Crosstalk within and beyond the Polycomb repressive system

The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.

Evaluating the Efficiency of Boron Nitride Coating in Single-Walled Carbon-Nanotube-Based 1D Heterostructure Films by Optical Spectroscopy

Single-walled carbon nanotube (SWCNT) films exhibit exceptional optical and electrical properties, making them highly promising for scalable integrated devices. Previously, we employed SWCNT films as templates for the chemical vapor deposition (CVD) synthesis of one-dimensional heterostructure films where boron nitride nanotubes (BNNTs) and molybdenum disulfide nanotubes (MoS2NTs) were coaxially nested over the SWCNT networks. In this work, we have further refined the synthesis method to achieve precise control over the BNNT coating in SWCNT@BNNT heterostructure films. The resulting structure of the SWCNT@BNNT films was thoroughly characterized using a combination of electron microscopy, UV-vis-NIR spectroscopy, Fourier-transform infrared (FT-IR) spectroscopy, and Raman spectroscopy. Specifically, we investigated the pressure effect induced by BNNT wrapping on the SWCNTs in the SWCNT@BNNT heterostructure film and demonstrated that the shifts of the SWCNT's G and 2D (G') modes in Raman spectra can be used as a probe of the efficiency of BNNT coating. In addition, we studied the impact of vacuum annealing on the removal of the initial doping in SWCNTs, arising from exposure to ambient atmosphere, and examined the effect of MoO3 doping in SWCNT films by using UV-vis-NIR spectroscopy and Raman spectroscopy. We show that through correlation analysis of the G and 2D (G') modes in Raman spectra, it is possible to discern distinct types of doping effects as well as the influence of applied pressure on the SWCNTs within SWCNT@BNNT heterostructure films. This work contributes to a deeper understanding of the strain and doping effect in both SWCNTs and SWCNT@BNNTs, thereby providing valuable insights for future applications of carbon-nanotube-based one-dimensional heterostructures.

The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response

Leucine-rich repeat kinase 2 (LRRK2), a Rab kinase associated with Parkinson's disease and several inflammatory diseases, has been shown to localize to stressed lysosomes and get activated to regulate lysosomal homeostasis. However, the mechanisms of LRRK2 recruitment and activation have not been well understood. Here, we found that the ATG8 conjugation system regulates the recruitment of LRRK2 as well as LC3 onto single membranes of stressed lysosomes/phagosomes. This recruitment did not require FIP200-containing autophagy initiation complex, nor did it occur on double-membrane autophagosomes, suggesting independence from canonical autophagy. Consistently, LRRK2 recruitment was regulated by the V-ATPase-ATG16L1 axis, which requires the WD40 domain of ATG16L1 and specifically mediates ATG8 lipidation on single membranes. This mechanism was also responsible for the lysosomal stress-induced activation of LRRK2 and the resultant regulation of lysosomal secretion and enlargement. These results indicate that the V-ATPase-ATG16L1 axis serves a novel non-autophagic role in the maintenance of lysosomal homeostasis by recruiting LRRK2.

Tex46 knockout male mice are sterile secondary to sperm head malformations and failure to penetrate through the zona pellucida

Each year, infertility affects 15% of couples worldwide, with 50% of cases attributed to men. It is assumed that sperm head shape is important for sperm-zona pellucida (ZP) penetration but research has yet to elucidate why. We generated testis expressed 46 (Tex46) knockout mice to investigate the essential roles of TEX46 in mammalian reproduction. We used RT-PCR to demonstrate that Tex46 was expressed exclusively in the male reproductive tract in mice and humans. We created Tex46-/- mice using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system and analyzed their fertility. Tex46 null spermatozoa underwent further evaluation using computer-assisted sperm analysis, light microscopy, and ultrastructural microscopy. We used immunoblot analysis to elucidate relationships between TEX46 and other acrosome biogenesis-related proteins. Mouse and human TEX46 are testis-enriched and encode a transmembrane protein which is conserved from amphibians to mammals. Loss of the mouse TEX46 protein causes male sterility primarily due to abnormal sperm head formation and secondary effects on sperm motility. Tex46 null spermatozoa morphologically lack the typical hooked sperm head appearance and fail to penetrate through the ZP. Electron microscopy of the testicular germ cells reveals malformation of the acrosomal cap, with misshapen sperm head tips and the appearance of a gap between the acrosome head and the nucleus. TEX46 is essential for sperm head formation, sperm penetration through the ZP, and male fertility in mice, and is a putative contraceptive target in men.

Heart rate reduction during voluntary deep diving in free-ranging loggerhead sea turtles

Air-breathing vertebrates exhibit cardiovascular responses to diving including heart rate reduction (diving bradycardia). Field studies on aquatic mammals and birds have shown that the intensity of bradycardia can vary depending on diving behaviour, such as the depth of dives and dive duration. However, in aquatic reptiles, the variation in heart rate during deep dives under natural conditions has not been fully investigated. In this study, we released five loggerhead sea turtles (Caretta caretta) outfitted with recorders into the sea and recorded their electrocardiogram, depth, water temperature and longitudinal acceleration. After 3 days, the recorders automatically detached from the turtles. The heart rate signals were detected from the electrodes placed on the surface of the plastron. The mean (±s.d.) heart rate of 12.8±4.1 beats min-1 during dives was significantly lower than that of 20.9±4.1 beats min-1 during surface periods. Heart rate during dives varied with dive depth, although it remained lower than that at the surface. When the turtle dived deeper than 140 m, despite the relatively high flipper stroke rate (approximately 19 strokes min-1), the heart rate dropped rapidly to approximately 2 beats min-1 temporarily. The minimum instantaneous heart rate during dives was lower at deeper dive depths. Our results indicate that loggerhead sea turtles show variations in the intensity of diving bradycardia depending on their diving behaviour, similar to that shown by marine mammals and birds.

New insights in ubiquitin-dependent Wnt receptor regulation in tumorigenesis

Wnt signaling plays a crucial role in embryonic development and homeostasis maintenance. Delicate and sensitive fine-tuning of Wnt signaling based on the proper timings and positions is required to balance cell proliferation and differentiation and maintain individual health. Therefore, homeostasis is broken by tissue hypoplasia or tumor formation once Wnt signal dysregulation disturbs the balance of cell proliferation. The well-known regulatory mechanism of Wnt signaling is the molecular reaction associated with the cytoplasmic accumulation of effector β-catenin. In addition to β-catenin, most Wnt effector proteins are also regulated by ubiquitin-dependent modification, both qualitatively and quantitatively. This review will explain the regulation of the whole Wnt signal in four regulatory phases, as well as the different ubiquitin ligases and the function of deubiquitinating enzymes in each phase. Along with the recent results, the mechanism by which RNF43 negatively regulates the surface expression of Wnt receptors, which has recently been well understood, will be detailed. Many RNF43 mutations have been identified in pancreatic and gastrointestinal cancers and examined for their functional alteration in Wnt signaling. Several mutations facilitate or activate the Wnt signal, reversing the RNF43 tumor suppressor function into an oncogene. RNF43 may simultaneously play different roles in classical multistep tumorigenesis, as both wild-type and mutant RNF43 suppress the p53 pathway. We hope that the knowledge obtained from further research in RNF43 will be applied to cancer treatment in the future despite the fully unclear function of RNF43.

