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Autophagy is the evolutionarily well-conserved process during which cell components are degraded and recycled. One of the crucial, but poorly understood steps of autophagy is autophagic body degradation in vacuole. To this day, no enzyme involved in this autophagy stage in plants has been identified. However, vacuolar processing enzymes (VPE) constitute great candidates as they are key vacuolar enzymes that activate other hydrolases. Our team is addressing this hypothesis by conducting studies on isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) cultured in vitro under various carbon (sugar) and nitrogen (asparagine) conditions. Sugar starvation induces autophagy, whereas asparagine (Asn) slows down autophagic body breakdown. So far, we detected a significantly higher VPE activity in sugar-starved axes (-S) than in sucrose-fed axes (+S), which was lowered in -S axes fed with asparagine (-S+Asn) and treated with autophagy inhibitors that interrupt this process at different stages. Ultrastructure observations, using a VPE inhibitor, showed an accumulation of autophagic bodies in the vacuoles of the -S axes. We performed the RNA-seq analysis and identified five transcripts of genes encoding VPE in each lupin species, within which four were most similar to the γVPE and one to the βVPE isoform of Arabidopsis thaliana. The RT-qPCR analysis revealed that only two γVPE-like genes showed higher levels of transcripts in the -S axes than in the +S axes. This may indicate that only given VPE participate in autophagic body degradation during sugar starvation-induced autophagy in lupin embryonic axes.

SEB Conference 2025

Study on the role of vacuolar processing enzymes (VPE) in autophagic body degradation during carbon starvation-induced autophagy

vacuole

protease

lupin

carbon starvation

autophagy

embryo

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Muscle fibre type distribution may be influenced by clinical state and differs between individuals. For example, chronic heart failure patients experience a shift from fast to show fibres, while sprinters have a larger fraction of fast fibres than non-sprinters. However, in vivo changes in fibre type distribution are accompanied by alterations in other muscle properties, most notably size and strength, making it difficult to isolate their effects on movement. This challenge can be overcome using predictive simulations, which synthesize motion and control based on a performance criterion. This study investigated the impact of fibre type distribution on gait biomechanics using predictive simulations.
We simulated walking (1.33 m/s) using the predictive simulation framework, PredSim. Ninety-two muscles were each represented by a Hill-type muscle model with two motor units containing all its slow and fast fibres, respectively. The baseline model used experimentally derived physiological cross-sectional area fractions for slow and fast fibres. These proportions were then varied from 6% to 96% slow fibres to assess their effects on walking biomechanics.
Metabolic cost of transport gradually decreased (~26% in total) as the fractions of slow fibres increased from 6% to 96%. Spatiotemporal characteristics, joint angles, joint torques, and muscle coordination were similar in most conditions, excepting at the highest slow fibre fractions (>86% slow). While the latter effects were modest during walking, we hypothesize that fibre type composition may have greater impacts on more demanding tasks, such as running. Overall, these findings suggest that muscle fibre type composition meaningfully affects gait biomechanics.

Muscle fibre type distribution influences walking biomechanics: A predictive simulation study

Genetic studies on the Arctic key fish species Polar cod, Boreogadus saida, from the Svalbard archipelago have been limited by relatively sparse sampling, primarily focusing on open-water areas with few or no fjord locations included. These studies have not yet provided conclusive evidence of genetic differentiation between Svalbard and other populations. This study therefore sought to ascertain whether a more extensive sampling program, encompassing 10 fjord stations along the north and west coast of Svalbard, could reveal functional differences on the transcriptomic level and indicate potential local adaptations, thereby providing insights into the presence of differentiated ecotypes. Thus, we conducted a RNASeq experiment along an environmental cline. The sampled stations varied from open water locations with well mixed water columns to closed, silled fjords with a strong thermocline, huge temperature differences across the water column (e.g., Billefjorden ΔT = 7 °C), and oxygen depletion in the deep-water layer (O2  < 70 % air saturation). The analysis revealed significant transcriptomic variation in response to the environmental gradient. The gene expression was primarily influenced by oceanic conditions (Atlantic or Arctic), local abiotic factors, and food availability, with primary production playing a key role in the different gene expression patterns observed between the clusters. These findings suggest local adaptation and the existence of four potential Polar cod ecotypes along the north-west coast of Svalbard and that a more detailed population-genomic analysis is essential to further explore the population structure of Polar cod in the high Arctic archipelago.

