Biology subjects

Kitajima, K.

Publications and source records attributed to Kitajima, K..

11 recordsLinked to original sources

bioRxiv2026

Crown-based growth strategies explain the distribution and co-occurrence of tree functional groups along environmental gradients

Elucidating interspecific variation in growth strategies across environments is critical for understanding tree diversity and distribution. However, a systematic analysis across diverse forests remains scarce due to limited large-tree crown measurements. We analysed 3,814 trees from 107 canopy species in 23 natural forests using forest census data and unmanned aerial vehicle. Relative growth rate (growth rate/biomass) was decomposed into growing space efficiency (growth rate/crown area) and crown area ratio (crown area/biomass). Relative growth rates were similar among functional groups (deciduous broadleaf, evergreen broadleaf, evergreen conifer), but their underlying components differed. Deciduous trees exhibited 34-43% higher crown area ratio but 24-27% lower growing space efficiency than evergreen broadleaf and conifer trees. Across environments, growing space efficiency correlated positively with mean annual temperature, likely from extended growing seasons while crown area ratio correlated negatively, particularly in deciduous species. Snow loading limited crown area ratio in evergreen species, while deciduous achieved higher values through avoiding snow loads. Correlation between crown area ratio and specific leaf area indicated a coordinated strategy between crowns and leaves. Different functional groups achieve comparable growth efficiency either through crown expansion or biomass production, explaining their distinct distribution as well as co-occurrence across broad environments.

ecology↗

bioRxiv2026

BRCA2 loss triggers a downward spiral of genomic instability via ROS-dependent metabolic collapse

BRCA2 plays a central role in maintaining genome integrity through homologous recombination and replication-fork protection, yet the compensatory networks sustaining BRCA2-deficient cells remain unclear. Here we show BRCA2 enforces a homeostatic mechanism aligning mitochondrial respiration with DNA repair capacity in both cancer and non-cancer contexts. Genome-wide CRISPR screening identified glutathione metabolism and base-excision repair as the key compensatory networks sustaining BRCA2-deficient cells by detoxifying mitochondria-derived reactive oxygen species. BRCA2 loss provokes an acute mitochondrial ROS surge, causing 8-oxoguanine accumulation and a systemic metabolic crisis marked by NAD+ and glutathione depletion. PARP inhibitor targets DNA replication vulnerabilities, increasing the cellular requirement for BRCA2. The resulting oxidative burden primes cells for TP53-dependent apoptosis in G1 during olaparib treatment, which extends cytotoxicity beyond canonical S-phase stress. These findings indicate BRCA2 prevents metabolic flux from outpacing repair capacity, providing a rationale for combining PARP inhibition with redox modulation to enhance efficacy and overcome resistance. HighlightsO_LIAcute BRCA2 loss induces ROS and mitochondrial dysfunction creating a metabolic scar C_LIO_LIOxidative lesions drive PARP hyperactivation and precipitate a cellular NAD crisis C_LIO_LIPARP inhibitors provoke TP53-dependent apoptosis in G1 beyond replication stress in S phase C_LIO_LIGlutathione deficiency exacerbates bone marrow failure under BRCA2 depletion C_LIO_LIBRCA2 tightly couples mitochondrial redox homeostasis to genomic maintenance C_LI

cell biology↗

bioRxiv2026

LeafContourEFD: a reproducible workflow for elliptic Fourier analysis with orientation normalization and lateral asymmetry

PremiseElliptic Fourier analysis is widely used to quantify leaf shape variation, but inconsistent normalization and orientation alignment can introduce biologically irrelevant variation. In addition, a reproducible workflow from raw images to normalized elliptic Fourier descriptors (EFDs) is still lacking. Methods and ResultsWe developed LeafContourEFD, a GUI application for reproducible leaf morphometrics. It integrates image segmentation, contour extraction, EFD calculation, and an extended normalization framework, termed oriented true EFD normalization, based on a user-defined biological reference axis. Analyses of Quercus serrata, Q. crispula, and Triadica sebifera showed that existing normalization methods can introduce orientation-related variance when the first-harmonic major axis does not match the leaf base-to-tip axis. In contrast, oriented true normalization removed these artifacts, yielding clearer shape transitions along principal components allowing shape variation among leaves to be captured while preserving biologically meaningful lateral asymmetry. ConclusionsLeafContourEFD improves interpretability and reproducibility in outline-based morphometrics and provides transparent outputs and metadata for data sharing and cross-study comparisons.

