High-throughput mechanical phenotyping and transcriptomics of single cells

The molecular system regulating cellular mechanical properties remains unexplored at single-cell resolution mainly due to a limited ability to combine mechanophenotyping with unbiased transcriptional screening. Here, we describe an electroporation-based lipid-bilayer assay for cell surface tension and transcriptomics (ELASTomics), a method in which oligonucleotide-labelled macromolecules are imported into cells via nanopore electroporation to assess the mechanical state of the cell surface and are enumerated by sequencing. ELASTomics can be readily integrated with existing single-cell sequencing approaches and enables the joint study of cell surface mechanics and underlying transcriptional regulation at an unprecedented resolution. We validate ELASTomics via analysis of cancer cell lines from various malignancies and show that the method can accurately identify cell types and assess cell surface tension. ELASTomics enables exploration of the relationships between cell surface tension, surface proteins, and transcripts along cell lineages differentiating from the haematopoietic progenitor cells of mice. We study the surface mechanics of cellular senescence and demonstrate that RRAD regulates cell surface tension in senescent TIG-1 cells. ELASTomics provides a unique opportunity to profile the mechanical and molecular phenotypes of single cells and can dissect the interplay among these in a range of biological contexts.

Nonvolatile optical phase shift in ferroelectric hafnium zirconium oxide

A nonvolatile optical phase shifter is a critical component for enabling the fabrication of programmable photonic integrated circuits on a Si photonics platform, facilitating communication, computing, and sensing. Although ferroelectric materials such as BaTiO3 offer nonvolatile optical phase shift capabilities, their compatibility with complementary metal-oxide-semiconductor fabs is limited. Hf0.5Zr0.5O2 is an emerging ferroelectric material, which exhibits complementary metal-oxide-semiconductor compatibility. Although extensively studied for ferroelectric transistors and memories, its application to photonics remains relatively unexplored. Here, we show the optical phase shift induced by ferroelectric Hf0.5Zr0.5O2. We observed a negative change in refractive index at a 1.55 μm wavelength in a pristine device regardless of the direction of the applied electric field. The nonvolatile phase shift was only observed once in a pristine device. This non-reversible phase shift can be attributed to the spontaneous polarization within the Hf0.5Zr0.5O2 film along the external electric field.

Evidence for a finite-momentum Cooper pair in tricolor d-wave superconducting superlattices

Fermionic superfluidity with a nontrivial Cooper-pairing, beyond the conventional Bardeen-Cooper-Schrieffer state, is a captivating field of study in quantum many-body systems. In particular, the search for superconducting states with finite-momentum pairs has long been a challenge, but establishing its existence has long suffered from the lack of an appropriate probe to reveal its momentum. Recently, it has been proposed that the nonreciprocal electron transport is the most powerful probe for the finite-momentum pairs, because it directly couples to the supercurrents. Here we reveal such a pairing state by the non-reciprocal transport on tricolor superlattices with strong spin-orbit coupling combined with broken inversion-symmetry consisting of atomically thin d-wave superconductor CeCoIn5. We find that while the second-harmonic resistance exhibits a distinct dip anomaly at the low-temperature (T)/high-magnetic field (H) corner in the HT-plane for H applied to the antinodal direction of the d-wave gap, such an anomaly is absent for H along the nodal direction. By carefully isolating extrinsic effects due to vortex dynamics, we reveal the presence of a non-reciprocal response originating from intrinsic superconducting properties characterized by finite-momentum pairs. We attribute the high-field state to the helical superconducting state, wherein the phase of the order parameter is spontaneously spatially modulated.

Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states

Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.

Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae

Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown function complements its function. Here, we identified frequent nonhomologous replacement of an essential component of DNA replication initiation, a replicative helicase loader gene, in Vibrionaceae. Our analysis of Vibrionaceae genomes revealed two genes with unknown function, named vdhL1 and vdhL2, that were substantially enriched in genomes without the known helicase-loader genes. These genes showed no sequence similarities to genes with known function but encoded proteins structurally similar with a viral helicase loader. Analyses of genomic syntenies and coevolution with helicase genes suggested that vdhL1/2 encodes a helicase loader. The in vitro assay showed that Vibrio harveyi VdhL1 and Vibrio ezurae VdhL2 promote the helicase activity of DnaB. Furthermore, molecular phylogenetics suggested that vdhL1/2 were derived from phages and replaced an intrinsic helicase loader gene of Vibrionaceae over 20 times. This high replacement frequency implies the host's advantage in acquiring a viral helicase loader gene.

