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Tsuda, S.

Publications and source records attributed to Tsuda, S..

12 recordsLinked to original sources

Developmental emergence of spatiotemporal coordination in cerebellar Purkinje cell populations

Coordinated activity across neuronal populations is fundamental to brain function, yet how such network-level organization emerges during development remains incompletely understood. Here, we performed whole-cerebellar calcium imaging at cellular scale in zebrafish larvae to examine the developmental maturation of Purkinje cell population dynamics. Visual stimulation recruited large, spatially organized populations of Purkinje cells whose responses depended on inferior olive input and were associated with optokinetic behavior. Notably, in the absence of stimuli, Purkinje cells formed transient assemblies exhibiting distance-dependent coordination. During development, long-range coordination progressively emerged, extending initially local correlations into distributed population-wide coordination. Early enucleation, but not dark rearing, disrupted the developmental refinement of long-range coordination and induced aberrant population clustering, suggesting that early retina-dependent signals contribute to cerebellar network development. Together, these findings reveal key organizational features underlying the developmental emergence of coordinated cerebellar population dynamics and suggest that early retina-dependent signals shape population-level organization.

neuroscience↗

Establishment of a transgenic strain for the whole brain calcium imaging in larval medaka fish (Oryzias latipes)

GCaMP-based calcium imaging is a powerful tool for investigating neural function in specific neurons. We generated transgenic (Tg) medaka strains expressing jGCaMP7s across extensive brain regions under the control of the gap43 promoter. Using these Tg larvae, calcium imaging successfully detected a tricaine-induced suppression of spontaneous neural activity and topographical visual responses in the optic tectum elicited by moving paramecia or optical fiber stimulation. These results indicate that our Tg medaka strains provide a versatile platform for investigating neural dynamics and their responses to various stimuli.

molecular biology↗

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zone are largely clustered to form complex porous structural unit called aggregates where highly diverse microbes coexist and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microbes exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. Yet, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus adequate cell extraction method from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) isolated from a topsoil of cultivated Acrisol. Using the same six individual aggregates, we performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion methods improved the extractability of bacterial cells compared to previous studies, the latter yielded higher number and more diverse microbes compared to the former. The analyses of nitrogen-cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to greater recovery of microbes strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microbes having the genes (i.e., potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. In addition, all six aggregates studied showed overall similarity in pore characteristics, phylum-level composition, and the microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggest that conventional methods employed for the extraction of cell and DNA may not be optimal. The current findings underscore the necessity to advance extraction methodologies, thereby facilitating a more comprehensive understanding of the microbial diversity and functioning within soil environments.

microbiology↗

Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states.

Single nucleotide variants (SNVs) contribute to cancer by altering the coding and the non-coding regions of the genome. Connecting SNVs to transcriptomic and epigenetic changes at the single-cell level remains challenging. To enable studies of rare cell populations harboring specific point mutations, we developed STAR-FACS, Specific-To-Allele PCR-FACS, to sort cells based on genomic allele alterations. We show that STAR-FACS can separate cells based on TERT promoter mutation status and is compatible with bulk and single-cell transcriptomic and epigenetic profiling. We demonstrate that glioblastoma cell lines derived from the same tumor but harboring distinct TERT promoter SNVs have different transcriptional programs.

cancer biology↗

A combination of two-enzyme system and enzyme engineering improved the activity of a new PET hydrolase identified from soil bacterial genome

We here report a novel PET hydrolase originating from a soil microbial genome sequence. This enzyme, bbPET0069, exhibits characteristics resembling a cutinase-like Type I PET-degrading enzyme but lacks disulfide bonds. Notably, bbPET0069 displayed remarkable synergy with Candida antarctica lipase B (CALB), demonstrating rapid and efficient PET degradation. To improve the PET degradation activity of bbPET0069, we employed a three-dimensional (3D) structural modeling to identify mutation sites around its substrate binding domain combined with a protein language model for effective mutation prediction. Through three initial rounds of directed evolution, we achieved a significant enhancement in PET degradation with CALB, resulting in a 12.6-fold increase compared to wild-type bbPET0069 without CALB. We confirmed its PET degradation activity in PET nanoparticles and films, and our proposed approach enabled efficient PET degradation to terephthalic acid monomers up to 95.5%. Our approach, which integrates a two-enzyme system with protein engineering, demonstrates the potential for enhancing the activity of emerging PET-degradation enzymes, which may possess unique attributes. Graphical AbstractA novel PET hydrolase, bbPET0069, was identified from a soil microbial genome. bbPET0069 and CALB showed remarkable synergy in PET degradation. Using surface feature analysis, PET degradation activity of bbPET0069 was significantly improved. This combination of a two-enzyme system and surface feature analysis holds promise for enhancing emerging PET-degradation enzymes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/578500v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@4c1c08org.highwire.dtl.DTLVardef@c47c74org.highwire.dtl.DTLVardef@1c6cd19org.highwire.dtl.DTLVardef@c32e73_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

The effects of paroxetine-induced transient apoptosis and brain remodeling on social behavior in developing zebrafish

