scholarly journals Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis

2021 ◽  
Author(s):  
Paola Cremonesi ◽  
Marco Severgnini ◽  
Alicia Romanò ◽  
Lorenza Sala ◽  
Mario Luini ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Bovine Milk ◽  
Microbial Populations ◽  
High Quality ◽  
Microbiota Analysis ◽  
The World

The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis.

scholarly journals Extraction of high molecular weight abaca DNA suitable for next-generation sequencing

2020 ◽  
Author(s):  
Rhosener Bhea Lu Koh ◽  
Cris Francis Cortez Barbosa ◽  
Vermando Masinsin Aquino ◽  
Leny Calano Galvez
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
High Molecular Weight ◽  
Dna Extraction ◽  
High Throughput ◽  
Next Generation ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Ctab Method ◽  
Generation Sequencing

Abstract Background The abaca (Musa textilis Née) is a fiber crop native to the Philippines with high economic value because of its fiber - the Manila hemp, known to be the strongest of all the natural fibers. DNA extraction in abaca is difficult due to its fibrous nature, high cellulose content and polyphenol compounds. Thus an optimized DNA extraction method is required for extracting high quality abaca DNA for next-generation sequencing applications. Results In this study, we have compared five different methods for the extraction of high molecular weight DNA from abaca leaves. The methods are the traditional CTAB method (Protocol 1), the CTAB with PVP method (Protocol 2), the CTAB with 0.3% β-mercaptoethanol method (Protocol 3), SDS-method (Protocol 4) and CTAB with Triton X-100 and PVP method (Protocol 5). Out of the five methods tested, traditional CTAB-method (Protocol 1), CTAB with 0.3% β-mercaptoethanol method (Protocol 3) and SDS-method (Protocol 4) have shown to be the most consistent in giving high molecular weight DNA with good yield and purity based on A260/A280 and A260/A230 absorption values. TissueLyserII was also utilized for homogenization for the three extraction protocols for applications in high-throughput DNA extraction. DNA from two abaca varieties were extracted using the CTAB with 0.3% β-mercaptoethanol method (Protocol 3) and were sent for NGS based on Illumina HiSeq platform having both passed the quality control for library preparation. Conclusion The CTAB with 0.3% β-mercaptoethanol method (Protocol 3) was found to be the simplest and most consistent method for extracting average yield DNA with high quality for NGS applications. The SDS-method (Protocol 4) was determined to have the shortest processing time and together with TissueLyserII is the most appropriate method for high-throughput extraction of abaca samples which will be useful for genotyping-by-sequencing (GBS) studies.

scholarly journals SILEX: A fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

2020 ◽  
Author(s):  
santiago vilanova ◽  
David Alonso ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
Edgar Garcia Fortea ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
High Quality ◽  
Extraction Protocol ◽  
Dna Extraction Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

scholarly journals Cost-Effective and Scalable DNA Extraction Method from Dried Blood Spots

2013 ◽  
Vol 59 (7) ◽  
pp. 1045-1051 ◽  
Author(s):  
Carlos A Saavedra-Matiz ◽  
Jason T Isabelle ◽  
Chad K Biski ◽  
Salvatore J Duva ◽  
Melissa L Sweeney ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Low Cost ◽  
Melting Curve Analysis ◽  
Molecular Testing ◽  
High Quality ◽  
Congenital Diseases ◽  
Cell Counts ◽  
Dna Extraction Method

BACKGROUND Dried blood spot (DBS) samples have been widely used in newborn screening (NBS) for the early identification of disease to facilitate the presymptomatic treatment of congenital diseases in newborns. As molecular genetics knowledge and technology progresses, there is an increased demand on NBS programs for molecular testing and a need to establish reliable, low-cost methods to perform those analyses. Here we report a flexible, cost-efficient, high-throughput DNA extraction method from DBS adaptable to small- and large-scale screening settings. METHODS Genomic DNA (g.DNA) was extracted from single 3-mm diameter DBS by the sequential use of red cell lysis, detergent-alkaline, and acid-neutralizing buffers routinely used in whole blood and plant tissue DNA extractions. We performed PCR amplification of several genomic regions using standard PCR conditions and detection methods (agarose gel, melting-curve analysis, TaqMan-based assays). Amplicons were confirmed by BigDye® Terminator cycle sequencing and compared with reference sequences. RESULTS High-quality g.DNA was extracted from hundreds of DBS, as proven by mutation detection of several human genes on multiple platforms. Manual and automated extraction protocols were validated. Quantification of g.DNA by Oligreen® fluorescent nucleic acid stain demonstrated a normal population distribution closely corresponding with white blood cell counts detected in newborn populations. CONCLUSIONS High-quality, amplifiable g.DNA is extractable from DBSs. Our method is adaptable, reliable, and scalable to low- and high-throughput NBS at low cost ($0.10/sample). This method is routinely used for molecular testing in the New York State NBS program.

scholarly journals SILEX: A fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

2020 ◽  
Author(s):  
santiago vilanova ◽  
David Alonso ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
Paola Ferrante ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
High Quality ◽  
Extraction Protocol ◽  
Dna Extraction Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract Background: The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results: SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions: A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

scholarly journals A high-throughput, high-quality plant genomic DNA extraction protocol

2013 ◽  
Vol 12 (4) ◽  
pp. 4526-4539 ◽  
Author(s):  
H. Li ◽  
J. Li ◽  
X.H. Cong ◽  
Y.B. Duan ◽  
L. Li ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Genomic Dna ◽  
High Quality ◽  
Genomic Dna Extraction ◽  
Extraction Protocol

