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Li D, Li QW, Xiang H, Yuan SS, Yang XP. A label-free activatable biosensor for in situ detection of exosomal microRNAs based on DNA-AgNCs and hairpin type nucleic acid probes. Anal Methods 2024; 16:1357-1362. [PMID: 38344752 DOI: 10.1039/d3ay02268d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Exosomal microRNA (miRNA) is a potential biomarker for cancer diagnosis, metastasis, and treatment. In situ detection of exosomal miRNA is an attractive option due to its simplicity and high accuracy. However, in situ exosomal miRNA detection has encountered challenges because of the low target abundance of targets and limited probe permeability. Herein, a label-free and activatable biosensor was developed for in situ exosomal miRNA assays by utilizing hairpin-shaped nucleic acid probes and DNA-hosted silver nanoclusters (DNA-AgNCs). The probe is directly internalized into the exosomes, and then hybridized with the target miRNA-21. Subsequently, the DNA-AgNCs are pulled closer to the G-rich sequence, ultimately leading to in situ red fluorescence activation. The biosensor not only can detect exosomal miRNA-21 but also distinguish cancer cells from normal cells. Under optimal reaction conditions, the detection limit (LOD) of exosomal miRNA-21 is 1.53 × 107 particles per mL. Furthermore, DNA-AgNCs are used as label-free signal elements for in situ detection of exosomal miRNAs for the first time, expanding the application of nanomaterials in this field. This strategy does not require tedious RNA extraction steps and expensive instruments, and may develop into a non-invasive diagnostic tool for ovarian cancer.
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Affiliation(s)
- Duo Li
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
| | - Qian-Wen Li
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
| | - Hui Xiang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
| | - Shi-Shan Yuan
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
| | - Xiao-Ping Yang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
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2
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Huang K, Meyers BC, Caplan JL. Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH. Methods Mol Biol 2024; 2784:101-111. [PMID: 38502481 DOI: 10.1007/978-1-0716-3766-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
- Molecular Imaging Core, Dana-Farber Cancer Institute, Boston, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
- Division of Plant Science and Technology, University of Missouri - Columbia, Columbia, MO, USA.
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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3
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Xie X, Sun Y, Peng J, Zhang Z, Wang M, Wang Z, Lei C, Huang Y, Nie Z. Collagen Anchoring Protein-Nucleic Acid Chimeric Probe for In Situ In Vivo Mapping of a Tumor-Specific Protease. Anal Chem 2023; 95:18487-18496. [PMID: 38057291 DOI: 10.1021/acs.analchem.3c03775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
In situ analysis of biomarkers in the tumor microenvironment (TME) is important to reveal their potential roles in tumor progression and early diagnosis of tumors but remains a challenge. In this work, a bottom-up modular assembly strategy was proposed for a multifunctional protein-nucleic chimeric probe (PNCP) for in situ mapping of cancer-specific proteases. PNCP, containing a collagen anchoring module and a target proteolysis-responsive isothermal amplification sensor module, can be anchored in the collagen-rich TME and respond to the target protease in situ and generate amplified signals through rolling cycle amplification of tandem fluorescent RNAs. Taking matrix metalloproteinase 2 (MMP-2), a tumor-associated protease, as the model, the feasibility of PNCP was demonstrated for the in situ detection of MMP-2 activity in 3D tumor spheroids. Moreover, in situ in vivo mapping of MMP-2 activity was also achieved in a metastatic solid tumor model with high sensitivity, providing a useful tool for evaluating tumor metastasis and distinguishing highly aggressive forms of tumors.
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Affiliation(s)
- Xuan Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Yuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Jialong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhenhua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Meixia Wang
- College of Biology, Hunan University, Changsha 410082, P. R. China
| | - Zeyuan Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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4
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Xu C, Yu J, Ning X, Xu M, He S, Wu J, Pu K. Semiconducting Polymer Nanospherical Nucleic Acid Probe for Transcriptomic Imaging of Cancer Chemo-Immunotherapy. Adv Mater 2023; 35:e2306739. [PMID: 37660291 DOI: 10.1002/adma.202306739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/27/2023] [Indexed: 09/04/2023]
Abstract
Real-time in vivo imaging of RNA can enhance the understanding of physio-pathological processes. However, most nucleic acid-based sensors have poor resistance to nucleases and limited photophysical properties, making them suboptimal for this purpose. To address this, a semiconducting polymer nanospherical nucleic acid probe (SENSE) for transcriptomic imaging of cancer immunity in living mice is developed. SENSE comprises a semiconducting polymer (SP) backbone covalently linked with recognition DNA strands, which are complemented by dye-labeled signal DNA strands. Upon detection of targeted T lymphocyte transcript (Gzmb: granzyme B), the signal strands are released, leading to a fluorescence enhancement correlated to transcript levels with superb sensitivity. The always-on fluorescence of the SP core also serves as an internal reference for tracking SENSE uptake in tumors. Thus, SENSE has the dual-signal channel that enables ratiometric imaging of Gzmb transcripts in the tumor of living mice for evaluating chemo-immunotherapy; moreover, it has demonstrated sensitivity and specificity comparable to flow cytometry and quantitative polymerase chain reaction, yet offering a faster and simpler means of T cell detection in resected tumors. Therefore, SENSE represents a promising tool for in vivo RNA imaging.
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Affiliation(s)
- Cheng Xu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Jie Yu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Xiaoyu Ning
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Mengke Xu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Shasha He
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Jiayan Wu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Kanyi Pu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
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5
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Zhong Y, Huang LX, Lin MT, Zhang ZY, Liu AL, Lei Y. A Y-shape-structured electrochemiluminescence biosensor based on carbon quantum dots and locked nucleic acid probe for microRNA determination with single-base resolution. Biosens Bioelectron 2023; 238:115583. [PMID: 37573643 DOI: 10.1016/j.bios.2023.115583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Since microRNAs (miRNAs) are predictors of tumorigenesis, accurate identification and quantification of miRNAs with highly similar sequences are expected to reflect tumor diagnosis and treatment. In this study, a highly selective and sensitive electrochemiluminescence (ECL) biosensor was constructed for miRNAs determination based on Y-shaped junction structure equipped with locked nucleic acids (LNA), graphene oxide-based nanocomposite to enrich luminophores, and conductive matrix. Specifically, two LNA-modified probes were designed for specific miRNA recognition, that is, a dual-amine functionalized hairpin capture probe and a signal probe. A Y-shaped DNA junction structure was generated on the electrode surface upon miRNA hybridizing across the two branches, so as to enhance the selectivity. Carbon quantum dots-polyethylene imine-graphene oxide (CQDs-PEI-GO) nanocomposites were developed to enrich luminophores CQDs, and thus enhancing the ECL intensity. For indirect signal amplification, an electrochemically activated poly(2-aminoterephthalic acid) (ATA) film decorated with gold nanoparticles was prepared on electrode as an effective matrix to accelerate the electron transfer. The fabricated ECL biosensor achieved sensitive determination of miRNA-222 with a limit-of-detection (LOD) as low as 1.95 fM (S/N = 3). Notably, Y-shaped junction structures equipped with LNA probes endowed ECL biosensor with salient single-base discrimination ability and anti-interference capacity. Overall, the proposed Y-shaped ECL biosensor has considerable promise for clinical biomarker determination.
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Affiliation(s)
- Yu Zhong
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Lin-Xiao Huang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Mu-Tu Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Zi-Yang Zhang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Ai-Lin Liu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
| | - Yun Lei
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
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6
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Wu P, Fang N, Tao Y, Wang Y, Jia W, Zhang H, Cai C, Zhu JJ. Enhancing the Reliability of SERS Detection in Ampicillin Using Oriented Tetrahedral Framework Nucleic Acid Probes and a Long-Range SERS Substrate. Anal Chem 2023; 95:14271-14278. [PMID: 37695688 DOI: 10.1021/acs.analchem.3c02356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Indirect surface-enhanced Raman scattering (SERS)-based methods are highly efficient in detecting and quantitatively analyzing trace antibiotics in complex samples. However, the poor reproducibility of indirect SERS assays caused by the diffusion and orientation changes of the probing molecules on SERS substrates still presents a significant challenge. To address this issue, this study reports the construction of a novel SERS sensing platform using tetrahedral framework nucleic acid (tFNA) as SERS probes in conjunction with a long-range SERS (LR-SERS) substrate. The tFNA was modified with sulfhydryl groups at three vertices and appended with a probing DNA at the remaining vertex, anchored on the substrate surface with a well-ordered orientation and stable coverage density, resulting in highly reproducible SERS signals. Owing to the weak SERS signal of tFNA inherited from its size being larger than the effective range of the enhancing electric field (E-field) of conventional SERS substrates, we utilized an LR-SERS substrate to enhance the signal of tFNA probes by capitalizing on its extended E-field. Correspondingly, the LR-SERS substrate demonstrated a 54-fold increase in the intensity of tFNA probes compared to the conventional substrate. Using this novel platform, we achieved a highly reliable detection of the antibiotic ampicillin with a wide linear range (10 fM to 1 nM), low detection limit (3.1 fM), small relative standard deviation (3.12%), and yielded quantitative recoveries of 97-102% for ampicillin in water, milk, and human serum samples. These findings, therefore, effectively demonstrate the achievement of highly reliable SERS detection of antibiotics using framework nucleic acids and an LR-SERS substrate.
