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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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2
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Martin NA, McLester-Davis LWY, Roy TR, Magruder MG, Hastings WJ, Drury SS. Monochrome Multiplex Quantitative PCR Telomere Length Measurement. J Vis Exp 2024:10.3791/66545. [PMID: 38587381 PMCID: PMC11080955 DOI: 10.3791/66545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Telomeres are ribonucleoprotein structures at the end of all eukaryotic chromosomes that protect DNA from damage and preserve chromosome stability. Telomere length (TL) has been associated with various exposures, biological processes, and health outcomes. This article describes the monochrome multiplex quantitative polymerase chain reaction (MMqPCR) assay protocol routinely conducted in our laboratory for measuring relative mean TL from human DNA. There are several different PCR-based TL measurement methods, but the specific protocol for the MMqPCR method presented in this publication is repeatable, efficient, cost-effective, and suitable for population-based studies. This detailed protocol outlines all information necessary for investigators to establish this assay in their laboratory. In addition, this protocol provides specific steps to increase the reproducibility of TL measurement by this assay, defined by the intraclass correlation coefficient (ICC) across repeated measurements of the same sample. The ICC is a critical factor in evaluating expected power for a specific study population; as such, reporting cohort-specific ICCs for any TL assay is a necessary step to enhance the overall rigor of population-based studies of TL. Example results utilizing DNA samples extracted from peripheral blood mononuclear cells demonstrate the feasibility of generating highly repeatable TL data using this MMqPCR protocol.
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Affiliation(s)
| | - Lauren W Y McLester-Davis
- Native American Center for Health Professions, University of Wisconsin-Madison; Department of Medicine, University of Wisconsin-Madison; Department of Biochemistry, University of Wisconsin-Madison
| | | | | | | | - Stacy S Drury
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital;
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3
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Cutrupi F, Rossi M, Cadonna M, Poznanski E, Manara S, Postinghel M, Palumbi G, Bellisomi M, Nicosia E, Allaria G, Dondero L, Veneri C, Mancini P, Ferraro GB, Rosa G, Suffredini E, Foladori P, Grasselli E. Evaluation of concentration procedures, sample pre-treatment, and storage condition for the detection of SARS-CoV-2 in wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106660-106670. [PMID: 37733200 PMCID: PMC10579110 DOI: 10.1007/s11356-023-29696-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Crucial information on the pandemic's spread has been gathered by monitoring the trend of SARS-CoV-2 in wastewater. This surveillance has highlighted that the initial concentration is a critical step of the analytical procedure due to the low viral titer that may be present in this matrix. This paper presents the results of the evaluation of two different wastewater concentration protocols to determine the most efficient and cost-effective. The two methods tested were the following: (a) a biphasic separation system with PEG-dextran and (b) a PEG/NaCl precipitation protocol. Other aspects of the detection method were also investigated including the influence of storage temperature on virus recovery and the heat treatment of pasteurization, which aims to make samples safer for operators and the environment. The PEG/NaCl precipitation method was found to perform better than the biphasic separation system, allowing for more sensitive identification of the presence of the virus and the detection of a higher viral titer than that identified with the biphasic separation in all results. Storage of the samples at 4.3±0.2°C for up to 3 weeks did not adversely affect the virus titer and the pasteurization pre-treatment increases operator safety and maintains the identification of the viral concentration.
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Affiliation(s)
- Francesca Cutrupi
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy.
| | - Michele Rossi
- Department of Biosciences, University of Milano, Via Celoria 26, 20134, Milano, Italy
| | - Maria Cadonna
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | | | - Serena Manara
- Department of Cellular Computational and Integrative Biology-CIBIO, Via Sommarive 9, 38123, Trento, Italy
| | - Mattia Postinghel
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | - Giulia Palumbi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Marta Bellisomi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Elena Nicosia
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
- Department of Health and Social Services, Liguria Region Administration, Piazza della Vittoria 119, 16121, Genova, Italy
| | - Giorgia Allaria
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Lorenzo Dondero
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Giuseppina Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Foladori
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy
| | - Elena Grasselli
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
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4
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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] [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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5
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Laveroni SL, Parks VR. Quantitative PCR of Alu Repeats Using PowerUp™ SYBR ® Green Master Mix. Methods Mol Biol 2023; 2685:149-174. [PMID: 37439981 DOI: 10.1007/978-1-0716-3295-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Quantitative PCR is one of the fundamental steps performed when processing routine casework in a forensic laboratory. Quantitative PCR of Alu repeats using a SYBR® Green master mix can produce calculated estimates of how much DNA was extracted from a sample. This process offers more efficiency, human specificity, and can be performed faster than other outdated quantification methods, such as slot blot or yield gel. A qPCR master mix is prepared and consists of Alu-F primers, Alu-R primers, water, and SYBR® Green master mix. The Alu-F and Alu-R primers target Alu sequences that are present hundreds of thousands of times throughout the human genome and are effective markers for human DNA quantification. During qPCR, the 7500 system facilitates the amplification of target Alu repeats. The SYBR® Green I fluorescent dye intercalates between the amplified dsDNA targets. During each amplification cycle, the 7500 system agitates the SYBR® Green I dye, resulting in a fluorescence signal that is recorded when it passes a specified Ct value. After qPCR amplification is complete, a standard curve is created and used to determine how much DNA a sample contains. This chapter provides instructions on how to accurately prepare a 96-well plate for qPCR, use the 7500 system and associated software to set up the qPCR amplification, and interpret the corresponding results produced.
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Affiliation(s)
- Sierra L Laveroni
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Victoria R Parks
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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6
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Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW. Long-Range Polymerase Chain Reaction. Methods Mol Biol 2023; 2967:181-192. [PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
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Affiliation(s)
- Ping Siu Kee
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Harsheni Karunanathie
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Simran D S Maggo
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
- Department of Pathology, Center for Personalized Medicine, Children's Hospital Los Angeles, California, LA, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Eng Wee Chua
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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7
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Aliev TA, Timralieva AA, Kurakina TA, Katsuba KE, Egorycheva YA, Dubovichenko MV, Kutyrev MA, Shilovskikh VV, Orekhov N, Kondratyuk N, Semenov SN, Kolpashchikov DM, Skorb EV. Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade. NANO SELECT 2022. [DOI: 10.1002/nano.202200092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - Nikita Orekhov
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- Bauman Moscow State Technical University Moscow Russia
| | - Nikolay Kondratyuk
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- National Research University Higher School of Economics Moscow Russia
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot Israel
| | - Dmitry M. Kolpashchikov
- ITMO University Saint Petersburg Russia
- University of Central Florida Chemistry Department Orlando Florida USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando Florida USA
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8
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Islam G, Gedge A, Lara-Jacobo L, Kirkwood A, Simmons D, Desaulniers JP. Pasteurization, storage conditions and viral concentration methods influence RT-qPCR detection of SARS-CoV-2 RNA in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153228. [PMID: 35090920 PMCID: PMC8788100 DOI: 10.1016/j.scitotenv.2022.153228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic presents many public health challenges including the tracking of infected individuals from local to regional scales. Wastewater surveillance of viral RNA has emerged as a complementary approach to track and monitor the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus in a variety of communities of different land use and population size. In the present study, we investigate how five different parameters (pasteurization, storage temperature, storage time, polyethylene glycol (PEG) concentration, and pellet mass) affect the detection of the SARS-CoV-2 N gene and fecal abundance indicator pepper mild mottle virus (PMMoV) gene. Pre-treatment of 24-h composite wastewater samples (n = 14) by pasteurization at 60 °C resulted in a significant reduction of total RNA concentration and copies of the SARS-CoV-2 N gene copies/L (paired Student's t-test, P < 0.05). Comparing the wastewater samples collected from 6 wastewater treatment plants (WWTPs) for a storage period of 7 and 14 days at 4 °C, -20 °C and -80 °C, demonstrated a decrease in SARS-CoV-2 N gene copies/L when samples were stored for 14 days at -20 °C. Polyethylene glycol-NaCl for purification and concentration of viral particles from the wastewater samples demonstrated that a short PEG incubation of 2 h during centrifugation at 4 °C was sufficient for the consistent detection of the SARS-CoV-2 N gene from a 30 mL sample volume. Combined, this paper presents method recommendations for developing a reliable, accurate, sensitive, and reproducible estimation of the SARS-CoV-2 virus in diverse domestic wastewater samples.
