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Tiwari S, Shahat A, Kastelic J, Thakor N, Thundathil J. Optimized total RNA isolation from bovine sperm with enhanced sperm head lysis. Biochem Cell Biol 2024; 102:194-205. [PMID: 37948675 DOI: 10.1139/bcb-2023-0231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Increasing evidence of sperm RNA's role in fertilization and embryonic development has provided impetus for its isolation and thorough characterization. Sperm are considered tough-to-lyse cells due to the compact condensed DNA in sperm heads. Lack of consensus among bovine sperm RNA isolation protocols introduces experimental variability in transcriptome studies. Here, we describe an optimized method for total RNA isolation from bovine sperm using the TRIzol reagent. This study critically investigated the effects of various lysis conditions on sperm RNA isolation. Sperm suspended in TRIzol were subjected to a combination of mechanical treatments (sonication and passage through a 30G needle and syringe) and chemical treatments (supplementation with reducing agents 1,4-dithiothreitol and tris(2-carboxyethyl) phosphine hydrochloride (TCEP)). Microscopic evaluation of sperm lysis confirmed preferential sperm tail versus sperm head lysis. Interestingly, only TCEP-supplemented TRIzol (both mechanical treatments) had progressive sperm head lysis and consistently yielded total sperm RNA. Furthermore, RNA integrity was confirmed based on the electrophoresis profile and an absence of genomic DNA and somatic cells (e.g., epithelial cells, spermatids, etc.) with RT-qPCR. Our findings highlighted the importance of sperm lysis, specifically of the sperm head using TCEP with mechanical treatment, in total RNA isolation and presented a bovine-specific sperm RNA isolation method to reduce experimental variabilities.
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Affiliation(s)
- Saurabh Tiwari
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Abdallah Shahat
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - John Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nehal Thakor
- Department of Chemistry & Biochemistry, University of Lethbridge, AB, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada
| | - Jacob Thundathil
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada
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Singh VV, Naseer A, Sellamuthu G, Jakuš R. An Optimized and Cost-Effective RNA Extraction Method for Secondary Metabolite-Enriched Tissues of Norway Spruce ( Picea abies). Plants (Basel) 2024; 13:389. [PMID: 38337922 PMCID: PMC10857598 DOI: 10.3390/plants13030389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Since the development of next-generation sequencing techniques and with the growing interest in transcriptomic studies, there is a demand for high-throughput RNA extraction techniques. General RNA extraction protocols are unreliable when it comes to the quality and quantity of isolated RNA obtained from different tissue types of different plant species. Despite Norway spruce (Picea abies) being one of the most significant and commercially valuable tree species in European forests, only limited genetic research is available. In this study, we developed a cetyltrimethylammonium bromide (CTAB) protocol by modifying the original method. We compared this CTAB protocol with other widely used methods for extracting RNA from different tissues (needle, phloem, and root) of Norway spruce, known for its richness in polyphenols, polysaccharides, and secondary metabolites. The modified CTAB method proves to be superior to the kit-based and TRIzol-based methods for extracting RNA from the metabolite-rich tissues of Norway spruce, resulting in high RNA quality and integrity values (RIN~7-9). The modified CTAB RNA extraction method is rapid, cost-effective, and relatively simple in yielding the desired RNA quality from Norway spruce tissues. It is optimal for RNA sequencing and other downstream molecular applications.
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Affiliation(s)
- Vivek Vikram Singh
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Aisha Naseer
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Gothandapani Sellamuthu
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
| | - Rastislav Jakuš
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 165 00 Prague, Czech Republic; (A.N.); (G.S.); (R.J.)
- Institute of Forest Ecology, Slovak Academy of Sciences, Štúrova 2, 960 53 Zvolen, Slovakia
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3
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Arthurs AL, McCullough D, Williamson JM, Jankovic-Karasoulos T, Smith MD, Roberts CT. Factors influencing RNA yield from placenta tissue. Placenta 2023; 140:80-83. [PMID: 37549440 DOI: 10.1016/j.placenta.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/12/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
High yield and integrity of placental RNA are crucial for placental transcriptomics studies. We assessed the effects of time to placental collection post-delivery; tissue storage, amount and method used for extraction; mode of delivery; and tissue type on total RNA yield. The optimal protocol for RNA extraction from placental tissue includes cryofreezing of the sample upon collection and RNA extraction from 50 mg of tissue using TRIzol reagent. Decidua yielded highest RNA quantity/mg of tissue, followed by villous tissue and the chorion. Comparisons with murine kidney and HEK293T show lower placental RNA yield, likely due to highly dense and heterogeneous tissue make-up and potential high placental nuclease activity.
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Affiliation(s)
- Anya L Arthurs
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia.
| | - Dylan McCullough
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Jessica M Williamson
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Tanja Jankovic-Karasoulos
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Melanie D Smith
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Claire T Roberts
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia.
