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Benites-Pariente JS, Samolski I, Ludeña Y, Villena GK. CRISPR/Cas9 mediated targeted knock-in of eglA gene to improve endoglucanase activity of Aspergillus fumigatus LMB-35Aa. Sci Rep 2024; 14:19661. [PMID: 39179646 PMCID: PMC11344075 DOI: 10.1038/s41598-024-70397-4] [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: 05/03/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
Bioeconomy goals for using biomass feedstock for biofuels and bio-based production has arisen the demand for fungal strains and enzymes for biomass processing. Despite well-known Trichoderma and Aspergillus commercial strains, continuous bioprospecting has revealed the fungal biodiversity potential for production of biomass degrading enzymes. The strain Aspergillus fumigatus LMB-35Aa has revealed a great potential as source of lignocellulose-degrading enzymes. Nevertheless, genetic improvement should be considered to increase its biotechnological potential. Molecular manipulation based on homologous direct recombination (HDR) in filamentous fungi poses a challenge since its low recombination rate. Currently, CRISPR/Cas9-mediated mutagenesis can enable precise and efficient editing of filamentous fungi genomes. In this study, a CRISPR/Cas9-mediated gene editing strategy for improving endoglucanase activity of A. fumigatus LMB-35Aa strain was successfully used, which constitutes the first report of heterologous cellulase production in filamentous fungi using this technology. For this, eglA gene from A. niger ATCC 10,864 was integrated into conidial melanin pksP gene locus, which facilitated the selection of edited events discerned by the emergence of albino colonies. Heterologous production of the EglA enzyme in a biofilm fermentation system resulted in a 40% improvement in endoglucanase activity of the mutant strain compared to the wild type.
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Affiliation(s)
- J S Benites-Pariente
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - I Samolski
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - Y Ludeña
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru
| | - G K Villena
- Laboratorio de Micología y Biotecnología "Marcel Gutiérrez-Correa", Universidad Nacional Agraria la Molina, 15024, Lima, Peru.
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2
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Velvizhi G, Jacqueline PJ, Shetti NP, K L, Mohanakrishna G, Aminabhavi TM. Emerging trends and advances in valorization of lignocellulosic biomass to biofuels. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118527. [PMID: 37429092 DOI: 10.1016/j.jenvman.2023.118527] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023]
Abstract
Sustainable technologies pave the way to address future energy demand by converting lignocellulosic biomass into fuels, carbon-neutral materials, and chemicals which might replace fossil fuels. Thermochemical and biochemical technologies are conventional methods that convert biomass into value-added products. To enhance biofuel production, the existing technologies should be upgraded using advanced processes. In this regard, the present review explores the advanced technologies of thermochemical processes such as plasma technology, hydrothermal treatment, microwave-based processing, microbial-catalyzed electrochemical systems, etc. Advanced biochemical technologies such as synthetic metabolic engineering and genomic engineering have led to the development of an effective strategy to produce biofuels. The microwave-plasma-based technique increases the biofuel conversion efficiency by 97% and the genetic engineering strains increase the sugar production by 40%, inferring that the advanced technologies enhances the efficiency. So understanding these processes leads to low-carbon technologies which can solve the global issues on energy security, the greenhouse gases emission, and global warming.
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Affiliation(s)
- G Velvizhi
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, Tamil Nadu, India.
| | - P Jennita Jacqueline
- CO(2) Research and Green Technology Centre, Vellore Institute of Technology (VIT), Vellore, 632 014, Tamil Nadu, India; School of Chemical Engineering, Vellore Institute of Technology (VIT), Vellore, 632 014, Tamil Nadu, India
| | - Nagaraj P Shetti
- Center for Energy and Environment, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, Karnataka, India
| | - Latha K
- Department of Mathematics, Easwari Engineering College, Chennai, 600 089, Tamil Nadu, India
| | - Gunda Mohanakrishna
- Center for Energy and Environment, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, Karnataka, India
| | - Tejraj M Aminabhavi
- Center for Energy and Environment, School of Advanced Sciences, KLE Technological University, Hubballi, 580 031, Karnataka, India; School of Engineering, UPES, Bidholi, Dehradun, Uttarakhand 248 007, India.
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3
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Transcriptome Analysis Reveals the Function of a G-Protein α Subunit Gene in the Growth and Development of Pleurotus eryngii. J Fungi (Basel) 2023; 9:jof9010069. [PMID: 36675890 PMCID: PMC9866537 DOI: 10.3390/jof9010069] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
Pleurotus eryngii is a commercially important edible fungus with high nutritional and economic value. However, few functional studies have examined key genes affecting the growth and development of P. eryngii. In this study, transformed strains, including over-expression (PeGNAI-OE) and RNA interference (PeGNAI-RNAi) lines, were constructed to elucidate the role of GNAI in P. eryngii growth. GNAI expression was found to affect the mycelial growth and the number of clamp connections. Moreover, the transformed strains were shown to have higher endogenous cAMP levels, thus affecting amylase and laccase activity. Fruiting experiments showed that GNAI expression revealed the formation of P. eryngii primordia and the number of buttons, while transcription analysis identified GNAI gene involvement in the growth and development of P. eryngii. Seven downstream genes regulated by GNAI were differentially expressed in PeGNAI-OE and PeGNAI-RNAi compared to wild type (WT). These genes may be related to mycelial growth and enzyme activity. They were involved in the MAPK signaling pathway, inositol phosphate metabolism, ascorbate, aldarate metabolism, and starch and sucrose metabolism. In summary, GNAI performs different physiological functions in regulating the growth and development of P. eryngii. Importantly, the molecular mechanisms of GNAI regulatory function are relatively complex and need further study.