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Affiliation(s)
- Golam Islam
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada.
| | - Ashley Gedge
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Linda Lara-Jacobo
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Andrea Kirkwood
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Denina Simmons
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
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9
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Holohan C, Hanrahan S, Feely N, Li P, O'Connell J, Moss C, Carr M, Tagit O, Lee GU. Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids. NANOSCALE 2021; 13:15659-15667. [PMID: 34533168 DOI: 10.1039/d1nr03933d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Our goal is to reinforce testing capabilities and identify weaknesses that could arise in resource-limited environments that do not have well-controlled cold chains. Method: The sensitivity of qRT-PCR analysis was studied in four VTM for synthetic single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) simulants of the SARS-CoV-2 genome. Results: The sensitivity and reproducibility of qRT-PCR for the synthetic ssRNA and dsDNA were found to be highly sensitive to VTM with the best results observed for ssRNA in HBSS and PBS-G. Surprisingly, the presence of epithelial cellular material with the ssRNA increased the sensitivity of the qRT-PCR assay. Repeated freeze-thaw cycling decreased the sensitivity of the qRT-PCR with two noted exceptions. Conclusions: The choice of VTM is critically important to defining the sensitivity of COVID-19 molecular diagnostics assays and this study suggests they can impact upon the stability of the SARS-CoV-2 viral genome. This becomes increasingly important if the virus structure is destabilised before analysis, which can occur due to poor storage conditions. This study suggests that COVID-19 testing performed with glycerol-containing PBS will produce a high level of stability and sensitivity. These results are in agreement with clinical studies reported for patient-derived samples.
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Affiliation(s)
- Cian Holohan
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
| | - Sophia Hanrahan
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
| | - Nathan Feely
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
| | - Peng Li
- Magnostics Ltd, Monkstown, Co. Dublin, Republic of Ireland.
| | - John O'Connell
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
| | - Catherine Moss
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Republic of Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Oya Tagit
- Magnostics Ltd, Monkstown, Co. Dublin, Republic of Ireland.
| | - Gil U Lee
- School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.
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10
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Sahoo S, Mandal S, Das P, Bhattacharya S, Chandy M. An analysis of the standard curve parameters of cytomegalovirus, BK virus and hepatitis B virus quantitative polymerase chain reaction from a clinical virology laboratory in eastern India. Indian J Med Microbiol 2021; 40:81-85. [PMID: 34602291 DOI: 10.1016/j.ijmmb.2021.09.007] [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: 05/27/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 11/05/2022]
Abstract
PURPOSE Quantitative real-time polymerase chain reactions (qPCRs) are important for accurate detection of nucleic acid target including that for viral load determination. Assessment of the quality of a PCR run is essential for quality control, diagnostics and research. In order to reduce subjectivity qPCR standard curves are accompanied with parametric values for slope, Y- intercept, correlation coefficient (R2) and PCR efficiency. In this study the performance of three qPCR assays-cytomegalovirus, hepatitis B virus and BK virus-with respect to standard curve parameters-slope, Y intercept, R2 and efficiency were examined. METHODS Using ideal values (Slope (minus 3.32); Y intercept = the number of PCR cycles; R2 = 1 and efficiency = 100%) we estimated the intra-assay variability (range) and deviation from ideal parameters (Δ). We also calculated the standard deviation (SD) and coefficient of variation (CV) for each of these parameters. We have evaluated the quality of each of the three viral load assays (CMV, HBV, BKV) using these statistical approach. RESULTS We found lab developed tests (CMV) to have least deviation from ideal Y intercept (limit of detection); however, commercial kit based assays had better linearity (scatter plot correlation between amplification factor and PCR efficiency). Using a scatter plot for the three assays we found the correlation with calculated amplification factor and PCR efficiency was most linear in case of BKV (0.9974), closely followed by the HBV assay (R2 = 0.9968). Although the CMV quantitative standards were least linear (0.868), the CV (coefficient of variation) was also the least in case of the CMV assay. CONCLUSION The study highlights an objective way of assessing qPCR assay quality and demonstrates a method to compare assays, validate tests and perform quality control.
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Affiliation(s)
- Sunanda Sahoo
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | - Sudipto Mandal
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | - Parijat Das
- Department of Microbiology, Tata Medical Center, Kolkata, India
| | | | - Mammen Chandy
- Department of Clinical Hematology, Tata Medical Center, Kolkata, India
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11
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Dahlhauser SD, Moor SR, Vera MS, York JT, Ngo P, Boley AJ, Coronado JN, Simpson ZB, Anslyn EV. Efficient molecular encoding in multifunctional self-immolative urethanes. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100393. [PMID: 34755143 PMCID: PMC8573738 DOI: 10.1016/j.xcrp.2021.100393] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular encoding in sequence-defined polymers shows promise as a new paradigm for data storage. Here, we report what is, to our knowledge, the first use of self-immolative oligourethanes for storing and reading encoded information. As a proof of principle, we describe how a text passage from Jane Austen's Mansfield Park was encoded in sequence-defined oligourethanes and reconstructed via self-immolative sequencing. We develop Mol.E-coder, a software tool that uses a Huffman encoding scheme to convert the character table to hexadecimal. The oligourethanes are then generated by a high-throughput parallel synthesis. Sequencing of the oligourethanes by self-immolation is done concurrently in a parallel fashion, and the liquid chromatography-mass spectrometry (LC-MS) information decoded by our Mol.E-decoder software. The passage is capable of being reproduced wholly intact by a third-party, without any purifications or the use of tandem MS (MS/MS), despite multiple rounds of compression, encoding, and synthesis.
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Affiliation(s)
| | - Sarah R. Moor
- University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Phuoc Ngo
- University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | - Eric V. Anslyn
- University of Texas at Austin, Austin, TX 78712, USA
- Lead contact
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12
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Narvaez Villarrubia CW, Tumas KC, Chauhan R, MacDonald T, Dattelbaum AM, Omberg K, Gupta G. Long-term stabilization of DNA at room temperature using a one-step microwave assisted process. EMERGENT MATERIALS 2021; 5:307-314. [PMID: 33778372 PMCID: PMC7986179 DOI: 10.1007/s42247-021-00208-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Long-term stabilization of DNA is needed for forensic, clinical, in-field operations and numerous other applications. Although freezing (<-20 °C) and dry storage are currently the preferential methods for long-term storage, a noticeable pre-analytical degradation of DNA over time, upfront capital investment and recurring costs have demonstrated a need for an alternative long-term room-temperature preservation method. Herein, we report a novel, fast (~5 min) silica sol-gel preparation method using a standard microwave-initiated polymerization reaction amenable to stabilization of DNA. The method involves use of one chemical, tetramethoxy silane (TMOS) and eliminates the use of alcohol as co-solvent and catalysts such as acids. In addition, the process involves minimal technical expertise, thus making it an ideal choice for resource-challenged countries and in-field applications. The sol-gel is capable to store and stabilize Escherichia coli DNA in ambient conditions for 210 days. DNA recovered from the sol-gel showed no significant nucleolytic and/or oxidative degradation, outperforming conventional storage conditions at -20 °C, and reported state-of-the-art technology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42247-021-00208-3.
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Affiliation(s)
| | - Keyla C. Tumas
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Rajat Chauhan
- Department of Bioengineering, University of Louisville, Louisville, KY 40292 USA
| | - Thomas MacDonald
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Andrew M. Dattelbaum
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Kristin Omberg
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Gautam Gupta
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40292 USA
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13
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Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics 2021; 22:69. [PMID: 33478392 PMCID: PMC7818915 DOI: 10.1186/s12864-021-07381-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging. Results Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation. Conclusion The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07381-z.