Correction to "Comprehensive Study of Preparation of Carboxy Group-Containing Cellulose Fibers from Dry-Lap Kraft Pulps by Catalytic Oxidation with Solid NaOCl"

[This corrects the article DOI: 10.1021/acssuschemeng.3c04750.].

Fluctuation of lysosomal protein degradation in neural stem cells of the postnatal mouse brain

Lysosomes are intracellular organelles responsible for degrading diverse macromolecules delivered from several pathways, including the endo-lysosomal and autophagic pathways. Recent reports have suggested that lysosomes are essential for regulating neural stem cells in developing, adult and aged brains. However, the activity of these lysosomes has yet to be monitored in these brain tissues. Here, we report the development of a new probe to measure lysosomal protein degradation in brain tissue by immunostaining. Our results indicate that lysosomal protein degradation fluctuates in neural stem cells of the hippocampal dentate gyrus, depending on age and brain disorders. Neural stem cells increase their lysosomal activity during hippocampal development in the dentate gyrus, but aging and aging-related disease reduce lysosomal activity. In addition, physical exercise increases lysosomal activity in neural stem cells and astrocytes in the dentate gyrus. We therefore propose that three different stages of lysosomal activity exist: the state of increase during development, the stable state during adulthood and the state of reduction due to damage caused by either age or disease.

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression

In this research, we elucidate the presence of around 11,000 housekeeping cis-regulatory elements (HK-CREs) and describe their main characteristics. Besides the trivial promoters of housekeeping genes, most HK-CREs reside in promoter regions and are involved in a broader role beyond housekeeping gene regulation. HK-CREs are conserved regions rich in unmethylated CpG sites. Their distribution highly correlates with that of protein-coding genes, and they interact with many genes over long distances. We observed reduced activity of a subset of HK-CREs in diverse cancer subtypes due to aberrant methylation, particularly those located in chromosome 19 and associated with zinc finger genes. Further analysis of samples from 17 cancer subtypes showed a significantly increased survival probability of patients with higher expression of these genes, suggesting them as housekeeping tumor suppressor genes. Overall, our work unravels the presence of housekeeping CREs indispensable for the maintenance and stability of cells.

Nonlinear and Emissive {[MIII(CN)6]3-···Polyresorcinol} (M = Fe, Co, Cr) Cocrystals Exhibiting an Ultralow Frequency Raman Response

Optically active functional noncentrosymmetric architectures might be achieved through the combination of molecules with inscribed optical responses and species of dedicated tectonic character. Herein, we present the new series of noncentrosymmetric cocrystal salt solvates (PPh4)3[M(CN)6](L)n·msolv (M = Cr(III), Fe(III), Co(III); L = polyresorcinol coformers, multiple hydrogen bond donors: 3,3',5,5'-tetrahydroxy-1,19-biphenyl, DiR, n = 2, or 5'-(3,5-dihydroxyphenyl)-3,3″,5,5″-tetrahydroxy-1,19:3',1″-terphenyl, TriRB, n = 1) denoted as MDiR and MTriRB, respectively. The hydrogen-bonded subnetworks {[M(CN)6]3-;Ln}∞ of dmp, neb, or dia topology are formed through structural matching between building blocks within supramolecular cis-bis(chelate)-like {[M(CN)6]3-;(H2L)2(HL)2} or tris(chelate)-like {[M(CN)6]3-;(H2L)3} fragments. The quantum-chemical analysis demonstrates the mixed electrostatic and covalent character of these interactions, with their strength clearly enhanced due to the negative charge of the hydrogen bond acceptor metal complex. The corresponding interaction energy is also dependent on the geometry of the contact and size matching of its components, rotational degree of freedom and extent of the π-electron system of the coformer, and overall fit to the molecular surroundings. Symmetry of the crystal lattices is correlated with the local symmetry of coformers and {complex;(coformer)n} hydrogen-bonded motifs characterized by the absence of the inversion center and mirror plane. All compounds reveal second-harmonic generation activity and photoluminescence diversified by individual UV-vis spectral characteristics of the components, and interesting low-frequency Raman scattering spectra within the subterahertz spectroscopic domain. Vibrational (infrared/Raman), UV-vis electronic absorption (experimental and calculated), and 57Fe Mössbauer spectra together with electrospray ionization mass spectrometry (ESI-MS) data are provided for the complete description of our systems.

Water vs. Organic Solvents: Water-Controlled Divergent Reactivity of 2-Substituted Indoles

Water is not a good solvent for most organic compounds, yet water can offer many benefits to some organic reactions, hence enriching organic chemistry. Herein, the unique divergent reactivity of 2-substituted indoles with ⋅NO sources is presented. The amount of water solvent was harnessed for a scalable, benign, and expedient synthesis of indolenine oximes, albeit with water's inability to dissolve the reactants. 2-Methoxyethyl nitrite, which has been tailored for reactions in water, empowered this protocol by enhancing the product selectivity. We further report on chemoselective transformations of the products that rely on their structural features. Our findings are expected to offer access to an underexplored chemical space. The platform is also applicable to oximinomalonate synthesis. Mechanistic studies revealed the important role of water in the reversal of stability between oxime and nitroso compounds, promoting the proton transfer.

Diverse contribution of amniogenic somatopleural cells to cardiovascular development: With special reference to thyroid vasculature

BACKGROUND

The somatopleure serves as the primordium of the amnion, an extraembryonic membrane surrounding the embryo. Recently, we have reported that amniogenic somatopleural cells (ASCs) not only form the amnion but also migrate into the embryo and differentiate into cardiomyocytes and vascular endothelial cells. However, detailed differentiation processes and final distributions of these intra-embryonic ASCs (hereafter referred to as iASCs) remain largely unknown.

RESULTS

By quail-chick chimera analysis, we here show that iASCs differentiate into various cell types including cardiomyocytes, smooth muscle cells, cardiac interstitial cells, and vascular endothelial cells. In the pharyngeal region, they distribute selectively into the thyroid gland and differentiate into vascular endothelial cells to form intra-thyroid vasculature. Explant culture experiments indicated sequential requirement of fibroblast growth factor (FGF) and vascular endothelial growth factor (VEGF) signaling for endothelial differentiation of iASCs. Single-cell transcriptome analysis further revealed heterogeneity and the presence of hemangioblast-like cell population within ASCs, with a switch from FGF to VEGF receptor gene expression.

CONCLUSION

The present study demonstrates novel roles of ASCss especially in heart and thyroid development. It will provide a novel clue for understanding the cardiovascular development of amniotes from embryological and evolutionary perspectives.

Differential peripheral memory T cell subsets sensitively indicate the severity of nonalcoholic fatty liver disease

AIM

Differential patterns of peripheral memory T cell subsets in nonalcoholic fatty liver disease (NAFLD) were assessed using flow cytometry (FCM) to elucidate their association with NAFLD severity and provide a new noninvasive method to sensitively detect the disease severity in addition to existing biomarkers.