plant biology↗

bioRxiv2026

Multi-omics definition of the sex-specific glycoproteome of murine tissues

Sex-specific differences in the glycoproteome remain poorly defined despite growing evidence that protein glycosylation is a key determinant of sex biology. Here we present a tissue-resolved glycoproteome atlas of adult male and female C57BL/6J mice, integrating transcriptomics, proteomics and glycoproteomics with sialic acid speciation and lectin microarray profiling across 19 tissues. Quantitative analysis of >26,800 protein- and site-specific N-glycoforms from 1,512 glycoproteins revealed highly distinct tissue glycoproteomes shaped by coordinated regulation of protein abundance and glyco-enzyme expression. Multi-omics integration identified strong glycophenotype-enzyme relationships, including control of tissue sialylation by Cmas and Cmah, suggesting rate-limiting roles in glycosylation. Pronounced sex-linked glycophenotypes were observed in salivary gland, liver and kidney, driven by differences in fucosylation, sialylation and protein abundance, whereas the brain glycome was largely conserved between sexes. An interactive online database (https://igcore.cloud/mta/atlas-viewer/) provides a resource for exploring sex-biased glycosylation across mouse tissues.

cell biology↗

bioRxiv2025

High density invasion by the shrub Ardisia crenata in Florida, USA is associated with altered soil chemical properties and microbial communities

Invasive plants can reshape soil ecosystems by altering chemical conditions and microbial communities. However, field evidence for how these effects scale with invader density, and whether responses are nonlinear, remains limited. We examined whether local stem density of the invasive shrub Ardisia crenata is associated with shifts in soil chemistry and soil microbiomes. The local density of A. crenata, which reproduces clonally with apomictic seeds, forms a gradient from high density to low density across invaded stands. Our results show strong differences in soil ecosystems with invasion, including consistently lower soil moisture, pH, organic matter, total carbon, total nitrogen, and electrical conductivity. These changes were accompanied by shifts in the community composition of soil prokaryotes and fungi, such as increased abundances of Acidothermus and Saitozyma with higher density of A. crenata. While the exact mechanisms causing these changes could not be established, increases of more labile above- and below-ground litter, as well as A. crenata specific secondary metabolites, were possible causal factors. We conclude that strong changes in soil ecosystems can be caused by invasive plants in a mesic forest understory, especially when they occur at high densities. Hence, to maintain healthy soil ecosystems, it is recommendable to control aggressive invasive plants such as A. crenata before they reach high densities.

ecology↗

bioRxiv2024

Anemonefish use sialic acid metabolism as Trojan horse to avoid giant sea anemone stinging

Anemonefish association with giant sea anemone is an iconic example of mutualistic symbiosis. Living inside the sea anemone without triggering the firing of highly toxic nematocysts present at the surface of sea anemone tentacles provides a unique shelter to the fish, which in return, by its territorial aggressiveness, protects the sea anemone from predators. The mechanisms by which the fish avoids triggering nematocysts discharge remain elusive. One hypothesis proposes that absence of sialic acids might disable nematocysts discharge. Here, we verified four predictions about the role of sialic acids in anemonefish protection: (i) sialic acid levels are lower in anemonefish mucus than in non-symbiotic and sensitive damselfish mucus; (ii) this decrease is specific to mucus and not observed in other organs; (iii) during post-embryonic development the levels of sialic acids are inversely correlated with the level of protection; (iv) the levels of sialic acids are minimal in sea anemone mucus. Taken together, our results allow us to propose a general model, in which anemonefish specifically regulates the level of sialic acids in their mucus to avoid nematocysts discharge. Our analysis also highlights several genes implicated in sialic acid removal as potential targets for allowing protection. Interestingly, our results also suggest that unrelated juveniles of damselfish (Dascyllus trimaculatus) capable to live in proximity with giant sea anemone may use the same mechanisms. Altogether, our data suggest that clownfish use sialic acids as a Trojan horse system to downplay the defenses of the sea anemones and illustrate the convergent tinkering used by fish to allow a mutualistic association with their hosts. Significance statementThe mutualistic relationship between anemonefish and giant sea anemones, where the fish shelter among the anemones tentacles while defending it from predators, is a classic example of symbiosis. However, how the fish avoids triggering the anemones venomous nematocysts has remained a mystery. This study reveals that the fish decrease the levels of sialic acids in their mucus, potentially preventing nematocyst discharge. This finding shed light on the mechanisms underlying this symbiotic relationship. Moreover, the discovery that unrelated damselfish may employ similar strategies underscores the broader significance of convergent adaptations in facilitating similar mutualistic associations in marine fishes.

