Biology subjects

Nakajima, Y.

Publications and source records attributed to Nakajima, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Topological defects and coherent myocardial chirality shape torsional heart contraction

The efficient pumping of the mammalian heart relies on torsional contractile motion generated by its highly ordered three-dimensional (3D) architecture of myocardial fibres. However, the topological principles governing how its complex geometry translates into contractile mechanics remain elusive. Here, we show that the mammalian heart forms a chiral nematic field, a biological analogue to 3D liquid crystals, whose topological organisation underlies its function. Analysis of 3D imaging data revealed disclination lines, continuous assemblies of topological defects characteristic of nematic systems, within the compact myocardium. Finite-element simulations reveal that these defects are not mere structural irregularities but can locally modulate contractile behaviour and reduce mechanical work. In heterotaxy hearts with reversed global anatomy (situs inversus), myocardial fibres retain a predominantly counter-clockwise twist, similar to that of the normal heart, but with a small clockwise component near the base. This decoupling of tissue-level chirality from systemic left-right patterning suggests that cardiac twist is an intrinsic property of the myocardial fibre. Mechanical simulations of situs inversus heart demonstrate that the coherence of transmural chirality, rather than its specific orientation, is critical for contractile efficiency. Together, these findings establish the heart as a topological material and reveal how organised chiral fields generate robust organ-level mechanical function.

biophysics↗

bioRxiv2026

Division of labor between ERK and Notch signaling coordinates distinct stem cell populations during jellyfish tentacle regeneration

Regeneration restores lost tissues through diverse cellular strategies that vary across species and tissue contexts. In many systems, regeneration involves blastema formation; however, how blastema formation is coordinated in tissues employing multiple stem/progenitor populations remains unclear. Here, we investigate tentacle regeneration in the hydrozoan jellyfish Cladonema, in which two distinct proliferative populations contribute to regeneration: resident homeostatic stem cells (RHSCs), which supply differentiated cell types, and repair-specific proliferative cells (RSPCs), which are transiently induced upon injury to form the blastema. While extensive cell death occurs shortly after injury, it is largely dispensable for blastema formation. Using pharmacological inhibition and cell proliferation analyses, we identify ERK/MAPK signaling as a key regulator of blastema formation. ERK signaling is rapidly activated at the injury site and selectively promotes proliferation of RSPCs without affecting RHSC proliferation. In contrast, inhibition of Notch signaling disrupts nematocyte differentiation and induces hyperproliferation of RHSCs, while leaving RSPC proliferation unchanged, indicating that Notch signaling governs the balance between differentiation and self-renewal in RHSCs. Together, these findings reveal a division of labor between conserved signaling pathways and support a model in which regeneration is achieved through spatially and functionally compartmentalized control of distinct stem cell populations.

developmental biology↗

bioRxiv2026

Aging disrupts tissue homeostasis and constrains blastema-mediated regeneration in the Cladonema medusa

Regenerative capacity varies widely across animals, yet aging is often accompanied by declining tissue homeostasis and regenerative potential. In many species, regeneration of complex structures relies on epimorphic programs that form a blastema, coordinating cell proliferation and pattern reorganization after injury. Although aging-associated regeneration defects have been documented in several bilaterian models, how aging shapes regeneration in early-branching metazoans with robust regenerative abilities remains unclear. Here, we investigate aging and regeneration in the medusa stage of Cladonema pacificum, a cnidarian that retains high regenerative capacity within a finite lifespan. We show that aging in Cladonema medusae is accompanied by progressive morphological and functional deterioration, including shrinkage of the umbrella and manubrium, tentacle shortening, and reduced reproductive output, along with increased DNA damage. At the cellular level, aging is associated with depletion of differentiated cell populations, including nematocytes and neurons, as well as reductions in stem cell-associated populations and proliferative activity in the tentacle bulb. Consistent with these changes, tentacle regeneration is markedly impaired in aged medusae and is characterized by delayed wound closure, defective blastema formation, and incomplete functional recovery. Together, our findings indicate that aging disrupts both tissue homeostasis and blastema-mediated regeneration in Cladonema medusae, establishing a tractable model for studying aging-regeneration interactions and supporting the view that aging imposes broadly shared constraints on regenerative systems across metazoans.

