Biology subjects

Becker, F.

Publications and source records attributed to Becker, F..

13 recordsLinked to original sources

bioRxiv2026

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

BackgroundEukaryotic genome annotation is currently bottlenecked by limitations in the generality, scalability or accuracy of computational methods and fewer than 20% of the genomes available at NCBI Datasets have associated gene annotations. Evidence-based pipelines such as BRAKER3 achieve high accuracy but require substantial extrinsic evidence and compute. Deep learning approaches have recently achieved large improvements in ab initio gene prediction accuracy. The end-to-end deep learning gene predictor Tiberius approaches the accuracy of evidence-based annotation on mammalian genomes without using any extrinsic evidence, but its published models were trained on mammals only, limiting its applicability across eukaryotes. ResultsWe extend Tiberius beyond mammals by training lineage-specific models for Mesan-giospermae, Fungi, Vertebrata, Insecta, Chlorophyta and Bacillariophyta, making the tool applicable to 92% of currently available eukaryotic assemblies. Across a benchmark of 33 species, Tiberius achieved higher exon-, transcript- and gene-level accuracy than the other evaluated ab initio methods, Helixer and ANNEVO, improving gene-level F1 score by 12-37 percentage points over Helixer and by 10-22 percentage points over ANNEVO, while also having the fastest runtimes overall. Compared with BRAKER3, which incorporates RNA-Seq and protein evidence, Tiberius approaches state-of-the-art accuracy in Mesangiospermae, Fungi, Bacillariophyta and Chlorophyta, while being on average 80 times faster when using a GPU. A reimplementation of the Tiberius backend reduced runtime by 31% compared to the previous implementation. Tiberius and its models are also available through a web server, which allows annotation of submitted assemblies without local resources. Furthermore, the Vertebrata model has been applied to annotate 2,948 vertebrate assemblies totalling nearly 6 trillion base pairs. ConclusionsTiberius is transferable well beyond Mammalia and reaches accuracy close to evidence-based annotation in several clades at a small fraction of the compute cost. This makes it a practical choice for highly accurate large-scale genome annotation, particularly when extrinsic evidence is unavailable or annotation throughput is limiting. Availability and implementationCode: https://github.com/Gaius-Augustus/Tiberius, web server: https://bioinf.uni-greifswald.de/tiberius.

bioinformatics↗

bioRxiv2026

Treatment with saturating dose of conventional anti-CD28 monoclonal antibody well tolerated in pig acute myocardial infarction model

CD4+ Foxp3+ regulatory T cells (Treg) efficiently foster wound healing after myocardial infarction (MI). Therapeutically shifting the balance between CD4+ Foxp3- conventional T cells (Tconv) and Treg towards Tregs enhanced survival in a mouse model of MI. Due to species-specific differences in cardiac wound healing and remodelling, it remains, however, unclear whether these findings can be translated into novel immunotherapies for human patients after MI. Therefore, we studied pigs whose cardiac wound healing after MI and the composition of the immune system are very close to humans. This includes the relevant complication of developing a cytokine release syndrome (CRS) after infusion of saturating amounts of a superagonistic anti-CD28 monoclonal antibody (mAb). To achieve the intended shift in the Treg/Tconv balance, we treated pigs three days after interventional MI induction with a non-superagonistic, i.e. conventional, anti-CD28 mAb, clone 3D11. Infusion of a saturating dose (1 mg/kg body weight) of mAb 3D11 was clinically well tolerated without signs of CRS induction or any other complications. Molecularly, mAb 3D11 infusion led to a downmodulation of CD28 expression on porcine T cells in vivo with the remaining CD28 molecules blocked from binding natural ligand proteins CD80 and CD86, as we show in this publication. Apart from modulating CD28 expression, treatment with mAb 3D11 did not induce any overt changes in the peripheral T cell compartment. However, after mAb 3D11 treatment, we observed Treg accumulation in the infarcted heart, particularly the border zone, on day 7 post-MI using immunofluorescence histology. Our findings thus suggest that even saturating doses of conventional anti-CD28 monoclonal antibodies could potentially be safely administered in patients to therapeutically shift the Treg/Tconv balance in the infarcted myocardium. This might be sufficient to enhance cardiac wound healing in patients short-term and prevent adverse remodelling long-term.

