1
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Zhang W, Jiao Y, Zhang Z, Zhang Y, Yu J, Gu Z. Transdermal gene delivery. J Control Release 2024; 371:516-529. [PMID: 38849095 DOI: 10.1016/j.jconrel.2024.06.013] [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] [Received: 02/28/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Gene delivery has revolutionized conventional medical approaches to vaccination, cancer, and autoimmune diseases. However, current gene delivery methods are limited to either intravenous administration or direct local injections, failing to achieve well biosafety, tissue targeting, drug retention, and transfection efficiency for desired therapeutic outcomes. Transdermal drug delivery based on various delivery strategies can offer improved therapeutic potential and superior patient experiences. Recently, there has been increased foundational and clinical research focusing on the role of the transdermal route in gene delivery and exploring its impact on the efficiency of gene delivery. This review introduces the recent advances in transdermal gene delivery approaches facilitated by drug formulations and medical devices, as well as discusses their prospects.
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Affiliation(s)
- Wentao Zhang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Jiao
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziru Zhang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuqi Zhang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Department of Burns and Wound Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jicheng Yu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Jinhua Institute of Zhejiang University, Jinhua 321299, China.
| | - Zhen Gu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, Key Laboratory for Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Jinhua Institute of Zhejiang University, Jinhua 321299, China; MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China.
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2
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Chung J, Billante A, Flatebo C, Leung KK, Gerson J, Emmons N, Kippin TE, Sepunaru L, Plaxco KW. Effects of storage conditions on the performance of an electrochemical aptamer-based sensor. SENSORS & DIAGNOSTICS 2024; 3:1044-1050. [PMID: 38882472 PMCID: PMC11170682 DOI: 10.1039/d4sd00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 06/18/2024]
Abstract
The electrochemical aptamer-based (EAB) sensor platform is the only molecular monitoring approach yet reported that is (1) real time and effectively continuous, (2) selective enough to deploy in situ in the living body, and (3) independent of the chemical or enzymatic reactivity of its target, rendering it adaptable to a wide range of analytes. These attributes suggest the EAB platform will prove to be an important tool in both biomedical research and clinical practice. To advance this possibility, here we have explored the stability of EAB sensors upon storage, using retention of the target recognizing aptamer, the sensor's signal gain, and the affinity of the aptamer as our performance metrics. Doing so we find that low-temperature (-20 °C) storage is sufficient to preserve sensor functionality for at least six months without the need for exogenous preservatives.
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Affiliation(s)
- Julia Chung
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Adriana Billante
- Department of Chemistry and Biochemistry, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Charlotte Flatebo
- Institute for Collaborative Biotechnologies, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Kaylyn K Leung
- Department of Chemistry and Biochemistry, University of California Santa Barbara Santa Barbara California 93106 USA
- Center for Bioengineering, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Julian Gerson
- Center for Bioengineering, University of California Santa Barbara Santa Barbara California 93106 USA
- Department of Psychological and Brain Sciences, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Nicole Emmons
- Center for Bioengineering, University of California Santa Barbara Santa Barbara California 93106 USA
- Department of Psychological and Brain Sciences, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Tod E Kippin
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara Santa Barbara California 93106 USA
- Department of Psychological and Brain Sciences, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Lior Sepunaru
- Department of Chemistry and Biochemistry, University of California Santa Barbara Santa Barbara California 93106 USA
| | - Kevin W Plaxco
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara Santa Barbara California 93106 USA
- Department of Chemistry and Biochemistry, University of California Santa Barbara Santa Barbara California 93106 USA
- Institute for Collaborative Biotechnologies, University of California Santa Barbara Santa Barbara California 93106 USA
- Center for Bioengineering, University of California Santa Barbara Santa Barbara California 93106 USA
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3
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [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: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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4
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Pali-Schöll I, Hermuth-Kleinschmidt K, Dramburg S, Agache I, Mayerhofer H, Jensen-Jarolim E, Goshua A, Nadeau KC. An EAACI review: Go green in health care and research. Practical suggestions for sustainability in clinical practice, laboratories, and scientific meetings. Allergy 2023; 78:2606-2622. [PMID: 37584433 PMCID: PMC10543587 DOI: 10.1111/all.15836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/10/2023] [Accepted: 07/22/2023] [Indexed: 08/17/2023]
Abstract
Health care professionals (HCPs) and researchers in the health care sector dedicate their professional life to maintaining and optimizing the health of their patients. To achieve this, significant amounts of resources are used and currently it is estimated that the health care sector contributes to more than 4% of net greenhouse gas (GHG) emissions. GHG emissions adversely impact planetary health and consequently human health, as the two are intricately linked. There are many factors of health care that contribute to these emissions. Hospitals and research labs also use high amounts of consumables which require large amounts of raw materials and energy to produce. They are further responsible for polluting the environment via disposal of plastics, drug products, and other chemicals. To maintain and develop state-of-the-art best practices and treatments, medical experts exchange and update their knowledge on methods and technologies in the respective fields at highly specialized scientific meetings. These meetings necessitate thousands of attendants traveling around the globe. Therefore, while the goal of HCPs is to care for the individual, current practices have an enormous (indirect) impact on the health of the patients by their negative environmental impacts. There is an urgent need for HCPs and researchers to mitigate these detrimental effects. The installation of a sustainability-manager at health care facilities and research organizations to implement sustainable practices while still providing quality health care is desirable. Increased use of telemedicine, virtual/hybrid conferences and green chemistry have recently been observed. The benefits of these practices need to be evaluated and implemented as appropriate. With this manuscript, we aim to increase the awareness about the negative impacts of the health care system (including health care research) on planetary and human health. We suggest some easy and highly impactful steps and encourage health care professionals and research scientists of all hierarchical levels to immediately implement them in their professional as well as private life to counteract the health care sector's detrimental effects on the environment.
