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1.
Front Microbiol. 2018 Jul 3;9:1457. doi: 10.3389/fmicb.2018.01457. eCollection 2018.

Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?

Author information

1
Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.
2
Wound Repair Unit, Center for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany.
3
Division of Plastic and Aesthetic Surgery, Rotkreuzklinikum München, Munich, Germany.

Abstract

The black yeast Exophiala dermatitidis is a polyextremophilic human pathogen, especially known for growing in man-made extreme environments. Reported diseases caused by this fungus range from benign cutaneous to systemic infections with 40% fatality rate. While the number of cases steadily increases in both immunocompromised and immunocompetent people, detailed knowledge about infection mechanisms, virulence factors and host response are scarce. To understand the impact of the putative virulence factor melanin on the infection, we generated a polyketide synthase (PKS1) mutant using CRISPR/Cas9 resulting in a melanin deficient strain. The mutant and the wild-type fungus were inoculated onto skin explants using an ex vivo skin organ culture model to simulate in vivo cutaneous infection. The difference between the mutant and wild-type transcriptional landscapes, as assessed by whole RNA-sequencing, were small and were observed in pathways related to the copper homeostasis, cell wall genes and proteases. Seven days after inoculation the wild-type fungus completely colonized the stratum corneum, invaded the skin and infected keratinocytes while the mutant had only partially covered the skin and showed no invasiveness. Our results suggest that melanin dramatically improves the invasiveness and virulence of E. dermatitidis during the first days of the skin infection.

KEYWORDS:

Exophiala dermatitidis; PKS1; black yeast; melanin; skin model; virulence

2.
Life (Basel). 2018 Jun 14;8(2). pii: E22. doi: 10.3390/life8020022.

Big Sound and Extreme Fungi-Xerophilic, Halotolerant Aspergilli and Penicillia with Low Optimal Temperature as Invaders of Historic Pipe Organs.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. Katja.Sterflinger@boku.ac.at.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. christian.voitl@boku.ac.at.
3
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. Ksenija.lopandic@boku.ac.at.
4
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. guadalupe.pinar@boku.ac.at.
5
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria. hakim.tafer@boku.ac.at.

Abstract

Recent investigations have shown that xerophilic fungi may pose a biodeterioration risk by threatening objects of cultural heritage including many types of materials, including wood, paint layers, organic glues or leather and even metal. Historic—and also new built—pipe organs combine all those materials. In this study, halotolerant aspergilli and penicillia with low optimal temperatures were shown to be the most frequent invaders of pipe organs. The fungi form white mycelia on the organic components of the organs with a clear preference for the bolus paint of the wooden pipes, the leather-made hinges of the stop actions and all parts fixed by organic glue. Physiological tests showed that the strains isolated from the instruments all show a halotolerant behavior, although none was halophilic. The optimum growth temperature is below 20 °C, thus the fungi are perfectly adapted to the cool and relatively dry conditions in the churches and organs respectively. The de-novo genome sequences analyses of the strains are currently ongoing and will reveal the genomic basis for the halotolerant behavior of the fungi.

KEYWORDS:

biodeterioration; pipe organs; xerophilic fungi

3.
Genome Announc. 2018 May 17;6(20). pii: e00343-18. doi: 10.1128/genomeA.00343-18.

Draft Genome Sequence of the Saccharomyces cerevisiae × Saccharomyces kudriavzevii HA1836 Interspecies Hybrid Yeast.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria ksenija.lopandic@boku.ac.at.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.

Abstract

Saccharomyces cerevisiae × Saccharomyces kudriavzevii interspecies hybrid yeasts have frequently been isolated from alcoholic fermentation environments. Here, we report the draft genome sequence of the S. cerevisiae × S. kudriavzevii HA1836 strain isolated from grapes from an Austrian vineyard.

4.
Genome Announc. 2018 Apr 26;6(17). pii: e00341-18. doi: 10.1128/genomeA.00341-18.

Draft Genome Sequence of the Interspecies Hybrid Saccharomyces pastorianus Strain HA2560, Isolated from a Municipal Wastewater Treatment Plant.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria ksenija.lopandic@boku.ac.at.

Abstract

Saccharomyces pastorianus is an industrially relevant yeast frequently isolated from brewing environments. Here, we report the draft genome sequence of the S. pastorianus HA2560 strain isolated from a municipal wastewater treatment plant.

