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Xing Y, Liang J, Dong F, Wu J, Shi J, Xu J, Wang J. Rapid Visual LAMP Method for Detection of Genetically Modified Organisms. ACS OMEGA 2023; 8:29608-29614. [PMID: 37599972 PMCID: PMC10433496 DOI: 10.1021/acsomega.3c03567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
We developed a novel loop-mediated isothermal amplification (LAMP) method using DNA captured on polyacrylamide microparticles (PAMMPs) as templates (PAMMPs@DNA-LAMP) for rapid qualitative detection of genetically modified organisms (GMOs). Here, DNA was extracted by a fast and cost-effective method using PAMMPs. Four LAMP primers were designed for the PAMMPs@DNA-LAMP method to detect the cauliflower mosaic virus 35S (CaMV35S) promotor in GMOs. We thus developed this method for rapid extraction of DNA (5-10 min) and fast amplification of DNA within ∼30 min at a constant temperature of 63 °C. Moreover, the DNA captured by PAMMPs (PAMMPs@DNA) could be effectively detected by both conventional and quantitative PCR (qPCR) and LAMP. The PAMMPs@DNA-LAMP method was validated with high specificity, sensitivity, and performance for practical sample analysis. This assay detected 0.01% target sequences, which had a high specificity like qPCR and better than the conventional PCR (cPCR). Furthermore, PAMMPs@DNA-LAMP was successfully used to extract and detect DNA from food samples of the major crops (soybean, maize, rice, etc.). In summary, a novel PAMMPs@DNA-LAMP assay has been developed, which has higher sensitivity and spends less time than the cPCR detection using the conventional DNA extracted process. This method offers a novel approach for rapid detection of GMOs in the field.
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Affiliation(s)
- Yujun Xing
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Key Laboratory for Control/Technology
and Standard for Agro-Product Safety and Quality, Ministry of Agriculture
and Rural Affairs/Collaborative Innovation Center for Modern Grain
Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jie Liang
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Fei Dong
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jirong Wu
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jianrong Shi
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Institute of Food Safety
and Nutrition, Jiangsu Academy of Agricultural
Sciences, Nanjing 210014, China
| | - Jianhong Xu
- Jiangsu
Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation
Base, Ministry of Science and Technology/Key Laboratory for Control/Technology
and Standard for Agro-Product Safety and Quality, Ministry of Agriculture
and Rural Affairs/Collaborative Innovation Center for Modern Grain
Circulation and Safety/Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jinke Wang
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering, Southeast
University, Nanjing 210096, China
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Cheng JT, Cao F, Chen XA, Li YQ, Mao XM. Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites. BMC Genomics 2020; 21:424. [PMID: 32580753 PMCID: PMC7315530 DOI: 10.1186/s12864-020-06813-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. A comprehensive survey of the genome and transcriptome of this endophytic fungus will help to understand its capacity to biosynthesize secondary metabolites and will lay the foundation for the development of this precious resource. RESULTS In this study, we reported the high-quality genome sequence of C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, larger than other typical filamentous fungi, and comprises 10,001 predicted genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for the mycotoxin aurovertins. In addition, several gene clusters were predicted to produce mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown that are potentially involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assays showed that only expression of the aurovertin gene cluster is much stronger than expression of the housekeeping genes under laboratory conditions, consistent with the observation that aurovertins are the predominant metabolites. Gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than expression of the housekeeping genes, which partially explained poor production of other secondary metabolites in this fungus. CONCLUSIONS Our omics data, along with bioinformatics analysis, indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce a profound number of secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.
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Affiliation(s)
- Jin-Tao Cheng
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Fei Cao
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
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Yang BC, Chen N, Liao B, Huang Y, Huang LN. Spencerozyma acididurans sp. nov., an acid-tolerant basidiomycetous yeast species isolated from acid mine drainage. Int J Syst Evol Microbiol 2019; 69:2828-2833. [PMID: 31274406 DOI: 10.1099/ijsem.0.003565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SYSU-17, representing a novel acid-tolerant yeast species which can grow at pH 2.0 weakly, was isolated from acid mine drainage collected in a tailing impoundment of the Fankou Lead/Zinc Mine, Guangdong Province, PR China. Phylogenetic analysis of strain SYSU-17 based on the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit ribosomal RNA (LSU rRNA) gene suggested that strain SYSU-17 was a novel species belonging to the genus Spencerozyma (class Microbotryomycetes, subphylum Pucciniomycotina). It differed from the type strain of the closest related species, Spencerozyma crocea CBS 2029T, by 0.7 % sequence divergence (three gaps and one nucleotide substitution out of 594 bp) in the D1/D2 domains of the LSU rRNA gene and 7.6 % sequence divergence (32 gaps and 22 nucleotide substitutions out of 714 bp) in the ITS region. In contrast to the physiological properties of S. crocea, the novel yeast species was unable to assimilate galactose, d-ribose, xylitol, succinate, d-xylose, ethanol, nitrate and nitrite. The name Spencerozyma acididurans sp. nov. is proposed and SYSU-17 is designated as the holotype.
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Affiliation(s)
- Bei-Cheng Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Nan Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yong Huang
- Guangdong Province Dabaoshan Mining Co. Ltd, Shaoguan 512128, PR China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin. Biol Proced Online 2018; 20:12. [PMID: 29881330 PMCID: PMC5984428 DOI: 10.1186/s12575-018-0077-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/19/2018] [Indexed: 11/23/2022] Open
Abstract
Background Although genomic DNA isolation using the Chelex 100 resin is rapid and inexpensive, the DNA obtained by this method has a low concentration in solution and contains suspended impurities. The presence of debris in the DNA solution may result in degradation of DNA on long term storage and inhibition of the polymerase chain reaction. In order to remove impurities and concentrate the DNA in solution, we have introduced modifications in the existing DNA isolation protocol using Chelex-100. We used ammonium acetate to precipitate proteins and a sodium acetate- isopropanol mixture to pellet out DNA which was washed with ethanol. Results A pure DNA pellet that can be dissolved in water or Tris-EDTA buffer and stored for a long time at − 80 °C was obtained. We also observed a 20-fold change in the DNA concentration following precipitation and re-dissolution. Conclusion Our method is different from other extraction methods since it uses non-toxic, easily available and inexpensive reagents as well as minimal amounts of blood or tissue samples for the DNA extraction process. Besides its use in sex determination and genotyping in lab animals as described in this paper, it may also have applications in forensic science and diagnostics such as the easy detection of pathogenic DNA in blood.
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