1
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Li W, Zhang S, Dang S, Gao L, Li G, Cheng D, Jiang L, Huang T, Zhai J. Establishment of an A/T-Rich Specifically MGB Probe digital droplet PCR Assays Based on SNP for Brucella wild strains and vaccine strains. Diagn Microbiol Infect Dis 2024; 110:116432. [PMID: 39024932 DOI: 10.1016/j.diagmicrobio.2024.116432] [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: 03/27/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
In recent years, immunization with the S2 live-attenuated vaccine has been recognized as the most economical and effective strategy for preventing brucellosis in Inner Mongolia, China. However, there are still challenges related to vaccine toxicity and the inability to distinguish between vaccine immunization and natural infection. Therefore, in this study, we developed a digital droplet polymerase chain reaction (ddPCR) assay based on single-nucleotide polymorphism (SNP) loci to identify wild Brucella strains and S2 vaccine strains. The assay demonstrated excellent linearity (R2> 0.99) with a lower detection limit of 10 copies/µL for both wild and vaccine strains. Additionally, the ddPCR assay outperformed the real-time fluorescent quantitative PCR (qPCR) assay in screening 50 clinical samples. We have established an effective and highly sensitive ddPCR assay for Brucella, providing an efficient method for detecting and differentiating wild strains of Brucella from the S2 vaccine strain.
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Affiliation(s)
- Wanyang Li
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Shuai Zhang
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Sheng Dang
- Keerqin District First People's Hospital, Tongliao 028000, China
| | - Lanzhu Gao
- Tongliao Infectious Disease Hospital, Tongliao 028000, China
| | - Guangchen Li
- Tongliao Infectious Disease Hospital, Tongliao 028000, China
| | - Dawei Cheng
- Beidahuang Industry Group General Hospital, Harbin 150000, China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou 350000, China
| | - Tianpeng Huang
- College of Public Health, Inner Mongolia Minzu University, Tongliao 028000, China; Brucellosis Prevention and Treatment Engineering Research Center of Inner Mongolia Autonomous Region, Tongliao 028000, China; Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao 028000, China
| | - Jingbo Zhai
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China; Brucellosis Prevention and Treatment Engineering Research Center of Inner Mongolia Autonomous Region, Tongliao 028000, China; Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao 028000, China.
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2
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Baron A, Hamane S, Gits-Muselli M, Legendre L, Benderdouche M, Mingui A, Ghelfenstein-Ferreira T, Alanio A, Dellière S. Dual quantitative PCR assays for the rapid detection of Trichophyton indotineae from clinical samples. Med Mycol 2024; 62:myae067. [PMID: 38977869 DOI: 10.1093/mmy/myae067] [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: 03/12/2024] [Revised: 06/24/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024] Open
Abstract
Trichophyton indotineae is an emerging species of the Trichophyton mentagrophytes complex (TMC), responsible for an epidemic of widespread hairless skin infections that is frequently (50-70%) resistant to terbinafine. In order to initiate appropriate treatment as quickly as possible without waiting for culture positivity (10-15 days) and molecular identification from the strain, we developed a dual quantitative PCR (qPCR) for the direct detection of T. indotineae in clinical samples. We first designed a T. indotineae-specific qPCR assay (TI-qPCR) targeting a single specific polymorphism in the internal transcribed spacer region. Although none of the 94 non-dermatophyte and 7 dermatophyte species were amplified, this TI-qPCR allowed amplification of other TMC species at a lower yield. With equal amounts (0.1 ng) of DNA per reaction, the mean quantitative cycle (Cq) values for T. indotineae and non-indotineae TMC were 27.9 (±0.1) and 38.9 (±0.3), respectively. Therefore, we normalized this assay against a previously validated pan-dermatophyte qPCR assay (PD-qPCR) and relied on the ΔCq [(TI-qPCR) - (PD-qPCR)] to identify T. indotineae versus other TMC species. Dual assay was validated using 86 clinical samples of culture-confirmed T. indotinea and 19 non-indotineae TMC cases. The mean ΔCq for non-indotineae TMC was 9.6 ± 2.7, whereas the ΔCq for T. indotinea was -1.46 ± 2.1 (P < .001). Setting the ΔCq at 4.5 as a cutoff value resulted in 100% specificity for the detection of T. indotineae. This dual qPCR assay quickly detects T. indotineae from skin scrapings, aiding in early diagnosis and treatment for patients with suspected infection.
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Affiliation(s)
- Audrey Baron
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Samia Hamane
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Maud Gits-Muselli
- Laboratoire de microbiologie, AP-HP, Hôpital Robert-Debré, F-75019 Paris, France
| | - Lina Legendre
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Mazouz Benderdouche
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Anselme Mingui
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
| | - Théo Ghelfenstein-Ferreira
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
- Institut Pasteur, Université de Paris Cité, CNRMA, Unité de Mycologie Translationnelle, F-75015 Paris, France
| | - Alexandre Alanio
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
- Institut Pasteur, Université de Paris Cité, CNRMA, Unité de Mycologie Translationnelle, F-75015 Paris, France
| | - Sarah Dellière
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, F-75010 Paris, France
- Institut Pasteur, Université de Paris Cité, Unité Immunobiologie d'Aspergillus, F-75015 Paris, France
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Zhang J, Chen M, Jiang H, Sun H, Ren J, Yang X, Liu S, Wang D, Huang Z, Liu J, Ma D, Guo X, Luo G. Atom-Modified gDNA Enhances Cleavage Activity of TtAgo Enabling Ultra-Sensitive Nucleic Acid Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403120. [PMID: 38728591 PMCID: PMC11267260 DOI: 10.1002/advs.202403120] [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: 03/26/2024] [Revised: 05/02/2024] [Indexed: 05/12/2024]
Abstract
The DNA-guided (gDNA) Argonaute from Thermus thermophilus (TtAgo) has little potential for nucleic acid detection and gene editing due to its poor dsDNA cleavage activity at relatively low temperature. Herein, the dsDNA cleavage activity of TtAgo is enhanced by using 2'-fluorine (2'F)-modified gDNA and developes a novel nucleic acid testing strategy. This study finds that the gDNA with 2'F-nucleotides at the 3'-end (2'F-gDNA) can promote the assembly of the TtAgo-guide-target ternary complex significantly by increasing its intermolecular force to target DNA and TtAgo, thereby providing ≈40-fold activity enhancement and decreasing minimum reaction temperature from 65 to 60 °C. Based on this outstanding advance, a novel nucleic acid testing strategy is proposed, termed FAST, which is performed by using the 2'F-gDNA/TtAgo for target recognition and combining it with Bst DNA polymerase for nucleic acid amplification. By integrating G-quadruplex and Thioflavin T, the FAST assay achieves one-pot real-time fluorescence analysis with ultra-sensitivity, providing a limit of detection up to 5 copies (20 µL reaction mixture) for miR-21 detection. In summary, an atom-modification-based strategy has been developed for enhancing the cleavage activity of TtAgo efficiently, thereby improving its practicability and establishing a TtAgo-based nucleic acid testing technology with ultra-sensitivity and high-specificity.
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Affiliation(s)
- Jun Zhang
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
- Key Laboratory of Bio‐Resource and Eco‐environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuan610064China
| | - Miaomiao Chen
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Huan Jiang
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Huifang Sun
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Jianing Ren
- Department of Oncology & Department of Rheumatology and ImmunologyAffiliated Hospital of North Sichuan Medical CollegeNanchong637000China
| | - Xin Yang
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Shanshan Liu
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Dongsheng Wang
- Department of Clinical LaboratorySichuan Cancer HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaChengdu610041China
| | - Zhen Huang
- Key Laboratory of Bio‐Resource and Eco‐environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduSichuan610064China
| | - Jianping Liu
- Department of Oncology & Department of Rheumatology and ImmunologyAffiliated Hospital of North Sichuan Medical CollegeNanchong637000China
| | - Daiyuan Ma
- Department of Oncology & Department of Rheumatology and ImmunologyAffiliated Hospital of North Sichuan Medical CollegeNanchong637000China
| | - Xiaolan Guo
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
| | - Guangcheng Luo
- Department of Clinical LaboratoryAffiliated Hospital of North Sichuan Medical CollegeSchool of Laboratory Medicine & Translational Medicine Research CenterNorth Sichuan Medical CollegeNanchong637000China
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4
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Pillai SP, Hill KK, Gans J, Smith TJ. Real-time PCR assays that detect genes for botulinum neurotoxin A-G subtypes. Front Microbiol 2024; 15:1382056. [PMID: 38873139 PMCID: PMC11169944 DOI: 10.3389/fmicb.2024.1382056] [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: 02/04/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.
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Affiliation(s)
- Segaran P. Pillai
- Office of the Commissioner, Food and Drug Administration, Department of Health and Human Services, Silver Spring, MD, United States
| | - Karen K. Hill
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States
| | - Jason Gans
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States
| | - Theresa J. Smith
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Tripathi M, Thakur Y, Syed R, Asatkar AK, Alqahtani MS, Das D, Agrawal R, Verma B, Pande R. In-vitro and in-silico analysis and antitumor studies of novel Cu(II) and V(V) complexes of N-p-Tolylbenzohydroxamic acid. Int J Biol Macromol 2024; 268:131768. [PMID: 38663706 DOI: 10.1016/j.ijbiomac.2024.131768] [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: 09/21/2023] [Revised: 03/07/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
Copper(L2Cu) and vanadium(L2VOCl) complexes of N-p-tolylbenzohydroxamic acid (LH) ligand have been investigated for DNA binding efficacy by multiple analytical, spectral, and computational techniques. The results revealed that complexes as groove binders as evidenced by UV absorption. Fluorescence studies including displacement assay using classical intercalator ethidium bromide as fluorescent probe also confirmed as groove binders. The viscometric analysis too supports the inferences as strong groove binders for both the complexes. Molecular docking too exposed DNA as a target to the complexes which precisely binds L2Cu, in the minor groove region while L2VOCl in major groove region. Molecular dynamic simulation performed on L2Cu complex revealing the interaction of complex with DNA within 20 ns time. The complex stacked into the nitrogen bases of oligonucleotides and the bonding features were intrinsically preserved for longer simulation times. In-vitro cytotoxicity study was undertaken employing MTT assay against the breast cancer cell line (MCF-7). Potential cytotoxic activities were observed for L2Cu and L2VOCl complexes with IC50 values of showing 71 % and 74 % of inhibition respectively.
