Biology subjects

Chiba, A.

Publications and source records attributed to Chiba, A..

6 recordsLinked to original sources

bioRxiv2026

Decoupling species richness and interaction frequency reveals how fungal interactions regulate wood decomposition

Wood decay fungi play a central role in forest carbon cycling, yet the mechanisms linking fungal biodiversity to decomposition remain unclear because species richness and interspecific interactions are rarely separated. Here, these effects were experimentally disentangled using a laboratory wood decomposition microcosm with four common wood-decay fungi. By manipulating the spatial arrangements of pre-colonized wood blocks, fungal species richness and the frequency of interspecific interactions were independently varied. Wood mass loss was quantified, and lignin and carbohydrate analyses were conducted to examine the changes in decay strategies and the potential accumulation of recalcitrant fungal products. Both fungal species richness and interspecific interactions enhanced wood decomposition, but their effects depended on species identity and combinations. Selection effects were observed when competitively dominant species replaced weaker competitors. Several species combinations showed decomposition rates exceeding those of pure cultures, indicating complementarity and facilitation by interspecific interactions. Generalized linear mixed models revealed that interaction frequency and species richness independently influenced decay rates in a species-specific manner. Chemical analyses revealed that interspecific interactions altered the relative loss of lignin and carbohydrates, indicating shifts in the enzymatic allocation and/or production of acid-insoluble fungal metabolites during competition. Our results indicate that competitive interactions among wood decay fungi often accelerate decomposition to offset energetic costs. However, deadlock interactions among basidiomycetes may promote the accumulation of recalcitrant fungal compounds, potentially slowing decomposition over longer timescales. We propose the "accumulated inhibitor hypothesis" to reconcile contrasting fungal diversity-decomposition relationships and highlight the importance of interaction frequency in fungal biodiversity-ecosystem functioning research.

ecology↗

bioRxiv2025

Endothelial-zippering proceeds by sensing heartbeat-driven force through Cadherin-6 during heart-vessel connection in zebrafish

The connection between the heart and great vessels established during embryogenesis is essential for circulation. However, how great veins adhere to the endocardium lining the inside lumen of the beating heart remains unknown. Here, using zebrafish, we demonstrate that the endocardium and great veins are sealed in a zipper-closing manner outside the beating heart. The gradual elongation of the endocardium, driven by convergent extension, organized this adhesion by pulling venous ECs along the anterior-posterior axis. Time-specific manipulation of the heart rate revealed that this endocardial elongation proceeds against heartbeat-driven force. From time-lapse imaging of adherens junctions, which would counterbalance mechanical forces, we found a specific contribution of Cadherin-6 instead of Cadherin-5 in sensing endocardium-specific mechanical force. This specificity was confirmed by the depletion of Cadherin-6 that caused endocardium deformation. Altogether, we propose Cadherin-6 mediated EC-zippering as a novel mechanism that updates the understanding of Cadherin usage in dynamic morphogenesis.

developmental biology↗

bioRxiv2022

Interactive Neurorobotics: Behavioral and Neural Dynamics of Agent Interactions

Interactive neurorobotics is a subfield which characterizes brain responses evoked during interaction with a robot, and their relationship with the behavioral responses. Gathering rich neural and behavioral data from humans or animals responding to agents can act as a scaffold for the design process of future social robots. The goals of this research can be broadly broken down into two categories. The first, seeks to directly study how organisms respond to artificial agents in contrast to biological or inanimate ones. The second, uses the novel affordances of the robotic platforms to investigate complex phenomena, such as responses to multisensory stimuli during minimally structured interactions, that would be difficult to capture with classical experimental setups. Here we argue that to realize the full potential of the approach, both goals must be integrated through methodological design that is informed by a deep understanding of the model system, as well as engineering and analytical considerations. We then propose a general framework for such experiments that emphasizes naturalistic interactions combined with multimodal observations and complementary analysis pipelines that are necessary to render a holistic picture of the data for the purpose of informing robotic design principles. Finally, we demonstrate this approach with an exemplar rat-robot social interaction task which included simultaneous multi-agent tracking and neural recordings.

