermore, MLPA is not apt to be interfered by the concentration and purity of DNA template.%目的 应用多重连接依赖性探针扩增(MLPA)技术对假肥大型肌营养不良(DMD及BMD)患者及其家系成员进行dystrophin基因分析,探讨MLPA定量技术在本病重复突变及携带者检测中的优势.方法 以355例DMD及BMD患者、46名缺失型患者之母和8名重复型患者之母为研究对象,应用MLPA技术对dystrophin基因全长外显子进行分析,对于单一外显子缺失的样本采用PCR及测序进行验证.结果 经MLPA分析,全部355例患者中190例为dystrophin基因缺失型患者,在其余非缺失型患者中检测出34

  17. 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

  18. 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.

  19. 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.

  20. Visual Detection of Potato leafroll virus by One-step Reverse Transcription Loop-Mediated Isothermal Amplification of DNA with Hydroxynaphthol Blue Dye

    NARCIS (Netherlands)

    Ahmadi, S.; Almasi, A.M.; Fatehi, F.; Struik, P.C.; Moradi, A.

    2013-01-01

    Loop-mediated isothermal amplification (LAMP) assay is a novel technique for amplifying DNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency. We applied reverse transcription loop-mediated isothermal amplification (RT-LAMP) to visually detect Potato leafroll vi

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Sequencing of simple sequence repeat anchored polymerase chain reaction amplification products of Biomphalaria glabrata

    Directory of Open Access Journals (Sweden)

    Caldeira Roberta L

    2002-01-01

    Full Text Available Simple sequence repeat anchored polymerase chain reaction amplification (SSR-PCR is a genetic typing technique based on primers anchored at the 5' or 3' ends of microsatellites, at high primer annealing temperatures. This technique has already been used in studies of genetic variability of several organisms, using different primer designs. In order to conduct a detailed study of the SSR-PCR genomic targets, we cloned and sequenced 20 unique amplification products of two commonly used primers, CAA(CT6 and (CA8RY, using Biomphalaria glabrata genomic DNA as template. The sequences obtained were novel B. glabrata genomic sequences. It was observed that 15 clones contained microsatellites between priming sites. Out of 40 clones, seven contained complex sequence repetitions. One of the repeats that appeared in six of the amplified fragments generated a single band in Southern analysis, indicating that the sequence was not widespread in the genome. Most of the annealing sites for the CAA(CT6 primer contained only the six repeats found within the primer sequence. In conclusion, SSR-PCR is a useful genotyping technique. However, the premise of the SSR-PCR technique, verified with the CAA(CT6 primer, could not be supported since the amplification products did not result necessarily from microsatellite loci amplification.

  6. 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

  7. Analysis of numerical stability and amplification matrices: Fourth-order Runge-Kutta methods

    Science.gov (United States)

    Kennedy, E. W.

    1979-01-01

    Amplification matrices, numerical kernels, stable, and exponentially stable numerical solutions are examined. The various techniques involved in these concepts are applied to certain systems that have Jordan forms, which are nondiagonal, with particular interest in the case of imaginary or zero eigenvalues.

  8. 应用多重连接依赖性探针扩增技术快速诊断遗传性压力敏感性周围神经病%Rapid diagnosis of hereditary neuropathy with liability to pressure palsies by multiplex ligation-dependent probe amplification

    Institute of Scientific and Technical Information of China (English)

    陈万金; 王丹妮; 何瑾; 许柳青; 胡微; 王柠

    2015-01-01

    目的 介绍多重连接依赖性探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术在遗传性压力敏感性周围神经病(hereditary neuropathy with liability to pressure palsies,HNPP)患者基因诊断中的应用.方法 应用MLPA技术检测8例临床拟诊为HNPP患者及5名健康对照者的周围髓鞘蛋白22(peripheral myelin protein 22,PMP22)基因、筑丝蛋白3基因及细胞色素c氧化酶组装蛋白10(cytochrome c oxidase assembly protein 10,COX10)基因外显子拷贝数.结果 7例临床拟诊的HNPP患者所检测的PMP22基因、筑丝蛋白3基因及COX10基因各外显子峰面积较健康对照明显减低,各基因的拷贝数为1,提示为大片段杂合缺失;另1例临床拟诊的HNPP患者所检测的PMP22基因、筑丝蛋白3基因及COX10基因峰面积正常,各基因拷贝数为2,未发现杂合缺失.结论 MLPA技术能快速、准确地对HNPP患者的HNPP相关基因进行定量分析,可用于HNPP患者的快速基因诊断.%Objective To introduce the application of multiplex ligation-dependent probe amplification (MLPA) assays in the diagnosis of patients with hereditary neuropathy with liability to pressure palsies (HNPP).Methods Copy numbers of the exons in peripheral myelin prolein 22 (PMP22) gene,tektin 3 (TEKT3) gene and cytochrome c oxidase assembly protein 10 (COX10) gene were analyzed by MLPA in 8 patients diagnosed with HNPP clinically and 5 normal controls.Results Among the 8 patients,7 patients were identified to have deletion mutations according to their reduced peak area of PMP22 gene,TEKT3 gene and COX10 gene compared with that of normal controls.One patient with normal peak area of PMP22 gene,TEKT3 gene and COX10 gene showed no deletion of these genes.Conclusions MLPA assays can detect the copy numbers of genes in HNPP region through semi-quantitative analysis in a rapid,accurate way,which may be utilized widely in the genetic diagnosis among HNPP patients.

  9. 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.

  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. 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

  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. Regenerative amplification and bifurcations in a burst-mode Nd:YAG laser.

    Science.gov (United States)

    Mance, Jason G; Slipchenko, Mikhail N; Roy, Sukesh

    2015-11-01

    An Nd:YAG-based burst-mode regenerative amplifier laser was developed that offers high extraction efficiency at high repetition rates with low seed energies. The regenerative amplification technique, combined with the burst-mode laser technology, shows promise as an efficient method for amplification of femtojoule-nanojoule pulses up to millijoule energies at repetition rates exceeding 100 kHz. Output energies at repetition rates near the inverse upper state lifetime are limited by bifurcations in the pulse energies of the burst. A model is developed and advantages and limitations are discussed.

  15. 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...

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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

  3. Use of RAPD and PCR double amplification in the study of ancient DNA

    Directory of Open Access Journals (Sweden)

    F. Balzano

    2011-01-01

    Full Text Available This project analysed the DNA extracted from bones of ancient sheep which have been brought to light in Sardinian different archaeological sites. In order to better analyse this highly fragmented DNA, a double amplification technique was chosen. The first approach consisted of RAPD-PCR abd the second one in classic PCR. The RAPD-PCR amplified random fragments and allowed the production of numerous amplicons. The products of RAPD amplification have been amplified, more specifically, by the second PCR using primers for a sequence of 176 bp of mitochondrial D-loop region. These DNA fragments have been sequenced and the sequence analysis has confirmed that it belonged to Ovis aries. Consequently, this provedure can be considered a valid tool to perform amplification of degraded DNA, such as ancient DNA.

  4. Towards rapid genotyping of resistant malaria parasites: could loop-mediated isothermal amplification be the solution?

    OpenAIRE

    Abdul-Ghani, Rashad

    2014-01-01

    Loop-mediated isothermal amplification (LAMP) is an innovative molecular technique that has been validated for point-of-care testing to diagnose malaria. Molecular detection and tracking of anti-malarial drug resistance is mainly based on highly sophisticated, costly and time-consuming techniques. With the validation of resistance-associated gene mutations in malaria parasites, there is a need to develop rapid, easy-to-use molecular tests for anti-malarial drug resistance genotyping. LAMP cou...

  5. Combinaison de faisceaux mutuellement incohérents par amplification paramétrique optique

    OpenAIRE

    Tropheme, Benoit,

    2012-01-01

    This work deals with a technique of combination of coherent beams: Optical Parametric Amplification (OPA) with Multiple Pumps. This technique is used to instantly transfer the energy of several pumps on one beam, without energy storage and thus avoiding thermal effects in the amplifying media. It can be useful to combine energy of numerous fiber lasers and to amplifiy with a high repetition rate very high energy lasers or broadband pulses. With a numerical and experimental study using BBO and...

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing

    Directory of Open Access Journals (Sweden)

    Plant Ramona N

    2006-08-01

    Full Text Available Abstract Background Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs or large scale (CGH array, FISH methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. Results All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Conclusion Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.

  12. Genealogy analysis of duchenne muscular dystrophy by multiplex ligation-dependent probe amplification and sequencing technology%MLPA及测序技术在DMD/BMD家系分析中的应用

    Institute of Scientific and Technical Information of China (English)

    古艳; 谢建生; 都莉; 韩春锡; 万琼

    2012-01-01

    Objective To analyze the DMD genealogy by MLPA technique in combine with DNA and cDNA sequencing technology. Methods There were 31 individuals accepted DMD gene diagnosis,including 6 DMD/BMD patients, 13 possible carriers and 6 healthy men in 2 DMD/BMD families,moreover 6 healthy women and men were selected from health examination people. Genomic DNA of the peripheral blood was extracted from the pedigrees' members with DMD. RNA was extracted from the bioptic muscle of the DMD patients and was reversed transcription to cDNA. Gene diagnosis was performed for theses pedigrees members using MLPA technique,the mutation was analyzed applying with DNA and/or cDNA sequence technique. Simultaneously,compare the effects of these methods on detecting DMD gene deletion. Results 4 patients of the first DMD family was deleted exon50,and the fetus was confirmed no DMD exons deletion. 2 patients were found deletion exon43 in the second family. MLPA analysis、DNA and cDNA sequencing technology showed the same result. Conclusion MLPA in company with DNA and cDNA sequencing technology could applied into clinical gene diagnosis for DMD.%目的 运用MLPA技术和DNA及cDNA测序技术对DMD/BMD进行家系分析,对患者、可能携带者基因诊断并探讨诊断流程的临床可行性.方法 对2个DMD/BMD家系中6例患者、13例女性可能携带者、6例男性家系成员,6例女性和男性健康对照共31例采集外周血提取DNA,运用MLPA技术分析对以上31例的DMD基因79个外显子;患者取右侧腓肠肌10~30 mg肌肉提取RNA,逆转录cDNA;分别进行DNA及cDNA序列测定,测序结果与MLPA结果进行比较.结果 经MLPA检测,家系1的4例患者均缺失DMD基因Exon50,家系2中2例患者均缺失Exon43.以上结果经肌肉cDNA测序证实了相应外显子缺失.结论 MLPA技术结合DNA及cDNA测序技术进行DMD家系分析具有可靠的临床应用价值.

  13. 多重探针连接依赖式扩增快速检测染色体非整倍体异常%Rapid detection of chromosomal aneuploidies by multiplex ligation-dependent probe amplification

    Institute of Scientific and Technical Information of China (English)

    范新萍; 王立荣; 肖白; 刘敬忠; 高淑英; 张璘; 张颖; 顾莹

    2008-01-01

    Objective To test whether multiplex ligation-dependent probe amplification(MLPA)could be used for the prenatal detection of the most common aneuploidies of chromosomes 13,18,21,X,and Y.Methods 34 cases including 22 blood samples(12 with trisomy 21,1 with monosomy X,one male witll extra Y and 8 healthy persons),4 cord blood samples with Down syndrome and 8 amniotic fluid samples ( 1 with trisomy 21 and 7 normal fetuses)were recruited into this study.All samples were confirmed by karvotype analysis. DNA was extracted from blood and amniotic lysate was incubated with proteinase K.MLPA was used to determine the relative copy numbers.Results The resuhs were available within 48 h and were concordant with karyotype analysis in all but one case of amniotic fluid that was suggested to be triploid sample 69,XXY by MLPA or contaminated by maternal blood.This sample actually was found containing a number of red blood cells after centfifugation in test. In total,the concordance rate with clinical characteristics was 97.1%.The Ratio values of 13,18,21,X in normal samples were approaching 1.0 except chromosome Y having slightly higher variation in relative copy number.The difference of ratio means between the normal and trisomy 21 samples was statistically significant by one-way ANOVA(F=298.906.P=0.000).Conclusion Computer assisted MLPA with high sensitivity is a rapid,simple,automatic and reliable method for detection of common chromosomal aneuploidies.%目的 评价多重探针连接依赖式扩增(muhiplex ligation-dependent probe amplification,MLPA)在常见染色体非整倍体异常及其在产前诊断中的应用价值.方法 收集经染色体核型分析证实的12例21三体、1例(45,X)、1例(47,XYY)患者,8名正常健康人外周血标本和4例21三体胎儿脐带血标本及1例21三体胎儿羊水、7例核型正常胎儿羊水,共计34份样本.提取外周血或脐带血基因组DNA,羊水标本蛋白酶K消化获得细胞裂解液,采用MLPA技术检测34

  14. 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

  15. Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification.

    Science.gov (United States)

    Speicher, M R; du Manoir, S; Schröck, E; Holtgreve-Grez, H; Schoell, B; Lengauer, C; Cremer, T; Ried, T

    1993-11-01

    We present a technique which allows the detection and chromosomal localization of DNA sequence copy number changes in solid tumor genomes from frozen sections and paraffin embedded, formalin fixed specimens. Based on comparative genomic hybridization and on universal DNA amplification procedures this technique is possible even if only a few tumor cells are available. We demonstrate the feasibility of this method to visualize complete and partial chromosome gains and losses and gene amplifications in archived solid tumor samples. PMID:8281155

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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...

  1. 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

  2. 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.

  3. Label-free and highly sensitive electrochemical detection of E. coli based on rolling circle amplifications coupled peroxidase-mimicking DNAzyme amplification.

    Science.gov (United States)

    Guo, Yuna; Wang, Yu; Liu, Su; Yu, Jinghua; Wang, Hongzhi; Wang, Yalin; Huang, Jiadong

    2016-01-15

    In this work, a simple, label-free, low cost electrochemical biosensor for highly sensitive and selective detection of Escherichia coli has been developed on the basis of rolling circle amplification (RCA) coupled peroxidase-mimicking DNAzyme amplification. A aptamer-primer probe (APP) containing anti-E. coli aptamer and a primer sequence complementary to a circular probe, which includes two G-quadruplex units, is used for recognizing target and triggering RCA-based polymerase elongation. Due to RCA coupled DNAzyme amplification strategy, the presence of target E. coli leads to the formation of numerous G-quadruplex oligomers on electrode, which folds into G-quadruplex/hemin complexs with the help of K(+) and hemin, thus generating extremely strong catalytic activity toward H2O2 and giving a remarkably strong electrochemical response. As far as we know, this work is the first time that RCA coupled peroxidase-mimicking DNAzyme amplification technique have been integrated into electrochemical assay for detecting pathogenic bacteria. Under optimal conditions, the proposed biosensor exhibits ultrahigh sensitivity toward E. coli with detection limits of 8cfumL(-1) and a detection range of 5 orders of magnitude. Besides, our biosensor also shows high selectivity toward target E. coli and has the advantages in its rapidness, low cost, simplified operations without the need of electrochemical labeling steps and additional labile reagents. Hence, the RCA coupled peroxidase-mimicking DNAzyme amplification-based electrochemical method might create a useful and practical platform for detecting E. coli and related food safety analysis and clinical diagnosis.

  4. Using DNS amplification DDoS attack for hiding data

    Science.gov (United States)

    Mehić, M.; Voznak, M.; Safarik, J.; Partila, P.; Mikulec, M.

