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Patnaik A, Rai SK, Dhaked RK. CRISPR-Cas12a assisted recombinase based strand invading isothermal amplification platform designed for targeted detection of Bacillus anthracis Sterne. Int J Biol Macromol 2024; 263:130216. [PMID: 38378112 DOI: 10.1016/j.ijbiomac.2024.130216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Detection of a pathogen is crucial prior to all prophylaxis and post exposure treatment, as it can prevent further disease manifestation. In this study, we have developed a nucleic acid pre-amplification based CRISPR diagnostic for detection and surveillance of Bacillus anthracis Sterne. Strand Invasion Based isothermal Amplification (SIBA) platform and Cas12a (CRISPR endo-nuclease) was used to develop CRISPR-SIBA, a multifaceted diagnostic platform. SIBA was employed as the isothermal pre-amplification platform. CRISPR-Cas12a based collateral trans-cleavage reaction was used to ensure and enhance the specificity of the system. Efficiency of the detection system was evaluated by detecting Bacillus anthracis Sterne in complex wastewater sample backgrounds. Previously reported, Prophage 3, Cya and Pag genes of Bacillus anthracis were used as targets for this assay. The amplification system provided reliable and specific detection readout, with a sensitivity limit of 100 colony forming units in 40 min. The endpoint fluorescence from CRISPR collateral cleavage reactions gave a detection limit of 105 to 106 CFUs. The experiments conducted in this study provide the evidence for SIBA's applicability and compatibility with CRISPR-Cas system and its efficiency to specifically detect Bacillus anthracis Sterne. CRISPR-SIBA can be translated into developing cost-effective diagnostics for pathogens in resource constrained settings.
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Affiliation(s)
- Abhinandan Patnaik
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Sharad Kumar Rai
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India.
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2
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Díez Rodríguez GR, Figueredo Lago JE, Armas Cayarga A, González González YJ, García de la Rosa I, Collazo Mesa T, López Reyes I, Batista Lozada Y, Rodríguez Calá FR, García Sánchez JB. A novel high-resolution melting analysis strategy for detecting cystic fibrosis-causing variants. Lab Med 2024; 55:185-197. [PMID: 37417450 DOI: 10.1093/labmed/lmad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Cystic fibrosis (CF), an autosomal recessive disease, is caused by variants in both alleles of the CF transmembrane conductance regulator (CFTR) gene. A new assay based on allele-specific polymerase chain reaction and high-resolution melting analysis was developed for the detection of 18 CF-causing CFTR variants previously identified in Cuba and Latin America. The assay is also useful for zygosity determination of mutated alleles and includes internal controls. The reaction mixtures were normalized and evaluated using blood samples collected on filter paper. The evaluation of analytical parameters demonstrated the specificity and sensitivity of the method to detect the included CFTR variants. Internal and external validations yielded a 100% agreement between the new assay and the used reference tests. This assay can complement CF newborn screening not only in Cuba but also in Latin America.
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Affiliation(s)
| | | | | | | | | | - Teresa Collazo Mesa
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
| | - Ixchel López Reyes
- National Center of Medical Genetics, Medical University of Havana, Playa, Havana, Cuba
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Omar RF, Boissinot M, Huletsky A, Bergeron MG. Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention. Infect Dis Rep 2024; 16:216-227. [PMID: 38525764 PMCID: PMC10961803 DOI: 10.3390/idr16020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.
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Affiliation(s)
- Rabeea F. Omar
- Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (M.B.); (A.H.); (M.G.B.)
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4
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Ding S, Shen T, Feng Z, Diao S, Yan Y, Du Z, Jin Y, Gu J, Zhou J, Liao M, Dong W. Development of a highly sensitive TaqMan method based on multi-probe strategy: its application in ASFV detection. Biol Methods Protoc 2024; 9:bpae011. [PMID: 38486874 PMCID: PMC10939455 DOI: 10.1093/biomethods/bpae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/19/2024] [Accepted: 02/17/2024] [Indexed: 03/17/2024] Open
Abstract
The establishment of high sensitive detection method for various pathogenic microorganisms remains constantly concerned. In the present study, multi-probe strategy was first systematically investigated followed by establishing a highly sensitive TaqMan real-time fluorescent quantitative PCR (qPCR) method for detecting African swine fever virus (ASFV). Briefly, four probes based on the B646L gene of ASFV were designed and the effects of different combinations of the probes in a single TaqMan qPCR assay on the detection sensitivity were investigated. As less as 0.5-5 copies/μl of the ASFV gene was detected by the established TaqMan qPCR assay. Furthermore, plasmid harboring the B646L in water samples could be concentrated 1000 times by ultrafiltration to enable a highly sensitive detection of trace viral nucleic acids. Moreover, no cross-reactivity was observed with other common clinical swine viruses such as PCV2, PCV3, PCV4, PEDV, PDCoV, CSFV, PRRSV, and PRV. When detecting 173 clinical porcine serum samples, the coincidence rate between the developed method and WOAH (World Organization of Animal Health) recommended method was 100%. This study might provide an integrated strategy to achieve higher detection sensitivity of trace pathogenic microorganisms and applicably sensitive TaqMan-based qPCR assays.
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Affiliation(s)
- Shuxiang Ding
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianren Shen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zixuan Feng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sujing Diao
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhenkun Du
- Zhoushan City Bureau of Agriculture and Rural Development, Zhejiang 316000, China
| | - Yulan Jin
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyan Gu
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Min Liao
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weiren Dong
- MOA Key Laboratory of Animal Virology, Zhejiang University Center for Veterinary Sciences, Hangzhou 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
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De Jesús Andino F, Davydenko A, Webb RJ, Robert J. The Binding, Infection, and Promoted Growth of Batrachochytrium dendrobatidis by the Ranavirus FV3. Viruses 2024; 16:154. [PMID: 38275964 PMCID: PMC10818972 DOI: 10.3390/v16010154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Increasing reports suggest the occurrence of co-infection between Ranaviruses such as Frog Virus 3 (FV3) and the chytrid fungus Batrachochytrium dendrobatidis (Bd) in various amphibian species. However, the potential direct interaction of these two pathogens has not been examined to date. In this study, we investigated whether FV3 can interact with Bd in vitro using qPCR, conventional microscopy, and immunofluorescent microscopy. Our results reveal the unexpected ability of FV3 to bind, promote aggregation, productively infect, and significantly increase Bd growth in vitro. To extend these results in vivo, we assessed the impact of FV3 on Xenopus tropicalis frogs previously infected with Bd. Consistent with in vitro results, FV3 exposure to previously Bd-infected X. tropicalis significantly increased Bd loads and decreased the host's survival.
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Affiliation(s)
- Francisco De Jesús Andino
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
| | - Anton Davydenko
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
| | - Rebecca J. Webb
- Veterinary Biosciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
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Chen CA, Ho NYJ, Hsiao HY, Lin SS, Lai PL, Tsai TT. Smartphone-assisted fluorescence-based detection of sunrise-type smart amplification process and a 3D-printed ultraviolet light-emitting diode device for the diagnosis of tuberculosis. Biosens Bioelectron 2024; 244:115799. [PMID: 37918047 DOI: 10.1016/j.bios.2023.115799] [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: 09/19/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Accurate and rapid diagnosis of infectious diseases plays a key role in clinical practice, especially in resource-limited countries. In this study, we integrated sunrise-type smart amplification process (s-SmartAmp), a convenient and sensitive isothermal amplification method for nucleic acid, into a portable 3D-printed device equipped with smartphone-assisted image analysis capabilities to develop a novel fluorescence-based sensing system for the on-site diagnosis of tuberculosis (TB). To increase the efficiency of fluorescence (or Förster) resonance energy transfer, two types of sunrise probe systems were compared to detect the IS6110 DNA sequence of TB. Subsequently, linear regression was conducted to compare the performance of s-SmartAmp and loop-mediated isothermal amplification (LAMP). The results indicated that, compared with LAMP, s-SmartAmp yielded more stable and precise results with lower background interference and high linear correlation coefficients (R2 = 0.9994 and 1, respectively) for the FAM-TAMRA and FITC-BHQ-1 probe system. The detection time was 45 min with a detection limit of 10 fg/μL. To evaluate the performance of our proposed on-site sensing system, we used s-SmartAmp 3D-printed ultraviolet light-emitting diode device to test multiple clinical samples of TB. Our findings suggest that the proposed system has the potential to achieve accurate and rapid on-site diagnosis of TB.
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Affiliation(s)
- Chung-An Chen
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hui-Yi Hsiao
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Song-Shu Lin
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Hyperbaric Oxygen Medical Research Laboratory, Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Po-Liang Lai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Spine Section and Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University, Taoyuan, Taiwan.
