Biology subjects

Juhasz, A.

Publications and source records attributed to Juhasz, A..

12 recordsLinked to original sources

bioRxiv2025

Scalable Assembly of Ascaris Mitogenomes from Whole-Genome Data Reveals a Novel Clade

The genus Ascaris is an important group of giant parasitic roundworms, infecting over 700 million people globally, with substantial economic losses in domestic pigs. Whilst species of Ascaris are morphologically indistinguishable, analysis of mitochondrial and selected nuclear DNA loci has revealed three clades (A, B, C), which may inflate with the addition of genomic data. Here, we present a bioinformatic pipeline for de novo assembly of complete mitochondrial genomes (mtDNA) from low-coverage whole-genome data through host-read depletion or mtDNA read enrichment, followed by mtDNA-specific assembly. Our approach yielded 149 high-quality Ascaris mtDNA assemblies, enabling the study of population-level diversity, including the identification of a novel clade (Clade D, designated here) associated with human samples from Ethiopia. Our analysis further revealed Clade C to comprise of pig-derived samples from Europe based on characterisation of worms isolated in Germany. Furthermore, genetic diversity across all mitochondrial loci was high (concatenated dataset: S = 1261; h = 94; {pi} = 0.0224), indicating substantial intraspecies variation. Our methods described here provide a scalable framework for mtDNA genome reconstruction with insights into roundworm population-genomic and phylogenetic studies.

genomics↗

bioRxiv2025

Characterisation of pouch secretions from breeding Tasmanian devils

Tasmanian devils (Sarcophilus harrisii), like all marsupials, give birth to altricial young. Here we employ proteomic analysis to identify components of devil pouch secretions (red oil) that may contribute to offspring survival and development. Proteins were extracted from 5 samples and analysed by liquid chromatography-tandem mass spectrometry. Peptide-level evidence revealed proteins involved in a diverse set of immune pathways, including those mediating iron-ion transport, defence responses to bacteria, innate immune responses, and antigen processing. A core set of 200 proteins was identified across at least three samples, 63 of which were associated with antimicrobial or immunoregulatory functions. These included immunoglobulins, components of complement and coagulation cascade, and antimicrobial proteins and peptides. For the first time, these findings highlight the Tasmanian devils red oil secretions as a source of immune proteins likely contributing to microbiome restructuring during lactation. Moreover, the data indicate that these proteins may act synergistically in pathways triggered by immune challenges or physiological stress. In briefMicrobial shifts in the Tasmanian devil pouch are critical for establishing a protective environment for the developing joey. This study confirms that Tasmanian devil red oil contains a diverse array of immune proteins that likely contribute to these microbial shifts.

zoology↗

bioRxiv2025

Edge computer vision produces microarthropod-based high-throughput biodiversity metrics

Soil fauna is crucial for carbon cycling, controlling organic matter decomposition and contributing to ecosystem services1-7. Soil microarthropods are top-down regulators in the decomposer food web and serve as fundamental indicators of soil health. Yet, routine field-level monitoring remains restricted to resource-intensive research, leaving a critical gap in arable land management and policy. To address this, we developed Edapholog(R) extractor, a fully automated laboratory device that detects and identifies live soil microarthropods via real-time, AI-based image analysis, enabling taxonomic identification. Here, we demonstrate its accuracy across 319 arable fields spanning ten European countries. We show that computer vision can support ecological interpretation in arable systems and long-term studies on conservation tillage and cover cropping, offering a scalable tool for integrating soil biodiversity metrics into regenerative agriculture and carbon farming. We validated the system against classical taxonomy and found that across [~]35,000 microarthropod individuals, the device achieved an overall accuracy of 86%, sensitivity of 75%, and specificity of 99% compared to manual identifications. Community composition analyses revealed high similarities (83%), with minimal richness differences (7%) and low species replacement (13%) across countries, indicating that the AI does not introduce taxonomic bias. When applied in a long-term field experiment, the system detected significant taxon-specific responses to conservation tillage, with effect sizes ranging from 0.5 to 4. Total abundance, richness, and a soil biological health index were 39%, 47%, and 150% higher, respectively, under conservation tillage compared to conventional ploughing. These effects were statistically consistent between the automated and classical methods. However, while manual microscopy required several hours per sample, the AI-based system delivered immediate results without the need for taxonomic expertise. Edapholog(R) extractor offers exciting opportunities for rapid, scalable soil biodiversity monitoring for future sustainable land management.

