A5005077366- Plant-Microbe Interactions and Immunity
- Plant Virus Research Studies
- Plant Reproductive Biology
- Plant Pathogens and Resistance
- Plant Disease Resistance and Genetics
- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- Potato Plant Research
- Bioinformatics and Genomic Networks
- Plant Pathogenic Bacteria Studies
- Scientific Computing and Data Management
- Biomedical and Engineering Education
- Machine Learning in Bioinformatics
- Chromosomal and Genetic Variations
- Phytoplasmas and Hemiptera pathogens
- Genetics, Bioinformatics, and Biomedical Research
- Algorithms and Data Compression
- Microbial Metabolic Engineering and Bioproduction
- Research Data Management Practices
- Plant Parasitism and Resistance
- Biomedical Text Mining and Ontologies
- Pineapple and bromelain studies
- Plant and Fungal Interactions Research
- Plant responses to water stress
- Cell Image Analysis Techniques
National Institute of Biology
2015-2025
Cornell University
2023
Genomics and Biotechnology of the Fruits Laboratory
2020
Universität Ulm
2018
ABSTRACT Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well ripe fruits, through predetermined abscission zones response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights deleterious effects of on chloroplast ultrastructure cells tomato flower pedicel zone, revealing spatiotemporal differential gene expression key...
Abstract Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation stress, however, remains limited. Here, we present a comprehensive molecular physiological high-throughput profiling potato tuberosum, cv. Désirée) under waterlogging applied single or in combinations designed mimic realistic future scenarios. Stress responses were...
SUMMARY Whereas the activation of resistance (R) proteins has been intensively studied, downstream signaling mechanisms leading to restriction pathogen remain mostly unknown. We studied immunity network response conditioned by potato Ny‐1 gene against virus Y. analyzed processes in cell death zone and surrounding tissue on biochemical expression levels order reveal spatiotemporal regulation immune response. show that transcriptional is dependent salicylic acid (SA). For some genes completely...
Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, floral. In addition, it contributes to the flavor foods, applied fragrance industry. nature, indole synthesized either from tryptophan bacterial tryptophanases (TNAs) or indole-3-glycerol phosphate (IGP) plant lyases (IGLs). While widely accepted that synthase α-subunit (TSA) has intrinsically low IGL activity absence of β-subunit, this study, we show Corynebacterium glutamicum...
Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current of biochemical, signaling, and regulatory molecular interactions in plants: highly curated model plant stress signaling (PSS; 543 reactions) large comprehensive network (488 390 interactions). Both were constructed by domain experts through systematic curation diverse literature database resources. SKM provides single entry point for...
Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by induction of cell death, manifested as formation necrotic lesions. While it known that salicylic acid key component in orchestration events restricting HR, exact function death still unknown. We show potato Y (PVY) can be detected outside zone Ny-1-mediated HR plants (cv. Rywal), observed individual infected cells or small clusters zone. By exploiting features temperature...
Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on genetic diversity highly heterozygous tetraploid Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack hinders further progress in potato research. In conducted investigation, we first merged and manually curated two existing partially-overlapping DM genome-based gene models, creating a union genes scaffold. Next, compiled available newly...
Potato is exceptionally sensitive to a wide range of stresses. Its successful interaction with beneficial symbionts would allow for environmentally friendly plant protection. We investigated the processes involved in colonisation potato Bacillus subtilis. RNAseq showed that at time biofilm establishment, immune responses interacting roots were attenuated, and complex transcriptional network was triggered, including ERFs, MYBs, NACs WRKYs. Interestingly, response intensified if plants are...
This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at Bay of Koper (Gulf Trieste, Northern Adriatic Sea) nearby bathing mussel farm areas. RoV NoV are released into Koper, with higher rates close discharge wastewater treatment plant, however, they can be detected recreational farming Our results...
Abstract Background Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress defenses, and a massive reprogramming of infected cells leading to major changes in whole homeostasis. The advances sequencing technologies allow simultaneous analysis multiple aspects viral infection at large scale, generating new insights into molecular mechanisms underlying plant-virus interactions....
Abstract 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 stress, however, remains limited. Here, we present a comprehensive molecular physiological high-throughput profiling potato ( Solanum tuberosum , cv. Desirée) under drought waterlogging applied single in combinations designed mimic realistic future scenarios. Stress-responses were...
Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function non-model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 plant immunity. We show that acts as a susceptibility factor. It negatively regulates immunity against virus Y and Ralstonia solanacearum, pathogens completely different modes action, thereby has than its orthologue tomato. Remarkably, destabilised healthy via autophagy pathway accumulates...
Abstract Background Rosaceae species are economically highly relevant crops. Their cultivation systems constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which them being plant elicitor peptides (Peps). Exogenous application Peps activates defense mechanisms and reduces the symptoms pathogen infection in various pathosystems. We have previously identified showed, an ex vivo system, that their topical...
The pathogenicity of intracellular plant pathogenic bacteria is associated with the action factors/effectors, but their physiological roles for most phytoplasma species, including ‘ Candidiatus Phytoplasma solani’ are unknown. Six putative factors/effectors from six different strains Ca . P. were selected by bioinformatic analysis. way in which they manipulate host cellular machinery was elucidated analyzing Nicotiana benthamiana leaves after Agrobacterium -mediated transient transformation...
Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of specifical biological system are responding particular perturbation, integrative approach superimposed on a prior knowledge network is shown to be advantageous.We have developed DiNAR, Differential Network Analysis R, user-friendly application with dynamic that integrates multiple condition and extensive...
Abstract Stress Knowledge Map (SKM, https://skm.nib.si ) is a publicly available resource containing two complementary knowledge graphs describing current of biochemical, signalling, and regulatory molecular interactions in plants: highly curated model plant stress signalling (PSS, 543 reactions) large comprehensive network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation diverse literature database resources. SKM provides single entrypoint for...
We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality low maintenance cost. It enables on-the-fly creation enriched directory tree structure (project/Investigation/Study/Assay) based on the ISA model, in standardised manner via consecutive batch files. Templates-based metadata is generated parallel at each...
Abstract While activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction pathogen remain mostly unknown. We studied immunity network response conditioned by potato Ny-1 gene against virus Y. analyzed processes in cell death zone and surrounding tissue on biochemical expression levels reveal spatiotemporal regulation immune response. show that transcriptional is dependent salicylic acid (SA). For some genes, completely lost...
Potato ( Solanum tuberosum ) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, despite frequent updates, they are not unified. This hinders comparison across versions, limits ability to reuse experimental data without significant re-analysis, leads missing or wrongly annotated genes. Here, we unify recent double monoploid v4 v6 by developing an automated merging protocol, resulting in Unified poTato genome (UniTato). We subsequently established...
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It associated with 'CandidatusPhytoplasma solani'. In symptomatic grapevines cv. 'Zweigelt' infected 'Ca. P. solani' compared uninfected grapevines, metabolic pathways phosphorylated sugar production were induced both at transcriptional level and of activity corresponding enzymes (Dermastia et al., 2021, Int. J. Mol. Sci.22: 3531). particular, expression gene coding for phosphoglucoisomerase was upregulated, resulting...
Plants respond to stress by redistributing resources from growth- defence-related processes, often resulting in decreased yields. Understanding the molecular mechanisms behind these growth-defence trade-offs can enhance breeding strategies help us design crop varieties with improved tolerance, yields and quality. To enable investigation of context metabolism an essential tuber crop, potato, here we develop a large-scale compartmentalised genome-scale metabolic model, Potato-GEM. Apart...
On 6th and 7th February 2018, a Think Tank took place in Ljubljana, Slovenia. It was follow-up of the “Big Data Training School for Life Sciences” held Uppsala, Sweden, September 2017. The focus on identifying topics interest optimising programme forthcoming “Advanced” Big Science, that we hope is again supported by COST Action CHARME (Harmonising standardisation strategies to increase efficiency competitiveness European life-science research - CA15110). aimed go into details several were...
Abstract Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on genetic diversity highly heterozygous tetraploid Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack hinders further progress in potato research. In conducted investigation, we first merged and manually curated two existing partially-overlapping DM genome-based gene models, creating a union genes scaffold. Next, compiled...
The “Advanced Big Data Training School for Life Sciences” took place during September 3-7, 2018, organized by the Management Group (DAMA-UPC) at Technical University of Catalonia (UPC) in Barcelona, Spain. It is follow-up training school first “Big Sciences”, held Uppsala, Sweden, 2017, which was defined and structured “Think Tank Hackathon”, Ljubljana, Slovenia, February 2018. aim this to get participants acquainted with emerging processing techniques field Computational Biology...