METHODS

We assessed the differential frequencies of peripheral memory T cell subsets in 103 patients with NAFLD according to the degree of liver fibrosis (FIB) using FCM analysis. We focused on the following populations: CCR7+ CD45RA+ naïve T, CCR7+ CD45RA- central memory T cells (TCM), CCR7- CD45RA- effector memory T, and CCR7- CD45RA+ terminally differentiated effector memory T (TEMRA) cells in CD4+ and CD8+ T, Th1, Th2, and Th17 cells, respectively. To evaluate the pathological progression of the disease, these frequencies were also examined according to the degree of the NAFLD activity score (NAS).

RESULTS

Several significant correlations were observed between laboratory parameters and peripheral memory T lymphocyte frequencies according to the degree of liver FIB and NAS in NAFLD. In univariate and multivariate analyses, the frequency of CD8+ TEMRA cells predicted severe FIB, and the predictive power was validated in an independent cohort. Furthermore, the frequencies of several memory T cell subsets sensitively indicated the pathological progression of NAFLD (Th17 TCM: steatosis, CD4+ TCM: lobular inflammation, and CD8+ TEMRA and effector memory T cells: hepatocellular ballooning).

CONCLUSIONS

Our results suggest that the analysis of peripheral memory T lymphocyte frequencies can noninvasively predict severe FIB and sensitively indicate the pathological progression of NAFLD.

Mechanisms of Non-Fresh Groundwater Presence at Water Tables in Highly Permeable Coastal Aquifers

Coastal aquifers with high hydraulic conductivities on the order of 10-2  m s-1 have unconventional salinity distributions with the presence of non-fresh groundwater at the water table over a wide swath near the coast. This study aims to unravel the mechanisms underlying the phenomenon via numerical simulations for variably saturated, density-driven flow and solute transport in porous media. The simulation results indicate that the existence of non-fresh groundwater at the water table is attributed to the upward mass flux in the saturated zone near the coast, which transports solute from deeper groundwater toward the water table. With high hydraulic conductivity, the upward mass flux becomes prominent at shallower elevations because of the high Darcy flux and the shallow saline groundwater. The upward mass flux has two main drivers, upward advection by the upward flow component and transverse dispersion by the seaward flow component. The advective mass flux dominates over the transverse dispersion in the deep part of the saturated zone where only groundwater with sea water salinity exists. In contrast, the transverse dispersion becomes more pronounced than the upward advection in the shallow saturated zone just beneath the water table and in the unsaturated zone immediately above the water table. Our findings help interpret the unconventional salinity distributions observed and elucidate the unique dynamics of groundwater flow and solute transport in highly permeable coastal aquifers.

Real-time detection of acetone gas molecules at ppt levels in an air atmosphere using a partially suspended graphene surface acoustic wave skin gas sensor

To improve the quality of modern life in the current society, low-power, highly sensitive, and reliable healthcare technology is necessary to monitor human health in real-time. In this study, we fabricated partially suspended monolayer graphene surface acoustic wave gas sensors (G-SAWs) with a love-mode wave to effectively detect ppt-level acetone gas molecules at room temperature. The sputtered SiO2 thin film on the surface of a black 36°YX-LiTaO3 (B-LT) substrate acted as a guiding layer, effectively reducing the noise and insertion loss. The G-SAWs exhibited enhanced gas response towards acetone gas molecules (800 ppt) in a real-time atmosphere. The high sensitivity of the G-SAW sensor can be attributed to the elasticity and surface roughness of the SiO2 film. In addition, the G-SAW sensor exhibited rapid response and recovery at room temperature. This study provides a potential strategy for diagnosing different stages of diabetes in the human body.

Tensile Stress Reduction and Strain Concentration of Epoxy Resin Caused by Heterogeneity: A Multiscale Approach Combining Molecular Dynamics Simulation and Finite Element Method

In this study, we investigated the effect of heterogeneity on the mechanical properties of epoxy resin by combining coarse-grained molecular dynamics (CG-MD) and finite element method (FEM) simulations. To evaluate the heterogeneity effect in the uniaxial elongation, heterogeneous and homogeneous FEM models of micrometer-scale cubic epoxy resin were constructed. For the heterogeneous FEM model, parameters of nanometer-scale elements were determined by CG-MD simulations, where nanometer-scale blocks have different cross-linked structures. For the homogeneous FEM model, the averaged parameters were used for all elements. The calculated stress-strain (S-S) curves of the heterogeneous model exhibit similar tensile stress values when compared to the experimental data, whereas the homogeneous model yields notably higher values. Moreover, a clear strain concentration associated with the formation of the shear band-like structure was observed in the heterogeneous model and not in the homogeneous model.

Using phenolic polymers to control the size and morphology of calcium carbonate microparticles

Calcium carbonate (CaCO3) is a naturally occurring mineral that occurs in biology and is used industrially. Due to its benign nature, CaCO3 microparticles have found use in the food and medical fields, where the specific size of the microparticles determine their functionality and potential applications. We demonstrate that phenolic polymers with different numbers of hydroxy groups can be used to control the diameter of CaCO3 microparticles in a range of 2-9 μm, and obtained particles were relatively uniform. The largest particles (∼9 μm in diameter) were obtained using poly(2,3,4,5-tetrahydroxystyrene) (P4HS), which showed the highest water solubility among the tested phenolic polymers. The polymer concentration and stirring speed influenced the size of microparticles, where the size of the obtained particles became smaller as the concentrations of phenolic polymers increased and as the stirring speed increased, both likely due to promoting the formation of a large number of individual crystal seeds by shielding seed-seed fusion and increasing the chances for precursor contact, respectively. The preparation time and temperature had a great influence on the morphology of the CaCO3 particles, where vaterite transforms into calcite over time. Specifically, aragonite crystals were observed at preparation temperature of 80 °C and vaterite particles with rough surfaces were obtained at 40 °C. Molecular weight and scale of reaction were also factors which affect the size and morphologies of CaCO3 particles. This research represents a facile method for producing relatively monodisperse CaCO3 microparticles with diameters that have previously proven difficult to access.

Acidic extracellular pH drives accumulation of N1-acetylspermidine and recruitment of protumor neutrophils

An acidic tumor microenvironment plays a critical role in tumor progression. However, understanding of metabolic reprogramming of tumors in response to acidic extracellular pH has remained elusive. Using comprehensive metabolomic analyses, we demonstrated that acidic extracellular pH (pH 6.8) leads to the accumulation of N1-acetylspermidine, a protumor metabolite, through up-regulation of the expression of spermidine/spermine acetyltransferase 1 (SAT1). Inhibition of SAT1 expression suppressed the accumulation of intra- and extracellular N1-acetylspermidine at acidic pH. Conversely, overexpression of SAT1 increased intra- and extracellular N1-acetylspermidine levels, supporting the proposal that SAT1 is responsible for accumulation of N1-acetylspermidine. While inhibition of SAT1 expression only had a minor effect on cancer cell growth in vitro, SAT1 knockdown significantly decreased tumor growth in vivo, supporting a contribution of the SAT1-N1-acetylspermidine axis to protumor immunity. Immune cell profiling revealed that inhibition of SAT1 expression decreased neutrophil recruitment to the tumor, resulting in impaired angiogenesis and tumor growth. We showed that antineutrophil-neutralizing antibodies suppressed growth in control tumors to a similar extent to that seen in SAT1 knockdown tumors in vivo. Further, a SAT1 signature was found to be correlated with poor patient prognosis. Our findings demonstrate that extracellular acidity stimulates recruitment of protumor neutrophils via the SAT1-N1-acetylspermidine axis, which may represent a metabolic target for antitumor immune therapy.

