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      Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus

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          Abstract

          Mitogen activated protein kinases (MAPKs) are highly conserved in eukaryotic organisms. In pathogenic fungi, their activities were assigned to different physiological functions including drug adaptation and resistance. Aspergillus fumigatus is a human pathogenic fungus, which causes life-threatening invasive infections. Therapeutic options against invasive mycoses are still limited. One of the clinically used drugs is caspofungin, which specifically targets the fungal cell wall biosynthesis. A systems biology approach, based on comprehensive transcriptome data sets and mathematical modeling, was employed to infer a regulatory network and identify key interactions during adaptation to caspofungin stress in A. fumigatus. Mathematical modeling and experimental validations confirmed an intimate cross talk occurring between the cell wall-integrity and the high osmolarity-glycerol signaling pathways. Specifically, increased concentrations of caspofungin promoted activation of these signalings. Moreover, caspofungin affected the intracellular transport, which caused an additional osmotic stress that is independent of glucan inhibition. High concentrations of caspofungin reduced this osmotic stress, and thus decreased its toxic activity. Our results demonstrated that MAPK signaling pathways play a key role during caspofungin adaptation and are contributing to the paradoxical effect exerted by this drug.

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          Pathogenesis of Aspergillus fumigatus in Invasive Aspergillosis.

          Aspergillus species are globally ubiquitous saprophytes found in a variety of ecological niches. Almost 200 species of aspergilli have been identified, less than 20 of which are known to cause human disease. Among them, Aspergillus fumigatus is the most prevalent and is largely responsible for the increased incidence of invasive aspergillosis (IA) in the immunocompromised patient population. IA is a devastating illness, with mortality rates in some patient groups reaching as high as 90%. Studies identifying and assessing the roles of specific factors of A. fumigatus that contribute to the pathogenesis of IA have traditionally focused on single-gene deletion and mutant characterization. In combination with recent large-scale approaches analyzing global fungal responses to distinct environmental or host conditions, these studies have identified many factors that contribute to the overall pathogenic potential of A. fumigatus. Here, we provide an overview of the significant findings regarding A. fumigatus pathogenesis as it pertains to invasive disease.
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            Gene regulatory network inference: data integration in dynamic models-a review.

            Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques. During the last decade, many systems biological approaches that base on genome-wide data have been developed to unravel the complexity of gene regulation. This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods. Standard GRN inference methods primarily use gene expression data derived from microarrays. However, the incorporation of additional information from heterogeneous data sources, e.g. genome sequence and protein-DNA interaction data, clearly supports the network inference process. This review focuses on promising modelling approaches that use such diverse types of molecular biological information. In particular, approaches are discussed that enable the modelling of the dynamics of gene regulatory systems. The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling.
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              The akuB(KU80) mutant deficient for nonhomologous end joining is a powerful tool for analyzing pathogenicity in Aspergillus fumigatus.

              To increase the frequency of homologous recombination, we inactivated the KU80 homologue in Aspergillus fumigatus (named akuB(KU80)). Homologous integration reached about 80% for both calcineurin A (calA) and polyketide synthase pksP (alb1) genes in the akuB(KU80) mutant to 3 and 5%, respectively, when using a wild-type A. fumigatus strain. Deletion of akuB(KU80) had no influence on pathogenicity in a low-dose murine infection model.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 September 2015
                2015
                : 10
                : 9
                : e0136932
                Affiliations
                [1 ]Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany
                [2 ]Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany
                [3 ]Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Adolf-Reichwein-Str. 23, 07745, Jena, Germany
                [4 ]Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747, Jena, Germany
                [5 ]Leibniz Junior Research Group—Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany
                Universidade de Sao Paulo, BRAZIL
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: RA RG OK AAB JL VV. Performed the experiments: RA CB JW JL VV. Analyzed the data: RA RG OK AAB JL VV. Contributed reagents/materials/analysis tools: RA CB JW JL VV. Wrote the paper: RA AAB JL VV.

                Article
                PONE-D-14-51849
                10.1371/journal.pone.0136932
                4565559
                26356475
                cc109cdf-0c7e-4db1-9a23-19bc76eb2fcd
                Copyright @ 2015

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 3 December 2014
                : 11 August 2015
                Page count
                Figures: 7, Tables: 1, Pages: 21
                Funding
                This work was supported by the ERA-NET PathoGenoMics programme ANTIFUN (The cell wall as a target to improve antifungal therapy against Aspergillosis), BFU2008-04709-E/BMC, (German Federal Ministry of Education and Research: BMBF FKZ 0315439). R.A. was supported by the DFG-founded excellence graduate school Jena School for Microbial Communication (JSMC). J.L. was supported by the DFG-founded CRC/Transregio 124 “FungiNet”. C.B. was supported by the “ARIADNE” Marie Curie Training Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Custom metadata
                All relevant data are within the paper and its Supporting Information files. RNA-Seq raw data are available on line at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=qzgdmcmaxranzml&acc=GSE55743.

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