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Kono, T.

Publications and source records attributed to Kono, T..

16 recordsLinked to original sources

Loss of the Y chromosome drives basal identity and metastatic potential via epigenetic reprogramming in pancreatic cancer

Loss of the Y chromosome (LOY) has been largely unexplored in pancreatic ductal adenocarcinoma (PDAC), and no mechanistic framework previously explained its role in tumor biology. We identify LOY as a recurrent, functionally consequential alteration affecting ~50% of male PDAC patients across two independent cohorts, with strong enrichment in advanced disease and, critically, in the basal subtype, establishing LOY as a clinically actionable biomarker. Comprehensive genomic profiling positions LOY as a distinct genetic event associated with TP53 mutations, implicating it in aggressive tumor evolution. Integrative analyses across bulk tumors, single-cell datasets and CRISPR-engineered PDAC models converge on epithelial-to-mesenchymal transition (EMT) as the dominant LOY-driven program. Y-chromosome deletion alone induces EMT transcriptional states, mesenchymal morphology and enhanced metastatic ability. Mechanistically, LOY disrupts epigenetic regulation through loss of Y-linked chromatin modifiers, reshaping DNA methylation at EMT- and basal-defining loci and reducing chemotherapy sensitivity. These findings establish LOY as a causal genetic driver of PDAC progression and a clinically accessible biomarker with direct therapeutic relevance.

cancer biology↗

Organ-resolved endothelial regulatory programs link aging and metabolic overload to vascular immune remodeling

Systemic aging and metabolic overload remodel the vasculature; however, how endothelial cells integrate these stresses across organs remains unclear. Using multi-organ single-cell and spatial transcriptomics with functional validation, we mapped endothelial and hematopoietic responses in adipose tissue, skeletal muscle, liver, and heart. Organ-specific endothelial transcriptional features were relatively preserved, whereas chronic stress selectively reconfigured regulatory programs: aging induced a conserved Irf/Stat-centered endothelial program, while high-fat diet engaged organ-biased lipid and remodeling programs. Spatial analysis revealed perivascular niches centered on aging-associated interferon-stimulated endothelial activation, with neighboring immune and stromal cells expressing C3 and LRP1-associated signals. Rather than simply amplifying inflammation, these niches contained mechanisms that restrained IFN activation, as C3 depletion upregulated vascular IRF7 expression. In parallel, the IFN downstream effector BST2 promoted anti-inflammatory macrophage differentiation and suppressed atherosclerosis. These findings define vascular inflammaging as an organ-resolved niche process in which endothelial IFN activation is coupled to local inflammatory restraint. HighlightsO_LIAging induces a shared endothelial type I IFN program across organs. C_LIO_LIA high-fat diet triggers organ-biased endothelial remodeling programs. C_LIO_LIPerivascular interferon niches couple inflammation with local restraint. C_LIO_LIIFN-induced endothelial BST2 promotes CD200R-associated macrophage regulatory features. C_LI

cell biology↗

Minimally invasive measurement of maternal transcripts enables predicting the developmental potential of mammalian zygotes

Maternal transcripts are stored in the oocyte cytoplasm during oogenesis and play a pivotal role in early embryonic development after fertilization. However, specific maternal transcripts that reflect the developmental potential of embryos have not been systematically identified, and the use of maternal transcript levels as an indicator of successful development has not been explored. Here, we link the maternal transcriptome to the zygotes developmental potential by examining transcripts in a single polar body. The transcriptome of a zygote or an oocyte was highly similar to that of its accompanying polar body in mouse, cow, and human. We have identified a set of maternal transcripts whose expression levels fluctuate between poor- and good-quality zygotes. Specifically, Sipa1and Zmym6 were identified as marker transcripts that accurately reflect the developmental potential of zygotes. Using these marker genes, combined with machine learning, the development of zygotes to the blastocyst stage was successfully predicted with more than 80% specificity as early as 12 hours after fertilization. Furthermore, our prediction platform significantly improved implantation rates and live births to term. Thus, we have demonstrated a minimally invasive method for identifying maternal transcripts associated with zygote developmental potential. Our developed prediction system provides a generalizable conceptual framework for human infertility treatment to reduce the risk of implantation failure by excluding embryos with low developmental potential, especially when early embryos are transferred, and for livestock propagation to assess selected expressed maternal trait-associated variants before embryo transfer.

