High throughput semi-automated extraction method for the creation of a collection from microbial fermentations of fungi and Actinomycetes

Planta Medica ◽  
2008 ◽  
Vol 74 (09) ◽  
Author(s):  
JR Tormo ◽  
N Tabanera ◽  
D Conway ◽  
P Ramos ◽  
A Redondo ◽  
...  
Keyword(s):  
High Throughput ◽  
Extraction Method ◽  
Automated Extraction ◽  
The Creation

scholarly journals Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Rachelle Bester ◽  
Glynnis Cook ◽  
Johannes H. J. Breytenbach ◽  
Chanel Steyn ◽  
Rochelle De Bruyn ◽  
...  
Keyword(s):  
High Throughput ◽  
Extraction Method ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Healthy Plant ◽  
Ion Torrent ◽  
Extraction Protocol ◽  
Zymo Research

Abstract Background High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. Methods Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. Results The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. Conclusions This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.

A high-throughput plant DNA extraction method for marker analysis

2003 ◽  
Vol 21 (1) ◽  
pp. 95-95 ◽  
Author(s):  
Angelo Karakousis ◽  
Peter Langridge
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Plant Dna ◽  
Dna Extraction Method ◽  
Marker Analysis

scholarly journals Evaluation of DNA levels recovered from forensic bone samples through the optimization of a semi-automated extraction method

2019 ◽  
Vol 7 (1) ◽  
pp. 614-616
Author(s):  
M.J. Caldeira ◽  
A.M. Bento ◽  
N. Gouveia ◽  
P. Brito ◽  
M.J. Porto
Keyword(s):  
Extraction Method ◽  
Automated Extraction

scholarly journals An Improved High-Throughput Lipid Extraction Method for the Analysis of Human Brain Lipids

Lipids ◽  
2013 ◽  
Vol 48 (3) ◽  
pp. 307-318 ◽  
Author(s):  
Sarah K. Abbott ◽  
Andrew M. Jenner ◽  
Todd W. Mitchell ◽  
Simon H. J. Brown ◽  
Glenda M. Halliday ◽  
...  
Keyword(s):  
Human Brain ◽  
High Throughput ◽  
Extraction Method ◽  
Lipid Extraction ◽  
Brain Lipids

scholarly journals High-throughput analysis of sulfatides in cerebrospinal fluid using automated extraction and UPLC-MS/MS

2017 ◽  
Vol 58 (7) ◽  
pp. 1482-1489 ◽  
Author(s):  
Maria Blomqvist ◽  
Jan Borén ◽  
Henrik Zetterberg ◽  
Kaj Blennow ◽  
Jan-Eric Månsson ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
High Throughput ◽  
Automated Extraction ◽  
High Throughput Analysis ◽  
Throughput Analysis

scholarly journals A new, harmless, high-throughput endosperm-based DNA extraction method for wheat

2019 ◽  
Vol 49 (9) ◽  
Author(s):  
Zhihui Ma ◽  
Yuquan Wang ◽  
Wenhui Wei ◽  
Zhengang Ru
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Seedling Emergence ◽  
Control Group ◽  
Suitable Alternative ◽  
Dna Extraction Method ◽  
High Throughput Method ◽  
Young Leaves ◽  
Non Destructive

ABSTRACT: In this study, a non-destructive, high-throughput, endosperm-based DNA extraction method was developed. To verify the non-destructive nature of this method, a germination test was performed on 288 seeds after sampling their endosperm, which gave a seedling emergence rate that was higher (97.6%) than that of the control group (92%). To confirm the feasibility of the new method, DNA was extracted from plants of a BC1F2 population by two different methods, namely, from endosperm using our rapid, high-throughput method (ER-DNA) and from young leaves emerging from the same sampled seed using the CTAB method (LC-DNA). The ER-DNA was undetectable by agarose gel electrophoresis, but was found to be an adequate replacement for LC-DNA for the amplification and detection of simple sequence repeats (SSRs). Further analysis revealed that ER-DNA was generally suitable for the generation of specific 500-750-bp fragments, but not for the amplification of 1,000-2,000-bp fragments. Our rapid, high-throughput method therefore has no deleterious effects on wheat seeds and yields DNA for SSR genotyping that is a suitable alternative to traditionally obtained DNA.

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