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Tayyrov A, Wei C, Fetz C, Goryachkin A, Schächle P, Nyström L, Künzler M. Cytoplasmic Lipases-A Novel Class of Fungal Defense Proteins Against Nematodes. Front Fungal Biol 2021; 2:696972. [PMID: 37744157 PMCID: PMC10512399 DOI: 10.3389/ffunb.2021.696972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/31/2021] [Indexed: 09/26/2023]
Abstract
Fungi are an attractive food source for predators such as fungivorous nematodes. Several fungal defense proteins and their protective mechanisms against nematodes have been described. Many of these proteins are lectins which are stored in the cytoplasm of the fungal cells and bind to specific glycan epitopes in the digestive tract of the nematode upon ingestion. Here, we studied two novel nematotoxic proteins with lipase domains from the model mushroom Coprinopsis cinerea. These cytoplasmically localized proteins were found to be induced in the vegetative mycelium of C. cinerea upon challenge with fungivorous nematode Aphelenchus avenae. The proteins showed nematotoxicity when heterologously expressed in E. coli and fed to several bacterivorous nematodes. Site-specific mutagenesis of predicted catalytic residues eliminated the in-vitro lipase activity of the proteins and significantly reduced their nematotoxicity, indicating the importance of the lipase activity for the nematotoxicity of these proteins. Our results suggest that cytoplasmic lipases constitute a novel class of fungal defense proteins against predatory nematodes. These findings improve our understanding of fungal defense mechanisms against predators and may find applications in the control of parasitic nematodes in agriculture and medicine.
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Affiliation(s)
- Annageldi Tayyrov
- Department of Biology, Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Chunyue Wei
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Céline Fetz
- Department of Biology, Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Aleksandr Goryachkin
- Department of Biology, Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Philipp Schächle
- Department of Biology, Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Laura Nyström
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, Zurich, Switzerland
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Zurich, Switzerland
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Tayyrov A, Schnetzler M, Gillis-Germitsch N, Schnyder M. Genetic diversity of the cardiopulmonary canid nematode Angiostrongylus vasorum within and between rural and urban fox populations. Infect Genet Evol 2020; 87:104618. [PMID: 33188914 DOI: 10.1016/j.meegid.2020.104618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 02/08/2023]
Abstract
Angiostrongylus vasorum is an emerging parasitic cardiopulmonary nematode of dogs, foxes, and other canids. In dogs, the infection causes respiratory and bleeding disorders along with other clinical signs collectively known as canine angiostrongylosis, while foxes represent an important wildlife reservoir. Despite the spread of A. vasorum across various countries in Europe and the Americas, little is known about the genetic diversity of A. vasorum populations at a local level in a highly endemic area. Thus, in the present study, we investigated the genetic diversity of 323 adult A. vasorum nematodes from 64 foxes living in the canton of Zurich, Switzerland. Among those, 279 worms isolated from 20 foxes were analyzed separately to investigate the genetic diversity of multiple worms within individual foxes. Part of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene was amplified and sequenced. Overall, 16 mitochondrial haplotypes were identified. The analysis of multiple worms per host revealed 12 haplotypes, with up to 5 different haplotypes in single individuals. Higher haplotype diversity (n = 10) of nematodes from foxes of urban areas than in rural areas (n = 7) was observed, with 5 shared haplotypes. Comparing our data with published GenBank sequences, five haplotypes were found to be unique within the Zurich nematode population. Interestingly, A. vasorum nematodes obtained from foxes in London and Zurich shared the same dominating haplotype. Further studies are needed to clarify if this haplotype has a different pathogenicity that may contribute to its dominance. Our findings show the importance of foxes as a reservoir for genetic parasite recombination and indicate that high fox population densities in urban areas with small and overlapping home ranges allow multiple infection events that lead to high genetic variability of A. vasorum.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Michèle Schnetzler
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Nina Gillis-Germitsch
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland.
