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Zhang Y, Li L, Li J, Ma Q. Integrating aptasensor with an explosive mass-tag signal amplification strategy for ultrasensitive and multiplexed analysis using a miniature mass spectrometer. Biosens Bioelectron 2024; 249:116010. [PMID: 38215638 DOI: 10.1016/j.bios.2024.116010] [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: 11/08/2023] [Revised: 12/23/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
Mass probes attached with aptamers and mass tags offer excellent specificity and sensitivity for multiplexed detection, wherein the dissociation of mass tags from the mass probes is as important as their labeling. Herein, aggregation-induced emission luminogen (AIEgen)-tagged mass probes (AIEMPs) were established to analyze estrogens, which integrated aptasensor with an explosive mass-tag signal amplification strategy via a simple ultrasound-assisted emulsification of nanoliposomes. The AIEMPs were assembled by the hybridization of aptamer-modified Fe3O4 nanoparticles (Fe NPs@Apt) and nanoliposomes loaded with massive AIEgen mass tags and partially complementary DNA strands (AIE NLs@cDNA). The aptamer was preferentially and specifically bound to estrogen, resulting in the detachment of AIE NLs from AIEMPs. Subsequently, the AIEMPs were deposited with electrospray solvents for explosive release of mass tags. Using nanoelectrospray ionization mass spectrometry (nanoESI-MS), the AIEMP-based aptasensor achieved ultrasensitive analysis of estrogens with limits of detection of 0.168-0.543 pg/mL and accuracies in the range of 87.9-114.0%. Compared to direct nanoESI-MS detection, the AIEMP-based aptasensor provides a signal amplification of four orders of magnitude. Furthermore, the utilization of different AIEMPs enables multiplexed detection of three estrogens with a miniature mass spectrometer, showing promising potential for on-site detection. This work expands the diversity of mass-tagging strategy and provides a versatile mass probe-based aptasensor platform for routine MS detection of trace analytes.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Consumer Product Quality Safety Inspection and Risk Assessment for State Market Regulation, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Linsen Li
- Key Laboratory of Consumer Product Quality Safety Inspection and Risk Assessment for State Market Regulation, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jingjing Li
- College of Chemistry, Tianjin Normal University, Tianjin 300387, China
| | - Qiang Ma
- Key Laboratory of Consumer Product Quality Safety Inspection and Risk Assessment for State Market Regulation, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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2
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Wu Z, Sun DW, Pu H. CRISPR/Cas12a and G-quadruplex DNAzyme-driven multimodal biosensor for visual detection of Aflatoxin B1. Spectrochim Acta A Mol Biomol Spectrosc 2023; 302:123121. [PMID: 37579713 DOI: 10.1016/j.saa.2023.123121] [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] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 08/16/2023]
Abstract
Aflatoxin B1 (AFB1) contamination severely threatens human and animal health, it is thus critical to construct a strategy for its rapid, accurate, and visual detection. Herein, a multimodal biosensor was proposed based on CRISPR/Cas12a cleaved G-quadruplex (G4) for AFB1 detection. Briefly, specific binding of AFB1 to the aptamer occupied the binding site of the complementary DNA (cDNA), and cDNA then activated Cas12a to cleave G4 into fragments. Meanwhile, the intact G4-DNAzyme could catalyze 3, 3', 5, 5'-tetramethylbenzidine (TMB) to form colourimetric/SERS/fluorescent signal-enhanced TMBox, and the yellow solution produced by TMBox under acidic conditions could be integrated with a smartphone application for visual detection. The colourimetric/SERS/fluorescent biosensor yielded detection limits of 0.85, 0.79, and 1.65 pg·mL-1, respectively, and was applied for detecting AFB1 in peanut, maize, and badam samples. The method is suitable for visual detection in naturally contaminated peanut samples and has prospective applications in the food industry.
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Affiliation(s)
- Zhihui Wu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
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3
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Qiao M, Liu Y, Wei M. Dual-signal output fluorescent aptasensor based on DNA programmability and gold nanoflowers for multiple mycotoxins detection. Anal Bioanal Chem 2023; 415:277-288. [PMID: 36376716 DOI: 10.1007/s00216-022-04403-x] [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: 09/01/2022] [Revised: 10/04/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Herein, a dual-signal output fluorescent aptamer sensor was constructed for the simultaneous detection of aflatoxin B1 (AFB1) and ochratoxin A (OTA) using the specific recognition ability of aptamers and the programmability of DNA. A functional capture probe (cDNA) was designed with the black hole quenching motif BHQ1 labeled at the 5' end and biotin (bio) labeled at the 3' end. The fluorescent dye Cy3-labeled aflatoxin B1 aptamer (AFB1-Apt) and the carboxyfluorescein FAM-labeled ochratoxin A aptamer (OTA-Apt) were used as two fluorescent probes. The cDNA is anchored to the quenching material gold nanoflowers (AuNFs) by the action of streptavidin (SA) and biotin. Its ends can be complementarily paired with two fluorescent probe bases to form a double-stranded structure. The fluorescence of Cy3 was quenched by AuNFs, and the fluorescence of FAM was quenched by BHQ1 through the fluorescence energy resonance transfer (FRET) effect, forming a fluorescence quenching system. Due to the high affinity of the target and the aptamer, the structure of the aptamer probe changes and detaches from the sensor when AFB1 and OTA are present, resulting in enhanced fluorescence. Under optimal conditions, the linear range of AFB1 was 0.1-100 ng/mL (R2 = 0.996), the limit of detection (LOD) was as low as 0.014 ng/mL, and the limit of quantification (LOQ) was 0.046 ng/mL. The linear range of OTA was 0.1-100 ng/mL (R2 = 0.995), the limit of detection (LOD) was as low as 0.027 ng/mL, and the limit of quantification (LOQ) was 0.089 ng/mL. The sensor had high accuracy in detecting both AFB1 and OTA in real sample analysis. The results of the t test show that there is no significant difference between the results of this study and the high-performance liquid phase (HPLC) method, indicating that the prepared sensor can be used as a potential platform for multiple mycotoxins detection.
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Affiliation(s)
- Mengxiang Qiao
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Henan University of Technology, Zhengzhou, 450001, People's Republic of China
| | - Yong Liu
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, People's Republic of China
| | - Min Wei
- College of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.
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4
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Li J, Yang Y, Li J, Li P, Qi H. Cell-Free Display Techniques for Protein Evolution. Adv Biochem Eng Biotechnol 2023; 185:59-90. [PMID: 37306697 DOI: 10.1007/10_2023_227] [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] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free protein synthesis (CFPS) with flexibility and controllability can provide a powerful platform for high-throughput screening of biomolecules, especially in the evolution of peptides or proteins. In this chapter, the emerging strategies for enhancing the protein expression level using different source strains, energy systems, and template designs in constructing CFPS systems are summarized and discussed in detail. In addition, we provide an overview of the ribosome display, mRNA display, cDNA display, and CIS display in vitro display technologies, which can couple genotype and phenotype by forming fusion complexes. Moreover, we point out the trend that improving the protein yields of CFPS itself can offer more favorable conditions for maintaining library diversity and display efficiency. It is hoped that the novel CFPS system can accelerate the development of protein evolution in biotechnological and medical applications.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Youhui Yang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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5
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Zhang H, Ye S, Huang L, Fan S, Mao W, Hu Y, Yu Y, Fu F. An electrochemical biosensor for the detection of aflatoxin B1 based on the specific aptamer and HCR biological magnification. Anal Methods 2022; 15:99-108. [PMID: 36484245 DOI: 10.1039/d2ay01682f] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Aflatoxin B1 (AFB1) is a highly toxic mycotoxin, which causes severe acute or cumulative poisoning. Therefore, it is important to develop sensitive and selective detection methods for AFB1 for the safety of food and medicinal herbs. Herein, we have developed a "signal-on" electrochemical aptasensor based on the high specificity of the aptamer and hybridization chain reaction (HCR) biological amplification for AFB1 detection. In this work, thiol-modified complementary DNA (cDNA) immobilized on the surface of a gold electrode (GE) served as an initiator DNA. When AFB1 was present, it competed with the cDNA for binding to the aptamers, which resulted in the detaching of aptamers from the cDNA-aptamer duplexes. Then, the single-stranded cDNA acted as an initiator to trigger the HCR signal amplification. Therefore, long double-stranded DNA (dsDNA) products were produced, which could load large amounts of methylene blue (MB) molecules to generate a distinct electrochemical signal. Under the optimized conditions, the proposed electrochemical aptasensor achieved the ultrasensitive detection of AFB1 with a linear detection range of 0.01-100 pg mL-1, and a limit of detection (LOD) down to 2.84 fg mL-1. Furthermore, the electrochemical aptasensor was successfully applied for detecting AFB1 in corn and two kinds of traditional Chinese medicine samples, indicating the potential value for AFB1 detection in practical samples.
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Affiliation(s)
- Hongyan Zhang
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Siying Ye
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Lishan Huang
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Shen Fan
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Weiwei Mao
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Yijin Hu
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Yuyan Yu
- Joint National Local Engineering Research Center of Fujian and Taiwan Chinese Medicine Molecular Biotechnology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Fengfu Fu
- Key Lab of Analysis and Detection for Food Safety of Ministry of Education, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China.
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6
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Zhan H, Yang S, Li C, Liu R, Chen W, Wang X, Zhao Y, Xu K. A highly sensitive competitive aptasensor for AFB 1 detection based on an exonuclease-assisted target recycling amplification strategy. Anal Methods 2022; 15:70-78. [PMID: 36477094 DOI: 10.1039/d2ay01617f] [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: 06/17/2023]
Abstract
Aflatoxin B1 (AFB1) is a typical mycotoxin found in agricultural products, and poses a huge threat to both humans and animals. Accurate and rapid measurement of AFB1 is essential for environmental analysis and food safety. Based on molecular docking simulation design and exonuclease-assisted target recycling amplification, we designed a competitive fluorescence aptasensor to detect AFB1 rapidly and sensitively. According to the molecular docking simulations, a complementary strand (cDNA) was designed by searching for potential binding sites of the aptamer, which had the lowest binding energy. Magnetic beads modified with biotin-Apt were used as the capture probe, while FAM-labeled cDNA acted as the reporter probe. By using EXO I for target recycling amplification, this aptasensor was highly sensitive and selective for AFB1. The detection limit of the suggested aptasensor under optimal conditions was 0.36 ng mL-1 (S/N = 3) in the range of 1-1000 ng mL-1 (R2 = 0.991). The developed aptasensor was successfully used to analyze AFB1 in oil samples.
