Biology subjects

Nagy, E.

Publications and source records attributed to Nagy, E..

13 recordsLinked to original sources

bioRxiv2026

Anthropogenic gradients shape Staphylococcus/Mammaliicoccus communities: Bacterial composition and resistance patterns as indicators of landscape hemeroby

Antimicrobial resistance (AMR) is one of the greatest challenges within the One Health continuum. Exploring transmission routes between health domains and determining their driving forces are key priorities for future research. This effort can be effectively supported by landscape epidemiology, a field of science that integrates methods from landscape ecology and epidemiology to unravel the complex interdependencies behind disease transmission. This exploratory study aimed to demonstrate that landscape diversity and the degree of hemeroby (anthropogenic impact) correlate with the composition of bacterial communities and their AMR profiles. To test this hypothesis, submandibular lymph nodes from Cervidae and Suidae were collected to detect Staphylococcus and Mammaliicoccus bacteria and characterise their AMR features using selective culture and the VITEK 2 Compact automated system. As a result, the bacterial community in the more natural landscape was more diverse, characterised by the dominance of Mammaliicoccus sciuri and pan-susceptible isolates of Staphylococcus hyicus, and it displayed a low-level, heterogeneous AMR profile. Within the more hemerobic landscape, the bacterial community was characterised by the dominance of Staphylococcus epidermidis, a human-adapted species, and the AMR profile showed signs of higher antimicrobial pressure from both public health and veterinary origins. Although this study was based on only two study sites and was therefore not suitable for drawing definite conclusions, the findings suggest that human impact manifests itself in both bacterial and AMR profiles. A high prevalence of mammaliicocci and a heterogeneous AMR profile appeared to be indicators of naturalness. Conversely, the dominance of a human-adapted bacterial species and the accumulation of AMR features characteristic of medical environments likely indicate higher degrees of hemeroby.

ecology↗

bioRxiv2026

Climate change and socioeconomic vulnerability: The Carpathian Basin as a potential hotspot in the dissemination of Dirofilaria repens in Europe

BackgroundDirofilaria repens is a zoonotic parasite expanding unnoticed across Europe due to climate change. We hypothesised that in this process, the Carpathian Basin has a facilitating effect. MethodsUsing 426 georeferenced European cases, the probability of infection occurrence was determined in relation to climatic factors, surface water availability, regional social deprivation, and stray dog population density. To analyse the potential impacts of ecological and social factors (deprivation and stray dog population density), the MaxEnt algorithm, and spatial Empirical Bayes smoothing and Bivariate Local Indicators of Spatial Association (BiLISA) index calculation were employed, respectively. ResultsMaxEnt analysis revealed that the mean warmest month temperature (22.8 - 25.1 {degrees}C), winter mean minimum temperature (> -2.1 {degrees}C), and summer precipitation (28.6 - 231 mm) have the strongest impact on the probability of the parasites occurrence in Europe. Social factors have significance in the eastern Balkans and the Carpathian Basin, but not in Western Europe. The Carpathian Basin appears to be a hotspot, similar to Mediterranean coastal areas. Furthermore, the Danube Valley acts as an ecological corridor for subtropical vector-borne parasites. ConclusionsOur findings confirm that summer warmth is the primary ecological driver of the parasites range expansion, which is facilitated by the Carpathian Basin due to climatic and socioeconomic conditions.

