Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes.

An important component of cellular biochemistry is the concentration of proteins and nucleic acids in non-membranous compartments1,2. These biomolecular condensates are formed from processes that include liquid-liquid phase separation. The multivalent interactions necessary for liquid-liquid phase separation have been extensively studied in vitro1,3. However, the regulation of this process in vivo is poorly understood. Here we identify an in vivo regulator of liquid-liquid phase separation through a genetic screen targeting factors required for Arabidopsis RNA-binding protein FCA function. FCA contains prion-like domains that phase-separate in vitro, and exhibits behaviour in vivo that is consistent with phase separation. The mutant screen identified a functional requirement for FLL2, a coiled-coil protein, in the formation of FCA nuclear bodies. FCA reduces transcriptional read-through by promoting proximal polyadenylation at many sites in the Arabidopsis genome3,4. FLL2 was required to promote this proximal polyadenylation, but not the binding of FCA to target RNA. Ectopic expression of FLL2 increased the size and number of FCA nuclear bodies. Crosslinking with formaldehyde captured in vivo interactions between FLL2, FCA and the polymerase and nuclease modules of the RNA 3'-end processing machinery. These 3' RNA-processing components colocalized with FCA in the nuclear bodies in vivo, which indicates that FCA nuclear bodies compartmentalize 3'-end processing factors to enhance polyadenylation at specific sites. Our findings show that coiled-coil proteins can promote liquid-liquid phase separation, which expands our understanding of the principles that govern the in vivo dynamics of liquid-like bodies.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape.

Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O. rufipogon. The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which together led to the loss of shattering.

Synthesis of a Gold-Silver Alloy Nanocluster within a Ring-Shaped Polyoxometalate and Its Photocatalytic Property.

Alloying is an effective method for modulating metal nanoclusters to enrich their structural diversity and physicochemical properties. Recent investigations have demonstrated that polyoxometalates (POMs) can act as effective multidentate ligands for silver (Ag) nanoclusters to endow them with synergistic properties, reactivity, catalytic properties, and stability. However, the application of POMs as ligands has been confined predominantly to monometallic nanoclusters. Herein, we report a synthetic method for fabricating surface-exposed gold (Au)-Ag alloy nanoclusters within a ring-shaped POM ([P8W48O184]40-). Reacting an Ag nanocluster stabilized by the ring-shaped POM with Au ions (Au+) was found to substitute several Ag atoms at the core of the nanocluster with Au atoms. The resultant {Au8Ag26} alloy nanocluster demonstrated superior photocatalytic activity and stability compared to the pristine Ag nanocluster in the aerobic oxidation of α-terpinene under visible-light irradiation. These findings provide fundamental insights into the formation and catalytic properties of POM-stabilized alloy nanoclusters and advance exploration into the synthesis and applications of diverse metal nanoclusters.

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36.

Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2 population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.

Wild and cultivated allele effects on rice phenotypic traits in reciprocal backcross populations between Oryza rufipogon and two cultivars, O. sativa Nipponbare and IR36.

A total of four populations of reciprocal backcross recombinant inbred lines were produced from a cross between a wild accession of Oryza rufipogon W630 and two major cultivars, O. sativa Japonica Nipponbare and Indica IR36. Using these populations, quantitative trait locus (QTL) analysis for eight morphological traits (culm length, panicle length, days to heading, panicle shape, pericarp color, hull color, seed shattering and seed awning) was carried out, and the putative QTL regions were compared among the populations. The QTLs with strong allele effects were commonly detected for culm length, panicle shape, pericarp color and hull color in all four populations, and their peak locations were close to the major genes of sd1, Spr3, Rc and Bh4, respectively. For panicle length and days to heading, some QTL regions overlapped between two or three populations. In the case of seed shattering and seed awning, strong wild allele effects at major loci were observed only in the populations with cultivated backgrounds. Since the wild and cultivated alleles have never been evaluated in the reciprocal genetic backgrounds, the present results provide new information on gene effects in breeding and domestication studies.

Direct Observation of Atomistic Reaction Process between Pt Nanoparticles and TiO2 (110).

The catalytic activity and selectivity of heterogeneous catalysts are governed by atomic and electronic structures at the heterointerface between noble metal nanoparticles (NPs) and oxide substrates. In specific chemical reactions, it is well-known that the catalytic activity is strongly suppressed by annealing in a reducing atmosphere, so-called strong metal-support interaction (SMSI). However, it is still unclear the formation process and atomistic origin of the SMSI. By preparing well-defined platinum (Pt) NPs supported on atomically flat TiO2 (110) substrate, we directly show the formation of chemically ordered Pt-Ti intermetallic NPs and impregnation of NPs into TiO2 substrate at high temperatures by using atomic-resolution scanning transmission electron microscopy combined with electron energy-loss spectroscopy. Furthermore, we observed negative charge transfer from the Pt-Ti intermetallic NPs to the TiO2 surface, which would strongly affect the catalytic activities.

