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Siddiqui HB, Golcez T, Çelik M, Sevgin B, Çoban M, Süder İ, Kaya Ö, Özören N, Pekkan K. Modulation of mechanosensitive genes during embryonic aortic arch development. Dev Dyn 2024. [PMID: 39096177 DOI: 10.1002/dvdy.728] [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: 12/21/2023] [Revised: 05/30/2024] [Accepted: 07/17/2024] [Indexed: 08/05/2024] Open
Abstract
BACKGROUND Early embryonic aortic arches (AA) are a dynamic vascular structures that are in the process of shaping into the great arteries of cardiovascular system. Previously, a time-lapsed mechanosensitive gene expression map was established for AA subject to altered mechanical loads in the avian embryo. To validate this map, we investigated effects on vascular microstructure and material properties following the perturbation of key genes using an in-house microvascular gene knockdown system. RESULTS All siRNA vectors show a decrease in the expression intensity of desired genes with no significant differences between vectors. In TGFβ3 knockdowns, we found a reduction in expression intensities of TGFβ3 (≤76%) and its downstream targets such as ELN (≤99.6%), Fbn1 (≤60%), COL1 (≤52%) and COL3 (≤86%) and an increase of diameter in the left AA (23%). MMP2 knockdown also reduced expression levels in MMP2 (≤30%) and a 6-fold increase in its downstream target COL3 with a decrease in stiffness of the AA wall and an increase in the diameter of the AA (55%). These in vivo measurements were confirmed using immunohistochemistry, western blotting and a computational growth model of the vascular extracellular matrix (ECM). CONCLUSIONS Localized spatial genetic modification of the aortic arch region governs the vascular phenotype and ECM composition of the embryo and can be integrated with mechanically-induced congenital heart disease models.
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Affiliation(s)
| | - Tansu Golcez
- Biomedical Sciences and Engineering Program, Koç University, Istanbul, Turkey
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
| | - Merve Çelik
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
| | - Börteçine Sevgin
- Biomedical Sciences and Engineering Program, Koç University, Istanbul, Turkey
| | - Mervenur Çoban
- Biomedical Sciences and Engineering Program, Koç University, Istanbul, Turkey
| | - İlke Süder
- Department of Molecular Biology and Genetics, Bogazici University, Turkey
| | - Özen Kaya
- Department of Molecular Biology and Genetics, Bogazici University, Turkey
- Department of Mechanical Engineering, Koç University, Istanbul, Turkey
| | - Nesrin Özören
- Department of Molecular Biology and Genetics, Bogazici University, Turkey
| | - Kerem Pekkan
- Biomedical Sciences and Engineering Program, Koç University, Istanbul, Turkey
- Department of Mechanical Engineering, Koç University, Istanbul, Turkey
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Spurlock N, Gabella WE, Nelson DJ, Evans DT, Pask ME, Schmitz JE, Haselton FR. Implementing L-DNA analogs as mirrors of PCR reactant hybridization state: theoretical and practical guidelines for PCR cycle control. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2840-2849. [PMID: 38567817 PMCID: PMC11079981 DOI: 10.1039/d4ay00083h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/22/2024] [Indexed: 05/12/2024]
Abstract
In previous reports, we described a PCR cycle control approach in which the hybridization state of optically labeled L-DNA enantiomers of the D-DNA primers and targets determined when the thermal cycle was switched from cooling to heating and heating to cooling. A consequence of this approach is that it also "adapts" the cycling conditions to compensate for factors that affect the hybridization kinetics of primers and targets. It assumes, however, that the hybridization state of the labeled L-DNA analogs accurately reflects the hybridization state of the D-DNA primers and targets. In this report, the Van't Hoff equation is applied to determine the L-DNA concentration and ratio of L-DNA strands required by this assumption. Simultaneous fluorescence and temperature measurements were taken during L-DNA controlled cycling, and the optical and thermal switch points compared as a function of both total L-DNA concentration and ratio of strands. Based on the Van't Hoff relationship and these experimental results, L-DNA best mirrors the hybridization of PCR primers and targets when total L-DNA concentration is set equal to the initial concentration of the D-DNA primer of interest. In terms of strand ratios, L-DNA hybridization behavior most closely matches the behavior of their D-DNA counterparts throughout the reaction when one of the L-DNA strands is far in excess of the other. The L-DNA control algorithm was then applied to the practical case of the SARS-CoV-2 N2 reaction, which has been shown to fail or have a delayed Cq when PCR was performed without nucleic acid extraction. PCR Cq values for simulated "unextracted" PCR samples in a nasopharyngeal background and in an NaCl concentration similar to that of viral transport media were determined using either the L-DNA control algorithm (N = 6) or preset cycling conditions (N = 3) and compared to water background controls run in parallel. For preset cycling conditions, the presence of nasopharyngeal background or a high salt background concentration significantly increased Cq, but the L-DNA control algorithm had no significant delay. This suggests that a carefully designed L-DNA-based control algorithm "adapts" the cycling conditions to compensate for hybridization errors of the PCR D-DNA reactants that produce false negatives.