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Sasi S, Krishnan S, Kodackattumannil P, Shamisi AA, Aldarmaki M, Lekshmi G, Kottackal M, Amiri KMA. DNA-free high-quality RNA extraction from 39 difficult-to-extract plant species (representing seasonal tissues and tissue types) of 32 families, and its validation for downstream molecular applications. Plant Methods 2023; 19:84. [PMID: 37568159 PMCID: PMC10416385 DOI: 10.1186/s13007-023-01063-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND High-purity RNA serves as the basic requirement for downstream molecular analysis of plant species, especially the differential expression of genes to various biotic and abiotic stimuli. But, the extraction of high-quality RNA is usually difficult from plants rich in polysaccharides and polyphenols, and their presence usually interferes with the downstream applications. The aim of the study is to optimize the extraction of high-quality RNA from diverse plant species/tissues useful for downstream molecular applications. RESULTS Extraction of RNA using commercially available RNA extraction kits and routine hexadecyltrimethylammonium bromide (CTAB) methods did not yield good quality DNA-free RNA from Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera. A reliable protocol for the extraction of high-quality RNA from mature leaves of these difficult-to-extract trees was optimized after screening nine different methods. The DNase I-, and proteinase K treatment-free modified method, consisting of extraction with CTAB method followed by TRIzol, yielded high-quality DNA-free RNA with an A260/A280 and A260/A230 ratios > 2.0. Extraction of RNA from Conocarpus, the most difficult one, was successful by avoiding the heat incubation of ground tissue in a buffer at 65 oC. Pre-warming of the buffer for 5-10 min was sufficient to extract good-quality RNA. RNA integrity number of the extracted RNA samples ranged between 7 and 9.1, and the gel electrophoresis displayed intact bands of 28S and 18S RNA. A cDNA library constructed from the RNA of P. cineraria was used for the downstream applications. Real-time qPCR analysis using the cDNA from P. cineraria RNA confirmed the quality. The extraction of good quality RNA from samples of the desert-growing P. cineraria (> 20-years-old) collected in alternate months of the year 2021 (January to December covering winter, spring, autumn, and the very dry and hot summer) proved the efficacy of the protocol. The protocol's broad applicability was further validated by extracting good-quality RNA from 36 difficult-to-extract plant species, including tissues such as roots, flowers, floral organs, fruits, and seeds. CONCLUSIONS The modified DNase I and Proteinase K treatment-free protocol enables to extract DNA-free, high-quality, intact RNA from a total of 39 difficult-to-extract plant species belonging to 32 angiosperm families is useful to extract good-quality RNA from dicots and monocots irrespective of tissue types and growing seasons.
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Affiliation(s)
- Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Preshobha Kodackattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Aysha Al Shamisi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
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Olejnik J, Hume AJ, Ross SJ, Scoon WA, Seitz S, White MR, Slutzky B, Yun NE, Mühlberger E. Art of the Kill: Designing and Testing Viral Inactivation Procedures for Highly Pathogenic Negative Sense RNA Viruses. Pathogens 2023; 12:952. [PMID: 37513799 PMCID: PMC10386221 DOI: 10.3390/pathogens12070952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The study of highly pathogenic viruses handled under BSL-4 conditions and classified as Select Agents frequently involves the transfer of inactivated materials to lower containment levels for downstream analyses. Adhering to Select Agent and BSL-4 safety regulations requires validation or verification of the inactivation procedures, which comes with an array of challenges for each method. This includes the use of cytotoxic reagents for chemical inactivation and defining the precise inactivation parameters for physical inactivation. Here, we provide a workflow for various inactivation methods using Ebola, Nipah, and Lassa viruses as our examples. We choose three distinct inactivation methods (TRIzol/TRIzol LS, aldehyde fixation using different fixatives, and heat) to highlight the challenges of each method and provide possible solutions. We show that, whereas published chemical inactivation methods are highly reliable, the parameters for heat inactivation must be clearly defined to ensure complete inactivation. In addition to the inactivation data, we also provide examples and templates for the documentation required for approval and use of inactivation SOPs, including an inactivation report, the procedure sections of developed SOPs, and an electronic inactivation certificate that accompanies inactivated samples. The provided information can be used as a roadmap for similar studies at high and maximum containment laboratories.
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Affiliation(s)
- Judith Olejnik
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Stephen J Ross
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
- Department of Biochemistry and Cell Biology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Whitney A Scoon
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Scott Seitz
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Mitchell R White
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Ben Slutzky
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Nadezhda E Yun
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
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Zhang H, Liu Y, Yu B, Lu R. An optimized TRIzol-based method for isolating RNA from adipose tissue. Biotechniques 2023. [PMID: 37232298 DOI: 10.2144/btn-2022-0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
High-quality RNA isolation from recalcitrant adipose tissue with high lipid content and low cell numbers is difficult. Many studies have made efforts to optimize methods for isolating RNA from adipose tissue through combinations of column-based kits and phenol-chloroform methods, or through in-house protocols. However, the considerable complexity of these protocols and the various kits/materials required hamper their wide use. Herein, we describe an optimized protocol based on TRIzol reagent, which is the most accessible ready-to-use reagent for nucleic acid and/or protein isolation in laboratories. This article provides a step-by-step protocol yielding sufficient and qualified RNA from lipid-rich specimens for downstream applications.
