Toward a high-resolution mechanism of intrinsically disordered protein self-assembly.

Membraneless organelles formed via the self-assembly of intrinsically disordered proteins (IDPs) play a crucial role in regulating various physiological functions. Elucidating the mechanisms behind IDP self-assembly is of great interest not only from a biological perspective but also for understanding how amino acid mutations in IDPs contribute to the development of neurodegenerative diseases and other disorders. Currently, two proposed mechanisms explain IDP self-assembly: (1) the sticker-and-spacer framework, which considers amino acid residues as beads to simulate the intermolecular interactions, and (2) the cross-ß hypothesis, which focuses on the ß-sheet interactions between the molecular surfaces constructed by multiple residues. This review explores the advancement of new models that provide higher resolution insights into the IDP self-assembly mechanism based on new findings obtained from structural studies of IDPs.

Importin alpha family NAAT/IBB domain: Functions of a pleiotropic long chameleon sequence.

Nuclear transport is essential for eukaryotic cell survival and regulates the movement of functional molecules in and out of the nucleus via the nuclear pore. Transport is facilitated by protein-protein interactions between cargo and transport receptors, which contribute to the expression and regulation of downstream genetic information. This chapter focuses on the molecular basis of the multifunctional nature of the importin α family, the representative transport receptors that bring proteins into the nucleus. Importin α performs multiple functions during the nuclear transport cycle through interactions with multiple molecules by a single domain called the IBB domain. This domain is a long chameleon sequence, which can change its conformation and binding mode depending on the interaction partners. By considering the evolutionarily conserved biochemical/physicochemical propensities of the amino acids constituting the functional complex interfaces, together with their structural properties, the mechanisms of switching between multiple complexes formed via IBB and the regulation of downstream functions are examined in detail. The mechanism of regulation by IBB indicates that the time has come for a paradigm shift in the way we view the molecular mechanisms by which proteins regulate downstream functions through their interactions with other molecules.

A case of cystic lymphangioma arising from the parauterine tissue.

A 57-year-old woman, gravida 3, para 3, with no complaints visited our hospital for right-sided adnexal tumor found incidentally in cancer screening. She had no medical history, surgical history, or gynecological disease. Imaging studies showed a 5-cm lobular cystic tumor on the right side of uterus. We suspected right hydrosalpinx and decided to perform diagnostic laparoscopy. During laparoscopy, the right adnexa was found to be atrophic, and the tumor was located in the broad ligament. The tumor was observed to be a multilocular cyst containing yellow fluid that developed from the right parauterine tissue. The tumor was resected from the surrounding tissue. Histological examination revealed that the multilocular cyst contained a vascular component surrounding the lymphatic endothelium and was decided to be a cystic lymphangioma. The patient was followed up and there was no evidence of recurrence at postoperative 7 months. We experienced a very rare case of lymphangioma arising from the parauterine tissue. The laparoscopic approach can assist with both diagnosis and treatment.

Enhanced High Thermal Conductivity Cellulose Filaments via Hydrodynamic Focusing.

Nanocellulose is regarded as a green and renewable nanomaterial that has attracted increased attention. In this study, we demonstrate that nanocellulose materials can exhibit high thermal conductivity when their nanofibrils are highly aligned and bonded in the form of filaments. The thermal conductivity of individual filaments, consisting of highly aligned cellulose nanofibrils, fabricated by the flow-focusing method is measured in dried condition using a T-type measurement technique. The maximum thermal conductivity of the nanocellulose filaments obtained is 14.5 W/m-K, which is approximately five times higher than those of cellulose nanopaper and cellulose nanocrystals. Structural investigations suggest that the crystallinity of the filament remarkably influence their thermal conductivity. Smaller diameter filaments with higher crystallinity, that is, more internanofibril hydrogen bonds and less intrananofibril disorder, tend to have higher thermal conductivity. Temperature-dependence measurements also reveal that the filaments exhibit phonon transport at effective dimension between 2D and 3D.

ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.

T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing ß-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.

The transcription factor Tbx5 regulates direction-selective retinal ganglion cell development and image stabilization.

