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Jo TS. Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples. Funct Integr Genomics 2023; 23:338. [PMID: 37975936 DOI: 10.1007/s10142-023-01269-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.
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Affiliation(s)
- Toshiaki S Jo
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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2
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Improve sample preparation process for miRNA isolation from the culture cells by using silica fiber membrane. Sci Rep 2020; 10:21132. [PMID: 33273557 PMCID: PMC7713297 DOI: 10.1038/s41598-020-78202-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/15/2020] [Indexed: 12/31/2022] Open
Abstract
In clinical applications of miRNAs, the purity and quality of the testing samples are very critical, especially the obtained tissue sample volume is limited. If the extracted miRNAs are contaminated or different in quality before analysis, it will increase the variance of the analysis result and make the medical information judgment incorrect and cannot be portable. Herein, we improved the commercially extraction kit by realizing the fundamental mechanism and hoped to serve finding optimal procedures for increasing the recovery of miRNAs extracted from cultured cells. In the adsorption process, the factors, like increasing the ethanol concentration or adding Ca2+, could influence the RNA adsorption were investigated. For the elution process, the effect caused by raising the elution temperature and raising the pH value of elution buffer was studied. Finally, the conditions for miRNA extraction are optimal modified by using a 65% (v/v) solution of ethanol in the adsorption process, and using TE buffer with the pH value of 8.0 and raising the temperature to 55 °C in the elution. According to the quantified results, the improved extraction kit can promote the recovery of endogenous miR-21 by about 6 times by using the optimal extraction conditions comparing with the miRNeasy Mini Kit.
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3
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Chen WY, Matulis D, Hu WP, Lai YF, Wang WH. Studies of the interactions mechanism between DNA and silica surfaces by Isothermal Titration Calorimetry. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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4
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Xu L, Sun L, Guan G, Huang Q, Lv J, Yan L, Ling L, Zhang Y. The effects of pH and salts on nucleic acid partitioning during phenol extraction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:305-320. [PMID: 30922157 DOI: 10.1080/15257770.2018.1533138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The partitioning of nucleic acids is sensitive to pH during phenol extraction. However, the exact effects of pH on phenol extraction had not been systematically investigated, and the mechanism of which were not fully elucidated. In this paper, we showed that the partitioning of nucleic acids was determined neither solely by the pH of the aqueous buffer being used, nor by the "pH of the phenol"; the latter is a completely wrong conception. We demonstrated that a key determinant for nucleic acid partitioning during phenol extraction was the equilibrated pH of the aqueous phase, which should be defined as the pH of phenol extraction. For example, when 50 mM NaAc-HAc buffer at pH of 3.47 was mixed with an equal volume of water-saturated phenol, the equilibrated pH of aqueous phase would be raised to ∼3.84. At this pH, almost all of genomic DNA partitioned into the phenol phase, and genomic DNA-free total RNA was retained in the aqueous phase. Several salts were found affecting the partitioning of nucleic acids during phenol extraction in different manners. Based on these results, a low-cost and efficient method for genomic DNA-free total RNA extraction was developed.
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Affiliation(s)
- Lei Xu
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Lu Sun
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Guoyu Guan
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Qianwu Huang
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Jun Lv
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Liang Yan
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Liefeng Ling
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
| | - Yao Zhang
- a Anhui Province Key Laboratory of Active Biological Macromolecules , Wannan Medical College , Wuhu , Anhui , China
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5
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Trujillo-Esquivel E, Franco B, Flores-Martínez A, Ponce-Noyola P, Mora-Montes HM. Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:404-9. [PMID: 27352216 DOI: 10.1080/15257770.2016.1184277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.
