Biology subjects

Kudoh, T.

Publications and source records attributed to Kudoh, T..

12 recordsLinked to original sources

bioRxiv2026

BeatRatePy - Automated Hight-Throughput Python-Based Beat Rate Quantification and Generation of Speed and Contraction Traces

Analysing cardiac motion from label free imaging can be difficult, especially when recordings vary in quality or show complex movement. We developed a Python-based pipeline that automatically measures beat rate, contraction, speed from transmitted light timelapse data. The workflow runs in a Jupyter notebook and uses straightforward steps that can be followed easily, making the analysis accessible including to users with limited coding experience. Using human iPSC-derived cardiomyocytes imaged on a Zeiss Cell Discoverer 7, the pipeline produced beat rates, contraction and contraction speed measurements that matched expected behaviour. To test wider use, we applied the same workflow to killifish larvae heart recordings and public datasets, changing only basic input parameters. The pipeline performed consistently across these different systems and did not require changes to the underlying code. By supporting clear parameter control and use across laboratories, microscopy platforms and repositories, this approach strengthens reproducible analysis of cardiac motion from label free imaging.

cell biology↗

bioRxiv2026

Chromosome-level assembly of the Arabian killifish as a novel biomedical model species.

The Arabian killifish (Aphaniops dispar) is an excellent model for studying human diseases such as fungal infections and cancer progression. The embryos possess a transparent chorion for live imaging and display an extended period of independent feeding (13 days post-fertilisation). They also exhibit broad thermal tolerance which enables live imaging at physiologically relevant human temperatures. However, omics resources for this species remain limited and restricts its use in genomics studies. We generated a 1.45 GB high-quality reference assembly with 24 chromosome-level scaffolds and N50 score of 60.64 Mb by combining long-read, long-range, and short-read sequencing. The A. dispar genome exhibits a high level of homozygosity (95.6%) with BUSCO gene completeness scores of 99.2% and 97.5% for the Actinopterygii and Cyprinodontiformes lineages, respectively. The genome is highly repetitive (58.7%) and the majority of these are DNA transposons. The mitochondrial genome is 81.55% similar to that of Aphanius iberus (the Spanish toothcarp), with minor structural modifications. A. dispar exhibits highly conserved synteny with Fundulus heteroclitus within the Cyprinodontoidei clade. Together, these findings provide a valuable genomic resource for comparative genomics within the teleost community.

genomics↗

bioRxiv2026

Title: A de novo transcriptomic atlas of early embryo development in the Arabian killifish

The Arabian killifish (Aphaniops dispar) is new tractable vertebrate model system for developmental, ecological and biomedical research, including drug screening, pharmacological and infection biology studies. It is a relatively small euryhaline teleost with broad thermal tolerance and adaptability across a wide range of salinities from freshwater to hypersaline habitats. The embryos and early larvae are tolerant to environmental stressors and exhibit a delayed period of nutritional independence before hatching. This advantage offers an extended window for experimenting on the early developmental processes. Here, we describe time-course gene expression profiling of Arabian killifish embryos across nine developmental time points, from the 1-cell stage to the larval pre-hatching stage. Clustering of dynamic expression profiles for 27,564 Trinity genes revealed coordinated transcriptional modules corresponding to the maternal, blastula, maternal-to-zygotic transition (MZT)-related, gastrulation, organogenesis and larval maturation stages. The maternal stage displayed a highly distinct expression profile, dominated by maternal-specific transcripts that are rapidly degraded during the MZT. The later stages, from 48 hpf onward, revealed a shift from early regulatory mechanisms to the expression of organogenesis-related genes. The ZGA stage showed the conserved up-regulation of many zinc finger-associated genes, consistent with zebrafish and other teleost genomes. Overall, embryo development in A. dispar is slower than in zebrafish, with equivalent stages occurring several hours later. We propose a delayed onset of zygotic genome activation (ZGA) in the blastula stage, corresponding to 6 hpf in the Arabian killifish. Taken together, this study provides a transcriptomic resource for mining embryo development-related genes in the Arabian killifish.

genomics↗

bioRxiv2025

Evaluating anaesthetics for improving scientific research and welfare using larval zebrafish