The diversity of visual input processed by the mammalian visual system requires the generation of many distinct retinal ganglion cell (RGC) types, each tuned to a particular feature. The molecular code needed to generate this cell-type diversity is poorly understood. Here, we focus on the molecules needed to specify one type of retinal cell: the upward-preferring ON direction-selective ganglion cell (up-oDSGC) of the mouse visual system. Single-cell transcriptomic profiling of up- and down-oDSGCs shows that the transcription factor Tbx5 is selectively expressed in up-oDSGCs. The loss of Tbx5 in up-oDSGCs results in a selective defect in the formation of up-oDSGCs and a corresponding inability to detect vertical motion. A downstream effector of Tbx5, Sfrp1, is also critical for vertical motion detection but not up-oDSGC formation. These results advance our understanding of the molecular mechanisms that specify a rare retinal cell type and show how disrupting this specification leads to a corresponding defect in neural circuitry and behavior.

Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain.

Importin α has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non-nuclear transport functions. In both nuclear transport and non-nuclear transport, a functional domain called the IBB domain (importin ß binding domain) plays a key role in regulating importin α behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin α function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin α IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across species and family members, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex-forming ability among family members and for functional switching.

Importin α2 association with chromatin: Direct DNA binding via a novel DNA-binding domain.

The nuclear transport of proteins is important for facilitating appropriate nuclear functions. The importin α family proteins play key roles in nuclear transport as transport receptors for copious nuclear proteins. Additionally, these proteins possess other functions, including chromatin association and gene regulation. However, these nontransport functions of importin α are not yet fully understood, especially their molecular-level mechanisms and consequences for functioning with chromatin. Here, we report the novel molecular characteristics of importin α binding to diverse DNA sequences in chromatin. We newly identified and characterized a DNA-binding domain-the Nucleic Acid Associating Trolley pole domain (NAAT domain)-in the N-terminal region of importin α within the conventional importin ß binding (IBB) domain that is necessary for nuclear transport of cargo proteins. Furthermore, we found that the DNA binding of importin α synergistically coupled the recruitment of its cargo protein to DNA. This is the first study to delineate the interaction between importin α and chromatin DNA via the NAAT domain, indicating the bifunctionality of the importin α N-terminal region for nuclear transport and chromatin association.

Modulation of Interfacial Thermal Transport between Fumed Silica Nanoparticles by Surface Chemical Functionalization for Advanced Thermal Insulation.

Since solid-state heat transport in a highly porous nanocomposite strongly depends on the thermal boundary conductance (TBC) between constituent nanomaterials, further suppression of the TBC is important for improving performance of thermal insulators. Here, targeting a nanocomposite fabricated by stamping fumed silica nanoparticles, we perform a wide variety of surface functionalizations on fumed silica nanoparticles by a silane coupling method and investigate the impact on the thermal conductivity (Km). The Km of the silica nanocomposite is approximately 20 and 9 mW/m/K under atmospheric and vacuum conditions at the material density of 0.2 g/cm3 without surface functionalization, respectively, and the experimental results indicate that the Km can be modulated depending on the chemical structure of molecules. The surface modification with a linear alkyl chain of optimal length significantly suppresses Km by approximately 30%, and the suppression can be further enhanced to approximately 50% with an infrared opacifier. The magnitude of suppression was found to sensitively depend on the length of the terminal chain. The magnitude is also related to the number of reactive silanol groups in the chemical structure, where the surface modification with fluorocarbon gives the largest suppression. The surface hydrophobization merits thermal insulation through significant suppression of the TBC, presumably by reducing the water molecules that otherwise would serve as heat conduction channels at the interface. On the other hand, when the chain length is long, the suppression is counteracted by the enhanced phonon transmission through the silane coupling molecules that grow with the chain length. This is supported by the analytical model and present simulation results, leading to prediction of the optimal chemical structure for better thermal insulation.

Weaker bonding can give larger thermal conductance at highly mismatched interfaces.

Thermal boundary conductance is typically positively correlated with interfacial adhesion at the interface. Here, we demonstrate a counterintuitive experimental result in which a weak van der Waals interface can give a higher thermal boundary conductance than a strong covalently bonded interface. This occurs in a system with highly mismatched vibrational frequencies (copper/diamond) modified by a self-assembled monolayer. Using finely controlled fabrication and detailed characterization, complemented by molecular simulation, the effects of bridging the vibrational spectrum mismatch and bonding at the interface are systematically varied and understood from a molecular dynamics viewpoint. The results reveal that the bridging and binding effects have a trade-off relationship and, consequently, that the bridging can overwhelm the binding effect at a highly mismatched interface. This study provides a comprehensive understanding of phonon transport at interfaces, unifying physical and chemical understandings, and allowing interfacial tailoring of the thermal transport in various material systems.

