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Li J, Ulloa GM, Mayor P, Santolalla Robles ML, Greenwood AD. Nucleic acid degradation after long-term dried blood spot storage. Mol Ecol Resour 2024; 24:e13979. [PMID: 38780145 DOI: 10.1111/1755-0998.13979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.
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Affiliation(s)
- Juan Li
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Gabriela M Ulloa
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- Grupo de Enfermedades Infecciosas Re-emergentes, Universidad Científica del Sur (UCSUR), Lima, Peru
| | - Pedro Mayor
- Programa de Pós-Graduação em Saúde e Produção Animal na Amazônia, Universidade Federal Rural da Amazônia (UFRA), Belém, Pará, Brazil
- ComFauna, Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica, Iquitos, Peru
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Meddly L Santolalla Robles
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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2
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Fonseca AA, Gonçalves VLDS, Barbosa AAS, Camargos MF. Use of FTA card for the detection of two RNA (CSFV and SV-A) and two DNA viruses (ASFVand SuHV-1) of importance in veterinary medicine. Braz J Microbiol 2024; 55:1961-1966. [PMID: 38589741 PMCID: PMC11153393 DOI: 10.1007/s42770-024-01309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
The FTA card has emerged as a promising alternative for nucleic acid extraction. The FTA card is a filter paper impregnated with chemicals that preserve and stabilize the genetic material present in the sample, allowing for its storage and transport at room temperature. The aim of this study was to test the card for the detection of RNA and DNA nucleic acids. Two RNA viruses (Senecavirus A and classical swine fever virus) and two DNA viruses (African swine fever virus and suid alphaherpesvirus 1) were tested, and in all cases, there was a decrease in sensitivity. The methods exhibited good repeatability and demonstrated a rapid and practical use for sample transport and nucleic acid extraction.
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3
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Si H, Tucciarone CM, Cecchinato M, Legnardi M, Mazzariol S, Centelleghe C. Comparison between Sampling Techniques for Virological Molecular Analyses: Dolphin Morbillivirus and Herpesvirus Detection from FTA ® Card and Frozen Tissue. Viruses 2023; 15:2422. [PMID: 38140663 PMCID: PMC10747605 DOI: 10.3390/v15122422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Stranded animals offer valuable information on marine mammal physiology and pathology; however, the decomposition state of the carcasses and lack of a rigorous cold chain for sample preservation can sometimes discourage diagnostic analyses based on nucleic acid detection. The present paper aims at evaluating the reliability of FTA® card tissue imprints as an alternative matrix to frozen tissues for virological analyses based on biomolecular methods. Given the contribution of Cetacean morbillivirus (CeMV) to strandings and the increase of herpesvirus detection in cetaceans, these two pathogens were selected as representative of RNA and DNA viruses. Dolphin morbillivirus (DMV) and herpesvirus presence was investigated in parallel on tissue imprints on FTA® cards and frozen tissues collected during necropsy of dolphins stranded in Italy. Samples were analysed by nested RT-PCR for DMV and nested-PCR for herpesvirus. Only one animal was positive for herpesvirus, hampering further considerations on this virus. DMV was detected in all animals, both in FTA® card imprints and tissue samples, with differences possibly related to the decomposition condition category of the carcasses. Tissue sampling on FTA® cards seems a promising alternative to frozen tissues for biomolecular analyses, especially when ensuring adequate storage and shipment conditions for frozen tissues is difficult.
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Affiliation(s)
- Haiyang Si
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Matteo Legnardi
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (H.S.); (M.C.); (M.L.)
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food Science (BCA), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (S.M.); (C.C.)
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food Science (BCA), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (S.M.); (C.C.)
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4
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Li W, Ma X, Yong YC, Liu G, Yang Z. Review of paper-based microfluidic analytical devices for in-field testing of pathogens. Anal Chim Acta 2023; 1278:341614. [PMID: 37709421 DOI: 10.1016/j.aca.2023.341614] [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: 03/11/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/16/2023]
Abstract
Pathogens cause various infectious diseases and high morbidity and mortality which is a global public health threat. The highly sensitive and specific detection is of significant importance for the effective treatment and intervention to minimise the impact. However, conventional detection methods including culture and molecular method gravely depend on expensive equipment and well-trained skilled personnel, limiting in the laboratory. It remains challenging to adapt in resource-limiting areas, e.g., low and middle-income countries (LMICs). To this end, low-cost, rapid, and sensitive detection tools with the capability of field testing e.g., a portable device for identification and quantification of pathogens, has attracted increasing attentions. Recently, paper-based microfluidic analytical devices (μPADs) have shown a promising tool for rapid and on-site diagnosis, providing a cost-effective and sensitive analytical approach for pathogens detection. The fast turn-round data collection may also contribute to better understanding of the risks and insights on mitigation method. In this paper, critical developments of μPADs for in-field detection of pathogens both for clinical diagnostics and environmental surveillance are reviewed. The future development, and challenges of μPADs for rapid and onsite detection of pathogens are discussed, including using the cross-disciplinary development with, emerging techniques such as deep learning and Internet of Things (IoT).