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Affiliation(s)
- Hongwei Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology & Visual Science, Guangzhou, 510060, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yaoming Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology & Visual Science, Guangzhou, 510060, China
| | - Bingcheng Yu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rong Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology & Visual Science, Guangzhou, 510060, China
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7
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Kao CY, Chang CT, Kuo PY, Lin CJ, Chiu HH, Liao HW. Sequential isolation of metabolites and lipids from a single sample to achieve multiomics by using TRIzol reagent. Talanta 2023; 258:124416. [PMID: 36889188 DOI: 10.1016/j.talanta.2023.124416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Simultaneous extraction of various types of biomolecule from a single sample can be beneficial for multiomics studies of unique specimens. An efficient and convenient sample preparation approach must be developed that can comprehensively isolate and extract biomolecules from one sample. TRIzol reagent is widely used in biological studies for DNA, RNA, and protein isolation. This study evaluated the feasibility of using TRIzol reagent for the simultaneous isolation of not only DNA, RNA, and proteins but also metabolites and lipids from a single sample. Through the comparison of known metabolites and lipids obtained using the conventional methanol (MeOH) and methyl-tert-butyl ether (MTBE) extraction methods, we determined the presence of metabolites and lipids in the supernatant during TRIzol sequential isolation. Finally, we performed untargeted metabolomics and lipidomics to examine metabolite and lipid alterations associated with the jhp0417 mutation in Helicobacter pylori by using the TRIzol sequential isolation protocol and MeOH and MTBE extraction methods. Metabolites and lipids with significant differences isolated using the TRIzol sequential isolation protocol were consistent with those obtained using the conventional MeOH and MTBE extraction methods. These results indicated that TRIzol reagent can be used to simultaneously isolate metabolites and lipids from a single sample. Thus, TRIzol reagent can be used in biological and clinical research, especially in multiomics studies.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chung-Te Chang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chia-Jen Lin
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Huai-Hsuan Chiu
- The Metabolomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, 10617, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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Takács R, Póliska S, Juhász T, Barna KB, Matta C. Isolation of High-Quality Total RNA from Small Animal Articular Cartilage for Next-Generation Sequencing. Curr Protoc 2023; 3:e692. [PMID: 36880775 DOI: 10.1002/cpz1.692] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Articular cartilage is characterized by a low density of chondrocytes surrounded by an abundant extracellular matrix (ECM) consisting of a dense mixture of collagens, proteoglycans, and glycosaminoglycans. Due to its low cellularity and high proteoglycan content, it is particularly challenging to extract high-quality total RNA suitable for sensitive high-throughput downstream applications such as RNA sequencing (RNA-Seq). Available protocols for high-quality RNA isolation from articular chondrocytes are inconsistent, resulting in suboptimal yield and compromised quality. This poses a significant difficulty in the application of RNA-Seq to study the cartilage transcriptome. Current protocols rely either on dissociation of cartilage ECM by collagenase digestion or pulverizing cartilage using various methods prior to RNA extraction. However, protocols for cartilage processing vary significantly depending on the species and source of cartilage within the body. Protocols for isolating RNA from human or large mammal (e.g., horse or cattle) cartilage samples are available, but this is not the case for chicken cartilage, despite the species being extensively used in cartilage research. Here, we present two improved RNA isolation protocols based on pulverization of fresh articular cartilage using a cryogenic mill or on enzymatic digestion using 1.2% (w/v) collagenase II. Our protocols optimize the collection and tissue processing steps to minimize RNA degradation and enhance RNA purity. Our results show that RNA purified from chicken articular cartilage using these methods has appropriate quality for RNA-Seq experiments. The procedure is applicable for RNA extraction from cartilage from other species such as dog, cat, sheep, and goat. The workflow for RNA-Seq analysis is also described here. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of total RNA from pulverized chicken articular cartilage Alternate Protocol: Extraction of total RNA from collagen-digested articular cartilage Support Protocol: Dissection of chicken articular cartilage from the knee joint Basic Protocol 2: RNA sequencing of total RNA from chicken articular cartilage.
