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Kopfnagel V, Klopp N, Bernemann I, Nizhegorodtseva N, Wilson R, Gronauer R, Seifert M, Illig T. Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA. Biopreserv Biobank 2024; 22:110-114. [PMID: 37074140 DOI: 10.1089/bio.2022.0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
The characterization of DNA methylation patterns to identify epigenetic markers for complex human diseases is an important and rapidly evolving part in biomedical research. DNA samples collected and stored in clinical biobanks over the past years are an important source for future epigenetic studies. Isolated gDNA is considered stable when stored at low temperatures for several years. However, the effect of multiple use and the associated repeated thawing of long-term stored DNA samples on DNA methylation patterns has not yet been investigated. In this study, we examined the influence of up to 10 freeze and thaw cycles on global DNA methylation by comparing genome-wide methylation profiles. DNA samples from 19 healthy volunteers were either frozen at -80°C or subjected to up to 10 freeze and thaw cycles. Genome-wide DNA methylation was analyzed after 0, 1, 3, 5, or 10 thaw cycles using the Illumina Infinium MethylationEPIC BeadChip. Evaluation of the global DNA methylation profile by beta-value density plots and multidimensional scaling plots revealed an expected clear participant-dependent variability, but a very low variability depending on the freeze and thaw cycles. In accordance, no significant difference in any of the methylated cytosine/guanine sites studied could be detected in the performed statistical analyses. Our results suggest that long-term frozen DNA samples are still suitable for epigenetic studies after multiple thaw cycles.
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Affiliation(s)
- Verena Kopfnagel
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Norman Klopp
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Inga Bernemann
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | | | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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Dierick E, Callens C, De Spiegelaere W, Ducatelle R, Van Immerseel F, Goossens E. Digital PCR: a tool in clostridial mutant selection and detection. Appl Microbiol Biotechnol 2023; 107:6973-6983. [PMID: 37704769 DOI: 10.1007/s00253-023-12779-8] [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: 06/30/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
The ClosTron mutagenesis system has enabled researchers to efficiently edit the clostridial genome. Since site-specific insertion of the mobile ClosTron insert may cause errors, validation is key. In this paper we describe the use of digital PCR (dPCR) as an alternative tool in selecting clostridial mutant strains. Clostridium perfringens chitinase mutant strains were constructed in which the mobile ClosTron intron was inserted into one of the chitinase genes. On-target insertion of the mobile intron was validated through conventional PCR. In order to confirm the absence of off-target insertions, dPCR was used to determine the amount of the ClosTron intron as well as the amount of a reference gene, located in close proximity to the interrupted gene. Subsequently, mutant strains containing an equivalent amount of both genes were selected as these do not contain additional off-target mobile ClosTron inserts. The outcome of this selection procedure was confirmed through a validated PCR-based approach. In addition to its application in mutant selection, dPCR can be used in other aspects of clostridial research, such as the distinction and easy quantification of different types of strains (wildtype vs. mutant) in complex matrices, such as faecal samples, a process in which other techniques are hampered by bacterial overgrowth (plating) or inhibition by matrix contaminants (qPCR). This research demonstrates that dPCR is indeed a high-throughput method in the selection of clostridial insertion mutants as well as a robust and accurate tool in distinguishing between wildtype and mutant C. perfringens strains, even in a complex matrix such as faeces. KEY POINTS: • Digital PCR as an alternative in ClosTron mutant selection • Digital PCR is an accurate tool in bacterial quantification in a complex matrix • Digital PCR is an alternative tool with great potential to microbiological research.
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Affiliation(s)
- Evelien Dierick
- Livestock Gut Health Team (LiGHT), Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Chana Callens
- Livestock Gut Health Team (LiGHT), Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
- Ghent University Digital PCR Consortium, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT), Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT), Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT), Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021; 11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advances in basic research have unveiled several strategies for improving the sensitivity and specificity of cell-free DNA (cfDNA) based assays, which is a prerequisite for broadening its clinical use. Included among these strategies is leveraging knowledge of both the biogenesis and physico-chemical properties of cfDNA towards the identification of better disease-defining features and optimization of methods. While good progress has been made on this front, much of cfDNA biology remains uncharted. Here, we correlated serial measurements of cfDNA size, concentration and nucleosome histone modifications with various cellular parameters, including cell growth rate, viability, apoptosis, necrosis, and cell cycle phase in three different cell lines. Collectively, the picture emerged that temporal changes in cfDNA levels are rather irregular and not the result of constitutive release from live cells. Instead, changes in cfDNA levels correlated with intermittent cell death events, wherein apoptosis contributed more to cfDNA release in non-cancer cells and necrosis more in cancer cells. Interestingly, the presence of a ~ 3 kbp cfDNA population, which is often deemed to originate from accidental cell lysis or active release, was found to originate from necrosis. High-resolution analysis of this cfDNA population revealed an underlying DNA laddering pattern consisting of several oligo-nucleosomes, identical to those generated by apoptosis. This suggests that necrosis may contribute significantly to the pool of mono-nucleosomal cfDNA fragments that are generally interrogated for cancer mutational profiling. Furthermore, since active steps are often taken to exclude longer oligo-nucleosomes from clinical biospecimens and subsequent assays this raises the question of whether important pathological information is lost.
