Belgium

Life is complex. The response of marine ectotherms to global changes stems from minute molecular alterations, with consequences scaling up through cellular functions to phenotypes to ecosystems. Another layer of complexity arises from the potential emergence of the interactive effects of multiple stressors. Whilst statistical and methodological developments, such as integrative frameworks and high-throughput omics, marked breakthroughs in clinical sciences, their use is lagging behind in aquatic sciences. Here, we explored a large-scale multilayer dataset on the response of the circumpolar Northern shrimp Pandalus borealis to combined ocean warming, acidification and hypoxia as the ideal opportunity to develop a framework implementing both different levels of the biological hierarchy and multiple stressors. Molecular (metabolomics, lipidomics, proteomics), cellular (enzymatic activity) and physiological (standard metabolic rates, maximum metabolic rates, aerobic scope) phenotypes of Northern shrimp from the Northwest Atlantic were integrated into multiomics and multilayer networks. Multivariate analyses show that the response of Northern shrimp strongly depends on the severity of their multistressor environment. Particularly, when hypoxia is superimposed to ocean acidification and warming, a positive synergistic effect emerges in multiomics profiles. Further analyses will help identify the key cellular functions that underpin the reduction in physiological performance and survival observed under combined ocean change drivers. Implementing integrative multiomics and multilayer approaches in marine and aquatic sciences will facilitate breakthroughs in life sciences, providing a greater understanding of how aquatic ectotherms will respond to ongoing environmental changes. Ultimately this new knowledge will inform more effective conservation measures and management strategies.

SEB Conference 2025

Beyond biomarkers: multiomics and multilayer networks as breakthroughs to predict the effects of global changes on aquatic ectotherms

combined stressors

multitraits

multiomics

omics

hypoxia

physiology

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SEB Conference 2024

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Seabirds are considered sentinels of marine ecosystem health. Black-legged kittiwakes (Rissa tridactyla) have experienced population declines as a result of prey shortages due to changing oceanographic conditions. Since 2019, a collaborative study on heart rate in black legged kittiwakes has been conducted by scientists at McGill University, University of Liverpool, University of Roehampton, and McMaster University at the Institute of Seabird Research and Conservation on Middleton Island, Alaska. To examine the indirect physiological effects of prey shortages, we used heart rate as a proxy of oxygen consumption and fine scale energetics. The recent development of a new prototype logger for birds has significantly improved data quality, with a 99% accuracy rate between manual and automatic heart rate measurements. In 2024, 45 kittiwakes were implanted with heart rate loggers and gps-accelerometers to identify which behaviours (flight, resting, etc.) required the most energy during different stages of the breeding season. Flapping flight was identified as the most energy-costly behaviour in kittiwakes, which is performed mainly during the chick-rearing stage. To examine the affect of supplemental feeding, 30 kittiwakes that were implanted with heart rate loggers were fed capelin three times a day for 10 days. Heart rate and body temperature differed significantly between fed and unfed birds after a feeding event. Our work will provide novel insights into the use of heart rate as a novel proxy of energetics and help to identify tipping points in which declines in prey availability could result in an energy deficit in kittiwakes and other seabirds.

Heart rate as a proxy of metabolic rate in black-legged kittiwakes (Rissa tridactyla)at Middleton Island, Alaska

Among vertebrates, patterns of movement vary considerably, from the lateral spine-based movements of fish to the predominantly limb-based movements of mammals. Yet, we know little about why these changes may have occurred in the course of evolution. Lizards form an interesting intermediate group where locomotion appears to be driven by both motion of their limbs and lateral spinal undulation with the extent varying between species. To understand the evolution and relative advantages of limb versus spine locomotion, we developed an empirically informed mathematical model, as well as used in-vivo data to inform a robotic model. Furthermore we have compared predictions from the mathematical model to in-vivo data from running and climbing lizards and data collected with the robotic model. Our mathematical model showed that, if limbs were allowed to grow longer, movements of the spine did not enable longer strides, since spinal movements reduced the achievable range of motion of the limbs. Yet, in-vivo data shows lateral spine movement is widespread among diverse group of lizards. Our robotic model was able to explain this disparity, showing that increased movement of the spine was energetically favorable. Our robot model also revealed that stability decreased with increased spine and limb range of motion, detailing the trade-off between speed and stability. Overall, our robotic model found a Pareto-optimal set of strides—when considering speed, efficiency, and stability—requiring both spine and limb movement, which closely agreed with movement patterns among lizards.