Determination of the optimal connector length to enhance stability of backbone-circularized granulocyte colony-stimulating factor

Improving protein stability is important for industrial applications, and one promising method for achieving this is backbone circularization. As connector length affects stability, predicting and elucidating a more stable connector length is necessary for development of the backbone circularization method. However, the relationship between connector length and protein stability has not been completely elucidated. Here, we determined the most stable connector length for granulocyte colony-stimulating factor by changing one residue at a time to produce connector length variants and then measuring their thermal stability. Analysis of the local structures obtained from the predicted structures of the circularized variants revealed that an approach using helix length, dihedral backbone angle, and number of unbonded hydrogen bond donors and acceptors is suitable for identifying connector lengths with higher stability.

SMG: self-supervised masked graph learning for cancer gene identification

Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data. Nevertheless, because of the limited labelled data, pinpointing CGs from a multitude of potential mutations remains an exceptionally challenging task. To address this, we propose a novel deep learning framework, termed self-supervised masked graph learning (SMG), which comprises SMG reconstruction (pretext task) and task-specific fine-tuning (downstream task). In the pretext task, the nodes of multi-omic featured protein-protein interaction (PPI) networks are randomly substituted with a defined mask token. The PPI networks are then reconstructed using the graph neural network (GNN)-based autoencoder, which explores the node correlations in a self-prediction manner. In the downstream tasks, the pre-trained GNN encoder embeds the input networks into feature graphs, whereas a task-specific layer proceeds with the final prediction. To assess the performance of the proposed SMG method, benchmarking experiments are performed on three node-level tasks (identification of CGs, essential genes and healthy driver genes) and one graph-level task (identification of disease subnetwork) across eight PPI networks. Benchmarking experiments and performance comparison with existing state-of-the-art methods demonstrate the superiority of SMG on multi-omic feature engineering.

Comparative Electronic Structures of the Chiral Helimagnets Cr1/3NbS2 and Cr1/3TaS2

Magnetic materials with noncollinear spin textures are promising for spintronic applications. To realize practical devices, control over the length and energy scales of such spin textures is imperative. The chiral helimagnets Cr1/3NbS2 and Cr1/3TaS2 exhibit analogous magnetic-phase diagrams with different real-space periodicities and field dependence, positioning them as model systems for studying the relative strengths of the microscopic mechanisms giving rise to exotic spin textures. Although the electronic structure of the Nb analogue has been experimentally investigated, the Ta analogue has received far less attention. Here, we present a comprehensive suite of electronic structure studies on both Cr1/3NbS2 and Cr1/3TaS2 using angle-resolved photoemission spectroscopy and density functional theory. We show that bands in Cr1/3TaS2 are more dispersive than their counterparts in Cr1/3NbS2, resulting in markedly different Fermi wavevectors. The fact that their qualitative magnetic phase diagrams are nevertheless identical shows that hybridization between the intercalant and host lattice mediates the magnetic exchange interactions in both of these materials. We ultimately find that ferromagnetic coupling is stronger in Cr1/3TaS2, but larger spin-orbit coupling (and a stronger Dzyaloshinskii-Moriya interaction) from the heavier host lattice ultimately gives rise to shorter spin textures.

Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide

Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.

TLR7/8 stress response drives histiocytosis in SLC29A3 disorders

Loss-of-function mutations in the lysosomal nucleoside transporter SLC29A3 cause lysosomal nucleoside storage and histiocytosis: phagocyte accumulation in multiple organs. However, little is known about the mechanism by which lysosomal nucleoside storage drives histiocytosis. Herein, histiocytosis in Slc29a3-/- mice was shown to depend on Toll-like receptor 7 (TLR7), which senses a combination of nucleosides and oligoribonucleotides (ORNs). TLR7 increased phagocyte numbers by driving the proliferation of Ly6Chi immature monocytes and their maturation into Ly6Clow phagocytes in Slc29a3-/- mice. Downstream of TLR7, FcRγ and DAP10 were required for monocyte proliferation. Histiocytosis is accompanied by inflammation in SLC29A3 disorders. However, TLR7 in nucleoside-laden splenic monocytes failed to activate inflammatory responses. Enhanced production of proinflammatory cytokines was observed only after stimulation with ssRNAs, which would increase lysosomal ORNs. Patient-derived monocytes harboring the G208R SLC29A3 mutation showed enhanced survival and proliferation in a TLR8-antagonist-sensitive manner. These results demonstrated that TLR7/8 responses to lysosomal nucleoside stress drive SLC29A3 disorders.

In vitro characterization of nonribosomal peptide synthetase-dependent O-(2-hydrazineylideneacetyl)serine synthesis indicates a stepwise oxidation strategy to generate the α-diazo ester moiety of azaserine

Azaserine, a natural product containing a diazo group, exhibits anticancer activity. In this study, we investigated the biosynthetic pathway to azaserine. The putative azaserine biosynthetic gene (azs) cluster, which contains 21 genes, including those responsible for hydrazinoacetic acid (HAA) synthesis, was discovered using bioinformatics analysis of the Streptomyces fragilis genome. Azaserine was produced by the heterologous expression of the azs cluster in Streptomyces albus. In vitro enzyme assays using recombinant Azs proteins revealed the azaserine biosynthetic pathway as follows. AzsSPTF and carrier protein (CP) AzsQ are used to synthesize the 2-hydrazineylideneacetyl (HDA) moiety attached to AzsQ from HAA. AzsD transfers the HDA moiety to the C-terminal CP domain of AzsN. The heterocyclization (Cy) domain of the nonribosomal peptide synthetase AzsO synthesizes O-(2-hydrazineylideneacetyl)serine (HDA-Ser) attached to its CP domain from l-serine and HDA moiety-attached AzsN. The thioesterase AzsB hydrolyzes it to yield HDA-Ser, which appears to be converted to azaserine by oxidation. Bioinformatics analysis of the Cy domain of AzsO showed that it has a conserved DxxxxD motif; however, two conserved amino acid residues (Thr and Asp) important for heterocyclization are substituted for Asn. Site-directed mutagenesis of two Asp residues in the DxxxxD motif (D193 and D198) and two substituted Asn residues (N414 and N447) indicated that these four residues are important for ester bond synthesis. These results showed that the diazo ester of azasrine is synthesized by the stepwise oxidation of the HAA moiety and provided another strategy to biosynthesize the diazo group.

regeneration factors expressed on myeloid expression in macrophage-like cells is required for tail regeneration in Xenopus laevis tadpoles

Xenopus laevis tadpoles can regenerate whole tails after amputation. We have previously reported that interleukin 11 (il11) is required for tail regeneration. In this study, we have screened for genes that support tail regeneration under Il11 signaling in a certain cell type and have identified the previously uncharacterized genes Xetrov90002578m.L and Xetrov90002579m.S [referred to hereafter as regeneration factors expressed on myeloid.L (rfem.L) and rfem.S]. Knockdown (KD) of rfem.L and rfem.S causes defects of tail regeneration, indicating that rfem.L and/or rfem.S are required for tail regeneration. Single-cell RNA sequencing (scRNA-seq) revealed that rfem.L and rfem.S are expressed in a subset of leukocytes with a macrophage-like gene expression profile. KD of colony-stimulating factor 1 (csf1), which is essential for macrophage differentiation and survival, reduced rfem.L and rfem.S expression levels and the number of rfem.L- and rfem.S-expressing cells in the regeneration bud. Furthermore, forced expression of rfem.L under control of the mpeg1 promoter, which drives rfem.L in macrophage-like cells, rescues rfem.L and rfem.S KD-induced tail regeneration defects. Our findings suggest that rfem.L or rfem.S expression in macrophage-like cells is required for tail regeneration.