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7
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Gamal M, Ibrahim MA. Introducing the f 0% method: a reliable and accurate approach for qPCR analysis. BMC Bioinformatics 2024; 25:17. [PMID: 38212692 PMCID: PMC10782791 DOI: 10.1186/s12859-024-05630-y] [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: 11/01/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among many other drawbacks. While other methods have been developed to analyze qPCR results, none has statistically proven to perform better than the CT method. Therefore, we aimed to develop a new qPCR analysis method that overcomes the limitations of the CT method. Our f0% [eff naught percent] method depends on a modified flexible sigmoid function to fit the amplification curve with a linear part to subtract the background noise. Then, the initial fluorescence is estimated and reported as a percentage of the predicted maximum fluorescence (f0%). RESULTS The performance of the new f0% method was compared against the CT method along with another two outstanding methods-LinRegPCR and Cy0. The comparison regarded absolute and relative quantifications and used 20 dilution curves obtained from 7 different datasets that utilize different DNA-binding dyes. In the case of absolute quantification, f0% reduced CV%, variance, and absolute relative error by 1.66, 2.78, and 1.8 folds relative to CT; and by 1.65, 2.61, and 1.71 folds relative to LinRegPCR, respectively. While, regarding relative quantification, f0% reduced CV% by 1.76, 1.55, and 1.25 folds and variance by 3.13, 2.31, and 1.57 folds regarding CT, LinRegPCR, and Cy0, respectively. Finally, f0% reduced the absolute relative error caused by LinRegPCR by 1.83 folds. CONCLUSIONS We recommend using the f0% method to analyze and report qPCR results based on its reported advantages. Finally, to simplify the usage of the f0% method, it was implemented in a macro-enabled Excel file with a user manual located on https://github.com/Mahmoud0Gamal/F0-perc/releases .
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Affiliation(s)
- Mahmoud Gamal
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Marwa A Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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Chubarov AS, Baranovskaya EE, Oscorbin IP, Yushin II, Filipenko ML, Pyshnyi DV, Vasilyeva SV, Lomzov AA. Phosphoramidate Azole Oligonucleotides for Single Nucleotide Polymorphism Detection by PCR. Int J Mol Sci 2024; 25:617. [PMID: 38203788 PMCID: PMC10778797 DOI: 10.3390/ijms25010617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Detection of the Kirsten rat sarcoma gene (KRAS) mutational status is an important factor for the treatment of various malignancies. The most common KRAS-activating mutations are caused by single-nucleotide mutations, which are usually determined by using PCR, using allele-specific DNA primers. Oligonucleotide primers with uncharged or partially charged internucleotide phosphate modification have proved their ability to increase the sensitivity and specificity of various single nucleotide mutation detection. To enhance the specificity of single nucleotide mutation detection, the novel oligonucleotides with four types of uncharged and partially charged internucleotide phosphates modification, phosphoramide benzoazole (PABA) oligonucleotides (PABAO), was used to prove the concept on the KRAS mutation model. The molecular effects of different types of site-specific PABA modification in a primer or a template on a synthesis of full-length elongation product and PCR efficiency were evaluated. The allele-specific PCR (AS-PCR) on plasmid templates showed a significant increase in analysis specificity without changes in Cq values compared with unmodified primer. PABA modification is a universal mismatch-like disturbance, which can be used for single nucleotide polymorphism discrimination for various applications. The molecular insights of the PABA site-specific modification in a primer and a template affect PCR, structural features of four types of PABAO in connection with AS-PCR results, and improvements of AS-PCR specificity support the further design of novel PCR platforms for various biological targets testing.
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Affiliation(s)
- Alexey S. Chubarov
- Correspondence: or (A.S.C.); (A.A.L.); Tel.: +7-913-763-1420 (A.S.C.); +7-(383)363-51-51 (A.A.L.)
| | | | | | | | | | | | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (E.E.B.); (I.P.O.); (I.I.Y.); (M.L.F.); (D.V.P.); (S.V.V.)
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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [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: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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González-Torralva F, Norsworthy JK. Overexpression of Acetyl CoA Carboxylase 1 and 3 ( ACCase1 and ACCase3), and CYP81A21 were related to cyhalofop resistance in a barnyardgrass accession from Arkansas. PLANT SIGNALING & BEHAVIOR 2023; 18:2172517. [PMID: 36722712 PMCID: PMC9897766 DOI: 10.1080/15592324.2023.2172517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] is the most difficult-to-control weed species of rice production systems worldwide. It has evolved resistance to different herbicide sites of action, including the acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. Target-site mutations conferring resistance to ACCase-inhibiting herbicides are well documented; however, the role of the different ACCase genes in conferring resistance to cyhalofop-p-butyl (cyhalofop), an ACCase-inhibiting herbicide, remains poorly understood. This research assessed the contribution of gene amplification and expression of ACCase genes in a cyhalofop-resistant barnyardgrass accession. Additionally, the expression of glutathione-S-transferases (GSTs) and cytochrome P450 monooxygenases (P450s) genes as possible contributors to resistance to cyhalofop were investigated. Results demonstrated that ACCase gene amplification does not contribute to cyhalofop resistance. However, ACCase1 and ACCase3 were found to be overexpressed in the cyhalofop-resistant barnyardgrass accession. At 24 h after cyhalofop treatment, an overexpression of 2.0- and 2.8-fold was detected in ACCase1 and ACCase3, respectively. In addition, CYP81A21 (a P450 gene) was found to be 2.5-fold overexpressed compared to the susceptible accession in the same time period. These results suggest that ACCase1, ACCase3, and CYP81A21 are crucial genes in contributing cyhalofop resistance in this barnyardgrass accession.
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Affiliation(s)
- Fidel González-Torralva
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Jason K. Norsworthy
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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Ping Y, Quanlin S, Yue H, Jing Z, Wenjun L. Screening and validation of double allele-specific binding F-primers for the measurement of antihypertensive pharmacogenomics. Front Med (Lausanne) 2023; 10:1269221. [PMID: 38173939 PMCID: PMC10761462 DOI: 10.3389/fmed.2023.1269221] [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: 07/29/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Objective Previous studies have proposed that genetic polymorphisms of CYP2D6*10, ADRB1, NPPA, CYP3A5*3, ACE, CYP2C9*3, and AGTR1 are involved in antihypertensive pharmacogenomics. The purpose of this study is to develop an amplification analysis using double allele-specific (AS) binding primers for accurate measurement of antihypertensive pharmacogenomics. Methods To establish a quadruplex quantitative PCR (qPCR) analysis for genotyping of CYP2D6*10, ADRB1 (1165 G>C), NPPA (2238 T>C) and CYP3A5*3, and a triplex qPCR analysis for genotyping of ACE (I/D), CYP2C9*3 and AGTR1 (1166 A>C), mismatch AS F-primers were screened by detection of plasmid/gDNA, and were validated by agreement analysis/reproducibility evaluation, in which the ΔCq (differences in threshold cycles between the wild-type F-primer-based amplification assay and the mutant-type F-primer-based amplification assay) was employed to determine genotypes. Results Seven pairs of primers were successfully selected through three rounds of F-primers screening. Except for ADRB1, the robustness assessment showed the amplification efficiency ranging from 0.9 to 1.1. In agreement analysis, two specimens in the training set (n = 203) were defined by the triplex analysis rather than NGS as heterozygotes for ACE, which was evidenced by gel electrophoresis. Reproducibility evaluation demonstrated that the coefficient of variation (CV) was <5%. Conclusion Multiplex amplification analysis using screened AS binding primers is a simple, reliable, and accurate tool to guide drug delivery in antihypertensive personalized treatment.
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Affiliation(s)
| | | | | | - Zhang Jing
- Institute of Biomedical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Lan Wenjun
- Institute of Biomedical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
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12
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Goyal S, Singh P, Sengupta S, Muthukrishnan AB, Jayaraman G. DNA-Aptamer-Based qPCR Using Light-Up Dyes for the Detection of Nucleic Acids. ACS OMEGA 2023; 8:47277-47282. [PMID: 38107963 PMCID: PMC10719997 DOI: 10.1021/acsomega.3c07599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/05/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is widely used in detection of nucleic acids, but existing methods either lack sequence-specific detection or are costly because they use chemically modified DNA probes. In this work, we apply a DNA aptamer and light-up dye-based chemistry for qPCR for nucleic acid quantification. In contrast to the conventional qPCR, in our method, we observe an exponential decrease in fluorescence upon DNA amplification. The qPCR method we developed produced consistent Ct vs log10 (DNA amount) standard curves, which have a linearfit with R2 value > 0.99. This qPCR technique was validated by quantifying gene targets from Streptococcus zooepidemicus (SzhasB) and Mycobacterium tuberculosis (MtrpoB). We show that our strategy is able to successfully detect DNA at as low as 800 copies/μL. To the best of our knowledge, this is the first study demonstrating the application of light-up dyes and DNA aptamers in qPCR.
