Relevant bibliographies by topics / Nucleic acids high throughput sequencing

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

Academic literature on the topic 'Nucleic acids high throughput sequencing'

Author: Grafiati
Published: 4 June 2021
Last updated: 18 February 2022

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Journal articles on the topic "Nucleic acids high throughput sequencing"

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Ng, Siemon, Cassandra Braxton, Marc Eloit, et al. "Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation." Viruses 10, no. 10 (2018): 566. http://dx.doi.org/10.3390/v10100566.

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A key step for broad viral detection using high-throughput sequencing (HTS) is optimizing the sample preparation strategy for extracting viral-specific nucleic acids since viral genomes are diverse: They can be single-stranded or double-stranded RNA or DNA, and can vary from a few thousand bases to over millions of bases, which might introduce biases during nucleic acid extraction. In addition, viral particles can be enveloped or non-enveloped with variable resistance to pre-treatment, which may influence their susceptibility to extraction procedures. Since the identity of the potential adventitious agents is unknown prior to their detection, efficient sample preparation should be unbiased toward all different viral types in order to maximize the probability of detecting any potential adventitious viruses using HTS. Furthermore, the quality assessment of each step for sample processing is also a critical but challenging aspect. This paper presents our current perspectives for optimizing upstream sample processing and library preparation as part of the discussion in the Advanced Virus Detection Technologies Interest group (AVDTIG). The topics include: Use of nuclease treatment to enrich for encapsidated nucleic acids, techniques for amplifying low amounts of virus nucleic acids, selection of different extraction methods, relevant controls, the use of spike recovery experiments, and quality control measures during library preparation.
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Matsvay, Alina, Daniel Kiselev, Andrey Ayginin, et al. "Metabarcoding-Like Approach for High Throughput Detection and Identification of Viral Nucleic Acids." Proceedings 50, no. 1 (2020): 136. http://dx.doi.org/10.3390/proceedings2020050136.

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Next generation sequencing (NGS) technologies have greatly enhanced our ability to identify new viral pathogens in various types of biological samples. This approach has led to the discovery of new viruses and has revealed hidden associations of viromes with many diseases. However, unlike the 16S rRNA, which allows for bacterial detection by metabarcoding, the diversity and variability of viral genomes render the creation of universal oligonucleotides for targeting all known and novel viruses impossible. While whole­genome sequencing solves this problem, its efficiency is inadequate due to the high cost per sample and relatively low sensitivity. Furthermore, the existing approaches to designing oligonucleotides for targeted PCR enrichment are usually incomprehensive, being oriented at detecting a particular viral species or a genus based on the presumption of its presence in the sample. In this study, we developed a computational pipeline for designing genus-specific oligonucleotides that would simultaneously cover a multitude of known viruses from different taxonomic groups. This new tool was used to design an oligonucleotide panel for targeted enrichment of viral nucleic acids in different types of samples, and its applicability for the detection of multiple viral genera at once was demonstrated. Next, we created a custom protocol for NGS library preparation adapted to the new primer panel, which was tested together on a number of samples and proved highly efficient in pathogen detection and identification. Since a reliable algorithm for bioinformatic analysis is crucial for rapid classification of the sequences, in this work, we developed an NGS­based data analysis module and demonstrated its functionality both for detecting novel viruses and analyzing virome diversity. This work was supported by an RSF (Russian Science Foundation) grant (No. 17-74-20096).
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Dahlman, James E., Kevin J. Kauffman, Yiping Xing, et al. "Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics." Proceedings of the National Academy of Sciences 114, no. 8 (2017): 2060–65. http://dx.doi.org/10.1073/pnas.1620874114.

