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Abstract Computed tomography (CT) is a non-invasive, three-dimensional imaging tool used in medical imaging, forensic science, industry and engineering, anthropology, and archaeology. The current study used high-resolution medical CT scanning of 431 animal skulls, including 399 dog skulls from 152 breeds, 14 cat skulls from 9 breeds, 14 skulls from 8 wild canid species (gray wolf, golden jackal, coyote, maned wolf, bush dog, red fox, Fennec fox, bat-eared fox), and 4 skulls from 4 wild felid species (wildcat, leopard, serval, caracal). This comprehensive and unique collection of CT image series of skulls can provide a solid foundation not only for comparative anatomical and evolutionary studies but also for the advancement of veterinary education, virtual surgery planning, and the facilitation of training in sophisticated machine learning methodologies.

Abstract The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

Abstract Assessing additive genetic variance is a crucial step in predicting the evolutionary response of a target trait. However, the estimated genetic variance may be sensitive to the methodology used, e.g., the way relatedness is assessed among the individuals, especially in wild populations where social pedigrees can be inaccurate. To investigate this possibility, we investigated the additive genetic variance in tarsus length, a major proxy of skeletal body size in birds. The model species was the collared flycatcher (Ficedula albicollis), a socially monogamous but genetically polygamous migratory passerine. We used two relatedness matrices to estimate the genetic variance: (1) based solely on social links and (2) a genetic similarity matrix based on a large array of single‐nucleotide polymorphisms (SNPs). Depending on the relatedness matrix considered, we found moderate to high additive genetic variance and heritability estimates for tarsus length. In particular, the heritability estimates were higher when obtained with the genetic similarity matrix instead of the social pedigree. Our results confirm the potential for this crucial trait to respond to selection and highlight methodological concerns when calculating additive genetic variance and heritability in phenotypic traits. We conclude that using a social pedigree instead of a genetic similarity matrix to estimate relatedness among individuals in a genetically polygamous wild population may significantly deflate the estimates of additive genetic variation.

IntroductionMacrophages significantly contribute to the regulation of vessel formation under physiological and pathological conditions. Although the angiogenesis-regulating role of alternatively polarized macrophages is quite controversial, a growing number of evidence shows that they can participate in the later phases of angiogenesis, including vessel sprouting and remodeling or regression. However, the epigenetic and transcriptional regulatory mechanisms controlling this angiogenesis-modulating program are not fully understood.ResultsHere we show that IL-4 can coordinately regulate the VEGFA-VEGFR1 (FLT1) axis via simultaneously inhibiting the proangiogenic Vegfa and inducing the antiangiogenic Flt1 expression in murine bone marrow-derived macrophages, which leads to the attenuated proangiogenic activity of alternatively polarized macrophages. The IL-4-activated STAT6 and IL-4-STAT6 signaling pathway-induced EGR2 transcription factors play a direct role in the transcriptional regulation of the Vegfa-Flt1 axis. We demonstrated that this phenomenon is not restricted to the murine bone marrow-derived macrophages, but can also be observed in different murine tissue-resident macrophages ex vivo and parasites-elicited macrophages in vivo with minor cell type-specific differences. Furthermore, IL-4 exposure can modulate the hypoxic response of genes in both murine and human macrophages leading to a blunted Vegfa/VEGFA and synergistically induced Flt1/FLT1 expression.DiscussionOur findings establish that the IL-4-activated epigenetic and transcriptional program can determine angiogenesis-regulating properties in alternatively polarized macrophages under normoxic and hypoxic conditions.