Seascape transcriptomics in Polar cod: profiling along an environmental cline

Understanding thermal physiology is critical for predicting population shifts due to climate change. During heatwaves, fish are particularly vulnerable due to increased energy demands and reduced oxygen levels in warmer waters. Current perceptions of heatwave risks often focus on short-term mortalities, neglecting fitness effects associated with sub-lethal physiological constraints.
In Atlantic salmon (Salmo salar), age at maturity, a key life-history trait, is genetically linked to aerobic scope — an essential metabolic attribute for energy allocation. Energy allocation is highly responsive to environmental temperatures, but how do different life history genotypes respond to heatwave temperatures?
First, we present a thermal performance curve for aerobic scope for juvenile salmon after acclimation. We also examine physiological differences between two vgll3 genotypes, which are linked to early or late maturation in adult salmon. We measured specific dynamic action, the metabolic cost of digestion and food assimilation, and aerobic scope of salmon juveniles at 15 and 20 °C to observe how fish manage energy expenditure as temperatures rise.
This study has significant implications for understanding the fitness of Atlantic Salmon and linking the effects of heatwaves to their life history and physiological fitness. Variation in how different genotypes respond to non-optimal temperatures allows for more accurate predictions of how populations may change in terms of genotypic structure and behaviour. This research is crucial for understanding evolutionary responses to climate change and for developing conservation strategies, both globally and within Finnish waters.

Is thermal performance during heatwaves predicted by life history genotypes in salmon?

Climate warming is directly affecting aquatic ectotherms. In addition, aquatic animals are constantly threatened by potential infections from various pathogens. Heatwaves and warming of habitats have been associated with increases in disease outbreaks and mortality in several ectotherms, suggesting the immune system can be an important component determining climate impacts. Fish rely heavily on the innate immune system with its generalist leukocytes in fighting pathogens, cell signalling, repairing wounds and regenerating tissue. The aim was therefore to investigate how temperature affects the immune response and regeneration. We did this byin vivoimaging of transgenic zebrafish (Danio rerio) larvae, with fluorescent neutrophils and macrophages, that were incubated at either 20°C, 28°C, 31°C, 33°C or 35°C. We performed tail amputations and observed the immune cell recruitment for 12 hours and tail regeneration over three days, while maintaining the thermal treatments. Both immune cell recruitment and regeneration were strongly affected by temperature. Recruitment of neutrophils was faster and higher in recruited cell numbers with increasing temperature. Macrophages, however, showed impaired recruitment at the highest temperature. Tissue regeneration displayed a typical thermal performance curve, where 20°C showed the slowest regeneration, increasing regeneration with temperature up to 35°C, over where it declined. These results suggest that fishes might be more vulnerable to infections at warm temperatures, and it is possible that the climate change driven disease outbreaks we observe in natural populations can be partly explained by a decreased function of the innate immune response.