ecology↗

bioRxiv2026

Reconstructing the hyphosphere using a hyphal release-capture soil microcosm

Fungal hyphae form spatially confined interfaces in soil that mediate close associations with bacteria, collectively referred to as the hyphosphere. Despite its recognized ecological importance, experimental access to hyphosphere-associated microbial communities under realistic soil and plant-associated conditions has remained limited. Here, we present a soil-mimetic microcosm that enables controlled reconstruction and recovery of hyphosphere bacterial communities embedded within plant-associated soil. The system integrates field-derived soil, a native soil microbial inoculum, living cotton seedlings, and a spatially constrained fungal inoculum housed within sterile cell-strainer assemblies, permitting hyphal extension into soil while preserving a recoverable fungal-soil boundary. Using the soil-borne plant pathogen Fusarium oxysporum f. sp. vasinfectum as a model filamentous fungus, we show that the microcosm enables reproducible recovery of hypha-associated soil microaggregates containing physically attached bacterial cells. Full-length 16S rRNA profiling revealed pronounced reductions in bacterial richness and evenness in hyphosphere samples relative to bulk and rhizosphere soils, consistent with recruitment of a restricted subset of the surrounding microbiota. Ordination analyses demonstrated clear compositional separation between soil and hyphosphere compartments, with convergence of hypha-associated communities across bulk and rhizosphere contexts. Phylogenetic turnover analyses indicated phylogenetic structuring, whereas taxonomic analyses identified a conserved set of bacterial genera consistently associated with hyphae alongside compartment-specific taxa influenced by soil and plant context. Together, these findings establish the novel hyphal release-and-capture microcosm as a reproducible, ecologically grounded platform for studying hyphosphere-associated bacterial communities in plant-associated soils.

microbiology↗

bioRxiv2025

Amino acid exchangeability and surface accessibility underpin the effects of single substitutions

Deep mutational scans have measured the effects of many mutations on many different proteins. Here we use a collection of such scans to perform a statistical meta-analysis of the effects of single amino acid substitutions. Specifically, we model the relative deleteriousness of each substitution in each deep mutational scan with respect to the identities of the wildtype and mutant residues, and the wildtype residues surface accessibility. This model explains much of the variance in mutational effects and quantifies physicochemical trends underlying them, including by yielding an empirical amino acid exchangeability matrix.

bioinformatics↗

bioRxiv2025

A Hit Prioritization Strategy for Compound Library Screening Using LiP-MS and Molecular Dynamics Simulations Applied to KRas G12D Inhibitors

An important step in screening small molecule libraries for drug discovery is hit prioritization and validation to rule out false positives, which is usually performed using biochemical and biophysical assays. The development of orthogonal assays that are highly sensitive and can accelerate the hit-to-lead process is valuable. Limited proteolysis combined with mass spectrometry (LiP-MS) is a technique used to study changes in protein structure upon ligand binding. In LiP-MS, proteins are exposed to low concentrations of proteases under native conditions. The resulting proteolytic pattern is sensitive to protein structure at the cleavage site, which can change upon ligand binding. We characterized the interaction of small molecule inhibitors of the KRas G12D mutant oncoprotein by LiP-MS combined with molecular dynamics (MD). Intact mass spectrometry and top-down analysis were used to detect and identify KRas G12D cleavage products in the presence and absence of inhibitors, thereby locating the cleavage sites in the protein. Cleavage sites protected upon compound binding correlated well with the switch II binding site. The degree of cleavage depends on binding affinity and the presence of specific functional groups in the inhibitors structure. A comparison of MD simulations for the ligand-free and ligand-bound proteins revealed the atomistic mechanisms by which the cleavage sites, located in flexible and disordered regions, are stabilized upon compound binding. We suggest that LiP-MS combined with MD (LiP-MS-MD) could be valuable in small molecule screening campaigns and add to the repertoire of available methods for high-quality hit selection in early-stage drug discovery.

biophysics↗

bioRxiv2025

Characterization of the KRas G12D-inhibitor interactions by HDX-MS and molecular dynamics simulations

Hydrogen-deuterium exchange (HDX) combined with mass spectrometry (MS) is a powerful technique for studying changes in protein structure and dynamics upon ligand binding. Protein-ligand complexes can result in increased protection of peptide-bond amides in HDX indicating protein structure stabilization. We have characterized the interaction of lead inhibitor candidates towards the KRas G12D oncoprotein by intact protein and bottom-up HDX-MS in combination with molecular dynamics (MD) simulations. Significant differences in HDX protection were detected upon inhibitor binding in the flexible switch-II pocket of the protein. We identified a correlation between ligand binding affinities and corresponding changes in protection. MD simulations of the free and inhibitor-bound KRas G12D proteins revealed changes in the hydrogen bond network of backbone amides in the switch-II region upon inhibitor binding, explaining the observed HDX protection. This combined HDX-MS and MD analysis approach provides a mechanistic picture of the KRas G12D protein-inhibitor interactions and may be a useful tool for future drug design efforts.

