TY - JOUR A1 - Brenzinger, Kristof A1 - Costa, Ohana Y. A. A1 - Ho, Adrian A1 - Koorneef, Guusje A1 - Robroek, Bjorn A1 - Molenaar, Douwe A1 - Korthals, Gerard A1 - Bodelier, Paul L. E. T1 - Steering microbiomes by organic amendments towards climate-smart agricultural soils JF - Biology and Fertility of Soils N2 - We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of specific organic amendments (especially digestate + compost). Unexpectedly, also the addition of mineral fertilizer in our mesocosms led to similar combined GHG emissions than one of the specific organic amendments. However, the application of organic amendments has the potential to increase soil C, which is not the case when using mineral fertilizer. While GHG emissions from cover crop residues were significantly higher compared to mineral fertilizer and the other organic amendments, crop growth was promoted. Furthermore, all organic amendments induced a shift in the diversity and abundances of key microbial groups. We show that organic amendments have the potential to not only lower GHG emissions by modifying the microbial community abundance and composition, but also favour crop growth-promoting microorganisms. This modulation of the microbial community by organic amendments bears the potential to turn soils into more climate-smart soils in comparison to the more conventional use of mineral fertilizers. KW - greenhouse gases KW - agricultural soils KW - organic amendment KW - flux measurements KW - microbial community abundance and compositions KW - plant growth Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-326930 VL - 57 IS - 8 ER - TY - JOUR A1 - Chumduri, Cindrilla A1 - Turco, Margherita Y. T1 - Organoids of the female reproductive tract JF - Journal of Molecular Medicine N2 - Healthy functioning of the female reproductive tract (FRT) depends on balanced and dynamic regulation by hormones during the menstrual cycle, pregnancy and childbirth. The mucosal epithelial lining of different regions of the FRT—ovaries, fallopian tubes, uterus, cervix and vagina—facilitates the selective transport of gametes and successful transfer of the zygote to the uterus where it implants and pregnancy takes place. It also prevents pathogen entry. Recent developments in three-dimensional (3D) organoid systems from the FRT now provide crucial experimental models that recapitulate the cellular heterogeneity and physiological, anatomical and functional properties of the organ in vitro. In this review, we summarise the state of the art on organoids generated from different regions of the FRT. We discuss the potential applications of these powerful in vitro models to study normal physiology, fertility, infections, diseases, drug discovery and personalised medicine. KW - female reproductive tract KW - organoids KW - reproductive health KW - pregnancy KW - fertility KW - infection KW - cancers Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-328374 VL - 99 IS - 4 ER - TY - JOUR A1 - Moris, Victoria C. A1 - Christmann, Katharina A1 - Wirtgen, Aline A1 - Belokobylskij, Sergey A. A1 - Berg, Alexander A1 - Liebig, Wolf-Harald A1 - Soon, Villu A1 - Baur, Hannes A1 - Schmitt, Thomas A1 - Niehuis, Oliver T1 - Cuticular hydrocarbons on old museum specimens of the spiny mason wasp, Odynerus spinipes (Hymenoptera: Vespidae: Eumeninae), shed light on the distribution and on regional frequencies of distinct chemotypes JF - Chemoecology N2 - The mason wasp Odynerus spinipes shows an exceptional case of intrasexual cuticular hydrocarbon (CHC) profile dimorphism. Females of this species display one of two CHC profiles (chemotypes) that differ qualitatively and quantitatively from each other. The ratio of the two chemotypes was previously shown to be close to 1:1 at three sites in Southern Germany, which might not be representative given the Palearctic distribution of the species. To infer the frequency of the two chemotypes across the entire distributional range of the species, we analyzed with GC–MS the CHC profile of 1042 dry-mounted specimens stored in private and museum collections. We complemented our sampling by including 324 samples collected and preserved