TY - JOUR A1 - Dhillon, Maninder Singh A1 - Dahms, Thorsten A1 - Kübert-Flock, Carina A1 - Liepa, Adomas A1 - Rummler, Thomas A1 - Arnault, Joel A1 - Steffan-Dewenter, Ingolf A1 - Ullmann, Tobias T1 - Impact of STARFM on crop yield predictions: fusing MODIS with Landsat 5, 7, and 8 NDVIs in Bavaria Germany JF - Remote Sensing N2 - Rapid and accurate yield estimates at both field and regional levels remain the goal of sustainable agriculture and food security. Hereby, the identification of consistent and reliable methodologies providing accurate yield predictions is one of the hot topics in agricultural research. This study investigated the relationship of spatiotemporal fusion modelling using STRAFM on crop yield prediction for winter wheat (WW) and oil-seed rape (OSR) using a semi-empirical light use efficiency (LUE) model for the Free State of Bavaria (70,550 km\(^2\)), Germany, from 2001 to 2019. A synthetic normalised difference vegetation index (NDVI) time series was generated and validated by fusing the high spatial resolution (30 m, 16 days) Landsat 5 Thematic Mapper (TM) (2001 to 2012), Landsat 7 Enhanced Thematic Mapper Plus (ETM+) (2012), and Landsat 8 Operational Land Imager (OLI) (2013 to 2019) with the coarse resolution of MOD13Q1 (250 m, 16 days) from 2001 to 2019. Except for some temporal periods (i.e., 2001, 2002, and 2012), the study obtained an R\(^2\) of more than 0.65 and a RMSE of less than 0.11, which proves that the Landsat 8 OLI fused products are of higher accuracy than the Landsat 5 TM products. Moreover, the accuracies of the NDVI fusion data have been found to correlate with the total number of available Landsat scenes every year (N), with a correlation coefficient (R) of +0.83 (between R\(^2\) of yearly synthetic NDVIs and N) and −0.84 (between RMSEs and N). For crop yield prediction, the synthetic NDVI time series and climate elements (such as minimum temperature, maximum temperature, relative humidity, evaporation, transpiration, and solar radiation) are inputted to the LUE model, resulting in an average R\(^2\) of 0.75 (WW) and 0.73 (OSR), and RMSEs of 4.33 dt/ha and 2.19 dt/ha. The yield prediction results prove the consistency and stability of the LUE model for yield estimation. Using the LUE model, accurate crop yield predictions were obtained for WW (R\(^2\) = 0.88) and OSR (R\(^2\) = 0.74). Lastly, the study observed a high positive correlation of R = 0.81 and R = 0.77 between the yearly R\(^2\) of synthetic accuracy and modelled yield accuracy for WW and OSR, respectively. KW - MOD13Q1 KW - precision agriculture KW - fusion KW - sustainable agriculture KW - decision making KW - winter wheat KW - oil-seed rape KW - crop models Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-311092 SN - 2072-4292 VL - 15 IS - 6 ER - TY - JOUR A1 - Brenner, Daniela A1 - Geiger, Nina A1 - Schlegel, Jan A1 - Diesendorf, Viktoria A1 - Kersting, Louise A1 - Fink, Julian A1 - Stelz, Linda A1 - Schneider-Schaulies, Sibylle A1 - Sauer, Markus A1 - Bodem, Jochen A1 - Seibel, Jürgen T1 - Azido-ceramides, a tool to analyse SARS-CoV-2 replication and inhibition — SARS-CoV-2 is inhibited by ceramides JF - International Journal of Molecular Sciences N2 - Recently, we have shown that C6-ceramides efficiently suppress viral replication by trapping the virus in lysosomes. Here, we use antiviral assays to evaluate a synthetic ceramide derivative α-NH2-ω-N3-C6-ceramide (AKS461) and to confirm the biological activity of C6-ceramides inhibiting SARS-CoV-2. Click-labeling with a fluorophore demonstrated that AKS461 accumulates in lysosomes. Previously, it has been shown that suppression of SARS-CoV-2 replication can be cell-type specific. Thus, AKS461 inhibited SARS-CoV-2 replication in Huh-7, Vero, and Calu-3 cells up to 2.5 orders of magnitude. The results were confirmed by CoronaFISH, indicating that AKS461 acts comparable to the unmodified C6-ceramide. Thus, AKS461 serves as a tool to study ceramide-associated cellular and viral pathways, such as SARS-CoV-2 infections, and it helped to identify lysosomes as the central organelle of C6-ceramides to inhibit viral replication. KW - ceramides KW - SARS-CoV-2 KW - azido-ceramides KW - sphingolipids Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-313581 SN - 1422-0067 VL - 24 IS - 8 ER - TY - JOUR A1 - Frank, Erik T. A1 - Kesner, Lucie A1 - Liberti, Joanito A1 - Helleu, Quentin A1 - LeBoeuf, Adria C. A1 - Dascalu, Andrei A1 - Sponsler, Douglas B. A1 - Azuma, Fumika A1 - Economo, Evan P. A1 - Waridel, Patrice A1 - Engel, Philipp A1 - Schmitt, Thomas A1 - Keller, Laurent T1 - Targeted treatment of injured nestmates with antimicrobial compounds in an ant society JF - Nature Communications N2 - Infected wounds pose a major mortality risk in animals. Injuries are common in the ant Megaponera analis, which raids pugnacious prey. Here we show that M. analis can determine