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Affiliation(s)
| | - Prashant Singh
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Sudeshna Sengupta
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Anantha Barathi Muthukrishnan
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Guhan Jayaraman
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
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Kim HR, Kim JM, Baek JS, Park J, Kim WI, Ku BK, Jeoung HY, Lee KK, Park CK. An Advanced Multiplex Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid and Reliable Detection of Porcine Epidemic Diarrhea Virus and Porcine Internal Positive Control. Viruses 2023; 15:2204. [PMID: 38005882 PMCID: PMC10674262 DOI: 10.3390/v15112204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
For rapid and reliable detection of porcine epidemic diarrhea virus (PEDV) from pig clinical samples, a multiplex, real-time, reverse transcription loop-mediated isothermal amplification (mqRT-LAMP) was developed using two sets of primers and assimilating probes specific to the PEDV N gene and the Sus scrofa β-actin gene, which was used as an endogenous internal positive control (EIPC) to avoid false-negative results. The assay specifically amplified both target genes of PEDV and EIPC in a single reaction without any interference but did not amplify other porcine viral nucleic acids. The limit of detection was 10 copies/μL, 100-fold lower than that of a reverse transcription-polymerase chain reaction (RT-PCR) and equivalent to that of quantitative/real-time RT-PCR (qRT-PCR). This assay has high repeatability and reproducibility with coefficients of variation < 4.0%. The positive signal of the mqRT-LAMP assay was generated within 25 min, demonstrating advantages in rapid detection of PEDV over RT-PCR or qRT-PCR assay, which require at least 2 h turnaround times. In clinical evaluation, the detection rate of PEDV by mqRT-LAMP assay (77.3%) was higher than that of RT-PCR assay (69.7%), and comparable to qRT-PCR (76.8%) with almost 100% concordance (kappa value 0.98). The developed mqRT-LAMP assay can serve as an advanced alternative method for PEDV diagnosis because it has high sensitivity and specificity, rapidity, and reliability even in resource-limited laboratories.
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Affiliation(s)
- Hye-Ryung Kim
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea; (H.-R.K.); (J.-M.K.); (J.-S.B.); (J.P.)
| | - Jong-Min Kim
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea; (H.-R.K.); (J.-M.K.); (J.-S.B.); (J.P.)
| | - Ji-Su Baek
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea; (H.-R.K.); (J.-M.K.); (J.-S.B.); (J.P.)
| | - Jonghyun Park
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea; (H.-R.K.); (J.-M.K.); (J.-S.B.); (J.P.)
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea;
| | - Bok Kyung Ku
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, Gimcheon 39660, Republic of Korea; (B.K.K.); (H.-Y.J.); (K.-K.L.)
| | - Hye-Young Jeoung
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, Gimcheon 39660, Republic of Korea; (B.K.K.); (H.-Y.J.); (K.-K.L.)
| | - Kyoung-Ki Lee
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, Gimcheon 39660, Republic of Korea; (B.K.K.); (H.-Y.J.); (K.-K.L.)
| | - Choi-Kyu Park
- College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu 41566, Republic of Korea; (H.-R.K.); (J.-M.K.); (J.-S.B.); (J.P.)
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14
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Banerjee P, Singh T, Qamar I. New Insights Into Pyridoxal Kinase Inhibitors and Their Antileukemic Effects. Cureus 2023; 15:e48176. [PMID: 38046746 PMCID: PMC10693352 DOI: 10.7759/cureus.48176] [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] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Pyridoxal kinase (PDXK) plays a pivotal role as an essential enzyme in cellular processes. It catalyzes the phosphorylation of pyridoxal, pyridoxamine, and pyridoxine to generate pyridoxal 5'-phosphate (PLP), the bioactive form of vitamin B6. An intriguing link has emerged between elevated expression levels of PDXK and PLP and various types of carcinomas, including leukemia. Leukemic cells have an increased need for vitamin B6 to sustain their survival and rapid growth, highlighting the potential of targeting PDXK-PLP as a promising therapeutic target in cancer treatment. To discover a novel and promising PDXK inhibitor, we conducted a comprehensive screening of compounds derived from both natural sources and drug-like databases. Our approach involved employing structure-based virtual screening and molecular docking techniques to attenuate the phosphorylation of PLP. Among the top six compounds, ZINC095099376 (referred to as C03) emerged as the most potent inhibitor of PDXK, primarily due to its exceptional binding affinity and remarkable specificity for the target protein. Furthermore, our investigation revealed that compound C03 establishes crucial interactions with key residues within the substrate binding site, indicating that it binds at the same site as the co-crystallized ligand. Remarkably, compound C03 inhibited the endogenous PDXK expression, showed anti-proliferative activity, and triggered an intrinsic pathway for apoptosis via the activation of key apoptotic factors in leukemic cells. In summary, these findings strongly indicate that compound C03 holds promise as a novel inhibitor of PDXK, offering the potential for the development of effective treatments for leukemia.
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Affiliation(s)
- Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, IND
| | - Tripti Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, IND
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, IND
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15
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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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16
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Lai JH, Keum JW, Lee HG, Molaei M, Blair EJ, Li S, Soliman JW, Raol VK, Barker CL, Fodor SPA, Fan HC, Shum EY. New realm of precision multiplexing enabled by massively-parallel single molecule UltraPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561546. [PMID: 37873291 PMCID: PMC10592712 DOI: 10.1101/2023.10.09.561546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
PCR has been a reliable and inexpensive method for nucleic acid detection in the past several decades. In particular, multiplex PCR is a powerful tool to analyze many biomarkers in the same reaction, thus maximizing detection sensitivity and reducing sample usage. However, balancing the amplification kinetics between amplicons and distinguishing them can be challenging, diminishing the broad adoption of high order multiplex PCR panels. Here, we present a new paradigm in PCR amplification and multiplexed detection using UltraPCR. UltraPCR utilizes a simple centrifugation workflow to split a PCR reaction into ∼34 million partitions, forming an optically clear pellet of spatially separated reaction compartments in a PCR tube. After in situ thermocycling, light sheet scanning is used to produce a 3D reconstruction of the fluorescent positive compartments within the pellet. At typical sample DNA concentrations, the magnitude of partitions offered by UltraPCR dictate that the vast majority of target molecules occupy a compartment uniquely. This single molecule realm allows for isolated amplification events, thereby eliminating competition between different targets and generating unambiguous optical signals for detection. Using a 4-color optical setup, we demonstrate that we can incorporate 10 different fluorescent dyes in the same UltraPCR reaction. We further push multiplexing to an unprecedented level by combinatorial labeling with fluorescent dyes - referred to as "comboplex" technology. Using the same 4-color optical setup, we developed a 22-target comboplex panel that can detect all targets simultaneously at high precision. Collectively, UltraPCR has the potential to push PCR applications beyond what is currently available, enabling a new class of precision genomics assays.
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17
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Wu Q, Hou Q, Wang P, Ding C, Lv S. Antifouling Electrochemiluminescence Biosensor Based on Bovine Serum Albumin Hydrogel for the Accurate Detection of p53 Gene in Human Serum. ACS APPLIED MATERIALS & INTERFACES 2023; 15:44322-44330. [PMID: 37672622 DOI: 10.1021/acsami.3c09737] [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: 09/08/2023]
Abstract
To detect biomarkers in complex samples, it is fundamental to avoid the nonspecific adsorption of impurities to improve the selectivity of biosensors. In this study, a sensitive antifouling electrochemiluminescence biosensor was proposed based on bovine serum albumin (BSA)- and exonuclease III (Exo III)-mediated nucleic acid cycle signal amplification strategy. Ti3C2Tx-NH4, which has a large surface area and high metal conductivity, was crosslinked with BSA to improve the conductivity of the sensing interface, which shows antifouling performance excellently due to the electrical neutrality and good hydrophilicity of BSA hydrogel. The cyclic amplification strategy based on Exo III and DNA hybridization chain reaction significantly amplified the electrochemiluminescence signal and improved the sensitivity of p53 gene detection. The linear range of the biosensor is 1 fM-1 nM with a detection limit of 0.26 fM. More importantly, the sensor showed excellent selectivity when it was used to detect the p53 gene in real samples, such as serum. Thus, this unique antifouling sensing interface is expected to construct various electrochemical biosensors in clinical diagnosis and biopathological analysis.
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Affiliation(s)
- Qiongwei Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qianqian Hou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Peipei Wang
- Department of Rehabilitation Medicine, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
- Department of Rehabilitation Medicine, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
| | - Shaoping Lv
- Department of Rehabilitation Medicine, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao 266042, China
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18
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Li C, Li F, Xie XN, Liang YS, Tian EW, Chao Z. Molecular quantification for differentiation of fresh and dried Jinqian Baihua She. J Pharm Biomed Anal 2023; 233:115444. [PMID: 37163873 DOI: 10.1016/j.jpba.2023.115444] [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: 11/28/2022] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
Freshly-used crude drugs have unique functions and advantages in TCM practice of treating diseases. Jinlong Capsule is a patent traditional Chinese medicine product effective for treatment of hepatocarcinoma, and fresh Jinqian Baihua She (JBS, the body of juvenile Bungarus multicinctus) is one of its important ingredients. The emergence of counterfeit fresh JBS, often identified as dried JBS with almost identical appearance, poses a difficult problem in the quality control of the product. Herein we report a molecular quantification-based method for differentiation of fresh and dried JBS by determining the copy number of a specific DNA marker in the samples. Using species-specific primers and TaqMan probes, we established a real-time quantitative PCR system for amplification of a fragment in the 658-bp cytochrome oxidase subunit I (COI) region from JBS specimens. The amplicon copy number in the muscle tissues ranged from 1.14 × 107 to 4.83 × 107 copies/mg in fresh JBS samples, as compared with 1.13 × 105-8.91 × 106 copies/mg in dried JBS samples. Based upon Fisher discriminant analysis, we used 1.27 × 107 copies/mg as the cut-off value for differentiating fresh and dried JBS, which was validated in the single-blinded validation test of fresh and dried JBS samples. This qPCR system may provide an efficient means for accurate identification of fresh JBS to improve the quality control of the medicinal product.
