Biology subjects

Rudolf, J.

Publications and source records attributed to Rudolf, J..

8 recordsLinked to original sources

bioRxiv2025

HSP90-mediated stress resilience in male gametophyte of Arabidopsis thaliana

Despite the accumulation of protective heat shock proteins (HSPs) during the male gametophyte development, pollen grains are highly sensitive to elevated temperatures. We performed transcriptomic analysis of five pollen developmental stages isolated from plants under normal and heat stress (H) conditions; uni-nuclear (UN), early bi-cellular (EB), bi-cellular (BC), tri-cellular (TC), and mature pollen (MPG). We show that the majority of genes that are up- or down-regulated under HS are specific for each stage, except BC stage that also exhibited the highest number of differentially expressed genes (DEGs) (>4000). This emphasize a complex, stage-dependent heat stress response, possibly dependent on HSP levels. Additionally, promoter motif analysis revealed that heat shock elements (HSEs) exhibit a stage- specific pattern of enrichment, which peaked in MP. To explore stage-specific influences of HSP90s in pollen development, we characterized a knockdown RNAi line, under normal and stress conditions in early- and late-stage RNAi lines using stage-specific promoters pJASON (JA90R) and pLAT52 (L90R). The hsp90 background leads to lower germination rate in both RNAi lines that is more pronounced under heat stress caused by significant alterations in heat stress control via impaired ABA signalling or ER stress response. Heat stress conditions also lead to a high percentage of nuclei shape and orientation defects in the L90R line pollen, pointing to the higher sensitivity of late stage development. We show this defect is linked to the down-regulation of DNA metabolism genes. Our complex dataset provides insight into stage-specific stress response on the level of single cell undergoing developmental changes.

plant biology↗

bioRxiv2025

Molecular and Phenotypic Characterization of Telomere Repeat Binding (TRBs) Proteins in Moss: Evolutionary and Functional Perspectives

Telomere repeat binding (TRB) proteins are plant-specific proteins with a unique domain structure distinct from telomere-binding proteins in animals and yeast. While extensively studied in seed plants, their role in early-diverging plant lineages remain largely unexplored. Here, we investigate TRB proteins in a model moss, Physcomitrium patens, to assess their evolutionary conservation and functional significance. Functional analysis using single knockout mutants revealed that individual PpTRB genes are essential for normal development, with mutants exhibiting defects in the two-dimensional (protonemal) stage and, more prominently, in the formation of three-dimensional (gametophore) structures. Some double mutants displayed telomere shortening, a phenotype also observed in TRB-deficient seed plants, indicating a conserved role for TRBs in telomere maintenance. Transcriptome profiling of TRB mutants revealed altered expression of genes associated with transcriptional regulation and stimulus response in protonema. Subcellular localization studies across various plant cell types confirmed that PpTRBs, like their seed plant counterparts, localize prevalently to the plant nucleus and mutually interact. In bryophytes, TRBs form a monophyletic group that mirrors the species phylogeny, whereas in seed plants, TRBs have diversified into two distinct monophyletic groups. Our findings provide the first comprehensive characterization of TRB proteins in non-vascular plants and demonstrate their conserved roles in telomere maintenance, with additional implications for plant development and gene regulation across land plant lineages. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/659030v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1fea36dorg.highwire.dtl.DTLVardef@9b5569org.highwire.dtl.DTLVardef@488d0org.highwire.dtl.DTLVardef@1b22c6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Shoot phenotyping of cytokinin receptors mutants revealed fluorescence parameters as early markers of drought stress

Plant phenotyping represents an increasing promise in plant research by providing a complex picture of plant development and fitness. In research focused on various environmental stresses, phenotyping can uncover markers that can sensitively assess the stress impact in very early stages before morphological changes. PlantScreenTM System represents a tool dedicated for shoot and root phenotyping in soil enabling high-precision, high-throughput phenotyping of small, mid-size and large plants. The system offers wide range of sensors providing the number of non-invasive analyses of morphological and physiological parameters as well as of pigments, water, or metabolite content. In our work, we combined phenotyping approaches to determine morphological changes and the status of the photosynthetic apparatus in Arabidopsis plants exposed to drought stress. Focused on morphology, the rosette area became smaller after seven days of drought stress when compared to control conditions. Interestingly, cytokinin signalling mutant ahk2 ahk3 revealed drought resistance compared to other genotypes. The fluorescent parameters showed higher sensitivity even in wild type. Non-photochemical quenching displayed values connected to reduced activity of photosynthetic apparatus after five days of drought stress. Taken together, acquired fluorescence parameters can serve as a marker of drought stress detection before morphological alterations occur. HighlightFluorescence parameters can serve as early markers of drought stress before morphological alterations appear. Shoot phenotyping of cytokinin receptor mutants showed drought resistance in the ahk2 ahk3 double mutant.

plant biology↗

bioRxiv2023

Night-time neuronal activation of Cluster N in a North American songbird

Night-migrating songbirds utilize the Earths magnetic field to help navigate to and from their breeding sites each year. A region of the avian forebrain called Cluster N has been shown to be activated during night migratory behavior and it has been implicated in processing geomagnetic information. Previous studies with night-migratory European songbirds have shown that neuronal activity at Cluster N is higher at night than during the day. Comparable work in North American migrants has only been performed in one species of swallows, so extension of examination for Cluster N in other migratory birds is needed. In addition, it is unclear if Cluster N activation is lateralized and the full extent of its boundaries in the forebrain have yet to be described. We used sensory-driven gene expression based on ZENK and the Swainsons thrush, a night-migratory North American songbird, to fill these knowledge gaps. We found elevated levels of gene expression in night-vs. day-active thrushes and no evidence for lateralization in this region. We further examined the anatomical extent of neural activation in the forebrain using 3D reconstruction topology. Our findings demonstrate that Swainsons thrushes possess an extensive bilateral night-activated Cluster N region in the forebrain similar to other European avian species, suggesting that Cluster N is highly conserved in nocturnal migrants.