    2014-05-01

    This paper concerns available steganographic techniques that can be used for sending hidden data through public network. Typically, in steganographic communication it is advised to use popular/often used method for sending hidden data and amount of that data need to be high as much as possible. We confirmed this by choosing a Domain Name System (DNS) as a vital protocol of each network and choosing Distributed denial of service (DDoS) attacks that are most popular network attacks currently represented in the world. Apart from characterizing existing steganographic methods we provide new insights by presenting two new techniques. The first one is network steganography solution which exploits free/unused protocols fields and is known for IP, UDP or TCP protocols, but has never been applied to DNS (Domain Name Server) which are the fundamental part of network communications. The second explains the usage of DNS Amplification DDoS Attack to send seamlessly data through public network. The calculation that was performed to estimate the total amount of data that can be covertly transferred by using these technique, regardless of steganalysis, is included in this paper.

  5. SBS mitigation with 'two-tone' amplification: a theoretical model

    Science.gov (United States)

    Bronder, T. J.; Shay, T. M.; Dajani, I.; Gavrielides, A.; Robin, C. A.; Lu, C. A.

    2008-02-01

    A new technique for mitigating stimulated Brillouin scattering (SBS) effects in narrow-linewidth Yb-doped fiber amplifiers is demonstrated with a model that reduces to solving an 8×8 system of coupled nonlinear equations with the gain, SBS, and four-wave mixing (FMW) incorporated into the model. This technique uses two seed signals, or 'two-tones', with each tone reaching its SBS threshold almost independently and thus increasing the overall threshold for SBS in the fiber amplifier. The wavelength separation of these signals is also selected to avoid FWM, which in this case possesses the next lowest nonlinear effects threshold. This model predicts an output power increase of 86% (at SBS threshold with no signs of FWM) for a 'two-tone' amplifier with seed signals at 1064nm and 1068nm, compared to a conventional fiber amplifier with a single 1064nm seed. The model is also used to simulate an SBS-suppressing fiber amplifier to test the regime where FWM is the limiting factor. In this case, an optimum wavelength separation of 3nm to 10nm prevents FWM from reaching threshold. The optimum ratio of the input power for the two seed signals in 'two-tone' amplification is also tested. Future experimental verification of this 'two-tone' technique is discussed.

  6. 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

  7. 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.

  8. Real-time DNA Amplification and Detection System Based on a CMOS Image Sensor.

    Science.gov (United States)

    Wang, Tiantian; Devadhasan, Jasmine Pramila; Lee, Do Young; Kim, Sanghyo

    2016-01-01

    In the present study, we developed a polypropylene well-integrated complementary metal oxide semiconductor (CMOS) platform to perform the loop mediated isothermal amplification (LAMP) technique for real-time DNA amplification and detection simultaneously. An amplification-coupled detection system directly measures the photon number changes based on the generation of magnesium pyrophosphate and color changes. The photon number decreases during the amplification process. The CMOS image sensor observes the photons and converts into digital units with the aid of an analog-to-digital converter (ADC). In addition, UV-spectral studies, optical color intensity detection, pH analysis, and electrophoresis detection were carried out to prove the efficiency of the CMOS sensor based the LAMP system. Moreover, Clostridium perfringens was utilized as proof-of-concept detection for the new system. We anticipate that this CMOS image sensor-based LAMP method will enable the creation of cost-effective, label-free, optical, real-time and portable molecular diagnostic devices. PMID:27302586

  9. The role of DNA amplification and cultural growth in complicated acute appendicitis

    Directory of Open Access Journals (Sweden)

    Francesca Tocchioni

    2016-09-01

    Full Text Available Bacterial growth of peritoneal fluid specimens obtained during surgical procedures for acute appendicitis may be useful to optimize further antibiotic therapy in complicated cases. DNA amplification represents a fast technique to detect microbial sequences. We aimed to compare the potential of DNA amplification versus traditional bacterial growth culture highlighting advantages and drawbacks in a surgical setting. Peritoneal fluid specimens were collected during surgery from 36 children who underwent appendectomy between May and December 2012. Real-time polymerase chain reaction (RT-PCR and cultures were performed on each sample. RT-PCR showed an amplification of 16S in 18/36 samples, Escherichia coli (in 7 cases, Pseudomonas aeruginosa (3, Fusobacterium necrophorum (3, Adenovirus (2, E.coli (1, Klebsiella pneumoniae (1, Serratia marcescens/Enterobacter cloacae (1. Bacterial growth was instead observed only in four patients (3 E.coli and 1 P.aeruginosa and Bacteroides ovatus. Preoperative C-reactive protein and inflammation degree, the most reliable indicators of bacterial translocation, were elevated as expected. DNA amplification was a quick and useful method to detect pathogens and it was even more valuable in detecting aggressive pathogens such as anaerobes, difficult to preserve in biological cultures; its drawbacks were the lack of biological growths and of antibiograms. In our pilot study RT-PCR and cultures did not influence the way patients were treated.

  10. 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

  11. Compensation of high-order phase distortions in chirped-pulse amplification system

    Science.gov (United States)

    Zhou, Bing; Jiang, Yong-Liang; Leng, Yu-xin; Chen, Xiao-Wei; Li, Ru-Xin; Xu, Zhi-Zhan

    2007-01-01

    Chirped-pulse amplification (CPA) technique has been widely used to generate ultra-intense femto-second pulses. In this scheme the seed pulses from an oscillator are stretched before amplification. The stretched pulses can support more energy extraction and effectively decrease the nonlinear effects in the gain media. The subsequent amplification in a CPA chain will result in a broadening of the output compressed pulses in temporal domain due to the gain narrowing and uncompensated phase distortions. In our experiment, using spectral modulation and phase pre-compensation system (Acoustic-Optics Programmable Dispersive Filter) between the oscillator and the stretcher, the effects of gain narrowing and high-order dispersions on the pulse duration in kHz chirped-pulse amplification system have been pre-compensated, and the spectral FWHM is expanded from 30nm to 50nm. The effects of GDD, TOD and FOD were investigated by scanning the four dispersion parameters respectively. By pre-compensating the high-order phase distortions with the phase measured by SPIDER, we successfully optimize the output duration from 51fs to 30fs, which is 1.07 times Fourier-transform-limitation.

  12. The Role of DNA Amplification and Cultural Growth in Complicated Acute Appendicitis

    Science.gov (United States)

    Tocchioni, Francesca; Tani, Chiara; Bartolini, Laura; Moriondo, Maria; Nieddu, Francesco; Pecile, Patrizia; Azzari, Chiara; Messineo, Antonio; Ghionzoli, Marco

    2016-01-01

    Bacterial growth of peritoneal fluid specimens obtained during surgical procedures for acute appendicitis may be useful to optimize further antibiotic therapy in complicated cases. DNA amplification represents a fast technique to detect microbial sequences. We aimed to compare the potential of DNA amplification versus traditional bacterial growth culture highlighting advantages and drawbacks in a surgical setting. Peritoneal fluid specimens were collected during surgery from 36 children who underwent appendectomy between May and December 2012. Real-time polymerase chain reaction (RT-PCR) and cultures were performed on each sample. RT-PCR showed an amplification of 16S in 18/36 samples, Escherichia coli (in 7 cases), Pseudomonas aeruginosa (3), Fusobacterium necrophorum (3), Adenovirus (2), E.coli (1), Klebsiella pneumoniae (1), Serratia marcescens/Enterobacter cloacae (1). Bacterial growth was instead observed only in four patients (3 E.coli and 1 P.aeruginosa and Bacteroides ovatus). Preoperative C-reactive protein and inflammation degree, the most reliable indicators of bacterial translocation, were elevated as expected. DNA amplification was a quick and useful method to detect pathogens and it was even more valuable in detecting aggressive pathogens such as anaerobes, difficult to preserve in biological cultures; its drawbacks were the lack of biological growths and of antibiograms. In our pilot study RT-PCR and cultures did not influence the way patients were treated. PMID:27777701

  13. Label-free detection of real-time DNA amplification using a nanofluidic diffraction grating

    Science.gov (United States)

    Yasui, Takao; Ogawa, Kensuke; Kaji, Noritada; Nilsson, Mats; Ajiri, Taiga; Tokeshi, Manabu; Horiike, Yasuhiro; Baba, Yoshinobu

    2016-08-01

    Quantitative DNA amplification using fluorescence labeling has played an important role in the recent, rapid progress of basic medical and molecular biological research. Here we report a label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Our detection system observed intensity changes during DNA amplification of diffracted light derived from the passage of a laser beam through nanochannels embedded in a microchannel. Numerical simulations revealed that the diffracted light intensity change in the nanofluidic diffraction grating was attributed to the change of refractive index. We showed the first case reported to date for label-free detection of real-time DNA amplification, such as specific DNA sequences from tubercle bacilli (TB) and human papillomavirus (HPV). Since our developed system allows quantification of the initial concentration of amplified DNA molecules ranging from 1 fM to 1 pM, we expect that it will offer a new strategy for developing fundamental techniques of medical applications.

  14. Single Cell Analysis of Dystrophin and SRY Gene by Using Whole Genome Amplification

    Institute of Scientific and Technical Information of China (English)

    徐晨明; 金帆; 黄荷凤; 陶冶; 叶英辉

    2001-01-01

    Objective To develop a reliable and sensitive method for detection of sex and multiloci of Duchenne muscular dystrophy (DMD) gene in single cell Materials & methods Whole genome of single cell were amplified by using 15-base random primers (primer extension preamplification, PEP), then a small aliquot of PEP product were analyzed by using locus-specific nest PCR amplification. The procedure was evaluated by detection dystrophin exons 8, 17, 19, 44, 45, 48 and human testis-determining gene (SRY)in single lymphocytes from known sources and single blastomeres from the couples with no family history of DMD.Results The amplification efficiency rate of six dystrophin exons from single lymphocytes and single blastomeres were 97. 2% (175/180) and 100% (60/60) respectively.Results of SRY showed that 100% (15/15) amplification in single male-derived lymphocytes and 0% (0/15) amplification in single female-derived lymphocytes. Conclusion The technique of single cell PEP-nest PCR for dystrophin exons 8, 17,19, 44, 45, 48 and SRY is highly specifc. PEP-nest PCR is suitable for Preimplantation genetic diagnosis (PGD) of DMD at single cell level.

  15. A Novel Cyclic Time to Digital Converter Based on Triple-Slope Interpolation and Time Amplification

    OpenAIRE

    M. Rezvanyvardom; E. Farshidi

    2015-01-01

    This paper investigates a novel cyclic time-to-digital converter (TDC) which employs triple-slope analog interpolation and time amplification techniques for digitizing the time interval between the rising edges of two input signals(Start and Stop). The proposed converter will be a 9-bit cyclic time-to-digital converter that does not use delay lines in its structure. Therefore, it has a low sensitivity to temperature, power supply and process (PVT) variations. The other advantages of the propo...

  16. The detection of Plasmodiophora brassicae using loop-mediated isothermal DNA amplification

    OpenAIRE

    Joanna Kaczmarek; Witold Irzykowski; Adam Burzyński; Małgorzata Jędryczka

    2014-01-01

    Plasmodiophora brassicae, the cause of clubroot, is a very serious problem preventing from successful and profitable cultivation of oilseed rape in Poland. The pathogen was found in all main growing areas of oilseed rape; it also causes considerable problems in growing of vegetable brassicas. The aim of this work was to elaborate fast, cheap and reliable screening method to detect P. brassicae. To achieve this aim the Loop-mediated isothermal DNA amplification (LAMP) technique has been elabor...

  17. Performance scaling via passive pulse shaping in cavity-enhanced optical parametric chirped-pulse amplification.

    Science.gov (United States)

    Siddiqui, Aleem M; Moses, Jeffrey; Hong, Kyung-Han; Lai, Chien-Jen; Kärtner, Franz X

    2010-06-15

    We show that an enhancement cavity seeded at the full repetition rate of the pump laser can automatically reshape small-signal gain across the interacting pulses in an optical parametric chirped-pulse amplifier for close-to-optimal operation, significantly increasing both the gain bandwidth and the conversion efficiency, in addition to boosting gain for high-repetition-rate amplification. Applied to a degenerate amplifier, the technique can provide an octave-spanning gain bandwidth.

  18. 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.

  19. 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...

  20. 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...

  1. Recombinase polymerase amplification as a promising tool in hepatitis C virus diagnosis

    Institute of Scientific and Technical Information of China (English)

    Hosam; Zaghloul; Mahmoud; El-shahat

    2014-01-01

    Hepatitis C virus(HCV)infection represents a significant health problem and represents a heavy load on some countries like Egypt in which about 20%of the total population are infected.Initial infection is usually asymptomatic and result in chronic hepatitis that give rise to complications including cirrhosis and hepatocellular carcinoma.The management of HCV infection should not only be focus on therapy,but also to screen carrier individuals in order to prevent transmission.In the present,molecular detection and quantification of HCV genome by real time polymerase chain reaction(PCR)represent the gold standard in HCV diagnosis and plays a crucial role in the management of therapeutic regimens.However,real time PCR is a complicated approach and of limited distribution.On the other hand,isothermal DNA amplification techniques have been developed and offer molecular diagnosis of infectious dieses at point-of-care.In this review we discuss recombinase polymerase amplification technique and illustrate its diagnostic value over both PCR and other isothermal amplification techniques.

  2. 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.

  3. 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.

  4. 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 ...

  5. 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.

  6. A new ultrasonic signal amplification method for detection of bacteria

    International Nuclear Information System (INIS)

    A new method is presented that increases the sensitivity of ultrasound-based techniques for detection of bacteria. The technique was developed for the detection of catalase-positive microorganisms. It uses a bubble trapping medium containing hydrogen peroxide that is mixed with the sample for microbiological evaluation. The enzyme catalase is present in catalase-positive bacteria, which induces a rapid hydrolysis of hydrogen peroxide, forming bubbles which remain in the medium. This reaction results in the amplification of the mechanical changes that the microorganisms produce in the medium. The effect can be detected by means of ultrasonic wave amplitude continuous measurement since the bubbles increase the ultrasonic attenuation significantly. It is shown that microorganism concentrations of the order of 105 cells ml−1 can be detected using this method. This allows an improvement of three orders of magnitude in the ultrasonic detection threshold of microorganisms in conventional culture media, and is competitive with modern rapid microbiological methods. It can also be used for the characterization of the enzymatic activity. (paper)

  7. 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...

  8. 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.

  9. 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.

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells.

    Science.gov (United States)

    Deng, Ruijie; Tang, Longhua; Tian, Qianqian; Wang, Ying; Lin, Lei; Li, Jinghong

    2014-02-24

    The ability to quantitate and visualize microRNAs (miRNAs) in situ in single cells would greatly facilitate the elucidation of miRNA-mediated regulatory circuits and their disease associations. A toehold-initiated strand-displacement process was used to initiate rolling circle amplification of specific miRNAs, an approach that achieves both stringent recognition and in situ amplification of the target miRNA. This assay, termed toehold-initiated rolling circle amplification (TIRCA), can be utilized to identify miRNAs at physiological temperature with high specificity and to visualize individual miRNAs in situ in single cells within 3 h. TIRCA is a competitive candidate technique for in situ miRNA imaging and may help us to understand the role of miRNAs in cellular processes and human diseases in more detail.