when wounds are infected and treat them accordingly. By applying a variety of antimicrobial compounds and proteins secreted from the metapleural gland to infected wounds, workers reduce the mortality of infected individuals by 90%. Chemical analyses showed that wound infection is associated with specific changes in the cuticular hydrocarbon profile, thereby likely allowing nestmates to diagnose the infection state of injured individuals and apply the appropriate antimicrobial treatment. This study demonstrates that M. analis ant societies use antimicrobial compounds produced in the metapleural glands to treat infected wounds and reduce nestmate mortality. KW - animal behaviour KW - chemical ecology KW - entomology KW - microbial ecology KW - proteomics Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-358081 VL - 14 ER - TY - JOUR A1 - Kárpáti, Zsolt A1 - Deutsch, Ferenc A1 - Kiss, Balázs A1 - Schmitt, Thomas T1 - Seasonal changes in photoperiod and temperature lead to changes in cuticular hydrocarbon profiles and affect mating success in Drosophila suzukii JF - Scientific Reports N2 - Seasonal plasticity in insects is often triggered by temperature and photoperiod changes. When climatic conditions become sub-optimal, insects might undergo reproductive diapause, a form of seasonal plasticity delaying the development of reproductive organs and activities. During the reproductive diapause, the cuticular hydrocarbon (CHC) profile, which covers the insect body surface, might also change to protect insects from desiccation and cold temperature. However, CHCs are often important cues and signals for mate recognition and changes in CHC composition might affect mate recognition. In the present study, we investigated the CHC profile composition and the mating success of Drosophila suzukii in 1- and 5-day-old males and females of summer and winter morphs. CHC compositions differed with age and morphs. However, no significant differences were found between the sexes of the same age and morph. The results of the behavioral assays show that summer morph pairs start to mate earlier in their life, have a shorter mating duration, and have more offspring compared to winter morph pairs. We hypothesize that CHC profiles of winter morphs are adapted to survive winter conditions, potentially at the cost of reduced mate recognition cues. KW - ecology KW - zoology Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-358095 VL - 13 ER - TY - JOUR A1 - Wu, Hao A1 - Zhao, Xiufeng A1 - Hochrein, Sophia M. A1 - Eckstein, Miriam A1 - Gubert, Gabriela F. A1 - Knöpper, Konrad A1 - Mansilla, Ana Maria A1 - Öner, Arman A1 - Doucet-Ladevèze, Remi A1 - Schmitz, Werner A1 - Ghesquière, Bart A1 - Theurich, Sebastian A1 - Dudek, Jan A1 - Gasteiger, Georg A1 - Zernecke, Alma A1 - Kobold, Sebastian A1 - Kastenmüller, Wolfgang A1 - Vaeth, Martin T1 - Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming JF - Nature Communications N2 - T cell exhaustion is a hallmark of cancer and persistent infections, marked by inhibitory receptor upregulation, diminished cytokine secretion, and impaired cytolytic activity. Terminally exhausted T cells are steadily replenished by a precursor population (Tpex), but the metabolic principles governing Tpex maintenance and the regulatory circuits that control their exhaustion remain incompletely understood. Using a combination of gene-deficient mice, single-cell transcriptomics, and metabolomic analyses, we show that mitochondrial insufficiency is a cell-intrinsic trigger that initiates the functional exhaustion of T cells. At the molecular level, we find that mitochondrial dysfunction causes redox stress, which inhibits the proteasomal degradation of hypoxia-inducible factor 1α (HIF-1α) and promotes the transcriptional and metabolic reprogramming of Tpex cells into terminally exhausted T cells. Our findings also bear clinical significance, as metabolic engineering of chimeric antigen receptor (CAR) T cells is a promising strategy to enhance the stemness and functionality of Tpex cells for cancer immunotherapy. KW - cytotoxic T cells KW - infection KW - lymphocyte differentiation KW - translational research Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-358052 VL - 14 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 - 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 - 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 - 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 - Maihoff, Fabienne A1 - Sahler, Simone A1 - Schoger, Simon A1 - Brenzinger, Kristof A1 - Kallnik, Katharina A1 - Sauer, Nikki A1 - Bofinger, Lukas A1 - Schmitt, Thomas A1 - Nooten, Sabine S. A1 - Classen, Alice T1 - Cuticular hydrocarbons of alpine bumble bees (Hymenoptera: Bombus) are species-specific, but show little evidence of elevation-related climate adaptation JF - Frontiers in Ecology and Evolution N2 - Alpine bumble bees are the