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Affiliation(s)
- Hongyan Zhan
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Si Yang
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Chenxi Li
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
| | - Rong Liu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
| | - Wenliang Chen
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, PR China
| | - Xiaoli Wang
- Department of Medical Imaging, Weifang Medical University, Weifang, Shandong 261053, China
| | - Yansong Zhao
- Department of Ophthalmology, Clinical Medical Institute, Affiliated Hospital, Weifang Medical University, Weifang, Shandong 261031, China
| | - Kexin Xu
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, PR China.
- School of Precision Instruments and Optoelectronics Engineering, Tianjin University, Tianjin 300072, PR China
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7
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Yang B, Zhao Z, Pan Y, Xie J, Zhou B, Li Y, Dong Y, Liu D. Shear-Thinning and Designable Responsive Supramolecular DNA Hydrogels Based on Chemically Branched DNA. ACS Appl Mater Interfaces 2021; 13:48414-48422. [PMID: 34633793 DOI: 10.1021/acsami.1c15494] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 06/13/2023]
Abstract
A novel supramolecular DNA hydrogel system was designed based on a directly synthesized chemically branched DNA. For the hydrogel formation, a self-dimer DNA with two sticky ends was designed as the linker to induce the gelation of B-Y. By programing the linker sequence, thermal and metal-ion responsiveness could be introduced into this hydrogel system. This supramolecular DNA hydrogel shows shear-thinning, designable responsiveness, and good biocompatibility, which will simplify the hydrogel composition and preparation process of the supramolecular DNA hydrogel and accelerate its biomedical applications.
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Affiliation(s)
- Bo Yang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhihan Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiayin Xie
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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8
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Yang H, Chen J, Liang Y, Zhang Y, Yin W, Xu Y, Liu SY, Dai Z, Zou X. A MOF-Shell-Confined I-Motif-Based pH Probe (MOFC-i) Strategy for Sensitive and Dynamic Imaging of Cell Surface pH. ACS Appl Mater Interfaces 2021; 13:45291-45299. [PMID: 34542269 DOI: 10.1021/acsami.1c13720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/13/2023]
Abstract
Dynamic imaging of cell surface pH is extremely challenging due to the slight changes in pH and the fast diffusion of secreted acid to the extracellular environment. In this work, we construct a novel metal-organic framework (MOF)-shell-confined i-motif-based pH probe (MOFC-i) strategy that enables sensitive and dynamic imaging of cell surface pH. The CY3- and CY5-labeled i-motif, which is hybridized via its short complementary chain with two-base mismatches, is optimized for sensing at physiological pH. After efficiently anchoring the optimized pH probes onto the cell membrane with the aid of cholesterol groups, a biocompatible microporous MOF shell is then formed around the cell by cross-linking ZIF-8 nanoparticles via tannic acid. The microporous MOF shell can confine secreted acid without inhibiting the normal physiological activities of cells; thus, the MOFC-i strategy can be used to monitor dynamic changes in the cell surface pH of living cells. Furthermore, this method can not only clearly distinguish the different metabolic behaviors of cancer cells and normal cells but also reveal drug effects on the cell surface pH or metabolism, providing promising prospects in pH-related diagnostics and drug screening.
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Affiliation(s)
- Huihui Yang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuling Liang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen Yin
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuzhi Xu
- Scientific Research Center, Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, China
| | - Si-Yang Liu
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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9
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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10
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Top O, Milferstaedt SWL, van Gessel N, Hoernstein SNW, Özdemir B, Decker EL, Reski R. Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms. Commun Biol 2021; 4:964. [PMID: 34385580 PMCID: PMC8361020 DOI: 10.1038/s42003-021-02486-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 07/26/2021] [Indexed: 12/18/2022] Open
Abstract
Production of biopharmaceuticals relies on the expression of mammalian cDNAs in host organisms. Here we show that the expression of a human cDNA in the moss Physcomitrium patens generates the expected full-length and four additional transcripts due to unexpected splicing. This mRNA splicing results in non-functional protein isoforms, cellular misallocation of the proteins and low product yields. We integrated these results together with the results of our analysis of all 32,926 protein-encoding Physcomitrella genes and their 87,533 annotated transcripts in a web application, physCO, for automatized optimization. A thus optimized cDNA results in about twelve times more protein, which correctly localizes to the ER. An analysis of codon preferences of different production hosts suggests that similar effects occur also in non-plant hosts. We anticipate that the use of our methodology will prevent so far undetected mRNA heterosplicing resulting in maximized functional protein amounts for basic biology and biotechnology.
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Affiliation(s)
- Oguz Top
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Stella W L Milferstaedt
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Bugra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, Freiburg, Germany.
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11
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Fuentealba NA, Moré G, Bravi ME, Unzaga JM, De Felice L, Salina M, Viegas M, Nabaes Jodar MS, Valinotto LE, Rivero FD, Di Lullo D, Pecoraro M, Panei CJ. First detection and molecular analysis of SARS-CoV-2 from a naturally infected cat from Argentina. Vet Microbiol 2021; 260:109179. [PMID: 34271305 PMCID: PMC8265177 DOI: 10.1016/j.vetmic.2021.109179] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has rapidly spread worldwide. Studies of transmission of the virus carried out in animals have suggested that certain animals may be susceptible to infection with SARS-CoV-2. The aim of the present study was to investigate the infection of SARS-CoV-2 in pets (18 cats and 20 dogs) from owners previously confirmed as COVID-19-positive. Oropharyngeal and rectal swabs were taken and analyzed by real-time RT-PCR assays, while blood samples were taken for antibody detection. Of the total pets analyzed, one cat was found reactive to SARS-CoV-2 by real-time RT-PCR of an oropharyngeal and a rectal swab. This cat presented only sneezing as a clinical sign. Serological analysis confirmed the presence of antibodies in the serum sample from this cat, as well as in the serum from another cat non-reactive to real-time RT-PCR. Complete sequence and phylogenetic analysis allowed determining that the SARS-CoV-2 genome belonged to the B.1.499 lineage. This lineage has been reported in different provinces of Argentina, mainly in the Metropolitan Area of Buenos Aires. This study notifies the first detection of the natural infection and molecular analysis of SARS-CoV-2 in a cat from Argentina whose owner where COVID-19-positive. Although there is currently no evidence that cats can spread COVID-19, results suggest that health authorities should test pets with COVID-19-positive owners.
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Affiliation(s)
- Nadia Analía Fuentealba
- Laboratorio de Virología, Facultad de Ciencias Veterinarias (FCV), Universidad Nacional de La Plata (UNLP), 60 & 118, La Plata, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Gastón Moré
- Laboratorio de Inmunoparasitología, FCV-UNLP, 60 & 118, La Plata, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Emilia Bravi
- Laboratorio de Virología, Facultad de Ciencias Veterinarias (FCV), Universidad Nacional de La Plata (UNLP), 60 & 118, La Plata, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Juan Manuel Unzaga
- Laboratorio de Inmunoparasitología, FCV-UNLP, 60 & 118, La Plata, Buenos Aires, Argentina
| | - Lorena De Felice
- Laboratorio de Inmunoparasitología, FCV-UNLP, 60 & 118, La Plata, Buenos Aires, Argentina
| | - Marcos Salina
- Laboratorio de Virología, Facultad de Ciencias Veterinarias (FCV), Universidad Nacional de La Plata (UNLP), 60 & 118, La Plata, Buenos Aires, Argentina
| | - Mariana Viegas
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Virología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Mercedes Soledad Nabaes Jodar
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Virología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Laura Elena Valinotto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Centro de investigaciones en Genodermatosis y Epidermólisis Ampollar (CIDEGEA), Hospital de Niños Dr. Ricardo Gutiérrez / Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernando David Rivero
- Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD), CONICET-UNSE, Santiago del Estero, Argentina
| | - David Di Lullo
- Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD), CONICET-UNSE, Santiago del Estero, Argentina
| | - Marcelo Pecoraro
- Laboratorio de Virología, Facultad de Ciencias Veterinarias (FCV), Universidad Nacional de La Plata (UNLP), 60 & 118, La Plata, Buenos Aires, Argentina
| | - Carlos Javier Panei
- Laboratorio de Virología, Facultad de Ciencias Veterinarias (FCV), Universidad Nacional de La Plata (UNLP), 60 & 118, La Plata, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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12
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Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021; 60:1971-1982. [PMID: 34121404 PMCID: PMC8256721 DOI: 10.1021/acs.biochem.1c00270] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 12/20/2022]
Abstract
Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that "jumps" across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.
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Affiliation(s)
- Thomas W. Christy
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Catherine A. Giannetti
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew J. Smola
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Jian Wang
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Nikolay V. Dokholyan
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Departments of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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13
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Lin Y, Zeng Y, Zhu Y, Shen J, Ye H, Jiang L. Plant Rho GTPase signaling promotes autophagy. Mol Plant 2021; 14:905-920. [PMID: 33794369 DOI: 10.1016/j.molp.2021.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/27/2021] [Accepted: 03/25/2021] [Indexed: 05/06/2023]
Abstract
The roles of Rho family guanosine triphosphatases (GTPases) of plants (ROPs) in modulating plant growth and development have been well characterized. However, little is known about the roles of ROP signaling pathways in regulating plant autophagy and autophagosome formation. In this study, we identify a unique ROP signaling mechanism, which mediates developmental to autophagic transition under stress conditions in the model plant Arabidopsis. Loss-of-function mutants of ROP8 showed stress-induced hypersensitive phenotypes and compromised autophagic flux. Similar to other ROPs in the ROP/RAC family, ROP8 exhibits both plasma membrane and cytosolic punctate localization patterns. Upon autophagic induction, active ROP8 puncta colocalize with autophagosomal markers and are degraded inside the vacuole. In human cells, RalB, an RAS subfamily GTPase, engages its effector Exo84 for autophagosome assembly. However, a RalB counterpart is missing in the plant lineage. Intriguingly, we discovered that plant ROP8 promotes autophagy via its downstream effector Sec5. Live-cell super-resolution imaging showed that ROP8 and Sec5 reside on phagophores for autophagosome formation. Taken together, our findings highlight a previously unappreciated role of an ROP8-Sec5 signaling axis in autophagy promotion, providing new insights into how plants utilize versatile ROP signaling networks to coordinate developmental and autophagic responses depending on environmental changes.
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Affiliation(s)
- Youshun Lin
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
| | - Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Ying Zhu
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hao Ye
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; Institute of Plant Molecular Biology and Agricultural Biotechnology, CUHK, Hong Kong, China; CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, N.T., Shenzhen, Hong Kong, 518057, China.
