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

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

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 advent

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2

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

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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 formulate

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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 mi

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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.

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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 descri

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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 wit

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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

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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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Zlatanova, Jordanka, and Andrei Mirzabekov. "Gel-Immobilized Microarrays for the Study of Nucleic Acids and Proteins." Microscopy and Microanalysis 5, S2 (1999): 1018–19. http://dx.doi.org/10.1017/s1431927600018419.

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Recently, a quantum leap has been achieved in the analysis of DNA and proteins through the advent of the biochip technology. This technology is a product of a broad interdisciplinary approach combining biochemical analysis, semiconductor manufacturing and computer software. Biochips can be defined as miniaturized ordered arrays of macro molecules or pieces thereof that are immobilized in a precise spatial manner on support media and can be used in highly automated, large-scale and high-throughput fashion to analyze biological material. The biochip can be used in a wide variety of areas related

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Radko, S. P., L. K. Kurbatov, K. G. Ptitsyn, et al. "Prospects for the use of third generation sequencers for quantitative profiling of transcriptome." Biomedical Chemistry: Research and Methods 1, no. 4 (2018): e00086. http://dx.doi.org/10.18097/bmcrm00086.

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Transcriptome profiling is widely employed to analyze transcriptome dynamics when studying various biological processes at the cell and tissue levels. Unlike the second generation sequencers, which sequence relatively short fragments of nucleic acids, the third generation DNA/RNA sequencers developed by biotechnology companies “PacBio” and “Oxford Nanopore Technologies” allow one to sequence transcripts as single molecules and may be considered as potential molecular counters capable to measure the number of copies of each transcript with high throughput, sensitivity, and specificity. In the p

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Kwit, Ewa, and Artur Rzeżutka. "Molecular methods in detection and epidemiologic studies of rabbit and hare viruses: a review." Journal of Veterinary Diagnostic Investigation 31, no. 4 (2019): 497–508. http://dx.doi.org/10.1177/1040638719852374.

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Various PCR-based assays for rabbit viruses have gradually replaced traditional virologic assays, such as virus isolation, because they offer high-throughput analysis, better test sensitivity and specificity, and allow vaccine and wild-type virus strains to be fully typed and differentiated. In addition, PCR is irreplaceable in the detection of uncultivable or fastidious rabbit pathogens or those occurring in low quantity in a tested sample. We provide herein an overview of the current state of the art in the molecular detection of lagomorph viral pathogens along with details of their targeted

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Desbrousses, Céline, Fabienne Archer, Adélie Colin, et al. "High-Throughput Sequencing (HTS) of newly synthetized RNAs enables one shot detection and identification of live mycoplasmas and differentiation from inert nucleic acids." Biologicals 65 (May 2020): 18–24. http://dx.doi.org/10.1016/j.biologicals.2020.03.002.

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15

Zehr, J. P., I. Hewson, and P. Moisander. "Molecular biology techniques and applications for ocean sensing." Ocean Science 5, no. 2 (2009): 101–13. http://dx.doi.org/10.5194/os-5-101-2009.

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Abstract. The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Molecular techniques can form the basis of remote instrumentation sensing technologies for marine microbial diversity and ecological function. Here we review some of the most commonly used molecular biological techniques. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitativ

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Zehr, J. P., I. Hewson, and P. H. Moisander. "Molecular biology techniques and applications for ocean sensing." Ocean Science Discussions 5, no. 4 (2008): 625–57. http://dx.doi.org/10.5194/osd-5-625-2008.

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Abstract. The study of marine microorganisms using molecular biological techniques is now widespread in the ocean sciences. These techniques target nucleic acids which record the evolutionary history of microbes, and encode for processes which are active in the ocean today. Here we review some of the most commonly used molecular biological techniques. Molecular biological techniques permit study of the abundance, distribution, diversity, and physiology of microorganisms in situ. These techniques include the polymerase chain reaction (PCR) and reverse-transcriptase PCR, quantitative PCR, whole

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Marais, Armelle, Chantal Faure, Gwenaëlle Comont, Thierry Candresse, Elodie Stempien, and Marie-France Corio-Costet. "Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum." Viruses 13, no. 3 (2021): 375. http://dx.doi.org/10.3390/v13030375.