developmental biology↗

bioRxiv2026

Structural basis for impaired oxygen evolution in extrinsic-protein-reconstituted photosystem II

Photosystem II (PSII) is a membrane-bound pigment-protein complex in oxygenic photosynthesis that catalyzes water splitting and oxygen evolution. Here, we present the X-ray crystallographic structure of a PsbO/V/U-reconstituted PSII from Thermosynechococcus vulcanus at 2.0 [A] resolution, revealing proper rebinding of the three extrinsic subunits, PsbO, PsbV, and PsbU. The overall geometry of the Mn4CaO5 cluster is largely preserved, although a subtle shortening of the Mn2-O2 bond suggests a minor local rearrangement. Structural analysis identifies perturbations that may underlie the reduced oxygen-evolving activity, including altered bicarbonate-binding interactions on the electron acceptor side and the loss of water molecules W658 and W660 in the O1 channel, disrupting a hydrogen-bond network critical for water delivery. In contrast, the Cl-1 and O4 channels remain intact. These findings suggest that disrupted water delivery and electron transport, together with minor rearrangements within the Mn4CaO5 cluster, may contribute to the decreased activity of the reconstituted PSII.

plant biology↗

bioRxiv2025

Purification and pigment analysis of diadinoxanthin-binding PSI-LHCI supercomplexes from Euglena gracilis strain Z

Euglena gracilis, a phototrophic flagellate, possesses light-harvesting complexes (LHCs) with a pigment composition distinct from that of land plants and green algae, despite notable similarities in LHC polypeptide sequences to green algae. Here, we purified photosystem I-LHCI (PSI-LHCI) supercomplexes from E. gracilis strain Z and characterized their biochemical and spectroscopic properties. The purified complex exhibited a unique pigment profile, notably including diadinoxanthin that is typically found in red-lineage organisms, setting E. gracilis apart from green-lineage organisms. The absorption spectrum displayed the Qy band of chlorophyll a at 675{square}nm, while the 77-K fluorescence-emission spectrum revealed a prominent peak at 732{square}nm, closely resembling those in land plants. These features suggest that long-wavelength chlorophylls bound to LHCI may be evolutionarily conserved. Nevertheless, the absence of neoxanthin, lutein, and violaxanthin further differentiates the Euglena LHCIs from other oxyphototrophs. Together, these results illuminate the evolutionary diversification of PSI-LHCI supercomplexes and offer insights into the unique pigment-binding features of the Euglena light-harvesting system.

plant biology↗

bioRxiv2025

Cross-Species Biomechanical Determinants of Shape Diversity

How complex molecular mechanisms translate into diverse multicellular shapes remains unclear. By leveraging the bi-layered architecture of six cnidarian species that diverged 500 million years ago, we show that modularity in supracellular mechanics governs larval shape diversity. Using active surface theory, quantitative imaging, and an inducible genetic system, we identify species-specific variations in three biomechanical modules. Basally aligned stress fibers drive axial elongation, while oral geometry and aboral rigidity define shape polarity. Remarkably, manipulating these modules transforms one species shape into another, demonstrating the causal relationship between module variation and shape diversity. Our analysis also uncovers instances of mechanical redundancies, where distinct module combinations generate similar shapes. These findings provide a general framework for how molecular complexity funnels into mesoscale mechanical determinants shaping morphological diversity.

