Relevant bibliographies by topics / Nucleic-acid Amplification and Quantification

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Nucleic-acid Amplification and Quantification'

Author: Grafiati
Published: 6 September 2023
Last updated: 7 September 2023

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Journal articles on the topic "Nucleic-acid Amplification and Quantification"

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Huggett, Jim, Clare Green, and Alimuddin Zumla. "Nucleic acid detection and quantification in the developing world." Biochemical Society Transactions 37, no. 2 (March 20, 2009): 419–23. http://dx.doi.org/10.1042/bst0370419.

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Techniques using nucleic acid amplification have not had the same amount of impact on research and clinical diagnosis in the developing world as that observed in the West. This is unsurprising when the costs and infrastructure required to perform nucleic acid amplification are considered. Despite this, nucleic acid amplification is being increasingly used in both research and diagnosis in countries such as Zambia and Tanzania. Scientific research in the developing world is made possible through the support and development of the necessary laboratory infrastructure and the establishment of special transport for the reagents and samples. This has enabled world-leading country-relevant research to be performed by local scientists on subjects ranging from rapid diagnosis of infectious diseases to measuring the RNA gene expression in an immune response. Concomitantly, the challenge presented by the need for tests that are more appropriate for a resource-poor setting has led to a number of newer methodologies for nucleic acid detection, which can be tailored to be performed in the field without the need for training in molecular biology. As nucleic acid amplification techniques become both simpler and cheaper, their impact is likely to play an increasingly crucial role in research and diagnosis in the developing world.
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Kreutz, Jason E., Jiasi Wang, Allison M. Sheen, Alison M. Thompson, Jeannette P. Staheli, Michael R. Dyen, Qinghua Feng, and Daniel T. Chiu. "Self-digitization chip for quantitative detection of human papillomavirus gene using digital LAMP." Lab on a Chip 19, no. 6 (2019): 1035–40. http://dx.doi.org/10.1039/c8lc01223g.

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Becherer, Lisa, Jacob Friedrich Hess, Sieghard Frischmann, Mohammed Bakheit, Hans Nitschko, Silvina Stinco, Friedrich Zitz, et al. "Point-of-Care System for HTLV-1 Proviral Load Quantification by Digital Mediator Displacement LAMP." Micromachines 12, no. 2 (February 5, 2021): 159. http://dx.doi.org/10.3390/mi12020159.

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This paper presents a universal point-of-care system for fully automated quantification of human T-cell lymphotropic virus type 1 (HTLV-1) proviral load, including genomic RNA, based on digital reverse RNA transcription and c-DNA amplification by MD LAMP (mediator displacement loop-mediated isothermal amplification). A disposable microfluidic LabDisk with pre-stored reagents performs automated nucleic acid extraction, reaction setup, emulsification, reverse transcription, digital DNA amplification, and quantitative fluorogenic endpoint detection with universal reporter molecules. Automated nucleic acid extraction from a suspension of HTLV-1-infected CD4+ T-lymphocytes (MT-2 cells) yielded 8 ± 7 viral nucleic acid copies per MT-2 cell, very similar to the manual reference extraction (7 ± 2 nucleic acid copies). Fully automated sample processing from whole blood spiked with MT-2 cells showed a comparable result of 7 ± 3 copies per MT-2 cell after a run time of two hours and 10 min.
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Mauk, Michael, Changchun Liu, Jinzhao Song, and Haim Bau. "Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification." Microarrays 4, no. 4 (October 20, 2015): 474–89. http://dx.doi.org/10.3390/microarrays4040474.

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Gullett, Jonathan C., and Frederick S. Nolte. "Quantitative Nucleic Acid Amplification Methods for Viral Infections." Clinical Chemistry 61, no. 1 (January 1, 2015): 72–78. http://dx.doi.org/10.1373/clinchem.2014.223289.