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Affiliation(s)
- Roland Takács
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tamás Juhász
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztina B Barna
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Csaba Matta
- Department of Anatomy, Histology, and Embryology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Snedden M, Singh L, Kyathanahalli C, Hirsch E. Toxic effects of trace phenol/guanidine isothiocyanate (P/GI) on cells cultured nearby in covered 96-well plates. BMC Biotechnol 2022; 22:35. [PMID: 36434619 PMCID: PMC9700959 DOI: 10.1186/s12896-022-00766-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND A mixture of phenol and guanidine isothiocyanate ("P/GI", the principal components of TRIzol™ and similar products) is routinely used to isolate RNA, DNA, and proteins from a single specimen. In time-course experiments of cells grown in tissue culture, replicate wells are often harvested sequentially and compared, with the assumption that in-well lysis and complete aspiration of P/GI has no effect on continuing cultures in nearby wells. METHODS To test this assumption, we investigated morphology and function of RAW 264.7 cells (an immortalized mouse macrophage cell line) cultured in covered 96-well plates for 4, 8, or 24 h at varying distances from a single control well or a well into which P/GI had been deposited and immediately aspirated completely. RESULTS Time- and distance-dependent disruptions resulting from proximity to a single well containing trace residual P/GI were seen in cell morphology (blebbing, cytoplasmic disruption, and accumulation of intracellular vesicles), cell function (pH of culture medium), and expression of genes related to inflammation (Tnfα) and autophagy (Lc3b). There was no transcriptional change in the anti-apoptotic gene Mcl1, nor the pro-apoptotic gene Hrk, nor in P/GI-unexposed control cultures. LPS-stimulated cells incubated near P/GI had lower expression of the cytokine Il6. These effects were seen as early as 4 h of exposure and at a distance of up to 3 well units from the P/GI-exposed well. CONCLUSIONS Exposure to trace residual quantities of P/GI in covered tissue culture plates leads to substantial disruption of cell morphology and function in as little as 4 h, possibly through induction of autophagy but not apoptosis. This phenomenon should be considered when planning time-course experiments in multi-well covered tissue culture plates.
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Affiliation(s)
- Madeline Snedden
- grid.240372.00000 0004 0400 4439Department of Obstetrics and Gynecology, NorthShore University HealthSystem, 2650 Ridge Ave, Suite 1538, Evanston, IL 60201 USA
| | - Lavisha Singh
- grid.240372.00000 0004 0400 4439Department of Statistics, NorthShore University HealthSystem, Evanston, IL USA
| | - Chandrashekara Kyathanahalli
- grid.240372.00000 0004 0400 4439Department of Obstetrics and Gynecology, NorthShore University HealthSystem, 2650 Ridge Ave, Suite 1538, Evanston, IL 60201 USA ,grid.170205.10000 0004 1936 7822Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL USA
| | - Emmet Hirsch
- grid.240372.00000 0004 0400 4439Department of Obstetrics and Gynecology, NorthShore University HealthSystem, 2650 Ridge Ave, Suite 1538, Evanston, IL 60201 USA ,grid.170205.10000 0004 1936 7822Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, Chicago, IL USA
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10
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Anderson ER, Prince T, Turtle L, Hughes GL, Patterson EI. Methods of SARS-CoV-2 Inactivation. Methods Mol Biol 2022; 2452:465-473. [PMID: 35554921 DOI: 10.1007/978-1-0716-2111-0_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Inactivation methods allow for hazard group 3 (HG3) pathogens to be disposed of and used safely in downstream experiments and assays to be carried out at lower containment levels. Commonly used viral inactivation methods include heat inactivation, fixation methods, ultraviolet (UV) light and detergent inactivation. Here we describe known methods used to inactivate SARS-CoV-2 for safe downstream biological assays.
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Affiliation(s)
- Enyia R Anderson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tessa Prince
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Lance Turtle
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals Foundation NHS Trust (member of Liverpool Health Partners), Liverpool, UK
| | - Grant L Hughes
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Edward I Patterson
- Department of Biological Sciences, Brock University, St. Catharines, Canada.
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11
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Amirouche A, Ait-Ali D, Nouri H, Boudrahme-Hannou L, Tliba S, Ghidouche A, Bitam I. TRIzol-based RNA extraction for detection protocol for SARS-CoV-2 of coronavirus disease 2019. New Microbes New Infect 2021; 41:100874. [PMID: 33815807 PMCID: PMC8010344 DOI: 10.1016/j.nmni.2021.100874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diagnostic testing is important for managing the 2019 novel coronavirus (SARS-CoV-2). We developed an optimized protocol for SARS-CoV-2 RNA extraction from the surface of the respiratory mucosa with nasopharyngeal swabs and compared the sensitivity of RNA extraction methods. RNA extraction was performed using three different procedures (TRIzol, QIAamp, VMT-TRIzol) from nine positive SARS-CoV-2 samples. SARS-CoV-2 was detected by real-time reverse transcriptase PCR (RT-PCR) using a detection kit for SARS-CoV-2 (Sun Yat-sen University). Compared to RT-PCR results, there were no discernible differences in detection rates when comparing the three different extraction procedures. On the basis of these results, the use of TRIzol as a transport medium and RNA extraction method for SARS-CoV-2 detection may be a helpful alternative for laboratories facing shortages of commercial testing kits.