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Affiliation(s)
- Chan Li
- Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China
| | - Fang Li
- Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xue-Na Xie
- Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yong-Shan Liang
- Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - En-Wei Tian
- Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China
| | - Zhi Chao
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China; Faculty of Medicinal Plant and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China.
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19
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Lamas A, Azinheiro S, Roumani F, Prado M, Garrido-Maestu A. Evaluation of the effect of outer primer structure, and inner primer linker sequences, in the performance of Loop-mediated isothermal amplification. Talanta 2023; 260:124642. [PMID: 37167680 DOI: 10.1016/j.talanta.2023.124642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
Loop-mediated isothermal amplification, or LAMP, is nowadays the most popular isothermal nucleic acid amplification technique. This technique implements a minimum of four primers, named outer (F3/B3) and inner primers (FIP/BIP). The inner primers hybridize in two distinct regions, and some studies have reported that the usage of a linker, typically composed of four thymines, in the middle of these primers can improve assay performance. In addition to this, dual-priming oligonucleotides, DPO, have been reported to provide highly specific reducing non-specific amplifications. Considering the large number of primers implemented in LAMP assays, in the current study the suitability of DPO primers replacing regular outer primers; and their combination with different linker sequences in the inner primers were explored. The results demonstrated that replacing standard F3/B3 by DPO primers does not significantly affect that overall performance of the assay, and provides additional stability to temperature changes. This observations were consistent regardless the type of linker implemented in the inner primers, out of which in the current study a linker composed of thymines significantly outperformed the other options tested, most likely due to a combination of sequence and physical structure.
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Affiliation(s)
- Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory, Department of Analytical Chemistry, Nutrition and Bromatology, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - Sarah Azinheiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Foteini Roumani
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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20
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Altindiş M, Kahraman Kilbaş EP. Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081421. [PMID: 37189522 DOI: 10.3390/diagnostics13081421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.
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Affiliation(s)
- Mustafa Altindiş
- Medical Microbiology Department, Faculty of Medicine, Sakarya University, Sakarya 54050, Türkiye
| | - Elmas Pınar Kahraman Kilbaş
- Medical Laboratory Techniques, Vocational School of Health Services, Fenerbahce University, Istanbul 34758, Türkiye
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21
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Kurup CP, Ahmed MU. Nanozymes towards Personalized Diagnostics: A Recent Progress in Biosensing. BIOSENSORS 2023; 13:bios13040461. [PMID: 37185536 PMCID: PMC10136715 DOI: 10.3390/bios13040461] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
This review highlights the recent advancements in the field of nanozymes and their applications in the development of point-of-care biosensors. The use of nanozymes as enzyme-mimicking components in biosensing systems has led to improved performance and miniaturization of these sensors. The unique properties of nanozymes, such as high stability, robustness, and surface tunability, make them an attractive alternative to traditional enzymes in biosensing applications. Researchers have explored a wide range of nanomaterials, including metals, metal oxides, and metal-organic frameworks, for the development of nanozyme-based biosensors. Different sensing strategies, such as colorimetric, fluorescent, electrochemical and SERS, have been implemented using nanozymes as signal-producing components. Despite the numerous advantages, there are also challenges associated with nanozyme-based biosensors, including stability and specificity, which need to be addressed for their wider applications. The future of nanozyme-based biosensors looks promising, with the potential to bring a paradigm shift in biomolecular sensing. The development of highly specific, multi-enzyme mimicking nanozymes could lead to the creation of highly sensitive and low-biofouling biosensors. Integration of nanozymes into point-of-care diagnostics promises to revolutionize healthcare by improving patient outcomes and reducing costs while enhancing the accuracy and sensitivity of diagnostic tools.
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Affiliation(s)
- Chitra Padmakumari Kurup
- Biosensors and Nanobiotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Minhaz Uddin Ahmed
- Biosensors and Nanobiotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
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22
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Mueller BL, Liberman MJ, Kolpashchikov DM. OWL2: a molecular beacon-based nanostructure for highly selective detection of single-nucleotide variations in folded nucleic acids. NANOSCALE 2023; 15:5735-5742. [PMID: 36880268 DOI: 10.1039/d2nr05590b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Hybridization probes have been used in the detection of specific nucleic acids for the last 50 years. Despite the extensive efforts and the great significance, the challenges of the commonly used probes include (1) low selectivity in detecting single nucleotide variations (SNV) at low (e.g. room or 37 °C) temperatures; (2) low affinity in binding folded nucleic acids, and (3) the cost of fluorescent probes. Here we introduce a multicomponent hybridization probe, called OWL2 sensor, which addresses all three issues. The OWL2 sensor uses two analyte binding arms to tightly bind and unwind folded analytes, and two sequence-specific strands that bind both the analyte and a universal molecular beacon (UMB) probe to form fluorescent 'OWL' structure. The OWL2 sensor was able to differentiate single base mismatches in folded analytes in the temperature range of 5-38 °C. The design is cost-efficient since the same UMB probe can be used for detecting any analyte sequence.
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Affiliation(s)
- Brittany L Mueller
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Mark J Liberman
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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23
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The Development of Diagnostic and Vaccine Strategies for Early Detection and Control of Human Brucellosis, Particularly in Endemic Areas. Vaccines (Basel) 2023; 11:vaccines11030654. [PMID: 36992237 DOI: 10.3390/vaccines11030654] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Brucellosis is considered one of the most serious zoonotic diseases worldwide. This disease affects both human and animal health, in addition to being one of the most widespread zoonotic illnesses in the Middle East and Northern Africa. Human brucellosis generally presents in a diverse and non-specific manner, making laboratory confirmation of the diagnosis critical to the patient’s recovery. A coordinated strategy for diagnosing and controlling brucellosis throughout the Middle East is required, as this disease cannot be known to occur without reliable microbiological, molecular, and epidemiological evidence. Consequently, the current review focuses on the current and emerging microbiological diagnostic tools for the early detection and control of human brucellosis. Laboratory assays such as culturing, serology, and molecular analysis can frequently be used to diagnose brucellosis. Although serological markers and nucleic acid amplification techniques are extremely sensitive, and extensive experience has been gained with these techniques in the laboratory diagnosis of brucellosis, a culture is still considered to be the “gold standard” due to the importance of this aspect of public health and clinical care. In endemic regions, however, serological tests remain the primary method of diagnosis due to their low cost, user-friendliness, and strong ability to provide a negative prediction, so they are commonly used. A nucleic acid amplification assay, which is highly sensitive, specific, and safe, is capable of enabling rapid disease diagnosis. Patients who have reportedly fully healed may continue to have positive molecular test results for a long time. Therefore, cultures and serological methods will continue to be the main tools for diagnosing and following up on human brucellosis for as long as no commercial tests or studies demonstrate adequate interlaboratory reproducibility. As there is no approved vaccine that prevents human brucellosis, vaccination-based control of animal brucellosis has become an important part of the management of human brucellosis. Over the past few decades, several studies have been conducted to develop Brucella vaccines, but the problem of controlling brucellosis in both humans and animals remains challenging. Therefore, this review also aims to present an updated overview of the different types of brucellosis vaccines that are currently available.