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Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Hratch M Baghdassarian
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Tiziano Pramparo
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Isaac Shamie
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Vahid Gazestani
- Department of Pediatrics, University of California, San Diego, USA.,Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Arjana Begzati
- Department of Medicine, University of California San Diego, San Diego, USA
| | - Shangzhong Li
- Department of Pediatrics, University of California, San Diego, USA.,Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Sarah Murray
- Department of Pathology, University of California San Diego, San Diego, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, USA. .,Department of Bioengineering, University of California San Diego, San Diego, USA. .,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, USA.
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14
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Iyer GR, Hasan Q. Alteration of methylation status in archival DNA samples: A qualitative assessment by methylation specific polymerase chain reaction. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:837-842. [PMID: 32649027 DOI: 10.1002/em.22398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression, which also facilitates genomic imprinting. Genomic imprinting is responsible for differential expression of genes based on parent of origin. Altered methylation of parental alleles results in imprinting disorders diagnosed by methylation specific polymerase chain reaction (MS-PCR) technique. With increasing evidence of genes under epigenetic influence, methylation studies are extensively performed on archival samples. To evaluate effect of storage and storage conditions on DNA methylation, a systematic MS-PCR based analysis was planned on an imprinted gene, SNRPN, located on chromosome 15q11.2. It was assessed by MS-PCR on fresh, 4 -20, and -80°C stored DNA samples for different time periods for systematic evaluation of methylation status. Technical factors like type of sample processing, method of DNA isolation, primer region polymorphism, sample heterogeneity were also evaluated. DNA methylation was observed to be altered for SNRPN gene after storage at -80°C from 2 months onwards. Long-term storage of DNA at -80°C results in altered DNA methylation status. This may lead to false MS-PCR diagnosis of imprinting disorders. Our proof of concept study should be followed with quantitative validation since the findings have critical implications in the present era of biobanking.
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Affiliation(s)
- Gayatri Rangarajan Iyer
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
- Department of Genetics, Osmania University, Tarnaka, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics & Molecular Medicine, Kamineni Hospitals, LB Nagar, Hyderabad, India
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15
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Beinhauerova M, Babak V, Bertasi B, Boniotti MB, Kralik P. Utilization of Digital PCR in Quantity Verification of Plasmid Standards Used in Quantitative PCR. Front Mol Biosci 2020; 7:155. [PMID: 32850953 PMCID: PMC7403525 DOI: 10.3389/fmolb.2020.00155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/19/2020] [Indexed: 01/07/2023] Open
Abstract
Quantitative PCR (qPCR) is a widely used method for nucleic acid quantification of various pathogenic microorganisms. For absolute quantification of microbial load by qPCR, it is essential to create a calibration curve from accurately quantified quantification standards, from which the number of pathogens in a sample is derived. Spectrophotometric measurement of absorbance is a routine method for estimating nucleic acid concentration, however, it may be affected by presence of other potentially contaminating nucleic acids or proteins and salts. Therefore, absorbance measurement is not reliable for estimating the concentration of stock solutions of quantification standards, based on which they are subsequently diluted. In this study, we utilized digital PCR (dPCR) for absolute quantification of qPCR plasmid standards and thus detecting possible discrepancies in the determination of the plasmid DNA number of standards derived from UV spectrophotometry. The concept of dPCR utilization for quantification of standards was applied on 45 qPCR assays using droplet-based and chip-based dPCR platforms. Using dPCR, we found that spectrophotometry overestimated the concentrations of standard stock solutions in the majority of cases. Furthermore, batch-to-batch variation in standard quantity was revealed, as well as quantitative changes in standards over time. Finally, it was demonstrated that droplet-based dPCR is a suitable tool for achieving defined quantity of quantification plasmid standards and ensuring the quantity over time, which is crucial for acquiring homogenous, reproducible and comparable quantitative data by qPCR.
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Affiliation(s)
- Martina Beinhauerova
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vladimir Babak
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia
| | - Barbara Bertasi
- Controllo Alimenti, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Maria Beatrice Boniotti
- Tecnologie Biologiche Applicate, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia.,Department of Hygiene and Technology of Food of Animal Origin and of Gastronomy, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia
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16
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Deslandes A, Berti V, Tandjaoui-Lambotte Y, Alloui C, Carbonnelle E, Zahar JR, Brichler S, Cohen Y. SARS-CoV-2 was already spreading in France in late December 2019. Int J Antimicrob Agents 2020; 55:106006. [PMID: 32371096 PMCID: PMC7196402 DOI: 10.1016/j.ijantimicag.2020.106006] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/23/2020] [Accepted: 04/25/2020] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 was already spreading in France in late December 2019, 1 month before the first official cases in the country. Early community spreading changes our knowledge of the COVID-19 epidemic. This new case changes our understanding of the epidemic, and modelling studies should adjust to these new data.
The COVID-19 epidemic is believed to have started in late January 2020 in France. Here we report a case of a patient hospitalised in December 2019 in an intensive care unit in a hospital in the north of Paris for haemoptysis with no aetiological diagnosis. RT-PCR was performed retrospectively on the stored respiratory sample and confirmed the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Based on this result, it appears that the COVID-19 epidemic started much earlier in France.
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Affiliation(s)
- A Deslandes
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France
| | - V Berti
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France
| | - Y Tandjaoui-Lambotte
- Réanimation polyvalente, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; INSERM U1272 Hypoxie et Poumon, Bobigny, France
| | - Chakib Alloui
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France
| | - E Carbonnelle
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, France
| | - J R Zahar
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; IAME, UMR 1137, Université Paris 13, Sorbonne Paris Cité, France.
| | - S Brichler
- Université Paris 13, Sorbonne Paris Cité, France, and Service de Microbiologie Clinique et Unité de Contrôle et de Prévention du Risque Infectieux, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France
| | - Yves Cohen
- Réanimation polyvalente, Groupe Hospitalier Paris Seine Saint-Denis, AP-HP, Bobigny, France; INSERM, U942, F-75010, Paris, France
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17
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Simon N, Shallat J, Williams Wietzikoski C, Harrington WE. Optimization of Chelex 100 resin-based extraction of genomic DNA from dried blood spots. Biol Methods Protoc 2020; 5:bpaa009. [PMID: 32665976 PMCID: PMC7334876 DOI: 10.1093/biomethods/bpaa009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/11/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Dried blood spots (DBS) are widely utilized as part of universal newborn screening and as a means of transporting samples from field sites. We use DBS from African field sites to assess for rare maternal-fetal cell exchange during pregnancy known as microchimerism. We aimed to develop a protocol to maximize the quantity of high-quality genomic DNA (gDNA) extracted from DBS. The total gDNA yield obtained from control DBS utilizing a Qiagen-based protocol and a Chelex® 100 resin-based protocol was first compared. Variations of the Chelex® protocol were subsequently tested to develop an optimized protocol. The gDNA was quantified by qPCR targeting the human beta-globin gene. DNA yield for a given experimental condition was normalized to a Chelex® control performed on the same day, and the total yields were compared using a Student's t-test. The control Chelex® protocol yielded 590% more DNA than the QIAamp® DNA Blood Mini Kit . The absolute efficiency of the control Chelex® protocol was 54%, compared to an absolute efficiency of 9% for the QIAamp® DNA Blood Mini Kit. Modification of the Chelex® protocol to include a second heat precipitation from the same DBS increased the gDNA yield by 29% (P < 0.001). Our optimized protocol including this modification increased the absolute efficiency of extraction to 68%. The gDNA extracted using the Chelex® protocol was stable through repeated freeze-thaw cycles. In a mock microchimerism experiment, rare donor alleles at a frequency of 10 in 100 000 could be identified in gDNA from DBS extracted using the optimized Chelex® protocol. Our findings may be of significance for a diverse range of applications that utilize DBS and require high-quality DNA, including newborn screening programs, pathogen and drug resistance screening from remote field sites, forensics, and rare allele detection.
