Biology subjects

Fischer, E.

Publications and source records attributed to Fischer, E..

16 recordsLinked to original sources

bioRxiv2026

Cross-Continental Analysis of Vampire Bat Betaherpesvirus Reveals Limited Interference Among Strains and Local Geographic Spread

Desmodus rotundus Betaherpesvirus (DrBHV) is a candidate vector for a transmissible vaccine targeting the circulation of rabies virus within its vampire bat reservoir. Studies assessing the potential for DrBHV as a vector have not considered its geographic range, potential for transboundary spread or how the diversity of wildtype DrBHV in natural bat populations might impede the spread of a modified vaccine strain. Here, by sequencing DrBHVs from vampire bats spanning 15 regions across 7 rabies-affected countries in Latin America and the Caribbean, we characterise the continent-scale distribution of DrBHV diversity and demonstrate widespread and apparently unconstrained co-infection. DrBHV occurred in all regions, forming a monophyletic clade consistent with a single introduction to vampire bats or host-virus co-speciation rather than frequent host switching. Phylogeographic analyses revealed cross-boundary spread that was predicted by geographic proximity. We identified 50 putative DrBHV strains and 79% of DrBHV-infected bats harboured multiple strains. No strains were over- or under-represented in co-infection and co-infections occurred proportionately to local strain prevalence. Whether strains circulated in given populations was predominantly driven by the geographic proximity of other populations containing that strain. The evolutionary relatedness of strains constrained neither rates of co-infection within individuals nor whether strains co-circulated within regions, suggesting vaccine vectors might be locally sourced rather than requiring imported, divergent strains to ameliorate interference. These results support the viability of DrBHV-vectored vaccines for mitigating rabies virus across Latin America and the Caribbean, despite widespread circulation of wildtype viruses.

genomics↗

bioRxiv2025

O-mannosylation and protein maturation check-points represent therapeutic opportunities in BRAF fusion protein oncogenesis

Fusions between protein-coding genes are common oncogenic drivers across cancers, typically pairing a proto-oncogene with partner that does not independently drive cancer. In all therapeutically actionable fusions, the proto-oncogene is the drug target, the contributions to oncogenicity of the fusion partner have largely been ignored. We studied the role of BRAF fusion partners and found that they are necessary for transformation. In the setting of KIAA1549::BRAF, the most common fusion protein across brain tumors, we found that KIAA1549 is necessary for the oncogenicity of KIAA1549::BRAF and engenders a striking and specific dependency on the protein O-mannosyltransferase complex (POMT1/2). Specifically, we show that genetic silencing or pharmacologic inhibition of the protein O-mannosyltransferase complex (POMT1/2) reverses fusion-induced transformation, thereby representing a novel and MAPK independent therapeutic target. Furthermore, POMT1/2 is required to glycosylate and enable maturation of the K::B fusion protein. These findings represent a proof-of-concept for targeting the partners in oncogenic fusions as a potential cancer therapeutic strategy.

cancer biology↗

bioRxiv2025

GRAPEVINE: A Reinforcement Failing Framework for AI-Guided Discovery of Hidden Spatial Dynamics in Adaptive Tumor Therapy

Artificial intelligence is revolutionizing scientific discovery in medicine, with reinforcement learning (RL) emerging as a promising tool for optimizing therapeutic strategies. Yet applying RL to complex scenarios such as therapy dynamics in solid tumors is constrained by the challenge of constructing training environments that are both computationally efficient and mechanistically interpretable. Here we introduce Reinforcement Failing, an AI-guided, human-in-the-loop discovery framework that shifts the focus from agent policy optimization to the refinement of the training environment itself. By combining multi-fidelity RL with group-relative performance evaluation across agent cohorts, Reinforcement Failing systematically reveals emergent mechanisms that first-principles models overlook. We apply this framework to adaptive therapy in solid tumors, which seeks to delay resistance-mediated treatment failure. In this setting, Reinforcement Failing uncovered a coupling between the mechanically driven collective motion of cells and spatially-heterogeneous proliferation that strongly influences therapy outcomes. Incorporating these emergent physical mechanisms into an augmented training environment improved cross-environment therapeutic performance and exposed potential pitfalls in translation. More broadly, these findings position Reinforcement Failing as a powerful artificial scientific discovery framework, capable of deciphering high-complexity processes at the interface of physics, machine learning, and medicine.