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Affiliation(s)
- Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ningning Fang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Yutong Tao
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Yuan Wang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Wenyu Jia
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
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7
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Wu K, Ma C, Wang Y. Functional Nucleic Acid Probes Based on Two-Photon for Biosensing. Biosensors (Basel) 2023; 13:836. [PMID: 37754070 PMCID: PMC10527542 DOI: 10.3390/bios13090836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.
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Affiliation(s)
- Kefeng Wu
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Yisen Wang
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
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8
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Ye Q, Zhang Z, Liu J, Wang X. Screen-printed electrode-based biosensors modified with functional nucleic acid probes and their applications in this pandemic age: a review. Anal Methods 2022; 14:2961-2975. [PMID: 35913361 DOI: 10.1039/d2ay00666a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Electrochemical methodology has probably been the most used sensing platform in the past few years as they provide superior advantages. In particular, screen-printed electrode (SPE)-based sensing applications stand out as they provide extraordinary miniaturized but robust and user-friendly detection system. In this context, we are focusing on the modification of SPE with functional nucleic acid probes and nanostructures to improve the electrochemical detection performance in versatile sensing applications, particularly in the fight against the COVID-19 pandemic. Aptamers are immobilized on the electrode surface to detect non-nucleic acid targets and complementary probes to recognize and capture nucleic acid targets. In a step further, SPE-based biosensors with the modification of self-assembled DNA nanostructures are emphasized as they offer great potential for the interface engineering of the electrode surface and promote the excellent performance of various interface reactions. By equipping with a portable potentiostat and a smartphone monitoring device, the realization of this SPE-based miniaturized diagnostic system for the further requirement of fast and POC detection is revealed. Finally, more novel and excellent works are previewed and future perspectives in this field are mentioned.
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Affiliation(s)
- Qingqing Ye
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Zhenqi Zhang
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Jian Liu
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Xuyao Wang
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
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9
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Erdem A, Eksin E. Impedimetric Sensing of Factor V Leiden Mutation by Zip Nucleic Acid Probe and Electrochemical Array. Biosensors (Basel) 2020; 10:bios10090116. [PMID: 32906640 PMCID: PMC7559847 DOI: 10.3390/bios10090116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 12/02/2022]
Abstract
A carbon nanofiber enriched 8-channel screen-printed electrochemical array was used for the impedimetric detection of SNP related to Factor V Leiden (FV Leiden) mutation, which is the most common inherited form of thrombophilia. FV Leiden mutation sensing was carried out in three steps: solution-phase nucleic acid hybridization between zip nucleic acid probe (Z-probe) and mutant type DNA target, followed by the immobilization of the hybrid on the working electrode area of array, and measurement by electrochemical impedance spectroscopy (EIS). The selectivity of the assay was tested against mutation-free DNA sequences and synthetic polymerase chain reaction (PCR) samples. The developed biosensor was a trustful assay for FV Leiden mutation diagnosis, which can effectively discriminate wild type and mutant type even in PCR samples.
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10
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Tian T, Li J, Xie C, Sun Y, Lei H, Liu X, Xia J, Shi J, Wang L, Lu W, Fan C. Targeted Imaging of Brain Tumors with a Framework Nucleic Acid Probe. ACS Appl Mater Interfaces 2018; 10:3414-3420. [PMID: 29299920 DOI: 10.1021/acsami.7b17927] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Development of agents for delivering drugs and imaging probes across the blood-brain barrier (BBB) remains a major challenge. In this study, we designed a biocompatible framework nucleic acid (FNA)-based imaging probe for brain tumor-targeting. We employed a typical type of FNAs, tetrahedral DNA nanostructures (TDNs), as the building block, which were modified with angiopep-2 (ANG), a 19-mer peptide derived from human Kunitz domain of aprotinin. This probe exhibited high binding efficiency with low-density lipoprotein receptor-related protein-1 (LRP-1) of BBB and glioma. We found that ANG-functionalized TDNs (ANG-TDNs) stayed intact for at least 12 h in serum, and that ANG modification effectively enhanced cellular uptake of TDNs in brain capillary endothelial cells and Uppsala 87 malignant glioma (U87MG) cells. Remarkably, studies in both in vitro and in vivo models revealed that ANG-TDNs could cross the BBB. Especially, in vivo imaging showed strong fluorescent signals in U87MG human glioblastoma xenograft in nude mice. This study establishes that the FNA-based platform provides a new theranostic tool for the study and therapy of brain tumors.
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Affiliation(s)
- Tian Tian
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine , Shanghai 201203, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Cao Xie
- Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, China
| | - Yanhong Sun
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Haozhi Lei
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Xinyi Liu
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiaoyun Xia
- School of Chemistry and Biology Engineering, Changsha University of Science and Technology , Changsha 410004, China
| | - Jiye Shi
- UCB Pharma , Slough, SL1 14EN Berkshire, U.K
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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11
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Giovanardi F, Cucinotta A, Vincetti L. Inhibited coupling guiding hollow fibers for label-free DNA detection. Opt Express 2017; 25:26215-26220. [PMID: 29041281 DOI: 10.1364/oe.25.026215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
The potentialities in using hollow core tube lattice fibers based on inhibited coupling wave-guiding for label-free DNA detection are numerically investigated and discussed here. The proposed sensing approach does not require any additional transducer component such as Bragg gratings, amplifying techniques such as nanoparticles nor coherent sources. It simply consists of the measurement of the transmittance of a piece of fiber some ten centimeters long. In case of matching DNA sequence, an additional bio-layer is laid down the dielectric-air interface causing a red shift of the transmission spectrum of the fiber. Results show a spectral sensitivity on the bio-layer with shift as high as 42 nm for every 10 nm of bio-layer and robustness against imperfect fiber coupling. The proposed approach can be easily applied to sensing of other complex molecular structures where the presence/absence of analyte can generate or not an additional layer.
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12
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Jensen HE, Jensen LK, Barington K, Pors SE, Bjarnsholt T, Boye M. Fluorescence in situ hybridization for the tissue detection of bacterial pathogens associated with porcine infections. Methods Mol Biol 2015; 1247:219-234. [PMID: 25399100 DOI: 10.1007/978-1-4939-2004-4_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence in situ hybridization (FISH) is an efficient technique for the identification of specific bacteria in tissue of both experimental and spontaneous infections. The method detects specific sequences of nucleic acids by hybridization of fluorescently labeled probes to complementary target sequences within intact cells. FISH allows direct histological localization of the bacteria in the tissue and thereby a correlation between the infection and the histopathological changes present. This chapter presents protocols for FISH identification of bacterial pathogens in fixed deparaffinized tissue samples mounted on glass slides. Two different methods are presented: one is illustrated with the use of peptide nucleic acid (PNA) that is carried out directly on glass slides (Method I), whereas the other is exemplified by using a DNA probe in a Shandon rack (Method II). In the two methods, both PNA and DNA probes can be used.