Functional roles of CD26/DPP4 in lipopolysaccharide-induced lung injury

Acute respiratory distress syndrome (ARDS) is characterized by dysregulated inflammation and increased permeability of lung microvascular cells. CD26/dipeptidyl peptidase-4 (DPP4) is a type II membrane protein that is expressed in several cell types and mediates multiple pleiotropic effects. We previously reported that DPP4 inhibition by sitagliptin attenuates lipopolysaccharide (LPS)-induced lung injury in mice. The current study characterized the functional role of CD26/DPP4 expression in LPS-induced lung injury in mice, isolated alveolar macrophages, and cultured lung endothelial cells. In LPS-induced lung injury, inflammatory responses [bronchoalveolar lavage fluid (BALF) neutrophil numbers and several proinflammatory cytokine levels] were attenuated in Dpp4 knockout (Dpp4 KO) mice. However, multiple assays of alveolar capillary permeability were similar between the Dpp4 KO and wild-type mice. TNF-α and IL-6 production was suppressed in alveolar macrophages isolated from Dpp4 KO mice. In contrast, in cultured mouse lung microvascular endothelial cells (MLMVECs), reduction in CD26/DPP4 expression by siRNA resulted in greater ICAM-1 and IL-6 expression after LPS stimulation. Moreover, the LPS-induced vascular monolayer permeability in vitro was higher in MLMVECs treated with Dpp4 siRNA, suggesting that CD26/DPP4 plays a protective role in endothelial barrier function. In summary, this study demonstrated that genetic deficiency of Dpp4 attenuates inflammatory responses but not permeability in LPS-induced lung injury in mice, potentially through differential functional roles of CD26/DPP4 expression in resident cellular components of the lung. CD26/DPP4 may be a potential therapeutic target for ARDS and warrants further exploration to precisely identify the multiple functional effects of CD26/DPP4 in ARDS pathophysiology.NEW & NOTEWORTHY We aimed to clarify the functional roles of CD26/DPP4 in ARDS pathophysiology using Dpp4-deficient mice and siRNA reduction techniques in cultured lung cells. Our results suggest that CD26/DPP4 expression plays a proinflammatory role in alveolar macrophages while also playing a protective role in the endothelial barrier. Dpp4 genetic deficiency attenuates inflammatory responses but not permeability in LPS-induced lung injury in mice, potentially through differential roles of CD26/DPP4 expression in the resident cellular components of the lung.

A multicolor suite for deciphering population coding of calcium and cAMP in vivo

cAMP is a universal second messenger regulated by various upstream pathways including Ca2+ and G-protein-coupled receptors (GPCRs). To decipher in vivo cAMP dynamics, we rationally designed cAMPinG1, a sensitive genetically encoded green cAMP indicator that outperformed its predecessors in both dynamic range and cAMP affinity. Two-photon cAMPinG1 imaging detected cAMP transients in the somata and dendritic spines of neurons in the mouse visual cortex on the order of tens of seconds. In addition, multicolor imaging with a sensitive red Ca2+ indicator RCaMP3 allowed simultaneous measurement of population patterns in Ca2+ and cAMP in hundreds of neurons. We found Ca2+-related cAMP responses that represented specific information, such as direction selectivity in vision and locomotion, as well as GPCR-related cAMP responses. Overall, our multicolor suite will facilitate analysis of the interaction between the Ca2+, GPCR and cAMP signaling at single-cell resolution both in vitro and in vivo.

Selective-plane-activation structured illumination microscopy

The background light from out-of-focus planes hinders resolution enhancement in structured illumination microscopy when observing volumetric samples. Here we used selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. Theoretical investigation of the imaging properties and experimental demonstrations show that selective plane activation is beneficial for imaging dense microstructures in cells and cell spheroids.

Persistent magnetic coherence in magnets

When excited, the magnetization in a magnet precesses around the field in an anticlockwise manner on a timescale governed by viscous magnetization damping, after which any information carried by the initial actuation seems to be lost. This damping appears to be a fundamental bottleneck for the use of magnets in information processing. However, here we demonstrate the recall of the magnetization-precession phase after times that exceed the damping timescale by two orders of magnitude using dedicated two-colour microwave pump-probe experiments for a Y3Fe5O12 microstructured film. Time-resolved magnetization state tomography confirms the persistent magnetic coherence by revealing a double-exponential decay of magnetization correlation. We attribute persistent magnetic coherence to a feedback effect, that is, coherent coupling of the uniform precession with long-lived excitations at the minima of the spin-wave dispersion relation. Our finding liberates magnetic systems from the strong damping in nanostructures that has limited their use in coherent information storage and processing.

hoxc12/c13 as key regulators for rebooting the developmental program in Xenopus limb regeneration

During organ regeneration, after the initial responses to injury, gene expression patterns similar to those in normal development are reestablished during subsequent morphogenesis phases. This supports the idea that regeneration recapitulates development and predicts the existence of genes that reboot the developmental program after the initial responses. However, such rebooting mechanisms are largely unknown. Here, we explore core rebooting factors that operate during Xenopus limb regeneration. Transcriptomic analysis of larval limb blastema reveals that hoxc12/c13 show the highest regeneration specificity in expression. Knocking out each of them through genome editing inhibits cell proliferation and expression of a group of genes that are essential for development, resulting in autopod regeneration failure, while limb development and initial blastema formation are not affected. Furthermore, the induction of hoxc12/c13 expression partially restores froglet regenerative capacity which is normally very limited compared to larval regeneration. Thus, we demonstrate the existence of genes that have a profound impact alone on rebooting of the developmental program in a regeneration-specific manner.