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Affiliation(s)
- Mamta Tripathi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India.
| | - Yamini Thakur
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India; Department of Chemistry, Govt. J. Yoganandam Chhattisgarh College, Raipur C.G. - 492001
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ashish Kumar Asatkar
- Department of Chemistry, Satya Narayan Agrawal Govt. Arts and Commerce College, Kohka-Neora, Dist. Raipur, CG 493114, India
| | - Mohammad S Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Rainy Agrawal
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
| | - Bharati Verma
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
| | - Rama Pande
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
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6
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Canalis E, Schilling L, Yu J, Denker E. NOTCH2 promotes osteoclast maturation and metabolism and modulates the transcriptome profile during osteoclastogenesis. J Biol Chem 2024; 300:105613. [PMID: 38159855 PMCID: PMC10837628 DOI: 10.1016/j.jbc.2023.105613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
Notch signaling plays a key regulatory role in bone remodeling and NOTCH2 enhances osteoclastogenesis, an effect that is mostly mediated by its target gene Hes1. In the present study, we explored mechanisms responsible for the enhanced osteoclastogenesis in bone marrow-derived macrophages (BMM) from Notch2tm1.1Ecan, harboring a NOTCH2 gain-of-function mutation, and control mice. Notch2tm1.1Ecan mice are osteopenic and have enhanced osteoclastogenesis. Bulk RNA-Seq and gene set enrichment analysis of Notch2tm1.1Ecan BMMs cultured in the presence of macrophage colony stimulating factor (M-CSF) and receptor activator of NF-κB ligand revealed enrichment of genes associated with enhanced cell metabolism, aerobic respiration, and mitochondrial function, all associated with osteoclastogenesis. These pathways were not enhanced in the context of a Hes1 inactivation. Analysis of single cell RNA-Seq data of pooled control and Notch2tm1.1Ecan BMMs treated with M-CSF or M-CSF and receptor activator of NF-κB ligand for 3 days identified 11 well-defined cellular clusters. Pseudotime trajectory analysis indicated a trajectory of clusters expressing genes associated with osteoclast progenitors, osteoclast precursors, and mature cells. There were an increased number of cells expressing gene markers associated with the osteoclast and with an unknown, albeit related, cluster in Notch2tm1.1Ecan than in control BMMs as well as enhanced expression of genes associated with osteoclast progenitors and precursors in Notch2tm1.1Ecan cells. In conclusion, BMM cultures display cellular heterogeneity, and NOTCH2 enhances osteoclastogenesis, increases mitochondrial and metabolic activity of osteoclasts, and affects cell cluster allocation in BMMs.
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; Department of Medicine, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA.
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Emily Denker
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
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Canalis E, Yu J, Singh V, Mocarska M, Schilling L. NOTCH2 sensitizes the chondrocyte to the inflammatory response of tumor necrosis factor α. J Biol Chem 2023; 299:105372. [PMID: 37865314 PMCID: PMC10692730 DOI: 10.1016/j.jbc.2023.105372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023] Open
Abstract
Notch regulates the immune and inflammatory response and has been associated with the pathogenesis of osteoarthritis in humans and preclinical models of the disease. Notch2tm1.1Ecan mice harbor a NOTCH2 gain-of-function and are sensitized to osteoarthritis, but the mechanisms have not been explored. We examined the effects of tumor necrosis factor α (TNFα) in chondrocytes from Notch2tm1.1Ecan mice and found that NOTCH2 enhanced the effect of TNFα on Il6 and Il1b expression. Similar results were obtained in cells from a conditional model of NOTCH2 gain-of-function, Notch22.1Ecan mice, and following the expression of the NOTCH2 intracellular domain in vitro. Recombination signal-binding protein for immunoglobulin Kappa J region partners with the NOTCH2 intracellular domain to activate transcription; in the absence of Notch signaling it inhibits transcription, and Rbpj inactivation in chondrocytes resulted in Il6 induction. Although TNFα induced IL6 to a greater extent in the context of NOTCH2 activation, there was a concomitant inhibition of Notch target genes Hes1, Hey1, Hey2, and Heyl. Electrophoretic mobility shift assay demonstrated displacement of recombination signal-binding protein for immunoglobulin Kappa J region from DNA binding sites by TNFα explaining the increased Il6 expression and the concomitant decrease in Notch target genes. NOTCH2 enhanced the effect of TNFα on NF-κB signaling, and RNA-Seq revealed increased expression of pathways associated with inflammation and the phagosome in NOTCH2 overexpressing cells in the absence and presence of TNFα. Collectively, NOTCH2 has important interactions with TNFα resulting in the enhanced expression of Il6 and inflammatory pathways in chondrocytes.
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; Department of Medicine, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA.
| | - Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Vijender Singh
- Computational Biology Core, Institute for System Genomics, UConn, Storrs, Connecticut, USA
| | - Magda Mocarska
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
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Chen W, Xu H, Dai S, Wang J, Yang Z, Jin Y, Zou M, Xiao X, Wu T, Yan W, Zhang B, Lin Z, Zhao M. Detection of low-frequency mutations in clinical samples by increasing mutation abundance via the excision of wild-type sequences. Nat Biomed Eng 2023; 7:1602-1613. [PMID: 37500748 DOI: 10.1038/s41551-023-01072-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
The efficiency of DNA-enrichment techniques is often insufficient to detect mutations that occur at low frequencies. Here we report a DNA-excision method for the detection of low-frequency mutations in genomic DNA and in circulating cell-free DNA at single-nucleotide resolution. The method is based on a competitive DNA-binding-and-digestion mechanism, effected by deoxyribonuclease I (DNase) guided by single-stranded phosphorothioated DNA (sgDNase), for the removal of wild-type DNA strands. The sgDNase can be designed against any wild-type DNA sequences, allowing for the uniform enrichment of all the mutations within the target-binding region of single-stranded phosphorothioated DNA at mild-temperature conditions. Pretreatment with sgDNase enriches all mutant strands with initial frequencies down to 0.01% and leads to high discrimination factors for all types of single-nucleotide mismatch in multiple sequence contexts, as we show for the identification of low-abundance mutations in samples of blood or tissue from patients with cancer. The method can be coupled with next-generation sequencing, droplet digital polymerase chain reaction, Sanger sequencing, fluorescent-probe-based assays and other mutation-detection methods.
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Affiliation(s)
- Wei Chen
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shenbin Dai
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yuewen Jin
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Mengbing Zou
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xianjin Xiao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Wei Yan
- Department of Dermatology, Peking University First Hospital, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses and National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | - Bin Zhang
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Department of Dermatology, Zhengzhou University, Affiliated Children's Hospital, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Zhimiao Lin
- Department of Dermatology, Peking University First Hospital, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses and National Clinical Research Center for Skin and Immune Diseases, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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9
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Canalis E, Mocarska M, Schilling L, Jafar-Nejad P, Carrer M. Antisense oligonucleotides targeting a NOTCH3 mutation in male mice ameliorate the cortical osteopenia of lateral meningocele syndrome. Bone 2023; 177:116898. [PMID: 37704069 PMCID: PMC10591917 DOI: 10.1016/j.bone.2023.116898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Lateral Meningocele Syndrome (LMS) is a monogenic disorder associated with NOTCH3 pathogenic variants that result in the stabilization of NOTCH3 and a gain-of-function. A mouse model (Notch3em1Ecan) harboring a 6691-TAATGA mutation in the Notch3 locus that results in a functional outcome analogous to LMS exhibits cancellous and cortical bone osteopenia. We tested Notch3 antisense oligonucleotides (ASOs) specific to the Notch36691-TAATGA mutation for their effects on Notch3 downregulation and on the osteopenia of Notch3em1Ecan mice. Twenty-four mouse Notch3 mutant ASOs were designed and tested for toxic effects in vivo, and 12 safe ASOs were tested for their impact on the downregulation of Notch36691-TAATGA and Notch3 mRNA in osteoblast cultures from Notch3em1Ecan mice. Three ASOs downregulated Notch3 mutant transcripts specifically and were tested in vivo for their effects on the bone microarchitecture of Notch3em1Ecan mice. All three ASOs were well tolerated. One of these ASOs had more consistent effects in vivo and was studied in detail. The Notch3 mutant ASO downregulated Notch3 mutant transcripts in osteoblasts and bone marrow stromal cells and had no effect on other Notch receptors. The subcutaneous administration of Notch3 mutant ASO at 50 mg/Kg decreased Notch36691-TAATGA mRNA in bone without apparent toxicity; microcomputed tomography demonstrated that the ASO ameliorated the cortical osteopenia of Notch3em1Ecan mice but not the cancellous bone osteopenia. In conclusion, a Notch3 ASO that downregulates Notch3 mutant expression specifically ameliorates the cortical osteopenia in Notch3em1Ecan mice. ASOs may become useful strategies in the management of monogenic disorders affecting the skeleton.
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, CT, USA; Department of Medicine, UConn Health, Farmington, CT, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, CT, USA.
| | - Magda Mocarska
- UConn Musculoskeletal Institute, UConn Health, Farmington, CT, USA
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, CT, USA
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10
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Zhou B, Yang G, Hu Z, Chen K, Guo W, Wang X, Du C. Development of a Real-Time Quantitative PCR Based on a TaqMan-MGB Probe for the Rapid Detection of Theileria haneyi. Microorganisms 2023; 11:2633. [PMID: 38004645 PMCID: PMC10673206 DOI: 10.3390/microorganisms11112633] [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: 09/05/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Equine piroplasmosis (EP) is a parasitic disease caused by Theileria equi (T. equi), Babesia caballi (B. caballi) and Theileria haneyi (T. haneyi). This disease is considered to be reportable by the World Organization for Animal Health (WOAH). Real-time quantitative PCR (qPCR) is regarded as a straightforward, rapid and sensitive diagnostic method to detect pathogens. However, qPCR has not been employed in the various epidemiological investigations of T. haneyi. In this study, we developed a new qPCR method to detect T. haneyi based on the chr1sco (chromosome 1 single-copy open reading frame (ORF)) gene, which has no detectable orthologs in T. equi or B. caballi. A TaqMan MGB probe was used in the development of the qPCR assay. A plasmid containing the chr1sco gene was constructed and used to establish the standard curves. The novel qPCR technique demonstrated great specificity for detecting additional frequent equine infectious pathogens and sensitivity for detecting diluted standard plasmids. This qPCR was further validated by comparison with an optimized nested PCR (nPCR) assay in the analysis of 96 clinical samples. The agreement between the nPCR assay and the established qPCR assay was 85.42%. The newly established method could contribute to the accurate diagnosis of T. haneyi infections in horses.
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Affiliation(s)
| | | | | | | | | | - Xiaojun Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (B.Z.); (G.Y.); (Z.H.); (K.C.); (W.G.)
| | - Cheng Du
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (B.Z.); (G.Y.); (Z.H.); (K.C.); (W.G.)
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11
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Huang X, Wang X, Zhou L, Kong F, Liu Y, Wang Z, Zhang H. TaqMan-MGB PCR Method for Rapid Detection of QoI Fungicide Resistance in Chinese Populations of Plasmopara viticola. PLANT DISEASE 2023; 107:3007-3013. [PMID: 36856651 DOI: 10.1094/pdis-12-22-2954-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Grape downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevine worldwide. Quinone outside inhibitor (QoI) fungicides are commonly used for the control of the pathogen in grape fields across China. However, their recurrent use could lead to the emergence of resistance against these compounds. Based on the most common mutation in resistant isolates, a glycine to alanine substitution at amino acid position 143 (G143A) in the cytochrome b protein, a TaqMan-MGB PCR was developed for the rapid detection of resistance to the QoI fungicide azoxystrobin in P. viticola. Specificity and sensitivity of this method showed it could specifically detect the point mutations linked with QoI resistance in P. viticola, and the detection limit was 0.2 pg. It could also quantify the resistance allele even in isolate mixtures containing as little as 5% QoI-resistant P. viticola strains. With this method, a large P. viticola population (n = 2,373) was screened, and QoI-resistant isolates were identified for the first time in China. The average frequencies of the resistant genotype from eight major-grapevine regions were up to 66%. Taken together, the results not only provide a novel tool for the rapid distinction and quantification of the QoI-resistant allele in P. viticola but also provide important references for fungicide selection and application, which will facilitate resistance management of grape downy mildew and improve grape production systems in Chinese vineyards.