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Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the fam

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Tyx, R. E., A. J. Rivera, L. M. Keong, and S. B. Stanfill. "An exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis." Applied Microbiology and Biotechnology 104, no. 2 (2019): 751–63. http://dx.doi.org/10.1007/s00253-019-10232-3.

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AbstractSmokeless tobacco (ST) products are used worldwide and are a major public health concern. In addition to harmful chemicals found in these products, microbes found in ST products are believed to be responsible for generating harmful tobacco-specific nitrosamines (TSNAs), the most abundant carcinogens in ST. These microbes also contribute endotoxins and other pro-inflammatory components. A greater understanding of the microbial constituents in these products is sought in order to potentially link select design aspects or manufacturing processes to avoidable increases in harmful constitue

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Cerutti, Heriberto, Xinrong Ma, Joseph Msanne, and Timothy Repas. "RNA-Mediated Silencing in Algae: Biological Roles and Tools for Analysis of Gene Function." Eukaryotic Cell 10, no. 9 (2011): 1164–72. http://dx.doi.org/10.1128/ec.05106-11.

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ABSTRACTAlgae are a large group of aquatic, typically photosynthetic, eukaryotes that include species from very diverse phylogenetic lineages, from those similar to land plants to those related to protist parasites. The recent sequencing of several algal genomes has provided insights into the great complexity of these organisms. Genomic information has also emphasized our lack of knowledge of the functions of many predicted genes, as well as the gene regulatory mechanisms in algae. Core components of the machinery for RNA-mediated silencing show widespread distribution among algal lineages, bu

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Tsui, Nancy B. Y., Peiyong Jiang, Yuen Fei Wong, et al. "Maternal Plasma RNA Sequencing for Genome-Wide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts." Clinical Chemistry 60, no. 7 (2014): 954–62. http://dx.doi.org/10.1373/clinchem.2014.221648.

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Abstract BACKGROUND Analysis of circulating RNA in the plasma of pregnant women has the potential to serve as a powerful tool for noninvasive prenatal testing and research. However, detection of circulating RNA in the plasma in an unbiased and high-throughput manner has been technically challenging. Therefore, only a limited number of circulating RNA species in maternal plasma have been validated as pregnancy- and placenta-specific biomarkers. METHODS We explored the use of massively parallel sequencing for plasma transcriptome profiling in first-, second-, and third-trimester pregnant women.

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Zolkefli, Nurhasliza, Siti Suhailah Sharuddin, Mohd Zulkhairi Mohd Yusoff, Mohd Ali Hassan, Toshinari Maeda, and Norhayati Ramli. "A Review of Current and Emerging Approaches for Water Pollution Monitoring." Water 12, no. 12 (2020): 3417. http://dx.doi.org/10.3390/w12123417.

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The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucle

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22

Li, Shouyi, Yuding Weng, Xiaoxiao Li, et al. "Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa." Nucleic Acids Research 49, no. 12 (2021): 6756–70. http://dx.doi.org/10.1093/nar/gkab506.

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Abstract The ability to fine tune global gene expression in response to host environment is critical for the virulence of pathogenic bacteria. The host temperature is exploited by the bacteria as a cue for triggering virulence gene expression. However, little is known about the mechanism employed by Pseudomonas aeruginosa to response to host body temperature. CspA family proteins are RNA chaperones that modulate gene expression. Here we explored the functions of P. aeruginosa CspA family proteins and found that CspC (PA0456) controls the bacterial virulence. Combining transcriptomic analyses,

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Lee, Jeeyun, Stefanie Mortimer, Gangwu Mei, et al. "Ultra-high-quality sequencing assay for comprehensive genetic panel analysis of tumor-derived circulating cell-free DNA in colorectal cancer patients." Journal of Clinical Oncology 32, no. 3_suppl (2014): 504. http://dx.doi.org/10.1200/jco.2014.32.3_suppl.504.