  18. Bioagent detection using miniaturized NMR and nanoparticle amplification : final LDRD report.

    Energy Technology Data Exchange (ETDEWEB)

    Clewett, C. F. M.; Adams, David Price; Fan, Hongyou; Williams, John D.; Sillerud, Laurel O.; Alam, Todd Michael; Aldophi, Natalie L. (New Mexico Resonance, Albuquerque, NM); McDowell, Andrew F. (New Mexico Resonance, Albuquerque, NM)

    2006-11-01

    This LDRD program was directed towards the development of a portable micro-nuclear magnetic resonance ({micro}-NMR) spectrometer for the detection of bioagents via induced amplification of solvent relaxation based on superparamagnetic nanoparticles. The first component of this research was the fabrication and testing of two different micro-coil ({micro}-coil) platforms: namely a planar spiral NMR {micro}-coil and a cylindrical solenoid NMR {micro}-coil. These fabrication techniques are described along with the testing of the NMR performance for the individual coils. The NMR relaxivity for a series of water soluble FeMn oxide nanoparticles was also determined to explore the influence of the nanoparticle size on the observed NMR relaxation properties. In addition, The use of commercially produced superparamagnetic iron oxide nanoparticles (SPIONs) for amplification via NMR based relaxation mechanisms was also demonstrated, with the lower detection limit in number of SPIONs per nanoliter (nL) being determined.

  19. Initial amplification of the HPV18 genome proceeds via two distinct replication mechanisms

    Science.gov (United States)

    Orav, Marit; Geimanen, Jelizaveta; Sepp, Eva-Maria; Henno, Liisi; Ustav, Ene; Ustav, Mart

    2015-01-01

    Determining the mechanism of HPV18 replication is paramount for identifying possible drug targets against HPV infection. We used two-dimensional and three-dimensional gel electrophoresis techniques to identify replication intermediates arising during the initial amplification of HPV18 episomal genomes. We determined that the first rounds of HPV18 replication proceed via bidirectional theta structures; however, a notable accumulation of almost fully replicated HPV18 genomes indicates difficulties with the completion of theta replication. We also observed intermediates that were created by a second replication mechanism during the initial amplification of HPV18 genomes. The second replication mechanism does not utilize specific initiation or termination sequences and proceeds via a unidirectional replication fork. We suggest a significant role for the second replication mechanism during the initial replication of the HPV18 genome and propose that the second replication mechanism is recombination-dependent replication. PMID:26522968

  20. Initial amplification of the HPV18 genome proceeds via two distinct replication mechanisms.

    Science.gov (United States)

    Orav, Marit; Geimanen, Jelizaveta; Sepp, Eva-Maria; Henno, Liisi; Ustav, Ene; Ustav, Mart

    2015-01-01

    Determining the mechanism of HPV18 replication is paramount for identifying possible drug targets against HPV infection. We used two-dimensional and three-dimensional gel electrophoresis techniques to identify replication intermediates arising during the initial amplification of HPV18 episomal genomes. We determined that the first rounds of HPV18 replication proceed via bidirectional theta structures; however, a notable accumulation of almost fully replicated HPV18 genomes indicates difficulties with the completion of theta replication. We also observed intermediates that were created by a second replication mechanism during the initial amplification of HPV18 genomes. The second replication mechanism does not utilize specific initiation or termination sequences and proceeds via a unidirectional replication fork. We suggest a significant role for the second replication mechanism during the initial replication of the HPV18 genome and propose that the second replication mechanism is recombination-dependent replication. PMID:26522968

  1. FLUORESCENCE IN SITU HYBRIDIZATION COMBINED WITH IMMUNOFLUORESCENT STAINING FOR RAPID DETECTION OF Nmyc AMPLIFICATION IN NEUROBLASTOMA

    Institute of Scientific and Technical Information of China (English)

    WANG Wei王伟; Marianne Ifversen; ZHAO Chun-ting赵春亭; WANG Hong-yi汪洪毅; ZHAO Hong-guo赵洪国

    2004-01-01

    Objective: To establish a method to improve the detection of disseminated tumor cells in bone marrow and peripheral blood samples of neuroblastoma patients and analysis of cytogenetic aberration. Methods: Immunofluorescent staining was performed using a cocktail of primary monoclonal neuroblastoma antibodies (14.G2a, 5.1H11). Fluorescence in situ hybridization was applied with fluorescent probes specific for Nmyc genes afterwards. A novel computer assisted scanning system for automatic search, image analysis and repositioning of these positive cells was developed. Fifty-six bone marrow and peripheral blood samples from 7 patients were evaluated by this method. Results: Fluorescence in situ hybridization can be combined with immunofluorescent staining in detecting Nmyc amplification in neuroblastoma patients. Fluorescence in situ hybridization results correlated well with data obtained by conventional cytogenetic procedures. Conclusion: The technique described allows search of tumor cells in the bone marrow as well as detection of Nmyc amplification in interphase nuclei.

  2. Rapid amplification of genetically modified organisms using a circular ferrofluid-driven PCR microchip.

    Science.gov (United States)

    Sun, Yi; Kwok, Yien-Chian; Foo-Peng Lee, Peter; Nguyen, Nam-Trung

    2009-07-01

    The use of genetically modified organisms (GMOs) as food and in food products is becoming more and more widespread. Polymerase chain reaction (PCR) technology is extensively used for the detection of GMOs in food products in order to verify compliance with labeling requirements. In this paper, we present a novel close-loop ferrofluid-driven PCR microchip for rapid amplification of GMOs. The microchip was fabricated in polymethyl methacrylate by CO2 laser ablation and was integrated with three temperature zones. PCR solution was contained in a circular closed microchannel and was driven by magnetic force generated by an external magnet through a small oil-based ferrofluid plug. Successful amplification of genetically modified soya and maize were achieved in less than 13 min. This PCR microchip combines advantages of cycling flexibility and quick temperature transitions associated with two existing microchip PCR techniques, and it provides a cost saving and less time-consuming way to conduct preliminary screening of GMOs.

  3. 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.

  4. 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

  5. Vorticity amplification near the stagnation point of landing gear wheels

    Science.gov (United States)

    Feltham, G.; Ekmekci, A.

    2014-04-01

    The vicinity near the forward stagnation point of landing-gear wheels has been found to support a mechanism for oncoming streams of weak vorticity to collect, grow, and amplify into discrete large-scale vortical structures that then shed with a distinct periodicity. To the authors' knowledge, such a flow phenomenon has never been reported before for landing gear wheels, which are in essence finite (three-dimensional) cylinders. To gain further insight into this phenomenon, a detailed experimental study has been undertaken employing the hydrogen bubble visualization and Particle Image Velocimetry techniques. A very thin platinum wire, similar to those used in hydrogen bubble visualization applications, was placed upstream of the wheel model to produce two streams of weak vorticity (with opposite sign) that convected toward the model. As the vorticity streams enter the stagnation region of the wheels, significant flow deceleration and vorticity stretching act to collect, grow, and amplify the incoming vorticity streams into large-scale vortical structures. Experiments were performed at a fixed Reynolds number, with a value of 32 500 when defined based on the diameter of the wheel and a value of 21 based on the diameter of the vorticity-generating upstream wire. First, to establish a baseline, the natural flow field (without the presence of an upstream wire) was characterized, where experimentally determined values for the stagnation boundary-layer thickness and the velocity profile along the stagnation streamline were both found to agree with the values provided in the literature for two-dimensional cylinders. Subsequently, the dynamics of vorticity collection, growth, amplification, and shedding were studied. The size, stand-off distance and the shedding frequency of the vortical structures forming near the stagnation region were all found to strongly depend on the impingement location of the inbound vorticity on the wheel. A simple relationship between the non

  6. 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.

  7. 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

  8. 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.

  9. 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...

  10. 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.

  11. Detection of genetically modified organisms (GMOs using isothermal amplification of target DNA sequences

    Directory of Open Access Journals (Sweden)

    La Mura Maurizio

    2009-02-01

    Full Text Available Abstract Background The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR. Here we have applied the loop-mediated isothermal amplification (LAMP method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene junctions. Results We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. Conclusion This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

  12. High concentration Yb-Er co-doped phosphate glass for optical fiber amplification

    International Nuclear Information System (INIS)

    We present the fabrication and characterization of two high concentration Yb3+-Er3+ co-doped double clad phosphate glass optical fibers (named A and B for short) manufactured by preform drawing, with the preform being obtained by the rod-in-tube technique. Optical amplification was demonstrated by core pumping 27 mm of fiber A (7/25/70 μm and NA = 0.17 between core and inner cladding) with a laser diode at 976 nm, achieving a 10.7 dB internal gain, i.e., 4.0 dB cm−1, for small signal input at 1535 nm. Amplification was also demonstrated in a cladding-pumped counter propagating configuration using both fibers A and B (12/48/140 μm and NA = 0.08). A maximum internal gain of 18.5 dB was achieved with 8 cm of fiber B, corresponding to an amplification of 2.3 dB cm−1, for small signal input at 1535 nm. (paper)

  13. Rapid detection of Bacillus anthracis by γ phage amplification and lateral flow immunochromatography.

    Science.gov (United States)

    Cox, Christopher R; Jensen, Kirk R; Mondesire, Roy R; Voorhees, Kent J

    2015-11-01

    New, rapid point-of-need diagnostic methods for Bacillus anthracis detection can enhance civil and military responses to accidental or deliberate dispersal of anthrax as a biological weapon. Current laboratory-based methods for clinical identification of B. anthracis require 12 to 120h, and are confirmed by plaque assay using the well-characterized γ typing phage, which requires an additional minimum of 24h for bacterial culture. To reduce testing time, the natural specificity of γ phage amplification was investigated in combination with lateral flow immunochromatography (LFI) for rapid, point-of-need B. anthracis detection. Phage-based LFI detection of B. anthracis Sterne was validated over a range of bacterial and phage concentrations with optimal detection achieved in as little as 2h from the onset of amplification with a threshold sensitivity of 2.5×10(4)cfu/mL. The novel use of γ phage amplification detected with a simple, inexpensive LFI assay provides a rapid, sensitive, highly accurate, and field-deployable method for diagnostic ID of B. anthracis in a fraction of the time required by conventional techniques, and without the need for extensive laboratory culture. PMID:26310605

  14. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.

    Science.gov (United States)

    Xu, Wentao; Wang, Chenguang; Zhu, Pengyu; Guo, Tianxiao; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo

    2016-04-21

    Techniques of isothermal amplification have recently made great strides, and have generated significant interest in the field of point-of-care detection. Nicking endonuclease-mediated isothermal amplification (NEMA) is an example of simple isothermal technology. In this paper, a real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) of improved specificity and sensitivity is described. First, we optimized the prohibition of de novo synthesis by choosing Nt·BstNBI endonuclease. Second, the whole genome was successfully amplified with Nt·BstNBI (6 U), betaine (1 M) and trehalose (60 mM) for the first time. Third, we achieved 10 pg sensitivity for the first time after adding a small molecular beacon that spontaneously undergoes a conformational change when hybridizing to target, and the practical test validated the assay's application. The small molecular beacon has a similar melting temperature to the reaction temperature, but is approximately 10 bp shorter than the length of a traditional molecular beacon. A new threshold regulation was also established for isothermal conditions. Finally, we established a thermodynamic model for designing small molecular beacons. This multistate model is more correct than the traditional algorithm. This theoretical and practical basis will help us to monitor SMB-NEMA in a quantitative way. In summary, our SMB-NEMA method allows the simple, specific and sensitive assessment of isothermal DNA quantification. PMID:27027375

  15. 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)....

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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, ...

  1. 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...

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. 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....

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.

    Directory of Open Access Journals (Sweden)

    Harish Bokkasam

    Full Text Available Molecular communication systems encounter similar constraints as telecommunications. In either case, channel crosstalk at the receiver end will result in information loss that statistical analysis cannot compensate. This is because in any communication channel there is a physical limit to the amount of information that can be transmitted. We present a novel and simple modified end amplification (MEA technique to generate reduced and defined amounts of specific information in form of short fragments from an oligonucleotide source that also contains unrelated and redundant information. Our method can be a valuable tool to investigate information overflow and channel capacity in biomolecular recognition systems.

  14. 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...

  15. 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.

  16. Nonlinear temporal pulse cleaning techniques and application

    Institute of Scientific and Technical Information of China (English)

    Yi; Xu; Jianzhou; Wang; Yansui; Huang; Yanyan; Li; Xiaomin; Lu; Yuxin; Leng

    2013-01-01

    Two different pulse cleaning techniques for ultra-high contrast laser systems are comparably analysed in this work.The first pulse cleaning technique is based on noncollinear femtosecond optical-parametric amplification(NOPA)and second-harmonic generation(SHG)processes.The other is based on cross-polarized wave(XPW)generation.With a double chirped pulse amplifier(double-CPA)scheme,although temporal contrast enhancement in a high-intensity femtosecond Ti:sapphire chirped pulse amplification(CPA)laser system can be achieved based on both of the techniques,the two different pulse cleaning techniques still have their own advantages and are suitable for different contrast enhancement requirements of different laser systems.

  17. Detection of APC gene germline mutation in Chinese familial adenomatous polyposis by direct sequencing in combination with multiplex ligation-dependent probe amplification%直接测序联合多重连接依赖探针扩增法检测家族性腺瘤性息肉病APC基因胚系突变

    Institute of Scientific and Technical Information of China (English)

    金鹏; 崔伟佳; 盛剑秋; 付蕾; 安贺娟; 李爱琴; 张明智; 韩英; 李世荣

    2010-01-01

    目的 研究中国家族性腺瘤性息肉病(FAP)患者APC基因胚系突变的特点.方法 对来自北京、河北、河南、安徽、内蒙古、山西、福建等地区的14个FAP家系先证者用直接测序法进行APC基因突变检测,对突变检测阴性者应用多重连接依赖探针扩增(MLPA)技术进行APE基因大片段缺失检测.结果 14例先证者中9例(64.3%)检测出APC基因微小突变,其中移码突变6例,剪接区突变2例,无义突变1例;2例(14.3%)检测出APC基因大片段缺失,微小突变与大片段缺失的总检出率为78.6%.c.2336-2337insT、c.3923-3929delAAGAAAA、c.532-2A>T和c.4179-4180GAdelinsT等4个微小突变和外显子11、10A缺失、外显子15 start缺失等2个大片段缺失为首次报道.结论 中国FAP患者APC基因的胚系突变类型多样,以移码突变居多,突变位点以第15外显子居多;直接测序法联合MLPA法检测大片段缺失可提高APC基因突变的检出率.%Objective To investigate the characteristics of APC gene germline mutation in Chinese patients with familial adenomatous polyposis ( FAP). Methods The genomic DNA was extracted from peripheral venous blood drawn from probands of 14 Chinese FAP families from Beijing, Hebei, Henan,Anhui, Inner Mongolia, Shanxi and Fujian. The APC gene was amplified by PCR and underwent direct sequencing. Large fragment deletion was detected by multiplex ligation-dependent probe amplification (MLPA) only in micromutation-negative samples found by sequencing. Results APC gene micromutations were found in 9 probands and the mieromutation detection rate was 64. 3%, including 6 frameshift mutations, 2 splicing mutations and 1 nonsense mutation. Large fragment deletions of APC gene were detected in 2 probands ( 14. 3% ). The total mutation detection rate of micromutation and large fragment deletion was 78. 6%. Four novel micmromutations and 2 novel large fragment deletions were found, including c. 2336-2337insT, c. 3923-3929delAAGAAAA, c

  18. Detection of MYCN Gene Amplification in Neuroblastoma by Fluorescence In Situ Hybridization: A Pediatric Oncology Group Study

    Directory of Open Access Journals (Sweden)

    Prasad Mathew

    2001-01-01

    Full Text Available To assess the utility of fluorescence in situ hybridization (FISH for analysis of MYCN gene amplification in neuroblastoma, we compared this assay with Southern blot analysis using tumor specimens collected from 232 patients with presenting characteristics typical of this disease. The FISH technique identified MYCN amplification in 47 cases, compared with 39 by Southern blotting, thus increasing the total number of positive cases by 21%. The major cause of discordancy was a low fraction of tumor cells (≤30% replacement in clinical specimens, which prevented an accurate estimate of MYCN copy number by Southern blotting. With FISH, by contrast, it was possible to analyze multiple interphase nuclei of tumor cells, regardless of the proportion of normal peripheral blood, bone marrow, or stromal cells in clinical samples. Thus, FISH could be performed accurately with very small numbers of tumor cells from touch preparations of needle biopsies. Moreover, this procedure allowed us to discern the heterogeneous pattern of MYCN amplification that is characteristic of neuroblastoma. We conclude that FISH improves the detection of MYCN gene amplification in childhood neuroblastomas in a clinical setting, thus facilitating therapeutic decisions based on the presence or absence of this prognostically important biologic marker.