Establishing anaesthesia for ensuring both animal welfare and compatibility with protocols required for different areas of scientific research is vital. Zebrafish (Danio rerio) are one of the most used animal models in research; however, little is known about the appropriateness of anaesthetic used for this species, especially for embryo-larval life stages. Using a combination of whole-brain functional imaging, quantification of cardiovascular performance, and behaviour, we explore the efficacy and tolerability of six widely used fish anaesthetics (2-phenoxyethanol, benzocaine, etomidate, MS222, isoeugenol and quinaldine sulfate) in larval zebrafish. We show that MS222 and quinaldine sulfate are the most suitable for achieving deep anaesthesia, while etomidate is better suited for studies focused on the cardiovascular system. Only quinaldine sulfate was found to be aversive. Our findings aid researchers for selecting the most suitable anaesthetic compounds and concentrations for their specific research goals, and the refinement of studies using anaesthesia in larval zebrafish.

physiology↗

bioRxiv2025

The retinoic acid receptor regulates development of a key evolutionary novelty - the molluscan shell

The shells of molluscs are iconic structures of invertebrate exoskeletons supporting and protecting their soft body parts. The shell matrix molecules are synthesized and secreted from a shell-producing tissue, the shell gland. Shell gland cells develop at the early trochophore stage of the larvae. To date, the molecular signalling pathways by which the shell gland forms and starts to secrete the shell remains elusive. Here we demonstrate in the Pacific oyster Crassostrea gigas and the limpet Nipponacmea fuscoviridis, that the retinoic acid receptor (RAR), is crucial for inducing shell gland formation. RAR is expressed in both species in the shell gland at the late gastrula to early trochophore stages prior to the first production of shell. Suppression of the RAR by chemical inhibitors or gene-knock-down lead to a complete loss of the larval shell. Transcriptomic and in situ hybridisation analyses revealed that the developmental regulatory genes that are normally expressed in the shell gland, including engrailed, are down-regulated in the RAR-suppressed embryos. Using the RAR functional assay carried out on zebrafish embryos, we also revealed that the oyster RAR cannot transduce the RA signal in zebrafish, indicating that the molluscan RAR is clearly different from vertebrate RARs in its binding capacity to the RA. Our finding represents a key example of adaptive evolution of developmental "toolkit" genes for the origin of a major novel trait, the molluscan shell, in animals.

developmental biology↗

bioRxiv2025

Physical disturbance induces heart stop in mangrove killifish, Kryptolebias marmoratus embryos

The mangrove killifish, Kryptolebias marmoratus, is a highly unique vertebrate species, known for its unusual sexual systems. It is one of two known self-fertilizing simultaneous hermaphroditic vertebrates, alongside the related Kryptolebias ocellatus1,2. While individuals can be born as primary males, most are born as hermaphrodites3 and some turn into secondary males later in life4. K. marmoratus is exceptionally tolerant of harsh and variable environmental conditions. This includes emersion as well as widely ranging salinities and temperatures5-7. Embryos can enter diapause, a state of arrested development, when conditions are unfavourable8,9.

developmental biology↗

bioRxiv2024

Ethanol down-regulates gastrula gene expression and cell movement, causing symptoms of foetal alcohol spectrum disorders

Foetal alcohol spectrum disorders (FASDs) occur in embryos when they are exposed to maternally supplied alcohol. To study the mechanisms of FASDs, the zebrafish embryo can serve as an excellent model as ethanol exposed zebrafish embryos exhibit common symptoms of human FASDs including microcephaly, incomplete neural plate closure, eye defects, craniofacial disorders and many other defects. Here we investigated the embryo development at gastrula stage when three germ layers develop with specific gene expressions and undergo dynamic cell movement including extension, convergence and epiboly, establishing the platform to form the head and body axis in the later development. Gastrula cell movement analyses using fluorescent transgenic zebrafish embryos revealed that ethanol induced dose dependent delay of extension, convergence and epiboly cell movement and associated gene expressions in all three germ layers. Our results suggest multiple targets of ethanol including gene expression and cell movement, consequently delay the key gene expression and cell localisation, causing irreversible developmental defects in the head and body axis formation.