Coordinating limbs and spine: (Pareto-) optimal locomotionin theory, in vivo, and in robots

Understanding the dynamics of blood flow and fuel delivery to the flight muscles of hovering hawkmoths is critical for evaluating the energy budget of these most energy-demanding organs. Flying hawkmoths significantly increase the body temperature and concentration of the lipoprotein nanoshuttles that deliver fuel from the fat body to the muscles. These changes directly affect blood viscosity and the dynamics of blood circulation. Using data on blood viscosity in resting hawkmoths (Sphingidae) and analyzing the structure of flight muscles from X-ray tomography data, we developed a series of models providing estimates of the drag forces exerted by the flowing blood on contracting muscles, pointing on important connection of muscular action with hemodynamics. We show that the flowing blood is able to deform muscle and hence this nontrivial coupling of blood flow and muscular contraction/relaxation leads to a viscoelastic reaction of the thorax.
This work was partially supported by NSF grants IOS 2014664 & 2422802.
[1] Brasovs A, Palaoro AV, Aprelev P, Beard CE, Adler PH, Kornev KG. 2023 Haemolymph viscosity in hawkmoths and its implications for hovering flight. Proc. R. Soc. B 290: 20222185

Hemodynamic mechanism of dissipation of muscular energy in hovering hawkmoths

Parasitised animals can differ dramatically in terms of their behaviour and cognitive performance from uninfected conspecifics. Yet, the causal direction of this relationship remains unclear: do parasites alter host behaviour/cognition, or do consistent differences in behaviour/cognition make hosts more susceptible to infection? We tackled these questions using wild-caught pumpkinseed sunfish (Lepomis gibbosus) to investigate the relationships among parasitism, behaviour and cognition. In a first study, we used fish body condition as a proxy for health status to help reveal correlations between parasites and host traits (i.e., exploration, boldness, cognition). Only individuals in relatively lower body condition displayed a negative relationship between parasite density and exploratory behaviours. However, there was no correlation between aversive learning, a measure of cognitive performance, and infection. Our results showed that body condition is important to consider when studying infection in wild populations as some patterns are only apparent when body condition is taken into consideration. In a second study, we measured exploration, activity, boldness and body condition before and after a semi-experimental infection using lake mesocosms where sunfish were naturally exposed to parasites. We found that behaviour strongly influenced infection susceptibility: bolder and less active fish acquired a higher density of parasites during the infection period. Following infection, fish body condition decreased with increasing cestode density, and activity decreased with increasing trematode density, suggesting that co-infection negatively impact hosts. These results highlight that two mechanisms may simultaneously operate: initial host behaviour influences their risk of infection, and infection alters the behaviour of infected hosts.

Double trouble: host behaviour influences and is influenced by co-infection with parasites

In the lab, diet has been found to greatly influence cognition, particularly during development. Specifically, high-fat high-sugar (HFHS) diets reduce learning and memory. One of the processes through which this occurs is the gut-brain axis, where the gut-microbiome influences how animals make decisions, such as during spatial exploration and navigation. In urban environments, species such as pigeons are often exposed to HFHS diets. In this study, we provided a HFHS diet and a control diet for 4 weeks to two groups of young racing pigeons, after which they all received the control diet (n=96). During treatment, the two groups did not differ in their gut-microbiota diversity, but from week 5 onwards young pigeons exposed to the HFHS diet had a higher gut-microbiota diversity than those raised on the control diet. When individuals were trained to return to their home loft, unlike what we predicted, individuals on the HFHS diet were (1) faster at finding the home loft, (2) faster at learning, (3) explored less and were (4) less cohesive and coordinated than individuals in the control group. Diet induced gut-microbiota diversity changes could explain behavioural differences in both social and individual navigation.

High-fat high-sugar diets and their effects on the gut microbiota and cognition of feral pigeons (Columba livia domestica)

The intricate DNA repair mechanisms organisms employ to rectify damage induced by environmental factors, such as UV rays, play a pivotal role in maintaining genomic stability. UV-induced damage leads to bulky lesions which are removed primarily by two Nucleotide excision repair (NER) pathways i.e., Global Genome Repair (GG-NER) and Transcription-Coupled Nucleotide Excision Repair (Tc-NER). In mammals Tc-NER involves the recruitment of CSA and CSB repair proteins when RNA polymerase halts at the damage site during transcription, resulting in transcription arrest followed by the formation of a repair bubble. This study aims to identify the proteins engaged in transcription-coupled DNA repair in Arabidopsis, offering insights into repair dynamics using the XR-seq method. Key proteins in mammalian Tc-NER are CSA and CSB for damage recognition and XPF\XPG serve as endonucleases responsible for DNA excision. Arabidopsis harbors homologs of key NER repair proteins CSA (AtCSA1 and AtCSA2), CSB (Chr24, Chr8), and XPF\XPG endonucleases (UVH3, UVH1, and ERCC1). Utilizing the XR-seq methodology allows the generation of genome-wide DNA repair maps at a single nucleotide level resolution. The main steps in XR-seq include Cell lysis, Immunoprecipitation, Adapter ligation, and Sequencing. We performed XR-seq for CSB homologs (Chr24 and Chr8) in Arabidopsis. Data shows the repair dymanics on transcribed strands for Chr24 and Chr8 knockouts compared to the normal wild type. Comparative protein alignments of these homologs also underscore potential functional differences. This research contributes to a comprehensive understanding of plant DNA repair processes and how they maintain genome integrity.

