1
|
Gao X, Liu S, Lv Y, Dai Q, Zhu L, Hu Z, Lu J, Zhou H, Jin J. Screening of Reference Genes for Quantitative Real-Time PCR Analysis in Tissues and during Testis Development, and Application to Analyze the Expression of kifc1 in Hemibarbus labeo (Teleostei, Cypriniformes, Cyprinidae). Animals (Basel) 2024; 14:2006. [PMID: 38998118 PMCID: PMC11240434 DOI: 10.3390/ani14132006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/27/2024] [Accepted: 06/30/2024] [Indexed: 07/14/2024] Open
Abstract
The selection of proper reference genes is vital for ensuring precise quantitative real-time PCR (qPCR) assays. This study evaluates the stability of the expression of nine candidate reference genes in different tissues and during testicular development in H. labeo. The results show that eef1a is recommended as a reference gene for qPCR analysis in tissues and during testicular development. Furthermore, we evaluated the optimal number of reference genes needed when calculating gene expression levels using the geomean method, revealing that two reference genes are sufficient. Specifically, eef1a and rps27 are recommended for analysis of gene expression in tissues, whereas eef1a and actb are advised for evaluating gene expression during testicular development. In addition, we examined the expression pattern of kifc1, a kinesin involved in the reshaping of spermatids. We detected peak expression levels of kifc1 in testes, with its expression initially increasing before decreasing throughout testicular development. The highest expression of kifc1 was observed in stage IV testes, the active period of spermiogenesis, suggesting a possible role for kifc1 in the regulation of the reshaping of spermatids and hence testicular development. This study represents the first investigation of reference genes for H. labeo, providing a foundation for studying gene expression patterns and investigating gene expression regulation during testicular development.
Collapse
Affiliation(s)
- Xinming Gao
- College of Ecology, Lishui University, Lishui 323000, China
| | - Siqi Liu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Yaoping Lv
- College of Ecology, Lishui University, Lishui 323000, China
| | - Qingmin Dai
- College of Ecology, Lishui University, Lishui 323000, China
| | - Ling Zhu
- College of Ecology, Lishui University, Lishui 323000, China
| | - Zehui Hu
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316100, China
| | - Junkai Lu
- Cixi Fisheries Technology Extension Center, Ningbo 315300, China
| | - Haidong Zhou
- Suichang Fisheries and Agricultural Machinery Technology Extension Station, Lishui 323399, China
| | - Jing Jin
- Zhejiang Fisheries Technology Extension Center, Hangzhou 311100, China
| |
Collapse
|
2
|
Freitas BCG, Dias DD, Reis LAM, Hernández LHA, Cereja GJGP, Aragão CF, da Silva SP, Nunes Neto JP, Elias CN, Cruz ACR. Evaluation of Multiple RNA Extraction Protocols for Chikungunya Virus Screening in Aedes aegypti Mosquitoes. Int J Mol Sci 2024; 25:6700. [PMID: 38928410 PMCID: PMC11204034 DOI: 10.3390/ijms25126700] [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: 05/13/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Chikungunya virus (Togaviridae, Alphavirus; CHIKV) is a mosquito-borne global health threat. The main urban vector of CHIKV is the Aedes aegypti mosquito, which is found throughout Brazil. Therefore, it is important to carry out laboratory tests to assist in the virus's diagnosis and surveillance. Most molecular biology methodologies use nucleic acid extraction as the first step and require quality RNA for their execution. In this context, four RNA extraction protocols were evaluated in Ae. aegypti experimentally infected with CHIKV. Six pools were tested in triplicates (n = 18), each containing 1, 5, 10, 20, 30, or 40 mosquitoes per pool (72 tests). Four commercial kits were compared: QIAamp®, Maxwell®, PureLink®, and PureLink® with TRIzol®. The QIAamp® and PureLink® with TRIzol® kits had greater sensitivity. Two negative correlations were observed: as the number of mosquitoes per pool increases, the Ct value decreases, with a higher viral load. Significant differences were found when comparing the purity and concentration of RNA. The QIAamp® protocol performed better when it came to lower Ct values and higher RNA purity and concentration. These results may provide help in CHIKV entomovirological surveillance planning.
Collapse
Affiliation(s)
- Bárbara Caroline Garcia Freitas
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, PA, Brazil; (B.C.G.F.); (D.D.D.); (L.A.M.R.); (J.P.N.N.)
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Daniel Damous Dias
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, PA, Brazil; (B.C.G.F.); (D.D.D.); (L.A.M.R.); (J.P.N.N.)
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Lúcia Aline Moura Reis
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, PA, Brazil; (B.C.G.F.); (D.D.D.); (L.A.M.R.); (J.P.N.N.)
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Leonardo Henrique Almeida Hernández
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Glennda Juscely Galvão Pereira Cereja
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Carine Fortes Aragão
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | - Joaquim Pinto Nunes Neto
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, PA, Brazil; (B.C.G.F.); (D.D.D.); (L.A.M.R.); (J.P.N.N.)
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| | | | - Ana Cecília Ribeiro Cruz
- Parasite Biology in the Amazon Region Graduate Program, Pará State University, Belém 66087-670, PA, Brazil; (B.C.G.F.); (D.D.D.); (L.A.M.R.); (J.P.N.N.)
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil; (L.H.A.H.); (G.J.G.P.C.); (C.F.A.); (S.P.d.S.)
| |
Collapse
|
3
|
Shen CH, Tang M, Li XF, Zhu L, Li W, Deng P, Zhai Q, Wu G, Yan XH. Evaluation of reference genes for quantitative expression analysis in Mylabris sibirica (Coleoptera, Meloidae). Front Physiol 2024; 15:1345836. [PMID: 38651047 PMCID: PMC11033477 DOI: 10.3389/fphys.2024.1345836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Mylabris sibirica is a hypermetamorphic insect whose adults feed on oilseed rape. However, due to a shortage of effective and appropriate endogenous references, studies on molecular functional genes in Mylabris sibirica, have been tremendously limited. In this study, ten internal reference genes (ACT, ARF1, AK, EF1α, GAPDH, α-TUB, RPL6, RPL13, RPS3 and RPS18) were tested and assessed under four selected treatments including adult ages, adult tissues, temperatures, and sex by RT-qPCR based on five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). Our findings showed that RPL6 and RPL13 were the most optimal internal reference gene combination for gene expression during various adult ages and under diverse temperatures; The combination of RPL6 and RPS18 was recommended to test gene transcription levels under different adult tissues. AK and RPL6 were the best reference genes in male and female adults. RPL6 and RPL13 were the most appropriate reference gene pair to estimate gene expression levels under four different tested backgrounds. The relative transcript levels of a uridine diphosphate (UDP)-N-acetylglucosamine-pyrophosphorylase (MsUAP), varied greatly according to normalization with the two most- and least-suited reference genes. This study will lay the basis for further molecular physiology and biochemistry studies in M. sibirica, such as development, reproduction, sex differentiation, cold and heat resistance.
Collapse
Affiliation(s)
- Chen-Hui Shen
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Min Tang
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiao-Fei Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Li Zhu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wei Li
- Northern Propagation Experiment Station, Center for Science and Technology Dissemination and Industrial Development, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, China
| | - Pan Deng
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qing Zhai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Gang Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiao-Hong Yan
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| |
Collapse
|
4
|
Hembrom PS, Deepthi M, Biswas G, Mappurath B, Babu A, Reeja N, Mano N, Grace T. Reference genes for qPCR expression in black tiger shrimp, Penaeus monodon. Mol Biol Rep 2024; 51:422. [PMID: 38485790 DOI: 10.1007/s11033-024-09409-5] [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: 12/02/2023] [Accepted: 03/01/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Gene expression profiling via qPCR is an essential tool for unraveling the intricate molecular mechanisms underlying growth and development. Identifying and validating the most appropriate reference genes is essential for qPCR experiments. Nevertheless, there exists a deficiency in a thorough assessment of reference genes concerning the expression of the genes in the research in the context of the growth and development of the Black Tiger Shrimp, P. monodon. This popular marine crustacean is extensively raised for human consumption. In this study, we assessed the expression stability of seven reference genes (ACTB, 18S, EF-1α, AK, PK, cox1, and CLTC) in adult tissues (hepatopancreas, gills, and stomach) of small and large polymorphs of P. monodon. METHODS AND RESULTS The stability of gene expressions was assessed utilizing NormFinder, BestKeeper, and geNorm, and a comprehensive ranking of these genes was conducted through the online tool RefFinder. In the overall ranking, 18S and CLTC emerged as the most stable genes in the hepatopancreas and stomach, while CLTC and AK exhibited significant statistical reliability in the gills of adult P. monodon. The validation of these identified stable genes was carried out using a growth-associated gene, insr-1. CONCLUSION The results indicated that 18S and CLTC stand out as the most versatile reference genes for conducting qPCR analysis focused on the growth of P. monodon. This study represents the first comprehensive exploration that identifies and assesses reference genes for qPCR analysis in P. monodon, providing valuable tools for research involving similar crustaceans.
Collapse
Affiliation(s)
- Preety Sweta Hembrom
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Mottakunja Deepthi
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Gourav Biswas
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Bhagya Mappurath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Adon Babu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Narchikundil Reeja
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Neeraja Mano
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Tony Grace
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
| |
Collapse
|
5
|
Lima OJF, Ribeiro JDS, Vasconcelos JDC, Ferraz MFI, Silva CEDMTDRE, Barros WMA, Vieira GR, David MCMM, Matos RJB. Environmental enrichment changes the effects of prenatal and postnatal undernutrition on memory, anxiety traits, Bdnf and TrkB expression in the hippocampus of male adult rats. Behav Brain Res 2024; 460:114817. [PMID: 38122904 DOI: 10.1016/j.bbr.2023.114817] [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: 06/22/2023] [Revised: 11/27/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Environmental factors such as undernutrition and environmental enrichment can promote changes in the molecular and behavioural mechanisms related to cognition. Herein, we investigated the effect of enriched environment stimulation in rats that were malnourished in the pre- and postnatal periods on changes in the gene expression of brain-derived neurotrophic factor and its receptor in the hippocampus, as well as on anxiety traits and memory. Early undernutrition promoted weight reduction, increased the risk analysis, reduced permanence in the open arm of the elevated plus-maze and induced a reduction in the gene expression of brain-derived neurotrophic factor and tropomyosin receptor kinase B. However, exposure to an enriched environment from 30 to 90 days' old maintained the malnourished phenotype, leading to weight reduction in the control group. In addition, the enriched environment did not alter the risk assessment in the undernourished group, but it did increase the frequency of labyrinth entries. Sixty-day exposure to the enriched environment resulted in a reversal in the gene expression of brain-derived neurotrophic factor and tropomyosin receptor kinase B in the hippocampus of malnourished rats and favoured of long-term memory in the object recognition test in the open-field. These results suggest that an enriched environment may have a protective effect in adult life by inducing changes in long-term memory and anxiety traits in animals that were undernourished in early life. Furthermore, reversing these effects of undernutrition involves mechanisms linked to the molecular signalling of brain-derived neurotrophic factor and tropomyosin receptor kinase B in the hippocampus.
