Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Folliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells.

Dynamic Dipolar Field of Spin Waves in Low-Dimensional Magnetic Systems: The Effects of Translational Symmetry Breaking

Magnon scatterings affect the performance of magnonic devices directly, and dynamic dipolar field (DDF) is crucial in the scattering potential. In this paper, a theoretical model of the DDF in low-dimensional magnetic systems is present, and simulations give the summation area to achieve good accuracy in the DDF calculation, though the dipolar field is a long-range interaction. Calculation in a finite-size thin film indicates that due to the breaking of translational symmetry, the DDF increases evidently in the borders and the corners. The DDF near the vertex of the thin film is several orders magnitude higher than that in the inside area, making the corners prominent in the magnon scatterings.

About the Solution of the Numerical Instability for Topological Solitons with Long Range Interaction

The computations of solutions of the field equations in the Model of Topological Particles, formulated with a scalar SU(2)-field, have shown instabilities leading to discrepancies between the numerical and analytical solutions. We identify the origin of these deviations in misalignments of the rotational axes corresponding to the SU(2) elements. The system of a single soliton we use as an example to show that a constraint suppressing the wave-like disturbances is able to lead to excellent agreement between the result of the numerical minimisation procedure and the analytical solution.

Long-range vector models at large N

We calculate various CFT data for the O(N) vector model with the long-range interaction, working at the next-to-leading order in the 1/N expansion. Our results provide additional evidence for the existence of conformal symmetry at the long-range fixed point, as well as the continuity of the CFT data at the long-range to short-range crossover point s* of the exponent parameter s. We also develop the N > 1 generalization of the recently proposed IR duality between the long-range and the deformed short-range models, providing further evidence for its non-perturbative validity in the entire region d/2 < s < s*.

Observation of roton-like dispersion relations in acoustic metamaterials

Roton dispersion relations, displaying a pronounced “roton” minimum at finite momentum, were firstly predicted by Landau and have been extensively explored in correlated quantum systems at low temperatures. Recently, the roton-like dispersion relations were theoretically extended to classical acoustics, which, however, have remained elusive in reality. Here, we report the experimental observation of roton-like dispersions in acoustic metamaterials with beyond-nearest-neighbour interactions at ambient temperatures. The resulting metamaterial supports multiple coexisting modes with different wavevectors and group velocities at the same frequency and broadband backward waves, analogous to the “return flow” termed by Feynman in the context of rotons. Moreover, by increasing the order of long-range interaction, we observe multiple rotons on a single dispersion band, which have never appeared in Landau’s prediction or any other condensed matter study. The realization of roton-like dispersions in metamaterials could pave the way to explore novel physics and applications on quantum-inspired phenomena in classical systems.

HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

Inverse Problem for Ising Connection Matrix with Long-Range Interaction

In the present paper, we examine Ising systems on d-dimensional hypercube lattices and solve an inverse problem where we have to determine interaction constants of an Ising connection matrix when we know a spectrum of its eigenvalues. In addition, we define restrictions allowing a random number sequence to be a connection matrix spectrum. We use the previously obtained analytical expressions for the eigenvalues of Ising connection matrices accounting for an arbitrary long-range interaction and supposing periodic boundary conditions.