Biology subjects

Miura, S.

Publications and source records attributed to Miura, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Loss of starch synthase IIa alleviates the negative impact of high temperature on rice starch during grain filling

High temperatures during grain filling stage are becoming increasingly frequent, compromising both grain and eating quality and thereby driving demand for heat-resilient cultivars. Such conditions are known to reduce the expression of granule-bound starch synthase I (GBSSI) and starch branching enzyme IIb (BEIIb), which are involved in starch biosynthesis, resulting in a decrease in amylose content and an increase in long-chain amylopectin. Thus, the present study introduced functional mutation in starch synthase IIa (SSIIa) that increases the proportion of short amylopectin chains to genetically compensate for the high-temperature-induced increase in amylopectin long chain. Rice lines carrying the ss2a mutation were grown at two locations with cooler (Akita) and warmer (Okayama) temperatures. Their grain traits, starch structure, and eating quality were compared. The ss2a mutant lines showed an increased proportion of short amylopectin chains as well as an increased apparent amylose content. Furthermore, these alterations in starch structure varied with the grain-filling temperature of the cultivation sites, ultimately affected eating quality. These results suggest that enriching short amylopectin chain via the ss2a mutation can counteract the increase in long amylopectin chain caused by high temperatures during grain filling, thereby maintaining a desirable starch structure and eating quality.

plant biology↗

bioRxiv2026

One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex

Defining what a species is remains one of the biggest questions in biology and directly challenges species delimitation in species complexes. The wide-spread Clarks' anemonefish Amphiprion clarkii has the widest range of all anemonefishes, from the Indian Ocean to the Central Pacific. However, the taxonomy of this species has been confused since its initial description due to its great variation in morphology and pigmentation even within the same locality. Here, we combined whole genome re-sequencing data from 166 individuals spanning most of the distribution of A. clarkii, including remote islands such as Ogasawara and Guam in the northwestern Pacific, and also including three individuals of the closely related A. tricinctus from the Marshall Islands. Our population genomic analyses reveal an unexpected level of divergence, with five deeply separated lineages corresponding to the Indian Ocean, Central Indo-Pacific, Melanesia, and the isolated population of Ogasawara. The fifth lineage comprises A. clarkii from Guam and A. tricinctus, revealing that A. tricinctus is phylogenetically nested within A. clarkii, challenging its current taxonomic status. The most divergent lineage, Melanesia, is genetically more distant from other A. clarkii lineages than several recognised species pairs within the Amphiprion genus, yet demographic modelling shows ongoing gene flow between all lineages. Together, our results highlight a hidden diversity and stress the necessity of an integrative taxonomic revision of the A. clarkii species complex.

evolutionary biology↗

bioRxiv2026

Hidden diversity and host specificity of Cladocopium symbionts revealed by phylotranscriptomics in giant sea anemones.

Giant sea anemones form an intricate, metabolically linked symbiosis with anemonefish (genus Amphiprion) and dinoflagellates (family Symbiodiniaceae). While the association between fish and anemone is well documented, the identity and distribution of resident Symbiodiniaceae remains poorly characterized. Here, we used RNA-sequencing of anemone tentacles and post-assembly filtering to recover Symbiodiniaceae sequences from Japanese anemones. Using transcriptome-wide phylogenetic approaches, we identified distinct Symbiodiniaceae strains in seven sea anemone species and four cryptic lineages of Entacmaea quadricolor. Phylogenies of 1300 and 214 nuclear genes resolved relationships among these symbionts with greater sensitivity than traditional molecular markers such as the Internal Transcribed Spacer 2 (ITS2) or partial 28S ribosomal DNA. Marker-based assessments indicate these Symbiodiniaceae as novel and specific to sea anemone hosts. Our transcriptome-wide phylogenies reveal previously undescribed Cladocopium (Clade C) strains associated with giant sea anemones, with symbionts clustering according to host species and lineage. Cophylogenetic analysis revealed significant phylogenetic congruence between anemone and Symbiodiniaceae, indicating a nonrandom association between host and symbiont evolutionary histories. Two sympatric cryptic lineages of E. quadricolor previously identified through host transcriptomics harbor distinct, specific Symbiodiniaceae assemblages. Analysis of genes under positive selection indicates functional divergence between these Symbiodiniaceae; three-dimensional reconstructions of symbiont cells using serial block-face scanning electron microscopy show consistent differences in cellular organization between two strains, further supporting their distinct functional identity. Together, our results uncover a hidden diversity of host-specific Symbiodiniaceae and suggest that cryptic diversification in giant sea anemones is mirrored by diversification of their algal symbionts within this tripartite symbiosis.