biophysics↗

bioRxiv2024

Uneven mitochondrial segregation during embryonic neurogenesis

Asymmetric divisions of vertebrate neural progenitors are critical for generating neurons while preserving the stem cell pool, ensuring proper central nervous system development. It was previously shown that the post-mitotic remodeling of mitochondrial activity in daughter cells influences neural fates. In this study, we demonstrate that unequal distribution of mitochondria during asymmetric mitosis plays a decisive role in triggering this differentiation process. Using live imaging to monitor mitochondrial segregation in individual progenitors and track their progenys fate within embryonic neural tissue, we show that daughter cells inheriting fewer mitochondria consistently differentiate into neurons, whereas their sibling receiving more mitochondria retains the progenitor status. Furthermore, experimental displacement of mitochondria during mitosis to force their unequal inheritance was sufficient to drive premature neuronal differentiation. Our findings establish a direct causal relationship between unequal mitochondrial inheritance and the asymmetric fate of sister cells in vivo, uncovering a key mechanism in neural development.

developmental biology↗

bioRxiv2024

CRISPR/Cas9-based somatic knock-in of reporters in the avian embryo in ovo

Gene editing and protein tagging are at the heart of modern developmental and cell biology. The advent of CRISPR/Cas9 based methods offers the possibility to develop customized approaches for genomic manipulations in non-classical experimental models. Here, we show that highly efficient somatic knock-ins of long DNA fragments can be achieved in the developing chick neural tube in ovo. We compare different types of repair matrices and different methods for the delivery of the CRISPR/Cas9 machinery, and find that an all plasmid-based approach and short arms of homology provide an easy and efficient method to achieve high frequencies of knock-in insertions with virtually no background signal. We use this method to target fluorescent reporters and dynamically monitor the subcellular distribution of endogenously expressed tagged proteins, as well as to insert the Gal4-VP16 transcription factor or the Cre recombinase at specific loci to label neural sub-populations in the chick embryonic spinal cord. Finally, we show that the method can also be applied to target the epiblast and somitic mesoderm.

developmental biology↗

bioRxiv2024

A low CDKN1c/p57kip2 expression in spinal progenitors drives the transition from proliferative to neurogenic modes of division

During vertebrate neurogenesis, a progressive transition from symmetric proliferative to asymmetric neurogenic divisions is critical to balance growth and differentiation. Using single-cell RNA-seq data from chick embryonic neural tube, we identify the cell cycle regulator Cdkn1c as a key regulator of this transition. While Cdkn1 is classically associated with neuronal cell cycle exit, we show that its expression initiates at low levels in neurogenic progenitors. Functionally targeting the onset of this expression impacts the course of neurogenesis: Cdkn1c knockdown impairs neuron production by favoring proliferative symmetric divisions. Conversely, inducing a low-level CDKN1c misexpression in self-expanding progenitors forces them to prematurely undergo neurogenic divisions. CDKN1c exerts this effect primarily by inhibiting the cyclin D-CDK complex and lengthening G1 phase duration. We propose that Cdkn1c acts as a dual driver of the neurogenic transition whose low level of expression first controls the progressive entry of progenitors into neurogenic modes of division before a higher expression mediates cell cycle exit in daughter cells. This highlights that the precise control of neurogenesis regulators expression levels sequentially imparts distinct functions, and is essential for proper neural development.