The effect of temperature on the immune response in zebrafish by in vivo imaging

Environmental stressors such as chemical and light pollution can have detrimental effects on the fitness of animals. One proposed link between these stressors and survival are telomeres, which play an important role in genome protection, ageing and somatic maintenance and are known to be shortened due to harsh environmental conditions. Amphibians are especially susceptible to environmental stressors because of their permeable skin and complex life cycle, characterized by metamorphosis from larvae to adults, making them an ideal model species to investigate possible effects of anthropogenic disturbance on telomere length. Therefore, we test the effects of chemical and light pollution on the telomere dynamics of the European green toad (Bufotes viridis) from larval stage until adulthood, in controlled lab experiments as well as in field studies in and around Vienna. We are developing a real-time quantitative polymerase chain reaction (qPCR) assay to analyze the relative telomere length (RTL) from DNA swabs from the larval, juvenile and adult stages. This longitudinal approach to understanding telomere dynamics of amphibians is the first one of this kind and the results will broaden our understanding about how anthropogenic disturbance acts on wildlife on a molecular basis and will therefore help to further improve animal conservation.

Telomere dynamics of the European green toad (Bufotes viridis) in the context of urbanization and pollution

Suspension feeders, organisms that retain food particles from water, have recently become of interest to inspire engineered filtration systems aiming for higher efficiency, energy savings, and reduced clogging. Among the 35 known suspension feeding mechanisms, only a few have been explored in detail for a biomimetic transfer, and even fewer have progressed to successful prototypes, patents, and commercial products. Based on my research of invertebrate and vertebrate suspension feeders, I experienced several challenges during the identification, analysis and transfer of biological particle separation processes. For example, constraints such as availability, protection statuses, and size posed difficulties when examining organisms like flamingos, manta rays, and whale sharks. A significant challenge was encountered in analysing the role of mucus in particle adhesion and transport in ascidians. Flow tank experiments using artificial mucus demonstrated limited particle retention capabilities compared to natural mucus. Despite these obstacles, promising results were achieved with ram-feeding fish. By integrating morphological, behavioural, and fluid-dynamical analyses, a prototype filter was developed with a self-cleaning mechanism capable of retaining 97.5% of microplastic fibres in a controlled lab environment. These findings underscore the potential of the biomimetic approach not only to advance filtration technology but also to deepen our understanding of these organisms, thereby supporting their conservation.

Overcoming Challenges in Studying Filter-Feeders for Bio-Inspired Filtration

The steroid hormone cortisol plays a crucial role in our response to stress, influencing various physiological systems, including the brain and immune system. These effects are mediated by two receptors: the mineralocorticoid receptor (MR) and the glucocorticoid receptor (GR). Both function as ligand-activated transcription factors, binding as homodimers to response elements in target genes. While MR and GR have been shown to form heterodimers, the physiological significance of MR/GR heterodimerization remains largely unexplored. In recent studies, we have demonstrated that MR/GR heterodimerization is essential for specific cortisol-driven effects on behaviour and immune function. To investigate this, we developed mutant MRs and GRs that could selectively form homo- or heterodimers and we expressed these receptors in zebrafish larvae from an MR/GR double knockout line. Behavioral analysis revealed that cortisol-induced hyperactivity occurred only under conditions of MR/GR heterodimerization. Similarly, cortisol’s inhibition of macrophage migration during inflammation also depended on heterodimer formation. To identify molecular targets of the MR/GR heterodimers, we next performed RNA-sequencing. Our findings showed that the heterodimers regulate distinct gene expression patterns. For example, genes involved in glutamatergic signalling were regulated, which was confirmed by CRISPR/Cas9-mediated gene editing of a response element in the gene encoding the metabotropic glutamate receptor 3, which abolished the cortisol-induced hyperactivity. In summary, our research establishes the physiological relevance of MR/GR heterodimerization in vivo, highlighting its central role in eliciting cortisol-induced responses to stress.