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14
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Shi L, Liu W, Li B, Yang CJ, Jin Y. Multichannel Paper Chip-Based Gas Pressure Bioassay for Simultaneous Detection of Multiple MicroRNAs. ACS Appl Mater Interfaces 2021; 13:15008-15016. [PMID: 33757287 DOI: 10.1021/acsami.1c01568] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 06/12/2023]
Abstract
Simultaneous detection of multi-biomarkers not only enhances the accuracy of disease diagnosis but also improves detection efficiency and reduces cost. It is vital to achieve portable, simple, low-cost, and simultaneous detection of biomarkers for point-of-care (POC) diagnostics in a low-resource setting. Herein, a multichannel paper chip-based gas pressure bioassay was developed for the simultaneous detection of multiple biomarkers by combining multichannel paper chips with a portable gas pressure meter. Four DNA tetrahedral probes (DTPs) were used as capture probes and were immobilized in different detection zones of the paper chips to improve hybridization efficiency and reduce nonspecific adsorption. The formation of a sandwich structure between target microRNAs (miRNAs), the capture probe, and platinum nanoparticles (PtNPs)-modified complementary DNA (PtNPs-cDNA) transformed biomolecular recognition into quantitative detection of gas pressure. Four lung cancer-related miRNAs were detected simultaneously by a portable gas pressure meter. There is a good linear relationship between gas pressure and the logarithm of miRNA concentration in the range of 10 pM to 100 nM. Compared with single-stranded DNA capture probe, the signal-to-noise (S/N) of DNA tetrahedral probes improved more than 3 times. Using ring-oven washing, the unbound reagents in all channels of the paper chip were simultaneously and continuously washed away, leading to a more cheap, simple, and fast separation than magnetic separation. Therefore, it offers a promising multichannel paper chip-based gas pressure bioassay for portable and simultaneous detection of multiple biomarkers.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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15
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Abstract
RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA structure and are now considered invaluable resources in the goal of relating structure to function. Recently, the power of deep sequencing and careful chemical probe design have merged, permitting researchers to obtain a holistic understanding of how RNA structure can be utilized to control RNA biology transcriptome-wide. Within this review, we outline the recent advancements in chemical probe design for interrogating RNA structures inside cells and discuss the recent advances in our understanding of RNA biology through the lens of chemical probing.
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Affiliation(s)
- Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chely M Garfio
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cellular Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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16
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He B, Wang K. A "signal off" aptasensor based on NiFe 2O 4 NTs and Au@Pt NRs for the detection of deoxynivalenol via voltammetry. Mikrochim Acta 2021; 188:23. [PMID: 33404751 DOI: 10.1007/s00604-020-04666-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/30/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
Abstract
A "signal off" aptasensor has been developed to detect deoxynivalenol (DON). DON aptamers (Apt) were used as biological recognition elements, nickel ferrite nanotubes (NiFe2O4 NTs) are used as the base material to increase the surface area of the electrode, and the Au@Pt NRs were used as carriers for loading signal labels thionine (Thi) and complementary strand (cDNA). In the presence of DON it will be specifically captured by Apt, then the competition mechanism was triggered; the signal molecules fall off from the electrode surface, which then causes the electrode signal to decrease. NiFe2O4 NTs and Au@Pt NRs were characterized by transmission electron microscope (TEM), scanning electron micrograph (SEM), energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD). The designed sensor provides a concentration range of 1 × 10-8 to 5 × 10-4 mg mL-1 and limit of detection of 3.02 × 10-9 mg mL-1. Determination of DON in corn meal samples was investigated and the recovery was 98.4 to 103.5%. The proposed aptasensor displayed good sensitivity, high specificity, and acceptable reproducibility. Graphical abstract Based on NiFe2O4 NTs as substrate material and Au@Pt NRs as signal label prepared DON aptasensor for the determination of DON.
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Affiliation(s)
- Baoshan He
- School of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Henan University of Technology, Lianhua Road 100#, Zhengzhou High & New Technology Industries Development Zone, Zhengzhou, 450001, Henan Province, People's Republic of China.
| | - Kai Wang
- School of Food Science and Technology, Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Henan University of Technology, Lianhua Road 100#, Zhengzhou High & New Technology Industries Development Zone, Zhengzhou, 450001, Henan Province, People's Republic of China
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17
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Srinivasan KA, Virdee SK, McArthur AG. Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data. Brief Funct Genomics 2020; 19:339-342. [PMID: 32415774 DOI: 10.1093/bfgp/elaa010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 11/12/2022] Open
Abstract
RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA library construction. Here, we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance.
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18
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Tao Z, Wei L, Wu S, Duan N, Li X, Wang Z. A colorimetric aptamer-based method for detection of cadmium using the enhanced peroxidase-like activity of Au-MoS 2 nanocomposites. Anal Biochem 2020; 608:113844. [PMID: 32763304 DOI: 10.1016/j.ab.2020.113844] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022]
Abstract
In this work, a colorimetric aptamer-based method for detection of cadmium using gold nanoparticles modified MoS2 nanocomposites as enzyme mimic is established. In short, biotinylated Cd2+ aptamers are immobilized by biotin-avidin binding on the bottoms of the microplate, the complementary strands of Cd2+ aptamers are connected to the Au-MoS2 nanocomposites which have the function of enhanced peroxidase-like activity. The csDNA-Au-MoS2 signal probe and target Cd2+ compete for binding Cd2+ aptamer, the color change can be observed by addition of chromogenic substrate, thereby realizing visual detection of Cd2+. The absorbance of the solution at 450 nm has a clear linear relationship with the Cd2+ concentration. The linear range is 1-500 ng/mL, and the limit of detection is 0.7 ng/mL. The assay was used to test white wine samples, the results are consistent with those of atomic absorption spectrometry; which prove that this method can be used for detection of Cd2+ in real samples.
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Affiliation(s)
- Zui Tao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Liting Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Xiang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China; Collaborative Innovation Center of Food Safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi, 214122, China.
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19
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Yang G, Zhao W, Qin C, Yang L, Meng X, Lu R, Yan X, Cao X, Zhang Y, Nie G. Molecular identification of grass carp igfbp2 and the effect of glucose, insulin, and glucagon on igfbp2 mRNA expression. Fish Physiol Biochem 2020; 46:1469-1482. [PMID: 32323051 DOI: 10.1007/s10695-020-00804-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
The GH (growth hormone)/IGFs (insulin-like growth factors) system has an important function in the regulation of growth. In this system, IGFBPs play a crucial regulatory role in IGF functions. As a member of the IGFBP family, IGFBP2 can bind to IGF and regulate IGF functions to regulate development and growth. In addition, IGFBP2 shows key regulatory functions in cell proliferation and metabolism. In this study, the igfbp2 gene was cloned from grass carp (Ctenopharyngodon idellus) liver. The ORF of grass carp igfbp2 is 834 bp long and encodes 277 amino acids. The tissue distribution results showed that igfbp2 is expressed in multiple tissues in grass carp and has a high expression level in the liver. In the OGTT, igfbp2 expression was significantly decreased in the liver and brain after 6 h of treatment with glucose. In vitro, igfbp2 expression in grass carp's primary hepatocytes was significantly suppressed by insulin after treatment for 6 and 12 h. Moreover, igfbp2 expression was markedly increased in a dose-dependent manner with glucagon incubation in grass carp's primary hepatocytes. To the best of our knowledge, this is the first report about Igfbp2 in grass carp. These results will provide a basis for the in-depth study of grass carp Igfbp2.
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Affiliation(s)
- Guokun Yang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Wenli Zhao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Chaobin Qin
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Liping Yang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xiaolin Meng
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xiao Yan
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xianglin Cao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Yanmin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China.
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20
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Al Kadi M, Jung N, Ito S, Kameoka S, Hishida T, Motooka D, Nakamura S, Iida T, Okuzaki D. UNAGI: an automated pipeline for nanopore full-length cDNA sequencing uncovers novel transcripts and isoforms in yeast. Funct Integr Genomics 2020; 20:523-536. [PMID: 31955296 PMCID: PMC7283198 DOI: 10.1007/s10142-020-00732-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Sequencing the entire RNA molecule leads to a better understanding of the transcriptome architecture. SMARTer (Switching Mechanism at 5'-End of RNA Template) is a technology aimed at generating full-length cDNA from low amounts of mRNA for sequencing by short-read sequencers such as those from Illumina. However, short read sequencing such as Illumina technology includes fragmentation that results in bias and information loss. Here, we built a pipeline, UNAGI or UNAnnotated Gene Identifier, to process long reads obtained with nanopore sequencing and compared this pipeline with the standard Illumina pipeline by studying the Saccharomyces cerevisiae transcriptome in full-length cDNA samples generated from two different biological samples: haploid and diploid cells. Additionally, we processed the long reads with another long read tool, FLAIR. Our strand-aware method revealed significant differential gene expression that was masked in Illumina data by antisense transcripts. Our pipeline, UNAGI, outperformed the Illumina pipeline and FLAIR in transcript reconstruction (sensitivity and specificity of 80% and 40% vs. 18% and 34% and 79% and 32%, respectively). Moreover, UNAGI discovered 3877 unannotated transcripts including 1282 intergenic transcripts while the Illumina pipeline discovered only 238 unannotated transcripts. For isoforms profiling, UNAGI also outperformed the Illumina pipeline and FLAIR in terms of sensitivity (91% vs. 82% and 63%, respectively). But the low accuracy of nanopore sequencing led to a closer gap in terms of specificity with Illumina pipeline (70% vs. 63%) and to a huge gap with FLAIR (70% vs 0.02%).
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Affiliation(s)
- Mohamad Al Kadi
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Nicolas Jung
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Shingo Ito
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Shoichiro Kameoka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Cykinso, Inc., Tokyo, 151-0053, Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, 171-0031, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, 565-0871, Japan
| | - Tetsuya Iida
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, 565-0871, Japan.
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan.
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Yamadaoka 3-1, Suita City, Osaka, Japan.
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Qiu G, Gai Z, Tao Y, Schmitt J, Kullak-Ublick GA, Wang J. Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection. ACS Nano 2020; 14:5268-5277. [PMID: 32281785 DOI: 10.1021/acsnano.0c0243910.1021/acsnano.0c02439.s001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ongoing outbreak of the novel coronavirus disease (COVID-19) has spread globally and poses a threat to public health in more than 200 countries. Reliable laboratory diagnosis of the disease has been one of the foremost priorities for promoting public health interventions. The routinely used reverse transcription polymerase chain reaction (RT-PCR) is currently the reference method for COVID-19 diagnosis. However, it also reported a number of false-positive or -negative cases, especially in the early stages of the novel virus outbreak. In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. For better sensing performance, the thermoplasmonic heat is generated on the same AuNIs chip when illuminated at their plasmonic resonance frequency. The localized PPT heat is capable to elevate the in situ hybridization temperature and facilitate the accurate discrimination of two similar gene sequences. Our dual-functional LSPR biosensor exhibits a high sensitivity toward the selected SARS-CoV-2 sequences with a lower detection limit down to the concentration of 0.22 pM and allows precise detection of the specific target in a multigene mixture. This study gains insight into the thermoplasmonic enhancement and its applicability in the nucleic acid tests and viral disease diagnosis.