developmental biology↗

bioRxiv2024

Flumequine, a fluoroquinolone in disguise

Fluoroquinolone resistance in E. coli isolates from livestock in Europe remains high even though the EMA restricted fluoroquinolone use in animals. However, flumequine, a quinolone similar to fluoroquinolones, is still used in livestock in the Netherland, Belgium, Greece or France. Therefore, we investigated whether flumequine selects for the same resistance mechanisms in E. coli. To accomplish this, we investigated and enumerated resistant and non-resistant E. coli isolates obtained from caecal fermentation assays and from broilers exposed to different concentrations of flumequine and enrofloxacin. Flumequine usage leads to approximately 3-fold increase of resistant E. coli in the caecal fermentation, comparable with enrofloxacin. After in vitro exposure to flumequine and enrofloxacin we detected the same SNPs (S83L, D87G) in gyrA. Furthermore, the same resistance-causing SNPs were found in phenotypic resistant E. coli isolates from broilers treated with enrofloxacin and flumequine. Flumequine induces similar resistance mechanisms as enrofloxacin and restriction for use should be the same.

microbiology↗

bioRxiv2024

A tunable and versatile chemogenetic near infrared fluorescent reporter

Near-infrared (NIR) fluorescent reporters provide additional colors for highly multiplexed imaging of cells and organisms, and enable imaging with less toxic light and higher contrast and depth. Here, we present the engineering of nirFAST, a small tunable chemogenetic NIR fluorescent reporter that is brighter than top-performing NIR fluorescent proteins in cultured mammalian cells. nirFAST is a small genetically encoded protein of 14 kDa that binds and stabilizes the fluorescent state of synthetic, highly cell-permeant, fluorogenic chromophores (so-called fluorogens) that are otherwise dark when free. Engineered to emit NIR light, nirFAST can also emit far-red or red lights through change of chromophore. nirFAST allows the imaging of proteins in live cultured mammalian cells, chicken embryo tissues and zebrafish larvae. Its near infrared fluorescence provides an additional color for high spectral multiplexing. We showed that nirFAST is well-suited for stimulated emission depletion (STED) nanoscopy, allowing the efficient imaging of proteins with subdiffraction resolution in live cells. nirFAST enabled the design of a chemogenetic green-NIR fluorescent ubiquitination-based cell cycle indicator (FUCCI) for the monitoring of the different phases of the cell cycle. Finally, bisection of nirFAST allowed the design of a fluorogenic chemically induced dimerization technology with NIR fluorescence readout, enabling the control and visualization of protein proximity.

cell biology↗

bioRxiv2023

Cigarette smoking promotes the spread of antimicrobial resistance in the human lung and the environment

While immediate health risks of cigarette smoking are well-established, indirect health impacts of cigarette-derived pollutants through proliferation of antimicrobial resistance (AMR) among bacteria remain understudied. Here, exposure to cigarette smoke condensate at relevant concentrations resulted in >2-fold elevated transfer rates of a multi-drug-resistance encoding plasmid between Pseudomonas strains in artificial lung sputum medium. This effect was connected to elevated reactive oxygen species production as part of the bacterial stress response when exposed to cigarette-derived toxicants. Similar results were obtained under exposure to cigarette ash leachate in environmental medium. Further, used cigarette filters enriched in toxic residues were submerged in a wastewater stream, and colonized by altered microbial communities compared to unused filters. These communities were significantly enriched in pathogens and AMR. Hence, filters could facilitate hitchhiking of high-risk bacteria to novel environments. We demonstrate that cigarette-derived compounds can promote the spread of AMR within the human lung and natural environments.

microbiology↗

bioRxiv2023

Anopheles salivary apyrase regulates blood meal hemostasis and drives malaria parasite transmission