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Affiliation(s)
- Nicholas Spurlock
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - William E Gabella
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, USA
| | - Dalton J Nelson
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - David T Evans
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Megan E Pask
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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Vasiljevic V, Obradovic J, Jurisic V. Significance of EGFR investigation in odontogenic keratocyst: a narrative review. Mol Biol Rep 2023; 50:7089-7098. [PMID: 37314601 DOI: 10.1007/s11033-023-08582-3] [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: 04/10/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND The recent classification of odontogenic keratocysts (OKSs) recognized them as benign neoplasms, although previous findings have revealed their aggressive nature. Immunohistochemical and molecular analyses have investigated OKSs, but the role of epidermal growth factor receptor (EGFR) has not been fully investigated, despite the importance of this oncogene in the process of carcinogenesis in tumors of epithelial origin. The EGFR protein is usually overexpressed, and the EGFR gene is mutated or amplified. AIMS OF STUDY This brief review aims to emphasize the importance of EGFR detection in these types of cysts. METHODS AND RESULTS It was revealed that the majority of the studies examined EGFR protein expression using immunohistochemical methods; however, considering EGFR gene variants, mutations were less explored in the previous period from 1992 to 2023. Although EGFR gene polymorphisms are clinically important, they were not identified in the present study. CONCLUSIONS In light of the current significance of EGFR variants, it would be beneficial to examine them in odontogenic lesions. This would enable resolving of discrepancies about their nature, and potentially enhance classifications OKCs in the future.
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Affiliation(s)
| | - Jasmina Obradovic
- Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, 34000, Kragujevac, Republic of Serbia
| | - Vladimir Jurisic
- Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovića 69, 34000, Kragujevac, Republic of Serbia.
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Memon A, Khidri FF, Waryah YM, Nigar R, Bhinder MA, Shaikh AM, Shaikh H, Waryah AM. Association of MSX1 Gene Variants with Nonsyndromic Cleft Lip and/or Palate in the Pakistani Population. Cleft Palate Craniofac J 2023:10556656231185218. [PMID: 37431261 DOI: 10.1177/10556656231185218] [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: 07/12/2023] Open
Abstract
OBJECTIVES This study investigated the association of MSX1 gene variants rs3821949 and rs12532 with nonsyndromic cleft lip and/or palate (NSCL/P) in the Pakistani population. DESIGN Comparative cross-sectional study.Setting: Multicenter of CL/P malformation.Patients/Participants: Unrelated Non-Syndromic cleft Lip/Palate patients and healthy controls were enrolled. METHODS One hundred (n = 100) subjects with NSCL/P and n = 50 unrelated healthy controls were enrolled in a multicenter comparative cross-sectional study. A tetra amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was performed to analyze MSXI gene single nucleotide variants (SNVs). RESULTS Among 100 NSCL/P subjects, the majority were males (56%; male: female = 1.27: 1). Most of the cases (74%) had cleft lip and palate (CLP) compared to isolated clefts. Genotyping of MSX1 gene variant rs3821949 showed an increased risk for NSCL/P in various genetic models (P < 0.0001), and the A allele exhibited a more than 4-fold increased risk among cases (OR = 4.22: 95% CI = 2.16-8.22; P < 0.0001). Our investigation found no significant difference between the rs12532 variation and NSCL/P. CONCLUSION Our study findings suggest that MSX1 gene variants may increase predisposition to NSCL/P in the Pakistani population. Further studies comprising large samples are required to identify the genetic aetiology of NSCL/P among our people.
