Biology subjects

Varga, V.

Publications and source records attributed to Varga, V..

13 recordsLinked to original sources

bioRxiv2026

Hippocampo-septal inhibitory feedback controls the medial septal circuit as a function of brain state, pyramidal cell activity and movement speed.

Encoding novel experiences and retrieving stored information rely on the hippocampal theta rhythm in several mammalian species. Coordination of putative pacemakers in the medial septum (MS) by the GABAergic hippocampo-septal (HS) feedback is hypothesized to be essential for theta genesis. In order to reveal how the HS-feedback controls the MS circuit, and through it hippocampal oscillations in general, we set out to uncover the behavior-related activity of HS neurons as well as how different components of the MS network are regulated by the HS-feedback. Utilizing computational modelling and in vivo optogenetic manipulation of the HS pathway, we show that the HS feedback is not required for theta generation, which is primarily governed by intra-MS connections. HS blockade did not alter the phase coupling of MS neurons to hippocampal theta rhythm nor the synchrony between rhythmic MS neurons but augmented ongoing theta and coupled mid-gamma oscillations in the hippocampus. By contrast, correlated activity between non-rhythmic MS neurons was sensitive to HS blockade. Moreover, the HS feedback scaled with hippocampal activity and running speed. In turn, modulation of MS neurons by running and ripples was diminished by the transient suppression of HS terminals. These findings suggest that the HS feedback exerts inhibitory control of the MS depending upon hippocampal output and movement speed.

neuroscience↗

bioRxiv2026

A preclinical resistance framework discovers the virulence risks of antibiotics in development

Several new antibiotics target multidrug-resistant pathogens, yet resistance is still evaluated mainly by drug-susceptibility, leaving consequences for bacterial pathogenicity poorly understood. Here, we develop a framework integrating resistance evolution, genomic surveillance and host-pathogen phenotyping to classify antibiotics by resistance potential and pathogenic consequences. Applying this framework to Klebsiella pneumoniae identified functionally distinct antibiotic candidates associated with elevated virulence risk. Resistance evolution rapidly increased virulence through clinically-relevant mutations, without direct selection for pathogenicity. Despite distinct genetic routes, resistance converged on cell-envelope rewiring. A single resistance mutation increased epithelial adhesion, intracellular colonization, macrophage immune-evasion, and tissue persistence in murine infection models, transforming K. pneumoniae into a more invasive and cytotoxic pathogen. Risk-profile analysis revealed partial decoupling of resistance and pathogenicity, with some low-resistance antibiotics yielding highly-virulent populations. These findings establish resistance-driven virulence as an underappreciated translational hazard and call for incorporating host-pathogen interactions into resistance surveillance and preclinical antibiotic development.

microbiology↗

bioRxiv2026

DeltaMut: An Integrative Database of AlphaFold2-Derived Missense Variant Structures

The widespread use of next-generation sequencing has led to a surge in the number of identified variants with uncertain effects on protein function. These variants pose a significant challenge in diagnostics and hinder patient treatment strategies. Numerous variant effect predictors (VEPs) are available to assess variant impact, but they primarily rely on sequence-derived information. The recent development of AlphaFold2 has raised questions about whether information retrieved from wild-type or predicted structures of missense variants can improve the predictive power of these algorithms. While the AlphaFold Protein Structure Database serves as a valuable resource for wild-type protein structures, a large-scale collection of missense variant structures is not available, limiting current efforts to wild-type conformations and a handful of modeled variants. To address this limitation, we developed DeltaMut, a comprehensive database containing over 77,000 protein structures, including 65,000 pathogenic and neutral missense variants. All structural models were generated using ParaFold, a high-performance computing-optimized implementation of AlphaFold2. The large-scale and systematic generation of variant protein structures distinguish DeltaMut as a unique resource for both expansive statistical studies and detailed, case-specific investigations of variant-induced structural changes. Furthermore, the DeltaMut database is freely accessible without registration. HighlightsO_LIDeltaMut is currently the largest database of AlphaFold2-predicted variant structures. C_LIO_LIContains 77,713 structures covering 12,101 wild-type and 65,612 variant proteins. C_LIO_LI70.6% of predicted structures have high or very high confidence (pLDDT [≥] 70). C_LIO_LIFreely accessible web server with visualization and download of variant models. C_LI

bioinformatics↗

bioRxiv2026

Assessing the impact of parental linear gene normalization on the performance of statistical models for circular RNA differential expression analysis

