Design of complicated all-α protein structures.

A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. Here, to expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing 'difficult-to-describe' α-helical protein structures composed of irregularly aligned α-helices like globins. Backbone structure libraries consisting of a myriad of α-helical structures with five or six helices were generated by combining 18 helix-loop-helix motifs and canonical α-helices, and five distinct topologies were selected for de novo design.

Assisting and eliminating memory effects of paste by adding polysaccharides.

A densely packed colloidal suspension, called a paste, is known to remember the direction of its motion because of its plasticity. Because the memory in the paste determines the preferential direction for crack propagation, the desiccation crack pattern morphology depends on memory of its motions (memory effect of paste). Two types of memory effects are memory of vibration and memory of flow.

A transcriptional program underlying the circannual rhythms of gonadal development in medaka.

To cope with seasonal environmental changes, organisms have evolved approximately 1-y endogenous circannual clocks. These circannual clocks regulate various physiological properties and behaviors such as reproduction, hibernation, migration, and molting, thus providing organisms with adaptive advantages. Although several hypotheses have been proposed, the genes that regulate circannual rhythms and the underlying mechanisms controlling long-term circannual clocks remain unknown in any organism.

Storage of Functional Sperm at Room Temperature in Zebrafish and Medaka.

The longevity of sperm in teleost such as zebrafish and medaka is short when isolated even in saline-balanced solution at a physiological temperature. In contrast, some internal fertilizers exhibit the long-term storage of sperm, >10 months, in the female reproductive tract. This evidence implies that sperm in teleost possesses the ability to survive for a long time under suitable conditions; however, these conditions are not well understood.

Chemogenetic Manipulation of Endogenous Proteins in Fission Yeast Using a Self-Localizing Ligand-Induced Protein Translocation System.

Cells sense extracellular stimuli through membrane receptors and process information through an intracellular signaling network. Protein translocation triggers intracellular signaling, and techniques such as chemically induced dimerization (CID) have been used to manipulate signaling pathways by altering the subcellular localization of signaling molecules. However, in the fission yeast , the commonly used FKBP-FRB system has technical limitations, and therefore, perturbation tools with low cytotoxicity and high temporal resolution are needed.

Cellular responses to compound stress induced by atmospheric-pressure plasma in fission yeast.

The stress response is one of the most fundamental cellular processes. Although the molecular mechanisms underlying responses to a single stressor have been extensively studied, cellular responses to multiple stresses remain largely unknown. Here, we characterized fission yeast cellular responses to a novel stress inducer, non-thermal atmospheric-pressure plasma.

ethnic-specific variant reducing binding of membrane-associated guanylate kinases causes focal epilepsy and behavioural disorder.

Pathogenic variants of affecting either its biosynthesis and/or its interactions with either LGI1 and/or PSD-95 have been recently identified in individuals with developmental and epileptic encephalopathy. Here, we describe a girl with seizures, delayed psychomotor development, and behavioural disorder, carrying a homozygous variant in (NM_021723.5:c.

An ABCB transporter regulates anisotropic cell expansion via cuticle deposition in the moss Physcomitrium patens.

Anisotropic cell expansion is crucial for the morphogenesis of land plants, as cell migration is restricted by the rigid cell wall. The anisotropy of cell expansion is regulated by mechanisms acting on the deposition or modification of cell wall polysaccharides. Besides the polysaccharide components in the cell wall, a layer of hydrophobic cuticle covers the outer cell wall and is subjected to tensile stress that mechanically restricts cell expansion.

Analysis of Plant-Specific ANTH Domain-Containing Protein in Marchantia polymorpha.

Membrane trafficking is a fundamental mechanism for protein and lipid transport in eukaryotic cells and exhibits marked diversity among eukaryotic lineages with distinctive body plans and lifestyles. Diversification of the membrane trafficking system is associated with the expansion and secondary loss of key machinery components, including RAB GTPases, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and adaptor proteins, during plant evolution. The number of AP180 N-terminal homology (ANTH) proteins, an adaptor family that regulates vesicle formation and cargo sorting during clathrin-mediated endocytosis, increases during plant evolution.

Picosecond-Scale Ultrafast Many-Body Dynamics in an Ultracold Rydberg-Excited Atomic Mott Insulator.

We report the observation and control of ultrafast many-body dynamics of electrons in ultracold Rydberg-excited atoms, spatially ordered in a three-dimensional Mott insulator (MI) with unity filling in an optical lattice. By mapping out the time-domain Ramsey interferometry in the picosecond timescale, we can deduce entanglement growth indicating the emergence of many-body correlations via dipolar forces. We analyze our observations with different theoretical approaches and find that the semiclassical model breaks down, thus indicating that quantum fluctuations play a decisive role in the observed dynamics.

