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Wang S, Wei R, Ma X, Guo J, Aizaz M, Li F, Wang J, Wang H, He H. The host protein CALCOCO2 interacts with bovine viral diarrhoea virus Npro, inhibiting type I interferon production and thereby promoting viral replication. Virulence 2024; 15:2289764. [PMID: 38047736 PMCID: PMC10730213 DOI: 10.1080/21505594.2023.2289764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Bovine viral diarrhoea-mucosal disease caused by bovine viral diarrhoea virus (BVDV) is a major infectious disease that affects the cattle industry. The nonstructural protein Npro of BVDV antagonizes the type I interferon (IFN-I) pathway, thereby escaping the host immune response. The exact mechanism by which Npro uses host proteins to inhibit IFN-I production is unclear. The host protein CALCOCO2 was identified as a binding partner of Npro using a yeast two-hybrid screen. The interaction between Npro and CALCOCO2 was confirmed by yeast co-transformation, co-immunoprecipitation assays, and GST pull-down assays. The stable overexpression of CALCOCO2 markedly promoted BVDV propagation, while the knockdown of CALCOCO2 significantly inhibited BVDV replication in MDBK cells. Interestingly, CALCOCO2 inhibited IFN-I and IFN-stimulated gene production in BVDV-infected cells. Ectopic expression of CALCOCO2 effectively reduced IRF3 protein levels via the proteasome pathway. CALCOCO2 was found to promote Npro-mediated ubiquitination degradation of IRF3 by interacting with IRF3. Our results demonstrate the molecular mechanism by which Npro recruits the CALCOCO2 protein to regulate IRF3 degradation to inhibit IFN-I production.
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Affiliation(s)
- Song Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Xiaomei Ma
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jin Guo
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Muhammad Aizaz
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Fangxu Li
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Wang
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongmei Wang
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongbin He
- Ruminant Diseases Research Center, College of Life Sciences, Shandong Normal University, Jinan, China
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Bissonnette N, Brousseau JP, Ollier S, Byrne AS, Ibeagha-Awemu EM, Tahlan K. Systematic assessment of the reliability of quantitative PCR assays targeting IS900 for the detection of Mycobacterium avium ssp. paratuberculosis presence in animal and environmental samples. J Dairy Sci 2024; 107:7165-7184. [PMID: 38754821 DOI: 10.3168/jds.2023-24566] [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: 12/18/2023] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the bacterium responsible for causing Johne's disease (JD), which is endemic to dairy cattle and also implicated in the etiology of Crohn's disease. The difficulty in diagnosing asymptomatic cows for JD makes this disease hard to control. Johne's disease is considered a priority under the One Health approach to prevent the spread of the causative agent to humans. Environmental screening is a strategic approach aimed at identifying dairy herds with animals infected with MAP. It serves as the initial step toward implementing more intensive actions to control the disease. Quantitative PCR (qPCR) technology is widely used for diagnosis. Given that genome sequencing is now much more accessible than ever before, it is possible to target regions of the MAP genome that allow for the greatest diagnostic sensitivity and specificity. The aim of this study was to identify among the published qPCR assays targeting IS900 the more cost-effective options to detect MAP and to validate them in the diagnostic context of JD. Mycobacterium avium ssp. paratuberculosis IS900 is a prime target because it is a multicopy genetic element. A total of 136 publications have reported on the use of IS900 qPCR assays over the past 3 decades. Among these records, 29 used the SYBR Green chemistry, and 107 used TaqMan technology. Aside from the 9 reports using commercial assays, 72 TaqMan reports cited previously published work, leaving us with 27 TaqMan qPCR designs. Upon closer examination, 5 TaqMan designs contained mismatches in primer or probe sequences. Additionally, others exhibited high similarity to environmental microorganisms or non-MAP mycobacteria. We assessed the performance of 6 IS900 qPCR designs and their sensitivity when applied to clinical or environmental samples, which varied from 4 to 56 fold overall. Additionally, we provide recommendations for testing clinical and environmental samples, as certain strategies used previously should be avoided due to poor qPCR design (e.g., the presence of mismatches) or a lack of specificity.
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Affiliation(s)
- N Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada.
| | - J-P Brousseau
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - S Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - A S Byrne
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - E M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - K Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
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Nandwa JO, Mehmood A, Mahjabeen I, Raheem KY, Hamadou M, Raimi MZ, Kayani MA. miR-4716-3p and the target AKT2 Gene/rs2304186 SNP are associated with blood cancer pathogenesis in Pakistani population. Noncoding RNA Res 2024; 9:695-703. [PMID: 38577021 PMCID: PMC10990746 DOI: 10.1016/j.ncrna.2024.03.005] [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: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
AKT2 is crucial for cancer cells' invasion, metastasis, and survival. It is a possible downstream gene target of cancer glycolysis-related microRNAs. The study investigated the role of miRNA-4716-3p, rs2304186, and the AKT2 gene in blood cancer pathogenesis. RT-qPCR was used to analyze AKT2 gene mRNA and miRNA-4716-3p expression in 200 blood cancer samples and 200 healthy controls. Furthermore, Tetra-ARMS PCR was used to examine the rs2304186 AKT2 SNP in 300 patients and 290 control samples. miRNA-4716-3p was shown to be significantly downregulated (p = 0.0294), whereas mRNA expression of the AKT2 gene was found to be significantly upregulated (p = 0.0034) in blood cancer patients compared to healthy individuals. miRNA-4716-3p downregulation (p = 0.0466) was more pronounced, while AKT2 upregulation was non-significant (p = 0.1661) in untreated patients compared to chemotherapy-treated patients. Blood cancer risk was significantly associated with the rs2304186 GT genotype (p = 0.0432), TT genotype (p = 0.0502), and mutant allele (T) frequency (p = 0.0008). Polymorphism rs2304186 was associated with an increased risk of blood cancer in dominant (p = 0.0011), recessive (p = 0.0502), and additive (p = 0.0008) genetic models. The results suggested that the rs2304186 and the deregulated expression of miRNA-4716-3p and AKT2 gene at the mRNA level may significantly increase the incidence of blood cancer, particularly in the Pakistani population. Therefore, these may function as suitable biomarkers for blood cancer diagnosis and prognosis. Additional, larger-scale investigations may be required to affirm these results.
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Affiliation(s)
- Jairus Olumasai Nandwa
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Department of Public Needs Research, Integrated Cancer Research Foundation of Kenya, Kenya
- Department of Genetics, Hebrew University of Jerusalem, Israel
| | - Azhar Mehmood
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | | | - Mamoudou Hamadou
- Department of Biological Sciences, Faculty of Science, University of Maroua, Cameroon
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Kamau MW, Witte C, Goosen W, Mutinda M, Villinger J, Getange D, Khogali R, von Fricken ME, Fèvre EM, Zimmerman D, Linton YM, Miller M. Comparison of test performance of a conventional PCR and two field-friendly tests to detect Coxiella burnetii DNA in ticks using Bayesian latent class analysis. Front Vet Sci 2024; 11:1396714. [PMID: 38962707 PMCID: PMC11220323 DOI: 10.3389/fvets.2024.1396714] [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: 03/06/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Introduction Coxiella burnetii (C. burnetii)-infected livestock and wildlife have been epidemiologically linked to human Q fever outbreaks. Despite this growing zoonotic threat, knowledge of coxiellosis in wild animals remains limited, and studies to understand their epidemiologic role are needed. In C. burnetii-endemic areas, ticks have been reported to harbor and spread C. burnetii and may serve as indicators of risk of infection in wild animal habitats. Therefore, the aim of this study was to compare molecular techniques for detecting C. burnetii DNA in ticks. Methods In total, 169 ticks from wild animals and cattle in wildlife conservancies in northern Kenya were screened for C. burnetii DNA using a conventional PCR (cPCR) and two field-friendly techniques: Biomeme's C. burnetii qPCR Go-strips (Biomeme) and a new C. burnetii PCR high-resolution melt (PCR-HRM) analysis assay. Results were evaluated, in the absence of a gold standard test, using Bayesian latent class analysis (BLCA) to characterize the proportion of C. burnetii positive ticks and estimate sensitivity (Se) and specificity (Sp) of the three tests. Results The final BLCA model included main effects and estimated that PCR-HRM had the highest Se (86%; 95% credible interval: 56-99%), followed by the Biomeme (Se = 57%; 95% credible interval: 34-90%), with the estimated Se of the cPCR being the lowest (24%, 95% credible interval: 10-47%). Specificity estimates for all three assays ranged from 94 to 98%. Based on the model, an estimated 16% of ticks had C. burnetii DNA present. Discussion These results reflect the endemicity of C. burnetii in northern Kenya and show the promise of the PCR-HRM assay for C. burnetii surveillance in ticks. Further studies using ticks and wild animal samples will enhance understanding of the epidemiological role of ticks in Q fever.
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Affiliation(s)
- Maureen W. Kamau
- Mpala Research Centre, Nanyuki, Kenya
- Division of Molecular Biology and Human Genetics, Department of Science, and Innovation – National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
- Global Health Program, Smithsonian National Zoo Conservation Biology Institute, Washington, DC, United States
| | - Carmel Witte
- Division of Molecular Biology and Human Genetics, Department of Science, and Innovation – National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
- The Center for Wildlife Studies, South Freeport, ME, United States
| | - Wynand Goosen
- Division of Molecular Biology and Human Genetics, Department of Science, and Innovation – National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | | | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Dennis Getange
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Rua Khogali
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Michael E. von Fricken
- College of Public Health and Health Professionals, Department of Environmental and Global Health University of Florida, Gainesville, FL, United States
| | - Eric Maurice Fèvre
- International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Dawn Zimmerman
- Veterinary Initiative for Endangered Wildlife, Bozeman, MT, United States
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU) Smithsonian Institution Museum Support Center, Suitland, MD, United States
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States
- Department of Entomology, Smithsonian Institution, National Museum of Natural History (NMNH), Washington, DC, United States
| | - Michele Miller
- Division of Molecular Biology and Human Genetics, Department of Science, and Innovation – National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
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Monfort-Lanzas P, Rusu EC, Parrakova L, Karg CA, Kernbichler DE, Rieder D, Lackner P, Hackl H, Gostner JM. ExonSurfer: a web-tool to design primers at exon-exon junctions. BMC Genomics 2024; 25:594. [PMID: 38867172 PMCID: PMC11170769 DOI: 10.1186/s12864-024-10456-2] [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: 01/23/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Reverse transcription quantitative PCR (RT-qPCR) with intercalating dyes is one of the main techniques to assess gene expression levels used in basic and applied research as well as in diagnostics. However, primer design for RT-qPCR can be complex due to the high demands on primer quality. Primers are best placed on exon junctions, should avoid polymorphic regions, be specific to the target transcripts and also prevent genomic amplification accurately, among others. Current software tools manage to meet all the necessary criteria only insufficiently. Here, we present ExonSurfer, a novel, user-friendly web-tool for qPCR primer design. RESULTS ExonSurfer combines the different steps of the primer design process, encompassing target selection, specificity and self-complementarity assessment, and the avoidance of issues arising from polymorphisms. Amplification of potentially contaminating genomic DNA is avoided by designing primers on exon-exon junctions, moreover, a genomic alignment is performed to filter the primers accordingly and inform the user of any predicted interaction. In order to test the whole performance of the application, we designed primer pairs for 26 targets and checked both primer efficiency, amplicon melting temperature and length and confirmed the targeted amplicon by Sanger sequencing. Most of the tested primers accurately and selectively amplified the corresponding targets. CONCLUSION ExonSurfer offers a comprehensive end-to-end primer design, guaranteeing transcript-specific amplification. The user interface is intuitive, providing essential specificity and amplicon details. The tool can also be used by command line and the source code is available. Overall, we expect ExonSurfer to facilitate RT-qPCR set-up for researchers in many fields.