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Nucleic acid therapeutics are limited by inefficient delivery to target tissues and cells and by an incomplete understanding of how nanoparticle structure affects biodistribution to off-target organs. Although thousands of nanoparticle formulations have been designed to deliver nucleic acids, most nanoparticles have been tested in cell culture contexts that do not recapitulate systemic in vivo delivery. To increase the number of nanoparticles that could be tested in vivo, we developed a method to simultaneously measure the biodistribution of many chemically distinct nanoparticles. We formulated nanoparticles to carry specific nucleic acid barcodes, administered the pool of particles, and quantified particle biodistribution by deep sequencing the barcodes. This method distinguished previously characterized lung- and liver- targeting nanoparticles and accurately reported relative quantities of nucleic acid delivered to tissues. Barcode sequences did not affect delivery, and no evidence of particle mixing was observed for tested particles. By measuring the biodistribution of 30 nanoparticles to eight tissues simultaneously, we identified chemical properties promoting delivery to some tissues relative to others. Finally, particles that distributed to the liver also silenced gene expression in hepatocytes when formulated with siRNA. This system can facilitate discovery of nanoparticles targeting specific tissues and cells and accelerate the study of relationships between chemical structure and delivery in vivo.
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Broberg, Martin, and James E. McDonald. "Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue." Methods and Protocols 2, no. 1 (2019): 15. http://dx.doi.org/10.3390/mps2010015.

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The application of high-throughput nucleic acid and protein sequencing technologies is transforming our understanding of plant microbiomes and their interactions with their hosts in health and disease. However, progress in studying host-microbiome interactions in above-ground compartments of the tree (the phyllosphere) has been hampered due to high concentrations of phenolic compounds, lignin, and other compounds in tree bark that severely limit the success of DNA, RNA, and protein extraction. Here we present modified sample-preparation and kit-based protocols for the extraction of host and microbiome DNA and RNA from oak (Quercus robus and Quercus petraea) bark tissue for subsequent high-throughput sequencing. In addition, reducing the quantity of bark tissue used for an established protein extraction protocol yielded high quality protein for parallel analysis of the oak-microbiota metaproteome. These procedures demonstrate the successful extraction of nucleic acids and proteins from oak tissue using as little as 50 mg of sample input, producing sufficient quantities for nucleic acid sequencing and protein mass spectrometry of tree stem tissues and their associated microbiota.
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Cui, Li, Tingting Zhao, Haibing Hu, Wen Zhang, and Xiuguo Hua. "Association Study of Gut Flora in Coronary Heart Disease through High-Throughput Sequencing." BioMed Research International 2017 (2017): 1–10. http://dx.doi.org/10.1155/2017/3796359.

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Objectives.We aimed to explore the impact of gut microbiota in coronary heart disease (CHD) patients through high-throughput sequencing.Methods.A total of 29 CHD in-hospital patients and 35 healthy volunteers as controls were included. Nucleic acids were extracted from fecal samples, followed byαdiversity and principal coordinate analysis (PCoA). Based on unweighted UniFrac distance matrices, unweighted-pair group method with arithmetic mean (UPGMA) trees were created.Results.After data optimization, an average of121312±19293reads in CHD patients and234372±108725reads in controls was obtained. Reads corresponding to 38 phyla, 90 classes, and 584 genera were detected in CHD patients, whereas 40 phyla, 99 classes, and 775 genera were detected in controls. The proportion of phylum Bacteroidetes (56.12%) was lower and that of phylum Firmicutes was higher (37.06%) in CHD patients than those in the controls (60.92% and 32.06%,P<0.05). PCoA and UPGMA tree analysis showed that there were significant differences of gut microbial compositions between the two groups.Conclusion.The diversity and compositions of gut flora were different between CHD patients and healthy controls. The incidence of CHD might be associated with the alteration of gut microbiota.
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Hugenholtz, Phil. "Guest commentary: The human microbiome and the promise of clinical ecology." Microbiology Australia 33, no. 3 (2012): 90. http://dx.doi.org/10.1071/ma12090.