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Affiliation(s)
- Guangyu Qiu
- Institute of Environmental Engineering, ETH Zürich, Zürich 8093, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf 8600, Switzerland
| | - Zhibo Gai
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zürich, Zürich 8091, Switzerland
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, PR China
| | - Yile Tao
- Institute of Environmental Engineering, ETH Zürich, Zürich 8093, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf 8600, Switzerland
| | - Jean Schmitt
- Institute of Environmental Engineering, ETH Zürich, Zürich 8093, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf 8600, Switzerland
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zürich, Zürich 8091, Switzerland
- Mechanistic Safety, CMO & Patient Safety, Global Drug Development, Novartis Pharma, Basel 4002, Switzerland
| | - Jing Wang
- Institute of Environmental Engineering, ETH Zürich, Zürich 8093, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf 8600, Switzerland
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22
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Qiu G, Gai Z, Tao Y, Schmitt J, Kullak-Ublick GA, Wang J. Dual-Functional Plasmonic Photothermal Biosensors for Highly Accurate Severe Acute Respiratory Syndrome Coronavirus 2 Detection. ACS Nano 2020; 14:5268-5277. [PMID: 32281785 PMCID: PMC7158889 DOI: 10.1021/acsnano.0c02439] [Citation(s) in RCA: 617] [Impact Index Per Article: 154.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
The ongoing outbreak of the novel coronavirus disease (COVID-19) has spread globally and poses a threat to public health in more than 200 countries. Reliable laboratory diagnosis of the disease has been one of the foremost priorities for promoting public health interventions. The routinely used reverse transcription polymerase chain reaction (RT-PCR) is currently the reference method for COVID-19 diagnosis. However, it also reported a number of false-positive or -negative cases, especially in the early stages of the novel virus outbreak. In this work, a dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction provides an alternative and promising solution for the clinical COVID-19 diagnosis. The two-dimensional gold nanoislands (AuNIs) functionalized with complementary DNA receptors can perform a sensitive detection of the selected sequences from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through nucleic acid hybridization. For better sensing performance, the thermoplasmonic heat is generated on the same AuNIs chip when illuminated at their plasmonic resonance frequency. The localized PPT heat is capable to elevate the in situ hybridization temperature and facilitate the accurate discrimination of two similar gene sequences. Our dual-functional LSPR biosensor exhibits a high sensitivity toward the selected SARS-CoV-2 sequences with a lower detection limit down to the concentration of 0.22 pM and allows precise detection of the specific target in a multigene mixture. This study gains insight into the thermoplasmonic enhancement and its applicability in the nucleic acid tests and viral disease diagnosis.
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Affiliation(s)
- Guangyu Qiu
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
| | - Zhibo Gai
- Department of Clinical Pharmacology and Toxicology,
University Hospital Zurich, University of Zürich,
Zürich 8091, Switzerland
- Experimental Center, Shandong University
of Traditional Chinese Medicine, Jinan 250355, PR
China
| | - Yile Tao
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
| | - Jean Schmitt
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
| | - Gerd A. Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology,
University Hospital Zurich, University of Zürich,
Zürich 8091, Switzerland
- Mechanistic Safety, CMO & Patient Safety, Global
Drug Development, Novartis Pharma, Basel 4002,
Switzerland
| | - Jing Wang
- Institute of Environmental Engineering,
ETH Zürich, Zürich 8093,
Switzerland
- Laboratory for Advanced Analytical Technologies, Empa,
Swiss Federal Laboratories for Materials Science and
Technology, Dübendorf 8600, Switzerland
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Terai T, Koike T, Nemoto N. Photocrosslinking of cDNA Display Molecules with Their Target Proteins as a New Strategy for Peptide Selection. Molecules 2020; 25:molecules25061472. [PMID: 32214008 PMCID: PMC7146492 DOI: 10.3390/molecules25061472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 12/29/2022] Open
Abstract
Binding peptides for given target molecules are often selected in vitro during drug discovery and chemical biology research. Among several display technologies for this purpose, complementary DNA (cDNA) display (a covalent complex of a peptide and its encoding cDNA linked via a specially designed puromycin-conjugated DNA) is unique in terms of library size, chemical stability, and flexibility of modification. However, selection of cDNA display libraries often suffers from false positives derived from non-specific binding. Although rigorous washing is a straightforward solution, this also leads to the loss of specific binders with moderate affinity because the interaction is non-covalent. To address this issue, herein, we propose a method to covalently link cDNA display molecules with their target proteins using light irradiation. We designed a new puromycin DNA linker that contains a photocrosslinking nucleic acid and prepared cDNA display molecules using the linker. Target proteins were also labeled with a short single-stranded DNA that should transiently hybridize with the linker. Upon ultraviolet (UV) light irradiation, cDNA display molecules encoding correct peptide aptamers made stable crosslinked products with the target proteins in solution, while display molecules encoding control peptides did not. Although further optimization and improvement is necessary, the results pave the way for efficient selection of peptide aptamers in multimolecular crowding biosystems.
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Affiliation(s)
- Takuya Terai
- Correspondence: (T.T.); or (N.N); Tel.: +81-48-858-3534 (T.T.); +81-48-858-3531 (N.N.)
| | | | - Naoto Nemoto
- Correspondence: (T.T.); or (N.N); Tel.: +81-48-858-3534 (T.T.); +81-48-858-3531 (N.N.)
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24
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Achouri N, Tomàs-Gamisans M, Triki S, Valero F, Miled N, Fendri A, Smichi N. Dissecting the Interaction Deficiency of a Cartilaginous Fish Digestive Lipase with Pancreatic Colipase: Biochemical and Structural Insights. Biomed Res Int 2020; 2020:3064290. [PMID: 32258111 PMCID: PMC7094207 DOI: 10.1155/2020/3064290] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 11/17/2022]
Abstract
A full-length cDNA encoding digestive lipase (SmDL) was cloned from the pancreas of the smooth-hound (Mustelus mustelus). The obtained cDNA was 1350 bp long encoding 451 amino acids. The deduced amino acid sequence has high similarity with known pancreatic lipases. Catalytic triad and disulphide bond positions are also conserved. According to the established phylogeny, the SmDL was grouped with those of tuna and Sparidae lipases into one fish digestive lipase cluster. The recently purified enzyme shows no dependence for bile salts and colipase. For this, the residue-level interactions between lipase-colipase are yet to be clearly understood. The structural model of the SmDL was built, and several dissimilarities were noticed when analyzing the SmDL amino acids corresponding to those involved in HPL binding to colipase. Interestingly, the C-terminal domain of SmDL which holds the colipase shows a significant role for colipase interaction. This is apt to prevent the interaction between fish lipase and the pancreatic colipase which and can provide more explanation on the fact that the classical colipase is unable to activate the SmDL.
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Affiliation(s)
- Neila Achouri
- University of Sfax, ENIS, Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Road of Soukra, BPW 1173-3038 Sfax, Tunisia
| | - Màrius Tomàs-Gamisans
- UAB, Universitat Autònoma de Barcelona, Departament d'Enginyeria Química, Biològica i Ambiental, Bellaterra Barcelona, Spain
| | - Soumaya Triki
- University of Sfax, Center of Biotechnology of Sfax, Laboratory of Molecular and Cellular Screening Processes, BP 111 7 Road Sidi Mansour km 6, Sfax, Tunisia
| | - Francisco Valero
- UAB, Universitat Autònoma de Barcelona, Departament d'Enginyeria Química, Biològica i Ambiental, Bellaterra Barcelona, Spain
| | - Nabil Miled
- University of Jeddah, College of Science, Department of Biological Sciences, Jeddah, Saudi Arabia
- Functional Genomics and Plant Physiology Unit, Higher Institute of Biotechnology of Sfax, 3038 Sfax, Tunisia
| | - Ahmed Fendri
- University of Sfax, ENIS, Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Road of Soukra, BPW 1173-3038 Sfax, Tunisia
| | - Nabil Smichi
- University of Sfax, ENIS, Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Road of Soukra, BPW 1173-3038 Sfax, Tunisia
- Mayo Clinic Arizona, 13400 Shea Boulevard, Scottsdale, AZ 85259, USA
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25
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Gu T, Li G, Tian Y, Chen L, Wu X, Zeng T, Xu Q, Vladyslav S, Chen G, Lu L. Molecular cloning, expression and mimicking antiviral activity analysis of retinoic acid-inducible gene-I in duck ( Anas platyrhynchos). J Genet 2020; 99:26. [PMID: 32366736] [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] [Indexed: 06/11/2023]
Abstract
Intracellular double-stranded RNA (dsRNA) is a chief sign of replication for many viruses. Pattern recognition receptors(PRRs) of the innate immune system detected the dsRNA and initiate the antiviral responses. Retinoic acid-inducible gene I (RIG-I), a member of PRRs, plays an essential regulatory role in dsRNA-induced signalling. In this study, the full-length complementary DNA (cDNA) of duck RIG-I (duRIG-I) was cloned using the reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of the cDNA ends (RACE). The cDNA of duRIG-I contained 97-bp 5'UTR, 141-bp 3'-UTR and 2802 bp complete open-reading frame (ORF) encoding 933 amino acids. Multiple sequence alignments showed that duRIG-I shared high similarity with RIG-I from other vertebrates. Quantitative real-time PCR (qRT-PCR) analysis revealed that duRIG-I mRNA was expressed in all tested tissues, with high levels in the liver, heart, spleen, kidney and thymus, while lower in the duodenum. duRIG-I could be induced by treatment with poly(I:C). Further, overexpression of duRIG-I significantly activated the transcription of poly(I:C)-induced IFN-b, IRF7, TRIF, Mx, STAT1 and STAT2 mRNA, and duRIG-I knockdown showed the opposite results. Overall, our results suggested that duRIG-I could be an important receptor for mimicking antiviral state in duck, which warrant further studies to show the possible mechanism.