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504 Background: Current approaches based on invasive biopsy genetic analysis can fail to capture an accurate picture of the real-time cancer profile due to limited spatial window of biopsy into residual disease throughout the body. Moreover, tumor rebiopsy has significant challenges to be widely used in practice for serial monitoring of disease progression or acquired resistance. Analysis of circulating tumor nucleic acids (ctDNA), on the other hand, presents a new tool for the monitoring and treatment of cancer. However, due to high-quality false positives in current NGS assays, the majority

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Chen, Xiaoyu, Francesca Tasca, Qian Wang, et al. "Expanding the editable genome and CRISPR–Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking." Nucleic Acids Research 48, no. 2 (2019): 974–95. http://dx.doi.org/10.1093/nar/gkz1121.

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Abstract Genome editing typically involves recombination between donor nucleic acids and acceptor genomic sequences subjected to double-stranded DNA breaks (DSBs) made by programmable nucleases (e.g. CRISPR–Cas9). Yet, nucleases yield off-target mutations and, most pervasively, unpredictable target allele disruptions. Remarkably, to date, the untoward phenotypic consequences of disrupting allelic and non-allelic (e.g. pseudogene) sequences have received scant scrutiny and, crucially, remain to be addressed. Here, we demonstrate that gene-edited cells can lose fitness as a result of DSBs at all

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Karamitros, Timokratis, Vasiliki Pogka, Gethsimani Papadopoulou, et al. "Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host–Pathogen Interactions." Microorganisms 9, no. 7 (2021): 1538. http://dx.doi.org/10.3390/microorganisms9071538.

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Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Fol

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Lin, Jimmy, Eric Ariazi, Michael Dzamba, et al. "Evaluation of a sensitive blood test for the detection of colorectal advanced adenomas in a prospective cohort using a multiomics approach." Journal of Clinical Oncology 39, no. 3_suppl (2021): 43. http://dx.doi.org/10.1200/jco.2021.39.3_suppl.43.

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43 Background: Blood-based screening tests for colorectal cancer (CRC) with high sensitivity and specificity are needed to improve adherence, facilitate early detection, and ultimately reduce mortality from CRC. Current stool-based tests have a sensitivity of 24-42% for colorectal advanced adenomas (AAs), while blood tests that rely on tumor-derived cell-free DNA (cfDNA) methylation signatures have shown limited sensitivity for AAs. Here we demonstrate the ability to detect AAs from blood using a multiomics test that incorporates both tumor- and immune-derived signatures, and compare it to the

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27

Zubov, V. V., D. A. Chemeris, R. G. Vasilov, V. E. Kurochkin, and Ya I. Alekseev. "Brief history of high-throughput nucleic acid sequencing methods." Biomics 13, no. 1 (2021): 27–46. http://dx.doi.org/10.31301/2221-6197.bmcs.2021-4.

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The processes occurring during the enzymatic growth of the DNA chain in the form of elongation of the molecules, the release of pyrophosphate, proton, thermal energy, and an increase in electrical impedance, which are used in various methods of high-throughput DNA sequencing by synthesis, are briefly considered. The detection of DNA chain growth is controlled by high-voltage gel electrophoresis and has limited scalability. As for mentioned above other by-products of DNA chain polymerization, their detection can be easily scalable, which has led to the emergence of methods for whole genome sequ

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Galigalidou, Chrysi, Anastasia Papadopoulou, Evangelia Stalika, et al. "High-Throughput T Cell Receptor (TR) Repertoire Analysis of Virus-Specific T Cells: Implications for T Cell Immunotherapy and Viral Infection Risk Stratification." Blood 132, Supplement 1 (2018): 2057. http://dx.doi.org/10.1182/blood-2018-99-118851.