evolutionary biology↗

bioRxiv2026

De novo transformer modeling improves recovery of genetic cell types from sparse single-cell RNA sequencing

Single-cell RNA sequencing (scRNA-seq) simultaneously provides gene-expression profiles and genetic variants from individual cells, creating an opportunity to relate cellular phenotypes to their somatic evolutionary histories. However, delineation of genetic type (GTs) from scRNA-seq remains difficult because most variant positions are unobserved in individual cells and the observed base calls contain substantial false-positive and false-negative errors. We evaluated some existing phylogenetic and imputation methods using one simulated dataset and two empirical tumor datasets. We found that extreme sparsity prevented reliable recovery of known or independently inferred GTs when multiple GTs were present. This led us to adapt the STICI transformer architecture to train a separate model de novo on each sparse cell-variant (CV) matrix. These data-specific models predicted millions of missing bases, greatly reducing matrix sparsity. Phylogenetic analyses of the imputed CV matrices showed substantially improved recovery of GTs in both simulated and empirical datasets. In the empirical dataset, transformer-based analysis also suggested finer-scale genetic structure within some previously reported GTs that was not apparent with the existing methods. These results demonstrate that highly sparse scRNA-seq datasets contain substantially more recoverable lineage information than previously appreciated and that de novo transformer modeling provides an effective approach for recovering much of this hidden information. Nevertheless, sequencing errors persisted, limiting reconstruction of cellular lineage structure and leaving significant room for methodological improvement before expression phenotypes can be examined reliably in the context of their cellular evolutionary relationships.

bioinformatics↗

bioRxiv2026

An evolvable and functionally partitioned network underlies developmental remodelling in teleosts

Comparative embryology has revealed that early animal development is based on highly conserved genetic programs. Beyond embryogenesis however, animals undergo remarkably diverse post-embryonic developmental transitions such as metamorphosis. Whether these transitions are also organised into conserved genetic programs remains largely unexplored. To identify conserved genetic programs underlying post-embryonic development, we examine metamorphic remodelling in five teleost fishes, spanning 200 million years of evolution. By integrating comparative co-expression networks, evolutionary genomics, phylogenetic modelling, and functional data in zebrafish, we uncovered a conserved post-embryonic developmental network. This conserved network comprises components involved in core cellular processes, and involved in development and physiology, both of which are under the control of thyroid hormone during metamorphosis. Despite evolutionary conservation at the coding sequence level, this network exhibits significant turnover in gene family copy number following the teleost-specific whole-genome duplication as well as lineage-specific expansions and contractions. The variation in gene copy numbers is associated with macroevolutionary variation in a number of ecological and morphological traits, including swimming performance, and trophic level. Cross-species tissue expression, zebrafish single-cell transcriptomics, and zebrafish perturbation phenotypes placed the implicated genes in biological contexts relevant to these traits. Together, our results provide evidence of an ancient, functionally partitioned post-embryonic developmental network that has diversified throughout teleost evolution. The heterochronic variation in network function, changes in endocrine activity, and gene-family turnover provide potential routes through which a shared developmental architecture contributed to the evolution of phenotypic diversity in teleosts.

evolutionary biology↗

bioRxiv2026

TGM2-mediated histone serotonylation is an epigenetic cardioprotective mechanism in HFpEF

Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome with incompletely understood molecular mechanisms. Histone serotonylation is a recently identified epigenetic modification in which serotonin is covalently conjugated to glutamine 5 of histone H3 in H3K4me3-marked nucleosomes. Here, we investigated the role of transglutaminase 2 (TGM2)-mediated histone serotonylation in HFpEF. In a mouse model of HFpEF induced by salty drinking water, unilateral nephrectomy and aldosterone infusion (SAUNA), cardiac H3K4me3Q5ser and nuclear TGM2 levels were increased. Cardiomyocyte-specific TGM2-deficient mice developed aggravated HFpEF phenotypes after SAUNA exposure, including worsened diastolic dysfunction, reduced exercise capacity, pulmonary congestion and delayed cardiomyocyte relaxation. CUT&RUN sequencing identified H3K4me3Q5ser-enriched regions predominantly around transcription start sites after SAUNA exposure, with notable enrichment at genes associated with G2/M checkpoint-related stress-response signaling. RNA sequencing further showed that activation of this pathway was impaired in SAUNA-exposed TGM2-deficient hearts. In cardiac myocytes, calcium-binding sites and nuclear localization of TGM2 support checkpoint-related stress-response gene activation in cardiac myocytes. Pharmacological WEE1 inhibition, which activates downstream CDK1-associated checkpoint signaling, partially rescued the aggravated HFpEF phenotype in TGM2-deficient mice. Finally, in patients with HFpEF, lower circulating serotonin levels were associated with adverse cardiac outcomes, and cardiomyocyte H3K4me3Q5ser levels correlated with serum serotonin concentrations. These findings suggest that cardiomyocyte TGM2-mediated histone serotonylation represents a stress-adaptive, cardioprotective epigenetic mechanism in HFpEF.

pathology↗

bioRxiv2026

Visualization of peripheral nerves in developing and regenerating limbs using a novel peripherin reporter line of Xenopus laevis

Peripherin (PRPH) is a class III intermediate filament protein expressed in peripheral nerves and upregulated during axon outgrowth and regeneration. In this study, we developed a transgenic Xenopus laevis line for long-term in vivo visualization of the peripheral nervous system. Deletion and motif analyses identified cis-regulatory regions within the promoter and intron 1 that are important for neuronal expression of the X. laevis prph gene. Stable lines exhibited robust EGFP reporter activity in developing neural primordia in embryos and in the peripheral nerves of tadpoles. Transgenic tadpoles enabled in vivo imaging of peripheral nerves throughout limb development. During larval limb regeneration, we observed modest early nerve entry into the blastema, recapitulating that seen in early limb development. In contrast, post-metamorphic limb blastemas displayed extensive innervation from the early phase of regeneration. Moreover, increased reporter activity in the nerves of the regenerating adult forelimb suggests regeneration-associated regulation of peripheral innervation and its potential role in blastema formation. This transgenic line will serve as a versatile tool for analyzing such large-scale neural remodeling across development, metamorphosis, and regeneration.

developmental biology↗

bioRxiv2026

A cyanobacterial adenine prenyltransferase enables longer-chain N6 prenylation

Adenine, a ubiquitous nucleobase found in biomolecules such as nucleic acids, cofactors, and signaling molecules, mediates diverse molecular interactions. Here, we identify TvAPT, an adenine prenyltransferase from the cyanobacterium Trichormus variabilis NIES-23. TvAPT efficiently catalyzes the unprecedented N6-prenylation of adenine-containing substrates using extended C10 and C15 prenyl donors, whereas canonical adenine prenyltransferases are generally limited to C5-dimethylallylation. X-ray structural analyses and protein engineering revealed that an enlarged prenyl-binding pocket enables the accommodation of extended prenyl donors, providing a structural basis for rationally tuning prenyl-donor preference. Together, these findings establish TvAPT as an adenine prenyltransferase that accepts a range of adenine-containing substrates, with a preference for nucleoside 5-monophosphates. Beyond expanding the known catalytic scope of adenine prenyltransferases, TvAPT provides access to nucleotide derivatives with enhanced membrane permeability and analogues of plant signaling molecules.