Collapse
Affiliation(s)
- Odair José Farias Lima
- Physical Education and Sports Science Nucleus, Academic Center of Vitória, Federal University of Pernambuco, Brazil
| | | | | | | | | | - Waleska Maria Almeida Barros
- Multicenter Postgraduate Program in Physiological Sciences, Academic Center of Vitória, Federal University of Pernambuco, Brazil
| | - Gilberto Ramos Vieira
- Postgraduate Program in Physical Education, Health Sciences Center, Federal University of Pernambuco, Brazil
| | | | | |
Collapse
|
6
|
Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [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: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
Collapse
Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
| |
Collapse
|
7
|
Rawat K, Gautam V, Sandhu A, Saha L. Detection and Characterization of Apoptosis-Related Proteins in Hippocampal Neurodegeneration: From mRNA Expression to Protein Quantification. Methods Mol Biol 2024; 2761:301-316. [PMID: 38427246 DOI: 10.1007/978-1-0716-3662-6_22] [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: 03/02/2024]
Abstract
The involvement of apoptosis in neurodegeneration can be detected by quantifying the apoptotic proteins in hippocampal lysate. Apoptosis can occur due to the overproduction of apoptotic proteins under the influence of external trigger or due to the overexpression of the apoptotic genes. Thus, the imbalance in the production of apoptotic proteins can be quantified using the Western blotting technique and the overexpression of apoptotic genes in hippocampal DNA can be quantified using the real-time quantification of mRNA expression of the apoptotic proteins. Here we provide the methodology of detecting the apoptosis-related proteins like Bax and Bcl-2 and their mRNA expression in hippocampal neurodegeneration. In this chapter, we have described the methodology for quantification of mRNA expression of these apoptosis-related proteins in the hippocampal lysate using the real-time quantitative polymerase chain reaction (qPCR) technique and the methodology of detection and characterization of respective protein expression in the hippocampal lysate using the Western blotting technique.
Collapse
Affiliation(s)
- Kajal Rawat
- Department of Pharmacology, Research Block B, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Vipasha Gautam
- Department of Pharmacology, Research Block B, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Arushi Sandhu
- Department of Pharmacology, Research Block B, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Lekha Saha
- Department of Pharmacology, Research Block B, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| |
Collapse
|
8
|
Dutta P, Mäkinen K. Absolute and Relative Quantification of Single-Stranded Positive-Sense RNA Viruses from Plant Tissue. Methods Mol Biol 2024; 2724:81-91. [PMID: 37987900 DOI: 10.1007/978-1-0716-3485-1_7] [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: 11/22/2023]
Abstract
Reverse transcription quantitative PCR (RT-qPCR) allows sensitive and specific measurement of mRNA transcripts from a given sample in a short period of time. Relative and absolute RT-qPCR are two strategies that could be used to quantify mRNA transcripts, based on the goal of the experiment. Here, we describe the protocol for the quantification of plant viral RNA transcripts from an infected sample using both strategies.
Collapse
Affiliation(s)
- Pinky Dutta
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
9
|
Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
Collapse
Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
| |
Collapse
|
10
|
Garcia-Raventós A, Muñoz-Mérida A, Lapiedra O, Unzeta M, Ferrandiz-Rovira M, Sol D. Identification of sex-linked SNP markers in wild populations of monomorphic birds. Mol Ecol Resour 2023; 23:1905-1913. [PMID: 37675830 DOI: 10.1111/1755-0998.13862] [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: 02/01/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Single-nucleotide polymorphism (SNP) analysis is a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we developed a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygous or homozygous for the Z-linked SNP, while females exhibit both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to identify the sex of individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable for discriminating males and females from a sample of 927 genotyped individuals at different maturity stages, with an accuracy of 99.5%. Since SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.
Collapse
Affiliation(s)
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | | | | | | | - Daniel Sol
- CREAF, Catalonia, Spain
- CSIC, Catalonia, Spain
| |
Collapse
|
11
|
Mao Y, Xu K, Miglietta L, Kreitmann L, Moser N, Georgiou P, Holmes A, Rodriguez-Manzano J. Deep Domain Adaptation Enhances Amplification Curve Analysis for Single-Channel Multiplexing in Real-Time PCR. IEEE J Biomed Health Inform 2023; 27:3093-3103. [PMID: 37028376 DOI: 10.1109/jbhi.2023.3257727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Data-driven approaches for molecular diagnostics are emerging as an alternative to perform an accurate and inexpensive multi-pathogen detection. A novel technique called Amplification Curve Analysis (ACA) has been recently developed by coupling machine learning and real-time Polymerase Chain Reaction (qPCR) to enable the simultaneous detection of multiple targets in a single reaction well. However, target classification purely relying on the amplification curve shapes faces several challenges, such as distribution discrepancies between different data sources (i.e., training vs testing). Optimisation of computational models is required to achieve higher performance of ACA classification in multiplex qPCR through the reduction of those discrepancies. Here, we proposed a novel transformer-based conditional domain adversarial network (T-CDAN) to eliminate data distribution differences between the source domain (synthetic DNA data) and the target domain (clinical isolate data). The labelled training data from the source domain and unlabelled testing data from the target domain are fed into the T-CDAN, which learns both domains' information simultaneously. After mapping the inputs into a domain-irrelevant space, T-CDAN removes the feature distribution differences and provides a clearer decision boundary for the classifier, resulting in a more accurate pathogen identification. Evaluation of 198 clinical isolates containing three types of carbapenem-resistant genes (blaNDM, blaIMP and blaOXA-48) illustrates a curve-level accuracy of 93.1% and a sample-level accuracy of 97.0% using T-CDAN, showing an accuracy improvement of 20.9% and 4.9% respectively. This research emphasises the importance of deep domain adaptation to enable high-level multiplexing in a single qPCR reaction, providing a solid approach to extend qPCR instruments' capabilities in real-world clinical applications.
Collapse
|
12
|
Oh D, De Spiegelaere W, Nauwynck HJ. Selection and validation of reference genes for RT-qPCR normalization of porcine alveolar macrophages (PAMs) for PRRSV studies. Sci Rep 2023; 13:8840. [PMID: 37258711 DOI: 10.1038/s41598-023-35873-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023] Open
Abstract
Porcine alveolar macrophages (PAMs) are widely used for in vitro studies of porcine respiratory viruses. Gene expression in these cells is altered by viral infection and cellular immune response. Real-time reverse transcription polymerase chain reaction (RT-qPCR) is a powerful technique for analyzing these changes. In order to obtain reliable quantitative RT-qPCR data and come to sound conclusions, stable reference genes are needed for normalization of target gene expression. In the present study, we evaluated the expression stability of nine reference genes in PAMs during cultivation and upon porcine reproductive and respiratory syndrome virus (PRRSV) inoculation. Using geNorm and NormFinder algorithms, we identified PSAP and GAPDH as the most stable reference genes under all experimental conditions. The selected reference genes were used for the normalization of CD163 expression under different conditions. This study demonstrates that selection of appropriate reference genes is essential for normalization and validation of RT-qPCR data across all experimental conditions. This study provides a new set of stable reference genes for future studies with porcine respiratory viruses in PAMs.
Collapse
Affiliation(s)
- Dayoung Oh
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Hans J Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| |
Collapse
|
13
|
Yan F, Li H, Chen X, Yu J, Su S, Li J, Ye W, Tang Y. Screening of Suitable Reference Genes for Immune Gene Expression Analysis Stimulated by Vibrio anguillarum and Copper Ions in Chinese Mitten Crab ( Eriocheir sinensis). Genes (Basel) 2023; 14:genes14051099. [PMID: 37239459 DOI: 10.3390/genes14051099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The reference gene expression is not always stable under different experimental conditions, and screening of suitable reference genes is a prerequisite in quantitative real-time polymerase chain reaction (qRT-PCR). In this study, we investigated gene selection, and the most stable reference gene for the Chinese mitten crab (Eriocheir sinensis) was screened under the stimulation of Vibrio anguillarum and copper ions, respectively. Ten candidate reference genes were selected, including arginine kinase (AK), ubiquitin-conjugating enzyme E2b (UBE), glutathione S-transferase (GST), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF-1α), α-tubulin (α-TUB), heat shock protein 90 (HSP90), β-actin (β-ACTIN), elongation factor 2 (EF-2) and phosphoglucomutase 2 (PGM2). Expression levels of these reference genes were detected under the stimulation of V. anguillarum at different times (0 h, 6 h, 12 h, 24 h, 48 h and 72 h) and copper ions in different concentrations (11.08 mg/L, 2.77 mg/L, 0.69 mg/L and 0.17 mg/L). Four types of analytical software, namely geNorm, BestKeeper, NormFinder and Ref-Finder, were applied to evaluate the reference gene stability. The results showed that the stability of the 10 candidate reference genes was in the following order: AK > EF-1α > α-TUB > GAPDH > UBE > β-ACTIN > EF-2 > PGM2 > GST > HSP90 under V. anguillarum stimulation. It was GAPDH > β-ACTIN > α-TUB > PGM2 > EF-1α > EF-2 > AK > GST > UBE > HSP90 under copper ion stimulation. The expression of E. sinensis Peroxiredoxin4 (EsPrx4) was detected when the most stable and least stable internal reference genes were selected, respectively. The results showed that reference genes with different stability had great influence on the accurate results of the target gene expression. In the Chinese mitten crab (E. sinensis), AK and EF-1α were the most suitable reference genes under the stimulation of V. anguillarum. Under the stimulation of copper ions, GAPDH and β-ACTIN were the most suitable reference genes. This study provided important information for further research on immune genes in V. anguillarum or copper ion stimulation.
