scholarly journals Genomic approaches and their contributions to understanding the European Neolithisation

2016 ◽  
Vol 43 ◽  
pp. 253-264
Author(s):  
Cristina Gamba
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
Significant Contribution ◽  
Cost Effective ◽  
Petrous Bone ◽  
Molecular Technique ◽  
Complete Genomes ◽  
Technical Advances ◽  
High Throughput Dna Sequencing ◽  
The Cost

The contribution of ancient DNA to the understanding of past events has been increasing exponentially in recent years. This is mainly due to the synergy of technical advances, such as the molecular technique of high-throughput DNA sequencing, which has allowed for the reconstruction of complete genomes as old as 750 000 years. Another step toward the cost-effective characterisation of ancient genomes is the sampling of petrous bone, which has allowed sequencing of the first ancient African genome. Here I review the significant contribution of ancient genomics to our understanding of the European Neolithisation process.

scholarly journals Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method

2021 ◽  
Author(s):  
Megh Singh Dhakad ◽  
Sanjib Gogoi ◽  
Ansu Kumari ◽  
Aashish Kumar Singh ◽  
Manoj B. Jais ◽  
...  
Keyword(s):  
Detection Method ◽  
Cost Effective ◽  
Molecular Technique ◽  
Rt Pcr ◽  
Index Method ◽  
Resource Limited ◽  
Qpcr Method ◽  
Kappa Value ◽  
The Cost ◽  
Higher Sensitivity

Background and Objectives: The entire globe is undergoing an unprecedented challenge of COVID-19. Considering the need of rapid and accurate diagnostic tests for SARS-CoV-2, this study was planned to evaluate the cost effective extraction free RT-PCR technique in comparison to the standard VTM based RT-qPCR method. Materials and Methods: Paired swabs from nasopharynx and oropharynx were collected for SARS-CoV-2 testing, from 211 adult patients (≥18 years) in VTM and plain sterile tubes (dry swabs). These samples were processed and RT-qPCR was carried out as per standard protocols. Results: 54.5% of the patients were females and 45.5% were males with sex ratio 1:1.19 (M: F). 38.86% were symptomatic, of which fever (86.59%), cough (79.23%) and breathlessness (46.34%) were the most common symptoms. The positivity by VTM based method and index method was 31.27% and 13.27% respectively. Of the 27 inconclusive results from index method, 37.04% were positive, 48.15% were negative by VTM based method. However, in 40 inconclusive results by VTM based method, 90% were negative and rest remained inconclusive by index method. The sensitivity and specificity of the index method were 39.39% and 85.71% respectively. The overall agreement between VTM based method and index method was 49.59% with estimated Kappa value of 0.19. Conclusion: VTM based method showed higher sensitivity compared to the index method. The higher positivity by VTM based method, suggests that VTM based method could plausibly be a better detection method of SARS-CoV-2. Still, the index method might add value in a resource limited setups for detection of SARS-CoV-2.  

scholarly journals A Method For Parallel, Automated, Thermal Cycling of Submicroliter Samples

2001 ◽  
Vol 11 (3) ◽  
pp. 441-447
Author(s):  
Jonathan Nakane ◽  
David Broemeling ◽  
Roger Donaldson ◽  
Andre Marziali ◽  
Thomas D. Willis ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Thermal Cycling ◽  
High Throughput ◽  
Dna Analysis ◽  
Detection Efficiency ◽  
Large Fraction ◽  
Cycle Sequencing ◽  
High Throughput Dna Sequencing ◽  
Reaction Volumes ◽  
The Cost

A large fraction of the cost of DNA sequencing and other DNA-analysis processes results from the reagent costs incurred during cycle sequencing or PCR. In particular, the high cost of the enzymes and dyes used in these processes often results in thermal cycling costs exceeding $0.50 per sample. In the case of high-throughput DNA sequencing, this is a significant and unnecessary expense. Improved detection efficiency of new sequencing instrumentation allows the reaction volumes for cycle sequencing to be scaled down to one-tenth of presently used volumes, resulting in at least a 10-fold decrease in the cost of this process. However, commercially available thermal cyclers and automated reaction setup devices have inherent design limitations which make handling volumes of <1 μL extremely difficult. In this paper, we describe a method for thermal cycling aimed at reliable, automated cycling of submicroliter reaction volumes.

scholarly journals Cost-Effective and High-Throughput Plasmonic Interference Coupled Nanostructures by Using Quasi-Uniform Anodic Aluminum Oxide

Coatings ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 420 ◽  
Author(s):  
Bae ◽  
Yu ◽  
Jung ◽  
Lee ◽  
Choi
Keyword(s):  
Aluminum Oxide ◽  
High Throughput ◽  
Anodic Aluminum Oxide ◽  
Noble Metals ◽  
Cost Effective ◽  
Plasmonic Nanostructures ◽  
Large Area ◽  
Plasmonic Material ◽  
Anodic Aluminum ◽  
The Cost

Large-area and uniform plasmonic nanostructures have often been fabricated by simply evaporating noble metals such as gold and silver on a variety of nanotemplates such as nanopores, nanotubes, and nanorods. However, some highly uniform nanotemplates are limited to be utilized by long, complex, and expensive fabrication. Here, we introduce a cost-effective and high-throughput fabrication method for plasmonic interference coupled nanostructures based on quasi-uniform anodic aluminum oxide (QU-AAO) nanotemplates. Industrial aluminum, with a purity of 99.5%, and copper were used as a base template and a plasmonic material, respectively. The combination of these modifications saves more than 18 h of fabrication time and reduces the cost of fabrication 30-fold. From optical reflectance data, we found that QU-AAO based plasmonic nanostructures exhibit similar optical behaviors to highly ordered (HO) AAO-based nanostructures. By adjusting the thickness of the AAO layer and its pore size, we could easily control the optical properties of the nanostructures. Thus, we expect that QU-AAO might be effectively utilized for commercial plasmonic applications.