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Affiliation(s)
- A Amirouche
- Laboratoire de Biochimie Appliquée, CHU de Bejaia, Bejaia, Algeria.,Faculté des Sciences de la Nature et de la Vie, CHU de Bejaia, Bejaia, Algeria
| | - D Ait-Ali
- Faculté des Sciences de la Nature et de la Vie, CHU de Bejaia, Bejaia, Algeria.,Laboratoire de Génie Biologique des Cancers, CHU de Bejaia, Bejaia, Algeria
| | - H Nouri
- Faculté des Sciences de la Nature et de la Vie, CHU de Bejaia, Bejaia, Algeria.,Laboratoire de Microbiologie Appliquée, CHU de Bejaia, Bejaia, Algeria
| | - L Boudrahme-Hannou
- Laboratoire de Génie Biologique des Cancers, CHU de Bejaia, Bejaia, Algeria.,Faculté de Médecine, Université de Bejaia, CHU de Bejaia, Bejaia, Algeria.,Service des maladies infectieuses, CHU de Bejaia, Bejaia, Algeria
| | - S Tliba
- Laboratoire de Génie Biologique des Cancers, CHU de Bejaia, Bejaia, Algeria.,Faculté de Médecine, Université de Bejaia, CHU de Bejaia, Bejaia, Algeria.,Service de Neurochirurgie, CHU de Bejaia, Bejaia, Algeria
| | - A Ghidouche
- Faculté des Sciences de la Nature et de la Vie, CHU de Bejaia, Bejaia, Algeria.,Laboratoire de Génie Biologique des Cancers, CHU de Bejaia, Bejaia, Algeria
| | - I Bitam
- Ecole Supérieure en Sciences de l'Aliment et des Industries Agroalimentaires (ESSAIA), El Harrach, Alger, Algeria.,Aix-Marseille Université, IRD, VITROME, IHU Méditerranée Infection, Marseille, France
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12
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Bo YY, Liang LD, Hua YJ, Zhao Z, Yao MS, Shan LB, Liang CZ. High-purity DNA extraction from animal tissue using picking in the TRIzol-based method. Biotechniques 2021; 70:186-90. [PMID: 33337248 DOI: 10.2144/btn-2020-0142] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
TRIzol is used for the extraction of RNA, DNA and proteins from tissues or cells. Here, we present a simple picking method to extract DNA from tissues using TRIzol. Spectrophotometric analysis showed that the 260/280 and 260/230 nm optical density ratio of the picking method's DNA is ideal and better than that obtained by the classic TRIzol method. Gel electrophoresis showed that there was no RNA contamination, and the DNA had not degraded. DNA extracted by the picking method had the same performance in restriction enzyme digestion and quantitative PCR as that obtained by the traditional method. Viral DNA in the infected tissue was also obtained. This modified method facilitates various molecular biology assays.
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13
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Bechmann VG, Hansen AT, Poulsen LK, Jensen BM. Quantity and Quality of Basophil RNA Depend on the RNA Extraction Technique. Methods Mol Biol 2020; 2163:241-5. [PMID: 32766981 DOI: 10.1007/978-1-0716-0696-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Basophils have been suggested to express low quantities of RNA, challenging the study of gene expression within these cells. However, the purification technique employed might have an impact on the quantity and quality of RNA purified from basophils. This chapter describes a method which gives an optimal RNA output using a TRIzol-based method in contrast to a commercial kit.
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14
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Maisarah Y, Hashida HN, Yusmin MY. The challenge of getting a high quality of RNA from oocyte for gene expression study. Vet Res Forum 2020; 11:179-184. [PMID: 32782748 PMCID: PMC7413007 DOI: 10.30466/vrf.2018.92133.2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/29/2018] [Indexed: 11/23/2022]
Abstract
The extraction of intact RNA from oocyte is quite challenging and time-consuming. A standard protocol using commercial RNA extraction kit, yields a low quantity of RNA in oocytes. In the past, several attempts in getting RNA for gene expression study ended up with a few different modified methods. Extraction of high-quality RNA from oocyte is important before further downstream analyses such as reverse transcription-polymerase chain reaction, quantitative polymerase chain reaction, or northern blot analysis. In this review, the efficiency of RNA extraction methods from all species oocytes was compared between published articles and our research to gather all possible methods of RNA extraction. Two different methods of RNA extraction that were proposed from various experiments were reviewed to determine the best method of RNA extraction from the oocyte. Modified TRIzol method can be concluded as an efficient RNA extraction method especially for good RNA from oocytes. Meanwhile, comparing RNA extraction kits to extract the RNA from oocytes or pre-implantation embryos, the micro RNA extraction kit type is the best. Therefore, an appropriate RNA extraction method is important to obtain high quality of total RNA for gene expression profiling analysis.