Plasmonic metallic nanoparticles, like Au, can be used to tune the optical properties of photonic nanoarchitectures occurring in butterfly wing scales possessing structural color. The effect of the nanoscale Au depends on the location and the amount deposited in the chitin-based photonic nanoarchitecture. The following three types of Au introduction methods were compared regarding the structural and optical properties of the resulting hybrid bio-nanocomposites: (i) growth of Au nanoparticles inside the nanopores of butterfly wing scales by a light-induced in situ chemical reduction of HAuCl4 in aqueous solution containing sodium citrate, as a new procedure we have developed, (ii) drop-drying of the aqueous Au sol formed during procedure (i) in the bulk liquid phase, and (iii) physical vapor deposition of Au thin film onto the butterfly wing. We investigated all three methods at two different Au concentrations on the wings of laboratory-bred blue-colored male Polyommatus icarus butterflies and characterized the optical properties of the resulting hybrid bio-nanocomposites. We found that the drop-drying and the in situ growth produced comparable redshift in the spectral position of the reflectance maximum associated with the chitin-based photonic nanoarchitecture in the wing scales, while the 5 nm or 15 nm thick Au layers vacuum deposited onto the butterfly wing behaved like an optical filter, without inducing spectral shift. The in situ growth in the photonic nanoarchitecture under intense illumination produced uniform Au nanoparticles located in the pores of the biological template, which is more advantageous for further applications. An additional benefit of this method is that the Au nanoparticles do not aggregate on drying, like in the case of drop-drying of preformed Au nanoparticles from the citrate-stabilized sol.

Heritable genetic variation is a prerequisite for adaptive evolution; however, our knowledge about the heritability of plastic traits, such as behaviors, is scarce, especially in wild populations. In this study, we investigated the heritability of song traits in the collared flycatcher (Ficedula albicollis), a small oscine passerine with complex songs involved in sexual selection. We recorded the songs of 81 males in a natural population and obtained various measures describing the frequency, temporal organization, and complexity of each song. As we had multiple songs from each individual, we were able to statistically account for the first time for the effect of within-individual variance on the heritability of song. Heritability was calculated from the variance estimates of animal models relying on a genetic similarity matrix based on Single Nucleotide Polymorphism screening. Overall, we found small additive genetic variance and heritability values in all song traits, highlighting the role of environmental factors in shaping bird song.

Photonic nanoarchitectures of butterfly wings can serve as biotemplates to prepare semiconductor thin films of ZnO by atomic layer deposition. The resulting biotemplated ZnO nanoarchitecture preserves the structural and optical properties of the natural system, while it will also have the features of the functional material. The ZnO-coated wings can be used directly in heterogeneous photocatalysis to decompose pollutants dissolved in water upon visible light illumination. We used the photonic nanoarchitectures of different Morpho butterflies with different structural colors as biotemplates and examined the dependence of decomposition rates of methyl orange and rhodamine B dyes on the structural color of the biotemplates and the thickness of the ZnO coating. Using methyl orange, we measured a ten-fold increase in photodegradation rate when the 20 nm ZnO-coated wings were compared to similarly coated glass substrates. Using rhodamine B, a saturating relationship was found between the degradation rate and the thickness of the deposited ZnO on butterfly wings. We concluded that the enhancement of the catalytic efficiency can be attributed to the slow light effect due to a spectral overlap between the ZnO-coated Morpho butterfly wings reflectance with the absorption band of dyes, thus the photocatalytic performance could be changed by the tuning of the structural color of the butterfly biotemplates. The photodegradation mechanism of the dyes was investigated by liquid chromatography–mass spectroscopy.

The photocatalytic activity of a flat surface can be increased by micro- and nanostructuring the interface to increase the area of the contact surface between the photocatalyst and the solute, and moreover, to optimize charge carrier transfer. Further enhancement can be achieved by using photonic nanostructures, which exhibit photonic band gap (PBG). Structurally coloured butterfly wings offer a rich ‘library’ of PBGs in the visible spectral range which can be used as naturally tuned sample sets for biotemplating. We used conformal atomic layer deposition of ZnO on the wings of various butterfly species (Arhopala asopia, Hypochrysops polycletus, Morpho sulkowskyi, Polyommatus icarus) possessing structural colour extending from the near UV to the blue wavelength range, to test the effects arising from the nanostructured surfaces and from the presence of different types of PBGs. Aqueous solutions of rhodamine B were used to test the enhancement of photocatalytic activity that was found for all ZnO-coated butterfly wings. The best reaction rate of decomposing rhodamine B when illuminated with visible light was found in 15 nm ZnO coated M. sulkowskyi wing, the reflectance of which had the highest overlap with the absorption band of the dye and had the highest reflectance intensity.