specifically for studying their CHCs. We were capable of reliably identifying the chemotypes in 91% of dry-mounted samples, some of which collected almost 200 years ago. We found both chemotypes to occur in the Far East, the presumed glacial refuge of the species, and their frequency to differ considerably between sites and geographic regions. The geographic structure in the chemotype frequencies could be the result of differential selection regimes and/or different dispersal routes during the colonization of the Western Palearctic. The presented data pave the route for disentangling these factors by providing information where to geographically sample O. spinipes for population genetic analyses. They also form the much-needed basis for future studies aiming to understand the evolutionary and geographic origin as well as the genetics of the astounding CHC profile dimorphism that O. spinipes females exhibit. KW - cuticular hydrocarbons KW - chemotypes KW - dry-mounted samples KW - collections KW - distribution Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-306999 SN - 0937-7409 SN - 1423-0445 VL - 31 IS - 5 ER - TY - THES A1 - König, Sebastian Thomas T1 - Temperature-driven assembly processes of Orthoptera communities: Lessons on diversity, species traits, feeding interactions, and associated faecal microorganisms from elevational gradients in Southern Germany (Berchtesgaden Alps) T1 - Temperaturabhängige Zusammensetzungsprozesse von Heuschreckengemeinschaften: Lektionen über die Diversität, Artmerkmale, Fraßinteraktionen, und Kot-Mikroorganismen von Höhengradienten in Süddeutschland (Berchtesgadener Alpen) N2 - Chapter I: Introduction Temperature is a major driver of biodiversity and abundance patterns on our planet, which becomes particularly relevant facing the entanglement of an imminent biodiversity and climate crisis. Climate shapes the composition of species assemblages either directly via abiotic filtering mechanisms or indirectly through alterations in biotic interactions. Insects - integral elements of Earth’s ecosystems - are affected by climatic variation such as warming, yet responses vary among species. While species’ traits, antagonistic biotic interactions, and even species’ microbial mutualists may determine temperature-dependent assembly processes, the lion’s share of these complex relationships remains poorly understood due to methodological constraints. Mountains, recognized as hotspots of diversity and threatened by rapidly changing climatic conditions, can serve as natural experimental settings to study the response of insect assemblages and their trophic interactions to temperature variation, instrumentalizing the high regional heterogeneity of micro- and macroclimate. With this thesis, we aim to enhance our mechanistic understanding of temperature-driven assembly processes within insect communities, exemplified by Orthoptera, that are significant herbivores in temperate mountain grassland ecosystems. Therefore, we combined field surveys of Orthoptera assemblages on grassland sites with molecular tools for foodweb reconstruction, primarily leveraging the elevational gradients offered by the complex topography within the Berchtesgaden Alpine region (Bavaria, Germany) as surrogate for temperature variation (space-for-time substitution approach). In this framework, we studied the effects of temperature variation on (1) species richness, abundance, community composition, and interspecific as well as intraspecific trait patterns, (2) ecological feeding specialisation, and (3) previously neglected links to microbial associates found in the faeces. Chapter II: Temperature-driven assembly processes Climate varies at multiple scales. Since microclimate is often overlooked, we assessed effects of local temperature deviations on species and trait compositions of insect communities along macroclimatic temperature gradients in Chapter II. Therefore, we employed joint species distribution modelling to explore how traits drive variation in the climatic niches of Orthoptera species at grassland sites characterized by contrasting micro- and macroclimatic conditions. Our findings revealed two key