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Kasu M, Ristow PG, Burrows AM, Kuplik Z, Gibbons MJ, D'Amato ME. Novel buffer for long-term preservation of DNA in biological material at room temperature 1. Biotechniques 2024:1-14. [PMID: 38949197 DOI: 10.1080/07366205.2024.2360813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish Pelagia noctiluca comb jelly Beroe sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.
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Affiliation(s)
- Mohaimin Kasu
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Peter G Ristow
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Adria Michelle Burrows
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Zafrir Kuplik
- Department of Biodiversity & Conservation Biology, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Mark J Gibbons
- Department of Biodiversity & Conservation Biology, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
| | - Maria E D'Amato
- Department of Biotechnology, Forensic DNA Laboratory, University of the Western Cape, Bellville, Western Cape, 7535, South Africa
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Pinazo-Durán MD, Zanón-Moreno V, García–Villanueva C, Martucci A, Peris-Martínez C, Vila-Arteaga J, García-Medina JJ, Andrés–Blasco I, Gallego–Martínez A, Nucci C, García–Feijoo J. Biochemical-molecular-genetic biomarkers in the tear film, aqueous humor, and blood of primary open-angle glaucoma patients. Front Med (Lausanne) 2023; 10:1157773. [PMID: 37305138 PMCID: PMC10251746 DOI: 10.3389/fmed.2023.1157773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Glaucoma is a chronic neurodegenerative disease, which is the leading cause of irreversible blindness worldwide. As a response to high intraocular pressure, the clinical and molecular glaucoma biomarkers indicate the biological state of the visual system. Classical and uncovering novel biomarkers of glaucoma development and progression, follow-up, and monitoring the response to treatment are key objectives to improve vision outcomes. While the glaucoma imaging field has successfully validated biomarkers of disease progression, there is still a considerable need for developing new biomarkers of early glaucoma, that is, at the preclinical and initial glaucoma stages. Outstanding clinical trials and animal-model study designs, innovative technology, and analytical approaches in bioinformatics are essential tools to successfully uncover novel glaucoma biomarkers with a high potential for translation into clinical practice. Methods To better understand the clinical and biochemical-molecular-genetic glaucoma pathogenesis, we conducted an analytical, observational, and case-comparative/control study in 358 primary open-angle glaucoma (POAG) patients and 226 comparative-control individuals (CG) to collect tears, aqueous humor, and blood samples to be processed for identifying POAG biomarkers by exploring several biological pathways, such as inflammation, neurotransmitter/neurotrophin alteration, oxidative stress, gene expression, miRNAs fingerprint and its biological targets, and vascular endothelial dysfunction, Statistics were done by using the IBM SPSS 25.0 program. Differences were considered statistically significant when p ≤ 0.05. Results Mean age of the POAG patients was 70.03 ± 9.23 years, and 70.62 ± 7.89 years in the CG. Malondialdehyde (MDA), nitric oxide (NO), interleuquin (IL)-6, endothelin-1 (ET-1), and 5 hydroxyindolacetic acid (5-HIAA), displayed significantly higher levels in the POAG patients vs. the CG (p < 0.001). Total antioxidant capacity (TAC), brain derived neurotrophic factor (BDNF), 5-hydroxy tryptamine (5-HT), solute carrier family 23-nucleobase transporters-member 2 (SLC23A2) gene, and the glutathione peroxidase 4 (GPX4) gene, showed significantly lower levelsin the POAG patients than in the CG (p < 0.001). The miRNAs that differentially expressed in tear samples of the POAG patients respect to the CG were the hsa miR-26b-5p (involved in cell proliferation and apoptosis), hsa miR-152-3p (regulator of cell proliferation, and extracellular matrix expression), hsa miR-30e-5p (regulator of autophagy and apoptosis), and hsa miR-151a-3p (regulator of myoblast proliferation). Discussion We are incredibly enthusiastic gathering as much information as possible on POAG biomarkers to learn how the above information can be used to better steer the diagnosis and therapy of glaucoma to prevent blindness in the predictable future. In fact, we may suggest that the design and development of blended biomarkers is a more appropriate solution in ophthalmological practice for early diagnosis and to predict therapeutic response in the POAG patients.
