Biology subjects

Kawai, H.

Publications and source records attributed to Kawai, H..

9 recordsLinked to original sources

bioRxiv2026

Ultrastructurally planar growth cones during neocortical axon navigation

Neurons extend axons toward spatially defined but often distant targets to establish brain circuits. Callosal projection neurons exemplify this organization, linking corresponding cortical territories between the two hemispheres. Growing axons rely on growth cones to regulate direction and speed through densely packed tissues. Although growth cone morphology and dynamics have been extensively characterized in cultured neurons and invertebrate models, how growth cones navigate the three-dimensional environment of the developing mammalian brain remains poorly explored. Here, we combined a genetically encoded electron microscopy (EM)-labeling strategy and zero-shot deep-learning-based tracing with high-resolution volume EM to reconstruct growth cones of identified callosal projection neurons in the developing mouse brain. Mediolaterally extending growth cones exhibited a planar, fan-shaped morphology, preferentially expanded along the dorsoventral axis. Filopodia extended from the edges of this plane and aligned predominantly with the same axis but showed no directional bias toward the growing direction. Longitudinal in vivo imaging revealed that increased growth cone complexity associated with filopodial extension coincided with lower instantaneous velocity but preceded accelerated extension. Together, these findings reveal a dorsoventrally oriented planar growth cone architecture in which filopodial extension precedes accelerated axon growth, suggesting a structural constraint that may restrict axon navigation to the callosal plane.

neuroscience↗

bioRxiv2025

Deep Learning Pipeline for Segmentation and Quantification of Overlapping Membranes in 2D Image

Quantitative morphological analysis is crucial for understanding cellular processes. While 3D Z-stack imaging offers high-resolution data, the complexity of 3D structures makes direct interpretation and manual annotation challenging and time-consuming, especially for large datasets. Maximum Intensity Projection (MIP) is a common strategy to create more interpretable 2D representations, but this inevitably leads to artificial overlaps between structures, significantly hindering accurate automated segmentation of individual instances by conventional methods or standard deep learning tools. To address this critical challenge in 2D projection analysis, we developed DeMemSeg, a deep learning pipeline based on Mask R-CNN, specifically designed to segment overlapping membrane structures, called prospore membranes (PSMs) during yeast sporulation. DeMemSeg was trained on a custom-annotated dataset, leveraging a systematic image processing workflow. Our optimized model accurately identifies and delineates individual, overlapping PSMs, achieving segmentation performance and derived morphological measurements that are statistically indistinguishable from expert manual annotation. Notably, DeMemSeg successfully generalized to segment PSMs from unseen data acquired from gip1{Delta} mutant cells, capturing the distinct morphological defects in PSMs. DeMemSeg thus provides a robust, automated solution for objective quantitative analysis of complex, overlapping membrane morphologies directly from widely used 2D MIP images, offering a practical tool and adaptable workflow to advance cell biology research.

cell biology↗

bioRxiv2024

Spike protein of the SARS-CoV-2 omicron variant interacts with actin

The omicron variant of SARS-CoV-2 is responsible for the COVID-19 pandemic, serving as a significant origin for the variants still being detected today. It affects the spike protein that most vaccines used to target when the Omicron strain was discovered. Here, we demonstrate that the receptor binding domain (RBD) of the Omicron variant of SARS-CoV-2 exhibits an increased affinity for human angiotensin-converting enzyme type 2 (hACE2) as a viral cell receptor compared to the prototype RBD. We also identified that {beta}- and {gamma}-actin are Omicron-specific binding partners of RBD. Protein complex predictions suggested that many of the Omicron-specific amino acid substitutions might be involved in the affinity of RBD and actin. Accordingly, we highlight the intriguing observation that proteins expected to localize to different cellular compartments exhibit strong binding.

biochemistry↗

bioRxiv2024

Transcriptional landscape of the dorsal raphe serotonin neurons rendering stress resiliency

