Tight junction membrane proteins regulate the mechanical resistance of the apical junctional complex

Epithelia must be able to resist mechanical force to preserve tissue integrity. While intercellular junctions are known to be important for the mechanical resistance of epithelia, the roles of tight junctions (TJs) remain to be established. We previously demonstrated that epithelial cells devoid of the TJ membrane proteins claudins and JAM-A completely lack TJs and exhibit focal breakages of their apical junctions. Here, we demonstrate that apical junctions fracture when claudin/JAM-A-deficient cells undergo spontaneous cell stretching. The junction fracture was accompanied by actin disorganization, and actin polymerization was required for apical junction integrity in the claudin/JAM-A-deficient cells. Further deletion of CAR resulted in the disruption of ZO-1 molecule ordering at cell junctions, accompanied by severe defects in apical junction integrity. These results demonstrate that TJ membrane proteins regulate the mechanical resistance of the apical junctional complex in epithelial cells.

Effect of defect-healing treatment on layered silicate precursors toward well-defined crosslinked frameworks

The synthesis of zeolites from two-dimensional layered precursors through interlayer crosslinking of the layers is a promising avenue for realizing meticulously designed synthesis routes. However, the presence of defective silanol species in the precursors hinders the achievement of desirable synthesis outcomes. This study focuses on PREFER-a layered precursor for FER-type zeolites-which was synthesized and subjected to a liquid-mediated defect-healing treatment that we recently developed. The defect-healing process involves the use of fluoride compounds for reconstruction and organic pore fillers to stabilize the framework. The effects of the treatment on the structure, composition, and iron insertion behavior of PREFER were examined. Characterization results revealed a reduction in the number of intralayer silanol defects, whereas interlayer silanols were unaffected by the defect-healing treatment. Furthermore, the subsequent alterations observed in the crosslinking behavior with iron atoms indicated that the defect-healing treatment may enhance the insertion of iron species between the layers in more homogeneous environments compared with the untreated precursor. These findings provide valuable insights into the prospects of controlled interlayer linkage in two-dimensional zeolite materials.

Development of an Enzyme Cascade System for the Synthesis of Enantiomerically Pure D-Amino Acids Utilizing Ancestral L-Amino Acid Oxidase

Enantiomerically pure D-amino acids hold significant potential as precursors for synthesizing various fine chemicals, including peptide-based drugs and other pharmaceuticals. This study focuses on establishing an enzymatic cascade system capable of converting various L-amino acids into their D-isomers. The system integrates four enzymes: ancestral L-amino acid oxidase (AncLAAO-N4), D-amino acid dehydrogenase (DAADH), D-glucose dehydrogenase (GDH), and catalase. AncLAAO-N4 initiates the process by converting L-amino acids to corresponding keto acids, which are then stereo-selectively aminated to D-amino acids by DAADH using NADPH and NH4Cl. Concurrently, any generated H2O2 is decomposed into O2 and H2O by catalase, while GDH regenerates NADPH from D-glucose. Optimization of reaction conditions and substrate concentrations enabled the successful synthesis of five D-amino acids, including a D-Phe derivative, three D-Trp derivatives, and D-phenylglycine, all with high enantiopurity (>99 % ee) at a preparative scale (>100 mg). This system demonstrates a versatile approach for producing a diverse array of D-amino acids.

Tumor endothelial cell-derived Sfrp1 supports the maintenance of cancer stem cells via Wnt signaling

Cancer stem cells (CSCs), which are critical targets for cancer therapy as they are involved in drug resistance to anticancer drugs, and metastasis, are maintained by angiocrine factors produced by particular niches that form within tumor tissue. Secreted frizzled-related protein 1 (Sfrp1) is an extracellular protein that modulates Wnt signaling. However, the cells that produce Sfrp1 in the tumor environment and its function remain unclear. We aimed to elucidate angiocrine factors related to CSC maintenance, focusing on Sfrp1. Although Sfrp1 is a Wnt pathway-related factor, its impact on tumor tissues remains unknown. We investigated the localization of Sfrp1 in tumors and found that it is expressed in some tumor vessels. Analysis of mice lacking Sfrp1 showed that tumor growth was suppressed in Sfrp1-deficient tumor tissues. Flow cytometry analysis indicated that CSCs were maintained in the early tumor growth phase in the Sfrp1 knockout (KO) mouse model of tumor-bearing cancer. However, tumor growth was inhibited in the late tumor growth phase because of the inability to maintain CSCs. Real-time PCR results from tumors of Sfrp1 KO mice showed that the expression of Wnt signaling target genes significantly decreased in the late stage of tumor growth. This suggests that Sfrp1, an angiocrine factor produced by the tumor vascular niche, is involved in Wnt signaling-mediated mechanisms in tumor tissues.

Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations

Lipid nanoparticles (LNPs) are essential carrier particles in drug delivery systems, particularly in ribonucleic acid delivery. In preparing lipid-based nanoparticles, microfluidic-based ethanol injection may produce precisely size-controlled nanoparticles. Ethanol is critical in LNP formation and post-treatment processes and affects liposome size, structure, lamellarity, and drug-loading efficiency. However, the effects of time-dependent changes in the ethanol concentration on the structural dynamics of liposomes are not clearly understood. Herein, we investigated ethanol-induced lipid bilayer changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations. The time-resolved SAXS measurement system revealed that single unilamellar liposomes were converted to multilamellar liposomes within 0.8 s of contact with ethanol, and the d-spacing was decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We conducted 1 μs MD simulations to understand the molecular-level structural changes in the liposomes. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed via time-resolved SAXS. Therefore, the post-treatment process to remove residual ethanol is critical in liposome formation.

Surface Depassivation via B-O Dative Bonds Affects the Friction Performance of B-Doped Carbon Coatings

Boron doping of diamond-like carbon coatings has multiple effects on their tribological properties. While boron typically reduces wear in cutting applications, some B-doped coatings show poor tribological performance compared with undoped films. This is the case of the tribological tests presented in this work in which an alumina ball is placed in frictional contact with different undoped and B-doped amorphous carbon coatings in humid air. With B-doped coatings, a higher friction coefficient at a steady state with respect to their undoped counterparts was observed. Estimates of the average contact shear stress based on experimental friction coefficients, surface topographies, and Persson's contact theory suggest that the increased friction is compatible with the formation of a sparse network of interfacial ether bonds leading to a mild cold-welding friction regime, as documented in the literature. Tight binding and density functional theory simulations were performed to investigate the chemical effect of B-doping on the interfacial properties of the carbon coatings. The results reveal that OH groups that normally passivate carbon surfaces in humid environments can be activated by boron and form B-O dative bonds across the tribological interfaces, leading to a mild cold-welding friction regime. Simulations performed on different tribological pairs suggest that this mechanism could be valid for B-doped carbon surfaces in contact with a variety of materials. In general, this study highlights the impact that subtle modifications in surface and interface chemistry caused by the presence of impurities can have on macroscopic properties, such as friction and wear.

