Biology subjects

Shimada, N.

Publications and source records attributed to Shimada, N..

8 recordsLinked to original sources

bioRxiv2026

A single-nucleus and spatial transcriptomic atlas of the Syrian hamster preoptic area across hibernation states

Hibernation is an extreme physiological state in certain mammals that is characterized by a reversible reduction in metabolic and thermogenic demands. Although the preoptic area has been implicated in the regulation of hibernation, comprehensive molecular and spatial resources for this brain region in hibernating mammals remain limited. Here, we present an integrated transcriptomic resource of the preoptic area generated using single-nucleus RNA sequencing (snRNA-seq) and Xenium-based spatial transcriptomics in a mammalian hibernator, Syrian hamster. The resource includes cross-species transcriptomic annotations relative to mouse preoptic area datasets, seasonal snRNA-seq datasets obtained under non-hibernating and hibernating conditions, and spatially resolved cell-type annotations generated from Xenium profiling. Together, these datasets provide a reference framework for identifying neuronal populations, examining molecular conservation across species and conditions, and integrating transcriptomic identity with spatial organization.

neuroscience↗

bioRxiv2026

A Master-Key DNA System Enabling Programmable Cross-Talks in Biomimetic Networks via An Artificial Chaperone

Biological systems operate through complex molecular networks programmed by genetic information; however, constructing artificial systems with multilayered control remains a significant challenge. Here, we report a simple and integrated master-key system governed by lock DNA and master key DNA, reversibly switching diverse downstream processes ON/OFF and achieving dynamic cross-talks among distinct molecular components. The system utilizes cationic copolymer chaperones as control nodes, based on poly(L-lysine) or poly(allylamine) grafted with hydrophilic side chains, with a peptide nucleic acid (PNA) plug-in that grants sequence-specificity. We demonstrated two proof-of-concept systems: a nucleic acid-based catalytic network responsive to microRNA let-7b and a peptide-mediated transformation of lipid bilayers from two-dimensional sheets to three-dimensional vesicles. Both systems exhibited precise, modular, and programmable control with high robustness, mimicking the governing role of nucleic acids in biological systems. This strategy provides a versatile design framework for constructing biomimetic molecular networks and studying biological systems.

bioengineering↗

bioRxiv2026

Adhesion-mediated transition to a mesenchymal-like, fan-shaped migration mode in Dictyostelium discoideum

Cells migrate with varying degrees of polarization and directional persistence as exemplified by epithelial, mesenchymal and amoeboid cell types. Depending on the physiological and developmental context, these states are often interchangeable, reflecting the plastic and adaptive nature of the cytoskeleton. However, general principles governing such motility-mode transitions remain poorly established, and it is unclear whether they apply to non-metazoan cells. Here, we report previously overlooked features of the amoebozoan Dictyostelium discoideum, demonstrating that it undergoes pronounced adhesion-dependent changes in both motility and morphology. Unlike the well-known pseudopodia-rich forms observed on weakly adhesive surfaces, cells on highly adhesive substrates adopt fan-shaped morphologies reminiscent of cultured mesenchymal cells. These cells are characterized by lamellipodia-like protrusions enriched in the SCAR/WAVE complex, large focal adhesion-like plaques, F-actin-independent front-rear gradients of Ras/Rap activity. Furthermore, they exhibit a marked increase in cortical stiffness dependent on F-actin, talins, and the RhoA homolog RacE. Their high directional persistence depends on the persistent localization of the SCAR/WAVE complex, talin-mediated substrate anchoring, and RacE-dependent stabilization of the cell rear. We propose that adhesion-engaged remodeling of cell polarity and cortical mechanics is an evolutionarily ancient feature that predates the specialization of adhesion receptors.

cell biology↗

bioRxiv2025

A nanobody-based degron system for targeted protein knockdown in Dictyostelium discoideum

