Czechia

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.


SEB Conference Prague 2024

Organization and function of the 3D barley genome

regulome

barley

hi-c

3d genome

interactome

enhancers

technical paper

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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

The mechanistic link between metabolic rate and foraging behaviour underpins several energy-based ecological theories, yet whether and how they interact remains unclear. Here we aimed to assess how modes of behaviour, in terms of cumulative space use, patch selection and time spent in an experimental resource patchy environment, are influenced by the foragers’ metabolic rate (SMR) and its main determinants i.e. body mass and temperature. We tested the individual behavioural patterns and metabolic rates of a model organism, the amphipod Gammarus insensibilis, across a range of body masses and temperatures. Our findings showed that body mass and temperature exert a major influence on foraging decisions and space use behaviour via their effects on metabolic rates. Individual cumulative space use was found to scale allometrically with body mass and exponentially with temperature, with patch giving-up time falling as body mass and temperature increased. Moreover, SMR had greater predictive power for behavioural patterns, explaining variation beyond that accounted for by body mass and temperature combined. Our results showed that cumulative space use scaled positively with mass-and-temperature-adjusted SMR (residual). Furthermore, the foraging decisions regarding patch choice and partitioning were strongly related to mass-and-temperature-adjusted SMR; individuals with higher mass-and-temperature-adjusted SMR initially preferred the most profitable patch and, as time progressed, abandoned the patch earlier compared to others. Our findings regarding the mechanistic relationship between behavioural patterns and metabolic rate across body mass and temperature shed light on higher-order energy-based ecological processes, with implications in the face of climate change.

Foraging decisions and space use behavior are linked to metabolic rate across temperatures

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

Birds are capable of incredible feats in the air, rapidly adapting flight to suit varying behavioural needs and environmental conditions. These feats are made possible through the interaction of biomechanical and sensory systems. One such system, mechanosensation, the ability to sense changes in aerodynamic forces caused by air flow, is thought to be critical for flight control. Notably in birds, vibration-based flow sensors are distributed throughout much of the wing surface; rather, they are localised at the base of the flight feathers. Therefore, it is flow-generated deformations of the passive and flexible flight feathers that are sensed by the flow sensors and not the airflow directly. The goal of this study is to understand how flow information is encoded by the feather aeroelastic response. Additionally, we aim to investigate how wing morphing behaviour can modify this structure-based signal processing. In a wind tunnel, we systematically altered the flow speed and direction acting on dried zebra finch (Taeniopygia guttata) wings in different morphs. By measuring and parametrising the shape of the frequency response under different flow conditions, we could then quantify how certain features of this vibration response can encode information on different flow characteristics. This study helps us understand the role wing structures play in flow sensing before any further neural signal processing and may inspire morphologically “smart” designs for distributed flow sensing in engineered structures.

Decoding aeroelastic response in flight feathers for flow sensing

The evolution of increased thermal tolerance in aquatic ectotherms may affect genetically correlated traits and alter physiological performances. Here, we report the correlated responses of a range of life history, behavioural and physiological traits to seven generations of artificial selection for increased (Up-selected) or decreased (Down-selected) acute upper thermal tolerance limit (CTmax) in zebrafish (Danio rerio). Contrary to the prediction of a trade-off between warming and cooling tolerance, the thermal window increased in the Up-selected lines. No change was observed in the aerobic metabolic scope or in the thermal sensitivity of resting and maximum metabolic rates, thus contradicting the hypothesis that thermal tolerance limits are controlled by aerobic scope. We also found no difference in brain heat shock protein levels between the selected lines, contradicting the hypothesized role of heat shock protein expression in the evolution of acute warming tolerance. Finally, fecundity, growth and swimming speed did not change in the Up-selected lines, but tended to decrease in the Down-selected lines, suggesting that the evolution of lower thermal tolerance is accompanied by a decrease in individual quality. These results suggest that selection due to acute heating events can benefit tolerance to cold, making individuals more resilient to extreme temperature events.

Selection on warming tolerance alters physiology and life history traits in zebrafish

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

Nuclear Pore Complexes (NPCs) are large macromolecular assemblies embedded into the nuclear envelope (NE). Their main function is to mediate the selective nucleocytoplasmic transport of macromolecules, although they are involved in other processes such as chromatin organization, and DNA repair. NPCs are organized into subcomplexes composed of repetitions of about 30 highly conserved nucleoporins (NUPs). The NUP107–160 complex is in the outer ring and is conserved between distantly related eukaryotes such as yeast and mammals. Here, we are going to focus on two Arabidopsis mutants deficient for this subcomplex: nup160 and nup96, also known as suppressor of auxin resistance1 (sar1) and sar3, respectively. NUP160 and NUP96 are critical for the nucleocytoplasmic transport of mRNAs and play important functions in auxin signalling, plant growth, and flowering time regulation, as well as in immune defence and cold stress tolerance. In the context of our global study about the possible role of NPCs during meiosis, we decided to explore the potential function of NUP160 and NUP96 during this cell division because the corresponding mutants show reduced fertility. The results of our study have demonstrated that meiosis is altered in a percentage of the meiocytes from these mutants, which would explain the reduction in the number of seeds. Our observations have revealed that the alteration of the NUP107-160 complex causes problems related to chromatin instability with abnormalities associated with condensation and fragmentation. The possible origins of these problems will be discussed.

The connection between structural nucleoporins and meiosis: when the chromatin collapses.

Paramutation represents a clear exception to the principles of inheritance established by Gregor Mendel in the 19th century. It involves the transfer of repressive epigenetic marks from a silent to an active allele and thereby violates Mendel's first law of independent allele segregation. By violating Mendel's first law of independent allele segregation, paramutation results from the transfer of repressive epigenetic marks from silent to active homologous alleles. It is best known from conspicuous pigmentation phenotypes in maize but the Paramutation phenomena was also reported across diverse plant and animal species. Paramutation-like events are common in tomato hybrids suggesting that paramutation may be less exceptional and rather a frequently co-occurring process during cross-hybridisation.



Here we use the classic example of paramutation in tomato – sulfurea (sulf), an understudied chlorosis phenotype associated with transgenerationally dependent allele segregation patterns – to dissect the epigenetic- and transgenerational mechanisms underlying paramutation in tomato plants. Our results show that the DNA- and histone-methyl transferases CMT3 and KYP are required for the maintenance of paramutation and that there is a change in chromatin architecture associated with the silent epiallele. We further demonstrate that in tomato the developmental and transgenerational maintenance of paramutation might be independent of sRNAs, which were previously suggested to explain the trans-communication between homologues as well as the maintenance of silent paramutated states across mitotic and meiotic divisions in maize. Together, our data significantly extends the current understanding of the paramutation model in plants by integrating existing concepts into a revised framework of non-Mendelian heredity.

Organization and function of the 3D barley genome

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Organization and function of the 3D barley genome

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Next from SEB Conference Prague 2024

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

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PRESENTATIONS

CONFERENCES

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RESOURCES

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