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Affiliation(s)
- Tiantian Gu
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China. ,
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Osho SO, Adeola O. Impact of dietary chitosan oligosaccharide and its effects on coccidia challenge in broiler chickens. Br Poult Sci 2019; 60:766-776. [PMID: 31483171 DOI: 10.1080/00071668.2019.1662887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/13/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022]
Abstract
1. Two experiments were conducted, the first to determine the optimum inclusion of chitosan oligosaccharide (COS) in broiler diets to support growth performance, digestive functions, intestinal morphology, and immune organs. The second experiment evaluated the immune-protective properties of COS on broiler chickens during coccidia challenge (CC).2. Experiment 1 investigated the effect of graded dietary concentration of COS in the diets of broiler chickens using eight cage replicates for each of the six diets. A corn-soybean meal-based diet was used as the basal diet and supplemented with 0.0, 0.5, 1.0, 1.5, 2.0, or 2.5 g of COS/kg feed to form the six treatments.3. The diet supplemented with 1.0 g COS/kg of feed provided the optimal inclusion level for broiler chickens regarding body weight (BW) gain, jejunal villus height, villus height to crypt depth ratio, and ileal energy digestibility at d 22 of age.4. Experiment 2 investigated the immune-protective properties of COS in broiler chickens during CC. A total of 224 male broiler chicks were randomly assigned to eight replicate cages in a 2 × 2 factorial arrangement of treatments with two COS concentrations (0 or 1 g of COS/kg of diet), with or without CC.5. On d 18 of age, birds in the CC group received twice the recommended coccidia vaccine dose of 30 doses/kg BW.6. Coccidia challenge reduced (P < 0.05) and dietary COS increased (P < 0.05) BW gain, and feed intake. Dietary COS mitigated (P < 0.05) the CC-induced effects on gain:feed. Dietary COS supplementation attenuated the CC-induced effects (P < 0.05) on the expression of occludin genes.7. In conclusion, dietary COS improved performance, and the immune-related beneficial impact of COS supplementation was associated with reduced expression of pro-inflammatory cytokine genes.
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Affiliation(s)
- S O Osho
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - O Adeola
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
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Zhu C, Liu D, Li Y, Shen X, Ma S, Liu Y, You T. Ratiometric electrochemical aptasensor for ultrasensitive detection of Ochratoxin A based on a dual signal amplification strategy: Engineering the binding of methylene blue to DNA. Biosens Bioelectron 2019; 150:111814. [PMID: 31740254 DOI: 10.1016/j.bios.2019.111814] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
A novel ratiometric electrochemical aptasensor was developed for Ochratoxin A (OTA) detection based on the binding of methylene blue (MB) to DNA with a dual signal amplification strategy. The formation of dsDNA structures between ferrocene-labeled complementary DNA (Fc-cDNA), the OTA aptamer, and complementary helper DNA (hDNA) caused Fc away from the electrode, and allowed dsDNA to bind with a certain amount of MB. Here, a small oxidation current of Fc (IFc) and a large oxidation current of MB (IMB) were obtained. In the presence of OTA, its specific recognition with the aptamer induced the release of aptamer and hDNA from the electrode and subsequently the formation of hairpin structure for cDNA, which caused Fc close to the electrode and a weaker binding ability with MB. Then, an increased IFc and a decreased IMB were obtained. Based on this principle, OTA could be accurately quantified by measuring the ratiometric signal of IFc/IMB. Herein, the dual signal amplification strategy of the introduction of hDNA and the binding with MB after the OTA recognition was exploited to amplify the response signal. The obtained aptasensor showed a linear detection range from 10 pg mL-1 to 10 ng mL-1 and a detection limit of 3.3 pg mL-1. The aptasensor was successfully applied to determine OTA in wheat, and the results were validated through HPLC-MS. Furthermore, by changing the target aptamers, this strategy could be universally used for the determination of various mycotoxins, showing promising potential applications for mycotoxins monitoring in agricultural products and foods.
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Affiliation(s)
- Chengxi Zhu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Dong Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Yuye Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiuli Shen
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Shuai Ma
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang Liu
- College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Tianyan You
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, High-tech Key Laboratory of Agricultural Equipment & Intelligentization of Jiangsu Province, School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, 212013, China.
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Chen X, Hao S, Zong B, Liu C, Mao S. Ultraselective antibiotic sensing with complementary strand DNA assisted aptamer/MoS 2 field-effect transistors. Biosens Bioelectron 2019; 145:111711. [PMID: 31563801 DOI: 10.1016/j.bios.2019.111711] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/25/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022]
Abstract
Although aptamer has been demonstrated as an important probe for antibiotic determination, the selective sensing of different antibiotics is still a challenge due to their structure similarities and wide folding degrees of aptamer. Herein, a field-effect transistor using MoS2 nanosheet as the channel and an aptamer DNA (APT) with its configuration shaped by a complementary strand DNA (CS) is employed for kanamycin (KAN) determination. This probe structure contributes to an enhanced selectivity and reliability with reduced device-to-device variations. This MoS2/APT/CS sensor shows time-dependent performance in antibiotic sensing. Prolonged detection time (20 s-300 s) leads to an enhanced sensitivity (1.85-4.43 M-1) and a lower limit of detection (1.06-0.66 nM), while a shorter detection time leads to a broader linear working range. A new sensing mechanism relying on charge release from probe is proposed, which is based on the "replacement reaction" between KAN and APT-CS. This sensor exhibits an extremely high selectivity (selectivity coefficient of 12.8) to kanamycin over other antibiotics including streptomycin, tobramycin, amoxicillin, ciprofloxacin and chloramphenicol. This work demonstrates the merits of probe engineering in label-free antibiotic detection with FET sensor, which presents significant promises in sensitive and selective chemical and biological sensing.
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Affiliation(s)
- Xiaoyan Chen
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Sibei Hao
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Boyang Zong
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Chengbin Liu
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Shun Mao
- Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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29
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Hou J, Gan Z, Chen SN, Nie P. Molecular and functional characterization of a short-type peptidoglycan recognition protein, PGRP-S in the amphibian Xenopus laevis. Dev Comp Immunol 2019; 98:13-19. [PMID: 30980872 DOI: 10.1016/j.dci.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/07/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Peptidoglycan recognition proteins (PGRPs) are a family of pattern recognition receptors (PRRs) involved in host antibacterial responses, and their functions have been characterized in most invertebrate and vertebrate animals. However, little information is available regarding the function of frog PGRPs. In this study, a short-type PGRP (termed Xl-PGRP-S) gene was identified in the African clawed frog, Xenopus laevis. The predicted protein of Xl-PGRP-S contains several structural features known in PGRPs, including a typical PGRP domain and two closely spaced conserved cysteines. Xl-PGRP-S gene was constitutively expressed in all tissues examined, with the highest expression level observed in muscle. As a typical PRR, Xl-PGRP-S is inducible after peptidoglycan (PGN) stimulation, and has an ability to bind PGN. In addition, Xl-PGRP-S has been proven to have Zn2+-dependent amidase activity and antibacterial activity against Edwardsiella tarda. The present study represents the first discovery on the function of frog PGRPs, thus contributing to a better understanding of the functional evolution of PGRPs in early tetrapods.
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Affiliation(s)
- Jing Hou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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Ma D, Fan J, Tian Y, Jiang P, Wang J, Zhu H, Bai J. Selection of reference genes for quantitative real-time PCR normalisation in largemouth bass Micropterus salmoides fed on alternative diets. J Fish Biol 2019; 95:393-400. [PMID: 31017661 DOI: 10.1111/jfb.13991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
The partial cDNA sequences of eight reference genes (actb, tuba1, gapdh58, gapdh59, eef1a1, RNA 18 s, pabpc1, ube2I) were cloned from largemouth bass Micropterus salmoides. The expression levels of these eight genes were compared in the various tissues (eye, spleen, kidney, gill, muscle, brain, liver, heart, gut and gonad) of M. salmoides fed on forage fish. The results showed that the candidate genes exhibited tissue-specific expression to various degrees and the stability ranking order was eef1a1 > tuba1 > RNA 18 s > pabpc1 > ube2I > actb > gapdh58 > gapdh59 among tissue types. Four candidate genes eef1a1, tuba1, RNA 18 s and actb were used to analyse the stability in liver tissues of largemouth bass between the forage-fish group and the formulated-feed group. The candidate genes also showed some changes in expression levels in the livers, while eef1a1 and tuba1 had the most stable expression in livers of fish fed on alternative diets within 10 candidates. So eef1a1 and tuba1 were recommended as optimal reference gene in quantitative real-time PCR analysis to normalise the expression levels of target genes in tissues and lives of the M. salmoides fed on alternative diets. In livers, the expression levels of gck normalised by eef1a1 and tuba1 showed the significant up-regulation in formulated feed group (P < 0.05) than those in forage-fish group. While sex difference has no significant effects on the expression levels of gck in both groups.
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Affiliation(s)
- Dongmei Ma
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiajia Fan
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Peng Jiang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huaping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Junjie Bai
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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31
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Potapov V, Fu X, Dai N, Corrêa IR, Tanner NA, Ong JL. Base modifications affecting RNA polymerase and reverse transcriptase fidelity. Nucleic Acids Res 2019; 46:5753-5763. [PMID: 29750267 PMCID: PMC6009661 DOI: 10.1093/nar/gky341] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/18/2018] [Indexed: 01/28/2023] Open
Abstract
Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing. Several modified bases, including methylated (m6A, m5C and m5U), hydroxymethylated (hm5U) and isomeric bases (pseudouridine), were examined. By comparing each modified base to the equivalent unmodified RNA base, we can determine how the modification affected cumulative RNA polymerase and reverse transcriptase fidelity. 5-hydroxymethyluridine and N6-methyladenosine both increased the combined error rate of T7 RNA polymerase and reverse transcriptases, while pseudouridine specifically increased the error rate of RNA synthesis by T7 RNA polymerase. In addition, we examined the frequency, mutational spectrum and sequence context of reverse transcription errors on DNA templates from an analysis of second strand DNA synthesis.
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Affiliation(s)
| | - Xiaoqing Fu
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- Dalian University of Technology, School of Life Science and Biotechnology, Dalian, Liaoning 116021, China
| | - Nan Dai
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Nathan A Tanner
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Jennifer L Ong
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- To whom correspondence should be addressed. Tel: +1 978 380 7448; Fax: +1 978 921 1350;
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Huang YL, Kawai G, Hasegawa A, Kannagi M, Masuda T. Impact of 5'-end nucleotide modifications of HIV-1 genomic RNA on reverse transcription. Biochem Biophys Res Commun 2019; 516:1145-1151. [PMID: 31284953 DOI: 10.1016/j.bbrc.2019.06.152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 11/20/2022]
Abstract
Reverse transcription of retroviral RNA is accomplished through a minus-strand strong stop cDNA (-sscDNA) synthesis and subsequent strand-transfer reactions. We have previously reported a critical role of guanosine (G) number at 5'-terminal of HIV-1 RNA for successful strand-transfer of -sscDNA. In this study, role(s) of the cap consisting of 7-methyl guanosine (7mG), a hallmark of transcripts generated by RNA polymerase II, at the 5'-end G nucleotide (5'-G) of HIV-1 RNA were examined. In parallel, contribution of highly conserved GGG tract located at the U3/R boundary in 3' terminal region of viral RNA (3'-GGG tract) was also addressed. The in vitro reverse transcription analysis using synthetic HIV-1 RNAs possessing the 5'-G with cap or triphosphate form demonstrated that the 5'-cap significantly increased strand-transfer efficiency of -sscDNA. Meanwhile, effect of the 5'-cap on the strand-transfer was retained in the reaction using mutant HIV-1 RNAs in which two Gs were deleted from the 3'-GGG tract. Lack of apparent contribution of the 3'-GGG tract during strand-transfer events in vitro was reproduced in the context of HIV-1 replication within cells. Instead, we noticed that the 3'-GGG tract might be required for efficient gene expression from proviral DNA. These results indicated that 7mG of the cap on HIV-1 RNA might not be reverse-transcribed and a possible role of the 3'-GGG tract to accept the non-template nucleotide addition during -sscDNA synthesis might be less likely. The 5'-G modifications of HIV-1 RNAs by the cap- or phosphate-removal enzyme revealed that the cap or monophosphate form of the 5'-G was preferred for the 1st strand-transfer compared to the triphosphate or non-phosphate form. Taken together, a status of the 5'-G determined strand-transfer efficiency of -sscDNA without affecting the non-template nucleotide addition, probably by affecting association of the 5'-G with 3'-end region of viral RNA.