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Affiliation(s)
- Isabella Pali-Schöll
- The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna Austria
- Institute of Pathophysiology and Allergy Research; Center of Physiology, Pathophysiology and Immunology; Medical University Vienna, Vienna Austria
| | | | - Stephanie Dramburg
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité Universitätsmedizin – Berlin, Berlin, Germany
| | - Ioana Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania
| | - Hanna Mayerhofer
- The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna Austria
- Institute of Pathophysiology and Allergy Research; Center of Physiology, Pathophysiology and Immunology; Medical University Vienna, Vienna Austria
| | - Erika Jensen-Jarolim
- The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna Austria
- Institute of Pathophysiology and Allergy Research; Center of Physiology, Pathophysiology and Immunology; Medical University Vienna, Vienna Austria
| | - Anna Goshua
- Stanford University School of Medicine, Stanford, CA
| | - Kari C. Nadeau
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA
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5
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Buko T, Tuczko N, Ishikawa T. DNA Data Storage. BIOTECH 2023; 12:44. [PMID: 37366792 DOI: 10.3390/biotech12020044] [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: 04/20/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.
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Affiliation(s)
- Tomasz Buko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Nella Tuczko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
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6
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Lizak A, Szweda R. Czy plastik może rozpocząć nową erę w archiwizacji danych? ARCHEION 2022. [DOI: 10.4467/26581264arc.22.014.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of information technology, many aspects of our lives are undergoing a digital transformation. An increasing number of users are going online every year, and constantly improving artificial intelligence is gaining popularity, which leads to the growing production of information. Nowadays, information is usually stored in data centres, which will be forced to increase their space with the constant flow of new bits of information. Together with the increase in their space, energy consumption and associated maintenance costs are escalating. In 2021, global data centre power consumption was 220–320 TWh, which is about 0.9–1.3% of global power consumption. Continuous power supply for database operations is responsible for about 1% of total carbon dioxide emissions. Furthermore, it has already been reported that with the exponentially growing amount of data, in about 20 years, the amount of silicon for microprocessors will no longer be sufficient to store all the information. Therefore, scientists are looking for alternatives to the currently used data storage solutions and are developing new technologies using chemical molecules. Recently, even plastic has been explored as a data carrier. In this work, we present examples of new technologies for data storage in polymers. We have discussed polymers as data carriers in comparison with currently used solutions and deliberated whether plastic can become a future material for information archiving.
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7
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Butterwort V, Dansby H, Zink FA, Tembrock LR, Gilligan TM, Godoy A, Braswell WE, Kawahara AY. A DNA Extraction Method for Insects From Sticky Traps: Targeting a Low Abundance Pest, Phthorimaea absoluta (Lepidoptera: Gelechiidae), in Mixed Species Communities. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:844-851. [PMID: 35391487 DOI: 10.1093/jee/toac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Invasive insects can cause catastrophic damage to ecosystems and cost billions of dollars each year due to management expenses and lost revenue. Rapid detection is an important step to prevent invasive insects from spreading, but improvements in detection capabilities are needed for bulk collections like those from sticky traps. Here we present a bulk DNA extraction method designed for the detection of Phthorimaea absoluta Meyrick (Lepidoptera: Gelechiidae), an invasive moth that can decimate tomato crops. We test the extraction method for insect specimens on sticky traps, subjected to different temperature and humidity conditions, and among mock insect communities left in the field for up to 21 d. We find that the extraction method yielded high success (>92%) in recovering target DNA across field and lab trials, without a decline in recovery after three weeks, across all treatments. These results may have a large impact on tomato growing regions where P. absoluta is in the early stages of invasion or not yet present. The extraction method can also be used to improve detection capabilities for other bulk insect collections, especially those using sticky traps, to the benefit of pest surveys and biodiversity studies.