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Affiliation(s)
- Xiaoqing Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xina Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Fanfang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Zhongyue Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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12
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Gordhan BG, Herrera C, Pillay AD, Seiphetlo T, Ealand CS, Machowski E, Singh N, Seatholo N, Otwombe K, Lebina L, Frise R, Scarlatti G, Chiodi F, Martinson N, Fox J, Kana BD. Evaluation of a human mucosal tissue explant model for SARS-CoV-2 replication. PLoS One 2023; 18:e0291146. [PMID: 37769001 PMCID: PMC10538748 DOI: 10.1371/journal.pone.0291146] [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: 05/24/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023] Open
Abstract
With the onset of COVID-19, the development of ex vivo laboratory models became an urgent priority to study host-pathogen interactions in response to the pandemic. In this study, we aimed to establish an ex vivo mucosal tissue explant challenge model for studying SARS-CoV-2 infection and replication. Nasal or oral tissue samples were collected from eligible participants and explants generated from the tissue were infected with various SARS-CoV-2 strains, including IC19 (lineage B.1.13), Beta (lineage B.1.351) and Delta (lineage B.1.617.2). A qRT-PCR assay used to measure viral replication in the tissue explants over a 15-day period, demonstrated no replication for any viral strains tested. Based on this, the ex vivo challenge protocol was modified by reducing the viral infection time and duration of sampling. Despite these changes, viral infectivity of the nasal and oral mucosa was not improved. Since 67% of the enrolled participants were already vaccinated against SARS-CoV-2, it is possible that neutralizing antibodies in explant tissue may have prevented the establishment of infection. However, we were unable to optimize plaque assays aimed at titrating the virus in supernatants from both infected and uninfected tissue, due to limited volume of culture supernatant available at the various collection time points. Currently, the reasons for the inability of these mucosal tissue samples to support replication of SARS-CoV-2 ex vivo remains unclear and requires further investigation.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Carolina Herrera
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Azure-Dee Pillay
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Thabiso Seiphetlo
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher Shawn Ealand
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Edith Machowski
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Natasha Singh
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Ntombexolo Seatholo
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Kennedy Otwombe
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Chiodi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Neil Martinson
- Faculty of Health Sciences, Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, MD, United States of America
| | - Julie Fox
- Guys and St. Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Bavesh Davandra Kana
- Faculty of Health Sciences, Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
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13
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Sui P, Sun Y, Shi Y, Ran W, Shi N, Sun D, Zheng J, Zhao J. Establishment and evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type canine distemper virus from vaccine strains. Heliyon 2023; 9:e19344. [PMID: 37662817 PMCID: PMC10469063 DOI: 10.1016/j.heliyon.2023.e19344] [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: 06/07/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
This study sought to establish a real-time reverse transcription (RT)-PCR method to differentially detect canine distemper virus (CDV) wild-type and vaccine strains. To this end, a pair of CDV universal primers and two specific minor groove binder (MGB) probes, harboring a T/C substitution in the hemagglutinin (H) gene, were designed. Using a recombinant plasmid expressing the H gene of the CDV wild-type or vaccine strain as standards, a sensitive and specific multiplex real-time RT-PCR was established for quantitative and differential detection of CDV wild-type and vaccine strains. The limit of detection for this multiplex assay was 22.5 copies/μL and 2.98 copies/μL of viral RNA for wild-type and vaccine strains, respectively. Importantly, the wild-type and vaccine MGB probes specifically hybridized different genotypes of wild-type CDV circulating in China as well as globally administered vaccine viruses, respectively, with no cross-reactivity observed with non-CDV viruses. Moreover, this method was successfully applied for the quantitative detection of CDV RNA in tissue samples of experimentally infected breeding foxes, raccoon dogs, and minks. Additionally, the multiplex real-time RT-PCR was able to detect the viral RNA in the whole blood samples as early as 3 days post-infection, 3 to 4 days prior to the onset of clinical signs in these CDV infection animals. Hence, the established multiplex real-time RT-PCR method is useful for differentiating wild-type CDV and vaccine strains in China, and for conducting canine distemper early diagnosis as well as dynamic mechanism of CDV replication studies in vivo.
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Affiliation(s)
- Ping Sui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Yiyang Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Yijun Shi
- Shandong Yantai Animal Disease Control Center, Yantai 264003, PR China
| | - Wei Ran
- Animal Husbandry and Fisheries, Guizhou Vocational College of Agriculture, Guiyang 551400, China
| | - Ning Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Jiasan Zheng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
| | - Jianjun Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China
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14
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Batson AM, Woodhall JW, du Toit LJ. Real-Time PCR Assays for Races of the Spinach Fusarium Wilt Pathogen, Fusarium oxysporum f. sp. spinaciae. PLANT DISEASE 2023; 107:2633-2642. [PMID: 36734942 DOI: 10.1094/pdis-11-22-2658-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is a significant limitation for producers of vegetative spinach and spinach seed crops during warm temperatures and/or on acid soils. Identification of isolates of F. oxysporum f. sp. spinaciae, and distinction of isolates of the two known races, entails time-intensive pathogenicity tests. In this study, two real-time PCR assays were developed: one for a candidate effector gene common to both races of F. oxysporum f. sp. spinaciae, and another for a candidate effector gene unique to isolates of race 2. The assays were specific to isolates of F. oxysporum f. sp. spinaciae (n = 44) and isolates of race 2 (n = 23), respectively. Neither assay amplified DNA from 10 avirulent isolates of F. oxysporum associated with spinach, 57 isolates of other formae speciales and Fusarium spp., or 7 isolates of other spinach pathogens. When the assays were used to detect DNA extracted from spinach plants infected with an isolate of race 1, race 2, or a 1:1 mixture of both races, the amount of target DNA detected increased with increasing severity of wilt. Plants infected with one or both isolates could be distinguished based on the ratio in copy number for each target locus. The real-time PCR assays enable rapid diagnosis of Fusarium wilt of spinach and will facilitate research on the epidemiology and management of this disease, as well as surveys on the prevalence of this understudied pathogen in regions of spinach and/or spinach seed production.
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Affiliation(s)
- Alex M Batson
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
| | - James W Woodhall
- University of Idaho Parma Research and Extension Center, Parma, ID 83360
| | - Lindsey J du Toit
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
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15
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Liu Y, Kumblathan T, Joyce MA, Tyrrell DL, Tipples G, Pang X, Li XF, Le XC. Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples. ACS MEASUREMENT SCIENCE AU 2023; 3:258-268. [PMID: 37600458 PMCID: PMC10152402 DOI: 10.1021/acsmeasuresciau.3c00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 08/22/2023]
Abstract
The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.
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Affiliation(s)
- Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Michael A. Joyce
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Graham Tipples
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
| | - Xiaoli Pang
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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16
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Wang S, Wang P, Liu J, Yang C, Li T, Yang J, Gu L, Wei M. Molecular detection of Nocardia: development and application of a real-time PCR assay in sputum and bronchoalveolar lavage fluid samples. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04619-4. [PMID: 37156981 DOI: 10.1007/s10096-023-04619-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
The diagnosis of pulmonary nocardiosis remains challenging. Rapid detection of Nocardia is of primary importance for early diagnosis and precise treatment of nocardiosis. In this study, our objective was to develop and validate a new TaqMan real-time PCR (qPCR) assay for rapidly detecting Nocardia spp. in respiratory samples. Based on published sequence data, primers in a conserved region of the 16S rRNA gene and a probe within that region that was specific for Nocardia were designed. The distinction effect of the qPCR assay was assessed between Nocardia and other respiratory-associated bacteria. Furthermore, the specificity and sensitivity of the assay were evaluated in respiratory clinical samples (n = 205), compared to the results of 16S rRNA gene amplicon sequencing and clinical diagnosis. The qPCR assay exhibited high specificity, sensitivity, repeatability, and reproducibility. The limit of detection of standard plasmid DNA was 3 × 102 copies/mL. Additionally, the qPCR assay was applied to the direct detection of 205 clinical respiratory samples. The specificity and sensitivity of the qPCR were all 100% compared to 16S rRNA gene amplicon sequencing, as well as 98.4% and 100% compared to clinical diagnosis respectively. The qPCR yielded results within 3 h of sample processing, compared to several days for culture, significantly reducing turnaround time. The results suggest that the new qPCR assay developed in this study provides reliable and rapid detection of Nocardia spp. in the respiratory tracts and is expected to reduce the time required for diagnosing and treating nocardiosis.
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Affiliation(s)
- Shuai Wang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Peng Wang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jun Liu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chunxia Yang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Tianmeng Li
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jingxian Yang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing, China
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Ming Wei
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
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17
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Chauhan RP, Fogel R, Limson J. Overview of Diagnostic Methods, Disease Prevalence and Transmission of Mpox (Formerly Monkeypox) in Humans and Animal Reservoirs. Microorganisms 2023; 11:1186. [PMID: 37317160 DOI: 10.3390/microorganisms11051186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mpox-formerly monkeypox-is a re-emerging zoonotic virus disease, with large numbers of human cases reported during multi-country outbreaks in 2022. The close similarities in clinical symptoms that Mpox shares with many orthopoxvirus (OPXV) diseases make its diagnosis challenging, requiring laboratory testing for confirmation. This review focuses on the diagnostic methods used for Mpox detection in naturally infected humans and animal reservoirs, disease prevalence and transmission, clinical symptoms and signs, and currently known host ranges. Using specific search terms, up to 2 September 2022, we identified 104 relevant original research articles and case reports from NCBI-PubMed and Google Scholar databases for inclusion in the study. Our analyses observed that molecular identification techniques are overwhelmingly being used in current diagnoses, especially real-time PCR (3982/7059 cases; n = 41 studies) and conventional PCR (430/1830 cases; n = 30 studies) approaches being most-frequently-used to diagnose Mpox cases in humans. Additionally, detection of Mpox genomes, using qPCR and/or conventional PCR coupled to genome sequencing methods, offered both reliable detection and epidemiological analyses of evolving Mpox strains; identified the emergence and transmission of a novel clade 'hMPXV-1A' lineage B.1 during 2022 outbreaks globally. While a few current serologic assays, such as ELISA, reported on the detection of OPXV- and Mpox-specific IgG (891/2801 cases; n = 17 studies) and IgM antibodies (241/2688 cases; n = 11 studies), hemagglutination inhibition (HI) detected Mpox antibodies in human samples (88/430 cases; n = 6 studies), most other serologic and immunographic assays used were OPXV-specific. Interestingly, virus isolation (228/1259 cases; n = 24 studies), electron microscopy (216/1226 cases; n = 18 studies), and immunohistochemistry (28/40; n = 7 studies) remain useful methods of Mpox detection in humans in select instances using clinical and tissue samples. In animals, OPXV- and Mpox-DNA and antibodies were detected in various species of nonhuman primates, rodents, shrews, opossums, a dog, and a pig. With evolving transmission dynamics of Mpox, information on reliable and rapid detection methods and clinical symptoms of disease is critical for disease management.