5.
Genome Announc. 2017 Nov 2;5(44). pii: e01242-17. doi: 10.1128/genomeA.01242-17.

Draft Genome Sequences of the Black Rock Fungus Knufia petricola and Its Spontaneous Nonmelanized Mutant.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria donatella.tesei@boku.ac.at.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.

Abstract

The fungal genus Knufia mostly comprises extremotolerant species from environmental sources, especially rock surfaces. The draft genome sequence of the rock fungus Knufia petricola presented here is the first whole-genome sequence of the only species among black fungi known to have a nonmelanized spontaneous mutant.

6.
Sci Rep. 2017 Sep 12;7(1):11436. doi: 10.1038/s41598-017-11807-8.

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda.

Author information

1
Department of Biotechnology, VIBT-EQ Extremophile Center, University of Natural Resources and Life Sciences, 1190, Vienna, Austria. barbara.blasi@boku.ac.at.
2
Department of Biotechnology, VIBT-EQ Extremophile Center, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.

Abstract

Cladophialophora immunda is an ascomycotal species belonging to the group of the black yeasts. These fungi have a thick and melanized cell wall and other physiological adaptations that allows them to cope with several extreme physical and chemical conditions. Member of the group can colonize some of the most extremophilic environments on Earth. Cladophialophora immunda together with a few other species of the order Chaetothyriales show a special association with hydrocarbon polluted environments. The finding that the fungus is able to completely mineralize toluene makes it an interesting candidate for bioremediation purposes. The present study is the first transcriptomic investigation of a fungus grown in presence of toluene as sole carbon and energy source. We could observe the activation of genes involved in toluene degradatation and several stress response mechanisms which allowed the fungus to survive the toluene exposure. The thorough comparative genomics analysis allowed us to identify several events of horizontal gene transfer between bacteria and Cladophialophora immunda and unveil toluene degradation steps that were previously reported in bacteria. The work presented here aims to give new insights into the ecology of Cladophialophora immunda and its adaptation strategies to hydrocarbon polluted environments.

7.
Front Cell Infect Microbiol. 2016 Oct 24;6:136. eCollection 2016.

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection.

Author information

1
Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria.
2
Department for Applied Genetics and Cell Biology, Molecular Plant Physiology and Crop Biotechnology, University of Natural Resources and Life Sciences Vienna, Austria.
3
Klinikum Bremen-Mitte, Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Biology and Chemistry, Center for Biomolecular Interactions Bremen, University Bremen Bremen, Germany.

Abstract

The black yeast Exophiala dermatitidis is a widespread polyextremophile and human pathogen, that is found in extreme natural habitats and man-made environments such as dishwashers. It can cause various diseases ranging from phaeohyphomycosis and systemic infections, with fatality rates reaching 40%. While the number of cases in immunocompromised patients are increasing, knowledge of the infections, virulence factors and host response is still scarce. In this study, for the first time, an artificial infection of an ex-vivo skin model with Exophiala dermatitidis was monitored microscopically and transcriptomically. Results show that Exophiala dermatitidis is able to actively grow and penetrate the skin. The analysis of the genomic and RNA-sequencing data delivers a rich and complex transcriptome where circular RNAs, fusion transcripts, long non-coding RNAs and antisense transcripts are found. Changes in transcription strongly affect pathways related to nutrients acquisition, energy metabolism, cell wall, morphological switch, and known virulence factors. The L-Tyrosine melanin pathway is specifically upregulated during infection. Moreover the production of secondary metabolites, especially alkaloids, is increased. Our study is the first that gives an insight into the complexity of the transcriptome of Exophiala dermatitidis during artificial skin infections and reveals new virulence factors.

KEYWORDS:

RNA sequencing; black yeast; fungal pathogens; skin infection; skin model; virulence

PMID:
27822460
PMCID:
PMC5075926
DOI:
10.3389/fcimb.2016.00136
[Indexed for MEDLINE]
Free PMC Article
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8.
BMC Genomics. 2016 Sep 29;17(1):763.

Genome sequence of the filamentous soil fungus Chaetomium cochliodes reveals abundance of genes for heme enzymes from all peroxidase and catalase superfamilies.

Author information

1
Department of Chemistry, Division of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria. marcel.zamocky@boku.ac.at.
2
Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava, Slovakia. marcel.zamocky@boku.ac.at.
3
Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190, Vienna, Austria.
4
Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551, Bratislava, Slovakia.
5
Department of Chemistry, Division of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria.

Abstract

BACKGROUND:

The ascomycetous family Chaetomiaceae (class Sordariomycetes) includes numerous soilborn, saprophytic, endophytic and pathogenic fungi which can adapt to various growth conditions and living niches by providing a broad armory of oxidative and antioxidant enzymes.

RESULTS:

We release the 34.7 Mbp draft genome of Chaetomium cochliodes CCM F-232 consisting of 6036 contigs with an average size of 5756 bp and reconstructed its phylogeny. We show that this filamentous fungus is closely related but not identical to Chaetomium globosum and Chaetomium elatum. We screened and critically analysed this genome for open reading frames coding for essential antioxidant enzymes. It is demonstrated that the genome of C. cochliodes contains genes encoding putative enzymes from all four known heme peroxidase superfamilies including bifunctional catalase-peroxidase (KatG), cytochrome c peroxidase (CcP), manganese peroxidase, two paralogs of hybrid B peroxidases (HyBpox), cyclooxygenase, linoleate diol synthase, dye-decolorizing peroxidase (DyP) of type B and three paralogs of heme thiolate peroxidases. Both KatG and DyP-type B are shown to be introduced into ascomycetes genomes by horizontal gene transfer from various bacteria. In addition, two putative large subunit secretory and two small-subunit typical catalases are found in C. cochliodes. We support our genomic findings with quantitative transcription analysis of nine peroxidase & catalase genes.

CONCLUSIONS:

We delineate molecular phylogeny of five distinct gene superfamilies coding for essential heme oxidoreductases in Chaetomia and from the transcription analysis the role of this antioxidant enzymatic armory for the survival of a peculiar soil ascomycete in various harsh environments.

KEYWORDS:

Chaetomium cochliodes; Heme-catalase super family; Peroxidase-catalase superfamily; Peroxidase-chlorite dismutase superfamily; Peroxidase-cyclooxygenase superfamily; Peroxidase-peroxygenase superfamily

9.
Geomicrobiol J. 2016 Mar 15;33(3-4):308-317. Epub 2016 Feb 25.

Pathogenic Yet Environmentally Friendly? Black Fungal Candidates for Bioremediation of Pollutants.

Author information

1
University of Natural Resources and Life Sciences Vienna, VIBT-Extremophile Center , Vienna , Austria.
2
GIRO Joint Research Unit IRTA-UPC, Torre Marimon, Caldes de Montbui , Barcelona , Catalonia , Spain.
3
CBS KNAW Fungal Biodiversity Center , Utrecht , The Netherlands.

Abstract

A collection of 163 strains of black yeast-like fungi from the CBS Fungal Biodiversity Center (Utrecht, The Netherlands), has been screened for the ability to grow on hexadecane, toluene and polychlorinated biphenyl 126 (PCB126) as the sole carbon and energy source. These compounds were chosen as representatives of relevant environmental pollutants. A microtiter plate-based culture assay was set up in order to screen the fungal strains for growth on the selected xenobiotics versus glucose, as a positive control. Growth was observed in 25 strains on at least two of the tested substrates. Confirmation of substrate assimilation was performed by cultivation on closed vials and analysis of the headspace composition with regard to the added volatile substrates and the generated carbon dioxide. Exophiala mesophila (CBS 120910) and Cladophialophora immunda (CBS 110551), both of the order Chaetothyriales and isolated from a patient with chronic sinusitis and a polluted soil sample, respectively, showed the ability to grow on toluene as the sole carbon and energy source. Toluene assimilation has previously been described for C. immunda but this is the first account for E. mesophila. Also, this is the first time that the capacity to grow on alkylbenzenes has been demonstrated for a clinical isolate. Assimilation of toluene could not be demonstrated for the human opportunistic pathogen Pseudoallescheria boydii (CBS 115.59, Microascales), but the results from microtiter plate assays suggest that strains of this species are promising candidates for further studies. The outstanding abilities of black yeast-like fungi to thrive in extreme environments makes them ideal agents for the bioremediation of polluted soils, and for the treatment of contaminated gas streams in biofilters. However, interrelations between hydrocarbonoclastic and potentially pathogenic strains need to be elucidated in order to avoid the possibility of biohazards occurring.

KEYWORDS:

Biofilter; black fungi; toluene

10.
Data Brief. 2015 Sep 2;5:372-5. doi: 10.1016/j.dib.2015.08.008. eCollection 2015 Dec.

Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions.

Author information

1
VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
2
Plant Biotechnology Unit, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
3
Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-IAC, 1060 Vienna, Austria.
4
Institute for Applied Genetics and Cell Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.

Abstract

In the current study a comparative proteomic approach was used to investigate the response of the human pathogen black yeast Exophiala dermatitidis toward temperature treatment. Protein functional analysis - based on cellular process GO terms - was performed on the 32 temperature-responsive identified proteins. The bioinformatics analyses and data presented here provided novel insights into the cellular pathways at the base of the fungus temperature tolerance. A detailed analysis and interpretation of the data can be found in "Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis" by Tesei et al. (2015) [1].

11.
Genome Announc. 2016 Feb 4;4(1). pii: e01580-15. doi: 10.1128/genomeA.01580-15.

Draft Genome of Debaryomyces fabryi CBS 789T, Isolated from a Human Interdigital Mycotic Lesion.

Author information

1
University of Natural Resources and Life Sciences Vienna, VIBT-Extremophile Center, Vienna, Austria.
2
University of Natural Resources and Life Sciences Vienna, VIBT-Extremophile Center, Vienna, Austria ksenija.lopandic@boku.ac.at.

Abstract

The yeast genus Debaryomyces comprises species isolated from various natural habitats, man-made environments, and clinical materials. Here, the draft genome of D. fabryi CBS 789(T), isolated from a human interdigital mycotic lesion, is presented.

12.
J Proteomics. 2015 Oct 14;128:39-57. doi: 10.1016/j.jprot.2015.07.007. Epub 2015 Jul 17.

Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis.

Author information

1
VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria. Electronic address: donatella.tesei@boku.ac.at.
2
Plant Biotechnology Unit, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
3
Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-IAC, 1060 Vienna, Austria.
4
VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
5
Institute for Applied Genetics and Cell Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.

Abstract

The black yeast Exophiala dermatitidis is a worldwide distributed agent of primary and secondary diseases in both immunocompromised and healthy humans, with a high prevalence in human-made environments. Since thermo-tolerance has a crucial role in the fungus persistence in man-dominated habitat and in its pathogenicity, three incubation temperatures (37, 45, 1 °C) and two time spans (1 h, 1 week) were selected to simulate different environmental conditions and to investigate the effect of temperature on the proteome of E. dermatitidis CBS 525.76. Using a novel protocol for protein extraction from black yeasts, 2-D DIGE could be applied for characterization of changes in total protein spot abundance among the experimental conditions. A total of 32 variable proteins were identified by mass spectrometry. Data about protein functions, localization and pathways were also obtained. A typical stress response under non-optimal temperature could not be observed at the proteome level, whereas a reduction of the metabolic activity, mostly concerning processes as the general carbon metabolism, was detected after exposure to cold. These results suggest that a fine protein modulation takes place following temperature treatment and a repertoire of stable protein might be at the base of E. dermatitidis adaptation to altered growth conditions.

SIGNIFICANCE:

E. dermatitidis is a pathogenic black yeast causing neurotropic infections, systemic and subcutaneous disease in a wide range of hosts, including humans. The discovery of the fungus high prevalence in man-made habitats, including sauna facilities, drinking water and dishwashers, generated concern and raised questions about the infection route. In the present work - which is the first contribution on E. dermatitidis proteome - the effect of different temperature conditions on the fungus protein pattern have been analyzed by using a gel-based approach and the temperature responsive proteins have been identified. The absence of a typical stress response following the exposure to non-optimal temperature was detected at the proteome level, along with a general reduction of the metabolic activity after exposure to cold. These results suggest that a very fine regulation of the protein expression as well as adaptations involving a basic set of stable proteins may be at the base of E. dermatitidis enormous ecological plasticity, which plays a role in the fungus distribution, also enabling the transition from natural to human habitat and to the human host.

KEYWORDS:

DIGE; Fungal proteomics; Pathogenic fungi; Thermo-tolerance; nLC-ESI-MS/MS

PMID:
26189359
DOI:
10.1016/j.jprot.2015.07.007
[Indexed for MEDLINE]
Free full text
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13.
Noncoding RNA. 2015 Jul 13;1(2):139-150. doi: 10.3390/ncrna1020139.

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster.

Author information

1
Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy. alberto.angrisani@unina.it.
2
Institut für Biotechnologie, Universität für Bodenkultur, Muthgasse 18, A-1190 Wien, Austria. htafer@gmail.com.
3
Bioinformatics Group, Department Computer Science, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig; University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. studla@bioinf.uni-leipzig.
4
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany. studla@bioinf.uni-leipzig.
5
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany. studla@bioinf.uni-leipzig.
6
Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria. studla@bioinf.uni-leipzig.
7
Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. studla@bioinf.uni-leipzig.
8
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. studla@bioinf.uni-leipzig.
9
Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy. mfuria@unina.it.

Abstract

A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.

KEYWORDS:

snoRNA, long non-coding RNA, sno-lncRNAs, Drosophila

14.
Environ Microbiol Rep. 2015 Dec;7(6):849-59. doi: 10.1111/1758-2229.12313. Epub 2015 Aug 19.

Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci's self-portrait.

Author information

1
Department of Biotechnology, Vienna Institute of Biotechnology (VIBT), University of Natural Resources and Life Sciences, Muthgasse 11, Vienna, 1190, Austria.
2
Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario (ICRCPAL), Ministero per i Beni e le Attivita Culturali, Via Milano 76, Rome, 00184, Italy. flavia.pinzari@entecra.it.

Abstract

Leonardo da Vinci's self-portrait is affected by foxing spots. The portrait has no fungal or bacterial infections in place, but is contaminated with airborne spores and fungal material that could play a role in its disfigurement. The knowledge of the nature of the stains is of great concern because future conservation treatments should be derived from scientific investigations. The lack of reliable scientific data, due to the non-culturability of the microorganisms inhabiting the portrait, prompted the investigation of the drawing using non-invasive and micro-invasive sampling, in combination with scanning electron microscope (SEM) imaging and molecular techniques. The fungus Eurotium halophilicum was found in foxing spots using SEM analyses. Oxalates of fungal origin were also documented. Both findings are consistent with the hypothesis that tonophilic fungi germinate on paper metabolizing organic acids, oligosaccharides and proteic compounds, which react chemically with the material at a low water activity, forming brown products and oxidative reactions resulting in foxing spots. Additionally, molecular techniques enabled a screening of the fungi inhabiting the portrait and showed differences when different sampling techniques were employed. Swabs samples showed a high abundance of lichenized Ascomycota, while the membrane filters showed a dominance of Acremonium sp. colonizing the drawing.

PMID:
26111623
PMCID:
PMC4959533
DOI:
10.1111/1758-2229.12313
[Indexed for MEDLINE]
Free PMC Article
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15.
PLoS One. 2015 Jun 10;10(6):e0127103. doi: 10.1371/journal.pone.0127103. eCollection 2015.

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response.

Author information

1
VIBT-Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.

Abstract

Exophiala dermatitidis (Wangiella dermatitidis) belongs to the group of the so-called black yeasts. Thanks in part to its thick and strongly melanized cell walls, E. dermatitidis is extremely tolerant to various kinds of stress, including extreme pH, temperature and desiccation. E. dermatitidis is also the agent responsible for various severe illnesses in humans, such as pneumonia and keratitis, and might lead to fatal brain infections. Due to its association with the human environment, its poly-extremophilic lifestyle and its pathogenicity in humans, E. dermatitidis has become an important model organism. In this study we present the functional analysis of the transcriptional response of the fungus at 1°C and 45°C, in comparison with that at 37°C, for two different exposition times, i.e. 1 hour and 1 week. At 1°C, E. dermatitidis uses a large repertoire of tools to acclimatize, such as lipid membrane fluidization, trehalose production or cytoskeleton rearrangement, which allows the fungus to remain metabolically active. At 45°C, the fungus drifts into a replicative state and increases the activity of the Golgi apparatus. As a novel finding, our study provides evidence that, apart from the protein coding genes, non-coding RNAs, circular RNAs as well as fusion-transcripts are differentially regulated and that the function of the fusion-transcripts can be related to the corresponding temperature condition. This work establishes that E. dermatitidis adapts to its environment by modulating coding and non-coding gene transcription levels and through the regulation of chimeric and circular RNAs.

PMID:
26061625
PMCID:
PMC4463862
DOI:
10.1371/journal.pone.0127103
[Indexed for MEDLINE]
Free PMC Article
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16.
Genome Announc. 2015 Apr 9;3(2). pii: e00203-15. doi: 10.1128/genomeA.00203-15.

Draft Genome Sequence of Exophiala mesophila, a Black Yeast with High Bioremediation Potential.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria katja.sterflinger@boku.ac.at.

Abstract

The fungal genus Exophiala comprises both pathogen species, which cause severe infections in humans, and environmental species, which are able to degrade alkylbenzene compounds. The draft genome sequence of Exophiala mesophila presented here is the first genome assembly of an alkylbenzene-degrading organism belonging to the genus Exophiala.

17.
Insect Biochem Mol Biol. 2015 Jun;61:69-78. doi: 10.1016/j.ibmb.2015.01.013. Epub 2015 Jan 29.

Developmentally regulated expression and expression strategies of Drosophila snoRNAs.

Author information

1
Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy.
2
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
3
Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy. Electronic address: mfuria@unina.it.

Abstract

Small nucleolar RNAs constitute a significant portion of the eukaryotic small ncRNA transcriptome and guide site-specific methylation or pseudouridylation of target RNAs. In addition, they can play diverse regulatory roles on gene expression, acting as precursors of smaller fragments able to modulate alternative splicing or operate as microRNAs. Defining their expression strategies and the full repertory of their biological functions is a critical, but still ongoing, process in most organisms. Considering that Drosophila melanogaster is one of the most advantageous model organism for genetic, functional and developmental studies, we analysed the whole genomic organization of its annotated snoRNAs - whose vast majority is known to be embedded in an intronic context - and show by GO term enrichment analysis that protein-coding genes involved in cell division and cytoskeleton organization are those mostly preferred as hosts. This finding was unexpected, and delineates an unpredicted link between snoRNA host genes and cell proliferation that might be of general relevance. We also defined by quantitative RT-PCR the expression of a representative subset of annotated specimens throughout the life cycle, providing a first overview on developmental profiling of the fly snoRNA transcriptome. We found that most of the tested specimens, rather than acting as housekeeping genes with uniform expression, exhibit dynamic developmental expression patterns; moreover, intronic snoRNAs harboured by the same host gene often exhibit distinct temporal profiles, indicating that they can be expressed uncoordinatedly. In addition to provide an updated outline of the fly snoRNA transcriptome, our data highlight that expression of these versatile ncRNAs can be finely regulated.

KEYWORDS:

Drosophila; Gene regulation; Genomic organization; ncRNA; snoRNA

PMID:
25641266
DOI:
10.1016/j.ibmb.2015.01.013
[Indexed for MEDLINE]
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18.
Genome Announc. 2015 Jan 29;3(1). pii: e01283-14. doi: 10.1128/genomeA.01283-14.

Draft Genome of Cladophialophora immunda, a Black Yeast and Efficient Degrader of Polyaromatic Hydrocarbons.

Author information

1
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria katja.sterflinger@boku.ac.at.
2
VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.
3
CBS Fungal Biodiversity Center, Utrecht, The Netherlands.

Abstract

The fungal genus Cladophialophora comprises many species which cause severe and even fatal infections in humans as well as environmental strains able to degrade polyaromatic hydrocarbons. The draft genome of Cladophialophora immunda presented here is the first whole-genome sequence within this important genus.

19.
Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):591-600. doi: 10.1002/wrna.1243. Epub 2014 Jul 9.

Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.

Author information

1
Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.

Abstract

The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60-70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat-derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat-derived RNAs from non-coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non-coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat-derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification.

PMID:
25045147
PMCID:
PMC4233971
DOI:
10.1002/wrna.1243
[Indexed for MEDLINE]
Free PMC Article
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20.
BMC Genomics. 2014 Jun 10;15:459. doi: 10.1186/1471-2164-15-459.

Structured RNAs and synteny regions in the pig genome.

Author information

1
Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg, Denmark. gorodkin@rth.dk.

Abstract

BACKGROUND:

Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals.

RESULTS:

We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog).

CONCLUSIONS:

We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02.

PMID:
24917120
PMCID:
PMC4124155
DOI:
10.1186/1471-2164-15-459
[Indexed for MEDLINE]
Free PMC Article
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