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Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | | | - Marielle Herzog
- Belgian Volition SRL, 22 Rue Phocas Lejeune, Parc Scientifique Crealys, 5032, Isnes, Belgium
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany.
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Matange K, Tuck JM, Keung AJ. DNA stability: a central design consideration for DNA data storage systems. Nat Commun 2021; 12:1358. [PMID: 33649304 PMCID: PMC7921107 DOI: 10.1038/s41467-021-21587-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Abstract
Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.
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Affiliation(s)
- Karishma Matange
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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Baoutina A, Bhat S, Partis L, Emslie KR. Storage Stability of Solutions of DNA Standards. Anal Chem 2019; 91:12268-12274. [DOI: 10.1021/acs.analchem.9b02334] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anna Baoutina
- National Measurement Institute (NMI), Lindfield, Sydney, New South Wales 2070, Australia
| | - Somanath Bhat
- National Measurement Institute (NMI), Lindfield, Sydney, New South Wales 2070, Australia
| | - Lina Partis
- National Measurement Institute (NMI), Lindfield, Sydney, New South Wales 2070, Australia
| | - Kerry R. Emslie
- National Measurement Institute (NMI), Lindfield, Sydney, New South Wales 2070, Australia
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Yoo HB, Park SR, Dong L, Wang J, Sui Z, Pavšič J, Milavec M, Akgoz M, Mozioğlu E, Corbisier P, Janka M, Cosme B, de V Cavalcante JJ, Flatshart RB, Burke D, Forbes-Smith M, McLaughlin J, Emslie K, Whale AS, Huggett JF, Parkes H, Kline MC, Harenza JL, Vallone PM. International Comparison of Enumeration-Based Quantification of DNA Copy-Concentration Using Flow Cytometric Counting and Digital Polymerase Chain Reaction. Anal Chem 2016; 88:12169-12176. [PMID: 28193036 DOI: 10.1021/acs.analchem.6b03076] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter. In addition, 2 orthogonal chemical-analysis methods based on nucleotide quantification, isotope-dilution mass spectrometry (IDMS) and capillary electrophoresis (CE) were applied to quantify a more concentrated solution of the plasmid. Although 9 dPCR results from 8 laboratories showed some dispersion (relative standard deviation [RSD] = 11.8%), their means were closely aligned with those of the FCM-based counting method and the orthogonal chemical-analysis methods, corrected for gravimetric dilution factors. Using the means of dPCR results, the RSD of all 4 methods was 1.8%, which strongly supported the validity of the recent enumeration approaches. Despite a good overall agreement, the individual dPCR results were not sufficiently covered by the reported measurement uncertainties. These findings suggest that some laboratories may not have considered all factors contributing to the measurement uncertainty of dPCR, and further investigation of this possibility is warranted.
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Affiliation(s)
- Hee-Bong Yoo
- Korea Research Institute of Standards and Science , Daejeon 34113, Republic of Korea.,University of Science and Technology , Daejeon 34141, Republic of Korea
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science , Daejeon 34113, Republic of Korea.,University of Science and Technology , Daejeon 34141, Republic of Korea
| | - Lianhua Dong
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Jing Wang
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Zhiwei Sui
- National Institute of Metrology , Beijing 100013, P.R. China
| | - Jernej Pavšič
- National Institute of Biology , 1000 Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology , 1000 Ljubljana, Slovenia
| | - Muslum Akgoz
- TUBITAK UME National Metrology Institute , Kocaeli 41470, Turkey
| | - Erkan Mozioğlu
- TUBITAK UME National Metrology Institute , Kocaeli 41470, Turkey
| | - Philippe Corbisier
- Institute for Reference Materials and Measurements, Joint Research Centre, European Commission , Geel 2440, Belgium
| | - Mátrai Janka
- Institute for Reference Materials and Measurements, Joint Research Centre, European Commission , Geel 2440, Belgium
| | - Bruno Cosme
- National Institute of Metrology, Quality and Technology , Xerém 25250-020, Brazil
| | | | | | - Daniel Burke
- National Measurement Institute Australia , Lindfield 2070, Australia
| | | | - Jacob McLaughlin
- National Measurement Institute Australia , Lindfield 2070, Australia
| | - Kerry Emslie
- National Measurement Institute Australia , Lindfield 2070, Australia
| | | | | | | | - Margaret C Kline
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
| | - Jo Lynne Harenza
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
| | - Peter M Vallone
- National Institute of Standards and Technology , Gaithersburg, Maryland 20899-1070, United States
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Yu H, Haskins JS, Su C, Allum A, Haskins AH, Salinas VA, Sunada S, Inoue T, Aizawa Y, Uesaka M, Kato TA. In vitro screening of radioprotective properties in the novel glucosylated flavonoids. Int J Mol Med 2016; 38:1525-1530. [DOI: 10.3892/ijmm.2016.2764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/22/2016] [Indexed: 11/06/2022] Open
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8
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Bulushev RD, Steinbock LJ, Khlybov S, Steinbock JF, Keyser UF, Radenovic A. Measurement of the position-dependent electrophoretic force on DNA in a glass nanocapillary. NANO LETTERS 2014; 14:6606-13. [PMID: 25343616 DOI: 10.1021/nl503272r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations.
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Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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