Czechia

Sharks have an unusual physiology, which remains largely a mystery. Opposed to most bony fish, elasmobranchs are isosmotic with seawater, and do so by accumulating extremely high levels of urea as an osmolyte. As urea is chaotropic, elasmobranchs release trimethylamine N-oxide (TMAO) into bodily fluids to protect proteins from urea toxicity, as well as improving resistance to high temperatures and pressures. In addition, elasmobranchs cannot directly oxidise lipids, which are converted to ketones, that are exported to other tissues. Elevated ketones acidify the blood in mammals, and the formation of acetone results in wasted energy. Moreover, in mammals this process is accessed in hypoglycaemic states due to glucose poor diets, starvation, and severe diabetes. To date there has been no work that interdigitates the role and influence of TMAO with energy metabolism in sharks. We also know little about how ketones and TMAO contribute to stressors such as hypoxia. Using high-resolution respirometry and a novel ATP-binding fluorophore, we addressed the effect of TMAO on mitochondrial ketone, lipid, pyrimidine and carbohydrate driven respiration, and ATP production, in cerebellum and heart of anoxia-tolerant epaulette sharks exposed to normoxia and 24h hypoxia.

SEB Conference 2024

TMAO regulates mitochondrial metabolism in brain and heart of the anoxia-tolerant epaulette shark Hemiscyllium ocellatum

respirometry

mitochondria

technical paper

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Natural populations of guppies in the Northern Range Mountains of Trinidad range from diverse, predator-rich communities in larger, higher order streams to small headwater tributaries with only one other fish species and reduced fish of predation. 1970’s vintage life history theory accurately predicts how life histories evolve in these tributaries, where guppies experience reduced mortality risk. They delay maturity and reduce investment in reproduction. The expected tradeoff is that reduced reproductive investment will be accompanied by the evolution of the ability to reproduce to more advanced ages and have extended lifespan. In fact, I found that the opposite was true. Guppies adapted to high predation communities begin to reproduce at an earlier age, invest more in reproduction, continue to reproduce to more advanced ages and have delayed accelerations in mortality risk relative to those adapted to low predation communities. These differences define those from high predation communities as super guppies and leads to the expectation that the low predation life history should never evolve, yet it does. How and why? The answer lies in the indirect consequences of life with and without predators. Predators create a guppy environment where guppy population densities are low and food is abundant. In the absence of predators, guppy populations soar and they deplete the environment of resources. The tradeoffs that favor the evolution of the low predation life history only appear as genotype by environment interactions that include the effects of population density and interspecific competition.

Guppy Life History Evolution - Insights on Costs and Tradeoffs Derived from 40 years of Research

The temperature-size rule predicts that for ectotherms, a rise in temperature induces a decrease in body size and an earlier age at maturity. However, this response is not universal and variations such as increased body size with earlier maturation or decreased body size with delayed maturation are also observed. Yet, most research on temperature-size responses does not account for the fact that global-change increases in mean temperatures are concomitant with changes in temperature variance. Furthermore, the temperature-induced changes on the nutritional environment of ectotherms are also rarely considered. Here, we develop a bioenergetic model of ectotherm body size and age at maturity as a function of temperature, food quantity and quality. The model is able to reproduce the entire spectrum of observed temperature-size and age responses. Simulations indicate that temperature variance shifts maturity towards smaller sizes while age is only slightly affected. When food quality becomes limiting, the effects on age at maturity strongly increase in particular at the warmer and colder boundaries of the ectotherm’s temperature breadth. We experimentally confirm this modulation of the temperature variance effects on size and age at maturity by food quality using the model organism Daphnia magna. Overall, our results indicate that accounting for the environmental changes that accompany the rise in mean temperature may yield different predictions on the amplitude and direction of the climate change effects on ectotherm body size-at-age than by considering mean temperature alone.

Ectotherm size-at-age in a warmer, more variable and resource-poor world

Trailing-edge (TE) fringes observed on owl wings are believed to play a crucial role in the silent flight of owls. The effects of TE fringes and underlying mechanisms on the aeroacoustic performance of owl wings, featured by curved leading edges, wavy TEs, and several feather slots at the wingtips, have not yet been addressed in association with real owl wings. In this study we for the first time constructed two 3D owl wing models, one with TE fringes and one without, based on real owl wing characteristics. Using large-eddy simulations and the Ffowcs Williams‒Hawkings analogy, the aeroacoustic characteristics of the wing models were analyzed. The results revealed that TE fringes effectively reduce aerodynamic noise without compromising aerodynamic performance. The study visualized the near-field flow dynamics, including nearfield flow and vortex structures, and flow fluctuations, demonstrating that the TE fringes break up large TE vortices, thereby suppressing TE flow fluctuations. Additionally, the fringes are observed to mitigate feather-slot interaction, effectively suppressing wingtip vortices. These combined mechanisms enhance the effectiveness of TE fringes in terms of aerodynamic force production and noise suppression. The findings contribute to understanding the role of TE fringes in silent owl flight and suggest the validity and feasibility of employing owl-inspired TE fringes in low-noise fluid machinery applications.