biochemistry↗

bioRxiv2026

Macrophage extracellular traps promote maladaptive cardiac remodelling and heart failure via PAD4-dependent mechanisms

AimsThe activation of inflammatory cells, particularly macrophages, plays a pivotal role in the pathogenesis of cardiac remodelling and heart failure. Emerging evidence indicates that extracellular traps released from inflammatory immune cells contribute to the progression of various pathologies. However, the clinical relevance and mechanistic role of macrophage extracellular traps (METs) in heart failure remain to be elucidated. Methods and ResultsEndomyocardial biopsy specimens from 69 patients with heart failure were analysed by fluorescent immunostaining to identify and quantify METs. The numbers of METs per myocardial tissue area in patients with heart failure showed a negative correlation with left ventricular (LV) ejection fraction and a positive correlation with LV end-diastolic diameter. Patients with higher MET counts had significantly lower event-free survival from the composite cardiac events. In a murine model of pressure overload by transverse aortic constriction (TAC), METs were most abundantly observed at 3 days post-TAC and remained detectable throughout the 4-week observation period. In vitro, time-dependent MET formation was induced by an intrinsic trigger of mitochondrial DNA in bone marrow-derived macrophages from wild-type (WT) mice, but not in peptidyl arginine deiminase 4 (PAD4)-deficient macrophages, indicating that PAD4 activity is indispensable for MET formation. The recipient mice transplanted with bone marrow cells from PAD4 knockout mice showed more preserved cardiac function, reduced myocardial fibrosis, and improved survival in response to TAC, compared to those transplanted with WT mice. Ex vivo analyses demonstrated that conditioned medium containing METs from WT macrophages induced fibroblast-to-myofibroblast transition via Toll-like receptor 4 signalling. ConclusionsPAD4-dependent MET formation from bone marrow-derived macrophages represents a novel driver of cardiac remodelling. Targeting MET formation may offer a potential therapeutic strategy for heart failure. Translational PerspectiveMacrophage extracellular traps (METs) are abundant in myocardial tissue from patients with heart failure with reduced ejection fraction and are associated with adverse left ventricular remodelling and worse clinical outcomes. These findings support myocardial MET burden as a potential tissue biomarker to improve risk stratification in heart failure patients. In mice, pressure overload induces MET formation, and hematopoietic PAD4 deficiency suppresses myocardial METs, attenuates fibrosis, preserves cardiac function, and improves survival. Mechanistically, mitochondrial DNA-enriched cardiomyocyte-derived exophers trigger PAD4-dependent METs, which activate cardiac fibroblasts through TLR4 signalling. Suppressing METs represents a potential therapeutic strategy to attenuate the progression of heart failure. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/711858v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@11b9b57org.highwire.dtl.DTLVardef@17386f7org.highwire.dtl.DTLVardef@1a1f002org.highwire.dtl.DTLVardef@942bbc_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2026

Glutathione acts as an exometabolite that rescues functionally distinct genetic mutations in fission yeast