most important pollinators in temperate mountain ecosystems. Although they are used to encounter small-scale successions of very different climates in the mountains, many species respond sensitively to climatic changes, reflected in spatial range shifts and declining populations worldwide. Cuticular hydrocarbons (CHCs) mediate climate adaptation in some insects. However, whether they predict the elevational niche of bumble bees or their responses to climatic changes remains poorly understood. Here, we used three different approaches to study the role of bumble bees’ CHCs in the context of climate adaptation: using a 1,300 m elevational gradient, we first investigated whether the overall composition of CHCs, and two potentially climate-associated chemical traits (proportion of saturated components, mean chain length) on the cuticle of six bumble bee species were linked to the species’ elevational niches. We then analyzed intraspecific variation in CHCs of Bombus pascuorum along the elevational gradient and tested whether these traits respond to temperature. Finally, we used a field translocation experiment to test whether CHCs of Bombus lucorum workers change, when translocated from the foothill of a cool and wet mountain region to (a) higher elevations, and (b) a warm and dry region. Overall, the six species showed distinctive, species-specific CHC profiles. We found inter- and intraspecific variation in the composition of CHCs and in chemical traits along the elevational gradient, but no link to the elevational distribution of species and individuals. According to our expectations, bumble bees translocated to a warm and dry region tended to express longer CHC chains than bumble bees translocated to cool and wet foothills, which could reflect an acclimatization to regional climate. However, chain lengths did not further decrease systematically along the elevational gradient, suggesting that other factors than temperature also shape chain lengths in CHC profiles. We conclude that in alpine bumble bees, CHC profiles and traits respond at best secondarily to the climate conditions tested in this study. While the functional role of species-specific CHC profiles in bumble bees remains elusive, limited plasticity in this trait could restrict species’ ability to adapt to climatic changes. KW - pollinators KW - altitudinal gradient KW - cuticular hydrocarbon KW - desiccation KW - mountain KW - global change KW - translocation experiment KW - drought stress Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-304420 SN - 2296-701X VL - 11 ER - TY - JOUR A1 - Liu, Ruiqi A1 - Friedrich, Mike A1 - Hemmen, Katherina A1 - Jansen, Kerstin A1 - Adolfi, Mateus C. A1 - Schartl, Manfred A1 - Heinze, Katrin G. T1 - Dimerization of melanocortin 4 receptor controls puberty onset and body size polymorphism JF - Frontiers in Endocrinology N2 - Xiphophorus fish exhibit a clear phenotypic polymorphism in puberty onset and reproductive strategies of males. In X. nigrensis and X. multilineatus, puberty onset is genetically determined and linked to a melanocortin 4 receptor (Mc4r) polymorphism of wild-type and mutant alleles on the sex chromosomes. We hypothesized that Mc4r mutant alleles act on wild-type alleles by a dominant negative effect through receptor dimerization, leading to differential intracellular signaling and effector gene activation. Depending on signaling strength, the onset of puberty either occurs early or is delayed. Here, we show by Förster Resonance Energy Transfer (FRET) that wild-type Xiphophorus Mc4r monomers can form homodimers, but also heterodimers with mutant receptors resulting in compromised signaling which explains the reduced Mc4r signaling in large males. Thus, hetero- vs. homo- dimerization seems to be the key molecular mechanism for the polymorphism in puberty onset and body size in male fish. KW - fluorescence lifetime imaging microscopy KW - Förster Resonance Energy Transfer KW - Mc4r KW - puberty KW - Xiphophorus Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-354261 SN - 1664-2392 VL - 14 ER - TY - JOUR A1 - Luther, Christian H. A1 - Brandt, Philipp A1 - Vylkova, Slavena A1 - Dandekar, Thomas A1 - Müller, Tobias A1 - Dittrich, Marcus T1 - Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans JF - Frontiers in Cellular and Infection Microbiology N2 - Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype. KW - sky kinases KW - kinase signaling KW - network analysis KW - transcriptome KW - transcriptional regulation KW - phosphoproteome KW - Candida albicans Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-311771 SN - 2235-2988 VL - 13 ER - TY - JOUR A1 - Kreß, Julia Katharina Charlotte A1 - Jessen, Christina A1 - Hufnagel, Anita A1 - Schmitz, Werner A1 - Da Xavier Silva, Thamara Nishida A1 - Ferreira Dos Santos, Ancély A1 - Mosteo, Laura A1 - Goding, Colin R. A1 - Friedmann Angeli, José Pedro A1 - Meierjohann, Svenja T1 - The integrated stress response effector ATF4 is an obligatory metabolic activator of NRF2 JF - Cell Reports N2 - Highlights • The integrated stress response leads to a general ATF4-dependent activation of NRF2 • ATF4 causes a CHAC1-dependent GSH depletion, resulting in NRF2 stabilization • An elevation of NRF2 transcript levels fosters this effect • NRF2 supports the ISR/ATF4 pathway by improving cystine and antioxidant supply Summary The redox regulator NRF2 becomes activated upon oxidative and electrophilic stress and orchestrates a response program associated with redox regulation, metabolism, tumor therapy resistance, and immune suppression. Here, we describe an unrecognized link between the integrated stress response (ISR) and NRF2 mediated by the ISR effector ATF4. The ISR is commonly activated after starvation or ER stress and plays a central role in tissue homeostasis and cancer plasticity. ATF4 increases NRF2 transcription and induces the glutathione-degrading enzyme CHAC1, which we now show to be critically important for maintaining NRF2 activation. In-depth analyses reveal that NRF2 supports ATF4-induced cells by increasing cystine uptake via the glutamate-cystine antiporter xCT. In addition, NRF2 upregulates genes mediating thioredoxin usage and regeneration, thus balancing the glutathione decrease. In conclusion, we demonstrate that the NRF2 response serves as second layer of the ISR, an observation highly relevant for the understanding of cellular resilience in health and disease. KW - NRF2 KW - ATF4 KW - integrated stress response KW - CHAC1 KW - melanoma KW - SLC7A11 KW - GSH Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350312 VL - 42 IS - 7 ER - TY - JOUR A1 - Steiner, Thomas A1 - Zachary, Marie A1 - Bauer, Susanne A1 - Müller, Martin J. A1 - Krischke, Markus A1 - Radziej, Sandra A1 - Klepsch, Maximilian A1 - Huettel, Bruno A1 - Eisenreich, Wolfgang A1 - Rudel, Thomas A1 - Beier, Dagmar T1 - Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae JF - mBio N2 - Small bacterial regulatory RNAs (sRNAs) have been implicated in the regulation of numerous metabolic pathways. In most of these studies, sRNA-dependent regulation of mRNAs or proteins of enzymes in metabolic pathways has been predicted to affect the metabolism of these bacteria. However, only in a very few cases has the role in metabolism been demonstrated. Here, we performed a combined transcriptome and metabolome analysis to define the regulon of the sibling sRNAs NgncR_162 and NgncR_163 (NgncR_162/163) and their impact on the metabolism of Neisseria gonorrhoeae. These sRNAs have been reported to control genes of the citric acid and methylcitric acid cycles by posttranscriptional negative regulation. By transcriptome analysis, we now expand the NgncR_162/163 regulon by several new members and provide evidence that the sibling sRNAs act as both negative and positive regulators of target gene expression. Newly identified NgncR_162/163 targets are mostly involved in transport processes, especially in the uptake of glycine, phenylalanine, and branched-chain amino acids. NgncR_162/163 also play key roles in the control of serine-glycine metabolism and, hence, probably affect biosyntheses of nucleotides, vitamins, and other amino acids via the supply of one-carbon (C\(_1\)) units. Indeed, these roles were confirmed by metabolomics and metabolic flux analysis, which revealed a bipartite metabolic network with glucose degradation for the supply of anabolic pathways and the usage of amino acids via the citric acid cycle for energy metabolism. Thus, by combined deep RNA sequencing (RNA-seq) and metabolomics, we significantly extended the regulon of NgncR_162/163 and demonstrated the role of NgncR_162/163 in the regulation of central metabolic pathways of the gonococcus. KW - sRNA KW - Neisseria gonorrhoeae KW - posttranscriptional regulation KW - amino acid transporter KW - bipartite metabolism Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-313323 VL - 14 ER - TY - JOUR A1 - Dhillon, Maninder Singh A1 - Dahms, Thorsten A1 - Kuebert-Flock, Carina A1 - Rummler, Thomas A1 - Arnault, Joel A1 - Steffan-Dewenter, Ingolf A1 - Ullmann, Tobias T1 - Integrating random forest and crop modeling improves the crop yield prediction of winter wheat and oil seed rape JF - Frontiers in Remote Sensing N2 - The fast and accurate yield estimates with the increasing availability and variety of global satellite products and the rapid development of new algorithms remain a goal for precision agriculture and food security. However, the consistency and reliability of suitable methodologies that provide accurate crop yield outcomes still need to be explored. The study investigates the coupling of crop modeling and machine learning (ML) to improve the yield prediction of winter wheat (WW) and oil seed rape (OSR) and provides examples for the Free State