zoology↗

bioRxiv2023

Non fire-adapted dry forest of Northwestern Madagascar: escalating and devastating trends revealed by remote-sensing data

Ankarafantsika National Park (ANP), the last significant remnant of Northwestern Madagascars tropical dry forests, is facing rapid degradation due to increased incidences of fire. This poses severe threats to biodiversity, local livelihoods, and vital ecosystem services. Our study, conducted on 3052 ha of ANPs pristine forests, employed advanced remote-sensing techniques to assess fire impacts during the past 37 years. Our aims were to understand historical fire patterns and evaluate forest recovery and susceptibility to repeated fires following initial burns. Using data from multiple Landsat satellite sensors, we constructed a time series of fire events since 1985, which revealed no fire activity before 2014. The Global Ecosystem Dynamics Investigation (GEDI) lidar sensor data were used to observe forest structure in both post-fire areas and undisturbed zones for comparison. We recorded six fire incidents from 2014-2021, during which the fire-affected area exponentially grew. A significant fire incident in October 2021 impacted 1052 hectares, 59% of which had experienced at least one fire in 2-4 years prior, with 60% experiencing 2 preceding incidents: one in 2017 and another in 2019. The initial fire drastically reduced plant cover and tree height, with subsequent fires causing minor additional loss. Post-fire recovery was negligible within the initial four years, even in patches without recurrent fires. The likelihood for an initial burn to trigger subsequent fires within a few years was high, leading to larger, more severe fires. We conclude that ANPs dry forests exhibit high vulnerability and low resilience to anthropogenic fires. Prompt preventive measures are essential to halt further fire spread and conserve the parks unique and invaluable biodiversity.

ecology↗

bioRxiv2022

Assembly of neuron- and radial glial cell-derived extracellular matrix molecules promotes radial migration of developing cortical neurons

Radial neuronal migration is a key neurodevelopmental event for proper cortical laminar organization. The multipolar-to-bipolar transition, a critical step in establishing neuronal polarity during radial migration, occurs in the subplate/intermediate zone (SP/IZ), a distinct region of the embryonic cerebral cortex. It has been known that the extracellular matrix (ECM) molecules are enriched in the SP/IZ. However, the molecular constitution and functions of the ECM formed in this region remain poorly understood. Here, we identified neurocan (NCAN) as a major chondroitin sulfate proteoglycan in the SP/IZ. NCAN binds to both radial glial cell-derived tenascin-C (TNC) and hyaluronan (HA), a large linear polysaccharide, forming a ternary complex of NCAN, TNC, and HA in the SP/IZ. Developing cortical neurons make contact with the ternary complex during migration. The enzymatic or genetic disruption of the ternary complex impairs radial migration by suppressing the multipolar-to-bipolar transition. Furthermore, both TNC and NCAN promoted the morphological maturation of cortical neurons in vitro. The present results provide evidence for the cooperative role of neuron- and radial glial cell-derived ECM molecules in cortical development.

neuroscience↗

bioRxiv2021

Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains

ST8SIA2 is the main factor regulating expression of the phenotype involved in schizophrenia. Lowered promoter activity of the ST8SIA2 gene is considered to be protective against schizophrenia by conferring tolerance to psychosocial stress. Here, we examined the promoter type composition of anatomically modern humans (AMHs) and archaic humans (AHs; Neanderthals and Denisovans), and compared the promoter activity at the population level (population promoter activity; PPA) between them. In AMHs, the TCT-type, showing the second lowest promoter activity, was most prevalent in the ancestral population of non-Africans. However, the detection of only the CGT-type from AH samples and recombination tracts in AH sequences showed that the CGT- and TGT-types, exhibiting the two highest promoter activities, were common in AH populations. Furthermore, interspecies gene flow occurred into AMHs from AHs and into Denisovans from Neanderthals, influencing promoter-type compositions independently in both AMHs and AHs. The difference of promoter-type composition makes PPA unique in each population. East and Southeast Asian populations show the lowest PPA. This results from the selective increase of the CGC-type, showing the lowest promoter activity, in these populations. Every non-African population shows significantly lower PPA than African populations, resulting from the TCT-type having the highest prevalence in the ancestral population of non-Africans. In addition, PPA reduction is also found among subpopulations within Africa via a slight increase of the TCT-type. These findings indicate a trend toward lower PPA in the spread of AMHs, interpreted as a continuous adaptation to psychosocial stress arising in migration. This trend is considered as genetic tuning for the evolution of collective brains. The inferred promoter-type composition of AHs differed markedly from that of AMHs, resulting in higher PPA in AHs than in AMHs. This suggests that the trend toward lower PPA is a unique feature in AMH spread.