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Affiliation(s)
- Ravendra P Chauhan
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
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18
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Van Poelvoorde LAE, Dufrasne FE, Van Gucht S, Saelens X, Roosens NHC. Development of Digital Droplet PCR Targeting the Influenza H3N2 Oseltamivir-Resistant E119V Mutation and Its Performance through the Use of Reverse Genetics Mutants. Curr Issues Mol Biol 2023; 45:2521-2532. [PMID: 36975535 PMCID: PMC10047791 DOI: 10.3390/cimb45030165] [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: 02/10/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
The monitoring of antiviral-resistant influenza virus strains is important for public health given the availability and use of neuraminidase inhibitors and other antivirals to treat infected patients. Naturally occurring oseltamivir-resistant seasonal H3N2 influenza virus strains often carry a glutamate-to-valine substitution at position 119 in the neuraminidase (E119V-NA). Early detection of resistant influenza viruses is important for patient management and for the rapid containment of antiviral resistance. The neuraminidase inhibition assay allows the phenotypical identification of resistant strains; however, this test often has limited sensitivity with high variability depending on the virus strain, drugs and assays. Once a mutation such as E119V-NA is known, highly sensitive PCR-based genotypic assays can be used to identify the prevalence of such mutant influenza viruses in clinical samples. In this study, based on an existing reverse transcriptase real-time PCR (RT-qPCR) assay, we developed a reverse transcriptase droplet digital PCR assay (RT-ddPCR) to detect and quantify the frequency of the E119V-NA mutation. Furthermore, reverse genetics viruses carrying this mutation were created to test the performance of the RT-ddPCR assay and compare it to the standard phenotypic NA assay. We also discuss the advantage of using an RT-ddPCR instead of qPCR method in the context of viral diagnostics and surveillance.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - François E Dufrasne
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Department of Infectious Diseases in Humans, Laboratory of Viral Diseases, Sciensano, Engelandstraat 642, 1180 Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
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19
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Harada T, Wakabayashi Y, Seto K, Lee K, Iyoda S, Kawatsu K. Real-time PCR assays to detect 10 Shiga toxin subtype (Stx1a, Stx1c, Stx1d, Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g) genes. Diagn Microbiol Infect Dis 2023; 105:115874. [PMID: 36529020 DOI: 10.1016/j.diagmicrobio.2022.115874] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/03/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
To develop subtyping methods for Shiga toxin (Stx)1a, Stx1c, Stx1d, Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g genes for epidemiological analyses of Shiga toxin-producing Escherichia coli (STEC), we developed 10 simplex real-time polymerase chain reaction (PCR) assays with reference to 284 valid stx sequences and evaluated their specificity and quantitative accuracy using STEC and non-STEC isolates and recombinant plasmids, respectively. Three stx1 and 5 stx2 subtype genes, except for stx2c and stx2d, were detected with high specificity using STEC isolates. However, some stx2a sequences potentially being close to both Stx2a and Stx2d cluster in neighbor-joining cluster analysis were positive for stx2a and stx2d by real-time PCR. For the stx2c assay, the number of real-time PCR cycles was reduced to avoid unnecessary false-positive results. Based on these considerations, the real-time PCR assays developed here might aid epidemiological investigations of infections or outbreaks caused by STEC harboring any of the stx subtype genes.
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Affiliation(s)
- Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan.
| | - Yuki Wakabayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kazuko Seto
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kentaro Kawatsu
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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20
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TaqMan Probes for Plant Species Identification and Quantification in Food and Feed Traceability. Methods Mol Biol 2023; 2638:301-314. [PMID: 36781651 DOI: 10.1007/978-1-0716-3024-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the last few years, the traceability and labeling of processed food and feeds have gained increasing importance due to the impact that mislabeling and product fraud may have on human/animal health or on the quality of final products, such as milk, cheese, and meat, as a consequence of animal dietary. The presence of contaminants or possible frauds due to the use of alternative plant materials in food and feeds can greatly impact the economy; therefore, they are becoming important targets for product certification by competent institutional services. This is especially relevant when complex matrixes are considered, in which the visual identification of the different components is quite difficult or even impossible. Despite the existence of mandatory traceability requirements for the analysis of feed/food composition addressed by European Community regulations, the labels do not always provide a sufficient guarantee about the ingredients and additive composition of those products. In this sense, the development of new methodologies that aim to assess the traceability of feed and food complex matrixes is crucial. In this chapter, a general protocol is presented for the establishment of quantitative real-time PCR-based techniques based on TaqMan assays applied to feed/food traceability, with a special focus on applications in the areas of food and feed security (e.g., for the detection of plant species involved in allergenic reactions), fraud detection (e.g., genetically modified organisms), and certification (e.g., protected denomination of origin).
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21
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Bergallo M, Tullio V, Roana J, Allizond V, Mandras N, Daprà V, Dini M, Comini S, Cavallo L, Gambarino S, Cuffini AM, Banche G. A Rapid and Specific Real-Time PCR Assay for the Detection of Clinically Relevant Mucorales Species. Int J Mol Sci 2022; 23:ijms232315066. [PMID: 36499395 PMCID: PMC9735628 DOI: 10.3390/ijms232315066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Infections triggered by filamentous fungi placed in the order Mucorales, phylum Zygomycota, can cause serious harm to immunocompromised patients. Since there is lack of a standardized PCR (polymerase chain reaction) assay for early diagnosis of this fungal infection, this work was aimed to develop a new PCR assay able to detect the presence of Mucorales genera in clinical specimens. Here, we describe a novel diagnostic TaqMan MGB probe assay for precise and rapid detection of the most common clinical species of Mucorales. Zygomycete-specific oligonucleotides were designed to specifically amplify and bind highly conserved sequences of fungal 28S rRNA gene. Additionally, we succeeded in differentiating Mucorales species (i.e., Rhizopus, Lichtheimia, Mucor, and Rhizomucor) in artificially infected serum samples, suggesting that the quantitative capability of this real-time PCR assay could potentially optimize the diagnosis of mucormycosis.
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Affiliation(s)
- Massimiliano Bergallo
- Cytoimmunodiagnostic Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Vivian Tullio
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Janira Roana
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Valeria Allizond
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Narcisa Mandras
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
- Correspondence:
| | - Valentina Daprà
- Cytoimmunodiagnostic Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Maddalena Dini
- Cytoimmunodiagnostic Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Sara Comini
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Lorenza Cavallo
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Stefano Gambarino
- Cytoimmunodiagnostic Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Anna Maria Cuffini
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
| | - Giuliana Banche
- Bacteriology and Mycology Laboratory, Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy
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22
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Wang Z, Kong L, Luo G, Zhang H, Sun F, Liang W, Wu W, Guo Z, Zhang R, Dou Y. Clinical impact of the PAI-1 4G/5G polymorphism in Chinese patients with venous thromboembolism. Thromb J 2022; 20:68. [PMID: 36376889 PMCID: PMC9662119 DOI: 10.1186/s12959-022-00430-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Background Venous thromboembolism (VTE) is a life-threatening cardiovascular syndrome that characterized by the imbalance of hemostasis and thrombosis and the formation of thrombi in the blood vessels. The aim of this study was to elucidate the clinical impact of the PAI-1 4G/5G polymorphism in Chinese patients with VTE. Methods A total of 169 subjects (89 VTE, 10 hyperbilirubinemia, 10 hyperlipidemia and 60 healthy controls) were recruited at Peking Union Medical College Hospital. The accuracy of the TaqMan-MGB RT-PCR method for detecting F5 G1691A (FVL) and PAI-1 4G/5G polymorphisms was evaluated by using sequencing method as the gold standard. Besides, the association of the PAI-1 4G/5G polymorphism with susceptibility, treatment efficacy and recurrence status of VTE in Chinese population were explored. Eventually, the plasma PAI-1 antigen levels and PAI-1 4G/5G polymorphisms were determined on additional 64 subjects (32 VTE and 32 healthy controls) simultaneously. Results The TaqMan-MGB RT-PCR method was proven to be highly accurate in determining the FVL and PAI-1 4G/5G polymorphisms without interference from bilirubin and lipids in the samples. No obvious correlation of the PAI-1 4G/5G polymorphism with VTE was observed in our study by using five genetic models (allele, genotype, dominant, recessive and additive). Additionally, we also observed that individuals with the 4G/5G genotype had lower neutrophil counts and neutrophil-to-lymphocyte ratio (NLR) than the 5G/5G genotype. Furthermore, we found that the patients with the 5G/5G genotype were more likely to achieve complete recanalization compared to the 4G/4G genotype. In addition, individuals carrying the 5G/5G genotype were more likely to develop a recurrence-free status as compared to individuals with the 4G/4G or 4G/5G genotypes. PAI-1 antigen levels in the VTE group were significantly higher than those in the HC group. However, there was no significant difference in the antigen levels of PAI-1 among subjects carrying various genotypes in the VTE group or HC group. Conclusion The PAI-1 4G/5G polymorphism has potential value in assessing the prognosis of Chinese patients with VTE. Our study has laid the foundation for the application of PAI-1 4G/5G polymorphism in the personalized management and monitoring of patients with VTE.
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23
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Shoop WK, Gorsuch CL, Bacman SR, Moraes CT. Precise and simultaneous quantification of mitochondrial DNA heteroplasmy and copy number by digital PCR. J Biol Chem 2022; 298:102574. [PMID: 36209825 PMCID: PMC9650046 DOI: 10.1016/j.jbc.2022.102574] [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: 06/23/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies and phenotypic consequences of mtDNA mutations depend on the mutant load surpassing a specific threshold. Additionally, changes in mtDNA copy number can impact mitochondrial ATP production, resulting in disease. Therefore, the precise determination of mtDNA heteroplasmy and copy number is crucial to the study of mitochondrial diseases. However, current methods can be imprecise, and quantifying small changes in either heteroplasmy or copy number is challenging. We developed a new approach to measure mtDNA heteroplasmy using a single digital PCR (dPCR) probe. This method is based on the observation that fluorescent-labeled probes in dPCR exhibit different intensities depending on the presence of a single nucleotide change in the sequence bound by the probe. This finding allowed us to precisely and simultaneously determine mtDNA copy number and heteroplasmy levels using duplex dPCR. We tested this approach in two different models (human and mouse), which proved faster and more internally controlled when compared to other published methods routinely used in the mitochondrial genetics field. We believe this approach could be broadly applicable to the detection and quantification of other mixed genetic variations.
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Affiliation(s)
- Wendy K Shoop
- Precision BioSciences, Durham, North Carolina, USA; University of Miami Miller School of Medicine, Miami, Florida, USA.
| | | | - Sandra R Bacman
- University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Carlos T Moraes
- University of Miami Miller School of Medicine, Miami, Florida, USA.
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24
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Nkosi NF, Oosthuizen MC, Quan M. Development and validation of a TaqMan® probe- based real-time PCR assay for detection of Ehrlichia canis. Ticks Tick Borne Dis 2022; 13:102055. [PMID: 36270114 DOI: 10.1016/j.ttbdis.2022.102055] [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: 10/20/2021] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 10/31/2022]
Abstract
Ehrlichiosis is a potentially fatal zoonotic tick-borne disease, caused by a pleomorphic Gram-negative bacterium. It occurs worldwide and affects humans, domestic and wild animals. Dogs infected with Ehrlichia canis develop canine monocytic ehrlichiosis (CME), a significant infectious disease of canines. TaqMan® based real-time PCR assays to detect Ehrlichia spp. affecting dogs were developed and a real-time PCR assay specific for E. canis validated. The efficiency of the assay was 93% and the 95% limit of detection was 33 E. canis plasmid copies/µl of blood (95% confidence interval: 23 - 58). The assay was specific for E. canis when tested against other haemoparasites. Consistent repeatability was observed, with an inter-run standard deviation (SD) range between 0.33 and 1.29 and an intra-run SD range between 0.04 and 1.14. Field samples were tested in parallel by both the E. canis real-time PCR assay and a reverse line blot hybridization assay. The results were in agreement for the two assays, with an exception of two out of 121 samples. Bayesian latent class analysis was used to calculate a diagnostic sensitivity of the E. canis real-time PCR assay of 90% and a specificity of 92%. This assay is a sensitive and reliable molecular detection method for E. canis and will be a useful tool for early diagnosis and timely treatment for this haemoparasite.
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Affiliation(s)
- Nokuzola F Nkosi
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Marinda C Oosthuizen
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Melvyn Quan
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, South Africa.
