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Villanueva-Saz S, Aranda MDC, Jiménez MDLÁ, de Andrés PJ, Verde M, Climent M, Lebrero Berna ME, Marteles Aragüés D, Fernández A. Serum protein electrophoresis in European mink ( Mustela lutreola): reference intervals and comparison of agarose gel electrophoresis and capillary zone electrophoresis. Vet Q 2024; 44:1-11. [PMID: 38389258 PMCID: PMC10896155 DOI: 10.1080/01652176.2024.2318195] [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] [Received: 08/07/2023] [Accepted: 12/29/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Knowledge of reference intervals for blood analytes, including serum protein fractions, is of great importance for the identification of infectious and inflammatory diseases and is often lacking in wild animal species. MATERIAL AND METHODS Serum samples were obtained from European minks enrolled in the breeding program (n = 55). Agarose gel electrophoresis (AGE) and capillary zone electrophoresis (CZE) were used to separate and identify protein fractions. Albumin, α1, α2, β, and γ-globulins fractions were identified in all mink sera by both electrophoresis methods. Reference intervals (90% CI) were determined following the 2008 guidelines of the Clinical Laboratory Standard Institute. The methods were compared using Passing-Bablok regression, Bland-Altman analysis, and Lin's concordance correlation. RESULTS A significant bias was found between methods for α1, α2, and γ-globulin. Lin's concordance correlation was considered unacceptable for α1, α2, and β-globulins. Differences for gender between methods were found for albumin and α2-globuins, which were higher for males than females. γ-globulins were higher for adults than young minks using both methods; however, α1 and α2-globulins were lower. CONCLUSION Both methods are adequate for identifying serum protein disorders, but the AGE and CZE methods are not equivalent. Therefore, reference intervals for each technique are required.
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Affiliation(s)
- Sergio Villanueva-Saz
- Animal Pathology Department, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Clinical Immunology Laboratory, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Aragon Agroalimentary Institute-IA2, Zaragoza University-CITA, Zaragoza, Spain
| | - María del Carmen Aranda
- FIEB Foundation (Fundación para la Investigación en etología y biodiversidad), Toledo, Spain
| | | | - Paloma Jimena de Andrés
- Department of Animal Medicine and Surgery, Veterinary Faculty, Complutense University of Madrid, Madrid, Spain
| | - Maite Verde
- Animal Pathology Department, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Clinical Immunology Laboratory, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Aragon Agroalimentary Institute-IA2, Zaragoza University-CITA, Zaragoza, Spain
| | - María Climent
- Department of Anatomy, Embryology and Animal Genetic, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
| | | | | | - Antonio Fernández
- Animal Pathology Department, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Clinical Immunology Laboratory, Veterinary Faculty, Zaragoza University, Zaragoza, Spain
- Aragon Agroalimentary Institute-IA2, Zaragoza University-CITA, Zaragoza, Spain
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2
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Tomioka Y, Akuta T, Tokunaga M, Arakawa T. Different behavior of Ferguson plot between agarose and polyacrylamide gels. Biophys Chem 2024; 307:107200. [PMID: 38367540 DOI: 10.1016/j.bpc.2024.107200] [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] [Received: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, our investigation extended to model proteins with acidic isoelectric points and larger molecular weights, namely Ferritin and caseinolytic peptidase B (ClpB). Notably, these proteins displayed distinct Ferguson plot slopes when subjected to agarose gel electrophoresis. Intriguingly, when polyacrylamide gel was employed, ClpB exhibited multiple bands, each with its unique Ferguson plot slope, deviating from the expected behavior based on molecular size. This divergence in Ferguson plot characteristics between agarose and polyacrylamide gels points to an interesting and complex interplay between protein properties and gel electrophoresis conditions.
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Affiliation(s)
- Yui Tomioka
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Teruo Akuta
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima-shi 890-0065, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
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3
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Bawane H, Kadam K, Mahale V, Kulkarni R. Comprehensive assessment of 12 commercial DNA-binding dyes as alternatives to ethidium bromide for agarose gel electrophoresis. Electrophoresis 2024; 45:442-450. [PMID: 37933673 DOI: 10.1002/elps.202300154] [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] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Staining and visualization of the nucleic acid bands on agarose gels using ethidium bromide (EB) has been a widely used technique in molecular biology. Although it is an efficient dye for this purpose, EB is known to be mutagenic and genotoxic in humans. This led to the emergence of various alternative dyes, which were claimed to be safer and more efficient than EB. However, these dyes portray varied sensitivity and interference with the electrophoretic mobility of nucleic acids. This work aimed at assessing ten nucleic acid-binding dyes and two prestained dyes for these properties by three staining techniques, such as precasting, preloading, and poststaining. Of these, preloading was not suitable for any of the dye while poststaining worked optimal for most of them. Precasting was suitable for only four dyes viz. DNA Stain G, SYBR™ safe, EZ-Vision® in-gel, and LabSafe™. Poststaining was, in general, a costlier method than precasting. The work gives a comprehensive understanding of the performance of nucleic acid-binding dyes for routine molecular biology experiments.
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Affiliation(s)
- Hemangi Bawane
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Komal Kadam
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Vinit Mahale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
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4
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Sowersby DS, Lewis LK. SURE gel electrophoresis: A method for improved detection and purification of dilute nucleic acid samples. Anal Biochem 2024; 684:115373. [PMID: 37926185 DOI: 10.1016/j.ab.2023.115373] [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] [Received: 10/06/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Agarose gel electrophoresis is performed routinely by molecular biologists as both an analytical and a preparative method for characterization of nucleic acids. Gel analysis of highly dilute DNA solutions is challenging because of the limited sensitivity of detection available with conventional methods. In this study a new approach is described for concentrating samples directly within gels called SURE (successive reloading) electrophoresis. The approach involves loading of dilute samples multiple times into a single well, with each loading followed by a brief pulse of electrical current before the next sample is loaded. The procedure generates single bands created by molecular stacking that exhibit strongly enhanced signal intensities and minimal band broadening. Using optimized voltages and time intervals as many as 20 successive loadings could be performed and up to 800 μL could be loaded into a single well. Gel extraction and fluorescent quantitation demonstrated that approximately 97 % of the DNA from each loading was incorporated into the resultant band. Highly dilute DNA samples (<0.0007 ng per microliter) could be readily detected after six loadings. The method produced good results with either TAE or TBE as electrophoresis buffers, using loading dyes with or without SDS, and in both minigels and large gels.
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Affiliation(s)
- Drew S Sowersby
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA.
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5
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Kalendar R, Ivanov KI, Samuilova O, Kairov U, Zamyatnin AA. Isolation of High-Molecular-Weight DNA for Long-Read Sequencing Using a High-Salt Gel Electroelution Trap. Anal Chem 2023; 95:17818-17825. [PMID: 37993972 DOI: 10.1021/acs.analchem.3c03894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW DNA that takes advantage of the fact that DNA's electrophoretic mobility decreases in a high-ionic-strength environment. The method begins with the separation of HMW DNA from various impurities by electrophoresis in an agarose gel-filled channel. After sufficient separation, a high-salt gel block is placed ahead of the DNA band of interest, leaving a gap between the separating gel and the high-salt gel that serves as a reservoir for sample collection. The DNA is then electroeluted from the separating gel into the reservoir, where its migration slows due to electrostatic shielding of the DNA's negative charge by excess counterions from the high-salt gel. As a result, the reservoir accumulates HMW DNA of high purity and integrity, which can be easily collected and used for long-read sequencing and other demanding applications without additional desalting. The method is simple and inexpensive, yields sequencing-grade HMW DNA even from difficult plant and soil samples, and has the potential for automation and scalability.
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Affiliation(s)
- Ruslan Kalendar
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Konstantin I Ivanov
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
| | - Olga Samuilova
- Department of Biological Chemistry, Institute of Biodesign and Modeling of Complex Systems, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
- HSE University, Faculty of Biology and Biotechnology, Moscow 117418, Russian Federation
| | - Ulykbek Kairov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
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Nakagawa M, Tomioka Y, Sakuma C, Kurosawa Y, Shibata T, Arakawa T, Akuta T. Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis. Electrophoresis 2023; 44:1446-1460. [PMID: 37294166 DOI: 10.1002/elps.202200255] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023]
Abstract
A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native-PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS-PAGE gels or the edge of the flat SDS-MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen-antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5-6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.