Major depressive disorder (MDD) is a serious and large social problem, yet the pathophysiology of MDD and the action mechanism of antidepressants are still poorly understood. A number of studies have reported that activation and inactivation of serotonin neurons in the dorsal raphe nucleus (DRN) cause antidepressant-like effects and depressive-like behaviors, respectively. Also, their physiological neural activities are increased when mice were chronically administered an SSRI and decreased in mice exposed to chronic social defeat stress (CSDS), a mouse model of depression. However, the molecular mechanism underlying these neural activity changes in DRN serotonin neurons remains unclear. In this study, we performed a DRN serotonin neuron-specific comprehensive gene expression analysis by using Translating Ribosome Affinity Purification (TRAP) technology in both chronic SSRI-treated mice as a model of antidepressant treatment and CSDS mice as a model of depression. It revealed that many gene expression changes were the opposite between SSRI-treated mice and CSDS-susceptible mice. Among these, we identified S100a10 as a prodepressive gene in DRN serotonin neurons, and we found that Interleukin-4 (IL-4) - Signal Transducer and Activator of Transcription 6 (STAT6) pathway and 5-HT1B receptor were the upstream and downstream molecules of S100a10, respectively. Our findings provide insights into molecular mechanisms underlying the action of antidepressants and stress resiliency.

pharmacology and toxicology↗

bioRxiv2024

Systematic mutagenesis assay promotes comprehension of the strand-bias laws for mutations induced by oxidative DNA damage

We have recently developed an efficient and sensitive method for analyzing mutations caused by various environmental and endogenous factors which utilizes nucleotide-barcoded supF shuttle vector libraries with a multiplexed NGS assay, referred to hereafter as supF NGS assay. Ionizing-radiation-induced cancer is known to be difficult to distinguish from spontaneous cancer, especially in the case of low-dose and low-dose-rate exposure, and discerning the underlying mechanisms of ionizing-radiation-induced cancer, especially the relationship between mutagenesis and carcinogenesis, is likely to be an arduous task. In the present study, we have attempted to address the mutations characteristic for exposure to low levels of ionizing radiation by using the supF NGS assay. As a result, a significant increase in mutations was detected at cytosines and guanines within 5-TC-3:5-GA-3 sites following chronic gamma-irradiation at a dose-rate of 1 Gy per day for the duration of 2 days. Since the number of detected mutations exceeded the expectations based on the quantity of DNA-damage induced by irradiation, we proceeded to explore the possibilities that a single DNA-lesion induced by irradiation may cause amplification of mutations. For this purpose, we utilized shuttle vector libraries with a single 8-oxo-7,8-dihydroguanine (8-oxo-G)-damaged residue introduced at different sites via an in vitro enzymatic method. Through a set of experiments, we revealed that a single 8-oxo-G-damaged residue can become a trigger for peripheral mutagenesis; intense generation of strand-biased mutations occured at 5-TC-3:5-GA-3 sites with specific localization in the secondary structures of single-stranded DNA, more frequently than not at sites different from the 8-oxo-G-damaged sites. Thus, this study provides a novel prospect for the role of DNA-lesions induced by environmentally or endogenously generated ROS in additional mutations. The high-performance mutagenesis assay presented in this study will advance research aimed at uncovering the mechanisms of mutagenesis and the intricacies relevant to carcinogenesis.

cell biology↗

bioRxiv2022

Development of a versatile high-throughput mutagenesis assay with multiplexed short read NGS using DNA-barcoded supF shuttle vector library amplified in non-SOS E. coli

A forward mutagenesis assay using the supF gene has been widely employed for the last several decades in studies addressing mutation frequencies and mutation spectra associated with various intrinsic and environmental mutagens. In this study, by using a supF shuttle vector and non-SOS-induced Escherichia coli with short read Next Generation Sequencing (NGS) technology, we present an advanced method for the study of mutations, which is simple, versatile, and cost-effective. We demonstrate the performance of our newly developed assay via pilot experiments with UV-irradiation, the results from which emerge more relevant than expected. The NGS data obtained from samples of the indicator E. coli grown on titer plates provides mutation frequency and spectrum data, and uncovers obscure mutations that cannot be detected by a conventional supF assay. Furthermore, a very small amount of NGS data from selection plates reveals the almost full spectrum of mutations in each specimen and offers us a novel insight into the mechanisms of mutagenesis, despite them being considered already well-known. We believe that the method presented here will contribute to future opportunities for research on mutagenesis, DNA repair, and cancer.

