Search bioRxiv⌕ Search

Biology subjects

Murata, K.

Publications and source records attributed to Murata, K..

At least 37 records · Page 2Linked to original sources

Wound-initiated hair regeneration by adhesive and shrinkable materials

Although there is a global demand for hair regrowth, particularly among middle-aged and older individuals, an effective hair growth technology has not yet been established1. Hair follicle neogenesis is restricted to the embryonic period, but hair regeneration accompanied by wound healing has been observed under some conditions2-4; however, the underlying mechanisms are unclear. Herein, we demonstrated that creating a wound without dermal defects effectively induced postneonatal hair follicle neogenesis. Separating the epidermis from the dermis by topical application of adhesive and shrinkable materials to mouse skin promoted epidermal regeneration, followed by new hair follicle formation. Hair follicle regeneration, accompanied by the upregulation of related genes, can be induced in mice, including middle-aged and aged mice, regardless of species, sex, skin location, or age. The cycle of the regenerated hair eventually synchronized with that of the surrounding physiological hairs. Our new hair regeneration technique based on reproduction of epidermis-dermis interactions provides a novel means to treat hair loss, including androgenetic alopecia.

cell biology↗

Endoplasmic reticulum patterns insect cuticle nanostructure

Insect cuticles with nano-level structures exhibit functional surface properties such as structural color and superhydrophobicity. Despite the enormous influence the cuticle has had on biomimetic industrial applications, molecular and cellular mechanisms of cuticular extracellular matrix (ECM) assembly into nanoscale structures remain poorly understood in insects and other taxa. Ghiradella (1989) described how a crystallin-like lattice of endoplasmic reticulum (ER) prefigures the patterning of the porous cuticle of the butterfly wing scale with structural color1. Building on that insight, we show that the nanopore structure of the olfactory (olf) organs, which serve as molecular filters in Drosophila, is built through a novel process in which ER material is trafficked to the plasma membrane mediated by the autophagy pathway. The process is controlled by the insect-specific protein Gore-tex/Osiris23 (Gox)2, which is localized to the tubular ER of olf hair cells. Gox recruits Ref(2)P, the fly counterpart of mammalian p62/SQSTM13, to initiate ER scission. The excised ER fragments are processed by autophagy to gain access to the plasma membrane and trigger membrane invagination, which plays a role in remodeling the cuticular envelope layer to the nanopore formation. This repurposing of the ER phagy for machinery to support the fabrication of nanoscale ECM by the Gox protein sheds light on the nanopatterning of insect cuticles and their genetic control.

developmental biology↗

A novel genetic mouse model of fatal aortic dissection reveals massive inflammatory cell infiltration in the thoracic aorta

BackgroundAortic dissection (AD) is the separation of medial layers of the aorta and is a major cause of death in patients with connective tissue disorders such as Marfan syndrome. However, molecular triggers instigating AD, its temporospatial progression, and how vascular cells in each vessel layer interact and participate in the pathological process remain incompletely understood. To unravel the underlying molecular mechanism of AD, we generated a spontaneous AD mouse model. MethodsWe incorporated a novel missense variant (p.G234D) in FBN1, the gene for fibrillin-1, identified in a non-syndromic familial AD patient into mice using CRISPR/Cas9 system. We performed histopathological analyses of the aortic lesions by histology, immunofluorescence staining, electron microscopy, synchrotron-based imaging and single-cell (sc)RNA-sequencing. Biochemical analysis was performed to examine the binding capacity of mutant human FBN1G234D protein to latent Tgf{beta} binding proteins (LTBPs), and signaling pathways in the mutant aortic wall were examined by western blot analysis. Results50% of the Fbn1G234D/G234D mutant mice died within 5 weeks of age from multiple intimomedial tears that expanded longitudinally and progressed to aortic rupture accompanied by massive immune cell infiltration. scRNA-sequencing, validated by immunostaining, revealed a significant increase in MHC class II-positive pro-inflammatory macrophages and monocytes at the site of intima tears with upregulation of MMP2/9 and marked disruption of elastic lamina. Subendothelial matrices, such as type IV collagen and laminin, expanded into the medial layer, where fibronectin expression was highly upregulated. Fbn1G234D/G234D endothelial cells exhibited altered mechanosensing with loss of parallel alignment to blood flow and upregulation of VCAM-1 and ICAM-1, all of which likely contributed to the infiltration of immune cells. Biochemically, FBN1G234D lost the ability to bind to latent TGF{beta} binding protein (LTBP)-1, -2, and -4, resulting in the downregulation of TGF{beta} signaling in the aortic wall. ConclusionsWe show that dynamic interactions involving endothelial cells (ECs) and macrophages/monocytes in the intima, where the ECM microenvironment is altered with the reduced TGF{beta} signaling, contributes to the initiation of AD. Our novel AD mouse model provides a unique opportunity to identify target molecules involved in the intimomedial tears that can be utilized for development of therapeutic strategies.