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24
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Fujita T, Nagata S, Fujii H. Oligoribonucleotide-Mediated Blockade of DNA Extension by Taq DNA Polymerases Increases Specificity and Sensitivity for Detecting Single-Nucleotide Differences. Anal Chem 2023; 95:3442-3451. [PMID: 36738294 DOI: 10.1021/acs.analchem.2c05186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Blocking PCR is a method that inhibits amplification of DNA possessing a nucleotide sequence complementary to that of a blocker; the method can be used to suppress amplification of target wild-type DNA while amplifying mutated DNA. Previously, we demonstrated that an oligoribonucleotide (ORN) functions as a cost-effective and sequence-specific blocker. This blocking PCR system, named ORN interference-PCR (ORNi-PCR), is compatible with DNA polymerases lacking 5'-3' exonuclease activity but not with those possessing the activity (e.g., Taq DNA polymerase), which can remove a hybridized ORN during DNA extension. Here, we demonstrate that under specific experimental conditions, an intact or phosphorothioated ORN strongly suppresses extension of target DNA by Taq DNA polymerases. This method was applied successfully to real-time ORNi-PCR and one-step real-time reverse transcription-ORNi-PCR using a dual-labeled fluorescent probe to detect a single-nucleotide mutation in DNA and RNA in a sequence-specific manner. The results reaffirm the utility of blocking PCR and provide technical hints for its improvement.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562 Aomori, Japan
| | - Shoko Nagata
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562 Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562 Aomori, Japan
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An Improved Duplex Real-Time Quantitative RT-PCR Assay with a Canine Endogenous Internal Positive Control for More Sensitive and Reliable Detection of Canine Parainfluenza Virus 5. Vet Sci 2023; 10:vetsci10020142. [PMID: 36851445 PMCID: PMC9965950 DOI: 10.3390/vetsci10020142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
A duplex real-time quantitative reverse transcription-polymerase chain reaction (dqRT-PCR) assay was successfully developed to simultaneously detect canine parainfluenza virus 5 (CPIV5) and a canine endogenous internal positive control (EIPC) in canine clinical samples. Two sets of primers and probes for the CPIV5 L and canine 16S rRNA genes were included in the dqRT-PCR assay to detect CPIV and monitor invalid results throughout the qRT-PCR process. The developed dqRT-PCR assay specifically detected CPIV5 but no other canine pathogens. Furthermore, 16S rRNA was stably amplified by dqRT-PCR assay in all samples containing canine cellular materials. The assay's sensitivity was determined as below ten RNA copies per reaction, with CPIV5 L gene standard RNA and 1 TCID50/mL with the CPIV5 D008 vaccine strain, which was 10-fold higher than that of the previous HN gene-specific qRT-PCR (HN-qRT-PCR) assays and was equivalent to that of the previous N gene-specific qRT-PCR (N-qRT-PCR) assays, respectively. Moreover, the Ct values of the CPIV5-positive samples obtained using the dqRT-PCR assay were lower than those obtained using the previous HN- and N-qRT-PCR assays, indicating that the diagnostic performance of the dqRT-PCR assay was superior to those of previous HN- and N-qRT-PCR assays. The calculated Cohen's kappa coefficient values (95% confidence interval) between dqRT-PCR and the HN- or N-specific qRT-PCR assays were 0.97 (0.90-1.03) or 1.00 (1.00-1.00), respectively. In conclusion, the newly developed dqRT-PCR assay with high sensitivity, specificity, and reliability will be a promising diagnostic tool for the detection of CPIV5 in clinical samples and useful for etiological and epidemiological studies of CPIV5 infection in dogs.
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Jeon GT, Kim HR, Kim JM, Baek JS, Shin YK, Kwon OK, Kang HE, Cho HS, Cheon DS, Park CK. Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples. Animals (Basel) 2023; 13:ani13040602. [PMID: 36830388 PMCID: PMC9951688 DOI: 10.3390/ani13040602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been frequently reported in companion dogs and cats worldwide during the ongoing coronavirus disease. However, RT-qPCR methods developed for humans have been used for the diagnosis of SARS-CoV-2 infections in suspected companion dogs and cats owing to the lack of the companion animal-tailored methods. Therefore, we developed a multiplex RT-qPCR (mRT-qPCR) using newly designed primers and probes targeting RdRp and N genes of all currently circulating SARS-CoV-2 variants as well as the canine or feline 16S rRNA gene as an endogenous internal positive control (EIPC) for reliable diagnosis of SARS-CoV-2 infection from suspected dogs and cats. The developed mRT-qPCR assay specifically detected the target genes of SARS-CoV-2 but no other canine or feline pathogens. Furthermore, canine and feline EIPCs were stably amplified by mRT-qPCR in samples containing canine- or feline-origin cellular materials. This assay has high repeatability and reproducibility, with an optimal limit of detection (<10 RNA copies per reaction) and coefficients of variation (<1.0%). The detection rate of SARS-CoV-2 of the developed mRT-qPCR was 6.6% for canine and feline nasopharyngeal samples, which was consistent with that of a commercial mRT-qPCR kit for humans. Collectively, the newly developed mRT-qPCR with canine and feline EIPC can efficiently diagnose and evaluate the viral load in field specimens and will be a valuable tool for etiological diagnosis, epidemiological study, and controlling SARS-CoV-2 infections in canine and feline populations.
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Affiliation(s)
- Gyu-Tae Jeon
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hye-Ryung Kim
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Min Kim
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji-Su Baek
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeun-Kyung Shin
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Oh-Kyu Kwon
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Hae-Eun Kang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Ho-Seong Cho
- Bio-Safety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | | | - Choi-Kyu Park
- Animal Disease Intervention Center, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-5973
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Kim JM, Kim HR, Jeon GT, Baek JS, Kwon OD, Park CK. Molecular Detection of Porcine Parainfluenza Viruses 1 and 5 Using a Newly Developed Duplex Real-Time RT-PCR in South Korea. Animals (Basel) 2023; 13:ani13040598. [PMID: 36830385 PMCID: PMC9951646 DOI: 10.3390/ani13040598] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Two species of porcine parainfluenza viruses (PPIV), PPIV1 and PPIV5, are globally distributed in pig herds and associated with porcine respiratory diseases, and a diagnostic tool for the simultaneous detection of the two viruses is required. In this study, a TaqMan probe-based duplex real-time reverse transcription polymerase chain reaction (dqRT-PCR) assay was first developed for the differential detection of PPIV1 and PPIV5 nucleocapsid protein (NP) genes in porcine clinical samples. The dqRT-PCR assay was highly sensitive, its limit of detection was approximately 10 RNA copies/reaction, it specifically amplified the targeted NP genes of PPIV1 and PPIV5 without cross-reacting with other porcine pathogens, and their clinical detection rates were 15.2% and 0.7%, respectively. The results from 441 clinical samples taken from 278 Korean domestic pig farms showed that the prevalence of PPIV1 and PPIV5 was 11.2% and 1.1%, respectively, and co-infection of both viruses was confirmed in a farm, suggesting that PPIV1 and PPIV5 are co-circulating in current Korean pig herds. Phylogenetic analysis based on the partial NP genes suggested that genetically diverse PPIV1 strains are circulating in Korean pig herds. The developed dqRT-PCR assay was found to be an accurate, reliable, and quantitative detection tool for PPIV1 and PPIV5 RNA in clinical pig samples and will be useful for etiological and epidemiological studies and the control of viral infections in the field.
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Medina-Lozano I, Arnedo MS, Grimplet J, Díaz A. Selection of Novel Reference Genes by RNA-Seq and Their Evaluation for Normalising Real-Time qPCR Expression Data of Anthocyanin-Related Genes in Lettuce and Wild Relatives. Int J Mol Sci 2023; 24:3052. [PMID: 36769376 PMCID: PMC9917471 DOI: 10.3390/ijms24033052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Lettuce is a popular vegetable source of bioactive compounds, like anthocyanins, powerful antioxidants present in red and semi-red varieties. Selection of reliable reference genes (RGs) for the normalization of real-time quantitative PCR (qPCR) data is crucial to obtain accurate gene expression results. Among the genes with totally unrelated biological functions, six candidate RGs (ADF2, CYB5, iPGAM, SCL13, TRXL3-3, and VHA-H) with low variation in expression according to RNA-seq analyses, were selected for future expression studies of anthocyanin-related genes in three different experiments: leaf colour comparison (green vs. red) in commercial varieties; tissue comparison (leaf vs. stem) in a wild relative; and drought stress experiment in commercial and traditional varieties, and a wild relative. Expression profiles of the candidate RGs were obtained by qPCR and their stability was assessed by four different analytical tools, geNorm, NormFinder, BestKeeper, and Delta Ct method, all integrated in RefFinder. All results considered, we recommend CYB5 to be used as RG for the leaf colour experiment and TRXL3-3 for the tissue and drought stress ones, as they were the most stable genes in each case. RNA-seq is useful to preselect novel RGs although validation by qPCR is still advisable. These results provide helpful information for gene expression studies in Lactuca spp. under the described conditions.