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Tayyrov A, Stanley CE, Azevedo S, Künzler M. Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. BMC Genomics 2019; 20:243. [PMID: 30909884 PMCID: PMC6434838 DOI: 10.1186/s12864-019-5607-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on the interaction of the model mushroom Coprinopsis cinerea by the fungivorous nematode Aphelenchus avenae on agar plates has shown that the this fungal defense response is most pronounced in the part of the mycelium that is in direct contact with the nematode. Hence, we hypothesized that, for a comprehensive characterization of this defense response, an experimental setup that maximizes the zone of direct interaction between the fungal mycelium and the nematode, was needed. RESULTS In this study, we conducted a transcriptome analysis of C. cinerea vegetative mycelium upon challenge with A. avenae using a tailor-made microfluidic device. The device was designed such that the interaction between the fungus and the nematode was confined to a specific area and that the mycelium could be retrieved from this area for analysis. We took samples from the confrontation area after different time periods and extracted and sequenced the poly(A)+ RNA thereof. The identification of 1229 differentially expressed genes (DEGs) shows that this setup profoundly improved sensitivity over co-cultivation on agar plates where only 37 DEGs had been identified. The product of one of the most highly upregulated genes shows structural homology to bacterial pore-forming toxins, and revealed strong toxicity to various bacterivorous nematodes. In addition, bacteria associated with the fungivorous nematode A. avenae were profiled with 16S rRNA deep sequencing. Similar to the bacterivorous and plant-feeding nematodes, Proteobacteria and Bacteroidetes were the most dominant phyla in A. avenae. CONCLUSIONS The use of a novel experimental setup for the investigation of the defense response of a fungal mycelium to predation by fungivorous nematodes resulted in the identification of a comprehensive set of DEGs and the discovery of a novel type of fungal defense protein against nematodes. The bacteria found to be associated with the fungivorous nematode are a possible explanation for the induction of some antibacterial defense proteins upon nematode challenge.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Claire E. Stanley
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Sophie Azevedo
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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Kombrink A, Tayyrov A, Essig A, Stöckli M, Micheller S, Hintze J, van Heuvel Y, Dürig N, Lin CW, Kallio PT, Aebi M, Künzler M. Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria. ISME J 2018; 13:588-602. [PMID: 30301946 PMCID: PMC6461984 DOI: 10.1038/s41396-018-0293-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/23/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022]
Abstract
Bacteria are the main nutritional competitors of saprophytic fungi during colonization of their ecological niches. This competition involves the mutual secretion of antimicrobials that kill or inhibit the growth of the competitor. Over the last years it has been demonstrated that fungi respond to the presence of bacteria with changes of their transcriptome, but the significance of these changes with respect to competition for nutrients is not clear as functional proof of the antibacterial activity of the induced gene products is often lacking. Here, we report the genome-wide transcriptional response of the coprophilous mushroom Coprinopsis cinerea to the bacteria Bacillus subtilis and Escherichia coli. The genes induced upon co-cultivation with each bacterium were highly overlapping, suggesting that the fungus uses a similar arsenal of effectors against Gram-positive and -negative bacteria. Intriguingly, the induced genes appeare to encode predominantly secreted peptides and proteins with predicted antibacterial activities, which was validated by comparative proteomics of the C. cinerea secretome. Induced members of two putative antibacterial peptide and protein families in C. cinerea, the cysteine-stabilized αβ-defensins (Csαβ-defensins) and the GH24-type lysozymes, were purified, and their antibacterial activity was confirmed. These results provide compelling evidence that fungi are able to recognize the presence of bacteria and respond with the expression of an arsenal of secreted antibacterial peptides and proteins.