pathology↗

Effects of diet particle size on growth performance of the edible cricket, Teleogryllus occipitalis (Orthoptera: Gryllidae)

Farming edible crickets has environmental and nutritional benefits, as well as social benefits such as livelihood diversification. Commercial feeds for poultry and fish farming are often used to feed crickets, and in recent years, crop and food-processing by-products have also been used to improve sustainability. However, the design of feed for crickets has not been standardized. Here, we investigated growth and development of the Asian field cricket, Teleogryllus occipitalis (Audinet-Serville) (Orthoptera: Gryllidae), fed on different forms of the same diet. Body weights and the rate of development were significantly greater in crickets fed on millimetre-order granules than in crickets fed on micrometre-order powder. The result suggests that the granular form is easier for T. occipitalis to grasp and ingest than the powdery form, or that greater hydrophobicity of the powdery form inhibits digestion. Simply feeding millimetre-order granules may contribute to the development of feed design for farming edible crickets.

zoology↗

Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy

Medusavirus is a giant virus classified into an independent family of Mamonoviridae. Medusavirus-infected amoebae release immature particles in addition to the virions. These particles were suggested to exhibit the maturation process of this virus, but the structure of these capsids during maturation remains unknown. Here, we applied a block-based reconstruction method in cryo-electron microscopy (cryo-EM) single particle analysis to these viral capsids, extending these resolutions to 7-10 [A]. The map revealed a novel network consisted of minor capsid proteins (mCPs), supporting major capsid proteins (MCPs). A predicted molecular model of the MCP fitted into the cryo-EM map clarified the boundaries between the MCP and the underlining mCPs and between the MCP and the outer spikes, identifying the molecular interactions between the MCP and these components. Several structural changes of mCPs were observed beneath the 5-fold vertices of immature particles, depending on the presence or absence of the underlying internal membrane. Furthermore, the lower part of penton proteins on the 5-fold vertices were also lost in the mature virions. These dynamic structural changes of mCPs exhibit important functions in the maturation process of medusavirus. ImportanceStructural changes in giant virus capsids during maturation have not been known. Medusavirus is a unique giant virus, where amoebae infected with the virus release immature particles in addition to mature virions. In this study, immature and mature medusavirus particles were investigated using cryo-electron microscopy, and firstly reported the structural changes in the viral capsid during maturation. In DNA empty particles, the conformation of the minor capsid proteins dynamically changed depending on the presence or absence of the underlying internal membranes. In DNA full particles, the lower part of the penton proteins was lost. These are the first report of the structural changes in the viral capsid during giant virus maturation.

molecular biology↗

Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 angstrom

While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating cancer cell toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.

biochemistry↗

Highly efficient transgenic mouse production using piggyBac and its application to rapid phenotyping at the founder generation

Pronuclear microinjection is the most popular method for producing transgenic (Tg) animals. Because the production efficiency is typically less than 20%, phenotypic characterization of Tg animals is generally performed on the next generation (F1) onwards. However, apart from in rodents, in many animal species with long generation times, it is desirable to perform phenotyping in the founder (F0) generation. In this study, we attempted to optimize a method of Tg mouse production to achieve higher Tg production efficiency using piggyBac transposon systems and established optimal conditions under which almost all individuals in the F0 generation were Tg. We also succeeded in generating bacterial artificial chromosome Tg mice with efficiency of approximately 70%. By combining this method with genome editing technology, we established a new strategy to perform phenotyping of mice with tissue-specific knockout using the F0 generation. Taking the obtained findings together, by using this method, experimental research using Tg animals can be carried out more efficiently.