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Affiliation(s)
- Anny Memon
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Oral Biology, Faculty of Dentistry, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Feriha Fatima Khidri
- Department of Biochemistry, Bilawal Medical College, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Yar Muhammad Waryah
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
- Department of Molecular Biology and Genetics, Sindh Institute of Ophthalmology and Visual Sciences, Hyderabad, Pakistan
| | - Roohi Nigar
- Department of Gynecology and Obstetrics, Bilawal Medical College, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics, University of Health Sciences, Lahore, Pakistan
| | | | - Hina Shaikh
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Department of Molecular Biology and Genetics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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Analyses of P16 INK4a gene promoter methylation relative to molecular, demographic and clinical parameters characteristics in non-small cell lung cancer patients: A pilot study. Mol Biol Rep 2023; 50:971-979. [PMID: 36378420 DOI: 10.1007/s11033-022-07982-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND The aim of this study was to examine the methylation status of p16INK4a promoter region in non small cell lung cancer (NSCLC) patients and their associations with single nucleotide polymorphisms (SNPs) of the epidermal growth factor receptor (EGFR) gene, as well as with demographic or clinical characteristics. METHODS Formalin-fixed and paraffin-embedded (FFPE) DNA samples extracted from 22 NSCLC patients were analyzed with methylation-specific polymerase chain reaction (PCR) method to obtain promoter methylation profile. The same cohort was genotyped for - 216G > T, -191 C > A, and 181,946 C > T EGFR SNPs. RESULTS There was a significant association between methylated p16INK4a in patients prior therapy (p = 0.017) since a significantly higher frequency of methylated p16INK4a was detected in these patients (40.9%) in comparison to frequency in patients after therapy (31.8%). Also, a higher frequency of methylated p16INK4a was detected among patients with leucopenia (p = 0.056). No associations were observed between the methylation status of the p16INK4a promoter region and EGFR SNPs or other clinical and demographic data in this cohort. CONCLUSION High frequency of methylation of the p16INK4a gene promoter was observed in NSCLC patients prior therapy and with leucopenia that can indicate their significance related to advanced clinical stage.
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Lafrance R, Valdez-Torres JB, Villicaña C, García-Estrada RS, Esparza-Araiza MJ, León-Félix J. Response Surface Methodology for Optimization of Multiplex-PCR Protocols for Detection of TYLCV, TSWV and Fol Molecular Markers: Analytical Performance Evaluation. Genes (Basel) 2023; 14:genes14020337. [PMID: 36833262 PMCID: PMC9956084 DOI: 10.3390/genes14020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/17/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Molecular markers linked to disease resistance genes which affect economically important crops are of great interest. In the case of tomato, a major focus on resistance breeding to multiple fungal and viral pathogens such as Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV) and Fusarium oxysporum f. sp. lycopersici (Fol), have led to the introgression of several resistance genes; therefore, molecular markers have become important in molecular-assisted selection (MAS) of tomato varieties resistant to those pathogens. However, assays that allow simultaneous evaluation of resistant genotypes, such as multiplex PCR, need to be optimized and evaluated to demonstrate their analytical performance, as many factors can affect them. This work aimed to generate multiplex PCR protocols for the joint detection of the molecular markers associated with pathogen resistance genes in tomato plants that are sensitive, specific and repeatable. For the optimization a central composite design of a response surface methodology (RSM-CCD) was used. For analytical performance evaluation, specificity/selectivity and sensibility (limit of detection and dynamic range) were analyzed. Two protocols were optimized: the first one with a desirability of 1.00, contained two markers (At-2 and P7-43) linked to I- and I-3-resistant genes. The second one with a desirability of 0.99, contained markers (SSR-67, SW5 and P6-25) linked to I-, Sw-5-, and Ty-3-resistant genes. For protocol 1, all the commercial hybrids (7/7) were resistant to Fol, and for protocol 2, two hybrids were resistant to Fol, one to TSWV and one to TYLCV with good analytical performance. In both protocols, the varieties considered susceptible to the pathogens, no-amplicon or susceptible amplicons, were observed. The optimized multiplex PCR protocols showed dynamic ranges from 5.97 up to 161.3 ng DNA. The limit of detection was 17.92 ng and 53.76 ng DNA for protocols 1 and 2, respectively, giving 100% positive results in the test replicates. This method allowed to develop optimized multiplex PCR protocols with few assays which translates into less time and resources, without sacrificing method performance.