Collapse
Affiliation(s)
- Fengyuan Yan
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hui Li
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xue Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Junjie Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Shengyan Su
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wei Ye
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yongkai Tang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| |
Collapse
|
14
|
Liu Y, Zhou J, Qiu Z, Hu P, Chen X, Yang Z. Identification and Validation of Reference Genes for Expression Analysis Using RT-qPCR in Leptocybe invasa Fisher and La Salle (Hymenoptera: Eulophidae). INSECTS 2023; 14:insects14050456. [PMID: 37233084 DOI: 10.3390/insects14050456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Leptocybe invasa (Hymenoptera: Eulophidae) is a globally intrusive pest. Despite extensive research into the physiological responses of this pest, our understanding of the molecular mechanisms still needs to be improved. We want to accurately investigate the expression of L. invasa's target genes, so it is imperative to select fitting reference genes. In this study, eight housekeeping genes' stability (RPS30, ACTR, 18S rRNA, ACT, RPL18, GAPDH, 28S rRNA, and TUB) was tested under five different experimental conditions, including male or female adults, somites (head, thorax, and abdomen), temperatures (0 °C, 25 °C, and 40 °C), diets (starvation, clear water, 10% honey water, Eucalyptus sap), and pesticides (acetone was used as a control, imidacloprid, monosultap). Gene stability was calculated using RefFinder, which integrates four algorithms (the ∆Ct method, geNorm, NormFinder, and BestKeeper). The findings implied that ACT and ACTR were the most accurate when comparing sexes. For analyzing different somites, 28S rRNA and RPL18 were ideal; the 28S rRNA and RRS30 were perfect for analyzing at different temperatures. The combination of ACT and GAPDH helped to analyze gene expression in different diets, and GAPDH and 28S rRNA were suitable for various pesticide conditions. Overall, this research offers a complete list of reference genes from L. invasa for precise analysis of target gene expression, which can improve the trustworthiness of RT-qPCR and lay the foundation for further investigations into the gene function of this pest.
Collapse
Affiliation(s)
- Ya Liu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Jing Zhou
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhisong Qiu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Ping Hu
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
| | - Xiao Chen
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhende Yang
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
| |
Collapse
|
15
|
Bălan AM, Bodolea C, Trancă SD, Hagău N. Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review. Healthcare (Basel) 2023; 11:healthcare11091345. [PMID: 37174887 PMCID: PMC10177880 DOI: 10.3390/healthcare11091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.
Collapse
Affiliation(s)
- Andrei-Mihai Bălan
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Constantin Bodolea
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Sebastian Daniel Trancă
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Emergency Department, The Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
| | - Natalia Hagău
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, "Regina Maria" Hospital, 400221 Cluj-Napoca, Romania
| |
Collapse
|
16
|
Luigi M, Taglienti A, Corrado CL, Cardoni M, Botti S, Bissani R, Casati P, Passera A, Miotti N, De Jonghe K, Everaert E, Olmos A, Ruiz-García AB, Faggioli F. Development and Validation of a Duplex RT-qPCR for Detection of Peach Latent Mosaic Viroid and Comparison of Different Nucleic-Acid-Extraction Protocols. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091802. [PMID: 37176860 PMCID: PMC10181016 DOI: 10.3390/plants12091802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Peach latent mosaic viroid (PLMVd) is an important pathogen that causes disease in peaches. Control of this viroid remains problematic because most PLMVd variants are symptomless, and although there are many detection tests in use, the reliability of PCR-based methods is compromised by the complex, branched secondary RNA structure of the viroid and its genetic diversity. In this study, a duplex RT-qPCR method was developed and validated against two previously published single RT-qPCRs, which were potentially able to detect all known PLMVd variants when used in tandem. In addition, in order to simplify the sample preparation, rapid-extraction protocols based on the use of crude sap or tissue printing were compared with commercially available RNA purification kits. The performance of the new procedure was evaluated in a test performance study involving five participant laboratories. The new method, in combination with rapid-sample-preparation approaches, was demonstrated to be feasible and reliable, with the advantage of detecting all different PLMVd isolates/variants assayed in a single reaction, reducing costs for routine diagnosis.
Collapse
Affiliation(s)
- Marta Luigi
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Anna Taglienti
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Carla Libia Corrado
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Marco Cardoni
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Simona Botti
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Rita Bissani
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Niccolò Miotti
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Kris De Jonghe
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Ellen Everaert
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Antonio Olmos
- IVIA Instituto Valenciano de Investigaciones Agrarias, 46113 Valencia, Spain
| | - Ana B Ruiz-García
- IVIA Instituto Valenciano de Investigaciones Agrarias, 46113 Valencia, Spain
| | - Francesco Faggioli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| |
Collapse
|
17
|
Yang S, Xian Q, Liu Y, Zhang Z, Song Q, Gao Y, Wen W. A Silicon-Based PDMS-PEG Copolymer Microfluidic Chip for Real-Time Polymerase Chain Reaction Diagnosis. J Funct Biomater 2023; 14:jfb14040208. [PMID: 37103298 PMCID: PMC10143339 DOI: 10.3390/jfb14040208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023] Open
Abstract
Polydimethylsiloxane (PDMS) has been widely used to make lab-on-a-chip devices, such as reactors and sensors, for biological research. Real-time nucleic acid testing is one of the main applications of PDMS microfluidic chips due to their high biocompatibility and transparency. However, the inherent hydrophobicity and excessive gas permeability of PDMS hinder its applications in many fields. This study developed a silicon-based polydimethylsiloxane-polyethylene-glycol (PDMS-PEG) copolymer microfluidic chip, the PDMS-PEG copolymer silicon chip (PPc-Si chip), for biomolecular diagnosis. By adjusting the modifier formula for PDMS, the hydrophilic switch occurred within 15 s after contact with water, resulting in only a 0.8% reduction in transmittance after modification. In addition, we evaluated the transmittance at a wide range of wavelengths from 200 nm to 1000 nm to provide a reference for its optical property study and application in optical-related devices. The improved hydrophilicity was achieved by introducing a large number of hydroxyl groups, which also resulted in excellent bonding strength of PPc-Si chips. The bonding condition was easy to achieve and time-saving. Real-time PCR tests were successfully conducted with higher efficiency and lower non-specific absorption. This chip has a high potential for a wide range of applications in point-of-care tests (POCT) and rapid disease diagnosis.
Collapse
Affiliation(s)
- Siyu Yang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
| | - Qingyue Xian
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Yiteng Liu
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Ziyi Zhang
- Division of Emerging Interdisciplinary Areas, Interdisciplinary Program Office, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
| | - Qi Song
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yibo Gao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Weijia Wen
- Thrust of Advanced Materials, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou 511400, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518000, China
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
18
|
Floridia V, Sfulcini M, D’Alessandro E, Cattaneo L, Mezzetti M, Liotta L, Trevisi E, Lopreiato V, Minuti A. Effect of Different Anticoagulant Agents on Immune-Related Genes in Leukocytes Isolated from the Whole-Blood of Holstein Cows. Genes (Basel) 2023; 14:406. [PMID: 36833333 PMCID: PMC9957540 DOI: 10.3390/genes14020406] [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: 01/10/2023] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Anticoagulants, such as ethylenediaminetetraacetic acid (EDTA), sodium citrate (Na-citrate), or heparin are normally used in hematological clinical tests to prevent coagulation. Although anticoagulants are fundamental for the correct application of clinical tests, they produce adverse effects in different fields, such as those involving specific molecular techniques; for instance, quantitative real time polymerase chain reactions (qPCR) and gene expression evaluation. For this reason, the aim of this study was to evaluate the expression of 14 genes in leukocytes that were isolated from the blood of Holstein cows, and which were collected in Li-heparin, K-EDTA, or Na-citrate tubes; then, they were analyzed using qPCR. Only the SDHA gene showed a significant dependence (p ≤ 0.05) on the anticoagulant that was used with the lowest expression; this was observed in Na-Citrate after being compared with Li-heparin and K-EDTA (p < 0.05). Although a variation in transcript abundance with the three anticoagulants was observed in almost all the investigated genes, the relative abundance levels were not statistically significant. In conclusion, the qPCR results were not influenced by the presence of the anticoagulant; thus, we had the opportunity to choose the test tube that was used in the experiment without interfering effects impacting the gene expression levels caused by the anticoagulant.
Collapse
Affiliation(s)
- Viviana Floridia
- Department of Veterinary Sciences, Università di Messina, Viale Palatucci, 13, 98168 Messina, Italy
| | - Marta Sfulcini
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, Università di Messina, Viale Palatucci, 13, 98168 Messina, Italy
| | - Luca Cattaneo
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Matteo Mezzetti
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Luigi Liotta
- Department of Veterinary Sciences, Università di Messina, Viale Palatucci, 13, 98168 Messina, Italy
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Vincenzo Lopreiato
- Department of Veterinary Sciences, Università di Messina, Viale Palatucci, 13, 98168 Messina, Italy
| | - Andrea Minuti
- Department of Animal Sciences, Food and Nutrition, Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| |
Collapse
|
19
|
Yao L, Jiang Y, Tan Z, Wu W. Construction of Very Low-Cost Loop Polymerase Chain Reaction System Based on Proportional-Integral-Derivative Temperature Control Optimization Algorithm and Its Application in Gene Detection. ACS OMEGA 2022; 7:46003-46011. [PMID: 36570205 PMCID: PMC9773339 DOI: 10.1021/acsomega.2c02975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/12/2022] [Indexed: 06/17/2023]
Abstract
Real-time polymerase chain reaction (PCR) technology is essential in nucleic acid detection and point-of-care testing (POCT). However, nowadays, the classical qPCR instrument has the deficiency of its bulky volume, high cost, and inconvenience to use; hence, a low-cost and easy-to-use PCR equipment was thus developed consisting of a hardware subsystem as well as a software subsystem based on an improved proportional-integral-derivative (PID) system. The proposed system not only could hold self-setting reaction cycles of temperature rising and falling automatically but also the temperature during the constant temperature stage was regulated steady based on improved temperature control algorithm, which proved its great effect compared with the reaction temperature derived from an infrared thermal imaging camera. The experimental results in gene detection research also could indicate its applicability and stability of our developed PCR system by using the amplification curve analysis, the melting curve analysis, and agarose gel electrophoresis analysis compared with the commercial PCR instrument, which illustrates the great potential application value of the proposed PCR system.