Depth sectioning using environmental and atomic-resolution STEM

(Scanning) transmission electron microscopy (TEM) images of samples in gas and liquid media are acquired with an environmental cell (EC) via silicon nitride membranes. The ratio of sample signal against the background is a significant factor for resolution. Depth-sectioning scanning TEM (STEM) is a promising technique that enhances the signal for a sample embedded in a matrix. It can increase the resolution to the atomic level, thereby enabling EC-STEM applications in important areas. This review introduces depth-sectioning STEM and its applications to high-resolution EC-STEM imaging of samples in gases and in liquids.

Reductive Retrocyclization of a Mangana(II)cyclopentasilane to Form Manganese(0) Bis(η2-disilene) Complexes

Ligand-exchange reactions on a mangana(II)cyclopentasilane complex that contains two THF ligands with aryl isocyanides led to the formation of manganese(0) bis(η2-disilene) complexes via a retrocyclization. In stark contrast, ligand-exchange reactions with CNtBu, an N-heterocyclic carbene, or pyridine-based ligands furnished manganese(II) complexes wherein the manganacyclopentasilane framework remained intact. The thermolysis of the obtained bis(η2-disilene) complex in the presence of mesityl isocyanide led to the formation of a cyclotetrasilane via the formal dimerization of the two η2-disilene moieties. The insertion of a mesityl isocyanide into the Mn-Siβ bond results in the formation of a manganese(II) complex supported by a [SiCSi]-type tridentate ligand scaffold.

Microfluidic Device for Simple Diagnosis of Plant Growth Condition by Detecting miRNAs from Filtered Plant Extracts

Plants are exposed to a variety of environmental stress, and starvation of inorganic phosphorus can be a major constraint in crop production. In plants, in response to phosphate deficiency in soil, miR399, a type of microRNA (miRNA), is up-regulated. By detecting miR399, the early diagnosis of phosphorus deficiency stress in plants can be accomplished. However, general miRNA detection methods require complicated experimental manipulations. Therefore, simple and rapid miRNA detection methods are required for early plant nutritional diagnosis. For the simple detection of miR399, microfluidic technology is suitable for point-of-care applications because of its ability to detect target molecules in small amounts in a short time and with simple manipulation. In this study, we developed a microfluidic device to detect miRNAs from filtered plant extracts for the easy diagnosis of plant growth conditions. To fabricate the microfluidic device, verification of the amine-terminated glass as the basis of the device and the DNA probe immobilization method on the glass was conducted. In this device, the target miRNAs were detected by fluorescence of sandwich hybridization in a microfluidic channel. For plant stress diagnostics using a microfluidic device, we developed a protocol for miRNA detection by validating the sample preparation buffer, filtering, and signal amplification. Using this system, endogenous sly-miR399 in tomatoes, which is expressed in response to phosphorus deficiency, was detected before the appearance of stress symptoms. This early diagnosis system of plant growth conditions has a potential to improve food production and sustainability through cultivation management.

Glu1022.53-Mediated Early Conformational Changes in the Process of Light-Induced Green Cone Pigment Activation

Ligand-triggered activation of G protein-coupled receptors (GPCRs) relies on the phenomenon of loose allosteric coupling, which involves conformational alterations spanning from the extracellular ligand-binding domain to the cytoplasmic region, where interactions with G proteins occur. During the GPCR activation process, several intermediate and equilibrium states orchestrate the movement of the flexible and rigid transmembrane (TM) segments of the GPCR. Monitoring early conformational changes is important in unraveling the structural intricacies of the loose allosteric coupling. Here, we focus on the lumi intermediate formed by thermal relaxation from the initial photointermediate, batho in primate green cone pigment (MG), a light-sensitive GPCR responsible for color vision. Our findings from light-induced Fourier transform infrared difference spectroscopy reveal its similarity with rhodopsin, which mediates twilight vision, specifically involving the flip motion of the β-ionone ring, the relaxation of the torsional structure of the retinal, and local perturbations in the α-helix upon lumi intermediate formation. Conversely, we observe a hydrogen bond modification specific to MG's protonated carboxylic acid, identifying its origin as Glu1022.53 situated in TM2. The weakening of the hydrogen bond strength at Glu1022.53 during the transition from the batho to the lumi intermediates corresponds to a slight outward movement of TM2. Additionally, within the X-ray crystal structure of the rhodopsin lumi intermediate, we note the relocation of the Met862.53 side chain in TM2, expanding the volume of the retinal binding pocket. Consequently, the position of 2.53 emerges as the early step in the conformational shift toward light-induced activation. Moreover, given the prevalence of IR-insensitive hydrophobic amino acids at position 2.53 in many rhodopsin-like GPCRs, including rhodopsin, the hydrogen bond alteration in the C═O stretching band at Glu1022.53 of MG can be used as a probe for tracing conformational changes during the GPCR activation process.

Site-Selective Photo-Crosslinking of Stilbene Pairs in a DNA Duplex Mediated by Ruthenium Photocatalyst

We herein report a method for site-selective photo-crosslinking of a DNA duplex. A stilbene pair was introduced into a DNA duplex and a ruthenium complex was conjugated with a triplex-forming oligonucleotide. We demonstrated that [2+2] photocycloaddition of the stilbene pair occurred upon irradiation with visible light when the ruthenium complex was in close proximity due to triplex formation. No reaction occurred when the ruthenium complex was not in proximity to the stilbene pair. The wavelength of visible light used was of lower energy than the wavelength of UV light necessary for direct excitation of stilbene. Quantum chemical calculation indicated that ruthenium complex catalyzed the photocycloaddition via triplet-triplet energy transfer. Site selectivity of this photo-crosslinking system was evaluated using a DNA duplex bearing two stilbene pairs as a substrate; we showed that the site of crosslinking was precisely regulated by the sequence of the oligonucleotide linked to the ruthenium complex. Since this method does not require orthogonal photoresponsive molecules, it will be useful in construction of complex photoresponsive DNA circuits, nanodevices and biological tools.

Control of Polar/Antipolar Layered Organic Semiconductors by the Odd-Even Effect of Alkyl Chain

Some rodlike organic molecules exhibit exceptionally high layered crystallinity when composed of a link between π-conjugated backbone (head) and alkyl chain (tail). These molecules are aligned side-by-side unidirectionally to form self-organized polar monomolecular layers, providing promising 2D materials and devices. However, their interlayer stacking arrangements have never been tunable, preventing the unidirectional arrangements of molecules in whole crystals. Here, it is demonstrated that polar/antipolar interlayer stacking can be systematically controlled by the alkyl carbon number n, when the molecules are designed to involve effectively weakened head-to-head affinity. They exhibit remarkable odd-even effect in the interlayer stacking: alternating head-to-head and tail-to-tail (antipolar) arrangement in odd-n crystals, and uniform head-to-tail (polar) arrangement in even-n crystals. The films show excellent field-effect transistor characteristics presenting unique polar/antipolar dependence and considerably improved subthreshold swing in the polar films. Additionally, the polar films present enhanced second-order nonlinear optical response along normal to the film plane. These findings are key for creating polarity-controlled optoelectronic materials and devices.