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Affiliation(s)
- Wenliang Li
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, Bedford, United Kingdom
| | - Xuanye Ma
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, Bedford, United Kingdom
| | - Yang-Chun Yong
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Guozhen Liu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, Bedford, United Kingdom.
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Reynolds J, Loeffler RS, Leigh PJ, Lopez HA, Yoon JY. Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests. BIOSENSORS 2023; 13:885. [PMID: 37754119 PMCID: PMC10526735 DOI: 10.3390/bios13090885] [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: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.
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Affiliation(s)
- Jocelyn Reynolds
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Reid S. Loeffler
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Preston J. Leigh
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Hannah A. Lopez
- Department of Neuroscience, The University of Arizona, Tucson, AZ 85721, USA;
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
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6
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Ranjan R, Biswal JK, Sahoo PK, Tripathy JP, Singh RP. Diagnostic application of formalin fixed archived tissues for detection of foot-and-mouth disease. J Virol Methods 2023:114754. [PMID: 37230193 DOI: 10.1016/j.jviromet.2023.114754] [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: 03/03/2023] [Revised: 05/01/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
Early and definitive disease diagnosis is critical for effective disease control. 50% buffered glycerine is commonly used viral transport medium, which is not always available and required cold chain. Tissues samples archived in 10% neutral buffered formalin (NBF) can preserve nucleic acid that can be used in molecular studies and disease diagnosis. The present study's goal was to detect the foot-and-mouth disease (FMD) viral genome in formalin-fixed archived tissue which may avoid cold chain during transportation. This study used FMD suspected samples preserved in 10% neutral buffered formalin from 0 to 730 days post fixation (DPF). All archived tissues were positive for FMD viral genome by multiplex RT-PCR and RT-qPCR up to 30 DPF, whereas archived epithelium tissues and thigh muscle were positive for FMD vial genome up to 120 DPF. FMD viral genome was detected in cardiac muscle up to 60 DPF and 120 DPF, respectively. The findings suggest that 10% neutral buffered formalin could be used for sample preservation and transportation for timely and accurate FMD diagnosis. More samples need to be tested before implementing the use of 10% neutral buffered formalin as a preservative and transportation medium. The technique may add value in ensuring biosafety measures for creation during disease free zone as well.
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Affiliation(s)
- Rajeev Ranjan
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India.
| | - Jitendra Kumar Biswal
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Prabin Kumar Sahoo
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Jagannath Prasad Tripathy
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
| | - Rabindra Prasad Singh
- ICAR-National Institute on Foot and Mouth Disease, International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar-752050, Odisha, India
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Rey Gomez LM, Hirani R, Care A, Inglis DW, Wang Y. Emerging Microfluidic Devices for Sample Preparation of Undiluted Whole Blood to Enable the Detection of Biomarkers. ACS Sens 2023; 8:1404-1421. [PMID: 37011238 DOI: 10.1021/acssensors.2c02696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Blood testing allows for diagnosis and monitoring of numerous conditions and illnesses; it forms an essential pillar of the health industry that continues to grow in market value. Due to the complex physical and biological nature of blood, samples must be carefully collected and prepared to obtain accurate and reliable analysis results with minimal background signal. Examples of common sample preparation steps include dilutions, plasma separation, cell lysis, and nucleic acid extraction and isolation, which are time-consuming and can introduce risks of sample cross-contamination or pathogen exposure to laboratory staff. Moreover, the reagents and equipment needed can be costly and difficult to obtain in point-of-care or resource-limited settings. Microfluidic devices can perform sample preparation steps in a simpler, faster, and more affordable manner. Devices can be carried to areas that are difficult to access or that do not have the resources necessary. Although many microfluidic devices have been developed in the last 5 years, few were designed for the use of undiluted whole blood as a starting point, which eliminates the need for blood dilution and minimizes blood sample preparation. This review will first provide a short summary on blood properties and blood samples typically used for analysis, before delving into innovative advances in microfluidic devices over the last 5 years that address the hurdles of blood sample preparation. The devices will be categorized by application and the type of blood sample used. The final section focuses on devices for the detection of intracellular nucleic acids, because these require more extensive sample preparation steps, and the challenges involved in adapting this technology and potential improvements are discussed.