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Integrating 1G with 2G Bioethanol Production by Using Distillers’ Dried Grains with Solubles (DDGS) as the Feedstock for Lignocellulolytic Enzyme Production. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
First-generation (1G) bioethanol is one of the most used liquid biofuels in the transport industry. It is generated by using sugar- or starch-based feedstocks, while second-generation (2G) bioethanol is generated by using lignocellulosic feedstocks. Distillers’ dried grains with solubles (DDGS) is a byproduct of first-generation bioethanol production with a current annual production of 22.6 million tons in the USA. DDGS is rich in fiber and valuable nutrients contents, which can be used to produce lignocellulolytic enzymes such as cellulases and hemicellulases for 2G bioethanol production. However, DDGS needs a pretreatment method such as dilute acid, ammonia soaking, or steam hydrolysis to release monosaccharides and short-length oligosaccharides as fermentable sugars for use in microbial media. These fermentable sugars can then induce microbial growth and enzyme production compared to only glucose or xylose in the media. In addition, selection of one or more suitable microbial strains, which work best with the DDGS for enzyme production, is also needed. Media optimization and fermentation process optimization strategies can then be applied to find the optimum conditions for the production of cellulases and hemicellulases needed for 2G bioethanol production. Therefore, in this review, a summary of all such techniques is compiled with a special focus on recent findings obtained in previous pieces of research conducted by the authors and by others in the literature. Furthermore, a comparison of such techniques applied to other feedstocks and process improvement strategies is also provided. Overall, dilute acid pretreatment is proven to be better than other pretreatment methods, and fermentation optimization strategies can enhance enzyme production by considerable folds with a suitable feedstock such as DDGS. Future studies can be further enhanced by the technoeconomic viability of DDGS as the on-site enzyme feedstock for the manufacture of second-generation bioethanol (2G) in first-generation (1G) ethanol plants, thus bridging the two processes for the efficient production of bioethanol using corn or other starch-based lignocellulosic plants.
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Cellulose-degrading enzymes: key players in biorefinery development. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01274-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Construction of CRISPR-Cas9 genome editing platform for white-rot fungus Cerrena unicolor BBP6 and its effects on extracellular ligninolytic enzyme biosynthesis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Raghav D, Jyoti A, Siddiqui AJ, Saxena J. Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches. J Appl Microbiol 2022; 133:287-310. [PMID: 35396804 DOI: 10.1111/jam.15574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
Abstract
There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.
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Affiliation(s)
- Divyangi Raghav
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Anupam Jyoti
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P O Box, Saudi Arabia
| | - Juhi Saxena
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
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Zhang T, Sun Y, Ma Z, Zhang J, Lv B, Li C. Developing iterative and quantified transgenic manipulations of non-conventional filamentous fungus Talaromyces pinophilus Li-93. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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Mondal S, Halder SK, Mondal KC. Tailoring in fungi for next generation cellulase production with special reference to CRISPR/CAS system. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2021; 2:113-129. [PMID: 38624901 PMCID: PMC8319711 DOI: 10.1007/s43393-021-00045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022]
Abstract
Cellulose is the utmost plenteous source of biopolymer in our earth, and fungi are the most efficient and ubiquitous organism in degrading the cellulosic biomass by synthesizing cellulases. Tailoring through genetic manipulation has played a substantial role in constructing novel fungal strains towards improved cellulase production of desired traits. However, the traditional methods of genetic manipulation of fungi are time-consuming and tedious. With the availability of the full-genome sequences of several industrially relevant filamentous fungi, CRISPR-CAS (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) technology has come into the focus for the proficient development of manipulated strains of filamentous fungi. This review summarizes the mode of action of cellulases, transcription level regulation for cellulase expression, various traditional strategies of genetic manipulation with CRISPR-CAS technology to develop modified fungal strains for a preferred level of cellulase production, and the futuristic trend in this arena of research.
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Affiliation(s)
- Subhadeep Mondal
- Center for Life Sciences, Vidyasagar University, Midnapore, 721102 West Bengal India
| | - Suman Kumar Halder
- Department of Microbiology, Vidyasagar University, Midnapore, 721102 West Bengal India
| | - Keshab Chandra Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, 721102 West Bengal India
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Rozhkova AM, Kislitsin VY. CRISPR/Cas Genome Editing in Filamentous Fungi. BIOCHEMISTRY (MOSCOW) 2021; 86:S120-S139. [PMID: 33827404 DOI: 10.1134/s0006297921140091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The review describes the CRISPR/CAS system and its adaptation for the genome editing in filamentous fungi commonly used for production of enzyme complexes, enzymes, secondary metabolites, and other compounds used in industrial biotechnology and agriculture. In the second part of this review, examples of the CRISPR/CAS technology application for improving properties of the industrial strains of fungi from the Trichoderma, Aspergillus, Penicillium, and other genera are presented. Particular attention is given to the efficiency of genome editing, as well as system optimization for specific industrial producers.
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Affiliation(s)
- Aleksandra M Rozhkova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Valeriy Yu Kislitsin
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
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12
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Jiang C, Lv G, Tu Y, Cheng X, Duan Y, Zeng B, He B. Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi. Front Microbiol 2021; 12:638096. [PMID: 33643273 PMCID: PMC7905030 DOI: 10.3389/fmicb.2021.638096] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yitian Duan
- School of Information, Renmin University of China, Beijing, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
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