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Affiliation(s)
- V Butterwort
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
| | - H Dansby
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
| | - F A Zink
- Department of Agricultural Biology, 1177 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - L R Tembrock
- Department of Agricultural Biology, 1177 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - T M Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, 2301 Research Boulevard, Suite 108, Fort Collins, CO 80526, USA
| | - A Godoy
- USDA-APHIS-PPQ-Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorfield Road, Building 6414, Edinburg, TX 78541, USA
| | - W E Braswell
- USDA-APHIS-PPQ-Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorfield Road, Building 6414, Edinburg, TX 78541, USA
| | - A Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32511, USA
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8
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Ezekannagha C, Becker A, Heider D, Hattab G. Design considerations for advancing data storage with synthetic DNA for long-term archiving. Mater Today Bio 2022; 15:100306. [PMID: 35677811 PMCID: PMC9167972 DOI: 10.1016/j.mtbio.2022.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/05/2022] [Accepted: 05/22/2022] [Indexed: 11/22/2022]
Abstract
Deoxyribonucleic acid (DNA) is increasingly emerging as a serious medium for long-term archival data storage because of its remarkable high-capacity, high-storage-density characteristics and its lasting ability to store data for thousands of years. Various encoding algorithms are generally required to store digital information in DNA and to maintain data integrity. Indeed, since DNA is the information carrier, its performance under different processing and storage conditions significantly impacts the capabilities of the data storage system. Therefore, the design of a DNA storage system must meet specific design considerations to be less error-prone, robust and reliable. In this work, we summarize the general processes and technologies employed when using synthetic DNA as a storage medium. We also share the design considerations for sustainable engineering to include viability. We expect this work to provide insight into how sustainable design can be used to develop an efficient and robust synthetic DNA-based storage system for long-term archiving.
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Affiliation(s)
- Chisom Ezekannagha
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
- Corresponding author.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, D-35043, Marburg, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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9
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Zhou Z, Zhang S, Yang G, Gao Y. Enhanced delivery efficiency and sustained release of biopharmaceuticals by complexation-based gel encapsulated coated microneedles: rhIFNα-1b example. Asian J Pharm Sci 2021; 16:612-622. [PMID: 34849166 PMCID: PMC8609446 DOI: 10.1016/j.ajps.2021.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/06/2021] [Accepted: 05/22/2021] [Indexed: 02/07/2023] Open
Abstract
Coated microneedles (MNs) are widely used for delivering biopharmaceuticals. In this study, a novel gel encapsulated coated MNs (GEC-MNs) was developed. The water-soluble drug coating was encapsulated with sodium alginate (SA) in situ complexation gel. The manufacturing process of GEC-MNs was optimized for mass production. Compared to the water-soluble coated MNs (72.02% ± 11.49%), the drug delivery efficiency of the optimized GEC-MNs (88.42% ± 6.72%) was steadily increased, and this improvement was investigated through in vitro drug release. The sustained-release of BSA was observed in vitro permeation through the skin. The rhIFNα-1b GEC-MNs was confirmed to achieve biosafety and 6-month storage stability. Pharmacokinetics of rhIFNα-1b in GEC-MNs showed a linearly dose-dependent relationship. The AUC of rhIFNα-1b in GEC-MNs (4.51 ng/ml·h) was bioequivalent to the intradermal (ID) injection (5.36 ng/ml·h) and significantly higher than water-soluble coated MNs (3.12 ng/ml·h). The rhIFNα-1b elimination half-life of GEC-MNs, soluble coated MNs, and ID injection was 18.16, 1.44, and 2.53 h, respectively. The complexation-based GEC-MNs have proved to be more efficient, stable, and achieve the sustained-release of water-soluble drug in coating MNs, constituting a high value to biopharmaceutical.
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Affiliation(s)
- Zequan Zhou
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suohui Zhang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,Beijing CAS Microneedle Technology Ltd, Beijing 102609, China
| | - Guozhong Yang
- Beijing CAS Microneedle Technology Ltd, Beijing 102609, China
| | - Yunhua Gao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Beijing CAS Microneedle Technology Ltd, Beijing 102609, China
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10
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Bennet D, Vo‐Dinh T, Zenhausern F. Current and emerging opportunities in biological medium‐based computing and digital data storage. NANO SELECT 2021. [DOI: 10.1002/nano.202100275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Devasier Bennet
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
| | - Tuan Vo‐Dinh
- Department of Biomedical Engineering Department of Chemistry Fitzpatrick Institute for Photonics Duke University Durham North Carolina USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
- Department of Basic Medical Sciences College of Medicine Phoenix The University of Arizona Phoenix Arizona USA
- Department of Biomedical Engineering; and BIO5 Institute College of Engineering The University of Arizona Tucson Arizona USA
- School of Pharmaceutical Sciences University of Geneva Geneva Switzerland
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11
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Tran TT, Yegoraw AA, Assen AM, Walkden-Brown SW, Gerber PF. Genomic Stability for PCR Detection of Infectious Laryngotracheitis Virus and Infectious Bronchitis Virus in Poultry Dust Samples Stored Under Different Conditions. Avian Dis 2021; 64:565-570. [PMID: 33647150 DOI: 10.1637/0005-2086-64.4.565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/12/2020] [Indexed: 11/05/2022]
Abstract
Dust collected from the poultry house has been increasingly used as a population-level sample to monitor the presence of pathogens or to evaluate the administration of live vaccines. However, there are no guidelines for the storage of this sample type. This study investigated the stability of infectious laryngotracheitis virus (ILTV), a DNA virus, and infectious bronchitis virus (IBV), an RNA virus, in poultry dust kept under temperature and moisture conditions that mimic on-farm and laboratory storage. Dust samples were collected from chicks spray vaccinated with a live IBV vaccine and inoculated with a field ILTV strain via eye drop. Samples were stored under different moisture conditions (dry = 2% moisture, moist = 22%-71% moisture) and temperatures (-20, 4, 25, and 37 C) for different durations (0, 7, and 14 days, and 1, 2, 3, and 4 mo) in a factorial arrangement, followed by quantitative PCR for detection of virus genome copies (GC). The length of storage, moisture level, and storage temperature affected the viral genome load for ILTV and IBV but did not affect the number of positive samples for each virus. All treatment combinations were ILTV positive for at least 4 mo. In dry dust samples, all storage temperatures or durations had quantifiable ILTV or IBV GC. Moisture addition had a detrimental effect on viral genome load, causing an overall reduction of 0.3 log 10 for ILTV GC (7.29 and 6.97 log 10, P = 0.0001), and 1.3 log 10 for IBV GC (5.95 and 4.66 log 10, P = 0.0001), which are unlikely to have biologic significance. In conclusion, dry dust can be stored at any temperature up to 37 C for at least 4 mo without loss in qPCR detection of ILTV or IBV GC. Collection or storage of moist dust should be avoided, or air drying prior to storage is recommended if only moist dust is available.