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Affiliation(s)
- Richecarde Lafrance
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán 80110, Sinaloa, Mexico
| | | | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A.C., Culiacán 80110, Sinaloa, Mexico
| | | | - Mayra Janeth Esparza-Araiza
- Centro de Innovación y Transferencia de Tecnología Agropecuaria de Sinaloa- Fundación Produce Sinaloa, A.C., Aguaruto 80308, Sinaloa, Mexico
| | - Josefina León-Félix
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán 80110, Sinaloa, Mexico
- Correspondence:
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Chung CZ, Söll D, Krahn N. Using selenocysteine-specific reporters to screen for efficient tRNA Sec variants. Methods Enzymol 2022; 662:63-93. [PMID: 35101219 DOI: 10.1016/bs.mie.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The unique properties of selenocysteine (Sec) have generated an interest in the scientific community to site-specifically incorporate Sec into a protein of choice. Current technologies have rewired the natural Sec-specific translation factor-dependent selenoprotein biosynthesis pathway by harnessing the canonical elongation factor (EF-Tu) to simplify the requirements for Sec incorporation in Escherichia coli. This strategy is versatile and can be applied to Sec incorporation at any position in a protein of interest. However, selenoprotein production is still limited by yield and serine misincorporation. This protocol outlines a method in E. coli to design and optimize tRNA libraries which can be selected and screened for by the use of Sec-specific intein-based reporters. This provides a fast and simple way to engineer tRNAs with enhanced Sec-incorporation ability.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States.
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
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9
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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Dhatterwal P, Mehrotra S, Mehrotra R. Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana. Methods Mol Biol 2022; 2392:115-123. [PMID: 34773619 DOI: 10.1007/978-1-0716-1799-1_9] [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: 06/13/2023]
Abstract
The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India.
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Lafrance R, Villicaña C, Valdéz-Torres JB, Martínez-Montoya H, Castillo-Ruiz O, Alemán-Castillo SE, Esparza-Araiza MJ, León-Félix J. Optimization of PCR-based TYLCV molecular markers by response surface methodology. Gene 2021; 785:145606. [PMID: 33771604 DOI: 10.1016/j.gene.2021.145606] [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: 08/29/2020] [Revised: 02/24/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most economically important vegetables worldwide. However, its production is affected by the tomato yellow leaf curl virus (TYLCV), causing the greatest devastation in the crop. One strategy to cope with TYLCV implies the use of resistant varieties, whose development can be accelerated by molecular markers. The aim of this study was to optimize endpoint PCR protocols for the detection of the molecular markers TG178, TG105A and P6-25, linked to Ty-1, Ty-2 and Ty-3 resistance genes, respectively, through a response surface methodology (RSM) using a central composite design (CCD) for four factors (temperature of annealing (Ta), DNA amount, MgCl2 and primer concentrations). Applicability, the limit of detection and dynamic range were also analyzed. The optimized PCR conditions were: for TG178: Ta = 60 °C, 90 ng DNA, 3.36 mM MgCl2 and 0.13 µM primers; for TG105A: Ta = 54.4 °C, 10 ng DNA, 1.5 mM MgCl2 and 0.9 µM primers; for P6-25, Ta = 52.5 °C, 50 ng DNA, 2.5 mM MgCl2 and 0.5 µM primers. Dynamic ranges varied from 0.42 to 103.3 ng of DNA, while the limit of detection was 3.82, 0.42 and 11.47 ng of DNA for the TG178, TG105A and P6-25 molecular makers respectively and was 100% positive in replicates. CCD allowed the optimization of PCR protocols for molecular markers, which may further apply in identifying TYLCV resistant tomato lines.
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Affiliation(s)
- Richecarde Lafrance
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán, Sinaloa, Mexico; Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A.C., Culiacán, Sinaloa, Mexico
| | | | - Humberto Martínez-Montoya
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | - Octelina Castillo-Ruiz
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | | | - Mayra Janeth Esparza-Araiza
- Centro de Innovación y Transferencia de Tecnología de Sinaloa- Fundacion Produce Sinaloa A.C. Aguaruto, Sinaloa, México
| | - Josefina León-Félix
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán, Sinaloa, Mexico.