Near-infrared PAINT localization microscopy via chromophore replenishment of phytochrome-derived fluorescent tag

Bacterial phytochromes are attractive molecular templates for engineering fluorescent proteins (FPs) because their near-infrared (NIR) emission significantly extends the spectral coverage of GFP-like FPs. Existing phytochrome-based FPs covalently bind heme-derived tetrapyrrole chromophores and exhibit constitutive fluorescence. Here we introduce Rep-miRFP, an NIR imaging probe derived from bacterial phytochrome, which interacts non-covalently and reversibly with biliverdin chromophore. In Rep-miRFP, the photobleached non-covalent adduct can be replenished with fresh biliverdin, restoring fluorescence. By exploiting this chromophore renewal capability, we demonstrate NIR PAINT nanoscopy in mammalian cells using Rep-miRFP.

Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography

The capability of focus control has been central to optical technologies that require both high temporal and spatial resolutions. However, existing varifocal lens schemes are commonly limited to the response time on the microsecond timescale and share the fundamental trade-off between the response time and the tuning power. Here, we propose an ultrafast holographic focusing method enabled by translating the speed of a fast 1D beam scanner into the speed of the complex wavefront modulation of a relatively slow 2D spatial light modulator. Using a pair of a digital micromirror device and a resonant scanner, we demonstrate an unprecedented refresh rate of focus control of 31 MHz, which is more than 1,000 times faster than the switching rate of a digital micromirror device. We also show that multiple micrometer-sized focal spots can be independently addressed in a range of over 1 MHz within a large volume of 5 mm × 5 mm × 5.5 mm, validating the superior spatiotemporal characteristics of the proposed technique - high temporal and spatial precision, high tuning power, and random accessibility in a three-dimensional space. The demonstrated scheme offers a new route towards three-dimensional light manipulation in the 100 MHz regime.

Highly efficient multi-resonance thermally activated delayed fluorescence material toward a BT.2020 deep-blue emitter

An ultrapure deep-blue multi-resonance-induced thermally activated delayed fluorescence material (DOB2-DABNA-A) is designed and synthesized. Benefiting from a fully resonating extended helical π-conjugated system, this compound has a small ΔEST value of 3.6 meV and sufficient spin-orbit coupling to exhibit a high-rate constant for reverse intersystem crossing (kRISC = 1.1 × 106 s-1). Furthermore, an organic light-emitting diode employing DOB2-DABNA-A as an emitter is fabricated; it exhibits ultrapure deep-blue emission at 452 nm with a small full width at half maximum of 24 nm, corresponding to Commission Internationale de l'Éclairage (CIE) coordinates of (0.145, 0.049). The high kRISC value reduces the efficiency roll-off, resulting in a high external quantum efficiency (EQE) of 21.6% at 1000 cd m-2.

StayGold variants for molecular fusion and membrane-targeting applications

Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.

Fabrication of Mie-resonant silicon nanoparticles using laser annealing for surface-enhanced fluorescence spectroscopy

Silicon nanostructures with unique Mie resonances have garnered considerable attention in the field of nanophotonics. Here, we present a simple and efficient method for the fabrication of silicon (Si) nanoparticle substrates using continuous-wave (CW) laser annealing. The resulting silicon nanoparticles exhibit Mie resonances in the visible region, and their resonant wavelengths can be precisely controlled. Notably, laser-annealed silicon nanoparticle substrates show a 60-fold enhancement in fluorescence. This tunable and fluorescence-enhancing silicon nanoparticle platform has tremendous potential for highly sensitive fluorescence sensing and biomedical imaging applications.

Surface spectroscopy and surface-bulk hybridization of Weyl semimetals

Weyl semimetal showing open-arc surface states is a prominent example of topological quantum matter in three dimensions. With the bulk-boundary correspondence present, nontrivial surface-bulk hybridization is inevitable but less understood. Spectroscopies have been often limited to verifying the existence of surface Fermi arcs, whereas its spectral shape related to the hybridization profile in energy-momentum space is not well studied. We present an exactly solvable formalism at the surface for a wide range of prototypical Weyl semimetals. The resonant surface state and the bulk influence coexist as a surface-bulk hybrid and are treated in a unified manner. Directly accessible to angle-resolved photoemission spectroscopy, we analytically reveal universal information about the system obtained from the spectroscopy of resonant topological states. We systematically find inhomogeneous and anisotropic singular responses around the surface-bulk merging borderline crossing Weyl points, highlighting its critical role in the Weyl topology. The response in scanning tunneling spectroscopy is also discussed. The results will provide much-needed insight into the surface-bulk-coupled physical properties and guide in-depth spectroscopic investigation of the nontrivial hybrid in many topological semimetal materials.

Association of homocysteine with white matter dysconnectivity in schizophrenia

Several studies have shown white matter (WM) dysconnectivity in people with schizophrenia (SZ). However, the underlying mechanism remains unclear. We investigated the relationship between plasma homocysteine (Hcy) levels and WM microstructure in people with SZ using diffusion tensor imaging (DTI). Fifty-three people with SZ and 83 healthy controls (HC) were included in this retrospective observational study. Tract-Based Spatial Statistics (TBSS) were used to evaluate group differences in WM microstructure. A significant negative correlation between plasma Hcy levels and WM microstructural disruption was noted in the SZ group (Spearman's ρ = -.330, P = 0.016) but not in the HC group (Spearman's ρ = .041, P = 0.712). These results suggest that increased Hcy may be associated with WM dysconnectivity in SZ, and the interaction between Hcy and WM dysconnectivity could be a potential mechanism of the pathophysiology of SZ. Further, longitudinal studies are required to investigate whether high Hcy levels subsequently cause WM microstructural disruption in people with SZ.