Collapse
Affiliation(s)
- Liping Yao
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou510500, China
| | - Yangyang Jiang
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou510500, China
| | - Zhongwei Tan
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou510500, China
| | - Wenming Wu
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou510500, China
- State
Key Laboratory of Microelectronics and Integrated Circuits, Fudan University, Shanghai200433, China
| |
Collapse
|
20
|
Liu X, Zhu H, Sabó J, Lánský Z, Neužil P. Improvement of the signal to noise ratio for fluorescent imaging in microfluidic chips. Sci Rep 2022; 12:18911. [PMID: 36344576 PMCID: PMC9640556 DOI: 10.1038/s41598-022-23426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Microfluidics systems can be fabricated in various ways using original silicon glass systems, with easy Si processing and surface modifications for subsequent applications such as cell seeding and their study. Fluorescent imaging of cells became a standard technique for the investigation of cell behavior. Unfortunately, high sensitivity fluorescent imaging, e.g., using total internal reflection fluorescence (TIRF) microscopy, is problematic in these microfluidic systems because the uneven surfaces of the silicon channels' bottoms affect light penetration through the optical filters. In this work, we study the nature of the phenomenon, finding that the problem can be rectified by using a silicon-on-insulator (SOI) substrate, defining the channel depth by the thickness of the top Si layer, and halting the etching at the buried SiO2 layer. Then the fluorescent background signal drops by = 5 times, corresponding to the limit of detection drop from = 0.05 mM to = 50 nM of fluorescein. We demonstrate the importance of a flat surface using TIRF-based single-molecule detection, improving the signal to a noise ratio more than 18 times compared to a conventional Si wafer. Overall, using very high-quality SOI substrates pays off, as it improves the fluorescence image quality due to the increase in signal-to-noise ratio. Concerning the cost of microfluidic device fabrication-design, mask fabrication, wafer processing, and device testing-the initial SOI wafer cost is marginal, and using it improves the system performance.
Collapse
Affiliation(s)
- Xiaocheng Liu
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
| | - Hanliang Zhu
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
| | - Ján Sabó
- grid.418095.10000 0001 1015 3316Institute of Biotechnology, Czech Academy of Science, Průmyslová 595, 252 50 Vestec, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Physical Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800 Prague 2, Czech Republic
| | - Zdeněk Lánský
- grid.418095.10000 0001 1015 3316Institute of Biotechnology, Czech Academy of Science, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Pavel Neužil
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
| |
Collapse
|
21
|
Koo SBN, Kim YS, Park CY, Lee DJ. Compact Camera Fluorescence Detector for Parallel-Light Lens-Based Real-Time PCR System. SENSORS (BASEL, SWITZERLAND) 2022; 22:8575. [PMID: 36366271 PMCID: PMC9654867 DOI: 10.3390/s22218575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The polymerase chain reaction is an important technique in biological research. However, it is time consuming and has a number of disadvantages. Therefore, real-time PCR technology that can be used in real-time monitoring has emerged, and many studies are being conducted regarding its use. Real-time PCR requires many optical components and imaging devices such as expensive, high-performance cameras. Therefore, its cost and assembly process are limitations to its use. Currently, due to the development of smart camera devices, small, inexpensive cameras and various lenses are being developed. In this paper, we present a Compact Camera Fluorescence Detector for use in parallel-light lens-based real-time PCR devices. The proposed system has a simple optical structure, the system cost can be reduced, and the size can be miniaturized. This system only incorporates Fresnel lenses without additional optics in order for the same field of view to be achieved for 25 tubes. In the center of the Fresnel lens, one LED and a complementary metal-oxide semiconductor camera were placed in directions that were as similar as possible. In addition, to achieve the accurate analysis of the results, image processing was used to correct them. As a result of an experiment using a reference fluorescent substance and double-distilled water, it was confirmed that stable fluorescence detection was possible.
Collapse
Affiliation(s)
- Seul-Bit-Na Koo
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Yu-Seop Kim
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Chan-Young Park
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Deuk-Ju Lee
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| |
Collapse
|
22
|
Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh. Sci Rep 2022; 12:18473. [PMID: 36323741 PMCID: PMC9630269 DOI: 10.1038/s41598-022-22588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.
Collapse
|
23
|
Leonaviciene G, Mazutis L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Res 2022; 51:e2. [PMID: 36268865 PMCID: PMC9841424 DOI: 10.1093/nar/gkac918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/29/2023] Open
Abstract
Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
Collapse
Affiliation(s)
- Greta Leonaviciene
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio av., Vilnius, LT-10257, Lithuania
| | - Linas Mazutis
- To whom correspondence should be addressed. Tel: +370 5 2234356;
| |
Collapse
|
24
|
Ma S, Wang K, Jiang Y, Guo Y, Zhang Y, Gao Y, Wu W. Development of a low-cost multi-channel nucleic acid detection PCR instrument and clinical detection application of COVID-19. Anal Chim Acta 2022; 1229:340338. [PMID: 36156217 PMCID: PMC9472591 DOI: 10.1016/j.aca.2022.340338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/01/2022]
Abstract
Since the COVID-19 outbreak at the end of December 2019, a variety of novel Coronavirus nucleic acid detection methods have been proposed at home and abroad. Because of the disadvantages of most existing PCR instruments on the market such as long reaction time and high cost, this study developed a more timesaving and cheaper two-channel real-time quantitative PCR instrument. In this instrument, a PCR system combining a thermal cycle system and real-time fluorescence quantitative technology was designed. The software system and data processing, optical system, thermal cycle module, and hardware module of the PCR instrument were studied. The low-cost, portable real-time quantitative PCR system has been validated with consistent results compared to Bio-rad CFX Connect. At the same time, the same samples were used for the contract experiment with the hospital instrument, and the amplification result was better than the existing instrument in the hospital.
Collapse
Affiliation(s)
- Shuang Ma
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, PR China
| | - Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, PR China
| | - Yangyang Jiang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, PR China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, PR China
| | - Yipeng Zhang
- School of Biomedical Engineering, Southern Medical University, PR China
| | - YingJun Gao
- School of Biotechnology and Health Sciences, Wuyi University, PR China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, PR China; Fudan University, Shanghai, 200433, PR China.
| |
Collapse
|
25
|
Miglietta L, Xu K, Chhaya P, Kreitmann L, Hill-Cawthorne K, Bolt F, Holmes A, Georgiou P, Rodriguez-Manzano J. Adaptive Filtering Framework to Remove Nonspecific and Low-Efficiency Reactions in Multiplex Digital PCR Based on Sigmoidal Trends. Anal Chem 2022; 94:14159-14168. [PMID: 36190816 PMCID: PMC9583074 DOI: 10.1021/acs.analchem.2c01883] [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] [Indexed: 11/28/2022]
Abstract
Real-time digital polymerase chain reaction (qdPCR) coupled with machine learning (ML) methods has shown the potential to unlock scientific breakthroughs, particularly in the field of molecular diagnostics for infectious diseases. One promising application of this emerging field explores single fluorescent channel PCR multiplex by extracting target-specific kinetic and thermodynamic information contained in amplification curves, also known as data-driven multiplexing. However, accurate target classification is compromised by the presence of undesired amplification events and not ideal reaction conditions. Therefore, here, we proposed a novel framework to identify and filter out nonspecific and low-efficient reactions from qdPCR data using outlier detection algorithms purely based on sigmoidal trends of amplification curves. As a proof-of-concept, this framework is implemented to improve the classification performance of the recently reported data-driven multiplexing method called amplification curve analysis (ACA), using available published data where the ACA is demonstrated to screen carbapenemase-producing organisms in clinical isolates. Furthermore, we developed a novel strategy, named adaptive mapping filter (AMF), to adjust the percentage of outliers removed according to the number of positive counts in qdPCR. From an overall total of 152,000 amplification events, 116,222 positive amplification reactions were evaluated before and after filtering by comparing against melting peak distribution, proving that abnormal amplification curves (outliers) are linked to shifted melting distribution or decreased PCR efficiency. The ACA was applied to assess classification performance before and after AMF, showing an improved sensitivity of 1.2% when using inliers compared to a decrement of 19.6% when using outliers (p-value < 0.0001), removing 53.5% of all wrong melting curves based only on the amplification shape. This work explores the correlation between the kinetics of amplification curves and the thermodynamics of melting curves, and it demonstrates that filtering out nonspecific or low-efficient reactions can significantly improve the classification accuracy for cutting-edge multiplexing methodologies.
Collapse
Affiliation(s)
- Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.,Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K
| | - Ke Xu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.,Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K
| | - Priya Chhaya
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K
| | - Louis Kreitmann
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K
| | - Kerri Hill-Cawthorne
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K
| | - Frances Bolt
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K
| |
Collapse
|
26
|
Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
Collapse
Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| |
Collapse
|
27
|
Hundreds-Dollar-Level Multiplex Integrated RT-qPCR Quantitative System for Field Detection. BIOSENSORS 2022; 12:bios12090706. [PMID: 36140090 PMCID: PMC9496240 DOI: 10.3390/bios12090706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.
