Biology subjects

Molnar, A.

Publications and source records attributed to Molnar, A..

10 recordsLinked to original sources

bioRxiv2026

5' Complementarity-Mediated End Joining (5'CMEJ) DNA repair

How cells choose among competing DNA double-strand break repair pathways, and whether the choice differs across the tree of life, remains poorly understood, limiting prediction of CRISPR editing outcomes, particularly in plants. Through a meta-analysis of 2,098 SpCas9 target sites across plants, animals, and an alga, we show that deletion patterns reflect cell-division status rather than taxonomic origin: dividing cells favour polymerase Theta-Mediated End Joining (TMEJ), whereas non-dividing cells employ a largely overlooked pathway, 5 Complementarity-Mediated End Joining (5CMEJ). Unlike the known resection-dependent pathways, which use 3 overhangs, 5CMEJ exploits the 5 overhangs generated by staggered SpCas9 cleavage.

molecular biology↗

bioRxiv2026

Silvicultural practices and interannual variation shape ectomycorrhizal fungal diversity and community composition in an oak-hornbeam forest in northern Hungary

Ectomycorrhizal (ECM) fungi are well-known for their crucial roles in forest health and productivity, yet their responses to various forest management practices are understudied, particularly in oak-dominated forests. The purpose of this study was to better understand the effects of silvicultural treatments on the diversity and community composition of ECM fungi in an oak-hornbeam forest in northern Hungary. We analyzed ITS2 rDNA metabarcoding data of soil-borne fungi to compare richness and community composition of ECM fungi among forest treatment types (clear-cutting, gap-cutting, preparation-cutting, tree retention in clear-cut areas, and control) and between sampling years (2020 and 2021). We found 268 ECM fungal genotypes, with the most diverse phylogenetic clades being /russula-lactarius (52), /tomentella-thelephora (47), /inocybe (40), /sebacina (27), and /cortinarius (20). We found significant compositional difference of ECM fungi among silvicultural treatments in both years, with some variations in richness. There were also small, but still significant compositional differences between the two years. Treatment effect was partly explained by altered environmental variables, such as relative humidity and soil temperature. These results highlight the importance of forest structure and the abiotic environment in driving community dynamics of plant-symbiotic fungi, with potential implications for forest health and productivity.

ecology↗

bioRxiv2026

A conserved photosynthetic cytochrome enhances growth in fluctuating light

Having at least one of the small soluble electron carriers cytochrome c6 (c6) and plastocyanin is indispensable for photosynthesis. It was believed that c6 had been lost from plants until a ubiquitous and highly conserved homologue, now named cytochrome c6A (c6A), was found in Arabidopsis thaliana. In spite of an early suggestion that c6A functioned like c6 in the photosynthetic electron transport chain it was soon shown to be unable to do so despite the strong structural homology between the two proteins. The function of c6A, and why it is apparently universal in plants and green algae, therefore remained unknown. Here, we show that, in the green alga Chlamydomonas reinhardtii, c6A confers a growth advantage under fluctuating light and is crucial for maintaining the light harvesting balance between photosystems I and II in photomixotrophic conditions. We show that in the absence of c6A, the light harvesting balance shifts towards PSII, leading to a more reduced plastoquinone pool and increased photooxidative stress. This study provides insights into how photosynthetic organisms acclimatize to stressful light conditions, indicating that c6A is important for this adaptation. These findings provide a basis for further mechanistic studies on a hypothesized role for c6A in thiol-based redox regulation in the thylakoid lumen, with implications for photoprotection mechanisms such as state transitions.

plant biology↗

bioRxiv2025

Infarctsize-AI: an efficient infarct size image analysis tool for small rodent myocardial infarction studies