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Affiliation(s)
- Elías Trujillo-Esquivel
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Bernardo Franco
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Alberto Flores-Martínez
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Patricia Ponce-Noyola
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Héctor M Mora-Montes
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
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6
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Simultaneous extraction of DNA and RNA from Escherichia coli BL 21 based on silica-coated magnetic nanoparticles. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5483-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Pavani KC, Baron EE, Faheem M, Chaveiro A, Da Silva FM. Optimisation of total RNA extraction from bovine oocytes and embryos for gene expression studies and effects of cryoprotectants on total RNA extraction. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715040076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Xu L, Tian C, Lu X, Ling L, Lv J, Wu M, Zhu G. Photoreactivation of Escherichia coli is impaired at high growth temperatures. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 147:37-46. [PMID: 25839748 DOI: 10.1016/j.jphotobiol.2015.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Photolyase repairs UV-induced lesions in DNA using light energy, which is the principle of photoreactivation. Active photolyase contains the two-electron-reduced flavin cofactor. We observed that photoreactivation of Escherichia coli was impaired at growth temperatures ⩾37°C, and growth in this temperature range also resulted in decreased photolyase protein levels in the cells. However, the levels of phr transcripts (encoding photolyase) were almost unchanged at the various growth temperatures. A lacZ-reporter under transcriptional control of the phr promoter showed no temperature-dependent expression. However, a translational reporter consisting of the photolyase N-terminal α/β domain-LacZ fusion protein exhibited lower β-galactosidase activity at high growth temperatures (37-42°C). These results indicated that the change in photolyase levels at different growth temperatures is post-transcriptional in nature. Limited proteolysis identified several susceptible cleavage sites in E. coli photolyase. In vitro differential scanning calorimetry and activity assays revealed that denaturation of active photolyase occurs at temperatures ⩾37°C, while apo-photolyase unfolds at temperatures ⩾25°C. Evidence from temperature-shift experiments also implies that active photolyase is protected from thermal unfolding and proteolysis in vivo, even at 42°C. These results suggest that thermal unfolding and proteolysis of newly synthesized apo-photolyase, but not active photolyase, is responsible for the impaired photoreactivation at high growth temperatures (37-42°C).
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Affiliation(s)
- Lei Xu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, Anhui, China; Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, China
| | - Changqing Tian
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, Anhui, China
| | - Xiaohua Lu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, China
| | - Liefeng Ling
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, China
| | - Jun Lv
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, China
| | - Mingcai Wu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, Anhui, China; Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, Anhui, China.
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9
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Sun N, Deng C, Zhao X, Zhou Q, Ge G, Liu Y, Yan W, Xia Q. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid. J Virol Methods 2014; 196:204-11. [DOI: 10.1016/j.jviromet.2013.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 10/26/2022]
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10
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Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: Application to viral nucleic acid extraction from serum. J Chromatogr A 2014; 1325:31-9. [DOI: 10.1016/j.chroma.2013.11.059] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 11/22/2013] [Accepted: 11/30/2013] [Indexed: 11/18/2022]
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11
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Rapid depletion of target proteins allows identification of coincident physiological responses. J Bacteriol 2012; 194:5932-40. [PMID: 22942249 DOI: 10.1128/jb.00913-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeted protein degradation is a powerful tool that can be used to create unique physiologies depleted of important factors. Current strategies involve modifying a gene of interest such that a degradation peptide is added to an expressed target protein and then conditionally activating proteolysis, either by expressing adapters, unmasking cryptic recognition determinants, or regulating protease affinities using small molecules. For each target, substantial optimization may be required to achieve a practical depletion, in that the target remains present at a normal level prior to induction and is then rapidly depleted to levels low enough to manifest a physiological response. Here, we describe a simplified targeted degradation system that rapidly depletes targets and that can be applied to a wide variety of proteins without optimizing target protease affinities. The depletion of the target is rapid enough that a primary physiological response manifests that is related to the function of the target. Using ribosomal protein S1 as an example, we show that the rapid depletion of this essential translation factor invokes concomitant changes to the levels of several mRNAs, even before appreciable cell division has occurred.
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