Collapse
|
28
|
Wang K, Wang Q, Peng C, Guo Y, Li Y, Zhou J, Wu W. Portable Heating System Based on a Liquid Metal Bath for Rapid PCR. ACS OMEGA 2022; 7:26165-26173. [PMID: 35936432 PMCID: PMC9352155 DOI: 10.1021/acsomega.2c01824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
With the outbreak of COVID-19 around the world, rapid and accurate detection of new coronaviruses is the key to stop the transmission of the disease and prevent and control the novel coronavirus, among which polymerase chain reaction (PCR) is the mainstream nucleic acid detection method. A temperature cycling device is the core of the PCR amplification micro-device. The precision of the temperature control and temperature change rate directly affect the efficiency of PCR amplification. This study proposes a new PCR method based on rapid PCR chip optimization of a liquid metal bath, which realizes precise and rapid temperature rise and fall control. We systematically explored the feasibility of using liquid metals with different melting points in the system and proposed a 47 °C bismuth-based liquid metal bath as the heat conduction medium of the system to optimize the system. The heat conduction properties of the thermally conductive silicone oil bath were compared. Compared with the thermally conductive silicone oil bath, thermal cycle efficiency is improved nearly 3 times. The average heating rate of the liquid metal bath is fast, and the temperature control stability is good, which can significantly reduce the hysteresis, and the temperature change curve is more gentle, which can greatly improve the efficiency of PCR amplification. The results of gene amplification using rat DNA as the template and SEC61A as the target also indicate that the system can be successfully used in PCR devices, and the types of PCR containers can be not limited to PCR tubes. Based on the experiment, we proved that the PCR method optimized by the liquid metal bath multi-gene rapid PCR chip can further improve the temperature response speed. It has the advantages of accurate data, fast response speed, low price, safety, and environmental protection and can effectively reduce the time of PCR and improve the application efficiency. As far as we know, this is the first international report on using a liquid metal bath to do rapid-cooling PCR.
Collapse
Affiliation(s)
- Kangning Wang
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou 516001, China
| | - Qingran Wang
- State
Key Laboratory of Luminescence and Applications, Changchun Institute
of Optics, Fine Mechanics and Physics, Chinese
Academy of Sciences, Changchun 130033, China
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Canfu Peng
- State
Key Laboratory of Luminescence and Applications, Changchun Institute
of Optics, Fine Mechanics and Physics, Chinese
Academy of Sciences, Changchun 130033, China
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Guo
- School
of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yan Li
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou 516001, China
| | - Jia Zhou
- State
Key Laboratory of Microelectronics and Integrated Circuits, Fudan University, Shanghai 200433, China
| | - Wenming Wu
- Institute
of Biological and Medical Engineering, Guangdong
Academy of Sciences, Guangzhou 516001, China
| |
Collapse
|
29
|
Gimenez C, Sánchez ML, Valdez HA, Rodriguez ME, Grasselli M. PCR-tips for rapid diagnosis of bacterial pathogens. Appl Microbiol Biotechnol 2022; 106:5729-5739. [PMID: 35915170 PMCID: PMC9343218 DOI: 10.1007/s00253-022-12069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022]
Abstract
Micropipette tips are currently among the most used disposable devices in bioresearch and development laboratories. Their main application is the fractionation of solutions. New functionalities have recently been added to this device, widening their applications. This paper analyzed disposable micropipette tips as reagent holders of PCR reagents. PCR has become a prevalent and often indispensable technique in biological laboratories for various applications, such as the detection of coronavirus and other infectious diseases. A functional micropipette tip was implemented to simplify PCR analysis and reduce the contamination chances of deoxynucleotides and specific primers. This disposable device is prepared by tip coating processes of reagents, using polyvinyl alcohol polymer and additives. The coated layer is optimized to load and release PCR reagents efficiently. As a proof of concept, we show that the detection of Bordetella pertussis, the etiological agent of whooping cough whose diagnostic relies on PCR, can be quickly done using practical-functional tips. This device is an excellent example of testing the functionality and contribution of molecular diagnostic PCR tips. KEY POINTS: • Functional micropipette tips are prepared by coating with dNTPs and primers. • Functional tips are used to replace dNTPs and primers in the PCR master mix. • PCR diagnostic of Bordetella pertussis is performed using functional tips.
Collapse
Affiliation(s)
- Claudia Gimenez
- Departamento de Ciencia y Tecnología, Laboratorio de Materiales Biotecnológicos (LaMaBio), Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.,GBEyB, Multidisciplinary Institute of Cell Biology (IMBICE, Dependent of the Argentine Research Council (CONICET), Scientific Research Commission, Province of Buenos Aires (CIC‑PBA) and UNLP), La Plata, Argentina
| | - Mirna L Sánchez
- Departamento de Ciencia y Tecnología, Laboratorio de Materiales Biotecnológicos (LaMaBio), Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.,GBEyB, Multidisciplinary Institute of Cell Biology (IMBICE, Dependent of the Argentine Research Council (CONICET), Scientific Research Commission, Province of Buenos Aires (CIC‑PBA) and UNLP), La Plata, Argentina
| | - Hugo A Valdez
- Laboratorio de Microbiología Celular e Inmunomecanismos, CINDEFI
- Centro de Investigación y Desarrollo en Fermentaciones Industriales Facultad de Ciencias Exactas (UNLP), La Plata, Argentina
| | - María E Rodriguez
- Laboratorio de Microbiología Celular e Inmunomecanismos, CINDEFI
- Centro de Investigación y Desarrollo en Fermentaciones Industriales Facultad de Ciencias Exactas (UNLP), La Plata, Argentina
| | - Mariano Grasselli
- Departamento de Ciencia y Tecnología, Laboratorio de Materiales Biotecnológicos (LaMaBio), Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina. .,GBEyB, Multidisciplinary Institute of Cell Biology (IMBICE, Dependent of the Argentine Research Council (CONICET), Scientific Research Commission, Province of Buenos Aires (CIC‑PBA) and UNLP), La Plata, Argentina.
| |
Collapse
|
30
|
Sampieri A, Monroy-Contreras R, Asanov A, Vaca L. Design of Hydrogel Silk-Based Microarrays and Molecular Beacons for Reagentless Point-of-Care Diagnostics. Front Bioeng Biotechnol 2022; 10:881679. [PMID: 35957640 PMCID: PMC9361048 DOI: 10.3389/fbioe.2022.881679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
We have developed a novel microarray system based on three technologies: 1) molecular beacons designed to interact with DNA targets at room temperature (25–27°C), 2) tridimensional silk-based microarrays containing the molecular beacons immersed in the silk hydrogel, and 3) shallow angle illumination, which uses separated optical pathways for excitation and emission. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing, and stringency control, and measure only end-point results, our microarray technology provides enhanced signal-to-background ratio (achieved by separating the optical pathways for excitation and emission, resulting in reduced stray light), performs analysis rapidly in one step without the need for labeling DNA targets, and measures the entire course of association kinetics between target DNA and the molecular beacons. To illustrate the benefits of our technology, we conducted microarray assays designed for the identification of influenza viruses. We show that in a single microarray slide, we can identify the virus subtype according to the molecular beacons designed for hemagglutinin (H1, H2, and H3) and neuraminidase (N1, N2). We also show the identification of human and swine influenza using sequence-specific molecular beacons. This microarray technology can be easily implemented for reagentless point-of-care diagnostics of several contagious diseases, including coronavirus variants responsible for the current pandemic.
Collapse
Affiliation(s)
- Alicia Sampieri
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | - Ricardo Monroy-Contreras
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
| | | | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, UNAM, Ciudad Universitaria, Mexico, Mexico
- *Correspondence: Luis Vaca,
| |
Collapse
|
31
|
Stevenson EM, Gaze WH, Gow NAR, Hart A, Schmidt W, Usher J, Warris A, Wilkinson H, Murray AK. Antifungal Exposure and Resistance Development: Defining Minimal Selective Antifungal Concentrations and Testing Methodologies. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:918717. [PMID: 37746188 PMCID: PMC10512330 DOI: 10.3389/ffunb.2022.918717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 09/26/2023]
Abstract
This scoping review aims to summarise the current understanding of selection for antifungal resistance (AFR) and to compare and contrast this with selection for antibacterial resistance, which has received more research attention. AFR is an emerging global threat to human health, associated with high mortality rates, absence of effective surveillance systems and with few alternative treatment options available. Clinical AFR is well documented, with additional settings increasingly being recognised to play a role in the evolution and spread of AFR. The environment, for example, harbours diverse fungal communities that are regularly exposed to antifungal micropollutants, potentially increasing AFR selection risk. The direct application of effect concentrations of azole fungicides to agricultural crops and the incomplete removal of pharmaceutical antifungals in wastewater treatment systems are of particular concern. Currently, environmental risk assessment (ERA) guidelines do not require assessment of antifungal agents in terms of their ability to drive AFR development, and there are no established experimental tools to determine antifungal selective concentrations. Without data to interpret the selective risk of antifungals, our ability to effectively inform safe environmental thresholds is severely limited. In this review, potential methods to generate antifungal selective concentration data are proposed, informed by approaches used to determine antibacterial minimal selective concentrations. Such data can be considered in the development of regulatory guidelines that aim to reduce selection for AFR.
Collapse
Affiliation(s)
- Emily M. Stevenson
- European Centre for Environment and Human Health, University of Exeter Medical School, Cornwall, United Kingdom
- Environment and Sustainability Institute, University of Exeter Medical School, Cornwall, United Kingdom
| | - William H. Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Cornwall, United Kingdom
- Environment and Sustainability Institute, University of Exeter Medical School, Cornwall, United Kingdom
| | - Neil A. R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Alwyn Hart
- Chief Scientist’s Group, Environment Agency, Horizon House, Bristol, England, United Kingdom
| | - Wiebke Schmidt
- Chief Scientist’s Group, Environment Agency, Horizon House, Bristol, England, United Kingdom
| | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Adilia Warris
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Helen Wilkinson
- Chief Scientist’s Group, Environment Agency, Horizon House, Bristol, England, United Kingdom
| | - Aimee K. Murray
- European Centre for Environment and Human Health, University of Exeter Medical School, Cornwall, United Kingdom
- Environment and Sustainability Institute, University of Exeter Medical School, Cornwall, United Kingdom
| |
Collapse
|
32
|
Zhou X, Schuh DA, Castle LM, Furst AL. Recent Advances in Signal Amplification to Improve Electrochemical Biosensing for Infectious Diseases. Front Chem 2022; 10:911678. [PMID: 35769443 PMCID: PMC9234564 DOI: 10.3389/fchem.2022.911678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
The field of infectious disease diagnostics is burdened by inequality in access to healthcare resources. In particular, “point-of-care” (POC) diagnostics that can be utilized in non-laboratory, sub-optimal environments are appealing for disease control with limited resources. Electrochemical biosensors, which combine biorecognition elements with electrochemical readout to enable sensitive and specific sensing using inexpensive, simple equipment, are a major area of research for the development of POC diagnostics. To improve the limit of detection (LOD) and selectivity, signal amplification strategies have been applied towards these sensors. In this perspective, we review recent advances in electrochemical biosensor signal amplification strategies for infectious disease diagnostics, specifically biosensors for nucleic acids and pathogenic microbes. We classify these strategies into target-based amplification and signal-based amplification. Target-based amplification strategies improve the LOD by increasing the number of detectable analytes, while signal-based amplification strategies increase the detectable signal by modifying the transducer system and keep the number of targets static. Finally, we argue that signal amplification strategies should be designed with application location and disease target in mind, and that the resources required to produce and operate the sensor should reflect its proposed application, especially when the platform is designed to be utilized in low-resource settings. We anticipate that, based on current technologies to diagnose infectious diseases, incorporating signal-based amplification strategies will enable electrochemical POC devices to be deployed for illnesses in a wide variety of settings.