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Affiliation(s)
- Henrik Elvang Jensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Ridebanevej 3, 1870, Frederiksberg C, Denmark,
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Iranmanesh Z, Mollaie HR, Arabzadeh SA, Zahedi MJ, Fazlalipour M, Ebrahimi S. Evaluation of the frequency of the IL-28 polymorphism (rs8099917) in patients with chronic hepatitis C using Zip nucleic acid probes, Kerman, Southeast of Iran. Asian Pac J Cancer Prev 2015; 16:1919-24. [PMID: 25773845 DOI: 10.7314/apjcp.2015.16.5.1919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Polymorphisms in the region of the interleukin IL-28 gene on chromosome 19 have been related with clearance of hepatitis C virus (HCV), a major human pathogen responsible for chronic hepatitis, cirrhosis and hepatocellular carcinoma. About 3% of the world's population is infected with HCV. The long-term response to therapy is influenced by many host and viral factors, and recent evidence has indicated that some host genetic polymorphisms related to IL-28 are the most powerful predictors of virological response in patients with HCV. This study assessed frequency of the IL-28 polymorphism (rs8099917) in 50 patients (39 men and 11 women ) with chronic hepatitis C using ZNA probe real time PCR new method . All patients were tested for genotype of HCV and the HCV viral load. In parallel, the levels of SGOT, SGPT and ALK enzymes were assessed. Treatment using Peg-interferon alpha with ribavirin was conducted for patients and subsequently samples were collected to detect any change in viral load or liver enzyme rates. The overall frequency of the TT allele is 74%, TG allele 20% and GG allele 6% and the percent of patients who had T allele was 84%. Clear reduction in viral load and liver enzymes was reported in patients with the T allele. Especially for genotype 1 which is relatively resistant to treatment, these alleles may have a role in this decline. In conclusion, we showed that IL-28 polymorphism rs8099917 strongly predicts virological response in HCV infection and that real-time PCR with Zip nucleic acid probes is a sensitive, specific and rapid detection method for detection of SNPs which will be essential for monitoring patients undergoing antiviral therapy.
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Affiliation(s)
- Zahra Iranmanesh
- Department of Medical Microbiology, Kerman University of Medical Sciences, Kerman, Iran E-mail :
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Ho TH, Dang KX, Lintula S, Hotakainen K, Feng L, Olkkonen VM, Verschuren EW, Tenkanen T, Haglund C, Kolho KL, Stenman UH, Stenman J. Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity. Nucleic Acids Res 2015; 43:e4. [PMID: 25378315 PMCID: PMC4288146 DOI: 10.1093/nar/gku1048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022] Open
Abstract
Here we provide the first strategy to use a competitive Extendable Blocking Probe (ExBP) for allele-specific priming with superior selectivity at the stage of reverse transcription. In order to analyze highly similar RNA variants, a reverse-transcriptase primer whose sequence matches a specific variant selectively primes only that variant, whereas mismatch priming to the alternative variant is suppressed by virtue of hybridization and subsequent extension of the perfectly matched ExBP on that alternative variant template to form a cDNA-RNA hybrid. This hybrid will render the alternative RNA template unavailable for mismatch priming initiated by the specific primer in a hot-start protocol of reverse transcription when the temperature decreases to a level where such mismatch priming could occur. The ExBP-based reverse transcription assay detected BRAF and KRAS mutations in at least 1000-fold excess of wild-type RNA and detection was linear over a 4-log dynamic range. This novel strategy not only reveals the presence or absence of rare mutations with an exceptionally high selectivity, but also provides a convenient tool for accurate determination of RNA variants in different settings, such as quantification of allele-specific expression.
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Affiliation(s)
- Tho H Ho
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Kien X Dang
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Susanna Lintula
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Kristina Hotakainen
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland Helsinki University Central Hospital, HUSLAB, Helsinki, 00029 HUS, Finland
| | - Lin Feng
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland
| | | | - Caj Haglund
- Department of Surgery, Helsinki University Central Hospital, Helsinki, 00029 HUS, Finland Research Program Unit, Translational Cancer Biology, University of Helsinki, Helsinki, FI-00014, Finland Haartman Institute, Department of Pathology, University of Helsinki, Helsinki, FI-00014, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, University of Helsinki, Helsinki, FI-00014, Finland
| | - Ulf-Hakan Stenman
- Haartman Institute, Department of Clinical Chemistry, Biomedicum Helsinki, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, 00290, Finland Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, FI-00014, Finland Department of Women's and Children's Health, Karolinska Institutet, Stockholm, SE-17176, Sweden
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Costa P, Couto I, Viveiros M, Inácio J. Nested and multiplex real-time PCR using dual-labeled probes: detecting and discriminating Mycobacterium tuberculosis complex members in cultures and animal tissues. Methods Mol Biol 2015; 1247:133-43. [PMID: 25399092 DOI: 10.1007/978-1-4939-2004-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Members of the Mycobacterium tuberculosis complex (MTC) are causative agents of tuberculosis (TB) in both humans and animals. In the last two decades, the accumulating knowledge of the nucleotide sequences of several genes, and of the whole genomes, of MTC members has allowed the development of novel molecular assays able to detect and discriminate between these species. However, despite the significant advances in the development of molecular assays for detecting MTC members in human samples, only a few assays have been described for detecting these agents in animal tissues. In this chapter we describe the use of two TaqMan (®)-based real-time PCR approaches, highly sensitive and specific and easy to perform, to detect and identify veterinary-relevant MTC species in both animal tissue samples and cultures.
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Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IP, Lisbon, Portugal
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Ou Q, Gu D, Zhang N, He J, Shao Y, Shi L, Liu C, Zhao C, Xu Y. [Preparation and performance assessment of Gamma-peptide nucleic acid gene chip detection system based on surface plasmon resonance]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2013; 30:1326-1329. [PMID: 24645620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aim of this study was to build a gene chip system with surface plasmon resonance (SPR) technique, for which Gamma-peptide nucleic acid (Gamma-PNA) functioned as a probe, in order to improve sensitivity and its specificity. With the use of self-assembled monolayer (SAM) technology, surface chemistry of two-dimensional structure was used. Gamma-PNA was designed according to the bioinformatics, and was plated on the SPR chip modified by SAM. Subsequently, relevant parameters of the experiment were ensured and optimized. The results showed that the performances of Gamma-PNA probe was little affected by the ion concentration of buffer, and it had a strong light signal in a stable state. As the ion concentration was 0, there were still good hybrid reactions; pH value had less influence upon Gamma-PNA probe, and acid environment of buffer could be better. Gamma-PNA probe combined with sensor technologies achieved made the probe with dispensable labels and real-time detection. It also improved the efficiency of the hybridization and the stability, providing the foundation for clinical application.
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Fontenete S, Guimarães N, Leite M, Figueiredo C, Wengel J, Filipe Azevedo N. Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes. PLoS One 2013; 8:e81230. [PMID: 24278398 PMCID: PMC3838382 DOI: 10.1371/journal.pone.0081230] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 10/10/2013] [Indexed: 12/16/2022] Open
Abstract
The understanding of the human microbiome and its influence upon human life has long been a subject of study. Hence, methods that allow the direct detection and visualization of microorganisms and microbial consortia (e.g. biofilms) within the human body would be invaluable. In here, we assessed the possibility of developing a variant of fluorescence in situ hybridization (FISH), named fluorescence in vivo hybridization (FIVH), for the detection of Helicobacter pylori. Using oligonucleotide variations comprising locked nucleic acids (LNA) and 2’-O-methyl RNAs (2’OMe) with two types of backbone linkages (phosphate or phosphorothioate), we were able to successfully identify two probes that hybridize at 37 °C with high specificity and sensitivity for H. pylori, both in pure cultures and in gastric biopsies. Furthermore, the use of this type of probes implied that toxic compounds typically used in FISH were either found to be unnecessary or could be replaced by a non-toxic substitute. We show here for the first time that the use of advanced LNA probes in FIVH conditions provides an accurate, simple and fast method for H. pylori detection and location, which could be used in the future for potential in vivo applications either for this microorganism or for others.
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Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Nuno Guimarães
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Marina Leite
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Céu Figueiredo
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- * E-mail:
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Zhao X, Huang WJ, Wei HJ, Wang Z, Li XY, Cheng YH, Tan MJ, Xiao N, Lan Y, Guo JF, Sui HT, Zhu WF, Du DD, Wang DY, Shu YL. [Development of a real-time reverse transcriptase PCR assay for detection of E119V amino acid change in neuraminidase of influenza A (H3N2) using the TaqMan-MGB probe]. Zhonghua Yu Fang Yi Xue Za Zhi 2013; 47:448-451. [PMID: 23958130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To develop a rapid duplex Real-time reverse transcription PCR (rRT-PCR) method to detect E119V mutation on neuraminidase (NA) of influenza A(H3N2) subtype with drug resistance to oseltamivir. METHODS Twenty-six NA genes of influenza A(H3N2) virus between 2000 and 2012 in GenBank database were selected as the target genes, and specific TaqMan-MGB probe was designed to target the E119V amino acid change in neuraminidase protein. rRT-PCR was then performed and evaluated for the sensitivity, specificity and reproducibility using virus with E119V mutation and clinical samples. RESULTS This study described the validation of a highly sensitive and specific duplex rRT-PCR for detection of substitutions leading to the E119V amino acid change in NA protein of influenza A(H3N2). Fluorescence signals could be detected even when diluted a A (H3N2) virus (HA = 8) into 10(-5) and linear correlation between the logarithm of the viral titer with the Ct values was observed. In addition, the assay was highly specific in that there was no cross-react with other respiratory viruses, nor did two TaqMan-MGB probes. E119V substitution in quasispecies with both sensitive and resistant viruses could be detected as well. The limit of detection was 5% for quasispecies with high concentrations and 50% for quasispecies with low concentrations. The average coefficient of variation (CV) for within-run assays was 2.32% and 0.57% for H3N2-119E and H3N2-119V primer/probe sets separately, 1.77% and 0.97% for average CV of between-run assays, which exhibited good repeatability. Sequence analysis of twenty NA genes verified glutamic acid (E) at amino acid site 119, which was in consistent with the results from our rRT-PCR method. CONCLUSION The assay developed in this study is highly sensitive and specific, and easy to operate; thereby it could be used for identification of A(H3N2) virus with E119V amino acid change in NA protein.
