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Sbruzzi RC, Feira MF, Cadore NA, Giudicelli GC, Kowalski TW, Gregianini TS, Chies JAB, Vianna FSL. An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. Biopreserv Biobank 2024; 22:166-173. [PMID: 37579075 DOI: 10.1089/bio.2022.0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.
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Affiliation(s)
- Renan C Sbruzzi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariléa F Feira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nathan A Cadore
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
| | - Thayne W Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - José A B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Tuwo M, Kuswinanti T, Nasruddin A, Tambaru E. Uncovering the presence of CVPD disease in citrus varieties of South Sulawesi, Indonesia: A molecular approach. J Genet Eng Biotechnol 2024; 22:100332. [PMID: 38494243 PMCID: PMC10980848 DOI: 10.1016/j.jgeb.2023.100332] [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: 03/19/2024]
Abstract
BACKGROUND The citrus vein phloem degeneration (CVPD) disease is one of important diseases that infects citrus plants and threatens global citrus production and quality due to its severe symptoms and rapid spread. In the 2000s, South Sulawesi Province as one of the citrus producers in Indonesia reported CVPD infection. To date, it is still uncertain as to whether the citrus production center has already been rid of the CVPD infection, keeping in mind the low prevalence of certified citrus saplings use and sub-optimal management of plantations by farmers. RESULTS Field observation results revealed varied chlorosis symptoms from young to productive cultivation, which certainly makes it appealing to find out the presence of the causative bacterium, as it has yet to be known whether all the leaves with positive chlorosis symptoms carry the bacterium Candidatus Liberibacter asiaticus. Citrus saplings that appear healthy may carry CVPD pathogens as the incubation period of CVPD pathogens in the host plant spans three to five months. Thus, it is necessary to find the right, rapid way to detect the presence of CVPD pathogens in the citrus plant. The most effective method to use is PCR as the bacterium Candidatus L. asiaticus is non-culturable in vitro, but it is detectable using 16S rDNA. Sampling of leaves with CVPD symptoms was conducted purposively from eight varieties in five citrus cultivation locations, i.e., Pangkep, Sidrap, Bantaeng, Luwu Utara, and Kepulauan Selayar Regencies. DNA isolation was carried out following the Genomic DNA Kit (Geneaid) procedure, followed by detection using the specific pathogenic primer pair OI1 (5' GCG CGT ATG CAA TAC GAG CGG C 3') and OI2c (5' GCC TCG CGA CTT CGC AAC CCA T 3'). CONCLUSION The PCR visualization result shows seven positive samples with DNA fragments measuring 1160 bp. The seven samples were samples of the Key lime, tangerine, Mandarin (cv. batu 55), and Mandarin (cv. selayar), each being derived from Sidrap, Luwu Utara, and Bantaeng. The average disease incidence rate was 66.56 %. Based on the field observation results, the insect vector Diaphorina citri was nowhere to be found in the five citrus cultivation locations in South Sulawesi.
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Affiliation(s)
- Mustika Tuwo
- Doctoral Program of Agricultural Science, Graduate School, Universitas Hasanuddin, Makassar 90245, South Sulawesi, Indonesia; Department of Biology, Faculty of Mathematics and Natural Science, Universitas Hasanuddin, Makassar 90245, South Sulawesi, Indonesia.
