Biology subjects

Fillinger, S.

Publications and source records attributed to Fillinger, S..

6 recordsLinked to original sources

bioRxiv2021

Directed evolution predicts cytochrome b G37V target site modification as probable adaptive mechanism towards the QiI fungicide fenpicoxamid in Zymoseptoria tritici.

Acquired resistance is a threat for antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms, as well as the highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complexIII of the respiratory chain at the ubiquinone reduction site (Qi site) of the mitochondrially encoded cytochrome b, a different site than the widely-used strobilurins which the respiratory complex by binding to the ubiquinol oxidation site (Qo site). We identified the G37V change, within the cytochrome b Qi site, as the most likely resistance mechanism to be selected in Z. tritici. This change triggered high fenpicoxamid resistance and halved the enzymatic activity of cytochrome b, despite no significant penalty for in vitro growth. In addition, we identified a negative cross-resistance between isolates harboring G37V or G143A, a Qo site change previously selected by strobilurins. Moreover, double mutants were less resistant to both QiIs and QoIs compared to single mutants. This work is a proof of concept that experimental evolution can be used to predict adaptation to fungicides, and provides new perspectives for the management of QiIs. Originality-Significance StatementO_LIThe highly adaptive traits of pathogens render evolutionary outcomes of antifungal treatments difficult to predict. C_LIO_LIWe used directed evolution to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. C_LIO_LIWe identified a target modification as the most likely resistance mechanism to be selected. C_LIO_LIThis change triggered high fenpicoxamid resistance and halved the activity of the target enzyme despite no significant penalty for in vitro growth. C_LIO_LIThis work supports the use of experimental evolution as a method to predict adaptation to fungicides and provides important information for the management of QiIs. C_LI

microbiology↗

bioRxiv2020

The failure of B cells to induce non-canonical MYD88 splice variants correlates with lymphomagenesis via sustained NF-κB signaling

Gain-of-function mutations of the TLR adaptor and oncoprotein MyD88 drive B cell lymphomagenesis via sustained NF-{kappa}B activation. In myeloid cells, sustained TLR activation and NF-{kappa}B activation lead to the induction of inhibitory MYD88 splice variants that restrain prolonged NF-{kappa}B activation. We therefore sought to investigate whether such a negative feedback loop exists in B cells. Analyzing MYD88 splice variants in normal B cells and different primary B cell malignancies, we observed that MYD88 splice variants in transformed B cells are dominated by the canonical, strongly NF-{kappa}B-activating isoform of MYD88 and contain at least three novel, so far uncharacterized signaling-competent splice isoforms. TLR stimulation in B cells unexpectedly reinforces splicing of NF-{kappa}B-promoting, canonical isoforms rather than the MyD88s, a negative regulatory isoform that is typically induced by TLRs in myeloid cells. This suggests that an essential negative feedback loop restricting TLR signaling in myeloid cells at the level of alternative splicing, is missing in B cells, rendering B cells vulnerable to sustained NF-{kappa}B activation and eventual lymphomagenesis. Our results uncover MYD88 alternative splicing as an unappreciated promoter of B cell lymphomagenesis and provide a rationale why oncogenic MYD88 mutations are exclusively found in B cells.

cancer biology↗

bioRxiv2019

Efficient data management infrastructure for the integration of imaging and omics data in life science research

As technical developments in omics and biomedical imaging drive the increase in quality, modality, and throughput of data generation in life sciences, the need for information systems capable of integrative, long-term storage and management of these heterogeneous digital assets is also increasing. Here, we propose an approach based on principles of Service Oriented Architecture design, to allow the integrated management and analysis of multi-omics and biomedical imaging data. The proposed architecture introduces an interoperable image management system, the OMERO server, into the backend of qPortal, a FAIR-compliant web-based platform for omics data management. The implementation of an integrated metadata model, the development of software components to enable the communication with the OMERO server, and an extension to the data management operations of established software, allows for FAIR management of heterogeneous omics and biomedical imaging data within an integrated system, which facilitates metadata queries from web-based scientific applications. The applicability of the proposed architecture is demonstrated in two prototypical use cases, a plant biology study using confocal scanning microscopy, and a clinical study on hepatocellular carcinoma, with data from a variety of medical imaging and omics modalities. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, as the joint analysis of omics and imaging data becomes not only desirable but necessary to derive novel insights into biological processes. In particular for powerful machine learning applications where the availability of large datasets with high quality phenotypic annotations is a requirement.

bioinformatics↗

bioRxiv2019

nf-core: Community curated bioinformatics pipelines

The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most pipelines are designed for execution on-premise, and the associated software dependencies are tightly coupled with the local compute environment. This leads to poor pipeline portability and reproducibility of the ensuing results - both of which are fundamental requirements for the validation of scientific findings. Here, we introduce nf-core: a framework that provides a community-driven, peer-reviewed platform for the development of best practice analysis pipelines written in Nextflow. Key obstacles in pipeline development such as portability, reproducibility, scalability and unified parallelism are inherently addressed by all nf-core pipelines. We are also continually developing a suite of tools that assist in the creation and development of both new and existing pipelines. Our primary goal is to provide a platform for high-quality, reproducible bioinformatics pipelines that can be utilized across various institutions and research facilities.

bioinformatics↗

bioRxiv2019

Comparative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain loss of pathogenicity phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways

O_LISignal transduction (ST) is essential for rapid adaptive responses to changing environmental conditions through rapid post-translational modifications of signalling proteins and downstream effectors that regulate the activity of target proteins and/or the expression of downstream genes. C_LIO_LIWe have performed a comparative proteomics study of ST mutants in the phytopathogenic fungus Botrytis cinerea during axenic growth under non-stressed conditions to decipher the roles of two kinases of the hyper-osmolarity pathway in B. cinerea physiology. We studied the mutants of the sensor histidine kinase Bos1 and of the MAP kinase Sak1. C_LIO_LIMultiplex shotgun proteomics detected 628 differential proteins between mutants and wild-type, 280 common to both mutants, indicating independent and shared regulatory functions for both kinases. Gene ontology analysis showed significant changes in proteins related to plant infection (secondary metabolism enzymes, lytic enzymes, proteins linked to osmotic, oxidative and cell wall stress) that may explain the virulence defects of both mutants. Intracellular accumulation of secreted proteins in the{Delta} bos1 histidine-kinase mutant suggests a potential secretion defect. The proteome data also highlight a new link between Sak1 MAPK, cAMP and Ca2+ signalling. C_LIO_LIThis study reveals the potential of proteomic analyses of signal transduction mutants to decipher their biological functions. C_LI

microbiology↗

bioRxiv2017

Plasticity of the MFS1 promoter leads to multi drug resistance in the wheat pathogen Zymoseptoria tritici

The ascomycete Zymoseptoria tritici is the causal agent of septoria leaf blotch on wheat. Disease control relies mainly on resistant wheat cultivars and on fungicide applications. The fungus displays a high potential to circumvent both methods. Resistance against all unisite fungicides has been observed over decades. A different type of resistance has emerged among wild populations with multi-drug resistant (MDR) strains. Active fungicide efflux through overexpression of the major-facilitator gene, MFS1, explains this emerging resistance mechanism. In this study, we identified as responsible mutations three types of inserts in the MFS1 promoter, two of which harboring potential transcription factor binding sites. We show, that type I insertion leads to MFS1 overexpression and consequently to MDR. Interestingly, all three inserts correspond to repeated elements of the Z. tritici genome.\n\nThese results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici and which contribute to its adaptive potential.

microbiology↗