ecology↗

bioRxiv2025

Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents

The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance (AMR). Here, we evaluate freshwater snails, which are geographically widespread aquatic invertebrates, as environmental reservoirs of ARGs. We collected faeces from eight gastropod genera at 15 freshwater locations across Malawi, Uganda, Zanzibar, and the United Kingdom, and conducted the first freshwater snail faecal metagenomics study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems in all countries. All ARGs that could be assembled into metagenome-assembled genomes (MAGs) were found within Proteobacteria, which dominated the faecal microbiomes and were strongly associated with the total ARG load. In Malawi, we linked blaOXA-181 (blaOXA-48-like), a previously mobilised carbapenemase gene, to Shewanella xiamenensis, the genes known progenitor. We detected another blaOXA-48-like gene by read-mapping from a sample in the United Kingdom. We identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations, with two mcr-7-like genes being found in an Aeromonas jandaei MAG in Uganda. Our findings highlight freshwater snail faeces as a One Health-relevant environmental reservoir of clinically important ARGs. Data SummaryShort reads from all samples sequenced in this study have been deposited in the Sequence Read Archive (SRA) under BioProject PRJNA1211045, with accession numbers SRX27371064 - SRX27371078. Data and code used to carry out analyses in R are available at https://github.com/amoreo71/freshwater_snail_faecal.

microbiology↗

bioRxiv2024

Multiomics plasticity in seed traits of pan-genome wheat cultivars

The molecular basis of cultivar-level variations in polyploid wheat that enables environmental adaptation while maintaining yield and quality in polyploid wheat remains poorly understood. We conducted a detailed phenotypic assessment and multiomics analysis of nine pan-genome polyploid wheat cultivars grown under control and drought conditions. We aimed to investigate the subgenome-level variations, cultivar differences and biochemical mechanisms affecting plant fitness under moderate drought stress. Intrinsic water use efficiency, grain yield, and grain protein content and quality differed among cultivars, supporting the plasticity of drought stress responses. Biased proteome and metabolome abundance changes in response to moderate drought stress during the vegetative stage indicate different strategies for the utilization of homeologous protein isoforms assigned to the A, B, and D subgenomes. Drought effects were detected at the protein level, but significant changes were observed in central carbon pathway metabolites and micronutrient profiles. The subgenomic localization of seed storage proteins highlight differences in nutrient reservoir accumulation and emphasizes the enhanced role of S-rich prolamins in the stress response. Subgenomic variations define cultivar phenotypes by producing molecules that accumulate and enable the underlying trade-offs between environmental adaptation and yield- or quality-related traits. These variations can be used to select crops with increased stress resistance without compromising yield.

plant biology↗

bioRxiv2024

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of these de novo annotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

genomics↗

bioRxiv2022

Exogenous DNA upregulates DUOX2 expression and function in human pancreatic cancer cells by activating the cGAS-STING signaling pathway

Pro-inflammatory cytokines upregulate the expression of the H2O2-producing NADPH oxidase dual oxidase 2 (DUOX2) which, when elevated, adversely affects survival from pancreatic ductal adenocarcinoma (PDAC). Because the cGAS-STING pathway is known to initiate pro-inflammatory cytokine expression following uptake of exogenous DNA, we examined whether activation of cGAS-STING could play a role in the generation of reactive oxygen species by PDAC cells. Here, we found that a variety of exogenous DNA species markedly increased the production of cGAMP, the phosphorylation of TBK1 and IRF3, and the translocation of phosphorylated IRF3 into the nucleus, leading to a significant, IRF3-dependent enhancement of DUOX2 expression, and a significant flux of H2O2 in PDAC cells. However, unlike the canonical cGAS-STING pathway, DNA-related DUOX2 upregulation was not mediated by NF-{kappa}B; and although exogenous IFN-{beta} significantly increased Stat1/2-associated DUOX2 expression, intracellular IFN-{beta} signaling that followed cGAMP or DNA exposure did not itself increase DUOX2 levels. Finally, DUOX2 upregulation subsequent to cGAS-STING activation was accompanied by the enhanced, normoxic expression of HIF-1 as well as DNA double strand cleavage, suggesting that cGAS-STING signaling may support the development of an oxidative, pro-angiogenic microenvironment that could contribute to the inflammation-related genetic instability of pancreatic cancer.

cancer biology↗

bioRxiv2022

Dexamethasone Inhibits Cytokine-Induced, DUOX2-Related VEGF-A Expression and DNA damage in Human Pancreatic Cancer Cells and Growth of Pancreatic Cancer Xenografts