biophysics↗

bioRxiv2022

Evaluation of acaricidal activity of lithium-chloride against Tetranychus urticae (Acari: Tetranychidae)

Tetranychus urticae is a severe threat and a major source of yield loss in some agricultural and horticultural crops. Control is greatly complicated due to the hidden lifestyle of the species. In addition to its direct damage, it is considered a vector for several viruses. The number of active substances used against it is limited, and the development of resistance means that sustainable control is not achieved. Therefore, there is a continuous need for new active substances. Lithium salts have been shown to be a promising alternative to control Varroa destructor, an apicultural mite pest. Therefore, in the present study, we investigated whether the contact efficacy of lithium chloride extends to other agricultural mite pests, such as the two-spotted spider mite. In the present pilot study, we report for the first time that the efficacy of lithium chloride extends to the two-spotted spider mite, showing 100% mortality at concentrations of 5.52 M, 2.76 M, and 1.38 M. It is to note, however, that the experiments did not cover residue and practical application aspects, and further extensive studies are needed in this area to clarify the relevance of the practical sub-classification.

zoology↗

bioRxiv2020

The Anti-histamine Azelastine, Identified by Computational Drug Repurposing, Inhibits SARS-CoV-2 Infection in Reconstituted Human Nasal Tissue In Vitro

BackgroundThe COVID-19 pandemic is an enormous threat for healthcare systems and economies worldwide that urgently demands effective preventive and therapeutic strategies. Unlike the development of vaccines and new drugs specifically targeting SARS-CoV-2, repurposing of approved or clinically tested drugs can provide an immediate solution. MethodsWe applied a novel computational approach to search among approved and clinically tested drugs from the DrugBank database. Candidates were selected based on Shannon entropy homology and predefined activity profiles of three small molecules with proven anti-SARS-CoV activity and a published data set. Antiviral activity of a predicted drug, azelastine, was tested in vitro in SARS-CoV-2 infection assays with Vero E6 monkey kidney epithelial cells and reconstituted human nasal tissue. The effect on viral replication was assessed by quantification of viral genomes by droplet digital PCR. FindingsThe computational approach with four independent queries identified major drug families, most often and in overlapping fashion anti-infective, anti-inflammatory, anti-hypertensive, anti-histamine and neuroactive drugs. Azelastine, an histamine 1 receptor-blocker, was predicted in multiple screens, and based on its attractive safety profile and availability in nasal formulation, was selected for experimental testing. Azelastine significantly reduced cytopathic effect and SARS-CoV-2 infection of Vero E6 cells with an EC50 of [~]6 M both in a preventive and treatment setting. Furthermore, azelastine in a commercially available nasal spray tested at 5-fold dilution was highly potent in inhibiting viral propagation in SARS-CoV-2 infected reconstituted human nasal tissue. InterpretationsAzelastine, an anti-histamine, available in nasal sprays developed against allergic rhinitis may be considered as a topical prevention or treatment of nasal colonization with SARS-CoV-2. As such, it could be useful in reducing viral spread and prophylaxis of COVID-19. Ultimately, its potential benefit should be proven in clinical studies. Fundingprovided by the Hungarian government to the National Laboratory of Virology and by CEBINA GmbH.

microbiology↗

bioRxiv2020

Development of Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (EFdA) by Wild-Type and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1