The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea

Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.

Fgf10 mutant newts regenerate normal hindlimbs despite severe developmental defects

In amniote limbs, Fibroblast Growth Factor 10 (FGF10) is essential for limb development, but whether this function is broadly conserved in tetrapods and/or involved in adult limb regeneration remains unknown. To tackle this question, we established Fgf10 mutant lines in the newt Pleurodeles waltl which has amazing regenerative ability. While Fgf10 mutant forelimbs develop normally, the hindlimbs fail to develop and downregulate FGF target genes. Despite these developmental defects, Fgf10 mutants were able to regenerate normal hindlimbs rather than recapitulating the embryonic phenotype. Together, our results demonstrate an important role for FGF10 in hindlimb formation, but little or no function in regeneration, suggesting that different mechanisms operate during limb regeneration versus development.

Effect of inorganic material surface chemistry on structures and fracture behaviours of epoxy resin

The mechanisms underlying the influence of the surface chemistry of inorganic materials on polymer structures and fracture behaviours near adhesive interfaces are not fully understood. This study demonstrates the first clear and direct evidence that molecular surface segregation and cross-linking of epoxy resin are driven by intermolecular forces at the inorganic surfaces alone, which can be linked directly to adhesive failure mechanisms. We prepare adhesive interfaces between epoxy resin and silicon substrates with varying surface chemistries (OH and H terminations) with a smoothness below 1 nm, which have different adhesive strengths by ~13 %. The epoxy resins within sub-nanometre distance from the surfaces with different chemistries exhibit distinct amine-to-epoxy ratios, cross-linked network structures, and adhesion energies. The OH- and H-terminated interfaces exhibit cohesive failure and interfacial delamination, respectively. The substrate surface chemistry impacts the cross-linked structures of the epoxy resins within several nanometres of the interfaces and the adsorption structures of molecules at the interfaces, which result in different fracture behaviours and adhesive strengths.

Large-scale cranial window for in vivo mouse brain imaging utilizing fluoropolymer nanosheet and light-curable resin

Two-photon microscopy enables in vivo imaging of neuronal activity in mammalian brains at high resolution. However, two-photon imaging tools for stable, long-term, and simultaneous study of multiple brain regions in same mice are lacking. Here, we propose a method to create large cranial windows covering such as the whole parietal cortex and cerebellum in mice using fluoropolymer nanosheets covered with light-curable resin (termed the 'Nanosheet Incorporated into light-curable REsin' or NIRE method). NIRE method can produce cranial windows conforming the curved cortical and cerebellar surfaces, without motion artifacts in awake mice, and maintain transparency for >5 months. In addition, we demonstrate that NIRE method can be used for in vivo two-photon imaging of neuronal ensembles, individual neurons and subcellular structures such as dendritic spines. The NIRE method can facilitate in vivo large-scale analysis of heretofore inaccessible neural processes, such as the neuroplastic changes associated with maturation, learning and neural pathogenesis.

Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability

DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.

Superconductivity in a van der Waals layered quasicrystal

Van der Waals layered transition-metal chalcogenides are drawing significant attention owing to their intriguing physical properties. This group of materials consists of abundant members with various elements, having a variety of different structures. However, they are all crystalline materials, and the physical properties of van der Waals layered quasicrystals have never been studied to date. Here, we report on the discovery of superconductivity in a van der Waals layered quasicrystal of Ta1.6Te. The electrical resistivity, magnetic susceptibility, and specific heat of the quasicrystal unambiguously validate the occurrence of bulk superconductivity at a transition temperature of ~1 K. This discovery can promote new research on assessing the physical properties of novel van der Waals layered quasicrystals as well as two-dimensional quasicrystals; moreover, it paves the way toward new frontiers of superconductivity in thermodynamically stable quasicrystals.

Deep generative design of RNA family sequences

RNA engineering has immense potential to drive innovation in biotechnology and medicine. Despite its importance, a versatile platform for the automated design of functional RNA is still lacking. Here, we propose RNA family sequence generator (RfamGen), a deep generative model that designs RNA family sequences in a data-efficient manner by explicitly incorporating alignment and consensus secondary structure information. RfamGen can generate novel and functional RNA family sequences by sampling points from a semantically rich and continuous representation. We have experimentally demonstrated the versatility of RfamGen using diverse RNA families. Furthermore, we confirmed the high success rate of RfamGen in designing functional ribozymes through a quantitative massively parallel assay. Notably, RfamGen successfully generates artificial sequences with higher activity than natural sequences. Overall, RfamGen significantly improves our ability to design functional RNA and opens up new potential for generative RNA engineering in synthetic biology.