Exposure to microbial products followed by loss of Tet2 promotes myelodysplastic syndrome via remodeling HSCs

Aberrant innate immune signaling in myelodysplastic syndrome (MDS) hematopoietic stem/progenitor cells (HSPCs) has been implicated as a driver of the development of MDS. We herein demonstrated that a prior stimulation with bacterial and viral products followed by loss of the Tet2 gene facilitated the development of MDS via up-regulating the target genes of the Elf1 transcription factor and remodeling the epigenome in hematopoietic stem cells (HSCs) in a manner that was dependent on Polo-like kinases (Plk) downstream of Tlr3/4-Trif signaling but did not increase genomic mutations. The pharmacological inhibition of Plk function or the knockdown of Elf1 expression was sufficient to prevent the epigenetic remodeling in HSCs and diminish the enhanced clonogenicity and the impaired erythropoiesis. Moreover, this Elf1-target signature was significantly enriched in MDS HSPCs in humans. Therefore, prior infection stress and the acquisition of a driver mutation remodeled the transcriptional and epigenetic landscapes and cellular functions in HSCs via the Trif-Plk-Elf1 axis, which promoted the development of MDS.

Intraperitoneal paclitaxel combined with FOLFOX/CAPOX plus bevacizumab for colorectal cancer with peritoneal carcinomatosis (the iPac-02 trial): study protocol of a single arm, multicenter, phase 2 study

BACKGROUND

The safety of intraperitoneally administrated paclitaxel (op PTX) was demonstrated in the phase I trial of ip PTX combined with conventional systemic chemotherapy for colorectal cancer with peritoneal carcinomatosis. Moreover, the median survival time was 29.3 months, which was longer than that observed in previous studies. Here, we planned the phase II trial of ip PTX: the iPac-02 trial.

METHODS

This multicenter, open-label, single assignment interventional clinical study includes patients with colorectal cancer with unresectable peritoneal carcinomatosis. FOLFOX-bevacizumab or CAPOX-bevacizumab is administered concomitantly as systemic chemotherapy. PTX 20 mg/m2 is administered weekly through the peritoneal access port in addition to these conventional systemic chemotherapies. The response rate is the primary endpoint. Progression-free survival, overall survival, peritoneal cancer index improvement rate, rate of negative peritoneal lavage cytology, safety, and response rate to peritoneal metastases are the secondary endpoints. A total of 38 patients are included in the study. In the interim analysis, the study will continue to the second stage if at least 4 of the first 14 patients respond to the study treatment. The study has been registered at the Japan Registry of Clinical Trials (jRCT2031220110).

RESULTS

We previously conducted phase I trial of ip PTX combined with conventional systemic chemotherapy for colorectal cancer with peritoneal carcinomatosis [1]. In the study, three patients underwent mFOLFOX, bevacizumab, and weekly ip PTX, and the other three patients underwent CAPOX, bevacizumab, and weekly ip PTX treatment. The dose of PTX was 20 mg/m [2]. The primary endpoint was the safety of the chemotherapy, and secondary endpoints were response rate, peritoneal cancer index improvement rate, rate of negative peritoneal lavage cytology, progression-free survival, and overall survival. Dose limiting toxicity was not observed, and the adverse events of ip PTX combined with oxaliplatin-based systemic chemotherapy were similar to those described in previous studies using systemic chemotherapy alone [3, 4]. The response rate was 25%, peritoneal cancer index improvement rate was 50%, and cytology in peritoneal lavage turned negative in all the cases. The progression-free survival was 8.8 months (range, 6.8-12 months), and median survival time was 29.3 months [5], which was longer than that observed in previous studies.

CONCLUSION

Here, we planned the phase II trial of ip paclitaxel combined with conventional chemotherapy for colorectal cancer with peritoneal carcinomatosis: the iPac-02 trial.

Sec16 and Sed4 interdependently function as interaction and localization partners at ER exit sites

COPII proteins assemble at ER exit sites (ERES) to form transport carriers. The initiation of COPII assembly in the yeast Saccharomyces cerevisiae is triggered by the ER membrane protein Sec12. Sec16, which plays a critical role in COPII organization, localizes to ERES independently of Sec12. However, the mechanism underlying Sec16 localization is poorly understood. Here, we show that a Sec12 homolog, Sed4, is concentrated at ERES and mediates ERES localization of Sec16. We found that the interaction between Sec16 and Sed4 ensures their correct localization to ERES. Loss of the interaction with Sec16 leads to redistribution of Sed4 from the ERES specifically to high-curvature ER areas, such as the tubules and edges of the sheets. The luminal domain of Sed4 mediates this distribution, which is required for Sed4, but not for Sec16, to be concentrated at ERES. We further show that the luminal domain and its O-mannosylation are involved in the self-interaction of Sed4. Our findings provide insight into how Sec16 and Sed4 function interdependently at ERES.

Quantitative Description of Bubble Formation in Response to Electrolyte Engineering

The green hydrogen economy is expected to play a crucial role in carbon neutrality, but industrial-scale water electrolysis requires improvements in efficiency, operation costs, and capital costs before broad deployment. Electrolysis operates at a high current density and involves the substantial formation of gaseous products from the electrode surfaces to the electrolyte, which may lead to additional resistance and a resulting loss of efficiency. A detailed clarification of the bubble departure phenomena against the electrode surface and the surrounding electrolytes is needed to further control bubbles in a water electrolyzer. This study clarifies how electrolyte properties affect the measured bubble detachment sizes from the comparisons with analytical expressions and dynamic simulations. Bubble behavior in various electrolyte solutions and operating conditions was described using various physical parameters. A quantitative relationship was then established to connect electrolyte properties and bubble departure diameters, which can help regulate the bubble management through electrolyte engineering.

Cryoelectron microscopic structure of the nucleoprotein-RNA complex of the European filovirus, Lloviu virus

Lloviu virus (LLOV) is a novel filovirus detected in Schreiber's bats in Europe. The isolation of the infectious LLOV from bats has raised public health concerns. However, the virological and molecular characteristics of LLOV remain largely unknown. The nucleoprotein (NP) of LLOV encapsidates the viral genomic RNA to form a helical NP-RNA complex, which acts as a scaffold for nucleocapsid formation and de novo viral RNA synthesis. In this study, using single-particle cryoelectron microscopy, we determined two structures of the LLOV NP-RNA helical complex, comprising a full-length and a C-terminally truncated NP. The two helical structures were identical, demonstrating that the N-terminal region determines the helical arrangement of the NP. The LLOV NP-RNA protomers displayed a structure similar to that in the Ebola and Marburg virus, but the spatial arrangements in the helix differed. Structure-based mutational analysis identified amino acids involved in the helical assembly and viral RNA synthesis. These structures advance our understanding of the filovirus nucleocapsid formation and provide a structural basis for the development of antifiloviral therapeutics.