4-ethynyl-2-fluoro-2-deoxyadenosine (EFdA, MK-8591, islatravir) is a nucleoside reverse transcriptase translocation inhibitor (NRTTI) with exceptional potency against WT and drug-resistant HIV strains. However, HIV resistance to EFdA is not well characterized. We therefore developed resistance to EFdA by serial passages using progressively increasing concentrations of EFdA. The starting virus was either WT or clinically relevant NRTI-resistant viruses K65R, M184V, and D67N/K70R/T215F/K219Q). In all cases, the selected mutations included M184V. Additional mutations in the RT connection domain (R358K and E399K) and one mutation in the RNase H domain (A502V) were noted. Site-specific mutagenesis validated the role for M184V as the primary determinant for resistance to EFdA; none of the connection domain mutations contributed significantly to phenotypic resistance to EFdA. A novel EFdA resistance mutation was also observed in the background of M184V. The A114S/M184V combination of mutations imparted higher resistance to EFdA (~24-fold) than M184V (-8-fold) or A114S (~2-fold) alone. Virus fitness data suggested that A114S affects HIV fitness by itself and in the presence of M184V. This is consistent with biochemical experiments that showed decreases in the enzymatic efficiency (kcat/Km) of WT RT vs. A114S (2.1-fold) and A114S/M184V/502V (6.5-fold), whereas there was no significant effect of A502V on RT or virus fitness. The observed EFdA resistance of M184V by itself and in combination with A114S combined with the strong published in vitro and in vivo data, confirm that EFdA is an excellent candidate as a potential HIV therapeutic.

microbiology↗

bioRxiv2019

Finding valuable bioactive components from Jerusalem artichoke (Helianthus tuberosus L.) leaf protein concentrate in a green biorefinery concept

Jerusalem artichoke is widely known for its inulin-enriched tubers. Recently the opportunity has been arisen to involve the whole plant in biorefinery concept due to its high lignocellulose biomass and tuber production. This paper focuses on the repeatedly harvestable green biomass of Jerusalem artichoke. Ultra-High Performance Liquid Chromatography-Electrospray Ionization/Mass Spectrometry (UHPLC-ESI-MS) was applied to identify the phytochemicals in Jerusalem artichoke leaf protein concentrate (JAPC) thermally extracted from green biomass of three clones, i.e., Alba, Fuseau and Kalevala. Amino acid and fatty acid profiles as well as yield of JAPC were also analyzed. The UHPLC-ESI-MS analyses showed that no toxic phytochemicals were identified in JAPC. The results revealed, also, that JAPC is not only essential-amino acids-rich but also contains substantial amounts of polyunsaturated fatty acids (66-68%) such as linolenic and linoleic acids. Linolenic acid represented 39-43% of total lipid content; moreover, the ratio between {omega}-6 and {omega}-3 essential fatty acids in JAPC was [~]0.6: 1. Using UHPLC-ESI-MS, the following hydroxylated methoxyflavones were for the first time identified in JAPC, i.e., dimethoxy-tetrahydroxyflavone, dihydroxy-methoxyflavone, hymenoxin and nevadensin. These compounds are medically important since they are referred to as anti-cancer, anti-inflammatory and antioxidants. Also, liquiritigenin - estrogenic-like compound - was identified in JAPC alongside the following terpenes, i,e., loliolide and dihydroactinidiolide. However, no remarkable differences of phytochemicals, fatty acids and amino acids composition were seen among Jerusalem artichoke clones. The green biomass of tested clones ranged between 5 to 5.6 kg m-2 and JAPC yield varied from 28.6 to 31.2 g DM kg-1 green biomass with total protein content, on average, of 33.3%. According to our knowledge, this paper is the first scientific report highlighting bioactive substances in JAPC such as PUFA phytochemicals. These results clearly prove that JAPC is a valuable product which can direct towards human and animal nutrition as well as it can serve as basic material for different industrial purposes.

plant biology↗

bioRxiv2018

RepB C-terminus mutation of an ori pRi vector affects plasmid copy number in Agrobacterium and transgene copy number in plants