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Affiliation(s)
- Pablo Monfort-Lanzas
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Elena Cristina Rusu
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
- SeqPlexing SL, Valencia, Spain
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucia Parrakova
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Cornelia A Karg
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Dorina-Elina Kernbichler
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
- Institute of Medical Biochemistry, Core Facility Metabolomics II, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Peter Lackner
- Department of Biosciences and Medical Biology, University of Salzburg, 5020, Salzburg, Austria
| | - Hubert Hackl
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Johanna M Gostner
- Institute of Medical Biochemistry, Biochemical Immunotoxicology Group, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria.
- Institute of Medical Biochemistry, Core Facility Metabolomics II, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria.
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Perez-Bou L, Gonzalez-Martinez A, Cabrera JJ, Juarez-Jimenez B, Rodelas B, Gonzalez-Lopez J, Correa-Galeote D. Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR. MICROBIAL ECOLOGY 2024; 87:71. [PMID: 38748252 PMCID: PMC11096201 DOI: 10.1007/s00248-024-02385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.
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Affiliation(s)
- Lizandra Perez-Bou
- Environmental Microbiology Group, Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan J Cabrera
- Nitrogen Metabolism Group, Zaidín Experimental Station, Spanish National Research Council, EEZ-CSIC, Granada, Spain
| | - Belen Juarez-Jimenez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Belen Rodelas
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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Ferrigno M, Frazzetto P, Prjibelski A, Tomescu AI, Puglia GD. PABLOG: a Primer Analysis tool using a Bee-Like approach on Orthologous Genes. PHYSIOLOGIA PLANTARUM 2024; 176:e14398. [PMID: 38894544 DOI: 10.1111/ppl.14398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
RNA-seq data is currently generated in numerous non-model organisms that lack a reference genome. Nevertheless, the confirmation of gene expression levels using RT-qPCR remains necessary, and the existing techniques do not seamlessly interface with the omics pipeline workflow. Developing primers for many targets by utilising orthologous genes can be a laborious, imprecise, and subjective process, particularly for plant species that are not commonly studied and do not have a known genome. We have developed a primer design tool, named PABLOG, that analyses the alignments generated from long or short RNA-seq reads and a reference orthologous gene. PABLOG scans, much like a bee searching several flowers for pollen, and presents a sorted list of potential exon-exon junction locations, ranked according to their reliability. Through computational analysis across the whole genomes of several non-model species, we demonstrate that PABLOG performs more effectively than other methods in identifying exon-exon junctions since it generates significantly fewer false-positive results. Examination of candidate regions at the gene level, in conjunction with laboratory studies, shows that the suggested primers successfully amplified particular targets in non-model plants without any presence of genomic contamination. Our tool includes a consensus sequence feature that enables the complete process of primer design, from aligning with the target gene to determining amplification parameters. The utility can be accessed via the GitHub repository located at: https://github.com/tools4plant-omics/PABLOG.
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Affiliation(s)
- Michele Ferrigno
- National Research Council of Italy, Institute for Agriculture and Forestry Systems in the Mediterranean, Catania, Italy
- Department of Mathematics and Computer Science, University of Catania, Catania, Italy
| | - Paola Frazzetto
- National Research Council of Italy, Institute for Agriculture and Forestry Systems in the Mediterranean, Catania, Italy
| | - Andrey Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | | | - Giuseppe Diego Puglia
- National Research Council of Italy, Institute for Agriculture and Forestry Systems in the Mediterranean, Catania, Italy
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Canturri A, Galina-Pantoja L, Vonnahme K, Pieters M. Detection of Mycoplasma hyopneumoniae viability using a PCR-based assay. Vet Microbiol 2024; 292:110058. [PMID: 38537399 DOI: 10.1016/j.vetmic.2024.110058] [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: 10/16/2023] [Revised: 03/09/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Mycoplasma hyopneumoniae detection in clinical specimens is accomplished by PCR targeting bacterial DNA. However, the high stability of DNA and the lack of relationship between bacterial viability and DNA detection by PCR can lead to diagnostic interpretation issues. Bacterial messenger RNA is rapidly degraded after cell death, and consequently, assays targeting mRNA detection can be used for the exclusive detection of viable bacterial cells. Therefore, this study aimed at developing a PCR-based assay for the detection of M. hyopneumoniae mRNA and at validating its applicability to differentiate viable from inert bacteria. Development of the RNA-based PCR encompassed studies to determine its analytical sensitivity, specificity, and repeatability, as well as its diagnostic accuracy. Comparisons between DNA and mRNA detection for the same target gene were performed to evaluate the ability of the RNA-based PCR to detect exclusively viable M. hyopneumoniae after bacterial inactivation using various methods. The RNA-based PCR was also compared to the DNA-based PCR as a tool to monitor the growth of M. hyopneumoniae in vitro. Under the conditions of this study, the developed RNA-based PCR assay detected only viable or very recently inactivated M. hyopneumoniae, while the DNA-based PCR consistently detected cells irrespective of their viability status. Changes in growth activity over time were only observable via RNA-based PCR. This viability PCR assay could be directly applied to evaluate the clearance of M. hyopneumoniae or to determine the viability of the bacterium at late stages of eradication programs.
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Affiliation(s)
- Albert Canturri
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA; Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | | | | | - Maria Pieters
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA; Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA; Swine Disease Eradication Center, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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9
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Lovatto M, Vidigal Filho PS, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Gilio TAS, Nascimento EA, Melotto M. Alterations in Gene Expression during Incompatible Interaction between Amendoim Cavalo Common Bean and Colletotrichum lindemuthianum. PLANTS (BASEL, SWITZERLAND) 2024; 13:1245. [PMID: 38732460 PMCID: PMC11085365 DOI: 10.3390/plants13091245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 05/13/2024]
Abstract
Anthracnose, caused by the fungus Colletotrichum lindemuthianum, poses a significant and widespread threat to the common bean crop. The use of plant genetic resistance has proven to be the most effective strategy for managing anthracnose disease. The Amendoim Cavalo (AC) Andean cultivar has resistance against multiple races of C. lindemuthianum, which is conferred by the Co-AC gene. Fine mapping of this resistance gene to common bean chromosome Pv01 enabled the identification of Phvul.001G244300, Phvul.001G244400, and Phvul.001G244500 candidate genes for further validation. In this study, the relative expression of Co-AC candidate genes was assessed, as well as other putative genes in the vicinity of this locus and known resistance genes, in the AC cultivar following inoculation with the race 73 of C. lindemuthianum. Gene expression analysis revealed significantly higher expression levels of Phvul.001G244500. Notably, Phvul.001G244500 encodes a putative Basic Helix-Loop-Helix transcription factor, suggesting its involvement in the regulation of defense responses. Furthermore, a significant modulation of the expression of defense-related genes PR1a, PR1b, and PR2 was observed in a time-course experiment. These findings contribute to the development of improved strategies for breeding anthracnose-resistant common bean cultivars, thereby mitigating the impact of this pathogen on crop yields and ensuring sustainable bean production.
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Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | | | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | | | - Eduardo A. Nascimento
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR 87020-900, Brazil
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Filindris T, Papakonstantinou E, Keramida M, Panteris E, Kalogeropoulos S, Georgopoulos N, Taniguchi F, Adonakis G, Harada T, Kaponis A. The effect of GnRH-a on the angiogenesis of endometriosis. Hormones (Athens) 2024:10.1007/s42000-024-00559-6. [PMID: 38639888 DOI: 10.1007/s42000-024-00559-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE Neoangiogenesis is necessary for adhesion and invasiveness of endometriotic lesions in women affected by endometriosis. Vascular endothelial growth factor (VEGF) is one of the main components of angiogenesis and is part of the major pathway tissue factor (TF)-protease activated receptor-2 (PAR-2)-VEGF that leads to neoangiogenesis. Specificity protein 1 (SP1) is a transcriptional factor that has recently been studied for its crucial role in angiogenesis via a specific pathway. We hypothesize that by blocking angiogenetic pathways we can suppress endometriotic lesions. Gonadotrophin-releasing hormone-agonists (GnRH-a) are routinely used, especially preoperatively, in endometriosis. It would be of great interest to clarify which angiogenetic pathways are affected and, thereby, pave the way for further research into antiangiogenetic effects on endometriosis. METHODS We used quantitative real-time polymerase chain reaction (qRT-PCR) to study mRNA expression levels of TF, PAR-2, VEGF, and SP1 in endometriotic tissues of women who underwent surgery for endometriosis and received GnRH-a (leuprolide acetate) preoperatively. RESULTS VEGF, TF, and PAR-2 expression is significantly lower in patients who received treatment (p < 0,001) compared to those who did not, whereas SP1 expression is not altered (p = 0.779). CONCLUSIONS GnRH-a administration does affect some pathways of angiogenesis in endometriotic lesions, but not all of them. Therefore, supplementary treatments that affect the SP1 pathway of angiogenesis should be developed to enhance the antiangiogenetic effect of GnRH-a in patients with endometriosis. TRIAL REGISTRATION Clinicaltrial.gov ID: NCT06106932.
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Affiliation(s)
- Theodoros Filindris
- Dept. of Obstetrics & Gynecology, Patras University School of Medicine, Patras, Greece
| | | | - Maria Keramida
- Dept. of Obstetrics & Gynecology, Patras University School of Medicine, Patras, Greece
| | - Eleftherios Panteris
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | | | - Neoklis Georgopoulos
- Dept. of Obstetrics & Gynecology, Patras University School of Medicine, Patras, Greece
| | - Fuminori Taniguchi
- Dept. of Obstetrics & Gynecology, Tottori University Faculty of Medicine, Yonago, Japan
| | - George Adonakis
- Dept. of Obstetrics & Gynecology, Patras University School of Medicine, Patras, Greece
| | - Tasuku Harada
- Dept. of Obstetrics & Gynecology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Apostolos Kaponis
- Dept. of Obstetrics & Gynecology, Patras University School of Medicine, Patras, Greece.