insights: (1) additive effects of micro- and macroclimate on the diversity, but (2) interactive effects on the abundance of several species, resulting in turnover and indicating that species possess narrower climatic niches than their elevational distributions might imply. This chapter suggests positive effects of warming on Orthoptera, but also highlights that the interplay of macro- and microclimate plays a pivotal role in structuring insect communities. Thus, it underscores the importance of considering both elements when predicting the responses of species to climate change. Additionally, this chapter revealed inter- and intraspecific effects of traits on the niches and distribution of species. Chapter III: Dietary specialisation along climatic gradients A crucial trait linked to the position of climatic niches is dietary specialisation. According to the ‘altitudinal niche-breadth hypothesis’, species of high-elevation habitats should be less specialized compared to their low-elevation counterparts. However, empirical evidence on shifts in specialization is scarce for generalist insect herbivores and existing studies often fail to control for the phylogeny and abundance of interaction partners. In Chapter III, we used a combination of field observations and amplicon sequencing to reconstruct dietary relationships between Orthoptera and plants along an extensive temperature gradient. We did not find close but flexible links between individual grasshopper and plant taxa in space. While interaction network specialisation increased with temperature, the corrected dietary specialisation pattern peaked at intermediate elevations on assemblage level. These nuanced findings demonstrate that (1) resource availability, (2) phylogenetic relationships, and (3) climate can affect empirical foodwebs intra- and interspecifically and, hence, the dietary specialisation of herbivorous insects. In this context, we discuss that the underlying mechanisms involved in shaping the specialisation of herbivore assemblages may switch along temperature clines. Chapter IV: Links between faecal microbe communities, feeding habits, and climate Since gut microbes affect the fitness and digestion of insects, studying their diversity could provide novel insights into specialisation patterns. However, their association with insect hosts that differ in feeding habits and specialisation has never been investigated along elevational climatic gradients. In Chapter IV, we utilized the dietary information gathered in Chapter III to characterize links between insects with distinct feeding behaviour and the microbial communities present in their faeces, using amplicon sequencing. Both, feeding and climate affected the bacterial communities. However, the large overlap of microbes at site level suggests that common bacteria are acquired from the shared feeding environment, such as the plants consumed by the insects. These findings emphasize the influence of a broader environmental context on the composition of insect gut microbial communities. Chapter V: Discussion & Conclusions Cumulatively, the sections of this dissertation provide support for the hypothesis that climatic conditions play a role in shaping plant–herbivore systems. The detected variation of taxonomic and functional compositions contributes to our understanding of assembly processes and resulting diversity patterns within Orthoptera communities, shedding light on the mechanisms that structure their trophic interactions in diverse climates. The combined results presented suggest that a warmer climate could foster an increase of Orthoptera species richness in Central European semi-natural grasslands, also because the weak links observed between insect herbivores and plants are unlikely to limit decoupled range shifts. However, the restructuring of Orthoptera communities in response to warmer temperatures depends on species' traits such as moisture preferences or phenology. Notably, we were able to demonstrate a crucial role of microclimate for many species, partly unravelling narrower climatic niches than their elevational ranges suggest. We found evidence that not only Orthoptera community