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Abstract We have developed a state-of-the-art apparatus for laser-based spin- and angle-resolved photoemission spectroscopy with micrometer spatial resolution (µ-SARPES). This equipment is realized by the combination of a high-resolution photoelectron spectrometer, a 6 eV laser with high photon flux that is focused down to a few micrometers, a high-precision sample stage control system, and a double very-low-energy-electron-diffraction spin detector. The setup achieves an energy resolution of 1.5 (5.5) meV without (with) the spin detection mode, compatible with a spatial resolution better than 10 µm. This enables us to probe both spatially-resolved electronic structures and vector information of spin polarization in three dimensions. The performance of µ-SARPES apparatus is demonstrated by presenting ARPES and SARPES results from topological insulators and Au photolithography patterns on a Si (001) substrate.

Abstract TaTe4, a metallic charge-density wave (CDW) material discovered decades ago, has attracted renewed attention due to its rich interesting properties, such as pressure-induced superconductivity and candidate nontrivial topological phase. Here, using high-resolution angle-resolved photoemission spectroscopy and ab initio calculation, we systematically investigate the electronic structure of TaTe4. At 26 K, we observe a CDW gap as large as 290 meV, which persists up to 500 K. The CDW-modulated band structure shows a complex reconstruction that closely correlates with the lattice distortion. Inside the CDW gap, there exist highly dispersive energy bands contributing to the remnant Fermi surface and metallic behavior in the CDW state. Interestingly, our ab initio calculation reveals that the large CDW gap mainly opens in the electronic states with out-of-plane orbital components, while the in-gap metallic states originate from in-plane orbitals, suggesting an orbital texture that couples with the CDW order. Our results shed light on the interplay between electron, lattice, and orbital in quasi-one-dimensional CDW materials.

CeSb undergoes a devil’s staircase sequence of extremely long-period modulations of the magnetically ordered 4f states. Here, the authors visualize how the devil’s staircase ordering impacts mobile electrons and collapses the well-defined band picture at the Fermi energy.

Abstract Conventional superconductivity is caused by electron-phonon coupling. The discovery of high-temperature superconductors raised the question of whether such strong electron-phonon coupling is realized in cuprates. Strong coupling with some collective excitation mode has been indicated by a dispersion “kink”. However, there is intensive debate regarding whether the relevant coupling mode is a magnetic resonance mode or an oxygen buckling phonon mode. This ambiguity is a consequence of the energy of the main prominent kink. Here, we show a new landscape of dispersion kinks. We report that heavily overdoping a Bi2Sr2CaCu2O8+δ superconductor results in a decline of the conventional main kink and a rise of another sharp kink, along with substantial energy shifts of both. Notably, the latter kink can be ascribed only to an oxygen-breathing phonon. Hence, the multiple phonon branches provide a consistent account of our data set on the multiple kinks. Our results suggest that strong electron-phonon coupling and its dramatic change should be incorporated into or reconciled with scenarios for the evolution of high-T c superconductivity.

In cuprates, superconductivity exists in a narrow window at high electron doping concentration with strong antiferromagnetic correlations. Here, the authors demonstrate superconductivity with no effect of antiferromagnetic order in a cuprate for a wide electron doping range following a protect anneal process.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

III-nitride quantum dots are proving to be promising for application to single photon emitting devices. Research around the globe is revealing several interesting properties of these emitters, including a wide range of emission wavelengths, high temperature operation, and deterministic polarization of the emitted photons. Here a review is given on the single photon emission properties of such III-nitride quantum dots. [ABSTRACT FROM AUTHOR]

The nature of the pseudogap (PG) in high transition temperature (high Tc) superconducting cuprates has been a major issue in condensed matter physics. It is still unclear whether the high Tt. superconductivity can be universally associated with the PG formation. Here we provide direct evidence of the existence of the PG phase via angle-resolved photoemission spectroscopy in another family of high Tc superconductor, iron pnictides. Our results reveal a composition-dependent PG formation in the multiband electronic structure of BaFe 2(AS1-x-Px)2. The PG develops well above the magnetostructural transition for low x, persists above the nonmagnetic superconducting dome for optimal x, and is destroyed for x ∼ 0.6, thus showing a notable similarity with cuprates. In addition, the PG formation is accompanied by inequivalent energy shifts in the zx/yz orbitals of iron atoms, indicative of a peculiar iron orbital ordering which breaks the fourfold rotational symmetry. [ABSTRACT FROM AUTHOR]

Ultrahigh resolution angle-resolved photoemission spectroscopy with low-energy photons is used to study the detailed momentum dependence of the well-known nodal ‘kink’ dispersion anomaly of Bi _2 Sr _2 CaCu _2 O _8+ _δ . We find that the kink's location transitions smoothly from a maximum binding energy of about 65 meV at the node of the d -wave superconducting gap to 55 meV roughly one-third of the way to the antinode. Meanwhile, the self-energy spectrum corresponding to the kink dramatically sharpens and intensifies beyond a critical point in momentum space. We discuss the possible bosonic spectrum in energy and momentum space that can couple to the k -space dispersion of the electronic kinks.