developmental biology↗

Redistribution of fragmented mitochondria ensure symmetric organelle partitioning and faithful chromosome segregation in mitotic mouse zygotes

In cleavage-stage embryos, preexisting organelles partition evenly into daughter blastomeres without significant cell growth after symmetric cell division. The presence of mitochondrial DNA within mitochondria and its restricted replication during preimplantation development makes their inheritance particularly important. While chromosomes are precisely segregated by the mitotic spindle, the mechanisms controlling mitochondrial partitioning remain poorly understood. In this study, we investigate the mechanism by which Dynamin-related protein 1 (Drp1) controls the mitochondrial redistribution and partitioning during embryonic cleavage. Depletion of Drp1 in mouse zygotes causes marked mitochondrial aggregation, and the majority of embryos arrest at the 2-cell stage. Clumped mitochondria are located in the center of mitotic Drp1-depleted zygotes with less uniform distribution, thereby preventing their symmetric partitioning. Asymmetric mitochondrial inheritance is accompanied by functionally inequivalent blastomeres with biased ATP and endoplasmic reticulum Ca2+ levels. We also find that marked mitochondrial centration in Drp1-depleted zygotes prevents the assembly of parental chromosomes, resulting in chromosome segregation defects and binucleation. Thus, mitochondrial fragmentation mediated by Drp1 ensure proper organelle positioning and partitioning into functional daughters during the first embryonic cleavage. Impact statementDepletion of Dynamin-related protein 1, a key regulator of mitochondrial fission, in mouse zygotes impair symmetric organelle partitioning and chromosome segregation leading to early developmental arrest.

developmental biology↗

Lipopolysaccharides derived from Porphyromonas gingivalis and Escherichia coli: differential and interactive effects on novelty-induced hyperlocomotion, blood cytokine levels and TRL4-related processes

Lipopolysaccharide (LPS), a component of the Gram-negative bacterial cell wall, activates Toll-like receptors (TLRs). Porphyromonas gingivalis (Pg) may be involved in the progression of periodontal disease. Mice exposed to a novel environment show hyperlocomotion that is inhibited by systemic administration of LPS derived from Escherichia coli (Ec-LPS). However, whether Pg-LPS influences novelty-induced locomotion is unknown. Accordingly, we carried out an open field test to analyse the effects of Pg-LPS. For comparison, effects of Ec-LPS were also studied. We also investigated the influence of systemic administration of Pg-LPS or Ec-LPS on IL-6, TNF-alpha, and IL-10 levels in blood, as they could be involved in the changes in locomotion. The TLR4 receptor antagonist TAK-242 was used to study the involvement of TLR4. Since Pg-LPS may block TLR4 in vitro, we analysed the effects of Pg-LPS on Ec-LPS-induced changes in behavioural and biochemical parameters. Male ddY mice were used. Compounds were administered intraperitoneally. Ec-LPS (840 {micro}g/kg), but not Pg-LPS (100, 500 and 840 {micro}g/kg), inhibited novelty-induced locomotion, which was reversed by TAK-242 (3.0 mg/kg). Ec-LPS (840 {micro}g/kg) increased blood levels of IL-6 and IL-10, which was antagonized by TAK-242 (3.0 mg/kg). However, TAK-242 did not inhibit Ec-LPS-induced increases in TNF-alpha levels in blood. Pg-LPS (100, 500, and 840 {micro}g/kg) did not alter blood IL-6, TNF-alpha, or IL-10 levels. The Ec-LPS-induced increase in blood IL-10, but not IL-6 and TNF-alpha, levels was inhibited by Pg-LPS (500 {micro}g/kg). These results suggest that TLR4 stimulation mediates the inhibition of novel environment-induced locomotion in mice following systemic administration of Ec-LPS, while also increasing blood IL-6 and IL-10 levels. In contrast, Pg-LPS did not exhibit these effects. The present study also provides in vivo evidence that Pg-LPS can inhibit TLR4-mediated increases in blood IL-10 levels, which is thought to prevent the development of periodontal disease.