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11
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Yu Z, Gao Z, Zeng Y, Li M, Xu G, Ren M, Zhu Y, Liu D. A delayed and unsynchronized ovary development as revealed by transcriptome of brain and pituitary of Coilia nasus. Front Mol Biosci 2024; 11:1361386. [PMID: 38665935 PMCID: PMC11043543 DOI: 10.3389/fmolb.2024.1361386] [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: 12/25/2023] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Coilia nasus is an anadromous fish that has been successfully domesticated in the last decade due to its high economic value. The fish exhibits a delayed ovary development during the reproductive season, despite breeding and selection for five to six offspring. The molecular mechanism of the delayed ovary development is still unknown, so the obstacles have not been removed in the large-scale breeding program. This study aims to investigate the key genes regulating ovarian development by comparing the transcriptomes of ovarian-stage IV and stage II brain/pituitary of Coilia nasus. Ovarian stages were validated by histological sections. A total of 75,097,641 and 66,735,592 high-quality reads were obtained from brain and pituitary transcriptomes, respectively, and alternatively spliced transcripts associated with gonadal development were detected. Compared to ovarian Ⅱ- brain, 515 differentially expressed genes (DEGs) were upregulated and 535 DEGs were downregulated in ovarian Ⅳ- brain, whereas 470 DEGs were upregulated and 483 DEGs were downregulated in ovarian Ⅳ- pituitary compared to ovarian Ⅱ- pituitary. DEGs involved in hormone synthesis and secretion and in the GnRH signaling pathway were screened. Weighted gene co-expression network analysis identified gene co-expression modules that were positively correlated with ovarian phenotypic traits. The hub genes Smad4 and TRPC4 in the modules were co-expressed with DEGs including Kiss1 receptor and JUNB, suggesting that ovarian development is controlled by a hypothalamic-pituitary-gonadal axis. Our results have provided new insights that advance our understanding of the molecular mechanism of C. nasus reproductive functions and will be useful for future breeding.
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Affiliation(s)
- Ziyan Yu
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Zongshuai Gao
- Department of Transfusion Medicine, Shanghai Sixth People’s Hospital Afffiliated to Shanghai Jiao Tong University School of Medicinel, Shanghai, China
| | - Yun Zeng
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Mingyou Li
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Mingchun Ren
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yunxia Zhu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dong Liu
- Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
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12
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de Oliveira PAA, Baboghlian J, Ramos COA, Mançano ASF, Porcari ADM, Girardello R, Ferraz LFC. Selection and validation of reference genes suitable for gene expression analysis by Reverse Transcription Quantitative real-time PCR in Acinetobacter baumannii. Sci Rep 2024; 14:3830. [PMID: 38360762 PMCID: PMC10869792 DOI: 10.1038/s41598-024-51499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterium considered an emerging multi-drug-resistant pathogen. Furthermore, this bacterium can survive in extreme environmental conditions, which makes it a frequent cause of nosocomial infection outbreaks. Gene expression analyses by Reverse Transcription Quantitative real-time PCR (RT-qPCR) depend on a reference gene, also called an endogenous gene, which is used to normalize the generated data and thus ensure an accurate analysis with minimal errors. Currently, gene expression analyses in A. baumannii are compromised, as there are no reports in the literature describing the identification of validated reference genes for use in RT-qPCR analyses. For this reason, we selected twelve candidate reference genes of A. baumannii and assessed their expression profile under different experimental and culture conditions. The expression stability of the candidate genes was evaluated by using statistical algorithms such as BestKeeper, geNorm, NormFinder, Delta CT, and RefFinder, in order to identify the most suitable candidate reference genes for RT-qPCR analyses. The statistical analyses indicated rpoB, rpoD, and fabD genes as the most adequate to ensure accurate normalization of RT-qPCR data in A. baumannii. The accuracy of the proposed reference genes was validated by using them to normalize the expression of the ompA gene, encoding the outer membrane protein A, in A. baumannii sensible and resistant to the antibiotic polymyxin. The present work provides suitable reference genes for precise RT-qPCR data normalization on future gene expression studies with A. baumannii.
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Affiliation(s)
| | - Juliana Baboghlian
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | | | | | - Andréia de Melo Porcari
- Laboratório Multidisciplinar de Pesquisa, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | - Raquel Girardello
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil.
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13
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Graf SD, Keber CU, Hattesohl A, Teply-Szymanski J, Hattesohl S, Guder M, Gercke N, Di Fazio P, Slater EP, Jesinghaus M, Denkert C, Bartsch DK, Lehman B. Mesenteric fibrosis in patients with small intestinal neuroendocrine tumors is associated with enrichment of alpha-smooth muscle actin-positive fibrosis and COMP-expressing stromal cells. J Neuroendocrinol 2024; 36:e13364. [PMID: 38246597 DOI: 10.1111/jne.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024]
Abstract
Neuroendocrine tumors of the small intestine (SI-NETs) often develop lymph node metastasis (LNM)-induced mesenteric fibrosis (MF). MF can cause intestinal obstruction as well as ischemia and render surgical resection technically challenging. The underlying pathomechanisms of MF are still not well understood. We examined mesenteric LNM and the surrounding stroma compartment from 24 SI-NET patients, including 11 with in situ presentation of strong MF (MF+) and 13 without MF (MF-). Differential gene expression was assessed with the HTG EdgeSeq Oncology Biomarker Panel comparing MF+ with MF- within LNM and paired stromal samples, respectively. Most interesting differentially expressed genes were validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in combination with validation of associated protein levels utilizing immunohistochemistry (IHC) staining of MF+ and MF- formalin-fixed, paraffin-embedded (FFPE) patient samples. Overall, 14 genes measured with a 2549-gene expression panel were differentially expressed in MF+ patients compared to MF-. Of those, nine were differentially expressed genes in LNM and five genes in the stromal tissue (>2-fold change, p < .05). The top hits included increased COMP and COL11A1 expression in the stroma of MF+ patients compared to MF-, as well as decreased HMGA2, COL6A6, and SLC22A3 expression in LNM of MF+ patients compared to LNM of MF- patients. RT-qPCR confirmed high levels of COMP and COL11A1 in stroma samples of MF+ compared to MF- patients. IHC staining confirmed the enrichment of α-smooth muscle actin-positive fibrosis in MF+ compared to MF- patients with corresponding increase of COMP-expressing stromal cells in MF+. Since COMP is associated with the known driver for fibrosis development transforming growth factor beta and with a cancer-associated fibroblasts enriched environment, it seems to be a promising new target for MF research.
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Affiliation(s)
- Sebastian D Graf
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
| | - Corinna U Keber
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Akira Hattesohl
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Julia Teply-Szymanski
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Sophia Hattesohl
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Marc Guder
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Norman Gercke
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
| | - Pietro Di Fazio
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
| | - Emily P Slater
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Carsten Denkert
- Institute of Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Detlef K Bartsch
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
| | - Bettina Lehman
- Department of Visceral, Thoracic and Vascular Surgery, Philipps-University Marburg, Marburg, Germany
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14
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Guo L, Ze X, Feng H, Liu Y, Ge Y, Zhao X, Song C, Jiao Y, Liu J, Mu S, Yao S. Identification and quantification of viable Lacticaseibacillus rhamnosus in probiotics using validated PMA-qPCR method. Front Microbiol 2024; 15:1341884. [PMID: 38298895 PMCID: PMC10828034 DOI: 10.3389/fmicb.2024.1341884] [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: 11/21/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
The identification and quantification of viable bacteria at the species/strain level in compound probiotic products is challenging now. Molecular biology methods, e.g., propidium monoazide (PMA) combination with qPCR, have gained prominence for targeted viable cell counts. This study endeavors to establish a robust PMA-qPCR method for viable Lacticaseibacillus rhamnosus detection and systematically validated key metrics encompassing relative trueness, accuracy, limit of quantification, linear, and range. The inclusivity and exclusivity notably underscored high specificity of the primers for L. rhamnosus, which allowed accurate identification of the target bacteria. Furthermore, the conditions employed for PMA treatment were fully verified by 24 different L. rhamnosus including type strain, commercial strains, etc., confirming its effective discrimination between live and dead bacteria. A standard curve constructed by type strain could apply to commercial strains to convert qPCR Cq values to viable cell numbers. The established PMA-qPCR method was applied to 46 samples including pure cultures, probiotics as food ingredients, and compound probiotic products. Noteworthy is the congruity observed between measured and theoretical values within a 95% confidence interval of the upper and lower limits of agreement, demonstrating the relative trueness of this method. Moreover, accurate results were obtained when viable L. rhamnosus ranging from 103 to 108 CFU/mL. The comprehensive appraisal of PMA-qPCR performances provides potential industrial applications of this new technology in quality control and supervision of probiotic products.
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Affiliation(s)
- Lizheng Guo
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Xiaolei Ze
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition & Health, Guangzhou, China
| | - Huifen Feng
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Yiru Liu
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Yuanyuan Ge
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Xi Zhao
- Microbiome Research and Application Center, BYHEALTH Institute of Nutrition & Health, Guangzhou, China
| | - Chengyu Song
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Yingxin Jiao
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Jiaqi Liu
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Shuaicheng Mu
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
| | - Su Yao
- China National Research Institute of Food and Fermentation Industries Co., LTD., China Center of Industrial Culture Collection, Beijing, China
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15
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Blay E, Hardyman E, Morovic W. PCR-based analytics of gene therapies using adeno-associated virus vectors: Considerations for cGMP method development. Mol Ther Methods Clin Dev 2023; 31:101132. [PMID: 37964893 PMCID: PMC10641278 DOI: 10.1016/j.omtm.2023.101132] [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] [Indexed: 11/16/2023]
Abstract
The field of gene therapy has evolved and improved so that today the treatment of thousands of genetic diseases is now possible. An integral aspect of the drug development process is generating analytical methods to be used throughout clinical and commercial manufacturing. Enumeration and identification assays using genetic testing are critical to ensure the safety, efficacy, and stability of many active pharmaceutical ingredients. While nucleic acid-based methods are already reliable and rapid, there are unique biological, technological, and regulatory aspects in gene therapies that must be considered. This review surveys aspects of method development and validation using nucleic acid-based testing of gene therapies by focusing on adeno-associated virus (AAV) vectors and their co-transfection factors. Key differences between quantitative PCR and droplet digital technologies are discussed to show how improvements can be made while still adhering to regulatory guidance. Example validation parameters for AAV genome titers are described to demonstrate the scope of analytical development. Finally, several areas for improving analytical testing are presented to inspire future innovation, including next-generation sequencing and artificial intelligence. Reviewing the broad characteristics of gene therapy assessment serves as an introduction for new researchers, while clarifying processes for professionals already involved in pharmaceutical manufacturing.