Abstract Individual animals can react to the changes in their environment by exhibiting behaviors in an individual‐specific way leading to individual differences in phenotypic plasticity. However, the effect of multiple environmental factors on multiple traits is rarely tested. Such a complex approach is necessary to assess the generality of plasticity and to understand how among‐individual differences in the ability to adapt to changing environments evolve. This study examined whether individuals adjust different song traits to varying environmental conditions in the collared flycatcher (Ficedula albicollis), a passerine with complex song. We also aimed to reveal among‐individual differences in behavioral responses by testing whether individual differences in plasticity were repeatable. The presence of general plasticity across traits and/or contexts was also tested. To assess plasticity, we documented (1) short‐scale temporal changes in song traits in different social contexts (after exposition to male stimulus, female stimulus or without stimuli), and (2) changes concerning the height from where the bird sang (singing position), used as a proxy of predation risk and acoustic transmission conditions. We found population‐level relationships between singing position and both song length (SL) and complexity, as well as social context‐dependent temporal changes in SL and maximum frequency (MF). We found among‐individual differences in plasticity of SL and MF along both the temporal and positional gradients. These among‐individual differences in plasticity were repeatable. Some of the plastic responses correlated across different song traits and environmental gradients. Overall, our results show that the plasticity of bird song (1) depends on the social context, (2) exists along different environmental gradients, and (3) there is evidence for trade‐offs between the responses of different traits to different environmental variables. Our results highlight the need to consider individual differences and to investigate multiple traits along multiple environmental axes when studying behavioral plasticity.

Collaboration of transcription factors (TFs) and their recognition motifs in DNA is the result of coevolution and forms the basis of gene regulation. However, the way how these short genomic sequences contribute to setting the level of gene products is not understood in sufficient detail. The biological problem to be solved by the cell is complex, because each gene requires a unique regulatory network in each cellular condition using the same genome. Thus far, only some components of these networks have been uncovered. In this review, we compiled the features and principles of the motif grammar, which dictates the characteristics and thus the likelihood of the interactions of the binding TFs and their coregulators. We present how sequence features provide specificity using, as examples, two major TF superfamilies, the bZIP proteins and nuclear receptors. We also discuss the phenomenon of “weak” (low affinity) binding sites, which appear to be components of several important genomic regulatory regions, but paradoxically are barely detectable by the currently used approaches. Assembling the complete set of regulatory regions composed of both weak and strong binding sites will allow one to get more comprehensive lists of factors playing roles in gene regulation, thus making possible the deeper understanding of regulatory networks.

The effects of salt stress condition on the growth, morphology, photosynthetic performance, and paramylon content were examined in the mixotrophic, unicellular, flagellate Euglena gracilis. We found that salt stress negatively influenced cell growth, accompanied by a decrease in chlorophyll (Chl) content. Circular dichroism (CD) spectroscopy revealed the changes in the macro-organization of pigment-protein complexes due to salt treatment, while the small-angle neutron scattering (SANS) investigations suggested a reduction in the thylakoid stacking, an effect confirmed by the transmission electron microscopy (TEM). At the same time, the analysis of the thylakoid membrane complexes using native-polyacrylamide gel electrophoresis (PAGE) revealed no significant change in the composition of supercomplexes of the photosynthetic apparatus. Salt stress did not substantially affect the photosynthetic activity, as reflected by the fact that Chl fluorescence yield, electron transport rate (ETR), and energy transfer between the photosystems did not change considerably in the salt-grown cells. We have observed notable increases in the carotenoid-to-Chl ratio and the accumulation of paramylon in the salt-treated cells. We propose that the accumulation of storage polysaccharides and changes in the pigment composition and thylakoid membrane organization help the adaptation of E. gracilis cells to salt stress and contribute to the maintenance of cellular processes under stress conditions.