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25
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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26
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Kostelansky F, Miletin M, Havlinova Z, Szotakova B, Libra A, Kucera R, Novakova V, Zimcik P. Thermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives. Nucleic Acids Res 2022; 50:10212-10229. [PMID: 36156152 PMCID: PMC9561273 DOI: 10.1093/nar/gkac777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/17/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations. However, the probes suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilisation is investigated. The study of large series of acridines revealed that optimal stabilisation is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through a two-carbon linker. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (Tm) of the duplex by almost 8°C for the best combination. The acridines interact with both single- and double-stranded DNAs with substantially preferred interaction for the latter. The study of interaction suggested higher affinity of the acridines toward the GC- than AT-rich sequences. Good discrimination of two point mutations was shown in practical application with HFE gene (wild type, H63D C > G and S65C A > C mutations). Acridine itself can also serve as a fluorophore and also allows discrimination of the fully matched sequences from those with point mutations in probes labelled only with acridine.
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Affiliation(s)
| | - Miroslav Miletin
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Zuzana Havlinova
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Barbora Szotakova
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Antonin Libra
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Radim Kucera
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Veronika Novakova
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Zimcik
- To whom correspondence should be addressed. Tel: +420 495067257;
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27
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A simple and smart AND-gate DNA nanoprobe for correlated enzymes tracking and cell-selective imaging. Biosens Bioelectron 2022; 217:114724. [PMID: 36166888 DOI: 10.1016/j.bios.2022.114724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Accurate cancer diagnosis and effective drug therapy entail sensitive and dynamic monitoring of intracellular key enzymes, since their expression level is closely related to disease progression. Simultaneous monitoring of correlated enzymes is promising to help unveiling mystery of cytobiological events during tumor progression and drug response, while is challenged by lacking of a robust and simple simultaneous detection strategy. In order to construct a simple and smart strategy which is complex design-avoided and doesn't need other auxiliary enzyme, here we develop an AND-gate strategy for simultaneously monitoring correlated enzymes which both are upregulated in cancer cells (telomerase and apurinic/apyrimidinic endonuclease 1). An innovative AND-gate DNA nanoprobe has been designed to avoid mutual interference and background noise, guaranteeing an enhanced fluorescent signal output upon catalyzation of dual enzymes. This AND-gate strategy achieves sensitive detection of two enzymes in an individual manner in test tube, through which the diagnostic potential of bladder cancer has been validated by telomerase detection in clinical urine sample. The AND-gate strategy enables specific intracellular imaging of dual enzymes in different cancer cell lines. Importantly, in contrast to traditional single-targeting strategies, AND-gate imaging of dual enzymes significantly improves cancer cell selectivity. Moreover, this strategy dynamically monitors enzymatic activity changes during chemoresistance induced by chemotherapeutic treatment. This simple and smart strategy has foreseeable prospect in the fields of disease diagnosis, drug prognosis evaluation, and precise fluorescence-guided surgery.
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28
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Imaizumi Y, Ishige T, Fujikawa T, Miyabe A, Murata S, Kawasaki K, Nishimura M, Taniguchi T, Igari H, Matsushita K. Development of multiplex S-gene-targeted RT-PCR for rapid identification of SARS-CoV-2 variants by extended S-gene target failure. Clin Chim Acta 2022; 536:6-11. [PMID: 36113557 PMCID: PMC9472704 DOI: 10.1016/j.cca.2022.08.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/15/2022]
Abstract
Background Tracking SARS-CoV-2 variants of concern (VOC) by genomic sequencing is time-consuming. The rapid screening of VOCs is necessary for clinical laboratories. In this study, we developed a rapid screening method based on multiplex RT-PCR by extended S-gene target failure (eSGTF), a false negative result caused by S-gene mutations. Methods Three S-gene target (SGT) regions (SGT1, codons 65–72; SGT2, codons 152–159; and SGT3, codons 370–377) and an N-gene region (for internal control) were detected in single-tube. Four types of VOC (Alpha, Delta, Omicron BA.1, and Omicron BA.2) are classified by positive/negative patterns of 3 S-gene regions (eSGTF pattern). Results The eSGTF patterns of VOCs were as follows (SGT1, SGT2, SGT3; P, positive; N, negative): Alpha, NPP; Delta, PNP; Omicron BA.1, NPN pattern; and Omicron BA.2, PPN. As compared with the S-gene sequencing, eSGTF patterns were identical to the specific VOCs (concordance rate = 96.7%, N = 206/213). Seven samples with discordant results had a minor mutation in the probe binding region. The epidemics of VOCs estimated by eSGTF patterns were similar to those in Japan. Conclusions Multiplex RT-PCR and eSGTF patterns enable high-throughput screening of VOCs. It will be useful for the rapid determination of VOCs in clinical laboratories.
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Affiliation(s)
- Yuri Imaizumi
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan.
| | - Tatsuki Fujikawa
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Akiko Miyabe
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Shota Murata
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Kenji Kawasaki
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Toshibumi Taniguchi
- Department of Infectious Disease, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Hidetoshi Igari
- Department of Infectious Disease, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ward, Chiba-city, Chiba 2608677, Japan
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29
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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30
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Lee HW, Ho WWH, Alexander BJR, Baskarathevan J. A Rapid qPCR for the Detection of Verticillium nonalfalfae MLST2 - A Highly Pathogenic Fungus on Kiwifruit. PLANT DISEASE 2022; 106:2348-2354. [PMID: 35350892 DOI: 10.1094/pdis-08-21-1819-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A highly pathogenic fungus characterized as Verticillium nonalfalfae multilocus sequence type 2 (MLST2) is an emerging fungal pathogen causing Verticillium wilt on kiwifruit. Although V. nonalfalfae MLST2 has not been reported outside Chile, there is a risk that this pathogen could spread through the global movement of germplasms to other countries. Current diagnostic methods for this fungus rely on a laborious and time-consuming plating assay for morphological identification and DNA sequence analysis. In this study, we describe the development and validation of a novel quantitative polymerase chain reaction (qPCR) assay for rapid and specific detection of V. nonalfalfae MLST2 in plant tissues. The assay targets the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene and was shown to detect all tested isolates of V. nonalfalfae MLST2 with a detection limit of approximately 2 pg of pathogen genomic DNA. There was no cross-reaction with V. nonalfalfae MLST1, other Verticillium species, or non-target fungal species found on kiwifruit. This assay was duplexed with a plant internal control for simultaneous detection of the pathogen and cytochrome oxidase gene from the host plant. This new specific and sensitive qPCR assay is a valuable molecular diagnostic tool for rapid screening of imported plant material and would also be useful for testing samples collected from field surveillance activities to monitor the presence of V. nonalfalfae MLST2.
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Affiliation(s)
- Hui Wen Lee
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
| | - Wellcome W H Ho
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
| | - Brett J R Alexander
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
| | - Jeyaseelan Baskarathevan
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
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Distinguishing Different Varieties of Oolong Tea by Fluorescence Hyperspectral Technology Combined with Chemometrics. Foods 2022; 11:foods11152344. [PMID: 35954110 PMCID: PMC9368096 DOI: 10.3390/foods11152344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/04/2022] Open
Abstract
Oolong tea is a semi-fermented tea that is popular among people. This study aims to establish a classification method for oolong tea based on fluorescence hyperspectral technology(FHSI) combined with chemometrics. First, the spectral data of Tieguanyin, Benshan, Maoxie and Huangjingui were obtained. Then, standard normal variation (SNV) and multiple scatter correction (MSC) were used for preprocessing. Principal component analysis (PCA) was used for data visualization, and with tolerance ellipses that were drawn according to Hotelling, outliers in the spectra were removed. Variable importance for the projection (VIP) > 1 in partial least squares discriminant analysis (PLS−DA) was used for feature selection. Finally, the processed spectral data was entered into the support vector machine (SVM) and PLS−DA. MSC_VIP_PLS−DA was the best model for the classification of oolong tea. The results showed that the use of FHSI could accurately distinguish these four types of oolong tea and was able to identify the key wavelengths affecting the tea classification, which were 650.11, 660.29, 665.39, 675.6, 701.17, 706.31, 742.34 and 747.5 nm. In these wavelengths, different kinds of tea have significant differences (p < 0.05). This study could provide a non-destructive and rapid method for future tea identification.
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32
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Dharmaraj K, Andersen MT, Alexander BJR, Toome-Heller M. A New TaqMan Real-Time PCR Assay for Detecting the Blueberry Pathogen Monilinia vaccinii- corymbosi. PLANT DISEASE 2022; 106:1826-1831. [PMID: 35077233 DOI: 10.1094/pdis-08-21-1737-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Monilinia vaccinii-corymbosi (Mvc) is an important fungal pathogen of blueberry, causing mummy berry disease. While the symptoms of the advanced stages of the disease can be obvious, diagnosing its early stages can be challenging. To facilitate fast and sensitive screening of asymptomatic or latently infected plant material for Mvc, we developed a specific TaqMan real-time PCR assay targeting the internal transcribed spacer (ITS) region. The assay was shown to be specific to Mvc and did not cross react with any of the other tested Monilinia species or other blueberry pathogens. Using the multicopy ITS region ensured high analytical sensitivity, enabling very low concentrations of Mvc DNA (0.1 pg) to be detected both in water and host DNA matrix. Comparable results were obtained in interlaboratory testing, showing that the assay is robust, and can be effectively used in other laboratories. Assay sensitivity was also confirmed on infected plant tissue, showing that it is effective in detecting the pathogen in infected asymptomatic stem tissue, as well as infected tissue that was mixed with healthy tissue at a ratio of 1:10 by weight. The assay was duplexed with a plant internal control (cytochrome oxidase gene) for simultaneous amplification of the pathogen and plant internal control in a single reaction. This new diagnostic tool can be used for sensitive and rapid screening of blueberry plants for the presence of Mvc in many different settings, e.g., for breeding programs, research, or biosecurity diagnostics.
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Affiliation(s)
- Karthikeyan Dharmaraj
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1072, New Zealand
| | - Mark T Andersen
- The New Zealand Institute for Plant & Food Research Ltd, Auckland 1142, New Zealand
| | - Brett J R Alexander
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1072, New Zealand
| | - Merje Toome-Heller
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1072, New Zealand
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33
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Kronenberger JA, Wilcox TM, Mason DH, Franklin TW, McKelvey KS, Young MK, Schwartz MK. eDNAssay: a machine learning tool that accurately predicts qPCR cross-amplification. Mol Ecol Resour 2022; 22:2994-3005. [PMID: 35778862 DOI: 10.1111/1755-0998.13681] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) sampling is a highly sensitive and cost-effective technique for wildlife monitoring, notably through the use of qPCR assays. However, it can be difficult to ensure assay specificity when many closely related species cooccur. In theory, specificity may be assessed in silico by determining whether assay oligonucleotides have enough base-pair mismatches with nontarget sequences to preclude amplification. However, the mismatch qualities required are poorly understood, making in silico assessments difficult and often necessitating extensive in vitro testing-typically the greatest bottleneck in assay development. Increasing the accuracy of in silico assessments would therefore streamline the assay development process. In this study, we paired 10 qPCR assays with 82 synthetic gene fragments for 530 specificity tests using SYBR Green intercalating dye (n = 262) and TaqMan hydrolysis probes (n = 268). Test results were used to train random forest classifiers to predict amplification. The primer-only model (SYBR Green-based) and full-assay model (TaqMan probe-based) were 99.6% and 100% accurate, respectively, in cross-validation. We further assessed model performance using six independent assays not used in model training. In these tests the primer-only model was 92.4% accurate (n = 119) and the full-assay model was 96.5% accurate (n = 144). The high performance achieved by these models makes it possible for eDNA practitioners to more quickly and confidently develop assays specific to the intended target. Practitioners can access the full-assay model via eDNAssay (https://NationalGenomicsCenter.shinyapps.io/eDNAssay), a user-friendly online tool for predicting qPCR cross-amplification.