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Affiliation(s)
| | - Rena Hirani
- Australian Red Cross Lifeblood, Sydney, New South Wales 2015, Australia
| | - Andrew Care
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - David W Inglis
- School of Engineering, Faculty of Science and Engineering and △School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
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8
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Abosrer F, Pezzoni G, Brocchi E, Castelli A, Baselli S, Grazioli S, Madani H, Kraim E, Dayhum A, Eldaghayes I. FTA Cards as a Rapid Tool for Collection and Transport of Infective Samples: Experience with Foot-and-Mouth Disease Virus in Libya. Animals (Basel) 2022; 12:ani12223198. [PMID: 36428427 PMCID: PMC9686888 DOI: 10.3390/ani12223198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/02/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a viral disease, widespread and highly contagious, that mainly affects cloven-hoofed domestic and wild animals. FMD can lead to high economic losses due to the reduction in animal production such as a drop in milk production, loss of body weight, and a high mortality rate in young ruminants. Sixteen samples were collected from animals showing typical clinical signs of FMD during the last FMD outbreak in Libya in 2018-2019. Flinders Technology Associates (FTA) cards impressed with blood, swabs, or vesicular epithelium samples were shipped to the WOAH FMD reference laboratory in Brescia, Italy, and tested for the detection of FMD viruses. Nucleic acids were extracted from the FTA cards, and molecular testing based on real-time RT-PCR assays was carried out, of which one was specifically designed for the detection of the FMD virus of serotype O, topotype O/East Africa-3 (O/EA-3), that was further confirmed by a sequence analysis of the VP1 gene. The phylogenetic analysis of the VP1 gene showed a nucleotide identity of more than 99% between the virus circulating in Libya and the FMD virus strains isolated in Algeria in 2019.
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Affiliation(s)
- Fadila Abosrer
- National Center for Animal Health, Tripoli P.O. Box 83252, Libya
- Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli, Tripoli P.O. Box 13662, Libya
| | - Giulia Pezzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
- Correspondence: (G.P.); (I.E.); Tel.: +39-030-2290614 (G.P.); +218-91-220-3195 (I.E.)
| | - Emiliana Brocchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Anna Castelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Stefano Baselli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Santina Grazioli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Hafsa Madani
- Institut National de la Médecine Vétérinaire, El Harrach, Alger P.O. Box 205, Algeria
| | - Elfurgani Kraim
- National Center for Animal Health, Tripoli P.O. Box 83252, Libya
| | - Abdunaser Dayhum
- Department of Preventive Medicine, Faculty of Veterinary Medicine, University of Tripoli, Tripoli P.O. Box 13662, Libya
| | - Ibrahim Eldaghayes
- Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli, Tripoli P.O. Box 13662, Libya
- Correspondence: (G.P.); (I.E.); Tel.: +39-030-2290614 (G.P.); +218-91-220-3195 (I.E.)
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9
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Zhou L, Lei Q, Guo J, Gao Y, Shi J, Yu H, Yin W, Cao J, Xiao B, Andreo J, Ettlinger R, Jeffrey Brinker C, Wuttke S, Zhu W. Long-term whole blood DNA preservation by cost-efficient cryosilicification. Nat Commun 2022; 13:6265. [PMID: 36270991 PMCID: PMC9587218 DOI: 10.1038/s41467-022-33759-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/30/2022] [Indexed: 12/25/2022] Open
Abstract
Deoxyribonucleic acid (DNA) is the blueprint of life, and cost-effective methods for its long-term storage could have many potential benefits to society. Here we present the method of in situ cryosilicification of whole blood cells, which allows long-term preservation of DNA. Importantly, our straightforward approach is inexpensive, reliable, and yields cryosilicified samples that fulfill the essential criteria for safe, long-term DNA preservation, namely robustness against external stressors, such as radical oxygen species or ultraviolet radiation, and long-term stability in humid conditions at elevated temperatures. Our approach could enable the room temperature storage of genomic information in book-size format for more than one thousand years (thermally equivalent), costing only 0.5 $/person. Additionally, our demonstration of 3D-printed DNA banking artefacts, could potentially allow 'artificial fossilization'.