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Affiliation(s)
- Neta Simon
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Jaclyn Shallat
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Whitney E Harrington
- Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
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18
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Tanner EEL, Wiraja C, Curreri CA, Xu C, Mitragotri S. Stabilization and Topical Skin Delivery of Framework Nucleic Acids using Ionic Liquids. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Eden E. L. Tanner
- School of Engineering and Applied Sciences Harvard University Pierce 211 Cambridge MA 02138 USA
| | - Christian Wiraja
- School of Chemical and Biomedical Engineering Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Christina A. Curreri
- School of Engineering and Applied Sciences Harvard University Pierce 211 Cambridge MA 02138 USA
| | - Chenjie Xu
- School of Chemical and Biomedical Engineering Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
- Department of Biomedical Engineering City University of Hong Kong 83 Tat Chee Avenue Kowloon Hong Kong SAR 999077 China
| | - Samir Mitragotri
- School of Engineering and Applied Sciences Harvard University Pierce 211 Cambridge MA 02138 USA
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19
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Oeser C, Pond M, Butcher P, Bedford Russell A, Henneke P, Laing K, Planche T, Heath PT, Harris K. PCR for the detection of pathogens in neonatal early onset sepsis. PLoS One 2020; 15:e0226817. [PMID: 31978082 PMCID: PMC6980546 DOI: 10.1371/journal.pone.0226817] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/05/2019] [Indexed: 11/21/2022] Open
Abstract
Background A large proportion of neonates are treated for presumed bacterial sepsis with broad spectrum antibiotics even though their blood cultures subsequently show no growth. This study aimed to investigate PCR-based methods to identify pathogens not detected by conventional culture. Methods Whole blood samples of 208 neonates with suspected early onset sepsis were tested using a panel of multiplexed bacterial PCRs targeting Streptococcus pneumoniae, Streptococcus agalactiae (GBS), Staphylococcus aureus, Streptococcus pyogenes (GAS), Enterobacteriaceae, Enterococcus faecalis, Enterococcus faecium, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium, a 16S rRNA gene broad-range PCR and a multiplexed PCR for Candida spp. Results Two-hundred and eight samples were processed. In five of those samples, organisms were detected by conventional culture; all of those were also identified by PCR. PCR detected bacteria in 91 (45%) of the 203 samples that did not show bacterial growth in culture. S. aureus, Enterobacteriaceae and S. pneumoniae were the most frequently detected pathogens. A higher bacterial load detected by PCR was correlated positively with the number of clinical signs at presentation. Conclusion Real-time PCR has the potential to be a valuable additional tool for the diagnosis of neonatal sepsis.
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Affiliation(s)
- Clarissa Oeser
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
- * E-mail:
| | - Marcus Pond
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Philip Butcher
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | | | - Philipp Henneke
- Pediatric Infectious Disease and Rheumatology, University Medical Center Freiburg, Freiburg, Germany
| | - Ken Laing
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Timothy Planche
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Paul T. Heath
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Kathryn Harris
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
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20
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Genetic profiling: Differentiation and identification of hazelnut cultivars (Corylus avellana L.) using RAPD-PCR. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Zupanič Pajnič I, Marrubini G, Pogorelc BG, Zupanc T, Previderè C, Fattorini P. On the long term storage of forensic DNA in water. Forensic Sci Int 2019; 305:110031. [PMID: 31707238 DOI: 10.1016/j.forsciint.2019.110031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/19/2022]
Abstract
A rectrospective study was conducted on the effect of the long term storage of 122 DNA samples resuspended in water, one of the elution media still suggested by well established protocols. These DNA samples come from four different kinds of forensically relevant samples (saliva swabs, FTA card bloodstains, nails and II° World War bones) extracted in 2008-2018 and stored at - 20°C (n=113 of groups #1-#5) and at +4°C (n=9 of the group #6), respectively. At the time of the present study (2019), quantitative PCR (qPCR) was employed as tool for assessing the degradation of the samples. The employment of the Human Quantifiler Kit showed that the median loss of DNA ranged from 17.8% to 66.6% in groups #1-#5 while it was 85.0% in group #6. However, it is likely that these values represent an underestimation due to the shortness of the qPCR probe (62 bp). Noteworthy, the DNA loss was statistically significant in each of the six groups (p values ≤ 0.0167). Thus, in agreement with the data on spontaneous DNA decay, no forensic DNA sample should be stored in water for long term periods. In conclusion, the results of this technical note warn against the use of water for this purpose.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia.
| | | | | | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia.
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy.
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Italy.
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22
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23
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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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24
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Ferro P, Ortega-Pinazo J, Martínez B, Jiménez Á, Gómez-Zumaquero JM, Hortas ML, Díaz T. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank 2019; 17:577-582. [PMID: 31429592 DOI: 10.1089/bio.2019.0024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.
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Affiliation(s)
- Pedro Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Jesús Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - Beatriz Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Álvaro Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | | | | | - Tatiana Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
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25
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Kielar C, Xin Y, Xu X, Zhu S, Gorin N, Grundmeier G, Möser C, Smith DM, Keller A. Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability. Molecules 2019; 24:E2577. [PMID: 31315177 PMCID: PMC6680526 DOI: 10.3390/molecules24142577] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023] Open
Abstract
DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 °C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Nelli Gorin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Christin Möser
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, 14476 Potsdam, Germany
| | - David M Smith
- DNA Nanodevices Unit, Department Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, 04103 Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Sciences, University of Leipzig, 04103 Leipzig, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
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26
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Ortega-Pinazo J, Díaz T, Martínez B, Jiménez A, Pinto-Medel MJ, Ferro P. Quality assessment on the long-term cryopreservation and nucleic acids extraction processes implemented in the andalusian public biobank. Cell Tissue Bank 2019; 20:255-265. [PMID: 30903409 DOI: 10.1007/s10561-019-09764-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
Human samples are commonly collected and long-term stored in biobanks for current and future analyses. Even though techniques for freezing human blood are well established, the storage time can compromise the cell viability as well as the yield and quality of nucleic acids (RNA and DNA) extracted from them. In this study, a protocol to obtain peripheral blood mononuclear cells (PBMCs) from 70 subjects, which were stored at - 196 °C from EDTA tubes for a long-term, was assessed. In parallel; a protocol to obtain DNA from the same subjects, which were stored at - 80 °C from citrate tubes, was also studied. Samples stored from 2008 to 2012 were studied and the results obtained showed that there were no statistically significant differences in the RNA or DNA extracted in terms of purity, integrity and functionality The freezing protocol used by the Málaga Biobank shows that viable PBMCs and DNA could be kept for a period of, at least, 10 years, with a high quality and performance. Furthermore, RNA extracted from these PBMCs presents also a good quality and performance. Therefore, the samples frozen according to the conditions of the protocols assessed in this study could be optimal for biomedical research.
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Affiliation(s)
- J Ortega-Pinazo
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - M J Pinto-Medel
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain.
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Ribeiro RM, Souza-Basqueira MD, Oliveira LCD, Salles FC, Pereira NB, Sabino EC. An alternative storage method for characterization of the intestinal microbiota through next generation sequencing. Rev Inst Med Trop Sao Paulo 2018; 60:e77. [PMID: 30517247 PMCID: PMC6282504 DOI: 10.1590/s1678-9946201860077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota has been the subject of various molecular studies mainly due to its importance and wide-ranging relationships with human hosts. However, the storage of fecal samples prior to DNA extraction is critical when characterizing the composition of intestinal microbiota. Therefore, we aimed to understand the effects of different fecal storage methods to characterize intestinal microbiota using Next Generation Sequencing (NGS) as well as to establish an alternative conservation method of bacterial genetic material in these samples using guanidine. Stool samples from 10 healthy volunteers were collected. Each sample was divided into five aliquots: one aliquot was extracted immediately after collection (fresh) and two aliquots were subjected to freezing at -20 °C or -80 °C and extracted after 48 h. The other two aliquots were stored in guanidine at room temperature or 4 °C and extracted after 48 h. The V4 hypervariable regions of the bacterial and archeal 16S rRNA gene were amplified by PCR and sequenced using an Ion Torrent PGM platform for NGS. The data were analyzed using QIIME software. Statistical significance was determined using a non-parametric Kruskal-Wallis test. A total of 11,494,688 reads with acceptable quality were obtained. Unweighted principal coordinate analysis (PCoA) revealed that the samples were clustered based on the host rather than by the storage group. At the phylum and genus levels, we observed statistically significant differences between two genera, Proteobacteria (p=0.013) and Suterella (p=0.004), comparing frozen samples with guanidine-stored samples. Our data suggest that the use of guanidine can preserve bacterial genetic materials as well as freezing, providing additional conveniences.
