Dataset Information

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing.

ABSTRACT: Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification. In this study, a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin (PVC) sheet. This modified method is named EZ-D, for EASY DNA extraction. Compared with the original cetyl trimethylammonium bromide (CTAB) method, DNA extracted by EZ-D is more efficient in polymerase chain reaction (PCR) amplification due to the more stable performance of the EZ-D stick. The EZ-D method is also faster, easier, and cheaper. PCR analyses showed that DNA extracted from several types of plant tissues by EZ-D was appropriate for specific identification of biological samples. A regular PCR reaction can detect the EZ-D-extracted DNA template at concentration as low as 0.1 ng/?L. Evaluation of the EZ-D showed that DNA extracts could be successfully amplified by PCR reaction for DNA fragments up to 3000 bp in length and up to 80% in GC content. EZ-D was successfully used for DNA extraction from a variety of plant species and plant tissues. Moreover, when EZ-D was combined with the loop-mediated isothermal amplification (LAMP) method, DNA identification of biological samples could be achieved without the need for specialized equipment. As an optimized DNA purification method, EZ-D shows great advantages in application and can be used widely in laboratories where equipment is limited and rapid results are required.

SUBMITTER: Wang Q

PROVIDER: S-EPMC7897602 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing.

Wang Qi Q Shen Xiaoxia X Qiu Tian T Wu Wei W Li Lin L Wang Zhi'an Z Shou Huixia H

Journal of Zhejiang University. Science. B 20210201 2

Nucleic acids in plant tissue lysates can be captured quickly by a cellulose filter paper and prepared for amplification after a quick purification. In this study, a published filter paper strip method was modified by sticking the filter paper on a polyvinyl chloride resin (PVC) sheet. This modified method is named EZ-D, for EASY DNA extraction. Compared with the original cetyl trimethylammonium bromide (CTAB) method, DNA extracted by EZ-D is more efficient in polymerase chain reaction (PCR) amp ...[more]

PMID: 33615751

Similar Datasets

Project description:Bones and teeth often represent the only sources of DNA available for identifying human remains. DNA in bones and teeth is generally better preserved than that in soft tissues because of the presence of hard connective tissue with a high level of calcium. Because of the extensive mineralisation, the choice of an efficient DNA extraction procedure is important to minimise the sampling of a high level of minerals and to remove polymerase chain reaction (PCR) inhibitors. Some protocols are available for DNA extraction from bones and teeth as part of the Qiagen EZ1 DNA Investigator Kit using the EZ1 Advanced XL automated purification platform. To improve the efficiency of DNA extraction from skeletal remains, the present study focuses on a modification to these already available protocols. In this study, different bones and teeth collected between 1 and 50 years after death were subjected to DNA extraction using the standard EZ1 protocol, a supplementary protocol, and a modified protocol. The modified approach included a decalcification step, whereas the Qiagen protocols worked directly on non-decalcified powder. In all three procedures, 150 mg samples were used for DNA extraction. We evaluated the quantity of DNA recovered from samples, the presence of any PCR inhibitors co-extracted, the level of DNA degradation, the quality of short tandem repeat (STR) profiles, and the reproducibility of the modified procedure. When compared with the other protocols, the modified protocol resulted in the best recovery of DNA that was free of PCR inhibitors. Additionally, the STR profiles were reliable and of high quality. In our opinion, the decalcification step increases DNA recovery by softening tissues, which allows lysis solutions to act more effectively. Furthermore, the use of two lysis solutions and the variation added to the EZ1 purification step allow for DNA recovery with quality and quantity superior to those of the previously available Qiagen-based protocols. These findings may be helpful solutions to the problems commonly encountered when dealing with difficult samples, such as bones and teeth.Key pointsBones and teeth often represent the only sources of DNA for identifying human remains.The choice of an efficient DNA extraction procedure is important for maximizing DNA recovery and removing PCR inhibitors.This study focuses on modifications to the previously available Qiagen-based protocols.The modified protocol enabled the best recovery of DNA, and both quality and quantity were superior to those of the previously available Qiagen-based protocols.The STR profiles obtained from samples extracted using the modified protocol were reliable and of high quality.