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Affiliation(s)
- Xiang Zhao
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, China
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Dai J, Peng H, Chen W, Cheng J, Wu Y. Development of multiplex real-time PCR for simultaneous detection of three Potyviruses in tobacco plants. J Appl Microbiol 2013; 114:502-8. [PMID: 23164070 DOI: 10.1111/jam.12071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/21/2012] [Accepted: 10/26/2012] [Indexed: 11/29/2022]
Abstract
AIMS To develop a multiplex real-time PCR assay using TaqMan probes for the simultaneous detection and quantification of Tobacco etch virus (TEV), Potato virus Y (PVY) and Tobacco vein banding mosaic virus (TVBMV). METHODS AND RESULTS Specific primer and probe combinations for TEV and TVBMV were developed from the coat protein region of the viral genome. To detect PVY, a primer and probe combination PVY-Univ F, PVY-Univ R and PVY-Univ P for amplifying the coat protein region of the virus genome was employed. The detection limit of multiplex real-time PCR for these viruses was 10 copies μl(-1) of the standard plasmid. The multiplex reaction was successful in the detection of these three pathogens, with no non-specific amplification and cross-reaction. CONCLUSIONS This multiplex real-time PCR provides a rapid, effective, specific and sensitive method for the simultaneous detection and quantification of the three pathogens on infected tobacco plants. SIGNIFICANCE AND IMPACT OF THE STUDY This multiplex real-time PCR will be useful not only for diagnostic, ecological, epidemiological and pathogenesis studies, but also for investigating host/virus or virus/virus interactions, in particular during mix infection.
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Affiliation(s)
- J Dai
- State Key Laboratory of Crop Stress Biology in Arid Areas and Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling, China
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20
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Abstract
The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (csh) was used as the template for PCR amplification and construction of a non-radioactive DIG labeled probe. The csh derived probe aided in the preliminary and rapid identification of L. plantarum from mixed cultures by colony hybridization. The method described here for the rapid identification of L. plantarum can also be applied for the rapid detection of other bacteria if a unique gene sequence can be identified from its complete genome sequence.
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Affiliation(s)
- Ilenys M Pérez-Díaz
- USDA-ARS, SAA Food Science Research Unit, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA.
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21
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Han KD, Mafi A, Johnson MD, Cohen M, Gbulie UB, Baker SB. Application of fluorescent in situ hybridization in the mouse xenograft model of human fat grafting. Aesthet Surg J 2012; 32:745-50. [PMID: 22859546 DOI: 10.1177/1090820x12452422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Determining the optimal technique for autologous fat grafting requires elucidation of the engraftment process at the cellular level. The nude mouse xenograft model for autologous human fat grafting is an excellent tool to evaluate the incorporation of grafted fat into the recipient. OBJECTIVES The authors present a murine xenograft model that uses fluorescent in situ hybridization (FISH) to differentiate between murine (host) cells and human (grafted) cells. METHODS Fat grafts were harvested from human abdominoplasty specimens, fixed, embedded in paraffin blocks, and cut into 5 µm sections. The sections were stained and used for in situ hybridization with fluorescently labeled murine and human nucleic acid reagents. A fluorescence microscope was used for photographic analysis of the grafts, allowing identification of murine and human cell populations based on the wavelength at which they stained. DAPI (4,'6-diamidino-2-phenylindole) counterstaining was also applied to confirm that the images obtained represented cell nuclei. RESULTS At 20× magnification, strong species-specific staining of cells was seen within the tissue sections, which allowed the authors to easily discriminate between graft-derived and host-derived cells. Using this approach, human fat xenografts were revealed to comprise a complex matrix of closely interacting graft- and host-derived structures. CONCLUSIONS FISH has the potential to be a powerful technique for distinguishing between murine and human cells in the nude mouse xenograft model of human fat grafting. By applying this technique, it may be possible to evaluate the engraftment process at a cellular level, which may ultimately allow clinicians to obtain more predictable results with grafted fat.
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Affiliation(s)
- Kevin D Han
- Department of Plastic Surgery, Georgetown University Medical Center, Washington, DC 20007, USA
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Rentoft M, Coates PJ, Laurell G, Nylander K. Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes. PLoS One 2012; 7:e35276. [PMID: 22530001 PMCID: PMC3328434 DOI: 10.1371/journal.pone.0035276] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/14/2012] [Indexed: 02/08/2023] Open
Abstract
Expression profiling techniques have been used to study the biology of many types of cancer but have been limited to some extent by the requirement for collection of fresh tissue. In contrast, formalin fixed paraffin embedded (FFPE) samples are widely available and represent a vast resource of potential material. The techniques used to handle the degraded and modified RNA from these samples are relatively new and all the pitfalls and limitations of this material for whole genome expression profiling are not yet clarified. Here, we analyzed 70 FFPE tongue carcinoma samples and 17 controls using the whole genome DASL array covering nearly 21000 genes. We identified that sample age is related to quality of extracted RNA and that sample quality influences apparent expression levels in a non-random manner related to gene probe sequence, leading to spurious results. However, by removing sub-standard samples and analysing only those 28 cancers and 15 controls that had similar quality we were able to generate a list of 934 genes significantly altered in tongue cancer compared to control samples of tongue. This list contained previously identified changes and was enriched for genes involved in many cancer-related processes such as tissue remodelling, inflammation, differentiation and apoptosis. Four novel genes of potential importance in tongue cancer development and maintenance, SH3BGL2, SLC2A6, SLC16A3 and CXCL10, were independently confirmed, validating our data. Hence, gene expression profiling can be performed usefully on archival material if appropriate quality assurance steps are taken to ensure sample consistency and we present some recommendations for the use of FFPE material based on our findings.
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Affiliation(s)
- Matilda Rentoft
- Department of Medical Biosciences/Pathology, Umeå University, Umeå, Sweden.
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Gao ZQ, Yue BF, He ZM. [Development and application of TaqMan MGB probe fluorescence quantitative PCR method for rapid detection of Clostridium piliforme]. Zhonghua Liu Xing Bing Xue Za Zhi 2012; 33:226-228. [PMID: 22575149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To develop a TaqMan MGB probe-based, sensitive and specific fluorescence quantitative PCR assay method for rapid detection of Clostridium piliforme. METHODS Primers and probes specific to 16S rRNA gene of Clostridium piliforme were designed. A TaqMan MGB probe-based, fluorescence quantitative PCR method was established. Specificity, sensitivity and stability of the method were assessed, followed by real-time quantitative PCR assay to detect Clostridium piliforme on 1156 clinical specimens during 2008-2011 and compared with conventional PCR assay. RESULTS The specificity of TaqMan MGB probe-based fluorescence quantitative PCR was high and did not show cross-reactivity with Helicobacter hepaticus, Helicobacter pylori, Campylobacter jejuni, Pasteurella pneumotropica, Escherichia coli or Pseudomonas aeruginosa. The detection limit was 2.2 copies/µl. The correlation coefficient and slope value of standard curve were 0.999 and -3.204, respectively and the efficiency of TaqMan MGB-based probe fluorescence quantitative PCR assay was 100%. When the TaqMan MGB-based probe fluorescence quantitative PCR assay was preformed to detect Clostridium piliforme on 1156 clinical specimens, a total of 101 specimens showed positive on Clostridium piliforme. However, only 44 specimens showed positive when conventional PCR was used. The real-time quantitative PCR for Clostridium piliforme could be completed within 2 hours. CONCLUSION The TaqMan MGB-based probe fluorescence quantitative PCR assay method was a reliable, specific, sensitive and useful tool for rapid detection of Clostridium piliforme.
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Affiliation(s)
- Zheng-qin Gao
- National Institutes for Food and Drug Control of China, Beijing, China.