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Affiliation(s)
- Roberto Marques Ribeiro
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Marcela de Souza-Basqueira
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Léa Campos de Oliveira
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Medicina Laboratorial (LIM 03), São Paulo, São Paulo, Brazil
| | - Flavia Cristina Salles
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Natalia Bueno Pereira
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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Müller HC, Van Bibber-Krueger CL, Ogunrinu OJ, Amachawadi RG, Scott HM, Drouillard JS. Effects of intermittent feeding of tylosin phosphate during the finishing period on feedlot performance, carcass characteristics, antimicrobial resistance, and incidence and severity of liver abscesses in steers. J Anim Sci 2018; 96:2877-2885. [PMID: 29718254 DOI: 10.1093/jas/sky166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/25/2018] [Indexed: 01/29/2023] Open
Abstract
Liver abscesses (LA) are a source of economic loss for feedlot cattle feedlots, and the 2017 veterinary feed directive has restricted further use of tylosin phosphate to prevention and control of LA. Our objective was to evaluate effects of intermittent tylosin phosphate feeding on incidence and severity of LA in feedlot cattle and presence of total antimicrobial-resistant Enterococcus spp. Steers (n = 312, 411.4 ± 6.71 kg) were blocked by initial BW and randomly assigned to a treatment group. Treatments included a negative control group (no tylosin phosphate throughout the finishing period), a positive control group (tylosin phosphate fed continuously throughout the finishing period), and a group that received tylosin phosphate off-label by feeding the drug on a repeated intermittent basis (1 wk on, 2 wk off). Steers were housed in 24 soil-surfaced pens with 13 steers per pen. Body weights of cattle were obtained every 28 d and at the end of 119 d the steers were weighed and harvested at a commercial abattoir. Fecal samples were collected on days 0, 21, and 118 to characterize antimicrobial-resistant Enterococcus spp. Total LA percentage was greater (P = 0.012) for the no tylosin phosphate treatment compared with the other treatments, but did not differ between the continuous tylosin phosphate treatment and the intermittently fed tylosin phosphate treatment (P = 0.716). No difference was observed among treatments for ADG (P = 0.21), DMI (P = 0.28), or G:F (P = 0.75). Marbling score was lower (P = 0.022) for tylosin phosphate treatment when compared with both intermittent treatment and continuous tylosin phosphate treatment. Enterococcus spp. bacterial counts did not differ by treatment group over time (P > 0.05); however, there was a strong period effect for macrolide resistance among all groups (P < 0.01), suggesting an important environmental component as cattle were first placed in pens and then progressed through the feeding period. We conclude that feeding tylosin phosphate intermittently during the finishing phase decreases the total percentage of LA and maintains feedlot performance and carcass characteristics to the same extent as feeding tylosin phosphate throughout the finishing phase; furthermore, we hypothesize that enteric antimicrobial resistance is a result of longer term antibiotic usage in a particular environment rather than a direct short-term result of the treatment during any given feeding period.
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Affiliation(s)
| | | | | | | | - H Morgan Scott
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - James S Drouillard
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS
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Liu LS, Gkranias N, Farias B, Spratt D, Donos N. Differences in the subgingival microbial population of chronic periodontitis in subjects with and without type 2 diabetes mellitus-a systematic review. Clin Oral Investig 2018; 22:2743-2762. [PMID: 30306333 DOI: 10.1007/s00784-018-2660-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The purpose of this systematic review was to evaluate the available evidence in the literature in regard to the subgingival microbial population of chronic periodontitis in subjects with type 2 diabetes mellitus (T2DM+PD) compared to non-diabetic subjects (NDM+PD). MATERIALS AND METHODS A literature search was conducted at Ovid MEDLINE and EMBASE database from 1980 to 2016, supplemented by hand searching as needed. Studies presenting with at least one of the primary outcomes (presence of any subgingival microorganisms, proportion and/or the amount of any subgingival plaque bacteria in T2DM+PD versus NDM+PD) were included. Screening, data extraction and quality assessment were conducted independently and in duplicate. RESULTS From 611 citations, 19 full-text papers were screened and 11 articles were included for critical appraisal by both reviewers. Some evidence of a difference in the microbial profile between chronic PD subjects with and without T2DM was identified. The strength of evidence is strongest in Tannerella forthysia (T .forsythia) which was reported to be less frequent in the diabetic (T2DM+PD) group in five of the studies, followed by a weaker strength of evidence for other periodontal pathogens such as Porphyromonas gingivalis (P. gingivalis) and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), which were also found less frequent in the diabetic (T2DM+PD) group . CONCLUSION Only few studies have compared T2DM+PD with NDM+PD. It is therefore strongly recommended that further studies which include four distinct groups of participants (NDM+PD, T2DM+PD, NDM+NPD, T2DM+NPD) instead of using intra-subject comparisons between healthy and diseased sites of the same subjects. CLINICAL RELEVANCE Differences in bacterial populations of T2DM+PD in comparison to NDM+PD subjects may indicate the need of different protocols for the treatment of the diabetic patients with periodontal disease.
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Affiliation(s)
- Linda Sun Liu
- Periodontology Unit, UCL Eastman Dental Institute, London, UK
| | - Nikolaos Gkranias
- Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), Turner Street, London, UK
| | - Bruna Farias
- Postgraduate Department, Federal University of Pernambuco, Recife, Brazil
| | - Dave Spratt
- Microbiology Department, UCL Eastman Dental Institute, London, UK
| | - Nikolaos Donos
- Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), Turner Street, London, UK.
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The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms. MICROMACHINES 2018; 9:mi9080367. [PMID: 30424300 PMCID: PMC6187716 DOI: 10.3390/mi9080367] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022]
Abstract
Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.
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Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA. Cancers (Basel) 2018; 10:cancers10060195. [PMID: 29891792 PMCID: PMC6025404 DOI: 10.3390/cancers10060195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/08/2018] [Accepted: 06/08/2018] [Indexed: 02/06/2023] Open
Abstract
Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability. The conservation of samples at room temperature (RT) by duplication can facilitate their protection. We describe a security system for the collection of non-small cell lung cancers (NSCLC) stored in the biobank of the Nice Hospital Center, France, by duplication and conservation of lyophilized (dried), encapsulated DNA kept at RT. Therefore, three frozen tissue collections from non-smoking, early stage and sarcomatoid carcinoma NSCLC patients were selected for this study. DNA was extracted, lyophilized and encapsulated at RT under anoxic conditions using the DNAshell technology. In total, 1974 samples from 987 patients were encapsulated. Six and two capsules from each sample were stored in the biobanks of the Nice and Grenoble (France) Hospitals, respectively. In conclusion, DNA maintained at RT allows for the conservation, duplication and durability of collections of interest stored in biobanks. This is a low-cost and safe technology that requires a limited amount of space and has a low environmental impact.
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The benefit of quality control charts (QCC) for routine quantitative BCR-ABL1 monitoring in chronic myeloid leukemia. PLoS One 2018; 13:e0196326. [PMID: 29689094 PMCID: PMC5916859 DOI: 10.1371/journal.pone.0196326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/11/2018] [Indexed: 11/23/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is state of the art in molecular monitoring of minimal residual disease in chronic myeloid leukemia (CML). In this context, maintenance of assay fidelity and detection of technical inaccuracy are crucial. Beside multiple common negative controls for the clinical sample preparations, quality control charts (QCC) are a common validation tool to sustain high process quality by continuously recording of qRT-PCR control parameters. Here, we report on establishment and benefit of QCC in qRT-PCR-based CML diagnostics. The absolute quantification of BCR-ABL1 fusion transcripts in patient samples is based on coamplification of a serially diluted reference plasmid (pME-2). For QCC establishment the measured Ct values of each pME-2 standard dilution (4–400,000) of a test set resembling 21 sequential qRT-PCR experiments were recorded and statistically evaluated. Test set data were used for determination of warning limits (mean +/- 2-fold standard deviation) and control (intervention) limits (mean +/- 3-fold standard deviation) to allow rapid detection of defined out-of-control situations which may require intervention. We have retrospectively analyzed QCC data of 282 sequential qRT-PCR experiments (564 reactions). Data evaluation using QCCs revealed three out-of-control situations that required intervention like experiment repeats, renewal of pME-2 standards, replacement of reagents or personnel re-training. In conclusion, with minimal more effort and hands-on time QCC rank among the best tools to grant high quality and reproducibility in CML routine molecular diagnosis.