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Affiliation(s)
- Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
- Abwiz Bio Inc., San Diego, California, USA
| | - Takashi Shibata
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
| | | | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., Takahagi-shi, Ibaraki, Japan
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7
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Raab J, Fink B, Bauer M. Appearance of ghost bands in gel electrophoresis depending on agarose concentration. Electrophoresis 2023; 44:1206-1209. [PMID: 37259607 DOI: 10.1002/elps.202300041] [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] [Received: 11/04/2022] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 06/02/2023]
Abstract
Standard agarose gel electrophoresis is a widely used method to analyse diversity of nucleic acids. Certain conditions, however, may give rise to artefactual bands. We report on artefactual bands frequently occurring, especially when partially homologous nucleic acids, such as splicing variants of DNA transcripts, are analysed simultaneously. Interestingly, to some extent agarose concentration may influence the occurrence of artefactual bands.
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Affiliation(s)
- Jana Raab
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Beate Fink
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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8
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Sato R, Tomioka Y, Sakuma C, Nakagawa M, Kurosawa Y, Shiba K, Arakawa T, Akuta T. Detection of concentration-dependent conformational changes in SARS-CoV-2 nucleoprotein by agarose native gel electrophoresis. Anal Biochem 2023; 662:114995. [PMID: 36427555 PMCID: PMC9681993 DOI: 10.1016/j.ab.2022.114995] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/02/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
The nucleoprotein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is abundantly expressed during infection, making it a diagnostic target protein. We analyzed the structure of the NP in solution using a recombinant protein produced in E. coli. A codon-optimized Profinity eXact™-tagged NP cDNA was cloned into pET-3d vector and transformed into E. coli T7 Express. The recombinant protein was first purified via chromatographic step using an affinity tag-based system that was followed by tag cleavage with sodium fluoride, resulting in proteolytic removal of the N-terminal tag sequence. The digested sample was then loaded directly onto a size exclusion chromatography run in the presence of L-Arg-HCl, resulting in removal of host nucleic acids and endotoxin. The molecular mass of the main NP fraction was determined by mass photometry as a dimeric form of NP, consistent with the blue native PAGE results. Interestingly, analysis of the purified NP by our newly developed agarose native gel electrophoresis revealed that it behaved like an acidic protein at low concentration despite its alkaline isoelectric point (theoretical pI = 10) and displayed a unique character of concentration-dependent charge and shape changes. This study should shed light into the behavior of NP in the viral life cycle.
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Affiliation(s)
- Ryo Sato
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
| | - Yasunori Kurosawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan; Abwiz Bio Inc., 9823 Pacific Heights Blvd., Suite J, San Diego, CA, 92121, USA.
| | - Kohei Shiba
- Refeyn Japan, K.K., 1-1-14, Sakuraguchi-cho, Nada-ku, Kobe, Hyogo, 6570036, Japan.
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA, 92130, USA.
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki, 318-0004, Japan.
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Parks VR, Torres DA. Yield Gel via Quantitative Gel Electrophoresis. Methods Mol Biol 2023; 2685:129-147. [PMID: 37439980 DOI: 10.1007/978-1-0716-3295-6_9] [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: 07/14/2023]
Abstract
Quantitative gel electrophoresis, also referred to as yield gel via gel electrophoresis, is an early quantification method that was developed to provide an estimate of the quality and the quantity of DNA extracted from evidence or reference samples. To conduct quantitative gel electrophoresis, an agarose gel that is combined with a nucleic acid gel stain is prepared. The gel stain intercalates between double-stranded DNA and can be visualized using UV light. DNA extract samples, along with DNA standards (ranging from 250 to 5 ng), and a 1 KB ladder are combined with a 6X loading dye and loaded on the agarose gel. Voltage is applied to facilitate DNA migration through the gel from the negative to the positive electrode, separating DNA fragments by size. After electrophoresis is complete, the results are visualized using UV light, and an image is captured for analysis. High-quality and -quantity DNA should contain a compact band comparable to that of the high molecular weight standards and ladder, with some smearing down the sample well. If a DNA extract sample does not produce a compact band and presents with only a smear, this is an indication that DNA degradation has occurred. This chapter provides instructions on how to successfully prepare an agarose gel, load DNA extract samples and corresponding controls, appropriately set up and run quantitative gel electrophoresis, interpret the results, and ensure comprehension of the method so troubleshooting can be performed if needed.
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Affiliation(s)
- Victoria R Parks
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Dayanara A Torres
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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Daves M, Piccin A, Vicidomini C, De Luisi A, Mega A. Utility of serum indices in a particular case of serum protein electrophoresis. Biochem Med (Zagreb) 2022; 32:030802. [PMID: 35966258 PMCID: PMC9344864 DOI: 10.11613/bm.2022.030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022] Open
Abstract
Screening and measurement of monoclonal (M) proteins are commonly performed using capillary zone electrophoresis (CZE). The identification of M-protein or monoclonal component (CM) is an essential requirement for diagnosis and monitoring of monoclonal gammopathies. The detection of CM has been largely improved by CZE. Capillary electrophoresis estimates CM more accurately, because absence of variation due to different dye binding affinities of proteins as instead seen with agarose gel electrophoresis. However, interferences can be present in CZE. This occurs because all substances absorbing at 200 nm can be identified. Recognition and handling of specimens exhibiting such interferences is essential to ensure accurate diagnostic and patient safety. We herein report on an unusual case of serum protein electrophoresis, to highlight that laboratory staff must be aware of and familiarise with the information provided by laboratory instruments. For example, in the case of serum indices, about specimen quality.
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Affiliation(s)
- Massimo Daves
- Clinical Biochemical Laboratory, Hospital of Bolzano, Bolzano, Italy
- Corresponding author:
| | - Andrea Piccin
- Northern Ireland Blood Transfusion Service, Belfast, UK
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | | | - Antonia De Luisi
- Clinical Biochemical Laboratory, Hospital of Bolzano, Bolzano, Italy
| | - Andrea Mega
- Division of Gastroenterology, Hospital of Bolzano, Bolzano, Italy
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Deb A, Gogoi P, Singh SK, Gooh Pattader PS. Noise-Activated Fast Locomotion of DNA through the Frictional Landscape of Nanoporous Gels. Langmuir 2022; 38:11764-11769. [PMID: 36037445 DOI: 10.1021/acs.langmuir.2c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
It is hypothesized that nonlinear solid friction between the gel matrix and DNA molecules inhibits the motion of DNA through the nanopores of the gel during electrophoresis. In this article, it is demonstrated that external noise can alleviate the effect of solid friction, thus enhancing the mobility of DNA in an electrophoretic setting. In the presence of noise, the mobility of DNA increases by more than ∼113% compared to conventional electrophoresis. Although at a high power of noise, DNA exhibits Arrhenius kinetics, at a low power of noise, super-Arrhenius kinetics suggests the collective behavior of the activated motion of DNA molecules. A stochastic simulation following modified Langevin dynamics with the asymmetric pore size distribution of the agarose gel successfully predicts the mobility of DNA molecules and reveals the salient features of the overall dynamics. This "noise lubricity" may have a broader applicability from molecular to macroscopic locomotion.
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Affiliation(s)
- Aniruddha Deb
- Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Prerona Gogoi
- Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Sunil K Singh
- Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Partho Sarathi Gooh Pattader
- Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
- Centre for Nanotechnology, Indian Institute of Technology, Guwahati 781039, Assam, India
- Jyoti and Bhupat Mehta School of Health Science & Technology, Indian Institute of Technology, Guwahati 781039, Assam, India
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12
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Tomioka Y, Nakagawa M, Sakuma C, Nagatoishi S, Tsumoto K, Arakawa T, Akuta T. Ladder observation of bovine serum albumin by high resolution agarose native gel electrophoresis. Int J Biol Macromol 2022; 215:512-520. [PMID: 35752339 DOI: 10.1016/j.ijbiomac.2022.06.118] [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] [Received: 03/29/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022]
Abstract
A commercially available bovine serum albumin (BSA) was examined by agarose native gel electrophoresis using two different agarose sources, UltraPure and MetaPhor agarose. While UltraPure agarose up to 5 % showed no clear separation of BSA oligomers, MetaPhor agarose clearly demonstrated oligomer bands above 4 %, indicating that the latter agarose has greater molecular sieving effects and is hence characterized to have high resolution for size differences, as probed by a greater slope of Ferguson plot. Physical properties are different between two agaroses. In general, UltraPure agarose has physical strength, while MetaPhor agarose is considerably fragile, but MetaPhor agarose solution is less viscous so that even 10 % gel can be made. Cause of oligomers was shown to be not associated with inter-chain disulfide bonds, but is due to association of native or native-like molecules.