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Affiliation(s)
- Maria D. Pinazo-Durán
- Ophthalmic Research Unit “Santiago Grisolia”, Foundation for Research in Health and Biomedicine (FISABIO), Valencia, Spain
- Cellular and Molecular Ophthalmobiology Group, Surgery Department, Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
- Spanish Network of Inflammatory Diseases: REI-RICORS (RD21/0002/0032) of the Institute of Health Carlos III (ISCIII), Spanish Government, Madrid, Spain
| | - Vicente Zanón-Moreno
- Spanish Network of Inflammatory Diseases: REI-RICORS (RD21/0002/0032) of the Institute of Health Carlos III (ISCIII), Spanish Government, Madrid, Spain
- Biosanitary Research Institute, Valencian International University (VIU), Valencia, Spain
| | | | - Alessio Martucci
- Ophthalmology Unit, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Cristina Peris-Martínez
- Spanish Network of Inflammatory Diseases: REI-RICORS (RD21/0002/0032) of the Institute of Health Carlos III (ISCIII), Spanish Government, Madrid, Spain
- Medical Ophthalmology FISABIO-FOM Center, Valencia, Spain
| | - Jorge Vila-Arteaga
- Department of Ophthalmology, University and Polytechnic Hospital “La Fe”, Valencia, Spain
| | - Jose J. García-Medina
- Ophthalmic Research Unit “Santiago Grisolia”, Foundation for Research in Health and Biomedicine (FISABIO), Valencia, Spain
- Spanish Network of Inflammatory Diseases: REI-RICORS (RD21/0002/0032) of the Institute of Health Carlos III (ISCIII), Spanish Government, Madrid, Spain
- Department of Ophthalmology, The General University Hospital “Morales Meseguer”, Murcia, Spain
- Department of Ophthalmology and Optometry, University of Murcia, Murcia, Spain
| | - Irene Andrés–Blasco
- Ophthalmic Research Unit “Santiago Grisolia”, Foundation for Research in Health and Biomedicine (FISABIO), Valencia, Spain
- Cellular and Molecular Ophthalmobiology Group, Surgery Department, Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
- Spanish Network of Inflammatory Diseases: REI-RICORS (RD21/0002/0032) of the Institute of Health Carlos III (ISCIII), Spanish Government, Madrid, Spain
| | - Alex Gallego–Martínez
- Ophthalmic Research Unit “Santiago Grisolia”, Foundation for Research in Health and Biomedicine (FISABIO), Valencia, Spain
- Cellular and Molecular Ophthalmobiology Group, Surgery Department, Faculty of Medicine and Odontology, University of Valencia, Valencia, Spain
| | - Carlo Nucci
- Ophthalmology Unit, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Julian García–Feijoo
- Department of Ophthalmology, The University Clinic Hospital “San Carlos”, Madrid, Spain
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Koitzsch KB, Anton CB, Koitzsch LO, Tjepkes TL, Schumann AC, Strasburg JL. A noninvasive and integrative approach for improving density and abundance estimates of moose. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Colby B. Anton
- Yellowstone Center for Resources, National Park Service Yellowstone National Park WY 82190 USA
| | | | - Tessa L. Tjepkes
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
| | - Abby C. Schumann
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
| | - Jared L. Strasburg
- Department of Biology University of Minnesota‐Duluth 207 Swenson Science Building, 1035 Kirby Drive Duluth MN 55812 USA
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Morinha F, Magalhães P, Blanco G. Standard guidelines for the publication of telomere qPCR results in evolutionary ecology. Mol Ecol Resour 2020; 20. [PMID: 32133733 DOI: 10.1111/1755-0998.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
Telomere length has been used as a proxy of fitness, aging and lifespan in vertebrates. In the last decade, dozens of articles reporting on telomere dynamics in the fields of ecology and evolution have been published for a wide range of taxa. With this growing interest, it is necessary to ensure the accuracy and reproducibility of telomere length measurement techniques. Real-time quantitative PCR (qPCR) is routinely applied to measure relative telomere length. However, this technique is highly sensitive to several methodological variables and the optimization of qPCR telomere assays remains highly variable between studies. Therefore, standardized guidelines are required to enable the optimization of robust protocols, and to help in judging the validity of the presented results. This review provides an overview of preanalytical and analytical factors that can lead to qPCR inconsistencies and biases, including: (a) sample type, collection and storage; (b) DNA extraction, storage and quality; (c) qPCR primers, laboratory reagents, and assay conditions; and (d) data analysis. We propose a minimum level of information for publication of qPCR telomere assays in evolutionary ecology considering the methodological pitfalls and sources of error. This review highlights the complexity of the optimization and validation of qPCR for telomere measurement per se, demonstrating the importance of transparency and clarity of reporting methodological details required for reliable, reproducible and comparable qPCR telomere assays. We encourage efforts to implement standardized protocols that ensure the rigour and quality of telomere dynamics studies.