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Affiliation(s)
- Yu-Lun Huang
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba, 275-0016, Japan
| | - Atsuhiko Hasegawa
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Mari Kannagi
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan.
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Müller C, Lukas P, Lemke S, Hildebrandt JP. Hirudin and Decorsins of the North American Medicinal Leech Macrobdella decora: Gene Structure Reveals Homology to Hirudins and Hirudin-like Factors of Eurasian Medicinal Leeches. J Parasitol 2019; 105:423-431. [PMID: 31163003] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Blood-sucking leeches, some of which are referred to as medicinal leeches, have caught attention not only because of their medical purposes, but also as study organisms to conduct research within fields as diverse as neurobiology, osmoregulation, ecology, and phylogeny. Of particular interest is the question whether hemophagy in leeches is of single origin or evolved independently several times. A key component in the saliva of hematophagous leeches is hirudin, a strong natural inhibitor of thrombin and hence the blood coagulation cascade. Multiple isoforms of hirudin have been described within and among several leech species and genera, often based on sequence data only. The identification of hirudin-like factors (HLFs) illustrated the necessity to underpin such predictions by functional tests. We overexpressed and purified the hirudin of the North American medicinal leech, Macrobdella decora, and proved its thrombin-inhibiting activity. In addition, analysis of the gene structure of both hirudin and some of the decorsins of M. decora clearly indicated conserved exon and intron positions when compared to genes of hirudins and HLFs of Eurasian medicinal leeches. Our data provide evidence for the incorporation of decorsins into the hirudin superfamily and support the concept of a single origin of blood feeding in jawed leeches.
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Affiliation(s)
- Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Phil Lukas
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Sarah Lemke
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany
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Wang J, Cheng J, Li Y, Yan H, Wu P, Zhu X, Liu L, Chen L, Chu W, Zhang J. Gene structure, recombinant expression and function characterization of Siniperca chuatsi Fsrp-3. J Fish Biol 2019; 94:714-724. [PMID: 30756375 DOI: 10.1111/jfb.13931] [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] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
A full-length complementary (c)DNA sequence encoding follistatin-related protein 3 (fsrp-3) was determined from skeletal muscle in Chinese mandarin fish Siniperca chuatsi, its molecular structure was characterised and its function suggested. The putative structure of S. chuatsi Fsrp-3 contains an N-terminal domain and two follistatin domains. Quantitative reverse-transcription (qRT)-PCR assays revealed that fsrp-3 messenger (m)RNA was differentially expressed among assayed tissues and was highly expressed in heart and intestine. fsrp-3 mRNA exhibited increasing expression from the larval to the juvenile stage (500 g). To investigate the potential function of S. chuatsi fsrp-3 in muscle growth, we constructed a Fsrp-3 prokaryotic expression system and injected the purified Fsrp-3 fusion protein into the dorsal muscle. Fsrp-3 administration significantly influenced cross-section area, satellite cell activation frequency and nuclear density of S. chuatsi muscle fibres. Following Fsrp-3 treatment, the expression of myogenic regulatory factors was up-regulated and decline in the expression of myostatin was observed. The study revealed that Fsrp-3 may affect muscle growth by regulating myogenic regulatory factor expression and antagonizing myostatin function to initiate satellite cell activation and differentiation in S. chuatsi.
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Affiliation(s)
- Jianhua Wang
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Jia Cheng
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
| | - Yulong Li
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
| | - Huiling Yan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Ping Wu
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
| | - Xin Zhu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Li Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Lin Chen
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
| | - Wuying Chu
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
| | - Jianshe Zhang
- Department of Bioscience and Environmental Engineering, Changsha University, Changsha, China
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Jiang GZ, Shi HJ, Xu C, Zhang DD, Liu WB, Li XF. Glucose-6-phosphate dehydrogenase in blunt snout bream Megalobrama amblycephala: molecular characterization, tissue distribution, and the responsiveness to dietary carbohydrate levels. Fish Physiol Biochem 2019; 45:401-415. [PMID: 30225750 DOI: 10.1007/s10695-018-0572-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
This study aimed to characterize the full-length cDNA of glucose-6-phosphate dehydrogenase (G6PD) from Megalobrama amblycephala with its responses to dietary carbohydrate levels characterized. The cDNA obtained covered 2768 bp with an open reading frame of 1572 bp. Sequence alignment and phylogenetic analysis revealed a high degree of conservation (77-97%) among most fish and other higher vertebrates. The highest transcription of G6PD was observed in kidney followed by liver, whereas relatively low abundance was detected in eye. Then, the transcriptions and activities of G6PD as well as lipid contents were determined in the liver, muscle, and the adipose tissue of fish fed two dietary carbohydrate levels (30 and 42%) for 12 weeks. Hepatic transcriptions of fatty acid synthetase (FAS), acetyl-CoA carboxylase α (ACCα), sterol regulatory element-binding protein-1 (SREBP1), and peroxisome proliferator-activated receptor γ (PPARγ) were also measured to corroborate the lipogenesis derived from carbohydrates. The G6PD expressions and activities in both liver and the adipose tissue as well as the lipid contents in whole-body, liver, and the adipose tissue all increased significantly after high-carbohydrate feeding. Hepatic transcriptions of FAS, ACCα, SREBP1, and PPARγ were also up-regulated remarkably by the intake of a high-carbohydrate diet. These results indicated that the G6PD of M. amblycephala shared a high similarity with that of other vertebrates. Its expressions and activities in tissues were both highly inducible by high-carbohydrate feeding, as also held true for the transcriptions of other enzymes and/or transcription factors involved in lipogenesis, evidencing an enhanced lipogenesis by high dietary carbohydrate levels.
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Affiliation(s)
- Guang-Zhen Jiang
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Hua-Juan Shi
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Chao Xu
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Ding-Dong Zhang
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wen-Bin Liu
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiang-Fei Li
- Key Laboratory of Aquaculture Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, People's Republic of China.
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Zhan Q, Shi X, Zhou J, Zhou L, Wei S. Drug-Controlled Release Based on Complementary Base Pairing Rules for Photodynamic-Photothermal Synergistic Tumor Treatment. Small 2019; 15:e1803926. [PMID: 30488638 DOI: 10.1002/smll.201803926] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Controlled drug release systems can enhance the safety and availability but avoid the side effect of drugs. Herein, the concept of DNA complementary base pairing rules in biology is used to design and prepare a photothermal-triggered drug release system. Adenine (A) modified polydopamine nanoparticles (A-PDA, photothermal reagent) can effectively bind with thymine (T) modified Zinc phthalocyanine (T-ZnPc, photosensitizer) forming A-PDA = T-ZnPc (PATP) complex based on A = T complementary base pairing rules. Similar to DNA, whose base pairing in double strands will break by heating, T-ZnPc can be effectively released from A-PDA after near infrared irradiation-triggered light-thermal conversion to obtain satisfactory photodynamic-photothermal synergistic tumor treatment. In addition, PDA can carry abundant Gd3+ to provide magnetic resonance imaging guided delivery and theranostic function.
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Affiliation(s)
- Qichen Zhan
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Key Laboratory of Applied Photochemistry, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Xianqing Shi
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Key Laboratory of Applied Photochemistry, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Jiahong Zhou
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Key Laboratory of Applied Photochemistry, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Lin Zhou
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Key Laboratory of Applied Photochemistry, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Shaohua Wei
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Key Laboratory of Applied Photochemistry, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
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Okada S, Ueda H, Noda Y, Suzuki T. Transcriptome-wide identification of A-to-I RNA editing sites using ICE-seq. Methods 2018; 156:66-78. [PMID: 30578846 DOI: 10.1016/j.ymeth.2018.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/15/2023] Open
Abstract
In A-to-I RNA editing, adenosine is converted to inosine in double-stranded regions of RNAs. Inosine, an abundant epitranscriptomic mark, contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect of A-to-I RNA editing on regulation of the epitranscriptome, accurate mapping of inosines is necessary. To this end, we established a biochemical method called inosine chemical erasing sequencing (ICE-seq) that enables unbiased and reliable identification of A-to-I RNA editing sites throughout the transcriptome. Here, we describe our updated protocol for ICE-seq in the human transcriptome.
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Affiliation(s)
- Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Ueda
- Biological Data Science Division, Research Center for Advanced Science and Technology (RCAST), University of Tokyo, Tokyo 153-8904, Japan
| | - Yuta Noda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Zhu Y, Qi C, Calandra C, Rao MS, Reddy JK. Cloning and identification of mouse steroid receptor coactivator-1 (mSRC-1), as a coactivator of peroxisome proliferator-activated receptor gamma. Gene Expr 2018; 6:185-95. [PMID: 9041124 PMCID: PMC6148307] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARgamma), a member of the nuclear receptor superfamily, is expressed predominantly in adipose tissue. Forced expression of the two isoforms of this receptor, PPARgamma1 and PPARgamma2, in fibroblasts initiates a transcriptional cascade that leads to the development of adipocyte phenotype. Using the yeast two-hybrid system and GAL4-PPARgamma as bait to screen mouse liver cDNA library, we isolated a mouse steroid receptor coactivator (mSRC-1) involved in nuclear hormone receptor transcriptional activity as a mPPARgamma interactive protein. mSRC-1 cDNA we isolated contains an open reading frame of 1447 amino acids and encodes a new member of the basic helix-loop-helix-PAS domain family. We show that the binding of mSRC-1 to mPPARgamma is ligand independent and coexpression of mSRC-1 with mPPARgamma increases the transcriptional activity of mPPARgamma in the presence of mPPARgamma ligand. We have identified the presence of two putative mPPARgamma binding sites in the mSRC-1, one between residues 620 and 789, and the second between residues 1231 and 1447. These two regions exhibit different degrees of binding affinity for mPPARgamma. We also show that mSRC-1 exhibits its own constitutive transcriptional activity in the yeast as well as in mammalian cells. These results suggest that mSRC-1 interacts with PPARgamma and plays a role in the PPARgamma-mediated signaling pathway.