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Affiliation(s)
- Yui Tomioka
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Masataka Nakagawa
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Chiaki Sakuma
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
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Green MR, Sambrook J. Transfer and Fixation of Denatured RNA in Agarose Gels to Membranes by Capillary Transfer. Cold Spring Harb Protoc 2022; 2022:2022/2/pdb.prot101774. [PMID: 35105784 DOI: 10.1101/pdb.prot101774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In most cases, fractionation of RNA by agarose gel electrophoresis is but a prelude to hybridization of the fractionated population to specific labeled probes that detect particular target mRNAs. RNA is first transferred from an agarose gel to a 2D support, usually a nylon membrane. This protocol presents the steps involved in the transfer of RNA from an agarose gel to a membranous support, facilitated by the upward flow of buffer, followed by various methods for fixation of the RNA to the membrane in preparation for hybridization. An alternative method for transfer by downward capillary flow is also given.
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14
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Green MR, Sambrook J. Separation of RNA according to Size: Electrophoresis of RNA through Agarose Gels Containing Formaldehyde. Cold Spring Harb Protoc 2022; 2022:2022/2/pdb.prot101758. [PMID: 35105783 DOI: 10.1101/pdb.prot101758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Samples of RNA may be denatured by treatment with formamide and separated by electrophoresis through agarose gels containing formaldehyde. In this method, RNA is fractionated by electrophoresis through an agarose gel containing 2.2 m formaldehyde.
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15
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Abid HA, Ong JW, Lin ES, Song Z, Liew OW, Ng TW. Low-cost Imaging of Fluorescent DNA in Agarose Gel Electrophoresis using Raspberry Pi cameras. J Fluoresc 2022; 32:443-448. [PMID: 35064858 PMCID: PMC8888377 DOI: 10.1007/s10895-021-02884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/27/2021] [Indexed: 01/13/2023]
Abstract
Low-cost analytical solutions built around microcomputers like the Raspberry Pi help to facilitate laboratory investigations in resource limited venues. Here, three camera modules (V1.3 with and without filter, as well as NoIR) that work with this microcomputer were assessed for their suitability in imaging fluorescent DNA following agarose gel electrophoresis. Evaluation of their utility was based on signal-to-noise (SNR) and noise variance metrics that were developed. Experiments conducted with samples were subjected to Polymerase Chain Reaction (PCR), and the amplified products were separated using gel electrophoresis and stained with Midori green. Image analysis revealed the NoIR camera performed the best with SNR and noise variance values of 21.7 and 0.222 respectively. In experiments conducted using UV LED lighting to simulate ethidium bromide (EtBr) excitation, the NoIR and V1.3 with filter removed cameras showed comparable SNR values.
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Affiliation(s)
- Hassan Ali Abid
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Jian Wern Ong
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Eric Shen Lin
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Zhixiong Song
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Oi Wah Liew
- Centre for Translational Medicine, Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, 117599, Singapore
| | - Tuck Wah Ng
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia.
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Salles TS, Cavalcanti AC, da Costa FB, Dias VZ, de Souza LM, de Meneses MDF, da Silva JAS, Amaral CD, Felix JR, Pereira DA, Boatto S, Guimarães MAAM, Ferreira DF, Azevedo RC. Genomic surveillance of SARS-CoV-2 Spike gene by sanger sequencing. PLoS One 2022; 17:e0262170. [PMID: 35051202 PMCID: PMC8775319 DOI: 10.1371/journal.pone.0262170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/25/2022] Open
Abstract
The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution.
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Affiliation(s)
- Tiago Souza Salles
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrea Cony Cavalcanti
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Central Laboratory of Public Health Noel Nutels - LACEN-RJ, Rio de Janeiro, Brazil
| | - Fábio Burack da Costa
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa Zaquieu Dias
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - José Antônio Suzano da Silva
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Applied Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cinthya Domingues Amaral
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jhonatan Ramos Felix
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Duleide Alves Pereira
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Stefanella Boatto
- Department of Applied Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Davis Fernandes Ferreira
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata Campos Azevedo
- Department of Virology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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17
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Figueroa S, Freire-Paspuel B, Vega-Mariño P, Velez A, Cruz M, Cardenas WB, Garcia-Bereguiain MA. High sensitivity-low cost detection of SARS-CoV-2 by two steps end point RT-PCR with agarose gel electrophoresis visualization. Sci Rep 2021; 11:21658. [PMID: 34737323 PMCID: PMC8568942 DOI: 10.1038/s41598-021-00900-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.
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Affiliation(s)
- Solange Figueroa
- One Health Research Group, Universidad de Las Americas, Quito, Ecuador
| | | | - Patricio Vega-Mariño
- Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos, Puerto Ayora, Ecuador
| | - Alberto Velez
- Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos, Puerto Ayora, Ecuador
| | - Marilyn Cruz
- Agencia de Regulación y Control de la Bioseguridad y Cuarentena para Galápagos, Puerto Ayora, Ecuador
| | - Washington B Cardenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
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18
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Holt CA, Cottyn B, Baumberger S, Kovacs-Schreiner K, Blacker AJ. High-Throughput Analysis of Lignin by Agarose Gel Electrophoresis. J Agric Food Chem 2020; 68:14297-14306. [PMID: 33200936 DOI: 10.1021/acs.jafc.0c06308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A high-throughput agarose gel electrophoresis (AGE) analytical method has been developed to separate lignin fractions according to their molecular weight (Mw), charge, and shape. Operating conditions to effect separation of species have been evaluated along with imaging parameters. Kraft, soda (Protobind), and Organosolv lignins showed distinct differences in migration. Bands were cut, extracted, and cross-analyzed by gel permeation chromatography (GPC), 1H NMR, and pyrolysis GC/MS to confirm their identity as lignin. The band intensity was correlated with lignin concentration by running serially diluted samples and imaging each lane to produce a precise calibration curve. The AGE technique was used to monitor and compare enzymatic, bacterial, chemical, and hydrothermal lignin digestions. Each method showed changes in lignin migration and band intensities over time. Low Mw species were seen in samples collected from the anode buffer tank. Though requiring further development, the AGE method can provide structural information about the lignin and is accessible to biological and chemistry laboratories.
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Affiliation(s)
- Christopher A Holt
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Stephanie Baumberger
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | | | - A John Blacker
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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19
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Nalbandian K, Piña-Aguilar RE, Morton CC. Resolving Breakpoints of Chromosomal Rearrangements at the Nucleotide Level Using Sanger Sequencing. Curr Protoc Hum Genet 2020; 108:e107. [PMID: 33369263 DOI: 10.1002/cphg.107] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Novel cytogenetic tools are increasingly based on genome sequencing for detecting chromosomal abnormalities. Different sequence-based techniques optimized for diagnosis of structural variants can be useful for narrowing down the localization of breakpoints of chromosomal abnormalities, but do not offer nucleotide resolution of breakpoints for proper interpretation of gene disruption. This protocol presents the characterization of structural variants at nucleotide resolution using Sanger sequencing after low-pass large-insert genome sequencing or other long-molecule methods. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Primer design for junction amplification at translocations and inversions Basic Protocol 2: Amplification of derivative chromosomes using a long-range polymerase Alternate Protocol: Amplification of derivative chromosomes using a hot-start polymerase Basic Protocol 3: Preparation of DNA for Sanger sequencing Basic Protocol 4: Interpretation and reporting of breakpoints based on Sanger sequencing.