immunology↗

bioRxiv2025

Low-dose infusion of a superagonistic anti-CD28 monoclonal antibody ameliorates inflammation after acute myocardial infarction in pigs

CD4+ Foxp3+ regulatory T cells (Treg) efficiently foster wound healing after myocardial infarction (MI). Moreover, therapeutic shifting of the balance between CD4+ Foxp3- conventional (Tconv) and Treg towards Treg enhances survival in mice after MI. Owing to the species-specific differences in cardiac wound healing and remodelling after MI, it remains unclear whether these findings can be translated into novel immunotherapies for patients with MI. Therefore, we tested the feasibility of therapeutic Treg activation after MI in pigs whose cardiac wound healing and the composition of the immune system are very close to humans. To activate Treg, we treated pigs three days after MI induction with a superagonistic anti-CD28 monoclonal antibody (mAb, CD28-SA; clone 4D12). To avoid induction of a cytokine release syndrome (CRS) we infused the CD28-SA at a low dose of 10 {micro}g/kg body weight. Low-dose CD28-SA treatment led to a local increase in porcine Treg among heart-infiltrating CD4+ T cells in comparison with the control mAb therapy (clone MOPC-21). Immunofluorescence histology showed that CD28-SA application particularly strengthened Treg accumulation in the infarct border zone. This was paralleled by a lower proportion of TNF-producing cells among cardiac monocytes and macrophages reflecting a shift away from inflammation and towards wound healing. Taken together, our findings in the pig MI model are the first to show that low-dose CD28-SA infusion is capable of ameliorating tissue inflammation in a species prone to CRS development after high-dose CD28-SA infusion. Moreover, the data highlight that therapeutically shifting the Treg/Tconv balance in MI patients might be feasible in order to enhance cardiac wound healing and prevent adverse remodelling.

immunology↗

bioRxiv2025

Bombus terrestris Complementary Sex Determiner (BtCSD) is identified as a conserved hymenopteran sex determination region: evolution, breeding, and conservation implications

All Hymenoptera (bees, sawflies, ants, wasps) are haplodiploid. Haploid males develop from unfertilized eggs and diploid females from fertilized eggs. Many species also have single locus complementary sex determination (sl-CSD): hemizygosity of a CSD gene results in normal males and heterozygosity in normal females, but homozygosity typically yields sterile diploid males. Populations that lose CSD allelic diversity to critical level, increasingly produce detrimental diploid males. Emblematic of this problem are the bumblebees. Bumblebees are one of the fastest declining animal groups worldwide, with CSD diversity loss playing a likely role, especially in isolated populations. Presently utilized and potential future species in agriculture are also challenged by diploid males in production. Population management of both requires exact knowledge of the CSD locus. Here we report the identity of Bombus terrestris CSD, a bumblebee model that is also a major commercial pollinator. As CSD must be reciprocally homozygous in diploid males and heterozygous in diploid females, we whole-genome-sequenced these for four colonies. From this, we identified B. terrestris CSD (BtCSD) on Chromosome 2: a 26 Kb region with a long non-coding RNA region (lncRNA) and a proximate hypervariable region. Comparative analyses indicated conservation of this region across infraorder Aculeata, including other bumblebees, mason bees, and ants. This supports a deep-rooted ancestral origin for BtCSD despite a lack of homology with con-familial honey bee csd and rapid evolutionary divergence of insect sex determination cascades. Our analyses do not support the lncRNA region as functional CSD, as proposed for other taxa, because of inadequate variation to constitute distinct alleles. Rather, a downstream region is implicated for its massive structural variation and candidate coding genes including Creld and two copies of aCOP. We discuss how this identification of BtCSD has critical implications for hymenopteran evolution and bumblebee population management.