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Abstract
Polymerase chain reaction (PCR) is an oft-used preparatory technique in amplifying specific DNA regions for downstream analysis. The size of an amplicon was initially limited by errors in nucleotide polymerization and template deterioration during thermal cycling. A variant of PCR, designated long-range PCR, was devised to counter these drawbacks and enable the amplification of large fragments exceeding a few kb. In this chapter we describe a protocol for long-range PCR, which we have adopted to obtain products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples.
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Affiliation(s)
- Eng Wee Chua
- Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia.
| | - Simran Maggo
- Department of Pathology and Carney Centre for Pharmacogenomics, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Carney Centre for Pharmacogenomics, University of Otago, Christchurch, New Zealand
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Dagnall CL, Hicks B, Teshome K, Hutchinson AA, Gadalla SM, Khincha PP, Yeager M, Savage SA. Effect of pre-analytic variables on the reproducibility of qPCR relative telomere length measurement. PLoS One 2017; 12:e0184098. [PMID: 28886139 PMCID: PMC5590866 DOI: 10.1371/journal.pone.0184098] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/17/2017] [Indexed: 12/17/2022] Open
Abstract
Telomeres, long nucleotide repeats and a protein complex at chromosome ends, shorten with each cell division and are susceptible to oxidative damage. Quantitative PCR (qPCR) is a widely-used technique to measure relative telomere length (RTL) in DNA samples but is challenging to optimize and significant lab-to-lab variability has been reported. In this study, we evaluated factors that may contribute to qPCR RTL measurement variability including DNA extraction methods, methods used for removing potential residual PCR inhibitors, sample storage conditions, and sample location in the PCR plate. Our results show that the DNA extraction and purification techniques, as well as sample storage conditions introduce significant variability in qPCR RTL results. We did not find significant differences in results based on sample location in the PCR plate or qPCR instrument used. These data suggest that lack of reproducibility in published association studies of RTL could be, in part, due to methodological inconsistencies. This study illustrates the importance of uniform sample handling, from DNA extraction through data generation and analysis, in using qPCR to determine RTL.
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Affiliation(s)
- Casey L. Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kedest Teshome
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Amy A. Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
| | - Payal P. Khincha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), Bethesda, Maryland, United States of America
- * E-mail:
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Huang D, Yan G, Skantar AM. Development of Real-Time and Conventional PCR Assays for Identifying Stubby Root Nematode Paratrichodorus allius. PLANT DISEASE 2017; 101:964-972. [PMID: 30682935 DOI: 10.1094/pdis-10-16-1431-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Paratrichodorus allius is an important pest on many crops, particularly on potato due to its ability to transmit Tobacco rattle virus causing corky ringspot disease on tubers. Detection and identification of P. allius are important for effective disease management. In this study, a rapid and reliable molecular diagnosis of this nematode targeting internal transcribed spacer ribosomal DNA was established. The specificity of the designed primers was evaluated using 29 nematode species and results showed that a single amplicon was produced from DNA of P. allius only. Detection sensitivity analysis indicated that a 9.6 × 10-4 ng of DNA template could be detected by conventional PCR and 1.92 × 10-4 ng of DNA by real-time PCR. The PCR assays amplified DNA of stubby root nematodes isolated from 18 soil samples in North Dakota and Minnesota, which were confirmed as P. allius by sequencing. Both conventional PCR and real-time PCR assays amplified target nematodes from complex nematode communities, supporting the success of this molecular diagnosis of P. allius. This is the first report of P. allius identification using the real-time PCR method and from nematode communities with other nematodes using conventional PCR. The new PCR assays provide rapid species identification and are suitable for use in diagnostic laboratories and detection of field infestations with P. allius.
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Affiliation(s)
- Danqiong Huang
- North Dakota State University, Department of Plant Pathology, Fargo 58102
| | - Guiping Yan
- North Dakota State University, Department of Plant Pathology, Fargo 58102
| | - Andrea M Skantar
- United States Department of Agriculture-Agricultural Research Service, Nematology Laboratory, Beltsville, MD 20705
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Karched M, Bhardwaj RG, Pauline EM, George S, Asikainen S. Effect of preparation method and storage period on the stability of saliva DNA. Arch Oral Biol 2017; 81:21-25. [PMID: 28460249 DOI: 10.1016/j.archoralbio.2017.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 02/13/2017] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
Saliva is an attractive source for oral microbial detection and quantification since sampling is non-invasive and rapid. OBJECTIVES To determine whether different saliva preparation methods or preservation time periods affect DNA stability. METHODS Saliva samples from 4 healthy adult volunteers were processed to obtain 3 different preparations: whole saliva, and after centrifugation pellet and supernatant. Purified DNA (MasterPure™) from each sample was divided into 4 aliquots, one for immediate analysis and 3 (stored at -80°C) for later analyses after 1 week and 2 and 6 months. DNA concentrations and qPCR based quantities of Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, Fusobacterium nucleatum, Filifactor alocis and Streptococcus mutans were determined. RESULTS DNA concentration did not decrease (P>0.05) during the 6-month period in any sample. Mean (SE) DNA concentrations (ng/μl) in whole saliva were 152.2 (51.2) and 147.8 (50) at day 0 and 6 months, respectively. Similarly, the values for pellet were 134.9 (42.5) and 133.6 (42.9), and for supernatant, 11 (1.9) and 8.9 (2.3), the difference being significant (P<0.001) between supernatant and whole saliva or pellet. The quantities of most bacterial species found at day 0 remained stable over the 6-month period in all saliva preparations. In supernatant, species quantities were lower (P<0.05) than in whole saliva or pellet. CONCLUSIONS DNA concentrations were comparable between whole saliva and pellet, suggesting that either of them can be used for DNA-based analyses. Our results also demonstrated that DNA extracted from saliva can be preserved at -80°C for at least 6 months without decrease in DNA concentration.
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Affiliation(s)
- Maribasappa Karched
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences, Faculty of Dentistry, Kuwait University, PO Box 24923, Safat 13110, Kuwait.