BackgroundCircular RNAs (circRNAs) emerged as promising non-invasive cancer biomarkers due to their stability, abundance in body fluids, and regulatory potential. However, circRNA differential expression analysis (DEA) remains challenging, largely owing to lack of consensus on important preprocessing strategies such as filtering and normalization. While well-established bulk RNA-sequencing frameworks are commonly applied to circRNA data, newer approaches such as CIRI-DE (part of CIRI3 suite) integrate both linear and circular transcript information to improve detection. Despite developments, an assessment of these integrative strategies is lacking, and the critical impact of filtering on DEA model performance has not been comprehensively evaluated. ResultsIn this study, we evaluated the impact of multiple normalization and filtering strategies on circRNA DEA using five experimental datasets, including two in-house blood platelet sets and semi-parametric simulated in silico datasets. Our results emphasize the importance of selecting an appropriate filtering threshold, as overly lenient filtering substantially reduced model performance across datasets. We found edgeRs filterByExpr() strategy particularly effective in handling zero counts in circRNA data, while also generating the most reliable results across most datasets. Furthermore, by incorporating linear and circular information as described in CIRI-DE, most methods identified a higher number of differentially expressed (DE) circRNAs compared to circular counts alone. Notably, circRNAs identified by both CIRI-DE and the modified bulk RNA-sequencing pipelines showed substantial overlap. ConclusionOur findings demonstrate that automated filtering combined with linear-aware normalization significantly enhances the sensitivity and reproducibility of circRNA DEA, providing a standardized framework for more reliable biomarker discovery in transcriptomic research.

bioinformatics↗

bioRxiv2025

Flagellar pocket collar biogenesis: Cytoskeletal organization and novel structures in a unicellular parasite

Understanding how cells build and organize their internal structures is a fundamental question in biology, with important implications for human health and disease. Trypanosomes are single-celled flagellated parasites that cause life-threatening diseases in human and animals. Their survival relies on a specialized compartment called the flagellar pocket (FP), which serves as a gateway for nutrient uptake, and immune evasion. The formation and function of the FP are supported by an intricate cytoskeletal structure known as the flagellar pocket collar (FPC). However, the mechanisms underlying its assembly remain poorly understood. In this study, we used cutting-edge ultrastructure expansion microscopy (U-ExM) to investigate FPC biogenesis in Trypanosoma brucei. We mapped the formation of the new microtubule quartet (nMtQ) alongside flagellum growth, providing new insights into its assembly. Additionally, we tracked the localization dynamics of key structural proteins - BILBO1, MORN1, and BILBO2 - during the biogenesis of the FPC and the hook complex (HC). Notably, we identified two previously undetected structures: the proFPC and the transient FPC-interconnecting fibre (FPC-IF), both of which appear to play crucial roles in linking and organizing cellular components during cell division. By uncovering these novel aspects of FPC biogenesis, our study significantly advances the understanding of cytoskeletal organization in trypanosomes and opens new avenues for exploring the functional significance of these structures.

microbiology↗

bioRxiv2025

Kinesin-3 KIF14 Regulates Intraflagellar Transport Dynamics in Primary Cilia

The primary cilium is an antenna-like organelle that plays a crucial role in development and homeostasis. Its growth and functions depend on the transport of cargo from the cilia base to the tip by intraflagellar transport (IFT) proteins and kinesin-2 motors. Primary cilia exhibit great variation in morphology and function across cell types and organisms. This diversity is thought to be conferred by the modulation of IFT by additional factors. However, examples of such non-canonical regulators, such as kinesin motors distinct from kinesin-2, are sparse. Thus, the involvement of non-canonical ciliary kinesins in intraciliary transport is unclear. Here, we show that a poorly characterized member of the kinesin-3 family, KIF14, plays a prominent role in primary cilia trafficking in human cells. Using live cell imaging and expansion microscopy, we demonstrate that KIF14 depletion leads to impaired IFT. Furthermore, using TIRF microscopy we show that the motility of KIF14 and its effects on cilia trafficking rely on the motor domain of KIF14, which drives the processive runs along the ciliary axoneme in cells and in vitro, in co-operation with the C-terminal CC1 domain. Finally, we demonstrate that C-terminal truncations of KIF14, including patient mutation Q1380x, disrupt IFT by causing traffic jam-like accumulations of ciliary components in the distal part of the primary cilia, leading to bulged tips of cilia. In summary, our data exemplify the role of a non-canonical ciliary kinesin in the regulation of ciliary trafficking and suggest a new paradigm for how kinesin-related trafficking defects may contribute to the pathology of disorder with a ciliary contribution.

cell biology↗

bioRxiv2025

A novel approach to tagging tubulin reveals microtubule assembly dynamics of the axoneme in Trypanosoma brucei