Partial mycoheterotrophy in the leafless orchid Eulophia zollingeri specialized on wood-decaying fungi

Although the absence of normal leaves is often considered a sign of full heterotrophy, some plants remain at least partially autotrophic despite their leafless habit. Leafless orchids with green stems and capsules probably represent a late evolutionary stage toward full mycoheterotrophy and serve as valuable models for understanding the pathways leading to this nutritional strategy. In this study, based on molecular barcoding and isotopic analysis, we explored the physiological ecology of the leafless orchid Eulophia zollingeri, which displays green coloration, particularly during its fruiting phase. Although previous studies had shown that E. zollingeri, in its adult stage, is associated with Psathyrellaceae fungi and exhibits high 13C isotope signatures similar to fully mycoheterotrophic orchids, it remained uncertain whether this symbiotic relationship is consistent throughout the orchid's entire life cycle and whether the orchid relies exclusively on mycoheterotrophy for its nutrition during the fruiting season. Our study has demonstrated that E. zollingeri maintains a specialized symbiotic relationship with Psathyrellaceae fungi throughout all life stages. However, isotopic analysis and chlorophyll data have shown that the orchid also engages in photosynthesis to meet its carbon needs, particularly during the fruiting stage. This research constitutes the first discovery of partial mycoheterotrophy in leafless orchids associated with saprotrophic non-rhizoctonia fungi.

Efficient Spin Interconversion by Molecular Conformation Dynamics of a Triplet Pair for Photon Up-Conversion in an Amorphous Solid

Solid-state materials with improved light-to-energy conversions in organic photovoltaics and in optoelectronics are expected to be developed by realizing efficient triplet-triplet annihilation (TTA) by manipulating the spin conversion processes to the singlet state. In this study, we elucidate the spin conversion mechanism for delayed fluorescence by TTA from a microscopic view of the molecular conformations. We examine the time evolution of the electron spin polarization of the triplet-pair state (TT state) in an amorphous solid-state system exhibiting highly efficient up-conversion emission by using time-resolved electron paramagnetic resonance. We clarified that the spin-state population of the singlet TT increased through the spin interconversion from triplet and quintet TT states during exciton diffusion with random orientation dynamics between the two triplets for the modulation of the exchange interaction, achieving a high quantum yield of up-conversion emission. This understanding provides us with a guide for the development of efficient light-to-energy conversion devices utilizing TTA.

Near-infrared imaging of phytochrome-derived autofluorescence in plant nuclei

Capturing images of the nuclear dynamics within live cells is an essential technique for comprehending the intricate biological processes inherent to plant cell nuclei. While various methods exist for imaging nuclei, including combining fluorescent proteins and dyes with microscopy, there is a dearth of commercially available dyes for live-cell imaging. In Arabidopsis thaliana, we discovered that nuclei emit autofluorescence in the near-infrared (NIR) range of the spectrum and devised a non-invasive technique for the visualization of live cell nuclei using this inherent NIR autofluorescence. Our studies demonstrated the capability of the NIR imaging technique to visualize the dynamic behavior of nuclei within primary roots, root hairs, and pollen tubes, which are tissues that harbor a limited number of other organelles displaying autofluorescence. We further demonstrated the applicability of NIR autofluorescence imaging in various other tissues by incorporating fluorescence lifetime imaging techniques. Nuclear autofluorescence was also detected across a wide range of plant species, enabling analyses without the need for transformation. The nuclear autofluorescence in the NIR wavelength range was not observed in animal or yeast cells. Genetic analysis revealed that this autofluorescence was caused by the phytochrome protein. Our studies demonstrated that nuclear autofluorescence imaging can be effectively employed not only in model plants but also for studying nuclei in non-model plant species.

Designer cell therapy for tissue regeneration

Cancer cell therapy, particularly chimeric antigen receptor (CAR) T-cell therapy for blood cancers, has emerged as a powerful new modality for cancer treatment. Therapeutic cells differ significantly from conventional drugs, such as small molecules and biologics, as they possess cellular information processing abilities to recognize and respond to abnormalities in the body. This capability enables the targeted delivery of therapeutic factors to specific locations and times. Various types of designer cells have been developed and tested to overcome the shortcomings of CAR T cells and expand their functions in the treatment of solid tumors. In particular, synthetic receptor technologies are a key to designing therapeutic cells that specifically improve tumor microenvironment. Such technologies demonstrate great potential for medical applications to regenerate damaged tissues as well that are difficult to cure with conventional drugs. In this review, we introduce recent developments in next-generation therapeutic cells for cancer treatment and discuss the application of designer therapeutic cells for tissue regeneration.

Active site tuning based on pseudo-binary alloys for low-temperature acetylene semihydrogenation

The development of an efficient catalytic system for low-temperature acetylene semihydrogenation using nonnoble metals is important for the cost-effective production of polymer-grade pure ethylene. However, it remains challenging owing to the intrinsic low activity. Herein, we report a flexibly tunable catalyst design concept based on a pseudo-binary alloy, which enabled a remarkable enhancement in the catalytic activity, selectivity, and durability of a Ni-based material. A series of (Ni1-xCux)3Ga/TiO2 catalysts exhibiting L12-type pseudo-binary alloy structures with various Cu contents (x = 0.2, 0.25, 0.33, 0.5, 0.6, and 0.75) were prepared for active site tuning. The optimal catalyst, (Ni0.8Cu0.2)3Ga/TiO2, exhibited outstandingly high catalytic activity among reported 3d transition metal-based systems and excellent ethylene selectivity (96%) and long-term stability (100 h) with near full conversion even at 150 °C. A mechanistic study revealed that Ni2Cu hollow sites on the (111) surface weakened the strong adsorption of acetylene and vinyl adsorbate, which significantly accelerated the hydrogenation process and inhibited undesired ethane formation.

2,2'-Tethered Binaphthyl-Embedded One-Handed Helical Ladder Polymers: Impact of the Tether Length on Helical Geometry and Chiroptical Property

Synthetic breakthroughs diversify the molecules and polymers available to chemists. We now report the first successful synthesis of a series of optically-pure 2,2'-tethered binaphthyl-embedded helical ladder polymers based on quantitative and chemoselective ladderization by the modified alkyne benzannulations using the 4-alkoxy-2,6-dimethylphenylethynyl group as the alkyne source, inaccessible by the conventional approach lacking the 2,6-dimethyl substituents. Due to the defect-free helix formation, the circular dichroism signal increased by more than 6 times the previously reported value. The resulting helical secondary structure can be fine-tuned by controlling the binaphthyl dihedral angle in the repeating unit with variations in the 2,2'-alkylenedioxy tethering groups by one carbon atom at a time. The optimization of the helical ladder structures led to a strong circularly polarized luminescence with a high fluorescence quantum yield (28 %) and luminescence dissymmetry factor (2.6×10-3 ).