Monocytes and macrophages express the transcription factor MAFB (V-maf musculoaponeurotic fibrosarcoma oncogene homolog B) and protect against ischemic acute kidney injury (AKI). However, the mechanism through which MAFB alleviates AKI in macrophages remains unclear. In this study, we induced AKI in macrophage lineage-specific Mafb-deficient mice (C57BL/6J) using the ischemia-reperfusion injury model to analyze these mechanisms. Our results showed that MAFB regulates the expression of Alox15 (arachidonate 15-lipoxygenase) in macrophages during ischemic AKI. The expression of ALOX15 was significantly decreased at the mRNA and protein levels in macrophages that infiltrated the kidneys of macrophage-specific Mafb-deficient mice at 24 h after ischemia-reperfusion injury. ALOX15 promotes the resolution of inflammation under acute conditions by producing specialized proresolving mediators by oxidizing essential fatty acids. Therefore, MAFB in macrophages promotes the resolution of inflammation in ischemic AKI by regulating the expression of Alox15. Moreover, MAFB expression in macrophages is upregulated via the COX-2/PGE2/EP4 pathway in ischemic AKI. Our in vitro assay showed that MAFB regulates the expression of Alox15 under the COX-2/PGE2/EP4 pathway in macrophages. PGE2 mediates the lipid mediator (LM) class switch from inflammatory LMs to specialized proresolving mediators. Therefore, MAFB plays a key role in the PGE2-mediated LM class switch by regulating the expression of Alox15. Our study identified a previously unknown mechanism by which MAFB in macrophages alleviates ischemic AKI and provides new insights into regulating the LM class switch in acute inflammatory conditions., (Copyright © 2024 by The American Association of Immunologists, Inc.)

The Bioinformation and DNA Data Bank of Japan Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides public databases that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), the DDBJ Center accepts and distributes nucleotide sequence data ranging from raw reads to assembled and annotated sequences with the National Center for Biotechnology Information and the European Bioinformatics Institute. Besides INSDC databases, the DDBJ Center provides databases for functional genomics (Genomic Expression Archive), metabolomics (MetaboBank), human genetic variations (TogoVar-repository) and human genetic and phenotypic data (Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics supercomputer, which is also a platform for the DDBJ Group Cloud (DGC) services for sharing and analysis of pre-publication data among research groups. This paper reports recent updates on the databases and the services of the DDBJ Center, highlighting the DGC service., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

In this community effort, we compare measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as a set of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method and/or their method of choice. Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively. These results are the most precise (intra-laboratory CVs ≤ 4.2%) and concordant (inter-laboratory CVs < 14%) community-derived absolute concentration values reported to date for four clinically used ceramides in the commonly analyzed SRM 1950. We demonstrate that calibration using authentic labelled standards dramatically reduces data variability. Furthermore, we show how the use of shared RM can correct systematic quantitative biases and help in harmonizing lipidomics. Collectively, the results from the present study provide a significant knowledge base for translation of lipidomic technologies to future clinical applications that might require the determination of reference intervals (RIs) in various human populations or might need to estimate reference change values (RCV), when analytical variability is a key factor for recall during multiple testing of individuals., (© 2024. The Author(s).)

Recently, unconventional antiferromagnets that enable the spin splitting (SS) of electronic states have been theoretically proposed and experimentally realized, where the magnetic sublattices containing moments pointing at different directions are connected by a novel set of symmetries. Such SS is substantial, k-dependent, and independent of the spin-orbit coupling (SOC) strength, making these magnets promising materials for antiferromagnetic spintronics. Here, combined with angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT) calculations, a systematic study on CrSb, a metallic spin-split antiferromagnet candidate with Néel temperature T N = 703 K, is conducted. The data reveal the electronic structure of CrSb along both out-of-plane and in-plane momentum directions, rendering an anisotropic k-dependent SS that agrees well with the calculational results. The magnitude of such SS reaches up to at least 0.8 eV at non-high-symmetry momentum points, which is significantly higher than the largest known SOC-induced SS. This compound expands the choice of materials in the field of antiferromagnetic spintronics and is likely to stimulate subsequent investigations of high-efficiency spintronic devices that are functional at room temperature., (© 2024 The Author(s). Advanced Science published by Wiley‐VCH GmbH.)