Solar radiation is a cheap and abundant energy for water remediation, hydrogen generation by water splitting, and CO2 reduction. Supported photocatalysts have to be tuned to the pollutants to be eliminated. Spectral engineering may be a handy tool to increase the efficiency or the selectivity of these. Photonic nanoarchitectures of biological origin with hierarchical organization from nanometers to centimeters are candidates for such applications. We used the blue wing surface of laboratory-reared male Polyommatus icarus butterflies in combination with atomic layer deposition (ALD) of conformal ZnO coating and octahedral Cu2O nanoparticles (NP) to explore the possibilities of engineering the optical and catalytic properties of hybrid photonic nanoarchitectures. The samples were characterized by UV-Vis spectroscopy and optical and scanning electron microscopy. Their photocatalytic performance was benchmarked by comparing the initial decomposition rates of rhodamine B. Cu2O NPs alone or on the butterfly wings, covered by a 5 nm thick layer of ZnO, showed poor performance. Butterfly wings, or ZnO coated butterfly wings with 15 nm ALD layer showed a 3 to 3.5 times enhancement as compared to bare glass. The best performance of almost 4.3 times increase was obtained for the wings conformally coated with 15 nm ZnO, deposited with Cu2O NPs, followed by conformal coating with an additional 5 nm of ZnO by ALD. This enhanced efficiency is associated with slow light effects on the red edge of the reflectance maximum of the photonic nanoarchitectures and with enhanced carrier separation through the n-type ZnO and the p-type Cu2O heterojunction. Properly chosen biologic photonic nanoarchitectures in combination with carefully selected photocatalyst(s) can significantly increase the photodegradation of pollutants in water under visible light illumination.

Non-photochemical quenching (NPQ) is an important photoprotective mechanism in plants and algae. Although the process is extensively studied, little is known about its relationship with ultrastructural changes of the thylakoid membranes. In order to better understand this relationship, we studied the effects of illumination on the organization of thylakoid membranes in Monstera deliciosa leaves. This evergreen species is known to exhibit very large NPQ and to possess giant grana with dozens of stacked thylakoids. It is thus ideally suited for small-angle neutron scattering measurements (SANS)—a non-invasive technique, which is capable of providing spatially and statistically averaged information on the periodicity of the thylakoid membranes and their rapid reorganizations in vivo. We show that NPQ-inducing illumination causes a strong decrease in the periodic order of granum thylakoid membranes. Development of NPQ and light-induced ultrastructural changes, as well as the relaxation processes, follow similar kinetic patterns. Surprisingly, whereas NPQ is suppressed by diuron, it impedes only the relaxation of the structural changes and not its formation, suggesting that structural changes do not cause but enable NPQ. We also demonstrate that the diminishment of SANS peak does not originate from light-induced redistribution and reorientation of chloroplasts inside the cells.