pharmacology and toxicology↗

bioRxiv2024

Melanophore and fluoroleucophore synergistically photo-protect the Arabian killifish, Aphanius dispar, embryo from ultraviolet light

Pigment cells in fish species play crucial roles in forming colour patterns of each species and other physiological characteristics including photoprotection. Research on photoprotection by pigment cells in animals has primarily concentrated on black pigment cells, known as melanophores. However, the roles of other pigment cells and their synergistic effects on UV protection remain poorly understood. In this study, we use the Arabian killifish embryos as a model for studying the mechanisms of UV protection by different pigment cells. This species features highly fluorescent pigment cells called fluoroleucophores and black pigment cells known as melanophores. The fluorescent pigments and black melanin pigments are generated by genes gch (GTP cyclohydrolase) and tyr (tyrosinase) respectively. We generated gch(-/-) and gch/tyr(-/-) double mutant lines using CRISPR/Cas9 genome editing and examined the UV sensitivity of these mutant embryos. Both morphology and gene expression data revealed that the gch/tyr(-/-) double mutant line exhibited the highest UV sensitivity, and the gch(-/-) line also demonstrated a greater stress response compared to wild type (WT). From the study, we have identified the synergistic role of black and fluorescent pigment cells in providing effective UV protection from the early stages of embryonic development.

developmental biology↗

bioRxiv2024

Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish infection

Candida auris is a critical priority fungal pathogen (World Health Organization). Clinical management is challenging due to a high mortality rate, rapidly increasing antifungal resistance, and frequent nosocomial outbreaks. A critical bottleneck in understanding virulence is the lack of gene expression profiling models during infection. We developed a fish embryo yolk-sac microinjection model using Aphanius dispar (Arabian killifish; AK) at human body temperature. This enabled interrogation of infection dynamics via dual host-pathogen RNA-seq across five major clades of C. auris (I-V). Host responses included heat shock, complement activation, and nutritional immunity, notably haem oxygenase (HMOX) expression during clade IV infection. We identified a pathogen transcriptional signature across all five clades of C. auris strongly enriched for putative xenosiderophore transmembrane transporters. We describe this novel family and a sub-clade of five putative haem transport-related (HTR) genes. Only the basal clade V isolate formed filaments, associated with canonical and atypical regulators of morphogenesis. Clades I and IV demonstrated increased virulence, accompanied by up-regulation of three HTR genes in clade IV, and the non-mating mating-type locus (MTL) gene PIKA in both clades. Our study provides new insight into C. auris pathogenesis, highlighting species-wide in vivo up-regulation of XTC genes during host tissue infection. Significance statementCandida auris is an emerging human fungal pathogen and global public health threat, yet in vivo transcriptomic analysis of tissue infection has remained elusive. Using yolk-sac infection in Arabian killifish, we profiled gene expression across five major C. auris clades. We found that the basal clade V uniquely undergoes filamentation during infection, while all clades upregulate members of a large, expanded family of xenosiderophore transporter candidate genes. These findings highlight the important roles for iron acquisition and morphological switching in pathogenesis, revealing potential mechanisms of immune evasion and fungal persistence, and identifying candidate targets for antifungal therapy.

microbiology↗

bioRxiv2024

The thermotolerant Arabian killifish, Aphanius dispar, as a novel infection model for human fungal pathogens