Previously, we demonstrated that pro-inflammatory cytokines enhance dual oxidase 2 (DUOX2)-dependent production of reactive oxygen species by human pancreatic ductal carcinoma (PDAC) cells, and that DUOX2 expression is significantly increased in patients with early stages of PDAC. In genetically-engineered mouse models of PDAC, dexamethasone (Dex) decreases formation of pancreatic intraepithelial neoplasia (PanIn) foci as well as PDAC invasiveness. Herein, we report that Dex, in a concentration- and time-dependent fashion, inhibited pro-inflammatory cytokine (IFN-{gamma}/LPS/IL-17A/IL-4)-mediated enhancement of DUOX2 expression in BxPC-3, CFPAC-1, and AsPC-1 human PDAC cell lines, as well as DUOX2-induced DNA damage. The inhibitory effects of Dex were abolished by pre-treatment with the Dex antagonist RU-486. Examination of the human DUOX2 promoter in silico revealed a putative negative glucocorticoid receptor (GR) binding element (IRnGRE). Western analysis, using nuclear extracts from Dex-treated PDAC cells, demonstrated that Dex activated the glucocorticoid receptor in PDAC cell nuclei in the presence of certain co-repressors, such as NCoR-1/2 and histone deacetylases (HDAC1, 2, and 3). Dex produced no anti-proliferative effects on PDAC cells in vitro. However, Dex significantly decreased the growth of BxPC-3 xenografts while decreasing inflammatory and immune cell infiltration of the microenvironment, as well as the mRNA expression of DUOX2 and VEGF-A, in BxPC-3 tumors. In contrast, Dex had no effect on the growth of xenografts developed from MIA-PaCa cells that are unresponsive to pro-inflammatory cytokines in culture. In summary, these studies suggest that suppression of inflammation-related DUOX2 expression by Dex could diminish the oxidative milieu supporting PDAC growth and development.

pharmacology and toxicology↗

bioRxiv2021

ELICE16INDURES (R): a plant immune-priming activator targeting jasmonate metabolism via TIFY and RHOMBOID proteins in Hordeum vulgare

Priming activity of plant-based allelochemicals is advanced research nowadays meaning a high potential in sustainable agriculture. The ELICE16INDURES(R) (RIMPH LTD, Hungary) plant conditioner of CO2 botanical extracts is rich in plant-active ingredients such as phenolic compounds, alkaloids, and flavonoids formulated in small multilamellar liposomes. This product was investigated in autumn barley (Hordeum vulgare). Field experiments of ELICE16INDURES showed augmented NDVI values interconnected with higher photosynthetic activity and yield increase. Background of the better vitality of plants was investigated by whole genomic gene expression profiling and showed an enhanced response to wounding, jasmonic acid, oxidative detoxification, and chloroplast activity. Among top50 differentially expressed genes the TIFY domain protein TIFY11B and RHOMBOID-like protein 2 related to JA signaling were up-regulated in field-collected samples. Phytotron experiments of barley were set up to validate and evaluate the transcriptomic effect of ELICE16INDURES. Well-studied priming active agents such as salicylic acid and beta-aminobutyric acid were compared with ELICE16INDURES and confirmed as priming inducer material with positive regulation of TIFY11B, TIFY3B, TIFY9, TIF10A, and RHOMBOID like protein 2 by using NGS GEx and RT-qPCR methods. One-sentence summaryELICE16INDURES(R) is a plant conditioner agent with a high amount of allelochemicals encapsulated into small multilamellar liposomes and found as an immune priming activator tested in H. vulgare field and phytotron cultures.

plant biology↗

bioRxiv2020

1RS.1BL molecular resolution provides novel contributions to wheat improvement

Wheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locus Rf multi. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.

genomics↗

bioRxiv2018

Wheat avenin-like protein and its significant Fusarium Head Blight resistant functions

Wheat Avenin-like proteins (TaALP) are atypical storage proteins belonging to the Prolamin superfamily. Previous studies on ALPs have focused on the proteins positive effects on dough strength, whilst no correlation has been made between TaALPs and the plant immune system. Here, we performed genome-wide characterization of ALP encoding genes in bread wheat. In silico analyses indicated the presence of critical peptides in TaALPs that are active in the plant immune system. Pathogenesis-related nucleotide motifs were also identified in the putative promoter regions of TaALP encoding genes. RT-PCR was performed on TaALP and previously characterised pathogenesis resistance genes in developing wheat caryopses under control and Fusarium graminearum infection conditions. The results showed that TaALP and NMT genes were upregulated upon F. graminearum inoculation. mRNA insitu hybridization showed that TaALP genes were expressed in the embryo, aleurone and sub-aleurone layer cells. Seven TaALP genes were cloned for the expression of recombinant proteins in Escherichia coli, which displayed significant inhibitory function on F. graminearum under anti-fungal tests. In addition, FHB index association analyses showed that allelic variations of two ALP genes on chromosome 7A were significantly correlated with FHB symptoms. Over-expression of an ALP gene on chromosome 7A showed an enhanced resistance to FHB. Yeast two Hybridization results revealed that ALPs have potential proteases inhibiting effect on metacaspases and beta-glucosidases. A vital infection process related pathogen protein, F. graminearum Beta-glucosidase was found to interact with ALPs. Our study is the first to report a class of wheat storage protein or gluten protein with biochemical functions. Due to its abundance in the grain and the important multi-functions, the results obtained in the current study are expected to have a significant impact on wheat research and industry.

molecular biology↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