Project description:BackgroundThe recent development of next-generation sequencing DNA marker technologies, such as genotyping-by-sequencing (GBS), generates thousands of informative single nucleotide polymorphism markers in almost any species, regardless of genomic resources. This enables poorly resourced or "orphan" crops/species access to high-density, high-throughput marker platforms which have revolutionised population genetics studies and plant breeding. DNA quality underpins success of GBS methods as the DNA must be amenable to restriction enzyme digestion and sequencing. A barrier to implementing GBS technologies is access to inexpensive, high-throughput extraction methods that yield sequencing-quality genomic DNA (gDNA) from plants. Several high-throughput DNA extraction methods are available, but typically provide low yield or poor quality gDNA, or are costly (US$6-$9/sample) for consumables.ResultsWe modified a non-organic solvent protocol to extract microgram quantities (1-13 μg) of sequencing-quality high molecular weight gDNA inexpensively in 96-well plates from either fresh, freeze-dried or silica gel-dried plant tissue. The protocol was effective for several easy and difficult-to-extract forage, crop, horticultural and common model species including Trifolium, Medicago, Lolium, Secale, Festuca, Malus, Oryza, and Arabidopsis. The extracted DNA was of high molecular weight and digested readily with restriction enzymes. Contrasting with other extraction protocols we assessed, Illumina-based sequencing of GBS libraries developed from this gDNA had very uniform high quality base-calls to the end of sequence reads. Furthermore, DNA extracted using this method has been sequenced successfully with the PacBio long-read platform. The protocol is scalable, readily automated without requirement for fume hoods, requires approximately three hours to process 192 samples (384-576 samples/day), and is inexpensive at US$0.62/sample for consumables.ConclusionsThis versatile, scalable and simple protocol yields high molecular weight genomic DNA suitable for restriction enzyme digestion and next-generation sequencing applications including GBS and long-read sequencing platforms such as PacBio. The low cost, high-throughput, and extraction of high quality gDNA from a range of fresh and dried source plant material makes this method suitable for many sequencing and genotyping applications including large-scale sample screening underpinning breeding programmes.

Project description:BACKGROUND:Nonmuscle invasive bladder cancer (NMIBC) is a chronic condition requiring intensive follow-up, repeated endoscopic examinations, tumor resections, and intravesical treatments that can occur every 3 months for life. In this clinical context, patient-reported outcomes (PROs) are a critical concern for patients and their managing clinicians. PROs have enormous potential to be integral to treatment assessment and recommendations for NMIBC; however, current PRO measures are inadequate for NMIBC because they lack key NMIBC-specific symptoms and side effects associated with contemporary treatments. OBJECTIVE:The overarching aim of this study was to develop and evaluate a patient-reported symptom index (SI) for individuals with NMIBC (the NMIBC-SI) that is acceptable to patients; reliable, valid, and responsive to differences between contemporary treatments for NMIBC; and fit for purpose as an endpoint in clinical trials. METHODS:The NMIBC-SI will be evaluated in 2 field tests across a total of 3 years. Field test 1 is a cross-sectional study design involving 225 adult NMIBC patients recruited while undergoing active treatment or those who completed final treatment within the past week. Data collected include patient demographics, clinical features of the tumor, risk category, treatment type, comorbidity, and PROs. Field test 2 is a prospective longitudinal study involving 225 newly diagnosed NMIBC-SI patients. Clinical data and patient-completed questionnaires will be collected at 4 time points during treatment: before tumor resection, 1 week after resection, end-of-induction intravesical therapy, and 1-year follow-up. Standard psychometric tests will be performed to assess the reliability, validity, responsiveness, and clinical utility of the NMIBC-SI. RESULTS:Participant recruitment to field test 1 commenced in February 2017. Recruitment for field test 2 is planned to commence in January 2018. Final results are expected to be published in 2019. The NMIBC-SI will be freely available for use via registration. CONCLUSIONS:This study protocol contains detailed methods that will be used across multiple international sites. Phase 2 in the development of the NMIBC-SI will enable a comprehensive evaluation of its reliability, validity, and responsiveness to ensure that the NMIBC-SI is fit for purpose in clinical research and provides an evidence base for the ongoing improvement of future therapies for NMIBC. TRIAL REGISTRATION:ClinicalTrials.gov NCT03091764; http://clinicaltrials.gov/ct2/showNCT03091764 (Archived by WebCite at http://www.webcitation.org/6umBhQeNX).

Dataset Information

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing.

Publications

Evaluation and application of an efficient plant DNA extraction protocol for laboratory and field testing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets