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Robert H. A. Coutts - One of the best experts on this subject based on the ideXlab platform.
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Completion of the sequence of the Aspergillus fumigatus partitivirus 1 genome
Archives of Virology, 2020Co-Authors: Charalampos Filippou, Robert H. A. Coutts, David A. Stevens, Raquel Sabino, Ioly Kotta-loizouAbstract:A Portuguese isolate of Aspergillus fumigatus was found to contain three double-stranded (ds) RNA elements ranging in size from 1.1 to 1.8 kbp and comprising the genome of a strain of Aspergillus fumigatus partitivirus 1 (AfuPV-1) previously thought to contain only the two largest dsRNA elements. The sequence of the smallest dsRNA element is described here, completing the sequence of the AfuPV-1 genome. Sequence analysis of the element revealed an open reading frame encoding a protein of unknown function similar in size and distantly related to elements previously identified in other members of the family Partitiviridae .
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multiplex detection of Aspergillus fumigatus mycoviruses
Viruses, 2018Co-Authors: Selin Ozkankotiloglu, Robert H. A. CouttsAbstract:Mycoviruses are viruses that naturally infect and replicate in fungi. They are widespread in all major fungal groups including plant and animal pathogenic fungi. Several dsRNA mycoviruses have been reported in Aspergillus fumigatus. Multiplex polymerase chain reaction (PCR) amplification is a version of PCR that enables amplification of different targets simultaneously. This technique has been widely used for detection and differentiation of viruses especially plant viruses such as those which infect tobacco, potato and garlic. For rapid detection, multiplex RT-PCR was developed to screen new isolates for the presence of A. fumigatus mycoviruses. Aspergillus fumigatus chrysovirus (AfuCV), Aspergillus fumigatus partitivirus (AfuPV-1), and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) dsRNAs were amplified in separate reactions using a mixture of multiplex primer pairs. It was demonstrated that in the presence of a single infection, primer pair mixtures only amplify the corresponding single virus infection. Mixed infections using dual or triple combinations of dsRNA viruses were also amplified simultaneously using multiplex RT-PCR. Up until now, methods for the rapid detection of Aspergillus mycoviruses have been restricted to small scale dsRNA extraction approaches which are laborious and for large numbers of samples not as sensitive as RT-PCR. The multiplex RT-PCR assay developed here will be useful for studies on determining the incidence of A. fumigatus mycoviruses. This is the first report on multiplex detection of A. fumigatus mycoviruses.
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profile and functional analysis of small rnas derived from Aspergillus fumigatus infected with double stranded rna mycoviruses
BMC Genomics, 2017Co-Authors: Irina Mohorianu, Robert H. A. Coutts, Selin Ozkan, Tamas Dalmay, Ping XuAbstract:Abstract Background Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencing. The A. fumigatus genome encodes essential components of the RNA silencing machinery, including Dicer, Argonaute and RNA-dependent RNA polymerase (RdRP) homologues. Active silencing of double-stranded (ds)RNA and the generation of small RNAs (sRNAs) has been shown for several mycoviruses and it is anticipated that a similar mechanism will be activated in A. fumigatus isolates infected with mycoviruses. Results To investigate the existence and nature of A. fumigatus sRNAs, sRNA-seq libraries of virus-free and virus-infected isolates were created using Scriptminer adapters and compared. Three dsRNA viruses were investigated: Aspergillus fumigatus partitivirus-1 (AfuPV-1, PV), Aspergillus fumigatus chrysovirus (AfuCV, CV) and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1, NK) which were selected because they induce phenotypic changes such as coloration and sectoring. The dsRNAs of all three viruses, which included two conventionally encapsidated ones PV and CV and one unencapsidated example NK, were silenced and yielded characteristic vsiRNAs together with co-incidental silencing of host fungal genes which shared sequence homology with the viral genomes. Conclusions Virus-derived sRNAs were detected and characterised in the presence of virus infection. Differentially expressed A. fumigatus microRNA-like (miRNA-like) sRNAs and small interfering RNAs (siRNAs) were detected and validated. Host sRNA loci which were differentially expressed as a result of virus infection were also identified. To our knowledge, this is the first study reporting the sRNA profiles of A. fumigatus isolates.
