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Wei Y, Li L, Liu Y, Xiang S, Zhang H, Yi L, Shang Y, Xu W. Identification techniques and detection methods of edible fungi species. Food Chem 2021; 374:131803. [PMID: 34915377 DOI: 10.1016/j.foodchem.2021.131803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 12/15/2022]
Abstract
Edible fungi have high nutritional value and great potential. Confusion among edible fungi species, and foodborne diseases due to toadstool poisoning or death induced by inadvertent consumption exist across the world. Therefore, edible fungi must be accurately identified. Based on different substances in edible fungi, there are different detection methods, and the same method can use different identification technology. Sensory identification methods include morphological and odor methods. Instrumental analysis methods based on chemical composition include chromatographic, mass spectrometry and spectral technology. Molecular biology identification methods based on nucleic acids include molecular marker technology, sequencing technology, isothermal amplification technology and endogenous reference gene method. Method is channel, and technology is the means. The principles, advantages, disadvantages and applications of various identification techniques and detection methods were discussed in this work to provide reference for the identification research of edible fungi and technical support for preventing food safety incidents caused by toadstools.
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Affiliation(s)
- Yuanmiao Wei
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Ling Li
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Yao Liu
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Shuna Xiang
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Hanyue Zhang
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Lunzhao Yi
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China
| | - Ying Shang
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, China.
| | - Wentao Xu
- Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
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Cowan AF, Elkins KM. Detection and Identification of Psilocybe cubensis DNA Using a Real-Time Polymerase Chain Reaction High Resolution Melt Assay. J Forensic Sci 2017; 63:1500-1505. [PMID: 29194645 DOI: 10.1111/1556-4029.13714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/03/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
Abstract
Psilocybe cubensis, or "magic mushroom," is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web-based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR® Green I, Radiant™ Green, or LCGreen Plus® intercalating dye; amplicon size was determined using agarose gel electrophoresis. The PCR assays were tested for amplifiability, specificity, reproducibility, robustness, sensitivity, and multiplexing with primers that target marijuana. The observed high resolution melt (HRM) temperatures for primer sets 1 and 7 were 78.85 ± 0.31°C and 73.22 ± 0.61°C, respectively, using SYBR® Green I dye and 81.67 ± 0.06°C and 76.04 ± 0.11°C, respectively, using Radiant™ Green dye.
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Affiliation(s)
- Ashley F Cowan
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
| | - Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
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Detection of Edible Mushroom Species by Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Makarevitch I, Martinez-Vaz B. Killing two birds with one stone: Model plant systems as a tool to teach the fundamental concepts of gene expression while analyzing biological data. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:166-173. [PMID: 27155065 DOI: 10.1016/j.bbagrm.2016.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/23/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022]
Abstract
Plants are ideal systems to teach core biology concepts due to their unique physiological and developmental features. Advances in DNA sequencing technology and genomics have allowed scientists to generate genome sequences and transcriptomics data for numerous model plant species. This information is publicly available and presents a valuable tool to introduce undergraduate students to the fundamental concepts of gene expression in the context of modern quantitative biology and bioinformatics. Modern biology classrooms must provide authentic research experiences to allow developing core competencies such as scientific inquiry, critical interpretation of experimental results, and quantitative analyses of large dataset using computational approaches. Recent educational research has shown that undergraduate students struggle when connecting gene expression concepts to classic genetics, phenotypic analyses, and overall flow of biological information in living organisms, suggesting that novel approaches are necessary to enhance learning of gene expression and regulation. This review describes different strategies and resources available to instructors willing to incorporate authentic research experiences, genomic tools, and bioinformatics analyses when teaching transcriptional regulation and gene expression in undergraduate courses. A variety of laboratory exercises and pedagogy materials developed to teach gene expression using plants are discussed. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Irina Makarevitch
- Department of Biology, Hamline University, Saint Paul, MN 55104, United States.