composition, specialisation, and traits varied along elevational gradients, but even microbial communities in the faeces of Orthoptera changed, which is a novel finding. This complex restructuring and reassembly of communities, coupled with the nonlinear specialisation of trophic interactions and a high diversity of associated bacteria, emphasize our currently incomplete comprehension of how ecosystems will develop under future climatic conditions, demanding caution in making simplified predictions for biodiversity change under climate warming. Since these predictions may benefit from including biotic interactions and both, micro- and macroclimate based on our findings, conservation authorities and practitioners must not neglect improving microclimatic conditions to ensure local survival of a diverse set of threatened and demanding species. In this context, mountains can play a pivotal role for biodiversity conservation since these offer heterogeneous microclimatic conditions in proximity that can be utilized by species with distinct niches. N2 - Kapitel I: Einleitung Die Temperatur ist eine wichtige Triebkraft hinter den Artenvielfalts- und Abundanzmustern auf unserem Planeten, was angesichts der Verflechtung der unmittelbar bevorstehenden Biodiversitäts- und Klimakrise besonders relevant ist. Das Klima strukturiert die Artenvielfalt direkt durch abiotische Filtermechanismen oder indirekt durch Veränderungen biotischer Wechselwirkungen. Insekten - wesentliche Bestandteile der Ökosysteme der Erde - sind von klimatischen Veränderungen wie der Erwärmung betroffen, reagieren aber je nach Art unterschiedlich. Während die Merkmale der Arten, antagonistische biotische Interaktionen und sogar die mikrobiellen Partner der Arten temperaturabhängige Zusammensetzungsprozesse bestimmen können, bleibt ein Großteil dieser komplexen Beziehungen aufgrund methodischer Einschränkungen nach wie vor schlecht verstanden. Gebirge, die als Hotspots der Diversität gelten und von sich rasch verändernden klimatischen Bedingungen bedroht sind, können durch Nutzung der großen regionalen Heterogenität der Klein- und Großklimate als natürliche Experimente dienen, um die Reaktion von Insektengemeinschaften und deren trophischen Interaktionen auf Temperaturänderungen zu untersuchen. Mit dieser Arbeit möchten wir einen Beitrag zum mechanistischen Verständnis der temperaturbedingten Zusammensetzungsprozesse von Insektengemeinschaften leisten, am Beispiel von Heuschrecken, die bedeutende Pflanzenfresser in Grünlandökosystemen der gemäßigten Breiten sind. Hierfür kombinierten wir Felduntersuchungen von Heuschreckengemeinschaften in Grünlandstandorten mit molekularen Methoden zur Rekonstruktion von Nahrungsbeziehungen, wobei wir hauptsächlich die Höhengradienten, die die komplexe Topografie der Berchtesgadener Alpenregion (Bayern, Deutschland) bietet, stellvertretend für Temperaturveränderungen verwendeten (Raum-Zeit-Substitutionsansatz). In diesem Rahmen untersuchten wir die Auswirkungen von Temperaturvariation auf (1) den Artenreichtum, die Abundanz, die Zusammensetzung der Gemeinschaft und die inter- und intraspezifischen Merkmalsmuster, (2) die ökologische Nahrungsspezialisierung und (3) die bis dato vernachlässigte Verbindung zu den mikrobiellen Begleitarten im Kot. Kapitel II: Temperaturabhängige Zusammensetzungsprozesse Das Klima variiert auf verschiedenen Ebenen. Da Veränderungen im Kleinklima oft vernachlässigt werden, haben wir in Kapitel II die Auswirkungen der lokalen Temperaturunterschiede auf die Arten- und Merkmalszusammensetzung von Insektengemeinschaften entlang makroklimatischer Temperaturgradienten untersucht. Hierfür haben wir die Methode der gemeinsamen Artenverteilungsmodellierung verwendet, um zu untersuchen, wie Artmerkmale die Unterschiede in klimatischen Nischen von Heuschreckenarten auf Grünlandstandorten mit gegensätzlichen mikro- und makroklimatischen Bedingungen beeinflussen. Unsere Ergebnisse brachten zwei wichtige Erkenntnisse zutage: (1) additive Auswirkungen des Mikro- und Makroklimas auf die Vielfalt, aber (2) interaktive Effekte auf die Häufigkeit mehrerer Arten, die sich in Zusammensetzungsunterschieden