Paul E Verweij - One of the best experts on this subject based on the ideXlab platform.
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selective flamingo medium for the isolation of Aspergillus fumigatus
Microorganisms, 2021Co-Authors: Jianhua Zhang, Paul E Verweij, Alfons J M Debets, Sijmen E SchoustraAbstract:For various studies in the clinic as well as the environment, it is essential to be able to selectively isolate Aspergillus fumigatus from samples containing bacteria as well as various other fungi (mainly Mucorales). Six agar media were compared for effectiveness in selectively isolating Aspergillus fumigatus from agricultural plant waste, woodchip waste, green waste, soil, grass and air samples collected in The Netherlands at a 48 °C incubation. The Flamingo Medium incubated at 48 °C, provided the most effective condition for the isolation of A. fumigatus from environmental samples, since it effectively inhibited the growth of competing fungi (mainly Mucorales) present in the environmental samples. Flamingo Medium reduced the number of colonies of Mucorales species by 95% and recovered an average of 20−30% more A. fumigatus colonies compared to the other media. We further confirmed that Flamingo Medium can inhibit the growth of clinical Mucorales, which occasionally present in patient’s tissue and can also be used for clinical applications. We suggest the use of Flamingo Medium as an efficient method for the study of A. fumigatus from important environmental niches for which there is increasing interest. Additionally, it can also be used in the clinic to isolate A. fumigatus especially from tissue contaminated with Mucorales.
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discovery and characterization of novel Aspergillus fumigatus mycoviruses
PLOS ONE, 2018Co-Authors: Jan Zoll, Paul E Verweij, Willem J. G. MelchersAbstract:In the last few years, increasing numbers of viruses infecting fungi have been identified. In this study, we used an in silico approach for the analysis of deep RNA sequencing data in order to discover and characterize putative genomic ssRNA or dsRNA mycovirus sequences in Aspergillus fumigatus. RNA sequencing reads of A. fumigatus strains were mapped against the A. fumigatus Af293 reference genome. Unmapped reads were collected for de novo assembly. Contigs were analyzed by Blastx comparison with a mycovirus protein database. Assembled viral genomes were used as template for remapping of RNA sequencing reads. In total, deep RNA sequencing results from 11 A. fumigatus strains were analyzed for the presence of mycoviral genomic RNAs. In 9 out of 11 strains, putative mycoviral RNA genomes were identified. Three strains were infected with two different mycovirus species. Two strains were infected with Aspergillus fumigatus polymycovirus type-1 (AfuPmV-1). Four strains contained fully recovered genomic RNA of unknown narna-like viruses designated as Aspergillus fumigatus narnavirus-1 and Aspergillus fumigatus narnavirus-2 (AfuNV-1 and AfuNV-2). Both viruses showed 38% amino acid sequence identity to Beihai narna-like virus-21. Three strains contained partially recovered genomic RNA of an unknown narna-like virus. Two strains contained fully recovered genomic RNAs of an unknown partitivirus designated as Aspergillus fumigatus partitivirus-2 (AfuPV-2) which showed 50% amino acid sequence identity to Alternaria alternata partitivirus-1. Finally, one strain contained fully recovered genomic RNA of an unknown mitovirus designated as Aspergillus fumigatus mitovirus-1 (AfuMV-1) which showed 34% amino acid sequence identity to Sclerotina sclerotiorum mitovirus. In silico analysis of deep RNA sequencing results showed that a majority of the A. fumigatus strains used here were infected with mycoviruses. Four novel A. fumigatus RNA mycoviruses could be identified: two different Aspergillus fumigatus narna-like viruses, one Aspergillus fumigatus partitivirus, and one Aspergillus fumigatus mitovirus.
