scholarly journals An Automated Sample Preparation System for Large-Scale DNA Sequencing

1999 ◽  
Vol 9 (5) ◽  
pp. 457-462 ◽  
Author(s):  
Andre Marziali ◽  
Thomas D. Willis ◽  
Nancy A. Federspiel ◽  
Ronald W. Davis
Keyword(s):  
Sample Preparation ◽  
Dna Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Low Cost ◽  
High Quality ◽  
Dna Templates ◽  
Sequencing Technologies ◽  
Front End ◽  
Automated Sample Preparation

Recent advances in DNA sequencing technologies, both in the form of high lane-density gels and automated capillary systems, will lead to an increased requirement for sample preparation systems that operate at low cost and high throughput. As part of the development of a fully automated sequencing system, we have developed an automated subsystem capable of producing 10,000 sequence-ready ssDNA templates per day from libraries of M13 plaques at a cost of $0.29 per sample. This Front End has been in high throughput operation since June, 1997 and has produced > 400,000 high-quality DNA templates.

scholarly journals Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0158502 ◽  
Author(s):  
Kamfai Chan ◽  
Mauricio Coen ◽  
Justin Hardick ◽  
Charlotte A. Gaydos ◽  
Kah-Yat Wong ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Molecular Detection ◽  
Low Cost ◽  
High Quality ◽  
3D Printers ◽  
Automated Sample Preparation

A Vision-Based Gap Detection Method during the Placement of Large-Scale Composite Structures

2011 ◽  
Vol 186 ◽  
pp. 11-15
Author(s):  
Li Cao ◽  
Wen Chen ◽  
Jun Xiao
Keyword(s):  
Image Processing ◽  
Video Processing ◽  
Composite Structures ◽  
Large Scale ◽  
Low Cost ◽  
High Quality ◽  
Detection Technology ◽  
Gap Measurement ◽  
Automatic Placement ◽  
On Line

Video processing technology is regarded as a low-cost detection technology in complex environment. Because the placement layer is thin and the surface is complex that causes high detection error and high cost in laser measurement. Two problems must be solved before using it in large-scale composite structures automatic placement. One is to obtain the high-quality and stable image, and the other is to improve efficiency of image processing. In this paper, a method obtaining the high quality placement gap images was studied. It made use of the optical characteristics of composite material’s surface texture. And some parameters were determined by experiments. To reduce the calculation cost of image processing, a placement gap measurement method based on line scanning was also proposed here. The method was effective in our detection experiments on an actual workpiece.

scholarly journals Automated Sample Preparation and Data Collection Workflow for High-Throughput In Vitro Metabolomics

Metabolites ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 52
Author(s):  
Julia M. Malinowska ◽  
Taina Palosaari ◽  
Jukka Sund ◽  
Donatella Carpi ◽  
Gavin R. Lloyd ◽  
...  
Keyword(s):  
Sample Preparation ◽  
High Throughput ◽  
High Throughput Screening ◽  
In Vitro Screening ◽  
Chemical Safety ◽  
Experimental Conditions ◽  
Well Location ◽  
Relative Standard ◽  
Automated Sample Preparation

Regulatory bodies have started to recognise the value of in vitro screening and metabolomics as two types of new approach methodologies (NAMs) for chemical risk assessments, yet few high-throughput in vitro toxicometabolomics studies have been reported. A significant challenge is to implement automated sample preparation of the low biomass samples typically used for in vitro screening. Building on previous work, we have developed, characterised and demonstrated an automated sample preparation and analysis workflow for in vitro metabolomics of HepaRG cells in 96-well microplates using a Biomek i7 Hybrid Workstation (Beckman Coulter) and Orbitrap Elite (Thermo Scientific) high-resolution nanoelectrospray direct infusion mass spectrometry (nESI-DIMS), across polar metabolites and lipids. The experimental conditions evaluated included the day of metabolite extraction, order of extraction of samples in 96-well microplates, position of the 96-well microplate on the instrument’s deck and well location within a microplate. By using the median relative standard deviation (mRSD (%)) of spectral features, we have demonstrated good repeatability of the workflow (final mRSD < 30%) with a low percentage of features outside the threshold applied for statistical analysis. To improve the quality of the automated workflow further, small method modifications were made and then applied to a large cohort study (4860 sample infusions across three nESI-DIMS assays), which confirmed very high repeatability of the whole workflow from cell culturing to metabolite measurements, whilst providing a significant improvement in sample throughput. It is envisioned that the automated in vitro metabolomics workflow will help to advance the application of metabolomics (as a part of NAMs) in chemical safety, primarily as an approach for high throughput screening and prioritisation.

scholarly journals Extensive Screening of Green Solvents for Safe and Sustainable UiO-66 Synthesis

2020 ◽  
Author(s):  
Diletta Morelli Venturi ◽  
Filippo Campana ◽  
Fabio Marmottini ◽  
Ferdinando Costantino ◽  
Luigi Vaccaro
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Metal Organic Framework ◽  
Dimethyl Formamide ◽  
Scale Production ◽  
Green Solvents ◽  
High Quality ◽  
Color Code ◽  
Large Scale Production ◽  
Metal Organic