Intrinsic factors responsible for brittle versus ductile nature of refractory high-entropy alloys

Refractory high-entropy alloys (RHEAs) are of interest for ultrahigh-temperature applications. To overcome their drawbacks - low-temperature brittleness and poor creep strength at high temperatures - improved fundamental understanding is needed. Using experiments, theory, and modeling, we investigated prototypical body-centered cubic (BCC) RHEAs, TiZrHfNbTa and VNbMoTaW. The former is compressible to 77 K, whereas the latter is not below 298 K. Hexagonal close-packed (HCP) elements in TiZrHfNbTa lower its dislocation core energy, increase lattice distortion, and lower its shear modulus relative to VNbMoTaW whose elements are all BCC. Screw dislocations dominate TiZrHfNbTa plasticity, but equal numbers of edges and screws exist in VNbTaMoW. Dislocation cores are compact in VNbTaMoW and extended in TiZrHfNbTa, and different macroscopic slip planes are activated in the two RHEAs, which we attribute to the concentration of HCP elements. Our findings demonstrate how ductility and strength can be controlled through the ratio of HCP to BCC elements in RHEAs.

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks

Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package 'transomics2cytoscape' for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape .

In vitro induction of patterned branchial arch-like aggregate from human pluripotent stem cells

Early patterning of neural crest cells (NCCs) in the craniofacial primordium is important for subsequent development of proper craniofacial structures. However, because of the complexity of the environment of developing tissues, surveying the early specification and patterning of NCCs is difficult. In this study, we develop a simplified in vitro 3D model using human pluripotent stem cells to analyze the early stages of facial development. In this model, cranial NCC-like cells spontaneously differentiate from neural plate border-like cells into maxillary arch-like mesenchyme after a long-term culture. Upon the addition of EDN1 and BMP4, these aggregates are converted into a mandibular arch-like state. Furthermore, temporary treatment with EDN1 and BMP4 induces the formation of spatially separated domains expressing mandibular and maxillary arch markers within a single aggregate. These results suggest that this in vitro model is useful for determining the mechanisms underlying cell fate specification and patterning during early facial development.

Ran-GTP assembles a specialized spindle structure for accurate chromosome segregation in medaka early embryos

Despite drastic cellular changes during cleavage, a mitotic spindle assembles in each blastomere to accurately segregate duplicated chromosomes. Mechanisms of mitotic spindle assembly have been extensively studied using small somatic cells. However, mechanisms of spindle assembly in large vertebrate embryos remain little understood. Here, we establish functional assay systems in medaka (Oryzias latipes) embryos by combining CRISPR knock-in with auxin-inducible degron technology. Live imaging reveals several unexpected features of microtubule organization and centrosome positioning that achieve rapid, accurate cleavage. Importantly, Ran-GTP assembles a dense microtubule network at the metaphase spindle center that is essential for chromosome segregation in early embryos. This unique spindle structure is remodeled into a typical short, somatic-like spindle after blastula stages, when Ran-GTP becomes dispensable for chromosome segregation. We propose that despite the presence of centrosomes, the chromosome-derived Ran-GTP pathway has essential roles in functional spindle assembly in large, rapidly dividing vertebrate early embryos, similar to acentrosomal spindle assembly in oocytes.

Neuronal DSCAM regulates the peri-synaptic localization of GLAST in Bergmann glia for functional synapse formation

In the central nervous system, astrocytes enable appropriate synapse function through glutamate clearance from the synaptic cleft; however, it remains unclear how astrocytic glutamate transporters function at peri-synaptic contact. Here, we report that Down syndrome cell adhesion molecule (DSCAM) in Purkinje cells controls synapse formation and function in the developing cerebellum. Dscam-mutant mice show defects in CF synapse translocation as is observed in loss of function mutations in the astrocytic glutamate transporter GLAST expressed in Bergmann glia. These mice show impaired glutamate clearance and the delocalization of GLAST away from the cleft of parallel fibre (PF) synapse. GLAST complexes with the extracellular domain of DSCAM. Riluzole, as an activator of GLAST-mediated uptake, rescues the proximal impairment in CF synapse formation in Purkinje cell-selective Dscam-deficient mice. DSCAM is required for motor learning, but not gross motor coordination. In conclusion, the intercellular association of synaptic and astrocyte proteins is important for synapse formation and function in neural transmission.

Coherent electronic coupling in quantum dot solids induces cooperative enhancement of nonlinear optoelectronic responses

Synchronized dynamics of quantum dot (QD) ensembles are essential for generating ultrafast and giant optical responses beyond those of individual QDs. Increasing the strength of the direct electronic coupling between QDs is a key strategy for the realization of cooperative quantum phenomena. Here, we observe a quantum cooperative effect on nonlinear photocurrents caused by the coherent electronic coupling in semiconductor QD solids. We measure quantum interference signals cooperatively generated in QD solids. We control the inter-QD distance with atomic precision using bidentate ligands that strongly link the QDs. The harmonic quantum interference signals are strongly enhanced when shortening the molecular length of the ligand. Furthermore, we clarify that the coherence length of multiexcitons extends to neighbouring QDs. This finding is direct evidence that multiexciton coherent tunnelling assists the ultrafast exciton delocalization. Cooperative enhancement in QD solids may find application in advanced quantum optoelectronics.