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Affiliation(s)
- Yusoff Maisarah
- Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia;
| | - Hashim Noor Hashida
- Biology Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur, Malaysia;
| | - Mohd-Yusuf Yusmin
- Biology Division, Centre for Foundation Studies in Science, University of Malaya, Kuala Lumpur, Malaysia;
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia.
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15
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Farrag M, Abri S, Leipzig ND. pH-dependent RNA isolation from cells encapsulated in chitosan-based biomaterials. Int J Biol Macromol 2020; 146:422-430. [PMID: 31904458 DOI: 10.1016/j.ijbiomac.2019.12.263] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 02/05/2023]
Abstract
Chitosan has emerged as a useful biomaterial employed in tissue engineering and drug delivery applications due to its tunable and interesting properties. However, chitosan is protonated at biological pH and thus carries positive charges, which renders chitosan incompatible with conventional methods of RNA extraction. RNA extraction is an important step in investigating cell responses and behavior through studying their gene expression transcriptional profiles. While some researchers have tried different techniques to improve the yield and purity of RNA extracted from cells encapsulated in chitosan-based biomaterials, no single study has investigated the effects of manipulating pH of the homogenate during RNA extraction on the yield and quality of total RNA. This study confirms the release and binding of RNA from chitosan to be pH dependent while analyzing the impact of pH changes during the tissue disruption and homogenization step of extraction on the resulting yield and quality of isolated RNA. This concept was applied to three commonly used methods of RNA extraction, using adult neural stem/progenitor cells (aNSPCs) encapsulated within methacrylamide chitosan (MAC) as a model chitosan-based bioscaffold. High pH conditions resulted in high yields with good quality using both TRIzol and CTAB. pH of the homogenate did not affect RNeasy spin columns, which worked best in neutral conditions with good quality, however, the overall yield was low. Results in total show that pH affected RNA interaction with a chitosan-based bioscaffold, and thus altered the concentration, purity, and integrity of isolated RNA, dependent on the method used.
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Affiliation(s)
- Mahmoud Farrag
- Integrated Bioscience Program, the University of Akron, Akron, OH, USA.
| | - Shahrzad Abri
- Department of Chemical, Biomolecular, and Corrosion Engineering, the University of Akron, Akron, OH, USA
| | - Nic D Leipzig
- Integrated Bioscience Program, the University of Akron, Akron, OH, USA; Department of Chemical, Biomolecular, and Corrosion Engineering, the University of Akron, Akron, OH, USA.
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16
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Alabi T, Patel SB, Bhatia S, Wolfson JA, Singh P. Isolation of DNA-free RNA from human bone marrow mononuclear cells: comparison of laboratory methods. Biotechniques 2020; 68:159-62. [PMID: 31870171 DOI: 10.2144/btn-2019-0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
RNA quality (purity and integrity) and quantity are of critical importance to ensure reliable gene expression analysis, reproducibility of RNA sequencing and microarray data and validation by RT-PCR. Currently available methods for isolating RNA either are labor intensive (requiring the use of toxic organic solvents and separate DNase treatment) or require automation (with extensive setup and startup costs). To optimize both the quality and quantity of RNA from bone marrow, we recommend stabilization and storage of bone marrow mononuclear cells in RNAprotect® Cell Reagent, followed by extraction using the RNeasy® Protect Cell Mini Kit (Qiagen, Hilden, Germany). This method achieves optimal quantity and high-quality RNA for sequencing and RT-PCR while remaining efficient and cost effective.
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Abstract
Astrocytoma is an invasive carcinoma occurring in the nervous system and currently lacks effective treatment options. A deeper understanding of the mechanisms of tumorigenesis and tumor progression is needed in order to develop novel therapeutic strategies. Recent advances in in vitro culture systems have demonstrated that the use of three-dimensional (3D) culture models could be more relevant for this purpose as compared to monolayer or two-dimensional (2D) models due to their resemblance to in vivo cancer pathology. High-throughput techniques such as RNA sequencing, microarray analyses and cloning could provide useful insights into the relevance of these systems to the native tissue. Previous studies have reported RNA extraction protocols needed for such applications. We have modified these protocols to suit the isolation of total RNA from monolayer and hydrogel cultures of astrocytoma established using basement membrane matrix, Geltrex™. We have used this method to demonstrate the differences in the expression of genes involved in autophagy, a process deregulated in many cancer types, in monolayer and hydrogel cultures using quantitative polymerase chain reaction (qPCR). This protocol can be adopted by the researchers who wish to understand the molecular basis of gene expression in hydrogel cultures of normal as well as cancer cell lines.