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Affiliation(s)
- Katarena Nalbandian
- Massachusetts College of Pharmacy and Health Sciences University, Boston, Massachusetts
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- These authors contributed equally to this work
| | - Raul E Piña-Aguilar
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
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20
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Meena B, Anburajan L, Varma KS, Vinithkumar NV, Kirubagaran R, Dharani G. A multiplex PCR kit for the detection of three major virulent genes in Enterococcus faecalis. J Microbiol Methods 2020; 177:106061. [PMID: 32950564 DOI: 10.1016/j.mimet.2020.106061] [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] [Received: 07/02/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 11/18/2022]
Abstract
A multiplex PCR kit that detects three major virulence genes, gelE, hyl and asaI, in Enterococcus faecalis was developed. Analyses of the available sequences of three major virulence genes and designed primers allowed us to develop the three-gene, multiplex PCR protocol that maintained the specificity of each primer pair. The resulting three amplicon bands for gelE, hyl and asaI were even and distinct with product sizes of 213, 273 and 713 bp, respectively. The multiplex PCR procedure was validated with a total of 243 E. faecalis strains that included 02 ATCC strains, 109 isolates from marine samples (sediment, water and sea foods), 22 isolates from cattle fodder, 79 isolates fresh water samples and 31 isolates from nosocomial samples. Specificity of the kit was indicated by amplification of only three major virulent genes gelE, hyl and asaI without any nonspecific bands. Tests for the limit of detection revealed that amplified genes from the sample with a minimum of 104 CFU/g or CFU/mL (10 cells/reaction) of E. faecalis and lower cell load samples, after a 3 h enrichment in NIOT-E. faecalis enrichment medium at 37 °C, a sensitivity level of 10 CFU/g or CFU/mL was achieved.
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Affiliation(s)
- Balakrishnan Meena
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Port Blair 744103, Andaman and Nicobar Islands, India.
| | - Lawrance Anburajan
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Port Blair 744103, Andaman and Nicobar Islands, India.
| | | | - Nambali Valsalan Vinithkumar
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Ramalingam Kirubagaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences, Govt. of India, Chennai 600100, India
| | - Gopal Dharani
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences, Govt. of India, Chennai 600100, India
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21
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Zhou L, Chandrasekaran AR, Punnoose JA, Bonenfant G, Charles S, Levchenko O, Badu P, Cavaliere C, Pager CT, Halvorsen K. Programmable low-cost DNA-based platform for viral RNA detection. Sci Adv 2020; 6:sciadv.abc6246. [PMID: 32978154 PMCID: PMC7518872 DOI: 10.1126/sciadv.abc6246] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/11/2020] [Indexed: 05/03/2023]
Abstract
Detection of viruses is critical for controlling disease spread. Recent emerging viral threats, including Zika virus, Ebola virus, and SARS-CoV-2 responsible for coronavirus disease 2019 (COVID-19) highlight the cost and difficulty in responding rapidly. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches that mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show nonenzymatic detection of viral RNA with selective and multiplexed detection between related viruses and viral strains. For clinical-level sensitivity in biological fluids, we paired the assay with sample preparation using either RNA extraction or isothermal preamplification. Our assay requires minimal laboratory infrastructure and is adaptable to other viruses, as demonstrated by quickly developing DNA nanoswitches to detect SARS-CoV-2 RNA in saliva. Further development and field implementation will improve our ability to detect emergent viral threats and ultimately limit their impact.
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Affiliation(s)
- Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Gaston Bonenfant
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Stephon Charles
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Oksana Levchenko
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Pheonah Badu
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Cassandra Cavaliere
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Cara T Pager
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
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Abstract
We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.
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23
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Heintz N, Gong S. Two-Step Bacterial Artificial Chromosome (BAC) Engineering: Verification of Co-Integrates and Selection of Resolved BAC Clones. Cold Spring Harb Protoc 2020; 2020:098087. [PMID: 32238594 DOI: 10.1101/pdb.prot098087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Successful modification of the bacterial artificial chromosome (BAC) after two-step BAC engineering is confirmed in two separate polymerase chain reactions (PCRs). The first reaction (5' co-integrate PCR) uses a forward 5' co-integrate primer (a sequence located upstream of the 5' end of the A-box) and a reverse 3' primer on the vector (175PA+50AT) or within the reporter sequence or mutated region as appropriate. The second reaction (3' co-integrate PCR) uses a forward 5' primer on the recA gene (RecA1300S) and a reverse 3' co-integrate primer (a sequence located downstream from the 3' end of the B-box). Those colonies shown to be positive in PCR analysis are further tested for sensitivity to UV light. After the resolution, colonies that have lost the excised recombination vector including sacB and recA genes become UV light sensitive.
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Volpe Chaves CE, do Valle Leone de Oliveira SM, Venturini J, Grande AJ, Sylvestre TF, Poncio Mendes R, Mello Miranda Paniago A. Accuracy of serological tests for diagnosis of chronic pulmonary aspergillosis: A systematic review and meta-analysis. PLoS One 2020; 15:e0222738. [PMID: 32182249 PMCID: PMC7077827 DOI: 10.1371/journal.pone.0222738] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic pulmonary aspergillosis (CPA) is a slow and progressive disease that develops in preexisting lung cavities of patients with tuberculosis sequelae, and it is associated with a high mortality rate. Serological tests such as double agar gel immunodiffusion test (DID) or counterimmunoelectrophoresis (CIE) test have been routinely used for CPA diagnosis in the absence of positive cultures. However, these tests have been replaced with enzyme-linked immunoassay (ELISA) and, a variety of methods. This systematic review compares ELISA accuracy to reference test (DID and/or CIE) accuracy in CPA diagnosis. It was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The study was registered in PROSPERO under the registration number CRD42016046057. We searched the electronic databases MEDLINE (PubMed), EMBASE (Elsevier), LILACS (VHL), Cochrane library, and ISI Web of Science. Gray literature was researched using Google Scholar and conference abstracts. We included articles with patients or serum samples from patients with CPA who underwent two serological tests: ELISA (index test) and IDD and/or CIE (reference test). We used the test accuracy as a result. Original articles were considered without a restriction of date or language. The pooled sensitivity, specificity, and summary receiver operating characteristic curves were estimated. We included 14 studies in the review, but only four were included in the meta-analysis. The pooled sensitivities and specificities were 0.93 and 0.97 for the ELISA test. These values were 0.64 and 0.99 for the reference test (DID and/or CIE). Analyses of summary receiver operating characteristic curves yielded 0.99 for ELISA and 0.99 for the reference test (DID and/or CIE). Our meta-analysis suggests that the diagnostic accuracy of ELISA is greater than the reference tests (DID and/or CIE) for early CPA detection.
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Affiliation(s)
- Cláudia Elizabeth Volpe Chaves
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Regional Hospital of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - James Venturini
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Antonio Jose Grande
- State University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Tatiane Fernanda Sylvestre
- Tropical Diseases Department, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo State, Brazil
| | - Rinaldo Poncio Mendes
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Tropical Diseases Department, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo State, Brazil
| | - Anamaria Mello Miranda Paniago
- Graduate Program in Infectious and Parasitic Diseases of Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
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25
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Abstract
In this protocol, DNA fragments are separated according to size by electrophoresis through low-melting-temperature agarose, and then recovered by melting the agarose and extracting with phenol:chloroform. The protocol works best for DNA fragments ranging in size from 0.5 to 5.0 kb. Yields of DNA fragments outside this range are usually lower, but often are sufficient for many purposes.
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26
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Cruz C, Houseley J. Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs. Methods Mol Biol 2020; 2062:83-103. [PMID: 31768973 DOI: 10.1007/978-1-4939-9822-7_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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Over the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide-urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.