Trailing-edge fringes enable robust aeroacoustic performance in owl flight: a computational study

Owls’ silent flight is commonly attributed to their special wing morphology combined with wingbeat kinematics. One of these special morphological features is the leading-edge serrations: rigid miniature hook-like patterns found at the primaries of the wings’ leading-edge. It is hypothesized that leading-edge serrations function as a passive flow control mechanism, impact the aerodynamic performance, supposedly alter the boundary layer over the wing, and the wake dynamics. We study the flow physics associated with owls’ leading-edge serrations using an owl wing with mimicked serrated geometry at Rec=40,000. We measured the flow characteristics of the boundary layer over the wing for various angles of attack (6o-20o) using PIV in a water channel. The experimental results suggest that leading-edge serrations modify the boundary layer over the wing. At low angles of attack (<20o), the serrations amplified the turbulence activity over the wing planform. At 20o, the serrations act to suppress existing turbulence conditions, presumably by causing an earlier separation closer to the leading-edge region, thus enabling the flow to reattach prior to shedding downstream. These results served as a benchmark for numerical simulations using DNS to elucidate the underlying mechanisms of the flow dynamics due to presence of these micro-structures. The 3D simulations shown that the serrations improve suction surface flow by promoting sustained flow reattachment via streamwise vorticity generation at the shear layer, prompting weaker reverse flow, and thus augmenting stall resistance. However, aerodynamic performance is negatively impacted due to the shear layer passing through the serration array which results in altered surface pressure distribution over the upper surface.

Fluid-wing interaction over inspired owl wing with leading edge serrations

Physiologically acclimation to temperature change is hypothesized to evolve in environments with high levels of temperature variation. However, this hypothesis has low explanatory power, meaning other factors must be in play. Behavioral thermoregulation can reduce the body temperature variation that organisms experience and selection on thermal physiology (the “Bogert Effect”). However, the interplay between behavioral thermoregulation and the evolution of thermal acclimation is rarely discussed. I will describe how the Bogert Effect applies to thermal acclimation, and use lizards as models to provide examples of how thermoregulation reduces seasonality in body temperatures and performance relative to null expectations from environmental data.

Behavioral thermoregulation and the evolution of thermal acclimation

The Atlantic bluefin tuna (ABFT), Thunnus thynnus, is an emblematic large and highly migratory pelagic fish with physiological specializations for its lifestyle, in-cluding partial endothermy and obligate ram ventilation. Even though general mi-gratory patterns are known, little information is available on the effects of body size and increased temperature on underlying biological migratory processes, which is of great interest in the context of ongoing climate change. We used high-resolution acoustic telemetry and heart rate biologgers to follow movements and cardiac activity for a year on twenty individuals (mass range 25 to 200 kg) held in a sea-pen (50m diameter and 30m depth) off the coast of Malta, Mediterranean Sea. During this period, in the summer 2023, a heat wave occurred with temperature increases of ~4˚C above the previous years’ summer average for about a week. Preliminary results indicate increased median daily depth use as temperature increased but only in smaller sized fish, larger fish seemed just to decrease their overall activity. The results will contribute to a better understanding of the behavioural and physiological responses of ABFT to environmental conditions, which is key to predicting their migratory behaviours in both current and future climates, and is essential for effective management of this highly exploited and socio-economically important species.

Physiological and behavioural responses to increased temperature in the Atlantic bluefin tuna

Small mammals are particularly vulnerable to increasing ambient heat loads and reduced food and water availability associated with climate change, given their high mass-specific metabolism, low thermal inertia, rapid water loss rate, and limited ability to store food and water. To better understand the mechanisms underlying this vulnerability, we implanted core body temperature and activity data loggers into meerkats (Suricata suricatta) and Cape ground squirrels (Xerus inauris), both of which are diurnal, and yellow mongooses (Cynictis penicillata), which exhibit some nocturnality, in the Kalahari of South Africa. We observed the behaviour of these habituated animals for one year while measuring black globe, air and burrow temperatures, solar radiation, wind, and rainfall. We also used infrared thermography to understand how surface body temperature relates to behaviour and core body temperature. Preliminary analyses indicate that animals avoided heat by retreating to shade and burrows, and responded to cold by shortening their active period and basking in the morning sun. These behavioural strategies may limit foraging time to replenish food and water. Our further analyses will assess the seasonal shifts in activity patterns and compare core body temperature patterns of all three species alongside their thermoregulatory behavioural strategies. We will also investigate the effects of reproductive behaviour and physiology (dispersal in males and pregnancy/lactation in females) on core body temperature. These findings will help us understand how small mammals in dryland environments respond to ongoing climate change and inform appropriate mitigation and conservation strategies.