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AbstractBACKGROUNDOver the past 2 decades there have been substantial improvements in the methods used to quantify viral nucleic acid in body fluids and in our understanding of how to use viral load measurements in the diagnosis and management of patients with a number of viral infections. These methods are now integrated into a wide range of diagnostic and treatment guidelines and commonly deployed in a variety of clinical settings.CONTENTQuantitative nucleic acid amplification methods that are used to measure viral load are described along with key issues and important variables that affect their performance. Particular emphasis is placed on those methods used in clinical laboratories as US Food and Drug Administration–cleared or laboratory-developed tests. We discuss the clinical applications of these methods in patients with HIV-1, hepatitis C virus, hepatitis B virus, cytomegalovirus, Epstein-Barr virus, and BK polyomavirus infections. Finally, the current challenges and future directions of viral load testing are examined.SUMMARYQuantitative nucleic acid amplification tests provide important information that can be used to predict disease progression, distinguish symptomatic from asymptomatic infection, and assess the efficacy of antiviral therapy. Despite the advances in technology, large challenges remain for viral testing related to accuracy, precision, and standardization. Digital PCR, a direct method of quantification of nucleic acids that does not rely on rate-based measurements or calibration curves, may address many of the current challenges.
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Zhang, Min, Jiajia Wu, Zhaoai Shi, Aocheng Cao, Wensheng Fang, Dongdong Yan, Qiuxia Wang, and Yuan Li. "Molecular Methods for Identification and Quantification of Foodborne Pathogens." Molecules 27, no. 23 (November 26, 2022): 8262. http://dx.doi.org/10.3390/molecules27238262.

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Foodborne pathogens that enter the human food chain are a significant threat worldwide to human health. Timely and cost-effective detection of them became challenging for many countries that want to improve their detection and control of foodborne illness. We summarize simple, rapid, specific, and highly effective molecular technology that is used to detect and identify foodborne pathogens, including polymerase chain reaction, isothermal amplification, loop-mediated isothermal amplification, nucleic acid sequence-based amplification, as well as gene chip and gene probe technology. The principles of their operation, the research supporting their application, and the advantages and disadvantages of each technology are summarized.
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Kurn, Nurith, Pengchin Chen, Joe Don Heath, Anne Kopf-Sill, Kathryn M. Stephens, and Shenglong Wang. "Novel Isothermal, Linear Nucleic Acid Amplification Systems for Highly Multiplexed Applications." Clinical Chemistry 51, no. 10 (October 1, 2005): 1973–81. http://dx.doi.org/10.1373/clinchem.2005.053694.

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Abstract Background: Global analysis of the genome, transcriptome, and proteome is facilitated by the recent development of tools for large-scale, highly parallel analysis. We describe a novel nucleic acid amplification system that generates products by several methods. 3′-Ribo-SPIA™ primes cDNA synthesis at the 3′ polyA tail, and whole transcript (WT)-Ribo-SPIA primes cDNA synthesis across the full length of the transcripts and thus provides whole-transcriptome amplification, independent of the 3′ polyA tail. Methods: We developed isothermal linear nucleic acid amplification systems, which use a single chimeric primer, for amplification of DNA (SPIA) and RNA (Ribo-SPIA). The latter allows mRNA amplification from as little as 1 ng of total RNA. Amplification efficiency was calculated based on the delta threshold cycle between nonamplified cDNA targets and amplified cDNA. The amounts and quality of total RNA and amplification products were determined after purification of the amplification products. GeneChip® array gene expression profiling and real-time PCR were used to test the accuracy and reproducibility of the method. Quantification of cDNA products (before and after amplification) at the 2 loci along the transcripts was used to assess product length (for evaluation of the 3′-initiated Ribo-SPIA) and equal representation throughout the length of the transcript (for evaluation of the whole transcript amplification system, WT-Ribo-SPIA™). Results: Ribo-SPIA–based global RNA amplification exhibited linearity over 6 orders of magnitude of transcript abundance and generated microgram amounts of amplified cDNA from as little as 1 ng of total RNA. Conclusions: The described methods enable comprehensive gene expression profiling and analysis from limiting biological samples. The WT-Ribo-SPIA procedure, which enables amplification of non–polyA-tailed RNA, is suitable for amplification and gene expression analysis of both eukaryotic and prokaryotic biological samples.
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Morcia, Caterina, Roberta Ghizzoni, Chiara Delogu, Lorella Andreani, Paola Carnevali, and Valeria Terzi. "Digital PCR: What Relevance to Plant Studies?" Biology 9, no. 12 (November 30, 2020): 433. http://dx.doi.org/10.3390/biology9120433.

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Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
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Warrior, Usha, Yihong Fan, Caroline A. David, Julie A. Wilkins, Evelyn M. McKeegan, James L. Kofron, and David J. Burns. "Application of QuantiGene™ Nucleic Acid Quantification Technology for High Throughput Screening." Journal of Biomolecular Screening 5, no. 5 (October 2000): 343–51. http://dx.doi.org/10.1177/108705710000500506.

