Biology subjects

Mimura, M.

Publications and source records attributed to Mimura, M..

13 recordsLinked to original sources

bioRxiv2026

Reconstitution in a minimal synthetic bacterium reveals distinct Mollicute MreB-based motility systems driven by orthogonal force directions

MreB, a bacterial actin homolog, is widely conserved in bacteria where it functions as a scaffold for a peptidoglycan synthesis. Intriguingly, members of the cell wall-lacking Mollicutes retain multiple mreB genes despite the absence of peptidoglycan. Previous work demonstrated that two MreB isoforms from Spiroplasma can reconstitute swimming motility in the minimal synthetic bacterium syn3B, indicating that MreB was repurposed for motility. Here, we expressed seven MreBs from Haloplasma contractile, an early-diverging Mollicute, in syn3B. Approximately 50% of cells elongated, and 15% exhibited curving and coiling movements that resembled Haloplasma but differed from Spiroplasma motility. Systematic analysis of isoform combinations revealed that movement requires specific MreB pairs, and that additional isoforms enhance motility efficiency. Cryo-electron tomography showed membrane-associated ribbons composed of MreB filaments. Mathematical modeling demonstrated that Haloplasma- and Spiroplasma-type movements can be reproduced by altering only the direction of force generation. Thus, diversification of force orientation within an actin homolog enabled independent evolution of distinct motility systems in Mollicutes.

Synthetic Biology↗

bioRxiv2024

Structural, genetic, and adaptive basis of superhydrophobicity in rice leaves

In most plants, leaf surfaces exhibit water-repellent properties, which protect against pathogens and weather. Plants such as lotus and rice have evolved outstanding water-repellent properties, so-called superhydrophobicity. However, the structural and genetic basis of these properties in crop plants remains unclear. In this study, we identified the genes and microstructures responsible for superhydrophobicity by analyzing water repellence in rice mutants and cultivars, as well as wild Oryza species. Analysis of the surface structure of mutant leaves revealed that the degree of water repellency in rice largely depends on the accumulation of cuticular wax. Meanwhile, although papillae differentiation contributes minorly to water repellency, it is suggested to play a crucial role in achieving superhydrophobicity. These morphological characteristics are regulated by at least five previously characterized genes. We also found that superhydrophobicity is present in ancestral species, is retained by most cultivated rice, and appears to have evolved independently of rice domestication. Understanding the mechanisms of water repellence and their applications should provide important insight into the natural design of water repellence, as well as a basis for future innovation.

plant biology↗

bioRxiv2024

Semi-automated navigation for efficient targeting of electron tomography to regions of interest in volume correlative light and electron microscopy

Electron microscopy is essential for the quantitative study of synaptic ultrastructure. At present, the correlation of functional and structural properties of the same synapse is extremely challenging. We introduce a novel integrated workflow designed to simplify sample navigation across spatial scales, allowing the identification of individual synapses from optical microscopy mouse brain image stacks that can be targeted for analysis using electron tomography imaging. We developed a software which has a function to register multimodal images using a novel segmentation-based image registration algorithm as well as a function to visualize all the registration results. Using our newly designed software we streamline mapping of high-resolution optical imaging onto reference maps using blood vessels as endogenous fiducial marks. Further we demonstrate significant improvements on the ultramicrotomy stage of volume Correlative Light and Electron Microscopy (vCLEM) workflows, providing real time guidance to targeted trimming to match previously acquired Regions Of Interest (ROIs), and reliable estimates of cutting depth relative to ROI, based on fluorescence imaging of TEM ready ultrathin sections. Using this workflow, we successfully targeted TEM tomography to the proximal axonal region containing the Axon Initial Segment identified using fluorescent light microscopy.

neuroscience↗

bioRxiv2024

Establishment of a rapid method to assemble and transfer DNA fragments into the JCVI-syn3B minimal synthetic bacterial genome

JCVI-syn3B (syn3B), a minimal synthetic bacterium that only possesses essential genes, facilitates the examination of heterogeneous gene functions in minimal life. Conventionally, Escherichia coli is used to construct DNA fragments for gene transfer into the syn3B genome through Cre/loxP system. However, the construction process is challenging and time-consuming due to various issues, including the inhibition of E. coli growth and unexpected recombination, especially with AT-rich DNA sequences such as those found in Mycoplasma genes. Therefore, in this study, we aimed to develop a new transformation method to overcome these issues. We assembled the vector and target DNA fragments using an in vitro homologous recombination system and subsequently transferred the products into the syn3B genome. We obtained approximately 103[~]104 recombinant colonies per milliliter of the original culture in eight days, which is four days shorter than the conventional period, without any recombination issues, even for AT-rich DNA. This method may be applicable to other gene manipulation systems based on Cre/loxP system. SignificanceA rapid and trouble free method was developed to transfer genes to the genome of minimal synthetic bacterium JCVI-Syn3B through Cre/loxP system. This method can be applied to Cre/loxP-based gene manipulation system in various research fields.