The protozoan parasite Trypanosoma brucei is a mono-flagellated cell during the G1-phase of its cell cycle. In order to duplicate, it assembles a new flagellum alongside the mature one, in which further elongation is prevented. Our group proposed a model where the mature flagellum is locked after construction to full length (Bertiaux et al. 2018) and access of new building blocks for elongation is exclusive to the new flagellum. To test this hypothesis directly, we developed a tool for the inducible expression of tagged tubulin. Alpha-tubulin that was tagged with an intragenic Ty-1-epitope behaved indistinguishable from untagged tubulin. Its incorporation was monitored after inducible expression, to follow the assembly dynamics of microtubules in the cell body, the mitotic spindle and the flagellum. In this study we observed that integration of tubulin occurs at the distal flagellum tip at a linear rate and is indeed restricted to the new flagellum in bi-flagellated cells. This is direct evidence that trypanosomes avoid competition between the two flagella by allowing tubulin incorporation only in the new organelle. However, by tracing flagella over several cell cycles we could also show that mature flagella do not remain locked indefinitely. The restriction is lifted briefly after the bi-flagellated cell has divided and the daughter cell inheriting the old flagellum shows incorporation of newly synthesized building blocks again. It then has to lock again before the cell can assemble a new flagellum. Our findings suggest regular incorporation of tubulin at the tip of previously locked flagella. This evidence was supported with an orthogonal approach, with which we monitored the incorporation of HaloTag-tagged radial spoke protein 4/6. Since flagellum length in trypanosomes is stable, this indicates that the entire axoneme is subject to regular events of transient disassembly followed by assembly at its distal tip.

cell biology↗

bioRxiv2024

Nimodipine reduces microglial activation in vitro as evidenced by morphological phenotype, phagocytic activity and next generation RNA sequencing

BackgroundNimodipine, an L-type voltage-gated calcium channel blocker, achieves vasorelaxation by suppressing Ca2+-dependent activation of cerebrovascular smooth muscle cells and is used to prevent delayed ischemic deficit following subarachnoid hemorrhage. Our preclinical drug repurposing studies raised the possibility that nimodipine may attenuate the pro-inflammatory shift in microglial function in response to brain injury. We analyzed the effects of nimodipine on activated microglia at the level of morphological and functional phenotypes, as well as their transcriptomic profile. MethodsLive brain slice preparations from C57BL/6 mice and primary microglia cultures from the cortex of neonatal Sprague Dawley rats were used. Brain slices were subjected to ischemia, and microglial cultures were activated with lipopolysaccharide (LPS; 20 ng/ml). Both preparations were treated with nimodipine (5-10-20 M). The degree of arborization was evaluated in Iba1-stained microglia and expressed as a transformation index (TI). Phagocytic activity of cultured microglia was visualized using fluorescent microbeads. TNF levels in the cultures were measured with ELISA. Total RNA was isolated from microglia and processed for next generation RNA sequencing to determine differentially expressed genes. ResultsNimodipine suppressed the ameboid morphological transformation and increased phagocytosis triggered by ischemia in brain slices and LPS in microglia cultures. At the transcriptional level, LPS resulted in a pro-inflammatory microglial phenotype, affecting the expression of cytokines, the complement system and phagocytosis-related genes. Focusing on the role of calcium in microglial activation, LPS increased RNA transcription of ionotropic purinergic and some TRP channels but decreased the expression of voltage- and ligand-gated calcium channels. In the endoplasmic reticulum, LPS downregulated gene expression of Ryr and IP3 receptors and increased transcription of the SERCA calcium pump gene. Nimodipine co-administered with LPS altered the expression of 110 genes in the opposite direction to LPS activation, of which at least 20 were associated with microglial immune response, 7 with cell adhesion and 2 with autophagy regulation. ConclusionThe effect of nimodipine goes beyond cerebral vasorelaxation. Nimodipine attenuates microglial activation by modulating Ca2+-dependent gene expression involved in intracellular signaling cascades to drive microglial immune responses. Consideration should be given to expanding the medical field of indication of nimodipine.

neuroscience↗

bioRxiv2022

ULK4 and Fused/STK36 interact to mediate assembly of a motile flagellum

Unc-51-like kinase (ULK) family serine-threonine protein kinase homologs have been linked to the function of motile cilia in diverse species. Mutations in Fused/STK36 and ULK4 in mice resulted in hydrocephalus and other phenotypes consistent with ciliary defects. How either protein contributes to the assembly and function of motile cilia is not well understood. Here we studied the phenotypes of ULK4 and Fused gene knockout (KO) mutants in the flagellated protist Leishmania mexicana. Both KO mutants exhibited a variety of structural defects of the flagellum cytoskeleton. Biochemical approaches indicate spatial proximity of these proteins and indicates a direct interaction between the N-terminus of LmxULK4 and LmxFused. Both proteins display a dispersed localisation throughout the cell body and flagellum, with enrichment near the flagellar base and tip. Fused/STK36 was previously shown to localise to mammalian motile cilia and we demonstrate here that ULK4 also localises to the motile cilia in mouse ependymal cells. Taken together these data suggest a model where the pseudokinase ULK4 is a positive regulator of the kinase Fused/STK36 in a pathway required for stable assembly of motile cilia. Summary StatementKnockout phenotypes in Leishmania, and confirmation of ULK4 ciliary localisation in mouse, show ULK4 and Fused/STK36 interact in a conserved pathway for stable assembly of motile cilia.