Microorganisms in nature form communities through diverse interactions, such as mutualism and competition, to adapt to their ecological environments. These interactions seem to be mediated by extracellular metabolites (exometabolites), yet the chemical and biological diversity underlying these processes remains largely unexplored. In this study, we examined the chemical basis of cell-cell communication in the fission yeast Schizosaccharomyces pombe by a genome-wide screen employing 3,420 viable gene deletion mutants. We identified 37 strains that exhibited growth defects in monoculture on a minimal medium but exhibited growth recovery in the vicinity of wild-type colonies (co-culture), suggesting that exometabolites secreted by wild-type cells compensated for the gene deletion. Both lipophilic and water-soluble fractions obtained by solvent partitioning of the wild-type culture supernatant promoted growth recovery. Among the 11 mutants rescued by the water-soluble fraction, six were cysteine auxotrophs, prompting analyses of thiol-containing metabolites by liquid chromatography-mass spectrometry (LC-MS), revealing the presence of glutathione (GSH) in the culture supernatant. GSH restored growth in most strains as a nutrient source. In contrast, GSH rescued cell morphology defects in the hob3{Delta} mutant, lacking the Bin/Amphiphysin/Rvs (BAR) adaptor protein Hob3, through a mechanism independent of nutrition. This research advances understanding of exometabolite-mediated interactions in S. pombe by highlighting the role of GSH as one of the communication molecules that influence cellular processes and shape microbial communities. Author summaryMicroorganisms secrete a wide range of metabolites that control microbial community behavior. These extracellular metabolites (exometabolites) include not only well-studied signaling molecules but also diverse primary and secondary metabolites, suggesting complex interactions among microbes. However, the molecular basis of these interactions remains poorly understood, partly due to challenges in detecting them experimentally. In this study, we surveyed exometabolites involved in cell-cell interactions in the model eukaryotic microorganism Schizosaccharomyces pombe. S. pombe secretes a wide variety of metabolites, including previously reported nitrogen signaling factors (NSFs) and glutathione identified in this work. By analyzing gene deletion mutants that depend on GSH for growth, we provide new insights into how microbes regulate collective behavior by sharing exometabolites.

microbiology↗

bioRxiv2026

Expanding and Decoding the Chemistry of Phospholipid Headgroup in Eukaryotes

Cellular membranes have diverse phospholipids, chemical differences in whose headgroups impact many biological processes. Phosphatidylcholine is an essential phospholipid for human health, but not universally required for life. The evolutionary mechanisms underlying phospholipid preferences remain poorly understood, due to the difficulty of investigating metabolite structure-activity relationships in a cellular context. Here, we developed a generalizable metabolic-rewiring method to manipulate phospholipid headgroups together and their biological effects. This approach utilizes synthetic media to hijack evolutionarily conserved phosphatidylcholine biosynthesis, leveraging xenobiotics as principal precursors for scalable headgroup transformations. By identifying over 100 artificial headgroups, we expanded the chemical diversity of xenobiotic phospholipids. Unexpectedly, we discovered that subtle headgroup alterations produced distinct mammalian cellular activities. We demonstrated that chemical headgroup modifications differentially elicited structure-dependent effects on phospholipid-protein interactions, calcium dynamics, transcriptomic profiles, and stem cell differentiation. Notably, cross-species comparison revealed that human and yeast cells have different headgroup preferences critical for cell life and death. As proof-of-concept, interactome analysis identified headgroup-sensitive human microproteins vital for mitochondrial respiration, but non-conserved in yeast. These results exemplify the evolutionary diversity of key phospholipid-protein interactions, illustrating why humans depend on phosphatidylcholine. Overall, our findings establish a programmable platform for elucidating and engineering phospholipid-driven cellular functions.

cell biology↗

bioRxiv2025

Loss of STARD7 Impairs Mitochondrial Phospholipid Homeostasis and Contributes to Mitochondrial Myopathy

Mitochondria are composed of phospholipid bilayers rich in phosphatidylcholine (PC). StAR-related lipid transfer domain-containing protein 7 (STARD7) functions as a lipid transfer protein that plays a crucial role in maintaining mitochondrial PC homeostasis. In this study, we investigated the physiological role of STARD7 in skeletal muscle using muscle-specific knockout (mKO) mice. STARD7 expression was markedly higher in the soleus, a mitochondria-dense slow-twitch muscle, compared with fast-twitch fibers. Although muscle fibers from mKO mice exhibited no apparent structural abnormalities, their endurance exercise capacity was markedly reduced. RNA-seq analysis revealed suppressed expression of fast-twitch-related genes accompanied by a reduction in fast-twitch fibers. At the mitochondrial level, respiratory chain complexes remained intact, but oxygen consumption was consistently decreased. Targeted lipidomic analysis showed decreased levels of PC, cardiolipin (CL), and coenzyme Q in mKO mitochondria, particularly in the soleus. Conversely, expression of CL biosynthetic enzymes was unchanged, and an in vitro binding assay indicated that STARD7 preferentially transfers linoleic acid-containing PC required for CL remodeling. Furthermore, electron microscopy revealed disorganized cristae structures, whereas 4-HNE-modified proteins, mtDNA content, and OPA1 processing remained unaffected. Together, these findings demonstrate that STARD7 plays an essential role for maintaining mitochondrial integrity and function in skeletal muscle, and its loss likely contributes to the pathogenesis of mitochondrial myopathy.