A native repABC replication origin, ori pRi, was previously reported as a single copy plasmid in Agrobacterium tumefaciens and can improve the production of transgenic plants with a single copy insertion of transgenes when it is used in binary vectors for Agrobacterium-mediated transformation. A high copy ori pRi variant plasmid, pTF::Ri, which does not improve the frequency of single copy transgenic plants, has been reported in the literature. Sequencing the high copy pTF::Ri repABC operon revealed the presence of two mutations: one silent mutation and one missense mutation that changes a tyrosine to a histidine (Y299H) in a highly conserved area of the C-terminus of the RepB protein (RepBY299H). Reproducing these mutations in the wild-type oriRi binary vector showed that Agrobacterium cells with the RepBY299H mutation grow faster on both solidified and in liquid medium, and have higher plasmid copy number as determined by ddPCR. In order to investigate the impact of the RepBY299H mutation on transformation and quality plant production, the RepBY299H mutated ori pRi binary vector was compared with the original wild-type ori pRi binary vector and a multi-copy oriV binary vector in canola transformation. Molecular analyses of the canola transgenic plants demonstrated that the multi-copy ori pRi with the RepBY299H mutation in Agrobacterium cells lost the advantage of generating high frequency single copy, backbone-free transgenic plants compared to using the single copy wild-type ori pRi binary vector.

molecular biology↗

bioRxiv2018

Direct immunosensing of avian influenza A virus in whole blood using hybrid nanocomposites

A sandwich-based electrochemical immunosensor was designed for detection of avian influenza virus (AIV) strains H5N1 and H4N6. This sensor was developed using gold-graphene nanocomposites, immobilized viral antibodies, and CdTe quantum dot electrochemical tagging. The nanocomposites were formed by the simultaneous reduction of a gold salt and graphene using hydroquinone as the reducing agent, thus producing non-spherical gold nanoparticles on graphene sheets. Viral antibodies were immobilized on nanocomposites and CdTe quantum dots through N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide and N-hydroxysuccinimide chemistry. Cyclic voltammetry studies were used to validate the detection of H5N1 surface protein and H4N6 inactivated virus. The immunosensor detected H5 protein in phosphate buffer solution (pH 7.4) with a limit of detection (LOD) of 10 fg/mL and a linear detection range was established for 10 ng/mL to 10 pg/mL. The biosensor detected H4N6 in three parts diluted whole chicken blood with a LOD of 1.28x10-7 hemagglutinating units (HAU). Commercial ELISA testing for H5N1 and H4N6 showed limits of detection of 10 ng/mL and 0.128 HAU, respectively. The sensor showed 106-fold increased detection of H4N6 virus in blood in comparison to its commercial ELISA kit counterpart. The developed immunosensor effectively change the way avian influenza is detected, monitored, and controlled; transforming time-consuming reactive methods, into rapid predictive technology.

bioengineering↗

bioRxiv2017

Self-assembled Star-shaped Chiroplasmonic Gold Nanoparticles for Ultrasensitive Chiro-immunosensor of Viruses

Near field optics and optical tunneling light-matter interaction in the superstructure of chiral nanostructures and semiconductor quantum dots exhibit strong optical rotation activity that may open a new window for chiral-based bioanalytes detection. Herein we report an ultrasensitive, chiro-immunosensor using superstructure of chiral gold nanohybrids (CAu NPs) and quantum dots (QDs). Self-assembling techniques were employed to create asymmetric plasmonic chiral nanostructures for extending the spectral range of circular dichroism (CD) response for obtaining superior plasmonic resonant coupling with the QDs excitonic state; this may help to achieve lower the limit of detection (LOD) values. As a result, the designed probe exhibited avian influenza A (H5N1) viral concentration at picomolar level, a significant improvement in sensitivity in comparison to a non-assembled CAu NPs based chiroassay. The practicability of the proposed sensing system was successfully demonstrated on several virus cultures including, avian influenza A (H4N6) virus, fowl adenovirus and coronavirus in blood samples. The results of our study highlights that exciton-plasmon interaction changes chirality and the self-assembled nanostructures are an efficient strategy for enhancing the sensitivity of plasmonic nanosensors.

bioengineering↗