niederschlagen und auf engere klimatische Nischen hinweisen, als es die Höhenverbreitung vermuten lässt. Dieses Kapitel deutet auf positive Auswirkungen einer Erwärmung auf Orthoptera hin, zeigt aber auch, dass das Zusammenspiel von Makro- und Mikroklima eine Schlüsselrolle bei der Strukturierung von Insektengemeinschaften spielt und beide Elemente bei der Vorhersage der Reaktionen von Arten auf den Klimawandel berücksichtigt werden sollten. Darüber hinaus wurden in diesem Kapitel die inter- und intraspezifischen Auswirkungen von Merkmalen auf die Nischen und die Verbreitung von Arten aufgezeigt. Kapitel III: Nahrungsspezialisierung entlang von Klimagradienten Ein entscheidendes Merkmal für die Lage der klimatischen Nische einer Art ist die Nahrungsspezialisierung. Nach der "Hypothese der Höhenlagen-abhängigen Nischenbreite" sollten Arten in hoch gelegenen Lebensräumen weniger spezialisiert sein als ihre Pendants in niedrigen Lagen. Empirische Belege für Verschiebungen in der Spezialisierung von generalistischen, herbivoren Insekten sind jedoch rar und es fehlt eine Berücksichtigung der Häufigkeit und Phylogenie von Interaktionspartnern. In Kapitel III haben wir eine Kombination aus Feldbeobachtungen und Amplikonsequenzierung verwendet, um die Nahrungsbeziehungen von Heuschrecken und Pflanzen entlang eines ausgedehnten Temperaturgradienten zu rekonstruieren. Wir konnten keine engen, sondern flexible Beziehungen zwischen einzelnen Herbivoren- und Pflanzentaxa feststellen. Während die Spezialisierung der Interaktionsnetzwerke mit der Temperatur zunahm, erreichte das korrigierte Muster der Nahrungsspezialisierung auf Gemeinschaftsebene seinen Höhepunkt in mittleren Höhenlagen. Diese differenzierten Ergebnisse zeigen, dass (1) die Verfügbarkeit von Ressourcen, (2) phylogenetische Beziehungen und (3) das Klima intra- und interspezifische empirische Nahrungsbeziehungen und damit die Nahrungsspezialisierung pflanzenfressender Insekten beeinflussen können. In diesem Kontext diskutieren wir, dass die zugrundeliegenden Mechanismen hinter der Nahrungsspezialisierung von herbivoren Insekten entlang von Temperaturgradienten wechseln könnten. Kapitel IV: Verbindungen zwischen Kotbakteriengemeinschaften, Ernährungsgewohnheiten und Klima. Da Darmbakterien die Fitness und Verdauung von Insekten beeinflussen, könnte die Untersuchung deren Vielfalt neue Erkenntnisse über Spezialisierungsmuster liefern. Ihre Verbindung mit Insekten, die sich in ihren Ernährungsgewohnheiten und ihrer Spezialisierung unterscheiden, wurde jedoch noch nie entlang klimatischer Höhengradienten untersucht. In Kapitel IV verwendeten wir Nahrungsinformationen aus Kapitel III, um mit Hilfe von Amplikonsequenzierung Verbindungen zwischen Insekten mit unterschiedlichem Ernährungsverhalten und mikrobiellen Gemeinschaften in deren Kot zu charakterisieren. Sowohl die Nahrung als auch das Klima hatten Auswirkungen auf die bakteriellen Gemeinschaften. Die große Überschneidung der Mikrobengemeinschaften auf Standortebene deutet jedoch darauf hin, dass gemeinsame Bakterien aus der geteilten Nahrungsumgebung, wie z.B. den von den Insekten verzehrten Pflanzen, stammen. Diese Ergebnisse unterstreichen den Einfluss eines breiteren Umweltkontextes auf die Zusammensetzung der mikrobiellen Gemeinschaften im Insektendarm. Kapitel V: Diskussion & Schlussfolgerungen Insgesamt stützen die Kapitel dieser Dissertation die Hypothese, dass klimatische Verhältnisse Pflanzen-Pflanzenfresser-Systeme prägen. Die festgestellten Unterschiede in der taxonomischen und funktionellen Zusammensetzung tragen zu unserem Verständnis der Zusammensetzungsprozesse und daraus resultierenden Diversitätsmustern von Heuschreckengemeinschaften sowie der Mechanismen bei, die deren trophische Interaktionen in verschiedenen Klimazonen strukturieren. Die Kombination der Ergebnisse deutet darauf hin, dass wärmeres Klima eine Zunahme des Heuschreckenartenreichtums in naturnahen Grünlandgebieten Mitteleuropas begünstigen könnte, auch weil die schwachen Verbindungen zwischen den herbivoren Insekten und Pflanzen entkoppelte Arealverschiebungen wahrscheinlich nicht limitieren. Jedoch könnten höhere Temperaturen