genomics↗

bioRxiv2025

Oncogene Silencing via ecDNA Micronucleation

Extrachromosomal DNA (ecDNA) contributes to cancer genome instability by enabling high-copy oncogene amplification, intratumoural heterogeneity and rapid genetic change. Micronuclei (MN) are frequently observed in chromosomally unstable cancers, yet their origins and relevance in ecDNA-driven tumours remain incompletely understood. Here, we investigate the relationship between ecDNA segregation errors and MN formation. We find that ecDNA frequently localizes to MN and represents a prominent source of MN content in ecDNA-positive cancer cells. Mitotic clustering of oncogene-bearing ecDNAs is associated with asymmetric inheritance and mis-segregation into MN. Transfer of oncogenes from ecDNA into MN is accompanied by reduced transcriptional output. Single-MN sequencing shows that individual MN are enriched for ecDNA to a degree that exceeds expectations from stochastic mis-segregation and that in MN oncogenes originating from multiple distinct ecDNAs coalesce. Using live-cell imaging, we observe that cells inheriting ecDNA-positive MN show limited proliferative capacity and an increased likelihood of cell death. In neuroblastoma patients with MYCN-amplified ecDNA, higher frequencies of ecDNA-positive MN at diagnosis are associated with improved event-free and overall survival. Together, these findings link ecDNA mis-segregation to MN formation and reduced cellular fitness, suggesting that ecDNA-positive MN may reflect a state of impaired oncogenic ecDNA function with potential relevance for clinical outcome.

cancer biology↗

bioRxiv2024

Putative EGF ligand and receptor of Echinococcus multilocularis that are critical for parasite development

The neglected zoonosis alveolar echinococcosis (AE) is caused by infiltrative growth of the metacestode larval stage of the cestode Echinococcus multilocularis within host organs. We previously demonstrated that metacestode growth depends on the mitotic activity of a population of parasite stem cells, called germinative cells, but it is not yet clear which molecular mechanisms govern Echinococcus stem cell dynamics such as cell-cycle progression, self-renewal and differentiation. Based on previous reports showing that epidermal growth factor (EGF) signalling contributes to Echinococcus stem cell regulation, we herein characterized three EGF receptors of the parasite and demonstrated by RNAi and inhibitor assays that one of these, EmER1, is crucial for the development of metacestode vesicles from parasite stem cells. We also showed that EmER1 serves as a target for afatinib, an EGF receptor inhibitor with profound anti-parasitic activities in vitro and in vivo. By bioinformatic analyses and membrane-bound yeast two-hybrid assays, we identified a parasite-derived, neuregulin-like cognate ligand for EmER1, EmNRG, the expression of which is strongly upregulated in metacestode vesicles during clonal expansion of germinative cells. Furthermore, we demonstrate that RNAi knockdown of the EmNRG encoding gene drastically affects the ability of germinative cells to produce metacestode vesicles. We propose that EmNRG and EmER1 form a cognate ligand-receptor system utilized by E. multilocularis to regulate asymmetric versus symmetric division decisions of stem cells. These data are relevant for further studies into Echinococcus stem cell dynamics and for the development of EGF signalling-based anti-infectives against echinococcosis.

microbiology↗

bioRxiv2024

Tiberius: End-to-End Deep Learning with an HMM for Gene Prediction

MotivationFor more than 25 years, learning-based eukaryotic gene predictors were driven by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently, Holst et al. demonstrated with their program Helixer that the accuracy of ab initio eukaryotic gene prediction can be improved by combining deep learning layers with a separate HMM postprocessor. ResultsWe present Tiberius, a novel deep learning-based ab initio gene predictor that end-to-end integrates convolutional and long short-term memory layers with a differentiable HMM layer. Tiberius uses a custom gene prediction loss and was trained for prediction in mammalian genomes and evaluated on human and two other genomes. It significantly outperforms existing ab initio methods, achieving F1-scores of 62% at gene level for the human genome, compared to 21% for the next best ab initio method. In de novo mode, Tiberius predicts the exon-intron structure of two out of three human genes without error. Remarkably, even Tiberiuss ab initio accuracy matches that of BRAKER3, which uses RNA-seq data and a protein database. Tiberiuss highly parallelized model is the fastest state-of-the-art gene prediction method, processing the human genome in under 2 hours. Availability and Implementationhttps://github.com/Gaius-Augustus/Tiberius Contact{lars.gabriel@uni-greifswald.de, mario.stanke@uni-greifswald.de}