Autism spectrum disorder (ASD) is a neurodevelopmental condition caused by various genetic and environmental factors. This disorder has the cardinal symptoms including impaired social behavior involving the amygdala. Ingesting antidepressants such as paroxetine in early pregnancy increases the risk of ASD in offspring. However, a comprehensive picture of the underlying pathogenic mechanisms remains elusive. Here we demonstrate that early exposure of zebrafish embryos to paroxetine retards neurogenesis in the optic tectum and the telencephalon that includes a region corresponding to the mammalian amygdala. Paroxetine-treated embryos exhibit impaired growth, with small heads and short body lengths resulting from transient apoptosis. This is reminiscent of the early-onset fetal growth restriction (FGR) associated with ASD. Interestingly, the delayed neurogenesis in the small heads was found to be restored after the cessation of paroxetine. This restoration was accompanied by extended retinotectal projections, suggesting brain-preferential remodeling. Finally, social behavior of the paroxetine-treated fish was examined. Our findings imply a biological mechanism underlying early exposure to paroxetine, a risk factor associated with the pathogenesis of ASD.

pharmacology and toxicology↗

Uncovering novel endolysins against methicillin-resistant Staphylococcus aureus using microbial single-cell genome sequencing

Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of endolysins is vital. We here propose microbial single-cell genome sequencing as an efficient tool to discover dozens of previously unknown endolysins, owing to its culture-independent sequencing method. As a proof-of-concept, we analyzed and recovered endolysin genes within prophage regions of Staphylococcus single-amplified genomes (SAGs) in human skin microbiome samples. We constructed a library of chimeric endolysins by shuffling domains of the natural endolysins and performed high-throughput screening against Staphylococcus aureus. One of the lead endolysins, bbst1027, exhibited desirable antimicrobial properties such as rapid bactericidal activity, no detectable resistance development, and in vivo efficacy. We foresee that this endolysin discovery pipeline is in principle applicable to any bacterial target, and boost the development of novel antimicrobial agents.

microbiology↗

In vivo long-term voltage imaging by genetically encoded voltage indicator reveals spatiotemporal dynamics of spinal cord neuronal populations during development

One of the central questions in neural development is how individual neurons assemble functional networks. To address this, it is essential to elucidate how coordinated activity emerges during development. However, tracking the functional maturation of neuronal populations over time remains challenging, as it requires long-term, non-invasive monitoring of membrane potential dynamics. Here, we developed a voltage imaging approach for zebrafish embryos using genetically encoded voltage indicators (GEVIs), enabling fast, direct and cell-type-specific measurements of membrane potentials from defined neuronal populations in a non-invasive manner. Using this approach, we detected coordinated voltage changes in spinal motor neurons with high spatiotemporal resolution. Depolarization and hyperpolarization events were observed at the population, single-cell, and subcellular levels. Notably, long-term voltage imaging revealed the early emergence and progressive maturation of membrane potential dynamics, characterized by increased firing rate, coupling strength and axonal outgrowth. This optical approach constitutes a significant advancement in the study of neural development, providing a powerful tool for investigating the spatiotemporal dynamics of neuronal populations in vivo.

neuroscience↗

Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing, revealed nine types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and the differentiation pathways involved in their maturation. We also discovered cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.

cell biology↗

Establishment of a novel method for the production of chimeric mouse embryos using oil droplets.

The production of chimeric animals is frequently necessary for the constructing genetically modified animals, and has gained popularity in regenerative medicine in the recent years for the reconstruction of xenogeneic organs. The aggregation method and the injection method are generally used for producing chimeric mice. In the aggregation method, the chimeras are produced by co-culturing embryos and stem cells, and keeping them physically adhered. In the injection method, the chimeras are produced by injecting stem cells into the zona pellucida using microcapillaries. These methods only focus on the generation of chimeric animals, and are not expected to produce reproducible results or allow quantitative evaluation. This study aimed to establish a novel method for producing chimeric embryos via droplets for improving on the conventional methods that are used for producing chimeric embryos. In this study, the embryonic stem cells and embryos were successfully isolated in the droplets, and the emergence of chimeric embryos was confirmed by co-culture for 6 hours. By this method, the control and operability of stem cell numbers can be regulated, and the method allows better reproducibility and quantification during the production of chimeric embryos. In addition to the conventional methods for producing chimeric embryo, the novel method described herein could be employed for the efficient production of chimeric animals.

bioengineering↗

High-throughput screening of high protein producer budding yeast using gel microdrop technology

The need for protein production has been growing over the years in various industries. We here present a high-throughput screening strategy to isolate high producer budding yeast clones from a mutagenized cell population using gel microdrop (GMD) technology. We use a microfluidic water-in-oil (W/O) emulsion method to produce monodisperse GMDs and a microfluidic cell sorter for damage-free sorting of GMDs by fluorescently quantifying secreted proteins. As a result, this high-throughput GMD screening method effectively selects high producer clones and improves protein production up to five-fold. We speculate that this screening strategy can be applied, in principle, to select any types of high producer cells (bacterial, fungal, mammalian, etc.) which produce arbitrary target protein as it does not depend on enzymes to be produced.

bioengineering↗

Uncovering cell-free protein expression dynamics by a promoter library with diverse strengths

Cell-free protein expression systems have been widely used for synthetic biology and metabolic engineering applications in recent years. Yet little is known about protein expression in the cell-free systems. Here we take a systems approach to uncover underlying dynamics of cell-free protein expression. We construct a set of T7 promoter variants to express proteins at different transcription rates in a reconstituted and E. coli extract-based cell-free systems. We find that the maximum expression level and the rate of protein synthesis as responses to the transcription rate change are different in the two cell-free systems, suggesting they are driven by different expression dynamics. We confirm this by constructing a simple mathematical model for each cell-free system, which well reproduce the experimental results and also identify different limiting factors for better protein expression in the two cell-free systems. In particular, they revealed there is a negative feedback effect in the mRNA-protein translation by the PURE system and also identified different limiting factors for better protein expression in the two cell-free systems.

synthetic biology↗