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Affiliation(s)
- Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Paula Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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Mitochondrial DNA analysis of a Viking age mass grave in Sweden. Forensic Sci Int Genet 2019; 42:268-274. [DOI: 10.1016/j.fsigen.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/12/2023]
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Muller R, Betsou F, Barnes MG, Harding K, Bonnet J, Kofanova O, Crowe JH. Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community. Biopreserv Biobank 2016; 14:89-98. [DOI: 10.1089/bio.2015.0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | | | - Keith Harding
- Damar Research Scientists, Damar, Cupar Muir, United Kingdom
| | - Jacques Bonnet
- Imagene, Genopole Campus 1, Evry, France
- Université de Bordeaux Segalen, Institut Bergonié, Bordeaux, France
| | - Olga Kofanova
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | - John H. Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, California
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Forensic Analysis of Mitochondrial and Autosomal Markers Using Pyrosequencing®. Methods Mol Biol 2016; 1315:379-96. [PMID: 26103912 DOI: 10.1007/978-1-4939-2715-9_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Forensic casework analyses often face challenges, such as limited genetic material with or without fragmentation and damage. To compensate for low amounts and degradation, shorter amplicons are often applied in the analysis. Also, a change of markers might be necessary using mitochondrial instead of autosomal markers. In addition, forensic research often involves analysis of large number of samples for marker evaluation and population-database compilation. Therefore, a flexible, robust but also rapid method for the detection of variation is highly useful. Pyrosequencing(®) is a rapid, reliable, easy-to-use method for sequence analysis. The method is well suited for rapid forensic analysis of a few targets or analysis of a single target in many samples. It allows sequencing of very short amplicons, which facilitates analysis of degraded DNA. Here we present the use of Pyrosequencing, a robust method for sensitive forensic analysis of mitochondrial DNA, autosomal STRs, and Y-chromosome STRs and SNPs.
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Buś MM, Nilsson M, Allen M. Analysis of Mitochondrial DNA from a Burned, Ninhydrin-Treated Paper Towel. J Forensic Sci 2016; 61:828-832. [DOI: 10.1111/1556-4029.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/11/2015] [Accepted: 08/15/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Magdalena M. Buś
- Department of Immunology, Genetics and Pathology; Science for Life Laboratory; Uppsala University; Box 815 S-751 08 Uppsala Sweden
| | - Martina Nilsson
- Swedish Police Authority; Stockholm Region; Division of investigation; Forensic Section; S-106 75 Stockholm Sweden
| | - Marie Allen
- Department of Immunology, Genetics and Pathology; Science for Life Laboratory; Uppsala University; Box 815 S-751 08 Uppsala Sweden
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Wang Y, Zheng H, Chen J, Zhong X, Wang Y, Wang Z, Wang Y. The Impact of Different Preservation Conditions and Freezing-Thawing Cycles on Quality of RNA, DNA, and Proteins in Cancer Tissue. Biopreserv Biobank 2015; 13:335-47. [PMID: 26484573 DOI: 10.1089/bio.2015.0029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yaogeng Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Chen
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaorong Zhong
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yanping Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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Bobrowiec PED, Lemes MR, Gribel R. Prey preference of the common vampire bat (Desmodus rotundus, Chiroptera) using molecular analysis. J Mammal 2015. [DOI: 10.1093/jmammal/gyu002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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