BackgroundsThe cellular slime mold Dictyostelium discoideum is a widely used model system for studying basic processes in cell and developmental biology. While genetic tools, such as targeted gene disruption by homologous recombination and genome editing using CRISPR/Cas9, are well-established in D. discoideum, efficient methods for conditional loss-of-function studies are limited. Here, we developed a nanobody-based degron system for D. discoideum based on ALFA-tagged protein recruitment to the Skp1-Cullin-F-box (SCF) complex. ResultsALFA-tagged Histone H1 was efficiently degraded by expressing anti-ALFA nanobody (NbALFA) fused to the D. discoideum FbxD F-box domain ( dictyGrad-ALFA). Cell type-specific targeting was achieved by expressing dictyGrad-ALFA under prestalk- and prespore-specific gene promoters. Furthermore, targeting of adenylyl cyclase A (ACA) resulted in the expected aggregation-deficient phenotype, validating the efficacy of dictyGrad-ALFA-mediated protein depletion. Cell type-specific ACA degradation delayed development but eventually resulted in normal fruiting bodies. Our ALFA-tag approach was further used for conditional knockdown in combination with the auxin-inducible degron 2 (AID2) system, which relies on indole-3-acetic acid (IAA)-dependent binding between NbALFA-mAID and a OsTIR-F-box-Skp1A fusion protein. We obtained efficient IAA-induced degradation in prestalk cells; however, efficiency was low in other cell types. ConclusionsTogether, these systems pave the way for conditional and cell type-specific protein degradation in D. discoideum, enabling functional analyses of essential genes for development and survival.

cell biology↗

bioRxiv2024

Effectiveness of Exercise Intervention in Preventing Active Arthritis Exacerbation in an SKG Mouse Model of Rheumatoid Arthritis

ObjectivesTo investigate the effects of low-intensity exercise on active arthritis in an SKG mouse model of human rheumatoid arthritis (RA) pathology. MethodsTwenty-four female SKG mice were divided into three groups: sedentary (control), AR (induced arthritis), and AREx (induced arthritis plus low-intensity exercise). Arthritis was induced via intraperitoneal administration of mannan. After a 2-week inflammation period, low-intensity treadmill exercise was performed only in the AREx group. Arthritis was assessed weekly during the rearing period. After 4 weeks of exercise, histological and bone morphometric analyses of the right ankle joint were performed. A histological analysis of the gastrocnemius muscle was also performed. Bulk mRNA sequencing was conducted on the left synovial membrane-fat pad (SM-FP) complex. ResultsThe synovitis score showed no change; however, the arthritis score was significantly lower in the AREx group than in the AR group (p<0.05), indicating that low-intensity exercise suppressed arthritis exacerbation. The calcaneal and talar bone volumes decreased in the AR group, whereas the AREx group showed no significant change. In the SM-FP complex tissue, the gene expression of inflammatory cytokines decreased in the AREx group compared with the AR group, particularly the suppression of IL6/Jak/Stat3. Immunohistochemical analysis revealed significantly decreased expression of pro-inflammatory cytokines and increased expression of anti-inflammatory cytokines in the synovium of the AREx group compared with the AR group (p<0.05). ConclusionLow-intensity exercise therapy for active RA showed anti-inflammatory and suppressive effects on arthritis exacerbation in SKG mice, a mouse model of human RA pathology. Key messagesO_LIExercise had an anti-inflammatory effect on SKG mice, a mouse model of rheumatoid arthritis. C_LIO_LIExercise suppresses pro-inflammatory cytokine pathways such as IL6/Jak/Stat3 signalling in the synovial-fat complex tissue. C_LIO_LIExercise therapy is effective in improving the pathophysiology of active rheumatoid arthritis. C_LI