synthetic biology↗

bioRxiv2022

Rice GLUCAN SYNTHASE-LIKE5 promotes Callose deposition in Anthers to maintain proper Male Meiosis Initiation and Progression

Callose is a plant cell-wall polysaccharide whose deposition is spatiotemporally regulated in various developmental processes and environmental stress responses. Appearance of callose in premeiotic anthers is a prominent histological hallmark for the onset of meiosis in flowering plants, whose biological role in meiosis is unknown till date. Here we show that rice GLUCAN SYNTHASE LIKE5 (OsGSL5), a callose synthase, localizes on the plasma membrane of pollen mother cells (PMCs), and is responsible for biogenesis of callose in anther locules through premeiotic and meiotic stages. In osgsl5 mutant anthers mostly lacking callose deposition, aberrant PMCs accompanied by aggregated, unpaired or multivalent chromosomes were frequently observed, and furthermore, a considerable number of mutant PMCs untimely progress into meiosis compared to wild type PMCs. Immunostaining of meiosis-specific protein PAIR2 in premeiotic PMCs revealed precocious meiosis entry in osgsl5 anthers. The findings of this study bestows new knowledge on function of callose in controlling timing of male meiosis initiation and progression, in addition to roles in microsporogenesis, in flowering plants.

developmental biology↗

bioRxiv2022

The oxytocin system regulates tearing

Tears are an exocrine physiological fluid secreted onto the ocular surface from the lacrimal apparatus in all mammals. Limited research has been conducted on the functional neuronal circuitry of tear production. In particular, the neuronal mechanisms of emotional tearing, which is a physiological reaction harmonized with enhanced emotional arousal and assumed to be unique to humans, remain unclear. We identified that the oxytocin neurons in the paraventricular hypothalamus is functionally projected to the oxytocin receptor-expressing neurons in the lacrimation center of the superior salivatory nucleus. Optogenetic activation or inhibition of these neurons and/or receptors can modulate the superior salivatory nucleus dependent tear secretion mediated through oxytocin. Moreover, we identified that maternal behavior, nociceptive behavior stimulation, and aversive memory retrieval are linked to tearing in mice, and that these emotional linked tearing are suppressed by optogenetic inhibition of the corresponding oxytocin system. Thus, tearing could be regulated through functional connections between central oxytocin systems in the paraventricular hypothalamus and the superior salivatory nucleus.

animal behavior and cognition↗

bioRxiv2021

Oscillatory population-level activity of dorsal raphe serotonergic neurons sculpts sleep structure

Dorsal raphe (DR) 5-HT neurons are involved in regulating sleep-wake transitions. Previous studies demonstrated that single-unit activity of DR 5-HT neurons is high during wakefulness, decreases during non-rapid eye movement (NREM) sleep, and ceases during rapid eye movement (REM) sleep. However, characteristics of the population-level activity of DR 5-HT neurons, which can influence the entire brain, are largely unknown. Here we measured population activities of 5-HT neurons in male and female mouse DR across the sleep-wake cycle by a ratiometric fiber photometry system. We found a slow oscillatory activity of compound intracellular Ca2+ signals during NREM sleep. The trough of concave 5-HT activity increased along with sleep progression, but the 5-HT activity level always returned to that seen in wake periods. When the trough reached the minimum level and remained there, REM sleep initiated. We also found a unique coupling of the oscillatory 5-HT activity and EEG power fluctuation, suggesting that EEG fluctuation is a proxy for 5-HT activity. Optogenetic activation of 5-HT neurons during NREM sleep triggered a high EMG power and induced wakefulness. Optogenetic inhibition induced REM sleep or sustained NREM with an EEG power increase and EEG fluctuation. These manipulations demonstrated a causal role of DR 5-HT neurons in sculpting sleep-wake structure. We also observed EEG fluctuations in human males during NREM sleep, implicating the existence of 5- HT oscillatory activity in humans. We propose that NREM sleep is not a monotonous state, but that it is dynamically regulated by the oscillatory population activity of DR 5- HT neurons. Significant statementPrevious studies have demonstrated single-cell 5-HT neuronal activity across sleep- wake conditions; however, population-level activities of these neurons are largely unknown. We monitored dorsal raphe (DR) 5-HT population activity using a fiber photometry system in mice and demonstrated that activity was highest during wakefulness, and lowest during rapid eye movement (REM) sleep. Surprisingly, during non-REM (NREM) sleep, the 5-HT population activity decreased with an oscillatory pattern, coinciding with EEG fluctuations. We examined the causal role of these 5-HT neuron activities by optogenetics and found that DR 5-HT neurons sculpted sleep-wake conditions by influencing EEG and EMG patterns. We found similar EEG fluctuations in a human sleep EEG study, suggesting the presence of oscillatory 5-HT neuron activity during NREM across species.