evolutionary biology↗

bioRxiv2019

Sox17 expression in endocardium precursor cells regulates heart development in mice

The endocardium is the endothelial component of the vertebrate heart and plays a key role in heart development. Cardiac progenitor cells (CPCs) that express the homeobox gene Nkx2-5 give rise to the endocardium. Where, when, and how the endocardium segregates during embryogenesis have remained largely unknown, however. We now show that Nkx2-5+ CPCs that express the Sry-type HMG box gene Sox17 specifically differentiate into the endocardium in mouse embryos. Approximately 20% to 30% of Nkx2-5+CPCs transiently express Sox17 from embryonic day (E) 7.5 to E8.5.Although Sox17 is not essential or sufficient for endocardium fate, it can bias the fate of CPCs toward the endocardium. On the other hand, Sox17 expression in the endocardium is required for heart development. Deletion of Sox17 specifically in the mesoderm markedly impaired endocardium development with regard to cell proliferation and behavior. The proliferation of cardiomyocytes, ventricular trabeculation, and myocardium thickening were also impaired in a non-cell-autonomous manner in the Sox17 mutant, resulting in anomalous morphology of the heart, likely as a consequence of down-regulation of NOTCH signaling. Changes in gene expression profile in both the endocardium and myocardium preceded the reduction in NOTCH-related gene expression in the mutant embryos, suggesting that Sox17 expression in the endocardium regulates an unknown signal required for nurturing of the myocardium. Our results thus provide insight into differentiation of the endocardium and its role in heart development. SignificanceThe endocardium is vital for vertebrate heart development; however, the molecular mechanisms regulating fate determination and differentiation remain largely unknown. Here, we show that a part of the earliest cardiac progenitor cells (CPCs) transiently and exclusively express Sry-type HMG box gene Sox17 in the mouse embryo. Sox17-expressing CPCs specifically differentiate to the endocardium. Sox17 biases the fate of CPCs toward the endocardium, and regulates proliferation and cellular behavior cell autonomously. Conversely, Sox17 in the endocardium regulates the myocardium non-cell autonomously. Notably, Sox17 is required for the ventricular trabeculation via the NOTCH signal that is not directly induced but maintained by Sox17. This study, thus, sheds light on endocardium development.

developmental biology↗

bioRxiv2017

Decomposing leaf mass into photosynthetic and structural components explains divergent patterns of trait variation within and among plant species

O_LIAcross the global flora, interspecific variation in photosynthetic and metabolic rates depends more strongly on leaf area than leaf mass. In contrast, intraspecific variation in these rates is strongly mass-dependent. These contrasting patterns suggest that the causes of variation in leaf mass per area (LMA) may be fundamentally different within vs. among species. C_LIO_LIWe developed a statistical modeling framework to decompose LMA into two conceptual components - metabolic LMAm (which determines photosynthetic capacity and dark respiration) and structural LMAs (which determines leaf toughness and potential leaf lifespan) - using leaf trait data from tropical forests in Panama and a global leaf-trait database. C_LIO_LIDecomposing LMA into LMAm and LMAs improves predictions of leaf trait variation (photosynthesis, respiration, and lifespan). We show that strong area-dependence of metabolic traits across species can result from multiple factors, including high LMAs variance and/or a slow increase in photosynthetic capacity with increasing LMAm. In contrast, strong mass-dependence of metabolic traits within species results from LMAm increasing from sunny to shady conditions. LMAm and LMAs were nearly independent of each other in both global and Panama datasets. C_LIO_LISynthesis: Our results suggest that leaf functional variation is multi-dimensional and that biogeochemical models should treat metabolic and structural leaf components separately. C_LI

ecology↗