biochemistry↗

bioRxiv2025

Cell-cell communication as underlying principle governing color pattern formation in fishes

The diverse pigmentation patterns of animals are crucial for predation avoidance and behavioral display, yet mechanisms underlying this diversity remain poorly understood. In zebrafish, Turing models have been proposed to explain stripe patterns, but it is unclear if they apply to other fishes. In anemonefish (Amphiprion ocellaris), we identified gja5b, a gene orthologous to zebrafish leopard and encoding a connexin involved in pigment cell communication, as responsible for the Snowflake phenotype. Using CRISPR/Cas9 and transgenesis, we recapitulate the Snowflake phenotype and show expression of gja5b in iridophores. A matching allele was recovered in zebrafish, revealing complementary requirements in both species. Our findings highlight conserved roles of gap junction mediated communication in pigment patterning across divergent teleosts.

developmental biology↗

bioRxiv2025

Decoding the constraints acting on a coastal fish using landscape transcriptomics

Understanding how wild organisms respond to complex mixtures of environmental stressors remains a major challenge in ecology1,2. To move beyond laboratory-based studies of the effect of individual stressors on model species, landscape transcriptomics - the study of how genome-wide expression patterns reveal environmental conditions - has been suggested3. Here, we apply landscape transcriptomics to the damselfish Chrysiptera cyanea, a sentinel species from Okinawas coastal ecosystems, by sampling juveniles and adults across 18 sites from natural to urbanized habitats. We uncover a striking molecular signature of urbanization: fish from human-impacted sites exhibit elevated expression of genes involved in inflammation and immune responses. Remarkably, their transcriptomes resemble those of overfed individuals from laboratory feeding experiments - suggesting that urban reefs act as "fast food" environments, offering energy-rich diets while imposing chronic stress. This pattern is illustrated by the altered expression of key genes in metabolic and stress pathways (e.g., downregulation of ppargc1a and insrb, indicative of dietary intake surplus and insulin resistance; upregulation of interleukins, chemokines, toll-like receptors and caspase linked to the immune response and inflammation). Our results demonstrate that wild transcriptomes capture the invisible biological costs of environmental degradation, positioning fish as living biosensors for coastal ecosystem health.

bioinformatics↗

bioRxiv2025

Socially regulated developmental plasticity in the color pattern of an anemonefish

Understanding the developmental basis of phenotypic plasticity is key to unraveling the origins of biodiversity. In coral reef fishes, color pattern changes during ontogeny can serve adaptive functions, yet the mechanisms and ecological contexts shaping these transitions remain largely unknown. Here, we investigated color pattern development in the tomato anemonefish (Amphiprion frenatus), which exhibits transient posterior white barring during early juvenile stages. We demonstrated that the timing of bar loss is plastic and modulated by the social environment, where juveniles cohabiting with adult conspecifics exhibited bar loss [~]24 days earlier than those isolated from adults. Through transcriptomic profiling, we identified gene expression changes implicating apoptosis- and autophagy-related pathways, as well as alterations in chromatophore development. Moreover, shifts in the expression of multiple thyroid hormone marker genes highlighted the potential neuroendocrinal integration of social cues that promoted bar loss. Ultrastructural analyses via transmission electron microscopy and in-situ assays indicated massive apoptosis of iridophores and associated dermal remodeling during the white-to-orange transition. The pharmacological inhibition of caspases delayed bar loss, confirming the functional role of programmed cell death. Behavioral trials revealed that adults responded differently to juveniles with/without the posterior bar, suggesting a role of transient barring in conflict avoidance during recruitment. Lastly, our evolutionary reconstruction of this plastic trait suggests that colony size is an important factor promoting this ontogenetic switch throughout anemonefishes. Our results provide compelling evidence for socially mediated plasticity in color pattern ontogeny with ecological and evolutionary implications for communication and species diversification in reef fishes.