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To identify inhibitors of interleukin-8 (IL-8) production, a high throughput assay was developed using the Quanti-Gene™ nucleic acid quantification kit that employs branched-chain DNA (bDNA) technology to measure the mRNA directly from cells. Unlike polymerase chain reaction and other technologies that employ target amplification, the QuantiGene system uses signal amplification. To perform the assay, various molecular probes capable of hybridizing with IL-8 mRNA were designed and synthesized. A human lung epithelial cell line was treated with interleukin-la (IL-la) to stimulate the IL-8 gene expression and the mRNA was measured using the QuantiGene system. The QuantiGene assay was sensitive, flexible, and reproducible and achieved equivalent or better sensitivity than promoter-reporter assays, and eliminated the time required for constructing a promoter-reporter system. Our data show that bDNA technology has the potential to be used as a high throughput screening assay.
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Li, Xue-Mei, Jie Luo, Ning-Bo Zhang, and Qing-Li Wei. "Nucleic acid quantification using nicking–displacement, rolling circle amplification and bio-bar-code mediated triple-amplification." Analytica Chimica Acta 881 (June 2015): 117–23. http://dx.doi.org/10.1016/j.aca.2015.05.011.

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Dissertations / Theses on the topic "Nucleic-acid Amplification and Quantification"

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Hernández-Neuta, Iván. "Nucleic acid analysis tools : Novel technologies and biomedical applications." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-146334.

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Nucleic acids are fundamental molecules of living organisms functioning essentially as the molecular information carriers of life. From how an organism is built to how it responds to external conditions, all of it, can be found in the form of nucleic acid sequences inside every single cell of every life form on earth. Therefore, accessing these sequences provides key information regarding the molecular identity and functional state of any living organism, this is very useful for areas like biomedicine, where accessing and understanding these molecular signatures is the key to develop strategies to understand, treat and diagnose diseases. Decades of research and technological advancements have led to the development of a number of molecular tools and engineering technologies that allow accessing the information contained in the nucleic acids. This thesis provides a general overview of the tools and technologies available for nucleic acid analysis, and proposes an illustrative concept on how molecular tools and emergent technologies can be combined in a modular fashion to design methods for addressing different biomedical questions. The studies included in this thesis, are focused on the particular use of the molecular tools named: padlock and selector probes, rolling circle amplification, and fluorescence detection of single molecules in combination with microfluidics and portable microscopy. By using this combination, it became possible to design and demonstrate novel approaches for integrated nucleic acid analysis, inexpensive digital quantification, mobile-phone based diagnostics and the description of viral infections. These studies represent a step forward towards the adoption of the selected group of tools and technologies, for the design and building of methods that can be used as powerful alternatives to conventional tools used in molecular diagnostics and virology.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Manuscript.

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Lee, Dong-Hun. "Nucleic acid amplification testing for screening of individual blood units." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2007. http://dare.uva.nl/document/48208.

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Daher, Rana. "Recombinase polymerase amplification technology : Assessment for nucleic acid-based acid-based point-of-care diagnostics." Doctoral thesis, Université Laval, 2015. http://hdl.handle.net/20.500.11794/26269.