Neuronal sensorimotor integration guiding salt concentration navigation in Caenorhabditis elegans

Animals navigate their environment by manipulating their movements and adjusting their trajectory which requires a sophisticated integration of sensory data with their current motor status. Here, we utilize the nematode Caenorhabditis elegans to explore the neural mechanisms of processing the sensory and motor information for navigation. We developed a microfluidic device which allows animals to freely move their heads while receiving temporal NaCl stimuli. We found that C. elegans regulates neck bending direction in response to temporal NaCl concentration changes in a way which is consistent with a C. elegans' navigational strategy which regulates traveling direction toward preferred NaCl concentrations. Our analysis also revealed that the activity of a neck motor neuron is significantly correlated with neck bending and activated by the decrease in NaCl concentration in a phase-dependent manner. By combining the analysis of behavioral and neural response to NaCl stimuli and optogenetic perturbation experiments, we revealed that NaCl decrease during ventral bending activates the neck motor neuron which counteracts ipsilateral bending. Simulations further suggest that this phase-dependent response of neck motor neurons can facilitate curving toward preferred salt concentrations.

Alkali metal bilayer intercalation in graphene

Alkali metal (AM) intercalation between graphene layers holds promise for electronic manipulation and energy storage, yet the underlying mechanism remains challenging to fully comprehend despite extensive research. In this study, we employ low-voltage scanning transmission electron microscopy (LV-STEM) to visualize the atomic structure of intercalated AMs (potassium, rubidium, and cesium) in bilayer graphene (BLG). Our findings reveal that the intercalated AMs adopt bilayer structures with hcp stacking, and specifically a C6M2C6 composition. These structures closely resemble the bilayer form of fcc (111) structure observed in AMs under high-pressure conditions. A negative charge transferred from bilayer AMs to graphene layers of approximately 1~1.5×1014 e-/cm-2 was determined by electron energy loss spectroscopy (EELS), Raman, and electrical transport. The bilayer AM is stable in BLG and graphite superficial layers but absent in the graphite interior, primarily dominated by single-layer AM intercalation. This hints at enhancing AM intercalation capacity by thinning the graphite material.

The nucleolar shell provides anchoring sites for DNA untwisting

DNA underwinding (untwisting) is a crucial step in transcriptional activation. DNA underwinding occurs between the site where torque is generated by RNA polymerase (RNAP) and the site where the axial rotation of DNA is constrained. However, what constrains DNA axial rotation in the nucleus is yet unknown. Here, we show that the anchorage to the nuclear protein condensates constrains DNA axial rotation for DNA underwinding in the nucleolus. In situ super-resolution imaging of underwound DNA reveal that underwound DNA accumulates in the nucleolus, a nuclear condensate with a core-shell structure. Specifically, underwound DNA is distributed in the nucleolar core owing to RNA polymerase I (RNAPI) activities. Furthermore, underwound DNA in the core decreases when nucleolar shell components are prevented from binding to their recognition structure, G-quadruplex (G4). Taken together, these results suggest that the nucleolar shell provides anchoring sites that constrain DNA axial rotation for RNAPI-driven DNA underwinding in the core. Our findings will contribute to understanding how nuclear protein condensates make up constraints for the site-specific regulation of DNA underwinding and transcription.

Replicating shear-mediated self-assembly of spider silk through microfluidics

The development of artificial spider silk with properties similar to native silk has been a challenging task in materials science. In this study, we use a microfluidic device to create continuous fibers based on recombinant MaSp2 spidroin. The strategy incorporates ion-induced liquid-liquid phase separation, pH-driven fibrillation, and shear-dependent induction of β-sheet formation. We find that a threshold shear stress of approximately 72 Pa is required for fiber formation, and that β-sheet formation is dependent on the presence of polyalanine blocks in the repetitive sequence. The MaSp2 fiber formed has a β-sheet content (29.2%) comparable to that of native dragline with a shear stress requirement of 111 Pa. Interestingly, the polyalanine blocks have limited influence on the occurrence of liquid-liquid phase separation and hierarchical structure. These results offer insights into the shear-induced crystallization and sequence-structure relationship of spider silk and have significant implications for the rational design of artificially spun fibers.

Automatic feature engineering for catalyst design using small data without prior knowledge of target catalysis

The empirical aspect of descriptor design in catalyst informatics, particularly when confronted with limited data, necessitates adequate prior knowledge for delving into unknown territories, thus presenting a logical contradiction. This study introduces a technique for automatic feature engineering (AFE) that works on small catalyst datasets, without reliance on specific assumptions or pre-existing knowledge about the target catalysis when designing descriptors and building machine-learning models. This technique generates numerous features through mathematical operations on general physicochemical features of catalytic components and extracts relevant features for the desired catalysis, essentially screening numerous hypotheses on a machine. AFE yields reasonable regression results for three types of heterogeneous catalysis: oxidative coupling of methane (OCM), conversion of ethanol to butadiene, and three-way catalysis, where only the training set is swapped. Moreover, through the application of active learning that combines AFE and high-throughput experimentation for OCM, we successfully visualize the machine's process of acquiring precise recognition of the catalyst design. Thus, AFE is a versatile technique for data-driven catalysis research and a key step towards fully automated catalyst discoveries.

HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence

Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation-qPCR, we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB-HKDC1 axis was essential for PINK1 (PTEN-induced kinase 1)/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels, with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and maintaining mitochondria-lysosome contact. Interestingly, HKDC1 regulated mitophagy and lysosomal repair independently of its prospective function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage-induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.

