Biology subjects

Zagorscak, M.

Publications and source records attributed to Zagorscak, M..

9 recordsLinked to original sources

bioRxiv2026

BoolDog: integrated Boolean and semi-quantitative network modelling in Python

SummaryBoolean and logic-based modeling approaches are well suited for the analysis of complex biological systems, particularly when detailed biochemical and kinetic information is unavailable. In such settings, biological pathways are represented as networks capturing system components and their interactions, providing a simplified yet informative abstraction of system behavior. While the structural topology of these networks is often well characterized, the absence of mechanistic detail limits the applicability of parameter-dependent modeling frameworks. To address this, we present BoolDog, a Python package for the construction, simulation, and analysis of Boolean and semi-quantitative Boolean networks. BoolDog supports synchronous simulation with events, attractor and steady-state identification, network visualization, and the systematic transformation of logic-based models into continuous ordinary differential equation (ODE) systems -- enabling the seamless integration of discrete and continuous modeling paradigms. Networks can be imported and exported across standard formats, and BoolDog integrates natively with established Python libraries for network analysis and visualisation, including NetworkX, igraph, and py4Cytoscape. Together, these capabilities provide a flexible, accessible, and interoperable platform for logic-based modeling of complex biological systems. Availability and implementationBoolDog is implemented in Python and available at https://github.com/NIB-SI/BoolDog/.

systems biology↗

bioRxiv2026

Potato yield can be predicted by using drone-captured and environmental measurements early in the growing season

Accurate pre-harvest prediction of crop yield informs variety selection, optimizes management, and accelerates breeding. As potato is the worlds leading non-grain staple, here we evaluate a diverse panel of varieties in a three-year field trial across five European locations. Canopy development and environmental parameters are monitored throughout the growing season using drone-based imaging, in-field sensors and gene expression measurements, while tuber yield and quality traits are quantified at harvest. We show that these data enable the identification of climate-resilient, high-yielding genotypes and support the development of machine learning models that explain over 80% of yield variation in independent test sets. Strikingly, measurements collected within the first two months after planting achieve predictive performance comparable to models trained on full-season data. Model interrogation further shows that over 70% of yield variation can already be predicted based on a simple five-parameter linear equation. Our framework thus demonstrates the potential of integrative field phenotyping and data-driven modeling to improve variety selection across heterogeneous environments.

plant biology↗

bioRxiv2025

An ERF transcription factor StPTI5, a novel regulator of endophyte community maintenance in potato

We have recently identified ERF transcription factor PTI5 as a susceptibility factor, negatively regulating immune response to diverse pathogens. Here we investigated the processes involved in colonisation of potato with beneficial organisms. RNAseq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and complex transcriptional network was triggered, with ethylene signalling being a central module and PTI5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While PTI5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in PTI5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the PTI5-silenced plants. PTI5 is thus involved both in blocking defence against harmful and blocking colonisation with beneficial microbes. Such mechanistic understanding of plant-microbe interaction paves the way for sustainable crop management.

plant biology↗

bioRxiv2024

Integration of multi-omics and deep phenotyping provides novel insights into multiple abiotic stress responses in potato

Potato is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, or flooding, which are severely exacerbated by climate change. Understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Desiree) under heat, drought and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress-responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising transcriptomics, proteomics, metabolomics and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analysed at the end of the stress period. Integrative analysis of multi-omics data was performed using a bioinformatic pipeline, which was established here, based on machine learning and knowledge networks. Overall, waterlogging had the most immediate and dramatic effects on potato plants, interestingly activating ABA-responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids and diverse stress induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies towards climate-adapted potato varieties. One Sentence SummaryIntegrated multi-omics analysis of high-throughput phenotyping in potato reveals distinct molecular signatures of acclimation to single and combined abiotic stresses related to climate change.

plant biology↗

bioRxiv2023

Evidence based Unification of poTato gene models with UniTato collaborative genome browser

Potato (Solanum tuberosum) is the most popular tuber crop and model organism. Though its gene models are frequently updated, they are not unified, leading to missing or wrongly annotated genes. Here, we thus unify the recent potato double monoploid v4 and v6 gene models by automatic merging. We established an Apollo web server that enables access to the Unified poTato genome annotation database (UniTato) as well as further community-based manual curation at unitato.nib.si. We demonstrate how the web server interface can help to resolve problems with missing or misplaced genes and can be used to further update them or consolidate a wider set of gene models or genome information. Genome annotation files and a comprehensive translation table are provided at github.com/NIB-SI/unitato.

plant biology↗

bioRxiv2023

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entrypoint for plant stress response investigations and the related growth tradeoffs. SKM provides interactive exploration of current knowledge. PSS is also formulated as qualitative and quantitative models for systems biology, and thus represents a starting point of a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation, design of validation experiments, or to gain new insights into experimental observations in plant biology.

plant biology↗

bioRxiv2021

pISA-tree - a data management framework for life science research projects using a standardised directory tree

We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in a standardised manner via consecutive batch files. Templates-based metadata is generated in parallel at each level enabling guided submission of experiment metadata. pISA-tree is complemented by two R packages, pisar and seekr. pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports. seekr enables synchronisation with the FAIRDOMHub repository. Applicability of pISA-tree was demonstrated in several national and international multi-partner projects. The system thus supports findable, accessible, interoperable and reusable (FAIR) research and is in accordance with the Open Science initiative. Source code and documentation of pISA-tree are available at https://github.com/NIB-SI/pISA-tree.

bioinformatics↗

bioRxiv2020

Spatial accumulation of salicylic acid is in effector-triggered immunity of potato against viruses regulated by RBOHD

While activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction of pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels to reveal spatiotemporal regulation of immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes, spatiotemporal regulation is completely lost in SA-deficient line, while the others show different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during resistance response. In plants with silenced RBOHD, the functionality of resistance response is perturbed and virus spread is not arrested at the site of infection. RBOHD is required for spatial accumulation of SA, and conversely RBOHD is under transcriptional regulation of SA signaling. Using spatially resolved RNA-Seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.

plant biology↗

bioRxiv2019

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Desiree, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.

plant biology↗