Relictithismia kimotsukiensis, a new genus and species of Thismiaceae from southern Japan with discussions on its phylogenetic relationship

The family Thismiaceae, known as "fairy lanterns" for their urn- or bell-shaped flowers with basally fused tepals, consists of non-photosynthetic flowering monocots mainly in tropical regions, extending into subtropical and temperate areas. Here, we propose a new mycoheterotrophic genus, Relictithismia Suetsugu & Tagane (Thismiaceae), with its monotypic species Relictithismia kimotsukiensis Suetsugu, Yas.Nakam. & Tagane from Kimotsuki Mountains in the Osumi Peninsula, Kagoshima Prefecture, Kyushu Island, southern Japan. Relictithismia resembles Haplothismia Airy Shaw in having a cluster of tuberous roots, a feature previously observed only in this genus within the family Thismiaceae. However, it differs in having solitary flowers (vs. 2-6-flowered pseudo-raceme in Haplothismia), anther thecae largely separated (vs. connate), and the presence of an annulus (vs. absent). Additionally, Relictithismia differs from the geographically overlapping genus Thismia Griff. in its stamen structure and the position of the annulus. In Relictithismia, the stamens lack connectives, and its free filaments arise from the annulus located inside the perianth mouth, while in Thismia, the stamens typically have connate connectives, forming a staminal tube pendulous from the annulus located at the mouth of the floral tube. Our morphological and phylogenetic data indicated that R. kimotsukiensis holds an early-diverging position within the family, situated outside the Old World Thismia clade. This paper offers an extensive description and color photographs of R. kimotsukiensis, complemented by notes on its phylogenetic relationship and evolutionary history.

Pseudo-Luciferase Activity of the SARS-CoV-2 Spike Protein for Cypridina Luciferin

Enzymatic reactions that involve a luminescent substrate (luciferin) and enzyme (luciferase) from luminous organisms enable a luminescence detection of target proteins and cells with high specificity, albeit that conventional assay design requires a prelabeling of target molecules with luciferase. Here, we report a luciferase-independent luminescence assay in which the target protein directly catalyzes the oxidative luminescence reaction of luciferin. The SARS-CoV-2 antigen (spike) protein catalyzes the light emission of Cypridina luciferin, whereas no such catalytic function was observed for salivary proteins. This selective luminescence reaction is due to the enzymatic recognition of the 3-(1-guanidino)propyl group in luciferin at the interfaces between the units of the spike protein, allowing a specific detection of the spike protein in human saliva without sample pretreatment. This method offers a novel platform to detect virus antigens simply and rapidly without genetic manipulation or antibodies.

Understanding and manipulating extracellular behaviors of Wnt ligands

Wnt, a family of secreted signaling proteins, serves diverse functions in embryogenesis, organogenesis, cancer, and stem cell functions. In the context of development, Wnt has been considered a representative morphogen, forming concentration gradients to give positional information to cells or tissues. However, although gradients are often illustrated in schemata, the reality of concentration gradients, or in other words, actual spatial distribution of Wnt ligands, and their behaviors in the extracellular space still remain poorly known. To understand extracellular behavior of Wnt ligands, quantitative analyses such as fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) are highly informative because Wnt dispersal involves physical and biochemical processes, such as diffusion and binding to or dissociation from cell surface molecules, including heparan sulfate proteoglycans (HSPGs). Here, I briefly discuss representative methods to quantify morphogen dynamics. In addition, I discuss molecular manipulations of morphogens, mainly focusing on use of protein binders, and synthetic biology of morphogens as indicators of current and future directions in this field.

Structure-based engineering of Tor complexes reveals that two types of yeast TORC1 produce distinct phenotypes

Certain proteins assemble into diverse complex states, each having a distinct and unique function in the cell. Target of rapamycin (Tor) complex 1 (TORC1) plays a central role in signalling pathways that allow cells to respond to the environment, including nutritional status signalling. TORC1 is widely recognised for its association with various diseases. The budding yeast Saccharomyces cerevisiae has two types of TORC1, Tor1-containing TORC1 and Tor2-containing TORC1, which comprise different constituent proteins but are considered to have the same function. Here, we computationally modelled the relevant complex structures and then, based on the structures, rationally engineered a Tor2 mutant that could form Tor complex 2 (TORC2) but not TORC1, resulting in a redesign of the complex states. Functional analysis of the Tor2 mutant revealed that the two types of TORC1 induce different phenotypes, with changes observed in rapamycin, caffeine and pH dependencies of cell growth, as well as in replicative and chronological lifespan. These findings uncovered by a general approach with huge potential - model structure-based engineering - are expected to provide further insights into various fields such as molecular evolution and lifespan.

Superlubricity of Silicon-Based Ceramics Sliding against Hydrogenated Amorphous Carbon in Ultrahigh Vacuum: Mechanisms of Transfer Film Formation

Tribological interfaces between silicon-based ceramics, such as Si3N4 or SiC, are characterized by high friction and wear in unlubricated conditions. A solution to this problem is to use them in combination with a hydrogenated amorphous carbon (a-C:H) countersurface from which a passivating carbon film is transferred onto the ceramic surface. However, the mechanisms underlying a stable film transfer process and the conditions that favor it remain elusive. Here, we present friction experiments in ultrahigh vacuum in which friction coefficients lower than 0.01 are achieved by sliding Si3N4 against a-C:H with 36 at. % hydrogen but not against a-C:H with 20 at. % hydrogen. Chemical surface analyses confirm that the superlubric interface forms via the transfer of a hydrocarbon nanofilm onto the Si3N4 surface. Quantum-mechanical simulations reveal that a stable passivating a-C:H film can only be transferred if, after initial cold welding of the tribological interface, the plastic shear deformation is localized within the a-C:H coating. This occurs if the yield shear stress for plastic flow of a-C:H is lower than that of the ceramic and of the shear strength of the a-C:H-ceramic interface, i.e., if the a-C:H hydrogen content ranges between ∼30 and ∼50 at. %. While the importance of a relatively high hydrogen content to achieve an efficient passivation of a-C:H surfaces in a vacuum is well-documented, this work reveals how the hydrogen content is also crucial for obtaining a stable a-C:H transfer film. These results can be extended to glass, SiC, and steel, supporting the generality of the proposed mechanism.

Interfacial negative magnetization in Ni encapsulated layer-tunable nested MoS2 nanostructure with robust memory applications

Combining interfacial interactions and layer-number tunability, the evolution of magnetism in low-dimensional diamagnetic systems like MoS2 is indeed an interesting area of research. To explore this, Ni nanophases with an average size of 12 nm were encapsulated in MoS2 and the magnetization dynamics were studied over the temperature range of 2-300 K. Surprisingly, the newly formed hybrid nanostructure was found to have a negative magnetization state with giant exchange bias that showed a reversible temperature-induced increase in both spin magnetic moment and coercivity. Density functional theory calculations proved an interfacial charge transfer interaction with a spin-polarized density of states. The magnetization state, along with giant exchange correlation among the magnetic clusters, suggested the possibility of robust thermomagnetic memory. The dc magnetization and relaxation, investigated with different measurement protocols, unveiled robust thermoremanent magnetization as a memory effect. The time-dependent magnetization study indicated that contributions from the negative magnetization state along with charge transfer induced spin states are responsible for the memory effect, which can be controlled by both temperature and external field.