Direct imaging of atomistic grain boundary migration.

Grain boundary (GB) migration plays an important role in modifying the microstructures and the related properties of polycrystalline materials, and is governed by the atomistic mechanism by which the atoms are displaced from one grain to another. Although such an atomistic mechanism has been intensively investigated, it is still experimentally unclear as to how the GB migration proceeds at the atomic scale. With the aid of high-energy electron-beam irradiation in atomic-resolution scanning transmission electron microscopy, we controllably triggered the GB migration in α-Al2O3 and directly visualized the atomistic GB migration as a stop motion movie. It was revealed that the GB migration proceeds by the cooperative shuffling of atoms on GB ledges along specific routes, passing through several different stable and metastable GB structures with low energies. We demonstrated that GB migration could be facilitated by the GB structural transformations between these low-energy structures.

Atomistic Origin of Li-Ion Conductivity Reduction at (Li3xLa2/3-x)TiO3 Grain Boundary.

Lithium lanthanum titanate (LLTO) is one of the excellent candidates for an electrolyte in the all-solid-state Li-ion battery, owing to the high Li-ion conductivity in the bulk. However, the Li-ion conductivity at the grain boundary (GB) is largely reduced, and it is therefore important to reveal the origin of Li-ion conductivity reduction at the GB. Here, by using atomic-resolution scanning transmission electron microscopy combined with atomic force microscopy, we investigate the charge states, Li-ion conductivities, atomic and electronic structures at the LLTO Σ5 and Σ13 GBs. Although the Σ5 GB has no significant influence on Li-ion conductivity, the Σ13 GB shows the evident reduction of Li-ion conductivity. We further elucidate that the Σ13 GB is positively charged by the formation of oxygen vacancies at the GB. Such a positive charge would form the Li-ion depletion layers adjacent to the GB, which causes the significant reduction of Li-ion conductivity.

Anataselike Grain Boundary Structure in Rutile Titanium Dioxide.

The formation of nanoscale phases at grain boundaries in polycrystalline materials has attracted much attention, since it offers a route toward targeted and controlled design of interface properties. However, understanding structure-property relationships at these complex interfacial defects is hampered by the great challenge of accurately determining their atomic structure. Here, we combine advanced electron microscopy together with ab initio random structure searching to determine the atomic structure of an experimentally fabricated Σ13 (221) [11̅0] grain boundary in rutile TiO2. Through careful analysis of the atomic structure and complementary electron energy-loss spectroscopy analysis we identify the existence of a unique nanoscale phase at the grain boundary with striking similarities to the bulk anatase crystal structure. Our results show a path to embed nanoscale anatase into rutile TiO2 and showcase how the atomic structure of even complex internal interfaces can be accurately determined using a combined theoretical and experimental approach.

[Case of Solitary Liver Metastasis of Breast Cancer Showing Minimal Differentiation from Intrahepatic Cholangiocarcinoma].

A 75-year-old woman presented to our department with a liver tumor. She had undergone left total mastectomy and axillary lymph node dissection for left breast cancer at the age of 67 years. Subsequently, she had taken an aromatase inhibitor. A follow-up abdominal echo revealed a 50 mm tumor in the liver. Based on examinations, she was diagnosed with an intrahepatic cholangiocarcinoma. She underwent laparoscopic lateral segment hepatectomy. Pathological diagnosis showed liver metastasis of the breast cancer. After surgery, she received hormonal therapy. After 5 months, multiple brain metastases appeared. She died 15 months after the liver operation.

Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume).

Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.

Two-Dimensional Room-Temperature Giant Antiferrodistortive SrTiO_{3} at a Grain Boundary.

The broken symmetry at structural defects such as grain boundaries (GBs) discontinues chemical bonds, leading to the emergence of new properties that are absent in the bulk owing to the couplings between the lattice and other parameters. Here, we create a two-dimensional antiferrodistortive (AFD) strontium titanate (SrTiO_{3}) phase at a Σ13(510)/[001] SrTiO_{3} tilt GB at room temperature. We find that such an anomalous room-temperature AFD phase with the thickness of approximate six unit cells is stabilized by the charge doping from oxygen vacancies. The localized AFD originated from the strong lattice-charge couplings at a SrTiO_{3} GB is expected to play important roles in the electrical and optical activity of GBs and can explain past experiments such as the transport properties of electroceramic SrTiO_{3}. Our study also provides new strategies to create low-dimensional anomalous elements for future nanoelectronics via grain boundary engineering.