The thylakoid membranes of vascular plants are differentiated into stacked granum and unstacked stroma regions. The formation of grana is triggered by the macrodomain formation of photosystem II and light-harvesting complex II (PSII-LHCII) and thus their lateral segregation from the photosystem I—light-harvesting complex I (PSI-LHCI) super-complexes and the ATP-synthase; which is then stabilized by stacking interactions of the adjacent PSII-LHCII enriched regions of the thylakoid membranes. The self-assembly and dynamics of this highly organized membrane system and the nature of forces acting between the PSII-LHCII macrodomains are not well understood. By using circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS) and transmission electron microscopy (TEM), we investigated the effects of Hofmeister salts on the organization of pigment-protein complexes and on the ultrastructure of thylakoid membranes. We found that the kosmotropic agent (NH4)2SO4 and the Hofmeister-neutral NaCl, up to 2 M concentrations, hardly affected the macro-organization of the protein complexes and the membrane ultrastructure. In contrast, chaotropic salts, NaClO4, and NaSCN destroyed the mesoscopic structures, the multilamellar organization of the thylakoid membranes and the chiral macrodomains of the protein complexes but without noticeably affecting the short-range, pigment-pigment excitonic interactions. Comparison of the concentration- and time-dependences of SANS, TEM and CD parameters revealed the main steps of the disassembly of grana in the presence of chaotropes. It begins with a rapid diminishment of the long-range periodic order of the grana membranes, apparently due to an increased stacking disorder of the thylakoid membranes, as reflected by SANS experiments. SANS measurements also allowed discrimination between the cationic and anionic effects—in stacking and disorder, respectively. This step is followed by a somewhat slower disorganization of the TEM ultrastructure, due to the gradual loss of stacked membrane pairs. Occurring last is the stepwise decrease and disappearance of the long-range chiral order of the protein complexes, the rate of which was faster in LHCII-deficient membranes. These data are interpreted in terms of a theory, from our laboratory, according to which Hofmeister salts primarily affect the hydrophylic-hydrophobic interactions of proteins, and the stroma-exposed regions of the intrinsic membrane proteins, in particular—pointing to the role of protein-water interface in the stacking interactions of granum thylakoid membranes.

Trace metal contaminations in natural waters, wetlands, and wastewaters pose serious threats to aquatic ecosystems—mainly via targeting microalgae. In this work, we investigated the effects of toxic amounts of chromium and cadmium ions on the structure and function of the photosynthetic machinery of Chlorella variabilis cells. To halt the propagation of cells, we used high concentrations of Cd and Cr, 50–50 mg L−1, in the forms of CdCl2 x 2.5 H2O and K2Cr2O7, respectively. Both treatments led to similar, about 50% gradual diminishment of the chlorophyll contents of the cells in 48 h, which was, however, accompanied by a small (~10%) but statistically significant enrichment (Cd) and loss (Cr) of ß-carotene. Both Cd and Cr inhibited the activity of photosystem II (PSII)—but with more severe inhibitions with Cr. On the contrary, the PsbA (D1) protein of PSII and the PsbO protein of the oxygen-evolving complex were retained more in Cr-treated cells than in the presence of Cd. These data and the higher susceptibility of P700 redox transients in Cr-treated cells suggest that, unlike with Cd, PSII is not the main target in the photochemical apparatus. These differences at the level of photochemistry also brought about dissimilarities at higher levels of the structural complexity of the photosynthetic apparatus. Circular dichroism (CD) spectroscopy measurements revealed moderate perturbations in the macro-organization of the protein complexes—with more pronounced decline in Cd-treated cells than in the cells with Cr. Also, as reflected by transmission electron microscopy and small-angle neutron scattering, the thylakoid membranes suffered shrinking and were largely fragmented in Cd-treated cells, whereas no changes could be discerned with Cr. The preservation of integrity of membranes in Cr-treated cells was most probably aided by high proportion of the de-epoxidized xanthophylls, which were absent with Cd. It can thus be concluded that beside strong similarities of the toxic effects of Cr and Cd, the response of the photosynthetic machinery of C. variabilis to these two trace metal ions substantially differ from each other—strongly suggesting different inhibitory and protective mechanisms following the primary toxic events.

Plants have evolved to maximize energy capture while protecting their photosynthetic machinery in response to rapid variation in light conditions. Here, the authors describe a chloroplast voltage-dependent anion channel that contributes to photoprotection by fine-tuning the ion balance across the thylakoid membrane.

Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators, which together establish a chromatin environment conducting to effective transcription. While cells with distinct TF profiles can have different functions, how different cells control overlapping genetic programs remains a question. In this paper, we show that the construction of estrogen receptor alpha-driven SEs is tissue-specific, both collaborating TFs and the active SE components greatly differ between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell lines have similar transcriptional outputs. These results delineate that despite the existence of a combinatorial code allowing alternative SE construction, a single master regulator might be able to determine the overall activity of SEs.