Anisotropic thermal conductivity measurement of organic thin film with bidirectional 3ω method.

Organic thin film materials with molecular ordering are gaining attention as they exhibit semiconductor characteristics. When using them for electronics, the thermal management becomes important, where heat dissipation is directional owing to the anisotropic thermal conductivity arising from the molecular ordering. However, it is difficult to evaluate the anisotropy by simultaneously measuring in-plane and cross-plane thermal conductivities of the film on a substrate because the film is typically as thin as tens to hundreds of nanometers and its in-plane thermal conductivity is low. Here, we develop a novel bidirectional 3ω system that measures the anisotropic thermal conductivity of thin films by patterning two metal wires with different widths and preparing the films on top and extracting the in-plane and cross-plane thermal conductivities using the difference in their sensitivities to the metal-wire width. Using the developed system, the thermal conductivity of spin-coated poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) with thickness of 70 nm was successfully measured. The measured in-plane thermal conductivity of PEDOT:PSS film was as high as 2.9 W m-1 K-1 presumably due to the high structural ordering, giving an anisotropy of 10. The calculations of measurement sensitivity to the film thickness and thermal conductivities suggest that the device can be applied to much thinner films by utilizing metal wires with a smaller width.

Mechanically Strong, Scalable, Mesoporous Xerogels of Nanocellulose Featuring Light Permeability, Thermal Insulation, and Flame Self-Extinction.

Scalability is a common challenge in the structuring of nanoscale particle dispersions, particularly in the drying of these dispersions for producing functional, porous structures such as aerogels. Aerogel production relies on supercritical drying, which exhibits poor scalability. A solution to this scalability limitation is the use of evaporative drying under ambient pressure. However, the evaporative drying of wet gels comprising nanoscale particles is accompanied by a strong capillary force. Therefore, it is challenging to produce evaporative-dried gels or "xerogels" that possess the specific structural profiles of aerogels such as mesoscale pores, high porosity, and high specific surface area (SSA). Herein, we demonstrate a structure of mesoporous xerogels with high porosity (∼80%) and high SSA (>400 m2 g-1) achieved by exploiting cellulose nanofibers (CNFs) as the building blocks with tunable interparticle interactions. CNFs are sustainable, wood-derived materials with high strength. In this study, the few-nanometer-wide CNFs bearing carboxy groups were structured into a stable network via ionic inter-CNF interaction. The outline of the resulting xerogels was then tailored into a regular, millimeter-thick, board-like structure. Several characterization techniques highlighted the multifunctionality of the CNF xerogels combining outstanding strength (compression E = 170 MPa, σ = 10 MPa; tension E = 290 MPa, σ = 8 MPa), moderate light permeability, thermal insulation (0.06-0.07 W m-1 K-1), and flame self-extinction. As a potential application of the xerogels, daylighting yet insulating, load-bearing wall members can be thus proposed.

Modular output circuits of the fastigial nucleus for diverse motor and nonmotor functions of the cerebellar vermis.

The cerebellar vermis, long associated with axial motor control, has been implicated in a surprising range of neuropsychiatric disorders and cognitive and affective functions. Remarkably little is known, however, about the specific cell types and neural circuits responsible for these diverse functions. Here, using single-cell gene expression profiling and anatomical circuit analyses of vermis output neurons in the mouse fastigial (medial cerebellar) nucleus, we identify five major classes of glutamatergic projection neurons distinguished by gene expression, morphology, distribution, and input-output connectivity. Each fastigial cell type is connected with a specific set of Purkinje cells and inferior olive neurons and in turn innervates a distinct collection of downstream targets. Transsynaptic tracing indicates extensive disynaptic links with cognitive, affective, and motor forebrain circuits. These results indicate that diverse cerebellar vermis functions could be mediated by modular synaptic connections of distinct fastigial cell types with posturomotor, oromotor, positional-autonomic, orienting, and vigilance circuits.

A common rule governing differentiation kinetics of mouse cortical progenitors.

