Standardization of an efficient protocol for isolation of RNA from Cuminum cyminum

Kanani, Poonam; Shukla, Yogesh; Modi, Arpan; Subhash, Narayanan; Kumar, Sushil

doi:10.1016/j.jksus.2018.12.008

Cited by 23 publications

(18 citation statements)

References 21 publications

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“…Routine molecular applications such as RT-PCR, NGS, RNA-seq require RNA with high purity and integrity [ 23 , 26 ]. At present, several methods and kits are available for extracting RNA from samples rich in polysaccharides, phenols and other secondary metabolites but they are mostly applied to plants tissues, leaves and woody species [ 20 , 21 , 23 , 26 , 33 , 37 , 38 ]. For this particular reason, five RNA isolation methods were compared in order to obtain high-quality RNA from Pseudomonas capeferrum TDA1 growing on aromatic compounds (phenol and 2,4-TDA) and succinate.…”

Section: Resultsmentioning

confidence: 99%

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An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

et al. 2021

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Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.

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Section: Resultsmentioning

confidence: 99%

“…Thus, polysaccharides can co-precipitate with RNA during the phenol/chloroform extraction steps [ 25 ]. Despite of these drawbacks, some modified protocols have been tested in plant leaves [ 52 ], seeds [ 37 ] and seedlings [ 53 ] obtaining high-quality RNA.…”

Section: Resultsmentioning

confidence: 99%

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

et al. 2021

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“…Two distinct methods of RNA extraction were evaluated to identify any impact of the RNA purification process on the quality of RNA (Table 1). Total RNA was extracted following the manufacturer's instructions of the commercial column-based system (QIAGEN RNeasy ® plant Mini Kit) and the non-commercial solvent phenol chloroform-based RNA extraction protocol [36]. DNA was successfully eliminated using DNase Digestion, DNase I, Bovine pancreas, > 1800 u, RNase Free (Biomatik), enabling us to continue with RNA free from DNA.…”

Section: Rna Extraction and Quality Assessmentmentioning

confidence: 99%

High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number

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Al‐Qurainy

Alshameri

et al. 2021

Biotechnology & Biotechnological Equipment

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Salinity is one of the most limiting constraints of crop production. Nevertheless, highly-tolerant crop plants (e.g. 'Guar' Cyamopsis tetragonoloba) can thrive well under salinity conditions. RNA-Seq plays a central role in identifying genes involved in the response mechanisms to salt stress in plant species. High-quality RNA, free of genomic DNA is a critical determinant for success in subsequent downstream experiments to shed light on tolerance mechanisms. In this research, an inspection of two different total RNA isolation protocols was employed for preparing highly pure and intact RNAs with good yield from Guar tissue under both high salinity and control conditions. The extracted RNA appeared in all quality metrics to be of adequate quantity and quality for most downstream applications, including high-throughput transcriptome sequencing and expression analysis. However, the outcomes showed that the most widely used RNA quality measurement, the RNA Integrity Number (RIN), is a poor indicator with a weak correlation to the integrity of RNA from this plant. In contrast to human and animal cells, plants have various ribosomal RNA species. Consequently, whenever the RNA was separated on an agarose gel, several RNA bands did appear, which gives the false impression of being unable to analyze the results of the bioanalyzer integrity. Low RIN number RNA samples were further processed by RNA-sequencing RNA-seq experiments from guar. RNA-seq analysis via Illumina's paired-end method was carried out to trace back and evaluate the extracted total RNA, resulting in high-quality data for subsequent stress tolerance research.

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“…Cumin belongs to the Apiaceae family, tribe Ammineae, and subtribe Carinae, and has 2n = 14 chromosomes 1,6,7 . Cumin is the second most popular seed species after black pepper 8 . It is an annual plant and is also one of the oldest and most cultivated aromatic and herbaceous natural products with numerous medicinal, nutraceutical, and pharmaceutical properties.…”

Section: Introductionmentioning

confidence: 99%

“…The aroma is mainly due to cuminol which makes up 2.5 -4.0% of the seed. The essential oils of cumin seeds primarily contain hydrocarbons and aldehydes 8 . The objective of this work is to provide a precise and up-to-date review of the ethnopharmacology, phyto-…”

Section: Introductionmentioning

confidence: 99%

Cumin (Cuminum cyminum L.): A review of its ethnopharmacology, phytochemistry

et al. 2020

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Introduction: Cumin (Cuminum cyminum L.) is an annual plant that is not only one of the most popular seed species but also one of the oldest and most cultivated aromatic and herbaceous natural products with numerous medicinal, nutraceutical, and pharmaceutical properties. It is widely used in the beverage, food, liquor, medicine, perfume, and toiletry industries. The objective of this work was to provide a precise and up-to-date review of the ethnopharmacology, phytochemistry, and biological activities of cumin. Methods: Information was gathered from the review of relevant literature obtained from various databases, such as Science Direct, Springer, PubMed, Google, and Google Scholar. Results: The various parts of the cumin plant (leaves, shoot, root, and flowers) contain similar and different chemical compounds. Conclusion: The medicinal and health potential of cumin is mainly attributed to its antioxidant, antibacterial, antifungal, anti-inflammatory, antidiabetic, insecticide, and immunomodulatory properties. More studies are, however, required to unravel novel components and applications of cumin.

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Standardization of an efficient protocol for isolation of RNA from Cuminum cyminum

Cited by 23 publications

References 21 publications

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene

High RNA quality extracted from the tolerant crop Cyamopsis tetragonoloba (L.) despite possession of low RNA integrity number

Cumin (Cuminum cyminum L.): A review of its ethnopharmacology, phytochemistry

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