Nanoarchitectonics of highly dispersed polythiophene on paper for accurate quantitative detection of metal ions

π-Conjugated polymers such as polythiophene provide intramolecular wire effects upon analyte capture, which contribute to sensitive detection in chemical sensing. However, inherent aggregation-induced quenching causes difficulty in fluorescent chemical sensing in the solid state. Herein, we propose a solid-state fluorescent chemosensor array device made of a paper substrate (PCSAD) for the qualitative and quantitative detection of metal ions. A polythiophene derivative modified by dipicolylamine moieties (1poly), which shows optical changes upon the addition of target metal ions (i.e., Cu2+, Cd2+, Ni2+, Co2+, Pb2+, Zn2+, and Hg2+), was highly dispersed on the paper substrate using office apparatus. In this regard, morphological observation of the PCSAD after printing of 1poly suggested the contribution of the fiber structures of the paper substrate to the homogeneous dispersion of 1poly ink to suppress aggregation-induced quenching. The optical changes in the PCSAD upon the addition of metal ions was rapidly recorded using a smartphone, which was further applied to imaging analysis and pattern recognition techniques for high-throughput sensing. Indeed, the printed PCSAD embedded with 1poly achieved the accurate detection of metal ions at ppm levels contained in river water. The limit of detection of the PCSAD-based sensing system using a smartphone (48 ppb for Cu2+ ions) is comparable to that of a solution-based sensing system using a stationary spectrophotometer (16 ppb for Cu2+ ions). Therefore, the methodology based on a combination of a paper-based sensor array and a π-conjugated polymer will be a promising approach for solid-state fluorescent chemosensors.

Structural and electronic characterization of fluorine-doped La0.5Sr0.5CoO3-δ using electron energy-loss spectroscopy

Perovskite oxides, ABO3, are potential catalysts for the oxygen evolution reaction, which is important in the production of hydrogen as a sustainable energy resource. Optimizing the chemical composition of such oxides by substitution or doping with additional elements is an effective approach to improving the activity of such catalysts. Here, we characterized the crystal and electronic structures of fluorine-doped La0.5Sr0.5CoO3-δ particles using scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS). High-resolution STEM imaging demonstrated the formation of a disordered surface phase caused by fluorine doping. In addition, spatially resolved EELS data showed that fluorine anions were introduced into the interiors of the particles and that Co ions near the surfaces were slightly reduced by fluorine doping in conjunction with the loss of oxygen ions. Peak fitting of energy-loss near-edge structure data demonstrated an unexpected nanostructure in the vicinity of the surface. An EELS characterization comprising elemental mapping together with an energy-loss near-edge structure analysis indicated that this nanostructure could not be assigned to Co-based materials but rather to the solid electrolyte BaF2. Complementary structural and electronic characterizations using STEM and EELS as demonstrated herein evidently have the potential to play an increasingly important role in elucidating the nanostructures of functional materials.

Dysregulation of stress granule dynamics by DCTN1 deficiency exacerbates TDP-43 pathology in Drosophila models of ALS/FTD

The abnormal aggregation of TDP-43 into cytoplasmic inclusions in affected neurons is a major pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although TDP-43 is aberrantly accumulated in the neurons of most patients with sporadic ALS/FTD and other TDP-43 proteinopathies, how TDP-43 forms cytoplasmic aggregates remains unknown. In this study, we show that a deficiency in DCTN1, a subunit of the microtubule-associated motor protein complex dynactin, perturbs the dynamics of stress granules and drives the formation of TDP-43 cytoplasmic aggregation in cultured cells, leading to the exacerbation of TDP-43 pathology and neurodegeneration in vivo. We demonstrated using a Drosophila model of ALS/FTD that genetic knockdown of DCTN1 accelerates the formation of ubiquitin-positive cytoplasmic inclusions of TDP-43. Knockdown of components of other microtubule-associated motor protein complexes, including dynein and kinesin, also increased the formation of TDP-43 inclusions, indicating that intracellular transport along microtubules plays a key role in TDP-43 pathology. Notably, DCTN1 knockdown delayed the disassembly of stress granules in stressed cells, leading to an increase in the formation of pathological cytoplasmic inclusions of TDP-43. Our results indicate that a deficiency in DCTN1, as well as disruption of intracellular transport along microtubules, is a modifier that drives the formation of TDP-43 pathology through the dysregulation of stress granule dynamics.

Distinct manifold encoding of navigational information in the subiculum and hippocampus

The subiculum (SUB) plays a crucial role in spatial navigation and encodes navigational information differently from the hippocampal CA1 area. However, the representation of subicular population activity remains unknown. Here, we investigated the neuronal population activity recorded extracellularly from the CA1 and SUB of rats performing T-maze and open-field tasks. The trajectory of population activity in both areas was confined to low-dimensional neural manifolds homoeomorphic to external space. The manifolds conveyed position, speed, and future path information with higher decoding accuracy in the SUB than in the CA1. The manifolds exhibited common geometry across rats and regions for the CA1 and SUB and between tasks in the SUB. During post-task ripples in slow-wave sleep, population activity represented reward locations/events more frequently in the SUB than in CA1. Thus, the CA1 and SUB encode information distinctly into the neural manifolds that underlie navigational information processing during wakefulness and sleep.

The absence of bumblebees on an oceanic island blurs the species boundary of two closely related orchids

Oceanic islands offer valuable natural laboratories for studying evolution. The Izu Islands, with their recent geological origin, provide an exceptional opportunity to explore the initial evolution on oceanic islands. Another noteworthy aspect is the absence of bumblebee species on most Izu Islands. We used ecological, morphological, and molecular data to investigate the impact of bumblebee absence on the evolution of two closely related orchid species, Goodyera henryi and Goodyera similis, focusing on Kozu Island, the Izu Islands. Our investigation revealed that while G. henryi exclusively relies on a bumblebee species for pollination on the mainland, G. similis is pollinated by scoliid wasps on both the mainland and the island. Intriguingly, all specimens initially categorized as G. henryi on Kozu Island are hybrids of G. henryi and G. similis, leading to the absence of pure G. henryi distribution on the island. These hybrids are pollinated by the scoliid wasp species that also pollinates G. similis on the island. The absence of bumblebees might result in sporadic and inefficient pollination of G. henryi by scoliid wasps, consequently promoting hybrid proliferation on the island. Our findings suggest that the absence of bumblebees can blur plant species boundaries.

Epstein-Barr virus lytic gene BNRF1 promotes B-cell lymphomagenesis via IFI27 upregulation

Epstein-Barr virus (EBV) is a ubiquitous human lymphotropic herpesvirus that is causally associated with several malignancies. In addition to latent factors, lytic replication contributes to cancer development. In this study, we examined whether the lytic gene BNRF1, which is conserved among gamma-herpesviruses, has an important role in lymphomagenesis. We found that lymphoblastoid cell lines (LCLs) established by BNRF1-knockout EBV exhibited remarkably lower pathogenicity in a mice xenograft model than LCLs produced by wild-type EBV (LCLs-WT). RNA-seq analyses revealed that BNRF1 elicited the expression of interferon-inducible protein 27 (IFI27), which promotes cell proliferation. IFI27 knockdown in LCLs-WT resulted in excessive production of reactive oxygen species, leading to cell death and significantly decreased their pathogenicity in vivo. We also confirmed that IFI27 was upregulated during primary infection in B-cells. Our findings revealed that BNRF1 promoted robust proliferation of the B-cells that were transformed by EBV latent infection via IFI27 upregulation both in vitro and in vivo.