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Affiliation(s)
- Emmanuel Blay
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Elaine Hardyman
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Wesley Morovic
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
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16
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Patel RH, Truong VB, Sabry R, Acosta JE, McCahill K, Favetta LA. SMAD signaling pathway is disrupted by BPA via the AMH receptor in bovine granulosa cells†. Biol Reprod 2023; 109:994-1008. [PMID: 37724935 DOI: 10.1093/biolre/ioad125] [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: 02/22/2023] [Revised: 07/18/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
Significant events that determine oocyte competence occur during follicular growth and oocyte maturation. The anti-Mullerian hormone, a positive predictor of fertility, has been shown to be affected by exposure to endocrine disrupting compounds, such as bisphenol A and S. However, the interaction between bisphenols and SMAD proteins, mediators of the anti-Mullerian hormone pathway, has not yet been elucidated. AMH receptor (AMHRII) and downstream SMAD expression was investigated in bovine granulosa cells treated with bisphenol A, bisphenol S, and then competitively with the anti-Mullerian hormone. Here, we show that 24-h bisphenol A exposure in granulosa cells significantly increased SMAD1, SMAD4, and SMAD5 mRNA expression. No significant changes were observed in AMHRII or SMADs protein expression after 24-h treatment. Following 12-h treatments with bisphenol A (alone or with the anti-Mullerian hormone), a significant increase in SMAD1 and SMAD4 mRNA expression was observed, while a significant decrease in SMAD1 and phosphorylated SMAD1 was detected at the protein level. To establish a functional link between bisphenols and the anti-Mullerian hormone signaling pathway, antisense oligonucleotides were utilized to suppress AMHRII expression with or without bisphenol exposure. Initially, transfection conditions were optimized and validated with a 70% knockdown achieved. Our findings show that bisphenol S exerts its effects independently of the anti-Mullerian hormone receptor, while bisphenol A may act directly through the anti-Mullerian hormone signaling pathway providing a potential mechanism by which bisphenols may exert their actions to disrupt follicular development and decrease oocyte competence.
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Affiliation(s)
- Rushi H Patel
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Vivien B Truong
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Reem Sabry
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Julianna E Acosta
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Kiera McCahill
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Laura A Favetta
- Reproductive Health and Biotechnology Lab, Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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17
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Da Silva CGN, Monteiro EDC, Diniz PP, Terra LA, Schwab S, Reis VM, Simoes-Araujo JL, Urquiaga S. Designing and validation of specific primers for the quantitative detection of bacteria in sugarcane inoculant. Braz J Microbiol 2023; 54:2627-2640. [PMID: 37843794 PMCID: PMC10689644 DOI: 10.1007/s42770-023-01144-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Endophytic diazotrophic plant growth-promoting bacteria Herbaspirillum rubrisubalbicans (HCC103), Herbaspirillum seropedicae (HRC54), Paraburkholderia tropica (Ppe8T), Gluconacetobacter diazotrophicus (Pal5T), and Nitrospirillum amazonense (CBAmC) have been used as inoculants for sugarcane. The genome sequences of these strains were used to design a set of specific primers for the real-time PCR (qPCR) assay. Primer specificity was confirmed by conventional PCR using the genomic DNAs of 25 related bacterial species and the five target strains. The qPCR assays were conducted using root and shoot samples from two sugarcane varieties (RB867515 and RB92579). These samples were collected both with and without inoculation, using the target strains specified in this study. The sugarcane plants were grown in a greenhouse, utilizing a substrate composed of sterile sand and vermiculite in a 2:1 ratio, for a duration of 55 days. The primers designed for this study successfully amplified target DNA fragments from each of the bacterial species, enabling their differentiation at the species level. The total bacterial population present in the sugarcane quantified using qPCR was on average 105.2 cells g-1 of fresh tissue. Across both evaluated varieties, it was observed that the population of inoculated bacteria tended to decrease over time and became more concentrated in the sugarcane roots compared to the aerial parts. The qPCR results suggest that both the host and the microbes influence the endophytic population and the bacterial number decreases with plant age.
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Affiliation(s)
- Cleudison Gabriel Nascimento Da Silva
- Instituto de Agronomia, Programa de Pós Graduação em Fitotecnia, Universidade Federal Rural Do Rio de Janeiro (UFRRJ), Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil.
| | - Edevaldo de Castro Monteiro
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Priscila Pereira Diniz
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Leonardo Araujo Terra
- Instituto de Agronomia, Programa de Pós Graduação em Ciência, Tecnologia e Inovação Agropecuária, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | | | | | - Segundo Urquiaga
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
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18
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Kumar C, Shrivastava K, Singh A, Chauhan V, Giri A, Gupta S, Sharma NK, Bose M, Sharma S, Varma-Basil M. Expression of mammalian cell entry genes in clinical isolates of M. tuberculosis and the cell entry potential and immunological reactivity of the Rv0590A protein. Med Microbiol Immunol 2023; 212:407-419. [PMID: 37787822 DOI: 10.1007/s00430-023-00781-w] [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: 05/31/2023] [Accepted: 08/31/2023] [Indexed: 10/04/2023]
Abstract
Mammalian cell entry (mce) operons play a vital role in cell invasion and survival of M. tuberculosis. Of the mce genes, the function of Rv0590A is still unknown. The present study was performed to investigate the function and immunogenic properties of the protein Rv0590A. Human leukemia monocytic cell line (THP-1) derived macrophages were infected with M. tuberculosis H37Rv at 3, 6, and 24 h of infection. The maximum colony forming units (CFU) were observed at 6 h (p < 0.005), followed by 3 h after infection. M. tuberculosis H37Rv and clinical isolates representative of Delhi/CAS, EAI, Beijing, Haarlem and Euro-American-superlineage were included in the study for expression analysis of mce1A, mce2A, mce3A, mce4A, and Rv0590A genes. Maximum upregulation of all mce genes was observed at 3 h of infection. All the five clinical isolates and H37Rv upregulated Rv0590A at various time points. Macrophage infection with M. tuberculosis H37Rv-overexpressing Rv0590A gene showed higher intracellular CFU as compared to that of wild-type H37Rv. Further, purified Rv0590A protein stimulated the production of TNFα, IFNγ, and IL-10 in macrophages. Thus, Rv0590A was found to be involved in cell invasion and showed good immunological response.
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Affiliation(s)
- Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Kamal Shrivastava
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Anupriya Singh
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Varsha Chauhan
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- Maharshi Dayanand University, Rohtak, Haryana, India
| | - Astha Giri
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- Deshbandhu College, University of Delhi, Delhi, India
| | - Shraddha Gupta
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Naresh Kumar Sharma
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
- University of Manitoba, Winnipeg, MB, Canada
| | - Mridula Bose
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India
| | - Sadhna Sharma
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, 110007, India.
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Lovatto M, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Mazucheli J, Vidigal Filho PS, Miranda EGR, Melotto M. Responsiveness of Candidate Genes on CoPv01CDRK/PhgPv01CDRK Loci in Common Bean Challenged by Anthracnose and Angular Leaf Spot Pathogens. Int J Mol Sci 2023; 24:16023. [PMID: 38003212 PMCID: PMC10671028 DOI: 10.3390/ijms242216023] [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: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 11/26/2023] Open
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01CDRK/PhgPv01CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01CDRK/PhgPv01CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.
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Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Josmar Mazucheli
- Departamento de Estatística, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | | | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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20
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Contreras E, Martín-Fernández L, Manaa A, Vicente-Carbajosa J, Iglesias-Fernández R. Identification of Reference Genes for Precise Expression Analysis during Germination in Chenopodium quinoa Seeds under Salt Stress. Int J Mol Sci 2023; 24:15878. [PMID: 37958860 PMCID: PMC10650251 DOI: 10.3390/ijms242115878] [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: 09/20/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chenopodium quinoa Willd. (quinoa), a member of the Amaranthaceae family, is an allotetraploid annual plant, endemic to South America. The plant of C. quinoa presents significant ecological plasticity with exceptional adaptability to several environmental stresses, including salinity. The resilience of quinoa to several abiotic stresses, as well as its nutritional attributes, have led to significant shifts in quinoa cultivation worldwide over the past century. This work first defines germination sensu stricto in quinoa where the breakage of the pericarp and the testa is followed by endosperm rupture (ER). Transcriptomic changes in early seed germination stages lead to unstable expression levels in commonly used reference genes that are typically stable in vegetative tissues. Noteworthy, no suitable reference genes have been previously identified specifically for quinoa seed germination under salt stress conditions. This work aims to identify these genes as a prerequisite step for normalizing qPCR data. To this end, germinating seeds from UDEC2 and UDEC4 accessions, with different tolerance to salt, have been analyzed under conditions of absence (0 mM NaCl) and in the presence (250 mM NaCl) of sodium chloride. Based on the relevant literature, six candidate reference genes, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Monensin sensitivity1 (MON1), Polypyrimidine tract-binding protein (PTB), Actin-7 (ACT7), Ubiquitin-conjugating enzyme (UBC), and 18S ribosomal RNA (18S), were selected and assessed for stability using the RefFinder Tool encompassing the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt in the evaluation. The data presented support the suitability of CqACT7 and CqUBC as reference genes for normalizing gene expression during seed germination under salinity stress. These recommended reference genes can be valuable tools for consistent qPCR studies on quinoa seeds.
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Affiliation(s)
- Estefanía Contreras
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Lucía Martín-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Arafet Manaa
- Laboratory of Extremophile Plants, Centre of Biotechnology de Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
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21
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Oldham RC, Held MA. Methods for detection and identification of beer-spoilage microbes. Front Microbiol 2023; 14:1217704. [PMID: 37637116 PMCID: PMC10448528 DOI: 10.3389/fmicb.2023.1217704] [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: 05/05/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
It is critical that breweries of all sizes routinely monitor the microbiome of their process to limit financial losses due to microbial contamination. Contamination by beer-spoiling microbes (BSMs) at any point during the brewing process may lead to significant losses for breweries if gone undetected and allowed to spread. Testing and detection of BSMs must be routine and rapid, and because even small breweries need the capability of BSM detection and identification, the method also needs to be affordable. Lactic acid bacteria (LAB) are responsible for most spoilage incidents, many of which have been shown to enter the viable but nonculturable (VBNC) state under conditions present in beer such as cold or oxidative stress. These bacteria are invisible to traditional methods of detection using selective media. This article describes several methods of BSM detection and identification that may be useful in the majority of craft breweries. While there are several genomic methods that meet some or many qualifications of being useful in craft breweries, real-time quantitative polymerase chain reaction (qPCR) currently best meets the desired method characteristics and holds the most utility in this industry, specifically SYBR Green qPCR. qPCR is a targeted method of detection and identification of microbes that is affordable, rapid, specific, sensitive, quantitative, and reliable, and when paired with valid DNA extraction techniques can be used to detect BSMs, including those in the VBNC state.
