Biology subjects

Nakamura, I.

Publications and source records attributed to Nakamura, I..

4 recordsLinked to original sources

bioRxiv2026

Comparative analyses of tailbeat frequency and stride length reveal how regionally endothermic fishes cruise fast

Cruising speed is a key factor affecting prey-search efficiency and migration range in continuously swimming animals. Tunas and lamnid sharks (e.g., white sharks) have convergently evolved traits for high-speed cruising, including the ability to maintain slow-twitch, aerobic red muscle (RM) warmer than ambient water, known as RM endothermy. Despite their well-known high cruising speeds, kinematic features underlying their elevated speeds remain unclear. Swim speed is the product of tailbeat frequency (TBF; Hz) and stride length (SL, the absolute distance traveled per tailbeat; m). RM endothermy is expected to elevate TBF by enhancing muscle contraction performance. Furthermore, within RM-endothermic fishes, tunas and lamnid sharks may exhibit distinct kinematic features because of differences in caudal fin morphology and tailbeat amplitude. Here, we compiled kinematic parameters from 20 fish species, including five RM-endothermic species, measured in the wild using animal-borne sensors. Comparative analyses showed that, for a given body mass and water temperature, RM-endothermic fishes exhibited 1.9 times higher cruising speed and TBF than ectothermic fishes, while SL remained similar. Within RM-endothermic fishes, tunas exhibited 2.3 times higher TBF than similar-sized lamnid sharks, whereas lamnid sharks showed 1.7 times longer SL than similar-sized tunas. These results indicate that RM endothermy is generally associated with higher TBF, while significant kinematic differences remain between tunas and lamnid sharks. This divergence may be partly explained by the greater caudal fin area and tailbeat amplitude in lamnid sharks. It may also reflect contrasting skeletal types of teleosts and elasmobranchs, which potentially influence body stiffness and swimming kinematics.

animal behavior and cognition↗

bioRxiv2026

Structural basis for monobody OP-4 binding to open-form adenylate kinase

Monobodies are fibronectin type-III-based binding proteins that specifically bind target proteins and regulate their functions. We previously identified monobodies that selectively recognize either the OPEN or CLOSED conformation of adenylate kinase (Adk), revealing that monobodies can discriminate distinct conformational states of a target protein. However, the molecular basis of OPEN-form recognition has remained unclear because the structure of the complex between an OPEN-form-specific monobody and Adk had not been determined. To address this issue, we determined the crystal structure of the complex between Adk and the OPEN-form-specific monobody OP-4, employing hierarchical clustering analysis of X-ray diffraction datasets. The structure revealed that OP-4 binds to the surface formed by the expanded LID and CORE domains of Adk. Mutations in the interface residues reduced the OP- 4-binding affinity, indicating that the crystallographically identified interface is also relevant in solution. In particular, R123 mutations markedly impaired OP-4 binding. Molecular dynamics simulations further suggested that the R123-D159-R156 hydrogen-bond network is retained in solution and may contribute to efficient complex formation. These findings establish the structural basis for monobody OP-4 binding to open-form Adk and identify the R123-centered interaction network as a key determinant of complex formation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/742914v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@67570forg.highwire.dtl.DTLVardef@84b9caorg.highwire.dtl.DTLVardef@1c1b782org.highwire.dtl.DTLVardef@f6ed05_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe crystal structure of the OPEN-form adenylate kinase/monobody OP-4 complex was successfully determined. C_LIO_LIThe crystal structure revealed that OP-4 binds to surface formed by the expanded LID and CORE domains in adenylate kinase. C_LIO_LIIsothermal titration calorimetry measurements for adenylate kinase mutants confirmed that the binding modes observed in solution are consistent with those observed in the crystal structure. C_LIO_LIMolecular dynamics simulations suggested that the R123-D159-R156 hydrogen bond network prior to OP-4 binding is important for complex formation. C_LI

biochemistry↗

bioRxiv2025

A SABATH family enzyme regulates development via the gibberellin-related pathway in the liverwort Marchantia polymorpha

The SABATH family enzymes are a group of plant-specific methyltransferases that catalyze the methylation of many small molecules, including several plant hormones. While this family emerged anciently before the evolution of land plants from streptophyte algae, little is known about their biological function in plant lineages other than angiosperms. Here, we identified 12 SABATH family genes from the liverwort Marchantia polymorpha and found that MpSABATH2 is essential for its development. Mpsabath2 mutants were severely inhibited in thallus growth and gemma cup formation, while spontaneously forming sexual branches under non-inductive conditions. These phenotypes resembled the developmental responses to far-red light, which was also supported by transcriptome analysis. Further genetic analysis connected this phenomenon with gibberellin (GA)-related metabolism. Blocking GA biosynthesis partially rescued Mpsabath2 phenotypes, which were restored by treatment with the GA precursor, ent-kaurenoic acid. Given that bryophyte and angiosperm SABATH proteins fall into distinct phylogenetic clades, our findings suggest that SABATH family enzymes independently acquired roles in developmental regulation through convergent or parallel evolution in land plants.

plant biology↗

bioRxiv2025

Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies

The Neotropical butterfly genus Adelpha Hubner exhibits remarkable species diversity and striking convergence in wing colour patterns potentially explained by mimicry, making it an exceptional model for exploring trait evolution and its relationship with speciation. To date, unresolved phylogenetic relationships hinder a comprehensive understanding of the evolutionary biology of the genus. Using a novel multi-marker dataset combining one mitochondrial and 15 nuclear gene fragments, we generate the most comprehensive phylogeny of the genus Adelpha to revisit its systematics and investigate the evolution of mimicry colour patterns. Our data set encompasses 83 of the 87 known extant species and six Limenitis species that were recently excluded from Adelpha (134 of c. 160 subspecies in total), collectively displaying 14 distinct mimicry patterns. We provide conclusive evidence that corroborates previous work on the polyphyly of Adelpha as historically conceived, and describe the genus Adelphina Paez & Willmott n. gen. to stabilize the nomenclature, both genera representing Neotropical limenitidines. The comprehensive phylogeny provided in this study lays a solid foundation for future research into the processes driving diversification within these species interacting through mimicry. Ancestral character state reconstruction reveals gradual evolution of mimicry pattern. The more common mimicry pattern IPHICLUS (forewing with orange subapical spot and white band) is inferred as ancestral, but repeated convergent evolution is also recovered. Evolutionary convergence is also observed for the second most abundant mimicry pattern, COCALA (orange-white banded). Increased rates of mimicry pattern evolution are also found toward the equator. These results underscore the complexity of mimicry evolution in the Neotropical limenitidines i.e., Adelpha and Adelphina, emphasizing the need to explore its interplay with other biotic and abiotic factors.

evolutionary biology↗