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Affiliation(s)
- J A Kronenberger
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - T M Wilcox
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - D H Mason
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - T W Franklin
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - K S McKelvey
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - M K Young
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
| | - M K Schwartz
- National Genomics Center for Wildlife and Fish Conservation, USFS Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA
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34
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Canalis E, Carrer M, Eller T, Schilling L, Yu J. Use of antisense oligonucleotides to target Notch3 in skeletal cells. PLoS One 2022; 17:e0268225. [PMID: 35536858 PMCID: PMC9089911 DOI: 10.1371/journal.pone.0268225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
Notch receptors are determinants of cell fate and function, and play an important role in the regulation of bone development and skeletal remodeling. Lateral Meningocele Syndrome (LMS) is a monogenic disorder associated with NOTCH3 pathogenic variants that result in the stabilization of NOTCH3 and a gain-of-function. LMS presents with neurological developmental abnormalities and bone loss. We created a mouse model (Notch3em1Ecan) harboring a 6691TAATGA mutation in the Notch3 locus, and heterozygous Notch3em1Ecan mice exhibit cancellous and cortical bone osteopenia. In the present work, we explored whether Notch3 antisense oligonucleotides (ASO) downregulate Notch3 and have the potential to ameliorate the osteopenia of Notch3em1Ecan mice. Notch3 ASOs decreased the expression of Notch3 wild type and Notch36691-TAATGA mutant mRNA expressed by Notch3em1Ecan mice in osteoblast cultures without evidence of cellular toxicity. The effect was specific since ASOs did not downregulate Notch1, Notch2 or Notch4. The expression of Notch3 wild type and Notch36691-TAATGA mutant transcripts also was decreased in bone marrow stromal cells and osteocytes following exposure to Notch3 ASOs. In vivo, the subcutaneous administration of Notch3 ASOs at 25 to 50 mg/Kg decreased Notch3 mRNA in the liver, heart and bone. Microcomputed tomography demonstrated that the administration of Notch3 ASOs ameliorates the cortical osteopenia of Notch3em1Ecan mice, and ASOs decreased femoral cortical porosity and increased cortical thickness and bone volume. However, the administration of Notch3 ASOs did not ameliorate the cancellous bone osteopenia of Notchem1Ecan mice. In conclusion, Notch3 ASOs downregulate Notch3 expression in skeletal cells and their systemic administration ameliorates cortical osteopenia in Notch3em1Ecan mice; as such ASOs may become useful strategies in the management of skeletal diseases affected by Notch gain-of-function.
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MESH Headings
- Abnormalities, Multiple
- Animals
- Bone Diseases, Metabolic/genetics
- Bone Diseases, Metabolic/metabolism
- Bone and Bones/diagnostic imaging
- Bone and Bones/metabolism
- Meningocele
- Mice
- Oligonucleotides, Antisense
- RNA, Messenger
- Receptor, Notch2/genetics
- Receptor, Notch2/metabolism
- Receptor, Notch3/genetics
- Receptor, Notch3/metabolism
- Receptors, Notch/genetics
- X-Ray Microtomography
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Affiliation(s)
- Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, United States of America
- Department of Medicine, UConn Health, Farmington, Connecticut, United States of America
- The UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, United States of America
| | - Michele Carrer
- Ionis Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Tabitha Eller
- The UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, United States of America
| | - Lauren Schilling
- The UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, United States of America
| | - Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, United States of America
- The UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, United States of America
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35
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Lu MD, Telwatte S, Kumar N, Ferreira F, Martin HA, Kadiyala GN, Wedrychowski A, Moron-Lopez S, Chen TH, Goecker EA, Coombs RW, Lu CM, Wong JK, Tsibris A, Yukl SA. Novel assays to investigate the mechanisms of latent infection with HIV-2. PLoS One 2022; 17:e0267402. [PMID: 35476802 PMCID: PMC9045618 DOI: 10.1371/journal.pone.0267402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Although there have been great advancements in the field of HIV treatment and prevention, there is no cure. There are two types of HIV: HIV-1 and HIV-2. In addition to genetic differences between the two types of HIV, HIV-2 infection causes a slower disease progression, and the rate of new HIV-2 infections has dramatically decreased since 2003. Like HIV-1, HIV-2 is capable of establishing latent infection in CD4+ T cells, thereby allowing the virus to evade viral cytopathic effects and detection by the immune system. The mechanisms underlying HIV latency are not fully understood, rendering this a significant barrier to development of a cure. Using RT-ddPCR, we previously demonstrated that latent infection with HIV-1 may be due to blocks to HIV transcriptional elongation, distal transcription/polyadenylation, and multiple splicing. In this study, we describe the development of seven highly-specific RT-ddPCR assays for HIV-2 that can be applied to the study of HIV-2 infections and latency. We designed and validated seven assays targeting different HIV-2 RNA regions along the genome that can be used to measure the degree of progression through different blocks to HIV-2 transcription and splicing. Given that HIV-2 is vastly understudied relative to HIV-1 and that it can be considered a model of a less virulent infection, application of these assays to studies of HIV-2 latency may inform new therapies for HIV-2, HIV-1, and other retroviruses.
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Affiliation(s)
- Michael D. Lu
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
| | - Sushama Telwatte
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Nitasha Kumar
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Fernanda Ferreira
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Holly Anne Martin
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Gayatri Nikhila Kadiyala
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Adam Wedrychowski
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Sara Moron-Lopez
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Tsui-Hua Chen
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Erin A. Goecker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States of America
| | - Robert W. Coombs
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States of America
| | - Chuanyi M. Lu
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Steven A. Yukl
- Department of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, United States of America
- Department of Medicine, San Francisco VA Health Care System, San Francisco, CA, United States of America
- * E-mail:
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36
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [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: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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Hair Follicle-Related MicroRNA-34a Serum Expression and rs2666433A/G Variant in Patients with Alopecia: A Cross-Sectional Analysis. Biomolecules 2022; 12:biom12050602. [PMID: 35625530 PMCID: PMC9138785 DOI: 10.3390/biom12050602] [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: 03/15/2022] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 01/10/2023] Open
Abstract
Alopecia areata (AA) is a type of immune-mediated alopecia. Recent studies have suggested microRNAs’ (miRNAs) implication in several cellular processes, including epidermal and hair follicle biology. Single nucleotide polymorphisms (SNPs) can modify gene expression levels, which may induce an autoimmune response. This case−control study included 480 participants (240 for each case/control group). MicroRNA-34a gene (MIR-34A) rs2666433A/G variant was genotyped using real-time allelic discrimination polymerase chain reaction (PCR). Additionally, circulatory miR-34a levels were quantified by quantitative reverse transcription PCR (qRT-PCR). On comparing between alopecia and non-alopecia cohorts, a higher frequency of A variant was noted among patients when compared to controls—A allele: 28 versus 18% (p < 0.001); A/A genotype: 9 versus 2%; A/G genotype: 39 versus 32% (p < 0.001). A/A and A/G carriers were more likely to develop alopecia under heterozygote comparison (OR = 1.83, 95% CI = 1.14−2.93), homozygote comparison (OR = 4.19, 95% CI = 1.33−13.1), dominant (OR = 2.0, 95% CI = 1.27−3.15), recessive (OR = 3.36, 95% CI = 1.08−10.48), over-dominant (OR = 1.65, 95% CI = 1.04−32.63), and log additive (OR = 1.91, 95% CI = 1.3−2.82) models. Serum miR-34a expression levels were upregulated in alopecia patients with a median and quartile fold change of 27.3 (1.42−2430). Significantly higher levels were more pronounced in A/A genotype patients (p < 0.01). Patients carrying the heterozygote genotype (rs2666433 * A/G) were two times more likely to develop more severe disease grades. Stratified analysis by sex revealed the same results. A high expression level was associated with concomitant autoimmune comorbidities (p = 0.001), in particular SLE (p = 0.007) and vitiligo (p = 0.049). In conclusion, the MIR34A rs2666433 (A/G) variant is associated with AA risk and severity in the studied population. Furthermore, high miR-34a circulatory levels could play a role in disease pathogenesis.
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38
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Lenoir C, Terrier J, Gloor Y, Gosselin P, Daali Y, Combescure C, Desmeules JA, Samer CF, Reny JL, Rollason V. Impact of the Genotype and Phenotype of CYP3A and P-gp on the Apixaban and Rivaroxaban Exposure in a Real-World Setting. J Pers Med 2022; 12:jpm12040526. [PMID: 35455642 PMCID: PMC9028714 DOI: 10.3390/jpm12040526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Apixaban and rivaroxaban are the two most prescribed direct factor Xa inhibitors. With the increased use of DOACs in real-world settings, safety and efficacy concerns have emerged, particularly regarding their concomitant use with other drugs. Increasing evidence highlights drug−drug interactions with CYP3A/P-gp modulators leading to adverse events. However, current recommendations for dose adjustment do not consider CYP3A/P-gp genotype and phenotype. We aimed to determine their impact on apixaban and rivaroxaban blood exposure. Three-hundred hospitalized patients were included. CYP3A and P-gp phenotypic activities were assessed by the metabolic ratio of midazolam and AUC0−6h of fexofenadine, respectively. Relevant CYP3A and ABCB1 genetic polymorphisms were also tested. Capillary blood samples collected at four time-points after apixaban or rivaroxaban administration allowed the calculation of pharmacokinetic parameters. According to the developed multivariable linear regression models, P-gp activity (p < 0.001) and creatinine clearance (CrCl) (p = 0.01) significantly affected apixaban AUC0−6h. P-gp activity (p < 0.001) also significantly impacted rivaroxaban AUC0−6h. The phenotypic switch (from normal to poor metabolizer) of P-gp led to an increase of apixaban and rivaroxaban AUC0−6h by 16% and 25%, respectively, equivalent to a decrease of 38 mL/min in CrCl according to the apixaban model. CYP3A phenotype and tested SNPs of CYP3A/P-gp had no significant impact. In conclusion, P-gp phenotypic activity, rather than known CYP3A/P-gp polymorphisms, could be relevant for dose adjustment.
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Affiliation(s)
- Camille Lenoir
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1206 Geneva, Switzerland
| | - Jean Terrier
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Department of Medicine, Division of General Internal Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (P.G.); (J.-L.R.)
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Yvonne Gloor
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
| | - Pauline Gosselin
- Department of Medicine, Division of General Internal Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (P.G.); (J.-L.R.)
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Youssef Daali
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1206 Geneva, Switzerland
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Christophe Combescure
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
- Department of Health and Community Medicine, Division of Clinical Epidemiology, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Jules Alexandre Desmeules
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1206 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Caroline Flora Samer
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Jean-Luc Reny
- Department of Medicine, Division of General Internal Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (P.G.); (J.-L.R.)