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Affiliation(s)
- Y Zhu
- Department of Pathology, Northwestern University Medical School, Chicago, IL 60611, USA
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Górski GK, Aros MC, Norton PA. Characterization of mouse fibronectin alternative mRNAs reveals an unusual isoform present transiently during liver development. Gene Expr 2018; 6:139-49. [PMID: 9041121 PMCID: PMC6148308] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fibronectins are found in many extracellular matrices as well as being abundant plasma proteins. The plasma isoforms of fibronectin, which are synthesized in the adult by liver hepatocytes, differ from those derived from most other cells and tissues due to alternative mRNA splicing. Studies in several vertebrates have indicated that FN alternative splicing is regulated spatially and temporally during development. The mouse represents an attractive organism in which to study the regulation of fibronectin splicing during development, but the patterns of fibronectin alternative splicing were not known for this species. Mouse fibronectin cDNA clones were isolated and sequenced, revealing > 95% identity with rat fibronectin at the amino acid level; all three segments that undergo alternative splicing are well conserved. RNase protection and RT-PCR were used to determine the patterns of alternative splicing that occur in fibroblasts and adult liver, sources of cellular and plasma fibronectins. Only A-B-mRNAs were detected in liver, and three V region variants were observed, corresponding to the protein isoforms V120, V95, and V0. Fibroblasts produced mRNAs that were heterogeneous for A and B splicing, but all RNAs contained V120. These patterns contrast with the embryonic form (B+A+V120). Characterization of fibronectin mRNAs from livers of fetal and newborn mice revealed that a significant level of B+ mRNA was present throughout late gestation, declining at birth. Little A+ mRNA was present, and the adult liver V region pattern was observed at all stages. Thus, fibronectin splicing changes during liver development are noncoordinate. One consequence of this temporal regulation is the transient synthesis of B+ mRNAs, including a novel isoform, B+A-V0.
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Affiliation(s)
- G K Górski
- Department of Medicine, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA 19107, USA
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Garson K, Duhig T, Fried M. Tissue-specific processing of the Surf-5 and Surf-4 mRNAs. Gene Expr 2018; 6:209-18. [PMID: 9196076 PMCID: PMC6148271] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The mouse surfeit locus is an unusually tight cluster of at least six "housekeeping" genes that do not share any sequence homology and whose gene organization may play a role in gene expression. The transcription of each of the five well-characterized genes (Surf-1 to -5) alternates with respect to its neighbor(s) and no more than 159 bp separates any two adjacent genes with the Surf-4 and Surf-2 genes overlapping at their 3' ends by 133 bp. In this work, the expression of the Surf-5 and Surf-4 genes has been examined in various mouse tissues. In addition to the ubiquitously expressed 3.5-kb Surf-5 mRNA, a second alternatively spliced Surf-5 mRNA, Surf-5b, was discovered that was highly expressed in the brain, heart, testis, and skeletal muscle. The alternative splice donor site of the Surf-5b mRNA is similar to splice donor sites found in neuron-specific mRNAs. Surf-5b encodes a unique protein, which, like the ubiquitous Surf-5 protein, has been found to be primarily located in the soluble fraction of the cytoplasm. The expression of the Surf-5b protein was also found to increase in embryonal carcinoma cells differentiated into neuronal cultures. Although the Surf-5 gene is highly conserved through evolution, the presence of the Surf-5b alternative splice may be restricted to higher vertebrates. The Surf-4 gene was ubiquitously expressed in eight different mouse tissues; however, the ratios of the three previously reported Surf-4 mRNAs (two of which are known to derive from different sites of polyadenylation) altered dramatically between tissues. The use of different forms of mRNA processing for regulation of tissue-specific expression of ubiquitously expressed genes is discussed.
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Affiliation(s)
- Ken Garson
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, P.O. Box 123, Lincoln’s Inn Fields, London WC2A 3PX UK
- Address correspondence to Mike Fried. Tel: 44-171-269-3297; Fax: 44-171-269-3581; E-mail:
| | - Trevor Duhig
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, P.O. Box 123, Lincoln’s Inn Fields, London WC2A 3PX UK
| | - Mike Fried
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, P.O. Box 123, Lincoln’s Inn Fields, London WC2A 3PX UK
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Austin CA, Lee KC, Swan RL, Khazeem MM, Manville CM, Cridland P, Treumann A, Porter A, Morris NJ, Cowell IG. TOP2B: The First Thirty Years. Int J Mol Sci 2018; 19:ijms19092765. [PMID: 30223465 PMCID: PMC6163646 DOI: 10.3390/ijms19092765] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Type II DNA topoisomerases (EC 5.99.1.3) are enzymes that catalyse topological changes in DNA in an ATP dependent manner. Strand passage reactions involve passing one double stranded DNA duplex (transported helix) through a transient enzyme-bridged break in another (gated helix). This activity is required for a range of cellular processes including transcription. Vertebrates have two isoforms: topoisomerase IIα and β. Topoisomerase IIβ was first reported in 1987. Here we review the research on DNA topoisomerase IIβ over the 30 years since its discovery.
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Affiliation(s)
- Caroline A Austin
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Ka C Lee
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Rebecca L Swan
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Mushtaq M Khazeem
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Catriona M Manville
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Peter Cridland
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Achim Treumann
- NUPPA, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Andrew Porter
- NUPPA, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Nick J Morris
- School of Biomedical Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Ian G Cowell
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Voorter CEM, Matern B, Tran TH, Fink A, Vidan-Jeras B, Montanic S, Fischer G, Fae I, de Santis D, Whidborne R, Andreani M, Testi M, Groeneweg M, Tilanus MGJ. Full-length extension of HLA allele sequences by HLA allele-specific hemizygous Sanger sequencing (SSBT). Hum Immunol 2018; 79:763-772. [PMID: 30107213 DOI: 10.1016/j.humimm.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/20/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 12/27/2022]
Abstract
The gold standard for typing at the allele level of the highly polymorphic Human Leucocyte Antigen (HLA) gene system is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, full-length sequence information is lacking for >90% of the HLA alleles. One of the goals of the 17th IHIWS workshop is to establish full-length sequences for as many HLA alleles as possible. In our component "Extension of HLA sequences by full-length HLA allele-specific hemizygous Sanger sequencing" we have used full-length hemizygous Sanger Sequence Based Typing to achieve this goal. We selected samples of which full length sequences were not available in the IPD-IMGT/HLA database. In total we have generated the full-length sequences of 48 HLA-A, 45 -B and 31 -C alleles. For HLA-A extended alleles, 39/48 showed no intron differences compared to the first allele of the corresponding allele group, for HLA-B this was 26/45 and for HLA-C 20/31. Comparing the intron sequences to other alleles of the same allele group revealed that in 5/48 HLA-A, 16/45 HLA-B and 8/31 HLA-C alleles the intron sequence was identical to another allele of the same allele group. In the remaining 10 cases, the sequence either showed polymorphism at a conserved nucleotide or was the result of a gene conversion event. Elucidation of the full-length sequence gives insight in the polymorphic content of the alleles and facilitates the identification of its evolutionary origin.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
| | - Ben Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Thuong Hien Tran
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annette Fink
- Transplantation Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Blanka Vidan-Jeras
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Sendi Montanic
- Tissue Typing Center, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Gottfried Fischer
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Ingrid Fae
- Department for Blood Group Serology and Blood Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Dianne de Santis
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Rebecca Whidborne
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, Australia
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
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Diniz MRV, Paiva ALB, Guerra-Duarte C, Nishiyama MY, Mudadu MA, de Oliveira U, Borges MH, Yates JR, Junqueira-de-Azevedo IDL. An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PLoS One 2018; 13:e0200628. [PMID: 30067761 PMCID: PMC6070231 DOI: 10.1371/journal.pone.0200628] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 12/06/2017] [Accepted: 06/29/2018] [Indexed: 01/23/2023] Open
Abstract
Phoneutria nigriventer is one of the largest existing true spiders and one of the few considered medically relevant. Its venom contains several neurotoxic peptides that act on different ion channels and chemical receptors of vertebrates and invertebrates. Some of these venom toxins have been shown as promising models for pharmaceutical or biotechnological use. However, the large diversity and the predominance of low molecular weight toxins in this venom have hampered the identification and deep investigation of the less abundant toxins and the proteins with high molecular weight. Here, we combined conventional and next-generation cDNA sequencing with Multidimensional Protein Identification Technology (MudPIT), to obtain an in-depth panorama of the composition of P. nigriventer spider venom. The results from these three approaches showed that cysteine-rich peptide toxins are the most abundant components in this venom and most of them contain the Inhibitor Cysteine Knot (ICK) structural motif. Ninety-eight sequences corresponding to cysteine-rich peptide toxins were identified by the three methodologies and many of them were considered as putative novel toxins, due to the low similarity to previously described toxins. Furthermore, using next-generation sequencing we identified families of several other classes of toxins, including CAPs (Cysteine Rich Secretory Protein-CRiSP, antigen 5 and Pathogenesis-Related 1-PR-1), serine proteinases, TCTPs (translationally controlled tumor proteins), proteinase inhibitors, metalloproteinases and hyaluronidases, which have been poorly described for this venom. This study provides an overview of the molecular diversity of P. nigriventer venom, revealing several novel components and providing a better basis to understand its toxicity and pharmacological activities.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- High-Throughput Nucleotide Sequencing
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Peptides/metabolism
- Proteomics
- Sequence Alignment
- Sequence Analysis, DNA
- Spider Venoms/metabolism
- Spiders/genetics
- Spiders/metabolism
- Toxins, Biological/genetics
- Toxins, Biological/metabolism
- Transcriptome
- Tumor Protein, Translationally-Controlled 1
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Affiliation(s)
- Marcelo R. V. Diniz
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana L. B. Paiva
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Clara Guerra-Duarte
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Milton Y. Nishiyama
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Ursula de Oliveira
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Márcia H. Borges
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - John R. Yates
- Department of Chemical Physiology and Molecular and Cellular Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
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Olsson S, Pinosio S, González-Martínez SC, Abascal F, Mayol M, Grivet D, Vendramin GG. De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses. Plant Mol Biol 2018; 97:337-345. [PMID: 29850988 DOI: 10.1007/s11103-018-0742-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/25/2018] [Indexed: 06/08/2023]
Abstract
We provide novel genomic resources for Taxus baccata in the form of a reference transcriptome, SSR and SNP markers, and orthologous single-copy genes, useful for phylogenomic and population genomic applications. English yew (T. baccata) is the only European representative of the Taxaceae family, a conifer group originated in the Jurassic period. The wide extent of environmental heterogeneity within the species' range, together with its long presence in Europe, make English yew an ideal species to investigate adaptive evolution in conifers. To enlarge the genomic resources available for this species, we used Illumina short read sequencing followed by de novo assembly to build the transcriptome of English yew. In addition to a fully annotated transcriptome as well as large sets of new potential SSR and SNP markers for T. baccata, we provide a data set of orthologous single-copy genes across three Taxus species using Picea sitchensis as outgroup, and discuss ortholog uses and limitations for phylogenomic and population genomic applications.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Sara Pinosio
- Istituto di Genomica Applicata (IGA), Via J. Linussio, 51, 33100, Udine, Italy
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, 50019, Sesto Fiorentino, FI, Italy
| | - Santiago C González-Martínez
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Federico Abascal
- Human Genetics Department, Sandhu Group, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Maria Mayol
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA-CIFOR, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain.