bioengineering↗

Regional random mutagenesis driven by multiple sgRNAs and diverse on-target genome editing events to identify functionally important elements in non-coding regions

Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. In contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea (ENU) and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR-& Transposase-based RegionaL Mutagenesis (CTRL-Mutagenesis). We demonstrated that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/557308v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@f70563org.highwire.dtl.DTLVardef@182dc6borg.highwire.dtl.DTLVardef@550e32org.highwire.dtl.DTLVardef@16f7dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

Post-acquisition super resolution for cryo-electron microscopy

Super resolution detector acquisition for cryo-EM has been used to improve the clarity of cryo-EM reconstructions. Recent reports have demonstrated achieving resolutions beyond the physical Nyquist limit using super resolution acquisition. Here, we demonstrate exceeding the physical Nyquist limitation by pre-processing the raw micrograph movies from "counting mode" data which has already reached physical Nyquist reconstruction resolution. To demonstrate functionality, micrograph movies of five datasets were pre-processed and demonstrate that it is possible to exceed the physical Nyquist limit via pixel doubling before motion correction. We call this "post-acquisition super resolution", or PASR. While this was originally developed for processing of giant virus datasets, where acquiring at high magnification is not always possible or desirable, it is also shown to work for smaller objects such as adeno-associated virus (AAV) and apoferritin, both of which are still high symmetry, and jack bean urease, with lower symmetry. PASR could reduce the magnification required to achieve desired resolutions, which may increase collection efficiency. PASR can also be of use for in vivo tomography and facilities with high storage demands. However, this method should only be used for data which is able to achieve the Nyquist limit without PASR pre-processing. It will not improve attained resolutions of data which does not already reach the Nyquist limit.

biophysics↗

An intra-oral flavor discrimination task in freely moving mice

Flavor plays a critical role in the pleasure of food. Flavor research has mainly focused on human subjects and revealed that many brain regions are involved in flavor perception. However, animal models for elucidating the mechanisms of neural circuits are lacking. Herein, we demonstrate the use of a novel behavioral task in which mice are capable of flavor discrimination. When the olfactory pathways of the mice were blocked, they could not perform the task. However, behavioral accuracy was not affected when the gustatory pathway was blocked by benzocaine. These results indicate that the mice performed this discrimination task mainly based on the intraoral flavor. We conclude that this novel task can contribute to research on the neural mechanisms of flavor perception.

neuroscience↗

Biochemical reactions between intra-articular tissues and joint instability in a rat model of osteoarthritis

AimsJoint instability is associated with various joint conditions including osteoarthritis (OA) and inflammation, and we have developed model which is determined to role of knee instability. Investigating cartilage maintenance factors such as hyaluronic acid (HA) and glycosaminoglycans (GAGs) can provide insights into the effect of the mechanical stress and the inhibitor used, with the following aims: 1) whether cartilage degeneration is inhibited in the new model, 2) whether combination TGF-{beta}1 inhibition mitigates cartilage degeneration, and to determine the role of TGF-{beta}1 in synovitis using fibroblasts. Main methodsWe used this novel model to investigate inhibition of OA progression with a focus on HA and GAGs, which help maintain the cartilage and synovial membrane. In detail, mechanical tests, X-ray, histological, and protein and mRNA expression analyses were used to determine the role of joint stability using in vivo model or fibroblast from synovial membrane. Key findingsJoint stability mitigated cartilage degeneration loss, decreased osteophytes, increased the expression levels of HA and GAGs in the synovial membrane, and decreased the release of pro-inflammatory factors in rats. Moreover, injection of TGF-{beta}1 inhibitor in an inflammatory synovial membrane promoted HA and GAGs expression. In synovial fibroblast cells, inhibition of TGF-{beta}1 over expression significantly inhibited the downregulation of pro-inflammatory factors and promoted the upregulation of lubrification for cartilage. SignificanceOur results suggest that joint instability is an independent mechanical factor for OA progression. The results provide novel insights into the association between OA and joint instability, which has significant human sciences implications. Research Highlights* Established a new experimental rat model of the different joint instability for elucidate osteoarthritis onset/progression * Using Histological staining to investigated the osteoarthritis including synovitis and osteophytes of the novel model * Using fibroblast from synovial membrane to investigated the fibrosis * Joint instability exacerbates articular cartilage degeneration and decreases HA and GAGs protein expressions in synovial membrane * TGF-{beta}1 inhibitor on early osteoarthritis joints may suppress synovial inflammation