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Victoria Rollason
- Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.L.); (J.T.); (Y.G.); (Y.D.); (J.A.D.); (C.F.S.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
- Correspondence:
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MicroRNA-17-92a-1 Host Gene (MIR17HG) Expression Signature and rs4284505 Variant Association with Alopecia Areata: A Case-Control Study. Genes (Basel) 2022; 13:genes13030505. [PMID: 35328059 PMCID: PMC8955921 DOI: 10.3390/genes13030505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 02/04/2023] Open
Abstract
Accumulating evidence indicates the implication of microRNAs (miRs) in cutaneous and hair follicle immunobiology. We evaluated, for the first time, the miR-17-92a-1 cluster host gene (MIR17HG) expression in peripheral blood of 248 unrelated alopecia areata (AA) patients compared to 244 matched controls using Real-Time qPCR. We also tested its association with different rs4284505A>G genotypes (based on TaqMan allelic discrimination PCR) and the available clinical data. The adjusted odds ratio (OR) and 95% confidence interval (CI) were calculated for each genetic association model. The upregulation of miR-17 was observed in the serum of patients with alopecia compared to controls (p-value = 0.004). The ROC curve showed high diagnostic performance of miR-17 in differentiating between patients and controls (AUC = 0.85, p-value < 0.001). rs4284505*A/G heterozygotes were more susceptible to the disease (OR = 1.57, 95% CI = 1.01−2.45) under the over-dominant model. Interestingly, patients with the rs4284505*G/G genotype had a higher level of miR-17 than those with the A/A and A/G genotypes. The G/G genotype was associated with the severe phenotype (p-value = 0.038). A/G carriers were the youngest (p-value < 0.001), had more frequent scalp infection (p-value = 0.006), exhibited the worst dermatology life quality index score (p-value = 0.037), and responded less to treatment (p-value = 0.033). In conclusion, MIR17HG expression and the rs4284505 variant were significantly associated with AA and could play a role in pathogenesis and phenotype in the Egyptian population. Further multi-center studies in other ethnicities are warranted to replicate the findings.
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Tan C, Yan Y, Guo N, Wang F, Wang S, Zhu L, Wang Y, Ma Y, Guo Y. Single-Tube Multiplex Digital Polymerase Chain Reaction Assay for Molecular Diagnosis and Prediction of Severity of Spinal Muscular Atrophy. Anal Chem 2022; 94:3517-3525. [PMID: 35137581 DOI: 10.1021/acs.analchem.1c04403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease characterized by the degeneration of motor neurons and progressive muscle atrophy. Accurate detection of SMN1 and SMN2 copy numbers is essential for SMA diagnosis, carrier screening, disease severity prediction, therapy, and prognosis. However, a method for SMN1 and SMN2 copy number determination that is simultaneously accurate, simple, rapid, multitargeted, and applicable to various samples has not previously been reported. Here, we developed a single-tube multiplex digital polymerase chain reaction (dPCR) assay for simultaneous determination of the copy numbers of SMN1 exons 7 and 8 and SMN2 exons 7 and 8. A total of 317 clinical samples, including peripheral blood, amniotic fluid, chorionic villus, buccal swabs, and dried blood spots, were collected to evaluate the performance of this dPCR-based assay. The test results were accurate for all the clinical samples. Our assay is accurate, rapid, easy to handle, and applicable to many types of samples and uses a small amount of DNA; it is a powerful tool for SMA molecular diagnosis, large-scale screening, and disease severity assessment.
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Affiliation(s)
- Chianru Tan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Na Guo
- TargetingOne Corporation, Beijing 100190, China
| | - Fang Wang
- TargetingOne Corporation, Beijing 100190, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | | | - Yipeng Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Kamminga S, Sidorov IA, Tadesse M, van der Meijden E, de Brouwer C, Zaaijer HL, Feltkamp MC, Gorbalenya AE. Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. iScience 2022; 25:103613. [PMID: 35036862 PMCID: PMC8749223 DOI: 10.1016/j.isci.2021.103613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/27/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.
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Affiliation(s)
- Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Igor A. Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Michaël Tadesse
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Caroline de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hans L. Zaaijer
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Mariet C.W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
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Elwazir MY, Hussein MH, Toraih EA, Al Ageeli E, Esmaeel SE, Fawzy MS, Faisal S. Association of Angio-LncRNAs MIAT rs1061540/MALAT1 rs3200401 Molecular Variants with Gensini Score in Coronary Artery Disease Patients Undergoing Angiography. Biomolecules 2022; 12:biom12010137. [PMID: 35053285 PMCID: PMC8773982 DOI: 10.3390/biom12010137] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as essential biomolecules with variable diagnostic and/or prognostic utility in several diseases, including coronary artery disease (CAD). We aimed for the first time to investigate the potential association of five angiogenesis-related lncRNAs (PUNISHER, SENCR, MIAT, MALAT1, and GATA6-AS) variants with CAD susceptibility and/or severity. TaqMan Real-Time genotyping for PUNISHER rs12318065A/C, SENCR rs12420823C/T, MIAT rs1061540C/T, MALAT1 rs3200401T/C, and GATA6-AS1 rs73390820A/G were run on the extracted genomic DNA from 100 unrelated patients with stable CAD undergoing diagnostic coronary angiography and from 100 controls. After adjusting covariates, the studied variants showed no association with disease susceptibility; however, MIAT*T/T genotype was associated with a more severe Gensini score. In contrast, MALAT1*T/C heterozygosity was associated with a lower score. The lipid profile, and to a lesser extent smoking status, male sex, weight, hypertension, and MALAT1 (T > C) (negative correlation), explained the variance between patients/control groups via a principal component analysis. Incorporating the principal components into a logistic regression model to predict CAD yielded a 0.92 AUC. In conclusion: MIAT rs1061540 and MALAT1 rs3200401 variants were associated with CAD severity and Gensini score in the present sample of the Egyptian population. Further large multi-center and functional analyses are needed to confirm the results and identify the underlying molecular mechanisms.
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Affiliation(s)
- Mohamed Y. Elwazir
- Department of Cardiology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Mohammad H. Hussein
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia;
| | - Safya E. Esmaeel
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Salwa Faisal
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
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Modarage K, Malik SA, Goggolidou P. Molecular Diagnostics of Ciliopathies and Insights Into Novel Developments in Diagnosing Rare Diseases. Br J Biomed Sci 2022; 79:10221. [PMID: 35996505 PMCID: PMC8915726 DOI: 10.3389/bjbs.2021.10221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
The definition of a rare disease in the European Union describes genetic disorders that affect less than 1 in 2,000 people per individual disease; collectively these numbers amount to millions of individuals globally, who usually manifest a rare disease early on in life. At present, there are at least 8,000 known rare conditions, of which only some are clearly molecularly defined. Over the recent years, the use of genetic diagnosis is gaining ground into informing clinical practice, particularly in the field of rare diseases, where diagnosis is difficult. To demonstrate the complexity of genetic diagnosis for rare diseases, we focus on Ciliopathies as an example of a group of rare diseases where an accurate diagnosis has proven a challenge and novel practices driven by scientists are needed to help bridge the gap between clinical and molecular diagnosis. Current diagnostic difficulties lie with the vast multitude of genes associated with Ciliopathies and trouble in distinguishing between Ciliopathies presenting with similar phenotypes. Moreover, Ciliopathies such as Autosomal Recessive Polycystic Kidney Disease (ARPKD) and Meckel-Gruber syndrome (MKS) present with early phenotypes and may require the analysis of samples from foetuses with a suspected Ciliopathy. Advancements in Next Generation Sequencing (NGS) have now enabled assessing a larger number of target genes, to ensure an accurate diagnosis. The aim of this review is to provide an overview of current diagnostic techniques relevant to Ciliopathies and discuss the applications and limitations associated with these techniques.
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Hossain MA, Brito-Rodriguez B, Sedger LM, Canning J. A Cross-Disciplinary View of Testing and Bioinformatic Analysis of SARS-CoV-2 and Other Human Respiratory Viruses in Pandemic Settings. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:163716-163734. [PMID: 35582017 PMCID: PMC8843158 DOI: 10.1109/access.2021.3133417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/04/2021] [Indexed: 05/26/2023]
Abstract
The SARS-Coronavirus-2 (SARS-CoV-2) infectious disease, COVID-19, has spread rapidly, resulting in a global pandemic with significant mortality. The combination of early diagnosis via rapid screening, contact tracing, social distancing and quarantine has helped to control the pandemic. The absence of real time response and diagnosis is a crucial technology shortfall and is a key reason why current contact tracing methods are inadequate to control spread. In contrast, current information technology combined with a new generation of near-real time tests offers consumer-engaged smartphone-based "lab-in-a-phone" internet-of-things (IoT) connected devices that provide increased pandemic monitoring. This review brings together key aspects required to create an entire global diagnostic ecosystem. Cross-disciplinary understanding and integration of both mechanisms and technologies for effective detection, incidence mapping and disease containment in near real-time is summarized. Available measures to monitor and/or sterilize surfaces, next-generation laboratory and smartphone-based diagnostic approaches can be brought together and networked for instant global monitoring that informs Public Health policy. Cloud-based analysis enabling real-time mapping will enable future pandemic control, drive the suppression and elimination of disease spread, saving millions of lives globally. A new paradigm is introduced - scaled and multiple diagnostics for mapping and spreading of a pandemic rather than traditional accumulation of individual measurements. This can do away with the need for ultra-precise and ultra-accurate analysis by taking mass measurements that can relax tolerances and build resilience through networked analytics and informatics, the basis for novel swarm diagnostics. These include addressing ethical standards, local, national and international collaborative engagement, multidisciplinary and analytical measurements and standards, and data handling and storage protocols.
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Affiliation(s)
- Md Arafat Hossain
- Department of Electrical and Electronic EngineeringKhulna University of Engineering & TechnologyKhulna9203Bangladesh
| | | | - Lisa M. Sedger
- Faculty of ScienceUniversity of Technology Sydney (UTS)SydneyNSW2007Australia
| | - John Canning
- interdisciplinary Photonic Laboratories (iPL), Global Big Data Technologies Centre (GBDTC), Faculty of Engineering and Information TechnologyUniversity of Technology Sydney (UTS)SydneyNSW2007Australia
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Efficient capturing and sensitive detection of hepatitis A virus from solid foods (green onion, strawberry, and mussel) using protamine-coated iron oxide (Fe 3O 4) magnetic nanoparticles and real-time RT-PCR. Food Microbiol 2021; 102:103921. [PMID: 34809947 DOI: 10.1016/j.fm.2021.103921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022]
Abstract
Hepatitis A virus (HAV) continues to be a public health concern and has caused large foodborne outbreaks and economic losses worldwide. Rapid detection of HAV in foods can help to confirm the source of outbreaks in a timely manner and prevent more people getting infected. In order to efficiently detect HAV at low levels of contamination in foods, rapid and easy-to-use techniques are required to separate and concentrate viral particles to a small volume. In the current study, HAV particles were eluted from green onion, strawberry, and mussel using glycine buffer (0.05 M glycine, 0.14 M NaCl, 0.2% (v/v) Tween 20, pH 9.0) and suspended viral particles were captured using protamine-coated magnetic nanoparticles (PMNPs). This process caused a selective concentration of the viral particles, which could be followed by quantitative real-time RT-PCR analysis. Results showed that pH, NaCl concentration, and PMNP amount used for the capturing had significant effects on the recovery efficiency of HAV (P < 0.05). The highest recovery rate was obtained at pH 9.0, 0.14 M NaCl, and 50 μL of PMNPs. The optimized PMNP capturing method enabled the rapid capture and concentration of HAV. A sensitive real-time RT-PCR test was developed with detection limits of 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, and 8.3 × 100 PFU/5 g of HAV in green onion, strawberry, and mussel, respectively. In conclusion, the PMNP method is rapid and convenient in capturing HAV from complex solid food samples and can generate concentrated HAV sample solutions suitable for high-sensitivity real time RT-PCR detection of the virus.