The gut microbiota influences physiological functions of the host, ranging from the maintenance of local gut homeostasis to systemic immunity and metabolism. Secreted phospholipase A 2 group X (sPLA 2 -X) is abundantly expressed in colonic epithelial cells but is barely detectable in metabolic and immune tissues. Despite this distribution, sPLA 2 -X-deficient (Pla2g10 -/- ) mice displayed variable obesity-related phenotypes that were abrogated after treatment with antibiotics or cohousing with Pla2g10 +/+ mice, suggesting the involvement of the gut microbiota. Under housing conditions where Pla2g10 -/- mice showed aggravation of diet-induced obesity and insulin resistance, they displayed increased colonic inflammation and epithelial damage, reduced production of polyunsaturated fatty acids (PUFAs) and lysophospholipids, decreased abundance of several Clostridium species, and reduced levels of short-chain fatty acids (SCFAs). These obesity-related phenotypes in Pla2g10 -/- mice were reversed by dietary supplementation with ω3 PUFAs or SCFAs. Thus, colonic sPLA 2 -X orchestrates ω3 PUFA-SCFA interplay via modulation of the gut microbiota, thereby secondarily affecting systemic metabolism., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Rationale and Objectives: Immune checkpoint inhibitors (ICIs) have improved lung cancer prognosis; however, ICI-related interstitial lung disease (ILD) is fatal and difficult to predict. Herein, we hypothesized that pre-existing lung inflammation on radiological imaging can be a potential risk factor for ILD onset. Therefore, we investigated the association between high uptake in noncancerous lung (NCL) on 18 F- FDG-PET/CT and ICI-ILD in lung cancer., Methods: Patients with primary lung cancer who underwent FDG-PET/CT within three months prior to ICI therapy were retrospectively included. Artificial intelligence was utilized for extracting the NCL regions (background lung) from the lung contralateral to the primary tumor. FDG uptake by the NCL was assessed via the SUVmax (NCL-SUVmax), SUVmean (NCL-SUVmean), and total glycolytic activity (NCL-TGA)defined as NCL-SUVmean×NCL volume [mL]. NCL-SUVmean and NCL-TGA were calculated using the following four SUV thresholds: 0.5, 1.0, 1.5, and 2.0., Results: Of the 165 patients, 28 (17.0%) developed ILD. Univariate analysis showed that high values of NCL-SUVmax, NCL-SUVmean 2.0 (SUV threshold=2.0), and NCL-TGA 1.0 (SUV threshold=1.0) were significantly associated with ILD onset (all p = 0.003). Multivariate analysis adjusted for age, tumor FDG uptake, and pre-existing interstitial lung abnormalities revealed that a high NCL-TGA 1.0 (≥149.45) was independently associated with ILD onset (odds ratio, 6.588; p = 0.002). Two-year cumulative incidence of ILD was significantly higher in the high NCL-TGA 1.0 group than in the low group (58.4% vs. 14.4%; p < 0.001)., Conclusion: High uptake of NCL on FDG-PET/CT is correlated with ICI-ILD development, which could serve as a risk stratification tool before ICI therapy in primary lung cancer., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Dr. Satoshi Watanabe reports: grants from Boehringer Ingelheim and Nippon Kayaku; lecture fees and speakers bureaus from AstraZeneca, Lilly, Chugai Pharma, Bristol-Myers, Novartis Pharma, Ono Pharmaceutical, Daiichi Sankyo, Taiho Pharmaceutical, Nippon Kayaku, Kyowa Hakko Kirin, Merck, Takeda Pharmaceutical and Celltrion, all outside the submitted work. Dr. Naohiro Yanagimura reports: lecture fees and speakers bureaus from MSD K.K and Honoraria, all outside the submitted work. Dr. Masashi Arita reports: lecture fees and speakers bureaus from Chugai Pharma, all outside the submitted work. Dr. Tomohiro Tanaka reports: lecture fees and speakers bureaus from Chugai and Takeda, all outside the submitted work. Dr. Koichiro Nozaki reports: lecture fees and speakers bureaus from AstraZeneca, Bristol-Myers, MSD, Taiho Pharmaceutical, Ono Pharmaceutical, and Chugai Pharmaceutical Co, all outside the submitted work. Dr. Yu Saida reports: lecture fees and speakers bureaus from Chugai, Lilly, Astra Zeneca, and Ono, all outside the submitted work. Dr. Toshiaki Kikuchi reports: grants from Nobelpharma, Boehringer Ingelheim, Taiho Pharmaceutical, KYORIN Pharmaceutical, Shionogi Pharma, Chugai Pharma, Asahi Kasei, Daiichi Sankyo, Nippon Kayaku and TEIJIN PHARMA; consulting fees from AN2 Therapeutics; lecture fees and speakers bureaus from Viatris, Astellas Pharma, Insmed, Boehringer Ingelheim, Terumo, Lilly, AstraZeneca, Daiichi Sankyo, KYORIN Pharmaceutical, Novartis Pharma, Merck, Bristol-Myers, NIPRO, Eisai, Ono Pharmaceutical, Chugai Pharma, GSK, Sumitomo Pharma, Kyowa Hakko Kirin, MSD, Sanofi, Shionogi Pharma, Meiji Seika Pharma and Taiho Pharmaceutical, all outside the submitted work. Dr. Hiroyuki Ishikawa reports: grants from Daiichi Sankyo, GE Healthcare Pharma, Guerbet, Nihon Medi-Physics, and PDRadiopharma; lecture fees from Bayer, Boehringer Ingelheim, Canon, Chugai Pharma, Eisai, FUJIFILM Medical, GE Healthcare Pharma, and Nihon Medi-Physics, all outside the submitted work. The remaining authors declare no conflict of interest., (Copyright © 2024 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.)

Persistent colonization and outgrowth of potentially pathogenic organisms in the intestine can result from long-term antibiotic use or inflammatory conditions, and may perpetuate dysregulated immunity and tissue damage 1,2 . Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment 3,4 , although an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy 5-7 . Here we isolated and down-selected commensal bacterial consortia from stool samples from healthy humans that could strongly and specifically suppress intestinal Enterobacteriaceae. One of the elaborated consortia, comprising 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby re-establishing colonization resistance and alleviating Klebsiella- and Escherichia-driven intestinal inflammation in mice. Harnessing these activities in the form of live bacterial therapies may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant Enterobacteriaceae infection., (© 2024. The Author(s).)

Embryo implantation is crucial for ensuring a successful pregnancy outcome and subsequent child health. The intrauterine environment during the peri-implantation period shows drastic changes in gene expression and cellular metabolism in response to hormonal stimuli and reciprocal communication with embryos. Here, we performed spatial transcriptomic analysis to elucidate the mechanisms underlying embryo implantation. Transcriptome data revealed that lipid metabolism pathways, especially arachidonic acid-related (AA-related) ones, were enriched in the embryo-receptive luminal epithelia. Cyclooxygenases (COXs), rate-limiting enzymes involved in prostaglandin production by AA, were spatiotemporally regulated in the vicinity of embryos during implantation, but the role of each COX isozyme in the uterus for successful pregnancy was unclear. We established uterine-specific COX2-knockout (uKO) and COX1/uterine COX2-double-KO (COX1/COX2-DKO) mice. COX2 uKO caused deferred implantation with failed trophoblast invasion, resulting in subfertility with reduced pregnancy rates and litter sizes. COX1/COX2 DKO induced complete infertility, owing to abrogated embryo attachment. These results demonstrate that both isozymes have distinct roles during embryo implantation. Spatial transcriptome and lipidome analyses revealed unique profiles of prostaglandin synthesis by each COX isozyme and spatiotemporal expression patterns of downstream receptors throughout the endometrium. Our findings reveal previously unappreciated roles of COXs at the fetomaternal interface to establish early pregnancy.