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Affiliation(s)
- Ryanne C. Oldham
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Quality Assurance and Quality Control Laboratory, Jackie O’s Brewery, Athens, OH, United States
| | - Michael A. Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
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22
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Pelisek J, Yundung Y, Reutersberg B, Meuli L, Rössler F, Rabin L, Kopp R, Zimmermann A. Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue. J Clin Med 2023; 12:5109. [PMID: 37568514 PMCID: PMC10420000 DOI: 10.3390/jcm12155109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2-4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA's disintegration state, is a better decision-making aid in choosing samples for omics analyses.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Yankey Yundung
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Benedikt Reutersberg
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Lorenz Meuli
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Fabian Rössler
- Department of Surgery and Transplantation, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Laetitia Rabin
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Reinhard Kopp
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Alexander Zimmermann
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
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23
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Seewald LA, Sabino IG, Montney KL, Delco ML. Synovial fluid mitochondrial DNA concentration reflects the degree of cartilage damage after naturally occurring articular injury. Osteoarthritis Cartilage 2023; 31:1056-1065. [PMID: 37028640 PMCID: PMC10524327 DOI: 10.1016/j.joca.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/27/2023] [Accepted: 03/19/2023] [Indexed: 04/09/2023]
Abstract
OBJECTIVE To evaluate mitochondrial DNA (mtDNA) release from injured chondrocytes and investigate the utility of synovial fluid mtDNA concentration in early detection of posttraumatic osteoarthritis. METHOD We measured mtDNA release using four models of osteoarthritis: in vitro interleukin-1β stimulation of cultured equine chondrocytes, ex vivo mechanical impact of bovine cartilage explants, in vivo mechanical impact of equine articular cartilage, and naturally occurring equine intraarticular fracture. In our in vivo model, one group was treated with an intraarticular injection of the mitoprotective peptide SS-31 following cartilage injury. mtDNA content was quantified using qPCR. For naturally occurring cases of joint injury, clinical data (radiographs, arthroscopic video footage) were scored for criteria associated with degenerative joint disease. RESULTS Chondrocytes released mtDNA in the acute time frame following inflammatory and mechanical cellular stress in vitro. mtDNA was increased in equine synovial fluid following experimental and naturally occurring injury to the joint surface. In naturally occurring posttraumatic osteoarthritis, we found a strong positive correlation between the degree of cartilage damage and mtDNA concentration (r = 0.80, P = 0.0001). Finally, impact-induced mtDNA release was mitigated by mitoprotective treatment. CONCLUSION Changes in synovial fluid mtDNA occur following joint injury and correlate with the severity of cartilage damage. Mitoprotection mitigates increases in synovial fluid mtDNA suggesting that mtDNA release may reflect mitochondrial dysfunction. Further investigation of mtDNA as a potentially sensitive marker of early articular injury and response to mitoprotective therapy is warranted.
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Affiliation(s)
- L A Seewald
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - I G Sabino
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - K L Montney
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - M L Delco
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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24
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Yang J, DeVore AN, Fu DA, Spicer MM, Guo M, Thompson SG, Ahlers-Dannen KE, Polato F, Nussenzweig A, Fisher RA. Rapid and precise genotyping of transgene zygosity in mice using an allele-specific method. Life Sci Alliance 2023; 6:e202201729. [PMID: 37037594 PMCID: PMC10087101 DOI: 10.26508/lsa.202201729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
Precise determination of transgene zygosity is essential for use of transgenic mice in research. Because integration loci of transgenes are usually unknown due to their random insertion, assessment of transgene zygosity remains a challenge. Current zygosity genotyping methods (progeny testing, qPCR, and NGS-computational biology analysis) are time consuming, prone to error or technically challenging. Here, we developed a novel method to determine transgene zygosity requiring no knowledge of transgene insertion loci. This method applies allele-specific restriction enzyme digestion of PCR products (RE/PCR) to rapidly and reliably quantify transgene zygosity. We demonstrate the applicability of this method to three transgenic strains of mice (Atm TgC3001L, Nes-Cre, and Syn1-Cre) harboring a unique restriction enzyme site on either the transgene or its homologous sequence in the mouse genome. This method is as accurate as the gold standard of progeny testing but requires 2 d instead of a month or more. It is also exceedingly more accurate than the most commonly used approach of qPCR quantification. Our novel method represents a significant technical advance in determining transgene zygosities in mice.
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Affiliation(s)
- Jianqi Yang
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | - Alison N DeVore
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | - Daniel A Fu
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | - Mackenzie M Spicer
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | - Mengcheng Guo
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | - Samantha G Thompson
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
| | | | - Federica Polato
- Laboratory of Genome Integrity, National Institutes of Health, Centre for Cancer Research, Bethesda, MD, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Institutes of Health, Centre for Cancer Research, Bethesda, MD, USA
| | - Rory A Fisher
- Departments of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA, USA
- Roy J and Lucille A Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
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25
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Siegl D, Kruchem M, Jansky S, Eichler E, Thies D, Hartwig U, Schuppan D, Bockamp E. A PCR protocol to establish standards for routine mycoplasma testing that by design detects over ninety percent of all known mycoplasma species. iScience 2023; 26:106724. [PMID: 37216121 PMCID: PMC10192841 DOI: 10.1016/j.isci.2023.106724] [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: 10/26/2022] [Revised: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Mycoplasma infection leads to false and non-reproducible scientific data and poses a risk to human health. Despite strict guidelines calling for regular mycoplasma screening, there is no universal and widely established standard procedure. Here, we describe a reliable and cost-effective PCR method that establishes a universal protocol for mycoplasma testing. The applied strategy utilizes ultra-conserved eukaryotic and mycoplasma sequence primers covering by design 92% of all species in the six orders of the class Mollicutes within the phylum Mycoplasmatota and is applicable to mammalian and many non-mammalian cell types. This method can stratify mycoplasma screening and is suitable as a common standard for routine mycoplasma testing.
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Affiliation(s)
- Dominik Siegl
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Marie Kruchem
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Sandrine Jansky
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Emma Eichler
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Dorothe Thies
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Udo Hartwig
- Department of Medicine III Hematology & Medical Oncology, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- ImmuneNTech GmbH, Wendelsheim 55234, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Ernesto Bockamp
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- ImmuneNTech GmbH, Wendelsheim 55234, Germany
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
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26
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Baettig CG, Zirngibl M, Smith KF, Lear G, Tremblay LA. Comparison between droplet digital PCR and reverse transcription-quantitative PCR methods to measure ecotoxicology biomarkers. MARINE POLLUTION BULLETIN 2023; 190:114829. [PMID: 36958116 DOI: 10.1016/j.marpolbul.2023.114829] [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: 01/24/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is currently the gold-standard technique for detecting and quantifying messenger RNA. However, without proper validation, the method may produce artefactual and non-reproducible cycle threshold values generating poor-quality data. The newer droplet digital PCR (ddPCR) method allows for the absolute quantification of targeted nucleic acids providing more sensitive and accurate measurements without requiring external standards. This study compared these two PCR-based methods to measure the expression of well-documented genes used in ecotoxicology studies. We exposed Mediterranean mussels (Mytilus galloprovincialis) to copper and analyzed gene expression in gills and digestive glands using RT-qPCR and ddPCR assays. A step-by-step methodology to optimize and compare the two technologies is described. After ten-fold serial complementary DNA dilution, both RT-qPCR and ddPCR exhibited comparable linearity and efficiency and produced statistically similar results. We conclude that ddPCR is a suitable method to assess gene expression in an ecotoxicological context. However, RT-qPCR has a shorter processing time and remains more cost-effective.
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Affiliation(s)
- Camille G Baettig
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand.
| | | | - Kirsty F Smith
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis A Tremblay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand
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27
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Frisk CA, Adams-Groom B, Smith M. Isolating the species element in grass pollen allergy: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163661. [PMID: 37094678 DOI: 10.1016/j.scitotenv.2023.163661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Grass pollen is a leading cause of allergy in many countries, particularly Europe. Although many elements of grass pollen production and dispersal are quite well researched, gaps still remain around the grass species that are predominant in the air and which of those are most likely to trigger allergy. In this comprehensive review we isolate the species aspect in grass pollen allergy by exploring the interdisciplinary interdependencies between plant ecology, public health, aerobiology, reproductive phenology and molecular ecology. We further identify current research gaps and provide open ended questions and recommendations for future research in an effort to focus the research community to develop novel strategies to combat grass pollen allergy. We emphasise the role of separating temperate and subtropical grasses, identified through divergence in evolutionary history, climate adaptations and flowering times. However, allergen cross-reactivity and the degree of IgE connectivity in sufferers between the two groups remains an area of active research. The importance of future research to identify allergen homology through biomolecular similarity and the connection to species taxonomy and practical implications of this to allergenicity is further emphasised. We also discuss the relevance of eDNA and molecular ecological techniques (DNA metabarcoding, qPCR and ELISA) as important tools in quantifying the connection between the biosphere with the atmosphere. By gaining more understanding of the connection between species-specific atmospheric eDNA and flowering phenology we will further elucidate the importance of species in releasing grass pollen and allergens to the atmosphere and their individual role in grass pollen allergy.
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Affiliation(s)
- Carl A Frisk
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway.
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Matt Smith
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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28
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Liu W, Zhu Y, Stellacci F. Recycling of Polymerase Chain Reaction (PCR) Kits. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:5524-5536. [PMID: 37041891 PMCID: PMC10081572 DOI: 10.1021/acssuschemeng.2c07309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/07/2023] [Indexed: 06/19/2023]
Abstract
Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginning of the pandemic, there was a shortage of PCR kits. So far, the ecosystem of a PCR kit is linear use; that is, kits are produced, used once, and disposed of as biolab waste. Here, we show that to mitigate the risk of future shortages, it is possible to envision recyclable PCR kits based on a more sustainable use of nucleic acid resources. A PCR kit is mainly composed of primers, nucleotides, and enzymes. In the case of a positive test, the free nucleotides are polymerized onto the primers to form longer DNA strands. Our approach depolymerizes such strands, keeping the primers and regenerating the nucleotides, i.e., returning the nucleic acid materials to the original state. The polymerized long DNA strands are hydrolyzed into nucleotide monophosphates that are then phosphorylated into triphosphates using a method that is developed from a recent publication. We used oligonucleotides with a 3'-terminal phosphorothioate (PS) backbone modification as nonhydrolyzable PCR primers, which are able to undergo the recycling process unchanged. The nuclease resistance of oligonucleotides with a ribose sugar modification was also evaluated, which showed worse recycling efficiency than PS-modified oligonucleotides. We successfully recycled both PCR primers and nucleotide monomers (∼75% yield). We demonstrate that the method allows for the direct reuse of PCR kits. We also show that the recycled primers can be isolated and then added to endpoint or quantitative PCR. This recycling approach provides a new path for circularly reusing nucleic acid materials in PCR kits.
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Affiliation(s)
- Weina Liu
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
| | - Yong Zhu
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
| | - Francesco Stellacci
- Institute
of Materials, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, Station 12, Lausanne 1015, Switzerland
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29
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Bogožalec Košir A, Lužnik D, Tomič V, Milavec M. Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. BIOSENSORS 2023; 13:bios13040463. [PMID: 37185538 PMCID: PMC10136035 DOI: 10.3390/bios13040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Dane Lužnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
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An Improved Duplex Real-Time Quantitative RT-PCR Assay with a Canine Endogenous Internal Positive Control for More Sensitive and Reliable Detection of Canine Parainfluenza Virus 5. Vet Sci 2023; 10:vetsci10020142. [PMID: 36851445 PMCID: PMC9965950 DOI: 10.3390/vetsci10020142] [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: 01/16/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
A duplex real-time quantitative reverse transcription-polymerase chain reaction (dqRT-PCR) assay was successfully developed to simultaneously detect canine parainfluenza virus 5 (CPIV5) and a canine endogenous internal positive control (EIPC) in canine clinical samples. Two sets of primers and probes for the CPIV5 L and canine 16S rRNA genes were included in the dqRT-PCR assay to detect CPIV and monitor invalid results throughout the qRT-PCR process. The developed dqRT-PCR assay specifically detected CPIV5 but no other canine pathogens. Furthermore, 16S rRNA was stably amplified by dqRT-PCR assay in all samples containing canine cellular materials. The assay's sensitivity was determined as below ten RNA copies per reaction, with CPIV5 L gene standard RNA and 1 TCID50/mL with the CPIV5 D008 vaccine strain, which was 10-fold higher than that of the previous HN gene-specific qRT-PCR (HN-qRT-PCR) assays and was equivalent to that of the previous N gene-specific qRT-PCR (N-qRT-PCR) assays, respectively. Moreover, the Ct values of the CPIV5-positive samples obtained using the dqRT-PCR assay were lower than those obtained using the previous HN- and N-qRT-PCR assays, indicating that the diagnostic performance of the dqRT-PCR assay was superior to those of previous HN- and N-qRT-PCR assays. The calculated Cohen's kappa coefficient values (95% confidence interval) between dqRT-PCR and the HN- or N-specific qRT-PCR assays were 0.97 (0.90-1.03) or 1.00 (1.00-1.00), respectively. In conclusion, the newly developed dqRT-PCR assay with high sensitivity, specificity, and reliability will be a promising diagnostic tool for the detection of CPIV5 in clinical samples and useful for etiological and epidemiological studies of CPIV5 infection in dogs.