scholarly journals Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Eveline Farias-Hesson ◽  
Jonathan Erikson ◽  
Alexander Atkins ◽  
Peidong Shen ◽  
Ronald W. Davis ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Sequencing ◽  
High Throughput ◽  
Magnetic Beads ◽  
Dna Barcode ◽  
Cost Effective ◽  
Dna Libraries ◽  
Emulsion Pcr ◽  
High Throughput Dna Sequencing ◽  
Sequencing Platforms

Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.

scholarly journals FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

2019 ◽  
Author(s):  
Michael M. Weinstein ◽  
Aishani Prem ◽  
Mingda Jin ◽  
Shuiquan Tang ◽  
Jeffrey M. Bhasin
Keyword(s):  
Rapid Assessment ◽  
Cost Effective ◽  
Bioinformatic Analysis ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bioinformatic Tools ◽  
Zymo Research ◽  
High Throughput Dna Sequencing ◽  
The Cost

ABSTRACTSummaryMicrobiome studies continue to provide tremendous insight into the importance of microorganism populations to the macroscopic world. High-throughput DNA sequencing technology (i.e., Next-generation Sequencing) has enabled the cost-effective, rapid assessment of microbial populations when combined with bioinformatic tools capable of identifying microbial taxa and calculating the diversity and composition of biological and environmental samples. Ribosomal RNA gene sequencing, where 16S and 18S rRNA gene sequences are used to identify prokaryotic and eukaryotic species, respectively, is one of the most widely-used techniques currently employed in microbiome analysis. Prior to bioinformatic analysis of these sequences, trimming parameters must be set so that post-trimming sequence information is maximized while expected errors in the sequences themselves are minimized. In this application note, we present FIGARO: a Python–based application designed to maximize read retention after trimming and filtering for quality. FIGARO was designed specifically to increase reproducibility and minimize trial-and-error in trimming parameter selection for a DADA2–based pipeline and will likely be useful for optimizing trimming parameters and minimizing sequence errors in other pipelines as well where paired-end overlap is required.Availability and implementationThe FIGARO application is freely available as source code at https://github.com/Zymo-Research/figaro.

scholarly journals Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

2020 ◽  
Author(s):  
Tatiana R. Feuerborn ◽  
Elle Palkopoulou ◽  
Tom van der Valk ◽  
Johanna von Seth ◽  
Arielle R. Munters ◽  
...  
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Simple Method ◽  
Laboratory Methods ◽  
Field Collection ◽  
Human Dna ◽  
Human Contamination ◽  
Reference Genomes

AbstractBackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

scholarly journals A Comparative Study of LAMP and PCR in Relation to Time and Cost

2022 ◽  
Vol 12 (2) ◽  
pp. 72-75
Author(s):  
Tanzila Rawnuck ◽  
Md Selim Reza ◽  
Mohammad Jahidur Rahman Khan ◽  
Rashida Akter Khanam ◽  
Saif Ullah Munshi
Keyword(s):  
Low Cost ◽  
Cost Effective ◽  
Molecular Techniques ◽  
Molecular Technique ◽  
Serum Samples ◽  
Setup Cost ◽  
Time Duration ◽  
Time Operation ◽  
The Cost ◽  
Short Time

Background: The Loop-mediated isothermal amplification (LAMP) represents a very sensitive, easy to use, and less time consuming diagnostic method. Aims: The aim was to establish a simple, cost-effective, molecular technique. Materials and methods: An analytical study was conducted using two hundred acute serum samples using two different molecular techniques; qPCR and LAMP to standardize a costeffective and less time-consuming technique. Results: The cost of in-house LAMP reagents was one-ninth of the cost of commercial qPCR. Consume cost was 23 times less than qPCR besides, lab setup cost was 92 times less than qPCR. More importantly, LAMP requires 5-6 times less time duration than qPCR. Conclusion: Due to its simple short-time operation with low cost, it would be a prevalent molecular technique globally, particularly in Bangladesh. J Shaheed Suhrawardy Med Coll 2020; 12(2): 72-75

scholarly journals Cost-effective, high-throughput, single-haplotype iterative mapping and sequencing for complex genomic structures

2017 ◽  
Author(s):  
Daniel W. Bellott ◽  
Ting-Jan Cho ◽  
Jennifer F. Hughes ◽  
Helen Skaletsky ◽  
David C. Page
Keyword(s):  
High Throughput ◽  
Cost Effective ◽  
Reference Sequence ◽  
Sequencing Technologies ◽  
A Genome ◽  
Time Required ◽  
Genomic Regions ◽  
The Cost ◽  
Genome Center ◽  
Library Preparation Protocol

AbstractReference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (SHIMS 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce SHIMS 2.0, an improved SHIMS protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to SHIMS 1.0, SHIMS 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.

scholarly journals Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Tatiana R. Feuerborn ◽  
Eleftheria Palkopoulou ◽  
Tom van der Valk ◽  
Johanna von Seth ◽  
Arielle R. Munters ◽  
...  
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Simple Method ◽  
Laboratory Methods ◽  
Field Collection ◽  
Human Dna ◽  
Human Contamination ◽  
Reference Genomes

Abstract Background After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Results Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. Conclusions We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

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