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Affiliation(s)
- Thanh T Tran
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia, 2351.,Faculty of Animal Sciences and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Addisu A Yegoraw
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia, 2351.,School of Veterinary Medicine, Wolaita Sodo University, Wolaita Sodo, Ethiopia
| | - Awol M Assen
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia, 2351.,School of Veterinary Medicine, Wollo University, Dessie, Ethiopia
| | - Stephen W Walkden-Brown
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia, 2351
| | - P F Gerber
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia, 2351
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12
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Xu C, Zhao C, Ma B, Liu H. Uncertainties in synthetic DNA-based data storage. Nucleic Acids Res 2021; 49:5451-5469. [PMID: 33836076 PMCID: PMC8191772 DOI: 10.1093/nar/gkab230] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/16/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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13
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Organick L, Nguyen BH, McAmis R, Chen WD, Kohll AX, Ang SD, Grass RN, Ceze L, Strauss K. An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage. SMALL METHODS 2021; 5:e2001094. [PMID: 34928102 DOI: 10.1002/smtd.202001094] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Indexed: 05/25/2023]
Abstract
Synthetic DNA has recently risen as a viable alternative for long-term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper, nine different methods used to preserve data files encoded in synthetic DNA are evaluated by accelerated aging of nearly 29 000 DNA sequences. In addition to a molecular count comparison, the DNA is also sequenced and analyzed after aging. These findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, the physical density of these methods is compared and a stability versus density trade-offs discussion provided.
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Affiliation(s)
- Lee Organick
- University of Washington, Paul G. Allen School of Computer Science and Engineering, Seattle, WA, 98195, USA
| | - Bichlien H Nguyen
- University of Washington, Paul G. Allen School of Computer Science and Engineering, Seattle, WA, 98195, USA
- Microsoft Research, Redmond, WA, 98052, USA
| | - Rachel McAmis
- University of Washington, Paul G. Allen School of Computer Science and Engineering, Seattle, WA, 98195, USA
| | - Weida D Chen
- ETH Zurich, Institute for Chemical and Bioengineering, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | - A Xavier Kohll
- ETH Zurich, Institute for Chemical and Bioengineering, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | | | - Robert N Grass
- ETH Zurich, Institute for Chemical and Bioengineering, Vladimir-Prelog-Weg 1, Zurich, 8093, Switzerland
| | - Luis Ceze
- University of Washington, Paul G. Allen School of Computer Science and Engineering, Seattle, WA, 98195, USA
| | - Karin Strauss
- University of Washington, Paul G. Allen School of Computer Science and Engineering, Seattle, WA, 98195, USA
- Microsoft Research, Redmond, WA, 98052, USA
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14
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Rowe AK, Donohue ME, Clare EL, Drinkwater R, Koenig A, Ridgway ZM, Martin LD, Nomenjanahary ES, Zakamanana F, Randriamanandaza LJ, Rakotonirina TE, Wright PC. Exploratory analysis reveals arthropod consumption in 10 lemur species using DNA metabarcoding. Am J Primatol 2021; 83:e23256. [PMID: 33818786 DOI: 10.1002/ajp.23256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Arthropods (insects, spiders, etc.) can fulfill major nutritional requirements for primates, particularly in terms of proteins, fats, vitamins, and minerals. Yet, for many primate species we know very little about the frequency and importance of arthropod consumption. Traditional methods for arthropod prey identification, such as behavioral observations and fecal dissections, offer limited taxonomic resolution and, as a result, underestimate true diversity. Metabarcoding arthropod DNA from primate fecal samples provides a promising but underused alternative. Here, we inventoried arthropod prey diversity in wild lemurs by sequencing two regions of the CO1 gene. Samples were collected opportunistically from 10 species of lemurs inhabiting three national parks in southern Madagascar using a combination of focal animal follows and live trapping. In total, we detected arthropod DNA in 98 of the 170 fecal samples analyzed. Although all lemur species included in these analyses showed evidence of arthropod consumption, those within the family Cheirogaleidae appeared to consume the highest frequency and diversity of arthropods. To our knowledge, this study presents the first evidence of arthropod consumption in Phaner pallescens, Avahi peyrierasi, and Propithecus verreauxi, and identifies 32 families of arthropods as probable food items that have not been published as lemur dietary items to date. Our study emphasizes the importance of arthropods as a nutritional source and the role DNA metabarcoding can play in elucidating an animal's diet.