cell biology↗

bioRxiv2021

Trypanosome morphogenesis involves recruitment of a pleckstrin homology domain protein by an orphan kinesin to the microtubule quartet

Kinesins are motor proteins found in all eukaryotic lineages that move along microtubules to mediate cellular processes such as mitosis and intracellular transport. In trypanosomatids, the kinesin superfamily has undergone a prominent expansion, resulting in one of the most diverse kinesin repertoires that includes the two kinetoplastid-restricted families X1 and X2. Here, we characterize in Trypanosoma brucei TbKifX2A, an orphaned X2 kinesin. TbKifX2A tightly interacts with TbPH1, a kinesin-like protein with a likely inactive motor domain, a rarely reported occurrence. Both TbKifX2A and TbPH1 localize to the microtubule quartet (MtQ), a characteristic but poorly understood cytoskeletal structure that wraps around the flagellar pocket as it extends to the cell body anterior. The proximal proteome of TbPH1 revealed two other interacting proteins, the flagellar pocket protein FP45 and intriguingly another X2 kinesin, TbKifX2C. Simultaneous ablation of TbKifX2A/TbPH1 results in the depletion of FP45 and TbKifX2C and also an expansion of the flagellar pocket, among other morphological defects. TbKifX2A is the first motor protein to be localized to the MtQ. The observation that TbKifX2C also associates with the MtQ suggests that the X2 kinesin family may have co-evolved with the MtQ, both kinetoplastid-specific traits.

molecular biology↗

bioRxiv2021

Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites

Expansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major, which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to rapidness of image acquisition and 3D reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic, and multivesicular tubule-associated microtubules of L. major. We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. 3D reconstruction of an entire volume of these cells provided details on morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.

cell biology↗

bioRxiv2021

Huygens synchronization of medial septal pacemaker neurons generates hippocampal theta oscillation

Episodic learning and memory retrieval are critically dependent on a hippocampal 4-12 Hz oscillatory clock signal, the theta oscillation. This clock is largely externally paced, by a network of GABAergic neurons in the medial septum (MS). Theoretical studies suggested a range of hypotheses how this network may achieve theta synchrony; however, experimental evidence is still lacking. By recording multiple single MS neurons and hippocampal local field potential oscillations simultaneously, with both acute and chronically implanted silicon probes, we show that MS pacemaker units oscillate at individual frequencies within the theta range in rodents. Synchronization of MS neuron frequencies, accompanied by an elevation of firing rates, was found to parallel hippocampal theta formation in multiple rodent model systems. This suggests a general mechanism for theta synchronization, akin to the synchronization of weakly coupled pendulum clocks observed by Huygens in the 17th century. We optogenetically identified the MS pacemaker units as parvalbumin-expressing GABAergic neurons, while the previously enigmatic MS glutamatergic neurons were mostly theta-activated non-rhythmic cells. Our data were consistent with a network model of partially connected single-compartment inhibitory pacemaker neurons, in which synchronization and de-synchronization in the frequency domain upon waxing and waning tonic excitatory drive was sufficient to toggle MS network output between theta and non-theta states. These results provide experimental and theoretical support to a frequency-synchronization mechanism for pacing hippocampal theta, which may serve as an inspirational prototype for the countless examples of synchronization processes in the central nervous system from Nematoda to Anthropoda to Chordate and Vertebrate phyla.

neuroscience↗

bioRxiv2019

Ultrafast Readout of Representations from Spatially Distributed Rodent Hippocampal Field Potentials

Spatiotemporal patterns of large-scale spiking and field potentials of the rodent hippocampus encode spatial representations during maze run, immobility and sleep. Here, we showed that multi-site hippocampal field potential amplitude at ultra-high frequency band (FPAuhf) provides not only a fast and reliable reconstruction of the rodents position in wake, but also a readout of replay content during sharp wave ripples. This FPAuhf feature may serve as robust real-time decoding strategy from large-scale (up to 100,000 electrodes) recordings in closed-loop experiments. Furthermore, we developed unsupervised learning approaches to extract low-dimensional spatiotemporal FPAuhf features during run and ripple periods, and to infer latent dynamical structures from lower-rank FPAuhf features. We also developed a novel optical flow-based method to identify propagating spatiotemporal LFP patterns from multi-site array recordings, which can be used for decoding application. Finally, we developed a prospective decoding strategy to predict animals future decision in goal-directed navigation.

neuroscience↗