| | - Betsy Martinez-Vaz
- Department of Biology, Hamline University, Saint Paul, MN 55104, United States
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Gang GH, Cho HJ, Kim HS, Kwack YB, Kwak YS. Analysis of Fungicide Sensitivity and Genetic Diversity among Colletotrichum Species in Sweet Persimmon. THE PLANT PATHOLOGY JOURNAL 2015; 31:115-22. [PMID: 26060430 PMCID: PMC4453992 DOI: 10.5423/ppj.oa.03.2015.0033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/12/2015] [Accepted: 04/17/2015] [Indexed: 05/09/2023]
Abstract
Anthracnose, caused by Colletotrichum gloeosporioides (C. gloeosporioides; Teleomorph: Glomerella cingulata), is the most destructive disease that affects sweet persimmon production worldwide. However, the biology, ecology, and genetic variations of C. gloeosporioides remain largely unknown. Therefore, in this study, the development of fungicide resistance and genetic diversity among an anthracnose pathogen population with different geographical origins and the exposure of this population to different cultivation strategies were investigated. A total of 150 pathogen isolates were tested in fungicide sensitivity assays. Five of the tested fungicides suppressed mycelial pathogen growth effectively. However, there were significant differences in the sensitivities exhibited by the pathogen isolates examined. Interestingly, the isolates obtained from practical management orchards versus organic cultivation orchards showed no differences in sensitivity to the same fungicide. PCR-restriction fragment length polymorphism (RFLP) analyses were performed to detect internal transcribed spacer regions and the β-tubulin and glutamine synthetase genes of the pathogens examined. Both the glutamine synthetase and β-tubulin genes contained a complex set of polymorphisms. Based on these results, the pathogens isolated from organic cultivation orchards were found to have more diversity than the isolates obtained from the practical management orchards.
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Affiliation(s)
- Geun-Hye Gang
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Hyun Ji Cho
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Hye Sun Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | | | - Youn-Sig Kwak
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 660-701,
Korea
- Corresponding author. Phone) 55-772-1922, FAX) 55-772-1929, E-mail)
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Millard JT, Chuang E, Lucas JS, Nagy EE, Davis GT. Case-Study Investigation of Equine Maternity via PCR-RFLP: A Biochemistry Laboratory Experiment. JOURNAL OF CHEMICAL EDUCATION 2013; 90:10.1021/ed300740r. [PMID: 24363455 PMCID: PMC3867210 DOI: 10.1021/ed300740r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A simple and robust biochemistry laboratory experiment is described that uses restriction fragment length polymorphism (RFLP) of polymerase chain reaction (PCR) products to verify the identity of a potentially valuable horse. During the first laboratory period, students purify DNA from equine samples and amplify two loci of mitochondrial DNA. During the second laboratory period, students digest PCR products with restriction enzymes and analyze the fragment sizes through agarose gel electrophoresis. An optional step of validating DNA extracts through realtime PCR can expand the experiment to three weeks. This experiment, which has an engaging and versatile scenario, provides students with exposure to key principles and techniques of molecular biology, bioinformatics, and evolution in a forensic context.
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Legorreta-Herrera M, Mosqueda-Romo NA, Hernández-Clemente F, Soto-Cruz I. Detection of an ABCA1 variant associated with type 2 diabetes mellitus susceptibility for biochemistry and genetic laboratory courses. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:409-418. [PMID: 24214147 DOI: 10.1002/bmb.20736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/19/2013] [Indexed: 06/02/2023]
Abstract
We selected diabetes mellitus for this laboratory exercise to provide students with an explicit model for scientific research concerning the association between the R230C polymorphism and susceptibility to type 2 diabetes mellitus, which is highly prevalent in the Mexican population. We used a collaborative project-based learning to engage students to direct their own learning process. Students worked in small groups with the same learning goal to research, organize data, and present seminars to experimentally genotype the C230 variant and correctly interpret their results. At the conclusion of this laboratory exercise, the students were able to demonstrate a clear understanding of the relevant biological molecular principles to genotype the C230 variant, showed technical competency to carry out the experimental protocols with proficiency, and interpret their results using statistical analyses. The students discussed their understanding of the genetic technologies and the broader social and ethical implications of the research. A randomly selected team was trained to work as a "sentinel" to monitor their classmates and ensure the proper application of techniques. Moreover, the evaluation of this exercise is shared between the students and the instructors; the students evaluate their own work and the performance of their classmates. At the end of the course, the students complete a questionnaire to anonymously provide feedback and information regarding their perception of the learning outcomes. Overall, the student feedback was positive, indicating that the exercise was useful and that it would help to prepare the students for professional practice.