Entamoeba histolytica is a protozoan parasite belonging to the phylum Amoebozoa that causes amebiasis, a global public health problem. E. histolytica alternates its form between a proliferative trophozoite and a dormant cyst. Trophozoite proliferation is closely associated with amebiasis symptoms and pathogenesis whereas cysts transmit the disease. Drugs are available for clinical use; however, they have issues of adverse effects and dual targeting of disease symptoms and transmission remains to be improved. Development of new drugs is therefore urgently needed. An untargeted lipidomics analysis recently revealed structural uniqueness of the Entamoeba lipidome at different stages of the parasite's life cycle involving very long (26-30 carbons) and/or medium (8-12 carbons) acyl chains linked to glycerophospholipids and sphingolipids. Here, we investigated the physiology of this unique acyl chain diversity in Entamoeba, a non-photosynthetic protist. We characterized E. histolytica fatty acid elongases (EhFAEs), which are typically components of the fatty acid elongation cycle of photosynthetic protists and plants. An approach combining genetics and lipidomics revealed that EhFAEs are involved in the production of medium and very long acyl chains in E. histolytica. This approach also showed that the K3 group herbicides, flufenacet, cafenstrole, and fenoxasulfone, inhibited the production of very long acyl chains, thereby impairing Entamoeba trophozoite proliferation and cyst formation. Importantly, none of these three compounds showed toxicity to a human cell line; therefore, EhFAEs are reasonable targets for developing new anti-amebiasis drugs and these compounds are promising leads for such drugs. Interestingly, in the Amoebazoan lineage, gain and loss of the genes encoding two different types of fatty acid elongase have occurred during evolution, which may be relevant to parasite adaptation. Acyl chain diversity in lipids is therefore a unique and indispensable feature for parasitic adaptation of Entamoeba., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Mi-ichi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Clinical studies have demonstrated that IL-4, a type 2 cytokine, plays an important role in the pathogenesis of chronic rhinosinusitis and eosinophilic asthma. However, the direct effect of IL-4 on eosinophils remains unclear., Objective: We aimed to elucidate the inflammatory effects of IL-4 on the functions of human eosinophils., Methods: A multiomics analysis comprising transcriptomics, proteomics, lipidomics, quantitative RT-PCR, and flow cytometry was performed by using blood eosinophils from healthy subjects stimulated with IL-4, IL-5, or a combination thereof., Results: Transcriptomic and proteomic analyses revealed that both IL-4 and IL-5 upregulate the expression of γ-gultamyl transferase 5, a fatty acid-metabolizing enzyme that converts leukotriene C 4 into leukotriene D 4 . In addition, IL-4 specifically upregulates the expression of IL-1 receptor-like 1 (IL1RL1), a receptor for IL-33 and transglutaminase-2. Additional transcriptomic analysis of cells stimulated with IL-13 revealed altered gene expression profiles, characterized by the upregulation of γ-gultamyl transferase 5, transglutaminase-2, and IL1RL1. The IL-13-induced changes were not totally different from the IL-4-induced changes. Lipidomic analysis revealed that IL-5 and IL-4 additively increased the extracellular release of leukotriene D 4 . In vitro experiments revealed that STAT6 and IL-4 receptor-α control the expression of these molecules in the presence of IL-4 and IL-13. Analysis of eosinophils derived from patients with allergic disorders indicated the involvement of IL-4 and IL-13 at the inflamed sites., Conclusions: IL-4 induces the proallergic phenotype of IL1RL1 high eosinophils, with prominent cysteinyl leukotriene metabolism via STAT6. These cellular changes represent potential therapeutic targets for chronic rhinosinusitis and eosinophilic asthma., Competing Interests: Disclosure statement Supported by the Japanese Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research Program (KAKENHI) (grants 15H05897, 15H05898, and 20H00495 [to M.A.]), Japan Science and Technology Agency program Exploratory Research for Advanced Technology (JST-ERATO) (grant JPMJER2101 [to M.A.]), Research Grant on Allergic Disease and Immunology from the Japan Agency for Medical Research and Development (grant 22ek0410097 [to J.M.]), JSPS Grant-in-Aid for Young Scientists (grant 20K17239 [to J.M.]), RIKEN Special Postdoctoral Researchers Program (to J.M.), GSK Japan Research Grant 2018 (to J.M.), and Grant-in-Aid for Research of the ONO Medical Research Foundation (to J.M.). Disclosure of potential conflict of interest: J. Miyata, K. Masaki, H. Kabata, and K. Fukunaga report receiving research grant support from GSK and AstraZeneca. J. Miyata and K. Fukunaga report receiving payments for lectures from GSK, AstraZeneca, and Sanofi. K. Masaki reports receiving payments for lectures from GSK and AstraZeneca, and GSK. H. Kabata reports receiving payments for lectures from AstraZeneca and Sanofi. The rest of the authors declare that they have no relevant conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Convergence provides clues to unveil the non-random nature of evolution. Intermediate paths toward convergence inform us of the stochasticity and the constraint of evolutionary processes. Although previous studies have suggested that substantial constraints exist in microevolutionary paths, it remains unclear whether macroevolutionary convergence follows stochastic or constrained paths. Here, we performed comparative genomics for hundreds of lactic acid bacteria (LAB) species, including clades showing a convergent gene repertoire and sharing fructose-rich habitats. By adopting phylogenetic comparative methods we showed that the genomic convergence of distinct fructophilic LAB (FLAB) lineages was caused by parallel losses of more than a hundred orthologs and the gene losses followed significantly similar orders. Our results further suggested that the loss of adhE, a key gene for phenotypic convergence to FLAB, follows a specific evolutionary path of domain architecture decay and amino acid substitutions in multiple LAB lineages sharing fructose-rich habitats. These findings unveiled the constrained evolutionary paths toward the convergence of free-living bacterial clades at the genomic and molecular levels., (© 2024. The Author(s).)