Collapse
Affiliation(s)
- Xingcheng Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Daena A. Schuh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Lauren M. Castle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ariel L. Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Ariel L. Furst,
| |
Collapse
|
33
|
Kostovska I, Trajkovska KT, Topuzovska S, Cekovska S, Labudovic D, Kostovski O, Spasovski G. Nephrinuria and podocytopathies. Adv Clin Chem 2022; 108:1-36. [PMID: 35659057 DOI: 10.1016/bs.acc.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The discovery of nephrin in 1998 has launched a new era in glomerular diseases research, emphasizing its crucial role in the structure and function of the glomerular filtration barrier. In the past 20 years, substantial advances have been made in understanding podocyte structure and function as well as the discovery of several podocyte-related proteins including nephrin. The glomerular filtration barrier is comprised of podocytes, the glomerular basement membrane and endothelial cells. Podocytes, with their specialized slit diaphragm, form the essential backbone of the glomerular filtration barrier. Nephrin is a crucial structural and functional feature of the slit diaphragm that prevents plasma protein, blood cell and macromolecule leakage into the urine. Podocyte damage results in nephrin release. Podocytopathies are kidney diseases in which podocyte damage drives proteinuria, i.e., nephrotic syndrome. Many kidney diseases involve podocytopathy including congenital nephrotic syndrome of Finnish type, diffuse mesangial sclerosis, minimal change disease, focal segmental glomerulosclerosis, collapsing glomerulonephropathy, diabetic nephropathy, lupus nephropathy, hypertensive nephropathy and preeclampsia. Recently, urinary nephrin measurement has become important in the early detection of podocytopathies. In this chapter, we elaborate the main structural and functional features of nephrin as a podocyte-specific protein, pathomechanisms of podocytopathies which result in nephrinuria, highlight the most commonly used methods for detecting urinary nephrin and investigate the diagnostic, prognostic and potential therapeutic relevance of urinary nephrin in primary and secondary proteinuric kidney diseases.
Collapse
Affiliation(s)
- Irena Kostovska
- Department of Medical and Experimental Biochemistry, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia.
| | - Katerina Tosheska Trajkovska
- Department of Medical and Experimental Biochemistry, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Sonja Topuzovska
- Department of Medical and Experimental Biochemistry, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Svetlana Cekovska
- Department of Medical and Experimental Biochemistry, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Danica Labudovic
- Department of Medical and Experimental Biochemistry, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Ognen Kostovski
- University Clinic of Abdominal Surgery, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Goce Spasovski
- University Clinic of Nephrology, Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| |
Collapse
|
34
|
Wang K, Jiang Y, Guo Y, Geng M, Wu W. An Optimized Thermal Feedback Methodology for Accurate Temperature Control and High Amplification Efficiency during Fluorescent qPCR. Bioengineering (Basel) 2022; 9:bioengineering9060237. [PMID: 35735480 PMCID: PMC9220086 DOI: 10.3390/bioengineering9060237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/27/2022] Open
Abstract
Traditional qPCR instrument is combined with CMOS and a personal computer, and a photoelectric feedback automatic fluorescence detection system is designed to realize quantitative real-time PCR. The key to reaction efficiency lies in how to ensure that the temperature of the detection reagent completely matches the set temperature. However, for most traditional real-time fluorescent PCR systems, the temperature cycling is controlled by detecting the temperature of the heating well plate. It cannot directly measure the temperature in the reaction reagent PCR tube, which will cause the deviation in the actual temperature of the reagent to be as expected. Therefore, in this paper, we raise a method of directly detecting the temperature in the reaction tube of the reagent during the temperature cycling is adopted. According to the deviation from the expected value, the set temperature of the PCR instrument is adjusted to make the actual temperature of the reagent closer to the expected value. Through this method, we also realized the temperature calibration and optimization of the TEC circulation system we built. Experiments show that this low-cost, portable real-time quantitative PCR system can detect and analyze pathogens in situ.
Collapse
Affiliation(s)
- Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yangyang Jiang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou 510006, China;
| | - Mingkun Geng
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China;
- Graduate School, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510000, China; (K.W.); (Y.J.)
- Correspondence:
| |
Collapse
|
35
|
Li J, Fu N, Ren L, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Monochamus saltuarius Under Bursaphelenchus xylophilus Treatment. Front Physiol 2022; 13:882792. [PMID: 35547586 PMCID: PMC9082747 DOI: 10.3389/fphys.2022.882792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
A special mutual relationship exists between the pine wood nematode (PWN) Bursaphelenchus xylophilus and its vector beetles of genus Monochamus, which enables PWN to spread, at the same time provides longhorned beetles with more weak hosts. PWN are attracted to the pupal chambers and then carried inside the trachea of beetle adults, which is a necessary part to complete the B. xylophilus infection cycle. The growth and immune responses of the vector beetle will affect this carrying process, however, they were rarely studied in Monochamus saltuarius. Real-time quantitative polymerase chain reaction (RT-qPCR), one of the most common methods for quantitative gene expression analysis, was performed to explore the key genes and pathways involved in the growth, development and immune responses of M. saltuarius at different developmental stages associated with infection of PWN and PWN treatment conditions. To enhance the accuracy of RT-qPCR data, the expression of target genes needs to be normalized with reference genes, which are stably expressed under varied experimental conditions. In our study, the stability of 14 candidate reference genes in M. saltuarius samples at different developmental stages associated with infection of PWN or PWN treatment conditions was evaluated using delta Ct, geNorm, NormFinder, BestKeeper and RefFinder algorithms. Moreover, KLF gene was used to validate the stability of the selected reference genes. Under experimental conditions of this study, RPL7 and TER were suitable reference genes at different developmental stages associated with infection of PWN. RPL7 and RPS5 were considered the most stable reference genes in the pupae treated with PWN. RPS5 and SNX6 could be used as reference genes in the adults treated with PWN. RPL7, EF1-γ, and RPS5 could be used as stable reference genes in all the samples. This work is the first to evaluate reference genes in M. saltuarius, laying a foundation for further gene expression experimental procedures and understanding the phoretic relationship between M. saltuarius and B. xylophilus.
Collapse
Affiliation(s)
- Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| |
Collapse
|
36
|
Papadakis G, Pantazis AK, Fikas N, Chatziioannidou S, Tsiakalou V, Michaelidou K, Pogka V, Megariti M, Vardaki M, Giarentis K, Heaney J, Nastouli E, Karamitros T, Mentis A, Zafiropoulos A, Sourvinos G, Agelaki S, Gizeli E. Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples. Sci Rep 2022; 12:3775. [PMID: 35260588 PMCID: PMC8904468 DOI: 10.1038/s41598-022-06632-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/27/2022] [Indexed: 02/08/2023] Open
Abstract
Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.
Collapse
Affiliation(s)
- G Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.
| | - A K Pantazis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - N Fikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - S Chatziioannidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - V Tsiakalou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - K Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - V Pogka
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - M Megariti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - M Vardaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - K Giarentis
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - J Heaney
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Nastouli
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - T Karamitros
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Mentis
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Zafiropoulos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - S Agelaki
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.,Department of Medical Oncology, University General Hospital, 71110, Heraklion, Greece
| | - E Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.
| |
Collapse
|
37
|
Saad-Hussein A, Soliman KM, Moubarz G. 18S rRNA gene sequencing for environmental aflatoxigenic fungi and risk of hepatic carcinoma among exposed workers. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 57:174-182. [PMID: 35236253 DOI: 10.1080/10934529.2022.2046428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Aspergillus exposure causes an increase in aflatoxin (AF) levels among exposed workers thereby increasing their risk of developing hepatocellular carcinoma (HCC). This study attempted to determine the presence of airborne aflatoxigenic fungi in environment of waste water treatment plant (WWTP); and study the hepatic cancer risks among exposed workers, emphasizing the role of glutathione S-transferases (GST) gene polymorphism protecting against the risk of hepatic cancer development due to exposure to AFs. The study isolated and identified different Aspergillus species producing AFs in air samples from WWTP sites using 18S ribosomal ribonucleic acid (18S rRNA) gene sequencing technique. GST gene polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). A significant increase in blood AF levels was found among WWTP exposed workers. The occurrence of GSTT1& M1 gene polymorphism in 6% of the workers was accompanied by significant decrease in the levels of AFs and alpha fetoprotein (AFP). In conclusion, Aspergillus-producing AFs were found in air of WWTP. Continuous exposure to AF-producing fungi caused elevated AF-levels in exposed workers. However only workers with heterozygous GSTT1& M1 genotypes can detoxify AFs, thereby decreasing the risk of HCC development among exposed workers.
Collapse
Affiliation(s)
- Amal Saad-Hussein
- Environmental & Occupational Medicine Department, National Research Centre, Dokki, Cairo, Egypt
| | - Kawther M Soliman
- Food Toxicology and Contaminants Department, National Research Centre, Dokki, Cairo, Egypt
| | - Gehan Moubarz
- Environmental & Occupational Medicine Department, National Research Centre, Dokki, Cairo, Egypt
| |
Collapse
|
38
|
Zhang Z, Weng Z, Yao J, Liu D, Zhang L, Zhang L, Xie G. Toehold-mediated nonenzymatic DNA strand displacement coupling UDG mediated PCR and multi-code magnetic beads for DNA genotyping. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
39
|
Development and validation of multiplex SYBR Green real-time PCR assays for detection and molecular surveillance of four tick-borne canine haemoparasites. Ticks Tick Borne Dis 2022; 13:101937. [DOI: 10.1016/j.ttbdis.2022.101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
|
40
|
Abstract
One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.