neuroscience↗

bioRxiv2021

Violet light modulates the central nervous system to regulate memory and mood

Light stimuli from the external environment serves as a signal. Photoreceptors receive photons at the outer nuclear layer of the retina. Non-visual photoreceptors, such as opsin5 (also known as OPN5 or neuropsin), are expressed in the retinal ganglion cells (RGCs) and hypothalamus to regulate the circadian cycle and body temperature. Here, we show that violet light (VL) stimuli received by OPN5-positive RGCs are transmitted to the habenula brain region. VL improves memory in aged mice and simultaneously increases neural architecture-related genes such as oligodendrocyte-related genes in the hippocampus. In addition, VL improves depressive-like behaviors in the social defeat stress model in an OPN5 dependent manner. Following VL exposure, cFos activation is observed at the nucleus accumbens (NAc) and the paraventricular thalamic nucleus (PVT). Taken together, the results indicate that violet light modulates brain function such as memory and mood by transmitting the signal from RGCs to the habenula region in the brain.

neuroscience↗

bioRxiv2021

Rice MEL2 regulates the timing of meiotic transition as a component of cytoplasmic RNA granules

Cytoplasmic RNA granules play important roles in gene expression at the post-transcriptional level. In this study, we found that the rice RNA-binding protein MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2), which contributes to the control of meiotic entry timing, was a constituent of RNA granules, frequently associating with processing bodies and stress granules in the cytoplasm of premeiotic spore mother cells. MEL2 has four conserved domains and a large intrinsically disordered region, which is often responsible for formation and maintenance of granular structures. MEL2-like proteins with diverse domain structures are widely conserved in land plants and charophyte algae. In basal land plants, MEL2-like proteins are exclusively expressed in the sporophyte, which expresses meiotic genes, suggesting the functional conservation of MEL2 among land plant species. We propose here that MEL2 participates in post-transcriptional regulation of meiotic genes as a component of RNA granules to ensure proper timing of the meiotic transition.

plant biology↗

bioRxiv2020

Regulation of the plastochron by three MANY-NODED DWARF genes in barley

The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf (mnd) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plastochron1 (pla1), pla2, and pla3 mutants in rice. In addition, the maturation of mnd leaves was accelerated, similar to pla mutants in rice. Several barley mnd alleles were derived from three loci--MND1, MND4, and MND8. Although MND4 coincided with a cytochrome P450 family gene that is a homolog of rice PLA1, we clarified that MND1 and MND8 encode an N-acetyltransferase-like protein and a MATE transporter-family protein, which are respectively orthologs of rice GW6a and maize BIGE1 and unrelated to PLA2 or PLA3. Expression analyses of the three MND genes revealed that MND1 and MND4 were expressed in limited regions of the shoot apical meristem and leaf primordia, but MND8 did not exhibit a specific expression pattern around the shoot apex. In addition, the expression levels of the three genes were interdependent among the various mutant backgrounds. Genetic analyses using the double mutants mnd4mnd8 and mnd1mnd8 indicated that MND1 and MND4 regulate the plastochron independently of MND8, suggesting that the plastochron in barley is controlled by multiple genetic pathways involving MND1, MND4, and MND8. Correlation analysis between leaf number and leaf blade length indicated that both traits exhibited a strong negative association among different genetic backgrounds but not in the same genetic background. We propose that MNDs function in the regulation of the plastochron and leaf growth and revealed conserved and diverse aspects of plastochron regulation via comparative analysis of barley and rice. Author summaryThe number of leaves produced during a plants lifetime is major determinant of plant architecture and affects the efficiency of photosynthesis and crop productivity. The leaf number is dependent on the temporal pattern of leaf initiation at the shoot apical meristem, which is termed the plastochron. The genetic factors involved in plastochron regulation have been identified in several plant species. However, whether the functions of plastochron-related genes and their genetic pathways are universal or diversified among different plant species is unclear. In this study, we investigated many-noded dwarf (mnd) mutants in barley, which exhibited a shortened plastochron and a decreased leaf blade length. The mutant alleles used in this study were derived from three loci, MND4, MND1, and MND8, which encode a cytochrome P450 family protein, an N-acetyltransferase-like protein, and a MATE transporter-family protein, respectively. Phenotypic and expression analyses revealed that these three MND genes affect the leaf production rate and leaf maturation program, but their expression levels were interdependent. In addition, the plastochron and leaf growth are closely related but independently regulated. We also analyzed the expression patterns and knockout mutants of rice MND orthologs to clarify whether their biological functions are conserved in rice and barley. This study provides insight into the genetic mechanisms of plastochron control in grass species.