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Wang LJ, Zhu M, Cao JJ, Gu HT, Lu XX. [Performance of locked nucleic acid probe real-time polymerase chain reaction in the detection of Aspergillus fumigatus]. Zhonghua Yi Xue Za Zhi 2011; 91:1268-1271. [PMID: 21756800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To evaluate the performance of locked nucleic acid (LNA) probe Real-time polymerase chain reaction (PCR) in the detection of Aspergillus fumigatus (A. fumigatus). METHODS All clinically cultured isolates of Aspergillus at our hospital were identified by morphology and DNA sequencing assay. The experimental group consists of A. fumigatus (n = 48) while the control group was made up of A. flavus (n = 55), A. versicolor (n = 16), A. nidulans (n = 10), A. sydowii (n = 5) and A. parasiticus (n = 1). The clinical samples consisted of A. fumigatus sinusitis tissue (n = 20) and bronchoalveolar lavage fluid (n = 1). DNA was extracted from all samples. A. fumigatus β-tubulin gene was targeted with LNA probe Real-time PCR assay. LNA probe Real-time PCR was evaluated with regards to specificity, efficiency, linear dynamic range in PCR amplification and limits of detection. RESULTS All clinical samples were positively amplified. The specificity was 100% and the PCR efficiency 98.2%. Linear dynamic range was at least six orders of magnitude and the limit of detection 2.5 pg. CONCLUSION LNA probe Real-time PCR is a promisingly accurate assay of rapidly detecting A. fumigatus practically and cost-efficiently.
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Affiliation(s)
- Li-Jun Wang
- Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
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Verma JS, Rawat D, Manzoor N, Deb M, Nair D. Evaluation of nucleic acid probe for rapid identification of Mycobacterium tuberculosis complex in extra-pulmonary culture isolates. J Commun Dis 2011; 43:11-15. [PMID: 23785877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Patients infected with Non-tuberculous mycobacteria (NTM) usually do not respond to conventional anti-tubercular treatment and are misdiagnosed as infection with multi-drug resistant strains of mycobacterium tuberculosis (M.tb) due to lack of correct species identification, particularly in the developing countries like India. One of the challenges faced by clinicians in the treatment of tuberculosis is the absence of an easy, reliable and rapid identification tool that can accurately differentiate disease caused by M.tb complex from NTM. Keeping this in consideration, the performance of species specific nucleic acid probe i.e. Accuprobe was assessed and compared with conventional niacin production, nitrate reductase assay techniques for identification of M.tb complex in 80 mycobacterial isolates obtained from different extra-pulmonary sites. Accuprobe identified 62 isolates (77.5%) as M. tuberculosis complex and remaining 18 isolates (22.5%) as NTM whereas 64 isolates (80%) were identified as M.tb and rest 16 (20%) were interpreted as NTM by conventional biochemical techniques. The overall agreement between both techniques was 96.9% The sensitivity, specificity, positive predictive value(PPV) and negative predictive value (NPV) shown by accuprobe were 96.9%, 100%, 96.9%, and 88.9% respectively. Thus, accuprobe has showed impressive sensitivity and specificity giving results in < 3 hrs from culture-positive isolates and have sure edge over conventional biochemical methods which are, nonetheless, labour intensive and cumbersome to perform thus delaying prompt mycobacterial identification.
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Affiliation(s)
- J S Verma
- Department of Microbiology, VMMC & Safdarjung Hospital, New Delhi, India
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Abstract
The ability to quantify miRNA abundance at the single-cell level and image its spatial distribution could lead to unique insight into the biological roles of miRNAs and miRNA-associated gene regulatory networks. This protocol describes a method for quantitatively imaging miRNAs in single cells using fluorescence in situ hybridization (FISH). The method combines the unique miRNA recognition properties of locked nucleic acid (LNA) with the signal amplification technology known as enzyme-labeled fluorescence (ELF). Although both approaches have previously been shown to increase detection specificity and/or sensitivity in FISH, combining these techniques into one protocol allows for single molecule detection. Specifically, individual miRNAs are identified as bright, photostable fluorescent spots. The dynamic range was found to span over three orders of magnitude and the average miRNA copy number per cell was within 17.5% of measurements acquired by quantitative RT-PCR.
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Affiliation(s)
- Jing Lu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP. Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes. BMC Plant Biol 2010; 10:85. [PMID: 20459672 PMCID: PMC3017814 DOI: 10.1186/1471-2229-10-85] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 05/07/2010] [Indexed: 05/11/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean. RESULTS To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent. CONCLUSIONS The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
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Affiliation(s)
- S Samuel Yang
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Wayne W Xu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruna Bucciarelli
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - John W Gronwald
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Carroll P Vance
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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28
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Abstract
In recent years, polymeric scaffolds have been used in several biomedical applications for the delivery of drugs or other biologically relevant molecules. Polymeric nanostructures possess different (and in some cases more powerful) properties respect to bulk materials. This, leaded academic researchers and industry to cooperate in developing pioneering nanostructured materials for industrial and biomedical applications. Moreover, the preparation and use of systems with multiple (multifunctional) properties (i.e., bioconjugation with superparamagnetic, fluorescent or targeting molecules) will represent in the future a viable and innovative tool for application in several clinical fields. This brief critical review collects and discusses some recent patents about the preparation and use of these multifunctional nanoparticles in biomedicine and in non-invasive bioimaging applications.
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Affiliation(s)
- Andrea Masotti
- Gene Expression-Microarrays Laboratory, IRCCS-Children's Hospital Bambino Gesù, P.za S.Onofrio 4, 00165 Rome, Italy.
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29
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Piao X, Sun L, Zhang T, Gan Y, Guan Y. Effects of mismatches and insertions on discrimination accuracy of nucleic acid probes. Acta Biochim Pol 2008; 55:713-720. [PMID: 19039337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 10/20/2008] [Accepted: 11/19/2008] [Indexed: 05/27/2023]
Abstract
Effective discrimination of non-complementary nucleotides is an important factor to ensure the accuracy of hybridization-based nucleic acid analyses. The current study investigates the effects of the chemical nature, the positions, the numbers, and the cooperative behavior of mismatches as well as insertions on 20-mer and 30-mer duplexes. We observed the hybridization stability trend affected by mismatches: G:T approximately G:G > G:A > A:A approximately T:T > A:C approximately T:C > C:C. The experimental data show that mismatches at the center of the oligonucleotide probes have a more profound destabilizing effect on the hybridization stability than those at either ends. Insertions also demonstrate a similar destabilizing effect as mismatches. These results provide useful information for designing DNA microarray nucleotide probes and for improving the discrimination accuracy of hybridization-based detections.
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Affiliation(s)
- Xianyu Piao
- Department of Biochemistry and Molecular Biology, China Medical University Shenyang, China
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30
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Xu W, Li JY, Li L, Yu H, Shen QD, Fan L, Qiao C, Hong M, Qian SX, Qiu HX. [Fluorescent in situ hybridization with a panel of probes detects molecular cytogenetic abnormalities in patients with chronic lymphocytic leukemia]. Zhonghua Yi Xue Za Zhi 2008; 88:2537-2540. [PMID: 19080644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
OBJECTIVE To explore the characteristics and prognostic significance of molecular cytogenetic aberrations in Chinese patients with chronic lymphocytic leukemia (CLL) and the significance thereof in diagnosis of CLL. METHODS A panel of probes (LSI D13S319, LSI p53, LSI ATM, CEP 12, LSI MYB, and LSI IGHC/IGHV) and interphase fluorescence in situ hybridization (FISH) were used to prospectively detect the cytogenetic abnormalities in 106 CLL patients, 82 males and 24 females, aged 62 (34 - 86). RESULTS Molecular cytogenetic aberrations were found in 79 of the 106 CLL patients (74.5%) and 35 patients (33.0%) showed more than two kinds of abnormalities. The most frequent abnormality detected was del (13q14) in 48 cases (45.3%), followed by trisomy of chromosome 12 in 27 patients (25.5%), IgH translocation in 25 patients (23.6%), del (17p13) in 17 patients (16.0%), del (11q22) in 11 patients (10.5%) and del (6q23) in 5 patients (4.7%). The Del (13q14) rate of the group younger than 60 was 56.5%, significantly higher than that of the group aged > or = 60 (36.7%, P = 0.033). There was no significant relationship between molecular cytogenetic aberrations and sex and Binet stages (both P > 0.05). Kaplan-Meier survival analysis showed that the survival time was shorter in the patients with p53 or ATM gene deletion. Patients with sole Del (13q14) had longer survival time than those with other abnormalities. CONCLUSION The frequencies of the chromosomal abnormalities in Chinese CLL patients are similar to those in Western countries. Panel FISH has greatly increased the sensitivity of cytogenetic analyses. Del (13q14) is the most frequent abnormality in CLL. Molecular cytogenetic aberrations detected with FISH have important prognostic significance in CLL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Asian People
- Chromosome Aberrations
- Cytogenetic Analysis
- Female
- Follow-Up Studies
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/ethnology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Nucleic Acid Probes
- Survival Rate
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Affiliation(s)
- Wei Xu
- Department of Hematology, First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
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31
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Salvi S, D'Orso F, Morelli G. Detection and quantification of genetically modified organisms using very short, locked nucleic acid TaqMan probes. J Agric Food Chem 2008; 56:4320-4327. [PMID: 18494480 DOI: 10.1021/jf800149j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-specific PCR is the preferred method in GMO detection because of its high specificity based on the flanking sequence of the exogenous integrant. The aim of this study was to evaluate the use of very short (eight-nucleotide long), locked nucleic acid (LNA) TaqMan probes in 5'-nuclease PCR assays for the detection and quantification of GMOs. Classic TaqMan and LNA TaqMan probes were compared for the analysis of the maize MON810 transgene. The performance of the two types of probes was tested on the maize endogenous reference gene hmga, the CaMV 35S promoter, and the hsp70/cryIA(b) construct as well as for the event-specific 5'-integration junction of MON810, using plasmids as standard reference molecules. The results of our study demonstrate that the LNA 5'-nuclease PCR assays represent a valid and reliable analytical system for the detection and quantification of transgenes. Application of very short LNA TaqMan probes to GMO quantification can simplify the design of 5'-nuclease assays.