developmental biology↗

bioRxiv2025

BubR1 and Mad2 regulate adult midgut remodeling in Drosophila diapause

Diapause is a survival strategy in which growth and aging are temporarily suspended, enabling animals to withstand unfavorable environments. Various insects, including the fruit fly Drosophila, enter reproductive diapause, or dormancy, in response to colder temperatures and/or shorter day lengths. During reproductive diapause, ovarian development halts, and non-reproductive organs also undergo remodeling at both morphological and metabolic levels: however, the mechanisms underlying this remodeling and its physiological impact remain largely unclear. Here, we show that the Drosophila adult midgut undergoes extensive remodeling in diapause, marked by a sustained suspension of growth due to the cell cycle arrest of intestinal stem cells (ISCs) that revert to normal upon returning to recovery conditions. During dormancy, BubR1 and Mad2, key regulators of mitosis, are highly expressed and localized in the cytoplasm of ISCs rather than at the kinetochore, and both BubR1 and Mad2 are essential for diapause-specific midgut remodeling. Furthermore, disruption of midgut growth arrest during diapause reduces the resistance to starvation in adult flies. Together, our findings identify a novel role for BubR1 and Mad2 in ISCs-promoting proper midgut remodeling during dormancy-and highlight the importance of this process for survival under adverse environments.

developmental biology↗

bioRxiv2024

Engineered coagulation factor VIII with enhanced secretion and coagulation potential for hemophilia A gene therapy

The major challenges of gene therapy for hemophilia A using adeno-associated virus (AAV) vectors are reducing vector doses and the long-term maintenance of stable factor VIII (FVIII). Here, we developed engineered human B-domain-deleted FVIIIs (FVIIISQs) with enhanced secretion and coagulation potential. Intracellular accumulation was markedly reduced in some engineered FVIIISQs, resulting in reduced unfolded protein responses. The administration of AAV vectors carrying engineered FVIIISQ to hemophilia A mice resulted in approximately eight-fold higher FVIII activity and four-fold higher FVIII antigen levels compared with wild-type FVIIISQ administration. The specific FVIII activity of the engineered FVIIISQ was 3.6 times higher than that of the wild-type FVIIISQ, and its binding to activated coagulation factor IX was significantly enhanced, which is supported by the structural analysis. In macaques, the administration of AAV5 vector carrying the engineered FVIIISQ without CpG sequences resulted in a supra-physiological increase in plasma FVIII activity at a dose one-thirtieth that of valoctocogene roxaparvovec (2 x 1012 vg/kg). The engineered FVIIISQ may thus provide stable, long-term therapeutic efficacy in AAV-mediated hemophilia A gene therapy even at low doses.

bioengineering↗

bioRxiv2024

Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638

Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with a red-lineage chlorophyll a/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin, {beta}-cryptoxanthin, and {beta}-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyll a in the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins, including RedCAP, in red algal PSI-LHCI supercomplexes.

plant biology↗

bioRxiv2024

The N-terminal extension region of BamE coordinates interaction between the β-barrel domain of BamA and BamD for efficient assembly

In the Gram-negative bacteria, the assembly of {beta}-barrel proteins into the outer membrane is mediated by the {beta}-barrel Assembly Machinery (BAM) complex. BamA is a central component of the BAM complex. The molecular mechanisms of BamA when the substrate protein is assembled has been well elucidated and further the inhibitors targeting key mechanisms of BamA have been isolated. Although the BAM complex is a multi-subunit machine and its coordination is necessary for full function, the molecular mechanism remains unclear. Here we report on a fine-tuning system with a subunit called BamE, which is required for the cooperation of two essential subunits BamA and BamD. BamE is a lipoprotein with an N-terminal extension region between the lipid-modifying cysteine on the N-terminus and the periplasmic folding domain. Our interaction mapping revealed that the N-terminal extension region of BamE interacts with the {beta}-barrel domain of BamA, which contains a catalytic site for assembly termed lateral gate. The mutational analysis demonstrated that the N-terminal extension region of BamE fine-tunes the assembly stage dependent BamA-BamD interaction, responsible for the crucial role for assembly and integrity of the outer membrane. We suggest that this fine-tuning system plays an important role in the substrate relay system from the receptor BamD to the insertase BamA. Furthermore, structure prediction-based analysis suspects that the C-terminal region of BamD acts as the replacement of BamE in BamE-less bacteria.