Development of Polymer-Lipid Hybrid Nanoparticles for Large-Sized Plasmid DNA Transfection

RNA and DNA delivery technologies using lipid nanoparticles (LNPs) have advanced significantly, as demonstrated by their successful application in mRNA vaccines. To date, commercially available RNA therapeutics include Onpattro, a 21 bp siRNA, and mRNA vaccines comprising 4300 nucleotides for COVID-19. However, a significant challenge remains in achieving efficient transfection, as the size of the delivered RNA and DNA increases. In contrast to RNA transfection, plasmid DNA (pDNA) transfection requires multiple steps, including cellular uptake, endosomal escape, nuclear translocation, transcription, and translation. The low transfection efficiency of large pDNA is a critical limitation in the development of artificial cells and their cellular functionalization. Here, we introduce polymer-lipid hybrid nanoparticles designed for efficient, large-sized pDNA transfection. We demonstrated that LNPs loaded with positively charged pDNA-polycation core nanoparticles exhibited a 4-fold increase in transfection efficiency for 15 kbp pDNA compared with conventional LNPs, which encapsulate a negatively charged pDNA-polycation core. Based on assessments of the size and internal structure of the polymer-lipid nanoparticles as well as hemolysis and cellular uptake analysis, we propose a strategy to enhance large-sized pDNA transfection using LNPs. This approach holds promise for accelerating the in vivo delivery of large-sized pDNA and advancing the development of artificial cells.

Accumulation of Immunity in Heavy-Tailed Sexual Contact Networks Shapes Mpox Outbreak Sizes

Many countries affected by the global outbreak of mpox in 2022 have observed a decline in cases. Our mathematical model accounting for heavy-tailed sexual partnership distributions suggests that mpox epidemics can hit the infection-derived herd immunity threshold and begin to decline, with <1% of sexually active men who have sex with men infected regardless of interventions or behavioral changes. We consistently found that many countries and US states experienced an epidemic peak, with cumulative cases of around 0.1% to 0.5% among men who have sex with men. The observed decline in cases may not necessarily be attributable to interventions or behavioral changes primarily.

Multiscale Modeling of Aqueous Electric Double Layers

From the stability of colloidal suspensions to the charging of electrodes, electric double layers play a pivotal role in aqueous systems. The interactions between interfaces, water molecules, ions and other solutes making up the electrical double layer span length scales from Ångströms to micrometers and are notoriously complex. Therefore, explaining experimental observations in terms of the double layer's molecular structure has been a long-standing challenge in physical chemistry, yet recent advances in simulations techniques and computational power have led to tremendous progress. In particular, the past decades have seen the development of a multiscale theoretical framework based on the combination of quantum density functional theory, force-field based simulations and continuum theory. In this Review, we discuss these theoretical developments and make quantitative comparisons to experimental results from, among other techniques, sum-frequency generation, atomic-force microscopy, and electrokinetics. Starting from the vapor/water interface, we treat a range of qualitatively different types of surfaces, varying from soft to solid, from hydrophilic to hydrophobic, and from charged to uncharged.

Effect of the bulkiness of alkyl ligands on the excited-state dynamics of ZnO nanocrystals

Organic ligands on the surface of nanocrystals (NCs) are extremely important in influencing various physical properties, such as dispersibility, electrical properties, and optical properties. Recent studies have revealed that a slight difference in the molecular structure of aliphatic organic ligands significantly affects the dispersibility of the NCs. On the other hand, the effects of the difference in the molecular structure of ligands on the excited-state dynamics of NCs remain elusive. In this study, we synthesized a series of colloidal ZnO NCs capped with different alkyl phosphonic acids and investigated their photophysical properties using emission decay measurements and transient absorption spectroscopy. The spectral shape and lifetime of the emission originating from the surface oxygen defects of ZnO NCs are almost the same irrespective of the alkyl phosphonic ligands used, indicating that the electronic states of the surface oxygen defects are not affected by the bulkiness of the ligand. On the other hand, the emission quantum yield correlates with the rate of carrier trapping by oxygen defects, suggesting that the rate of carrier trapping reflects the number of oxygen defects. Revealing the detailed relationship between molecular structures of organic ligands and the optical properties of NCs is important for advanced photofunctional superstructures using semiconductor NCs.

A Versatile Comonomer Additive for Radically Recyclable Vinyl-derived Polymers

Radically-formed, vinyl-derived polymers account for over 30 % of polymer production. Connected through stable carbon-carbon bonds, these materials are notoriously challenging to chemically recycle. Herein, we report universal copolymerization of a cyclic allyl sulfide (CAS) additive with multiple monomers under free-radical conditions, to introduce main-chain dynamic motifs. Backbone allyl sulfides undergo post-polymerization radical rearrangement via addition-fragmentation-transfer (AFT) that fosters both chain scission and extension. Scission is selectively induced through allyl sulfide exchange with small molecule thiyl radicals, resulting in oligomers as low as 14 % of the initial molar mass. Crucially, oligomers retain allyl sulfide end groups, enabling their extension with monomer under radical conditions. Extended, i.e., recycled, product molar mass is tunable through the ratio of monomer to oligomer, and can surpass that of the initial copolymer. Two scission-extension cycles are demonstrated in copolymers with methyl methacrylate and styrene without escalation in dispersity. In illustration of forming higher-value products, i.e., upcycling, we synthesized block copolymers through the extension of oligomers with a different vinyl monomer. Collectively, our approach to chemical recycling is unparalleled in its ability to 1) function in a variety of vinyl-derived polymers, 2) complete radical closed-loop cycling, and 3) upcycle waste material.

Domino-Redox Reaction Induced by An Electrochemically Triggered Conformational Change

The concept of a domino-type reaction has been applied in a wide range of fields such as synthetic organic chemistry, material engineering, and life science. To extend the domino concept to redox chemistry, we designed and synthesized a dimeric quinodimethane (QD) with a nonplanar dithiin spacer. The domino-redox properties can be activated by raising the temperature, based on a thermally equilibrated twisted conformation of QD, which has a higher HOMO level that is more readily oxidized. After one QD unit is oxidized (trigger), steric repulsion and electronic interaction between electrophores make the neighboring QD unit adopt a twisted conformation (domino process), which facilitates the following oxidation. Thus, a domino-redox reaction was achieved for the first time by a change in the HOMO level due to a drastic change in the molecular conformation.

The left-right reversed visual feedback of the hand affects multisensory interaction within peripersonal space

The interaction between vision and touch, known as the crossmodal congruency effect, has been extensively investigated in several research studies. Recent studies have revealed that the crossmodal congruency effect involves body representations. However, it is unclear how bodily information (e.g., location, posture, motion) is linked to visual and tactile inputs. Three experiments were conducted to investigate this issue. In Experiment 1, participants performed a crossmodal congruency task in which both their hand appearance and the motor trajectories were left-right reversed. The results showed that the crossmodal congruency effect was not observed in the reversal condition, whereas participants showed significant crossmodal congruency in the control condition, in which there was no visual manipulation of the hand. In Experiments 2 and 3, where either the hand appearance or motor trajectory was left-right reversed individually, a significant crossmodal congruency effect was observed. This study demonstrated that visual manipulation of hand appearance and motor trajectories both affected the crossmodal congruency effect, although neither showed a dominant effect that solely altered the crossmodal congruency effect. The present results provide insights into the relationship between visual-tactile interactions and bodily information.