The balance between proliferation and differentiation of stem cells and progenitors determines the size of an adult brain region. While the molecular mechanisms regulating proliferation and differentiation of cortical progenitors have been intensively studied, an analysis of the kinetics of progenitor choice between self-renewal and differentiation in vivo is, due to the technical difficulties, still unknown. Here we established a descriptive mathematical model to estimate the probability of self-renewal or differentiation of cortical progenitor behaviors in vivo, a variable we have termed the expansion coefficient. We have applied the model, one which depends only on experimentally measured parameters, to the developing mouse cortex where the expansive neuroepithelial cells and neurogenic radial glial progenitors are coexisting. Surprisingly, we found that the expansion coefficients of both neuroepithelium cells and radial glial progenitors follow the same developmental trajectory during cortical development, suggesting a common rule governing self-renewal/differentiation behaviors in mouse cortical progenitor differentiation.

Tuba8 Drives Differentiation of Cortical Radial Glia into Apical Intermediate Progenitors by Tuning Modifications of Tubulin C Termini.

Most adult neurons and glia originate from radial glial progenitors (RGs), a type of stem cell typically extending from the apical to the basal side of the developing cortex. Precise regulation of the choice between RG self-renewal and differentiation is critical for normal development, but the mechanisms underlying this transition remain elusive. We show that the non-canonical tubulin Tuba8, transiently expressed in cortical progenitors, drives differentiation of RGs into apical intermediate progenitors, a more restricted progenitor type lacking attachment to the basal lamina. This effect depends on the unique C-terminal sequence of Tuba8 that antagonizes tubulin tyrosination and Δ2 cleavage, two post-translational modifications (PTMs) essential for RG fiber maintenance and the switch between direct and indirect neurogenesis and ultimately distinct neuronal lineage outcomes. Our work uncovers an instructive role of a developmentally regulated tubulin isotype in progenitor differentiation and provides new insights into biological functions of the cellular tubulin PTM "code."

New method for determining fibrinogen and FDP threshold criteria by artificial intelligence in cases of massive hemorrhage during delivery.

AIM: To investigate the feasibility of a novel method using artificial intelligence (AI), in which the fibrinogen criterion was determined by the quantitative relation between the distributions of fibrin/fibrinogen degradation products (FDPs) and fibrinogen. METHODS: A dataset of 154 deliveries comprising more than 2000 g of blood lost due to hemorrhage, excluding disseminated intravascular coagulation (DIC), among patients from eight national perinatal centers in Japan from 2011 to 2015 were obtained. The fibrinogen threshold criterion was identified by using the function that best fit the distributions of FDP as determined by AI. FDP production was described by differential equations using a dataset containing fibrinogen levels less than the fibrinogen criterion and solved numerically. RESULTS: A fibrinogen level of 237 mg/dL as the threshold criterion was obtained. The FDP threshold criteria were 2.0 and 8.5 mg/dL for no coagulopathy and a failed coagulation system, respectively. CONCLUSION: The fibrinogen threshold criterion for patients with massive hemorrhage excluding DIC at delivery were obtained by selecting the functions that best fit the distributions of FDP data by using AI.

Graded Coexpression of Ion Channel, Neurofilament, and Synaptic Genes in Fast-Spiking Vestibular Nucleus Neurons.

Computations that require speed and temporal precision are implemented throughout the nervous system by neurons capable of firing at very high rates, rapidly encoding and transmitting a rich amount of information, but with substantial metabolic and physical costs. For economical fast spiking and high throughput information processing, neurons need to optimize multiple biophysical properties in parallel, but the mechanisms of this coordination remain unknown. We hypothesized that coordinated gene expression may underlie the coordinated tuning of the biophysical properties required for rapid firing and signal transmission. Taking advantage of the diversity of fast-spiking cell types in the medial vestibular nucleus of mice of both sexes, we examined the relationship between gene expression, ionic currents, and neuronal firing capacity. Across excitatory and inhibitory cell types, genes encoding voltage-gated ion channels responsible for depolarizing and repolarizing the action potential were tightly coexpressed, and their absolute expression levels increased with maximal firing rate. Remarkably, this coordinated gene expression extended to neurofilaments and specific presynaptic molecules, providing a mechanism for coregulating axon caliber and transmitter release to match firing capacity. These findings suggest the presence of a module of genes, which is coexpressed in a graded manner and jointly tunes multiple biophysical properties for economical differentiation of firing capacity. The graded tuning of fast-spiking capacity by the absolute expression levels of specific ion channels provides a counterexample to the widely held assumption that cell-type-specific firing patterns can be achieved via a vast combination of different ion channels.SIGNIFICANCE STATEMENT Although essential roles of fast-spiking neurons in various neural circuits have been widely recognized, it remains unclear how neurons efficiently coordinate the multiple biophysical properties required to maintain high rates of action potential firing and transmitter release. Taking advantage of diverse fast-firing capacities among medial vestibular nucleus neurons of mice, we identify a group of ion channel, synaptic, and structural genes that exhibit mutually correlated expression levels, which covary with firing capacity. Coexpression of this fast-spiking gene module may be a basic strategy for neurons to efficiently and coordinately tune the speed of action potential generation and propagation and transmitter release at presynaptic terminals.