BackgroundMyocardial infarct size (IS) is the gold standard end-point in shorth-term studies on cardioprotection. However, IS quantification in rodent models with standard Evans Blue and 2,3,5-triphenyltetrazolium chloride (TTC) staining is time-consuming and prone to inter-observer variance. Therefore, we aimed to develop an artificial intelligence (AI)-based application to reduce time and inter-observer variability of IS analysis in rodent acute myocardial infarction (MI) models. MethodsWe used TTC/Evans blue-stained heart slice images of independent laboratories from previously published projects. Rat (n = 325 and 248 slices) and mouse (n = 77 slices) datasets were used to train deep learning segmentation models with three different neural network architectures, which were combined into a single AI analysis. AI analysis was compared with manual analysis on rat data from a training laboratory (internal data, n = 496 slices, n = 41 whole-hearts) and data from independent laboratories (external data, n = 60 and 62 slices). Additionally, two independent evaluators performed manual and AI-assisted analysis, consisting of AI-analysis and its manual correction, on internal (n = 36 slices) and external data (n = 37 slices). ResultsLins concordance correlation coefficient (CCC) between IS/AAR values from manual and AI analysis was 0.844 with 95% CI of [0.814; 0.869] for images of internal data heart slices. On external data heart slices, AI accurately annotated slice area and AAR but failed to annotate infarcted area. On internal whole-heart data, CCC between AI and AI-assisted IS/AAR was 0.894 with 95% CI of [0.812; 0.942]. AI-assisted analysis reduced evaluation time on both internal and external datasets and increased region overlap for AAR between the two independent evaluators on dependent data. ConclusionsAI-assisted analysis significantly reduced analysis time and inter-observer variability. For optimal performance, lab-specific AI training is recommended. Infarctsize-AI is available at https://infarctsize.com. Translational perspectiveMyocardial infarct size (IS) is the gold-standard end-point in shorth-term studies to assess potential cardioprotective therapies against acute myocardial infarction (AMI). However, IS quantification in rodent AMI models is time-consuming and prone to inter-observer variance. Therefore, we developed an AI-based software that can reduce analysis time and inter-observer variability and facilitate documentation, which facilitates the clinical translation of potential cardioprotective therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=34 SRC="FIGDIR/small/688527v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@187c938org.highwire.dtl.DTLVardef@1ab8bb4org.highwire.dtl.DTLVardef@160dc68org.highwire.dtl.DTLVardef@264617_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Nurseries and garden centres as hubs of alien plant invasions

The growing global horticultural trade is having a steadily increasing impact on the rate at which alien species are introduced into new areas, partly because horticultural trade also entails the unintentional dispersal of many contaminant species. Although there are reports about noteworthy occurrences of alien plant species in garden centres, this phenomenon has hardly been studied systematically. To bridge this knowledge gap, we conducted systematic field surveys in 12 garden centres in Hungary to assess their alien flora. We hypothesised that (i) the number of alien species inhabiting a garden centre is positively correlated with its size, (ii) relative to their size, garden centres host a disproportionately large proportion of the local alien flora, and (iii) alien species inhabiting garden centres differ from the regional alien flora in their traits. We recorded altogether 93,788 individuals of 67 introduced species, seven of which have not yet been reported from the country. There was considerable variability in the number of species and individuals found in each garden centre, but there was no correlation between the size of the garden centres and the number of species they host. Despite their relatively small size, the studied garden centres hosted a considerable proportion of the local alien flora, indicating that they strongly accumulate alien species and that they can act as invasion hubs for several alien species. Alien species inhabiting garden centres differed from the regional alien flora in some of their trait values, indicating that the species that are most successful at establishing populations inside garden centres are both good dispersers and possess an effective resource-acquisitive strategy. We conclude that established alien plant populations in garden centres may induce local invasions, and in the meantime, individuals and seeds inside the containers of ornamental plants are regularly transported to distant areas by the customers. Therefore, plant species dispersed as contaminants of horticultural stock need to be better considered in invasion biology to reduce the threat they may present.

ecology↗

bioRxiv2023

Alkaline and loess grasslands with contrasting richness and biomass patterns are not separated on the CSR strategy spectrum.

Studying the relationship between biodiversity patterns and processes in vegetation has been at the centre of interest in vegetation ecology for several decades. By studying the biomass of loess and alkaline grasslands along a water and salinity gradient, we aimed to analyse species diversity and CSR functional type patterns. We aimed to test the following hypotheses: i) The biomass and species richness scores and the species composition are significantly different between the sampled grassland community types. ii) The sampled communities are well separated based on the CSR strategy spectrum. iii) The amount of green biomass and litter are positively correlated with competitiveness and negatively with stress tolerance. The biomass and species richness scores and the species composition of the sampled communities along the sampled gradients were significantly different; the highest species richness, evenness and Shannon diversity values were found in loess grasslands. The highest level of litter accumulation was found in alkaline meadows. The communities were well separated in the ordinations but surprisingly, calculation of coordinates for CSR strategy types have not shown clear separation of the grassland community types. Based on the results we can conclude that the current CSR classification is too robust to delineate grassland communities in alkaline landscapes which are markedly different in composition. We point out that the CSR classification is based on the magnitude of stress, and it is not able to differentiate between the various forms of stress which might be responsible for the marked compositional differences. Therefore, developing an index focusing specifically on the functional characterisation of stressed communities and able to differentiate between different forms of stress (e.g., water and/or salinity stress) would be highly beneficial for future studies.

ecology↗

bioRxiv2023

The chloroplastic phosphate transporter CrPHT4-7 supports phosphate homeostasis and photosynthesis in Chlamydomonas