of Bavaria (70,550 km2), Germany, in 2019. The main objectives are to find whether a coupling approach [Light Use Efficiency (LUE) + Random Forest (RF)] would result in better and more accurate yield predictions compared to results provided with other models not using the LUE. Four different RF models [RF1 (input: Normalized Difference Vegetation Index (NDVI)), RF2 (input: climate variables), RF3 (input: NDVI + climate variables), RF4 (input: LUE generated biomass + climate variables)], and one semi-empiric LUE model were designed with different input requirements to find the best predictors of crop monitoring. The results indicate that the individual use of the NDVI (in RF1) and the climate variables (in RF2) could not be the most accurate, reliable, and precise solution for crop monitoring; however, their combined use (in RF3) resulted in higher accuracies. Notably, the study suggested the coupling of the LUE model variables to the RF4 model can reduce the relative root mean square error (RRMSE) from −8% (WW) and −1.6% (OSR) and increase the R 2 by 14.3% (for both WW and OSR), compared to results just relying on LUE. Moreover, the research compares models yield outputs by inputting three different spatial inputs: Sentinel-2(S)-MOD13Q1 (10 m), Landsat (L)-MOD13Q1 (30 m), and MOD13Q1 (MODIS) (250 m). The S-MOD13Q1 data has relatively improved the performance of models with higher mean R 2 [0.80 (WW), 0.69 (OSR)], and lower RRMSE (%) (9.18, 10.21) compared to L-MOD13Q1 (30 m) and MOD13Q1 (250 m). Satellite-based crop biomass, solar radiation, and temperature are found to be the most influential variables in the yield prediction of both crops. KW - crop modeling KW - random forest KW - machine learning KW - NDVI KW - satellite KW - landsat KW - sentinel-2 KW - winter wheat Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-301462 SN - 2673-6187 VL - 3 ER - TY - JOUR A1 - Maihoff, Fabienne A1 - Friess, Nicolas A1 - Hoiss, Bernhard A1 - Schmid‐Egger, Christian A1 - Kerner, Janika A1 - Neumayer, Johann A1 - Hopfenmüller, Sebastian A1 - Bässler, Claus A1 - Müller, Jörg A1 - Classen, Alice T1 - Smaller, more diverse and on the way to the top: Rapid community shifts of montane wild bees within an extraordinary hot decade JF - Diversity and Distributions N2 - Aim Global warming is assumed to restructure mountain insect communities in space and time. Theory and observations along climate gradients predict that insect abundance and richness, especially of small‐bodied species, will increase with increasing temperature. However, the specific responses of single species to rising temperatures, such as spatial range shifts, also alter communities, calling for intensive monitoring of real‐world communities over time. Location German Alps and pre‐alpine forests in south‐east Germany. Methods We empirically examined the temporal and spatial change in wild bee communities and its drivers along two largely well‐protected elevational gradients (alpine grassland vs. pre‐alpine forest), each sampled twice within the last decade. Results We detected clear abundance‐based upward shifts in bee communities, particularly in cold‐adapted bumble bee species, demonstrating the speed with which mobile organisms can respond to climatic changes. Mean annual temperature was identified as the main driver of species richness in both regions. Accordingly, and in large overlap with expectations under climate warming, we detected an increase in bee richness and abundance, and an increase in small‐bodied species in low‐ and mid‐elevations along the grassland gradient. Community responses in the pre‐alpine forest gradient were only partly consistent with community responses in alpine grasslands. Main Conclusion In well‐protected temperate mountain regions, small‐bodied bees may initially profit from warming temperatures, by getting more abundant and diverse. Less severe warming, and differences in habitat openness along the forested gradient, however, might moderate species responses. Our study further highlights the utility of standardized abundance data for revealing rapid changes in bee communities over only one decade. KW - Alps KW - altitudinal gradient KW - body size KW - climate change KW - global warming KW - hymenoptera KW - pollinator KW - range shifts Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312126 VL - 29 IS - 2 ER - TY - INPR A1 - Dandekar, Thomas T1 - Analysing the phase space of the standard model and its basic four forces from a qubit phase transition perspective: implications for large-scale structure generation and early cosmological events N2 - The phase space for the standard model of the basic four forces for n quanta includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. We replace the “big bang” by a condensation event (interacting qubits become decoherent) and inflation by a crystallization event – the crystal unit