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Affiliation(s)
- Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Andreas Koenig
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, Stony Brook University, Stony Brook, New York, USA
| | - Zachary M Ridgway
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - Luke D Martin
- School of Archaeology and Anthropology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eva S Nomenjanahary
- Department of Biological Anthropology, University of Antananarivo, Antananarivo, Madagascar
| | | | | | | | - Patricia C Wright
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, Stony Brook University, Stony Brook, New York, USA
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15
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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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16
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Matange K, Tuck JM, Keung AJ. DNA stability: a central design consideration for DNA data storage systems. Nat Commun 2021; 12:1358. [PMID: 33649304 PMCID: PMC7921107 DOI: 10.1038/s41467-021-21587-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Abstract
Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.
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Affiliation(s)
- Karishma Matange
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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17
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Tan X, Ge L, Zhang T, Lu Z. Preservation of DNA for data storage. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The preservation of DNA has attracted significant interest of scientists in diverse research fields from ancient biological remains to the information field. In light of the different DNA safekeeping requirements (e.g., storage time, storage conditions) in these disparate fields, scientists have proposed distinct methods to maintain the DNA integrity. Specifically, DNA data storage is an emerging research, which means that the binary digital information is converted to the sequences of nucleotides leading to dense and durable data storage in the form of synthesized DNA. The intact preservation of DNA plays a significant role because it is closely related to data integrity. This review discusses DNA preservation methods, aiming to confirm an appropriate one for synthetic oligonucleotides in DNA data storage. First, we analyze the impact factors of the DNA long-term storage, including the intrinsic stability of DNA, environmental factors, and storage methods. Then, the benefits and disadvantages of diverse conservation approaches (e.g., encapsulation-free, chemical encapsulation) are discussed. Finally, we provide advice for storing non-genetic information in DNA in vitro. We expect these preservation suggestions to promote further research that may extend the DNA storage time.
The bibliography includes 99 references.
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18
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Oosting T, Hilario E, Wellenreuther M, Ritchie PA. DNA degradation in fish: Practical solutions and guidelines to improve DNA preservation for genomic research. Ecol Evol 2020; 10:8643-8651. [PMID: 32884647 PMCID: PMC7452763 DOI: 10.1002/ece3.6558] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/26/2020] [Accepted: 06/10/2020] [Indexed: 12/02/2022] Open
Abstract
The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol >99.5%) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making samples unsuitable for next-generation sequencing. Here, we conclude that DESS was the most promising solution when storing samples for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing sample preservation protocols and provides both practical and economical advice to improve DNA preservation when sampling for genome-wide applications.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant & Food Research LtdAucklandNew Zealand
| | - Maren Wellenreuther
- Nelson Seafood Research UnitThe New Zealand Institute for Plant & Food Research LtdNelsonNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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19
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Dong Y, Sun F, Ping Z, Ouyang Q, Qian L. DNA storage: research landscape and future prospects. Natl Sci Rev 2020; 7:1092-1107. [PMID: 34692128 PMCID: PMC8288837 DOI: 10.1093/nsr/nwaa007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/06/2020] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.
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Affiliation(s)
- Yiming Dong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fajia Sun
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qi Ouyang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Long Qian
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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20
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Abstract
Molecular data storage is an attractive alternative for dense and durable information storage, which is sorely needed to deal with the growing gap between information production and the ability to store data. DNA is a clear example of effective archival data storage in molecular form. In this Review, we provide an overview of the process, the state of the art in this area and challenges for mainstream adoption. We also survey the field of in vivo molecular memory systems that record and store information within the DNA of living cells, which, together with in vitro DNA data storage, lie at the growing intersection of computer systems and biotechnology.
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Affiliation(s)
- Luis Ceze
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Karin Strauss
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.,Microsoft Research, Redmond, WA, USA
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21
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deWaard JR, Ratnasingham S, Zakharov EV, Borisenko AV, Steinke D, Telfer AC, Perez KHJ, Sones JE, Young MR, Levesque-Beaudin V, Sobel CN, Abrahamyan A, Bessonov K, Blagoev G, deWaard SL, Ho C, Ivanova NV, Layton KKS, Lu L, Manjunath R, McKeown JTA, Milton MA, Miskie R, Monkhouse N, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Radulovici AE, Steinke C, Warne CP, Hebert PDN. A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples. Sci Data 2019; 6:308. [PMID: 31811161 PMCID: PMC6897906 DOI: 10.1038/s41597-019-0320-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 01/08/2023] Open
Abstract
The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.