<p>Zirconium based Metal-Organic Framework UiO-66 is to date considered one of the benchmark compound among stable MOFs and it has attracted a huge attention for its employment in many strategic applications. Large scale production of UiO-66 for industrial purposes requires the use of safe and green solvents, fulfilling the green chemistry principles and able to replace the use of <i>N,N</i>-Dimethyl-Formamide (DMF), which, despite its toxicity, is still considered the most efficient solvent for obtaining UiO-66 of high quality. Herein we report on a survey of about 40 different solvents with different polarity, boiling point and acidity, used for the laboratory scale synthesis of high quality UiO-66 crystals. The solvents were chosen according the European REACH Regulation 1907/2006 among those having low cost, low toxicity and fully biodegradable. Concerning MOF synthesis, the relevant parameters chosen for establishing the quality of the results obtained are the degree are the crystallinity, microporosity and specific surface area, yield and solvent recyclability. Taking into account also the chemical physical properties of all the solvents, a color code was assigned in order to give a final green assessment for the UiO-66 synthesis. Defectivity of the obtained products, the use of acidic modulators and the use of alternative Zr-salts have been also taken into consideration. Preliminary results lead to conclude that GVL (γ-valerolactone) is among the most promising solvents for replacing DMF in UiO-66 MOF synthesis. </p>

scholarly journals Extensive Screening of Green Solvents for Safe and Sustainable UiO-66 Synthesis

2020 ◽  
Author(s):  
Diletta Morelli Venturi ◽  
Filippo Campana ◽  
Fabio Marmottini ◽  
Ferdinando Costantino ◽  
Luigi Vaccaro
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Metal Organic Framework ◽  
Dimethyl Formamide ◽  
Scale Production ◽  
Green Solvents ◽  
High Quality ◽  
Color Code ◽  
Large Scale Production ◽  
Metal Organic

<p>Zirconium based Metal-Organic Framework UiO-66 is to date considered one of the benchmark compound among stable MOFs and it has attracted a huge attention for its employment in many strategic applications. Large scale production of UiO-66 for industrial purposes requires the use of safe and green solvents, fulfilling the green chemistry principles and able to replace the use of <i>N,N</i>-Dimethyl-Formamide (DMF), which, despite its toxicity, is still considered the most efficient solvent for obtaining UiO-66 of high quality. Herein we report on a survey of about 40 different solvents with different polarity, boiling point and acidity, used for the laboratory scale synthesis of high quality UiO-66 crystals. The solvents were chosen according the European REACH Regulation 1907/2006 among those having low cost, low toxicity and fully biodegradable. Concerning MOF synthesis, the relevant parameters chosen for establishing the quality of the results obtained are the degree are the crystallinity, microporosity and specific surface area, yield and solvent recyclability. Taking into account also the chemical physical properties of all the solvents, a color code was assigned in order to give a final green assessment for the UiO-66 synthesis. Defectivity of the obtained products, the use of acidic modulators and the use of alternative Zr-salts have been also taken into consideration. Preliminary results lead to conclude that GVL (γ-valerolactone) is among the most promising solvents for replacing DMF in UiO-66 MOF synthesis. </p>

scholarly journals A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Kucharski ◽  
Jaishree Tripathi ◽  
Sourav Nayak ◽  
Lei Zhu ◽  
Grennady Wirjanata ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Rna Extraction ◽  
Transcriptome Data ◽  
High Quality ◽  
Diverse Range ◽  
Human Haemoglobin ◽  
Infected Blood ◽  
Blood Samples ◽  
Total Rna

Abstract Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest  2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to  date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.

scholarly journals Genetics of non-syndromic childhood obesity and the use of high-throughput DNA sequencing technologies

2017 ◽  
Vol 31 (10) ◽  
pp. 1549-1561 ◽  
Author(s):  
Ana Carolina Proença da Fonseca ◽  
Claudio Mastronardi ◽  
Angad Johar ◽  
Mauricio Arcos-Burgos ◽  
Gilberto Paz-Filho
Keyword(s):  
Childhood Obesity ◽  
Dna Sequencing ◽  
High Throughput ◽  
Sequencing Technologies ◽  
High Throughput Dna Sequencing

scholarly journals LRez: C ++ API and toolkit for analyzing and managing Linked-Reads data

2021 ◽  
Author(s):  
Pierre Morisse ◽  
Claire Lemaitre ◽  
Fabrice Legeai
Keyword(s):  
Genome Assembly ◽  
Low Cost ◽  
Variant Calling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
High Quality ◽  
Dna Molecule ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Genomic Regions

Abstract Motivation Linked-Reads technologies combine both the high-quality and low cost of short-reads sequencing and long-range information, through the use of barcodes tagging reads which originate from a common long DNA molecule. This technology has been employed in a broad range of applications including genome assembly, phasing and scaffolding, as well as structural variant calling. However, to date, no tool or API dedicated to the manipulation of Linked-Reads data exist. Results We introduce LRez, a C ++ API and toolkit which allows easy management of Linked-Reads data. LRez includes various functionalities, for computing numbers of common barcodes between genomic regions, extracting barcodes from BAM files, as well as indexing and querying BAM, FASTQ and gzipped FASTQ files to quickly fetch all reads or alignments containing a given barcode. LRez is compatible with a wide range of Linked-Reads sequencing technologies, and can thus be used in any tool or pipeline requiring barcode processing or indexing, in order to improve their performances. Availability and implementation LRez is implemented in C ++, supported on Unix-based platforms, and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module. Supplementary information Supplementary data are available at Bioinformatics Advances

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