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Affiliation(s)
- Cristina Cruz
- Epigenetics Programme, Babraham Institute, Cambridge, UK
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27
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Kim JH, Park Y, Kim WJ, Kim AY, Nguyen P, Lyu DP, Lee HS, Koh YH. Developing molecular diagnostics for detection of red imported fire ants using two genes, Sinv11108 and Sinv11977. Arch Insect Biochem Physiol 2019; 102:e21610. [PMID: 31452246 DOI: 10.1002/arch.21610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Aggressive red imported fire ants (RIFAs) are expanding their habitat due to active international trade and global warming. To prevent infestation and settlement, RIFAs must be removed during the quarantine process. Because RIFAs are social insects and have different morphological characteristics depending on their castes, non-ant taxonomists have difficulty confirming RIFAs based on their morphological characteristics alone. The disadvantages of previously reported RIFA molecular diagnostics are that they require additional steps, such as restriction enzyme digestion followed by agarose gel electrophoresis separation or DNA sequence verification for polymerase chain reaction (PCR)-amplified products. To overcome these drawbacks, two RIFA-specific genes were selected and used to develop diverse PCR-based RIFA molecular diagnostic techniques. We found that RIFAs could be confirmed by conventional PCR targeting of two RIFA-specific genes followed by agarose electrophoresis separation. In addition, TaqMan probe real-time PCR methods had the advantage of confirming RIFAs immediately after the reactions were completed by observing fluorescence indexes. Finally, multiplex PCRs enhanced RIFA specificity and sensitivity. The new molecular diagnostic methods developed in this study had the advantages of reducing false positive and negative results together with high specificity and sensitivity for RIFAs.
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Affiliation(s)
- Ji-Hye Kim
- Department of Biomedical Gerontology, Hallym University, Chuncheon, Gangwon-do, Korea
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do, Korea
| | - Youngjin Park
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do, Korea
| | | | - A-Young Kim
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do, Korea
| | - Phuong Nguyen
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do, Korea
| | - Dong Pyo Lyu
- Department of Forest Science, SangJi University, Wonju, Gangwon-do, Korea
| | - Heung Sik Lee
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do, Korea
| | - Young Ho Koh
- Department of Biomedical Gerontology, Hallym University, Chuncheon, Gangwon-do, Korea
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do, Korea
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Biaz A, Raiss C, El-Amin G, Uwingabiye J, El-Machtani-Idrissi S, Dami A, Ouzzif Z, Bouhsain S. Better Resolution of Gel Electrophoresis than that of Capillary Electrophoresis: About a Case Report. Clin Lab 2019; 65. [PMID: 31710450 DOI: 10.7754/clin.lab.2019.190424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Motohashi K. Development of highly sensitive and low-cost DNA agarose gel electrophoresis detection systems, and evaluation of non-mutagenic and loading dye-type DNA-staining reagents. PLoS One 2019; 14:e0222209. [PMID: 31498824 PMCID: PMC6733488 DOI: 10.1371/journal.pone.0222209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/23/2019] [Indexed: 11/18/2022] Open
Abstract
Highly sensitive and low-cost DNA agarose gel detection systems were developed using non-mutagenic and loading dye-type DNA-staining reagents. The DNA detection system that used Midori Green Direct and Safelook Load-Green, both with an optimum excitation wavelength at ~490 nm, could detect DNA-fragments at the same sensitivity to that of the UV (312 nm)-transilluminator system combined with ethidium bromide, after it was excited by a combination of cyan LED light and a shortpass filter (510 nm). The cyan LED system can be also applied to SYBR Safe that is widely used as a non-toxic dye for post-DNA-staining. Another DNA-detection system excited by black light was also developed. Black light used in this system had a peak emission at 360 nm and caused less damage to DNA due to lower energy of UV rays with longer wavelength when compared to those of short UV rays. Moreover, hardware costs of the black light system were ~$100, less than 1/10 of the commercially available UV (365 nm) transilluminator (>$1,000). EZ-Vision and Safelook Load-White can be used as non-mutagenic and loading dye-type DNA-staining reagents in this system. The black light system had a greater detection sensitivity for DNA fragments stained by EZ-Vision and Safelook Load-White compared with the commercially available imaging system using UV (365 nm) transilluminator.
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Affiliation(s)
- Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo Motoyama, Kita-Ku, Kyoto, Japan
- * E-mail:
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Green MR, Sambrook J. Recovery of DNA from Agarose Gels Using Glass Beads. Cold Spring Harb Protoc 2019; 2019:2019/9/pdb.prot100453. [PMID: 31481493 DOI: 10.1101/pdb.prot100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This DNA recovery protocol uses glass beads and a solution of sodium iodide/sodium sulfite as a chaotropic agent to disrupt the agarose gel.
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Abstract
Background: The forkhead box O3 (FOXO3) and p27Kip1 are two important genes in breast cancer progression. In the present study we analyzed the effect of simultaneous FOXO3 silencing and p27Kip1 activation on breast cancer cell survival and the potential targets of these changes in cancer molecular pathways. Materials and methods: The present study involved the cloning of FOXO3a shRNA and p27Kip1 genes under the control of the bidirectional survivin promoter to down- and up-regulate FOXO3 and p27Kip1 genes, respectively. After transfection of the recombinant expression vector into the breast cancer cell line, the inhibition of cell growth was assessed by MTS and flow cytometry assays. Following the extraction of total mRNA and protein, the expression of target genes was evaluated by qPCR and Western blotting in both treated and untreated cell lines. Then, the downstream protein responses were examined by 2 D electrophoresis. The differentially expressed proteins were also identified by mass spectrometry. Results: Rates of cell proliferation were significantly inhibited in the transfected cell line 72 h post-transfection. Proteomic profiling of the cell line resulted in the identification of seven novel protein markers in breast cancer responsive to these changes in expression of FOXO3 and p27Kip1. The changes in expression of these markers suggested that certain signaling pathways contribute to the development of breast cancer. Conclusion: Simultaneous silencing of FOXO3 and activation of p27Kip1 in MDA-MB-231 cells caused alterations in the expression level of several genes involved in apoptosis, cell proliferation, cell cycle control, tissue invasion, drug resistance, and metastasis. It seems that the identified genes might serve as useful biomarkers for breast cancer.
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Affiliation(s)
- Sabah Mayahi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Masood Golalipour
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ahad Yamchi
- Department of Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | | | - Majid Shahbazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- AryaTinaGene Biopharmaceutical Company, Gorgan, Iran
- CONTACT Majid Shahbazi Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, 4916668197, Iran
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Chandrasekaran AR, MacIsaac M, Dey P, Levchenko O, Zhou L, Andres M, Dey BK, Halvorsen K. Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches. Sci Adv 2019; 5:eaau9443. [PMID: 30891499 PMCID: PMC6415953 DOI: 10.1126/sciadv.aau9443] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/29/2019] [Indexed: 05/03/2023]
Abstract
MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive and often requires amplification, labeling, or radioactive probes. Here, we report a single-step, nonenzymatic microRNA detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNA-activated conditional looping of engineered switches), our assay has subattomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells and multiplex our detection for several microRNAs from one biological sample. We demonstrate 1-hour detection without expensive equipment or reagents, making this assay a compelling alternative to quantitative polymerase chain reaction and Northern blotting.
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Affiliation(s)
| | - Molly MacIsaac
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Oksana Levchenko
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Madeline Andres
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Bijan K. Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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Woith E, Melzig MF. Extracellular Vesicles from Fresh and Dried Plants-Simultaneous Purification and Visualization Using Gel Electrophoresis. Int J Mol Sci 2019; 20:ijms20020357. [PMID: 30654488 PMCID: PMC6359398 DOI: 10.3390/ijms20020357] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 12/12/2022] Open
Abstract
Although animal-derived extracellular vesicles (EVs) are moving increasingly into scientific focus, EVs from other kingdoms remain underestimated and our knowledge of them is still expandable, probably due to the lack of an easy and broadly executable isolation, purification and visualization method. Using differential centrifugation with subsequent agarose gel electrophoresis, we were able to simplify the terms of EV isolation. EVs from Nicotiana tabacum L., Vinca minor L., and Viscum album L. were purified, even though they did not migrate into the gel matrix. If 3,3- Dihexyloxacarbocyanine iodide (DiOC 6 ) is added to the specimen in excess, membranous components can already be detected by eye, or with higher sensitivity, using a UV transilluminator. The sample preparation can be adjusted to the EV species of interest. Moreover, EVs are separated from small charged contaminants and dye excess, because these impurities can pass the gel matrix, while EVs themselves are retained in the pocket. Significantly, we isolated EVs from dried plant material, which is-to our knowledge-the first proof that EVs are stable enough to overcome the drying process of plant material.