The picornavirus genome encodes a large, single polyprotein that is processed by viral proteases to form an active replication complex. The replication complex is formed with the viral genome, host proteins, and viral proteins that are produced/translated directly from each of the viral genomes (viral proteins provided in cis ). Efficient complementation in vivo of replication complex formation by viral proteins provided in trans , thus exogenous or ectopically expressed viral proteins, remains to be demonstrated. Here, we report an efficient trans complementation system for the replication of defective poliovirus (PV) mutants by a viral polyprotein precursor in HEK293 cells. Viral 3AB in the polyprotein, but not 2BC, was processed exclusively in cis . Replication of a defective PV replicon mutant, with a disrupted cleavage site for viral 3C pro protease between 3C pro and 3D pol (3C/D[A/G] mutant) could be rescued by a viral polyprotein provided in trans . Only a defect of 3D pol activity of the replicon could be rescued in trans ; inactivating mutations in 2C ATPase/hel , 3B, and 3C pro of the replicon completely abrogated the trans -rescued replication. An intact N-terminus of the 3C pro domain of the 3CD pro provided in trans was essential for the trans -active function. By using this trans complementation system, a high-titer defective PV pseudovirus (PV pv ) (>10 7 infectious units per mL) could be produced with the defective mutants, whose replication was completely dependent on trans complementation. This work reveals potential roles of exogenous viral proteins in PV replication and offers insights into protein/protein interaction during picornavirus infection., Importance: Viral polyprotein processing is an elaborately controlled step by viral proteases encoded in the polyprotein; fully processed proteins and processing intermediates need to be correctly produced for replication, which can be detrimentally affected even by a small modification of the polyprotein. Purified/isolated viral proteins can retain their enzymatic activities required for viral replication, such as protease, helicase, polymerase, etc. However, when these proteins of picornavirus are exogenously provided (provided in trans ) to the viral replication complex with a defective viral genome, replication is generally not rescued/complemented, suggesting the importance of viral proteins endogenously provided (provided in cis ) to the replication complex. In this study, I discovered that only the viral polymerase activity of poliovirus (PV) (the typical member of picornavirus family) could be efficiently rescued by exogenously expressed viral proteins. The current study reveals potential roles for exogenous viral proteins in viral replication and offers insights into interactions during picornavirus infection., Competing Interests: The author declares no conflict of interest.

An earthquake with a moment magnitude of 7.5 (Mw) struck the northern Noto Peninsula, Ishikawa Prefecture, Japan, at 16:10 local time on January 1, 2024. This earthquake triggered a tsunami that propagated along the coastline of Ishikawa, Toyama, and Niigata Prefectures facing the Sea of Japan and significantly damaged coastal communities and infrastructure. Approximately 70 researchers from 23 universities or other institutes throughout Japan formed a joint research group to conduct a post-tsunami survey along a 340 km stretch of the coast. Based on the watermarks and traces of the tsunami, the inundation and run-up heights were surveyed using total stations, automatic optical levels, laser range finders, and a real-time kinematic (RTK) Global Navigation Satellite System (GNSS). The tidal correction was adjusted using astronomical tidal tables. In total, 303 survey records have been compiled, generating the NP2024TS (Noto Peninsula 2024 Tsunami Survey) dataset. This dataset provides comprehensive information on the inundation and run-up heights of the tsunami, which is useful for understanding tsunami characteristics and validating numerical tsunami models., (© 2024. The Author(s).)

The generation of hydrogen as a clean energy carrier by photocatalysis, as a zero-emission technology, is of significant scientific and industrial interest. However, the main drawback of photocatalytic hydrogen generation from water splitting is its low efficiency compared to traditional chemical or electrochemical methods. Zinc oxide (ZnO) with the wurtzite phase is one of the most investigated photocatalysts for hydrogen production, but its activity still needs to be improved. In this study, an oxygen-deficient high-pressure ZnO rocksalt phase is stabilized using a high-pressure torsion (HPT) method, and the product is used for photocatalysis under ambient pressure. The simultaneous introduction of oxygen vacancies and the rocksalt phase effectively improved photocatalytic hydrogen production to levels comparable to benchmark P25 TiO 2 , due to improving light absorbance and providing active sites for photocatalysis without any negative effect on electron-hole recombination. These results confirm the high potential of high-pressure phases for photocatalytic hydrogen generation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The inner mitochondrial membrane (IMM) undergoes dynamic morphological changes, which are crucial for the maintenance of mitochondrial functions as well as cell survival. As the dynamics of the membrane are governed by its lipid components, a fluorescent probe that can sense spatiotemporal alterations in the lipid properties of the IMM over long periods of time is required to understand mitochondrial physiological functions in detail. Herein, we report a red-emissive IMM-labeling reagent with excellent photostability and sensitivity to its environment, which enables the visualization of the IMM ultrastructure using super-resolution microscopy as well as of the lipid heterogeneity based on the fluorescence lifetime at the single mitochondrion level. Combining the probe and fluorescence lifetime imaging microscopy (FLIM) showed that peroxidation of unsaturated lipids in the IMM by reactive oxygen species caused an increase in the membrane order, which took place prior to mitochondrial swelling., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Aim: The effects of iron on vascular calcification in rats and vascular smooth muscle cells were recently reported, but clinical studies on iron and vascular calcification are scant. We studied the associations of absolute iron deficiency, coronary artery calcification and mortality in patients with maintenance haemodialysis (MHD)., Methods: Transferrin saturation (TSAT), ferritin, mean corpuscular haemoglobin (MCH) and Agatston coronary artery calcium score (CACS) were studied at baseline in MHD patients and followed up for 3 years. Cox proportional hazard analyses for mortality and linear regression analyses for CACS were performed., Results: In 306 patients, the median age was 67 (56-81) years, dialysis duration was 76 (38-142) months, and diabetes prevalence was 42.5%. Fifty-two patients had died by 3 years. Patients with absolute iron deficiency (TSAT <20% and ferritin <100 ng/mL) (n = 102) showed significantly higher CACS (p = .0266) and C-reactive protein (p = .0011), but a lower frequency of iron formulation administration compared with patients without absolute iron deficiency at baseline (n = 204). Absolute iron deficiency was a significant predictor for 3-year cardiovascular (CV) mortality (hazard ratio: 2.08; p = .0466), but not for 3-year all-cause mortality. CACS was significant predictor for both 3-year CV and all-cause mortality (p <.05). Absolute iron deficiency and MCH were significant determinants of CACS (p < .05)., Conclusion: MHD patients with absolute iron deficiency showed significantly higher CACS than others, and absolute iron deficiency was a significant risk factor for coronary artery calcification and 3-year CV mortality in MHD patients, but was not a significant predictor for 3-year all-cause mortality., (© 2024 Asian Pacific Society of Nephrology.)