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triazole resistance surveillance in Aspergillus fumigatus
Medical Mycology, 2018Co-Authors: Agustin Resendiz Sharpe, Katrien Lagrou, Jacques F Meis, Anuradha Chowdhary, Shawn R Lockhart, Paul E VerweijAbstract:Triazole resistance is an increasing concern in the opportunistic mold Aspergillus fumigatus. Resistance can develop through exposure to azole compounds during azole therapy or in the environment. Resistance mutations are commonly found in the Cyp51A-gene, although other known and unknown resistance mechanisms may be present. Surveillance studies show triazole resistance in six continents, although the presence of resistance remains unknown in many countries. In most countries, resistance mutations associated with the environment dominate, but it remains unclear if these resistance traits predominately migrate or arise locally. Patients with triazole-resistant Aspergillus disease may fail to antifungal therapy, but only a limited number of cohort studies have been performed that show conflicting results. Treatment failure might be due to diagnostic delay or due to the limited number of alternative treatment options. The ISHAM/ECMM Aspergillus Resistance Surveillance working group was set up to facilitate surveillance studies and stimulate international collaborations. Important aims are to determine the resistance epidemiology in countries where this information is currently lacking, to gain more insight in the clinical implications of triazole resistance through a registry and to unify nomenclature through consensus definitions.
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Mycovirus genomic RNA segments found in Aspergillus fumigatus strains.
2018Co-Authors: Jan Zoll, Paul E Verweij, Willem J. G. MelchersAbstract:Mycovirus genomic RNA segments found in Aspergillus fumigatus strains.
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Schematic representation of the genomic organization of the novel narnaviridae Aspergillus fumigatus narnavirus-1 (AfuNV1), Aspergillus fumigatus narnavirus-2 (AfuNV2), and Aspergillus fumigatus mitovirus-1 (AfuMV).
2018Co-Authors: Jan Zoll, Paul E Verweij, Willem J. G. MelchersAbstract:Schematic representation of the genomic organization of the novel narnaviridae Aspergillus fumigatus narnavirus-1 (AfuNV1), Aspergillus fumigatus narnavirus-2 (AfuNV2), and Aspergillus fumigatus mitovirus-1 (AfuMV).
Selin Ozkan - One of the best experts on this subject based on the ideXlab platform.
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profile and functional analysis of small rnas derived from Aspergillus fumigatus infected with double stranded rna mycoviruses
BMC Genomics, 2017Co-Authors: Irina Mohorianu, Robert H. A. Coutts, Selin Ozkan, Tamas Dalmay, Ping XuAbstract:Abstract Background Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencing. The A. fumigatus genome encodes essential components of the RNA silencing machinery, including Dicer, Argonaute and RNA-dependent RNA polymerase (RdRP) homologues. Active silencing of double-stranded (ds)RNA and the generation of small RNAs (sRNAs) has been shown for several mycoviruses and it is anticipated that a similar mechanism will be activated in A. fumigatus isolates infected with mycoviruses. Results To investigate the existence and nature of A. fumigatus sRNAs, sRNA-seq libraries of virus-free and virus-infected isolates were created using Scriptminer adapters and compared. Three dsRNA viruses were investigated: Aspergillus fumigatus partitivirus-1 (AfuPV-1, PV), Aspergillus fumigatus chrysovirus (AfuCV, CV) and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1, NK) which were selected because they induce phenotypic changes such as coloration and sectoring. The dsRNAs of all three viruses, which included two conventionally encapsidated ones PV and CV and one unencapsidated example NK, were silenced and yielded characteristic vsiRNAs together with co-incidental silencing of host fungal genes which shared sequence homology with the viral genomes. Conclusions Virus-derived sRNAs were detected and characterised in the presence of virus infection. Differentially expressed A. fumigatus microRNA-like (miRNA-like) sRNAs and small interfering RNAs (siRNAs) were detected and validated. Host sRNA loci which were differentially expressed as a result of virus infection were also identified. To our knowledge, this is the first study reporting the sRNA profiles of A. fumigatus isolates.