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Palowski A, Balestreri C, Urriola PE, van de Ligt JLG, Sampedro F, Dee S, Shah A, Yancy HF, Shurson GC, Schroeder DC. Survival of a surrogate African swine fever virus-like algal virus in feed matrices using a 23-day commercial United States truck transport model. Front Microbiol 2022; 13:1059118. [PMID: 36569067 PMCID: PMC9782974 DOI: 10.3389/fmicb.2022.1059118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
African swine fever virus (ASFV) is a member of the nucleocytoplasmic large DNA viruses (NCLDVs) and is stable in a variety of environments, including animal feed ingredients as shown in previous laboratory experiments and simulations. Emiliania huxleyi virus (EhV) is another member of the NCLDVs, which has a restricted host range limited to a species of marine algae called Emiliania huxleyi. This algal NCLDV has many similar morphological and physical characteristics to ASFV thereby making it a safe surrogate, with results that are applicable to ASFV and suitable for use in real-world experiments. Here we inoculated conventional soybean meal (SBMC), organic soybean meal (SBMO), and swine complete feed (CF) matrices with EhV strain 86 (EhV-86) at a concentration of 6.6 × 107 virus g-1, and then transported these samples in the trailer of a commercial transport vehicle for 23 days across 10,183 km covering 29 states in various regions of the United States. Upon return, samples were evaluated for virus presence and viability using a previously validated viability qPCR (V-qPCR) method. Results showed that EhV-86 was detected in all matrices and no degradation in EhV-86 viability was observed after the 23-day transportation event. Additionally, sampling sensitivity (we recorded unexpected increases, as high as 49% in one matrix, when virus was recovered at the end of the sampling period) rather than virus degradation best explains the variation of virus quantity observed after the 23-day transport simulation. These results demonstrate for the first time that ASFV-like NCLDVs can retain viability in swine feed matrices during long-term transport across the continental United States.
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Affiliation(s)
- Amanda Palowski
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Cecilia Balestreri
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Pedro E. Urriola
- Department of Animal Science, College of Food Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul, MN, United States
| | - Jennifer L. G. van de Ligt
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Fernando Sampedro
- Environmental Health Sciences Division, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Scott Dee
- Pipestone Applied Research, Pipestone Veterinary Services, Pipestone, MN, United States
| | | | - Haile F. Yancy
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD, United States
| | - Gerald C. Shurson
- Department of Animal Science, College of Food Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul, MN, United States
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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High-throughput primer design by scoring in piecewise logistic model for multiple polymerase chain reaction variants. Sci Rep 2022; 12:21136. [PMID: 36477468 PMCID: PMC9729204 DOI: 10.1038/s41598-022-25561-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: 08/16/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Polymerase chain reaction (PCR) variants requiring specific primer types are widely used in various PCR experiments, including generic PCR, inverse PCR, anchored PCR, and ARMS PCR. Few tools can be adapted for multiple PCR variants, and many tools select primers by filtration based on the given parameters, which result in frequent design failures. Here we introduce PrimerScore2, a robust high-throughput primer design tool that can design primers in one click for multiple PCR variants. It scores primers using a piecewise logistic model and the highest-scored primers are selected avoiding the issue of design failure and the necessity to loosen parameters to redesign, and it creatively evaluates specificity by predicting the efficiencies of all target/non-target products. To assess the prediction accuracy of the scores and efficiencies, two next generation sequencing (NGS) libraries were constructed-a 12-plex and a 57-plex-and the results showed that 17 out of 19 (89.5%) low-scoring pairs had a poor depth, 18 out of 19 (94.7%) high-scoring pairs had a high depth, and the depth ratios of the products were linearly correlated with the predicted efficiencies with a slope of 1.025 and a coefficient of determination (R2) 0.935. 116-plex and 114-plex anchored PCR panels designed by PrimerScore2 were applied to 26 maternal plasma samples with male fetuses, the results showed that the predicted fetal DNA fractions were concordant with fractions measured in gold standard method (Y fractions). PrimerScore2 was also used to design 77 monoplex Sanger sequencing primers, the sequencing results indicated that all the primers were effective.
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Zhang H, Gao J, Chen J, Peng Y, Han Z. RNA-dependent RNA polymerase could extend the lasting validity period of exogenous dsRNA. PEST MANAGEMENT SCIENCE 2022; 78:4569-4578. [PMID: 35831266 DOI: 10.1002/ps.7076] [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: 11/24/2021] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Previous studies have found that pesticide double-stranded (ds)RNA usually has a long-lasting validity period in plants. However, it is uncertain if any factors in plants could extend dsRNA duration. It has been reported that RNA-dependent RNA polymerases (RdRP) in plants and some other eukaryotes could catalyze RNA amplification and be involved in RNAi (interference). Thus, this study evaluated the effect of RdRP on the tissue content, activity, and duration of exogenous dsRNA. RESULTS We found that RdRP knockdown in Arabidopsis thaliana had no significant effect on tissue contents of reporter dsRNA parent molecules (8.91% reduction), but it caused significant decrease in the tissue contents of derived short fragments of 200, 120 and 59 bp tested (51.22%, 52.83% and 59.35%, respectively). Aphid inoculation tests showed that the same dose of insecticidal dsAgZFP exhibited a significantly lower lethal effect (mortality 58.8%) in the plants with RdRP knockdown than in the control plants with normal RdRP (86.0%). For Caenorhabditis elegans, the worms treated simultaneously with dsRdRP and reporter dsRNA had similar body contents to reporter dsRNA parent molecules and its long-fragment derivative (200 bp) as the control (1.28- and 1.07-fold greater, respectively). However, 120- and 59-bp short-fragment derivatives were significantly reduced by 28.78% and 59.84%, respectively, which also diminished faster in the descendants. CONCLUSIONS We conclude that RdRP could significantly enhance the tissue content of dsRNA derivatives by catalyzing amplification, thus improving dsRNA activity and extending its lasting validity period. Otherwise, RNAi by exogenous dsRNA was proven to be noninheritable in A. thaliana. This work confirmed the merit of dsRNA as a plant protectant. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jing Gao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yue Peng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Arenas F, Morte A, Navarro-Ródenas A. Design and Validation of qPCR-Specific Primers for Quantification of the Marketed Terfezia claveryi and Terfezia crassiverrucosa in Soil. J Fungi (Basel) 2022; 8:1095. [PMID: 36294660 PMCID: PMC9605127 DOI: 10.3390/jof8101095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Desert truffle crop is a pioneer in southeastern Spain, a region where native edible hypogeous fungi are adapted to the semiarid areas with low annual rainfall. Terfezia claveryi Chatin was the first species of desert truffle to be cultivated, and has been increasing in recent years as an alternative rainfed crop in the Iberian Peninsula. However, its behaviour in the field has yet not been investigated. For this purpose, specific primers were designed for the soil DNA quantification of both T. claveryi and Terfezia crassiverrucosa and a real-time qPCR protocol was developed, using the ITS rDNA region as a target. Moreover, a young desert truffle orchard was sampled for environmental validation. The results showed the highest efficiency for the TerclaF3/TerclaR1 primers pair, 89%, and the minimal fungal biomass that could be reliable detected was set at 4.23 µg mycelium/g soil. The spatial distribution of fungal biomass was heterogeneous, and there was not a direct relationship between the quantity of winter soil mycelium and the location/productivity of desert truffles. This protocol could be applied to tracking these species in soil and understand their mycelial dynamics in plantations and wild areas.
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Affiliation(s)
- Francisco Arenas
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), Campus de Espinardo, 30100 Murcia, Spain
- Forest Science and Technology Centre of Catalonia (CTFC), Carretera de Sant Llorenç de Morunys, Km 2, 25280 Solsona, Spain
| | - Asunción Morte
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), Campus de Espinardo, 30100 Murcia, Spain
| | - Alfonso Navarro-Ródenas
- Departamento de Biología Vegetal (Botánica), Facultad de Biología, Universidad de Murcia, CEIR Campus Mare Nostrum (CMN), Campus de Espinardo, 30100 Murcia, Spain
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Chávez-Luzanía RA, Montoya-Martínez AC, Parra-Cota FI, de Los Santos-Villalobos S. Pangenomes-identified singletons for designing specific primers to identify bacterial strains in a plant growth-promoting consortium. Mol Biol Rep 2022; 49:10489-10498. [PMID: 36125674 DOI: 10.1007/s11033-022-07927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND The use of plant growth-promoting microorganisms represents a sustainable way to increase agricultural yields and plant health. Thus, the identification and tracking of these microorganisms are determinants for validating their positive effects on crops. Pangenomes allow the identification of singletons that can be used to design specific primers for the detection of the studied strains. OBJECTIVE This study aimed to establish a strategy based on the use of whole-genome sequencing and pangenomes for designing and validating primer sets for detecting Bacillus cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65, a promising beneficial bacterial consortium for wheat. METHODS AND RESULTS The identification of singletons of TE3T, TRQ8, and TRQ65 was performed by pangenomes using the Kbase platform and subsequently analyzed using BLAST®. The identified DNA regions were used for primer design in AlleleID version 7. Primers were validated by multiplex PCR using pure template DNA from each studied strain, combinations of two or three DNA from these strains, and DNA from agricultural soil samples enriched (and not) with the bacterial consortium. Here, we report the first design of primers capable of detecting and identifying the beneficial strains TE3T, TRQ8, and TRQ65. CONCLUSIONS The use of pangenomes allowed the distinction of unique sequences that enables the design of primers for specific identification of the studied bacterial strains. This strategy can be widely used for the design of primer sets to detect other strains of interest for combating biopiracy, and commercial protection of biological products, among other applications.