Collapse
Affiliation(s)
- Brian M. Schmidt
- Michigan Medicine, Department of
Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, Ann Arbor,
MI, USA
- Brian M. Schmidt, DPM, Assistant Professor,
Department of Internal Medicine, Division of Metabolism, Endocrinology, and
Diabetes, University of Michigan Medical School, 24 Frank Lloyd Wright Drive,
Lobby C, Ann Arbor, MI 48106, USA.
| |
Collapse
|
41
|
Miłobedzka A, Ferreira C, Vaz-Moreira I, Calderón-Franco D, Gorecki A, Purkrtova S, Dziewit L, Singleton CM, Nielsen PH, Weissbrodt DG, Manaia CM. Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127407. [PMID: 34629195 DOI: 10.1016/j.jhazmat.2021.127407] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 05/10/2023]
Abstract
Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.
Collapse
Affiliation(s)
- Aleksandra Miłobedzka
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; Institute of Evolutionary Biology, University of Warsaw, Warsaw, Poland.
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | | | - Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Caitlin M Singleton
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
| |
Collapse
|
42
|
Shen CH, Peng LJ, Zhang YX, Zeng HR, Yu HF, Jin L, Li GQ. Reference Genes for Expression Analyses by qRT-PCR in Phthorimaea operculella (Lepidoptera: Gelechiidae). INSECTS 2022; 13:insects13020140. [PMID: 35206714 PMCID: PMC8879603 DOI: 10.3390/insects13020140] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022]
Abstract
Due to a lack of effective internal references, studies on functional genes in Phthorimaea operculella, a serious Lepidopteran pest attacking potatoes worldwide, have been greatly limited. To select suitable endogenous controls, ten housekeeping genes of actin (ACT), α-tubulin (α-TUB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1α), 18S and 28S ribosomal RNA (18S, 28S), ribosomal protein genes RPL4, RPL13 and RPL27 and superoxide dismutase (SOD) were tested. Their expression levels were determined under three different experimental conditions (developmental stages, tissues/organs and temperatures) using qRT-PCR technology. The stability was evaluated with five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). The results clarified that RPL13, EF1α and RPL27 are ranked as the best reference gene combination for measuring gene expression levels among different developing stages and under various temperatures; EF1α and RPL13 are recommended to normalize the gene expression levels among diverse tissues. EF1α and RPL13 are the best reference genes in all the experimental conditions. To validate the utility of the selected reference pair, EF1α and RPL13, we estimated the tissue-biased expression level of chitin synthase A gene (PoChSA). As expected, PoChSA was abundantly expressed in ectodermally derived epidermal cells, and lowly transcribed in the midgut. These findings will lay the foundation for future research on the molecular physiology and biochemistry of P. operculella.
Collapse
Affiliation(s)
| | | | | | | | | | - Lin Jin
- Correspondence: ; Tel.: +86-25-84395248
| | | |
Collapse
|
43
|
Selection and Validation of Reliable Reference Genes for Gene Expression Studies in Different Genotypes and TRV-Infected Fruits of Peach (Prunus persica L. Batsch) during Ripening. Genes (Basel) 2022; 13:genes13010160. [PMID: 35052500 PMCID: PMC8775616 DOI: 10.3390/genes13010160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a powerful tool to detect and quantify transcription abundance, and the stability of the reference gene determines its success. However, the most suitable reference gene for different genotypes and tobacco rattle virus (TRV) infected fruits was unclear in peach (Prunus persica L. Batsch). In this study, 10 reference genes were selected and gene expression was characterized by RT-qPCR across all samples, including different genotypes and TRV-infected fruits during ripening. Four statistical algorithms (geNorm, NormFinder, BestKeeper, and RefFinder) were used to calculate the stability of 10 reference genes. The geNorm analysis indicated that two suitable reference genes should be used for gene expression normalization. In general, the best combination of reference genes was CYP2 and Tua5 for TRV-infected fruits and CYP2 and Tub1 for different genotypes. In 18S, GADPH, and TEF2, there is an unacceptable variability of gene expression in all experimental conditions. Furthermore, to confirm the validity of the reference genes, the expression levels of PpACO1, PpEIN2, and PpPL were normalized at different fruit storage periods. In summary, our results provide guidelines for selecting reliable reference genes in different genotypes and TRV-infected fruits and lay the foundation for accurate evaluation of gene expression for RT-qPCR analysis in peach.
Collapse
|
44
|
Zhao X, Geng Y, Hu T, Zhao Y, Yang S, Hao D. Evaluation of Optimal Reference Genes for qRT-PCR Analysis in Hyphantria cunea (Drury). INSECTS 2022; 13:97. [PMID: 35055939 PMCID: PMC8778541 DOI: 10.3390/insects13010097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022]
Abstract
The relative quantification of gene expression is mainly achieved through reverse transcription-quantitative PCR (qRT-PCR); however, its reliability and precision rely on proper data normalization using one or more optimal reference genes. Hyphantria cunea (Drury) has been an invasive pest of forest trees, ornamental plants, and fruit trees in China for many years. Currently, the molecular physiological role of reference genes in H. cunea is unclear, which hinders functional gene study. Therefore, eight common reference genes, RPS26, RPL13, UBI, AK, RPS15, EIF4A, β-actin, α-tub, were selected to evaluate levels of gene expression stability when subjected to varied experimental conditions, including developmental stage and gender, different tissues, larvae reared on different hosts and different larval density. The geNorm, BestKeeper, ΔCt method, and NormFinder statistical algorithms were used to normalize gene transcription data. Furthermore, the stability/suitability of these candidates was ranked overall by RefFinder. This study provides a comprehensive evaluation of reference genes in H. cunea and could help select reference genes for other Lepidoptera species.
Collapse
Affiliation(s)
- Xudong Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (Y.G.); (T.H.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yishu Geng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (Y.G.); (T.H.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Tianyi Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (Y.G.); (T.H.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yongang Zhao
- Forest Station of Huaian District, Huaian 223001, China; (Y.Z.); (S.Y.)
| | - Suling Yang
- Forest Station of Huaian District, Huaian 223001, China; (Y.Z.); (S.Y.)
| | - Dejun Hao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (X.Z.); (Y.G.); (T.H.)
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
45
|
Fan X, Li X, Zhang T, Xu J, Shi Z, Wu Z, Wu J, Pan D, Du L. A Novel qPCR Method for the Detection of Lactic Acid Bacteria in Fermented Milk. Foods 2021; 10:3066. [PMID: 34945617 PMCID: PMC8700909 DOI: 10.3390/foods10123066] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022] Open
Abstract
The number of live lactic acid bacteria (LAB) is an important quality indicator for yogurt, the quantitative testing of LAB has become an important task in the evaluation of product quality and function. By analyzing and comparing the performance of 16S rRNA gene and tuf gene used in absolute quantification, the tuf gene with copy number 1 was selected as the target gene of six LAB. By drawing a standard curve to achieve qualitative and quantitative detection of six strains of LAB, the detection range was found to be 1 × 103-1 × 108 copies/µL. The traditional plate colony count and Flow Cytometry (FCM) were compared with the method of qPCR, which was used in this experiment. Meanwhile, the confocal laser microscope combined with STYO 9 and propidium iodide dyes was used to determine that the content of viable bacteria in the yogurt was more than 90%, which proved that the detection result using qPCR method was closer to the true level of LAB in yogurt. Compared with the existing methods, the method in this study allowed the qualitative and quantitative detection of the six kinds of LAB in yogurt, and the distribution of live and dead bacteria in yogurt could be calculated.
Collapse
Affiliation(s)
- Xiankang Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Xiefei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Tao Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jue Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Zihang Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jihuan Wu
- Ningbo Yifule Biotechnology Co., Ltd., Ningbo 315500, China;
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Lihui Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| |
Collapse
|
46
|
Sulo P, Šipková B. DNA diagnostics for reliable and universal identification of Helicobacter pylori. World J Gastroenterol 2021; 27:7100-7112. [PMID: 34887630 PMCID: PMC8613642 DOI: 10.3748/wjg.v27.i41.7100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/11/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reliable diagnostics are a major challenge for the detection and treatment of Helicobacter pylori (H. pylori) infection. Currently at the forefront are non-invasive urea breath test (UBT) and stool antigen test (SAT). Polymerase chain reaction (PCR) is not endorsed due to nonspecific primers and the threat of false-positives. The specificity of DNA amplification can be achieved by nested PCR (NPCR), which involves two rounds of PCR. If the primers are properly designed for the variable regions of the 16S rRNA gene, it is not difficult to develop an NPCR assay for the unambiguous identification of H. pylori. Elaborate NPCR for a 454 bp amplicon was validated on 81 clinical biopsy, stool, and saliva samples, each from the same individuals, and compared with available H. pylori assays, namely histology, rapid urease test, SAT, and 13C-UBT. The assay was much more sensitive than simple PCR, and it was equally sensitive in biopsy samples as the 13C-UBT test, which is considered the gold standard. In addition, it is sufficiently specific because sequencing of the PCR products exclusively confirmed the presence of H. pylori-specific DNA. However, due to the threshold and lower abundance, the sensitivity was much lower in amplifications from stool or saliva. Reliable detection in saliva also complicates the ability of H. pylori to survive in the oral cavity aside from and independent of the stomach. The reason for the lower sensitivity in stool is DNA degradation; therefore, a new NPCR assay was developed to obtain a shorter 148 bp 16S rRNA amplicon. The assay was validated on stool samples from 208 gastroenterological patients and compared to SAT results. Surprisingly, this NPCR revealed the presence of H. pylori in twice the number of samples as SAT, indicating that many patients are misdiagnosed, not treated by antibiotics, and their problems are interpreted as chronic. Thus, it is unclear how to properly diagnose H. pylori in practice. In the first approach, SAT or UBT is sufficient. If samples are negative, the 148 bp amplicon NPCR assay should be performed. If problems persist, patients should not be considered negative, but due to threshold H. pylori abundance, they should be periodically tested. The advantage of NPCR over UBT is that it can be used universally, including questionable samples taken from patients with achlorhydria, receiving proton pump inhibitors, antibiotics, bismuth compound, intestinal metaplasia, or gastric ulcer bleeding.