Mosquito salivary proteins play a crucial role in regulating hemostatic responses at the bite site during blood feeding. In this study, we investigate the function of Anopheles gambiae salivary apyrase (AgApyrase) in Plasmodium transmission. Our results demonstrate that salivary apyrase interacts with and activates tissue plasminogen activator, facilitating the conversion of plasminogen to plasmin, a human protein previously shown to be required for Plasmodium transmission. Microscopy imaging shows that mosquitoes ingest a substantial amount of apyrase during blood feeding which reduces coagulation in the blood meal by enhancing fibrin degradation and inhibiting platelet aggregation. Supplementation of Plasmodium infected blood with apyrase significantly enhanced Plasmodium infection in the mosquito midgut. In contrast, AgApyrase immunization inhibited Plasmodium mosquito infection and sporozoite transmission. This study highlights a pivotal role for mosquito salivary apyrase for regulation of hemostasis in the mosquito blood meal and for Plasmodium transmission to mosquitoes and to the mammal host, underscoring the potential for new strategies to prevent malaria transmission.

microbiology↗

bioRxiv2023

A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms.

Knowledge of who infected whom during an outbreak of an infectious disease is important to determine risk factors for transmission and to design effective control measures. Both whole-genome sequencing of pathogens and epidemiological data provide useful information about the transmission events and underlying processes. Existing models to infer transmission trees usually assume that the pathogen is introduced only once from outside into the population of interest. However, this is not always true. For instance, SARS-CoV-2 is suggested to be introduced multiple times in mink farms in the Netherlands from the SARS-CoV-2 pandemic among humans. Here, we developed a Bayesian inference method combining whole-genome sequencing data and epidemiological data, allowing for multiple introductions of the pathogen in the population. Our method does not a priori split the outbreak into multiple phylogenetic clusters, nor does it break the dependency between the processes of mutation, within-host dynamics, transmission, and observation. We implemented our method as an additional feature in the R-package phybreak. On simulated data, our method identifies the number of introductions with high accuracy. Moreover, when a single introduction was simulated, our method produces similar estimates of parameters and transmission trees as the existing package. When applied to data from a SARS-CoV-2 outbreak in Dutch mink farms, the method provides strong evidence for 13 introductions, which is 20 percent of all infected farms. Using the new feature of the phybreak package, transmission routes of a more complex class of infectious disease outbreaks can be inferred which will aid infection control in future outbreaks.

evolutionary biology↗

bioRxiv2022

Multi-omic profiling of breast cancer cells uncovers stress MAPK-associated sensitivity to AKT degradation

Over 50% of human tumors display hyperactivation of the serine/threonine kinase AKT. Despite evidence of clinical efficacy, there remains scope to improve upon the therapeutic window of the current generation of AKT inhibitors. Here we report the development of a second-generation AKT degrader, INY-05-040, which outperformed catalytic AKT inhibition with respect to cellular suppression of AKT-driven phenotypes in breast cancer cell lines. A systematic growth inhibition screen across 288 cancer cell lines confirmed a substantially higher potency for INY-05-040 (median GI50adj = 1.1 {micro}M) compared to our first-generation AKT degrader (INY-03-041; median GI50adj = 3.1 {micro}M), with both compounds outperforming catalytic AKT inhibition with GDC-0068 (median GI50adj > 10 {micro}M). Using multi-omic profiling and causal network integration in breast cancer cells, we demonstrate that the enhanced efficacy of INY-05-040 is associated with sustained suppression of AKT signaling, followed by a potent induction of the stress mitogen activated protein kinase (MAPK) c-Jun N-terminal kinase (JNK). Further integration of growth inhibition assays with publicly available transcriptomic, proteomic, and reverse phase protein array (RPPA) measurements established low baseline JNK signaling as a biomarker for breast cancer sensitivity to AKT degradation. Collectively, our study presents a systematic framework for mapping the network-wide signaling effects of therapeutically relevant compounds, and identifies INY-05-040 as a potent pharmacological suppressor of AKT signaling.