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Affiliation(s)
- Inés Medina-Lozano
- Department of Plant Sciences, Agrifood Research and Technology Centre of Aragon (CITA), Avd. Montañana 930, 50059 Zaragoza, Spain
- AgriFood Institute of Aragon–IA2, CITA-University of Zaragoza, 50013 Zaragoza, Spain
| | - María Soledad Arnedo
- Ramiro Arnedo S.A. Paraje La Molina 54, Las Norias de Daza, 04716 Almería, Spain
| | - Jérôme Grimplet
- Department of Plant Sciences, Agrifood Research and Technology Centre of Aragon (CITA), Avd. Montañana 930, 50059 Zaragoza, Spain
- AgriFood Institute of Aragon–IA2, CITA-University of Zaragoza, 50013 Zaragoza, Spain
| | - Aurora Díaz
- Department of Plant Sciences, Agrifood Research and Technology Centre of Aragon (CITA), Avd. Montañana 930, 50059 Zaragoza, Spain
- AgriFood Institute of Aragon–IA2, CITA-University of Zaragoza, 50013 Zaragoza, Spain
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Uh YR, Jang CS. Establishing DNA markers to differentiate Agastache rugosa and Pogostemon cablin, which are confusedly used as medicinal herbs, using real-time PCR. Food Sci Biotechnol 2023; 32:239-247. [PMID: 36647523 PMCID: PMC9839904 DOI: 10.1007/s10068-022-01176-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/07/2022] [Accepted: 09/06/2022] [Indexed: 01/19/2023] Open
Abstract
Agastache rugosa and Pogostemon cablin are used as medicinal herbs and aromatic plants and belong to the family Lamiaceae. Despite differences in composition and physicochemical properties, both plants are frequently sold as the medical substance "Kwakhyang" in some Asian countries. Molecular markers were established to distinguish between the two plants using quantitative real-time PCR. Species-specific primers were designed in the nuclear internal transcribed spacer region of ribosomal DNA and in the chloroplast genes matK, rbcL, and rpoB. Six primer sets were tested, the correlation coefficient was higher than 0.99, and the slope was approximately - 3.36 to - 3.58. Efficiency ranged from 90.13 to 98.52%. The developed real-time PCR assay was validated with 14 off-target species, and its reliability was verified through blind testing of 14 commercial products. The assay developed here may help protect consumer rights, and the designed primers can be used to distinguish between the target species. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-022-01176-y.
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Affiliation(s)
- Yo Ram Uh
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, 24341 Republic of Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon, 24341 Republic of Korea
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Chubarov AS, Oscorbin IP, Novikova LM, Filipenko ML, Lomzov AA, Pyshnyi DV. Allele-Specific PCR for PIK3CA Mutation Detection Using Phosphoryl Guanidine Modified Primers. Diagnostics (Basel) 2023; 13:diagnostics13020250. [PMID: 36673060 PMCID: PMC9858071 DOI: 10.3390/diagnostics13020250] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Phosphoryl guanidine (PG) is the novel uncharged modification of internucleotide phosphates of oligonucleotides. Incorporating PG modification into PCR primers leads to increased discrimination between wild-type and mutated DNA, providing extraordinary detection limits in an allele-specific real-time polymerase chain reaction (AS-PCR). Herein, we used PG-modification to improve the specificity of AS primers with unfavorable Pyr/Pur primer's 3'-end mismatch in the template/primer complex. Two mutations of the PIK3CA gene (E542K, E545K) were chosen to validate the advantages of the PG modification. Several primers with PG modifications were synthesized for each mutation and assessed using AS-PCR with the plasmid controls and DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissues. The assay allows the detection of 0.5% of mutated DNA on the wild-type DNA plasmid template's background with good specificity. Compared with ddPCR, the primers with PG-modification demonstrated 100% specificity and 100% sensitivity on the DNA from FFPE with mutation presence higher than 0.5%. Our results indicate the high potential of PG-modified primers for point mutation detection. The main principle of the developed methodology can be used to improve the specificity of primers regardless of sequences.
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Wang Z, Chen J, Song J, Kong L, Wang X, Xu T, Lin S, Dou Y. Plasminogen Activator Inhibitor-1 4G/5G (rs1799889) Polymorphism in Chinese Patients with Diabetes Mellitus and Hypertension. Diabetes Metab Syndr Obes 2023; 16:1133-1147. [PMID: 37122677 PMCID: PMC10132305 DOI: 10.2147/dmso.s410682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
Objective To determine the plasminogen activator inhibitor-1 (PAI-1) 4G/5G (rs1799889) genotype of the subjects in a robust detection method and to explore the association of the PAI-1 4G/5G polymorphism with susceptibility to diabetes mellitus (DM) and hypertension (HTN) as well as clinical characteristics. Methods This study recruited 208 patients (68 patients were diagnosed with DM, 70 patients with HTN and 70 patients with DM combined with HTN) and 132 healthy controls (HC). A subset of the population was selected to evaluate the accuracy of the Real-time PCR (RT-PCR) method for detecting PAI-1 4G/5G polymorphism by using the sequencing method as the gold standard. Furthermore, the association of the PAI-1 4G/5G polymorphism with genetic susceptibility to DM and HTN was explored. Moreover, variations in clinical characteristics among individuals with various PAI-1 genotypes were also analyzed in the DM group, the HTN group and the DM+HTN group. Results There was a high concordance between the RT-PCR method and the sequencing method in determining the PAI-1 4G/5G polymorphism. No association was observed between the PAI-1 4G/5G polymorphism and susceptibility to DM, HTN and DM+HTN, respectively. There were no statistical differences in all study indicators among individuals that carrying various genotypes in the HC group. There were several variations in clinical characteristics among individuals harboring different PAI-1 4G/5G genotypes in the DM group, the HTN group and the DM+HTN group. Conclusion The RT-PCR method can accurately identify the PAI-1 4G/5G genotype in different individuals. The PAI-1 4G/5G polymorphism may not be associated with genetic susceptibility to DM, HTN and DM+HTN, but differences in clinical characteristics among individuals with various genotypes may provide a reference for disease assessment and personalized treatment of patients.
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Affiliation(s)
- Ziran Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Jintu Chen
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, People’s Republic of China
| | - Jingjing Song
- Department of Clinical Laboratory, Anhui Provincial Maternal and Child Health Hospital, Hefei, Anhui, People’s Republic of China
| | - Lingjun Kong
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Xuanzhi Wang
- Department of Medical Laboratory, North Sichuan Medical College, Nanchong, Sichuan, People’s Republic of China
| | - Tengda Xu
- Department of Health Management, Peking Union Medical College Hospital, Beijing, People’s Republic of China
| | - Songbai Lin
- Department of Health Management, Peking Union Medical College Hospital, Beijing, People’s Republic of China
| | - Yaling Dou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Correspondence: Yaling Dou, Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China, Email
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Li S, Wu Y, Zheng H, Li H, Zheng Y, Nan J, Ma J, Nagarajan D, Chang JS. Antibiotics degradation by advanced oxidation process (AOPs): Recent advances in ecotoxicity and antibiotic-resistance genes induction of degradation products. CHEMOSPHERE 2023; 311:136977. [PMID: 36309060 DOI: 10.1016/j.chemosphere.2022.136977] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic contamination could cause serious risks of ecotoxicity and resistance gene induction. Advanced oxidation processes (AOPs) such as Fenton, photocatalysis, activated persulfate, electrochemistry and other AOPs technologies have been proven effective in the degradation of high-risk, refractory organic pollutants such as antibiotics. However, due to the limited mineralization ability, a large number of degradation intermediates will be produced in the oxidation process. The residual or undiscovered ecological risks of degradation products are potential safety hazards and problems necessitating comprehensive studies. In-depth investigations especially on the full assessments of ecotoxicity and resistance genes induction capability of antibiotic degradation products are important issues in reducing the environmental problems of antibiotics. Therefore, this review presents an overview of the current knowledge on the efficiency of different AOPs systems in reducing antibiotics toxicity and antibiotic resistance.
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Affiliation(s)
- Shuo Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China; Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Wu
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Heshan Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Hongbin Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Jun Nan
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Ma
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
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Ma C, Li H, Lu S, Li X, Wang S, Wang W. Ocular Lesions in Brucella Infection: A Review of the Literature. Infect Drug Resist 2022; 15:7601-7617. [PMID: 36579126 PMCID: PMC9791996 DOI: 10.2147/idr.s394497] [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: 10/22/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Ocular lesions due to Brucella infection are uncommon and easily overlooked in clinical management, but must be differentiated from non-infectious eye diseases and treated promptly to protect the patient's vision. We reviewed the relevant literature and identified 47 patients with ocular complications of Brucella infection. Among them, 28 showed ocular neuropathy, 15 presented with uveitis, and four patients displayed other ocular symptoms. Ocular symptoms accompanying Brucella infection require prompt diagnosis and treatment. The main methods of diagnosis are intraocular fluid tests and blood tests. Early diagnosis and treatment with suitable antibiotics are central to protecting the patient's vision. Notably, in terms of mechanism of injury, Brucella infection is chronic and cannot be eliminated by phagocytes, and can cause damage to the eye by inducing autoimmune reactions, antigen-antibody complex production, release of endogenous and exogenous toxins, and bacterial production of septic thrombi in the tissues. In this review, we summarize the ocular symptoms, diagnosis, treatment and prognosis of Brucella infection, and discuss the mechanisms of Brucella in ocular lesions, providing a reference for the diagnosis and treatment of Brucella ocular lesions.