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Yao M, Zhang X, Gao Y, Song S, Xu D, Yan L. Development and application of multiplex PCR method for simultaneous detection of seven viruses in ducks. BMC Vet Res 2019; 15:103. [PMID: 30935399 PMCID: PMC6444421 DOI: 10.1186/s12917-019-1820-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/25/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Major viruses, including duck-origin avian influenza virus, duck-origin Newcastle disease virus, novel duck parvovirus, duck hepatitis A virus, duck Tembusu virus, fowl adenovirus, and duck enteritis virus, pose great harm to ducks and cause enormous economic losses to duck industry. This study aims to establish a multiplex polymerase chain reaction (m-PCR) method for simultaneous detection of these seven viruses. RESULTS Specific primers were designed and synthesized according to the conserved region of seven viral gene sequences. Then, seven recombinant plasmids, as the positive controls, were reconstructed in this study. Within the study, D-optimal design was adopted to optimize PCR parameters. The optimum parameters for m-PCR were annealing temperature at 57 °C, Mg2+ concentration at 4 mM, Taq DNA polymerase concentration at 0.05 U/μL, and dNTP concentration at 0.32 mM. With these optimal parameters, the m-PCR method produced neither cross-reactions among these seven viruses nor nonspecific reactions with other common waterfowl pathogens. The detection limit of m-PCR for each virus was 1 × 104 viral DNA copies/μL. In addition, the m-PCR method could detect a combination of several random viruses in co-infection analysis. Finally, the m-PCR method was successfully applied to clinical samples, and the detection results were consistent with uniplex PCR. CONCLUSION Given its rapidity, specificity, sensitivity, and convenience, the established m-PCR method is feasible for simultaneous detection of seven duck-infecting viruses and can be applied to clinical diagnosis of viral infection in ducks.
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Affiliation(s)
- Ming Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiyu Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunfei Gao
- Nanjing Tianbang Bio-Industry co., LTD, Nanjing, 211102, China
| | - Suquan Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danning Xu
- Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Zhongkai University of Agricultural and Engineering, Guangzhou, 510225, China.
| | - Liping Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Detection Center of Terrestrial Wildlife Disease, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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13
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Pullulan reduces the non-specific amplification of loop-mediated isothermal amplification (LAMP). Anal Bioanal Chem 2019; 411:1211-1218. [DOI: 10.1007/s00216-018-1552-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/23/2018] [Accepted: 12/14/2018] [Indexed: 01/12/2023]
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14
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Epidermal Growth Factor Receptor Gene in Non-Small-Cell Lung Cancer: The Importance of Promoter Polymorphism Investigation. Anal Cell Pathol (Amst) 2018; 2018:6192187. [PMID: 30406002 PMCID: PMC6204164 DOI: 10.1155/2018/6192187] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/05/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Recently, epidermal growth factor receptor (EGFR) was a key molecule in investigation of lung cancer, and it was a target for a new therapeutic strategy, based on molecular analyses. In this review, we have summarized some issues considering the role of EGFR in lung cancer, its coding gene, and its promoter gene polymorphisms (SNPs) -216G/T and -191C/A in non-small-cell lung cancer (NSCLC). The position of the SNPs indicates their significant role in EGFR regulation. The accumulation of knowledge regarding SNPs lately suggests their significant and important role in the onset of carcinogenesis, the prediction of the onset of metastases, the response to therapy with TKI inhibitors, and the onset of toxic effects of the applied therapy. Based on this, we suggest further studies of the relationship of clinical significance to SNPs in patients with lung tumors.