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Affiliation(s)
- Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Alex V Borisenko
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Angela C Telfer
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kate H J Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Monica R Young
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Crystal N Sobel
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie L deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Kara K S Layton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Jaclyn T A McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Megan A Milton
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Norm Monkhouse
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Connor P Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
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22
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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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23
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Colin B, Deprez B, Couturier C. High-Throughput DNA Plasmid Transfection Using Acoustic Droplet Ejection Technology. SLAS DISCOVERY 2018; 24:492-500. [PMID: 30290128 DOI: 10.1177/2472555218803064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Labcyte Echo acoustic liquid handler allows accurate droplet ejection at high speed from a source well plate to a destination plate. It has already been used in various miniaturized biological assays, such as quantitative PCR (q-PCR), quantitative real-time PCR (q-RT-PCR), protein crystallization, drug screening, cell dispensing, and siRNA transfection. However, no plasmid DNA transfection assay has been published so far using this dispensing technology. In this study, we evaluated the ability of the Echo 550 device to perform plasmid DNA transfection in 384-well plates. Due to the high throughput of this device, we simultaneously optimized the three main parameters of a transfection process: dilution of the transfection reagent, DNA amount, and starting DNA concentration. We defined a four-step protocol whose optimal settings allowed us to transfect HeLa cells with up to 90% efficiency and reach a co-expression of nearly 100% within transfected cells in co-transfection experiments. This fast, reliable, and automated protocol opens new ways to easily and rapidly identify optimal transfection settings for a given cell type. Furthermore, it permits easy software-based transfection control and multiplexing of plasmids distributed on wells of a source plate. This new development could lead to new array applications, such as human ORFeome protein expression or CRISPR-Cas9-based gene function validation in nonpooled screening strategies.
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Affiliation(s)
- Béatrice Colin
- 1 Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, Lille, France
| | - Benoit Deprez
- 1 Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, Lille, France
| | - Cyril Couturier
- 1 Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, Lille, France
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24
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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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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. MICROBIOME 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Miernyk KM, DeByle CK, Rudolph KM. Evaluation of Two Matrices for Long-Term, Ambient Storage of Bacterial DNA. Biopreserv Biobank 2017; 15:529-534. [PMID: 29130748 DOI: 10.1089/bio.2017.0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Culture-independent molecular analyses allow researchers to identify diverse microorganisms. This approach requires microbiological DNA repositories. The standard for DNA storage is liquid nitrogen or ultralow freezers. These use large amounts of space, are costly to operate, and could fail. Room temperature DNA storage is a viable alternative. In this study, we investigated storage of bacterial DNA using two ambient storage matrices, Biomatrica DNAstable® Plus and GenTegra® DNA. METHODS We created crude and clean DNA extracts from five Streptococcus pneumoniae isolates. Extracts were stored at -30°C (our usual DNA storage temperature), 25°C (within the range of temperatures recommended for the products), and 50°C (to simulate longer storage time). Samples were stored at -30°C with no product and dried at 25°C and 50°C with no product, in Biomatrica DNAstable Plus or GenTegra DNA. We analyzed the samples after 0, 1, 2, 4, 8, 16, 32, and 64 weeks using the Nanodrop 1000 to determine the amount of DNA in each aliquot and by real-time PCR for the S. pneumoniae genes lytA and psaA. Using a 50°C storage temperature, we simulated 362 weeks of 25°C storage. RESULTS The average amount of DNA in aliquots stored with a stabilizing matrix was 103%-116% of the original amount added to the tubes. This is similar to samples stored at -30°C (average 102%-121%). With one exception, samples stored with a stabilizing matrix had no change in lytA or psaA cycle threshold (Ct) value over time (Ct range ≤2.9), similar to samples stored at -30°C (Ct range ≤3.0). Samples stored at 25°C with no stabilizing matrix had Ct ranges of 2.2-5.1. CONCLUSION DNAstable Plus and GenTegra DNA can protect dried bacterial DNA samples stored at room temperature with similar effectiveness as at -30°C. It is not effective to store bacterial DNA at room temperature without a stabilizing matrix.
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Affiliation(s)
- Karen M Miernyk
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
| | - Carolynn K DeByle
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
| | - Karen M Rudolph
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
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Schmidt O, Hausmann A, Cancian de Araujo B, Sutrisno H, Peggie D, Schmidt S. A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys). Biodivers Data J 2017; 5:e20006. [PMID: 29134041 PMCID: PMC5676197 DOI: 10.3897/bdj.5.e20006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).
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Affiliation(s)
- Olga Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Axel Hausmann
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | | | - Hari Sutrisno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djunijanti Peggie
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Stefan Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
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Li Q, Wang X, Liu X, Liao Q, Sun J, He X, Yang T, Yin J, Jia J, Li X, Colotte M, Bonnet J. Long-Term Room Temperature Storage of Dry Ribonucleic Acid for Use in RNA-Seq Analysis. Biopreserv Biobank 2017; 15:502-511. [PMID: 29022740 DOI: 10.1089/bio.2017.0024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
RNA is an essential biological material for research in genomics and translational medicine. As such, its storage for biobanking is an important field of study. Traditionally, long-term storage in the cold (generally freezers or liquid nitrogen) is used to maintain high-quality (in terms of quantity and integrity) RNA. Room temperature (RT) preservation provides an alternative to the cold, which is plagued by serious problems (mainly cost and safety), for RNA long-term storage. In this study, we evaluated the performance of several RT storage procedures, including the RNAshell® from Imagene, where the RNA is dried and kept protected from the atmosphere, and the vacuum drying of RNA with additives such as the Imagene stabilization solution and a home-made trehalose solution. This evaluation was performed through accelerated (equivalent to 10 years for RNAshell) aging and real-time studies (4 years). To check RNA quality and integrity, we used RNA integrity number values and RNA-seq. Our study shows that isolation from atmosphere offers a superior protective effect for RNA storage compared with vacuum drying alone, and demonstrates that RNAshell permits satisfactory RNA quality for long-term RT storage. Thus, the RNA quality could meet the demand of downstream applications such as RNA-seq.