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Affiliation(s)
- Liang Zhou
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Qi Lei
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Jimin Guo
- grid.266832.b0000 0001 2188 8502Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, NM 87131 USA
| | - Yuanyuan Gao
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Jianjun Shi
- grid.459319.30000 0001 0175 0741Science and Technology on Advanced Functional Composites Technology, Aerospace Research Institute of Materials & Processing Technology, Beijing, 100076 P. R. China
| | - Hong Yu
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Wenxiang Yin
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Jiangfan Cao
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Botao Xiao
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
| | - Jacopo Andreo
- grid.473251.60000 0004 6475 7301BCMaterials, Basque Center for Materials, UPV/EHU Science Park, 48940 Leioa, Spain
| | - Romy Ettlinger
- grid.11914.3c0000 0001 0721 1626School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom
| | - C. Jeffrey Brinker
- grid.266832.b0000 0001 2188 8502Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, NM 87131 USA
| | - Stefan Wuttke
- grid.473251.60000 0004 6475 7301BCMaterials, Basque Center for Materials, UPV/EHU Science Park, 48940 Leioa, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Wei Zhu
- grid.79703.3a0000 0004 1764 3838MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 P. R. China
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10
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Role of Paper-Based Sensors in Fight against Cancer for the Developing World. BIOSENSORS 2022; 12:bios12090737. [PMID: 36140122 PMCID: PMC9496559 DOI: 10.3390/bios12090737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Cancer is one of the major killers across the globe. According to the WHO, more than 10 million people succumbed to cancer in the year 2020 alone. The early detection of cancer is key to reducing the mortality rate. In low- and medium-income countries, the screening facilities are limited due to a scarcity of resources and equipment. Paper-based microfluidics provide a platform for a low-cost, biodegradable micro-total analysis system (µTAS) that can be used for the detection of critical biomarkers for cancer screening. This work aims to review and provide a perspective on various available paper-based methods for cancer screening. The work includes an overview of paper-based sensors, the analytes that can be detected and the detection, and readout methods used.
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11
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Resmi PE, Suneesh PV, Ramachandran T, Babu TGS. Paper based micro/nanofluidics devices for biomedical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:159-190. [PMID: 35033283 DOI: 10.1016/bs.pmbts.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This chapter details the significance, fabrication and biomedical applications of paper-based microfluidic devices. The first part of the chapter describes the importance of paper diagnostic devices, highlighting pretreatment, dipsticks, lateral flow assays, and microPADs. Various methods followed for the fabrication of the paper analytical devices are discussed in the second part. The last part is about some of the important biomedical applications of paper analytical devices. Finally, the challenges and research gaps in the paper microfluidics for biomedical applications are presented.
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Affiliation(s)
- P E Resmi
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - P V Suneesh
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India; Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - T Ramachandran
- Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - T G Satheesh Babu
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India; Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India.
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12
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Optimizing Release of Nucleic Acids of African Swine Fever Virus and Influenza A Virus from FTA Cards. Int J Mol Sci 2021; 22:ijms222312915. [PMID: 34884719 PMCID: PMC8657678 DOI: 10.3390/ijms222312915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 01/29/2023] Open
Abstract
FTA cards and related products simplify the collection, transport, and transient storage of biological sample fluids. Here, we have compared the yield and quality of DNA and RNA released from seven different FTA cards using seven releasing/extraction methods with eleven experimental eluates. For the validation, dilution series of African swine fever virus (ASFV) positive EDTA blood and Influenza A virus (IAV) positive allantoic fluid were used. Based on our data, we conclude that direct PCR amplification without the need for additional nucleic acid extraction and purification could be suitable and more convenient for ASFV DNA release from FTA cards. In contrast, IAV RNA loads can be amplified from FTA card punches if a standard extraction procedure including a lysis step is applied. These differences between the amplifiable viral DNA and RNA after releasing and extraction are not influenced by the type of commercial FTA card or the eleven different nucleic acid releasing procedures used for the comparative analyses. In general, different commercial FTA cards were successfully used for the storage and recovery of the ASFV and IAV genetic material suitable for PCR. Nevertheless, the usage of optimized nucleic acid releasing protocols could improve the recovery of the viral genome of both viruses. Here, the application of Chelex® Resin 100 buffer mixed with 1 × Tris EDTA buffer (TE, pH 8.0) or with TED 10 (TE buffer and Dimethylsulfoxid) delivered the best results and can be used as a universal method for releasing viral DNA and RNA from FTA cards.