Short-term memory capacity analysis of Lu3Fe4Co0.5Si0.5O12-based spin cluster glass towards reservoir computing

Reservoir computing is a brain heuristic computing paradigm that can complete training at a high speed. The learning performance of a reservoir computing system relies on its nonlinearity and short-term memory ability. As physical implementation, spintronic reservoir computing has attracted considerable attention because of its low power consumption and small size. However, few studies have focused on developing the short-term memory ability of the material itself in spintronics reservoir computing. Among various magnetic materials, spin glass is known to exhibit slow magnetic relaxation that has the potential to offer the short-term memory capability. In this research, we have quantitatively investigated the short-term memory capability of spin cluster glass based on the prevalent benchmark. The results reveal that the magnetization relaxation of Co, Si-substituted Lu₃Fe₅O₁₂ with spin glass behavior can provide higher short-term memory capacity than ferrimagnetic material without substitution. Therefore, materials with spin glass behavior can be considered as potential candidates for constructing next-generation spintronic reservoir computing with better performance.

Reconfigurable magnon interference by on-chip dynamic wavelength conversion

Spin waves (SWs), an ultra-low power magnetic excitation in ferro or antiferromagnetic media, have tremendous potential as transport less data carriers for post-CMOS technology using their wave interference properties. The concept of magnon interference originates from optical interference, resulting in a historical taboo of maintaining an identical wavevector for magnon interference-based devices. This makes the attainment of on-chip design reconfigurability challenging owing to the difficulty in phase tuning via external fields. Breaking the taboo, this study explores a novel technique to systematically control magnon interference using asymmetric wavevectors from two different SW modes (magnetostatic surface SWs and backward volume magnetostatic SWs) in a microstructured yttrium iron garnet crossbar. Using this system, we demonstrate phase reconfigurability in the interference pattern by modulating the thermal landscape, modifying the dispersion of the interfering SW modes. Thus, we manifest that such a tunable interference can be used to implement reconfigurable logic gates operating between the XNOR and XOR modes by using symmetric and asymmetric interference, respectively.

A CRISPR-del-based pipeline for complete gene knockout in human diploid cells

The advance of CRISPR/Cas9 technology has enabled us easily to generate gene knockout cell lines by introducing insertion-deletion mutations (indels) at the target site via the error-prone non-homologous end joining repair system. Frameshift-promoting indels can disrupt gene functions by generation of a premature stop codon. However, there is growing evidence that targeted genes are not always knocked out by the indel-based gene disruption. Here, we established a pipeline of CRISPR-del, which induces a large chromosomal deletion by cutting two different target sites, to perform 'complete' gene knockout efficiently in human diploid cells. Quantitative analyses show that the frequency of gene deletion with this approach is much higher than that of conventional CRISPR-del methods. The lengths of the deleted genomic regions demonstrated in this study are longer than those of 95% of the human protein-coding genes. Furthermore, the pipeline enabled the generation of a model cell line having a bi-allelic cancer-associated chromosomal deletion. Overall, these data lead us to propose that the CRISPR-del pipeline is an efficient and practical approach for producing 'complete' gene knockout cell lines in human diploid cells.

Comparing the structure-function relationship between the visual fields measured with variational Bayes linear regression and SITA standard

PURPOSE

We recently constructed an algorithm to measure visual field (VF) using the variational Bayes linear regression (VBLR). This algorithm enabled a faster VF measurement than the Swedish interactive thresholding algorithm (SITA) standard while maintaining the test-retest reproducibility (Murata H, et al. Br J Ophthalmol 2021). The current study aimed to compare the structure-function relationship between the SITA standard and VBLR.

METHOD

In 78 eyes of 56 patients with primary open-angle glaucoma, VF measurements were conducted using both SITA standard and VBLR VF, as well as spectral-domain optical coherence tomography. The structure-function relationship was investigated between visual sensitivity and circumpapillary retinal nerve fiber layer in the whole VF. This analysis was repeated for each of the 12 sectors (30 degrees). The strength of the structure-function relationship was evaluated using the second-order bias-corrected Akaike Information Criterion (AICc) index.

RESULT

In the whole VF, AICc values of SITA standard and VBLR were 601.6 and 597.3, respectively. The relative likelihood that VBLR had a better structure-function relationship than the SITA standard was 88.2% (when the entire field was averaged) or 99.9% (when all test points were analyzed in the pointwise manner). With the sector-wise analysis, SITA standard had a better structure-function relationship than VBLR in 1 sector (Superior sector in the retina), whereas VBLR had a better structure-function relationship than SITA standard in 4 sectors (Supero-Nasal, Infero-Nasal, Inferior, and Infero-Temporal sectors) with >95% relative likelihood.

CONCLUSION

Although it depends on locations and similar between SITA standard and VBLR-VF, but VBLR-VF had a better structure-function relationship than the SITA standard overall.

sconce: a cosmic web finder for spherical and conic geometries

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called sconce (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (scms) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard scms method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as sconce-scms and has been made publicly available.

Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis

Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.

Application of a Machine Learning Algorithm for Structural Brain Images in Chronic Schizophrenia to Earlier Clinical Stages of Psychosis and Autism Spectrum Disorder: A Multiprotocol Imaging Dataset Study

BACKGROUND AND HYPOTHESIS

Machine learning approaches using structural magnetic resonance imaging (MRI) can be informative for disease classification; however, their applicability to earlier clinical stages of psychosis and other disease spectra is unknown. We evaluated whether a model differentiating patients with chronic schizophrenia (ChSZ) from healthy controls (HCs) could be applied to earlier clinical stages such as first-episode psychosis (FEP), ultra-high risk for psychosis (UHR), and autism spectrum disorders (ASDs).

STUDY DESIGN

Total 359 T1-weighted MRI scans, including 154 individuals with schizophrenia spectrum (UHR, n = 37; FEP, n = 24; and ChSZ, n = 93), 64 with ASD, and 141 HCs, were obtained using three acquisition protocols. Of these, data regarding ChSZ (n = 75) and HC (n = 101) from two protocols were used to build a classifier (training dataset). The remainder was used to evaluate the classifier (test, independent confirmatory, and independent group datasets). Scanner and protocol effects were diminished using ComBat.

STUDY RESULTS

The accuracy of the classifier for the test and independent confirmatory datasets were 75% and 76%, respectively. The bilateral pallidum and inferior frontal gyrus pars triangularis strongly contributed to classifying ChSZ. Schizophrenia spectrum individuals were more likely to be classified as ChSZ compared to ASD (classification rate to ChSZ: UHR, 41%; FEP, 54%; ChSZ, 70%; ASD, 19%; HC, 21%).

CONCLUSION

We built a classifier from multiple protocol structural brain images applicable to independent samples from different clinical stages and spectra. The predictive information of the classifier could be useful for applying neuroimaging techniques to clinical differential diagnosis and predicting disease onset earlier.