animal behavior and cognition↗

bioRxiv2021

Conserved and context-dependent roles for Pdgfrb signaling during zebrafish vascular mural cell development

Platelet derived growth factor beta and its receptor, Pdgfrb, play essential roles in the development of vascular mural cells, including pericytes and vascular smooth muscle. To determine if this role was conserved in zebrafish, we analyzed pdgfb and pdgfrb mutant lines. Similar to mouse, pdgfb and pdgfrb mutant zebrafish lack brain pericytes and exhibit anatomically selective loss of vascular smooth muscle coverage. Despite these defects, pdgfrb mutant zebrafish did not otherwise exhibit circulatory defects at larval stages. However, beginning at juvenile stages, we observed severe cranial hemorrhage and vessel dilation associated with loss of pericytes and vascular smooth muscle cells in pdgfrb mutants. Similar to mouse, pdgfrb mutant zebrafish also displayed structural defects in the glomerulus, but normal development of hepatic stellate cells. We also noted defective mural cell investment on coronary vessels with concomitant defects in their development. Together, our studies support a conserved requirement for Pdgfrb signaling in mural cells. In addition, these mutants provide an important model for definitive investigation of mural cells during early embryonic stages without confounding secondary effects from circulatory defects. Summary statementGenetic analysis in zebrafish demonstrates the conserved role of Pdgfb/Pdgfrb signaling in pericyte and vascular smooth muscle cell formation during vascular development in vertebrates.

developmental biology↗

bioRxiv2019

Labeling proteins within Drosophila embryos by combining FRET reporters, position-specific genomic integration, and GAL4-reponsive expression

Protein interaction network (PIN) or interactome has been mapped vigorously for the entire genome. We recognize, nonetheless, that such a map could illuminate profound insights had its context been revealed. We describe a scalable protein lableling method that could re-supply natural context back to the map of protein interactome. Genetically encoded fluorescent proteins, position-specific genomic integration and GAL4-responsive expression control enable labeling proteins A, B and C each with a either an eGFP, mCherry or NirFP in specified cells of optically transparent animals such as Drosophila embryos. While following multiple proteins through development and behavior, these labels offer separable pairs of Forster resonance energy transfer between proteins A and B and proteins B and C. We test and observe FRET interactions between specific protein pairs controlling cytoskeleton, nuclear signaling and cell polarity. By using our protein labeling method, it will be possible to map protein interaction network in situ -- isPIN.

developmental biology↗

bioRxiv2019

Periosteum-derived Osteocrin regulates bone growth through both endochondral ossification and intramembranous ossification

During development of long bones, two mechanistically distinct processes contribute to long- and short-axis growth. Endochondral ossification in the growth plate leads to the long-axis growth, while intramembranous ossification including apposition in the periosteum regulates the short axis growth. Here, we show that periosteal osteoblast-derived secretory peptide, Osteocrin (OSTN), promotes both types of long bone growth through potentiation of signaling by C-type natriuretic peptide (CNP), because OSTN inhibits the clearance of CNP by binding to natriuretic peptide receptor 3 (NPR3). The mice lacking OSTN showed less bone mass in trabecular and cortical regions than the control mice, suggesting the dual functions of OSTN in long bone growth. We found that OSTN regulated trabecular bone formation by inducing proliferation and maturation of chondrocytes possibly through enhancing CNP-dependent signaling. Besides the contribution of OSTN to long axis growth, we demonstrated that OSTN together with CNP induced osteoblast differentiation of periosteum-derived multipotent progenitor cells expressing NPR3. These data suggest that OSTN induces long bone growth through endochondral ossification and osteoblast specification of multipotent progenitor cells in the periosteum.

developmental biology↗