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Dhatterwal P, Mehrotra S, Mehrotra R. Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana. BMC Res Notes 2017; 10:638. [PMID: 29183338 PMCID: PMC5706289 DOI: 10.1186/s13104-017-2982-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/22/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. RESULT Results show that successful amplification can be achieved by performing a 2-step PCR at a lower extension temperature of 65 °C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0 mM. The results also suggest that the DNA concentration of about 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
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White SJ, Laros JF, Bakker E, Cambon‐Thomsen A, Eden M, Leonard S, Lochmüller H, Matthijs G, Mattocks C, Patton S, Payne K, Scheffer H, Souche E, Thomassen E, Thompson R, Traeger‐Synodinos J, Vooren S, Janssen B, den Dunnen JT. Critical points for an accurate human genome analysis. Hum Mutat 2017; 38:912-921. [DOI: 10.1002/humu.23238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/13/2017] [Accepted: 04/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Stefan J. White
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Jeroen F.J. Laros
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
- GenomeScan Leiden The Netherlands
| | - Egbert Bakker
- Clinical GeneticsLeiden University Medical Center The Netherlands
| | - Anne Cambon‐Thomsen
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Martin Eden
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | - Samantha Leonard
- Epidemiology and Public Health Analyses, Inserm and Université Toulouse III Paul Sabatier Toulouse UMR 1027 France
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | - Simon Patton
- Central Manchester University Hospitals Foundation Trust, EMQN Manchester UK
| | - Katherine Payne
- Manchester Centre for Health Economics, University of Manchester Manchester UK
| | | | | | - Ellen Thomassen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
| | - Rachel Thompson
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne UK
| | | | | | | | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center The Netherlands
- Clinical GeneticsLeiden University Medical Center The Netherlands
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Li A, Zhou B, Alves CS, Xu B, Guo R, Shi X, Cao X. Mechanistic Studies of Enhanced PCR Using PEGylated PEI-Entrapped Gold Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2016; 8:25808-25817. [PMID: 27599792 DOI: 10.1021/acsami.6b09310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The polymerase chain reaction (PCR) is considered an excellent technique and is widely used in both molecular biology research and various clinical applications. However, the presence of byproducts and low output are limitations generally associated with this technique. Recently, the use of nanoparticles (NPs) has been shown to be very effective at enhancing PCR. Although mechanisms underlying this process have been suggested, most of them are mainly based on PCR results under certain situations without abundant systematic experimental strategy. In order to overcome these challenges, we synthesized a series of polyethylene glycol (PEG)-modified polyethylenimine (PEI)-entrapped gold nanoparticles (PEG-Au PENPs), each having different gold contents. The role of the synthesized NPs in improving the PCR technique was then systematically evaluated using the error-prone two-round PCR and GC-rich PCR (74% GC content). Our results suggest a possible mechanism of PCR enhancement. In the error-prone two-round PCR system, the improvement of the specificity and efficiency of the technique using the PEG-Au PENPs mainly depends on surface-charge-mediated electrostatic interactions. In the GC-rich PCR system, thermal conduction may be the dominant factor. These important findings offer a breakthrough in understanding the mechanisms involved in improving PCR amplification, as well as in the application of nanomaterials in different fields, particularly in biology and medicine.
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Affiliation(s)
- Aijun Li
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Benqing Zhou
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Carla S Alves
- CQM-Centro de Quimica da Madeira, Universidade da Madeira , Campus da Penteada, 9020-105 Funchal, Portugal
| | - Bei Xu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Rui Guo
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Xiangyang Shi
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
- CQM-Centro de Quimica da Madeira, Universidade da Madeira , Campus da Penteada, 9020-105 Funchal, Portugal
| | - Xueyan Cao
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
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Jurišić V, Obradović J, Tošić N, Pavlović S, Kulić M, Djordjević N. Effects of DMSO, glycerol, betaine and their combinations in detecting single nucleotide polymorphisms of epidermal growth factor receptor (EGFR) gene promoter sequence in non-small-cell lung cancer (NSCLC) patients. J Pharm Biomed Anal 2016; 128:275-279. [DOI: 10.1016/j.jpba.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