Puff turbulence in the limit of strong buoyancy

We provide a numerical validation of a recently proposed phenomenological theory to characterize the space-time statistical properties of a turbulent puff, both in terms of bulk properties, such as the mean velocity, temperature and size, and scaling laws for velocity and temperature differences both in the viscous and in the inertial range of scales. In particular, apart from the more classical shear-dominated puff turbulence, our main focus is on the recently discovered new regime where turbulent fluctuations are dominated by buoyancy. The theory is based on an adiabaticity hypothesis which assumes that small-scale turbulent fluctuations rapidly relax to the slower large-scale dynamics, leading to a generalization of the classical Kolmogorov and Kolmogorov-Obukhov-Corrsin theories for a turbulent puff hosting a scalar field. We validate our theory by means of massive direct numerical simulations finding excellent agreement. This article is part of the theme issue 'Scaling the turbulence edifice (part 2)'.

Effective Connectivity and Criminal Sentencing Decisions: Dynamic Causal Models in Laypersons and Legal Experts

This magnetic resonance imaging study is designed to obtain relevant implications for criminal justice and explores the effective connectivity underlying expertise. Laypersons and experts considered sentences for remorseful and remorseless defendants, respectively, with and without mitigation, in hypothetical murder cases. Two groups revealed no differential activation. However, dynamic causal modeling analysis found distinct patterns of connectivity associated with subjects’ expertise and mitigating factors. In sentencing for remorseful defendants, laypersons showed increased strength in all bidirectional connections among activated regions of Brodmann area (BA) 32, BA23, the right posterior insula, and the precuneus. In contrast, legal experts sentenced based on mitigation reasoning, showed increased strength only in the bidirectional connection between the insula and the precuneus. When sentencing for remorseless ones without mitigation, both laypersons and experts increased the connection strength, but with reverse directionality, between regions; legal experts strengthened connectivity from BA10 to other regions, that is, the right anterior insula and BA23, but the directionality was reversed in laypersons. In addition, the strength of connection to BA32 and BA10 was correlated with changes in punishments by mitigating factors. This is a crucial result that establishes the validity of the connectivity estimates, which were uninformed by the independent (behavioral) differences in the severity of punishment.

Foxp3+ CD4+ regulatory T cells control dendritic cells in inducing antigen-specific immunity to emerging SARS-CoV-2 antigens

Regulatory T (Treg) cells, which constitute about 5-10% of CD4+T cells expressing Foxp3 transcription factor and CD25(IL-2 receptor α chain), are key regulators in controlling immunological self-tolerance and various immune responses. However, how Treg cells control antigen-specific immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear. In this study, we examined the effect of transient breakdown of the immunological tolerance induced by Treg-cell depletion on adaptive immune responses against administered SARS-CoV-2 antigen, spike protein 1 (S1). Notably, without the use of adjuvants, transient Treg-cell depletion in mice induced anti-S1 antibodies that neutralized authentic SARS-CoV-2, follicular helper T cell formation and S1-binding germinal center B cell responses, but prevented the onset of developing autoimmune diseases. To further clarify the mechanisms, we investigated maturation of dendritic cells (DCs), which is essential to initiate antigen-specific immunity. We found that the transient Treg-cell depletion resulted in maturation of both migratory and resident DCs in draining lymph nodes that captured S1-antigen. Moreover, we observed S1-specific CD4+ T cells and CD8+ T cells with interferon-γ production. Thus, captured S1 was successfully presented by DCs, including cross-presentation to CD8+ T cells. These data indicate that transient Treg-cell depletion in the absence of adjuvants induces maturation of antigen-presenting DCs and succeeds in generating antigen-specific humoral and cellular immunity against emerging SARS-CoV-2 antigens. Finally, we showed that SARS-CoV-2 antigen-specific immune responses induced by transient Treg-cell depletion in the absence of adjuvants were compatible with those induced with an effective adjuvant, polyriboinosinic:polyribocytidyl acid (poly IC) and that the combination of transient Treg-cell depletion with poly IC induced potent responses. These findings highlight the capacity for manipulating Treg cells to induce protective adaptive immunity to SARS-CoV-2 with activating antigen-presenting DCs, which may improve the efficacy of ongoing vaccine therapies and help enhance responses to emerging SARS-CoV-2 variants.

Programmable and sequential Gaussian gates in a loop-based single-mode photonic quantum processor

A quantum processor to import, process, and export optical quantum states is a common core technology enabling various photonic quantum information processing. However, there has been no photonic processor that is simultaneously universal, scalable, and programmable. Here, we report on an original loop-based single-mode versatile photonic quantum processor that is designed to be universal, scalable, and programmable. Our processor can perform arbitrarily many steps of programmable quantum operations on a given single-mode optical quantum state by time-domain processing in a dynamically controlled loop-based optical circuit. We use this processor to demonstrate programmable single-mode Gaussian gates and multistep squeezing gates. In addition, we prove that the processor can perform universal quantum operations by injecting appropriate ancillary states and also be straightforwardly extended to a multimode processor. These results show that our processor is programmable, scalable, and potentially universal, leading to be suitable for general-purpose applications.

Three-dimensional quantification of twisting in the Arabidopsis petiole

Organisms have a variety of three-dimensional (3D) structures that change over time. These changes include twisting, which is 3D deformation that cannot happen in two dimensions. Twisting is linked to important adaptive functions of organs, such as adjusting the orientation of leaves and flowers in plants to align with environmental stimuli (e.g. light, gravity). Despite its importance, the underlying mechanism for twisting remains to be determined, partly because there is no rigorous method for quantifying the twisting of plant organs. Conventional studies have relied on approximate measurements of the twisting angle in 2D, with arbitrary choices of observation angle. Here, we present the first rigorous quantification of the 3D twisting angles of Arabidopsis petioles based on light sheet microscopy. Mathematical separation of bending and twisting with strict definition of petiole cross-sections were implemented; differences in the spatial distribution of bending and twisting were detected via the quantification of angles along the petiole. Based on the measured values, we discuss that minute degrees of differential growth can result in pronounced twisting in petioles.

Roles of the ClC chloride channel CLH-1 in food-associated salt chemotaxis behavior of C. elegans

The ability of animals to process dynamic sensory information facilitates foraging in an ever-changing environment. However, molecular and neural mechanisms underlying such ability remain elusive. The ClC anion channels/transporters play a pivotal role in cellular ion homeostasis across all phyla. Here, we find a ClC chloride channel is involved in salt concentration chemotaxis of Caenorhabditis elegans. Genetic screening identified two altered-function mutations of clh-1 that disrupt experience-dependent salt chemotaxis. Using genetically encoded fluorescent sensors, we demonstrate that CLH-1 contributes to regulation of intracellular anion and calcium dynamics of salt-sensing neuron, ASER. The mutant CLH-1 reduced responsiveness of ASER to salt stimuli in terms of both temporal resolution and intensity, which disrupted navigation strategies for approaching preferred salt concentrations. Furthermore, other ClC genes appeared to act redundantly in salt chemotaxis. These findings provide insights into the regulatory mechanism of neuronal responsivity by ClCs that contribute to modulation of navigation behavior.