die Zusammensetzung von Heuschreckengemeinschaften je nach den Merkmalen der Arten wie deren Feuchtigkeitsvorlieben oder der Schlupfphänologie verändern. Darüber hinaus konnten wir nachweisen, dass das Mikroklima für viele Arten eine entscheidende Rolle spielt, da es teilweise engere klimatische Nischen aufdeckt, als ihre Höhenverbreitung vermuten lassen. Wir fanden Hinweise darauf, dass sich nicht nur die Zusammensetzung, Spezialisierung und Merkmale der Heuschreckengemeinschaften entlang der Höhengradienten ändern, sondern dass sogar die mikrobiellen Gemeinschaften im Kot variieren, was eine neue Erkenntnis darstellt. Diese komplexe Umstrukturierung und Neuzusammensetzung von Gemeinschaften in Kombination mit der nichtlinearen Spezialisierung von Interaktionen und einer hohen Vielfalt an assoziierten Bakterien unterstreichen unser noch immer begrenztes Verständnis davon, wie sich Ökosysteme unter zukünftigen Klimabedingungen entwickeln werden, und mahnen zur Vorsicht bei vereinfachten Vorhersagen über die Veränderung der biologischen Vielfalt im Zuge der Klimaerwärmung. Da solche Vorhersagen auf Grundlage unserer Ergebnisse vom Einbezug biotischer Wechselwirkungen und des Mikro- und Makroklimas profitieren können, dürfen Naturschutzverantwortliche eine Verbesserung der mikroklimatischen Bedingungen nicht vernachlässigen, um das lokale Überleben einer Vielzahl bedrohter und anspruchsvoller Arten zu sichern. In diesem Zusammenhang können Berge eine entscheidende Rolle für den Erhalt der biologischen Vielfalt spielen, da sie in räumlicher Nähe heterogene mikroklimatische Bedingungen bieten, die von Arten mit unterschiedlichen Nischen genutzt werden können. KW - Heuschrecken KW - Mikroklima KW - Bayerische Alpen KW - Nahrung KW - Mikrobiom KW - biotic interactions KW - plant-herbivore-interactions KW - elevational gradients Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-354608 ER - TY - JOUR A1 - Däullary, Thomas A1 - Imdahl, Fabian A1 - Dietrich, Oliver A1 - Hepp, Laura A1 - Krammer, Tobias A1 - Fey, Christina A1 - Neuhaus, Winfried A1 - Metzger, Marco A1 - Vogel, Jörg A1 - Westermann, Alexander J. A1 - Saliba, Antoine-Emmanuel A1 - Zdzieblo, Daniela T1 - A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection JF - Gut Microbes N2 - Infection research largely relies on classical cell culture or mouse models. Despite having delivered invaluable insights into host-pathogen interactions, both have limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models in vitro. Here, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our model to enteric infection research in the human context. Infection assays coupled to spatio-temporal readouts recapitulated the established key steps of epithelial infection by this pathogen in our model. Besides, we detected the upregulation of olfactomedin 4 in infected cells, a hitherto unrecognized aspect of the host response to Salmonella infection. Together, this primary human small intestinal tissue model fills the gap between simplistic cell culture and animal models of infection, and shall prove valuable in uncovering human-specific features of host-pathogen interplay. KW - intestinal enteroids KW - biological scaffold KW - Salmonella Typhimurium KW - OLFM4 KW - NOTCH KW - filamentous Salmonella Typhimurium KW - bacterial migration KW - bacterial virulence KW - 3D tissue model KW - olfactomedin 4 KW - infection Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350451 VL - 15 IS - 1 ER - TY - JOUR A1 - Caliskan, Aylin A1 - Dangwal, Seema A1 - Dandekar, Thomas T1 - Metadata integrity in bioinformatics: bridging the gap between data and knowledge JF - Computational and Structural Biotechnology Journal N2 - In the fast-evolving landscape of biomedical research, the emergence of big data has presented researchers with extraordinary opportunities to explore biological complexities. In biomedical research, big data imply also a big responsibility. This is not only due to genomics data being sensitive information but also due to genomics data being shared and re-analysed among the scientific community. This saves valuable resources and can even help to find new insights