Comparative assessment of four RNA extraction methods and modification to obtain high-quality RNA from Parthenium hysterophorus leaf

Ahmad, Javed; Baig, Mohd Affan; Ali, Arlene Asthana; Al-Huqail, Asma A.; Ibrahim, Mohamed M.; Qureshi, M. Irfan

doi:10.1007/s13205-017-1003-3

Cited by 20 publications

(16 citation statements)

References 23 publications

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“…Plant gene expression analysis, cloning, transcriptomic and other research often need to isolate and purify RNA from tissues and high purity, high concentration and good integrity RNA is always a must [ 17 , 26 ]. At present, a large number of methods have been exploited or modified [ 27 – 30 ]. But plants have large differences in composition and this requires suitable approaches for different types of plants.…”

Section: Resultsmentioning

confidence: 99%

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

Liu

Han

et al. 2018

PLoS ONE

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Acquiring high quality RNA is the basis of plant molecular biology research, plant genetics and other physiological investigations. At present, a large number of nucleotide isolation methods have been exploited or modified, such as commercial kits, CTAB, SDS methods and so on. Due to the nature of different plants, extraction methods vary. Moreover, efficiency of certain approach cannot be guaranteed due to composition of different plants and extracting high quality RNA from plants rich in polysaccharides and polyphenols are often difficult. The physical and chemical properties of polysaccharides which are similar to nucleic acids and other secondary metabolites will be coprecipitated with RNA irreversibly. Therefore, how to remove polysaccharides and other secondary metabolites during RNA extraction is the primary challenge. Dendrobium huoshanense is an Orchidaceae perennial herb that is rich in polysaccharides and other secondary metabolites. By using D. huoshanense as the subject, we improved the method originated from CHAN and made it suitable for plants containing high amount of polysaccharides and polyphenols. The extracted total RNA was clear and non-dispersive, with good integrity and no obvious contamination with DNA and other impurities. And it was also evaluated by gel electrophoresis, nucleic acid quantitative detector and PCR assessment. Thus, as a simple approach, it is suitable and efficient in RNA isolation for plants rich in polysaccharides and polyphenols.

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Section: Resultsmentioning

confidence: 99%

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

Liu

Han

et al. 2018

PLoS ONE

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“…21, 22 and 36 protein spots were up-regulated in both ML and HL stress treatments. The 3,8,15,16,28,30,32,35, 37 and 38 protein spots were down regulated in both ML and HL stress treatments. These proteins represent candidate proteins which are associated with ML and HL stress responses in P. hysterophorus.…”

Section: Changes In Expression Of Proteinsmentioning

confidence: 94%

Parthenium hysterophorus steps up Ca-regulatory pathway in defence against highlight intensities