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Affiliation(s)
- Qiyuan Li
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaopan Liu
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiuyan Liao
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jia Jia
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Marthe Colotte
- 2 Imagene, Production Platform , Rue Henri Desbruères, Evry, France
| | - Jacques Bonnet
- 3 Institut Bergonié, Université de Bordeaux , Bordeaux, France .,4 Imagene, R&D Department, Université de Bordeaux , ENSTBB, Bordeaux, France
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Huang LH, Lin PH, Tsai KW, Wang LJ, Huang YH, Kuo HC, Li SC. The effects of storage temperature and duration of blood samples on DNA and RNA qualities. PLoS One 2017; 12:e0184692. [PMID: 28926588 PMCID: PMC5604973 DOI: 10.1371/journal.pone.0184692] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/29/2017] [Indexed: 11/21/2022] Open
Abstract
DNA and RNA samples from blood are the common examination target for non-invasive physical tests and/or biomedical studies. Since high-quality DNA and RNA samples guarantee the correctness of these tests and/or studies, we investigated the effects of storage temperature and storage duration of whole blood on DNA and RNA qualities. Subjects were enrolled to donate blood samples which were stored for different durations and at different temperatures, followed by the examinations on RNA quality, qPCR, DNA quality and DNA methylation. For RNA, we observed obvious quality decline with storage duration longer than 24 hours. Storage at low temperature does not keep RNA samples from degradation. And, storing whole blood samples in freezer dramatically damage RNA. For DNA, quality decline was not observed even with storage duration for 15 days. However, DNA methylation significantly altered with storage duration longer than three days. Storage duration within 24 hours is critical for collecting high-quality RNA samples for next-generation sequencing (NGS) assays (RIN≧8). If microarray assays are expected (RIN≧7), storage duration within 32 hours is acceptable. Although DNA is resistant within 15 days when kept in whole blood, DNA quantity dramatically decreases owing to WBC lysis. In addition, duration for more than three days significantly alter DNA methylation status, globally and locally. Our result provides a reference for dealing with blood samples.
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Affiliation(s)
- Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Hsien Lin
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Liang-Jen Wang
- Department of Child and Adolescent Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ying-Hsien Huang
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
- Department of Pediatrics, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ho-Chang Kuo
- Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
- * E-mail: (HCK); (SCL)
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
- * E-mail: (HCK); (SCL)
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Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp. J Microbiol Methods 2016; 127:68-73. [DOI: 10.1016/j.mimet.2016.05.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 11/18/2022]
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Muller R, Betsou F, Barnes MG, Harding K, Bonnet J, Kofanova O, Crowe JH. Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community. Biopreserv Biobank 2016; 14:89-98. [DOI: 10.1089/bio.2015.0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | | | - Keith Harding
- Damar Research Scientists, Damar, Cupar Muir, United Kingdom
| | - Jacques Bonnet
- Imagene, Genopole Campus 1, Evry, France
- Université de Bordeaux Segalen, Institut Bergonié, Bordeaux, France
| | - Olga Kofanova
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | - John H. Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, California
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Zhirnov V, Zadegan RM, Sandhu GS, Church GM, Hughes WL. Nucleic acid memory. NATURE MATERIALS 2016; 15:366-70. [PMID: 27005909 PMCID: PMC6361517 DOI: 10.1038/nmat4594] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Nucleic acid memory has a retention time far exceeding electronic memory. As an alternative storage media, DNA surpasses the information density and energy of operation offered by flash memory.
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Affiliation(s)
- Victor Zhirnov
- Semiconductor Research Corporation, 1101 Slater Road, Durham, North Carolina 27703, USA
| | - Reza M Zadegan
- Department of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725-2090, USA
| | - Gurtej S Sandhu
- Micron Technology, Inc., PO Box 6, 8000 South Federal Way, Boise, Idaho 83707-0006, USA
| | - George M Church
- Department of Genetics, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - William L Hughes
- Department of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725-2090, USA
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Kashiwagi T, Maxwell EA, Marshall AD, Christensen AB. Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success. PeerJ 2015; 3:e1188. [PMID: 26413431 PMCID: PMC4581770 DOI: 10.7717/peerj.1188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 07/23/2015] [Indexed: 12/04/2022] Open
Abstract
Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.
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Affiliation(s)
- Tom Kashiwagi
- Molecular Fisheries Laboratory, University of Queensland , St. Lucia, QLD , Australia ; Marine Megafauna Foundation , Truckee, CA , USA ; Current affiliation: Center for Fisheries, Aquaculture and Aquatic Sciences, Southern Illinois University Carbondale , Carbondale, IL , USA
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Ellervik C, Vaught J. Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking. Clin Chem 2015; 61:914-34. [DOI: 10.1373/clinchem.2014.228783] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Abstract
BACKGROUND
Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized medicine for diagnostic or prognostic purposes.