in silico. To fully use these opportunities, detailed and correct metadata are imperative. This includes not only the availability of metadata but also their correctness. Metadata integrity serves as a fundamental determinant of research credibility, supporting the reliability and reproducibility of data-driven findings. Ensuring metadata availability, curation, and accuracy are therefore essential for bioinformatic research. Not only must metadata be readily available, but they must also be meticulously curated and ideally error-free. Motivated by an accidental discovery of a critical metadata error in patient data published in two high-impact journals, we aim to raise awareness for the need of correct, complete, and curated metadata. We describe how the metadata error was found, addressed, and present examples for metadata-related challenges in omics research, along with supporting measures, including tools for checking metadata and software to facilitate various steps from data analysis to published research. Highlights • Data awareness and data integrity underpins the trustworthiness of results and subsequent further analysis. • Big data and bioinformatics enable efficient resource use by repurposing publicly available RNA-Sequencing data. • Manual checks of data quality and integrity are insufficient due to the overwhelming volume and rapidly growing data. • Automation and artificial intelligence provide cost-effective and efficient solutions for data integrity and quality checks. • FAIR data management, various software solutions and analysis tools assist metadata maintenance. KW - meta-data KW - error KW - annotation KW - error-transfer KW - wrong labelling KW - patient data KW - control group KW - tools overview Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-349990 SN - 2001-0370 VL - 21 ER - TY - JOUR A1 - Caliskan, Aylin A1 - Caliskan, Deniz A1 - Rasbach, Lauritz A1 - Yu, Weimeng A1 - Dandekar, Thomas A1 - Breitenbach, Tim T1 - Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning JF - Computational and Structural Biotechnology Journal N2 - Machine learning techniques are excellent to analyze expression data from single cells. These techniques impact all fields ranging from cell annotation and clustering to signature identification. The presented framework evaluates gene selection sets how far they optimally separate defined phenotypes or cell groups. This innovation overcomes the present limitation to objectively and correctly identify a small gene set of high information content regarding separating phenotypes for which corresponding code scripts are provided. The small but meaningful subset of the original genes (or feature space) facilitates human interpretability of the differences of the phenotypes including those found by machine learning results and may even turn correlations between genes and phenotypes into a causal explanation. For the feature selection task, the principal feature analysis is utilized which reduces redundant information while selecting genes that carry the information for separating the phenotypes. In this context, the presented framework shows explainability of unsupervised learning as it reveals cell-type specific signatures. Apart from a Seurat preprocessing tool and the PFA script, the pipeline uses mutual information to balance accuracy and size of the gene set if desired. A validation part to evaluate the gene selection for their information content regarding the separation of the phenotypes is provided as well, binary and multiclass classification of 3 or 4 groups are studied. Results from different single-cell data are presented. In each, only about ten out of more than 30000 genes are identified as carrying the relevant information. The code is provided in a GitHub repository at https://github.com/AC-PHD/Seurat_PFA_pipeline. KW - single cell analysis KW - machine learning KW - explainability of machine learning KW - principal KW - feature analysis KW - model reduction KW - feature selection Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-349989 SN - 2001-0370 VL - 21 ER - TY - JOUR A1 - Engstler, Markus A1 - Beneke, Tom T1 - Gene editing and