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Affiliation(s)
- Sergio Salvi
- Unità di Nutrizione Sperimentale, Istituto Nazionale di Ricerca per gli Alimenti e la Nutrizione, Via Ardeatina 546, 00178 Roma, Italy
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32
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Abstract
We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarrays. The detection and screening of duplex DNA binders are important because these molecules, in many cases, are potential anticancer agents as well as toxins. Triplex DNA binders are also promising drug candidates. These molecules, in conjunction with triplex-forming oligonucleotides, could potentially be used to achieve control of gene expression by interfering with transcription factors that bind to DNA. Therefore, the ability to screen for these molecules in a high-throughput fashion could dramatically improve the drug screening process. The assay reported here provides excellent discrimination between strong, intermediate, and weak duplex and triplex DNA binders in a high-throughput fashion.
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Affiliation(s)
| | | | - Chad A. Mirkin
- *Author to whom correspondence should be addressed. ; Phone: (847) 467-3327; Fax: (847) 467-5123
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33
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Calmels TP, Mazurais D. In situ hybridization: a technique to study localization of cardiac gene expression. Methods Mol Biol 2007; 366:159-80. [PMID: 17568124 DOI: 10.1007/978-1-59745-030-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In situ hybridization allows the detection of specific gene transcripts in tissues, cells or, chromosomes. In the cardiovascular field, this powerful and rapid methodology provides precious insights into the complex gene organization and expression within an heterogeneous cell population. This technique is particularly useful to elucidate the genes and pathways involved in cardiac cells processes (differentiation, proliferation, apoptosis) or in the development of cardiovascular pathologies. In situ hybridization allows the precise localization of gene transcripts to the different heart regions and to individual cell types such as working cardiomyocytes, cells from conductive tissues and blood vessels displaying specific functions. This chapter describes the different technical procedures that are of crucial importance to carry on sensitive and specific in situ hybridization experiments in heart samples. The detection of transcripts within paraformaldehyde-fixed, paraffin-embedded cardiac tissue samples is illustrated here with the detection of cardiac sphingosine-1-phosphate receptor expression.
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Affiliation(s)
- Thierry P Calmels
- Bioproject Biotech, Pharmacology Department, Saint Grégoire Cedex, France
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34
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Rossi S, Lesignoli F, Germini A, Faccini A, Sforza S, Corradini R, Marchelli R. Identification of PCR-amplified genetically modified organisms (GMOs) DNA by peptide nucleic acid (PNA) probes in anion-exchange chromatographic analysis. J Agric Food Chem 2007; 55:2509-16. [PMID: 17326652 DOI: 10.1021/jf062063s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with high affinity and specificity, have been used as specific probes in order to assess the identity of the peaks observed. Two different protocols were adopted in order to obtain single-stranded DNA: amplification with an excess of one primer or digestion of one DNA strand. The single-stranded DNA was mixed with the PNA probe, and the presence of a specific sequence was revealed through detection of the corresponding PNA:DNA peak with significantly different retention time. Advantages and limits of this approach are discussed. The method was tested with reference materials and subsequently applied to commercial samples.
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Affiliation(s)
- Stefano Rossi
- Dipartimento di Chimica Organica e Industriale Università di Parma, Viale G. P. Usberti 17/A, I-43100 Parma, Italy
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35
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Bonvicini F, Mirasoli M, Gallinella G, Zerbini M, Musiani M, Roda A. PNA-based probe for quantitative chemiluminescent in situ hybridisation imaging of cellular parvovirus B19 replication kinetics. Analyst 2007; 132:519-23. [PMID: 17525808 DOI: 10.1039/b701664f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To allow the ultrasensitive localization and the quantitative detection of parvovirus B19 nucleic acids in single infected cells at various times post-infection, a peptide nucleic acid (PNA)-based in situ hybridisation (ISH) assay with chemiluminescent detection has been developed. The assay is based on the use of a biotin-labelled PNA probe detected by a streptavidin-linked alkaline phosphatase and a chemiluminescent dioxetane phosphate derivative substrate. The luminescent signal was quantified and imaged with an ultrasensitive nitrogen-cooled CCD camera connected to an epifluorescence microscope. The assay was used to analyze the parvovirus B19 infection process in cell cultures and to quantify the amount of viral nucleic acids at different times after infection. The chemiluminescent ISH-PNA assay is characterized by high resolution providing a sharp localization of B19 nucleic acids within single cells, with higher sensitivity with respect to conventional colorimetric ISH detection. Thanks to the high detectability and wide linear range of chemiluminescence detection, an objective evaluation of the percentage of infected cells, which reached its maximum at 24 h after infection, following a B19 virus infectious cycle could be accurately evaluated. Chemiluminescence detection also allowed the quantitative analysis of viral nucleic acids at the single-cell level, showing a continuous increase of the content of viral nucleic acids in infected cells with time after infection. The developed chemiluminescent ISH-PNA assay could thus represent a potent tool for the assessment of viral infections and for the quantitative evaluation of the virus nucleic acid load of infected cells in virus studies and diagnostics.
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Affiliation(s)
- Francesca Bonvicini
- Department of Clinical and Experimental Medicine, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
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36
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Abstract
We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA ("expanded DNA") and yDNA ("wide DNA"). The large component bases are fluorescent, and they display high stacking affinity. When singly substituted into natural DNA, they are destabilizing because the benzo-expanded base pair size is too large for the natural helix. However, when all base pairs are expanded, xDNA and yDNA form highly stable, sequence-selective double helices. The size-expanded DNAs are candidates for components of new, functioning genetic systems. In addition, the fluorescence of expanded DNA bases makes them potentially useful in probing nucleic acids.
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37
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Liu ZC, Shin DS, Shokouhimehr M, Lee KN, Yoo BW, Kim YK, Lee YS. Light-directed synthesis of peptide nucleic acids (PNAs) chips. Biosens Bioelectron 2007; 22:2891-7. [PMID: 17236754 DOI: 10.1016/j.bios.2006.12.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 11/23/2006] [Accepted: 12/01/2006] [Indexed: 11/30/2022]
Abstract
We report herein the light-directed synthesis of peptide nucleic acids (PNAs) microarray using PNA monomers protected by photolabile protecting groups and a maskless technique that uses a digital micromirror array system to form virtual masks. An ultraviolet image from the virtual mask was cast onto the active surface of a glass substrate, which was mounted in a flow cell reaction chamber connected to a peptide synthesizer. Light exposure was followed by automatic chemical coupling cycles and these steps were repeated with different virtual masks to grow the desired PNA probes in a selected pattern. In a preliminary experiment, an array of PNA probes with dimensions of 4.11 mm x 4.11 mm was generated on each slide. Each synthesis region in the final array measured 210 microm x 210 microm for a total of 256 sites. The center-to-center space was 260 microm. It was observed from the hybridization pattern of the fluorescently labeled oligonucleotide targets that the fluorescence intensities of the matched, and mismatched sequences showed substantial difference, demonstrating specificity in the identification of complementary sequences. This opens the way to exploit processes from the microelectronics industry for the fabrication of PNA microarrays with high densities.