Role of qGZn9a in controlling grain zinc concentration in rice, Oryza sativa L.

KEY MESSAGE: A candidate gene responsible for higher grain zinc accumulation in rice was identified, which was probably associated with a partial defect in anther dehiscence. Zinc (Zn) is an essential mineral element in many organisms. Zn deficiency in humans causes various health problems; therefore, an adequate dietary Zn intake is required daily. Rice, Oryza sativa, is one of the main crops cultivated in Asian countries, and one of the breeding scopes of rice is to increase the grain Zn levels. Previously, we found that an Australian wild rice strain, O. meridionalis W1627, exhibits higher grain Zn levels than cultivated rice, O. sativa Nipponbare, and identified responsible genomic loci. An increase in grain Zn levels caused by one of the loci, qGZn9a, is associated with fertility reduction, but how this negative effect on grain productivity is regulated remains unknown. In this study, we artificially trimmed spikelets on the flowering day and found that a reduction in number of seeds was associated with an increase in the grain Zn levels. We also found that a partial defect in anther dehiscence correlated with the increase in grain Zn levels in plants carrying the W1627 chromosomal segment at qGZn9a in a Nipponbare genetic background. Among eight candidate genes in the qGZn9a region, three were absent from the corresponding region of W1627; one of these, Os09g0384900, encoding a DUF295 protein with an unknown function, was found to be specifically expressed in the developing anther, thereby suggesting that the gene may be involved in the regulation of anther dehiscence. As fertility and grain Zn levels are essential agronomic traits in rice, our results highlight the importance of balancing these two traits.

Direct Measurement of Electronic Band Structures at Oxide Grain Boundaries.

Grain boundaries (GBs) modulate the macroscopic properties in polycrystalline materials because they have different atomic and electronic structures from the bulk. Despite the progress on the understanding of GB atomic structures, knowledge of the localized electronic band structures is still lacking. Here, we experimentally characterized the atomic structures and the band gaps of four typical GBs in α-Al2O3 by scanning transmission electron microscopy and valence electron energy-loss spectroscopy (EELS). It was found that the band gaps of the GBs are narrowed by 0.5-2.1 eV compared with that of 8.8 eV in the bulk. By combing core-loss EELS with first-principles calculations, we elucidated that the band gap reductions directly correlate with the decrease of the coordination numbers of Al and O ions at the GBs. These results provide in-depth understanding between the local atomic and electronic band structures for GBs and demonstrate a novel electronic-structure analysis for crystalline defects.

Atomic Scale Origin of Enhanced Ionic Conductivity at Crystal Defects.

In oxide materials, the presence of dislocations often strongly affects the properties of thin film and multilayer devices. Although it was reported that ionic conduction can be enhanced by introducing dislocations in ionic conductors, the underlying mechanism of such enhancement remains unclear. Here we analyzed the ionic conduction enhancement in an yttria-stabilized zirconia (YSZ) single edge dislocation from a structural point of view, using atomic resolution scanning transmission electron microscopy (STEM). First, the atomic structure and chemistry of a dislocation in YSZ were characterized by STEM and energy dispersive X-ray spectroscopy (EDS). A relative ionic conduction variation map around the dislocation was then estimated based on the well-established strain-conductivity and chemistry-conductivity relationships in YSZ. We propose that a faster ionic conductivity path can be formed around the dislocation core due to the coupling of the tensile strain field and dopant segregation, which could account for enhanced ionic conductivity along dislocations.

Adaptive Voxel Matching for Temporal CT Subtraction.

Temporal subtraction (TS) technique calculates a subtraction image between a pair of registered images acquired from the same patient at different times. Previous studies have shown that TS is effective for visualizing pathological changes over time; therefore, TS should be a useful tool for radiologists. However, artifacts caused by partial volume effects degrade the quality of thick-slice subtraction images, even with accurate image registration. Here, we propose a subtraction method for reducing artifacts in thick-slice images and discuss its implementation in high-speed processing. The proposed method is based on voxel matching, which reduces artifacts by considering gaps in discretized positions of two images in subtraction calculations. There are two different features between the proposed method and conventional voxel matching: (1) the size of a searching region to reduce artifacts is determined based on discretized position gaps between images and (2) the searching region is set on both images for symmetrical subtraction. The proposed method is implemented by adopting an accelerated subtraction calculation method that exploit the nature of liner interpolation for calculating the signal value at a point among discretized positions. We quantitatively evaluated the proposed method using synthetic data and qualitatively using clinical data interpreted by radiologists. The evaluation showed that the proposed method was superior to conventional methods. Moreover, the processing speed using the proposed method was almost unchanged from that of the conventional methods. The results indicate that the proposed method can improve the quality of subtraction images acquired from thick-slice images.