biochemistry↗

bioRxiv2024

PD-1 negatively regulates helper T cell differentiation into Th2

Programmed Cell Death Protein-1 (PD-1) represents endogenous mechanisms of negative immunoregulation. While the modulation of effector functions has been the major focus of PD-1 research, quick PD-1 upregulation in naive T cells starting 1 h after priming raised a possibility that PD-1 also affects the development of effector T cells. The role of PD-1 in functional differentiation into Th1 and Th2 has been unclear. In murine naive CD4+ T cell activation, we found that PD-1 stimulation during the early stage of T cell activation strongly impaired Th2 cell development, while Th1 cell induction was relatively resistant to this immunosuppressive signaling. The steep decline in Th2 cell induction suggested the significance of PD-1 in allergic inflammation. Treatment with anti-human PD-1 agonist antibody inhibited allergic inflammation in human PD-1-knock-in mice as shown by the reduction of Th2 cells, IgE levels and eosinophilic infiltration. This study shows that PD-1 regulates not only the intensity but also the quality of immune response by deviating Th differentiation. PD-1 stimulators are projected to be valuable in suppressing various forms of inflammatory activities, but the efficacy against Th2-dominant immune response may be particularly high.

immunology↗

bioRxiv2024

BMP4 regulates asymmetric Pkd2 distribution in mouse nodal immotile cilia and ciliary mechanosensing required for left-right determination

BackgroundMouse nodal immotile cilia mechanically sense the bending direction for left-right (L-R) determination and activate the left-side-specific signaling cascade, leading to increased Nodal activity. Asymmetric distribution of Pkd2, a crucial channel for L-R determination, on immotile cilia has been reported recently. However, the causal relationship between the asymmetric Pkd2 distribution and direction-dependent flow sensing is not well understood. Furthermore, the underlying molecular mechanism directing this asymmetric Pkd2 distribution remains unclear. ResultsThe effects of several recombinant proteins and inhibitors on the Pkd2 distribution were analyzed using super-resolution microscopy. Notably, bone morphogenetic protein 4 (BMP4) affected the Pkd2 distribution. Additionally, three-dimensional manipulation of nodal immotile cilia using optical tweezers revealed that excess BMP4 caused defects in the mechanosensing ability of the cilia. ConclusionsExperimental data together with model calculations suggest that BMP4 regulates the asymmetric distribution of Pkd2 in nodal immotile cilia, thereby affecting the ability of these cilia to sense the bending direction for L-R determination. This study, for the first time, provides insight into the relationship between the asymmetric protein distribution in cilia and their function.

developmental biology↗

bioRxiv2024

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex

Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

plant biology↗

bioRxiv2023

Structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-[A] resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

plant biology↗

bioRxiv2023

Acto3D: user- and budget-friendly software for multichannel high-resolution three-dimensional imaging

Advances in fluorescence microscopy and tissue-clearing technology have revolutionized three-dimensional (3D) imaging of fluorescently labeled tissues, organs, and embryos. However, the complexity and high cost of existing software and computer solutions for such imaging limit its widespread adoption by researchers with limited resources. We here introduce Acto3D as a user- and budget-friendly, open-source computer software application designed to streamline the generation and observation of high-resolution 3D images of targets labeled with multiple fluorescent probes. Acto3D features an intuitive interface that simplifies the importation, visualization, and analysis of data sets, has an associated tool for annotation of vascular lumens, and incorporates multiple fluorescence channels for comprehensive imaging. Underpinned by an integrated graphics processing unit, Acto3D allows accurate image reconstruction and efficient data processing without the need for expensive high-performance computers. We validated the software by imaging mouse embryonic structures. Acto3D thus constitutes a cost-effective and efficient platform to support biological research.