  19. 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

  20. A novel dendritic surfactant for enhanced microcystin-LR detection by double amplification in a quartz crystal microbalance biosensor.

    Science.gov (United States)

    Xia, Yuetong; Zhang, Jianping; Jiang, Long

    2011-08-01

    Enhanced sensitivity for the hepatotoxin microcystin-LR (MC-LR) was achieved in a quartz crystal microbalance (QCM) system via double amplification. For primary amplification, an innovative interface on the QCM was obtained as a matrix by the vesicle layer formed by our synthetic dendritic surfactant, bis (amidoethyl-carbamoylethyl) octadecylamine (C18N3). The vesicle matrix was then functionalised by an optimised concentration of monoclonal antibodies against MC-LR (anti-MC-LR) to detect the analyte. The results showed that a detection limit of 100 ng/mL was achieved by primary amplification. To achieve higher sensitivity, secondary amplification was implemented with anti-MC-LR gold nanoparticle (AuNPs) conjugates as probes, which lowered the detection limit for MC-LR to 1 ng/mL (the maximum concentration recommended by the World Health Organization [WHO] in drinking water for humans). The QCM immunosensor reported here has advantages such as high sensitivity, portability, simplicity, and cost-effectiveness for MC-LR detection. It would be uniquely superior compared with current MC-LR detection techniques for on-the-spot water detection. Furthermore, the methodology described here is also potentially significant in many fields for the routine monitoring of environmental and food safety.

  1. Amplification of 9q34 in childhood adrenocortical tumors: a specific feature unrelated to ethnic origin or living conditions

    Directory of Open Access Journals (Sweden)

    Figueiredo B.C.

    2000-01-01

    Full Text Available Adrenocortical tumors (ACT in children under 15 years of age exhibit some clinical and biological features distinct from ACT in adults. Cell proliferation, hypertrophy and cell death in adrenal cortex during the last months of gestation and the immediate postnatal period seem to be critical for the origin of ACT in children. Studies with large numbers of patients with childhood ACT have indicated a median age at diagnosis of about 4 years. In our institution, the median age was 3 years and 5 months, while the median age for first signs and symptoms was 2 years and 5 months (N = 72. Using the comparative genomic hybridization technique, we have reported a high frequency of 9q34 amplification in adenomas and carcinomas. This finding has been confirmed more recently by investigators in England. The lower socioeconomic status, the distinctive ethnic groups and all the regional differences in Southern Brazil in relation to patients in England indicate that these differences are not important to determine 9q34 amplification. Candidate amplified genes mapped to this locus are currently being investigated and Southern blot results obtained so far have discarded amplification of the abl oncogene. Amplification of 9q34 has not been found to be related to tumor size, staging, or malignant histopathological features, nor does it seem to be responsible for the higher incidence of ACT observed in Southern Brazil, but could be related to an ACT from embryonic origin.

  2. Developing Novel Interface and Signal Amplification Strategies for Study of Biological Interactions by Surface Plasmon Resonance(SPR) and SPRimaing

    OpenAIRE

    Liu, Ying

    2012-01-01

    Surface plasmon resonance (SPR) has been widely used as a powerful analytical technique for the study of a broad range of biomolecular interactions. With the capability of real-time detection, SPR allows convenient and nondestructive measurement of analyte concentration and binding kinetics. To improve the performance of SPR biosensing, we have developed a series of novel methods that lead to ultrasensitive detection via signal amplification by coupling inline atom transfer radical polymeriza...

  3. Mtp-40 and alpha antigen gene fragment amplification for the detection of Mycobacterium tuberculosis in Colombian clinical specimens

    OpenAIRE

    Alfonso Rosalba; Romero Rosa Elena; Patarroyo Manuel Elkin; Murillo Luis Angel

    2002-01-01

    In this study, the use of Mtp-40 and alpha antigen polymerase chain reaction (PCR) amplification fragments for the precise tuberculosis (TB) diagnosis was evaluated. One hundred and ninety two different samples were obtained from 113 patients with suspected TB. Mtp-40 and alpha antigen protein genes were amplified by the PCR technique and compared to both the "gold standard" (culture) test, as well as the clinical parameters (including a clinical record and X-ray film exam in 113 patients). T...

  4. 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...

  5. Molecular Technique to Understand Deep Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  6. 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

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Electrochemical etching amplification of low-let recoil particle tracks in polymers for fast neutron dosimetry

    International Nuclear Information System (INIS)

    An electrochemical etching method for the amplification of fast-neutron-induced recoil particle tracks in polymers was investigated. The technique gave superior results over those obtained by conventional etching methods especially when polycarbonate foils were used for recoil particle track amplification. Electrochemical etching systems capable of multi-foil processing were designed and constructed to demonstrate the feasibility of the techniques for large-scale neutron dosimetry. Electrochemical etching parameters were studied including the nature or type of the polymer foil used, foil thickness and its effect on etching time, the applied voltage and its frequency, the chemical composition, concentration, and temperature of the etchant, distance and angle between the electrodes, and the type of particles such as recoil particles including protons. Recoil particle track density, mean track diameter, and optical density as functions of the mentioned parameters were determined. Each parameter was found to have a distinct effect on the etching results in terms of the measured responses. Several new characteristics of this fast neutron dosimetry method were studied especially for personnel dosimetry using various radiation sources such as nuclear reactors, medical cyclotrons, and isotopic neutron sources. The dose range, neutron energy dependence, directional response, fading characteristics, neutron threshold energy, etc. were investigated

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. Novel degenerate PCR method for whole genome amplification applied to Peru Margin (ODP Leg 201 subsurface samples

    Directory of Open Access Journals (Sweden)

    Amanda eMartino

    2012-01-01

    Full Text Available A degenerate PCR-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. The method, which we have called Random Amplification Metagenomic PCR (RAMP, involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3’ end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10X. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin, and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa show that community analysis can be sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low biomass samples.

  9. Experimental amplification of an entangled photon: what if the detection loophole is ignored?

    CERN Document Server

    Pomarico, Enrico; Sekatski, Pavel; Zbinden, Hugo; Gisin, Nicolas

    2011-01-01

    The experimental verification of quantum features, such as entanglement, at large scales is extremely challenging because of environment-induced decoherence. Indeed, measurement techniques for demonstrating the quantumness of multiparticle systems in the presence of losses are difficult to define and, if not sufficiently accurate, they provide wrong conclusions. We present a Bell test where one photon of an entangled pair is amplified and then detected by threshold detectors, whose signals undergo postselection. The amplification is performed by a classical machine, which produces a fully separable micro-macro state. However, by adopting such a technique, one can surprisingly observe a violation of the CHSH inequality. This is due to the fact that ignoring the detection loophole, opened by the postselection and the system losses, can lead to misinterpretations, such as claiming the micro-macro entanglement in a setup where evidently there is not. By using threshold detectors and postselection, one can only in...

  10. Evaluation of gene amplification and protein expression of HER-2/neu in esophageal squamous cell carcinoma using Fluorescence in situ Hybridization (FISH) and immunohistochemistry

    International Nuclear Information System (INIS)

    Esophageal squamous cell carcinoma (ESCC) is the sixth most frequent neoplasia in Brazil. It is usually associated with a poor prognosis because it is often at an advanced stage when diagnosed and there is a high frequency of lymph node metastases. It is important to know what prognostic factors can facilitate diagnosis, optimize therapeutic decisions, and improve the survival of these patients. A member of the epidermal growth factor receptor (EGFR) family, c-erbB-2, has received much attention because of its therapeutic implications; however, few studies involving fluorescence in situ hybridization (FISH) analysis of HER-2/neu gene amplification and protein expression in ESCC have been conducted. The aim of this study was to verify the presence of HER-2/neu gene amplification using FISH, and to correlate the results with immunohistochemical expression and clinical-pathological findings. One hundred and ninety-nine ESCC cases were evaluated using the Tissue Microarray (TMA) technique. A polyclonal antibody against c-erbB-2 was used for immunohistochemistry. Analyses were based on the membrane staining pattern. The results were classified according to the Herceptest criteria (DAKO): negative (0/1+), potential positive (2+) and positive (3+). The FISH reactions were performed according to the FISH HER2 PharmDx (DAKO) protocol. In each case, 100 tumor nuclei were evaluated. Cases showing a gene/CEN17 fluorescence ratio ≥ 2 were considered positive for gene amplification. The c-erbB-2 expression was negative in 117/185 cases (63.2%) and positive in 68 (36.8%), of which 56 (30.3%) were 2+ and 12 (6.5%) were 3+. No significant associations were found among protein expression, clinicopathological data and overall survival. Among the 47 cases analyzed, 38 (80.9%) showed no gene amplification while 9 (19.1%) showed amplification, as demonstrated by FISH. Cases that were negative (0/1+) and potential positive (2+) for c-erbB-2 expression by immunohistochemistry showed no

  11. Amplification of Whole Tumor Genomes and Gene-by-Gene Mapping of Genomic Aberrations from Limited Sources of Fresh-Frozen and Paraffin-Embedded DNA

    OpenAIRE

    Bredel, Markus; Bredel, Claudia; Juric, Dejan; Kim, Young; Vogel, Hannes; Harsh, Griffith R.; Recht, Lawrence D.; Pollack, Jonathan R.; Sikic, Branimir I.

    2005-01-01

    Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffin-embedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of ...

  12. Genomic amplification of the human telomerase gene (hTERC associated with human papillomavirus is related to the progression of uterine cervical dysplasia to invasive cancer

    Directory of Open Access Journals (Sweden)

    Liu Hongqian

    2012-10-01

    Full Text Available Abstract Background Human papillomavirus (HPV infection plays an etiological role in the development of cervical dysplasia and cancer. Amplification of human telomerase gene (hTERC and over expression of telomerase were found to be associated with cervical tumorigenesis. This study was performed to analyze genomic amplification of hTERC gene, telomerase activity in association with HPV infection in different stages of cervical intraepithelial neoplasia (CIN and cervical cancer. We were studying the role of hTERC in the progression of uterine cervical dysplasia to invasive cancer, and proposed an adjunct method for cervical cancer screening. Methods Exfoliated cervical cells were collected from 114 patients with non neoplastic lesion (NNL, n=27, cervical intraepithelial neoplasia (CIN1, n=26, CIN2, n=16, CIN3, n=24 and cervical carcinoma (CA, n=21, and analyzed for amplification of hTERC with two-color fluorescence in situ hybridization (FISH probe and HPV-DNA with Hybrid Capture 2. From these patients, 53 were taken biopsy to analyze telomerase activity by telomeric repeat amplification protocol (TRAP and expression of human telomerase reverse transcriptase (hTERT, with immunohistochemistry (IHC. All biopsies were clinically confirmed by phathologists. Results Amplification of hTERC was significantly associated with the histologic diagnoses (p Conclusions hTERC ampliffication can be detected with FISH technique on exfoliated cervical cells. Amplification of hTERC and HPV infection are associated with more progressive CIN3 and CA. The testing of hTERC amplification might be a supplementary to cytology screening and HPV test, especially high-risk patients. Virtual slides The virtual slide(s for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1857134686755648.

  13. A FRET based aptasensor coupled with non-enzymatic signal amplification for mercury (II) ion detection.

    Science.gov (United States)

    Chu-Mong, Ketsarin; Thammakhet, Chongdee; Thavarungkul, Panote; Kanatharana, Proespichaya; Buranachai, Chittanon

    2016-08-01

    In this work, the idea of incorporating a non-enzymatic signal amplification with a regular aptasensor was tested. In this proof of principle, the sensor was designed for the detection of mercury (II) ions (Hg(2+)) based on the Förster Resonance Energy Transfer (FRET), and the catalyzed hairpin assembly (CHA) technique that was used as the signal amplification method. This sensor comprised a mercury aptamer-catalyst complex (Apt-C) and two types of hairpin DNA: H1 labeled with fluorescein and H2 labeled with tetramethylrhodamine. In the presence of Hg(2+), two facing thymine bases in the mercury aptamer strand were coordinated with one mercury ion. This caused the release of the catalyst for the catalyzed hairpin assembly (CHA) reaction that turned H1 and H2 hairpins into H1-H2 hybrids. FRET was then used to report the hairpin-duplex transformation. The sensor showed excellent specificity towards Hg(2+) over other possible interfering cations present at even a 100 fold greater concentrations. It had a linear range of 10.0-200.0nM, and a good detection limit of 7.03±0.18nM, which is lower than the regulatory mercury limit for drinking water (10nM or 2ppb). The sensor was used to detect spiked Hg(2+) in nine real surface water samples collected from three different areas. Acceptable recoveries and small standard deviations indicated that the sensor was practically applicable, and the proposed idea to incorporate a CHA amplification in a regular aptasensor was not only feasible but beneficial. The same principles can be applied to develop sensors for various different targets. PMID:27216687

  14. Micromachined polymerase chain reaction system for multiple DNA amplification of upper respiratory tract infectious diseases.

    Science.gov (United States)

    Liao, Chia-Sheng; Lee, Gwo-Bin; Wu, Jiunn-Jong; Chang, Chih-Ching; Hsieh, Tsung-Min; Huang, Fu-Chun; Luo, Ching-Hsing

    2005-01-15

    This paper presents a micro polymerase chain reaction (PCR) chip for the DNA-based diagnosis of microorganism genes and the detection of their corresponding antibiotic-resistant genes. The micro PCR chip comprises cheap biocompatible soda-lime glass substrates with integrated thin-film platinum resistors as heating/sensing elements, and is fabricated using micro-electro-mechanical-system (MEMS) techniques in a reliable batch-fabrication process. The heating and temperature sensing elements are made of the same material and are located inside the reaction chamber in order to ensure a uniform temperature distribution. This study performs the detection of several genes associated with upper respiratory tract infection microorganisms, i.e. Streptococcus pneumoniae, Haemopilus influenze, Staphylococcu aureus, Streptococcus pyogenes, and Neisseria meningitides, together with their corresponding antibiotic-resistant genes. The lower thermal inertia of the proposed micro PCR chip relative to conventional bench-top PCR systems enables a more rapid detection operation with reduced sample and reagent consumption. The experimental data reveal that the high heating and cooling rates of the system (20 and 10 degrees C/s, respectively) permit successful DNA amplification within 15 min. The micro PCR chip is also capable of performing multiple DNA amplification, i.e. the simultaneous duplication of multiple genes under different conditions in separate reaction wells. Compared with the large-scale PCR system, it is greatly advantageous for fast diagnosis of multiple infectious diseases. Multiplex PCR amplification of two DNA segments in the same well is also feasible using the proposed micro device. The developed micro PCR chip provides a crucial tool for genetic analysis, molecular biology, infectious disease detection, and many other biomedical applications. PMID:15590288

  15. Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis.