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Affiliation(s)
| | | | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones forestales, Agrícolas y Pecuarias, Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, SON, México
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36
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Ben Amor F, Elleuch J, Farhat A, Barkallah M, Smith KF, Ben Neila I, Fendri I, Abdelkafi S. Development of a novel TaqMan qPCR assay for rapid detection and quantification of Gymnodinium catenatum for application to harmful algal bloom monitoring in coastal areas of Tunisia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:63953-63963. [PMID: 35469376 DOI: 10.1007/s11356-022-20273-3] [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: 01/28/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Gymnodinium catenatum is a dinoflagellate known to cause paralytic shellfish poisoning (PSP), commonly associated with human muscular paralysis, neurological symptoms, and, in extreme cases, death. In the present work, we developed a real-time PCR-based assay for the rapid detection of the toxic microalgal species, G. catenatum, in environmental bivalve mollusc samples as well as seawater samples. G. catenatum-specific primers and probe were designed on the ITS1-5.8S-ITS2 rDNA region. Hydrolysis probe qPCR assay was optimized. ITS1-5.8S-ITS2 rDNA region copy numbers per G. catenatum cell genome were estimated to be 122.73 ± 5.54 copies/cell, allowing cell quantification. The application of the optimized qPCR assay for G. catenatum detection and quantification in field samples has been conducted, revealing high sensitivity (detection of around 1.3105 cells/L of seawater samples. Thus, the designed hydrolysis probe qPCR assay could be considered an efficient tool for phytoplankton monitoring whilst ensuring accuracy and sensitivity and providing cost and time savings.
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Affiliation(s)
- Faten Ben Amor
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Sfax, Tunisia
| | - Ameni Farhat
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, B.P. 1171, 1117, 3029, Sfax, Tunisia
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Sfax, Tunisia
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, B.P. 1171, 1117, 3029, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, University of Sfax, Sfax, Tunisia.
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Salmon M, White HE, Zizkova H, Gottschalk A, Motlova E, Cerveira N, Colomer D, Coriu D, Franke GN, Gottardi E, Izzo B, Jurcek T, Lion T, Schäfer V, Venturi C, Vigneri P, Zawada M, Zuna J, Hovorkova L, Koblihova J, Klamova H, Markova MS, Srbova D, Benesova A, Polivkova V, Zackova D, Mayer J, Roeder I, Glauche I, Ernst T, Hochhaus A, Polakova KM, Cross NCP. Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy. Leukemia 2022; 36:1879-1886. [PMID: 35676453 PMCID: PMC9252903 DOI: 10.1038/s41375-022-01612-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022]
Abstract
Several studies have reported that chronic myeloid leukaemia (CML) patients expressing e14a2 BCR::ABL1 have a faster molecular response to therapy compared to patients expressing e13a2. To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC) BCR::ABL1 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories (n = 10). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 (p = 0.015), and the amplification efficiency was 2% greater (P = 0.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels of BCR::ABL1/GUSB were identified at diagnosis for patients expressing e13a2 (n = 67) compared to e14a2 (n = 78) when analysed by RT-qPCR (P = 0.0005) but not ddPCR (P = 0.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending on BCR::ABL1 transcript type; these differences are small but may need to be considered for optimal patient management.
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Affiliation(s)
- Matthew Salmon
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Helen E White
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Hana Zizkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Eliska Motlova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Nuno Cerveira
- Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Dolors Colomer
- Pathology Department, Hospital Clinic, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBERONC, Barcelona, Spain
| | - Daniel Coriu
- Fundeni Clinical Institute, Hematology Department, Bucharest, Romania.,Hematology Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Georg N Franke
- University of Leipzig Medical Center, Department for Hematology, Cellular Therapies and Hemostaseology, Leipzig, Germany
| | - Enrico Gottardi
- Laboratory of Chemical and Clinical Analysis "Area 3" A.O.U San Luigi Gonzaga-Orbassano, Turin, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology University 'Federico II' and CEINGE - Advanced Biotechnologies, Naples, Italy
| | - Tomas Jurcek
- Center of Molecular Biology and Gene Therapy, Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Thomas Lion
- Labdia Labordiagnostik / St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Vivien Schäfer
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Claudia Venturi
- IRCSS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Paolo Vigneri
- University of Catania, Department of Clinical and Experimental Medicine, Center of Experimental Oncology and Hematology, Catania, Italy
| | | | - Jan Zuna
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Lenka Hovorkova
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Dana Srbova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Adela Benesova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vaclava Polivkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Daniela Zackova
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany. Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | | | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK. .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
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Lahnsteiner F. Seasonal differences in thermal stress susceptibility of diploid and triploid brook trout, Salvelinus fontinalis (Teleostei, Pisces). JOURNAL OF FISH BIOLOGY 2022; 101:276-288. [PMID: 35633147 DOI: 10.1111/jfb.15118] [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: 03/14/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Many physiological processes of teleost fish show periodicity due to intrinsic rhythms. It may be hypothesized that also susceptibility to thermal stress differs seasonally. To shed more light on this problem the following experiment was conducted. Diploid and triploid Salvelinus fontinalis were kept at an acclimation temperature of 9°C and at a natural photoperiod typical for the Northern Hemisphere during their entire live. During eight different periods of the year, different subgroups were exposed to a 32 day lasting thermal stress of 20°C. Rate of fish maintaining equilibrium, daily growth rate, condition factor, viscerosomatic index and hepato-somatic index were measured. Complementary mRNA expression of genes characterizing growth (GHR1, GHR2), proteolysis (Protreg, Protα5), stress (Hsp47, Hsp90) and respiratory energy metabolism (ATPJ52) was determined. Seasonal differences in thermal stress susceptibility of 2n and 3n S. fontinalis were detected. It was highest from September to December and moderate from January to March. During the remaining period of the year, susceptibility to thermal stress was minimal. Increased thermal stress susceptibility was related to decreased rates of fish maintaining equilibrium, decreased growth rates, reduction of viscera and liver mass and changes in mRNA expression of genes characterizing proteolysis, growth, respiratory energy metabolism and stress. The differences in seasonal stress susceptibility were minor between 2n and 3n S. fontinalis. The data are valuable for ecology and fish culture to identify periods when animals are most susceptible to thermal stress.
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Affiliation(s)
- Franz Lahnsteiner
- Federal Agency for Water Management, Institute for Water Ecology, Fisheries and Lake Research, Mondsee, Austria
- Fishfarm Kreuzstein, Unterach, Austria
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Persson S, Larsson C, Simonsson M, Ellström P. rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. BMC Bioinformatics 2022; 23:239. [PMID: 35717145 PMCID: PMC9206141 DOI: 10.1186/s12859-022-04781-0] [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: 03/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT‑PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04781-0.
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Affiliation(s)
- Sofia Persson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Dag Hammarskjölds väg 56 A, 752 37, Uppsala, Sweden. .,Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden.
| | - Christina Larsson
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Dag Hammarskjölds väg 56 A, 752 37, Uppsala, Sweden
| | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden
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Abstract
Gene therapy, cell therapy and vaccine research have led to an increased use of qPCR/ddPCR in bioanalytical laboratories. CROs are progressively undertaking the development and validation of qPCR and ddPCR assays. Currently, however, there is limited regulatory guidance for the use of qPCR and a complete lack of any regulatory guidelines for the use of the newer ddPCR to support regulated bioanalysis. Hence, the Global CRO Council in Bioanalysis (GCC) has issued this White Paper to provide; 1) a consensus on the different validation parameters required to support qPCR/ddPCR assays; 2) a harmonized approach to their validation and 3) a consistent development of standard operating procedures (SOPs) for all the bioanalytical laboratories using these techniques.
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Development and Comparison of Seminested PCR, qPCR, and LAMP for the Rapid Detection of Arthrinium phaeospermum, the Causal Agent of Bamboo Blight. FORESTS 2022. [DOI: 10.3390/f13060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bambusa pervariabilis × Dendrocalamopsis grandis blight is a newly discovered disease in bamboos that has caused substantial economic loss to the affected areas. With the purpose of carrying out rapid detection of Bambusa pervariabilis × Dendrocalamopsis grandis blight caused by Arthrinium phaeospermum during the incubation period, three sets of detection assays were established: seminested PCR, real-time quantitative PCR, and LAMP. The specificity, sensitivity, and effectiveness of these assays were also detected. The results showed that the three assays were able to specifically amplify the target bands from five strains of Arthriniumphaeospermum from different sources, but none of the other 18 strains were able to obtain the specific bands. The sensitivity of the established seminested PCR, LAMP, and real-time quantitative PCR assays were 100, 10, and 1 pg/μL, respectively. The presence of A. phaeospermum could be detected in the early stage of disease using the total DNA of infected hybrid bamboo tissue as a template. The three systems established in this study are of great significance for the early diagnosis and rapid detection of hybrid bamboo blight.
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Geiselhardt F, Peters M, Jo WK, Schadenhofer A, Puff C, Baumgärtner W, Kydyrmanov A, Kuiken T, Piewbang C, Techangamsuwan S, Osterhaus ADME, Beineke A, Ludlow M. Development and Validation of a Pan-Genotypic Real-Time Quantitative Reverse Transcription-PCR Assay To Detect Canine Distemper Virus and Phocine Distemper Virus in Domestic Animals and Wildlife. J Clin Microbiol 2022; 60:e0250521. [PMID: 35491822 PMCID: PMC9116185 DOI: 10.1128/jcm.02505-21] [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: 12/17/2021] [Accepted: 04/09/2022] [Indexed: 11/20/2022] Open
Abstract
Canine distemper virus (CDV) is an animal morbillivirus belonging to the family Paramyxoviridae and has caused major epizootics with high mortality levels in susceptible wildlife species. In recent years, the documented genetic diversity of CDV has expanded, with new genotypes identified in India, the Caspian Sea, and North America. However, no quantitative real-time PCR (RT-qPCR) that has been validated for the detection of all genotypes of CDV is currently available. We have therefore established and characterized a pan-genotypic probe-based RT-qPCR assay based on the detection of a conserved region of the phosphoprotein (P) gene of CDV. This assay has been validated using virus strains representative of six genotypes of CDV in different sample types, including frozen tissue, formalin-fixed paraffin-embedded tissue sections, and virus isolates. The primers and probe target sequences were sufficiently conserved to also enable detection of the phocine distemper virus strains responsible for epizootics in harbor seals in the North Sea in 1988 and 2002. Comparison with two recently published RT-qPCR assays for CDV showed that under equivalent conditions the primers and probe set reported in this study were more sensitive in detecting nucleic acids from an Asia-4 genotype, which displays sequence variation in primer and probe binding sites. In summary, this validated new pan-genotypic RT-qPCR assay will facilitate screening of suspected distemper cases caused by novel genotypes for which full genome sequences are unavailable and have utility in detecting multiple CDV strains in geographical regions where multiple genotypes cocirculate in wildlife.