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Abstract Viral infections, mainly by cytomegalovirus (CMV), Epstein Barr virus (EBV) and polyomavirus type I (BKV), are major causes of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). As effective immune responses against human viruses rely on an armamentarium of T-cell receptor (TR) repertoire capable of recognizing a broad range of antigenic peptides of those pathogens, reconstitution of antiviral immunity, either by spontaneous generation of endogenous virus-specific T cells (VSTs) or by adoptive immunotherapy with VSTs, plays a critical role to

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Chiodi, Claudia, Matteo Moro, Andrea Squartini, et al. "High-Throughput Isolation of Nucleic Acids from Soil." Soil Systems 4, no. 1 (2019): 3. http://dx.doi.org/10.3390/soilsystems4010003.

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DNA-based technologies have become widespread tools for soil microbiological analyses in recent years. DNA extraction from the soil is a key step for these approaches: it is a challenge for researchers as it is still both expensive and time-consuming when large surveys are planned. The aim of this study was to develop a high-throughput automated protocol for DNA extraction and purification from soil. The protocol was based on the BioSprint 96 platform and compared for validation with another automated procedure and two commercial column-based kits. To evaluate the performances of the protocols

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Meyer, Matthias, Udo Stenzel, Sean Myles, Kay Prüfer, and Michael Hofreiter. "Targeted high-throughput sequencing of tagged nucleic acid samples." Nucleic Acids Research 35, no. 15 (2007): e97. http://dx.doi.org/10.1093/nar/gkm566.

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Komarova, Natalia, Daria Barkova, and Alexander Kuznetsov. "Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology." International Journal of Molecular Sciences 21, no. 22 (2020): 8774. http://dx.doi.org/10.3390/ijms21228774.

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Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HT

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Wroclawska, E., J. O. Brant, T. P. Yang, and K. Moore. "100 ASSESSMENT OF LOCUS-SPECIFIC DNA METHYLATION: OPTIMIZATION FOR BOVINE EMBRYOS." Reproduction, Fertility and Development 21, no. 1 (2009): 150. http://dx.doi.org/10.1071/rdv21n1ab100.

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Assessment of chromatin remodeling in early embryos is a major focus of studies today, and evaluation of DNA methylation at specific loci is one approach to study these epigenetic modifications. Our objective was to optimize the bisulfite sequencing methodology for use with very small cell numbers originating from pre-implantation embryos, making the process more time- and cost-efficient. The optimized steps include bisulfite conversion of small samples, bisulfite primer design, high-throughput plasmid DNA amplification, and preparation for sequencing. Methylation at 2 loci, Satellite I and Oc

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Chen, Zheng, Ting Chen, Atul Sathe, Yuqing He, Xiao-bo Zhang, and Jian-li Wu. "Identification of a Novel Semi-Dominant Spotted-Leaf Mutant with Enhanced Resistance to Xanthomonas oryzae pv. oryzae in Rice." International Journal of Molecular Sciences 19, no. 12 (2018): 3766. http://dx.doi.org/10.3390/ijms19123766.

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Many spotted-leaf mutants show enhanced disease resistance to multiple pathogen attacks; however, the mechanisms are largely unknown. Here, we reported a novel semi-dominant spotted-leaf mutant 24 (spl24) obtained from an ethyl methane sulfonate (EMS)-induced IR64 mutant bank. spl24 developed tiny brown lesions on the leaf tip and spread down gradually to the leaf base as well as the sheath at the early heading stage. The performances of major agronomic traits such as the plant height, panicle length, number of panicles/plant, and 1000-grain weight were significantly altered in spl24 when comp

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Srivatsan, Seergazhi, and Michael Famulok. "Functional Nucleic Acids in High Throughput Screening and Drug Discovery." Combinatorial Chemistry & High Throughput Screening 10, no. 8 (2007): 698–705. http://dx.doi.org/10.2174/138620707782507359.