Energy efficiency in computing was identified as low energy usage of the hardware for a while. However, nowadays, we can talk about energy efficiency in terms of software as well. Therefore, we have to investigate how the different design decisions and programming language constructs affect the energy consumption. The green computing is a relatively new research area, guidelines are required for the software developers in terms of energy efficiency. In our research we are focusing on the functional programming language Erlang. We have investigated the effect of different language constructs (such as higher order functions), parallelism, data structures and styles of programming on energy usage. Additionally we present a tool to measure and visualise the consumed energy.

A fabrication method of a multifunctional hybrid material is achieved by using the insoluble organic nacre matrix of the Haliotis laevigata shell infiltrated with gelatin as a confined reaction environment. Inside this organic scaffold magnetite nanoparticles (MNPs) are synthesized. The amount of MNPs can be controlled through the synthesis protocol therefore mineral loadings starting from 15 wt % up to 65 wt % can be realized. The demineralized organic nacre matrix is characterized by small-angle and very-small-angle neutron scattering (SANS and VSANS) showing an unchanged organic matrix structure after demineralization compared to the original mineralized nacre reference. Light microscopy and confocal laser scanning microscopy studies of stained samples show the presence of insoluble proteins at the chitin surface but not between the chitin layers. Successful and homogeneous gelatin infiltration in between the chitin layers can be shown. The hybrid material is characterized by TEM and shows a layered structure filled with MNPs with a size of around 10 nm. Magnetic analysis of the material demonstrates superparamagnetic behavior as characteristic for the particle size. Simulation studies show the potential of collagen and chitin to act as nucleators, where there is a slight preference of chitin over collagen as a nucleator for magnetite. Colloidal-probe AFM measurements demonstrate that introduction of a ferrogel into the chitin matrix leads to a certain increase in the stiffness of the composite material.

Adipocyte differentiation and function have become the major research targets due to the increasing interest in obesity and related metabolic conditions. Although, late stages of adipogenesis have been extensively studied, the early phases remain poorly understood. Here we present that supplementing ascorbic acid (AsA) to the adipogenic differentiation cocktail enables the robust and efficient differentiation of mouse embryonic stem cells (mESCs) to mature adipocytes. Such ESC-derived adipocytes mimic the gene-expression profile of subcutaneous isolated adipocytes in vivo remarkably well, much closer than 3T3-L1 derived ones. Moreover, the differentiated cells are in a monolayer, allowing a broad range of genome-wide studies in early and late stages of adipocyte differentiation to be performed.

PolyCarboxylate ether-based superplasticizers (PCEs) are a type of comb-shaped copolymers used as polymeric dispersants in cementitious materials. PCEs have a high degree of dispersity, which limits the suitability of conventional characterization techniques, such as Size Exclusion Chromatography (SEC). Properties of PCEs strongly depend on their molecular structure and a comprehensive characterization is needed to fully understand the structure–property relationships. PCEs with well-defined molecular structures were synthesized to study their solution conformation by SEC and scattering techniques. The combined use of SEC, dynamic light scattering and small-angle neutron scattering allowed us to demonstrate the validity of a scaling law describing the radius of gyration of comb-shaped copolymers as a function of their molecular structure. Moreover, we show that the use of SEC with standard calibration, although widely spread, is not adequate for PCEs.

The architectural and historic research of planned cities maybe the most neglected section of our history of architecture,our city planning and our urban design. This may be due to thefact that as inseparable the settlement or neighborhood is fromthe community, from the residents and from the sociologicalenvironment determined by the culture, as extensive is theresearch area. This concerns especially the settlements whichwere organized and planned in one period and where thefunction is fixed and the original society of the settlement isdefined. Moreover, even the settling and the circumstances ofthe population show a special peculiarity. The organization ofthe supplies has also its own history. The social development andthe transformation of demands is also an unknown originatorworthy of research that effected significantly the metamorphosisof these neighborhoods and cities.