bioinformatics↗

bioRxiv2023

The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis

Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5-untranslated region (5-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37{degrees}C. The trxA gene is transcribed into two mRNA isoforms, of which the short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25{degrees}C suggesting partially open structures available to the ribosome in the living cell. Upstream of katY we uncovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37{degrees}C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with temperature regulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37{degrees}C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature. Author summaryThe external conditions dramatically change when a bacterial pathogen enters a mammalian host. Sensing the new situation and rapidly responding to it is of critical importance for pathogens, like Yersinia pseudotuberculosis, since they often circulate between their environmental reservoirs and a warm-blooded host. Many virulence-related genes encode a temperature-sensitive mRNA element, a so-called RNA thermometer (RNAT), in the 5-end of their transcript. Melting of this structure at 37{degrees}C allows ribosome binding and translation initiation. The host immune system typically fights microbial pathogens by the production of reactive oxygen species (ROS). Here, we find that several ROS defense genes in Yersinia are upregulated at host body temperature to counteract the ROS attack. In particular, the massive RNAT-mediated upregulation of the catalase KatY confers protection against H2O2 at 37{degrees}C. Our study reveals a close regulatory link between temperature sensing and the oxidative stress response in a notorious food borne pathogen.

microbiology↗

bioRxiv2022

Conformational dynamics and target-dependent myristoyl switch of calcineurin B homologous protein 3

Calcineurin B homologous protein 3 (CHP3) is an EF-hand Ca2+-binding protein involved in regulation of cancerogenesis, cardiac hypertrophy and neuronal development via interactions with sodium/proton exchangers (NHEs) and signalling proteins. CHP3 binds Ca2+ with micromolar affinity providing the basis to respond to intracellular Ca2+ signals. Ca2+ binding and myristoylation are important for CHP3 function but the underlying molecular mechanism remained elusive. Here, we show that Ca2+ binding and myristoylation independently affect conformational dynamics and functions of human CHP3. Ca2+ binding increased flexibility and hydrophobicity of CHP3 indicative of an open conformation. CHP3 in open Ca2+-bound conformation had higher affinity for NHE1 and associated stronger with lipid membranes compared to the closed Mg2+-bound conformation. Myristoylation enhanced flexibility of CHP3 and decreased its affinity to NHE1 independently of the bound ion, but did not affect its binding to lipid membranes. The data exclude the proposed Ca2+-myristoyl switch for CHP3. Instead, they document a Ca2+-independent exposure of the myristoyl moiety induced by binding of the target peptide to CHP3 enhancing its association to lipid membranes. We name this novel regulatory mechanism "target-dependent myristoyl switch". Taken together, the interplay of Ca2+ binding, myristoylation and target binding allows for a context-specific regulation of CHP3 functions.

biochemistry↗

bioRxiv2022

Honey Bees Get Map Coordinates from the Dance

Honeybees (Apis mellifera carnica) communicate the rhumb line to a food source (its direction and distance from the hive) by means of a waggle dance. We ask whether bees recruited by the dance use it only as a flying instruction or also translate it into a location vector in a map-like memory, so that information about spatial relations of environmental cues informs their attempts to find the source. The flights of recruits captured on exiting the hive and released at distant sites were tracked by radar. The recruits performed first a straight flight in the direction of the rhumb line. However, the vector portions of their flights and the ensuing tortuous search portions were strongly and differentially affected by the release site. Searches were biased toward the true location of the food and away from the location specified by translating the rhumb line origin to the release site. We conclude that by following the dance a recruit gets two messages, a polar flying instruction (the rhumb line) and its conversion to Cartesian map coordinates.

animal behavior and cognition↗

bioRxiv2022

Targeting Echinococcus multilocularis PIM kinase for improving anti-parasitic chemotherapy