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Metagenomics, the application of high-throughput sequencing to nucleic acids extracted directly from environmental samples, made its debut in 2004 through two high-profile papers in Science (Sargasso Sea) and Nature (acid mine drainage). A key strength of the approach is the ability to circumvent the well-known cultivation bottleneck and lay bare the genetic blueprints of ecologically important members of the microbial community, many of which cannot be easily obtained in culture.
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Israeli, Ofir, Efi Makdasi, Inbar Cohen-Gihon, et al. "A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood." Future Science OA 6, no. 6 (2020): FSO476. http://dx.doi.org/10.2144/fsoa-2020-0013.

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High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, Y. pestis, F. tularensis and B. anthracis spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5–5.9 orders of magnitude, in samples with bacteria spiked-in at 103–105 CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8–9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.
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Agrawal, Megha. "Next Generation Sequencing Technology in Clinical Diagnostics." Biotechnology Kiosk 2, no. 7 (2020): 10–17. http://dx.doi.org/10.37756/bk.20.2.7.2.

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The promise of next generation sequencing offers hope for the current DNA sequencing technology to evolve from the applications in basic research to transition to the clinical diagnostics. This advancement in the sequencing technology is happening in part due to the introduction of high throughput and benchtop instruments that offer fully automated cost-effective sequencing along with faster assay times. This development is believed to remove the bottleneck of the complex and cumbersome library preparation that include isolation of nucleic acids and the resulting amplified and barcoded DNA with sequencing adapters. Here, we present a brief overview of the principles of next generation sequencing and automation of library preparation along with the diagnostic applications of next generation sequencing in human immunogenetics. Finally, an outlook is presented.
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Busi, Susheel Bhanu, Paraskevi Pramateftaki, Jade Brandani, et al. "Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams." PeerJ 8 (October 27, 2020): e9973. http://dx.doi.org/10.7717/peerj.9973.

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Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.
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Blanco, Celia, Samuel Verbanic, Burckhard Seelig, and Irene A. Chen. "EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides." Journal of Molecular Evolution 88, no. 6 (2020): 477–81. http://dx.doi.org/10.1007/s00239-020-09954-0.

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Dissertations / Theses on the topic "Nucleic acids high throughput sequencing"

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Oman, Kenji. "Nucleic Acid High-Throughput Sequencing Studies Present Unique Challenges in Analysis and Interpretation." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1437681208.

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Marandat, Gregory. "Développement et mise en œuvre d'approches métatranscriptomiques pour le suivi microbiologique de digesteurs anaérobies." Thesis, Paris, AgroParisTech, 2015. http://www.theses.fr/2015AGPT0005.