Biosensing with Surface-Charge-Modulated Graphene Field-Effect Transistors beyond Nonlinear Electrolytic Screening

In field-effect transistor (FET) biosensors, charge screening in electrolyte solutions limits the sensitivity, thereby restricting the applicability of FET sensors. This is particularly pronounced in graphene FET (GFET) biosensors, where the bare graphene surface possesses a strongly negative charge, which impedes the high sensitivity of GFETs owing to nonlinear electrolytic screening at the interfaces between graphene and liquid. In this study, we counteracted the negative surface charge of graphene by decorating positively charged compounds and demonstrated the sensing of C-reactive protein (CRP) with surface-charge-modulated GFETs (SCM-GFETs). We integrated multiple SCM-GFETs with anti-CRP antibodies and nonfunctionalized GFETs into a chip and measured differentials to eliminate background changes to improve measurement reliability. The FET response corresponded to the fluorescence images, which visualized the specific adsorption of CRP. The estimated dissociation constant was consistent with previously reported values; this supports the conclusion that the results are attributed to specific adsorption. Conversely, the signal in GFETs without decoration was obscured by noise because of nonlinear electrolytic screening, further emphasizing the significance of surface-charge modulation. The limit of detection of the system was determined to be 2.9 nM. This value has the potential to be improved through further optimization of the surface charges to align with specific applications. Our devices effectively circumvent nonlinear electrolytic screening, opening the door for further advancements in GFET biosensor technology.

AtMYB50 regulates root cell elongation by upregulating PECTIN METHYLESTERASE INHIBITOR 8 in Arabidopsis thaliana

Plant root development involves multiple signal transduction pathways. Notably, phytohormones like auxin and cytokinin are well characterized for their molecular mechanisms of action. Reactive oxygen species (ROS) serve as crucial signaling molecules in controlling root development. The transcription factor, UPBEAT1 (UPB1) is responsible for maintaining ROS homeostasis at the root tip, influencing the transition from cell proliferation to differentiation. While UPB1 directly regulates peroxidase expression to control ROS homeostasis, it targets genes other than peroxidases, suggesting its involvement in root growth through non-ROS signals. Our investigation focused on the transcription factor MYB50, a direct target of UPB1, in Arabidopsis thaliana. By analyzing multiple fluorescent proteins and conducting RNA-seq and ChIP-seq, we unraveled a step in the MYB50 regulatory gene network. This analysis, in conjunction with the UPB1 regulatory network, demonstrated that MYB50 directly regulates the expression of PECTIN METHYLESTERASE INHIBITOR 8 (PMEI8). Overexpressing PMEI8, similar to the MYB50, resulted in reduced mature cell length. These findings establish MYB50 as a regulator of root growth within the UPB1 gene regulatory network. Our study presents a model involving transcriptional regulation by MYB50 in the UPB1 regulated root growth system and sheds light on cell elongation via pectin modification.

Functional characterization of four opsins and two G alpha subtypes co-expressed in the molluscan rhabdomeric photoreceptor

BACKGROUND

Rhabdomeric photoreceptors of eyes in the terrestrial slug Limax are the typical invertebrate-type but unique in that three visual opsins (Gq-coupled rhodopsin, xenopsin, Opn5A) and one retinochrome, all belonging to different groups, are co-expressed. However, molecular properties including spectral sensitivity and G protein selectivity of any of them are not determined, which prevents us from understanding an advantage of multiplicity of opsin properties in a single rhabdomeric photoreceptor. To gain insight into the functional role of the co-expression of multiple opsin species in a photoreceptor, we investigated the molecular properties of the visual opsins in the present study.

RESULTS

First, we found that the fourth member of visual opsins, Opn5B, is also co-expressed in the rhabdomere of the photoreceptor together with previously identified three opsins. The photoreceptors were also demonstrated to express Gq and Go alpha subunits. We then determined the spectral sensitivity of the four visual opsins using biochemical and spectroscopic methods. Gq-coupled rhodopsin and xenopsin exhibit maximum sensitivity at ~ 456 and 475 nm, respectively, and Opn5A and Opn5B exhibit maximum sensitivity at ~ 500 and 470 nm, respectively, with significant UV sensitivity. Notably, in vitro experiments revealed that Go alpha was activated by all four visual opsins, in contrast to the specific activation of Gq alpha by Gq-coupled rhodopsin, suggesting that the eye photoreceptor of Limax uses complex G protein signaling pathways.

CONCLUSIONS

The eye photoreceptor in Limax expresses as many as four different visual opsin species belonging to three distinct classes. The combination of opsins with different spectral sensitivities and G protein selectivities may underlie physiological properties of the ocular photoreception, such as a shift in spectral sensitivity between dark- and light-adapted states. This may be allowed by adjustment of the relative contribution of the four opsins without neural networks, enabling a simple strategy for fine-tuning of vision.

Characteristics of patients with COVID-19 who have deteriorating chest X-ray findings within 48 h: a retrospective cohort study

The severity of chest X-ray (CXR) findings is a prognostic factor in patients with coronavirus disease 2019 (COVID-19). We investigated the clinical and genetic characteristics and prognosis of patients with worsening CXR findings during early hospitalization. We retrospectively included 1656 consecutive Japanese patients with COVID-19 recruited through the Japan COVID-19 Task Force. Rapid deterioration of CXR findings was defined as increased pulmonary infiltrates in ≥ 50% of the lung fields within 48 h of admission. Rapid deterioration of CXR findings was an independent risk factor for death, most severe illness, tracheal intubation, and intensive care unit admission. The presence of consolidation on CXR, comorbid cardiovascular and chronic obstructive pulmonary diseases, high body temperature, and increased serum aspartate aminotransferase, potassium, and C-reactive protein levels were independent risk factors for rapid deterioration of CXR findings. Risk variant at the ABO locus (rs529565-C) was associated with rapid deterioration of CXR findings in all patients. This study revealed the clinical features, genetic features, and risk factors associated with rapid deterioration of CXR findings, a poor prognostic factor in patients with COVID-19.

Visible Light Responsive Dinuclear Zinc Complex Consisting of Proximally Arranged Two d10 -Zinc Centers

So far, Zn(II)-based d10 complexes have been known to be colorless unless they are accompanied by chromophoric groups, and therefore both fundamental and advanced photophysical performance of Zn centers of complexes, especially in visible-light regions has been unexplored. Here, we first demonstrate a dinuclear Zn(II) complex that shows visible light absorption using an orbital distributed over closely contacted two Zn centers experimentally determined by X-ray crystallography. A contrastive study demonstrated that intermetallic orbital interaction in dinuclear Zn(II) complex is responsible for capturing visible light to exhibit orangish yellow color, whereas an analogous one without such an interaction is colorless. This work demonstrates that introduction of Zn-Zn interactions to Zn(II) molecules contradicts the common notion that Zn is unresponsive to visible light and expands the photophysical field of zinc chemistry.