Analysis Criteria for Choosing Energy Efficient High-Quality Light Sources and Luminaires

2018 ◽  
pp. 113-119
Author(s):  
Gennady Ya. Vagin ◽  
Eugene B. Solntsev ◽  
Oleg Yu. Malafeev
Keyword(s):  
Energy Efficiency ◽  
Energy Efficient ◽  
National Standards ◽  
Light Sources ◽  
The European Union ◽  
High Quality ◽  
Eu Directive ◽  
The World ◽  
A New Technique ◽  
Energy Labelling

The article analyses critera applying to the choice of energy efficient high quality light sources and luminaires, which are used in Russian domestic and international practice. It is found that national standards GOST P 54993–2012 and GOST P 54992– 2012 contain outdated criteria for determining indices and classes of energy efficiency of light sources and luminaires. They are taken from the 1998 EU Directive #98/11/EU “Electric lamps”, in which LED light sources and discharge lamps of high intensity were not included. A new Regulation of the European Union #874/2012/EU on energy labelling of electric lamps and luminaires, in which these light sources are taken into consideration, contains a new technique of determining classes of energy efficiency and new, higher classes are added. The article has carried out a comparison of calculations of the energy efficiency classes in accordance with GOST P 54993 and with Regulation #874/2012/EU, and it is found out that a calculation using GOST P 54993 gives underrated energy efficiency classes. This can lead to interdiction of export for certain light sources and luminaires, can discredit Russian domestic manufacturer light sources and does not correspond to the rules of the World Trade Organization (WTO).

BROADCASTING PRODUCTS OF THE RADIO STATION «LVIVSKA KHVYLYA»: THE GENRE AND THEMATIC CHARACTERISTICS

2019 ◽  
Vol 25242644 ◽  
pp. 54-57
Author(s):  
Vitalii Handziuk
Keyword(s):  
Radio Station ◽  
High Quality ◽  
Fm Radio ◽  
The World

The main principles of developing of a program concept, target, genre-thematic and audience intended purposes of the Ukrainian FM-radio station «Lvivska khvylya» radio series are considered. It’s concluded that the radio «Lvivskа khvylya» successfully creates the actual, original content of the broadcast, hold onto the genres of radio journalism and the formula of radio success – a beautiful and cheerful mood, a friendly and relaxed atmosphere, a lively conversation; promptly informs the audience about current and important events in the country and in the world; journalists create high-quality content – informational, analytical, entertainment and musical radio series.

A Bibliometric Analysis of Global Research on Lophomonas sp. in Scopus (1933-2019)

2020 ◽  
Vol 20 ◽  
Author(s):  
Masoud Keighobadi ◽  
Maryam Nakhaei ◽  
Ali Sharifpour ◽  
Ali Akbar Khasseh ◽  
Sepideh Safanavaei ◽  
...  
Keyword(s):  
Bibliometric Analysis ◽  
International Collaboration ◽  
Research Articles ◽  
High Quality ◽  
The Real ◽  
The Us ◽  
The World ◽  
Scopus Database ◽  
Number Of Publications ◽  
Global Research

Background: This study was designed to analyze the global research on Lophomonas spp. using bibliometric techniques. Methods: A bibliometric research was carried out using the Scopus database. The analysis unit was the research articles conducted on Lophomonas spp. Results: Totally, 56 articles about Lophomonas spp. were indexed in the Scopus throughout 1933-2019 ( 87 years ) with the following information: (A) The first article was published in 1933; (B) 21 different countries contributed in studies related to Lophomonas spp.; (C) China ranked first with 16 publications about Lophomonas spp.; and (D) “Brugerolle, G” and “Beams, H.W.” from France and the US participated in 4 articles respectively, as the highest number of publications in the Lophomonas spp. network. Discussion: After 87 years, Lophomonas still remains unknown for many researchers and physicians around the world. Further studies with high quality and international collaboration are urgently needed to determine different epidemiological aspects and the real burden of the mysterious parasite worldwide.

scholarly journals A dataset on affiliation of venture capitalists in China between 2000 and 2016

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jin Chen ◽  
Tianyuan Chen ◽  
Yifei Song ◽  
Bin Hao ◽  
Ling Ma
Keyword(s):  
Data Sources ◽  
Venture Capitalists ◽  
High Quality ◽  
Public Agency ◽  
Multiple Data Sources ◽  
Multiple Data ◽  
Multi Stage ◽  
The World ◽  
Prior Literature ◽  
Innovation And Entrepreneurship

AbstractPrior literature emphasizes the distinct roles of differently affiliated venture capitalists (VCs) in nurturing innovation and entrepreneurship. Although China has become the second largest VC market in the world, the unavailability of high-quality datasets on VC affiliation in China’s market hinders such research efforts. To fill up this important gap, we compiled a new panel dataset of VC affiliation in China’s market from multiple data sources. Specifically, we drew on a list of 6,553 VCs that have invested in China between 2000 and 2016 from CVSource database, collected VC’s shareholder information from public sources, and developed a multi-stage procedure to label each VC as the following types: GVC (public agency-affiliated, state-owned enterprise-affiliated), CVC (corporate VC), IVC (independent VC), BVC (bank-affiliated VC), FVC (financial/non-bank-affiliated VC), UVC (university endowment/spin-out unit), and PenVC (pension-affiliated VC). We also denoted whether a VC has foreign background. This dataset helps researchers conduct more nuanced investigations into the investment behaviors of different VCs and their distinct impacts on innovation and entrepreneurship in China’s context.

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