microbiology↗

Single cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers

BackgroundThe encoding of cell intrinsic resistance states in breast cancer reflects the contributions of genomic and non-genomic variation. However, identifying the potential contributions of each requires accurate measurement and subtraction of the contribution of clonal fitness from co-measurement of transcriptional states. Somatic genomic variation in gene dosage, copy number variation, is the dominant mutational mechanism in breast cancer contributing to transcriptional variation and has recently been shown to contribute to platinum chemotherapy resistance states. Here we deploy time series measurements of triple negative breast cancer single cell transcriptomes in conjunction with co-measured single cell copy number associated clonal fitness to identify the contributions of genomic and non-genomic mechanisms to drug associated transcription states. ResultsWe generated serial scRNA-seq data (126,556 cells) from triple negative breast cancer (TNBC) patient-derived xenograft (PDX) experiments over 2.5 years in duration, and matched it against genomic copy number single cell data from the same biological samples. We show that the cell memory of transcriptional states of TNBC tumors serially exposed to platinum identifies distinct clonal responses within individual tumours. Copy-number clones with high drug fitness leading to clonal sweeps exhibit less transcriptional reversion, whereas clones with weak drug fitness exhibit highly dynamic transcription on drug withdrawal. Pathway analysis shows that copy number associated and copy number independent transcripts converge on epithelial-mesenchymal transition (EMT) and cytokine signaling states associated with resistance. We show from trajectory analysis that transcriptional reversion exhibits hysteresis, indicating that new intermediate transcriptional states are generated by platinum exposure. ConclusionsWe discovered that copy number clones with strong genotype associated fitness under platinum became fixed in their states, resulting in minimal transcriptional reversion on drug withdrawal. In contrast clones with weaker fitness undergo non-genomic transcriptional plasticity and these distinct responses co-exist within single tumours. Together the data suggest that copy number associated and copy number independent transcriptional states may contribute to platinum drug resistance within individual tumours. The dominance of genomic or non-genomic mechanisms within individual polyclonal tumours has implications for approaches to restoration of drug sensitivity and re-treatment strategies. Data availabilityUploaded Data URL: https://ega-archive.org/studies/EGAS00001007242 Github manuscript: https://github.com/molonc/drug_resistant_material/

genomics↗

Quantitative environmental DNA metabarcoding reflects quantitative capture data of fish community obtained by electrical shocker

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity. HighlightsO_LIeDNA analysis and capture surveys of fishes were conducted at a total of 21 sites. C_LIO_LIQuantitative eDNA metabarcoding (qMiSeq) successfully quantified the eDNA of fishes. C_LIO_LIFor each site, the estimated eDNA conc. reflected the abundance and biomass of fishes. C_LIO_LIFor each taxon, the estimated eDNA conc. were comparable among sites. C_LIO_LIqMiSeq is a suitable and useful tool for quantitative monitoring of fish community. C_LI