    Science.gov (United States)

    Santiago-Felipe, S; Tortajada-Genaro, L A; Puchades, R; Maquieira, A

    2014-02-01

    Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR-ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA-ELISA combination is proposed for amplification at a low, constant temperature (40°C) in a short time (40 min), for the hybridisation of labelled products to specific 5'-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA-ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA-ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings.

  16. 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.

  17. 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)

  18. 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)

  19. 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

  20. 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

  1. 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...

  2. 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.

  3. 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

  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. Direct Amplification of Sound By Light

    CERN Document Server

    Zhao, C; Fan, Y; Miao, S Grass H; Blair, D G; Hosken, D; Brooks, A; Veitch, P J; Munch, J; Slagmolen, B J J; McClelland, D E

    2007-01-01

    The principles of parametric interactions have been widely used in physics, including low noise microwave amplifiers, optical parametric oscillators (OPOs) and optical spring interactions with mechanical resonators. In the case of opto-mechanical interactions a mechanical mode modulates the length of an optical cavity, thereby changing the resonance condition of the optical mode. In recent experiments this interaction has been used to "cool" thermally excited mechanical modes of small acoustic resonators through the associated time dependent radiation pressure forces acting on the resonator. Such techniques are examples of two-mode parametric interactions in which the optical mode linewidth is sufficiently broad that the mechanical frequency occurs within the linewidth of a single mode. Here we present the first observation of three-mode opto-acoustic parametric interactions. In this case energy in an optical cavity mode is scattered into another optical cavity mode by its interaction with an acoustic mode in...

  6. 联合应用MLPA技术和基因测序技术检测DMD基因单个外显子缺失突变%Use of MLPA and gene sequencing technologies to detect a single exon deletion mutation in DMD gene

    Institute of Scientific and Technical Information of China (English)

    莫桂玲; 胡朝晖; 喻长顺; 詹益鑫; 朱庆义

    2011-01-01

    目的 提高检测DMD基因单个外显子缺突变失的准确率,为DMD家系成员的遗传咨询和产前基因诊断提供准确的依据.方法 收集2009-2010年送本实验室进行DMD基因检测的血样185例,提取外周血DNA,以美国病理学家协会提供的DNA质控品分别为阴性和阳性对照,联合应用MLPA技术、PCR技术和基因测序技术,分析其DMD基因单个外显子的缺失情况.结果 185例样品中,有7例MLPA结果显示为DMD基因单个外显子缺失,经过PCR技术和基因测序技术验证后,其中的6例确实为DMD基因单个外显子的缺失,1例为67号外显子的微小突变.结论 联合应用MLPA技术、PCR技术和基因测序技术,可以提高检测DMD基因单个外显子缺失的准确率,避免将单个外显子的微小突变误判为缺失突变,为DMD家系成员的遗传咨询和产前基因诊断提供准确的依据.%Objective To improve the accuracy of detection of a single exon deletion and provide an accurate basis of genetic counseling and prenatal gene diagnosis of the family members.Methods 185 blood samples were collected and the DMD gene was delected between 2009 to 2010. DNA samples from the College of American Pathologists were used as negative control and positive control. A single exon deletion mutation in DMD gene was detected by MLPA, PCR and gene sequencing technologies..Results In the term of 185 blood samples, the MLPA results showed that there existed single exon deletion mutations in DMD gene of 7 cases. PCR and gene sequencing were used to confirm, and a new mutation (c.9760_9781dup22/p.Pro3261LeufsX5) in DMD gene exon 67 was found just in one blood sample.Conclusion MLPA、PCR and gene sequencing technology are combined to improve the accuracy of detection of a single exon deletion and provide an accurate basis of genetic counseling and diagnosis of prenatal gene in the family members.

  7. Laser-enhanced ionization of mercury atoms in an inert atmosphere with avalanche amplification of the signal.

    Science.gov (United States)

    Clevenger, W L; Matveev, O I; Cabredo, S; Omenetto, N; Smith, B W; Winefordner, J D

    1997-07-01

    A new method for laser-enhanced ionization detection of mercury atoms in an inert gas atmosphere is described. The method, which is based on the avalanche amplification of the signal resulting from the ionization from a selected Rydberg level reached by a three-step laser excitation of mercury vapor in a simple quartz cell, can be applied to the determination of this element in various matrices by the use of conventional cold atomization techniques. The overall (collisional + photo) ionization efficiency is investigated at different temperatures, and the avalanche amplification effect is reported for Ar and P-10 gases at atmospheric pressure. It is shown that the amplified signal is related to the number of charges produced in the laser-irradiated volume. Under amplifier noise-limited conditions, a detection limit of ∼15 Hg atoms/laser pulse in the interaction region is estimated. PMID:21639354

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

    Directory of Open Access Journals (Sweden)

    Chen Hao-tai

    2011-11-01

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

  9. Experimental techniques; Techniques experimentales

    Energy Technology Data Exchange (ETDEWEB)

    Roussel-Chomaz, P. [GANIL CNRS/IN2P3, CEA/DSM, 14 - Caen (France)

    2007-07-01

    This lecture presents the experimental techniques, developed in the last 10 or 15 years, in order to perform a new class of experiments with exotic nuclei, where the reactions induced by these nuclei allow to get information on their structure. A brief review of the secondary beams production methods will be given, with some examples of facilities in operation or under project. The important developments performed recently on cryogenic targets will be presented. The different detection systems will be reviewed, both the beam detectors before the targets, and the many kind of detectors necessary to detect all outgoing particles after the reaction: magnetic spectrometer for the heavy fragment, detection systems for the target recoil nucleus, {gamma} detectors. Finally, several typical examples of experiments will be detailed, in order to illustrate the use of each detector either alone, or in coincidence with others. (author)

  10. 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

  11. Rapid genome detection of Schmallenberg virus and bovine viral diarrhea virus by use of isothermal amplification methods and high-speed real-time reverse transcriptase PCR.

    Science.gov (United States)

    Aebischer, Andrea; Wernike, Kerstin; Hoffmann, Bernd; Beer, Martin

    2014-06-01

    Over the past few years, there has been an increasing demand for rapid and simple diagnostic tools that can be applied outside centralized laboratories by using transportable devices. In veterinary medicine, such mobile test systems would circumvent barriers associated with the transportation of samples and significantly reduce the time to diagnose important infectious animal diseases. Among a wide range of available technologies, high-speed real-time reverse transcriptase quantitative PCR (RT-qPCR) and the two isothermal amplification techniques loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) represent three promising candidates for integration into mobile pen-side tests. The aim of this study was to investigate the performance of these amplification strategies and to evaluate their suitability for field application. In order to enable a valid comparison, novel pathogen-specific assays have been developed for the detection of Schmallenberg virus and bovine viral diarrhea virus. The newly developed assays were evaluated in comparison with established standard RT-qPCR using samples from experimentally or field-infected animals. Even though all assays allowed detection of the target virus in less than 30 min, major differences were revealed concerning sensitivity, specificity, robustness, testing time, and complexity of assay design. These findings indicated that the success of an assay will depend on the integrated amplification technology. Therefore, the application-specific pros and cons of each method that were identified during this study provide very valuable insights for future development and optimization of pen-side tests. PMID:24648561

  12. 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.

  13. Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence

    OpenAIRE

    Mingming Zhao; Yuhua Shi; Lan Wu; Licheng Guo; Wei Liu; Chao Xiong; Song Yan; Wei Sun; Shilin Chen

    2016-01-01

    Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nucl...

  14. Molecular cytogenetic analysis of formalin-fixed, paraffin-embedded solid tumors by comparative genomic hybridization after universal DNA-amplification

    OpenAIRE

    Speicher, Michael R.; Manoir, Stanislas du; Schröck, Evelin; Holtgreve-Grez, Heidi; Schoell, B; Lengauer, Christoph; Cremer, Thomas; Ried, Thomas

    1993-01-01

    We present a technique which allows the detection and chromosomal localization of DNA sequence copy number changes in solid tumor genomes from frozen sections and paraffin embedded, formalin fixed specimens. Based on comparative genomic hybridization and on universal DNA amplification procedures this technique is possible even if only a few tumor cells are available. We demonstrate the feasibility of this method to visualize complete and partial chromosome gains and losses and gene amplificat...

  15. 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

  16. 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...

  17. Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis

    Energy Technology Data Exchange (ETDEWEB)

    Santiago-Felipe, S.; Tortajada-Genaro, L.A.; Puchades, R.; Maquieira, A., E-mail: amaquieira@qim.upv.es

    2014-02-06

    Graphical abstract: -- Highlights: •Recombinase polymerase amplification is a powerful DNA method operating at 40 °C. •The combination RPA–ELISA gives excellent performances for high-throughput analysis. •Screening of food safety threats has been done using standard laboratory equipment. •Allergens, GMOs, bacteria, and fungi have been successfully determined. -- Abstract: Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR–ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA–ELISA combination is proposed for amplification at a low, constant temperature (40 °C) in a short time (40 min), for the hybridisation of labelled products to specific 5′-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA–ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA–ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings.

  18. Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Recombinase polymerase amplification is a powerful DNA method operating at 40 °C. •The combination RPA–ELISA gives excellent performances for high-throughput analysis. •Screening of food safety threats has been done using standard laboratory equipment. •Allergens, GMOs, bacteria, and fungi have been successfully determined. -- Abstract: Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR–ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA–ELISA combination is proposed for amplification at a low, constant temperature (40 °C) in a short time (40 min), for the hybridisation of labelled products to specific 5′-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA–ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA–ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings

  19. An empirical approach for quantifying loop-mediated isothermal amplification (LAMP using Escherichia coli as a model system.

    Directory of Open Access Journals (Sweden)

    Sowmya Subramanian

    Full Text Available Loop mediated isothermal amplification (LAMP is a highly efficient, selective and rapid DNA amplification technique for genetic screening of pathogens. However, despite its popularity, there is yet no mathematical model to quantify the outcome and no well-defined metric for comparing results that are available. LAMP is intrinsically complex and involves multiple pathways for gene replication, making fundamental modelling nearly intractable. To circumvent this difficulty, an alternate, empirical model is introduced that will allow one to extract a set of parameters from the concentration versus time curves. A simple recipe to deduce the time to positive, Tp--a parameter analogous to the threshold cycling time in polymerase chain reaction (PCR, is also provided. These parameters can be regarded as objective and unambiguous indicators of LAMP amplification. The model is exemplified on Escherichia coli strains by using the two gene fragments responsible for vero-toxin (VT production and tested against VT-producing (O157 and O45 and non-VT producing (DH5 alpha strains. Selective amplification of appropriate target sequences was made using well established LAMP primers and protocols, and the concentrations of the amplicons were measured using a Qubit 2.0 fluorometer at specific intervals of time. The data is fitted to a generalized logistic function. Apart from providing precise screening indicators, representing the data with a small set of numbers offers significant advantages. It facilitates comparisons of LAMP reactions independently of the sampling technique. It also eliminates subjectivity in interpretation, simplifies data analysis, and allows easy data archival, retrieval and statistical analysis for large sample populations. To our knowledge this work represents a first attempt to quantitatively model LAMP and offer a standard method that could pave the way towards high throughput automated screening.

  20. New perspectives on assessing amplification effects.

    Science.gov (United States)

    Souza, Pamela E; Tremblay, Kelly L

    2006-09-01

    Clinicians have long been aware of the range of performance variability with hearing aids. Despite improvements in technology, there remain many instances of well-selected and appropriately fitted hearing aids whereby the user reports minimal improvement in speech understanding. This review presents a multistage framework for understanding how a hearing aid affects performance. Six stages are considered: (1) acoustic content of the signal, (2) modification of the signal by the hearing aid, (3) interaction between sound at the output of the hearing aid and the listener's ear, (4) integrity of the auditory system, (5) coding of available acoustic cues by the listener's auditory system, and (6) correct identification of the speech sound. Within this framework, this review describes methodology and research on 2 new assessment techniques: acoustic analysis of speech measured at the output of the hearing aid and auditory evoked potentials recorded while the listener wears hearing aids. Acoustic analysis topics include the relationship between conventional probe microphone tests and probe microphone measurements using speech, appropriate procedures for such tests, and assessment of signal-processing effects on speech acoustics and recognition. Auditory evoked potential topics include an overview of physiologic measures of speech processing and the effect of hearing loss and hearing aids on cortical auditory evoked potential measurements in response to speech. Finally, the clinical utility of these procedures is discussed. PMID:16959734

  1. Detection of Clostridium perfringens alpha toxin gene in lambs by loop mediated isothermal amplification

    Directory of Open Access Journals (Sweden)

    B. Radhika

    2016-01-01

    Full Text Available Aim: The loop mediated isothermal amplification (LAMP was standardized for rapid detection of Clostridium perfringens. Materials and Methods: A total of 120 fecal samples were collected from enterotoxemia suspected lambs were used for screening of C. perfringens cpa gene by LAMP. The specificity of the LAMP amplified products was tested by digesting with restriction enzyme XmnI for alpha toxin gene. Results: Out of 120 samples screened 112 (93.3% samples were positive by both LAMP and polymerase chain reaction (PCR for detection of cpa gene which indicated the equal sensitivity of both the tests. The enzyme produced single cut in 162 base pair amplified product of alpha toxin gene at 81 base pair resulting in a single band in gel electrophoresis. Conclusion: Both LAMP and PCR for detection of cpa gene indicated the equal sensitivity of both the tests. Standardization of LAMP reaction for amplification of epsilon and beta toxin genes will help to identify the C. perfringens toxin types from the clinical samples. The test could be a suitable alternative to the PCR in detection of toxin types without the help of sophisticated machinery like thermal cycler. Considering its simplicity in operation and high sensitivity, there is the potential use of this technique in clinical diagnosis and surveillance of infectious diseases.

  2. Sensitive colorimetric detection of Listeria monocytogenes based on isothermal gene amplification and unmodified gold nanoparticles.