neuroscience↗

bioRxiv2021

Comprehensive analysis of behavioral dynamics in the protochordate Ciona intestinalis

Vertebrate nervous systems can generate a remarkable diversity of behaviors. However, our understanding of how behaviors may have evolved in the chordate lineage is limited by the lack of neuroethological studies leveraging our closest invertebrate relatives. Here we combine high-throughput video acquisition with pharmacological perturbations of bioamine signaling to systematically reveal the global structure of the motor behavioral repertoire in the Ciona intestinalis larvae. Most of Cionas postural variance can be captured by six basic shapes, which we term "Eigencionas". Motif analysis of postural time series further demonstrated that bioamines influence numerous stereotyped behavioral maneuvers including "startle-like" and "beat-and-glide". Employing computational modeling of swimming dynamics and spatio-temporal embedding of postural features revealed that subtle behavioural differences are generated at the levels of motor modules and the transitions between, both modulated by bioamines. Finally, we show that flexible motor module usage gives rise to diverse behaviors in response to different light stimuli.

animal behavior and cognition↗

bioRxiv2020

Fine-tuning of Epithelial EGFR signals Supports Coordinated Mammary Gland Development

During puberty, robust morphogenesis occurs in the mammary gland; stem- and progenitor-cells develop into mature basal- and luminal-cells to form the ductal tree. The receptor signals that govern this process in mammary epithelial cells (MECs) are incompletely understood. The EGFR has been implicated and here we focused on EGFRs downstream pathway component Rasgrp1. We find that Rasgrp1 dampens EGF-triggered signals in MECs. Biochemically and in vitro, Rasgrp1 perturbation results in increased EGFR-Ras-PI3K-AKT and mTORC1-S6 kinase signals, increased EGF-induced proliferation, and aberrant branching-capacity in 3D cultures. However, in vivo, Rasgrp1 perturbation results in delayed ductal tree maturation with shortened branches and reduced cellularity. Rasgrp1-deficient MEC organoids revealed lower frequencies of basal cells, the compartment that incorporates stem cells. Molecularly, EGF effectively counteracts Wnt signal-driven stem cell gene signature in organoids. Collectively, these studies demonstrate the need for fine-tuning of EGFR signals to properly instruct mammary epithelium during puberty.

cell biology↗

bioRxiv2020

The Internal Structure of Metacommunities

Current analyses of metacommunity data largely focus on global attributes across the entire metacommunity, such as mean alpha, beta, and gamma diversity, as well as the partitioning of compositional variation into single estimates of contributions of space and environmental effects and, more recently, possible contributions of species interactions. However, this view neglects the fact that different species and sites in the landscape can vary widely in how they contribute to these metacommunity-wide attributes. We argue for a new conceptual framework with matched analytics with the goals of studying the complex and interactive relations between process and pattern in metacommunities that is focused on the variation among species and among sites which we call the internal structure of the metacommunity. To demonstrate how the internal structure could be studied, we create synthetic data using a process-based colonization-extinction metacommunity model. We then use Joint Species Distribution Models to estimate how the contributions of space, environment and biotic interactions driving metacommunity assembly differ among species and sites. We find that this approach to the internal structure of metacommunities provides useful information about the distinct ways that different species and different sites contribute to metacommunity structure. Although it has limitations, our work points at a more general approach to understand how other possible complexities might affect internal structure and might thus be incorporated into a more cohesive metacommunity theory.

ecology↗

bioRxiv2018

Quantitative analysis reveals the basic behavioural repertoire of the urochordate Ciona intestinalis.

Quantitative analysis of animal behaviour in model organisms is becoming an increasingly essential approach for tackling the great challenge of understanding how activity in the brain gives rise to behaviour. In addition, behavioural analysis can provide insight on the molecular basis of nervous system development and function as demonstrated by genetic screens focused on behavioural phenotyping in some genetically tractable model organisms. The progress in building low-cost automated tracking setups, together with advances in computer vision machine learning have expanded the repertoire of organisms which are amenable to quantitative behavioural analysis. Here we used automated image-based tracking to extract behavioural features from an organism of great importance in understanding the evolution of chordates, the free swimming larval form of the tunicate Ciona intestinalis which has a compact and fully mapped nervous system composed of only 231 neurons. We analysed hundreds of videos of larvae and we extracted basic geometric and physical descriptors of larval behaviour. Most importantly, we used machine learning methods to create an objective ontology of behaviours for C. intestinalis larvae. We identified eleven behavioural modes using agglomerative clustering. This approach enabled us to produce a quantitative description of the basic larval behavioural repertoire. Furthermore, we tested the robustness of this repertoire by comparing different rearing conditions and ages. Using our pipeline for quantitative behavioural analysis, we successfully reproduced the known photoresponsive behaviour and the first demonstration to our knowledge that C. intestinalis larvae exhibit sensory arousal and thigmotaxis, both of which can be modulated by the anxiotropic drug modafinil. Remarkably, by comparing the behaviour between animals assayed individually or in small groups, we found that crowd size influences larval behaviour. This study shows that C. intestinalis larval behaviour can be broken down to a set of stereotyped behaviours that are used to different extents in a context-dependent manner. Furthermore, it raises exciting possibilities such as mapping behaviour to specific neurons of this compact chordate nervous system and it paves the way for comparative quantitative behavioural studies as a means to reconstruct the evolution of behaviour, especially in the chordate lineage.

animal behavior and cognition↗