Ultrafast Encapsulation of Metal Nanoclusters into MFI Zeolite in the Course of Its Crystallization: Catalytic Application for Propane Dehydrogenation.

Encapsulating metal nanoclusters into zeolites combines the superior catalytic activity of the nanoclusters with high stability and unique shape selectivity of the crystalline microporous materials. The preparation of such bifunctional catalysts, however, is often restricted by the mismatching in time scale between the fast formation of nanoclusters and the slow crystallization of zeolites. We herein demonstrate a novel strategy to overcome the mismatching issue, in which the crystallization of zeolites is expedited so as to synchronize it with the rapid formation of nanoclusters. The concept was demonstrated by confining Pt and Sn nanoclusters into a ZSM-5 (MFI) zeolite in the course of its crystallization, leading to an ultrafast, in situ encapsulation within just 5 min. The Pt/Sn-ZSM-5 exhibited exceptional activity and selectivity with stability in the dehydrogenation of propane to propene. This method of ultrafast encapsulation opens up a new avenue for designing and synthesizing composite zeolitic materials with structural and compositional complexity.

Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa 'Nipponbare'.

KEY MESSAGE: A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, 'Nipponbare', was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci. Asian cultivated rice, Oryzasativa, was domesticated from its wild ancestor, O.rufipogon. Loss of seed shattering is one of the most recognisable traits selected during rice domestication. Three quantitative trait loci (QTLs), qSH1, qSH3, and sh4, were previously reported to be involved in the loss of seed shattering of Japonica cultivated rice, O.sativa 'Nipponbare'. However, the introgression line (IL) carrying 'Nipponbare' alleles at these three loci in the genetic background of wild rice, O.rufipogon W630, showed a lower value for detaching a grain from the pedicel than 'Nipponbare'. Here, we investigated abscission layer formation in the IL and found a partially formed abscission layer in the central region between the epidermis and vascular bundles. Based on QTL-seq analysis using the F2 population obtained from a cross between 'Nipponbare' and the IL, we detected two novel loci qCSS3 and qCSS9 (QTL for the Control of Seed Shattering in rice on chromosomes 3 and 9), which were found to be involved in the difference in seed-shattering degree between 'Nipponbare' and W630. Then, we further focused on qCSS3 in order to understand its potential role on the loss of seed shattering. The candidate region of qCSS3 was found to be located within a 526-kb region using substitution mapping analysis. Interestingly, the qCSS3 candidate region partially overlaps the selective sweep detected for Japonica but not for Indica rice cultivars, suggesting that this region harbours the mutation at a novel seed-shattering locus specifically selected for non-seed-shattering behaviour in Japonica cultivars.

Transition-Metal Distribution in Brownmillerite Ca2FeCoO5.

Ca2Fe2-xCoxO5 (0 ≤ x ≤ 1) with higher Co content, which crystallizes in a brownmillerite-type structure, is currently one of the best oxygen-evolution-reaction (OER) catalysts. Identifying the Fe/Co occupancies at the octahedral (Oh) and tetrahedral (Td) sites in the structure is the foundation for the understanding of the role of cobalt in each site and the exploration of further improvement in the OER activity. Here, we investigate the Fe/Co distribution in Ca2FeCoO5 by means of atomic-resolution energy dispersive X-ray spectroscopy in scanning transmission electron microscopy and dynamical image simulations combined with systematic density functional theory calculations. Our careful microscopic study reveals the absence of long-range Fe/Co order within the transition-metal (TM) layers, but cobalt is slightly enriched at the Td and Oh sites in the as-synthesized (1100 °C) and 800 °C annealed for a month samples, respectively. The observed Co site preferences are interpretable from the viewpoints of TM ionic size effect and ligand field effect, which are competitive around a crossover point at a certain temperature between 800 and 1100 °C. We also elucidate that the as-synthesized sample with Co enrichment at the Td site shows the better OER activity, and the optimum annealing temperature for more OER active Ca2FeCoO5 should be higher than the crossover temperature.

[Multiple Pulmonary Inflammatory Myofibroblastic Tumor].

A 67-year-old man visited hospital because of prolonged cough. Chest computed tomography (CT) revealed multiple tumors in bilateral lungs. Transbronchial lung biopsy did not reveal malignancy. Because antibiotic treatment was ineffective, partial resection of the right lung was performed for establishing the diagnosis. The pathological diagnosis was inflammatory myofibroblastic tumor. The postoperative course was uneventful. After 6 months postsurgery, he complained of breathing difficulty and exacerbation of the lesions was found by chest CT. By methylprednisolone pulse therapy, the symptom was improved, and the size of lesions reduced. Since this event, he has been administered oral prednisolone (PSL) 10 mg/day, and the exacerbation of the disease has not been noted.