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Cette thèse de doctorat porte dans l’ensemble une étude approfondie sur une technologie émergente pour l’amplification isotherme des acides nucléiques appelée recombinase polymerase amplification (RPA). L’introduction porte une description détaillée sur la RPA. Cette revue de littérature documente et discute les diverses applications de la RPA en soulignant les connaissances actuelles concernant les applications diagnostiques. Malgré la composition complexe de la RPA (6 à 7 protéines dans le même mélange réactionnel), cette dernière s’avère une technologie rapide (générant des résultats < 20 min), spécifique et sensible (détection de l’ordre de quelques copies de génome), et largement appliquée dans différentes disciplines. Ces avantages nous permettent de croire que la RPA possède la flexibilité nécessaire pour être utilisée comme outil de diagnostic rapide des maladies infectieuses en réduisant le temps d’obtention des résultats à moins d’une heure au lieu de 2 à 3 jours avec les tests de cultures standards. En conséquence, il sera possible d’intégrer la RPA dans des plateformes microfluidiques ou laboratoire sur puce qui permettent la préparation d’échantillons, l’amplification et la détection des acides nucléiques des microbes causant des infections. En premier lieu, les travaux de cette thèse ont généré des lignes directrices additionnelles pour la conception des amorces/sondes RPA. En second lieu, nos travaux ont permis de développer un essai diagnostic RPA pour la détection des streptocoques du groupe B, responsables de la septicémie et la méningite chez les nouveau-nés. Cet essai fut le premier à évaluer la performance de la RPA avec des échantillons cliniques humains. Ce test diagnostic RPA a été comparé à une méthode de référence, la réaction en chaîne par polymérase (PCR). Cette démonstration sur des échantillons cliniques nous à inciter à pousser notre étude pour réaliser le dernier objectif de ce projet qui consistait à automatiser la RPA par intégration dans un système microfluidique miniaturisé centripète. Une collaboration avec des experts en génies et en matériaux a permis de générer un dispositif microfluidique appelé blade ainsi de l’instrument impliqué dans l’opération des différentes tâches mécanistiques. Ces résultats préliminaires suggèrent qu’il sera important d’offrir un système automatisé complet applicable au chevet du patient. Par conséquence, il sera possible d’exécuter une analyse complète des agents infectieux en moins d’une heure sans le besoin des procédures complexes de préparation et de transport des échantillons cliniques ni le recours à du personnel qualifié.
This dissertation consists of an exhaustive study on an emerging technology for isothermal amplification of nucleic acids called recombinase polymerase amplification (RPA). The introduction of this thesis is a detailed description of the RPA. This review documents and discusses the various applications of this technology by pointing to the current knowledge about RPA for diagnostic applications. Despite the complex composition of RPA (6 to 7 proteins in the same reaction mixture), the latter was shown to be rapid (generating results in < 20 min), specific and sensitive (detecting few target genome copies), and applied widely in different fields. Based on these advantages, we assume that RPA has a flexibility allowing it to be used for the rapid diagnosis of infectious diseases thus reducing time-to-result to less than an hour. Consequently, it will be possible to integrate RPA in microfluidic platforms providing a lab-on chip system. The first part of this doctoral project generated additional guidelines for RPA primers/probes design to develop specific RPA diagnostic assays. Second, we developed an RPA diagnostic test for the detection of group B streptococci, responsible for sepsis and meningitis in newborns. This assay was the first to evaluate RPA with human clinical samples. This diagnostic test was compared to a reference method, the polymerase chain reaction (PCR). This demonstration with clinical samples served to carry out the final objective of this project that was to automate RPA in a miniaturized microfluidic centripetal system. Collaboration with engineers and experts in materials has generated the microfluidic device called "blade" and the instrument involved in the operation of various mechanistic tasks. These preliminary results suggested that it will be important to provide an automated system applicable at bedside. Consequently, it will be possible to perform a complete analysis of infectious agents in less than an hour without the need for complex procedures for the preparation and transport of clinical specimens or the assistance of qualified personnel.
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Matinyenya, Brian. "Novel and newer nucleic acid amplification tests for the diagnosis of TB." Master's thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20680.

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Background: Current tools for TB diagnosis have suboptimal accuracy, perform poorly in diagnosing extra-pulmonary TB, and are not point of care; hence results have a slow turn-around time. Objective: This project evaluated the diagnostic accuracy of the promising novel loop mediated isothermal amplification (LAMP) assay on sputum, and that of the semi-automated Xpert MTB/RIF (Xpert) test on non-sputum specimens (bronchoalveolar lavage fluid [BALF], tracheal aspirates, and cerebrospinal fluid [CSF]) from South African patients with suspected TB (the accuracy of Xpert using these fluids was unknown at the time this work was performed). Methodology: Biological samples (sputum, tracheal aspirates, BALF, or CSF) were collected from patients with suspected TB. Liquid culture served as the reference standard for the diagnosis of definite TB. Accuracy was evaluated according to HIV and smear microscopy status, where appropriate. The relationship between test performance and bacterial load (culture time-to-positivity [TTP]) was also compared. For the evaluation of LAMP, 2 spot sputa of approximately 4 ml were collected from 301 patients (60 μl of sputum was used for the assay). For the evaluation of Xpert on BALF, 152 patients who were sputum scarce or smear-negative were recruited (1 ml of the BALF aliquot or a re-suspended pellet from 10 ml BALF was used). For the evaluation of Xpert on tracheal aspirates, 120 tracheal aspirates from patients enrolled in the intensive care unit (ICU) were tested. For the evaluation of Xpert on CSF, 235 patients with suspected TBM had a lumbar puncture with 1 ml of CSF or where available a re-suspended pellet from 3 ml of CSF evaluated using Xpert.
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Syed, Shahida Nina. "Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9617.