cancer biology↗

bioRxiv2021

An engineered multifunctional protein tag for advanced fluorescence imaging

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we present the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of live-cell compatible fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. We showed that the ability to tune the fluorescence color and properties through simple molecular modulation provides an unprecedent experimental versatility for imaging proteins in live cells, including delicate cultured hippocampal neurons, and in multicellular organisms. The ability to tune the spectral properties and fluorescence performance enables to match the spectral specifications and requirements of the most advanced imaging techniques, and allowed us to achieve efficient stimulated emission depletion (STED) nanoscopy of fusion proteins in live cells and live primary cultured neurons.

molecular biology↗

bioRxiv2020

Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2

An outbreak of a novel coronavirus, now named SARS-CoV-2, causing respiratory disease and a [~]2% case fatality rate started in Wuhan, China in December 2019. Following unprecedented rapid global spread, the World Health Organization declared COVID-19 a pandemic on March 11, 2020. Although data on disease in humans are emerging at a steady pace, certain aspects of the pathogenesis of SARS-CoV-2 can only be studied in detail in animal models, where repeated sampling and tissue collection is possible. Here, we show that SARS-CoV-2 causes respiratory disease in infected rhesus macaques, with disease lasting 8-16 days. Pulmonary infiltrates, a hallmark of human disease, were visible in lung radiographs of all animals. High viral loads were detected in swabs from the nose and throat of all animals as well as in bronchoalveolar lavages; in one animal we observed prolonged rectal shedding. Taken together, the rhesus macaque recapitulates moderate disease observed in the majority of human cases. The establishment of the rhesus macaque as a model of COVID-19 will increase our understanding of the pathogenesis of this disease and will aid development and testing of medical countermeasures.

microbiology↗

bioRxiv2018

Individuals with 22q11.2 deletion syndrome show intact prediction but reduced adaptation in responses to repeated sounds: evidence from Bayesian mapping

Background: One of the most common copy number variants, the 22q11.2 microdeletion, confers a increased risk for schizophrenia. Since schizophrenia has been associated with an aberrant neural response to repeated stimuli through both reduced adaptation and prediction, we here hypothesized that this may also be the case in nonpsychotic individuals with a 22q11.2 deletion. Methods: We recorded high-density EEG from 19 individuals with 22q11.2 deletion syndrome (12-25 years), as well as 27 healthy volunteers with comparable age and sex distribution, while they listened to a sequence of sounds arranged in a roving oddball paradigm. Using posterior probability maps and dynamic causal modelling we tested three different models accounting for repetition dependent changes in cortical responses as well as in effective connectivity; namely an adaptation model, a prediction model, and a model including both adaptation and prediction. Results: Repetition-dependent changes were parametrically modulated by a combination of adaptation and prediction and were apparent in both cortical responses and in the underlying effective connectivity. This effect was reduced in individuals with a 22q11.2 deletion and was negatively correlated with negative symptom severity. Follow-up analysis showed that the reduced effect of the combined adaptation and prediction model seen in individuals with 22q11.2 deletion was driven by reduced adaptation rather than prediction failure. Conclusions: Our findings suggest that adaptation is reduced in individuals with a 22q11.2 deletion, which can be interpreted in light of the framework of predictive coding as a failure to suppress prediction errors.

neuroscience↗

bioRxiv2018

Losing maternal care: Neotenic gene expression in the preoptic area of avian brood parasites

Parental care for is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species were compared. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in maternal behavior across vertebrates. Using comparative transcriptomic approaches, we identified gene expression patterns associated with brood parasitism and evaluated two alternative explanations for the evolution of brood parasitism: reduced expression of parental-related genes in the POA versus retention of juvenile (neotenic) gene expression. While we did not find evidence for large scale gene downregulation, expression patterns did reflect substantial evidence for neotenic POA gene expression in parasitic birds. Differentially expressed genes with previously established roles in parental care were identified. Targeted examination of these selected candidate genes in additional hypothalamic regions revealed species differences in gene expression patterns is not POA-specific. Together, these results provide new insights into neurogenomics underlying maternal behavior loss in avian brood parasites.

animal behavior and cognition↗