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Jia Z, Han X, Tsuda K. An Efficient Method for DNA Purification-Free PCR from Plant Tissue. Curr Protoc 2021; 1:e289. [PMID: 34748285 DOI: 10.1002/cpz1.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amplification of genomic DNA fragments by PCR is necessary for plant molecular biology approaches such as genotyping. While this is a routine molecular technique in a modern laboratory, there are still significant hurdles when analyzing a large number of samples or collecting and storing samples while in the field. Because PCR amplification directly from plant tissue is often unsuccessful due to various inhibitors, genomic DNA purification is usually required, which involves laborious and time-consuming procedures or costly materials, particularly when using commercial kits. These undermine scalability and use in less-equipped settings. In addition, plant tissues and purified DNA need to be stored under proper conditions to avoid degradation. Here, we describe a low-cost, high-throughput PCR method to amplify genomic DNA fragments from plant tissue pounded to cellulose-based filter paper without the need for DNA purification or special equipment for sample storage. In this protocol, a small punch of plant tissue is pounded to a commercially available or homemade DNA storage card and directly placed into a PCR mixture containing Tween-20, a non-ionic detergent, directly followed by PCR. We also describe the steps to prepare a homemade DNA storage card, which is easy to make and can be stored with plant tissue at room temperature for a long time without any special equipment, allowing us to test the same sample multiple times. We have used this method in at least eleven plant species, including arabidopsis, tomato, soybean, potato, cotton, and rice. Altogether, our method decreases labor and cost, thereby increasing throughput and making plant DNA-based molecular diagnostic assays accessible to resource-limited settings, including classrooms, and facilitating sample collection in the field. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Making a homemade cellulose-based DNA storage card Basic Protocol 2: Pounding plant tissue on a DNA storage card Basic Protocol 3: DNA-purification free PCR.
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Affiliation(s)
- Zhengnan Jia
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaowei Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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Skeen HR, Cooper NW, Hackett SJ, Bates JM, Marra PP. Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird. Mol Ecol 2021; 30:5900-5916. [PMID: 34580952 DOI: 10.1111/mec.16170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 01/04/2023]
Abstract
Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.
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Affiliation(s)
- Heather R Skeen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Nathan W Cooper
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
| | - Shannon J Hackett
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - John M Bates
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, Washington, District of Columbia, USA
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15
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Alyethodi RR, Singh U, Kumar S, Alex R, Sengar GS, Raja TV, Deb R, Prakash B. Designing, optimization, and validation of whole blood direct T-ARMS PCR for precise and rapid genotyping of complex vertebral malformation in cattle. BMC Biotechnol 2021; 21:36. [PMID: 34022869 PMCID: PMC8141239 DOI: 10.1186/s12896-021-00696-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/11/2021] [Indexed: 12/04/2022] Open
Abstract
Background DNA testing in the cattle industry undergoes multiple hurdles. Successful genotyping involves the transportation of samples from the field to the laboratory in a chilled environment followed by DNA extraction, and finally, a specific genotyping protocol is followed. Various researches are focused on overcoming these issues. Microcards offer blood transportation at ambient temperature. Direct PCR methods can save the time of DNA extraction but available only for simplex PCR. Tetra Primer-Amplification Refractory Mutation System based Polymerase Chain Reaction (T-ARMS PCR) can make DNA testing faster in a low-cost setting. The present study was aimed to design, optimize, and validate a T-ARMS PCR for faster DNA testing of SNP responsible for Complex Vertebral Malformation (CVM)-an important genetic disease of the cattle industry. Further, a direct T-ARMS PCR from whole blood was developed to avoid the DNA extraction steps. Lastly, using the optimized protocol, genotyping of blood spotted on Microcard eliminates the need for cold chain maintenance in the transportation of samples. Results The present study demonstrated a novel T-ARMS PCR-based genotyping of the SNP rs438228855, which is responsible for CVM. Here, wild genotypes were recognized by 389 bp and 199 bp bands in agarose gel, while the carrier genotype showed an additional 241 bp band. The developed protocol was validated using PCR-Primer Introduced Restriction Analysis (PCR-PIRA) and sequencing. The present study further established a direct T-ARMS PCR for this SNP from whole blood. Different conditions such as heparin and EDTA treated blood, the need for pre-treatment, and two different DNA Polymerases for the direct PCR were optimized. Finally, our optimized protocol successfully genotyped the whole blood samples dried on Insta™DNA cards. Conclusions The present study reported the usefulness of primer modified T-ARMS PCR for detecting CVM for the first time. To the best of our knowledge, direct PCR in T-ARMS PCR has never been reported. Lastly, the use of microcards in the developed protocol can make the assay useful in the DNA testing of field samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00696-5.
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Affiliation(s)
- R R Alyethodi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Garacharma, Andaman and Nicobar Islands, 744101, India.