cell guarantees same symmetries everywhere. Interacting qubits solidify and form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, large-scale structure of voids and filaments, supercluster formation, galaxy formation, dominance of matter and life-friendliness. We prove qubit interactions to be 1,2,4 or 8 dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field. Hence, vacuum energy gets low only inside the qubit crystal. Condensed mathematics may advantageously model free / bound qubits in phase space. KW - phase space KW - cosmology KW - emergent time KW - qubit KW - phase transition KW - bit Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-298580 ER - TY - THES A1 - Solvie, Daniel Alexander T1 - Molecular Mechanisms of MYC as Stress Resilience Factor T1 - Molekulare Mechanismen von MYC als Stressresistenzfaktor N2 - Cancer is one of the leading causes of death worldwide. The underlying tumorigenesis is driven by the accumulation of alterations in the genome, eventually disabling tumor suppressors and activating proto-oncogenes. The MYC family of proto-oncogenes shows a strong deregulation in the majority of tumor entities. However, the exact mechanisms that contribute to MYC-driven oncogenesis remain largely unknown. Over the past decades, the influence of the MYC protein on transcription became increasingly apparent and was thoroughly investigated. Additionally, in recent years several publications provided evidence for so far unreported functions of MYC that are independent of a mere regulation of target genes. These findings suggest an additional role of MYC in the maintenance of genomic stability and this role is strengthened by key findings presented in this thesis. In the first part, I present data revealing a pathway that allows MYC to couple transcription elongation and DNA double-strand break repair, preventing genomic instability of MYC-driven tumor cells. This pathway is driven by a rapid transfer of the PAF1 complex from MYC onto RNAPII, a process that is mediated by HUWE1. The transfer controls MYC-dependent transcription elongation and, simultaneously, the remodeling of chromatin structure by ubiquitylation of histone H2B. These regions of open chromatin favor not only elongation but also DNA double-strand break repair. In the second part, I analyze the ability of MYC proteins to form multimeric structures in response to perturbation of transcription and replication. The process of multimerization is also referred to as phase transition. The observed multimeric structures are located proximal to stalled replication forks and recruit factors of the DNA-damage response and transcription termination machinery. Further, I identified the HUWE1-dependent ubiquitylation of MYC as an essential step in this phase transition. Cells lacking the ability to form multimers display genomic instability and ultimately undergo apoptosis in response to replication stress. Both mechanisms present MYC as a stress resilience factor under conditions that are characterized by a high level of transcriptional and replicational stress. This increased resilience ensures oncogenic proliferation. Therefore, targeting MYC’s ability to limit genomic instability by uncoupling transcription elongation and DNA repair or disrupting its ability to multimerize presents a therapeutic window in MYC-dependent tumors. N2 - Tumorerkrankungen sind eine der häufigsten Todesursachen weltweit. Für die Entstehung und Entwicklung eines Tumors sind Veränderungen im Genom verantwortlich, wobei Proto-Onkogene aktiviert und Tumorsuppressorgene inaktiviert werden. Die MYC-Familie der Proto-Onkogene ist in der Mehrzahl der menschlichen Tumorerkrankungen stark dereguliert. Der genaue Mechanismus, der in MYC-getriebenen Tumoren eine Rolle spielt, ist aber weiterhin ungeklärt. In den letzten Jahrzehnten wurde die Funktion von MYC als Transkriptionsfaktor in den Vordergrund gestellt. Veröffentlichungen der letzten Jahre deuten zusätzlich auf mehrere, bisher unbekannte Funktionen hin, die unabhängig von einer bloßen Regulation von Zielgenen sind und auf eine zusätzliche Rolle bei der Erhaltung der genomischen Stabilität hinweisen. Diese Rolle wird durch wesentliche Ergebnisse dieser Doktorarbeit gestärkt. In dem ersten Teil der Doktorarbeit präsentiere ich einen Pathway, der es MYC ermöglicht, transkriptionelle Elongation und Doppelstrangbruch-Reparatur zu koppeln, wodurch genomische Instabilität in MYC-gesteuerten Tumorzellen limitiert wird. Dieser Pathway wird durch einen schnellen Transfer des PAF1-Komplexes von MYC auf die RNAPII angetrieben, bei dem HUWE1 eine essenzielle Rolle einnimmt. Der Transfer steuert die MYC-abhängige transkriptionelle Elongation und gleichzeitig die Öffnung der Chromatinstruktur. Dies geschieht durch Ubiquitylierung des Histons H2B zugunsten von sowohl transkriptioneller Elongation als auch der DNA-Doppelstrangbruchreparatur. In