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Affiliation(s)
- Manasi P Jogalekar
- Molecular Biology Program, New Mexico State University, Las Cruces, NM, USA
| | - Elba E Serrano
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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18
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Chan KK, Kwok CS, Sze ET, Lee FW. Evaluation of the Use of TRIzol-Based Protein Extraction Approach for Gel-Based Proteomic Analysis of Dried Seafood Products and Chinese Tonic Foods. Int J Mol Sci 2018; 19:E1998. [PMID: 29987231 DOI: 10.3390/ijms19071998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Although the emergence of gel-free approaches has greatly enhanced proteomic studies, two-dimensional gel electrophoresis (2-DE) remains one of the most widely used proteomic techniques for its high resolving power, relatively low cost, robustness, and high resolution. Preparation of high-quality protein samples remains the key in high-quality 2-DE for proteomic analysis. Samples with high endogenous levels of interfering molecules, such as salts, nucleic acids, lipids, and polysaccharides, would yield a low-quality 2-DE gel and hinder the analysis. Recently, a TRIzol-based protein extraction method has gained prominence and has attracted attention due to its promising performance in high-quality 2-DE. The authors evaluate the use of this approach for four valuable dried food products, namely two dried seafood products (abalone slices and whelk slices) and two traditional Chinese tonic foods (ganoderma and caterpillar fungus). The results indicate that 2-DE gels obtained through the TRIzol-based method are of high-quality and are comparable to those obtained through the trichloroacetic acid⁻acetone method in terms of spot number, spot intensity, and resolution. The TRIzol-based method is generally applicable to dried food samples and is simple and fast, which greatly streamlines the protein extraction procedure. Additionally, it enables the concurrent extraction and analysis of RNA, DNA, and protein from the same sample.
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19
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Ziros PG, Chartoumpekis DV, Sykiotis GP. A Simple Protocol for High Efficiency Protein Isolation After RNA Isolation from Mouse Thyroid and Other Very Small Tissue Samples. Methods Mol Biol 2016; 1449:383-93. [PMID: 27613051 DOI: 10.1007/978-1-4939-3756-1_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
As a dedicated hormone-secreting organ, the thyroid gland possesses a complement of proteostatic systems, including antioxidant, unfolded protein, and autophagic responses. The vast majority of animal investigations of thyroid physiology and, more recently, proteostasis, have utilized as model the rat, rather than the mouse. This is due to the very small size of the thyroid gland in the latter, with a total weight of ~2 mg (~1 mg per thyroid lobe). However, this strategy has limited the utilization of genetic approaches, such as taking advantage of the various transgenic and knockout mouse models. Here, we describe a simple and highly efficient protocol for the simultaneous isolation of mRNA, micro-RNA and 150-200 μg of protein from as little as 1 mg of mouse thyroid tissue, the average weight of one of the two thyroid lobes, thus preserving the other lobe for immunohistochemical or other analyses. While our workflow is similar to other protocols published in the literature and/or proposed by commercial reagent providers, we have introduced a key modification that addresses efficiently the most challenging step of the protein isolation process: the solubilization of the protein pellet after RNA extraction and protein precipitation. We demonstrate the feasibility of our approach and its utility for downstream analyses (including Western blotting) that facilitate the comparative study of proteostatic pathways in the mouse thyroid. We have also successfully applied this protocol on samples from mouse liver, brown and white adipose tissue, as well as from rodent cell lines.
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Abstract
Isolation of high-quality and nondegraded RNA is a prerequisite for many modern molecular biology applications. A variety of RNA extraction products and protocols are available for the standard model organisms, yet species-specific peculiarities of less well studied organisms often require specific protocol adaptations. Here we describe a robust RNA extraction protocol for planarians that is widely used in the community. The protocol combines tissue homogenization in TRIzol with phenol-chloroform extraction and subsequent purification over commercial columns. The purified RNA can be used for many downstream applications, such as cDNA synthesis and next-generation sequencing (NGS, RNA-seq).
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Affiliation(s)
- Shang-Yun Liu
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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21
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Kopec AM, Rivera PD, Lacagnina MJ, Hanamsagar R, Bilbo SD. Optimized solubilization of TRIzol-precipitated protein permits Western blotting analysis to maximize data available from brain tissue. J Neurosci Methods 2017; 280:64-76. [PMID: 28192129 DOI: 10.1016/j.jneumeth.2017.02.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/24/2017] [Accepted: 02/06/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Techniques simultaneously assessing multiple levels of molecular processing are appealing because molecular signaling underlying complex neural phenomena occurs at complementary levels. The TRIzol method isolates RNA and DNA, but protein retrieval is difficult due to inefficient solubilization of precipitated protein pellets. NEW METHOD We optimized a buffer for the efficient solubilization of protein from TRIzol-precipitated brain tissue for Western blotting analysis, which was also more effective at directly homogenizing brain tissue than RIPA buffer. RESULTS Protein yield during solubilization, in addition to protein yield via direct homogenization, is increased by optimizing concentrations of chemicals in a standard lysis buffer. Effective incubation parameters for both total protein yield and the analysis of post-translational modifications is remarkably flexible. Importantly, different neural cell types and protein classes are represented in solubilized protein samples. Moreover, we used dissociated mouse brain tissue to isolate microglia from other cell types and successfully resolved cell type-specific proteins from these small and difficult to attain samples. COMPARISON WITH EXISTING METHOD(S) Solubilization buffers to date have been comprised primarily of SDS or urea; the data herein demonstrate that components common to lysis buffers can also enhance protein solubilization both after direct homogenization and after precipitation. CONCLUSIONS This method is suitable for assessing gene and protein expression from a single brain sample, allowing for a more comprehensive evaluation of neural phenomena while minimizing the number of subjects.