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La digestion anaérobie est une stratégie attractive pour traiter et valoriser les déchets organiques, par la co-production de biogaz, fertilisants, chaleur et électricité. Ces bioprocédés utilisent les capacités des microorganismes à convertir la matière organique complexe en composés plus simples. Les biomasses représentent le "moteur microbien" des réacteurs, et influencent leurs performances. Un suivi microbiologique est important, or pour des communautés complexes, les techniques classiques de biologie sont chronophages et limitées. La récente démocratisation du séquençage d’ADN de nouvelle génération et de la bioinformatique a levé de nombreux verrous.Ce doctorat concerne le développement et l’implémentation d’outils moléculaires culture-indépendants, basés sur le séquençage d’ARN de communautés complexes de microorganismes, aussi appelés métatranscriptomiques. Ces approches ont permis de caractériser les consortia procaryotiques fonctionnels de digesteurs anaérobie. Six types de réacteurs, traitant différent substrats (ordures ménagères, boues activées et effluent papetier), ont été analysés. Une méta-analyse de 33 jeux de données métatranscriptomiques a mis en évidence des taxons communs et spécifiques aux différents bioréacteurs, ainsi que de nombreuses fonctions génétiques, associées à des métabolismes d’intérêt (Carbone, Azote et Soufre).Les résultats obtenus montrent le potentiel des outils métatranscriptomiques pour l’analyse d’échantillons environnementaux complexes. Ces outils de nouvelle génération, semblent être incontournables pour l’ingénierie microbiologique. Ils permettent d’interroger le "savoir universel" (bases de données biologiques), offrant ainsi une vision holistique de la composition et de la fonction de communautés complexes de microorganismes. Les principales limites concernent l’incomplétude des bases de données, les problématiques techniques et bioinformatiques, ainsi que l’intégration globale de ce nouveau savoir<br>Anaerobic digestion bioreactors appear nowadays environmentally attractive because they allow treating and valorizing organic waste, by production of added value biogas, fertilizers, heat and electricity. Such bioprocesses employ natural abilities of complex microbial communities to convert complex organic matter into simpler molecules. Anaerobic digestion microbiomes represent the "microbial engine" of reactors, which ultimately sustain its performance. Solving dysfunctions or start phase issues is difficult especially without a microbiological monitoring. Classical microbiological and molecular tools show limitations dealing with complex communities, but recently the arrival of next-generation DNA sequencers and bioinformatics open locks.New culture-independent molecular tools, based on RNA sequencing of complex microbial communities, also called metatranscriptomic approaches, were developed and implemented, in order to monitor the microbial consortia of anaerobic digesters. Six types of reactors were analyzed. They treated different substrates (solid waste, activated sludge and paper mill effluent), which spanned from lab to industrial scale. A meta-analysis of thirty-three metatranscriptomic datasets permitted to highlight specific and core groups of taxa present in bioreactors, as well as numerous genetic functions related to Carbon, Nitrogen and Sulfur metabolisms.The results obtained from this work show the power of metatranscriptomics, to analyze complex environmental samples. Metatranscriptomics appears as an unavoidable tool for microbial community engineering, interestingly enabling an interrogation of the "universal knowledge" (biological databases), and giving a holistic picture about the structure and function of complex microbial communities. Some limits however still remain in relation to the incompleteness of databases, technical and bioinformatics issues, biological interpretations, as well as in the integration of this new knowledge in an inclusive picture
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Largy, Eric. "Ciblage d’acides nucléiques G-quadruplexes : synthèse et développement de méthodes pour l’analyse et le criblage de ligands sélectifs multimodaux." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA112257.

