1
|
Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method. Mol Biol Rep 2021; 48:3629-3635. [PMID: 33893925 PMCID: PMC8065318 DOI: 10.1007/s11033-021-06349-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.
Collapse
|
2
|
Yen YC, Yang CY, Mena KD, Cheng YT, Yuan CS, Chen PS. Jumping on the bed and associated increases of PM 10, PM 2.5, PM 1, airborne endotoxin, bacteria, and fungi concentrations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 245:799-809. [PMID: 30502709 DOI: 10.1016/j.envpol.2018.11.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 06/09/2023]
Abstract
Jumping on the bed is a favorite behavior of children; however, no study has investigated the increased air pollutants resulting from jumping on the bed. Therefore, we aimed to investigate the elevated concentrations of particulate matter (PM) and bioaerosols from jumping on the bed and making the bed. Simulation of jumping on the bed and making the bed was performed at sixty schoolchildren's houses in Taiwan. PM10, PM2.5, PM1 (PM with aerodynamic diameter less than 10, 2.5, and 1 μm, respectively) and airborne bacteria, fungi and endotoxin concentrations were simultaneously measured over simulation and background periods. Our results show the increase of PM10, PM2.5, PM1, airborne bacteria and fungi through the behavior of jumping on the bed (by 414 μg m-3, 353 μg m-3, 349 μg m-3, 6569 CFU m-3 and 978 CFU m-3, respectively). When making the bed, the PM10, PM2.5, PM1, airborne bacteria and fungi also significantly increased by 4.69 μg m-3, 4.09 μg m-3, 4.15 μg m-3, 8569 CFU m-3, and 779 CFU m-3, respectively. Airborne endotoxin concentrations significantly increased by 21.76 EU m-3 following jumping on the bed and making the bed. Moreover, when jumping on the bed, higher PM2.5 and PM1 concentrations in houses with furry pets rather than no furry pets, and less airborne fungi in apartments than in townhouses were found. For making the bed, lower airborne fungi was found in houses using essential oils rather than no essential oils using. The airborne endotoxin concentrations were positively associated with furry pets and smokers in the homes and negatively correlated to the home with window opening with a statistical significance during the periods of jumping on the bed and making the bed. In conclusion, significant increases of PM and bioaerosols during jumping on the bed and making the bed may need to be concerned.
Collapse
Affiliation(s)
- Yu-Chuan Yen
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chun-Yuh Yang
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Kristina Dawn Mena
- Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, TX, United States
| | - Yu-Ting Cheng
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Chung-Shin Yuan
- Institute of Environmental Engineering, College of Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Pei-Shih Chen
- Department of Public Health, College of Health Science, Kaohsiung Medical University, Kaohsiung City, Taiwan; Institute of Environmental Engineering, College of Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung City, Taiwan.
| |
Collapse
|
3
|
O’Brien CE, McCarthy CGP, Walshe AE, Shaw DR, Sumski DA, Krassowski T, Fitzpatrick DA, Butler G. Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade. PLoS One 2018; 13:e0198957. [PMID: 29944657 PMCID: PMC6019693 DOI: 10.1371/journal.pone.0198957] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/28/2018] [Indexed: 11/18/2022] Open
Abstract
Diutina catenulata (Candida catenulata) is an ascomycetous yeast that has been isolated from humans, animals and environmental sources. The species is a contaminant of dairy products, and has been linked to superficial and invasive infections in both humans and animals. Previous phylogenetic analyses have assigned the species to the Saccharomycetales, but failed to identify its specific clade. Here, we report the genome sequence of an environmental isolate of D. catenulata. Examination of the tRNA repertoire and coding potential of this species shows that it translates the CUG codon as serine and not leucine. In addition, two phylogenetic analyses using 204 ubiquitous gene family alignments and 3,826 single-copy genes both confirm the placement of the species in the Debaryomycetaceae/Metschnikowiaceae, or CTG-Ser clade. The sequenced isolate contains an MTLα idiomorph. However, unlike most MTL loci in related species, poly (A) polymerase (PAP) is not adjacent to MTLα1.
Collapse
Affiliation(s)
- Caoimhe E. O’Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Charley G. P. McCarthy
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Annie E. Walshe
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dennis R. Shaw
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Deirdre A. Sumski
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Tadeusz Krassowski
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David A. Fitzpatrick
- Department of Biology, Genome Evolution Laboratory, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
4
|
Mueller-Rompa S, Janke T, Schwaiger K, Mayer M, Bauer J, Genuneit J, Braun-Fahrlaender C, Horak E, Boznanski A, von Mutius E, Ege MJ. Identification of fungal candidates for asthma protection in a large population-based study. Pediatr Allergy Immunol 2017; 28:72-78. [PMID: 27711990 DOI: 10.1111/pai.12665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Exposure to molds has been related to asthma risk both positively and negatively, depending on the environmental setting. The pertinent results are based on generic markers or culturing methods although the majority of present fungi cannot be cultured under laboratory conditions. The aim of the present analysis was to assess environmental dust samples for asthma-protective fungal candidates with a comprehensive molecular technique covering also non-cultivable and non-viable fungi. METHODS Mattress dust samples of 844 children from the GABRIELA study were analyzed by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) of the fungus-specific internal transcribed spacer (ITS) region. Known asthma candidate species were tested for their associations with asthma, and further gel positions were sought to explain the above. As a second, data-driven, analysis, we tested the association of each individual gel position with asthma. RESULTS In the hypothesis-driven approach, Penicillium chrysogenum emerged with an odds ratio of 0.80 (95% confidence interval 0.66-0.96; p = 0.020). The effect size was changed by 39% toward the null when adjusting for the two bands 683 (DNA of Metschnikowia sp., Aureobasidium spp.) and 978 (DNA of Epicoccum spp., Galactomyces spp., uncultured Penicillium). The data-driven approach yielded an additional band (containing DNA of Pseudotaeniolina globosa) with reduced risk of asthma (OR = 0.80 [0.66-0.96], p = 0.012). CONCLUSIONS A large population-based study revealed several fungal taxa with inverse associations with childhood asthma. Molds produce a variety of bioactive compounds with detrimental but also beneficial immunoregulatory capacities, which renders them promising targets for further asthma research.