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Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of RNA and DNA replication during cell division. However, the reversible hybridisation of complementary nucleic acids is equally crucial in nearly all molecular biology technologies, ranging from nucleic acid amplification technologies, such as the polymerase chain reaction, and DNA biosensors to next generation sequencing. For nucleic acid amplification technologies, controlled DNA denaturation and renaturation is particularly essential and achieved by cycling elevated temperatures. Although this is by far the most commonly used method, the management of rapid temperature changes requires bulky instrumentation and intense power supply. These factors so far precluded the development of true point-of-care tests for molecular diagnostics. This Thesis explored the possibility of using electrochemical means to control reversible DNA hybridisation by using electroactive intercalators. First, fluorescence-based melting curve analysis was employed to gain an in depth understanding of the reversible process of DNA hybridisation. Fundamental properties, such as stability of the double helix, were investigated by studying the effect of common denaturing agents, such as formamide and urea, pH and monovalent salt concentration. Thereafter, four different electroactive intercalators and their effect on the thermodynamic stability of duplex DNA were screened. The intercalators investigated were methylene blue, thionine, daunomycin and adriamycin. Absorbance-based melting curve analysis revealed a significant increase of the melting temperature of duplex DNA in the presence of oxidised daunomycin. This was not observed in the presence of chemically reduced daunomycin, which confirmed the hypothesis that switching of the redox-state of daunomycin altered its properties from DNA binding to non-binding. Accordingly this altered the thermodynamic stability of duplex DNA. The difference in the stability of duplex DNA, as a direct result of the redox-state of daunomycin, was exploited to drive cyclic electrochemically controlled DNA denaturation and renaturation under isothermal conditions. This proof-of-principle was demonstrated using complementary synthetic 20mer and 40mer DNA oligonucleotides. Analysis with in situ UV–vis and circular dichroism spectroelectrochemistry, as two independent techniques, indicated that up to 80 % of the duplex DNA was reversibly hybridised. Five cycles of DNA denaturation and renaturation were achieved and gel electrophoresis as well as NMR showed no degradation of DNA or daunomycin. As no extreme conditions were implicated, no covalent modification of DNA was required and isothermal conditions were kept, this finding has great potential to simplify future developments of miniaturised and portable bioanalytical systems for nucleic acid-based molecular diagnostics.
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Thomas, Alistair Owen. "Detection of bacterial gene expression by a novel isothermic nucleic acid amplification technology." Thesis, University of Bath, 2004. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410924.

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A novel probe-based technique called Signal-Mediated Amplification Reaction Technology (SMART) was optimised for detection of RNA targets in order to quantify gene expression. The SMART assay was used to quantify both 23 S rRNA in P. aeruginosa PAOl and gfpmuti mRNA in the plasmid-borne rpoSwgfpmvXi fusions P. aeruginosa SS429 and SS431. However, the assay was not sufficiently sensitive to detect gfpmvfo mRNA from the chromosomal rpoS::gfpmut3 fusion P. aeruginosa SS336. SDS-PAGE analysis of outer membrane proteins of P. aeruginosa PAOl revealed that cells grown in a reported iron-replete chemically defined medium CDMio were in fact limiting for iron. Modifications to the growth medium such as increased iron concentration, reduction in pH and the addition of citrate and ascorbate all failed to produce an iron-replete phenotype. This was achievable only when MOPSO buffer was replaced with phosphate buffer, indicating that by some unknown mechanism MOPSO can reduce iron availability in minimal media. The effects of nutrient limitation on rpoS expression in P. aeruginosa planktonic and biofilm culture were investigated using direct fluorescence measurement of rpoS::gfpmut3 chromosomal and plasmid fusions. In planktonic culture, nutrient-replete and magnesium-limited conditions resulted in an increase in rpoS expression whilst minimal levels of rpoS expression were seen in both iron-limited and glucose-limited conditions. Furthermore, minimal expression of rpoS was noted in P. aeruginosa biofilms in glucose, magnesium and iron-limited conditions.
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Xiao, Linlin. "Detection of Viable Foodborne Pathogens and Spoilage Microorganisms by Nucleic Acid Amplification Based Platforms." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1308284180.