Lysophagy protects against propagation of α-synuclein aggregation through ruptured lysosomal vesicles

The neuron-to-neuron propagation of misfolded α-synuclein (αSyn) aggregates is thought to be key to the pathogenesis of synucleinopathies. Recent studies have shown that extracellular αSyn aggregates taken up by the endosomal-lysosomal system can rupture the lysosomal vesicular membrane; however, it remains unclear whether lysosomal rupture leads to the transmission of αSyn aggregation. Here, we applied cell-based αSyn propagation models to show that ruptured lysosomes are the pathway through which exogenous αSyn aggregates transmit aggregation, and furthermore, this process was prevented by lysophagy, i.e., selective autophagy of damaged lysosomes. αSyn aggregates accumulated predominantly in lysosomes, causing their rupture, and seeded the aggregation of endogenous αSyn, initially around damaged lysosomes. Exogenous αSyn aggregates induced the accumulation of LC3 on lysosomes. This LC3 accumulation was not observed in cells in which a key regulator of autophagy, RB1CC1/FIP200, was knocked out and was confirmed as lysophagy by transmission electron microscopy. Importantly, RB1CC1/FIP200-deficient cells treated with αSyn aggregates had increased numbers of ruptured lysosomes and enhanced propagation of αSyn aggregation. Furthermore, various types of lysosomal damage induced using lysosomotropic reagents, depletion of lysosomal enzymes, or more toxic species of αSyn fibrils also exacerbated the propagation of αSyn aggregation, and impaired lysophagy and lysosomal membrane damage synergistically enhanced propagation. These results indicate that lysophagy prevents exogenous αSyn aggregates from escaping the endosomal-lysosomal system and transmitting aggregation to endogenous cytosolic αSyn via ruptured lysosomal vesicles. Our findings suggest that the progression and severity of synucleinopathies are associated with damage to lysosomal membranes and impaired lysophagy.

Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activator

About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.

RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations

Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.

An archetype and scaling of developmental tissue dynamics across species

Morphometric studies have revealed the existence of simple geometric relationships among various animal shapes. However, we have little knowledge of the mathematical principles behind the morphogenetic dynamics that form the organ/body shapes of different species. Here, we address this issue by focusing on limb morphogenesis in Gallus gallus domesticus (chicken) and Xenopus laevis (African clawed frog). To compare the deformation dynamics between tissues with different sizes/shapes as well as their developmental rates, we introduce a species-specific rescaled spatial coordinate and a common clock necessary for cross-species synchronization of developmental times. We find that tissue dynamics are well conserved across species under this spacetime coordinate system, at least from the early stages of development through the phase when basic digit patterning is established. For this developmental period, we also reveal that the tissue dynamics of both species are mapped with each other through a time-variant linear transformation in real physical space, from which hypotheses on a species-independent archetype of tissue dynamics and morphogenetic scaling are proposed.

Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping

Overexpression of antibody light chains in small plasma cell clones can lead to misfolding and aggregation. On the other hand, the formation of amyloid fibrils from antibody light chains is related to amyloidosis. Although aggregation of antibody light chain is an important issue, atomic-level structural examinations of antibody light chain aggregates are sparse. In this study, we present an antibody light chain that maintains an equilibrium between its monomeric and tetrameric states. According to data from X-ray crystallography, thermodynamic and kinetic measurements, as well as theoretical studies, this antibody light chain engages in 3D domain swapping within its variable region. Here, a pair of domain-swapped dimers creates a tetramer through hydrophobic interactions, facilitating the revelation of the domain-swapped structure. The negative cotton effect linked to the β-sheet structure, observed around 215 nm in the circular dichroism (CD) spectrum of the tetrameric variable region, is more pronounced than that of the monomer. This suggests that the monomer contains less β-sheet structures and exhibits greater flexibility than the tetramer in solution. These findings not only clarify the domain-swapped structure of the antibody light chain but also contribute to controlling antibody quality and advancing the development of future molecular recognition agents and drugs.

Microautophagy regulated by STK38 and GABARAPs is essential to repair lysosomes and prevent aging

Lysosomes are degradative organelles and signaling hubs that maintain cell and tissue homeostasis, and lysosomal dysfunction is implicated in aging and reduced longevity. Lysosomes are frequently damaged, but their repair mechanisms remain unclear. Here, we demonstrate that damaged lysosomal membranes are repaired by microautophagy (a process termed "microlysophagy") and identify key regulators of the first and last steps. We reveal the AGC kinase STK38 as a novel microlysophagy regulator. Through phosphorylation of the scaffold protein DOK1, STK38 is specifically required for the lysosomal recruitment of the AAA+ ATPase VPS4, which terminates microlysophagy by promoting the disassembly of ESCRT components. By contrast, microlysophagy initiation involves non-canonical lipidation of ATG8s, especially the GABARAP subfamily, which is required for ESCRT assembly through interaction with ALIX. Depletion of STK38 and GABARAPs accelerates DNA damage-induced cellular senescence in human cells and curtails lifespan in C. elegans, respectively. Thus, microlysophagy is regulated by STK38 and GABARAPs and could be essential for maintaining lysosomal integrity and preventing aging.

Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches

Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.