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Affiliation(s)
- Ashley M Kopec
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Phillip D Rivera
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Richa Hanamsagar
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Staci D Bilbo
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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22
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Mölder T, Speek M. [Letter to the Editor] Accelerated RNA-RNA hybridization by concentrated guanidinium thiocyanate solution in single-step RNA isolation. Biotechniques 2016; 61:61-5. [PMID: 27528070 DOI: 10.2144/000114441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/09/2016] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Mart Speek, Department of Gene Technology, Akadeemia tee 15, Room 129, Tallinn University of Technology, Tallinn 19086, Estonia. E-mail: mart.speek@ttu.ee.
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Majumdar G, Vera S, Elam MB, Raghow R. A streamlined protocol for extracting RNA and genomic DNA from archived human blood and muscle. Anal Biochem 2015; 474:25-7. [PMID: 25579785 DOI: 10.1016/j.ab.2014.12.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/30/2014] [Indexed: 11/26/2022]
Abstract
We combined the TRIzol method of nucleic acid extraction with QIAamp columns to achieve coextraction of RNA and genomic DNA from peripheral blood mononuclear cells (PBMCs) and biopsied skeletal muscle, both stored at -80 °C for many months. Total RNA was recovered from the upper aqueous phase of TRIzol. The interphase and organic phases were precipitated with ethanol, digested with proteinase K, and filtered through QIAamp MinElute columns to recover DNA. The combined protocol yielded excellent quality and quantity of nucleic acids from archived human PBMCs and muscle and may be easily adapted for other tissues.
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Affiliation(s)
- Gipsy Majumdar
- Department of Veterans Affairs Medical Center, Memphis, TN 38104, USA; Department of Pharmacology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Santiago Vera
- Department of Veterans Affairs Medical Center, Memphis, TN 38104, USA
| | - Marshall B Elam
- Department of Veterans Affairs Medical Center, Memphis, TN 38104, USA; Department of Pharmacology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Rajendra Raghow
- Department of Veterans Affairs Medical Center, Memphis, TN 38104, USA; Department of Pharmacology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Lee JTY, Cheung KMC, Leung VYL. Correction for concentration overestimation of nucleic acids with phenol. Anal Biochem 2014; 465:179-86. [PMID: 25132565 DOI: 10.1016/j.ab.2014.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 07/31/2014] [Accepted: 08/05/2014] [Indexed: 12/13/2022]
Abstract
We report a computational method based on ultraviolet (UV) spectra for correcting the overestimated concentrations of nucleic acid samples contaminated with TRIzol/phenol. The derived correction formulas were validated using RNA solutions, double-stranded DNA solutions, and single-stranded oligonucleotide solutions. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with SYBR Green was performed to assess the level of TRIzol contamination that can be tolerated for gene expression quantification. After the correction, the accuracy of the RNA concentrations was greatly improved and there was no significant difference in the threshold cycle (Ct) values for GAPDH and ACAN genes in RT-qPCR obtained for RNA contaminated with up to 0.1% TRIzol (phenol level index [PLI]∼5.8-5.9). Similarly, accuracy improvements were also observed for DNA or oligonucleotides contaminated with phenol using different concentration correction formulas. In addition, the Ct values and amplification efficiency of DNA in qPCR were not affected by TRIzol contamination below 1%. This computational method is easy and convenient to use and reduces the concentration overestimations greatly.
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Affiliation(s)
- Juliana T Y Lee
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Hong Kong.
| | - Kenneth M C Cheung
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Hong Kong.
| | - Victor Y L Leung
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Hong Kong.
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Yamaguchi H, Hasegawa K, Esumi M. Protein from the fraction remaining after RNA extraction is useful for proteomics but care must be exercised in its application. Exp Mol Pathol 2013; 95:46-50. [PMID: 23707946 DOI: 10.1016/j.yexmp.2013.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/15/2013] [Indexed: 01/20/2023]
Abstract
Simultaneous isolation of mRNA and proteins from a single small biopsy specimen can be useful for integrated omics studies. Here, we have improved the method for extracting protein from the fraction remaining after RNA isolation by TRIzol reagent, for application in protein and proteome analyses. Protein yield was reduced by half, but the patterns developed on 2D gels were equivalent to conventional urea extractions. Thus, although quantitative profiles of individual proteins were different from conventionally-isolated samples, overall profiles were similar. Therefore, this particular protein source is useful for proteomics but care must be exercised in its application.
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