BackgroundThe potentially lethal zoonosis alveolar echinococcosis (AE) is caused by the metacestode larval stage of the tapeworm Echinococcus multilocularis. Current AE treatment options are limited and rely on surgery as well as on chemotherapy involving benzimidazoles (BZ). BZ treatment, however, is parasitostatic only, must be given for prolonged time periods, and is associated with adverse side effects. Novel treatment options are thus urgently needed. Methodology/Principal findingsBy applying a broad range of kinase inhibitors to E. multilocularis stem cell cultures we identified the proto-oncogene PIM kinase as a promising target for anti-AE chemotherapy. The gene encoding the respective E. multilocularis ortholog, EmPIM, was characterized and in situ hybridization assays indicated its expression in parasite stem cells. By yeast two-hybrid assays we demonstrate interaction of EmPIM with E. multilocularis CDC25, indicating an involvement of EmPIM in parasite cell cycle regulation. Small molecule compounds SGI-1776 and CX-6258, originally found to effectively inhibit human PIM kinases, exhibited detrimental effects on in vitro cultured parasite metacestode vesicles and prevented the formation of mature vesicles from parasite stem cell cultures. To improve compound specificity for EmPIM, we applied a high throughput in silico modelling approach, leading to the identification of compound Z196138710. When applied to in vitro cultured metacestode vesicles and parasite cell cultures, Z196138710 proved equally detrimental as SGI-1776 and CX-6258, but displayed significantly reduced toxicity towards human HEK293T and HepG2 cells. Conclusions/SignificanceRepurposing of kinase inhibitors initially designed to affect mammalian kinases for helminth disease treatment is often hampered by adverse side effects of respective compounds on human cells. Here we demonstrate the utility of high throughput in silico approaches to design small molecule compounds of higher specificity for parasite cells. We propose EmPIM as a promising target for respective approaches towards AE treatment. Author summaryThe larva of the tapeworm E. multilocularis grows tumor-like within the host liver, thus causing the lethal disease alveolar echinococcosis (AE). Anti-parasitic treatment relies on chemotherapy with benzimidazoles, which do not kill the parasite and must be applied for years. As druggable enzymes with key functions in growth control, protein kinases are promising drug targets and many kinase inhibitors have been identified during cancer research. Optimized for binding to human kinases, however, repurposing of such drugs for parasitic disease treatment is associated with adverse side effects. Herein, the authors applied an in silico approach to identify small molecule compounds that show higher specificity for a parasite kinase, EmPIM, over its mammalian homologs. The authors demonstrate expression of EmPIM in Echinococcus stem cells, which are the drivers of parasite growth, and show that mammalian PIM kinase inhibitors SGI-1776 and CX-6258 also affect parasite development in vitro. Finally, they show that one of the in silico screened compounds is equally effective against the parasite as SGI-1776 and CX-6258, but significantly less toxic to human cells. These results demonstrate the utility of in silico approaches to identify parasite-specific kinase inhibitors.

microbiology↗

bioRxiv2022

Meiosis in the human pathogen Aspergillus fumigatus has the highest known number of crossovers

Evidence from both population genetics and a laboratory sexual cycle indicate that sex is common in the fungus Aspergillus fumigatus. However, the impact of sexual reproduction has remained unclear. Here, we show that meiosis in A. fumigatus involves the highest known recombination rate, producing ~29 crossovers per chromosome. This represents the highest known crossover rate for any Eukaryotic species. We validate this recombination rate by mapping resistance to acriflavine, a common genetic marker. We further show that this recombination rate can produce the commonly encountered TR34/L98H azole-resistant cyp51A haplotype in each sexual event, facilitating its rapid and global spread. Understanding the consequences of this unparalleled crossover rate will not only enrich our genetic understanding of this emergent human pathogen, but of meiosis in general. One-Sentence SummaryGenetic exchange between chromosomes during sex in Aspergillus fumigatus is higher than in any other known organism.

genetics↗

bioRxiv2019

VARUS: Sampling Complementary RNA Reads from the Sequence Read Archive

Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However, selecting a subset of available experiments, sequencing runs and reads for this purpose is a nontrivial task and complicated by the inhomogeneity of the data.\n\nThis article presents the software VARUS that selects, downloads and aligns reads from NCBIs Sequence Read Archive, given only the species binomial name and genome. VARUS automatically chooses runs from among all archived runs to randomly select subsets of reads. The objective of its online algorithm is to cover a large number of transcripts adequately when network bandwidth and computing resources are limited. For most tested species VARUS achieved both a higher sensitivity and specificity with a lower number of downloaded reads than when runs were manually selected. At the example of twelve eukaryotic genomes, we show that RNA-Seq that was sampled with VARUS is well-suited for fully-automatic genome annotation with BRAKER.\n\nWith VARUS, genome annotation can be automatized to the extent that not even the selection and quality control of RNA-Seq has to be done manually. This introduces the possibility to have fully automatized genome annotation loops over potentially many species without incurring a loss of accuracy over a manually supervised annotation process.

bioinformatics↗