developmental biology↗

bioRxiv2023

Highly regenerative species-specific genes improve age-associated features in the adult Drosophila midgut

BackgroundThe remarkable regenerative abilities observed in planarians and cnidarians are closely linked to the active proliferation of adult stem cells and the precise differentiation of their progeny, both of which typically deteriorate during aging in low regenerative animals. While regeneration-specific genes conserved in highly regenerative organisms may confer regenerative abilities and long-term maintenance of tissue homeostasis, it remains unclear whether introducing these regenerative genes into low regenerative animals can improve their regeneration and aging processes. ResultsHere we ectopically express high regenerative species-specific JmjC domain-encoding genes (HRJDs) in Drosophila, a widely used low regenerative model organism. Surprisingly, HRJD expression impedes tissue regeneration in the developing wing disc but extends organismal lifespan when expressed in the intestinal stem cell lineages of the adult midgut under non-regenerative conditions. Notably, HRJDs enhance the proliferative activity of intestinal stem cells while maintaining their differentiation fidelity, ameliorating age-related decline in gut barrier functions. ConclusionsThese findings together suggest that the introduction of highly regenerative species-specific genes can improve stem cell functions and promote a healthy lifespan when expressed in aging animals.

developmental biology↗

bioRxiv2023

Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth

Post-developmental organ resizing improves organismal fitness under constantly changing nutrient environments. Although stem cell abundance is a fundamental determinant of adaptive resizing, our understanding of its underlying mechanisms remains primarily limited to the regulation of stem cell division. Here we demonstrate that nutrient fluctuation induces dedifferentiation in the Drosophila adult midgut to drive adaptive intestinal growth. From lineage tracing and single-cell RNA-sequencing, we identify a subpopulation of enteroendocrine cells (EEs) that convert into functional intestinal stem cells (ISCs) in response to dietary glucose and amino acids by activating the JAK-STAT pathway. Genetic ablation of EE-derived ISCs severely impairs ISC expansion and midgut growth despite the retention of resident ISCs, and in silico modeling further indicates that EE dedifferentiation enables efficient increase in the midgut cell number while maintaining epithelial cell composition. Our findings uncover a physiologically-induced dedifferentiation that ensures ISC expansion during adaptive organ growth in concert with nutrient conditions.

developmental biology↗

bioRxiv2023

Ciliary protein CEP290 regulates focal adhesion via microtubule system in non-ciliated cells

Almost all differentiated mammalian cells have primary cilia on their surface. Ciliary dysfunction causes ciliopathy in humans. Centrosomal protein 290 (CEP290) is a ciliary protein that causes ciliopathies, localizes at the cilial base in ciliated cells, whereas it localizes to the centrosome in non-ciliated proliferating cells. The cilia-dependent function of CEP290 has been extensively studied; however, the cilia-independent function, which is likely responsible for the wider phenotypic spectra of CEP290-related ciliopathies, remains largely unknown. Here, we examined cilia-independent functions of CEP290 in non-ciliated cells. Our study showed that Cep290 function loss suppresses microtubule elongation due to microtubule organizing center malfunction. Surprisingly, CEP290 forms a complex with the adenomatous polyposis coli (APC) protein encoded by the adenomatous polyposis coli gene. The APC-CEP290 complex exists in the centrosome and on microtubule fibers. Notably, the reduced focal adhesion formation is likely responsible for the Cep290 mutant phenotypes, including impaired directed cell migration, shrunken cell shape, and reduced adhesive capacity to the extracellular matrix. The APC-CEP290 complex is consistently important for transporting a focal adhesion molecule, paxillin, to focal adhesions in non-ciliated cells. Thus, our findings provide a novel platform to better understand the ciliopathies.

cell biology↗