Project description:We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 24 to 84 hours with 12 hours intervals.
Project description:Multisite modification is a basic way of conferring functionality to proteins and a key component of post-translational modification networks. Additional interest in multisite modification stems from its capability of acting as complex information processors. In this paper, we connect two seemingly disparate themes: symmetry and multisite modification. We examine different classes of random modification networks of substrates involving separate or common enzymes. We demonstrate that under different instances of symmetry of the modification network (invoked explicitly or implicitly and discussed in the literature), the biochemistry of multisite modification can lead to the symmetry being broken. This is shown computationally and consolidated analytically, revealing parameter regions where this can (and in fact does) happen, and characteristics of the symmetry-broken state. We discuss the relevance of these results in situations where exact symmetry is not present. Overall, through our study we show how symmetry breaking (i) can confer new capabilities to protein networks, including concentration robustness of different combinations of species (in conjunction with multiple steady states); (ii) could have been the basis for ordering of multisite modification, which is widely observed in cells; (iii) can significantly impact information processing in multisite modification and in cell signalling networks/pathways where multisite modification is present; and (iv) can be a fruitful new angle for engineering in synthetic biology and chemistry. All in all, the emerging conceptual synthesis provides a new vantage point for the elucidation and the engineering of molecular systems at the junction of chemical and biological systems.
Project description:The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion may be independent of exon size, and therefore could be dependent on intron-exon boundaries. All genomes examined have two distinctive classes of exons, each with different evolutionary histories. In the framework proposed in this article, these two classes of exons can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. We note that one of these exon classes comprises mostly alternatively spliced exons.
Project description:Because of their unique electronic properties, cyclic molecular structures ranging from benzene to natural light-harvesting complexes have received much attention. Rigid ?-conjugated templated porphyrin nanorings serve as excellent model systems here because they possess well-defined structures that can readily be controlled and because they support highly delocalized excitations. In this study, we have deliberately modified a series of six-porphyrin nanorings to examine the impact of lowering the rotational symmetry on their photophysical properties. We reveal that as symmetry distortions increase in severity along the series of structures, spectral changes and an enhancement of radiative emission strength occur, which derive from a transfer of oscillator strength into the lowest (k = 0) state. We find that concomitantly, the degeneracy of the dipole-allowed first excited (k = ±1) state is lifted, leading to an ultrafast polarization switching effect in the emission from strongly symmetry-broken nanorings.
Project description:Tissue morphogenesis comprises the self-organized creation of various patterns and shapes. Although detailed underlying mechanisms are still elusive in many cases, an increasing amount of experimental data suggests that chemical morphogen and mechanical processes are strongly coupled. Here, we develop and test a minimal model of the axis-defining step (i.e., symmetry breaking) in aggregates of the Hydra polyp. Based on previous findings, we combine osmotically driven shape oscillations with tissue mechanics and morphogen dynamics. We show that the model incorporating a simple feedback loop between morphogen patterning and tissue stretch reproduces a wide range of experimental data. Finally, we compare different hypothetical morphogen patterning mechanisms (Turing, tissue-curvature, and self-organized criticality). Our results suggest the experimental investigation of bigger (i.e., multiple head) aggregates as a key step for a deeper understanding of mechanochemical symmetry breaking in Hydra.
Project description:Spectrally rich but geometrically simple plasmonic metallic nanoparticles are highly favored in nanophotonics. However, they remain elusive owing to the symmetry-induced mode degeneracy and interband transition-induced plasmonic damping. Hence, most nanoparticles exhibit a single major extinction peak originating from the lowest-order dipole resonance. In this study, we uncover that even a simple tetrahedral nanoparticle supports rich spectral features due to symmetry breaking. This discovery runs counter to the reported gold tetrahedral nanoparticles, where only a single extinction peak was observed. We find that, in the case of a tetrahedral nanoparticle, the plasmonic quadrupole vertex mode becomes a bright mode and hybridizes with the dipole vertex mode, which splits the extinction peak and contributes to spectral diversity and tunability. The peak splitting is also found to be sensitively dependent on the roundness of vertices and edges. Furthermore, the tetrahedral depolarization factors are determined using the previously generalized absorption coefficient. We envision that this work will not only help fill the gap in understanding the optical properties enriched by symmetry breaking but also guide the superior probe design by combining spectral tunability with geometric simplicity of the nanoparticle.
Project description:Plants and animals use plumes, barbs, tails, feathers, hairs and fins to aid locomotion. Many of these appendages are not actively controlled, instead they have to interact passively with the surrounding fluid to generate motion. Here, we use theory, experiments and numerical simulations to show that an object with a protrusion in a separated flow drifts sideways by exploiting a symmetry-breaking instability similar to the instability of an inverted pendulum. Our model explains why the straight position of an appendage in a fluid flow is unstable and how it stabilizes either to the left or right of the incoming flow direction. It is plausible that organisms with appendages in a separated flow use this newly discovered mechanism for locomotion; examples include the drift of plumed seeds without wind and the passive reorientation of motile animals.
Project description:Spatial evolution game has traditionally assumed that players interact with direct neighbors on a single network, which is isolated and not influenced by other systems. However, this is not fully consistent with recent research identification that interactions between networks play a crucial rule for the outcome of evolutionary games taking place on them. In this work, we introduce the simple game model into the interdependent networks composed of two networks. By means of imitation dynamics, we display that when the interdependent factor α is smaller than a threshold value α(C), the symmetry of cooperation can be guaranteed. Interestingly, as interdependent factor exceeds α(C), spontaneous symmetry breaking of fraction of cooperators presents itself between different networks. With respect to the breakage of symmetry, it is induced by asynchronous expansion between heterogeneous strategy couples of both networks, which further enriches the content of spatial reciprocity. Moreover, our results can be well predicted by the strategy-couple pair approximation method.