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Affiliation(s)
- Chao Ma
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Haoyu Li
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan, People’s Republic of China,Hunan Clinical Research Centre of Ophthalmic Disease, Changsha, Hunan, People’s Republic of China
| | - Shuwen Lu
- Department of Ophthalmology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, People’s Republic of China
| | - Xian Li
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, England,School of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, the University of Manchester, Manchester, England
| | - Shuai Wang
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Wenzhan Wang
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China,Correspondence: Wenzhan Wang, Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, Henan, 450052, People’s Republic of China, Tel +86 371-66278091, Email
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Artika IM, Dewi YP, Nainggolan IM, Siregar JE, Antonjaya U. Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis. Genes (Basel) 2022; 13:genes13122387. [PMID: 36553654 PMCID: PMC9778061 DOI: 10.3390/genes13122387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.
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Affiliation(s)
- I Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor 16680, Indonesia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
- Correspondence:
| | - Yora Permata Dewi
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Ita Margaretha Nainggolan
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Ungke Antonjaya
- Eijkman Oxford Clinical Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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Chen S, Sun Y, Fan F, Chen S, Zhang Y, Zhang Y, Meng X, Lin JM. Present status of microfluidic PCR chip in nucleic acid detection and future perspective. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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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McGuire CC, Robert JR. Developmental exposure to thyroid disrupting chemical mixtures alters metamorphosis and post-metamorphic thymocyte differentiation. Curr Res Toxicol 2022; 3:100094. [PMID: 36407672 PMCID: PMC9672424 DOI: 10.1016/j.crtox.2022.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
While there is some evidence to suggest that disruption of the thyroid hormone (TH)-axis during perinatal development may weaken T cell immunity later in life, data are currently lacking on whether environmentally relevant thyroid disrupting chemicals (TDCs) can induce similar outcomes. To fill this gap in knowledge, X. laevis tadpoles were exposed to an environmentally relevant mixture of TDCs, either during early tadpole development, or immediately before and during metamorphosis, to assess T cell differentiation and anti-viral immune response against FV3 infection after metamorphosis. Extending our previous study showing a delay in metamorphosis completion, here we report that TDC exposure prior to metamorphosis reduced the frequency of surface MHC-II + splenic lymphocytes and weakened some aspects of the anti-viral immune response. TDC exposure during metamorphosis slowed post-metamorphic migration of the thymus reduced the renewal of cortical thymocytes and splenic CD8 + T cells. The results indicate that TDC exposure during perinatal development may perturb the formation of T cell immunity later in life.
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Affiliation(s)
- Connor C. McGuire
- University of Rochester Department of Microbiology and Immunology, 601 Elmwood Avenue, Rochester, NY 14642, 2USA
- University of Rochester Department Environmental Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Jacques R. Robert
- University of Rochester Department of Microbiology and Immunology, 601 Elmwood Avenue, Rochester, NY 14642, 2USA
- University of Rochester Department Environmental Medicine, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Koo SBN, Kim YS, Park CY, Lee DJ. Compact Camera Fluorescence Detector for Parallel-Light Lens-Based Real-Time PCR System. SENSORS (BASEL, SWITZERLAND) 2022; 22:8575. [PMID: 36366271 PMCID: PMC9654867 DOI: 10.3390/s22218575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The polymerase chain reaction is an important technique in biological research. However, it is time consuming and has a number of disadvantages. Therefore, real-time PCR technology that can be used in real-time monitoring has emerged, and many studies are being conducted regarding its use. Real-time PCR requires many optical components and imaging devices such as expensive, high-performance cameras. Therefore, its cost and assembly process are limitations to its use. Currently, due to the development of smart camera devices, small, inexpensive cameras and various lenses are being developed. In this paper, we present a Compact Camera Fluorescence Detector for use in parallel-light lens-based real-time PCR devices. The proposed system has a simple optical structure, the system cost can be reduced, and the size can be miniaturized. This system only incorporates Fresnel lenses without additional optics in order for the same field of view to be achieved for 25 tubes. In the center of the Fresnel lens, one LED and a complementary metal-oxide semiconductor camera were placed in directions that were as similar as possible. In addition, to achieve the accurate analysis of the results, image processing was used to correct them. As a result of an experiment using a reference fluorescent substance and double-distilled water, it was confirmed that stable fluorescence detection was possible.
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Affiliation(s)
- Seul-Bit-Na Koo
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Yu-Seop Kim
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Chan-Young Park
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
| | - Deuk-Ju Lee
- School of Software, Hallym University, Chuncheon-si 24252, Korea
- Bio-IT Research Center, Hallym University, Chuncheon-si 24252, Korea
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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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Fan J, Wei X, Dong H, Zhang Y, Zhou Y, Xu M, Xiao G. Advancement in Analytical Techniques for Determining the Activity of β-Site Amyloid Precursor Protein Cleaving Enzyme 1. Crit Rev Anal Chem 2022:1-13. [PMID: 36227582 DOI: 10.1080/10408347.2022.2132812] [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: 01/18/2023]
Abstract
Alzheimer's disease (AD) is a degenerative disease of the central nervous system. The pathogenesis is still not fully clear. One of the main histopathological manifestations is senile plaques formed by β-amyloid (Aβ) accumulation. Aβ is generated from the sequential proteolysis of amyloid precursor protein (APP) by β-secretase [i.e. β-site APP cleaving enzyme 1 (BACE1)] and γ-secretase, with a rate-limiting step controlled by BACE1 activity. Therefore, inhibiting BACE1 activity has become a potential therapeutic strategy for AD. The development of reliable detection methods for BACE1 activity plays an important role in early diagnosis of AD and evaluation of the therapeutic effect of new drugs for AD. This article has reviewed the recent advances in BACE1 activity detection techniques. The challenges of applying these analysis techniques to early clinical diagnosis of AD and development trends of the detection techniques have been prospected.
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Affiliation(s)
- Jie Fan
- College of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, China
| | - Xiuhua Wei
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, China
| | - Hui Dong
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, China
| | - Yintang Zhang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, China
| | - Yanli Zhou
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, China
| | - Guoqing Xiao
- College of Materials Science and Engineering, Xi'an University of Architecture and Technology, Xi'an, China
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Soga K, Nakamura K, Egi T, Narushima J, Yoshiba S, Kishine M, Mano J, Kitta K, Takabatake R, Shibata N, Kondo K. Development and Validation of a New Robust Detection Method for Low-Content DNA Using ΔΔCq-Based Real-Time PCR with Optimized Standard Plasmids as a Control Sample. Anal Chem 2022; 94:14475-14483. [PMID: 36205585 PMCID: PMC9583069 DOI: 10.1021/acs.analchem.2c03680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Real-time polymerase
chain reaction (PCR) is the gold standard
for DNA detection in many fields, including food analysis. However,
robust detection using a real-time PCR for low-content DNA samples
remains challenging. In this study, we developed a robust real-time
PCR method for low-content DNA using genetically modified (GM) maize
at concentrations near the limit of detection (LOD) as a model. We
evaluated the LOD of real-time PCR targeting two common GM maize sequences
(P35S and TNOS) using GM maize event MON863 containing a copy of P35S
and TNOS. The interlaboratory study revealed that the LOD differed
among laboratories partly because DNA input amounts were variable
depending on measurements of DNA concentrations. To minimize this
variability for low-content DNA samples, we developed ΔΔCq-based
real-time PCR. In this study, ΔCq and ΔΔCq are as
follows: ΔCq = Cq (P35S or TNOS) – Cq (SSIIb; maize endogenous
gene), ΔΔCq = ΔCq (analytical sample) – ΔCq
(control sample at concentrations near the LOD). The presence of GM
maize was determined based on ΔΔCq values. In addition,
we used optimized standard plasmids containing SSIIb, P35S, and TNOS
with ΔCq equal to the MON863 genomic DNA (gDNA) at concentrations
near the LOD as a control sample. A validation study indicated that
at least 0.2% MON863 gDNA could be robustly detected. Using several
GM maize certified reference materials, we have demonstrated that
this method was practical for detecting low-content GM crops and thus
for validating GM food labeling. With appropriate standards, this
method would be applicable in many fields, not just food.