The relationships between ambient heat load, behaviour and body temperature in small diurnal mammals in a dryland environment

DNA-protein crosslinks (DPCs) are highly toxic DNA lesions represented by covalently trapped proteins to DNA molecules. If not repaired, DPCs physically block DNA replication- and transcription-associated complex. Due to the structural and chemical diversity of the crosslinked proteins and a variety of potentially affected DNA/chromatin contexts, DPCs are very challenging lesions to repair. Although specific proteins have been linked with DPC repair, as a whole it is still only poorly understood, especially in plants. We recently described cytidine analog zebularine as a potent inducer of Type 1 DPCs between DNA methyltransferase MET1 (an ortholog of the mammalian DNMT1) and DNA in the model plant Arabidopsis thaliana. The MET1 crosslinks are greatly enriched at the heterochromatic fraction of 45S rDNA repeats (Prochazkova et al., 2022).
We performed a forward-directed genetic screen to identify the molecular factors contributing to the mitigation of zebularine-induced DPCs in Arabidopsis. The SMC5/6 complex subunits were among the first characterized candidates (Dvořák Tomaštíková et al., 2023). Genetic interaction and sensitivity assays revealed that the SMC5/6 complex is essential for plant DPC repair and works parallel to the nucleolytic and proteolytic pathways. We showed that the SUMO accumulates at the crosslinked foci induced by zebularine, and the SMC5/6 complex SUMO E3 ligase subunit NSE2 is responsible for the SUMOylation. Of particular interest is a splice variant mutation in the NSE2 SUMO domain that allowed us to uncouple SUMO-related and developmental functions of the SMC5/6 complex. Further screening identified additional candidates involved in the SUMO modification. 
In summary, our forward-directed genetic screen shows the importance of SUMO in DPC repair in plants and identifies mutations that can be of great interest for further structural and functional studies. Importantly, we identified an additional 50 complementation groups including not yet characterized Arabidopsis proteins or proteins that have not yet been connected with DNA damage repair. This points not only to the complexity of DPC repair but also to the power of the forward-directed screen. 


Out of the haze of DNA-protein crosslink repair in plants

In nature, plants and microorganisms communicate with each other by exchanging different signaling compounds including volatile compounds (VCs), some of which have biostimulating properties. In Arabidopsis, VCs from the fungal phytopathogen Penicillium aurantiogriseum promote growth, photosynthesis and root hair (RH) proliferation and hyper-elongation through mechanisms involving ethylene, auxin and photosynthesis signaling. A striking alteration in the proteome of roots of fungal VC-treated plants involves strong up-regulation of RALF22. To test the possible involvement of the RALF22 in the fungal VC-promoted RH changes, we characterized the RH responses of ralf22 and fer-4 plants impaired in RALF22 and its receptor FERONIA to VCs emitted by P. aurantiogriseum. We found that these plants were unresponsive in terms of VC-promoted RH elongation and proliferation. Unlike in WT roots, fungal VCs did not enhance the transcript levels of RALF22 in roots of fer-4 and ethylene- and auxin- insensitive mutants, and those of RH-related, ethylene-responsive genes (e.g. RSL4, RHD2, PRX1 and PRX44) in ralf22 and fer-4 roots. Finally, we identified ethylene as the bioactive fungal VC, as VCs of ΔefeA strains of P. aurantiogriseum cultures impaired in ethylene synthesis weakly promoted RH proliferation and elongation in exposed plants. Collectively, our results demonstrate that RALF22-FERONIA complex is a key determinant of the ethylene, auxin and photosynthesis signaling-mediated RH response to fungal ethylene emissions.

RAPID ALKALINIZATION FACTOR 22 is a key modulator of the root hair growth responses to fungal ethylene emissions in Arabidopsis

Chromatin located in the cell nucleus is folded into a hierarchy of structures of increasing complexity, from nucleosomes and chromatin fibres to chromatin loops, domains, chromatin compartments and chromosome territories. Its flexible spatial arrangement must ensure that the correct gene expression programs are executed at the right time and in the right cell type and that the chromatin can be rapidly reorganized into highly condensed structures – metaphase chromosomes. The elucidation of these processes is facilitated by chromosome conformation capture (3C) techniques, especially Hi-C, which provides genome-wide information about chromatin contacts in the three-dimensional space. 
We applied Hi-C to study spatial genome organisation in barley – a model for large-genome cereals. First, we combined Hi-C with flow sorting of metaphase chromosomes and nuclei at G1, S and G2 phase, respectively, and analysed chromatin dynamics during the cell cycle. We observed surprisingly small changes in higher-order chromatin structure between chromosomes and interphase nuclei isolated from root tips but a striking difference between G1 from root-tip and leaf tissue, indicating a different chromatin arrangement in the interphase between rapidly cycling and non-cycling cells. Furthermore, we used the Hi-C data to delineate active and silenced chromatin compartments in the barley genome and provided evidence for their impact on gene expression. Last, we combined barley interactome data with several epigenomic datasets to identify functional chromatin interactions. This allowed us to predict 1754 distal cis-regulatory elements (enhancers or silencers) and their target genes, which will be further validated by reporter assays and bioinformatics approaches. 
This research was supported by the Czech Science Foundation, award number 21-18794S, and from the project TowArds Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the ERDF Programme Johannes Amos Comenius.


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