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Affiliation(s)
- Eric Woith
- Institute of Pharmacy-Pharmaceutical Biology, Dahlem Center of Plant Sciences, Freie Universitaet Berlin, Koenigin-Luise-Str. 2+4, D-14195 Berlin, Germany.
| | - Matthias F Melzig
- Institute of Pharmacy-Pharmaceutical Biology, Dahlem Center of Plant Sciences, Freie Universitaet Berlin, Koenigin-Luise-Str. 2+4, D-14195 Berlin, Germany.
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Abstract
Electrophoresis through agarose or polyacrylamide gels is used to separate, analyze, identify, and purify DNA fragments. The technique is simple, rapid to perform, and capable of resolving fragments of DNA that cannot be separated adequately by other procedures, such as density gradient centrifugation. The location of bands of DNA within the gel can be determined directly by staining with low concentrations of fluorescent intercalating dyes, such as ethidium bromide or SYBR Gold; bands containing as little as 20 pg of double-stranded DNA can then be detected by direct examination of the gel in ultraviolet (UV) light. If necessary, these bands of DNA can be recovered from the gel.
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Abstract
This protocol describes steps for the preparation and running of agarose gels and for staining and visualization of DNA in gels using three dyes: ethidium bromide, SYBR Gold, and SYBR Green 1.
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Pott C, Brüggemann M, Ritgen M, van der Velden VHJ, van Dongen JJM, Kneba M. MRD Detection in B-Cell Non-Hodgkin Lymphomas Using Ig Gene Rearrangements and Chromosomal Translocations as Targets for Real-Time Quantitative PCR. Methods Mol Biol 2019; 1956:199-228. [PMID: 30779036 DOI: 10.1007/978-1-4939-9151-8_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 06/09/2023]
Abstract
Minimal residual disease (MRD) diagnostics is of high clinical relevance in patients with indolent B-cell non-Hodgkin lymphomas (B-NHL) and serves as a surrogate parameter to evaluate treatment effectiveness and long-term prognosis. MRD diagnostics performed by real-time quantitative PCR (RQ-PCR) is still the gold standard and currently the most sensitive and the most broadly applied method in follicular lymphoma (FL) and mantle cell lymphoma (MCL). Alternatively, droplet digital PCR (ddPCR) can be used for MRD monitoring in multiple myeloma, mantle cell lymphoma, and follicular lymphoma with comparable sensitivity, accuracy, and reproducibility.The most broadly applicable MRD target in B-NHL is the junctional regions of the rearranged immunoglobulin heavy chain gene (IGHV). Chromosomal translocations like the t(14;18) translocation in FL and t(11;14) translocation in MCL can be used as MRD target in selected lymphoma subtypes. In patients with B-cell chronic lymphocytic leukemia, both flow-cytometry and RQ-PCR are equally suited for MRD assessment as long as a sensitivity of 10-4 shall be achieved.MRD diagnostics targeting the IGHV gene is complex and requires extensive knowledge and experience because the junctional regions of each lymphoma have to be identified before the patient-specific RQ-PCR assays can be designed for MRD monitoring. In addition, the presence and load of somatic hypermutation (SHM) within the rearranged IG heavy variable (IGHV) gene occurring as during B-cell development of germinal center and post-germinal center lymphomas may hamper appropriate primer binding leading to false-negative results. The translocations mentioned above have the advantage that consensus forward primers and probes, both placed in the breakpoint regions of chromosome 18 in FL and chromosome 11 in MCL, can be used in combination with a reverse primer placed in the IGH joining region of chromosome 14. RQ-PCR-based methods can reach a good sensitivity (≤10-4). This chapter provides all relevant background information and technical aspects for the complete laboratory process from detection of the clonal IGHV gene rearrangement and the chromosomal translocations at diagnosis to the actual MRD measurements in clinical follow-up samples of B-NHL. However, it should be noted that MRD diagnostics for clinical treatment protocols has to be accompanied by regular international quality control rounds to ensure the reproducibility and reliability of the MRD results.
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Affiliation(s)
- Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany.
| | - Monika Brüggemann
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Ritgen
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Michael Kneba
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
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Csako G. Isoelectric Focusing in Agarose Gel for Detection of Oligoclonal Bands in Cerebrospinal and Other Biological Fluids. Methods Mol Biol 2019; 1855:387-401. [PMID: 30426434 DOI: 10.1007/978-1-4939-8793-1_33] [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: 06/09/2023]
Abstract
Isoelectric focusing (IEF) coupled with immunodetection (immunofixation or immunoblotting) has become the leading technique for the detection and study of oligoclonal bands (OCBs) in cerebrospinal fluid (CSF) and also is increasingly used in other body fluids such as the tear and serum. Limited commercial availability of precast agarose IEF gels for research and a need for customization prompted reporting a detailed general protocol for the preparation and casting of agarose IEF gel along with sample, control, and isoelectric point marker preparation and carrying out the focusing itself for CSF OCBs. However, the method is readily adaptable to the use of other body fluid specimens and, possibly, research specimens such as culture fluids as well.
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Affiliation(s)
- Gyorgy Csako
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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38
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Cunningham NR, Kokona B, Quinn JM, Fairman R. Size Analysis of C9orf72 Dipeptide Repeat Proteins Expressed in Drosophila melanogaster Using Semidenaturing Detergent Agarose Gel Electrophoresis. Methods Mol Biol 2019; 2039:91-101. [PMID: 31342421 DOI: 10.1007/978-1-4939-9678-0_7] [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: 06/10/2023]
Abstract
This chapter supplements Chapter 6 on sample preparation and analysis using an analytical ultracentrifuge with fluorescence detection. In this related chapter, we describe how semidenaturing detergent agarose gel electrophoresis can be used to complement the analytical ultracentrifugation work, often as a prelude to careful biophysical analysis to help screen conditions to improve the success of sedimentation velocity experiments. We describe preparation of crude lysates made using Drosophila melanogaster and provide a protocol giving detailed instructions for successful fractionation of protein aggregates using SDD-AGE. While limited in resolving power, this method can identify fractionation in three pools based on sample migration in the gel: that of a monomer or limiting small oligomer species; intermediate aggregation pools, which are typically heterogeneous, represented as high retention smears; and large-scale aggregation, found caught up in the wells.
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Affiliation(s)
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Jeanne M Quinn
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, PA, USA.
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Stelling MP, de Bento AA, Caloba P, Vilanova E, Pavão MSG. Methods for Isolation and Characterization of Sulfated Glycosaminoglycans from Marine Invertebrates. Methods Mol Biol 2019; 1952:55-70. [PMID: 30825165 DOI: 10.1007/978-1-4939-9133-4_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 06/09/2023]
Abstract
Marine invertebrates produce different kinds of sulfated polysaccharides. These glycans play essential roles in several biological processes and the study of these molecules is promising in a variety of fields. In the following sections, we describe the materials and methods used for the extraction, purification, and characterization of marine invertebrate-derived glycosaminoglycans.
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Affiliation(s)
- Mariana P Stelling
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ananda A de Bento
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philippe Caloba
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo Vilanova
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauro S G Pavão
- Laboratório de Bioquímica e Biologia Celular de Glicoconjugados, Programa de Glicobiologia, Instituto de Bioquímica Médica Leopoldo de Meis and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Ream JA, Lewis LK, Lewis KA. Horizontal Agarose Gel Mobility Shift Assay for Protein-RNA Complexes. Methods Mol Biol 2019; 1855:363-370. [PMID: 30426432 PMCID: PMC10636705 DOI: 10.1007/978-1-4939-8793-1_31] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recent advances in agarose gel electrophoresis protocols established conditions for the high-resolution separation of DNA and RNA using higher voltages combined with short run times. We subsequently developed a protocol for using these conditions to measure the binding affinity of a protein for an RNA ligand on an agarose gel. This native gel mobility shift assay is highly accessible, using common molecular biology reagents found in most laboratories. Here, we describe the protocol for carrying out native agarose gel electrophoresis to characterize the binding affinity of a protein for an RNA ligand. The electrophoresis time is less than 10 min, which minimizes the dissociation of protein and ligand. We have used the p19 siRNA binding protein and its cognate dsRNA ligand to demonstrate strategies for identifying optimal conditions to measure apparent binding constants using this agarose gel shift system.
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Affiliation(s)
- Jennifer A Ream
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - L Kevin Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Karen A Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA.