Reversing Unknown Qubit-Unitary Operation, Deterministically and Exactly.

We report a deterministic and exact protocol to reverse any unknown qubit-unitary operation, which simulates the time inversion of a closed qubit system. To avoid known no-go results on universal deterministic exact unitary inversion, we consider the most general class of protocols transforming unknown unitary operations within the quantum circuit model, where the input unitary operation is called multiple times in sequence and fixed quantum circuits are inserted between the calls. In the proposed protocol, the input qubit-unitary operation is called 4 times to achieve the inverse operation, and the output state in an auxiliary system can be reused as a catalyst state in another run of the unitary inversion.

Harnessing Deep Learning to Analyze Cryptic Morphological Variability of Marchantia polymorpha.

Characterizing phenotypes is a fundamental aspect of biological sciences, although it can be challenging due to various factors. For instance, the liverwort Marchantia polymorpha is a model system for plant biology and exhibits morphological variability, making it difficult to identify and quantify distinct phenotypic features using objective measures. To address this issue, we utilized a deep-learning-based image classifier that can handle plant images directly without manual extraction of phenotypic features and analyzed pictures of M.

Shared GABA transmission pathology in dopamine agonist- and antagonist-induced dyskinesia.

Dyskinesia is involuntary movement caused by long-term medication with dopamine-related agents: the dopamine agonist 3,4-dihydroxy-L-phenylalanine (L-DOPA) to treat Parkinson's disease (L-DOPA-induced dyskinesia [LID]) or dopamine antagonists to treat schizophrenia (tardive dyskinesia [TD]). However, it remains unknown why distinct types of medications for distinct neuropsychiatric disorders induce similar involuntary movements. Here, we search for a shared structural footprint using magnetic resonance imaging-based macroscopic screening and super-resolution microscopy-based microscopic identification.

Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly.

Brain development is orchestrated by both innate and experience-dependent mechanisms, but their relative contributions are difficult to disentangle. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum, thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections.

Evolution of dispersal under spatio-temporal heterogeneity.

Theoretical studies over the past decades have revealed various factors that favor or disfavor the evolution of dispersal. Among these, environmental heterogeneity is one driving force that can impact dispersal traits, because dispersing individuals can obtain a fitness benefit through finding better environments. Despite this potential benefit, some previous works have shown that the existence of spatial heterogeneity hinders evolution of dispersal.

Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga.

Reef-building corals thrive in oligotrophic environments due to their possession of endosymbiotic algae. Confined to the low pH interior of the symbiosome within the cell, the algal symbiont provides the coral host with photosynthetically fixed carbon. However, it remains unknown how carbon is released from the algal symbiont for uptake by the host.

Stretching the limits of extracellular signal-related kinase (ERK) signaling - Cell mechanosensing to ERK activation.

Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK-ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues.

Width-dependent band gap of arm-chair graphene nanoribbons formed on vicinal SiC substrates by MBE.

Formation and electronic states of graphene nanoribbons with arm-chair edges (AGNR) are studied on the SiC(0001) vicinal surfaces toward the [11-00] direction. The surface step and terrace structures of both 4H and 6H-SiC substrates are used as the growth templates of one-dimensional arrays of AGNRs, which are prepared using the carbon molecular beam epitaxy followed by hydrogen intercalation. A band gap is observed above the-band maximum by angle-resolved photoelectron spectroscopy (ARPES) for the both samples.

Development of advanced photon calibrator for Kamioka gravitational wave detector (KAGRA).

The Kamioka Gravitational wave detector (KAGRA) cryogenic gravitational-wave observatory has commenced joint observations with the worldwide gravitational wave detector network. Precise calibration of the detector response is essential for accurately estimating parameters of gravitational wave sources. A photon calibrator is a crucial calibration tool used in laser interferometer gravitational-wave observatory, Virgo, and KAGRA, and it was utilized in joint observation 3 with GEO600 in Germany in April 2020.

Kangaroo endogenous retrovirus (KERV) forms megasatellite DNA with a simple repetition pattern in which the provirus structure is retained.

The kangaroo endogenous retrovirus (KERV) was previously reported to have undergone a rapid copy number increase in the red-necked wallaby; however, the mode of amplification was left to be clarified. The present study revealed that the long terminal repeat (LTR) (0.6 kb) and internal region (2.