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Additional file 2: of Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses
2017Co-Authors: Selin Ozkan, Irina Mohorianu, Tamas Dalmay, Robert CouttsAbstract:Quantile normalisation. MA plots and distributions of DE (calculated using offset fold change method, OFC) separated per size class. In the MA plots, the average abundance (in log 2) is shown on the axis and the OFC (with offset = 20) is shown on the y axis. The CV, NK and PV correspond to Aspergillus fumigatus chrysovirus (AfuCV), a strain of Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) and Aspergillus fumigatus partitivirus-1 (AfuPV-1), respectively. (PDF 5547 kb
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Additional file 3 of Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses
2017Co-Authors: Selin Ozkan, Irina Mohorianu, Tamas Dalmay, Robert CouttsAbstract:Presence plots indicating the distribution and abundance of (A) Aspergillus fumigatus chrysovirus (AfuCV) and (B) Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1)-derived sRNAs along the 4 segments of the related genomes. Double-stranded RNA segments are shown as 1, 2, 3 and 4 respectively. Colour code for the lines are red, green, orange and blue for 19 nt, 20 nt, 21 nt and 22 nt, respectively. Genomic coordinates were represented on the x axis. On the y axis, the point cumulative abundance of all incident reads (in linear scale) was represented. (PDF 8465 kb
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Additional file 8: of Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses
2017Co-Authors: Selin Ozkan, Irina Mohorianu, Tamas Dalmay, Robert CouttsAbstract:Histograms showing the differentially expressed (−2 ≥ DE or DE ≥ 2) sRNA loci and annotations. The sRNA loci of all three viruses were identified and expressions plotted for CV (A), NK (B) and PV (C). The CV, NK and PV correspond to Aspergillus fumigatus chrysovirus (AfuCV), a strain of Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) and Aspergillus fumigatus partitivirus-1 (AfuPV-1), respectively. Annotations of the regions of putative sources of sRNAs were presented in red to indicate those differentially expressed in virus-infected cases and in blue to indicate the ones differentially expressed in virus-free examples. Comparisons were made for all three combinations (1_1: virus_free_rep1 and virus_infected_rep_1; 1_2: virus_free_rep1 and virus_infected_rep_2; 2_1: virus_free_rep2 and virus_infected_rep_1; 2_2: virus_free_rep2 and virus_infected_rep_2). (PDF 1446 kb
Ioly Kotta-loizou - One of the best experts on this subject based on the ideXlab platform.
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Completion of the sequence of the Aspergillus fumigatus partitivirus 1 genome
Archives of Virology, 2020Co-Authors: Charalampos Filippou, Robert H. A. Coutts, David A. Stevens, Raquel Sabino, Ioly Kotta-loizouAbstract:A Portuguese isolate of Aspergillus fumigatus was found to contain three double-stranded (ds) RNA elements ranging in size from 1.1 to 1.8 kbp and comprising the genome of a strain of Aspergillus fumigatus partitivirus 1 (AfuPV-1) previously thought to contain only the two largest dsRNA elements. The sequence of the smallest dsRNA element is described here, completing the sequence of the AfuPV-1 genome. Sequence analysis of the element revealed an open reading frame encoding a protein of unknown function similar in size and distantly related to elements previously identified in other members of the family Partitiviridae .
Christian Hertweck - One of the best experts on this subject based on the ideXlab platform.
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bacterium induces cryptic meroterpenoid pathway in the pathogenic fungus Aspergillus fumigatus
ChemBioChem, 2013Co-Authors: Claudia Konig, Kirstin Scherlach, Volker Schroeckh, Fabian Horn, Sandor Nietzsche, Axel A Brakhage, Christian HertweckAbstract:Stimulating encounter: The intimate, physical interaction between the soil-derived bacterium Streptomyces rapamycinicus and the human pathogenic fungus Aspergillus fumigatus led to the activation of an otherwise silent polyketide synthase (PKS) gene cluster coding for an unusual prenylated polyphenol (fumicycline A). The meroterpenoid pathway is regulated by a pathway-specific activator gene as well as by epigenetic factors.
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Biosynthesis and function of gliotoxin in Aspergillus fumigatus
Applied Microbiology and Biotechnology, 2012Co-Authors: Daniel H. Scharf, Axel A Brakhage, Thorsten Heinekamp, Nicole Remme, Peter Hortschansky, Christian HertweckAbstract:Gliotoxin (GT) is the prototype of the epidithiodioxopiperazine (ETP)-type fungal toxins. GT plays a critical role in the pathobiology of Aspergillus fumigatus . It modulates the immune response and induces apoptosis in different cell types. The toxicity has been attributed to the unusual intramolecular disulfide bridge, which is the functional motif of all ETPs. Because of the extraordinary structure and activity of GT, this fungal metabolite has been the subject of many investigations. The biosynthesis of GT involves unprecedented reactions catalysed by recently discovered enzymes. Here, we summarize the recent progress in elucidating the GT biosynthetic pathway and its role in virulence.