| | - U Singh
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Kumar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Alex
- Animal genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - G S Sengar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - T V Raja
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Deb
- ICAR-National Research centre on Pig, Guwahati, Assam, India
| | - B Prakash
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
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Long-Term Preservation and Storage of Faecal Samples in Whatman ® Cards for PCR Detection and Genotyping of Giardia duodenalis and Cryptosporidium hominis. Animals (Basel) 2021; 11:ani11051369. [PMID: 34065892 PMCID: PMC8151430 DOI: 10.3390/ani11051369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Preservation and conservation of biological specimens, including faecal samples, is a challenge in remote areas or poor-resource settings where the cold chain cannot be maintained. This study aims at evaluating the suitability of filter cards for long-term storage of faecal samples of animal and human origin positive to the diarrhoea-causing protozoan parasites, Giardia duodenalis and Cryptosporidium hominis. Three commercially available Whatman® Filter Cards were comparatively assessed: the FTA® Classic Card, the FTA® Elute Micro Card, and the 903 Protein Saver Card. Human faecal samples positive to G. duodenalis (n = 5) and C. hominis (n = 5) were used to impregnate the selected cards at given storage (1 month, 3 months, and 6 months) periods and temperature (-20 °C, 4 °C, and room temperature) conditions. Parasite DNA was detected by PCR-based methods. Sensitivity assays and quality control procedures to assess suitability for genotyping purposes were conducted. Overall, all three Whatman® cards were proven useful for the detection and molecular characterisation of G. duodenalis and C. hominis under the evaluated conditions. Whatman® cards represent a simple, safe, and cost-effective option for the transportation, preservation, and storage of faecal samples without the need of the cold chain.
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Shalaby AG, Bakry NR, Mohamed AAE, Khalil AA. Evaluating Flinders Technology Associates card for transporting bacterial isolates and retrieval of bacterial DNA after various storage conditions. Vet World 2020; 13:2243-2251. [PMID: 33281363 PMCID: PMC7704315 DOI: 10.14202/vetworld.2020.2243-2251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Flinders Technology Associates (FTA) cards simplify sample storage, transport, and extraction by reducing cost and time for diagnosis. This study evaluated the FTA suitability for safe transport and storage of Gram-positive and Gram-negative bacterial cells of animal origin on its liquid culture form and from organ impression smears (tissues) under the same routine condition of microbiological laboratory along with detecting their nucleic acid over different storage conditions. Materials and Methods: Increase in bacterial count from 104 to 107 (colony-forming units/mL) of 78 isolates representing seven bacterial species was applied onto cards. FTA cards were grouped and inoculated by these bacteria and then stored at different conditions of 24-27°C, 4°C, and −20°C for 24 h, for 2 weeks, for 1 and 3 month storage, respectively. Bacteriological examination was done, after which bacterial DNA was identified using specific primers for each bacterial type and detected by polymerase chain reaction (PCR). Results: The total percentage of recovered bacteria from FTA cards was 66.7% at 24-27°C for 24 h, the detection limit was 100% in Gram-positive species, while it was 57.4% in Gram-negative ones. Regarding viable cell detection from organ impression smears, it was successful under the previous conditions. No live bacterial cells were observed by bacteriological isolation rather than only at 24-27°C for 24 h storage. All bacterial DNA were sufficiently confirmed by the PCR technique at different conditions. Conclusion: Overall, the FTA card method was observed to be a valid tool for nucleic acid purification for bacteria of animal origin in the form of culture or organ smears regardless of its Gram type and is used for a short time only 24 h for storage and transport of live bacteria specifically Gram-positive type. Moreover, the bacterial nucleic acid was intact after storage in −20°C for 3 months and was PCR amplifiable.
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Affiliation(s)
- Azhar G Shalaby
- Department of Biotechnology Unit, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Centre, Dokki, Giza, Egypt
| | - Neveen R Bakry
- Department of Epidemiology Unit, Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Centre, Dokki, Giza, Egypt
| | - Abeer A E Mohamed
- Department of Buffalo Diseases, Animal Health Research Institute, Dokki, Giza, Egypt
| | - Ashraf A Khalil
- Institute of Biotechnology and Genetic Engineering, City of Scientific Research and Technology Applications, Borg Elarab, Alexandria, Egypt
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Deliorman M, Sukumar P, Alnemari R, Qasaimeh MA. A Method to Efficiently Cryopreserve Mammalian Cells on Paper Platforms. Bio Protoc 2020; 10:e3764. [PMID: 33659422 DOI: 10.21769/bioprotoc.3764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 01/11/2023] Open
Abstract
This protocol describes a simple method to cryopreserve mammalian cells within filter papers as an alternative to conventional slow-freezing approach. The method involves treating paper fibers with fibronectin, using low concentrations of the cryoprotectant dimethyl sulfoxide (DMSO), and slow freezing cells to -80 °C at a 1 °C min-1 rate. In our method, the biocompatibility, large surface area, 3D porosity and fiber flexibility of the paper, in combination with the fibronectin treatment, yield recovery of cells comparable to conventional approaches, with no additional fine-tuning to freezing and thawing procedures. We expect that the paper-based cryopreservation method will bring several advantages to the field of preserving mammalian cells, including accommodation of a higher number of cells within a unit volume and no cell loss after release. The method requires a minimal storage space, where paper platforms with large areas can be rolled and/or folded and stored in stocks, and allows for efficient transportation/distribution of cells in an on-demand manner. Moreover, an additional feature of this method includes the formation and cryopreservation of cellular spheroids and 3D cell cultures.