Periportal hepatocyte proliferation at midgestation governs maternal glucose homeostasis in mice

The maternal liver is challenged by metabolic demands throughout pregnancy. However, hepatocyte dynamics and their physiological significance in pregnancy remain unclear. Here, we show in mice that hepatocyte proliferation is spatiotemporally regulated in each liver lobular zone during pregnancy, with transient proliferation of periportal and pericentral hepatocytes during mid and late gestation, respectively. Using adeno-associated virus (AAV)-8-mediated expression of the cell cycle inhibitor p21 in hepatocytes, we show that inhibition of hepatocyte proliferation during mid, but not late, gestation impairs liver growth. Transcriptionally, genes involved in glucose/glycogen metabolism are downregulated in late pregnancy when midgestational hepatocyte proliferation is attenuated. In addition, hepatic glycogen storage is abolished, with concomitant elevated blood glucose concentrations, glucose intolerance, placental glycogen deposition, and fetal overgrowth. Laser capture microdissection and RNA-seq analysis of each liver lobular zone show zone-specific changes in the transcriptome during pregnancy and identify genes that are periportally expressed at midgestation, including the hyaluronan-mediated motility receptor (Hmmr). Knockdown of Hmmr in hepatocytes by AAV8-shHmmr suppresses periportal hepatocyte proliferation at midgestation and induces impaired hepatic glycogen storage, glucose intolerance, placental glycogen deposition and fetal overgrowth. Our results suggest that periportal hepatocyte proliferation during midgestation is critical for maternal glycogen metabolism and fetal size.

Percolation-induced gel-gel phase separation in a dilute polymer network

Cosmic large-scale structures, animal flocks and living tissues can be considered non-equilibrium organized systems created by dissipative processes. Replicating such properties in artificial systems is still difficult. Herein we report a dissipative network formation process in a dilute polymer-water mixture that leads to percolation-induced gel-gel phase separation. The dilute system, which forms a monophase structure at the percolation threshold, spontaneously separates into two co-continuous gel phases with a submillimetre scale (a dilute-percolated gel) during the deswelling process after the completion of the gelation reaction. The dilute-percolated gel, which contains 99% water, exhibits unexpected hydrophobicity and induces the development of adipose-like tissues in subcutaneous tissues. These findings support the development of dissipative structures with advanced functionalities for distinct applications, ranging from physical chemistry to tissue engineering.

Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility

The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported. Here we employ transgenic techniques to the allotetraploid plant A. kamchatica. We find that when the dominant SCR-B is repaired by removing a transposable element insertion, self-incompatibility is restored. This suggests that SCR was responsible for the evolution of self-compatibility. By contrast, the reconstruction of recessive SCR-D cannot restore self-incompatibility. These data indicate that the insertion in SCR-B conferred dominant self-compatibility to A. kamchatica. Dominant self-compatibility supports the prediction that dominant mutations increasing selfing rate can pass through Haldane's sieve against recessive mutations. The dominance regulation between subgenomes inherited from progenitors contrasts with previous studies on novel epigenetic mutations at polyploidization termed genome shock.

Wavefront control of subcycle vortex pulses via carrier-envelope-phase tailoring

The carrier-envelope phase (CEP) of an ultrashort laser pulse is becoming more crucial to specify the temporal characteristic of the pulse's electric field when the pulse duration becomes shorter and attains the subcycle regime; here, the pulse duration of the intensity envelope is shorter than one cycle period of the carrier field oscillation. When this subcycle pulse involves a structured wavefront as is contained in an optical vortex (OV) pulse, the CEP has an impact on not only the temporal but also the spatial characteristics owing to the spatiotemporal coupling in the structured optical pulse. However, the direct observation of the spatial effect of the CEP control has not yet been demonstrated. In this study, we report on the measurement and control of the spatial wavefront of a subcycle OV pulse by adjusting the CEP. To generate subcycle OV pulses, an optical parametric amplifier delivering subcycle Gaussian pulses and a Sagnac interferometer as a mode converter were integrated and provided an adequate spectral adaptability. The pulse duration of the generated OV pulse was 4.7 fs at a carrier wavelength of 1.54 µm. To confirm the wavefront control with the alteration of the CEP, we developed a novel [Formula: see text]-2[Formula: see text] interferometer that exhibited spiral fringes originating from the spatial interference between the subcycle OV pulse and the second harmonic of the subcycle Gaussian pulse producing a parabolic wavefront as a reference; this resulted in the successful observation of the rotation of spiral interference fringes during CEP manipulation.

Antiferromagnetic topological insulator with selectively gapped Dirac cones

Antiferromagnetic (AF) topological materials offer a fertile ground to explore a variety of quantum phenomena such as axion magnetoelectric dynamics and chiral Majorana fermions. To realize such intriguing states, it is essential to establish a direct link between electronic states and topology in the AF phase, whereas this has been challenging because of the lack of a suitable materials platform. Here we report the experimental realization of the AF topological-insulator phase in NdBi. By using micro-focused angle-resolved photoemission spectroscopy, we discovered contrasting surface electronic states for two types of AF domains; the surface having the out-of-plane component in the AF-ordering vector displays Dirac-cone states with a gigantic energy gap, whereas the surface parallel to the AF-ordering vector hosts gapless Dirac states despite the time-reversal-symmetry breaking. The present results establish an essential role of combined symmetry to protect massless Dirac fermions under the presence of AF order and widen opportunities to realize exotic phenomena utilizing AF topological materials.

Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.