Oncolytic herpes simplex virus type 1 (HSV-1) in combination with lenalidomide for plasma cell neoplasms

Oncolytic viruses exert an anti-tumour effect through two mechanisms: direct oncolytic and indirect immune-mediated mechanisms. Although oncolytic herpes simplex virus type 1 (HSV-1) has been approved for melanoma treatment and is being examined for its applicability to a broad spectrum of malignancies, it is not known whether it has an anti-myeloma effect. In the present study, we show that the third-generation oncolytic HSV-1, T-01, had a direct oncolytic effect on five of six human myeloma cell lines in vitro. The anti-tumour effect was enhanced in the presence of peripheral blood mononuclear cells (PBMCs) from healthy individuals and, to a lesser extent, from patients with myeloma. The enhancing effect of PBMCs was abrogated by blocking type I interferons (IFNs) or by depleting plasmacytoid dendritic cells (pDCs) or natural killer (NK) cells, suggesting that pDC-derived type I IFNs and NK cells dominated the anti-tumour effect. Furthermore, the combination of T-01 and lenalidomide exhibited enhanced cytotoxicity, and the triple combination of T-01, lenalidomide and IFN-α had a maximal effect. These data indicate that oncolytic HSV-1 represents a viable therapy for plasma cell neoplasms through direct oncolysis and immune activation governed by pDCs and NK cells. Lenalidomide is likely to augment the anti-myeloma effect of HSV-1.

Crystal growth control of rod-shaped ε-Fe2O3 nanocrystals

Herein we report crystal growth control of rod-shaped ε-Fe2O3 nanocrystals by developing a synthesis based on the sol-gel technique using β-FeO(OH) as a seed in the presence of a barium cation. ε-Fe2O3 nanocrystals are obtained over a wide calcination temperature range between 800 °C and 1000 °C. A low calcination temperature (800 °C) provides an almost cubic rectangular-shaped ε-Fe2O3 nanocrystal with an aspect ratio of 1.4, whereas a high calcination temperature (1000 °C) provides an elongated rod-shaped ε-Fe2O3 nanocrystal with an aspect ratio of 3.3. Such systematic anisotropic growth of ε-Fe2O3 is achieved due to the wide calcination temperature in the presence of barium cations. The surface energy and the anisotropic adsorption of barium on the surface of ε-Fe2O3 can explain the anisotropic crystal growth of rod-shaped ε-Fe2O3 along the crystallographic a-axis. The present work may provide important knowledge about how to control the anisotropic crystal shape of nanomaterials.

The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regeneration

Plants form calluses and regenerate new organs when incubated on phytohormone-containing media. While accumulating evidence suggests that these regenerative processes are governed by transcriptional networks orchestrating wound response and developmental transitions, it remains unknown if posttranslational regulatory mechanisms are involved in this process. In this study, we demonstrate that SAP AND MIZ1 DOMAIN- CONTAINING LIGASE1 (SIZ1), an E3 ligase-catalyzing attachment of the SMALL UBIQUITIN-LIKE MODIFIER (SUMO) to proteins, regulates wound-induced signal transduction and organ regeneration in Arabidopsis (Arabidopsis thaliana). We show that loss-of-function mutants for SIZ1 exhibit overproduction of shoot meristems under in vitro tissue culture conditions, while this defect is rescued in a complementation line expressing pSIZ1::SIZ1 RNA sequencing analysis revealed that siz1-2 mutants exhibit enhanced transcriptional responses to wound stress, resulting in the hyper-induction of over 400 genes immediately after wounding. Among them, we show that elevated levels of WOUND INDUCED DEDIFFERENTIATION1 (WIND1) and WIND2 contribute to the enhanced shoot regeneration observed in siz1 mutants, as expression of the dominant-negative chimeric protein WIND1-SRDX (SUPERMAN repression domain) in siz1-3 mutants partly rescues this phenotype. Although compromised SIZ1 function does not modify the transcription of genes implicated in auxin-induced callus formation and/or pluripotency acquisition, it does lead to enhanced induction of cytokinin-induced shoot meristem regulators such as WUSCHEL, promoting the formation of WUSCHEL-expressing foci in explants. This study thus suggests that SIZ1 negatively regulates shoot regeneration in part by repressing wound-induced developmental reprogramming.

Impaired mucociliary motility enhances antigen-specific nasal IgA immune responses to a cholera toxin-based nasal vaccine

Nasal mucosal tissues are equipped with physical barriers, mucus and cilia, on their surface. The mucus layer captures inhaled materials, and the cilia remove the inhaled materials from the epithelial layer by asymmetrical beating. The effect of nasal physical barriers on the vaccine efficacy remains to be investigated. Tubulin tyrosine ligase-like family, member 1 (Ttll1) is an essential enzyme for appropriate movement of the cilia on respiratory epithelium, and its deficiency (Ttll1-KO) leads to mucus accumulation in the nasal cavity. Here, when mice were intra-nasally immunized with pneumococcal surface protein A (PspA, as vaccine antigen) together with cholera toxin (CT, as mucosal adjuvant), Ttll1-KO mice showed higher levels of PspA-specific IgA in the nasal wash and increased numbers of PspA-specific IgA-producing plasma cells in the nasal passages when compared with Ttll1 hetero (He) mice. Mucus removal by N-acetylcysteine did not affect the enhanced immune responses in Ttll1-KO mice versus Ttll1-He mice. Immunohistological and flow cytometry analyses revealed that retention time of PspA in the nasal cavity in Ttll1-KO mice was longer than that in Ttll1-He mice. Consistently, uptake of PspA by dendritic cells was higher in the nasopharynx-associated lymphoid tissue (NALT) of Ttll1-KO mice than that of Ttll1-He mice. These results indicate that the ciliary function of removing vaccine antigen from the NALT epithelial layer is a critical determinant of the efficacy of nasal vaccine.

Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans

BACKGROUND

Annotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has been limited due to the lack of quantitative information on the location and identity of neurons.

RESULTS

Here, we present a dataset that facilitates the annotation of neuronal identities, and demonstrate its application in a comprehensive analysis of whole-brain imaging. We systematically identified neurons in the head region of 311 adult worms using 35 cell-specific promoters and created a dataset of the expression patterns and the positions of the neurons. We found large positional variations that illustrated the difficulty of the annotation task. We investigated multiple combinations of cell-specific promoters driving distinct fluorescence and generated optimal strains for the annotation of most head neurons in an animal. We also developed an automatic annotation method with human interaction functionality that facilitates annotations needed for whole-brain imaging.

CONCLUSION

Our neuron ID dataset and optimal fluorescent strains enable the annotation of most neurons in the head region of adult C. elegans, both in full-automated fashion and a semi-automated version that includes human interaction functionalities. Our method can potentially be applied to model species used in research other than C. elegans, where the number of available cell-type-specific promoters and their variety will be an important consideration.

What is the origin of macroscopic friction?

What is the origin of molecular friction, and how can macroscopic friction be explained in terms of molecular friction? To elucidate the origins of molecular and macroscopic friction, we conducted density functional theory calculations and double-direct shear tests at normal stresses ranging from 5 to 60 MPa for mica surfaces. Frictional forces between mica surfaces were theoretically predicted to oscillate periodically every 30° of sliding direction, in agreement with previous experimental findings. This result affirms that the potential energy roughness of mica under sliding is the origin of molecular friction, which depends on the normal stress and sliding direction. The discovered mechanism of molecular friction can quantitatively explain experimentally observed macroscopic friction of mica when the presence of wear particles is taken into consideration.