In eukaryotic cells, phosphorus is assimilated and utilized primarily as phosphate (Pi). Pi homeostasis is mediated by transporters that have not yet been adequately characterized in green algae. This study reports on CrPHT4-7 from Chlamydomonas reinhardtii, a member of the PHT4 transporter family, which exhibits remarkable similarity to AtPHT4;4 from Arabidopsis thaliana, a chloroplastic ascorbate transporter. Using fluorescent protein tagging we show that CrPHT4-7 resides in the chloroplast envelope membrane. Crpht4-7 mutants, generated by the CRISPR/Cas12a-mediated single-strand templated repair, show retarded growth especially in high light, enhanced sensitivity to phosphorus limitation, reduced ATP level, strong ascorbate accumulation and diminished non-photochemical quenching in high light. Conversely, CrPHT4-7 overexpressing lines exhibit enhanced biomass accumulation under high light conditions in comparison with the wild-type strain. Expressing CrPHT4-7 in a yeast strain lacking Pi transporters substantially recovered its slow growth phenotype demonstrating that it transports Pi. Even though CrPHT4-7 shows a high degree of similarity to AtPHT4;4, it does not display any significant ascorbate transport activity in yeast or intact algal cells. Thus, the results demonstrate that CrPHT4-7 functions as a chloroplastic Pi transporter essential for maintaining Pi homeostasis and photosynthesis in Chlamydomonas reinhardtii. One-sentence summaryWe demonstrate that the CrPHT4-7 transporter of Chlamydomonas reinhardtii is located in the chloroplast envelope membrane and contributes to maintaining phosphate homeostasis and photosynthesis.

plant biology↗

bioRxiv2022

PADAPT 1.0 - the Pannonian Database of Plant Traits

We present PADAPT 1.0, the Pannonian Database of Plant Traits which relies on regional data sources and integrates existing data and new measurements on a wide range of traits and attributes of the plant species of the Pannonian Biogeographical Region and makes it freely accessible at www.padapt.eu. The current version covers the species of the region occurring in Hungary (cc. 90% of the regions flora) and consists of 126,337 records on 2745 taxa. There are 53 plant attributes in PADAPT 1.0 organised in six major groups: (i) Habitus and strategy, (ii) Reproduction, (iii) Kariology, (iv) Distribution and conservation, (v) Ecological indicator values, and (vi) Leaf traits. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Data collection will continue in the future and the PADAPT team welcomes researchers interested in contributing with data. The main task before an updated version of the database is to include species of the Pannonian region not covered by the current version. In conclusion, although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.

ecology↗

bioRxiv2022

Heritage of ancient cultures supports conservation: a continent-wide perspective from the Eurasian steppes

Civilisations including ancient ones, have shaped the global ecosystems in many ways through a co-evolution of landscapes and humans. However, the cultural legacies of ancient and lost civilisations are seldom considered in conservation. Here using a continental-scale dataset containing over 1,000 data records on the localities, land cover, protection status and cultural values related to ancient steppic burial mounds (so-called kurgans), we evaluated how these iconic and widespread landmarks can contribute to grassland conservation in the Eurasian steppes, which is one of the most endangered biomes on Earth. By using Bayesian logistic generalized regressions and proportional odds logistic regressions, we aimed to reveal the potential of mounds in preserving grasslands considering landscapes with different levels of land use transformation. We also compared the conservation potential of mounds situated inside and outside protected areas and assessed whether the presence of cultural, historical or spiritual values support the maintenance of grasslands on them. We revealed that kurgans have enormous importance in preserving grasslands in transformed landscapes outside protected areas, where they can act as habitat islands, and provide an additional pillar for conservation by contributing to habitat conservation and improvement of habitat connectivity. We found that besides their steep slopes hindering ploughing, the existence of cultural, historical or religious values could almost double the chance for grassland occurrence on kurgans due to the related extensive land use and the respect of local communities. As the estimated number of steppic mounds is about 600,000 and also similar historical features exist in all continents, our results can be upscaled to a global level. Our results also suggest that an integrative socio-ecological approach in conservation might support the positive synergistic effects of conservational, landscape and cultural values.

ecology↗

bioRxiv2019

Loss of a glutaredoxin gene underlies parallel evolution of trichome patter in Antirrhinum

Most angiosperms produce trichomes--epidermal hairs that have protective or more specialised roles. In almost all species trichomes are multicellular and, in the majority, secretory. Despite the importance of multicellular trichomes for plant protection and as a source of high-value products, little is known about the mechanisms that control their development. Here we use natural variation between Antirrhinum (snapdragon) species to examine how trichome distribution is regulated and has evolved. We show that a single gene, Hairy (H), which is needed to repress trichome fate, underlies variation in trichome distribution patterns between all Antirrhinum species except one. H encodes an epidermis-specific glutaredoxin and trichome distribution within individual plants reflects the location of H expression. Gene phylogenies and functional tests suggest that H gained its trichome-repressing role late in eudicot evolution and that Antirrhinum species with widespread trichomes evolved multiple times from a largely bald ancestor though independent losses of H activity. We also find evidence for an evolutionary reversal involving a suppressor mutation, and for a pleiotropic effect of H that might constrain the evolution of trichome patterns.

plant biology↗