Candida albicans: a fungal pathogen, can cause superficial and fatal infections in humans. An important virulence factor in C. albicans dissemination is the transformation from yeast to an invasive hyphal form, which is favoured at human body temperature. Zebrafish, a useful model for studying C. albicans infections, cannot survive at 37{degrees}C. Arabian killifish, Aphanius dispar, an emerging teleost model can tolerate temperatures up to 40 {degrees}C for up to 12 days (independent feeding time) allowing for longer analysis compared to zebrafish. This study introduces A. dispar as a thermo-relevant and a more accurate reporter of the virulence mechanisms relevant to C. albicans as a human pathogen. Using A. dispar, we tested virulence at human skin (30 {degrees}C), body temperature (37 {degrees}C) and a high fever condition (40{degrees}C). Infection by C. albicans at 37{degrees}C and 40{degrees}C significantly increased virulence, reduced survival of AKF embryos and formed invasive hyphal network compared to 30 {degrees}C. Two mutant strains of C. albicans. pmr1{Delta} (with aberrant cell surface glycans) exhibited reduced virulence at 37{degrees}C, whereas rsr1{Delta} (lacking a cell polarity marker) showed less virulence at 30 {degrees}C. Additionally, anti-fungal treatment rescued AKF survival in a dose-dependent manner, indicating AKFs potential for in vivo drug testing. Our data indicates the quantitative and qualitative importance of examining virulence traits at physiologically relevant temperatures and demonstrates an equivalence to findings for systemic infection derived in mouse models. The A. dispar embryo therefore provides an excellent in vivo model system for assessing virulence, drug-testing, and real-time imaging of host-pathogen interactions. Significance StatementThe virulence of many pathogens is dependent on host temperature. We demonstrate that the A. dispar embryo provides an excellent new thermo-relevant alternative to zebrafish and mouse models, which have limitations in terms of the range of temperatures that can be assessed in real-time. In this study, we have assessed C. albicans temperature-based virulence, focusing on human body and human skin temperatures (37, 40 and 30 {degrees}C, respectively) by examining different genetic backgrounds of C. albicans strains. The results indicate different C. albicans strains with genetic background show varied virulence depending on temperature indicating importance of examination of virulence mechanisms at physiological temperatures.

animal behavior and cognition↗

bioRxiv2024

Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish, Kryptolebias marmoratus

From an ENU-mutated mangrove killifish line R228, we have identified and isolated a novel mutant line, no-fin-ray/nfr in which fin ray development is largely reduced. Besides the reduction of the fin, the nfr mutant also exhibited other phenotype associated with ectodermal cell lineages including loss of scales, deformation in the gill structure such as decreasing the number of gill filaments, the reduction in the number of jaw teeth, pharyngeal teeth and gill rakers. Illumina RNAseq with 12 embryos each from mutants, siblings and the parental WT strain Hon9 identified a mutation in the edaradd in a highly conserved C-terminal death domain. Edaradd is known as a cytoplasmic accessory protein for the Ectodysplasin A (EDA) signalling pathway. To confirm the crucial role of edaradd during fin development, CRISPR RNAs were designed to knock out the gene in another killifish species, Arabian killifish. Indeed, Arabian killifish edaradd crispants showed a potent reduction of the fin development with 100% frequency. Furthermore, EDA crispants also showed identical phenotypes to that of edaradd crispants, confirming the fin defect in the mutants/crispants is caused by the signalling pathway of the EDA in the killifish species. These data demonstrate a powerful genetic approach using isogenic self-fertilising mangrove killifish as a tool for identifying mutants and their mutation, and revealed the crucial role of edaradd in the fish fin development and other ectoderm derived epithelial tissues.

developmental biology↗

bioRxiv2021

Estrogen regulates early embryonic development of the olfactory sensory system via estrogen responsive glia

Estrogen is well-known to regulate development of sexual dimorphisms of the brain, however its role in the brain during early embryonic development prior to sex-differentiation is unclear. Using estrogen biosensor zebrafish models, we found that estrogen activity in the embryonic brain occurs specifically in a type of glia located within the OB, which we name estrogen-responsive olfactory bulb/EROB cells. With estrogen activity, EROB cells extend their ramified projections that overlay the OB outermost layer and tightly interact with olfactory sensory neurons (OSNs) at the olfactory glomeruli. Pharmacologically inhibiting estrogen activity and/or EROB cell ablation impedes olfactory glomerular development, including OSN pathfinding, topological organisation of olfactory glomeruli and inhibitory neurogenesis in the OB. Furthermore, activation of this estrogen/EROB-dependent mechanism decreases the intrinsic neuronal activity primarily in the OB, and this alteration of estrogen signalling disrupts olfaction-mediated behaviour. We propose that estrogen acts on glia to regulate development of functional OB circuits, thereby modulating the local intrinsic excitability in the OB and olfaction-mediated behaviour. Our data also suggest a possibility that the estrogen/EROB cascade may be an important site of action for environmental estrogens causative of neurodevelopmental impairments in animals and humans.

developmental biology↗