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L’objectif de ces travaux de thèse était l’étude des interactions de petites molécules avec les multiples structures de l’ADN quadruplex via i) le développement et l’utilisation d’un test haut-débit pour l’analyse des interactions ligand-ADN quadruplex et le criblage de chimiothèques/ciblothèques et ii) la préparation de composés aux modes d’interactions multiples (empilement/sillon, covalent/non-covalent, etc.), sélectifs (quadruplex vs. duplex et intra-quadruplex) et éventuellement fonctionnalisés (biotine, fluorophore, etc.). La première partie des travaux a été centrée sur le développement du test G4-FID (G-quadruplex Fluorescent Intercalator Displacement) qui est une méthode semi-quantitative permettant l’évaluation de l’affinité et de la sélectivité de petites molécules pour l’ADN quadruplex par déplacement d’une sonde off/on, le Thiazole Orange (TO). Le test a notamment été transposé avec succès de la cuve vers la microplaque (HT-G4-FID). D’autre part, nous avons montré l’intérêt de fluorophores alternatifs, TO-PRO-3 et Hoechst 33258, aux caractéristiques spectrales complémentaires à TO. Cette méthode d’analyse a également été utilisée avec succès pour l’identification de nouveaux ligands sélectifs d’ADN quadruplex et la mise en évidence des relations structure-activité ainsi que des sélectivités structurales. La deuxième partie des travaux a été consacrée à la préparation et à l’étude de nouveaux ligands d’ADN quadruplex. Ces ligands possèdent des particularités, soit dans leur mode d’interaction (sillons, coordination) soit par leur bifonctionnalité (biotinylés, fluorescents). Nous avons ainsi préparé un ligand de quadruplex polyhétéroaryle acyclique (TOxaPy) possédant une sélectivité inattendue pour certaines structures de l’ADN quadruplex. D’autre part, nous avons montré que les complexes de dérivés de terpyridine peuvent être adaptés, en changeant le ligand organique et/ou la nature du métal, de façon à interagir avec l’ADN quadruplex par interaction covalentes et/ou non covalentes<br>The aim of this thesis work was to study the interactions of small molecules with multiple structures of quadruplex DNA via i) the development and use of a high-throughput test for the analysis of ligand-quadruplex DNA interactions and screening of chemical libraries and ii) the preparation of compounds with multiple binding modes (stacking/groove, covalent/non-covalent, etc..) selective (quadruplex vs. duplex and intra-quadruplex) and possibly functionalized (biotin, fluorophore, etc.). The first part of the work was focused on the development of the G4-FID (G-quadruplex Intercalator Fluorescent Displacement) assay, which is a semi-quantitative method for evaluating the affinity and selectivity of small molecules for quadruplex DNA by displacing an off/on probe, the Thiazole Orange (TO). The test has been implemented successfully with microplate (HT-G4-FID). On the other hand, we have shown the importance of alternative fluorophores, TO-PRO-3 and Hoechst 33258, with complementary spectral characteristics. This method of analysis has also been successfully used for the identification of new selective ligands of quadruplex DNA and the identification of structure-activity relationships and structural selectivities. The second part of the work was devoted to the preparation and study of new DNA quadruplex ligands. These ligands possess particular characteristics either in their mode of interaction (grooves, coordination) or by their bifunctionality (biotinylated, fluorescent). We have prepared an acyclic polyheteroaryle quadruplex ligand (TOxaPy) with an unexpected selectivity for certain structures of quadruplex DNA. Furthermore, we showed that complexes of terpyridine derivatives can be tailored by changing the organic ligand and / or the metal in order to interact with quadruplex DNA by covalent and / or non-covalent interaction
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Books on the topic "Nucleic acids high throughput sequencing"

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Carpousis, Agamemnon J. High-Density Sequencing Applications in Microbial Molecular Genetics. Elsevier Science & Technology, 2018.

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(Editor), Michael McClelland, and Arthur B. Pardee (Editor), eds. Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series). Eaton Publishing Company/Biotechniques Books, 1999.

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Book chapters on the topic "Nucleic acids high throughput sequencing"

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Marais, Armelle, Chantal Faure, Bernard Bergey, and Thierry Candresse. "Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7683-6_4.

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Xu, Wentao. "Recent Progress in High-Throughput Detection Technology for Food Safety." In Functional Nucleic Acids Detection in Food Safety. Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-1618-9_9.

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Yamanluirt, Gokay, Eric J. Berns, Albert Xue, et al. "Exploration of the Nanomedicine-Design Space with High-throughput Screening and Machine Learning*." In Spherical Nucleic Acids. Jenny Stanford Publishing, 2020. http://dx.doi.org/10.1201/9781003056713-109.

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Yamankurt, Gokay, Eric J. Berns, Albert Xue, et al. "Exploration of the Nanomedicine-Design Space with High-throughput Screening and Machine Learning*." In Spherical Nucleic Acids. Jenny Stanford Publishing, 2020. http://dx.doi.org/10.1201/9781003056713-21.

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Yamanluirt, Gokay, Eric J. Berns, Albert Xue, et al. "Exploration of the Nanomedicine-Design Space with High-throughput Screening and Machine Learning*." In Spherical Nucleic Acids. Jenny Stanford Publishing, 2020. http://dx.doi.org/10.4324/9780429200151-109.

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Rajkhowa, Sanchaita, and Ramesh C. Deka. "Protein-Ligand Docking Methodologies and Its Application in Drug Discovery." In Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0115-2.ch008.