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Affiliation(s)
- Zheng-Chun Liu
- School of Chemical and Biological Engineering, Seoul National University, Kwanak-Gu, Seoul 151-742, South Korea.
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38
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Wiedro K, Stachowska E, Chlubek D. [Real-time polymerase chain reaction (RT-PCR)]. Ann Acad Med Stetin 2007; 53:5-9. [PMID: 18595479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The work present PCR (Polymerase Chain Reaction) with the real time analysis of the increase of product allowing quick detection, duplication and identification of even slight amounts of nucleic acids. Essential methods used in molecular diagnostics, based on marked probes and fluorescence phenomenon were discussed. Increased sensitivity of technology, the possibility of analysis and visualization of products during the time of reaction, enabled the progress of highly effective diagnostics applications.
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Affiliation(s)
- Katarzyna Wiedro
- Zakład Biochemii Katedry Biochemii i Chemii Medycznej Pomorskiej Akademii Medycznej w Szczecinie, Szczecin
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39
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Yesilkaya H, Meacci F, Niemann S, Hillemann D, Rüsch-Gerdes S, Barer MR, Andrew PW, Oggioni MR. Evaluation of molecular-Beacon, TaqMan, and fluorescence resonance energy transfer probes for detection of antibiotic resistance-conferring single nucleotide polymorphisms in mixed Mycobacterium tuberculosis DNA extracts. J Clin Microbiol 2006; 44:3826-9. [PMID: 17021120 PMCID: PMC1594805 DOI: 10.1128/jcm.00225-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of fluorescence resonance energy transfer, molecular-beacon, and TaqMan probes to detect single nucleotide polymorphism (SNP) in the presence of a wild-type allele was evaluated using drug resistance-conferring SNPs in mixed Mycobacterium tuberculosis DNA. It was found that both the absolute quantity and the ratio of alleles determine the detection sensitivity of the probe systems.
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Affiliation(s)
- Hasan Yesilkaya
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, United Kingdom
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40
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Lefmann M, Schweickert B, Buchholz P, Göbel UB, Ulrichs T, Seiler P, Theegarten D, Moter A. Evaluation of peptide nucleic acid-fluorescence in situ hybridization for identification of clinically relevant mycobacteria in clinical specimens and tissue sections. J Clin Microbiol 2006; 44:3760-7. [PMID: 17021106 PMCID: PMC1594750 DOI: 10.1128/jcm.01435-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 08/05/2006] [Indexed: 11/20/2022] Open
Abstract
With fluorescently labeled PNA (peptide nucleic acid) probes targeting 16S rRNA, we established a 3-h fluorescence in situ hybridization (FISH) procedure for specific visualization of members of the Mycobacterium tuberculosis complex, M. leprae, M. avium, and M. kansasii. Probe specificity was tested against a panel of 25 Mycobacterium spp. and 10 gram-positive organisms. After validation, probes were used to identify 52 mycobacterial culture isolates. Results were compared to conventional genotypic identification with amplification-based methods. All isolates (M. tuberculosis complex, n = 24; M. avium, n = 7; M. kansasii, n = 1) were correctly identified by FISH. In addition, the technique was used successfully for visualization of mycobacteria in biopsies from infected humans or animals. In conclusion, PNA-FISH is a fast and accurate tool for species-specific identification of culture-grown mycobacteria and for direct visualization of these organisms in tissue sections. It may be used successfully for both research and clinical microbiology.
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Affiliation(s)
- Michael Lefmann
- Institut für Mikrobiologie und Hygiene, Charité-Universitätsmedizin Berlin, Dorotheenstr. 96, 10117 Berlin, Germany.
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Abstract
SNPmasker is a comprehensive web interface for masking large eukaryotic genomes. The program is designed to mask SNPs from recent dbSNP database and to mask the repeats with two alternative programs. In addition to the SNP masking, we also offer population-specific substitution of SNP alleles in genomic sequence according to SNP frequencies in HapMap Phase II data. The input to SNPmasker can be defined in chromosomal coordinates or inserted as a sequence. The sequences masked by our web server are most useful as a preliminary step for different primer and probe design tasks. The service is available at http://bioinfo.ebc.ee/snpmasker/ and is free for all users.
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Affiliation(s)
- Reidar Andreson
- Department of Bioinformatics, University of TartuEstonia
- Estonian Biocentre, TartuEstonia
| | - Tarmo Puurand
- Department of Bioinformatics, University of TartuEstonia
| | - Maido Remm
- Department of Bioinformatics, University of TartuEstonia
- Estonian Biocentre, TartuEstonia
- To whom correspondence should be addressed. Tel: +372 7375001; Fax: +372 7420286;
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42
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Li YM, Wang JY, Chen Y, Shao JB, Wang J, Tong Y. [Detection of mtDNA*LHON G11778A mutation by real-time polymerase chain reaction using TaqMan-MGB probe technology]. Zhonghua Yan Ke Za Zhi 2006; 42:728-32. [PMID: 17081446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
OBJECTIVE To develop a simple, rapid and reliable real-time PCR assay based on TaqMan technology using a new MGB probe for detecting mtDNA(*)LHON G11778A mutation and heteroplasmy directly. METHODS Twenty patients with suspicion of Leber hereditary optic neuropathy (LHON) and their maternal relatives had undergone molecular genetic evaluation. Seventeen normal individuals were used as the controls. A real-time PCR involved two MGB probes (wild-type and mutation-type) in a single tube on the iCycler IQ real-time detection system was used to detect the mtDNA(*)LHON G11778A mutation. The results were then compared with the DNA sequence analysis of the PCR products. A linear standard curve was obtained by pUCm LHON-G and pUCm LHON-A clone. RESULTS In the controls (wild type), the reaction of VIC-labeled MGB probe was positive and the channel of FAM reaction was negative, the DNA sequence was 100% matched to previously published data. In 20 LHON patients and their maternal relatives, 12 cases showed mutations in DNA sequence analysis, all of them were LHON mtDNA mutation. While 5 other cases showed the combination of LHON mtDNA mutation and wide type gene phenotype, the rate of Ct value in wild type versus gene mutation was over 25%. DNA sequence analysis showed 8 of LHON mtDNA belonged to wild types and 3 cases were heteroplasmy, and the rate of Ct value in gene mutation versus wild type was lower than 25%. CONCLUSION This real-time PCR assay is a simple, rapid and reliable method for the detection of genotyping mtDNA mutations as well as for quantifying heteroplasmy.
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Affiliation(s)
- Yu-min Li
- Zheyi Eye Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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Schulz R, Menheniott TR, Woodfine K, Wood AJ, Choi JD, Oakey RJ. Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. Nucleic Acids Res 2006; 34:e88. [PMID: 16855283 PMCID: PMC1524921 DOI: 10.1093/nar/gkl461] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/26/2006] [Accepted: 06/15/2006] [Indexed: 01/06/2023] Open
Abstract
Genomic imprinting refers to a specialized form of epigenetic gene regulation whereby the expression of a given allele is dictated by parental origin. Defining the extent and distribution of imprinting across genomes will be crucial for understanding the roles played by imprinting in normal mammalian growth and development. Using mice carrying uniparental disomies or duplications, microarray screening and stringent bioinformatics, we have developed the first large-scale tissue-specific screen for imprinted gene detection. We quantify the stringency of our methodology and relate it to previous non-tissue-specific large-scale studies. We report the identification in mouse of four brain-specific novel paternally expressed transcripts and an additional three genes that show maternal expression in the placenta. The regions of conserved linkage in the human genome are associated with the Prader-Willi Syndrome (PWS) and Beckwith-Wiedemann Syndrome (BWS) where imprinting is known to be a contributing factor. We conclude that large-scale systematic analyses of this genre are necessary for the full impact of genomic imprinting on mammalian gene expression and phenotype to be elucidated.