pathology↗

Structure and its transformation of elliptical nege-like virus Tanay virus

Negeviruses that infect insects are recently identified virus species that are phylogenetically related to several plant viruses. They exhibit a unique virion structure, an elliptical core with a short projection. Negeviruses encode two structural proteins, a glycoprotein that forms a short projection, and an envelope protein that forms an elliptical core. The glycoprotein has been reported only in the negeviruses genes, and not in phylogenetically related plant viruses genes. In this report, we first describe the three-dimensional electron cryo-microscopy (cryo-EM) structure of Tanay virus (TANAV), one of the nege-like viruses. TANAV particle demonstrates a periodical envelope structure consisting of three layers surrounding the centered viral RNA. The elliptical core dynamically changes its shape under acidic and even low detergent conditions to form bullet-like or tubular shapes. The further cryo-EM studies on these transformed TANAV particles reveal their overall structural rearrangement. These findings suggest putative geometries of TANAV and its transformation in the life cycle, and the potential importance of the short projection for enabling cell entry to the insect hosts. Impact statementNegeviridae has recently been declared as a virus family that includes virus species exhibiting a unique particle structure that differs from other known viruses. They are known to be common mosquito viruses isolated around the world, but also phylogenetically related to several plant viruses that impair crop production. Therefore, the negeviruses may also play a role in plant ecosystems that threaten agriculture. However, the mechanism of infection and assembly of the negeviruses as well as their structure were unknown. In this study, intact and dissociated structures of the TANAV were first examined using cryo-EM single particle analysis (SPA) and electron cryo-tomography (cryo-ET). These results reveal new structural geometries of the TANAV particle and its dynamic transformation under acidic and even low-detergent conditions, providing new insights into the infection and assembly mechanism in negeviruses.

biophysics↗

The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers

As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in the low light, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). Its architecture exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, a Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and a Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of OtPSI-LHCI-Lhcp supercomplex is likely due to a state transition-like mechanism induced by light intensity change. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to weak coupling of the chlorophyll a603-a609 pair in OtLhca1-4.

plant biology↗

Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover

The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na+ transport and demonstrates an off-axis rotor assembly. Recent single molecular studies of the isolated V1 domain have indicated that there are subpauses within the three major states of the pseudo three-fold symmetric rotary enzyme. However, there was no structural evidence for these. Herein we activated the EhV-ATPase complex with ATP and identified multiple structures consisting of a total of six states of this complex by using cryo-electron microscopy. The orientations of the rotor complex during turnover, especially in the intermediates, were not as perfectly uniform as expected. The densities in the nucleotide binding pockets in the V1 domain indicated the different catalytic conditions for the six conformations. The off-axis rotor and its interactions with the stator a-subunit during rotation suggests that this non-uniform rotor rotation is performed through the entire complex.

molecular biology↗

Oxytocin and Emotional Tear in Dogs

In humans, tear volume increases in emotional arousal. No studies have investigated the relationship of emotional arousal and tear volume in animals. We measured tear volume in dogs before and after reunion with their owners. Tear volume increased significantly during owner, but not familiar non-owner, reunions but not during reunions with familiar non-owners. When oxytocin instillation was applied to dogs, the tear volume increased, suggesting that oxytocin can mediate the emotion-induced tear secretion in dogs. When the photos of dogs face in which artificial tear was applied to the dogs eyes, the positive impression of these photo increased. These suggest that emotional tear can facilitate human-dog emotional connection.

animal behavior and cognition↗

Particle morphology of medusavirus inside and outside the cells reveals a new maturation process of giant viruses