Aim: We studied the effects of overhydration (OH), Kt/Vurea and β2-microglobulin (β2-MG) on coronary artery calcification and mortality in patients undergoing haemodialysis (HD)., Methods: The Agatston coronary artery calcium score (CACS), postdialysis body composition using bioimpedance analysis, single-pool Kt/Vurea and predialysis β2-MG at baseline were assessed and followed up for 3 years in patients undergoing HD. We performed logistic regression analyses for a CACS ≥400 and Cox proportional hazard analyses for all-cause and cardiovascular mortality., Results: The study involved 338 patients with a median age of 67 (56-74) years, dialysis duration of 70 (33-141) months and diabetes prevalence of 39.1% (132/338). Patients with a CACS ≥400 (n = 222) had significantly higher age, dialysis duration, male prevalence, diabetes prevalence, C-reactive protein, predialysis β2-MG, OH, extracellular water/total body water and overhydration/extracellular water (OH/ECW) but significantly lower Kt/Vurea than patients with a CACS <400 (n = 116) (p < .05). OH/ECW, Kt/Vurea and predialysis β2-MG were significant predictors of a CACS ≥400 (p < .05) after adjusting for age, dialysis duration, serum phosphate and magnesium. In all patients, cut-off values of OH/ECW, Kt/Vurea and predialysis β2-MG for a CACS ≥400 were 16%, 1.74 and 28 mg/L, respectively. After adjusting for dialysis duration, OH/ECW ≥16%, Kt/Vurea ≥1.74 and β2-MG ≥28 mg/L were significant predictors of 3-year all-cause mortality but not 3-year cardiovascular mortality., Conclusion: Higher OH/ECW, higher predialysis β2-MG and lower Kt/Vurea values are significant risk factors for a CACS ≥400 and 3-year all-cause mortality in patients undergoing maintenance HD., (© 2024 Asian Pacific Society of Nephrology.)

The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Suetake H et al.)

Background: Although polioviruses (PVs) replicate in lymphoid tissue of both the pharynx and ileum, research on polio vaccine-induced mucosal immunity has predominantly focused on intestinal neutralizing and binding antibody levels measured in stool., Methods: To investigate the extent to which routine immunization with intramuscularly injected inactivated polio vaccine (IPV) may induce nasal and pharyngeal mucosal immunity, we measured PV type-specific neutralization and immunoglobulin (Ig) G, IgA, and IgM levels in nasal secretions, adenoid cell supernatants, and sera collected from 12 children, aged 2 to 5 years, undergoing planned adenoidectomies. All participants were routinely immunized with IPV and had no known contact with live PVs., Results: PV-specific mucosal neutralization was detected in nasal and adenoid samples, mostly from children who had previously received four IPV doses. Across the three PV serotypes, both nasal (Spearman's rho ≥ 0.87, p≤0.0003 for all) and adenoid (Spearman's rho ≥0.57, p≤0.05 for all) neutralization titers correlated with serum neutralization titers. In this small study sample, there was insufficient evidence to determine which Ig isotype(s) was correlated with neutralization., Conclusions: Our findings provide policy-relevant evidence that routine immunization with IPV may induce nasal and pharyngeal mucosal immunity. The observed correlations of nasal and pharyngeal mucosal neutralization with serum neutralization contrast with previous observations of distinct intestinal and serum responses to PV vaccines. Further research is warranted to determine which antibody isotype(s) correlate with polio vaccine-induced nasal and pharyngeal mucosal neutralizing activity and to understand the differences from intestinal mucosal immunity., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolved chemical entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically-resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry. SCIENTIFIC CONTRIBUTION: This new extension to the InChI standard would enable improved annotation of analytical datasets characterizing chemical entities, supporting the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles of data stewardship for chemical datasets, ultimately promoting Open Science in chemistry., (© 2024. The Author(s).)

Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

The activities of the transient receptor potential vanilloid 4 (TRPV4), a Ca 2+ -permeable nonselective cation channel, are controlled by its surrounding membrane lipids (e.g., cholesterol, phosphoinositides). The transmembrane region of TRPV4 contains a cholesterol recognition amino acid consensus (CRAC) motif and its inverted (CARC) motif located in the plasmalemmal cytosolic leaflet. TRPV4 localizes in caveolae, a bulb-shaped cholesterol-rich domain at the plasma membrane. Here, we visualized the spatiotemporal interactions between TRPV4 and cholesterol at the plasma membrane in living cells by dual-color single-molecule imaging using total internal reflection fluorescence microscopy. To this aim, we labeled cholesterol at the cytosolic leaflets of the plasma membrane using a cholesterol biosensor, D4H. Our single-molecule tracking analysis showed that the TRPV4 molecules colocalize with D4H-accessible cholesterol molecules mainly in the low fluidity membrane domains in which both molecules are highly clustered. Colocalization of TRPV4 and D4H-accessible cholesterol was observed both inside and outside of caveolae. Agonist-evoked TRPV4 activation remarkably decreased colocalization probability and association rate between TRPV4 and D4H-accessible cholesterol molecules. Interestingly, upon TRPV4 activation, the particle density of D4H-accessible cholesterol molecules was decreased and the D4H-accessible cholesterol molecules in the fast-diffusing state were increased at the plasma membrane. The introduction of skeletal dysplasia-associated R616Q mutation into the CRAC/CARC motif of TRPV4, which reduced the interaction with cholesterol clusters, could not alter the D4H-accessible cholesterol dynamics. Mechanistically, TRPV4-mediated Ca 2+ influx and the C-terminal calmodulin-binding site of TRPV4 are essential for modulating the plasmalemmal D4H-accessible cholesterol dynamics. We propose that TRPV4 remodels its surrounding plasmalemmal environment by manipulating cholesterol dynamics through Ca 2+ influx., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Purpose: This study investigated the combined effect of lower-extremity muscle power training and regular cardiac rehabilitation on muscle strength, balance function, and walking ability of older adults with heart failure., Methods: Thirty-one patients, comprising 17 males and 14 females, aged between 66 and 89 years and diagnosed with non-severe heart failure, were randomly assigned to either the intervention group (n = 15) or control group (n = 16). Both groups participated in a 12-week regular rehabilitation program, with the intervention group receiving additional lower-extremity muscle power training. Various outcome measures, including muscle strength (the five-times-sit-to-stand test and knee extensor peak torque), balance function (Berg balance scale and functional reach test), and walking ability (4-m walk and Timed Up-and-Go tests) were assessed at baseline and 12 weeks after the intervention., Results: Of the 31 participants, 27 completed the study protocol. The intervention group demonstrated significantly greater improvement in the five-times-sit-to-stand test time, indicating enhanced lower-extremity muscle power compared to the control group. Both groups showed significant differences in the Berg balance scale, functional reach test, 4-m walk test, and Timed Up-and-Go test between baseline and 12 weeks. However, the effect sizes for the changes during the study period were larger in the intervention group (d = 0.74-1.19) than the control group (d = 0.57-0.96)., Conclusion: Combining lower-extremity muscle power training with regular cardiac rehabilitation may lead to additional improvements in muscle function for older adults with heart failure, resulting in enhanced dynamic balance and walking ability., Trial Registration Number/date of Registration: UMIN000032087/April 4, 2018., (© 2023. The Author(s), under exclusive licence to European Geriatric Medicine Society.)

Background: Disruption of intestinal barrier caused by intestinal ischemia due to hemorrhagic shock is associated with the pathogenesis of multiple organ dysfunction (MOD) after severe trauma. Mesenteric lymph (ML) plays an important role as a route for transporting inflammatory mediators, including lipids. Postbiotics, such as 10-hydroxy-cis-12-octadecenoic acid (HYA), have received much attention as a treatment option. However, the relationship between postbiotics and MOD has yet to be clarified. The aim of the present study was to analyze lipid metabolites derived from gut microbiota in the intestinal ischemia-reperfusion (IR) rat model., Methods: Male Sprague-Dawley rats underwent laparotomy, and their ML duct and superior mesenteric artery were exposed. The superior mesenteric artery was clamped for 60 minutes, followed by 120 minutes of reperfusion. The ML and the plasma were collected before and after intestinal IR. Lipids were extracted from plasma and ML, and liquid chromatography-tandem mass spectrometry was performed., Results: The concentration of linoleic acid in plasma samples was not different before and after IR; however, the linoleic acid concentration in the ML samples increased after intestinal IR. Eicosapentaenoic acids and docosahexaenoic related to linoleic acids showed similar changes with IR-induced increase in the ML. The concentration of HYA, a linoleic acid-derived bioactive metabolite produced by gut bacteria, was high in ML samples, while that in plasma samples was low. The relative increase rate of HYA in ML samples after IR was higher than that of the plasma samples (the ML samples: relative increase, 3.23 ± 1.36; the plasma samples: relative increase, 0.95 ± 0.35; n = 3, p = 0.048)., Conclusion: The present study demonstrated increased linoleic acids and high concentrations of HYA, lipid metabolites derived from gut bacteria in the ML after intestinal IR. These findings may contribute to clarifying the relation between gut microbiota and MOD after severe trauma., (Copyright © 2023 American Association for the Surgery of Trauma.)

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan., (© 2024 The Authors. Genes to Cells published by Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.)

Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Japanese Biochemical Society.)