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CORAL, LUCIA. "HIGH-RESOLUTION NUCLEIC ACID ANALYSIS WITH A DNA NANOTECHNOLOGY APPROACH." Doctoral thesis, Università degli Studi di Trieste, 2017. http://hdl.handle.net/11368/2908115.

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The goal of my research program is to develop a DNA-based nanosensor for nucleic acids analysis. I plan to use DNA Origami nanostructures that are formed by a-few-thousand-nucleotides-long, circular, single stranded (ss)DNA “scaffold” folded to form a specific shape by the action of a few hundreds of short (approx. 30 nucleotides) ssDNA “staples”, which hybridize over non-consecutive regions of the scaffold. Staples can be incorporated within the structure with well-defined stoichiometry and some of them can be designed to serve as highly-specific receptor for short nucleic acids sequences. I plan to introduce a restriction site within staples adjacent to such probes to permit their steric protection from enzymatic degradation as a consequence of a probe-target recognition event in their vicinity. The restriction reaction, therefore, “writes” the amount of target molecules captured on the nanosensors by permanently modifying certain target-specific staples within the DNA nanostructure. In turn, the amount of such modified staples is associated with the amount of target molecules captured on the nanosensor surface from the solution, and can be subsequently analyzed with standard DNA quantification techniques such as quantitative PCR (qPCR), or high-throughput DNA sequencing. This research plan is based on recent results obtained in our laboratory showing that, in self-assembled DNA structures, restriction enzymatic reactions are steric-regulated in a step-wise fashion. Therefore, one goal of this PhD thesis is the development of a quantitative assay to evaluate the efficiency of enzymatic reactions within such nanostructures, as well as staples incorporation and stability for aiding fundamental studies of enzymatic reactions in DNA nanostructures. Specifically, the restriction quantification method proposed is based on a linear PCR (L-PCR) amplification reaction that involves staple-specific carriers (70-nucleotide-long ssDNA) that can fully hybridize to staple fragments produced by the enzymatic cutting. The polymerase action leads to the formation of a duplex DNA fragment 70 base pairs (bp) long for each cleaved staple, whereas the hybridization of un-cleaved staples on the carrier prevents such polymerase reaction. To study staples incorporation efficiency, the same protocol can be used, but DNA carriers are designed to hybridize the full length of the DNA staple sequence. I prepared L-PCR samples to evaluate next-generation sequencing (NGS) quantification accuracy and L-PCR efficiency. As a proof-of-concept, I analyzed 5 staples of a triangular DNA nanostructure and obtained information on their incorporation efficiency or cleavage. This thesis also describes the design and development of a DNA based nanosensor for improving the accuracy of short nucleic acid quantification with qPCR. The work aims at coupling qPCR with a self-assembled nanosensor, which can help overcome amplification and retro-transcription reaction bias, and circumvent the detection threshold of 2-fold concentration variation, without requiring updates to traditional qPCR instrumentation. Components of such sensor are three consecutive “foot-loop” DNA probes each carrying a target-complementary sequence in the loop. Probes are assembled over a common scaffold that joins their “feet”. Each “foot” carries a restriction site and upon hybridization of three copies of the same target molecule on the respective loops, the site of each foot is destabilized (termed “bingo” configuration). Only in this case, the whole scaffold is protected from enzymatic cleavage and can be amplified with PCR. Target and bingo-scaffold concentrations are correlated by power function of 3. The results obtained demonstrate the increased accuracy of the Bingo-qPCR assay with respect to standard qPCR in evaluating small variation of enzymatic activity, and prove the feasibility of the target detection switch-based reaction.
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Choi, Kwan-yue. "A molecular epidemiology study on conjunctivitis using conventional nucleic acid amplification technologies and resequencing microarray." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B44248465.

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Choi, Kwan-yue, and 蔡君如. "A molecular epidemiology study on conjunctivitis using conventional nucleic acid amplification technologies and resequencing microarray." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B44248465.

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Books on the topic "Nucleic-acid Amplification and Quantification"

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Myers, Meagan B., and Cynthia A. Schandl, eds. Clinical Applications of Nucleic Acid Amplification. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2950-5.

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A, Toranzos Gary, ed. Environmental applications of nucleic acid amplification techniques. Lancaster, PA: Technomic Pub. Co., 1997.