| | - Radhika G Bhardwaj
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences, Faculty of Dentistry, Kuwait University, PO Box 24923, Safat 13110, Kuwait
| | - Eunice M Pauline
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences, Faculty of Dentistry, Kuwait University, PO Box 24923, Safat 13110, Kuwait
| | - Swapna George
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences, Faculty of Dentistry, Kuwait University, PO Box 24923, Safat 13110, Kuwait
| | - Sirkka Asikainen
- Oral Microbiology Research Laboratory, Department of Bioclinical Sciences, Faculty of Dentistry, Kuwait University, PO Box 24923, Safat 13110, Kuwait
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Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, Dobbin KK, Alvarez J, Robbins PB, Selvan SR, Streicher HZ, Butterfield LH, Thurin M. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation. J Immunother Cancer 2016; 4:76. [PMID: 27895917 PMCID: PMC5109744 DOI: 10.1186/s40425-016-0178-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
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Affiliation(s)
- Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | | | - Rachael Hawtin
- Nodality, Inc, 170 Harbor Way, South San Francisco, 94080 CA USA
| | - Sylvia Janetzki
- ZellNet Consulting, Inc, 555 North Avenue, Fort Lee, 07024 NJ USA
| | - Jenny Zhang
- Covaris Inc, 14 Gill St, Woburn, MA 01801 USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, College of Public Health, The University of Georgia, 101 Buck Road, Athens, 30602 GA USA
| | - John Alvarez
- Janssen Research & Development, LLC, Spring House, PA 19477 USA
| | | | - Senthamil R Selvan
- Omni Array Biotechnology, 15601 Crabbs Branch Way, Rockville, 20855 MD USA
| | - Howard Z Streicher
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Magdalena Thurin
- National Cancer Institute, Cancer Diagnosis Program, DCTD, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA ; Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
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Evaluation of the performance of quantitative detection of the Listeria monocytogenes prfA locus with droplet digital PCR. Anal Bioanal Chem 2016; 408:7583-7593. [PMID: 27558101 PMCID: PMC5061835 DOI: 10.1007/s00216-016-9861-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/03/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
Abstract
Fast and reliable pathogen detection is an important issue for human health. Since conventional microbiological methods are rather slow, there is growing interest in detection and quantification using molecular methods. The droplet digital polymerase chain reaction (ddPCR) is a relatively new PCR method for absolute and accurate quantification without external standards. Using the Listeria monocytogenes specific prfA assay, we focused on the questions of whether the assay was directly transferable to ddPCR and whether ddPCR was suitable for samples derived from heterogeneous matrices, such as foodstuffs that often included inhibitors and a non-target bacterial background flora. Although the prfA assay showed suboptimal cluster formation, use of ddPCR for quantification of L. monocytogenes from pure bacterial cultures, artificially contaminated cheese, and naturally contaminated foodstuff was satisfactory over a relatively broad dynamic range. Moreover, results demonstrated the outstanding detection limit of one copy. However, while poorer DNA quality, such as resulting from longer storage, can impair ddPCR, internal amplification control (IAC) of prfA by ddPCR, that is integrated in the genome of L. monocytogenes ΔprfA, showed even slightly better quantification over a broader dynamic range. Evaluating the absolute quantification potential of ddPCR targeting Listeria monocytogenes prfA ![]()
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Payne DA, Baluchova K, Peoc'h KH, van Schaik RHN, Chan KCA, Maekawa M, Mamotte C, Russomando G, Rousseau F, Ahmad-Nejad P. Pre-examination factors affecting molecular diagnostic test results and interpretation: A case-based approach. Clin Chim Acta 2016; 467:59-69. [PMID: 27321365 DOI: 10.1016/j.cca.2016.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. METHODS The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. CONCLUSIONS The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics.
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Affiliation(s)
- Deborah A Payne
- Molecular Services, APP-UniPath LLC, American Pathology Partners-UniPath, 6116 East Warren Ave., Denver, CO, USA.
| | - Katarina Baluchova
- Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Biomedical Center Martin, Division of Oncology, Mala Hora 4C, 036 01 Martin, Slovakia; Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, Department of Molecular Biology, Mala Hora 4C, 036 01 Martin, Slovakia
| | - Katell H Peoc'h
- AP-HP Hôpital Beaujon, Service de Biochimie clinique, Clichy F-92118, France; Université Paris Diderot, UFR de Médecine site Bichat, INSERM UMRs-1149, Paris, France
| | - Ron H N van Schaik
- Department Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - K C Allen Chan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
| | - Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Cyril Mamotte
- School of Biomedical Sciences and CHIRI Biosciences, Curtin University, Perth, Australia
| | - Graciela Russomando
- Molecular Biology and Biotechnology Department, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay
| | - François Rousseau
- Department of Medical Biology, Direction médicale des services hospitaliers, CHU de Québec - Université Laval, Québec City, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, Canada
| | - Parviz Ahmad-Nejad
- Institute for Medical Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS Hospital, Heusnerstraße 40, 42283 Wuppertal, Witten/Herdecke University, Germany
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Madrigal RG, Shaw SD, Witkowski LA, Sisson BE, Blodgett GP, Chaffin MK, Cohen ND. Use of Serial Quantitative PCR of the vapA Gene of Rhodococcus equi in Feces for Early Detection of R. equi Pneumonia in Foals. J Vet Intern Med 2016; 30:664-70. [PMID: 26806422 PMCID: PMC4913589 DOI: 10.1111/jvim.13828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/13/2015] [Accepted: 12/16/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Current screening tests for Rhodococcus equi pneumonia in foals lack adequate accuracy for clinical use. Real-time, quantitative PCR (qPCR) for virulent R. equi in feces has not been systematically evaluated as a screening test. OBJECTIVE The objective of this study was to evaluate the accuracy of qPCR for vapA in serially collected fecal samples as a screening test for R. equi pneumonia in foals. ANIMALS One hundred and twenty-five foals born in 2011 at a ranch in Texas. METHODS Fecal samples were collected concurrently with thoracic ultrasonography (TUS) screening examinations at ages 3, 5, and 7 weeks. Affected (pneumonic) foals (n = 25) were matched by age and date-of-birth to unaffected (n = 25) and subclinical (ie, having thoracic TUS lesions but no clinical signs of pneumonia) foals (n = 75). DNA was extracted from feces using commercial kits and concentration of virulent R. equi in feces was determined by qPCR. RESULTS Subsequently affected foals had significantly greater concentrations of vapA in feces than foals that did not develop pneumonia (unaffected and subclinical foals) at 5 and 7 weeks of age. Accuracy of fecal qPCR, however, was poor as a screening test to differentiate foals that would develop clinical signs of pneumonia from those that would remain free of clinical signs (including foals with subclinical pulmonary lesions attributed to R. equi) using receiver operating characteristic (ROC) methods. CONCLUSIONS AND CLINICAL IMPORTANCE In the population studied, serial qPCR on feces lacked adequate accuracy as a screening test for clinical R. equi foal pneumonia.
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Affiliation(s)
- R G Madrigal
- Department of Large Animal Clinical Sciences, College of Biomedical Sciences and Veterinary Medicine, Texas A&M University, College Station, TX
| | - S D Shaw
- Department of Large Animal Clinical Sciences, College of Biomedical Sciences and Veterinary Medicine, Texas A&M University, College Station, TX
| | - L A Witkowski
- Laboratory of Veterinary Epidemiology and Economics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - B E Sisson
- Department of Large Animal Clinical Sciences, College of Biomedical Sciences and Veterinary Medicine, Texas A&M University, College Station, TX
| | | | - M K Chaffin
- Department of Large Animal Clinical Sciences, College of Biomedical Sciences and Veterinary Medicine, Texas A&M University, College Station, TX
| | - N D Cohen
- Department of Large Animal Clinical Sciences, College of Biomedical Sciences and Veterinary Medicine, Texas A&M University, College Station, TX
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Factors Affecting the Use of Human Tissues in Biomedical Research: Implications in the Design and Operation of a Biorepository. Methods Mol Biol 2016; 1381:1-38. [PMID: 26667452 DOI: 10.1007/978-1-4939-3204-7_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The availability of high-quality human tissues is necessary to advance medical research. Although there are inherent and induced limitations on the use of human tissues in research, biorepositories play critical roles in minimizing the effects of such limitations. Specifically, the optimal utilization of tissues in research requires tissues to be diagnosed accurately, and the actual specimens provided to investigators must be carefully described (i.e., there must be quality control of each aliquot of the tissue provided for research, including a description of any damage to tissues). Tissues also should be collected, processed, stored, and distributed (i.e., handled) uniformly under a rigorous quality management system (QMS). Frequently, tissues are distributed to investigators by tissue banks which have collected, processed, and stored them by standard operating procedures (SOPs). Alternatively, tissues for research may be handled via SOPs that are modified to the specific requirements of investigators (i.e., using a prospective biorepository model). The primary goal of any type of biorepository should be to ensure its specimens are of high quality and are utilized appropriately in research; however, approaches may vary based on the tissues available and requested. For example, extraction of specific molecules (e.g., microRNA) to study molecular characteristics of a tissue may require less clinical annotation than tissues that are utilized to identify how the molecular expression might be used to clarify a clinical outcome of a disease or the response to a specific therapy. This review focuses on the limitations of the use of tissues in research and how the design and operations of a tissue biorepository can minimize some of these limitations.
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Herrmann DC, Maksimov P, Hotop A, Groß U, Däubener W, Liesenfeld O, Pleyer U, Conraths FJ, Schares G. Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II. Int J Med Microbiol 2014; 304:911-6. [PMID: 25037927 DOI: 10.1016/j.ijmm.2014.06.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany.