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Affiliation(s)
- Franziska Geiselhardt
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine (TiHo-RIZ), Hannover, Germany
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Arnsberg, Germany
| | - Wendy K. Jo
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine (TiHo-RIZ), Hannover, Germany
| | - Alina Schadenhofer
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine (TiHo-RIZ), Hannover, Germany
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | | | - Aidyn Kydyrmanov
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Almaty, Kazakhstan
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Animal Virome and Diagnostic Development Research Group, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine (TiHo-RIZ), Hannover, Germany
| | - Andreas Beineke
- Chemisches und Veterinäruntersuchungsamt Westfalen, Arnsberg, Germany
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine (TiHo-RIZ), Hannover, Germany
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Zhang L, Cai Y, Zhang M, Du G, Wang J. Selection and Evaluation of Candidate Reference Genes for Quantitative Real-Time PCR in Aboveground Tissues and Drought Conditions in Rhododendron Delavayi. Front Genet 2022; 13:876482. [PMID: 35495151 PMCID: PMC9046656 DOI: 10.3389/fgene.2022.876482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022] Open
Abstract
There has been no systematic identification and screening of candidate reference genes for normalization of quantitative real-time PCR (qRT-PCR) results in Rhododendron delavayi to date. Therefore, the present study used GAPDH, Act, EF1, Tub-, Tub-5, UEC1, TATA, TATA-2, UEP, TIP41, and Ubiquitin to predict their stabilities on different aboveground tissues (matured leaves (ML), stem tips (STM), and flower buds (FB)) at different developmental stages (young and adult plants) using five statistical algorithms: Delta Ct method, BestKeeper, geNorm, Normfinder, and RefFinder. The findings were confirmed using ML obtained from plants that had been stressed by drought. By using RefFinder with ML samples collected under drought conditions, it was determined that the top five most stable reference genes were GAPDH > UEC1 > Actin > Tubulin- > Tubulin—5, whereas the least stable reference gene was Ubiquitin. In addition, under control conditions, UEC1, UEC2, Actin, and GAPDH were selected as the highest stable potential reference genes at the juvenile stage of R. delavayi with ML and STM. When ML and STM were combined with drought-stressed samples, TIP41, GAPDH, or their combination proved to be the most effective qRT-PCR primers. The findings will aid in the improvement of the precision and reliability of qRT-PCR data and laying the groundwork for future gene functional studies in R. delavayi.
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Affiliation(s)
- Lu Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Yanfei Cai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
| | - Mingchao Zhang
- School of Agriculture, Yunnan University, Kunming, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, China
- *Correspondence: Guanghui Du, ; Jihua Wang,
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Shvets D, Vinogradova S. Occurrence and Genetic Characterization of Grapevine Pinot Gris Virus in Russia. PLANTS (BASEL, SWITZERLAND) 2022; 11:1061. [PMID: 35448789 PMCID: PMC9028157 DOI: 10.3390/plants11081061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is a widespread grapevine pathogen associated with symptoms of leaf mottling and deformation. In order to study the distribution and genetic diversity of GPGV in Russia, we tested 1347 grapevine samples from 3 regions of Russia-the Krasnodar Krai, Stavropol Krai, and Republic of Crimea-using duplex real-time RT-PCR. GPGV was detected in 993 grapevines, both symptomatic and asymptomatic. In 119 isolates, we sequenced complete movement protein (MP) and coat protein (CP) genes of the GPGV genome. The percentage of identity of the obtained nucleotide MP/CP sequences with the closest isolates from the GenBank was 97.75-99.56%. A phylogenetic analysis showed that these Russian GPGV isolates are mainly grouped with previously described representative asymptomatic isolates. New post-translational modifications of the MP and CP at the positions of polymorphisms in the genomes of Russian isolates were predicted. The present work is the first study on the distribution and genetic diversity of GPGV in Russia.
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Neris D, Mattiello L, Zuñiga G, Purgatto E, Menossi M. Reduction of ethylene biosynthesis in sugarcane induces growth and investment in the non-enzymatic antioxidant apparatus. PLANT CELL REPORTS 2022; 41:979-993. [PMID: 35226115 DOI: 10.1007/s00299-022-02832-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Lower ethylene production in sugarcane results in plants with higher stature, expression of growth-promoting genes, higher photosynthetic rate, and increased antioxidant compounds. The hormone ethylene is involved in critical processes in sugarcane, such as the growth and accumulation of sucrose. The lack of mutants for ethylene biosynthesis or signaling genes makes it difficult to understand the role of this phytohormone throughout sugarcane development. This study aimed to evaluate the physiology and development of sugarcane plants with low ethylene production. To achieve this goal, we used RNA interference to silence three genes, ScACS1, ScACS2, and ScACS3, encoding 1-aminocyclopropane-1-carboxylic acid synthases (ACS), responsible for a limiting step of the ethylene biosynthesis pathway. Sugarcane plants with reduced ethylene levels presented increased growth, faster germination of lateral gems, and activation of non-enzymatic antioxidant mechanisms. We observed an augmentation in the expression of ScACO5, which encodes the final enzyme regulating ethylene biosynthesis, and ScERF1, encoding a transcription factor, linked to the ethylene response. The increase in plant height was correlated with higher expression of ScPIF3, ScPIF4, and ScPIF5, which encode for transcription factors related to growth induction. Interestingly, there was also an increase in the expression of the ScGAI gene, which encodes a DELLA protein, a growth repressor. The final content of sucrose in the stems was not affected by the low levels of ethylene, although the rate of CO2 assimilation was reduced. This study reports for the first time the impacts of low endogenous production of ethylene in sugarcane and provides helpful insights on the molecular mechanisms behind ethylene responses.
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Affiliation(s)
- Daniel Neris
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Gustavo Zuñiga
- Faculty of Chemistry and Biology, University of Santiago de Chile, Santiago, Chile
| | - Eduardo Purgatto
- Faculty of Pharmaceutical Sciences, São Paulo University, São Paulo, SP, Brazil
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Cell-Free Paper-Based Analysis of Gut Microbiota and Host Biomarkers. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:351-374. [PMID: 34985756 DOI: 10.1007/978-1-0716-1998-8_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The gut microbiome and its interactions with the host have been shown to affect several aspects of human health and disease. Investigations to elucidate these mechanisms typically involve sequence analysis of fecal samples. To support these studies, we present methods to design RNA toehold switch sensors to detect microbial and host transcripts. The sensors are embedded in paper-based, cell-free reactions that enable affordable and rapid analysis of microbiome samples.
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Juszkiewicz DJ, White NE, Stolarski J, Benzoni F, Arrigoni R, Baird AH, Hoeksema BW, Wilson NG, Bunce M, Richards ZT. Full Title: Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach. Mol Phylogenet Evol 2022; 172:107469. [DOI: 10.1016/j.ympev.2022.107469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
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Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale. Microorganisms 2022; 10:microorganisms10020341. [PMID: 35208796 PMCID: PMC8875355 DOI: 10.3390/microorganisms10020341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/17/2022] [Accepted: 01/29/2022] [Indexed: 02/01/2023] Open
Abstract
Ornithobacterium rhinotracheale (ORT) has been associated with poultry respiratory disease worldwide. The organism is fastidious and isolation is challenging. One TaqMan real-time PCR (qPCR) assay has been developed for the detection of ORT. However, during validating the ORT qPCR, the assay performance was suboptimal. During the in silico evaluation, deviations from the basic parameters for primers and probes designs (e.g., presence of stable undesirable primer-dimers) were observed. The suboptimal design led to low efficiency and low sensitivity of the assay. Initially, modification on the probe was carried out to improve the performance of the assay. However, the assay’s performance (efficiency and sensitivity) was still suboptimal. In this manuscript, we describe the development of a new qPCR assay and the comparison of its performance with the currently available assay. A highly efficient, sensitive, and specific qPCR assay was developed with approximately 1000-folds reduction in the limit of detection (from 3 × 106 plasmid DNA copies/mL to 1 × 103 plasmid DNA copies/mL). Additionally, the efficiency of the new assay (E = 98.70%) was significantly better than the current assay (E = 73.18%). The newly developed assay is an improved diagnostic tool for the sensitive and efficient diagnosis of ORT from clinical samples.
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49
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RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step. Int J Mol Sci 2022; 23:ijms23031303. [PMID: 35163227 PMCID: PMC8835954 DOI: 10.3390/ijms23031303] [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: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
Reverse transcription of RNA coupled to amplification of the resulting cDNA by the polymerase chain reaction (RT-PCR) is one of the principal molecular technologies in use today, with applications across all areas of science and medicine. In its real-time, fluorescence-based usage (RT-qPCR), it has long been a core technology driving the accurate, rapid and sensitive laboratory diagnosis of infectious diseases. However, RT-qPCR protocols have changed little over the past 30 years, with the RT step constituting a significant percentage of the time taken to complete a typical RT-qPCR assay. When applied to research investigations, reverse transcription has been evaluated by criteria such as maximum yield, length of transcription, fidelity, and faithful representation of an RNA pool. Crucially, however, these are of less relevance in a diagnostic RT-PCR test, where speed and sensitivity are the prime RT imperatives, with specificity contributed by the PCR component. We propose a paradigm shift that omits the requirement for a separate high-temperature RT step at the beginning of an RT-qPCR assay. This is achieved by means of an innovative protocol that incorporates suitable reagents with a revised primer and amplicon design and we demonstrate a proof of principle that incorporates the RT step as part of the PCR assay setup at room temperature. Use of this modification as part of a diagnostic assay will of course require additional characterisation, validation and optimisation of the PCR step. Combining this revision with our previous development of fast qPCR protocols allows completion of a 40 cycle RT-qPCR run on a suitable commercial instrument in approximately 15 min. Even faster times, in combination with extreme PCR procedures, can be achieved.
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Nunes VV, Silva-Mann R, Souza JL, Calazans CC. Pharmaceutical, food potential, and molecular data of Hancornia speciosa Gomes: a systematic review. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:525-543. [PMID: 35068695 PMCID: PMC8764503 DOI: 10.1007/s10722-021-01319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Hancornia speciosa Gomes is a fruit and medicinal tree species native to South America, which in Brazil is considered of potential economic value and priority for research and development. We present a map of the state-of-art, including articles, patents, and molecular data of the species to identify perspectives for future research. The annual scientific production, intellectual, social, and conceptual structure were evaluated, along with the number of patent deposits, components of the plant used, countries of deposit, international classification and assignees, and the accessibility of available molecular data. Brazil has the most significant publications (306) between 1992 and 2020. Technological products (29) have been developed from different tissues of the plant. Most of the articles and patents were developed by researchers from public universities from different regions of Brazil. The molecular data are sequences of nucleotides (164) and proteins (236) of the chloroplast genome and are described to identify the species as DNA barcodes and proteins involved in photosynthesis. The compilation and report of scientific, technological, and molecular information in the present review allowed the identification of new perspectives of research to be developed based on the gaps in knowledge regarding the species and perspectives for the definition of future research. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10722-021-01319-w.
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Affiliation(s)
- Valdinete Vieira Nunes
- Post-Graduation Program in Agriculture and Biodiversity, Universidade Federal de Sergipe, São Cristóvão, Sergipe Brazil
| | - Renata Silva-Mann
- Department of Agronomic Engineering, Universidade Federal de Sergipe, São Cristóvão, Sergipe Brazil
| | - Juliana Lopes Souza
- Post-Graduation Program in Agriculture and Biodiversity, Universidade Federal de Sergipe, São Cristóvão, Sergipe Brazil
| | - Crislaine Costa Calazans
- Post-Graduation Program in Agriculture and Biodiversity, Universidade Federal de Sergipe, São Cristóvão, Sergipe Brazil
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