Collapse
Affiliation(s)
- Pavol Sulo
- Department of Biochemistry, Comenius University, Bratislava 842 15, Slovakia
| | - Barbora Šipková
- Department of Biochemistry, Comenius University, Bratislava 842 15, Slovakia
| |
Collapse
|
47
|
Wang Y, Wang Q, Bergmann SM, Li Y, Li B, Lv Y, Yin J, Yang G, Qv Y, Wang Y, Zeng W. Development and comparative evaluation of real-time PCR and real-time RPA assays for detection of tilapia lake virus. Mol Cell Probes 2021; 60:101776. [PMID: 34740779 DOI: 10.1016/j.mcp.2021.101776] [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: 07/26/2021] [Revised: 10/04/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022]
Abstract
Tilapia lake virus (TiLV) is a newly emerged pathogen responsible for high mortality and economic losses in the global tilapia industry. Early and accurate diagnosis is an important priority for TiLV disease control. In order to evaluate the methodology in the molecular diagnosis of TiLV, we compared newly developed quantitative real-time PCR (qPCR) and real-time recombinase polymerase amplification (real-time RPA) assays regarding their sensitivities, specificities and detection effect on clinical samples. Real-time RPA amplified the target pathogen in less than 30 min at 39 °C with a detection limit of 620 copies, while qPCR required about 60 min with a detection limit of 62 copies. Both assays were specific for TiLV and there were no cross-reactions observed with other common fish pathogens. The assays were validated using 35 tissue samples from clinically infected and 60 from artificially infected animals. The sensitivities for the real-time RPA and qPCR assays were 93.33 and 100%, respectively, and the specificity was 100% for both. Both methods have their advantages and can play their roles in different situations. The qPCR is more suitable for quantitative analysis and accurate detection of TiLV in a diagnostic laboratory, whereas real-time RPA is more suitable for the diagnosis of clinical diseases and preliminary screening for TiLV infection in poorly equipped laboratories as well as in fish farms.
Collapse
Affiliation(s)
- Yahui Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Qing Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Yingying Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Bo Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Yuefeng Lv
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Jiyuan Yin
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China
| | - Guang Yang
- College of Fisheries, Tianjin Agriculture University, Tianjin, China
| | - Yang Qv
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China
| | - Yingying Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong China.
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.
| |
Collapse
|
48
|
Nasrollahi F, Haghniaz R, Hosseini V, Davoodi E, Mahmoodi M, Karamikamkar S, Darabi MA, Zhu Y, Lee J, Diltemiz SE, Montazerian H, Sangabathuni S, Tavafoghi M, Jucaud V, Sun W, Kim H, Ahadian S, Khademhosseini A. Micro and Nanoscale Technologies for Diagnosis of Viral Infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100692. [PMID: 34310048 PMCID: PMC8420309 DOI: 10.1002/smll.202100692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.
Collapse
Affiliation(s)
- Fatemeh Nasrollahi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Elham Davoodi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Mechanical and Mechatronics EngineeringUniversity of WaterlooWaterlooONN2L 3G1Canada
| | - Mahboobeh Mahmoodi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Biomedical EngineeringYazd BranchIslamic Azad UniversityYazd8915813135Iran
| | | | - Mohammad Ali Darabi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Junmin Lee
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Sibel Emir Diltemiz
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of ChemistryFaculty of ScienceEskisehir Technical UniversityEskisehir26470Turkey
| | - Hossein Montazerian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | | | - Maryam Tavafoghi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Wujin Sun
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Han‐Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| |
Collapse
|
49
|
Fiddler JL, Clarke SL. Evaluation of candidate reference genes for quantitative real-time PCR analysis in a male rat model of dietary iron deficiency. GENES & NUTRITION 2021; 16:17. [PMID: 34600467 PMCID: PMC8487497 DOI: 10.1186/s12263-021-00698-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Quantitative real-time polymerase chain reaction (qPCR) is a reliable and efficient method for quantitation of gene expression. Due to the increased use of qPCR in examining nutrient-gene interactions, it is important to examine, develop, and utilize standardized approaches for data analyses and interpretation. A common method used to normalize expression data involves the use of reference genes (RG) to determine relative mRNA abundance. When calculating the relative abundance, the selection of RG can influence experimental results and has the potential to skew data interpretation. Although common RG may be used for normalization, often little consideration is given to the suitability of RG selection for an experimental condition or between various tissue or cell types. In the current study, we examined the stability of gene expression using BestKeeper, comparative delta quantitation cycle, NormFinder, and RefFinder in a variety of tissues obtained from iron-deficient and pair-fed iron-replete rats to determine the optimal selection among ten candidate RG. RESULTS Our results suggest that several commonly used RG (e.g., Actb and Gapdh) exhibit less stability compared to other candidate RG (e.g., Rpl19 and Rps29) in both iron-deficient and iron-replete pair-fed conditions. For all evaluated RG, Tfrc expression significantly increased in iron-deficient animal livers compared to the iron-replete pair-fed controls; however, the relative induction varied nearly 4-fold between the most suitable (Rpl19) and least suitable (Gapdh) RG. CONCLUSION These results indicate the selection and use of RG should be empirically determined and RG selection may vary across experimental conditions and biological tissues.
Collapse
Affiliation(s)
- Joanna L Fiddler
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14850-6301, USA.
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Stephen L Clarke
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| |
Collapse
|
50
|
Chiu RYT, Kojima N, Mosley GL, Cheng KK, Pereira DY, Brobeck M, Chan TL, Zee JST, Kittur H, Chung CYT, Tsang E, Maran K, Yung RWH, Leung ACP, Siu RHP, Ng JPL, Choi TH, Fung MW, Chan WS, Lam HY, Lee KH, Parkin S, Chao FC, Ho SKN, Marshak DR, Ma ESK, Klausner JD. Evaluation of the INDICAID COVID-19 Rapid Antigen Test in Symptomatic Populations and Asymptomatic Community Testing. Microbiol Spectr 2021; 9:e0034221. [PMID: 34346748 PMCID: PMC8552729 DOI: 10.1128/spectrum.00342-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/24/2021] [Indexed: 12/03/2022] Open
Abstract
As the COVID-19 pandemic progresses, there is an increasing need for rapid, accessible assays for SARS-CoV-2 detection. We present a clinical evaluation and real-world implementation of the INDICAID COVID-19 rapid antigen test (INDICAID rapid test). A multisite clinical evaluation of the INDICAID rapid test using prospectively collected nasal (bilateral anterior) swab samples from symptomatic subjects was performed. The INDICAID rapid test demonstrated a positive percent agreement (PPA) and negative percent agreement (NPA) of 85.3% (95% confidence interval [95% CI], 75.6% to 91.6%) and 94.9% (95% CI, 91.6% to 96.9%), respectively, compared to laboratory-based reverse transcriptase PCR (RT-PCR) using nasal specimens. The INDICAID rapid test was then implemented at COVID-19 outbreak screening centers in Hong Kong as part of a testing algorithm (termed "dual-track") to screen asymptomatic individuals for prioritization for confirmatory RT-PCR testing. In one approach, preliminary positive INDICAID rapid test results triggered expedited processing for laboratory-based RT-PCR, reducing the average time to confirmatory result from 10.85 h to 7.0 h. In a second approach, preliminary positive results triggered subsequent testing with an onsite rapid RT-PCR, reducing the average time to confirmatory result to 0.84 h. In 22,994 asymptomatic patients, the INDICAID rapid test demonstrated a PPA of 84.2% (95% CI, 69.6% to 92.6%) and an NPA of 99.9% (95% CI, 99.9% to 100%) compared to laboratory-based RT-PCR using combined nasal/oropharyngeal specimens. The INDICAID rapid test has excellent performance compared to laboratory-based RT-PCR testing and, when used in tandem with RT-PCR, reduces the time to confirmatory positive result. IMPORTANCE Laboratory-based RT-PCR, the current gold standard for COVID-19 testing, can require a turnaround time of 24 to 48 h from sample collection to result. The delayed time to result limits the effectiveness of centralized RT-PCR testing to reduce transmission and stem potential outbreaks. To address this, we conducted a thorough evaluation of the INDICAID COVID-19 rapid antigen test, a 20-minute rapid antigen test, in both symptomatic and asymptomatic populations. The INDICAID rapid test demonstrated high sensitivity and specificity with RT-PCR as the comparator method. A dual-track testing algorithm was also evaluated utilizing the INDICAID rapid test to screen for preliminary positive patients, whose samples were then prioritized for RT-PCR testing. The dual-track method demonstrated significant improvements in expediting the reporting of positive RT-PCR test results compared to standard RT-PCR testing without prioritization, offering an improved strategy for community testing and controlling SARS-CoV-2 outbreaks.
Collapse
Affiliation(s)
- Ricky Y. T. Chiu
- Phase Scientific International Ltd., Garden Grove, California, USA
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Noah Kojima
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Garrett L. Mosley
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Kwok Kin Cheng
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - David Y. Pereira
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Matthew Brobeck
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Jonpaul Sze-Tsing Zee
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Harsha Kittur
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | | | - Eric Tsang
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Kajal Maran
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Raymond Wai-Hung Yung
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Alex Chin-Pang Leung
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Ryan Ho-Ping Siu
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | | | - Tsz Hei Choi
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Mei Wai Fung
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Ho Yin Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Koon Hung Lee
- Department of Hospital Administration, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Sean Parkin
- CityHealth Urgent Care, Alameda, California, USA
| | - Felix C. Chao
- Phase Scientific International Ltd., Garden Grove, California, USA
| | - Stephen Ka-Nung Ho
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Daniel R. Marshak
- Phase Scientific International Ltd., Garden Grove, California, USA
- Phase Scientific International Ltd., Hong Kong, People’s Republic of China
| | - Edmond Shiu-Kwan Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, People’s Republic of China
| | - Jeffrey D. Klausner
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California
| |
Collapse
|