    Science.gov (United States)

    Fu, Zhongyu; Zhou, Xiaoming; Xing, Da

    2013-12-15

    Listeria monocytogenes (L. monocytogenes), one of most problematic food-borne bacteria, is mainly transmitted through the food chain and may cause listeriosis. Therefore, the development of rapid and sensitive L. monocytogenes detection technique has become an urgent task. In this study, we proposed a method using hyperbranching rolling circle amplification (HRCA) combined with gold nanoparticle (GNP) based colorimetric strategy to offer an isothermal, highly sensitive and specific assay for the detection of L. monocytogenes. First, a linear padlock probe targeting a specific sequence in the hly gene was designed and followed with a ligation by Taq DNA ligase. After ligation, further amplification by HRCA with a thiolated primer and an unlabeled primer is performed. The resulting thiolated HRCA products were then captured onto GNP surface and made GNP more salt-tolerant. Detection of the bacteria can be achieved by a facilitated GNP based colorimetric testing using naked eyes. Through this approach, as low as 100 aM synthetic hly gene targets and about 75 copies of L. monocytogenes can be detected. The specificity is evaluated by distinguishing target L. monocytogenes from other bacteria. The artificial contaminated food samples were also detected for its potential applications in real food detection. This method described here is ideal for bacteria detection due to its simplicity and high sensitivity. PMID:23948710

  3. Chemically induced DNA hypomethylation in breast carcinoma cells detected by the amplification of intermethylated sites

    International Nuclear Information System (INIS)

    Compromised patterns of gene expression result in genomic instability, altered patterns of gene expression and tumour formation. Specifically, aberrant DNA hypermethylation in gene promoter regions leads to gene silencing, whereas global hypomethylation events can result in chromosomal instability and oncogene activation. Potential links exist between environmental agents and DNA methylation, but the destabilizing effects of environmental exposures on the DNA methylation machinery are not understood within the context of breast cancer aetiology. We assessed genome-wide changes in methylation patterns using a unique methylation profiling technique called amplification of intermethylated sites (AIMS). This method generates easily readable fingerprints that represent the investigated cell line's methylation profile, based on the differential cleavage of DNA with methylation-specific isoschisomeric restriction endonucleases. We validated this approach by demonstrating both unique and reoccurring sites of genomic hypomethylation in four breast carcinoma cell lines treated with the cytosine analogue 5-azacytidine. Comparison of treated with control samples revealed individual bands that exhibited methylation changes, and these bands were excized and cloned, and the precise genomic location individually identified. In most cases, these regions of hypomethylation coincided with susceptible target regions previously associated with chromosome breakage, rearrangement and gene amplification. Similarly, we observed that acute benzopyrene exposure is associated with altered methylation patterns in these cell lines. These results reinforce the link between environmental exposures, DNA methylation and breast cancer, and support a role for AIMS as a rapid, affordable screening method to identify environmentally induced DNA methylation changes that occur in tumourigenesis

  4. Rapid and Sensitive Detection of Didymella bryoniae by Visual Loop-Mediated Isothermal Amplification Assay

    Science.gov (United States)

    Yao, Xiefeng; Li, Pingfang; Xu, Jinghua; Zhang, Man; Ren, Runsheng; Liu, Guang; Yang, Xingping

    2016-01-01

    Didymella bryoniae is a pathogenic fungus that causes gummy stem blight (GSB) in Cucurbitaceae crops (e.g., cantaloupe, muskmelon, cucumber, and watermelon). GSB produces lesions on the stems and leaves, and can also be spread by seeds. Here, we developed a rapid, visual, and sensitive loop-mediated amplification (LAMP) assay for D. bryoniae detection based on sequence-characterized amplified regions (GenBank accession nos GQ872461 and GQ872462) common to the two random amplification of polymorphic DNA group genotypes (RGI and RGII) of D. bryoniae; ideal conditions for detection were optimized for completion in 45 min at 63°C. The sensitivity and specificity of the LAMP assay were further analyzed in comparison with those of a conventional polymerase chain reaction (PCR). The sensitivity of the LAMP assay was 1000-fold higher than that of conventional PCR with a detection limit of 0.1 fg μL-1 of targeted DNA. The LAMP assay could be accomplished in about 45 min, with the results visible to the naked eye. The assay showed high specificity in discriminating all D. bryoniae isolates from seven other fungal pathogens that occur in Cucurbitaceae crops. The LAMP assay also detected D. bryoniae infection in young muskmelon leaves with suspected early symptoms of GSB disease. Hence, the technique has great potential for developing rapid and sensitive visual detection methods for the D. bryoniae pathogen in crops and seeds. This method has potential application in early prediction of disease and reducing the risk of epidemics.

  5. Application of sequence-independent amplification (SIA) for the identification of RNA viruses in bioenergy crops.

    Science.gov (United States)

    Agindotan, Bright O; Ahonsi, Monday O; Domier, Leslie L; Gray, Michael E; Bradley, Carl A

    2010-10-01

    Miscanthus x giganteus, energycane, and Panicum virgatum (switchgrass) are three potential biomass crops being evaluated for commercial cellulosic ethanol production. Viral diseases are potentially significant threats to these crops. Therefore, identification of viruses infecting these bioenergy crops is important for quarantine purposes, virus resistance breeding, and production of virus-free planting materials. The application is described of sequence-independent amplification, for the identification of RNA viruses in bioenergy crops. The method involves virus partial purification from a small amount of infected leaf tissue (miniprep), extraction of viral RNA, amplification of randomly primed cDNAs, cloning, sequencing, and BLAST searches for sequence homology in the GenBank. This method has distinct advantage over other virus characterization techniques in that it does not require reagent specific to target viruses. Using this method, a possible new species was identified in the genus Marafivirus in switchgrass related to Maize rayado fino virus, its closest relative currently in GenBank. Sugarcane mosaic virus (SCMV), genus Potyvirus, was identified in M.xgiganteus, energycane, corn (Zea mays), and switchgrass. Other viruses identified were: Maize dwarf mosaic virus (MDMV), genus Potyvirus, in johnsongrass (Sorghum halepense); Soil borne wheat mosaic virus (SBWMV), genus Furovirus, in wheat (Triticum aestivum); and Bean pod mottle virus (BPMV), genus Comovirus, in soybean (Glycine max). The method was as sensitive as conventional RT-PCR. This is the first report of a Marafivirus infecting switchgrass, and SCMV infecting both energycane and M. x giganteus.

  6. Brillouin amplification in phase coherent transfer of optical frequencies over 480 km fiber

    CERN Document Server

    Terra, O; Schnatz, H

    2010-01-01

    We describe the use of fiber Brillouin amplification (FBA) for the coherent transmission of optical frequencies over a 480 km long optical fiber link. FBA uses the transmission fiber itself for efficient, bi-directional coherent amplification of weak signals with pump powers around 30 mW. In a test setup we measured the gain and the achievable signal-to-noise ratio (SNR) of FBA and compared it to that of the widely used uni-directional Erbium doped fiber amplifiers (EDFA) and to our recently built bi-directional EDFA. We measured also the phase noise introduced by the FBA and used a new and simple technique to stabilize the frequency of the FBA pump laser. We then transferred a stabilized laser frequency over a wide area network with a total fiber length of 480 km using only one intermediate FBA station. After compensating the noise induced by the fiber, the frequency is delivered to the user end with an uncertainty below 2x10-18 and an instability sigma(tau) = 2x10-14/(tau/second).

  7. Rapid amplification of genetically modified organisms using a circular ferrofluid-driven PCR microchip.

    Science.gov (United States)

    Sun, Yi; Kwok, Yien-Chian; Foo-Peng Lee, Peter; Nguyen, Nam-Trung

    2009-07-01

    The use of genetically modified organisms (GMOs) as food and in food products is becoming more and more widespread. Polymerase chain reaction (PCR) technology is extensively used for the detection of GMOs in food products in order to verify compliance with labeling requirements. In this paper, we present a novel close-loop ferrofluid-driven PCR microchip for rapid amplification of GMOs. The microchip was fabricated in polymethyl methacrylate by CO2 laser ablation and was integrated with three temperature zones. PCR solution was contained in a circular closed microchannel and was driven by magnetic force generated by an external magnet through a small oil-based ferrofluid plug. Successful amplification of genetically modified soya and maize were achieved in less than 13 min. This PCR microchip combines advantages of cycling flexibility and quick temperature transitions associated with two existing microchip PCR techniques, and it provides a cost saving and less time-consuming way to conduct preliminary screening of GMOs. PMID:19399482

  8. Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Johanna Hasmats

    Full Text Available Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74% of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.

  9. Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

    Science.gov (United States)

    Hasmats, Johanna; Gréen, Henrik; Orear, Cedric; Validire, Pierre; Huss, Mikael; Käller, Max; Lundeberg, Joakim

    2014-01-01

    Exome sequence capture and massively parallel sequencing can be combined to achieve inexpensive and rapid global analyses of the functional sections of the genome. The difficulties of working with relatively small quantities of genetic material, as may be necessary when sharing tumor biopsies between collaborators for instance, can be overcome using whole genome amplification. However, the potential drawbacks of using a whole genome amplification technology based on random primers in combination with sequence capture followed by massively parallel sequencing have not yet been examined in detail, especially in the context of mutation discovery in tumor material. In this work, we compare mutations detected in sequence data for unamplified DNA, whole genome amplified DNA, and RNA originating from the same tumor tissue samples from 16 patients diagnosed with non-small cell lung cancer. The results obtained provide a comprehensive overview of the merits of these techniques for mutation analysis. We evaluated the identified genetic variants, and found that most (74%) of them were observed in both the amplified and the unamplified sequence data. Eighty-nine percent of the variations found by WGA were shared with unamplified DNA. We demonstrate a strategy for avoiding allelic bias by including RNA-sequencing information.

  10. X-ray Chirped Pulse Amplification: towards GW Soft X-ray Lasers

    Directory of Open Access Journals (Sweden)

    Marta Fajardo

    2013-07-01

    Full Text Available Extensive modeling of the seeding of plasma-based soft X-ray lasers is reported in this article. Seminal experiments on amplification in plasmas created from solids have been studied in detail and explained. Using a transient collisional excitation scheme, we show that a 18 µJ, 80 fs fully coherent pulse is achievable by using plasmas pumped by a compact 10 Hz laser. We demonstrate that direct seeding of plasmas created by nanosecond lasers is not efficient. Therefore, we propose and fully study the transposition to soft X-rays of the Chirped Pulse Amplification (CPA technique. Soft X-ray pulses with energy of 6 mJ and 200 fs duration are reachable by seeding plasmas pumped by compact 100 J, sub-ns, 1 shot/min lasers. These soft X-ray lasers would reach GW power, corresponding to an increase of 100 times as compared to the highest peak power achievable nowadays in the soft X-ray region (30 eV–1 keV. X-ray CPA is opening new horizon for soft x-ray ultra-intense sources.

  11. 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...

  12. 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.

  13. 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

  14. 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...

  15. Application of Isothermal Amplification Techniques for Identification of Madurella mycetomatis, the Prevalent Agent of Human Mycetoma

    NARCIS (Netherlands)

    Ahmed, Sarah A; van de Sande, Wendy W J; Desnos-Ollivier, Marie; Fahal, Ahmed H; Mhmoud, Najwa A; de Hoog, G S

    2015-01-01

    Appropriate diagnosis and treatment of eumycetoma may vary significantly depending on the causative agent. To date, the most common fungus causing mycetoma worldwide is Madurella mycetomatis. This species fails to express any recognizable morphological characteristics, and reliable identification ca

  16. Improved diagnosis of contagious bovine pleuropneumonia (CBPP) by standard serological techniques and DNA amplification

    International Nuclear Information System (INIS)

    The aim was to improve the diagnosis of contagious bovine pleuropneumonia (CBPP) in Botswana by the implementation and establishment of the OIE standard complement fixation test (CFT) method, and to demonstrate a diagnostic system in a 96 well format coupled with a colorimetric detection of the PCR amplified product suitable for moderate to high sample numbers for the detection of Mycoplasma mycoides mycoides SC (MmmSC) from nasal swabs, lung tissue and cultures

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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 ...

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Development of a quantitative fluorescence single primer isothermal amplification-based method for the detection of Salmonella.

    Science.gov (United States)

    Wang, Jianchang; Li, Rui; Hu, Lianxia; Sun, Xiaoxia; Wang, Jinfeng; Li, Jing

    2016-02-16

    Food-borne disease caused by Salmonella has long been, and continues to be, an important global public health problem, necessitating rapid and accurate detection of Salmonella in food. Real time PCR is the most recently developed approach for Salmonella detection. Single primer isothermal amplification (SPIA), a novel gene amplification technique, has emerged as an attractive microbiological testing method. SPIA is performed under a constant temperature, eliminating the need for an expensive thermo-cycler. In addition, SPIA reactions can be accomplished in 30 min, faster than real time PCR that usually takes over 2h. We developed a quantitative fluorescence SPIA-based method for the detection of Salmonella. Using Salmonella Typhimurium genomic DNA as template and a primer targeting Salmonella invA gene, we showed the detection limit of SPIA was 2.0 × 10(1)fg DNA. Its successful amplification of different serotypic Salmonella genomic DNA but not non-Salmonella bacterial DNA demonstrated the specificity of SPIA. Furthermore, this method was validated with artificially contaminated beef. In conclusion, we showed high sensitivity and specificity of SPIA in the detection of Salmonella, comparable to real time PCR. In addition, SPIA is faster and more cost-effective (non-use of expensive cyclers), making it a potential alternative for field detection of Salmonella in resource-limited settings that are commonly encountered in developing countries.

  11. Genetic signatures from amplification profiles characterize DNA mutation in somatic and radiation-induced sports of chrysanthemum

    International Nuclear Information System (INIS)

    The chrysanthemum (Dendranthema grandiflora Tzvelev.) cultivars 'Dark Charm', 'Salmon Charm', 'Coral Charm' and 'Dark Bronze Charm' are either radiation-induced mutants or spontaneous sports of 'Charm' and constitute a family or series of plants that primarily differ in flower color. These cultivars, which were difficult to differentiate genetically by DNA amplification fingerprinting (DAF), were easily identified by using arbitrary signatures from amplification profiles (ASAP). Genomic DNA was first amplified with three standard octamer arbitrary primers, all of which produced monomorphic profiles. Products from each of these DNA fingerprints were subsequently reamplified using four minihairpin decamer primers. The 12 primer combinations produced signatures containing approximately 37% polymorphic character loci, which were used to estimate genetic relationships between cultivars. Forty-six (32%) unique amplification products were associated with individual cultivars. The number of ASAP polymorphisms detected provided an estimate of the mutation rate in the mutant cultivars, ranging from 0.03% to 1.6% of nucleotide changes within an average of 18 kb of arbitrary amplified DAF sequence. The ASAP technique permits the clear genetic identification of somatic mutants and radiation-induced sports that are genetically highly homogeneous and should facilitate marker assisted breeding and protection of plant breeders rights of varieties or cultivars

  12. A SPR biosensor based on signal amplification using antibody-QD conjugates for quantitative determination of multiple tumor markers.

    Science.gov (United States)

    Wang, Huan; Wang, Xiaomei; Wang, Jue; Fu, Weiling; Yao, Chunyan

    2016-01-01

    The detection of tumor markers is very important in early cancer diagnosis; however, tumor markers are usually present at very low concentrations, especially in the early stages of tumor development. Surface plasmon resonance (SPR) is widely used to detect biomolecular interactions; it has inherent advantages of being high-throughput, real-time, and label-free technique. However, its sensitivity needs essential improvement for practical applications. In this study, we developed a signal amplification strategy using antibody-quantum dot (QD) conjugates for the sensitive and quantitative detection of α-fetoprotein (AFP), carcinoembryonic antigen (CEA) and cytokeratin fragment 21-1 (CYFRA 21-1) in clinical samples. The use of a dual signal amplification strategy using AuNP-antibody and antibody-QD conjugates increased the signal amplification by 50-folds. The constructed SPR biosensor showed a detection limit as low as 0.1 ng/mL for AFP, CEA, and CYFRA 21-1. Moreover, the results obtained using this SPR biosensor were consistent with those obtained using the electrochemiluminescence method. Thus, the constructed SPR biosensor provides a highly sensitive and specific approach for the detection of tumor markers. This SPR biosensor can be expected to be readily applied for the detection of other tumor markers and can offer a potentially powerful solution for tumor screening. PMID:27615417

  13. 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...

  14. 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.

  15. 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.

  16. 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...

  17. 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...

  18. 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.

  19. 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.)

  20. 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;...

  1. 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...

  2. 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.

  3. 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.

  4. 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 ...

  5. Spectral Phase Modulation and chirped pulse amplification in High Gain Harmonic Generation

    CERN Document Server

    Wu, Zilu; Krinsky, Sam; Loos, Henrik; Murphy, James; Shaftan, Timur; Sheehy, Brian; Shen, Yuzhen; Wang, Xijie; Yu Li Hua

    2004-01-01

    High Gain Harmonic Generation (HGHG), because it produces longitudinally coherent pulses derived from a coherent seed, presents remarkable possibilities for manipulating FEL pulses. If spectral phase modulation imposed on the seed modulates the spectral phase of the HGHG in a deterministic fashion, then chirped pulse amplification, pulse shaping, and coherent control experiments at short wavelengths become possible. In addition, the details of the transfer function will likely depend on electron beam and radiator dynamics and so prove to be a useful tool for studying these. Using the DUVFEL at the National Synchrotron Light Source at Brookhaven National Laboratory, we present spectral phase analyses of both coherent HGHG and incoherent SASE ultraviolet FEL radiation, applying Spectral Interferometry for Direct Electric Field Reconstruction (SPIDER), and assess the potential for employing compression and shaping techniques.