Collapse
Affiliation(s)
- Susanne Mueller-Rompa
- Dr von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Tobias Janke
- Chair of Animal Hygiene, Technische Universität München, Munich, Germany
| | - Karin Schwaiger
- Chair of Animal Hygiene, Technische Universität München, Munich, Germany
| | - Melanie Mayer
- Chair of Animal Hygiene, Technische Universität München, Munich, Germany
| | - Johann Bauer
- Chair of Animal Hygiene, Technische Universität München, Munich, Germany
| | - Jon Genuneit
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Charlotte Braun-Fahrlaender
- Swiss Tropical and Public Health Institute Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Erika von Mutius
- Dr von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany.,The German Center for Lung Research (DZL), München, Germany
| | - Markus J Ege
- Dr von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany.,The German Center for Lung Research (DZL), München, Germany
| | | |
Collapse
|
5
|
Rajatileka S, Luyt K, Williams M, Harding D, Odd D, Molnár E, Váradi A. Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand conformational polymorphism (SSCP), pyrosequencing and Sanger sequencing. BMC Genet 2014; 15:80. [PMID: 24996834 PMCID: PMC4112986 DOI: 10.1186/1471-2156-15-80] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirement for basic equipment accessible in most laboratories and low cost. This technique was previously used to detect rs4354668:A > C (g.-181A > C) SNP in the promoter of astroglial glutamate transporter (EAAT2) and the same approach was initially used here to investigate this promoter region in a cohort of newborns. Results Unexpectedly, four distinct DNA migration patterns were identified by SSCP. Sanger sequencing revealed two additional SNPs: g.-200C > A and g.-168C > T giving a rise to a total of ten EAAT2 promoter variants. SSCP failed to distinguish these variants reliably and thus pyrosequencing assays were developed. g.-168C > T was found in heterozygous form in one infant only with minor allele frequency (MAF) of 0.0023. In contrast, g.-200C > A and -181A > C were more common (with MAF of 0.46 and 0.49, respectively) and showed string evidence of linkage disequilibrium (LD). In a systematic comparison, 16% of samples were miss-classified by SSCP with 25-31% errors in the identification of the wild-type and homozygote mutant genotypes compared to pyrosequencing or Sanger sequencing. In contrast, SSCP and pyrosequencing of an unrelated single SNP (rs1835740:C > T), showed 94% concordance. Conclusion Our data suggest that SSCP cannot always detect reliably several closely located SNPs. Furthermore, caution is needed in the interpretation of the association studies linking only one of the co-inherited SNPs in the EAAT2 promoter to human diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anikó Váradi
- Centre for Research in Biosciences, Department of Biological, Biomedical and Analytical Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK.
| |
Collapse
|
6
|
Katra I, Arotsker L, Krasnov H, Zaritsky A, Kushmaro A, Ben-Dov E. Richness and diversity in dust stormborne biomes at the southeast mediterranean. Sci Rep 2014; 4:5265. [PMID: 24919765 PMCID: PMC4053720 DOI: 10.1038/srep05265] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/15/2014] [Indexed: 12/26/2022] Open
Abstract
Dust storms include particulate matter that is transported over land and sea with biota that could impact downwind ecosystems. In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared. The bio-assemblages in the collected dust samples were affiliated with scores of different taxa. Distinct patterns of richness and diversity of the two events were influenced by the origins of the air masses: Ev13 was rich with reads affiliated to Betaproteobacteria and Embryophyta, consistent with a European origin. Ev12, originated in north-Africa, contained significantly more of the Actinobacteria and fungi, without conifers. The abundance of bacterial and eukaryotic reads demonstrates dissemination of biological material in dust that may impose health hazards of pathogens and allergens, and influence vegetation migration throughout the world.
Collapse
Affiliation(s)
- Itzhak Katra
- Department of Geography and Environmental Development, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel
| | - Luba Arotsker
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel
| | - Helena Krasnov
- Department of Geography and Environmental Development, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel
| | - Arieh Zaritsky
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel
| | - Ariel Kushmaro
- 1] Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel [2] National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel [3] School of Materials Science and Engineering, Nanyang Technological University, Singapore 637819 (Singapore)
| | - Eitan Ben-Dov
- 1] National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84104, Israel [2] Department of Life Sciences, Achva Academic College MP Shikmim, 79800, Israel
| |
Collapse
|