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Montmayeur, Anna M., Terry Fei Fan Ng, Alexander Schmidt, et al. "High-Throughput Next-Generation Sequencing of Polioviruses." Journal of Clinical Microbiology 55, no. 2 (2016): 606–15. http://dx.doi.org/10.1128/jcm.02121-16.

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ABSTRACTThe poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcript

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Dayaram, Anisha, Kyriakos Tsangaras, Selvaraj Pavulraj, et al. "Novel Divergent Polar Bear-Associated Mastadenovirus Recovered from a Deceased Juvenile Polar Bear." mSphere 3, no. 4 (2018): e00171-18. http://dx.doi.org/10.1128/msphere.00171-18.

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ABSTRACTPolar bears in captivity can be exposed to opportunistic pathogens not present in their natural environments. A 4-month-old polar bear (Ursus maritimus) living in an isolated enclosure with his mother in the Tierpark Berlin, Berlin, Germany, was suffering from severe abdominal pain, mild diarrhea, and loss of appetite and died in early 2017. Histopathology revealed severe hepatic degeneration and necrosis without evidence of inflammation or inclusion bodies, although a viral infection had been suspected on the basis of the clinical signs. We searched for nucleic acids of pathogens by s

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Huang, Shuo, Mercedes Romero-Ruiz, Oliver K. Castell, Hagan Bayley, and Mark I. Wallace. "High-throughput optical sensing of nucleic acids in a nanopore array." Nature Nanotechnology 10, no. 11 (2015): 986–91. http://dx.doi.org/10.1038/nnano.2015.189.

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38

Kossen, Karl, Narendra K. Vaish, Vasant R. Jadhav, et al. "High-Throughput Ribozyme-Based Assays for Detection of Viral Nucleic Acids." Chemistry & Biology 11, no. 6 (2004): 807–15. http://dx.doi.org/10.1016/j.chembiol.2004.03.029.

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39

Iwanaga, Masanobu. "High-Sensitivity High-Throughput Detection of Nucleic Acid Targets on Metasurface Fluorescence Biosensors." Biosensors 11, no. 2 (2021): 33. http://dx.doi.org/10.3390/bios11020033.

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Worldwide infection disease due to SARS-CoV-2 is tremendously affecting our daily lives. High-throughput detection methods for nucleic acids are emergently desired. Here, we show high-sensitivity and high-throughput metasurface fluorescence biosensors that are applicable for nucleic acid targets. The all-dielectric metasurface biosensors comprise silicon-on-insulator nanorod array and have prominent electromagnetic resonances enhancing fluorescence emission. For proof-of-concept experiment on the metasurface biosensors, we have conducted fluorescence detection of single-strand oligoDNAs, which

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He, Sha, Yi Zhang, Pei Wang, et al. "Multiplexed microfluidic blotting of proteins and nucleic acids by parallel, serpentine microchannels." Lab on a Chip 15, no. 1 (2015): 105–12. http://dx.doi.org/10.1039/c4lc00901k.

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Dorado, Gabriel, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez, and Pilar Hernández. "Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review." Biomolecules 11, no. 8 (2021): 1111. http://dx.doi.org/10.3390/biom11081111.

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new

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Gallego, Diego, Leonardo Darré, Pablo D. Dans, and Modesto Orozco. "VeriNA3d: an R package for nucleic acids data mining." Bioinformatics 35, no. 24 (2019): 5334–36. http://dx.doi.org/10.1093/bioinformatics/btz553.