molecular biology↗

bioRxiv2021

MeDUsA: A novel system for automated axon quantification to evaluate neuroaxonal degeneration

BackgroundDrosophila is an excellent model organism for studying human neurodegenerative diseases (NDs), and the rough eye phenotype (REP) assay is a convenient experimental system for analysing the toxicity of ectopically expressed human disease genes. However, the association between REP and axonal degeneration, an early sign of ND, remains unclear. To address this question, we developed a method to evaluate axonal degeneration by quantifying the number of retinal R7 axons in Drosophila; however, it requires expertise and is time-consuming. Therefore, there is a need for an easy-to-use software that can automatically quantify the axonal degeneration. ResultWe created MeDUsA (a method for the quantification of degeneration using fly axons), which is a standalone executable computer program based on Python that combines a pre-trained deep-learning masking tool with an axon terminal counting tool. This software automatically quantifies the number of axons from a confocal z-stack image series. Using this software, we have demonstrated for the first time directly that axons degenerate when the causative factors of NDs (Syn, Tau, TDP-43, HTT) were expressed in the Drosophila eye. Furthermore, we compared axonal toxicity of the representative causative genes of NDs and their pathological alleles with REP and found no significant correlation between them. ConclusionsMeDUsA rapidly and accurately quantifies axons in Drosophila eye. By simplifying and automating time-consuming manual efforts requiring significant expertise, it enables large-scale, complex research efforts on axonal degeneration, such as screening to identify genes or drugs that mediate axonal toxicity caused by ND disease proteins.

pathology↗

bioRxiv2021

A quantitative model of sporadic axonal degeneration in the Drosophila visual system

In human neurodegenerative diseases, neurons undergo axonal degeneration months to years before they die. Here, we developed a system modelling early degenerative events in Drosophila adult photoreceptor cells. Thanks to the stereotypy of their axonal projections, this system delivers quantitative data on sporadic and progressive axonal degeneration of photoreceptor cells. Using this method, we show that exposure of adult flies to a constant light stimulation for several days overcomes the intrinsic resilience of R7 photoreceptors and leads to progressive axonal degeneration. This was not associated with apoptosis. We furthermore provide evidence that loss of synaptic integrity between R7 and a postsynaptic partner preceded axonal degeneration, thus recapitulating features of human neurodegenerative diseases. Finally, our experiments uncovered that neurotransmission to postsynaptic partners of R7 and their response are required to initiate degeneration, suggesting that postsynaptic cells signal back to the photoreceptor to maintain axonal structure. This model can be used to dissect cellular circuit mechanisms involved in the early events of axonal degeneration, allowing for a better understanding of how neurons cope with stress and lose their resilience capacities.

neuroscience↗

bioRxiv2021

An interactive deep learning-based approach reveals mitochondrial cristae topologies

Outer and inner mitochondrial membranes are highly specialized structures with distinct functional properties. Reconstructing complex 3D ultrastructural features of mitochondrial membranes at the nanoscale requires analysis of large volumes of serial scanning electron tomography data. While deep-learning-based methods improved in sophistication recently, time-consuming human intervention processes remain major roadblocks for efficient and accurate analysis of organelle ultrastructure. In order to overcome this limitation, we developed a deep-learning image analysis platform called Python-based Human-In-the-LOop Workflows (PHILOW). Our implementation of an iterative segmentation algorithm and Three-Axis-Prediction method not only improved segmentation speed, but also provided unprecedented ultrastructural detail of whole mitochondria and cristae. Using PHILOW, we found that 42% of cristae surface exhibits tubular structures that are not recognizable in light microscopy and 2D electron microscopy. Furthermore, we unraveled a fundamental new regulatory function for the dynamin-related GTPase Optic Atrophy 1 (OPA1) in controlling the balance between lamellar versus tubular cristae subdomains.

cell biology↗