| | - Tutik Kuswinanti
- Department of Plant Pest and Disease, Faculty of Agriculture, Universitas Hasanuddin, Makassar 90245, South Sulawesi, Indonesia
| | - Andi Nasruddin
- Department of Plant Pest and Disease, Faculty of Agriculture, Universitas Hasanuddin, Makassar 90245, South Sulawesi, Indonesia
| | - Elis Tambaru
- Department of Biology, Faculty of Mathematics and Natural Science, Universitas Hasanuddin, Makassar 90245, South Sulawesi, Indonesia
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Zhang B, Zhang Q, Yang L, Zheng H, Pang G, Zhao M, Sun B, Cao J. Role of miR-584-5p in Lipopolysaccharide-Stimulated Human Bronchial Epithelial Cell Inflammation and Apoptosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:2408682. [PMID: 35449817 PMCID: PMC9017489 DOI: 10.1155/2022/2408682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022]
Abstract
Acute lung injury (ALI)/acute respiratory distress syndrome is a common clinical syndrome characterized by respiratory failure. MicroRNAs (miRNAs) are closely related to ALI and acute respiratory distress syndrome. TargetScan software analysis showed that miR-584-5p can bind to the 3' noncoding region of TLR4, which is involved in the occurrence and development of ALI, thereby affecting the inflammatory pathway and inflammation development. Thus, we aimed to determine whether miR-584-5p affects ALI. Human bronchial epithelial (16-HBE) cells were transfected with miR-584-5p mimics or inhibitors and then stimulated with lipopolysaccharide (LPS).The cell viability, apoptosis, release of proinflammatory factors, mTOR, and NF-κB pathway protein expression were evaluated respectively. Mimic584 increased, whereas inhibitor584 decreased, LPS-stimulated inflammation. The protein expression of inflammatory factors was significantly increased in 16-HBE cells in the mimic584 + LPS group and decreased in the inhibitor584 + LPS group. Mimic584 activated mTOR and the NF-κB-related proteins P65 and p-p65, whereas inhibitor584 inactivated the proteins in 16-HBE cells. Overexpression of miR-584 significantly promoted apoptosis in LPS-stimulated 16-HBE cells. There were no differences in the proliferation and cell cycle of LPS-stimulated 16-HBE cells regardless of mimic584 or inhibitor584 transfection. Collectively, we demonstrated that inhibitor584 can alleviate ALI-induced expression of inflammatory factors via mTOR signaling and the NF-κB pathway. In conclusion, we found that inhibitor584 transfection could be a potential therapeutic strategy for ALI.
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Affiliation(s)
- Bo Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Qing Zhang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Linying Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Hongfei Zheng
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Guifen Pang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Mingzhen Zhao
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Bo Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei, China
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin 300052, China
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Zou Z, Guo L, Ahmadi P, Hartjen P, Gosau M, Smeets R, Kluwe L. Two simple and inexpensive methods for preparing DNA suitable for digital PCR from a small number of cells in 96-well plates. J Clin Lab Anal 2020; 35:e23513. [PMID: 32761657 PMCID: PMC7843281 DOI: 10.1002/jcla.23513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Background Although DNA of high quality can be easily prepared from cultured cells with commercially available kits, many studies involve a large number of samples which increases the cost drastically. We optimized two simple and inexpensive methods for preparing DNA suitable for digital PCR from a small number of cells directly from wells of 96‐well plates. Methods Cells (number: 103‐104) were lysed with a Direct PCR® lysis buffer or a 10% Chelex100® solution. The lysates were further purified and concentrated by means of DNA precipitation with a blue‐colored glycogen as a carrier. PCR and digital PCR were used to evaluate the efficiency of the two methods. Results For 1000 cells from one primary culture and two tumor cell lines, DNA was reproducible and obtained with recovery rate (obtained/expected amount of DNA) in the range of 50%‐90% as measured by the fluorometer dyes instrument Qubit. Using 8 out of a total of 10 µL DNA solution for 1000 cells, both conventional PCR and digital PCR were successful. For digital PCR, more than 1600 positive droplets were obtained for DNA from 1000 cells using the Direct PCR® method, corresponding to a yield efficiency of approximately 80%. Further reducing the number of cells down to 100 would be possible with 160 positive droplets expected. Both reagents are inexpensive (0.08€/sample). Conclusions Two methods are efficient, especially the Direct PCR® reagent‐based method provides a simple and inexpensive method for preparing DNA suitable for digital PCR from small number of cells.
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Affiliation(s)
- Ziang Zou
- Laboratory for Tumor Genetics and Regenerative Medicine, Department of Neurology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Linna Guo
- Department of Oral and Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Parimah Ahmadi
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philip Hartjen
- Department of Oral and Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Gosau
- Department of Oral and Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Smeets
- Department of Oral and Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Lan Kluwe
- Laboratory for Tumor Genetics and Regenerative Medicine, Department of Neurology, University Hospital Hamburg-Eppendorf, Hamburg, Germany.,Department of Oral and Maxillofacial Surgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
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