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Lee, Helen H., Stephen A. Morse, and Ørjan Olsvik, eds. Nucleic Acid Amplification Technologies Application to Disease Diagnosis. Boston, MA: Birkhäuser Boston, 1996. http://dx.doi.org/10.1007/978-1-4612-2454-9.

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Zhang, Shusheng, Sai Bi, and Xinyue Song, eds. Nucleic Acid Amplification Strategies for Biosensing, Bioimaging and Biomedicine. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-7044-1.

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Lauerman, Lloyd Herman. Nucleic acid amplification assays for diagnosis of animal diseases. [Madison, Wis.]: American Association of Veterinary Laboratory Diagnosticians, 1998.

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Giulio, Pisani, ed. Nucleic acid amplification technology (NAT) for the detection of Hepatitis C Virus (HCV) in plasma pools: Validation report. Roma: Istituto superiore di sanità, 2000.

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New York Academy of Sciences. Pharmaceutical science to improve the human condition: Prix Galien 2010 : winners and finalist candidates of the Prix Galien USA, International, and Pro Bono Humanitarian Awards 2010. Malden, MA: Wiley Periodicals, 2011.

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McNerney, Ruth. Evaluation of the role of nucleic acid amplification tests in the routine diagnosis of tuberculosis in developing countries with a high prevalence of HIV infection: Report of a three year collaborative research project (1996-1999). Lusaka: s.n., 2000.

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Scialpi, Angela, and Alessio Mengoni, eds. La PCR e le sue varianti. Florence: Firenze University Press, 2008. http://dx.doi.org/10.36253/978-88-6453-159-5.

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The book "La PCR e le sue varianti" is designed as a reference tool for those whose laboratory activities deal with methods based on nucleic acid amplification. The text provides the theoretical bases of the polymerase chain reaction (PCR) and its variants (e.g. RT-PCR, quantitative PCR, isothermic PCR) in a rapid and concise manner and describes the principal applications used for genetic identification and the study of genetic polymorphism, in the form of a protocol that can be easily consulted by the users.
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Bernd, Kochanowski, and Reischl Udo, eds. Quantitative PCR protocols. Totowa, N.J: Humana Press, 1999.

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Book chapters on the topic "Nucleic-acid Amplification and Quantification"

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Cross, L., C. Potts, and J. G. Anson. "Sensitive and Rapid Detection and Quantification of Nucleic Acids." In Methods in DNA Amplification, 19–26. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4615-2530-1_3.

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Zhang, Zhenhao, Weimin Tian, Wei Ren, Zhengping Li, and Chenghui Liu. "Quantification of Site-Specific 5-Formylcytosine by Integrating Peptide Nucleic Acid-Clamped Ligation with Loop-Mediated Isothermal Amplification." In Springer Protocols Handbooks, 77–91. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1229-3_8.

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Yoda, Minami, Jean-Luc Garden, Olivier Bourgeois, Aeraj Haque, Aloke Kumar, Hans Deyhle, Simone Hieber, et al. "Nucleic Acid Amplification." In Encyclopedia of Nanotechnology, 1911. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-90-481-9751-4_100600.

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Shen, Feng. "SlipChip Device for Digital Nucleic Acid DNA nucleic acid amplification Nucleic acid amplification Amplification." In Methods in Molecular Biology, 123–32. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6734-6_10.

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Lehmann, Marc, and Roland P. H. Schmitz. "Nucleic Acid Amplification Techniques." In Modern Techniques for Pathogen Detection, 55–111. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2015. http://dx.doi.org/10.1002/9783527687978.ch3.

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Ørum, Henrik, Christoph Kessler, and Troels Koch. "Peptide Nucleic Acid." In Nucleic Acid Amplification Technologies Application to Disease Diagnosis, 29–48. Boston, MA: Birkhäuser Boston, 1997. http://dx.doi.org/10.1007/978-1-4612-2454-9_3.

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Pannu, Neesh, Xiaoyan Wen, John A. Kellum, John Fildes, N. Al-Subaie, Mark Hamilton, Susan M. Lareau, et al. "Nucleic Acid Amplification Tests (NAAT)." In Encyclopedia of Intensive Care Medicine, 1579. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-00418-6_3224.

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Kessler, Harald H., and Evelyn Stelzl. "Isothermal Nucleic Acid Amplification Methods." In Clinical Virology Manual, 137–44. Washington, DC, USA: ASM Press, 2016. http://dx.doi.org/10.1128/9781555819156.ch12.