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Hawash Y, Ghonaim MM, Al-Shehri SS. An Improved PCR-RFLP Assay for Detection and Genotyping of Asymptomatic Giardia lamblia Infection in a Resource-Poor Setting. THE KOREAN JOURNAL OF PARASITOLOGY 2016; 54:1-8. [PMID: 26951972 PMCID: PMC4792328 DOI: 10.3347/kjp.2016.54.1.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/18/2015] [Accepted: 11/04/2015] [Indexed: 11/23/2022]
Abstract
Laboratory workers, in resource-poor countries, still consider PCR detection of Giardia lamblia more costly and more time-consuming than the classical parasitological techniques. Based on 2 published primers, an in-house one-round touchdown PCR-RFLP assay was developed. The assay was validated with an internal amplification control included in reactions. Performance of the assay was assessed with DNA samples of various purities, 91 control fecal samples with various parasite load, and 472 samples of unknown results. Two cysts per reaction were enough for PCR detection by the assay with exhibited specificity (Sp) and sensitivity (Se) of 100% and 93%, respectively. Taking a published small subunit rRNA reference PCR test results (6%; 29/472) as a nominated gold standard, G. lamblia was identified in 5.9% (28/472), 5.2%, (25/472), and 3.6% (17/472) by PCR assay, RIDA® Quick Giardia antigen detection test (R-Biopharm, Darmstadt, Germany), and iodine-stained smear microscopy, respectively. The percent agreements (kappa values) of 99.7% (0.745), 98.9% (0.900), and 97.7% (0.981) were exhibited between the assay results and that of the reference PCR, immunoassay, and microscopy, respectively. Restriction digestion of the 28 Giardia-positive samples revealed genotype A pattern in 12 and genotype B profile in 16 samples. The PCR assay with the described format and exhibited performance has a great potential to be adopted in basic clinical laboratories as a detection tool for G. lamblia especially in asymptomatic infections. This potential is increased more in particular situations where identification of the parasite genotype represents a major requirement as in epidemiological studies and infection outbreaks.
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Affiliation(s)
- Yoursry Hawash
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia ; Department of Medical Parasitology, National Liver Institute, Menoufia University, Shebin El-Koom, Menoufia 23513, Egypt
| | - M M Ghonaim
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia ; Medical Microbiology and Immunology Department, Faculty of Medicine, Menoufia University, Shebin El-Koom, Menoufia 23513, Egypt
| | - S S Al-Shehri
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
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Frequencies of EGFR single nucleotide polymorphisms in non-small cell lung cancer patients and healthy individuals in the Republic of Serbia: a preliminary study. Tumour Biol 2016; 37:10479-86. [DOI: 10.1007/s13277-016-4930-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/28/2016] [Indexed: 01/06/2023] Open
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Kalinska-Bienias A, Kostrzewa G, Malejczyk M, Ploski R, Majewski S. Possible association between actinic keratosis and the rs7208422 (c.917A→T, p.N306l) polymorphism of the EVER2 gene in patients without epidermodysplasia verruciformis. Clin Exp Dermatol 2014; 40:318-23. [PMID: 25495765 DOI: 10.1111/ced.12506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND Mutations of the EVER1 and EVER2 genes cause epidermodysplasia verruciformis (EV), a genodermatosis associated with squamous cell carcinoma (SCC). Recently, it has been found that the rs7208422 (c.917A→T, p.N306l) polymorphism in the EVER2 gene is related to an increased risk of SCC in patients with conditions other than EV. We hypothesized that this polymorphism might be also associated with actinic keratoses (AK). AIM To determine whether the rs7208422 polymorphism of the EVER2 gene is associated with AK in non-EV patients. METHODS We genotyped rs7208422 in 65 patients with AK and 274 controls, using reverse transcription PCR. RESULTS We detected a trend towards an association between AK and the TT genotype of rs7208422; the frequency of this genotype was 38.5% in patients with AK and 26.3% in controls (OR = 1.75, P < 0.06 for recessive model of inheritance). We also found an association between rs7208422 TT and both the age at which AK appeared and the extent of the AK. This variant was more frequent in patients who had AK onset before the age of 70 years compared with those whose age of onset was above 70 years (OR = 3.14, P = 0.03 for the recessive model; OR = 2.05, P = 0.04 for allelic comparison) and more frequent in AK involving > 3 body areas (OR = 3.14, P = 0.03 for the recessive model; OR = 2.34, P = 0.01 for allelic comparison). These associations remained significant in a multivariate regression analysis, showing that both parameters were independently associated with the TT genotype (P = 0.031). CONCLUSIONS This study indicates a potential role of the rs7208422 (c.917A→T, P.N306l) polymorphism of the EVER2 gene in AK.
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Affiliation(s)
- A Kalinska-Bienias
- Department of Dermatology and Immunodermatology, Medical University of Warsaw, Warsaw, Poland
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