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Affiliation(s)
- Daland C Herrmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Laboratory for Toxoplasmosis, Südufer 10, Greifswald-Insel Riems, Germany
| | - Pavlo Maksimov
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Laboratory for Toxoplasmosis, Südufer 10, Greifswald-Insel Riems, Germany
| | - Andrea Hotop
- German National Consulting Laboratory for Toxoplasmosis, Institute of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- German National Consulting Laboratory for Toxoplasmosis, Institute of Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Walter Däubener
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Oliver Liesenfeld
- Charité-Universitätsmedizin Berlin, Institute for Microbiology and Hygiene, Campus Benjamin Franklin, Berlin, Germany
| | - Uwe Pleyer
- Charité-Universitätsmedizin Berlin, Department of Ophthalmology, Campus Virchow Clinic, Berlin, Germany
| | - Franz J Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Laboratory for Toxoplasmosis, Südufer 10, Greifswald-Insel Riems, Germany
| | - Gereon Schares
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, National Reference Laboratory for Toxoplasmosis, Südufer 10, Greifswald-Insel Riems, Germany.
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Jumbri K, Abdul Rahman MB, Abdulmalek E, Ahmad H, Micaelo NM. An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies. Phys Chem Chem Phys 2014; 16:14036-46. [PMID: 24901033 DOI: 10.1039/c4cp01159g] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL-DNA could be used as a basis for future development of specific ILs for nucleic acid technology.
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Affiliation(s)
- K Jumbri
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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44
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Viljoen CD, Thompson GG, Sreenivasan S. Stability of ultramer as copy number standards in real-time PCR. Gene 2013; 516:143-5. [DOI: 10.1016/j.gene.2012.12.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/02/2012] [Indexed: 11/17/2022]
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Chandran A, Ghoshdastidar D, Senapati S. Groove binding mechanism of ionic liquids: a key factor in long-term stability of DNA in hydrated ionic liquids? J Am Chem Soc 2012. [PMID: 23181803 DOI: 10.1021/ja304519d] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid sample storage is of paramount importance in biotechnology and forensic sciences. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here, we employ molecular dynamics simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental results show that DNA maintains the native B-conformation in ILs. Simulation results further suggest that, apart from the electrostatic association of IL cations with the DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contributes significantly to DNA stability. Circular dichroism spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL ions were seen to disrupt the water cage around DNA, including the spine of hydration in the minor groove. This partial dehydration by ILs likely prevents the hydrolytic reactions that denature DNA and helps stabilize DNA for the long term. The detailed understanding of IL-DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acid solutes.
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Affiliation(s)
- Aneesh Chandran
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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46
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Johnson BJ, Melde BJ, Dinderman MA, Lin B. Stabilization of RNA through absorption by functionalized mesoporous silicate nanospheres. PLoS One 2012; 7:e50356. [PMID: 23226266 PMCID: PMC3511576 DOI: 10.1371/journal.pone.0050356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/24/2012] [Indexed: 11/29/2022] Open
Abstract
The potential for encapsulating RNA within tunable, semi-permeable structures for storage and transportation purposes offers an interesting approach to the reduction of stringent storage requirements that often hamper the field application of genetic analysis methods. In this study, we assessed the potential for application of functionalized, porous silicate sorbents in maintaining nucleic acid integrity. Mesoporous silica nanoparticles (MSNs) with and without incorporated stabilizing reagents were used to encapsulate triosephosphate isomerase mRNA of Arabidopsis thaliana. The absorption, elution, and the long-term stability of the RNA were monitored by using quantitative real-time RT-PCR. The results indicate that adsorbed RNA can be eluted from the sorbents using simple buffers and employed directly for downstream molecular diagnostic assays without any further processing. RNA integrity can be maintained for extended time periods under refrigeration temperatures in the presence of covalently immobilized stabilizing compounds. This study provides initial evidence of the potential for application of MSNs in transportation and storage. They may also have utility in sample collection and processing in restrictive environments.
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Affiliation(s)
| | | | | | - Baochuan Lin
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington D.C., United States of America
- * E-mail:
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47
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Vlčková K, Mrázek J, Kopečný J, Petrželková KJ. Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla). J Microbiol Methods 2012; 91:45-51. [DOI: 10.1016/j.mimet.2012.07.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
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Durdiaková J, Kamodyová N, Ostatníková D, Vlková B, Celec P. Comparison of different collection procedures and two methods for DNA isolation from saliva. Clin Chem Lab Med 2012; 50:643-7. [DOI: 10.1515/cclm.2011.814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe non-invasive, flexible and easy sample collection makes saliva an interesting source of DNA for research and diagnostic purposes. The aim of our study was to find the most suitable collection method for biological material from the oral cavity and the most effective DNA isolation technique for further analytic applications.DNA was isolated from swabs, Salivette saliva, whole saliva and samples collected with a commercial set for scraping of buccal cells. Phenol-chloroform extraction and isolation using a silica membrane based commercial kit were compared. Quantity of bacterial and human genomic DNA was estimated using real time PCR. The effects of storage conditions on DNA recovery were assessed.Sample collection techniques significantly affected the quantity of DNA for both, silica membrane based and phenol-chloroform isolations. Whole saliva provided the largest number of bacterial and human genome copies after both extraction methods. Storage for 36 months at –20°C reduced recovery of human genomic DNA five times after silica membrane based extraction and 10 times after phenol-chloroform isolation.Whole saliva was found to be the most suitable material for human and bacterial DNA isolation. Both compared methods are useful considering the quantity of extracted DNA.
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49
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Rossmanith P, Wagner M. The challenge to quantify Listeria monocytogenes--a model leading to new aspects in molecular biological food pathogen detection. J Appl Microbiol 2010; 110:605-17. [PMID: 21182577 DOI: 10.1111/j.1365-2672.2010.04915.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In this work, we discuss the latest insights concerning advantages and disadvantages and the nature of microbiological and molecular methods for quantitative food pathogen detection. The assessment of molecular methods must be brought on a basis that considers the nature of molecular methods and their underlying mechanism. A potential approach to setting up the development, validation and structure of an analytical chain is presented based on quantitative real-time PCR (qPCR). This is analysed exemplary on the basis of recent work using the model organism Listeria monocytogenes. Several prerequisites for successful quantitative detection of this pathogen will be discussed. In particular, sample preparation, controls for all methodical steps and the validation of the core assay qPCR are addressed, which constitute the basis for a reliable analytical detection chain for molecular biological pathogen detection from food. Microbiological methods are analysed based on growth of the single cell, which is the fundament of these traditional methods.
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Affiliation(s)
- P Rossmanith
- Christian Doppler Laboratory for Molecular Food Analytics, Vienna, Austria
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50
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Rossmanith P, Röder B, Frühwirth K, Vogl C, Wagner M. Mechanisms of degradation of DNA standards for calibration function during storage. Appl Microbiol Biotechnol 2010; 89:407-17. [PMID: 20967442 DOI: 10.1007/s00253-010-2943-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/07/2010] [Accepted: 10/09/2010] [Indexed: 02/06/2023]
Abstract
Establishment of molecular diagnostics offering quantitative technology is directly associated with real-time polymerase chain reaction (PCR). This rapid, accurate and sensitive method requires careful execution, including reliable calibration standards. The storage of such standards is crucial to prevent nucleic acid decay and to ensure stable results using real-time PCR. In this study, a broad investigation of possible causes of DNA degradation during storage was performed, including GC-content of the fragments, long-term storage, rapid freeze-and-thaw experiments, genomic DNA and short DNA fragments of different species, the influence of shear stress and the effect of nuclease remaining after DNA isolation. Several known chemical DNA degradation mechanisms have been matched with the experimental data through a process of elimination. Protocols for practical application, as well as a theoretical model describing the underlying mechanisms of deviation of real-time PCR results due to decay of standard DNA, have been developed. Primary amines in the buffer composition, which enhance depurination of the DNA helix, and shear stress due to ice crystal formation, could be identified as major sources of interaction. This results in degradation of the standard DNA, as well as in the probability of occurrence of mismatches affecting real-time PCR performance.
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Affiliation(s)
- Peter Rossmanith
- Christian Doppler Laboratory for Molecular Food Analytics, Veterinärplatz 1, 1210 Vienna, Austria.
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