dem zweiten Teil der Doktorarbeit analysiere ich die Fähigkeit von MYC-Proteinen, als Reaktion auf eine Störung der Transkription und/oder Replikation multimere Strukturen bilden zu können. Diese Fähigkeit wird auch als Phasentrennung bezeichnet. Die multimere Strukturen befinden sich in der Nähe von blockierten Replikationsgabeln und rekrutieren Faktoren der DNA-Schadensreaktion und der Transkriptionsterminationsmaschinerie. Die HUWE1-abhängige Ubiquitylierung von MYC habe ich als wesentlichen Schritt der Phasentrennung identifiziert. Zellen ohne die Fähigkeit zur Bildung von Multimeren zeigen als Reaktion auf Replikationsstress exzessive genomische Instabilität und letztendlich Apoptose auf. Beide Mechanismen machen MYC zu einem Faktor, der genomische Instabilität als Resultat von unphysiologischem Transkriptions- und Replikationsstress limitiert und damit die onkogene Zellteilung gewährleistet. Eine gezielte Beeinflussung der aufgeführten Mechanismen, durch welche MYC die genomische Instabilität limitiert, kann bei MYC-abhängigen Tumoren von großem therapeutischem Nutzen sein. KW - MYC KW - Krebsforschung KW - DNS-Schädigung KW - DNS-Reparatur KW - Oncogenes Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-305398 ER - TY - THES A1 - Sauerwein, Till T1 - Implementation and application of bioinformatical software for the analysis of dual RNA sequencing data of host and pathogen during infection T1 - Implementierung und Anwendung bioinformatischer Software für die Analyse von dual RNA-Sequenzierdaten von Wirt und Erreger während Infektion N2 - Since the advent of high-throughput sequencing technologies in the mid-2010s, RNA se- quencing (RNA-seq) has been established as the method of choice for studying gene expression. In comparison to microarray-based methods, which have mainly been used to study gene expression before the rise of RNA-seq, RNA-seq is able to profile the entire transcriptome of an organism without the need to predefine genes of interest. Today, a wide variety of RNA-seq methods and protocols exist, including dual RNA sequenc- ing (dual RNA-seq) and multi RNA sequencing (multi RNA-seq). Dual RNA-seq and multi RNA-seq simultaneously investigate the transcriptomes of two or more species, re- spectively. Therefore, the total RNA of all interacting species is sequenced together and only separated in silico. Compared to conventional RNA-seq, which can only investi- gate one species at a time, dual RNA-seq and multi RNA-seq analyses can connect the transcriptome changes of the species being investigated and thus give a clearer picture of the interspecies interactions. Dual RNA-seq and multi RNA-seq have been applied to a variety of host-pathogen, mutualistic and commensal interaction systems. We applied dual RNA-seq to a host-pathogen system of human mast cells and Staphylo- coccus aureus (S. aureus). S. aureus, a commensal gram-positive bacterium, can become an opportunistic pathogen and infect skin lesions of atopic dermatitis (AD) patients. Among the first immune cells S. aureus encounters are mast cells, which have previously been shown to be able to kill the bacteria by discharging antimicrobial products and re- leasing extracellular traps made of protein and deoxyribonucleic acid (DNA). However, S. aureus is known to evade the host’s immune response by internalizing within mast cells. Our dual RNA-seq analysis of different infection settings revealed that mast cells and S. aureus need physical contact to influence each other’s gene expression. We could show that S. aureus cells internalizing within mast cells undergo profound transcriptome changes to adjust their metabolism to survive in the intracellular niche. On the host side, we found out that infected mast cells elicit a type-I interferon (IFN-I) response in an autocrine manner and in a paracrine manner to non-infected bystander-cells. Our study provides the first evidence that mast cells are capable to produce IFN-I upon infection with a bacterial pathogen. N2 - Seit dem Aufkommen von Hochdurchsatz-Sequenziertechnologien Mitte der 2010er Jahre hat sich RNA-Sequenzierung (RNA-seq) als Methode der Wahl für die Untersuchung von Genexpression etabliert. Im Vergleich zu Microarray-basierten Methoden, die vor dem Aufkommen von RNA-seq hauptsächlich zur Untersuchung der Genexpression verwendet wurden, kann mit RNA-seq das gesamte Transkriptom eines Organismus charakterisiert werden, ohne dass die Gene von Interesse vorab definiert werden müssen. Heute gibt es ei- ne Vielzahl von RNA-seq-Methoden und Protokollen, darunter Dual RNA-seq und Multi RNA-seq. Dual RNA-seq und Multi RNA-seq untersuchen gleichzeitig die Transkriptome von zwei bzw. mehreren Arten. Dazu wird die gesamte RNA aller interagierenden Arten gemeinsam sequenziert und nur in silico aufgetrennt. Im Vergleich zur herkömmlichen RNA-seq, bei der jeweils nur eine Spezies untersucht