In-Depth Quantification of Cell Division and Elongation Dynamics at the Tip of Growing Arabidopsis Roots Using 4D Microscopy, AI-Assisted Image Processing and Data Sonification

One of the fundamental questions in plant developmental biology is how cell proliferation and cell expansion coordinately determine organ growth and morphology. An amenable system to address this question is the Arabidopsis root tip, where cell proliferation and elongation occur in spatially separated domains, and cell morphologies can easily be observed using a confocal microscope. While past studies revealed numerous elements of root growth regulation including gene regulatory networks, hormone transport and signaling, cell mechanics and environmental perception, how cells divide and elongate under possible constraints from cell lineages and neighboring cell files has not been analyzed quantitatively. This is mainly due to the technical difficulties in capturing cell division and elongation dynamics at the tip of growing roots, as well as an extremely labor-intensive task of tracing the lineages of frequently dividing cells. Here, we developed a motion-tracking confocal microscope and an Artificial Intelligence (AI)-assisted image-processing pipeline that enables semi-automated quantification of cell division and elongation dynamics at the tip of vertically growing Arabidopsis roots. We also implemented a data sonification tool that facilitates human recognition of cell division synchrony. Using these tools, we revealed previously unnoted lineage-constrained dynamics of cell division and elongation, and their contribution to the root zonation boundaries.

Transcriptomic Interpretation on Explainable AI-Guided Intuition Uncovers Premonitory Reactions of Disordering Fate in Persimmon Fruit

Deep neural network (DNN) techniques, as an advanced machine learning framework, have allowed various image diagnoses in plants, which often achieve better prediction performance than human experts in each specific field. Notwithstanding, in plant biology, the application of DNNs is still mostly limited to rapid and effective phenotyping. The recent development of explainable CNN frameworks has allowed visualization of the features in the prediction by a convolutional neural network (CNN), which potentially contributes to the understanding of physiological mechanisms in objective phenotypes. In this study, we propose an integration of explainable CNN and transcriptomic approach to make a physiological interpretation of a fruit internal disorder in persimmon, rapid over-softening. We constructed CNN models to accurately predict the fate to be rapid softening in persimmon cv. Soshu, only with photo images. The explainable CNNs, such as Gradient-weighted Class Activation Mapping (Grad-Class Activation Mapping (CAM)) and guided Grad-CAM, visualized specific featured regions relevant to the prediction of rapid softening, which would correspond to the premonitory symptoms in a fruit. Transcriptomic analyses to compare the featured regions of the predicted rapid-softening and control fruits suggested that rapid softening is triggered by precocious ethylene signal-dependent cell wall modification, despite exhibiting no direct phenotypic changes. Further transcriptomic comparison between the featured and non-featured regions in the predicted rapid-softening fruit suggested that premonitory symptoms reflected hypoxia and the related stress signals finally to induce ethylene signals. These results would provide a good example for the collaboration of image analysis and omics approaches in plant physiology, which uncovered a novel aspect of fruit premonitory reactions in the rapid-softening fate.

Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico

With advances in high-throughput, large-scale in vivo measurement and genome modification techniques at the single-nucleotide level, there is an increasing demand for the development of new technologies for the flexible design and control of cellular systems. Computer-aided design is a powerful tool to design new cells. Whole-cell modeling aims to integrate various cellular subsystems, determine their interactions and cooperative mechanisms, and predict comprehensive cellular behaviors by computational simulations on a genome-wide scale. It has been applied to prokaryotes, yeasts, and higher eukaryotic cells, and utilized in a wide range of applications, including production of valuable substances, drug discovery, and controlled differentiation. Whole-cell modeling, consisting of several thousand elements with diverse scales and properties, requires innovative model construction, simulation, and analysis techniques. Furthermore, whole-cell modeling has been extended to multiple scales, including high-resolution modeling at the single-nucleotide and single-amino acid levels and multicellular modeling of tissues and organs. This review presents an overview of the current state of whole-cell modeling, discusses the novel computational and experimental technologies driving it, and introduces further developments toward multihierarchical modeling on a whole-genome scale.

Projective Measurement-Based Quantum Phase Difference Estimation Algorithm for the Direct Computation of Eigenenergy Differences on a Quantum Computer

Quantum computers are capable of calculating the energy difference of two electronic states using the quantum phase difference estimation (QPDE) algorithm. The Bayesian inference-based implementations for the QPDE have been reported so far, but in this approach, the quality of the calculated energy difference depends on the input wave functions being used. Here, we report the inverse quantum Fourier transformation-based QPDE with Na of ancillary qubits, which allows us to compute the difference of eigenenergies based on the single-shot projective measurement. As proof-of-concept demonstrations, we report numerical experiments for the singlet-triplet energy difference of the hydrogen molecule and the vertical excitation energies of halogen-substituted methylenes (CHF, CHCl, CF2, CFCl, and CCl2) and formaldehyde (HCHO).

Complexation study of a 1,3-phenylene-bridged cyclic hexa-naphthalene with fullerenes C60 and C70 in solution and 1D-alignment of fullerenes in the crystals

To investigate the host ability of a simple macrocycle, 1,3-phenylene-bridged naphthalene hexamer N6, we evaluated the complexation of N6 with fullerenes in toluene and in the crystals. The complexes in the solid-state demonstrate the one-dimensional alignment of fullerenes. The single-crystals of the C60@N6 composite have semiconductive properties revealed by photoconductivity measurements.

Lumicrine signaling: Extracellular regulation of sperm maturation in the male reproductive tract lumen

The behaviors of cells, tissues, and organs are controlled by the extracellular environment in addition to their autonomous regulatory system. Dysfunction of extracellular regulatory mechanisms affects not only the development and survival of organisms but also successful reproduction. In this review article, a novel extracellular regulatory mechanism regulating the mammalian male reproductive ability will be briefly summarized. In terrestrial vertebrates, spermatozoa generated in the testis are transported through the lumen of the male reproductive tract and become functionally mature during the transport. Recent studies with gene-modified animals are unveiling the luminal extracellular environment of the reproductive tract to function not only as the pathway of sperm transport and the site of sperm maturation but also as the channel for cellular communication to regulate sperm maturation. Of special interest is the molecular mechanism of lumicrine signaling, a transluminal secreted signal transduction in the male reproductive tract lumen as a master regulator of sperm maturation and male reproductive ability. The general significance of such transluminal signaling in the context of cell biology will also be discussed.

Association between ABO blood group/genotype and COVID-19 in a Japanese population

An association between coronavirus disease 2019 (COVID-19) and the ABO blood group has been reported. However, such an association has not been studied in the Japanese population on a large scale. Little is known about the association between COVID-19 and ABO genotype. This study investigated the association between COVID-19 and ABO blood group/genotype in a large Japanese population. All Japanese patients diagnosed with COVID-19 were recruited through the Japan COVID-19 Task Force between February 2020 and October 2021. We conducted a retrospective cohort study involving 1790 Japanese COVID-19 patients whose DNA was used for a genome-wide association study. We compared the ABO blood group/genotype in a healthy population (n = 611, control) and COVID-19 patients and then analyzed their associations and clinical outcomes. Blood group A was significantly more prevalent (41.6% vs. 36.8%; P = 0.038), and group O was significantly less prevalent (26.2% vs. 30.8%; P = 0.028) in the COVID-19 group than in the control group. Moreover, genotype OO was significantly less common in the COVID-19 group. Furthermore, blood group AB was identified as an independent risk factor for most severe diseases compared with blood group O [aOR (95% CI) = 1.84 (1.00-3.37)]. In ABO genotype analysis, only genotype AB was an independent risk factor for most severe diseases compared with genotype OO. Blood group O is protective, whereas group A is associated with the risk of infection. Moreover, blood group AB is associated with the risk of the "most" severe disease.