Enhancing Thermal Boundary Conductance of Graphite-Metal Interface by Triazine-Based Molecular Bonding.

Thermal boundary conductance between graphite and metal plays an important role in developing thermally conductive composites and contacts for thermal management. On the basis of the premise that the thermal boundary conductance (TBC) correlates with interfacial bonding strength, we conducted triazine-based molecular-bonding process to improve interfacial adhesion forces between a-axis of highly oriented pyrolytic graphite and aluminum. The surface coverage of molecular bonding at the interface is estimated by the X-ray photoelectron spectroscopy and thermal boundary conductance is measured by the time-domain thermoreflectance method. It is found that the TBC is directly proportional to the surface coverage of covalently bonded triazine linkers, with the proportionality constant for their increment rates being about unity. The experimental finding is supported by the corresponding simulation using the atomic Green's function method, which exhibits the same linear dependence on the surface coverage.

Revealing How Topography of Surface Microstructures Alters Capillary Spreading.

Wetting phenomena, i.e. the spreading of a liquid over a dry solid surface, are important for understanding how plants and insects imbibe water and moisture and for miniaturization in chemistry and biotechnology, among other examples. They pose fundamental challenges and possibilities, especially in dynamic situations. The surface chemistry and micro-scale roughness may determine the macroscopic spreading flow. The question here is how dynamic wetting depends on the topography of the substrate, i.e. the actual geometry of the roughness elements. To this end, we have formulated a toy model that accounts for the roughness shape, which is tested against a series of spreading experiments made on asymmetric sawtooth surface structures. The spreading speed in different directions relative to the surface pattern is found to be well described by the toy model. The toy model also shows the mechanism by which the shape of the roughness together with the line friction determines the observed slowing down of the spreading.

Current status of intensity-modulated radiation therapy for prostate cancer: History, clinical results and future directions.

External beam radiotherapy has changed dramatically over several decades with the improvement of computer hardware and software, and machinery developments. Intensity-modulated radiation therapy is the most sophisticated technique for all cancer treatment with radiation therapy, and is widely disseminated and available for daily use in many countries. Several retrospective and prospective studies have shown that intensity-modulated radiation therapy reduces the radiation dose in the organs at risk with diminished rates of acute and late toxicity, even with higher doses (>74 Gy). An important technique for the clinical use of intensity-modulated radiation therapy is image-guided radiation therapy. The clinical benefit for prostate image-guided radiation therapy has been assessed by comparing the outcomes of patients with either the image-guided radiation therapy or non-image-guided radiation therapy technique. These studies have shown that image-guided radiation therapy significantly decreases acute and late rectal and bladder toxicities. Randomized trials and meta-analysis have shown that higher doses result in better biochemical control. More recently, hypofractionated radiation therapy comparing hypofractionated radiation therapy versus conventional fractionated radiation therapy have shown that hypofractionated radiation therapy produces biochemical control and toxicity rated similar to those produced by conventional fractionated radiation therapy. The clinical use of ultrahypofractionated radiation therapy and simultaneous integrated boost technique is necessary to evaluate its further safety and benefits. Intensity-modulated radiation therapy is also widely accepted in the field of salvage therapy and for the patients with distant oligometastases. The purpose of the present review is to summarize the history of intensity-modulated radiation therapy, new techniques for intensity-modulated radiation therapy, hypofractionation and future directions for prostate cancer.