plant biology↗

bioRxiv2019

Cortical surface architecture endophenotype and correlates of clinical diagnosis of autism spectrum disorder

AimPrior structural MRI studies demonstrated atypical gray matter characteristics in siblings of individuals with autism spectrum disorder (ASD). However, they did not clarify which aspect of gray matter presents the endophenotype. Further, because they did not enroll siblings of TD people, they underestimated the difference between individuals with ASD and their unaffected siblings. The current study aimed to solve these questions.\n\nMethodsWe recruited 30 pairs of adult male siblings (15 of them have an ASD endophenotype, other 15 pairs not) and focused on four gray matter parameters: cortical volume and three surface-based parameters (cortical thickness, fractal dimension, and sulcal depth [SD]). First, we sought to identify a pattern of an ASD endophenotype, comparing the four parameters. Then, we compared individuals with ASD and their unaffected siblings in the cortical parameters to identify neural correlates for the clinical diagnosis accounting for the difference between TD siblings.\n\nResultsA sparse logistic regression with a leave-one-pair-out cross-validation showed the highest accuracy for the identification of an ASD endophenotype (73.3%) with the SD compared with the other three parameters. A bootstrapping analysis accounting for the difference in the SD between TD siblings showed a significantly large difference between individuals with ASD and their unaffected siblings in six out of 68 regions-of-interest accounting for multiple comparisons.\n\nConclusionsThis proof-of-concept study suggests that an ASD endophenotype emerges in SD and that neural correlates for the clinical diagnosis can be dissociated from the endophenotype when we accounted for the difference between TD siblings. (248/250 words)

neuroscience↗

bioRxiv2018

Machine learning approach to identify resting-state functional connectivity pattern serving as an endophenotype of autism spectrum disorder

Endophenotype refers to a measurable and heritable component between genetics and diagnosis and exists in both individuals with a diagnosis and their unaffected siblings. We aimed to identify a pattern of endophenotype consisted of multiple connections. We enrolled adult male individuals with autism spectrum disorder (ASD) endophenotype (i.e., individuals with ASD and their unaffected siblings) and individuals without ASD endophenotype (i.e., pairs of typical development (TD) siblings) and utilized a machine learning approach to classify people with and without endophenotypes, based on resting-state functional connections (FCs). A sparse logistic regression successfully classified people as to the endophenotype (area under the curve=0.78, classification accuracy=75%), suggesting the existence of endophenotype pattern. A binomial test identified that nine FCs were consistently selected as inputs for the classifier. The least absolute shrinkage and selection operator with these nine FCs predicted severity of communication impairment among individuals with ASD (r=0.68, p=0.021). In addition, two of the nine FCs were statistically significantly correlated with the severity of communication impairment (r=0.81, p=0.0026 and r=-0.60, p=0.049). The current findings suggest that an ASD endophenotype pattern exists in FCs with a multivariate manner and is associated with clinical ASD phenotype.

neuroscience↗

bioRxiv2017

Aberrant cerebellar-default-mode functional connectivity underlying auditory verbal hallucinations in schizophrenia revealed by multi-voxel pattern analysis of resting-state functional connectivity MRI data

Past neuroimaging studies have reported that aberrant functional connectivity (FC) underlying auditory verbal hallucinations (AVHs) in schizophrenia is highly distributed over multiple functional networks. There is thus a need for exploratory approaches without limiting analysis to particular seed regions or functional networks, to identify FC alterations underlying AVH. We applied a multi-voxel pattern analysis (MVPA) of FC together with a series of post-hoc FC analyses to resting-state fMRI data acquired from 25 patients with schizophrenia and 25 matched healthy controls. First, the MVPA revealed multiple clusters exhibiting altered FC patterns in schizophrenia. Subsequent multiple linear regression analysis using scores of these clusters identified that FC alteration in the right cerebellum crus I was significantly associated with the severity of AVH. Furthermore, post-hoc FC analysis with the right crus I as a seed revealed significant FC alterations with regions distributed across multiple functional networks, including speech, default-mode, thalamus, and cerebellum. Subsequent linear regression analyses further demonstrated that, among these regions, only reduced FC in the left precuneus was significantly associated with the severity of AVH. Our unbiased exploratory analysis of FC data revealed a novel evidence for the crucial role of FC between cerebellar and default-mode networks in AVH. (198 words)

neuroscience↗