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Affiliation(s)
- Reiner Schulz
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
| | - Trevelyan R. Menheniott
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
| | - Kathryn Woodfine
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
| | - Andrew J. Wood
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
| | - Jonathan D. Choi
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
| | - Rebecca J. Oakey
- King's College London, School of Medicine at Guy's, King's College and St. Thomas' Hospitals, Department of Medical and Molecular Genetics8th Floor Guy's Tower, London SE1 9RT, UK
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Bar-Or C, Bar-Eyal M, Gal TZ, Kapulnik Y, Czosnek H, Koltai H. Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results. BMC Genomics 2006; 7:110. [PMID: 16677401 PMCID: PMC1482311 DOI: 10.1186/1471-2164-7-110] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 05/08/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the approaches for conducting genomics research in organisms without extant microarray platforms is to profile their expression patterns by using Cross-Species Hybridization (CSH). Several different studies using spotted microarray and CSH produced contradicting conclusions in the ability of CSH to reflect biological processes described by species-specific hybridization (SSH). RESULTS We used a tomato-spotted cDNA microarray to examine the ability of CSH to reflect SSH data. Potato RNA was hybridized to spotted cDNA tomato and potato microarrays to generate CSH and SSH data, respectively. Difficulties arose in obtaining transcriptomic data from CSH that reflected those obtained from SSH. Nevertheless, once the data was filtered for those corresponding to matching probe sets, by restricting proper cutoffs of probe homology, the CSH transcriptome data showed improved reflection of those of the SSH. CONCLUSIONS This study evaluated the relative performance of CSH compared to SSH, and proposes methods to ensure that CSH closely reflects the biological process analyzed by SSH.
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Affiliation(s)
- Carmiya Bar-Or
- Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture of the Hebrew University of Jerusalem, Rehovot, Israel
| | - Meira Bar-Eyal
- Department of Nematology, ARO Volcani Center, Bet Dagan, Israel
| | - Tali Z Gal
- Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, Israel
| | - Yoram Kapulnik
- Depatment of Agronomy & Natural Resources, ARO Volcani Center, Bet Dagan, Israel
| | - Henryk Czosnek
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture of the Hebrew University of Jerusalem, Rehovot, Israel
| | - Hinanit Koltai
- Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, Israel
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Schatz P, Distler J, Berlin K, Schuster M. Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection. Nucleic Acids Res 2006; 34:e59. [PMID: 16670426 PMCID: PMC1456329 DOI: 10.1093/nar/gkl218] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The methylation of CpG dinucleotides has become a topic of great interest in cancer research, and the methylation of promoter regions of several tumor suppressor genes has been identified as a marker of tumorigenesis. Evaluation of DNA methylation markers in tumor tissue requires hundreds of samples, which must be analyzed quantitatively due to the heterogeneous composition of biological material. Therefore novel, fast and inexpensive methods for high throughput analysis are needed. Here we introduce a new assay based on peptide nucleic acid (PNA)-library hybridization and subsequent MALDI-TOF analysis. This method is multiplexable, allows the use of standard 384 well automated pipetting, and is more specific and flexible than established methods, such as microarrays and MS-SNuPE. The approach was used to evaluate three candidate colon cancer methylation markers previously identified in a microarray study. The methylation of the genes Ade-nomatous polyposis coli (APC), glycogen synthase kinase-beta-3 (GSK3beta) and eyes absent 4 (EYA4) was analyzed in 12 colon cancer and 12 normal tissues. APC and EYA4 were confirmed as being differentially methylated in colon cancer patients whereas GSK3beta did not show differential methylation.
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Affiliation(s)
| | | | | | - Matthias Schuster
- To whom correspondence should be addressed. Tel: +49 30 24345100; Fax: +49 30 24345555;
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Tamiya S. [Immunohistochemistry and in situ hybridizattion--method and pathological significance]. Fukuoka Igaku Zasshi 2006; 97:92-8. [PMID: 16768180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Sadafumi Tamiya
- Department of Health Sciences, School of Medicine, Kyushu University
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Liu D, Lawrence ML, Austin FW, Ainsworth AJ, Pace LW. PCR detection of pathogenic Leptospira genomospecies targeting putative transcriptional regulator genes. Can J Microbiol 2006; 52:272-7. [PMID: 16604124 DOI: 10.1139/w05-120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Leptospira comprises multiple genomospecies that demonstrate varied pathogenic potential. The availability of rapid and precise diagnostic procedures to differentiate pathogenic from nonpathogenic Leptospira spp. is therefore essential to prevent an otherwise easily treatable malaise from developing into a life-threatening disease. In this report, we conducted an investigation on the diagnostic potential of Leptospira genes encoding putative tran scriptional regulators. While PCR primers derived from transcriptional regulator gene la1137 recognized all 24 pathogenic Leptospira strains representing seven species, those from la1937, la3231, la3825, and la4130 detected 19 of the 24 Leptospira strains. However, none of these primers reacted with four nonpathogenic Leptospira species or other common bacteria. The putative transcriptional regulator genes la1137, la1937, la3231, la3825, and la4130 are present in pathogenic Leptospira strains, making them potential targets for diagnostic applications. Further characterization of these genes and their proteins may help elucidate the molecular mechanisms of leptospiral virulence and pathogenicity and pave the way for potential development of novel control strategies against leptospirosis.Key words: Leptospira, pathogenic, transcriptional regulator gene, PCR, identification.
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Affiliation(s)
- Dongyou Liu
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS 39762, USA.
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Nanda I, Karl E, Volobouev V, Griffin DK, Schartl M, Schmid M. Extensive gross genomic rearrangements between chicken and Old World vultures (Falconiformes: Accipitridae). Cytogenet Genome Res 2006; 112:286-95. [PMID: 16484785 DOI: 10.1159/000089883] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 08/10/2005] [Indexed: 11/19/2022] Open
Abstract
The karyotypes of most birds consist of a small number of macrochromosomes and numerous microchromosomes. Intriguingly, most accipitrids which include hawks, eagles, kites, and Old World vultures (Falconiformes) show a sharp contrast to this basic avian karyotype. They exhibit strikingly few microchromosomes and appear to have been drastically restructured during evolution. Chromosome paints specific to the chicken (GGA) macrochromosomes 1-10 were hybridized to metaphase spreads of three species of Old World vultures (Gyps rueppelli, Gyps fulvus, Gypaetus barbatus). Paints of GGA chromosomes 6-10 hybridize only to single chromosomes or large chromosome segments, illustrating the existence of high chromosome homology. In contrast, paints of the large macrochromosomes 1-5 show split hybridization signals on the chromosomes of the accipitrids, disclosing excessive chromosome rearrangements which is in clear contrast to the high degree of chromosome conservation substantiated from comparative chromosome painting in other birds. Furthermore, the GGA chromosome paint hybridization patterns reveal remarkable interchromosomal conservation among the two species of the genus Gyps.
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Affiliation(s)
- I Nanda
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Duan ZY, Guo YQ, Liu JX. [Application of modern molecular biology techniques to study micro-ecosystem in the rumen]. Wei Sheng Wu Xue Bao 2006; 46:166-9. [PMID: 16579489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The microbial community inhabiting in the rumen is characterized by its high population density, wide diversity and interactive complexity. However, until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional characterization) which probably only account for 10% to 20% of the rumen microbial population. Modem molecular biology techniques provide effective methods to study the micro-ecosystem in the rumen. The use of molecular techniques based on nucleic acid probes is likely to revolutionize the approach to microbial ecology in the rumen and provide, not simply a refinement or increased understanding but a complete description of rumen community for the first time. Modem molecular techniques based on sequence comparisons of nucleic acids may be used to explore molecular characterization and provide a classification scheme which predicts natural evolutionary relationships. Genetic fingerprinting techniques that provide a pattern or profile of genetic diversity have been applied in a variety of environmental studies for the analysis of microbial communities. Whole-cell hybridization is a powerful technique which may be used to study the structure and function of microbial communities in situ and describe the expression of key enzymes. Real-time quantitative PCR technique may be conducted to accurately quantify the target microorganisms in the rumen. Development of these procedures and techniques will result in greater insights into community structure and activity of rumen microbial communities in relation to functional interactions, spatial and temporal relationships between different microorganisms and between microorganisms and feed particles. The successful development and application of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural environment with their genetic potential and in situ activities.
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Affiliation(s)
- Zhi-yong Duan
- Institute of Dairy Science, Zhejiang University, Hangzhou 310029, China.
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Abstract
The polymerase chain reaction (PCR) has become one of the most important tools in molecular diagnostics, providing exquisite sensitivity and specificity for detection of nucleic acid targets. Real-time monitoring of PCR has simplified and accelerated PCR laboratory procedures and has increased information obtained from specimens including routine quantification and differentiation of amplification products. Clinical diagnostic applications and uses of real-time PCR are growing exponentially, real-time PCR is rapidly replacing traditional PCR, and new diagnostic uses likely will emerge. This review analyzes the scope of present and potential future clinical diagnostic applications of this powerful technique. Critical discussions focus on basic concepts, variations, data analysis, instrument platforms, signal detection formats, sample collection, assay design, and execution of real-time PCR.
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Affiliation(s)
- Bernhard Kaltenboeck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
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