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Sun H, Fan J, Chu H, Gao Y, Fang J, Wu Q, Ding H, Zhuo X, Kong Q, Lv H, Zheng B, Lu S. RPA-CRISPR/Cas12a-LFA combined with a digital visualization instrument to detect Toxoplasma gondii in stray dogs and cats in Zhejiang province, China. Microbiol Spectr 2024; 12:e0399823. [PMID: 38809001 PMCID: PMC11218441 DOI: 10.1128/spectrum.03998-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/14/2024] [Indexed: 05/30/2024] Open
Abstract
Toxoplasma gondii, which causes toxoplasmosis, is prevalent in warm-blooded animals, such as cats, dogs, and humans. T. gondii causes economic losses to livestock production and represents a potential risk to public health. Dogs and cats are common hosts in the epidemiology of toxoplasmosis. The current molecular diagnostic tools for T. gondii infection require high technical skills, a laboratory environment, and complex instruments. Herein, we developed a recombinase polymerase amplification (RPA)-clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) assay to detect T. gondii. The lowest limit of detection of the assay was 31 copies/μL for the T. gondii B1 gene. In addition, we established a visual RPA-CRISPR/Cas12a lateral flow band assay (RPA-CRISPR/Cas12a-LFA) combined with a digital visualization instrument, which minimized the problem of false-negative results for weakly positive samples and avoided misinterpretation of the results by the naked eye, making the LFA assay results more accurate. The assay established in this study could identify T. gondii within 55 min with high accuracy and sensitivity, without cross-reaction with other tested parasites. The developed assay was validated by establishing a mouse model of toxoplasmosis. Finally, the developed assay was used to investigate the prevalence of T. gondii in stray cats and dogs in Zhejiang province, Eastern China. The positive rates of T. gondii infection in stray cats and dogs were 8.0% and 4.0%, respectively. In conclusion, the RPA-CRISPR/Cas12a-LFA is rapid, sensitive, and accurate for the early diagnosis of T. gondii, showing promise for on-site surveillance. IMPORTANCE Toxoplasma gondii is a virulent pathogen that puts millions of infected people at risk of chronic disease reactivation. Hosts of T. gondii are distributed worldwide, and cats and dogs are common hosts of T. gondii. Therefore, rapid diagnosis of early T. gondii infection and investigation of its prevalence in stray dogs and cats are essential. Here, we established a visual recombinase polymerase amplification-clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a-assay combined with a lateral flow band assay and a digital visualization instrument. Detailed analyses found that the assay could be used for the early diagnosis of T. gondii without false-negative results. Moreover, we detected the prevalence of T. gondii in stray cats and dogs in Zhejiang province, China. Our developed assay provides technical support for the early diagnosis of T. gondii and could be applied in prevalence surveys of T. gondii in stray dogs and cats.
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Affiliation(s)
- Hao Sun
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Jiyuan Fan
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Hongkun Chu
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Yafan Gao
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Jiawen Fang
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Qinli Wu
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Haojie Ding
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Xunhui Zhuo
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - QingMing Kong
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - HangJun Lv
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Bin Zheng
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
| | - Shaohong Lu
- Laboratory of Pathogen Biology, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Research Center of Novel Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Bio-tech Vaccine of Zhejiang Province, School of Basic Medicine and Forensics, Hangzhou Medical College, Hangzhou, China
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Subbotin SA. Rapid Detection of the Strawberry Foliar Nematode Aphelenchoides fragariae Using Recombinase Polymerase Amplification Assay with Lateral Flow Dipsticks. Int J Mol Sci 2024; 25:844. [PMID: 38255917 PMCID: PMC10815920 DOI: 10.3390/ijms25020844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Rapid and reliable diagnostic methods for plant-parasitic nematodes are critical for facilitating the selection of effective control measures. A diagnostic recombinase polymerase amplification (RPA) assay for Aphelenchoides fragariae using a TwistAmp® Basic Kit (TwistDx, Cambridge, UK) and AmplifyRP® Acceler8® Discovery Kit (Agdia, Elkhart, IN, USA) combined with lateral flow dipsticks (LF) has been developed. In this study, a LF-RPA assay was designed that targets the ITS rRNA gene of A. fragariae. This assay enables the specific detection of A. fragariae from crude nematode extracts without a DNA extraction step, and from DNA extracts of plant tissues infected with this nematode species. The LF-RPA assay showed reliable detection within 18-25 min with a sensitivity of 0.03 nematode per reaction tube for crude nematode extracts or 0.3 nematode per reaction tube using plant DNA extracts from 0.1 g of fresh leaves. The LF-RPA assay was developed and validated with a wide range of nematode and plant samples. Aphelenchoides fragariae was identified from seed samples in California. The LF-RPA assay has great potential for nematode diagnostics in the laboratory with minimal available equipment.