The spot urinary sodium-to-potassium (Na/K) ratio is a simple measure of salt loading and has been shown to be associated with elevated blood pressure (BP) in middle-aged and older adults. This study aimed to evaluate the association between the spot urinary Na/K ratio and BP in 457 healthy adolescents aged 12-15 years in a school-based setting. The mean urinary Na/K ratio was 4.99 ± 2.76, and no significant difference was found between the boys and girls. When the participants were stratified based on urinary Na/K ratio quartile, age- and sex-adjusted systolic and diastolic BP gradually increased as Na/K ratio increased (systolic BP: 106.1, 106.9, 108.2, and 111.5 mmHg, P trend  < 0.001; diastolic BP: 62.0, 62.4, 63.1, 64.3 mmHg, P trend  = 0.022). The systolic and diastolic BP were more closely associated with urinary Na/K ratio than with Na and K levels, as well as estimated daily salt intake. In the multiple regression analysis, the urinary Na/K ratio was significantly associated with systolic BP (β = 0.144, P < 0.001) and diastolic BP (β = 0.114, P = 0.015) independent of potential confounding factors. An additional subgroup analysis revealed that the BP of the group with both high salt intake (≥8.5 g/day) and high Na/K ratio (≥6.60) was significantly higher than that of the group with high salt intake alone (systolic BP, 115.0 vs. 109.1 mmHg, P < 0.001; diastolic BP, 66.0 vs. 62.5 mmHg, P = 0.017). These results suggest that the urinary Na/K ratio is associated with BP levels in healthy adolescents and may be useful for assessing salt loading and its effects on BP elevation., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Lipid transport is an essential cellular process with importance to human health, disease development, and therapeutic strategies. Type IV P-type ATPases (P4-ATPases) have been identified as membrane lipid flippases by utilizing nitrobenzoxadiazole (NBD)-labeled lipids as substrates. Among the 14 human type IV P-type ATPases, ATP10D was shown to flip NBD-glucosylceramide (GlcCer) across the plasma membrane. Here, we found that conversion of incorporated GlcCer (d18:1/12:0) to other sphingolipids is accelerated in cells exogenously expressing ATP10D but not its ATPase-deficient mutant. These findings suggest that 1) ATP10D flips unmodified GlcCer as well as NBD-GlcCer at the plasma membrane and 2) ATP10D can translocate extracellular GlcCer, which is subsequently converted to other metabolites. Notably, exogenous expression of ATP10D led to the reduction in cellular hexosylceramide levels. Moreover, the expression of GlcCer flippases, including ATP10D, also reduced cellular hexosylceramide levels in fibroblasts derived from patients with Gaucher disease, which is a lysosomal storage disorder with excess GlcCer accumulation. Our study highlights the contribution of ATP10D to the regulation of cellular GlcCer levels and maintaining lipid homeostasis., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Enterovirus A71 (EV-A71) infection involves a variety of receptors. Among them, two transmembrane protein receptors have been investigated in detail and shown to be critical for infection: P-selectin glycoprotein ligand-1 (PSGL-1) in lymphocytes (Jurkat cells), and scavenger receptor class B member 2 (SCARB2) in rhabdomyosarcoma (RD) cells. PSGL-1 and SCARB2 have been reported to be expressed on the surface of Jurkat and RD cells, respectively. In the work reported here, we investigated the roles of PSGL-1 and SCARB2 in the process of EV-A71 entry. We first examined the expression of SCARB2 in Jurkat cells, and detected it within the cytoplasm, but not on the cell surface. Further, using PSGL-1 and SCARB2 knockout cells, we found that although both PSGL-1 and SCARB2 are essential for virus infection of Jurkat cells, virus attachment to these cells requires only PSGL-1. These results led us to evaluate the cell surface expression and the roles of SCARB2 in other EV-A71-susceptible cell lines. Surprisingly, in contrast to the results of previous studies, we found that SCARB2 is absent from the surface of RD cells and other susceptible cell lines we examined, and that although SCARB2 is essential for infection of these cells, it is dispensable for virus attachment. These results indicate that a receptor other than SCARB2 is responsible for virus attachment to the cell and probably for internalization of virions, not only in Jurkat cells but also in RD cells and other EV-A71-susceptible cells. SCARB2 is highly concentrated in lysosomes and late endosomes, where it is likely to trigger acid-dependent uncoating of virions, the critical final step of the entry process. Our results suggest that the essential interactions between EV-A71 and SCARB2 occur, not at the cell surface, but within the cell., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Nishimura et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Spatial, momentum and energy separation of electronic spins in condensed-matter systems guides the development of new devices in which spin-polarized current is generated and manipulated 1-3 . Recent attention on a set of previously overlooked symmetry operations in magnetic materials 4 leads to the emergence of a new type of spin splitting, enabling giant and momentum-dependent spin polarization of energy bands on selected antiferromagnets 5-10 . Despite the ever-growing theoretical predictions, the direct spectroscopic proof of such spin splitting is still lacking. Here we provide solid spectroscopic and computational evidence for the existence of such materials. In the noncoplanar antiferromagnet manganese ditelluride (MnTe 2 ), the in-plane components of spin are found to be antisymmetric about the high-symmetry planes of the Brillouin zone, comprising a plaid-like spin texture in the antiferromagnetic (AFM) ground state. Such an unconventional spin pattern, further found to diminish at the high-temperature paramagnetic state, originates from the intrinsic AFM order instead of spin-orbit coupling (SOC). Our finding demonstrates a new type of quadratic spin texture induced by time-reversal breaking, placing AFM spintronics on a firm basis and paving the way for studying exotic quantum phenomena in related materials., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Gaucher disease (GD) is a recessively inherited lysosomal storage disorder characterized by a deficiency of lysosomal glucocerebrosidase (GBA1). This deficiency results in the accumulation of its substrate, glucosylceramide (GlcCer), within lysosomes. Here, we investigated lysosomal abnormalities in fibroblasts derived from patients with GD. It is noteworthy that the cellular distribution of lysosomes and lysosomal proteolytic activity remained largely unaffected in GD fibroblasts. However, we found that lysosomal membranes of GD fibroblasts were susceptible to damage when exposed to a lysosomotropic agent. Moreover, the susceptibility of lysosomal membranes to a lysosomotropic agent could be partly restored by exogenous expression of wild-type GBA1. Here, we report that the lysosomal membrane integrity is altered in GD fibroblasts, but lysosomal distribution and proteolytic activity is not significantly altered.Key words: glucosylceramide, lysosome, Gaucher disease, lysosomotropic agent.

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

We have developed a state-of-the-art apparatus for laser-based spin- and angle-resolved photoemission spectroscopy with micrometer spatial resolution (µ-SARPES). This equipment is realized by the combination of a high-resolution photoelectron spectrometer, a 6 eV laser with high photon flux that is focused down to a few micrometers, a high-precision sample stage control system, and a double very-low-energy-electron-diffraction spin detector. The setup achieves an energy resolution of 1.5 (5.5) meV without (with) the spin detection mode, compatible with a spatial resolution better than 10 µm. This enables us to probe both spatially-resolved electronic structures and vector information of spin polarization in three dimensions. The performance of µ-SARPES apparatus is demonstrated by presenting ARPES and SARPES results from topological insulators and Au photolithography patterns on a Si (001) substrate., (© 2024. The Author(s).)