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Loens, Katherine, D. Ursi, H. Goossens, and M. Ieven. "Nucleic Acid Sequence-Based Amplification." In Medical Biomethods Handbook, 273–91. Totowa, NJ: Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-870-6:273.

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Mosammaparast, Nima, and Alexander J. McAdam. "Real-Time Nucleic Acid Quantification." In Advanced Techniques in Diagnostic Microbiology, 345–53. Boston, MA: Springer US, 2012. http://dx.doi.org/10.1007/978-1-4614-3970-7_19.

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Conference papers on the topic "Nucleic-acid Amplification and Quantification"

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Stanoszek, Lauren, Thomas Blomquist, Erin L. Crawford, Bradly Austermiller, Casey Spitzer, Paige FS Willey, and James C. Willey. "Abstract 2232: Effectiveness evaluation of an in vitro nucleic acid amplification test for quantification of BCR-ABL fusion transcript variants in human whole blood." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-2232.

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Weigl, Bernhard H., Gonzalo Domingo, Jay Gerlach, Dennis Tang, Darrel Harvey, Nick Talwar, Alex Fichtenholz, Bill van Lew, and Paul LaBarre. "Non-instrumented nucleic acid amplification assay." In MOEMS-MEMS 2008 Micro and Nanofabrication, edited by Wanjun Wang and Claude Vauchier. SPIE, 2008. http://dx.doi.org/10.1117/12.763650.

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Song, B. F., Q. Song, W. Jin, Q. C. Tian, and Y. Mu. "Absolute Nucleic Acid Quantification System and Analysis." In 2015 International Conference on Industrial Technology and Management Science. Paris, France: Atlantis Press, 2015. http://dx.doi.org/10.2991/itms-15.2015.410.

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Hollenstein, Marcel. "Modified nucleoside triphosphates in rolling circle amplification." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414103.

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Ménová, Petra, and Michal Hocek. "Preparation of modified oligonucleotides by nicking enzyme amplification reaction." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414324.

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Liu, Mingdian, Zheyan Tang, Hosein Monshat, Yuxin Zhao, and Meng Lu. "Portable instrument for paper-based isothermal nucleic acid amplification tests." In CLEO: Applications and Technology. Washington, D.C.: OSA, 2020. http://dx.doi.org/10.1364/cleo_at.2020.jtu2f.13.

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LaBarre, Paul, David Boyle, Kenneth Hawkins, and Bernhard Weigl. "Instrument-free nucleic acid amplification assays for global health settings." In SPIE Defense, Security, and Sensing, edited by Sárka O. Southern, Kevin N. Montgomery, Carl W. Taylor, Bernhard H. Weigl, B. V. K. Vijaya Kumar, Salil Prabhakar, and Arun A. Ross. SPIE, 2011. http://dx.doi.org/10.1117/12.882868.

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Hassibi, Arjang, Thomas H. Lee, Ronald W. Davis, and Nader Pourmand. "Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays." In Biomedical Optics 2003, edited by Dan V. Nicolau and Ramesh Raghavachari. SPIE, 2003. http://dx.doi.org/10.1117/12.478095.

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Efimov, V. A., O. G. Chakhmakhcheva, M. V. Choob, and D. Archdeacon. "Using chimeric DNA/RNA molecular beacons for target-specific signal amplification." In XIIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2002. http://dx.doi.org/10.1135/css200205308.

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Riedl, Jan, and Cynthia J. Burrows. "Site-specific labeling of DNA base modifications for amplification of DNA damage." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414091.

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Reports on the topic "Nucleic-acid Amplification and Quantification"

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James, Conrad D., Kenneth Roy Pohl, Mark Steven Derzon, Jaime McClain, and Komandoor Achyuthan. Quantification of false positive reduction in nucleic acid purification on hemorrhagic fever DNA. Office of Scientific and Technical Information (OSTI), November 2006. http://dx.doi.org/10.2172/899359.

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Shen, Yanqin, Likui Fang, Bo Ye, and Guocan Yu. Diagnostic accuracy of nucleic acid amplification tests for abdominal tuberculosis: a protocol of systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, June 2020. http://dx.doi.org/10.37766/inplasy2020.6.0030.

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Yu, Guocan, Yanqin Shen, Xudong Xu, and Lihua Lin. Nucleic acid amplification techniques for rapid diagnosis of non-tuberculous mycobacteria: A protocol of systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2020. http://dx.doi.org/10.37766/inplasy2020.11.0076.

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