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Affiliation(s)
- Sergei A Subbotin
- Plant Pest Diagnostic Centre, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448, USA
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Ma L, Zhu M, Meng Q, Wang Y, Wang X. Real-time detection of Seneca Valley virus by one-tube RPA-CRISPR/Cas12a assay. Front Cell Infect Microbiol 2024; 13:1305222. [PMID: 38259970 PMCID: PMC10800940 DOI: 10.3389/fcimb.2023.1305222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Senecavirus A (SVA) is a highly contagious virus that causes vesicular disease in pigs. At present, laboratory detection methods, such as virus isolation and polymerase chain reaction (PCR), required precision instruments and qualified personnel, making them unsuitable for point-of-care tests (POCT). Fortunately, the emergence of CRISPR/Cas system has provided new opportunities for fast and efficient pathogen detection. Methods This study successfully developed a precise and sensitive detection platform for diagnosing SVA by combining the CRISPR system with recombinase polymerase amplification (RPA). Results The minimum detection limit of the assay was 10 copies of the SVA genome. Meanwhile, the assay demonstrated high specificity. To validate the effectiveness of this system, we tested 85 swine clinical samples and found that the fluorescence method had a 100% coincidence rate compared to RT-qPCR. Discussion Overall, the RPA-CRISPR/Cas12a assay established in our study is a highly effective method for detecting SVA and holds great potential for practical applications in the resource-limited settings.
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Affiliation(s)
- Lei Ma
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
| | - Mengjie Zhu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Qingfeng Meng
- Testing Technology R&D Department, Shanghai Kaiwosha Biotechnology Co., Ltd, Shanghai, China
| | - Yao Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xueping Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
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Zhang K, Sun Z, Shi K, Yang D, Bian Z, Li Y, Gou H, Jiang Z, Yang N, Chu P, Zhai S, Wei Z, Li C. RPA-CRISPR/Cas12a-Based Detection of Haemophilus parasuis. Animals (Basel) 2023; 13:3317. [PMID: 37958075 PMCID: PMC10648042 DOI: 10.3390/ani13213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Haemophilus parasuis (H. parasuis, HPS) is a prominent pathogenic bacterium in pig production. Its infection leads to widespread fibrinous inflammation in various pig tissues and organs, often in conjunction with various respiratory virus infections, and leads to substantial economic losses in the pig industry. Therefore, the rapid diagnosis of this pathogen is of utmost importance. In this study, we used recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR) technology to establish a convenient detection and analysis system for H. parasuis that is fast to detect, easy to implement, and accurate to analyze, known as RPA-CRISPR/Cas12a analysis. The process from sample to results can be completed within 1 h with high sensitivity (0.163 pg/μL of DNA template, p < 0.05), which is 104 -fold higher than the common PCR method. The specificity test results show that the RPA-CRISPR/Cas12a analysis of H. parasuis did not react with other common pig pathogens, including Streptococcus suis type II and IX, Actinobacillus pleuropneumoniae, Escherichia coli, Salmonella, Streptococcus suis, and Staphylococcus aureus (p < 0.0001). The RPA-CRISPR/Cas12a assay was applied to 15 serotypes of H. parasuis clinical samples through crude extraction of nucleic acid by boiling method, and all of the samples were successfully identified. It greatly reduces the time and cost of nucleic acid extraction. Moreover, the method allows results to be visualized with blue light. The accurate and convenient detection method could be incorporated into a portable format as point-of-care (POC) diagnostics detection for H. parasuis at the field level.
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Affiliation(s)
- Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Zeyi Sun
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Keda Shi
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Nanling Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Shaolun Zhai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
| | - Zhanyong Wei
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China; (K.Z.); (Z.S.); (K.S.); (D.Y.); (Z.B.); (Y.L.); (H.G.); (Z.J.); (N.Y.); (P.C.); (S.Z.)
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Zhao F, Wang P, Wang H, Liu S, Sohail M, Zhang X, Li B, Huang H. CRISPR/Cas12a-mediated ultrasensitive and on-site monkeypox viral testing. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2105-2113. [PMID: 37066613 DOI: 10.1039/d2ay01998a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spread of the monkeypox virus (MPXV) from Central and West Africa to previously non-endemic regions has caused a global panic. In this context, the rapid, specific, and ultrasensitive detection of MPXV is crucial to contain its spread, though such technology has seldom been reported. Herein, we proposed an MPXV assay combining recombinase-aided amplification (RAA) and CRISPR/Cas12a. This assay targeted the highly conserved MPXV F3L gene and demonstrates a low detection limit (LOD) of 101 copies per μL. By leveraging the high specificity nature of RAA and CRISPR/Cas12a, we rationally optimized probes and conditions to achieve high selectivity that differentiates MPXV from other orthopox viruses and current high-profile viruses. To facilitate on-site screening of potential MPXV carriers, a kit integrating lateral flow strips was developed, enabling naked-eye MPXV detection with a LOD of 104 copies per μL. Our RAA-Cas12a-MPXV assay was able to detect MPXV without the need for sophisticated operation and expensive equipment. We believe that this assay can be rapidly deployed in emerging viral outbreaks for on-site surveillance of MPXV.
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Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Haoxuan Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Sirui Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
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