CONTENT
The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues.
SUMMARY
The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
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Affiliation(s)
- Christina Ellervik
- Department of Research, Nykoebing Falster Hospital, Nykoebing Falster, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA
| | - Jim Vaught
- International Society for Biological and Environmental Repositories, Vancouver, Canada
- Editor-in-Chief, Biopreservation and Biobanking, Vancouver, Canada
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Dauner AL, Gilliland TC, Mitra I, Pal S, Morrison AC, Hontz RD, Wu SJL. Evaluation of nucleic acid stabilization products for ambient temperature shipping and storage of viral RNA and antibody in a dried whole blood format. Am J Trop Med Hyg 2015; 93:46-53. [PMID: 25940193 PMCID: PMC4497903 DOI: 10.4269/ajtmh.15-0110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 11/07/2022] Open
Abstract
Loss of sample integrity during specimen transport can lead to false-negative diagnostic results. In an effort to improve upon the status quo, we used dengue as a model RNA virus to evaluate the stabilization of RNA and antibodies in three commercially available sample stabilization products: Whatman FTA Micro Cards (GE Healthcare Life Sciences, Pittsburgh, PA), DNAstāble Blood tubes (Biomātrica, San Diego, CA), and ViveST tubes (ViveBio, Alpharetta, GA). Both contrived and clinical dengue-positive specimens were stored on these products at ambient temperature or 37°C for up to 1 month. Antibody and viral RNA levels were measured by enzyme-linked immunosorbent assay (ELISA) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays, respectively, and compared with frozen unloaded controls. We observed reduced RNA and antibody levels between stabilized contrived samples and frozen controls at our earliest time point, and this was particularly pronounced for the FTA cards. However, despite some time and temperature dependent loss, a 94.6-97.3% agreement was observed between stabilized clinical specimens and their frozen controls for all products. Additional considerations such as cost, sample volume, matrix, and ease of use should inform any decision to incorporate sample stabilization products into a diagnostic testing workflow. We conclude that DNAstāble Blood and ViveST tubes are useful alternatives to traditional filter paper for ambient temperature shipment of clinical specimens for downstream molecular and serological testing.
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Affiliation(s)
| | | | | | - Subhamoy Pal
- *Address correspondence to Subhamoy Pal, Viral and Rickettsial Diseases Department, Naval Medical Research Center, Building 17, Suite 2B, NSA Bethesda, MD 20889. E-mail:
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Zhou J, Wu J, Zhao X, Shen W, Liu X, Xu C, Jin H. Biostorage and Quality Control for Human Peripheral Blood Leukocytes. Biopreserv Biobank 2015; 13:13-9. [PMID: 25686042 DOI: 10.1089/bio.2014.0094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jiayi Zhou
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Jing Wu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Xiaoyan Zhao
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
| | - Weihong Shen
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Xiaoyan Liu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Congjian Xu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
| | - Hongyan Jin
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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Evaluation of DNA/RNAshells for Room Temperature Nucleic Acids Storage. Biopreserv Biobank 2015; 13:49-55. [DOI: 10.1089/bio.2014.0060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Udtha M, Flores R, Sanner J, Nomie K, Backes E, Wilbers L, Caldwell J. The Protection and Stabilization of Whole Blood at Room Temperature. Biopreserv Biobank 2014; 12:332-6. [DOI: 10.1089/bio.2014.0026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Malini Udtha
- Department of Nursing Systems, The University of Texas Health Science Center at Houston School of Nursing, Houston, Texas
| | - Rene Flores
- Department of Research Compliance, Integrity, and Education, The University of Texas Health Science Center at Houston School of Nursing, Houston, Texas
| | - Jennifer Sanner
- Department of Nursing Systems, The University of Texas Health Science Center at Houston School of Nursing, Houston, Texas
| | - Krystle Nomie
- Department of Nursing Systems, The University of Texas Health Science Center at Houston School of Nursing, Houston, Texas
| | - Elizabeth Backes
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, Missouri
| | - Luke Wilbers
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, Missouri
| | - James Caldwell
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, Missouri
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Willows-Munro S, Schoeman MC. Influence of killing method on Lepidoptera DNA barcode recovery. Mol Ecol Resour 2014; 15:613-8. [PMID: 25229871 DOI: 10.1111/1755-0998.12331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022]
Abstract
The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study, we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). Previous studies have suggested that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and as such may not be appropriate for the collection of insects for DNA-based research. All Lepidoptera collected produced DNA barcodes of good quality, and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis.
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Affiliation(s)
- Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa
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Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW, de Bruyn M. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 2014; 29:358-67. [DOI: 10.1016/j.tree.2014.04.003] [Citation(s) in RCA: 515] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/07/2023]
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do Nascimento C, dos Santos JN, Pedrazzi V, Pita MS, Monesi N, Ribeiro RF, de Albuquerque RF. Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA–DNA hybridization method. Arch Oral Biol 2014; 59:12-21. [DOI: 10.1016/j.archoralbio.2013.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/16/2013] [Accepted: 10/15/2013] [Indexed: 11/29/2022]
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