Ahmad

Baig

Amna

et al. 2020

Sci Rep

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Parthenium hysterophorus exhibits tolerance to a great extent against abiotic stresses including high light intensities. in this study, P. hysterophorus was subjected to three different light intensities viz. control (CL, 250 µmol photons m −2 s −1), moderately high (ML, 500 µmol photons m −2 s −1) and high (HL, 1000 µmol photons m −2 s −1) for assessment of biochemical and physiological responses at 3 and 5 days after treatment (DAT). Proteomic responses were also observed at 5 DAT. Level of oxidative stress marker, abundance of H 2 o 2 and o 2 − was highest in leaves exposed to HL followed by ML treatment. Biomass accumulation, photosynthetic parameters, chloroplast and mitochondrial integrity were also affected by both ML and HL treatments. Differential protein expression data showed modulation of thirty-eight proteins in ML and HL intensities. P. hysterophorus exhibited good ability to survive in ML then HL treatment as demonstrated by enhancement of the antioxidant system and photosynthesis. furthermore, P. hysterophorus mobilized some key proteins related to calcium signaling, which in turn coordinate physiological homeostasis under stress. proline and total soluble sugar content were high under stress; however, results of simulated experiment of our study indicate such accumulation of osmolytes may inhibit photon-availability to chloroplast. these results clarify our understanding of the mechanisms underlying the light stress tolerance of P. hysterophorus. Light is one of the primary essential environmental factors that affect growth and development of plants. Any slight change in light intensity, duration and quality can influence the rate, pattern of growth and development which can significantly influence the productivity at mass scale 1,2. Sensitivity of a plant to high intensities of light may lead to failure in acclimation responses leading to cellular damage and ultimately to the death of plants 3. As the light energy absorption exceeds capacity of its usage in the chloroplasts, oxygenic photosynthesis electron transport is elevated, generating excessive reactive oxygen species (ROS) through photochemical energy conversion 4. ROS damages cellular components including photosynthetic reaction centers and peripherical light-harvesting structures. Such light-induced damages might decrease photosynthetic activity, known as photoinhibition which is still poorly understood 5,6. Also, how do plants respond to highlight intensities at a cellular level and what might be rescue mechanisms are still in need of full understanding. Under light stress, role of calcium could also be crucial in protection of plants and thylakoids 7,8 besides other protective mechanisms 1,9-11. Such mechanisms primarily, and effectively, include defence pathways those operate through modulation of proteome profiles 12-14. The efficiency of defense depends on degree of modulation, and qualitative composition of a proteome decides the degree of threshold to withstand abiotic stress. Compared to crop plants, weeds are generally much mor...

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“…Lung tissues (100 mg) were ground into powder using liquid nitrogen prior to the addition of 1 ml TRIzol (Thermo Fisher Scientific, Inc.) for lysis. Following lysis, total RNA was extracted using the phenol chloroform method ( 20 ). The purity of RNA was determined by A260/A280 using ultraviolet spectrophotometry (Nanodrop ND2000; Thermo Fisher Scientific, Inc.).…”

Section: Methodsmentioning

confidence: 99%

MicroRNA-215 suppresses the proliferation, migration and invasion of non-small cell lung carcinoma cells through the downregulation of matrix metalloproteinase-16 expression

et al. 2018

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The present study investigated the expression of microRNA (miR)-215 in non-small cell lung carcinoma (NSCLC) at tissue and cellular levels, as well as its biological functions and mechanism of action. A total of 56 patients with NSCLC were included in the present study. NSCLC tissues and tumor-adjacent normal tissues were resected and collected. Reverse transcription-quantitative polymerase chain reaction was used to measure the expression of miR-215. Following transfection with miR-215 mimics, A549 cell proliferation, migration and invasion were determined using a Cell Counting Kit-8 and Transwell assay. Western blotting was employed to measure the expression of matrix metalloproteinase (MMP)-16 protein. A dual-luciferase reporter assay was conducted to determine the existence of a direct interaction between miR-215 and the MMP-16 gene. Reduced expression of miR-215 in NSCLC was closely associated with lymphatic metastasis and TNM staging. Overexpression of miR-215 inhibited the proliferation of A549 cells in vitro. Upregulated expression of miR-215 inhibited the migration and invasion of A549 cells in vitro. miR-215 exerted its biological functions possibly by regulating the expression of MMP-16. Elevated expression of MMP-16 promoted the proliferation, migration and invasion of A549 cells. miR-215 regulated the proliferation, migration and invasion of A549 cells by binding with the seed 3′-untranslated region of MMP-16 mRNA. The present study demonstrates that reduced expression of miR-215 in NSCLC is negatively associated with lymphatic metastasis and TNM staging. In addition, miR-215 acts as a tumor suppressor gene by inhibiting the proliferation, migration and invasion of NSCLC cells via the downregulation of MMP-16 expression.

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Comparative assessment of four RNA extraction methods and modification to obtain high-quality RNA from Parthenium hysterophorus leaf

Cited by 20 publications

References 23 publications

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

Parthenium hysterophorus steps up Ca-regulatory pathway in defence against highlight intensities

MicroRNA-215 suppresses the proliferation, migration and invasion of non-small cell lung carcinoma cells through the downregulation of matrix metalloproteinase-16 expression

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