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Affiliation(s)
- M Legorreta-Herrera
- Molecular Immunology Laboratory, Facultad de Estudios Superiores Zaragoza, UNAM, Mexico
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Weinlander KM, Hall DJ, De Stasio EA. RFLP analysis and allelic discrimination with real-time PCR using the human lactase persistence trait: A pair of molecular genetic investigations. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 38:167-171. [PMID: 21567819 DOI: 10.1002/bmb.20357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We describe here two open-ended laboratory investigations for an undergraduate laboratory course that uses students' DNA as templates for quantitative real-time PCR and for traditional PCR followed by RFLP analysis. Students are captivated by the immediacy of the application and the relevance of the genotypes and traits, lactase persistence or nonpersistence, under study. Concepts ranging from nucleotide polymorphisms to natural selection can be demonstrated and reinforced by these laboratories. Students have a high degree of success with the laboratories and both objective and self-assessments of student learning indicate that concepts and techniques are better understood following implementation of these laboratory investigations.
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Chang MM, Digennaro P, Macula A. PCR cloning of partial nbs sequences from grape (Vitis aestivalis Michx). BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2009; 37:355-360. [PMID: 21567771 DOI: 10.1002/bmb.20320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R genes. Here, we report a 4-week undergraduate laboratory exercise that mimics the research environment to PCR-clone partial nbs sequences using degenerate primers corresponding to the phosphate-binding loop (P-loop) and GLPL motifs within the NBS domain of potential R gene products from the North American grape, Vitis aestivalis Michx. Students were able to complete the laboratory procedures successfully and obtained four different clones, among which three are new. Through the laboratory exercise, students learned a variety of important molecular techniques including genomic DNA isolation, DNA quantification, PCR, agarose gel electrophoresis, DNA extraction from agarose gel, ligation, bacterial transformation, and plasmid DNA isolation and purification. They also used currently available web-based bioinformatic programs for sequence analysis. The laboratory exercise provides students the hands-on experience on PCR cloning and shows them how it is done in a research environment. The clones obtained may be further tested for their potential use as markers to differentiate resistant cultivars from the susceptible ones, a useful tool in breeding programs.
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Affiliation(s)
- Ming-Mei Chang
- Department of Biology, State University of New York at Geneseo, Geneseo, New York 14454.
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Asraoui JF, Sayar NP, Knio KM, Smith CA. Fly diversity revealed by PCR-RFLP of mitochondrial DNA. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2008; 36:354-362. [PMID: 21591219 DOI: 10.1002/bmb.20220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this article, we describe an inexpensive, two-session undergraduate laboratory activity that introduces important molecular biology methods in the context of biodiversity. In the first session, students bring tentatively identified flies (order Diptera, true flies) to the laboratory, extract DNA, and amplify a region of the mitochondrial gene NADH dehydrogenase subunit 1. In the second session, the students digest the PCR product with a restriction enzyme, visualize the resulting fragments by agarose gel electrophoresis, and analyze their results with comparison to known sequences. The diversity of flies and their importance as disease vectors, agriculture pests, pollinators, models of speciation, and in the case of Drosophila melanogaster, as a genetic model organism, offer many perspectives with which to appeal to students' interests. The laboratory exercise can be linked as a module to topics in biodiversity, bioinformatics, entomology, evolution, and mutagenesis.
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Affiliation(s)
- Jimmy F Asraoui
- Department of Biology, American University of Beirut, Beirut, Lebanon
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Amenkhienan E, Smith EJ. A web-based genetic polymorphism learning approach for high school students and science teachers*. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2006; 34:30-33. [PMID: 21638628 DOI: 10.1002/bmb.2006.49403401030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using freely available bioinformatics tools on the Internet to detect single nucleotide polymorphisms in genomic DNA and gene-based sequences to evaluate variation or polymorphism. Similar tools were also used to show the functional effect, if any, of the single nucleotide polymorphisms. A total of 25 science teachers and 60 students from high schools in Alabama and Virginia participated in the program that ranged from 2 to 4 weeks. Seventy percent of the teachers have now developed a web-based module to teach at least two lessons involving DNA variation and how it influences other disciplines, including evolution. Among former high school students, five are in Ph.D. programs in genetics or related subjects, and 80% are in medical school or in college in a biology or pre-med major. The exercise is simple to implement, and the cost is relatively low, requiring only a computer with an Internet connection. It also provides a foundation for introducing students to the theory of evolution, a concept that remains controversial in high school science curricula. Similar programs, if properly implemented, may result in fostering more interest in the biological sciences among prospective college students and ensure a good foundation in the pipeline for career biologists and scientists.
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Affiliation(s)
- Ehichoya Amenkhienan
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia 24061-0306,; The University of Mary Washington, Fredericksburg, Virginia 22406
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