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Montague TG, Almansoori A, Gleason EJ, Copeland DS, Foley K, Kraves S, Alvarez Saavedra E. Gene expression studies using a miniaturized thermal cycler system on board the International Space Station. PLoS One 2018; 13:e0205852. [PMID: 30379894 PMCID: PMC6209215 DOI: 10.1371/journal.pone.0205852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/02/2018] [Indexed: 02/02/2023] Open
Abstract
The distance and duration of human spaceflight missions is set to markedly increase over the coming decade as we prepare to send astronauts to Mars. However, the health impact of long-term exposure to cosmic radiation and microgravity is not fully understood. In order to identify the molecular mechanisms underpinning the effects of space travel on human health, we must develop the capacity to monitor changes in gene expression and DNA integrity in space. Here, we report successful implementation of three molecular biology procedures on board the International Space Station (ISS) using a miniaturized thermal cycler system and C. elegans as a model organism: first, DNA extraction–the initial step for any type of DNA analysis; second, reverse transcription of RNA to generate complementary DNA (cDNA); and third, the subsequent semi-quantitative PCR amplification of cDNA to analyze gene expression changes in space. These molecular procedures represent a significant expansion of the budding molecular biology capabilities of the ISS and will permit more complex analyses of space-induced genetic changes during spaceflight missions aboard the ISS and beyond.
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Affiliation(s)
- Tessa G. Montague
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | | | | | - Kevin Foley
- Boeing, Houston, TX, United States of America
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Silva NNT, Reis LES, Lima AA. Comparison of Capillary Electrophoresis, AGE, and PAGE for MTHFR Polymorphism Analysis in FFPE Cervical Samples. Ann Clin Lab Sci 2018; 48:587-593. [PMID: 30373862] [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] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
BACKGROUND Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism analysis could help in diagnosis, treatment, and prognosis of some pathologies, since it has been associated with the development of cardiovascular diseases, defects in neural tube formation, psychiatric disorders, and cancer. Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) is the most commonly used technique to analyze this polymorphism. Usually, RFLP products are evaluated by agarose gel electrophoresis (AGE) or polyacrylamide gel electrophoresis (PAGE). However, capillary electrophoresis (CE) may represent an alternative for MTHFR C677T polymorphism analysis by PCR-RFLP. Thus, the aim of this study was to compare CE, AGE, and PAGE to MTHFR C677T polymorphism analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) cervical samples. METHODS 150 biopsy blocks of cervical samples were analyzed. MTHFR polymorphism was evaluated by PCR-RFLP, and the products generated were analyzed by CE, AGE, and PAGE. Concordance between the methods was evaluated by rate agreement, Kappa coefficient, and McNemars's Test. RESULTS Eight samples (5.4%) showed discordant results according to CE and PAGE or AGE. Differences of CC and CT frequencies were observed between CE and AGE (p=0.016): CC genotype varied from 68.0% to 72.7%, and CT varied from 23.3% to 27.3%. Besides, Kappa coefficient between CE and AGE, or PAGE was very high (κ>0.81). CONCLUSION Capillary electrophoresis presented high agreement with PAGE and AGE, and may be an accurate, safe, and quick alternative method for MTHFR polymorphism analysis.
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Affiliation(s)
- Nayara Nascimento Toledo Silva
- Departamento de Análises Clínicas, Universidade Federal de Ouro Preto, Campus Universitário Morro do Cruzeiro s/n, Ouro Preto, Minas Gerais, Brasil
| | - Levi Eduardo Soares Reis
- Departamento de Análises Clínicas, Universidade Federal de Ouro Preto, Campus Universitário Morro do Cruzeiro s/n, Ouro Preto, Minas Gerais, Brasil
| | - Angélica Alves Lima
- Departamento de Análises Clínicas, Universidade Federal de Ouro Preto, Campus Universitário Morro do Cruzeiro s/n, Ouro Preto, Minas Gerais, Brasil
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Dai W, Zhang J, Meng X, He J, Zhang K, Cao Y, Wang D, Dong H, Zhang X. Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection. Theranostics 2018; 8:2646-2656. [PMID: 29774065 PMCID: PMC5956999 DOI: 10.7150/thno.24480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 01/28/2023] Open
Abstract
As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification. Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process. In the present of target miRNA, the stem of the corresponding hairpin detection probe (HDP) will be unfolded and expose the concealed domain. The corresponding hairpin assistant probe (HAP) then replaces the hybridized target miRNA to form specific HDP/HAP complexes and releases miRNA based on thermodynamically driven entropy gain process, and the released miRNA triggers the next recycle to produce tremendous corresponding HDP/HAP complexes. Results: The results showed that the CHA gel assay can detect miRNA at fM levels and shows good capability of discriminating miRNA family members and base-mismatched miRNAs. It is able to analyze miRNAs extracted from cell lysates, which are consistent with the results of conventional polymerase chain reaction (PCR) method. Depending on the length of the designed hairpin probes, the CHA gel assay consisting of different hairpin probes effectively discriminated and simultaneously detected multiple miRNAs in homogenous solution and miRNAs extracted from cell lysates. Conclusion: The work highlights the practical use of a conventional gel electrophoresis for sensitive interesting nucleic acid sequences detection.
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Affiliation(s)
- Wenhao Dai
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Jing Zhang
- School of Petrochemical Engineering, School of Food Science and Technology, Changzhou University, Changzhou 213164, P.R. China
| | - Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Jie He
- School of Computer and Communication Engineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Kai Zhang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Yu Cao
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Dongdong Wang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, Beijing Key Lab for Bioengineering and Sensing Technology, School of Chemistry and bioengineering, University of Science & Technology Beijing, Beijing 100083, P.R. China
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Zamorano Cuervo N, Osseman Q, Grandvaux N. Virus Infection Triggers MAVS Polymers of Distinct Molecular Weight. Viruses 2018; 10:E56. [PMID: 29385716 PMCID: PMC5850363 DOI: 10.3390/v10020056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
The mitochondrial antiviral signaling (MAVS) adaptor protein is a central signaling hub required for cells to mount an antiviral response following virus sensing by retinoic acid-inducible gene I (RIG-I)-like receptors. MAVS localizes in the membrane of mitochondria and peroxisomes and in mitochondrial-associated endoplasmic reticulum membranes. Structural and functional studies have revealed that MAVS activity relies on the formation of functional high molecular weight prion-like aggregates. The formation of protein aggregates typically relies on a dynamic transition between oligomerization and aggregation states. The existence of intermediate state(s) of MAVS polymers, other than aggregates, has not yet been documented. Here, we used a combination of non-reducing SDS-PAGE and semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) to resolve whole cell extract preparations to distinguish MAVS polymerization states. While SDD-AGE analysis of whole cell extracts revealed the formation of previously described high molecular weight prion-like aggregates upon constitutively active RIG-I ectopic expression and virus infection, non-reducing SDS-PAGE allowed us to demonstrate the induction of lower molecular weight oligomers. Cleavage of MAVS using the NS3/4A protease revealed that anchoring to intracellular membranes is required for the appropriate polymerization into active high molecular weight aggregates. Altogether, our data suggest that RIG-I-dependent MAVS activation involves the coexistence of MAVS polymers with distinct molecular weights.
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Affiliation(s)
- Natalia Zamorano Cuervo
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
| | - Quentin Osseman
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| | - Nathalie Grandvaux
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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Abstract
OBJECTIVE Agarose gel electrophoresis has been the mainstay technique for the analysis of DNA samples of moderate size. In addition to separating linear DNA molecules, it can also resolve different topological forms of plasmid DNAs, an application useful for the analysis of the reactions of DNA topoisomerases. However, gel electrophoresis is an intrinsically low-throughput technique and suffers from other potential disadvantages. We describe the application of the QIAxcel Advanced System, a high-throughput capillary electrophoresis system, to separate DNA topoisomers, and compare this technique with gel electrophoresis. RESULTS We prepared a range of topoisomers of plasmids pBR322 and pUC19, and a 339 bp DNA minicircle, and compared their separation by gel electrophoresis and the QIAxcel System. We found superior resolution with the QIAxcel System, and that quantitative analysis of topoisomer distributions was straightforward. We show that the QIAxcel system has advantages in terms of speed, resolution and cost, and can be applied to DNA circles of various sizes. It can readily be adapted for use in compound screening against topoisomerase targets.