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Affiliation(s)
- Keisuke Soga
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
| | - Kosuke Nakamura
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
| | - Tomohiro Egi
- Food and Agricultural Materials Inspection Center: Saitama Shintoshin National Government Building, Kensato Building 2-1, Shintoshin, Chuo-ku, Saitama-Shi330-9731, Saitama, Japan
| | - Jumpei Narushima
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
| | - Satoko Yoshiba
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
| | - Masahiro Kishine
- National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba305-8642, Ibaraki, Japan
| | - Junichi Mano
- National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba305-8642, Ibaraki, Japan
| | - Kazumi Kitta
- National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba305-8642, Ibaraki, Japan
| | - Reona Takabatake
- National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba305-8642, Ibaraki, Japan
| | - Norihito Shibata
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi210-9501, Kanagawa, Japan
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Li M, Ge S, Zhang J, Wu S, Wu H, Zhuang LL. Mechanism and performance of algal pond assisted constructed wetlands for wastewater polishing and nutrient recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156667. [PMID: 35705127 DOI: 10.1016/j.scitotenv.2022.156667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/30/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
The limitation of oxygen and carbon source restricted the TN removal in constructed wetland (CW). Algal pond (AP) could produce oxygen and fix CO2 to improve C/N ratio in water. Therefore, an AP-CW system was established under laboratory conditions to deeply explore the effect of nutrient load distribution and microalgae addition in CWs on pollutant removal. This study showed that AP-CW could remove 49.7% TN and 90.0% TP with no carbon addition in CWs. The significant removal of NH4-N by AP advanced the location of denitrification in CWs. To enhance TN removal, different dosage of microalgae were intermittently added at 20 and 10 cm respectively below the inlet of the vertical flow CW1 and CW2, where the rest NH4-N has been almost oxidized into nitrate. The addition of microalgae influenced the microflora and effluent quality. Microalgae dosage in denitrification area significantly increased the absolute abundance of Σnir. The best TN removal of AP-CW could reach 91.3% when 8 g (dry weight) microalgae was added. However, unlike previous knowledge, microalgae as an organic carbon source would also release N and P during decomposition, leading to increased nutrients in the effluent. The optimal dosage of microalgae was 1 g/5 d in this study. The position and amount of microalgae addition in CWs should be adjusted based on water property and element flow to achieve the best pollutant removal and biomass harvest.
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Affiliation(s)
- Mengting Li
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Shuhan Ge
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Jian Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China; Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Shubiao Wu
- Department of Agroecology, Aarhus University, Blichers All'e 20, 8830 Tjele, Denmark
| | - Haiming Wu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China
| | - Lin-Lan Zhuang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China.
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Chávez-Luzanía RA, Montoya-Martínez AC, Parra-Cota FI, de Los Santos-Villalobos S. Pangenomes-identified singletons for designing specific primers to identify bacterial strains in a plant growth-promoting consortium. Mol Biol Rep 2022; 49:10489-10498. [PMID: 36125674 DOI: 10.1007/s11033-022-07927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND The use of plant growth-promoting microorganisms represents a sustainable way to increase agricultural yields and plant health. Thus, the identification and tracking of these microorganisms are determinants for validating their positive effects on crops. Pangenomes allow the identification of singletons that can be used to design specific primers for the detection of the studied strains. OBJECTIVE This study aimed to establish a strategy based on the use of whole-genome sequencing and pangenomes for designing and validating primer sets for detecting Bacillus cabrialesii TE3T, Priestia megaterium TRQ8, and Bacillus paralicheniformis TRQ65, a promising beneficial bacterial consortium for wheat. METHODS AND RESULTS The identification of singletons of TE3T, TRQ8, and TRQ65 was performed by pangenomes using the Kbase platform and subsequently analyzed using BLAST®. The identified DNA regions were used for primer design in AlleleID version 7. Primers were validated by multiplex PCR using pure template DNA from each studied strain, combinations of two or three DNA from these strains, and DNA from agricultural soil samples enriched (and not) with the bacterial consortium. Here, we report the first design of primers capable of detecting and identifying the beneficial strains TE3T, TRQ8, and TRQ65. CONCLUSIONS The use of pangenomes allowed the distinction of unique sequences that enables the design of primers for specific identification of the studied bacterial strains. This strategy can be widely used for the design of primer sets to detect other strains of interest for combating biopiracy, and commercial protection of biological products, among other applications.
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Affiliation(s)
| | | | - Fannie Isela Parra-Cota
- Campo Experimental Norman E. Borlaug, Instituto Nacional de Investigaciones forestales, Agrícolas y Pecuarias, Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, SON, México
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Analysis of Pathogenic Vibrio Contamination in Marine Products along China Based on Fluorescence Quantitative PCR. J FOOD QUALITY 2022. [DOI: 10.1155/2022/9572064] [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
At present, aquatic product pollution has become the main root of frequent food safety problems and causes economic losses. Vibrio is one of the main pathogens causing foodborne diseases. In this study, in order to uncover the pollution status of pathogenic Vibrio in the marine products of China, a total of 646 aquatic products were collected and analyzed from 10 coastal cities in China. Five kinds of pathogenic Vibrio were separated from these samples and monitored to explore the relationship between pollution and the pathogen. Real-time fluorescence quantitative PCR was adopted to detect foodborne Vibrio quantitatively in marine aquatic products. Aquatic pathogenic Vibrio was collected in different regions, different types of aquatic products, and different sampling places, and the difference in detection rate was statistically significant through statistical analysis. This study made a frame for the pollution degree of pathogenic Vibrio in marine products in China and established the dominant flora of pathogenic Vibrio in different types of aquatic products, which provides a theoretical basis for food safety supervision departments to take targeted prevention and control measures.
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Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [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: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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Hundreds-Dollar-Level Multiplex Integrated RT-qPCR Quantitative System for Field Detection. BIOSENSORS 2022; 12:bios12090706. [PMID: 36140090 PMCID: PMC9496240 DOI: 10.3390/bios12090706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.
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47
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Jin Z, Pan Z, Wang Z, Kong L, Zhong M, Yang Y, Dou Y, Sun JL. CYSLTR1 rs320995 (T927C) and GSDMB rs7216389 (G1199A) Gene Polymorphisms in Asthma and Allergic Rhinitis: A Proof-of-Concept Study. J Asthma Allergy 2022; 15:1105-1113. [PMID: 36034974 PMCID: PMC9400812 DOI: 10.2147/jaa.s371120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background and Objective Asthma and allergic rhinitis have been reported to be strongly associated with genetic factors. The aim of this study was to evaluate the accuracy of the TaqMan-MGB (minor groove binder) qPCR method for detecting CYSLTR1 rs320995 (T927C) and GSDMB rs7216389 (G1199A) gene polymorphisms as well as to explore the association of CYSLTR1 rs320995 and GSDMB rs7216389 polymorphisms with genetic susceptibility of Chinese patients with asthma and allergic rhinitis. Methods In this study, 310 asthmatic patients and 60 healthy individuals were recruited in Peking Union Medical College Hospital. The CYSLTR1 rs320995 (T927C) and GSDMB rs7216389 (G1199A) gene polymorphisms in each group were analyzed by TaqMan-MGB qPCR and DNA sequencing which was regarded as the gold standard. After the validation of this method, additional 71 patients with allergic rhinitis and 72 patients with asthma combined with allergic rhinitis were selected and tested by using TaqMan-MGB qPCR. Results The TaqMan-MGB qPCR results were fully consistent with DNA sequencing results (Kappa = 1, P<0.001). In addition, the results of the TaqMan-MGB qPCR assay were not affected by bilirubin and lipids. We found differential distribution of CYSLTR1 rs320995 genotypes in female patients with asthma combined with allergic rhinitis (χ 2=6.172, P=0.046, statistical power = 0.591). Specifically, the TT genotype is more frequent in women suffering from asthma with allergic rhinitis, whereas the TC genotype is more prevalent in healthy women. However, no such associations were observed in the GSDMB rs7216389 polymorphism. Conclusion We have established a reliable TaqMan-MGB qPCR method for the detection of CYSLTR1 rs320995 and GSDMB rs7216389 polymorphisms. Moreover, the CYSLTR1 rs320995 polymorphism may be associated with genetic susceptibility of Chinese female patients with asthma and allergic rhinitis. Multicenter studies with larger sample sizes are required in the future.
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Affiliation(s)
- Zhengshuo Jin
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China.,Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Zhouxian Pan
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Ziran Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Lingjun Kong
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Min Zhong
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yongshi Yang
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Yaling Dou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Jin-Lyu Sun
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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Mafra I, Honrado M, Amaral JS. Animal Species Authentication in Dairy Products. Foods 2022; 11:foods11081124. [PMID: 35454711 PMCID: PMC9027536 DOI: 10.3390/foods11081124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Milk is one of the most important nutritious foods, widely consumed worldwide, either in its natural form or via dairy products. Currently, several economic, health and ethical issues emphasize the need for a more frequent and rigorous quality control of dairy products and the importance of detecting adulterations in these products. For this reason, several conventional and advanced techniques have been proposed, aiming at detecting and quantifying eventual adulterations, preferentially in a rapid, cost-effective, easy to implement, sensitive and specific way. They have relied mostly on electrophoretic, chromatographic and immunoenzymatic techniques. More recently, mass spectrometry, spectroscopic methods (near infrared (NIR), mid infrared (MIR), nuclear magnetic resonance (NMR) and front face fluorescence coupled to chemometrics), DNA analysis (real-time PCR, high-resolution melting analysis, next generation sequencing and droplet digital PCR) and biosensors have been advanced as innovative tools for dairy product authentication. Milk substitution from high-valued species with lower-cost bovine milk is one of the most frequent adulteration practices. Therefore, this review intends to describe the most relevant developments regarding the current and advanced analytical methodologies applied to species authentication of milk and dairy products.
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Affiliation(s)
- Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
- Correspondence: (I.M.); (J.S.A.)
| | - Mónica Honrado
- CIMO, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal;
| | - Joana S. Amaral
- CIMO, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal;
- Correspondence: (I.M.); (J.S.A.)
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50
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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