ecology↗

Topoisomerase 2b induces DNA breaks to regulate human papillomavirus replication

Topoisomerases regulate higher order chromatin structures through the transient breaking and re-ligating of one or both strands of the phosphodiester backbone of duplex DNA. TOP2{beta} is a type II topoisomerase that induces double strand DNA breaks at topological-associated domains (TADS) to relieve torsional stress arising during transcription or replication. TADS are anchored by CTCF and SMC1 cohesin proteins in complexes with TOP2{beta}. Upon DNA cleavage a covalent intermediate DNA-TOP2{beta} (TOP2{beta}cc) is transiently generated to allow for strand passage. The tyrosyl-DNA phosphodiesterase TDP2 can resolve TOP2{beta}cc but failure to do so quickly can lead to long-lasting DNA breaks. Given the role of CTCF/SMC1 proteins in the HPV life cycle we investigated if TOP2{beta} proteins contribute to HPV pathogenesis. Our studies demonstrated that levels of both TOP2{beta} and TDP2 were substantially increased in cells with high risk HPV genomes and this correlated with high amounts of DNA breaks. Knockdown of TOP2{beta} with shRNAs reduced DNA breaks by over 50% as determined through COMET assays. Furthermore this correlated with substantially reduced formation of repair foci such as {gamma}H2AX, pCHK1 and pSMC1 indicative of impaired activation of DNA damage repair pathways. Importantly, knockdown of TOP2{beta} also blocked HPV genome replication. Our previous studies demonstrated that CTCF /SMC1 factors associate with HPV genomes at sites in the late regions of HPV31 and these correspond to regions that also bind TOP2{beta}. This study identifies TOP2{beta} as responsible for enhanced levels of DNA breaks in HPV positive cells and as a regulator of viral replication.

microbiology↗

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

Tumour fitness landscapes underpin selection in cancer, impacting etiology, evolution and response to treatment. Progress in defining fitness landscapes has been impeded by a lack of timeseries perturbation experiments over realistic intervals at single cell resolution. We studied the nature of clonal dynamics induced by genetic and pharmacologic perturbation with a quantitative fitness model developed to ascribe quantitative selective coefficients to individual cancer clones, enable prediction of clone-specific growth potential, and forecast competitive clonal dynamics over time. We applied the model to serial single cell genome (>60,000 cells) and transcriptome (>58,000 cells) experiments ranging from 10 months to 2.5 years in duration. We found that genetic perturbation of TP53 in epithelial cell lines induces multiple forms of copy number alteration that confer increased fitness to clonal populations with measurable consequences on gene expression. In patient derived xenografts, predicted selective coefficients accurately forecasted clonal competition dynamics, that were validated with timeseries sampling of experimentally engineered mixtures of low and high fitness clones. In cisplatin-treated patient derived xenografts, the fitness landscape was inverted in a time-dependent manner, whereby a drug resistant clone emerged from a phylogenetic lineage of low fitness clones, and high fitness clones were eradicated. Moreover, clonal selection mediated reversible drug response early in the selection process, whereas late dynamics in genomically fixed clones were associated with transcriptional plasticity on a fixed clonal genotype. Together, our findings outline causal mechanisms with implication for interpreting how mutations and multi-faceted drug resistance mechanisms shape the etiology and cellular fitness of human cancers.

cancer biology↗

Cigarette Smoke Exposure Impairs β-Cell Function Through Activation of Oxidative Stress and Ceramide Accumulation

