Comparative analysis and innovation of a simple and rapid method for high-quality RNA and DNA extraction of kiwifruit

Afshar-Mohammadian, Mansour; Rezadoost, Mohammad Hossein; Fallah, Seyyed Fatemeh

doi:10.1016/j.mex.2018.03.008

Cited by 8 publications

(8 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Plant DNA extraction protocols are often reported for only one or a few species, or are suitable only for specific applications [1–4]. In our experience, commercial kits, expensive for large-scale projects, are frequently inefficient for DNA extraction from challenging plant tissues rich in polyphenols or polysaccharides.…”

Section: Introductionmentioning

confidence: 99%

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

et al. 2018

View full text Add to dashboard Cite

Modern genotyping techniques, such as SNP analysis and genotyping by sequencing (GBS), are hampered by poor DNA quality and purity, particularly in challenging plant species, rich in secondary metabolites. We therefore investigated the utility of a pre-wash step using a buffered sorbitol solution, prior to DNA extraction using a high salt CTAB extraction protocol, in a high throughput or miniprep setting. This pre-wash appears to remove interfering metabolites, such as polyphenols and polysaccharides, from tissue macerates. We also investigated the adaptability of the sorbitol pre-wash for RNA extraction using a lithium chloride-based protocol. The method was successfully applied to a variety of tissues, including leaf, cambium and fruit of diverse plant species including annual crops, forest and fruit trees, herbarium leaf material and lyophilized fungal mycelium. We consistently obtained good yields of high purity DNA or RNA in all species tested. The protocol has been validated for thousands of DNA samples by generating high data quality in dense SNP arrays. DNA extracted from Eucalyptus spp. leaf and cambium as well as mycelium from Trichoderma spp. was readily digested with restriction enzymes and performed consistently in AFLP assays. Scaled-up DNA extractions were also suitable for long read sequencing. Successful RNA quality control and good RNA-Seq data for Eucalyptus and cashew confirms the effectiveness of the sorbitol buffer pre-wash for high quality RNA extraction.

show abstract

Section: Introductionmentioning

confidence: 99%

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The list of primers is given in Table 1 . After obtaining the IC50 at 48 hours of eugenol, whole-cell RNA was isolated using the Sinagen plus RNAX kit [ 9 ]. The purity and concentration of the extracted RNA were checked using a Nano-Drop ND-1000TM (Thermo Scientific) spectrophotometer at 260/280 nm, and samples displaying 1.8 and 1.9 were examined by electrophoresis on a 1.5% agar gel.…”

Section: Methodsmentioning

confidence: 99%

A Metabolomic Investigation of Eugenol on Colorectal Cancer Cell Line HT-29 by Modifying the Expression of APC, p53, and KRAS Genes

Ghodousi-Dehnavi

Hosseini

Arjmand

et al. 2021

Evidence-Based Complementary and Alternative Medicine

View full text Add to dashboard Cite

Colorectal cancer is one of the most lethal cancers with a high mortality rate. Chemotherapy results in drug resistance in some cases; hence, herbal medicines are sometimes used in adjunct with it. Eugenol has been reported to have anti-inflammatory, antioxidant, and anticancer properties. Metabolomics is a study of metabolic changes within an organism using high-throughput technology. The purpose of this research was to investigate the anticancer effects of eugenol and variations in p53, KRAS, and APC gene expression and metabolic changes associated with the abovementioned gene expressions using 1HNMR spectroscopy. The MTT method was used to determine cell viability and its IC50 detected. After treating HT-29 cells with IC50 concentration of eugenol, RNA was extracted and cDNA was obtained from them and the expression of p53, KRAS, and APC genes was measured using the qRT-PCR technique. Metabolites were extracted using the chloroform-ethanol method, lyophilized, and sent for 1HNMR spectroscopy using the 1D-NOESY protocol. Chemometrics analysis such as PLS-DA was performed, and differentiated metabolites were identified using the Human Metabolome Database. Integrated metabolic analysis using the metabolites and gene expression was performed by the MetaboAnalyst website. The observed IC50 for eugenol was 500 μM, and the relative expression of APC and p53 genes in the treated cells increased compared to the control group, and the expression of KRAS oncogene gene decreased significantly. The crucial changes in convergent metabolic phenotype with genes were identified. The results indicate that eugenol exhibits its antitumor properties by targeting a specific biochemical pathway in the cell’s metabolome profile due to changes in genes involved in colon cancer.

show abstract

“…RNA concentrations were measured spectrophotometrically using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and only samples with A260/A280 of 1.8-2.0 were used for further analysis. The RNA quality was checked with an RNA gel for two clear bands of 18S and 28S rRNAs [19].…”

Section: Rna Extraction From Rice Endospermmentioning

confidence: 99%

Levels and Expression Patterns of Endogenous Hormones during Seed Germination of Dongxiang Wild Rice

Liao¹,

Luo²,

Zuo³

et al. 2021

Pol. J. Environ. Stud.

View full text Add to dashboard Cite

Comparative analysis and innovation of a simple and rapid method for high-quality RNA and DNA extraction of kiwifruit

Abstract: Graphical abstract

Cited by 8 publications

References 17 publications

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications

A Metabolomic Investigation of Eugenol on Colorectal Cancer Cell Line HT-29 by Modifying the Expression of APC, p53, and KRAS Genes

Levels and Expression Patterns of Endogenous Hormones during Seed Germination of Dongxiang Wild Rice

Contact Info

Product

Resources

About