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Affiliation(s)
- Lesley A. Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Rachel E. Hipkin
- Qiagen Ltd., Skelton House, Lloyd St. North, Manchester, M15 6SH UK
- Present Address: Fluidigm Ltd, 12 New Fetter Lane, London, EC4A 1JP UK
| | - Michael M. Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: University Centre, Blackburn College, University Close, Blackburn, Lancashire BB2 1LH UK
| | - Nicolas P. Burton
- Inspiralis Ltd, Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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46
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Jensen MBF, Schjørring S, Björkman JT, Torpdahl M, Litrup E, Nielsen EM, Niskanen T. External quality assessment for molecular typing of Salmonella 2013-2015: performance of the European national public health reference laboratories. Eur J Clin Microbiol Infect Dis 2017; 36:1923-1932. [PMID: 28573470 PMCID: PMC5602099 DOI: 10.1007/s10096-017-3015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
We report the results of three consecutive External Quality Assessments (EQAs) for molecular subtyping of Salmonella to assess the performance of the European national public health reference laboratories (NPHRLs). The EQA included the molecular typing methods used for European enhanced surveillance of human Salmonella infections: pulsed field gel electrophoresis (PFGE), including gel analysis by the use of the software BioNumerics, and 5-locus multiple locus variable number of tandem repeat analysis (MLVA) for serovar Typhimurium. The participation in the PFGE laboratory part was higher (27/35) than in the gel analysis (19/35) and MLVA (15/35), suggestive of the need for capacity building in methods requiring specialized equipment (MLVA) or software (gel analysis). The majority (25/27) of the participating NPHRLs produced inter-laboratory comparable PFGE gel(s). Two laboratories continued to produce low-quality gels and should have additional technical assistance in the future. In particular, two gel quality evaluation parameters, measuring "image acquisition and running conditions" and "bands", were identified to cause gel quality problems throughout the EQAs. Despite the high number of laboratories participating in the PFGE laboratory part, the participation in gel analysis was low, although increasing. In the MLVA part, the NPHRLs correctly assigned 96% (405/420) allelic profiles according to the nomenclature. In conclusion, the EQAs identified critical parameters for unsuccessful performance and helped to offer assistance to those laboratories that needed it most. The assessments supported the development of quality in molecular typing and promoted the harmonization of subtyping methods used for EU/EEA-wide surveillance of human Salmonella infections.
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Affiliation(s)
- M B F Jensen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - S Schjørring
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
- European Programme for Public Health Microbiology Training, European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
| | - J T Björkman
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - M Torpdahl
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E Litrup
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E M Nielsen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark.
| | - T Niskanen
- European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
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Abstract
Agarose gel electrophoresis may be used to purify fragmented genomic DNA after ligation of adaptors. After electrophoresis, the region of the gel containing the desired size range of DNA is excised, and the DNA is subsequently extracted from the gel and purified by passage through a spin column.
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LaFrentz BR, García JC, Dong HT, Waldbieser GC, Rodkhum C, Wong FS, Chang SF. Optimized reverse primer for 16S-RFLP analysis and genomovar assignment of Flavobacterium columnare. J Fish Dis 2017; 40:1103-1108. [PMID: 27982441 DOI: 10.1111/jfd.12583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Affiliation(s)
- B R LaFrentz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - J C García
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - H T Dong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - G C Waldbieser
- USDA-ARS, Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, USA
| | - C Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - F S Wong
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore city, Singapore
| | - S F Chang
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore city, Singapore
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Dahmani F, Benkirane S, Kouzih J, Woumki A, Mamad H, Masrar A. [Epidemiological profile of hemoglobinopathies: a cross-sectional and descriptive index case study]. Pan Afr Med J 2017; 27:150. [PMID: 28904678 PMCID: PMC5567958 DOI: 10.11604/pamj.2017.27.150.11477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Hemoglobinopathies are congenital disorders resultimg from hemoglobin abnormalities. Major forms are often severe, their management is difficult and associated with a great psychosocial impact on patients and their families. They are classified as rare diseases and are still insufficiently known by health professionals. This lack of knowledge is at the origin of diagnostic errors, delay in their management and therefore high morbidity and mortality rate for these patients. In 2008, the World Health Organization (WHO) has published data on hemoglobinopathies epidemiology: more than 330.000 cases of hemoglobinopathy occur each year (83% of cases of sickle cell anemia, 17 % of cases of thalassemia). Hemoglobin disorders are responsible for approximately 3.4% of deaths among people under the age of 5. At the global level, approximately 7% of pregnant women would be carriers of a form of thalassemia and 1% of couples are at risk. However, they are relatively frequent in some regions of the globe where consanguineous marriages are common. We conducted a descriptive cross-sectional study based on two surveys, the first in May 2015 and the second in June of the same year. It was performed in the immunization days to deliver pneumococcal vaccine to the index cases and it was aimed to describe the epidemiological features of families at risk of hemoglobinopathies (index case study), whose index cases were treated in the Department of Pediatrics at the Provincial Hospital El Idrisi, Kenitra, Morocco. After having collected the epidemiological data from patients, laboratory tests were performed including: blood count with red blood cells morphological assessment using the MGG assay and automatic numbering of reticulocytes; hemoglobin electrophoresis at alkaline pH (8.8) and then at acid pH (5.4) on agarose gel and densitometric integration. 275 patients had laboratory profiles compatible with hemoglobinopathy. The majority of these patients were born to consanguineous marriages (83.1%) and came from the north regions of Morocco. This family survey allowed to identify families at risk with a high frequency of sickle cell anemia. Our results confirm the existence of hemoglobinopathies variants among Moroccan population.
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Affiliation(s)
- Fatima Dahmani
- Équipe de Recherche en Hématologie, Laboratoire d'Hématologie, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
| | - Souad Benkirane
- Équipe de Recherche en Hématologie, Laboratoire d'Hématologie, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
| | - Jaafar Kouzih
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
| | - Aziz Woumki
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
| | - Hassan Mamad
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
| | - Azlarab Masrar
- Équipe de Recherche en Hématologie, Laboratoire d'Hématologie, Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
- Laboratoire Central d'Hématologie, Centre Hospitalier Ibn Sina, Rabat, Maroc
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50
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Qin Q, Miao J, Wang S, Yu Q, Li M, He F, Wang G. [Association between intestinal flora and immunity in middle-aged and aged people by PCR-DGGE]. Wei Sheng Yan Jiu 2017; 46:40-45. [PMID: 29903150] [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] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To analyze whether the effects of the aging caused changes in intestinal flora to the immunity by evaluating the potent association between the intestinal flora and their immunity of middle-aged and aged healthy subjects based on profiling the composition of their fecal bacteria and testing their immune parameters. METHODS Total 99 healthy volunteers aged 50- 75 were recruited. Blood samples collected from them were analyzed for CD3~+T cell, CD4~+T cell, CD8~+T cell, serum Ig A, Ig M and Ig G with flow cytometer( FCM) and immunoturbidimetry. The fecal samples were also collected from them. The genomic DNA of fecal bacteria was extracted and amplified with the universal primers of bacterial 16S rRNA V6- V8 region by PCR. The DNA amplifications were tested with denaturing gradient gel electrophoresis( DGGE). Cluster analysis, principal component analysis( PCA) and variance analysis were used to characterize fecal bacteria composition andanalyze the association with observed immune parameters. RESULTS The fecal microbiota were highly polymorphic and greatly varied among the tested subjects. CD3~+T cell and CD4~+/CD8~+ levels correlated with intestinal flora structure. Intestinal flora richness( S) of population with high CD4~+/ CD8~+ level was lower compared with population with normal or low CD4~+/ CD8~+ level. However, no apparent association was observed between serum Ig A, Ig M, Ig G levels and the fecal microbiota among the tested subjects. CONCLUSION The decrease in the diversity of intestinal flora might affect CD8~+T cell based innate immunity of host. The deep association could exist between intestinal flora and their immunity in middle-aged and aged people.
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Affiliation(s)
- Qianqian Qin
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Junjie Miao
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Shuyue Wang
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Qian Yu
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Ming Li
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Fang He
- West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Guoqing Wang
- West China School of Public Health, Sichuan University, Chengdu 610041, China
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