Identification  of Arabidopsis Proteins Involved in Nucleotide Excision Repair

Mechanical deformations of DNA are ubiquitous in Biology and occurs as part of critical processes involved in the reading, repair, copying, and packaging of genetic information. Therefore, such processes may be regulated by the local mechanical pliability of DNA to accommodate physical deformations. We have developed high-throughput technology to measure how local sequence impacts local DNA bendability via a “mechanical code”. We show that via the mechanical code, genomes encoded regulatory information impacting diverse cellular processes such as gene expression, nucleosome organization and remodelling, transcription factor binding, and DNA supercoiling by topoisomerases. We are currently exploring how chemical alterations to DNA such as via epigenetic modifications or DNA damage may alter the mechanical code, resulting in downstream functional consequences. We are also investigating how variations in DNA mechanics impact the genome-wide variations in DNA supercoiling, ultimately allowing environmental factors that control supercoiling to impact broad cellular gene expression programmes in complex ways. Overall, we advance our understanding of how physical forces have impacted the evolution of genomes.

Deciphering the mechanical code of DNA and its impact on cellular processes

AI literacy and the readiness to apply a range of simple and complex technologies in schools and universities represent significant challenges that our institutions must address as they progress. The uncertainty surrounding when staff and students should employ these technologies perpetuates numerous challenges that disciplines and educationalists must resolve. However, while questions about how these technologies are being adopted arise, it is crucial to consider where their utility can be maximised for both staff and students, as well as the base level of literacy needed to access the various present and emerging tools (Stanković et al., 2024). Nurfidari et al. (2024) argue that overviews and introductions to available technologies and their utilisation in various roles are necessary for both staff and students. Particularly when integrating systems into student and staff roles, it is essential to consider how we can support staff in using these new technologies, whether in teaching-focused roles or other capacities.
How do we ensure students can engage with the technology while simultaneously developing their skills and ethical uses? Therefore, we must reflect on how we intend to embed these tools to benefit our communities, rather than merely expanding the user base, while also considering the lifelong learning needs of both students and staff (Simeunović & Ružičić, 2024).

Enhancing AI Literacy and Technological Integration in Education: Challenges and Strategies

The efficiency of water uptake by plants from the soil is shaped by root system architecture and influenced by anatomical features, such as hydrophobic barriers and aerenchyma formation. While root architecture determines the spatial distribution of roots, root anatomy influences local hydraulic properties like radial and axial conductances.Water movement through root tissues occurs via apoplastic and cell-to-cell pathways. Apoplastic flow can be blocked by hydrophobic barriers like lignin and suberin, while cell-to-cell flow is regulated by plasmodesmata and aquaporins. These features collectively define radial conductivity and axial conductance, which are crucial for estimating a plant's water uptake capacity.While these hydraulic properties have been extensively studied in monocotyledons, there is a knowledge gap regarding woody dicotyledons. Dicots present significant anatomical differences, including secondary growth and different hydrophobic deposition patterns, which can substantially impact hydraulic dynamics.Here we use computational models to investigate how anatomical features influence root hydraulic properties in tomato (used as a model species). We characterized the root anatomy of 30-day-old tomato plants and developed a secondary growth module to a generator of root anatomy. We also monitored suberin and lignin deposition in the endodermis and exodermis, establishing a spatiotemporal atlas of their maturation, coupled with recent litterature data. We used a hydraulic solver of root anatomy hydraulics to estimate local hydraulic properties and conducted in silico analysis to assess the impact of various factors on root hydraulic conductance and water uptake profiles.This research provides valuable insights into the hydraulic dynamics of dicotyledonous roots.Correspondence: marco.dagostino@uclouvain.be

Influence of secondary growth, apoplastic barriers and developmental anatomy on root hydraulic properties: In Silico analysis

Engineering staple crops like Zea mays to associate with N2 -fixing rhizobia or to enhance existing associations with arbuscular mycorrhizal fungi (AMF) are two strategies being pursued to improve the sustainability of food production by reducing the need for synthetic fertilizers. The effectiveness of such strategies may vary depending on soil nutrient conditions in the field as well as the developmental stage of the plant. We developed the first metabolic models describing the symbiotic nutrient exchange between a plant and AMF and validated its predictions by comparing them with empirical data from a field study comparing plants with and without AMF. Measured and predicted growth rate benefits – 31% vs. 19%, respectively – aligned closely, and predicted carbon allocation from the plant host to AMF mirrored prior literature estimates. Next, we developed a model quantifying the costs of N2 -fixation by rhizobia on a hypothetical Zea mays plant engineered to harbor rhizobia in nodules. Our model predicts relative growth rate penalties ranging from 12.8 to 3.4%, depending on developmental stage, associated with obtaining organic nitrogen from rhizobia rather than synthetic fertilizer. These penalties are lower than those previously predicted for legumes due to the lower nitrogen content of Zea mays biomass, making the potential symbiosis with rhizobia in Zea mays especially economically viable. Finally, we built a model of the plant in association with both rhizobia and AMF and found that, under conditions of moderate to severe nutrient deprivation, these strategies are predicted to have substantial synergy with one another.

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Heart rate as a proxy of metabolic rate in black-legged kittiwakes (Rissa tridactyla)at Middleton Island, Alaska

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