molecular biology↗

bioRxiv2022

Evolutionary stability of social commitment

Conflict resolution between individual cells and a group is essential for multicellularity. The social amoeba Dictyostelium discoideum switches between solitary growth and social fruitification depending on nutrient availability. Under starvation, cells form fruiting bodies consisting of spores and non-viable altruistic stalk cells. Once cells socially committed, they complete fruitification even with a renewed source of nutrients. This social commitment is puzzling because it deprives individual cells of benefits of quickly resuming solitary growth. One idea posits that traits that facilitate premature de-commitment are somehow hindered from being selected. We studied outcomes of premature de-commitment by forced refeeding. We show that when refed cells resume sociality together with non-refed cells, besides some becoming solitary outside of fruiting bodies, a large fraction was redirected to a sub-region of altruistic stalk regardless of their original fate. The refed cells exhibited reduced cohesivity and were sorted out to the altruistic positions in morphogenesis. Furthermore, a theoretical model considering evolution of cell-cell association revealed a valley in the fitness landscape that prevents invasion of de-committing mutants. Our results provide a general scheme that naturally penalizes withdrawal from a society by evolving a specific division of labor that less cohesive individuals become altruists. Significance StatementEvolution of unicellular to multicellular organisms must resolve conflicts of reproductive interests between individual cells and the group. In the social amoeba Dictyostelium, a transition from a solitary to multicellular group occurs under starvation. Once cells commit themselves to multicellular organization, the process continues even when shifting to an environment that favors solitary growth. Our study revealed that cells forced to partially revert to a de-committed state take an altruistic role through interaction with socially committed cells. The de-committed cells exhibited reduced cohesivity and were sorted out to altruistic positions in morphogenesis. This inevitably penalizes selfish cells that revert to solitary growth too quickly. Our results explain group-level behavior that is apparently difficult to understand from an individual-level fitness.

evolutionary biology↗

bioRxiv2018

Tissue self-organization based on collective cell migration by contact activation of locomotion and chemotaxis

Despite their central role in multicellular organization, navigation rules that dictate cell rearrangement remain much to be elucidated. Contact between neighboring cells and diffusive attractant molecules are two of the major determinants of tissue-level patterning, however in most cases, molecular and developmental complexity hinders one from decoding the exact governing rules of individual cell movement. A primordial example of tissue patterning by cell rearrangement is found in the social amoeba Dictyostelium discoideum where the organizing center or the tip self-organize as a result of sorting of differentiating prestalk and prespore cells. Due to its relatively simple and conditional multicellularity, the system provides a rare case where the process can be fully dissected into individual cell behavior. By employing microfluidics and microsphere-based manipulation of navigational cues at the single-cell level, here we uncovered a previously overlooked mode of Dictyostelium cell migration that is strictly directed by cell-cell contact. The cell-cell contact signal is mediated by E-set Ig-like domain containing heterophilic adhesion molecules TgrB1/TgrC1 that act in trans to induce plasma membrane recruitment of SCAR complex and formation of dendritic actin networks, and the resulting cell protrusion competes with those induced by chemoattractant cAMP. Furthermore, we demonstrate that both prestalk and prespore cells can protrude towards the contact signal as well as to chemotax towards cAMP, however when given both signals, prestalk cells orient towards the chemoattractant whereas prespore cells choose the contact signal. These data suggest a new model of cell sorting by competing juxtacrine and diffusive cues each with potential to drive its own mode of collective cell migration. The present findings not only resolve the long standing question of how cells sort in Dictyostelium but also cast light on the remarkable parallels in collective cell migration that evolved independently in metazoa and amoebozoa.

cell biology↗

bioRxiv2018

Reverse transcription-PCR using a Primer Set Targeting the 3D Region Detects Foot-and-Mouth Disease Virus with High Sensitivity

Because foot-and-mouth disease (FMD) has the potential to spread extensively, methods used for its diagnosis must be rapid and accurate. Therefore, reverse transcription-PCR (RT-PCR) plays an important diagnostic role. Here we designed the primer set FM8/9 to amplify 644 bases of the conserved 3D region of all seven serotypes of FMD virus (FMDV). We compared the performance of RT-PCR assays using FM8/9 with that using the primer set 1F/R targeting the 5-UTR described in the manual of the World Organization for Animal Health. The detection limits of the RT-PCR assays were determined for 14 strains representing all serotypes. Compared with the sensitivities of the RT-PCR assay using 1F/R, those using FM8/9 were 101-to 104-fold higher for eight strains. To assess the validity of the methods for analyzing clinical samples, sera and saliva samples from pigs and cows infected with FMDV were collected daily and analyzed using the two PCR assays. The FM8/9 assay detected FMDV from all infected pigs and cows for longer times compared with the 1F/R assay, therefore revealing higher sensitivity for the clinical samples. Our results suggest that the FM8/9 RT-PCR assay is highly sensitive and is therefore suitable for the diagnosis of FMD.

microbiology↗