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Molecular docking is a key tool in structural biology and computer-assisted drug design. Molecular docking is a method which predicts the preferred orientation of a ligand when bound in an active site to form a stable complex. It is the most common method used as a structure-based drug design. Here, the authors intend to discuss the various types of docking methods and their development and applications in modern drug discovery. The important basic theories such as sampling algorithm and scoring functions have been discussed briefly. The performances of the different available docking software have also been discussed. This chapter also includes some application examples of docking studies in modern drug discovery such as targeted drug delivery using carbon nanotubes, docking of nucleic acids to find the binding modes and a comparative study between high-throughput screening and structure-based virtual screening.
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Rajkhowa, Sanchaita, and Ramesh C. Deka. "Protein-Ligand Docking Methodologies and Its Application in Drug Discovery." In Oncology. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-0549-5.ch035.

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Molecular docking is a key tool in structural biology and computer-assisted drug design. Molecular docking is a method which predicts the preferred orientation of a ligand when bound in an active site to form a stable complex. It is the most common method used as a structure-based drug design. Here, the authors intend to discuss the various types of docking methods and their development and applications in modern drug discovery. The important basic theories such as sampling algorithm and scoring functions have been discussed briefly. The performances of the different available docking software have also been discussed. This chapter also includes some application examples of docking studies in modern drug discovery such as targeted drug delivery using carbon nanotubes, docking of nucleic acids to find the binding modes and a comparative study between high-throughput screening and structure-based virtual screening.
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Szabo, Arthur G. "Fluorescence principles and measurement." In Spectrophotometry and Spectrofluorimetry. Oxford University Press, 2000. http://dx.doi.org/10.1093/oso/9780199638130.003.0006.

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Fluorescence spectrometry is the most extensively used optical spectroscopic method in analytical measurement and scientific investigation. During the past five years more than 60000 scientific articles have been published in which fluorescence spectroscopy has been used. The large number of applications ranges from the analytical determination of trace metals in the environment to pH measurements in whole cells under physiological conditions. In the scientific research laboratory, fluorescence spectroscopy is being used or applied to study the fundamental physical processes of molecules; structure-function relationships and interactions of biomolecules such as proteins and nucleic acids; structures and activity within whole cells using such instrumentation as confocal microscopy; and DNA sequencing in genomic characterization. In analytical applications the use of fluorescence is dominant in clinical laboratories where fluorescence immunoassays have largely replaced radioimmunoassay techniques. There are two main reasons for this extensive use of fluorescence spectroscopy. Foremost is the high level of sensitivity and wide dynamic range that can be achieved. There are a large number of laboratories that have reported single molecule detection. Secondly, the instrumentation required is convenient and for most purposes can be purchased at a modest cost. While improvements and advances continue to be reported fluorescence instrumentation has reached a high level of maturity. A review of the physical principles of the fluorescence phenomenon permits one to understand the origins of the information content that fluorescence measurements can provide. A molecule absorbs electromagnetic radiation through a quantum mechanical process where the molecule is transformed from a ‘ground’ state to an ‘excited’ state. The energy of the absorbed photon of light corresponds to the energy difference between these two states. In the case of light in the ultraviolet and visible spectral range of 200 nm to 800 nm that corresponds to energies of 143 to 35.8 kcal mol-1. The absorption of light results in an electronic transition in the atom or molecule. In atoms this involves the promotion of an electron from an outer shell orbital to an empty orbital of higher energy.
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Raychaudhuri, Soumya. "Functional Genomics." In Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.003.0009.