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Affiliation(s)
| | - Pavithra Sukumar
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Roaa Alnemari
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mohammad A Qasaimeh
- Division of Engineering, New York University Abu Dhabi, Abu Dhabi, UAE.,Department of Mechanical and Aerospace Engineering, New York University, New York, USA
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Jia B, Colling A, Stallknecht DE, Blehert D, Bingham J, Crossley B, Eagles D, Gardner IA. Validation of laboratory tests for infectious diseases in wild mammals: review and recommendations. J Vet Diagn Invest 2020; 32:776-792. [PMID: 32468923 DOI: 10.1177/1040638720920346] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Evaluation of the diagnostic sensitivity (DSe) and specificity (DSp) of tests for infectious diseases in wild animals is challenging, and some of the limitations may affect compliance with the OIE-recommended test validation pathway. We conducted a methodologic review of test validation studies for OIE-listed diseases in wild mammals published between 2008 and 2017 and focused on study design, statistical analysis, and reporting of results. Most published papers addressed Mycobacterium bovis infection in one or more wildlife species. Our review revealed limitations or missing information about sampled animals, identification criteria for positive and negative samples (case definition), representativeness of source and target populations, and species in the study, as well as information identifying animals sampled for calculations of DSe and DSp as naturally infected captive, free-ranging, or experimentally challenged animals. The deficiencies may have reflected omissions in reporting rather than design flaws, although lack of random sampling might have induced bias in estimates of DSe and DSp. We used case studies of validation of tests for hemorrhagic diseases in deer and white-nose syndrome in hibernating bats to demonstrate approaches for validation when new pathogen serotypes or genotypes are detected and diagnostic algorithms are changed, and how purposes of tests evolve together with the evolution of the pathogen after identification. We describe potential benefits of experimental challenge studies for obtaining DSe and DSp estimates, methods to maintain sample integrity, and Bayesian latent class models for statistical analysis. We make recommendations for improvements in future studies of detection test accuracy in wild mammals.
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Affiliation(s)
- Beibei Jia
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Axel Colling
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David E Stallknecht
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - David Blehert
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - John Bingham
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Beate Crossley
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Debbie Eagles
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
| | - Ian A Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada (Jia, Gardner).,CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (Colling, Bingham, Eagles).,Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA (Stallknecht).,U.S. Geological Survey, National Wildlife Health Center, Madison, WI (Blehert).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Crossley)
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Buxhofer-Ausch V, Ausch C, Reiner A, Müllner-Ammer K, Schmid A, Kriwanek S, Sebesta C, Halwachs-Baumann G, Kriegshäuser G. SFRP1 promotor methylation analysis of FTA card touch-prep samples derived from colonic polyps. Exp Mol Pathol 2020; 114:104397. [PMID: 32007530 DOI: 10.1016/j.yexmp.2020.104397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023]
Abstract
Whatman FTA® cards provide the most reliable method for DNA storage and extraction, however, the literature lacks reports on the epigenetic analysis of FTA card-derived tumor DNA. Therefore, this study aimed at demonstrating that punches from colonic adenoma samples preserved on FTA filter cards are suitable for methylation analysis by real-time methylation-specific PCR (MSP). Genomic DNA was isolated from a total of 40 sporadic colorectal adenoma samples stored on FTA cards for a median of 59.60 (range 48-72) months. After bisulfite treatment, deaminated DNA was analyzed by SYBR Green real-time MSP using primers specific for methylated and unmethylated promotor sequences of the secreted frizzled-related protein 1 (SFRP1) gene. Amplifiable DNA could be isolated from all FTA card punches while SFRP1 promotor methylation was present in 34/40 (85.0%) colorectal adenomas. Our results indicate that genomic DNA isolated from colonic tumor samples preserved on FTA cards is suitable for downstream methylation detection methodologies such as MSP even after prolonged storage periods.
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Affiliation(s)
- Veronika Buxhofer-Ausch
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Ordensklinikum Linz Elisabethinen, Linz, Austria; Medical Faculty, Johannes Kepler University Linz, Austria
| | - Christoph Ausch
- Department of Surgery, Hospital Göttlicher Heiland, Austria.