Medusavirus, a giant virus, is phylogenetically closer to eukaryotes than the other giant viruses and has been recently classified as an independent species. However, details of its morphology and maturation process in host cells remain unclear. Here, we investigated the particle morphology of medusavirus inside and outside infected cells using conventional transmission electron microscopy (C-TEM) and cryo-electron microscopy (cryo-EM). The C-TEM of amoeba infected with the medusavirus showed four types of particles: empty, DNA-full, and the corresponding intermediates. Time-dependent changes in the proportion and following intracellular localization of these particles suggested a new maturation process for the medusavirus. Empty particles and viral DNAs were produced independently in the cytoplasm and nucleus, respectively, and only empty particles located near the nucleus incorporated the viral DNA into the capsid. All four types of particles were also found outside the cells. The cryo-EM of these particles showed that the intact capsid structure, covered with three different types of spikes, was conserved among all particle types, although with minor size-related differences. The internal membrane exhibited a structural array similar to that of the capsid, interacted closely with the capsid, and displayed open membrane structures in the empty and empty-intermediate particles. This result suggests that the open structures in the internal membrane are used for an exchange of scaffold proteins and viral DNA during the maturation process. This new model of the maturation process of medusavirus provides insight into the structural and behavioral diversity of giant viruses. ImportanceGiant viruses exhibit diverse morphologies and maturation processes. In the present study, medusavirus showed four types of particle morphologies both inside and outside the infected cells, when propagated in the laboratory using amoeba culture. Time-course analysis of the medusavirus particles in the infected cells reveals a new maturation process. Empty viral particles and viral DNAs were produced independently in the cytoplasm and nucleus, and only the empty particles located near the nucleus incorporated the viral DNA. Consequently, many immature particles, along with mature virions, were released from the host cells. Except for showing a small change in size, the capsid structures were well preserved during the maturation process. The empty viral particles and corresponding intermediates showed open membrane structures, which are presumably used for exchanging scaffold proteins and viral DNAs.

microbiology↗

BITC induces cardiomyocyte proliferation and heart regeneration

Cardiomyocyte proliferation is an evolutionarily conserved mechanism that supports cardiac regeneration in vertebrates. Mammalian cardiomyocytes are arrested from the cell cycle shortly after birth, and therefore mammals lose the ability to regenerate injured myocardium for the rest of their lives. Pharmacological induction of cardiomyocyte proliferation has gained a lot of interest in recent years, as researchers strive to achieve heart tissue regeneration. Here we show that a small chemical, benzyl isothiocyanate (BITC), induced cardiomyocyte proliferation through activation of the cyclin-dependent kinase (CDK) pathway. BITC treatment also allowed heart regeneration in the infarcted neonatal heart, even after the regeneration period in mice. Furthermore, administration of BITC to adult mice in parallel with mild hypoxia (10% O2) induced cell cycle reentry and tissue regeneration in the adult heart. Our findings thus suggest that pharmacological activation of the CDK pathway using BITC, concurrently with the activation of hypoxia-related signaling pathways, may be a promising approach to inducing cardiac regeneration in patients with heart disease.

pharmacology and toxicology↗

The 4.4 A structure of the giant Melbournevirus virion belonging to the Marseilleviridae family

Members of Marseilleviridae, one family of icosahedral giant viruses classified in 2012 have been identified worldwide in all types of environments. The virion shows a characteristic internal membrane extrusion at the five-fold vertices of the capsid, but its structural details need to be elucidated. We now report the 4.4 [A] cryo-electron microscopy structure of the Melbournevirus capsid. An atomic model of the major capsid protein (MCP) shows a unique cup structure on the trimer that accommodates additional proteins. A polyalanine model of the penton base protein shows internally extended N- and C-terminals, which indirectly connect to the internal membrane extrusion. The Marseilleviruses share the same orientational organisation of the MCPs as PBCV-1 and CroV, but do not appear to possess a protein akin to the "tape measure" of these viruses. Minor capsid proteins named PC-{beta}, zipper, and scaffold are proposed to control the dimensions of the capsid during assembly.

microbiology↗