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Yu J, Schilling L, Eller T, Canalis E. Hairy and enhancer of split 1 is a primary effector of NOTCH2 signaling and induces osteoclast differentiation and function. J Biol Chem 2021; 297:101376. [PMID: 34742737 PMCID: PMC8633688 DOI: 10.1016/j.jbc.2021.101376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Notch2tm1.1Ecan mice, which harbor a mutation replicating that found in Hajdu–Cheney syndrome, exhibit marked osteopenia because of increased osteoclast number and bone resorption. Hairy and enhancer of split 1 (HES1) is a Notch target gene and a transcriptional modulator that determines osteoclast cell fate decisions. Transcript levels of Hes1 increase in Notch2tm1.1Ecan bone marrow–derived macrophages (BMMs) as they mature into osteoclasts, suggesting a role in osteoclastogenesis. To determine whether HES1 is responsible for the phenotype of Notch2tm1.1Ecan mice and the skeletal manifestations of Hajdu–Cheney syndrome, Hes1 was inactivated in Ctsk-expressing cells from Notch2tm1.1Ecan mice. Ctsk encodes the protease cathepsin K, which is expressed preferentially by osteoclasts. We found that the osteopenia of Notch2tm1.1Ecan mice was ameliorated, and the enhanced osteoclastogenesis was reversed in the context of the Hes1 inactivation. Microcomputed tomography revealed that the downregulation of Hes1 in Ctsk-expressing cells led to increased bone volume/total volume in female mice. In addition, cultures of BMMs from CtskCre/WT;Hes1Δ/Δ mice displayed a decrease in osteoclast number and size and decreased bone-resorbing capacity. Moreover, activation of HES1 in Ctsk-expressing cells led to osteopenia and enhanced osteoclast number, size, and bone resorptive capacity in BMM cultures. Osteoclast phenotypes and RNA-Seq of cells in which HES1 was activated revealed that HES1 modulates cell–cell fusion and bone-resorbing capacity by supporting sealing zone formation. In conclusion, we demonstrate that HES1 is mechanistically relevant to the skeletal manifestation of Notch2tm1.1Ecan mice and is a novel determinant of osteoclast differentiation and function.
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Affiliation(s)
- Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Lauren Schilling
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Tabitha Eller
- UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA
| | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Health, Farmington, Connecticut, USA; UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut, USA; Department of Medicine, UConn Health, Farmington, Connecticut, USA.
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Detection and Clinical Implications of Monovalent Rotavirus Vaccine-Derived Virus Strains in Children with Gastroenteritis in Alberta, Canada. J Clin Microbiol 2021; 59:e0115421. [PMID: 34406795 DOI: 10.1128/jcm.01154-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
While rotavirus vaccine programs effectively protect against severe rotavirus gastroenteritis, rotavirus vaccine strains have been identified in the stool of vaccinated children and their close contacts suffering from acute gastroenteritis. The prevalence of vaccine strains, the emergence of vaccine-derived strains, and their role in acute gastroenteritis are not well studied. We developed a locked nucleic acid reverse transcription real-time PCR assay (LNA-RTqPCR) to detect the monovalent rotavirus vaccine (RV1) Rotarix nonstructural protein 2 (NSP2) in children with acute gastroenteritis and healthy controls, and validated it using sequence-confirmed RV1 strains. The association between RV1-derived strains and gastroenteritis was determined using logistic regression. The new assay exhibited 100% (95% CI 91.7%, 100%) diagnostic sensitivity and 99.4% (95% CI 96.2%, 100%) diagnostic specificity, with a detection limit of 9.86 copies/reaction and qPCR efficiency of 99.7%. Using this assay, we identified the presence of RV1-derived NSP2 sequences in 7.7% of rotavirus gastroenteritis cases and 98.6% of rotavirus-positive healthy children (94.4% had previously received the RV1). Among gastroenteritis cases, those whose stool contained RV1-derived strains had milder gastroenteritis symptoms compared to that of natural rotavirus infections. We observed no significant association between RV1-derived strains and gastroenteritis (odds ratio [OR] 0.98; 95% CI 0.60, 1.72). Our study demonstrated that the new assay is suitable for monitoring RV1-derived rotavirus strain circulation and that the RV1-derived strains are not associated with development of gastroenteritis symptoms.
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Takahashi S, Takada S, Yamanaka H, Masuda R, Kasai A. Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel. PLoS One 2021; 16:e0255576. [PMID: 34529685 PMCID: PMC8445453 DOI: 10.1371/journal.pone.0255576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 07/19/2021] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) analysis with species-specific primer/probe sets is promising as a tool to quantify fish abundance and distribution. Nevertheless, several factors could reduce the accuracy of this method. Here, we aimed to analyze whether intraspecific variability and diel activity rhythm affect eDNA detection in Japanese eels (Anguilla japonica). For this purpose, we performed tank experiments focusing on two points. First, we assessed the effects of base pair sequences with probe region polymorphism on eDNA detection. Next, we evaluated the influences of diel rhythm, activity, and individual differences in eDNA release rate on eDNA concentration. We examined the base pair sequences of the probe regions of 20 individuals and found genetic mismatches in two of them. The eDNA concentration was estimated to be much lower in these variants than it was in the other individuals. We conducted a rearing experiment on four non-variant individuals to explore the influences of diel activity and inter-individual differences in eDNA detection. Nocturnal eel activity was reflected in the eDNA detection but the inter-individual differences remained large. The observed weak positive correlations between eDNA concentration and activity suggest that eDNA emission is highly dependent on basal metabolism. The present study suggests that consideration of polymorphic sites at the probe region and diel activity rhythms should improve the accuracy and precision of abundance estimation through eDNA. Such fine-tuning is applicable not only for eels but also for other fishes to be targeted by eDNA technology.
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Affiliation(s)
- Sayaka Takahashi
- Oita Junior College, Oita, Japan
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Maizuru Fisheries Research Station, Kyoto University, Nagahama, Maizuru, Kyoto, Japan
- * E-mail:
| | - Shingo Takada
- Division of Marine Bioresource and Environmental Science, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Hiroki Yamanaka
- Faculty of Advanced Science and Technology, Ecology and Environmental Engineering Course, Ryukoku University, Otsu, Shiga, Japan
- Center for Biodiversity Science, Ryukoku University, Otsu, Shiga, Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Kyoto University, Nagahama, Maizuru, Kyoto, Japan
| | - Akihide Kasai
- Faculty of Fisheries Sciences, Division of Marine Bioresource and Environmental Science, Hokkaido University, Hakodate, Hokkaido, Japan
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Zabaleta N, Dai W, Bhatt U, Hérate C, Maisonnasse P, Chichester JA, Sanmiguel J, Estelien R, Michalson KT, Diop C, Maciorowski D, Dereuddre-Bosquet N, Cavarelli M, Gallouët AS, Naninck T, Kahlaoui N, Lemaitre J, Qi W, Hudspeth E, Cucalon A, Dyer CD, Pampena MB, Knox JJ, LaRocque RC, Charles RC, Li D, Kim M, Sheridan A, Storm N, Johnson RI, Feldman J, Hauser BM, Contreras V, Marlin R, Tsong Fang RH, Chapon C, van der Werf S, Zinn E, Ryan A, Kobayashi DT, Chauhan R, McGlynn M, Ryan ET, Schmidt AG, Price B, Honko A, Griffiths A, Yaghmour S, Hodge R, Betts MR, Freeman MW, Wilson JM, Le Grand R, Vandenberghe LH. An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates. Cell Host Microbe 2021; 29:1437-1453.e8. [PMID: 34428428 PMCID: PMC8346325 DOI: 10.1016/j.chom.2021.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 pandemic has affected more than 185 million people worldwide resulting in over 4 million deaths. To contain the pandemic, there is a continued need for safe vaccines that provide durable protection at low and scalable doses and can be deployed easily. Here, AAVCOVID-1, an adeno-associated viral (AAV), spike-gene-based vaccine candidate demonstrates potent immunogenicity in mouse and non-human primates following a single injection and confers complete protection from SARS-CoV-2 challenge in macaques. Peak neutralizing antibody titers are sustained at 1 year and complemented by functional memory T cell responses. The AAVCOVID vector has no relevant pre-existing immunity in humans and does not elicit cross-reactivity to common AAVs used in gene therapy. Vector genome persistence and expression wanes following injection. The single low-dose requirement, high-yield manufacturability, and 1-month stability for storage at room temperature may make this technology well suited to support effective immunization campaigns for emerging pathogens on a global scale.
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Affiliation(s)
- Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Wenlong Dai
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Urja Bhatt
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cécile Hérate
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Jessica A Chichester
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julio Sanmiguel
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Reynette Estelien
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kristofer T Michalson
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cheikh Diop
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dawid Maciorowski
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nathalie Dereuddre-Bosquet
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Anne-Sophie Gallouët
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Nidhal Kahlaoui
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Julien Lemaitre
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Wenbin Qi
- Novartis Gene Therapies, San Diego, CA, USA
| | | | - Allison Cucalon
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Cecilia D Dyer
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Betina Pampena
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James J Knox
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Dan Li
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Maya Kim
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Abigail Sheridan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Nadia Storm
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rebecca I Johnson
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vanessa Contreras
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Romain Marlin
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Raphaël Ho Tsong Fang
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Catherine Chapon
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France; National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Eric Zinn
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Aisling Ryan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dione T Kobayashi
- Translational Innovation Fund, Mass General Brigham Innovation, Cambridge, MA, USA
| | - Ruchi Chauhan
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Marion McGlynn
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | | | - Anna Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | - Michael R Betts
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mason W Freeman
- Center for Computational & Integrative Biology, Department of Medicine, and Translational Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James M Wilson
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, Fontenay-aux-Roses, France.
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA; Ocular Genomics Institute, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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Müştak IB, Müştak HK. Detection and differentiation of Salmonella Enteritidis and Salmonella Typhimurium by multiplex quantitative PCR from different poultry matrices. Br Poult Sci 2021; 63:171-178. [PMID: 34402333 DOI: 10.1080/00071668.2021.1966751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
1. The aim of this study was to develop a multiplex quantitative polymerase chain reaction (qPCR) based molecular diagnostic kit for rapid diagnosis of Salmonella enterica serovar Enteritidis and S. enterica serovar Typhimurium serotypes, which are frequently isolated worldwide from poultry samples.2. Detection and discrimination of S. Enteritidis and S. Typhimurium were performed by targeting the sdf and the STM4492 (putative cytoplasmic protein) gene, respectively. The invA (invasion protein) gene was used to detect Salmonella spp. as a target gene, since it is considered a standard. In this study, a total of 200 bacterial strains (178 Salmonella spp. strains and 22 other genera) were used to test the specificity and sensitivity of the developed kit. The limit of detection (LOD) of the assays was determined to be 100-101 cfu/25 g from chicken meat samples artificially contaminated by litter and 100-101 cfu/ml for cloacal swab samples.3. The multiplex qPCR results were 100% compatible with conventional serotyping results while the specificity and sensitivity values were 100%. These findings indicated that the newly developed multiplex qPCR technique can provide an alternative method to conventional serotyping of S. Enteritidis and S. Typhimurium in laboratories lacking adequate infrastructure.
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Affiliation(s)
- I B Müştak
- Department of Microbiology, Ankara University Faculty of Veterinary Medicine, Ankara, Turkey
| | - H K Müştak
- Department of Microbiology, Ankara University Faculty of Veterinary Medicine, Ankara, Turkey
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