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The overarching purpose of this chapter is to introduce the reader to some of the essential elements of biology, genomics, and bioinformatics. It is by no means a comprehensive description of these fields, but rather the bare minimum that will be necessary to understand the remainder of the book. In the first section we introduce the primary biological molecules: nucleic acids and proteins. We discuss genetic information flow in living beings and how genetic material in DNA is translated into functional proteins. In the second section we present a short primer on probability theory; we review some of the basic concepts. In the third section we describe how biological sequences are obtained and the common strategies employed to analyze them. In the fourth section, we describe the methods used to collect high throughput gene expression data. We also review the popular methods used to analyze gene expression data. There are many other important areas of functional genomics that we do not address at all in this chapter. New experimental and analytical methods are constantly emerging. For the sake of brevity we focused our discussion on the areas that are most applicable to the remainder of the book. But, we note that many of the analytical methods presented here can be applied widely and without great difficulty to other data types than the ones they have been presented with. Here we present a focused review of molecular biology designed to give the reader a sufficient background to comprehend the remainder of the book. A thorough discussion is beyond the scope of this book and the interested reader is referred to other textbooks (Alberts, Bray et al. 1994; Stryer 1995; Nelson, Lehninger et al. 2000). The central dogma of molecular biology is a paradigm of information flow in living organisms (see Plate 2.1). Information is stored in the genomic deoxyriboculeic acid (DNA). DNA polymerase, a protein that synthesizes DNA, can replicate DNA so that it can be passed on to progeny after cell division.
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Conference papers on the topic "Nucleic acids high throughput sequencing"

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Whelan, Rebecca J., Arvinder Kapur, Mildred Felder, Jamie Shallcross, and Manish S. Patankar. "Abstract B42: Identification of nucleic acid aptamers for ovarian cancer biomarkers using multiple selection modes and high-throughput sequencing." In Abstracts: AACR Special Conference: Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; October 17-20, 2015; Orlando, FL. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1557-3265.ovca15-b42.

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Phaneuf, Christopher R., Nikita Pak, and Craig R. Forest. "Rapid, Low-Cost, Microfluidic Thermocycler for High-Throughput Genetic Diagnostics." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19714.

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Conventional instrumentation for amplifying nucleic acids by the polymerase chain reaction (PCR), which involves repeated temperature cycling, suffers from slow heating rates (e.g., 3 C/s) and large, costly sample volumes (i.e., 50 μL). Performing PCR is often the most time-consuming step in genetic sample preparation for common procedures such as pathogen detection and forensics. Faster thermocycling can reduce overall runtime and facilitate time-sensitive analyses. Smaller reaction volumes require fewer expensive reagents. Efforts to miniaturize genetic sample preparation have been largely confined to glass devices that are relatively expensive and require elaborate fabrication methods. Landers [1] has used glass microchips fabricated by wet etching to perform PCR, in which volumes of approximately 270 nL can be cycled 25 times with a tungsten filament lamp in only 5 min. Other developments include the work of Yasuda [2] and Faris [3], using infrared laser radiation to perform real-time PCR in 10–30 nL droplets suspended in mineral oil with amplification times of 3.5 and 6 min, respectively. Still, these devices can only perform a single reaction at a time.
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3

Zhang, Jun, Sheng Yan, Dan Yuan, Gursel Alici, Nam-trung Nguyen, and Weihua Li. "High Throughput Cell-Free Extraction of Plasma by an Integrated Microfluidic Device Combining Inertial Microfluidics and Membrane." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6717.

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Abstract:
Plasma is a host of various analytes such as proteins, metabolites, circulating nucleic acids (CNAs), pathogens. The key process of plasma extraction is to eliminate the contamination from blood cells. Conventional methods, such as centrifugation and membrane filtration, are generally lab-intensive, time consuming and even dangerous. In this study, we report an integrated microfluidic device that combines inertial microfluidics and membrane filter. The integrated microfluidic device was evaluated by the diluted (x1/10, x1/20) whole blood, and the quality of the extracted blood plasma was tested. It was found that quality of extracted blood plasma from integrated device was equivalent to that obtained by the centrifugation. This study demonstrates a significant progress towards the practical application of inertial microfluidics with membrane filter for high-throughput and high efficient blood plasma extraction.
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