| | - Angelika Reiner
- Department of Pathology, Donauspital, Vienna - SMZO, Austria
| | | | - Alfons Schmid
- Department of Internal Medicine 2, Donauspital - SMZO, Vienna, Austria
| | | | - Christian Sebesta
- Department of Internal Medicine 2, Donauspital - SMZO, Vienna, Austria
| | | | - Gernot Kriegshäuser
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital, Steyr, Austria; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University, Graz, Austria
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22
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West FL, Algee-Hewitt BF. Cadaveric blood cards: Assessing DNA quality and quantity and the utility of STRs for the individual estimation of trihybrid ancestry and admixture proportions. Forensic Sci Int Synerg 2020; 2:114-122. [PMID: 32412010 PMCID: PMC7219121 DOI: 10.1016/j.fsisyn.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/04/2023]
Abstract
As part a body donation program, blood samples were collected and stored on untreated (non-FTA) blood cards. The blood cards were evaluated in terms of DNA preservation and STR typing success with resulting profiles assessed with special consideration given to profile matching for positive identification and biogeographic ancestry estimation. While STR profiles were successfully generated for all samples, results indicate that the time interval between date of death and sample collection have an impact on DNA quantity and quality. There is a statistically significant decrease in relative fluorescent unit (RFU) values with increasing time interval between date of death and sample collection, indicating degradation in the blood card samples related to the post-mortem interval prior to sample collection. The STR profiles were used to estimate ancestry and admixture using the program STRUCTURE, demonstrating utility of these markers beyond individual identification purposes, with caveats for application based on population history.
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Affiliation(s)
- Frankie L. West
- Forensic Science Program, Western Carolina University, USA
- Corresponding author.
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Carnt NA, Cipriani V, Stapleton FJ, Calder V, Willcox MD. Association study of single nucleotide polymorphisms in IL-10 and IL-17 genes with the severity of microbial keratitis. Cont Lens Anterior Eye 2019; 42:658-661. [DOI: 10.1016/j.clae.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/19/2019] [Accepted: 06/25/2019] [Indexed: 01/20/2023]
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Caza F, Joly de Boissel PG, Villemur R, Betoulle S, St-Pierre Y. Liquid biopsies for omics-based analysis in sentinel mussels. PLoS One 2019; 14:e0223525. [PMID: 31581216 PMCID: PMC6776352 DOI: 10.1371/journal.pone.0223525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transcriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in mussels to assess the quality of aquatic ecosystems.
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Affiliation(s)
- France Caza
- INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | | | | | - Stéphane Betoulle
- Université Reims Champagne-Ardenne, UMR-I 02 SEBIO, Stress environnementaux et Biosurveillance des milieux aquatiques, Reims, France
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Wu SG, Pan W, Liu H, Byrne-Steele ML, Brown B, Depinet M, Hou X, Han J, Li S. High throughput sequencing of T-cell receptor repertoire using dry blood spots. J Transl Med 2019; 17:47. [PMID: 30777078 PMCID: PMC6379990 DOI: 10.1186/s12967-019-1796-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/09/2019] [Indexed: 11/12/2022] Open
Abstract
Background Immunology research, particularly next generation sequencing (NGS) of the immune T-cell receptor β (TCRβ) repertoire, has advanced progression in several fields, including treatment of various cancers and autoimmune diseases. This study aimed to identify the TCR repertoires from dry blood spots (DBS), a method that will help collecting real-world data for biomarker applications. Methods Finger-prick blood was collected onto a Whatman filter card. RNA was extracted from DBS of the filter card, and fully automated multiplex PCR was performed to generate a TCRβ chain library for next generation sequencing (NGS) analysis of unique CDR3s (uCDR3). Results We demonstrated that the dominant clonotypes from the DBS results recapitulated those found in whole blood. According to the statistical analysis and laboratory confirmation, 40 of 2-mm punch disks from the filter cards were enough to detect the shared top clones and have strong correlation in the uCDR3 discovery with whole blood. uCDR3 discovery was neither affected by storage temperatures (room temperature versus − 20 °C) nor storage durations (1, 14, and 28 days) when compared to whole blood. About 74–90% of top 50 uCDR3 clones of whole blood could also be detected from DBS. A low rate of clonotype sharing, 0.03–1.5%, was found among different individuals. Conclusions The DBS-based TCR repertoire profiling method is minimally invasive, provides convenient sampling, and incorporates fully automated library preparation. The system is sensitive to low RNA input, and the results are highly correlated with whole blood uCDR3 discovery allowing study scale-up to better understand the relationship and mutual influences between the immune and diseases. Electronic supplementary material The online version of this article (10.1186/s12967-019-1796-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shang-Gin Wu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, 10002, Taiwan.,Department of Internal Medicine, National Taiwan University Cancer Center, National Taiwan University, Taipei, 10672, Taiwan
| | - Wenjing Pan
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.,iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Hongna Liu
- iCubate Inc., Huntsville, AL, 35806, USA
| | | | - Brittany Brown
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Mollye Depinet
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Xiaohong Hou
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA. .,iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA.
| | - Song Li
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA.
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