Mineralocorticoid and glucocorticoid receptor heterodimers drive distinct cortisol-induced stress responses

GCN2 is an evolutionarily conserved serine/threonine protein kinase that acts as a sensor of amino acid deficiency and phosphorylates eIF2α; this inhibits global translation initiation but allows expression of ATF4 and activation of the integrated stress response (ISR). Here we show that we show that eight different inhibitors of the RAF protein kinases (RAFi) paradoxically activate GCN2 leading to eIF2α -dependent (and ERK1/2-independent) ATF4 and CHOP expression. The GCN2 kinase inhibitor A-92, GCN2 RNAi, GCN2 knock-out or ISRIB (an eIF2α antagonist) all reverse RAFi-induced expression of ATF4 and CHOP indicating that RAFi require GCN2 to activate the ISR.  RAFi also activate full-length recombinant GCN2in vitroand in cells. Activation of the ISR by RAFi is abolished by a GCN2 kinase dead mutation, whilst a M802A gatekeeper mutant is activated at lower RAFi concentrations, demonstrating that RAFi bind directly to the GCN2 kinase domain; this is supported by mechanistic structural models of RAFi interacting with GCN2.  RAFi may therefore serve as novel probes for GCN2 function in the ISR and proteostasis. Our results may also be relevant to the clinical use of RAFi in cancer.

A novel class of small molecule activators of GCN2, an amino acid-sensing protein kinase

A non-destructive multi-omic approach was adopted to integrate phenome (imaging phenotyping and physiological gas exchange) and volatilome analyses (detection of Volatile Organic Compounds, VOCs) to investigate plant-plant communication in tomato (Solanum lycopersicum). A wild-type (WT) and a mutant (MT) for a gene putatively encoding for an odor receptor were analyzed. WT and MT plants (receivers) were closed in containers, together with WT plants previously subjected to water stress (emitters). The VOCs released by the emitters are supposed to function as chemical signals, enhancing defensive mechanisms (priming) of neighboring plants against future stressors. After 24 hours, a subset of WT and MT receivers was subjected to water stress to evaluate the priming effect. The preliminary analysis of phenomic data reveals differences between stressed and non-stressed plants, hindering the detection of the priming response. The Principal Component Analysis of volatilome data confirms this separation and further distinguishes between WT and MT plants. Statistical and supervised machine learning methodologies can significantly enhance the analysis of complex datasets. To this end, we are implementing models capable of identifying common latent components across -omic analyses, rigorously selecting the most informative features, improving both the interpretability and robustness of the analysis. This approach has proven particularly effective for datasets with limited sample sizes and is expected to enable the identification of potential critical biomarkers and distinctive response patterns. The innovative integration of multi-omics and artificial intelligence techniques opens new avenues for studying plant communication while advancing both fundamental knowledge and applied research strategies.

AI-driven multi-omics analysis of plant-plant communication in tomato, using Feature Extraction and Statistical Machine Learning

Water scarcity, impacted by climate change, threatens grapevine production and quality. To select varieties more adapted to constraining conditions, a key lever could be to explore genetic progress margins around the well-known trade-off between carbon gain and water loss. A major bottleneck that hampers such advances is the lack of methods for measuring fine functioning traits on thousands of plants as required for genetic analyses, and easily usable in field settings. To overcome this limitation, we deployed an original approach to predict photosynthesis, water-use efficiency and other constitutive leaf traits using high-throughput measurements of poro-fluorometry and near-infrared spectroscopy on a grapevine diversity panel of 250 cultivars grown both in a greenhouse with different watering regimes, and in the vineyard. All these cultivars were resequenced, yielding 1.6M genomic variants, which were used to perform genome-wide association studies with single-locus linear mixed-model and LocalScore algorithms. We found large genetic variability for all traits studied in the greenhouse, with genomic heritability ranging from 0.14 to 0.38. Thirty-six QTLs were detected, with some co-localizations, such as a main genomic region associated with net photosynthesis, electron transport rate, and transpiration. Interestingly, additional regions were detected, specifically associated with either photosynthesis or transpiration, highlighting genetic margins to maintain photosynthesis under drought together with a lower water use. Our findings provide valuable insights into how photosynthesis responds to multiple environmental factors in field settings. This is particularly relevant for perennial crops such as grapevine, where cumulative effects of adverse conditions over years deserve major attention.

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Muscle fibre type distribution influences walking biomechanics: A predictive simulation study

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