  6. Development of a loop-mediated isothermal amplification assay for rapid detection of Burkholderia mallei.

    Science.gov (United States)

    Mirzai, S; Safi, S; Mossavari, N; Afshar, D; Bolourchian, M

    2016-01-01

    The present study was conducted to establish a Loop-mediated isothermal amplification (LAMP) technique for the rapid detection of B. mallei the etiologic agent of glanders, a highly contagious disease of equines. A set of six specific primers targeting integrase gene cluster were designed for the LAMP test. The reaction was optimized using different temperatures and time intervals. The specificity of the assay was evaluated using DNA from B.pseudomallei and Pseudomonas aeruginosa. The LAMP products were analyzed both visually and under UV light after electrophoresis. The optimized conditions were found to be at 63ºC for 60 min. The assay showed high specificity and sensitivity. It was concluded that the established LAMP assay is a rapid, sensitive and practical tool for detection of B. mallei and early diagnosis of glanders. PMID:27609471

  7. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains

    DEFF Research Database (Denmark)

    Wales, Nathan; Andersen, Kenneth; Cappellini, Enrico;

    2014-01-01

    from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical...... resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA...... extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated...

  8. Bacteriophage amplification assay for detection of Listeria spp. using virucidal laser treatment

    Directory of Open Access Journals (Sweden)

    I.C. Oliveira

    2012-09-01

    Full Text Available A protocol for the bacteriophage amplification technique was developed for quantitative detection of viable Listeria monocytogenes cells using the A511 listeriophage with plaque formation as the end-point assay. Laser and toluidine blue O (TBO were employed as selective virucidal treatment for destruction of exogenous bacteriophage. Laser and TBO can bring a total reduction in titer phage (ca. 10(8 pfu/mL without affecting the viability of L. monocytogenes cells. Artificially inoculated skimmed milk revealed mean populations of the bacteria as low as between 13 cfu/mL (1.11 log cfu/mL, after a 10-h assay duration. Virucidal laser treatment demonstrated better protection of Listeria cells than the other agents previously tested. The protocol was faster and easier to perform than standard procedures. This protocol constitutes an alternative for rapid, sensitive and quantitative detection of L. monocytogenes.

  9. Single Cell HLA Matching Feasibility by Whole Genomic Amplification and Nested PCR

    Institute of Scientific and Technical Information of China (English)

    Xiao-hong Li; Fang-yin Meng

    2004-01-01

    @@ PCR based single-cell DNA analysis has been widely used in forensic science, preimplantation genetic diagnosis and so on. However, the original sample cannot be efficiently retrieved following single cell PCR, consequently the amount of information gained is limited. HLA system is too sophisticated that it is very hard to complete HLA typing by single cell. A Taq polymerase-based method using random primers to amplify whole genome termed as whole genome amplification (WGA) has demonstrated to be a useful method in increasing the copies of minimum sample. We establish a technique in this study to amplify HLA-A and HLA-B loci at same time in a single cell using WGA.

  10. Applications of Light Amplification by Stimulated Emission of Radiation (Lasers) for Restorative Dentistry.

    Science.gov (United States)

    Najeeb, Shariq; Khurshid, Zohaib; Zafar, Muhammad Sohail; Ajlal, Syed

    2016-01-01

    Light amplification by stimulated emission of radiation (laser) has been used widely in a range of biomedical and dental applications in recent years. In the field of restorative dentistry, various kinds of lasers have been developed for diagnostic (e.g. caries detection) and operative applications (e.g. tooth ablation, cavity preparation, restorations, bleaching). The main benefits for laser applications are patient comfort, pain relief and better results for specific applications. Major concerns for using dental lasers frequently are high cost, need for specialized training and sensitivity of the technique, thereby compromising its usefulness particularly in developing countries. The main aim of this paper is to evaluate and summarize the applications of lasers in restorative dentistry, including a comparison of the applications of lasers for major restorative dental procedures and conventional clinical approaches. A remarkable increase in the use of lasers for dental application is expected in the near future. PMID:26642047

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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...

  1. A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wei [College of Food Science and Engineering, Ocean University of China, Qingdao 266003 (China); Zhao, Shiming [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China); Mao, Yiping [Yueyang Institute for Food and Drug Control, Yueyang 430198 (China); Fang, Zhiyuan [Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou 510095 (China); Lu, Xuewen [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China); Zeng, Lingwen, E-mail: zeng6@yahoo.com [Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China)

    2015-02-25

    Highlights: • Limit of detection as low as 10 CFU mL{sup −1}Escherichia coli O157:H7. • No need of antibodies and substituted with aptamers. • Isothermal strand displacement amplification for signal amplification. • Results observed by the naked eye. • Great potential application in the area of food control. - Abstract: Foodborne diseases caused by pathogens are one of the major problems in food safety. Convenient and sensitive point-of-care rapid diagnostic tests for food-borne pathogens have been a long-felt need of clinicians. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. These methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive aptamer based biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). In this assay, two different aptamers specific for the outmembrane of E. coli O157:H7 were used. One of the aptamers was used for magnetic bead enrichment, and the other was used as a signal reporter for this pathogen, which was amplified by isothermal strand displacement amplification (SDA) and further detected by a lateral flow biosensor. Only the captured aptamers on cell membrane were amplified, limitations of conventional DNA amplification based method such as false-positive can be largely reduced. The generated signals (red bands on the test zone of a lateral flow strip) can be unambiguously read out by the naked eye. As low as 10 colony forming units (CFU) of E. coli O157:H7 were detected in this study. Without DNA extraction, the reduced handling and simpler equipment requirement render this assay a simple and rapid alternative to conventional methods.

  2. 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 ...

  3. 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

  4. High and Stable Conversion Efficiency Obtaining in Single-Stage Multi-Crystal Optical Parametric Chirped Pulse Amplification System

    Institute of Scientific and Technical Information of China (English)

    JIANG Yong-Liang; LENG Yu-Xin; ZHAO Bao-Zhen; WANG Cheng; LIANG Xiao-Yan; LU Hai-He; XU Zhi-Zhan

    2005-01-01

    @@ An optical parametric chirped-pulse amplification system is demonstrated to provide 32.9% pump-to-signal con-version efficiency. Special techniques are used to make the signal and pump pulses match with each other inboth spectral and temporal domains. The broadband 9.5-mJ pulses are produced at the repetition rate of 1 Hzwith the gain of over 1.9 × 108. The output energy fluctuation of 7.8% is achieved for the saturated amplificationprocess against the pump fluctuation of 10%.

  5. Molecular techniques for detection of genetic variation in horticultural crops

    International Nuclear Information System (INIS)

    The application of molecular techniques in cultivar identification and classification of some horticultural fruit crops are briefly reviewed in this paper. Two distinct approaches have been utilized including electrophoresis of polymorphic isozymes and DNA Amplification Fingerprintings; DAFs. Such markers were successfully employed in distinguishing genetic variability and generated genetic relatedness dendrogram among closely related cultivars of Salacca species, and Lansium domesticum Correa. (author)

  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. Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

    Science.gov (United States)

    Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

    2016-07-19

    We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

  8. Screening for copy number alterations in loci associated with autism spectrum disorders by two-color multiplex ligation-dependent probe amplification

    DEFF Research Database (Denmark)

    Bremer, Anna; Giacobini, Maibritt; Nordenskjöld, Magnus;

    2010-01-01

    identified in a subgroup of individuals with ASD using array technology. Adequate genetic testing for these genomic imbalances have not yet been widely implemented in the diagnostic setting due to lack of feasible and cost-effective methods as well as difficulties to interpret the clinical significance...... detection of multiple loci in a single reaction. We screened 148 autistic patients for 15 different loci covering 26 genes and found a 15q11-13 interstitial duplication that had escaped detection by conventional karyotyping in 1.3% of the patients. Synthetic probe MLPA allows for a flexible analysis...... of a continuously increasing number of CNAs associated with autism. Our result show that MLPA assay is an easy and cost-effective method for the identification of selected CNAs in diagnostic laboratories....

  9. Genetic Analysis and Its Clinical Effect of Spontaneous Abortion after Assisted Reproductive Techniques%辅助生殖技术治疗后自然流产胚胎的遗传学分析及其临床效应

    Institute of Scientific and Technical Information of China (English)

    段程颖; 李红; 刘敏娟; 陈瑛; 孙健; 丁扬; 丁洁; 王玮

    2014-01-01

    Objective:To analyze the chromosome abnormalities of spontaneous abortion tissues after assisted reproductive techniques (ART),and to discuss the relationship between genetic change and clinical feature. Methods:40 cases of spontaneous abortion villuses from ART, and 113 cases from natural pregnancy as control, were studied by the routine G banding karyotyping after the standard cell culture and harvest. Those cases of culture failure or without culture were analyzed by the multiplex ligation-dependent probe amplification (MLPA). Results: ①There was no significant difference in the rates of abnormal karyotyping between the ART group (50%, 20 cases) and the control group(53.1%,60 cases,P>0.05).②There were no significant differences in the rates of abnormal karyotyping when analyzed those parameters, including women age, primary or secondary infertility, infertility cause (male, female, or both), cycle type (fresh or frozen) (P>0.05). Although there was significant difference in this rate when analyzed IVF method (routine IVF and ICSI) in the limited cases(P<0.05), it should be further studied in more cases. Conclusions:Chromosome abnomalities are the main reason of spontaneous abortion after ART. The combined genetic techniques to detect the spontaneous abortion tissues are helpful for the ART treatment of infertility.%目的:研究辅助生殖技术(ART)后自然流产胚胎的染色体异常率及遗传学改变与临床相关性。方法:选取经ART治疗妊娠后自然流产患者绒毛40例作为实验组,并选取正常自然流产患者绒毛113例作为对照组。2组绒毛经细胞培养,常规染色体制备后进行核型分析,培养失败或无法培养的绒毛应用多重连接依赖的探针扩增(MLPA)技术进行检测。结果:①实验组染色体核型异常20例,异常率为50.0%;对照组染色体异常核型60例,异常率53.1%,2组异常率差异无统计学意义(P>0.05);②实验组妊娠妇女不

  10. Monosomy of chromosome 17 in breast cancer during interpretation of HER2 gene amplification

    Science.gov (United States)

    Brunelli, Matteo; Nottegar, Alessia; Bogina, Giuseppe; Caliò, Anna; Cima, Luca; Eccher, Albino; Vicentini, Caterina; Marcolini, Lisa; Scarpa, Aldo; Pedron, Serena; Brunello, Eleonora; Knuutila, Sakari; Sapino, Anna; Marchiò, Caterina; Bria, Emilio; Molino, Annamaria; Carbognin, Luisa; Tortora, Giampaolo; Jasani, Bharat; Miller, Keith; Merdol, Ibrahim; Zanatta, Lucia; Laurino, Licia; Wirtanen, Tiina; Zamboni, Giuseppe; Marconi, Marcella; Chilosi, Marco; Manfrin, Erminia; Martignoni, Guido; Bonetti, Franco

    2015-01-01

    Monosomy of chromosome 17 may affect the assessment of HER2 amplification. Notably, the prevalence ranges from 1% up to 49% due to lack of consensus in recognition. We sought to investigate the impact of monosomy of chromosome 17 to interpretation of HER2 gene status. 201 breast carcinoma were reviewed for HER2 gene amplification and chromosome 17 status. FISH analysis was performed by using double probes (LSI/CEP). Absolute gene copy number was also scored per each probe. HER2 FISH test was repeated on serial tissue sections, ranging in thickness from 3 to 20 µm. Ratio was scored and subsequently corrected by monosomy after gold control test using the aCGH method to overcome false interpretation due to artefactual nuclear truncation. HER2 immunotests was performed on all cases. 26/201 cases were amplified (13%). Single signals per CEP17 were revealed in 7/201 (3.5%) cases. Five out of 7 cases appeared monosomic with aCGH (overall, 5/201, 2.5%) and evidenced single signals in >60% of nuclei after second-look on FISH when matching both techniques. Among 5, one case showed amplification with a pattern 7/1 (HER2/CEP17>2) of copies (3+ at immunotest); three cases revealed single signals per both probes (LSI/CEP=1) and one case revealed a 3:1 ratio; all last 4 cases showed 0/1+ immunoscore. We concluded that: 1) monosomy of chromosome 17 may be observed in 2.5% of breast carcinoma; 2) monosomy of chromosome 17 due to biological reasons rather than nuclear truncation was observed when using the cut-off of 60% of nuclei harboring single signals; 3) the skewing of the ratio due to single centromeric 17 probe may lead to false positive evaluation; 4) breast carcinomas showing a 3:1 ratio (HER2/CEP17) usually show negative 0/1+ immunoscore and <6 gene copy number at FISH. PMID:26328251

  11. 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

  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. Improved PCR amplification for molecular analysis using DNA from long-term preserved formalin-fixed, paraffin-embedded lung cancer tissue specimens.

    Science.gov (United States)

    Taga, Masataka; Eguchi, Hidetaka; Shinohara, Tomoko; Takahashi, Keiko; Ito, Reiko; Yasui, Wataru; Nakachi, Kei; Kusunoki, Yoichiro; Hamatani, Kiyohiro

    2013-01-01

    Archival tissue specimens are valuable resources of materials for molecular biological analyses in retrospective studies, especially for rare diseases or those associated with exposure to uncommon environmental events. Although successful amplification with PCR is essential for analysis of DNA extracted from archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens, we have often encountered problems with poor PCR amplification of target fragments. To overcome this, we examined whether heat treatment in alkaline solution could efficiently restore the PCR template activity of DNA that had already been extracted from FFPE lung cancer tissue specimens. The effect of the heat treatment was assessed by PCR for the TP53 gene and other lung cancer-related gene loci. The heat treatment of DNA samples in borate buffer resulted in successful PCR amplification of DNA fragments ranging from 91 to 152 bp. This technique for restoration of template activity of DNA for PCR amplification is very simple and economical, and requires no special apparatus, so it may be applicable for molecular analysis of DNA samples from FFPE tissue specimens at various laboratories.

  15. 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 $\\sim 100$ ...

  16. Loop-mediated isothermal amplification (LAMP method for rapid detection of Trypanosoma brucei rhodesiense.

    Directory of Open Access Journals (Sweden)

    Zablon Kithinji Njiru

    Full Text Available Loop-mediated isothermal amplification (LAMP of DNA is a novel technique that rapidly amplifies target DNA under isothermal conditions. In the present study, a LAMP test was designed from the serum resistance-associated (SRA gene of Trypanosoma brucei rhodesiense, the cause of the acute form of African sleeping sickness, and used to detect parasite DNA from processed and heat-treated infected blood samples. The SRA gene is specific to T. b. rhodesiense and has been shown to confer resistance to lysis by normal human serum. The assay was performed at 62 degrees C for 1 h, using six primers that recognised eight targets. The template was varying concentrations of trypanosome DNA and supernatant from heat-treated infected blood samples. The resulting amplicons were detected using SYTO-9 fluorescence dye in a real-time thermocycler, visual observation after the addition of SYBR Green I, and gel electrophoresis. DNA amplification was detected within 35 min. The SRA LAMP test had an unequivocal detection limit of one pg of purified DNA (equivalent to 10 trypanosomes/ml and 0.1 pg (1 trypanosome/ml using heat-treated buffy coat, while the detection limit for conventional SRA PCR was approximately 1,000 trypanosomes/ml. The expected LAMP amplicon was confirmed through restriction enzyme RsaI digestion, identical melt curves, and sequence analysis. The reproducibility of the SRA LAMP assay using water bath and heat-processed template, and the ease in results readout show great potential for the diagnosis of T. b. rhodesiense in endemic regions.