developmental biology↗

bioRxiv2025

Functional impact of pathogenic Runt domain mutations in Runx2 in vivo: Insights into the skeletal and dental anomalies of cleidocranial dysplasia

Runt-related transcription factor 2 (RUNX2) is essential for skeletogenesis, and mutations in its gene cause cleidocranial dysplasia (CCD), an autosomal dominant skeletal disorder. The evolutionarily conserved 128-amino acid Runt homology domain (RHD) of human RUNX2 is essential for DNA binding and heterodimerization, and serves as a mutation hotspot associated with severe CCD phenotypes. To elucidate the functional impact of pathogenic RHD mutations in vivo, we generated two novel mouse lines: one carrying a missense mutation, c.695G>A (p.R232Q) (Runx2m/+), corresponding to the human RUNX2 c.674G>A (p.R225Q), and the other harboring a frameshift mutation, c.697_698delGA (p.E233TfsTer9) (Runx2112/+), causing a premature stop codon. Homozygous Runx2m/mand Runx2112/112 mice lacked membranous ossification, whereas heterozygous Runx2m/+ and Runx2112/+ mice displayed typical CCD-like skeletal features, including an open anterior fontanelle and clavicle hypoplasia. Unexpectedly, heterozygotes carrying pathogenic mutations in RHD developed an accessory root-like protrusion at the furcation of three-rooted maxillary first molars, representing a previously unrecognized dental phenotype during root development. Dual luciferase assays revealed impaired transactivation of the p.R232Q mutant Runx2 on the osteocalcin enhancer/promoter. Wild-type Runx2 was robustly expressed in osteoblasts and hypertrophic chondrocytes during bone formation, but the mutant Runx2 exhibited reduced expression in hypertrophic chondrocytes and partially impaired nuclear localization, resulting in arrested osteoblast and chondrocyte maturation. Our mutant mouse model provides a valuable in vivo platform to study CCD pathogenesis, mechanisms of tooth root furcation, and therapeutic interventions targeting dysfunctional RHD.

genetics↗

bioRxiv2024

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

The number of high-quality genomes is rapidly growing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with a coverage of 94.5x, the genome of the Sapphire Devil, Chrysiptera cyanea was assembled and annotated. The final assembly consisted of 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%. 28,173 genes were identified. Comparative analyses with available chromosome-scale assemblies for related species identified contig-chromosome correspondences. This genome will be useful to use as a comparison to study the specific adaptations linked to symbiosis life of the closely related anemonefish. Furthermore, this species is present in most tropical coastal areas in the Indo-West Pacific and could become a model for environmental monitoring. This work will allow to expand coral reef research efforts and highlights the power of long-read assemblies to retrieve high quality genomes.

genomics↗

bioRxiv2024

A microendovascular system can record precise neural signals from cortical and deep vessels with minimal invasiveness

Minimally invasive intravascular electroencephalography (ivEEG) signals are a promising tool for developing clinically feasible brain-computer interfaces (BCIs) that restore communication and motor functions in paralyzed patients. However, current ivEEG techniques can only record signals from the superior sagittal sinus (SSS), making it challenging to record motor responses related to hand and mouth movements from brain regions distant from the SSS, despite their critical role in BCIs. Here, using micro intravascular electrodes, ivEEGs recorded from the cortical or deep veins of eight pigs could measure cortical activities with greater signal power and better spatial resolution than those recording in the SSS, thus allowing mapping of the sensorimotor and visual functional areas. Additionally, electrical stimulation in the cortical vein between the micro intravascular electrodes induced muscle contractions contralateral to the stimulated area in five anesthetized pigs. These results demonstrate that ivEEG using micro intravascular electrodes is a promising tool for developing BCIs.

neuroscience↗