| | - Giovanni G Vendramin
- Division of Florence, Institute of Biosciences and Bioresources, National Research Council, 50019, Sesto Fiorentino, FI, Italy
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45
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Zhang XS, Pei JJ, Zhao LG, Tang F, Fang XY. RNA-Seq analysis and comparison of the enzymes involved in ionone synthesis of three cultivars of Osmanthus. J Asian Nat Prod Res 2018; 20:649-661. [PMID: 29629568 DOI: 10.1080/10286020.2018.1453503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
To comprehend the molecular mechanisms that control the differences in the composition of Osmanthus essential oils, the RNA-seq data and differentially expressed genes in different cultivar Osmanthus were studied. cDNA libraries of "jinqiugui," "baijie," and "rixianggui" were sequenced using Illumina HiSeq TM 2000. All of the enzymes involved in ionone synthesis were verified. DEGs were revealed and their enriched pathways were analyzed. A total of 20 DEGsencoding four enzymes that were potential candidates involved in ionone biosynthesis, as well as ispH, GPPS, ZDS, and CCD. It provided a way for Osmanthus oil monomer material to be synthesized in vitro.
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Affiliation(s)
- Xue-Song Zhang
- a Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , Nanjing 210037 , China
- b College of Tea and Food Science and Technology , Jiangsu Polytechnic College of Agriculture and Forestry , Jurong 212400 , China
| | - Jian-Jun Pei
- a Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , Nanjing 210037 , China
| | - Lin-Guo Zhao
- a Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , Nanjing 210037 , China
| | - Feng Tang
- c International Centre for Bamboo and Rattan , Beijing 100714 , China
| | - Xian-Ying Fang
- a Co-Innovation Center for Sustainable Forestry in Southern China , Nanjing Forestry University , Nanjing 210037 , China
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46
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Zheng T, Chen Z, Ju Y, Zhang H, Cai M, Pan H, Zhang Q. Reference gene selection for qRT-PCR analysis of flower development in Lagerstroemia indica and L. speciosa. PLoS One 2018; 13:e0195004. [PMID: 29579116 PMCID: PMC5868847 DOI: 10.1371/journal.pone.0195004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 12/03/2017] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a prevalent method for gene expression analysis, depending on the stability of the reference genes for data normalization. Lagerstroemia indica and L. speciosa are popular ornamental plants which are famous for the long flowering period. However, no systematic studies on reference genes in Lagerstroemia have yet been conducted. In the present study, we selected nine candidate reference genes (GAPDH, TUA, TUB, 18S, RPII, EF-1α, ATC, EIF5A and CYP) and evaluated their expression stability in different tissues during floral development of L. indica and L. speciosa using four algorithms (geNorm, NormFinder, BestKeeper and, RefFinder). Results showed that RPII and EF-1α were the most stably expressed and suitable reference genes for both of Lagerstroemia species. Moreover, ACT exhibited high expression stability in L. indica and GAPDH was a suitable reference gene for L. speciosa in different flower development stages. TUB was an unsuitable reference gene for gene expression normalization due to significant variations in expression across all samples. Finally, we verified the reliability of the selected candidate reference genes by amplifying an AGAMOUS homolog (LsAG1) of Arabidopsis thaliana. This study provides a list of suitable reference genes, thereby broadening the genetic basis of the gene expression patterns in Lagerstroemia species.
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Affiliation(s)
- Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Zhilin Chen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yiqian Ju
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Han Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Ming Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Forestry University, Beijing, China
- National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, China
- * E-mail:
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Murolo S, De Miccolis Angelini RM, Faretra F, Romanazzi G. Phenotypic and Molecular Investigations on Hypovirulent Cryphonectria parasitica in Italy. Plant Dis 2018; 102:540-545. [PMID: 30673478 DOI: 10.1094/pdis-04-17-0517-re] [Citation(s) in RCA: 3] [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: 06/09/2023]
Abstract
Chestnut blight is caused by the fungus Cryphonectria parasitica. As one of the most ecologically important diseases of Castanea spp., C. parasitica can rapidly kill trees. In Europe, mitigation of disease severity took place spontaneously through colonization of C. parasitica by mycoviruses, which reduced the virulence of the fungus. In the framework of a survey, 138 C. parasitica isolates were identified, and virulent/hypovirulent phenotypes were determined through morphological properties and pathogenicity tests. For a pool of four hypovirulent isolates, dsRNA was extracted, cDNA synthesized, and a library subjected to next-generation sequencing. The bioinformatics analysis allowed detecting and reconstructing the complete genome of Cryphonectria hypovirus 1 (CHV-1), denoted as CHV-1 Marche. When compared with the available genomes of other hypoviruses that affected the virulence of C. parasitica, available in databases, CHV-1 Marche showed some nucleotide diversity. The approach used in this study was effective to explore the virome inside a pool of hypovirulent C. parasitica isolates. Next-generation sequencing allowed us to exclude the presence of any other ssRNA and dsRNA viruses infecting the fungus and determine CHV-1 as the only responsible of hypovirulence of C. parasitica in the analyzed samples.
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Affiliation(s)
- Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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48
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Román J, Castillo A, Cottet L, Mahn A. Kinetic and structural study of broccoli myrosinase and its interaction with different glucosinolates. Food Chem 2018; 254:87-94. [PMID: 29548477 DOI: 10.1016/j.foodchem.2018.01.179] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 08/07/2017] [Revised: 01/11/2018] [Accepted: 01/30/2018] [Indexed: 11/17/2022]
Abstract
Myrosinase is a glycosylated enzyme present in the Brassicaceae family that catalyzes the hydrolysis of glucoraphanin to yield sulforaphane, recognized as a health-promoting compound found in cruciferous foods. Broccoli myrosinase has been poorly characterized. In this work, the enzyme was purified from broccoli florets and its kinetic behaviour was analyzed. The cDNA of broccoli myrosinase was isolated and sequenced to obtain the amino acids sequence of the enzyme. A three-dimensional structural model of a broccoli myrosinase subunit was built and used to perform molecular docking simulations with glucoraphanin and other glucosinolates. Kinetic data were adjusted to the Two-Binding Sites Model that describes substrate inhibition, obtaining R2 higher than 97%. The docking simulations confirmed the existence of two substrate-binding sites in the monomer, and allowed identifying the residues that interact with the substrate in each site. Our findings will help to design strategies to better exploit the health-promoting properties of broccoli.
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Affiliation(s)
- Juan Román
- Doctorate Program in Food Science and Technology, Faculty of Technology, University of Santiago of Chile, Chile.
| | - Antonio Castillo
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Chile.
| | - Luis Cottet
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile, Chile.
| | - Andrea Mahn
- Department of Chemical Engineering, Faculty of Engineering, University of Santiago of Chile, Chile.
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Zhou Y, Yuan C, Ruan S, Zhang Z, Meng J, Xi Z. Exogenous 24-Epibrassinolide Interacts with Light to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Cabernet Sauvignon (Vitis vinifera L.). Molecules 2018; 23:molecules23010093. [PMID: 29315208 PMCID: PMC6017727 DOI: 10.3390/molecules23010093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/04/2022] Open
Abstract
Anthocyanins and proanthocyanidins (PAs) are crucial factors that affect the quality of grapes and the making of wine, which were stimulated by various stimuli and environment factors (sugar, hormones, light, and temperature). The aim of the study was to investigate the influence of exogenous 24-Epibrassinolide (EBR) and light on the mechanism of anthocyanins and PAs accumulation in grape berries. Grape clusters were sprayed with EBR (0.4 mg/L) under light and darkness conditions (EBR + L, EBR + D), or sprayed with deionized water under light and darkness conditions as controls (L, D), at the onset of veraison. A large amount of anthocyanins accumulated in the grape skins and was measured under EBR + L and L treatments, whereas EBR + D and D treatments severely suppressed anthocyanin accumulation. This indicated that EBR treatment could produce overlay effects under light, in comparison to that in dark. Real-time quantitative PCR analysis indicated that EBR application up-regulated the expression of genes (VvCHI1, VvCHS2, VvCHS3, VvDFR, VvLDOX, VvMYBA1) under light conditions. Under darkness conditions, only early biosynthetic genes of anthocyanin biosynthesis responded to EBR. Furthermore, we also analyzed the expression levels of the BR-regulated transcription factor VvBZR1 (Brassinazole-resistant 1) and light-regulated transcription factor VvHY5 (Elongated hypocotyl 5). Our results suggested that EBR and light had synergistic effects on the expression of genes in the anthocyanin biosynthesis pathway.
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Affiliation(s)
- Yali Zhou
- College of Enology, Northwest A&F University, Yangling 712100, China.
| | - Chunlong Yuan
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Shicheng Ruan
- Chateau Changyu Rena Co., Ltd., Xianyang 712000, China.
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Jiangfei Meng
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Zhumei Xi
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
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Abstract
The accurate and quantitative detection of 5-methylcytosine is of great importance in the field of epigenetics. The method of choice is usually bisulfite sequencing because of the high resolution and the possibility to combine it with next generation sequencing. Nevertheless, also this method has its limitations. Following the bisulfite treatment DNA strands are no longer complementary such that in a subsequent PCR amplification the DNA methylation patterns information of only one of the two DNA strand is preserved. Several years ago Hairpin Bisulfite sequencing was developed as a method to obtain the pattern information on complementary DNA strands. The method requires fragmentation (usually by enzymatic cleavage) of genomic DNA followed by a covalent linking of both DNA strands through ligation of a short DNA hairpin oligonucleotide to both strands. The ligated covalently linked dsDNA products are then subjected to a conventional bisulfite treatment during which all unmodified cytosines are converted to uracils. During the treatment the DNA is denatured forming noncomplementary ssDNA circles. These circles serve as a template for a locus specific PCR to amplify chromosomal patterns of the region of interest. As a result one ends up with a linearized product, which contains the methylation information of both complementary DNA strands.
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Affiliation(s)
- Pascal Giehr
- Department of Biological Sciences, Genetics/Epigenetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Jörn Walter
- Department of Biological Sciences, Genetics/Epigenetics, Saarland University, Saarbrücken, Saarland, Germany.
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