  17. Rapid and Sensitive Detection of Didymella bryoniae by Visual Loop-Mediated Isothermal Amplification Assay.

    Science.gov (United States)

    Yao, Xiefeng; Li, Pingfang; Xu, Jinghua; Zhang, Man; Ren, Runsheng; Liu, Guang; Yang, Xingping

    2016-01-01

    Didymella bryoniae is a pathogenic fungus that causes gummy stem blight (GSB) in Cucurbitaceae crops (e.g., cantaloupe, muskmelon, cucumber, and watermelon). GSB produces lesions on the stems and leaves, and can also be spread by seeds. Here, we developed a rapid, visual, and sensitive loop-mediated amplification (LAMP) assay for D. bryoniae detection based on sequence-characterized amplified regions (GenBank accession nos GQ872461 and GQ872462) common to the two random amplification of polymorphic DNA group genotypes (RGI and RGII) of D. bryoniae; ideal conditions for detection were optimized for completion in 45 min at 63°C. The sensitivity and specificity of the LAMP assay were further analyzed in comparison with those of a conventional polymerase chain reaction (PCR). The sensitivity of the LAMP assay was 1000-fold higher than that of conventional PCR with a detection limit of 0.1 fg μL(-1) of targeted DNA. The LAMP assay could be accomplished in about 45 min, with the results visible to the naked eye. The assay showed high specificity in discriminating all D. bryoniae isolates from seven other fungal pathogens that occur in Cucurbitaceae crops. The LAMP assay also detected D. bryoniae infection in young muskmelon leaves with suspected early symptoms of GSB disease. Hence, the technique has great potential for developing rapid and sensitive visual detection methods for the D. bryoniae pathogen in crops and seeds. This method has potential application in early prediction of disease and reducing the risk of epidemics. PMID:27625648

  18. 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

  19. 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...

  20. 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.

  1. 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....

  2. 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).

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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.

  15. 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

  16. 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

  17. Acquired Techniques

    DEFF Research Database (Denmark)

    Lunde Nielsen, Espen; Halse, Karianne

    2013-01-01

    Acquired Techniques - a Leap into the Archive, at Aarhus School of Architecture. In collaboration with Karianne Halse, James Martin and Mika K. Friis. Following the footsteps of past travelers this is a journey into tools and techniques of the architectural process. The workshop will focus upon...

  18. 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.

  19. Experimental approach for estimating seismic amplification effects at the top of a ridge and their implication on ground motion predictions: the case of Narni (Central Italy).

    Science.gov (United States)

    Lovati, Sara; Bakavoli, Mohammad; Massa, Marco; Ferretti, Gabriele; Pacor, Francesca; Paolucci, Roberto

    2010-05-01

    From March to September 2009 a dense velocimetric network was installed in correspondence of Narni, a little village in central Italy, built on the top of a massive limestone ridge. The network was planned with the aim to investigate possible local site effects due to the morphology of the ridge, characterized by slopes ranging from 22° to 35° and a maximum difference of quota between top and bottom of 230 m. Three stations were installed at the base of the hill and other 7 monitored the crest. A remarkable dataset was obtained, composed by about 700 earthquakes, the great amount of which occurred after the 06th April 2009, Mw 6.3, L'Aquila earthquake. Site amplifications related to the ridge morphological features were investigated through empirical techniques with and without reference site, computing Spectral Standard Ratio, SSR and Horizontal to Vertical spectral ratio, HVSR. Directional spectral analyses were also performed . The agreement between the results coming from HVSR and SSR techniques allows us to assess with reliability a clear amplification effect for frequencies ranging between 3 and 5 Hz for all stations installed on the crest: in particular, SSR results show an amplification level with respect to the reference station up to 4.5. The highest amplification level (almost double) were observed when the direction perpendicular to the main elongation of the ridge is taken into account. Finally, considering the L'Aquila events with Mw > 4.5 and merging the information coming from the reference and non-reference site techniques, it was possible to recognize further amplification effects, at frequency lower than 1 Hz, probably related not to the morphology of the area but to source and/or polarization effects. Bidimensional numerical simulations were then computed in order to compare the results coming from the experiment with those obtained through numerical modeling. A hybrid finite-boundary element method based on code named HYBRID has been used for

  20. Amplification of Vorticity Near the Stagnation Point of Landing Gear Wheels

    Science.gov (United States)

    Feltham, Graham; Ekmekci, Alis

    2013-11-01

    In this experimental investigation, a stream of steady weak vorticity impinging near the stagnation point of a landing gear wheel is shown to grow and amplify into large-scale vortices that coherently shed from the point of generation. To produce the upstream vorticity, a platinum wire of 100 micron diameter, similar to that used in hydrogen bubble visualization technique, is placed upstream of the wheel model. Experiments are conducted in a recirculating water channel. The wheel diameter is D = 152 mm. The Reynolds number based on the wire diameter is 21 and based on the wheel diameter is 32,500. Qualitative understanding of the vorticity amplification and eventual vortex shedding near the stagnation region of the wheel is achieved by employing the hydrogen bubble visualization technique while quantitative insight is collected using Particle Image Velocimetry (PIV). The size and frequency of the shed vortices are found to depend on the wheel geometry as well as the magnitude and impingement point of the inbound vorticity.

  1. Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes

    Directory of Open Access Journals (Sweden)

    Georg Walch

    2016-04-01

    Full Text Available Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success.

  2. Large-scale solvent-swelling-based amplification of microstructured sharkskin

    International Nuclear Information System (INIS)

    Sophisticated biomimetic microstructures/nanostructures have attracted attention worldwide, but their fabrication technique significantly restricts their application. This study uses natural sharkskin to investigate amplification (i.e., the bioscaling forming process) and thus acquire a complex microstructure that cannot be fabricated by traditional micromachining techniques. The bioscaling forming process adjusts the optimal function region of natural surfaces by utilizing the solvent-swelling effect of polydimethylsiloxane. To accurately replicate amplified sharkskin, the swelling ratio and rate in gaseous and liquid n-hexane were investigated. Epoxy resin was used to produce a positive sharkskin mold. A comparison between the microstructure of the original and amplified sharkskin shows that the swelling ratio can reach a maximum of 34% with gaseous n-hexane and 39% with liquid n-hexane. The accuracy of bioscaling forming was higher than 95%. The drag-reducing effect was also tested. When the sharkskin was amplified 1.34 times, the optimal velocity range of the drag reduction moved from 5.0 to 3.5 m s−1. (paper)

  3. Experimental amplification of an entangled photon: what if the detection loophole is ignored?

    Energy Technology Data Exchange (ETDEWEB)

    Pomarico, Enrico; Sanguinetti, Bruno; Sekatski, Pavel; Zbinden, Hugo; Gisin, Nicolas, E-mail: enrico.pomarico@unige.ch [Group of Applied Physics, University of Geneva, 1211 Geneva (Switzerland)

    2011-06-15

    The experimental verification of quantum features, such as entanglement, at large scales is extremely challenging because of environment-induced decoherence. Indeed, measurement techniques for demonstrating the quantumness of multiparticle systems in the presence of losses are difficult to define, and if they are not sufficiently accurate they can provide wrong conclusions. We present a Bell test where one photon of an entangled pair is amplified and then detected by threshold detectors, whose signals undergo postselection. The amplification is performed by a classical machine, which produces a fully separable micro-macro state. However, by adopting such a technique one can surprisingly observe a violation of the Clauser-Horne-Shimony-Holt inequality. This is due to the fact that ignoring the detection loophole opened by the postselection and the system losses can lead to misinterpretations, such as claiming micro-macro entanglement in a setup where evidently it is not present. By using threshold detectors and postselection, one can only infer the entanglement of the initial pair of photons, and so micro-micro entanglement, as is further confirmed by the violation of a nonseparability criterion for bipartite systems. How to detect photonic micro-macro entanglement in the presence of losses with the currently available technology remains an open question.

  4. Lasing dynamics study by femtosecond time-resolved fluorescence non-collinear optical parametric amplification spectroscopy

    Science.gov (United States)

    Wei, Dang; Qing, Liao; Peng-Cheng, Mao; Hong-Bing, Fu; Yu-Xiang, Weng

    2016-05-01

    Femtosecond time-resolved fluorescence non-collinear optical parametric amplification spectroscopy (FNOPAS) is a versatile technique with advantages of high sensitivity, broad detection bandwidth, and intrinsic spectrum correction function. These advantages should benefit the study of coherent emission, such as measurement of lasing dynamics. In this letter, the FNOPAS was used to trace the lasing process in Rhodamine 6G (R6G) solution and organic semiconductor nano-wires. High-quality transient emission spectra and lasing dynamic traces were acquired, which demonstrates the applicability of FNOPAS in the study of lasing dynamics. Our work extends the application scope of the FNOPAS technique. Project supported by the National Natural Science Foundation of China (Grant Nos. 20925313 and 21503066), the Innovation Program of Chinese Academy of Sciences (Grant No. KJCX2-YW-W25), the Postdoctoral Project of Hebei University, China, and the Project of Science and Technology Bureau of Baoding City, China (Grant No. 15ZG029).

  5. A New Two-Branch Amplification Architecture and its Application with Various Modulated Signals

    Institute of Scientific and Technical Information of China (English)

    W. Hamdane; A. B. Kouki; F. Gagnon

    2011-01-01

    This paper proposes a new two-branch amplification architecture that combines baseband signal decomposition with RF front-end optimization. In the proposed architecture, the filtered modulated signals are separated into two components that are then amplified independently and combined to regenerate an amplified version of the original signal. A branch with an efficient amplifier transmits a low-varying envelope signal that contains the main part of the information. Another branch amplifies the residual portion of the signal. The baseband decomposition and parameters of the RF part are optimized to find the configuration that gives the best power efficiency and linearity. For M-ary quadrature amplitude modulation (M-QAM) signals, this technique is limited in terms of power efficiency. However, for filtered continuous phase modulation (CPM) signals, especially for minimum shift keying (MSK) and Gaussian MSK (GMSK) signals, high power efficiency can be achieved with no significant impact on the overall linearity. The results show that this technique gives better performance than the single-ended ctass-B amplifier.

  6. Highly sensitive chemiluminescence technology for protein detection using aptamer-based rolling circle amplification platform

    Institute of Scientific and Technical Information of China (English)

    Zhi-Juan Cao; Qian-Wen Peng; Xue Qiu; Cai-Yun Liu; Jian-Zhong Lu

    2011-01-01

    A robust, selective and highly sensitive chemiluminescent (CL) platform for protein assay was presented in this paper. This novel CL approach utilized rolling circle amplification (RCA) as a signal enhancement technique and the 96-well plate as the immobilization and separation carrier. Typically, the antibody immobilized on the surface of 96-well plate was sandwiched with the protein target and the aptamer-primer sequence. This aptamer-primer sequence was then employed as the primer of RCA. Based on this design, a number of the biotinylated probes and streptavidin-horseradish peroxidase (SA-HRP) were captured on the plate, and the CL signal was amplified. In summary, our results demonstrated a robust biosensor with a detection limit of 10 fM that is easy to be established and utilized, and devoid of light source. Therefore, this new technique .will broaden the perspective for future development of DNA-based biosensors for the detection of other protein biomarkers related to clinical diseases, by taking advantages of high sensitivity and selectivity.

  7. 滚环DNA扩增的原理、应用和展望%Principle, application and the future:Rolling circle DNA amplification

    Institute of Scientific and Technical Information of China (English)

    肖乐义; 祁自柏; 薛歧庚; 董建军; 杨占清

    2004-01-01

    Rolling circle DNA amplification (RCA) is an isothermal signal amplification method. The phi 29 DNA polymerase is able to synthesize DNA chains more than 70 kilobase pairs in length and achieve a 10\\+5-fold linear and a 10\\+9-fold or more exponential amplification. The product produced by RAC can be linked to the DNA primers or antibodies which immobilized on supporter (such as glass, microplate etc.) that make the RCA especially suitable for the researches about biochip. As a new technique RCA is well suited to on-chip signal amplification that not only provide the sensibitity and specificity of analysis but also keep the multiplexing of stereo-analysis. RCA is also a trace molecular detection method and will be exploited in research and detection of extremely trace biomacromolecule or biomarkers.%滚环DNA扩增(Rolling circle DNA amplification, RCA)是一种等温信号扩增方法,其线性扩增倍数为105,指数化扩增能力大于109,产生的扩增产物连接在固相支持物(如玻片、微孔板等)表面的DNA引物或抗体上(适宜作生物芯片研究).RCA是一种适合在芯片上(on-chip)进行信号扩增的新技术,它既能提供研究分析的敏感性和特异性,又能保持立体分析的多元性.RCA亦是一种痕量的分子检测方法,可用于极其微量的生物大分子和生物标志的检测与研究.

  8. Rapid and sensitive detection of Citrus Bacterial Canker by loop-mediated isothermal amplification combined with simple visual evaluation methods

    Directory of Open Access Journals (Sweden)

    Vojnov Adrian A

    2010-06-01

    Full Text Available Abstract Background Citrus Bacterial Canker (CBC is a major, highly contagious disease of citrus plants present in many countries in Asia, Africa and America, but not in the Mediterranean area. There are three types of Citrus Bacterial Canker, named A, B, and C that have different genotypes and posses variation in host range within citrus species. The causative agent for type A CBC is Xanthomonas citri subsp. citri, while Xanthomonas fuscans subsp. aurantifolii, strain B causes type B CBC and Xanthomonas fuscans subsp. aurantifolii strain C causes CBC type C. The early and accurate identification of those bacteria is essential for the protection of the citrus industry. Detection methods based on bacterial isolation, antibodies or polymerase chain reaction (PCR have been developed previously; however, these approaches may be time consuming, laborious and, in the case of PCR, it requires expensive laboratory equipment. Loop-mediated isothermal amplification (LAMP, which is a novel isothermal DNA amplification technique, is sensitive, specific, fast and requires no specialized laboratory equipment. Results A loop-mediated isothermal amplification assay for the diagnosis of Citrus Bacterial Canker (CBC-LAMP was developed and evaluated. DNA samples were obtained from infected plants or cultured bacteria. A typical ladder-like pattern on gel electrophoresis was observed in all positive samples in contrast to the negative controls. In addition, amplification products were detected by visual inspection using SYBRGreen and using a lateral flow dipstick, eliminating the need for gel electrophoresis. The sensitivity and specificity of the assay were evaluated in different conditions and using several sample sources which included purified DNA, bacterium culture and infected plant tissue. The sensitivity of the CBC-LAMP was 10 fg of pure Xcc DNA, 5 CFU in culture samples and 18 CFU in samples of infected plant tissue. No cross reaction was observed with DNA

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. "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).

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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...

  20. 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.

  1. 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.

  2. 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...

  3. 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.

  4. 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 ...

  5. 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.

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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

  11. 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...

  12. [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

  13. 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....

  14. 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

  15. 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

  16. 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

  17. 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.…

  18. 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.

  19. 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.

  20. 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.