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Affiliation(s)
- Anja Kombrink
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Annageldi Tayyrov
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Andreas Essig
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Martina Stöckli
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.,rqmicro AG, Brandstrasse 24, 8952, Schlieren, Switzerland
| | - Sebastian Micheller
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - John Hintze
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.,Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen, Denmark
| | - Yasemin van Heuvel
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Natalia Dürig
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Chia-Wei Lin
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Pauli T Kallio
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Markus Aebi
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
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Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 2015; 4:e06974. [PMID: 26175406 PMCID: PMC4501334 DOI: 10.7554/elife.06974] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/16/2015] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga. DOI:http://dx.doi.org/10.7554/eLife.06974.001 Single-celled parasites cause many severe diseases in humans and animals. The apicomplexans form probably the most successful group of these parasites and include the parasites that cause malaria. Apicomplexans infect a broad range of hosts, including humans, reptiles, birds, and insects, and often have complicated life cycles. For example, the malaria-causing parasites spread by moving from humans to female mosquitoes and then back to humans. Despite significant differences amongst apicomplexans, these single-celled parasites also share a number of features that are not seen in other living species. How and when these features arose remains unclear. It is known from previous work that apicomplexans are closely related to single-celled algae. But unlike apicomplexans, which depend on a host animal to survive, these algae live freely in their environment, often in close association with corals. Woo et al. have now sequenced the genomes of two photosynthetic algae that are thought to be close living relatives of the apicomplexans. These genomes were then compared to each other and to the genomes of other algae and apicomplexans. These comparisons reconfirmed that the two algae that were studied were close relatives of the apicomplexans. Further analyses suggested that thousands of genes were lost as an ancient free-living algae evolved into the apicomplexan ancestor, and further losses occurred as these early parasites evolved into modern species. The lost genes were typically those that are important for free-living organisms, but are either a hindrance to, or not needed in, a parasitic lifestyle. Some of the ancestor's genes, especially those that coded for the building blocks of flagella (structures which free-living algae use to move around), were repurposed in ways that helped the apicomplexans to invade their hosts. Understanding this repurposing process in greater detail will help to identify key molecules in these deadly parasites that could be targeted by drug treatments. It will also offer answers to one of the most fascinating questions in evolutionary biology: how parasites have evolved from free-living organisms. DOI:http://dx.doi.org/10.7554/eLife.06974.002
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Affiliation(s)
- Yong H Woo
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hifzur Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | | | - Martin Kolisko
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jan Michálek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alka Saxena
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Annageldi Tayyrov
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alaguraj Veluchamy
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Shahjahan Ali
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Axel Bernal
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Javier del Campo
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jaromír Cihlář
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Eva Hajdušková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jan Janouškovec
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Fred D Mast
- Seattle Biomedical Research Institute, Seattle, United States
| | - Diego Miranda-Saavedra
- Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, Madrid, Spain
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raeece Naeem
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mridul Nair
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aswini K Panigrahi
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neil D Rawlings
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eriko Padron-Regalado
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nadira Samad
- School of Botany, University of Melbourne, Parkville, Australia
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jon Wilkes
- Wellcome Trust Centre For Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel E Neafsey
- Broad Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Christian Doerig
- Department of Microbiology, Monash University, Clayton, Australia
| | - Chris Bowler
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197 INSERM U1024, Paris, France
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Thomas J Templeton
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross F Waller
- School of Botany, University of Melbourne, Parkville, Australia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Abstract
In this study, real-time polymerase chain reaction (PCR) was used for identifying the effects of different temperatures and times of heat treatment on the DNA of meat products. For this purpose, beef, pork, and chicken were baked at 200 °C for 10, 20, 30, 40, 50 min, and for 30 min at 30, 60, 90, 120, 150, 180, 210 °C and also cooked by boiling at 99 °C for 10, 30, 60, 90, 120, 150, 180, 210, and 240 min. The DNA was then extracted from all samples after the heat treatment. Further, a region of 374, 290, and 183-bp of mitochondrial DNA of beef, pork, and chicken, respectively, was amplified by real-time PCR. It was found that baking and boiling of the beef, pork, and chicken resulted in decreases in the detectable copy numbers of specific genes, which varied with the heating time and degree. The results indicated that species determination and quantification using real-time PCR are affected by the temperature, duration of the heat treatment, and size of the DNA fragment to be amplified.
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Affiliation(s)
- Ergün Şakalar
- Genetics and Bioengineering Dept, Fatih Univ, İstanbul, Turkey.
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