scalable functional genomic screening in Leishmania species using the CRISPR/Cas9 cytosine base editor toolbox LeishBASEedit JF - eLife N2 - CRISPR/Cas9 gene editing has revolutionised loss-of-function experiments in Leishmania, the causative agent of leishmaniasis. As Leishmania lack a functional non-homologous DNA end joining pathway however, obtaining null mutants typically requires additional donor DNA, selection of drug resistance-associated edits or time-consuming isolation of clones. Genome-wide loss-of-function screens across different conditions and across multiple Leishmania species are therefore unfeasible at present. Here, we report a CRISPR/Cas9 cytosine base editor (CBE) toolbox that overcomes these limitations. We employed CBEs in Leishmania to introduce STOP codons by converting cytosine into thymine and created http://www.leishbaseedit.net/ for CBE primer design in kinetoplastids. Through reporter assays and by targeting single- and multi-copy genes in L. mexicana, L. major, L. donovani, and L. infantum, we demonstrate how this tool can efficiently generate functional null mutants by expressing just one single-guide RNA, reaching up to 100% editing rate in non-clonal populations. We then generated a Leishmania-optimised CBE and successfully targeted an essential gene in a plasmid library delivered loss-of-function screen in L. mexicana. Since our method does not require DNA double-strand breaks, homologous recombination, donor DNA, or isolation of clones, we believe that this enables for the first time functional genetic screens in Leishmania via delivery of plasmid libraries. KW - CRISPR/Cas9 KW - Leishmania KW - cytosine base editor (CBE) toolbox KW - gene editing KW - scalable functional genomic screening KW - LeishBASEedit Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350002 VL - 12 ER - TY - JOUR A1 - Salihoglu, Rana A1 - Srivastava, Mugdha A1 - Liang, Chunguang A1 - Schilling, Klaus A1 - Szalay, Aladar A1 - Bencurova, Elena A1 - Dandekar, Thomas T1 - PRO-Simat: Protein network simulation and design tool JF - Computational and Structural Biotechnology Journal N2 - PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server. KW - network simulation KW - protein analysis KW - signalling pathways KW - dynamic protein-protein interactions KW - optogenetics KW - oncolytic virus KW - DNA storage Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350034 SN - 2001-0370 VL - 21 ER - TY - JOUR A1 - Conrad, David A1 - Kehl, Alexandra A1 - Müller, Tobias A1 - Klopfleisch, Robert A1 - Aupperle-Lellbach, Heike T1 - Immunohistochemical and molecular genetic analysis of canine digital mast cell tumours JF - Animals N2 - Grading, immunohistochemistry and c-kit mutation status are criteria for assessing the prognosis and therapeutic options of canine cutaneous mast cell tumours (MCTs). As a subset, canine digital MCTs have rarely been explored in this context. Therefore, in this retrospective study, 68 paraffin-embedded canine digital MCTs were analysed, and histological grading was assessed according to Patnaik and Kiupel. The immunohistochemical markers KIT and Ki67 were used, as well as polymerase chain reaction (PCR) for mutational screening in c-kit exons 8, 9, 11 and 14. Patnaik grading resulted in 22.1% grade I, 67.6% grade II and 10.3% grade III tumours. Some 86.8% of the digital MCTs were Kiupel low-grade. Aberrant KIT staining patterns II and III were found in 58.8%, and a count of more than 23 Ki67-positive cells in 52.3% of the cases. Both parameters were significantly associated with an internal tandem duplication (ITD) in c-kit exon 11 (12.7%). French Bulldogs, which tend to form well-differentiated cutaneous MCTs, had a higher proportion of digital high-grade MCTs and ITD in c-kit exon 11 compared with mongrels. Due to its retrospective nature, this study did not allow for an analysis of survival data. Nevertheless, it may contribute to the targeted characterisation of digital MCTs. KW - dog KW - digit KW - toe KW - CD117 KW - Ki67 KW - KIT KW - grading KW - PCR KW - sequencing KW - c-kit Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-319199 SN - 2076-2615 VL - 13 IS - 10 ER -