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Abstract Summary veriNA3d is an R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures. In addition to single-structure analyses, veriNA3d also implements functions to handle whole datasets of mmCIF/PDB structures that could be retrieved from public/local repositories. Our package aims to fill a gap in the data mining of nucleic acids structures to produce flexible and high throughput analysis of structural databases. Availability and implementation http://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d. Supplementary information Supplementary dat

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Das, Jagotamoy, Ivaylo Ivanov, Tina S. Safaei, Edward H. Sargent, and Shana O. Kelley. "Combinatorial Probes for High-Throughput Electrochemical Analysis of Circulating Nucleic Acids in Clinical Samples." Angewandte Chemie International Edition 57, no. 14 (2018): 3711–16. http://dx.doi.org/10.1002/anie.201800455.

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Das, Jagotamoy, Ivaylo Ivanov, Tina S. Safaei, Edward H. Sargent, and Shana O. Kelley. "Combinatorial Probes for High-Throughput Electrochemical Analysis of Circulating Nucleic Acids in Clinical Samples." Angewandte Chemie 130, no. 14 (2018): 3773–78. http://dx.doi.org/10.1002/ange.201800455.

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Fountain, Kenneth J., Martin Gilar, and John C. Gebler. "Electrospray ionization mass spectrometric analysis of nucleic acids using high-throughput on-line desalting." Rapid Communications in Mass Spectrometry 18, no. 12 (2004): 1295–302. http://dx.doi.org/10.1002/rcm.1481.

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Zhang, Chenguang, Gongchen Sun, Satyajyoti Senapati, and Hsueh-Chia Chang. "A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification." Lab on a Chip 19, no. 22 (2019): 3853–61. http://dx.doi.org/10.1039/c9lc00818g.

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We report a new Bifurcated Continuous Field-Flow Fractionation (BCFFF) microfluidic chip for isolation and purification of nucleic acids from blood plasma with high and concentration-independent yield. The platform is ideal for isolation and quantification of small miRNAs.

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Jeong, Sinyoung, Homan Kang, Myeong Geun Cha, et al. "Two-dimensional SERS encoding method for on-bead peptide sequencing in high-throughput bioanalysis." Chemical Communications 55, no. 18 (2019): 2700–2703. http://dx.doi.org/10.1039/c8cc10224d.

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Shaffer, Justin P., Clarisse Marotz, Pedro Belda-Ferre, et al. "A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities." BioTechniques 70, no. 3 (2021): 149–59. http://dx.doi.org/10.2144/btn-2020-0153.

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One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environm

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Chen, Zhu, Changhu Xiao, Manling Tang, et al. "Advances in Fully Automated Nucleic Acid Extraction System Based on Magnetic Nanobeads." Nanoscience and Nanotechnology Letters 11, no. 12 (2019): 1633–43. http://dx.doi.org/10.1166/nnl.2019.3051.

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Using magnetic nanobeads (MNBs) to extract nucleic acids is an efficient, inexpensive, easy automation, high throughput and good repeatability, instead of the traditional nucleic acid extraction (NAE) methods. Advances in fully automated MNBs-based nucleic acid extraction systems (MNAES) can push the frontiers of point-of-care testing (POCT) devices towards low-cost, automation, and enhanced accuracy molecular-level diagnostics. So, this paper introduces the pipettingbased MNAES with position of magnetic separation kit or tip, and based on magnetic bar MNAES with blending manner is shock or ro

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Wu, Lin Hui, Jian Li Liu, Jing Zeng, and Ji Zhao. "Comparison of DNA Extraction and Purification Methods from Different Soils for Metagenomic Sequencing." Advanced Materials Research 955-959 (June 2014): 306–9. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.306.

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There is an increased interest in the extraction of nucleic acids from various environmental samples, since only a minority of naturally occurring microbes can be cultured using standard techniques. Nucleic acids extraction and purification from soils are extremely challenging due to the low biomass, high organic contents and high variability of soil types. This has been regarded as one of the major difficulties that hamper the development of soil microbial ecology study. No commercial nucleic acids kits currently available are capable of preparing the DNAs without modifications. The cost can

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