wird, können Dual RNA-seq- und Multi RNA-seq-Analysen die Transkriptomveränderungen der untersuchten Spezies mit- einander in Verbindung bringen und so ein klareres Bild der Wechselwirkungen zwischen den Spezies vermitteln. Dual RNA-seq und Multi RNA-seq wurden bereits auf eine Viel- zahl von Wirt-Pathogen-, mutualistischen und kommensalen Interaktionssystemen ange- wendet. Wir haben Dual RNA-seq auf ein Wirt-Pathogen-System aus menschlichen Mastzellen und S. aureus angewendet. S. aureus, ein kommensales grampositives Bakterium, kann zu ei- nem opportunistischen Erreger werden und Hautläsionen von Patienten mit atopischer Dermatitis (AD) infizieren. Zu den ersten Immunzellen, auf die S. aureus trifft, gehören Mastzellen, die nachweislich in der Lage sind, das Bakterium abzutöten, indem sie antimi- krobielle Produkte abgeben und extrazelluläre Fallen aus Proteinen und DNA freisetzen. Es ist jedoch bekannt, dass S. aureus die Immunantwort des Wirts umgehen kann, indem es in die Mastzellen internalisiert wird. Unsere Dual RNA-seq-Analyse verschiedener In- fektionssituationen ergab, dass Mastzellen und S. aureus physischen Kontakt benötigen, um ihre Genexpression gegenseitig zu beeinflussen. Wir konnten zeigen, dass S. aureus Zellen, die von Mastzellen internalisiert werden, tiefgreifende Transkriptomveränderungen durchlaufen, um ihren Stoffwechsel für das ̈Uberleben in der intrazellulären Nische an- zupassen. Auf Seite des Wirts fanden wir heraus, dass infizierte Mastzellen eine IFN-I (Interferon Typ I)-Antwort auf autokrine und auf parakrine Weise auf nicht-infizierte, in der Nähe befindliche Zellen auslösen. Unsere Studie liefert den ersten Beweis dafür, dass Mastzellen bei einer Infektion mit einem bakteriellen Erreger in der Lage sind, IFN-I zu produzieren. Um die bioinformatische Analyse von Dual RNA-seq und Multi RNA-seq zu erleichtern, haben wir ein umfangreiches Update des bereits existierenden RNA-seq-Analysepro- gramms READemption veröffentlicht. Die neue Version READemption 2 ermöglicht es den Nutzern, Dual RNA-seq- und Multi RNA-seq-Daten einer beliebigen Anzahl von Spe- zies auf bequeme Weise zu analysieren, während es weiterhin möglich ist, herkömmliche RNA-seq-Projekte zu analysieren, die nur eine Spezies untersuchen. Bei der Entwicklung wurde Wert darauf gelegt, die Qualität der Software durch die Einhaltung bewährter Verfahren für die Entwicklung wissenschaftlicher Software hoch zu halten. KW - Biologie KW - biology Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-303075 ER - TY - JOUR A1 - Mehmood, Rashid A1 - Alsaleh, Alanoud A1 - Want, Muzamil Y. A1 - Ahmad, Ijaz A1 - Siraj, Sami A1 - Ishtiaq, Muhammad A1 - Alshehri, Faizah A. A1 - Naseem, Muhammad A1 - Yasuhara, Noriko T1 - Integrative molecular analysis of DNA methylation dynamics unveils molecules with prognostic potential in breast cancer JF - BioMedInformatics N2 - DNA methylation acts as a major epigenetic modification in mammals, characterized by the transfer of a methyl group to a cytosine. DNA methylation plays a pivotal role in regulating normal development, and misregulation in cells leads to an abnormal phenotype as is seen in several cancers. Any mutations or expression anomalies of genes encoding regulators of DNA methylation may lead to abnormal expression of critical molecules. A comprehensive genomic study encompassing all the genes related to DNA methylation regulation in relation to breast cancer is lacking. We used genomic and transcriptomic datasets from the Cancer Genome Atlas (TGCA) Pan-Cancer Atlas, Genotype-Tissue Expression (GTEx) and microarray platforms and conducted in silico analysis of all the genes related to DNA methylation with respect to writing, reading and erasing this epigenetic mark. Analysis of mutations was conducted using cBioportal, while Xena and KMPlot were utilized for expression changes and patient survival, respectively. Our study identified multiple mutations in the genes encoding regulators of DNA methylation. The expression profiling of these showed significant differences between normal and disease tissues. Moreover, deregulated expression of some of the genes, namely DNMT3B, MBD1, MBD6, BAZ2B, ZBTB38, KLF4, TET2 and TDG, was correlated with patient prognosis. The current study, to our best knowledge, is the first to provide a comprehensive molecular and genetic profile of DNA methylation machinery genes in breast cancer and identifies DNA methylation machinery as an important determinant of the disease progression. The findings of this study will advance our understanding of the etiology of the disease and may serve to identify alternative targets for novel therapeutic strategies in cancer. KW - DNA methylation KW - epigenetic modification KW - breast cancer KW - genomics KW - in silico analysis Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-321171 SN - 2673-7426 VL - 3 IS - 2 SP - 434 EP - 445 ER -