ObjectivesEpidemiological studies indicate that first- and second-hand cigarette smoke (CS) exposure are important risk factors for the development of type 2 diabetes (T2D). Additionally, elevated diabetes risk has been reported to occur within a short period of time after smoking cessation, and health risks associated with smoking are increased when combined with obesity. At present, the mechanisms underlying these associations remain incompletely understood. The objective of this study was to test the impact of CS exposure on pancreatic {beta}-cell function using rodent and in vitro models.\n\nMethodsBeginning at 8 weeks of age, C57BL/6J mice were concurrently fed high fat-diet (HFD) and exposed to CS for 11 weeks, followed by an additional 11 weeks of smoking cessation with continued HFD exposure. Glucose tolerance testing was performed during CS exposure and during the cessation period. Cultured {beta}-cells (INS-1) and primary islets were exposed ex vivo to CS extract (CSE), and {beta}-cell function and viability were tested. Since CS increases ceramide in lungs cells and these bioactive sphingolipids have been implicated in pancreatic {beta}-cell dysfunction in diabetes, islet and {beta}-cell sphingolipid levels were measured in islets from CS-exposed mice and in CSE-treated islets and INS-1 cells using liquid chromatography-tandem mass spectrometry.\n\nResultsCompared to HFD-fed ambient air-exposed mice, HFD-fed and CS- exposed mice had reduced weight gain and better glucose tolerance during the active smoking period. Following smoking cessation, CS-mice exhibited rapid weight gain and a significantly greater increase in glucose intolerance compared to non-smoking control mice. CS-exposed mice had higher serum proinsulin/insulin ratios, indicative of {beta}-cell dysfunction, significantly lower {beta}-cell mass (p=0.02), and reduced {beta}-cell proliferation (p=0.006), and increased islet ceramide accumulation. Ex vivo exposure of isolated islets to CSE was sufficient to increase islet ceramide accumulation, reduce insulin gene expression and glucose-stimulated insulin secretion, and increase {beta}-cell oxidative and ER stress. Treatment with the antioxidant N-acetylcysteine, markedly attenuated the effects of CSE on ceramide levels, restored {beta}-cell function and survival, and increased cyclin D2 expression, while also reducing activation of {beta}-cell ER and oxidative stress.\n\nConclusionsOur results indicate that CS exposure inhibits insulin production, processing, and secretion and reduced {beta}-cell viability and proliferation. These effects were linked to increased {beta}-cell oxidative and ER stress and ceramide accumulation. Mice fed HFD continued to experience detrimental effects of CS exposure even during smoking cessation. Elucidation of mechanisms by which CS exposure impairs {beta}-cell function in synergy with obesity will help design therapeutic and preventive interventions for both active and former smokers.

molecular biology↗

The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research

The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced relative. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate the highest quality molluscan assembly to date. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.

genomics↗

Evaluation of biodiversity metrics through environmental DNA metabarcoding outperforms visual and capturing surveys

O_LIInformation on alpha (local), beta (between habitats), and gamma (regional) diversity is fundamental to understanding biodiversity as well as the function and stability of community dynamics. Methods like environmental DNA (eDNA) metabarcoding are currently considered useful to investigate biodiversity. C_LIO_LIWe compared the performance of eDNA metabarcoding with visual and capture surveys for estimating alpha and gamma diversity of river fish communities, and nestedness and turnover in particular. C_LIO_LIIn five rivers across west Japan, by comparison to visual/capture surveys, eDNA metabarcoding detected more species in the study sites (i.e., alpha diversity). Consequently the overall number of species in the region (i.e., gamma diversity) was higher. In particular, the species found by visual/capture surveys were encompassed by those detected by eDNA metabarcoding. C_LIO_LIEstimates of community diversity within rivers differed between survey methods. Although we found that the methods show similar levels of community nestedness and turnover within the rivers, visual/capture surveys showed more distinct community differences from upstream to downstream. Our results suggest that eDNA metabarcoding may be a suitable method for community assemblage analysis, especially for understanding regional community patterns, for fish monitoring in rivers. C_LI

ecology↗

Paternal age affects offspring's behavior possibly via an epigenetic mechanism recruiting a transcriptional repressor REST

Advanced paternal age has deleterious effects on mental health of next generation. Using a mouse model, we have confirmed that offspring derived from aged fathers showed impairments in behavior and abnormalities in the brain structure and activity. Comprehensive target DNA methylome analyses revealed in aged sperm more hypo-methylated genomic regions, in which REST/NRSF binding motif was enriched. Gene set enrichment analyses also identified enrichment of "REST/NRSF target genes", in addition to "Late-fetal genes" and autism spectrum disorder-related "SFARI genes", in up-regulated genes of developing brains from aged father. Indeed, gene sets near hypo-methylated genomic regions with REST/NRSF binding motif were also enriched in up-regulated genes of developing brains. Taken altogether, DNA hypo-methylation due to paternal aging in sperm will induce leaky expression of REST/NRSF target genes in the developing brain, thereby causing neuronal abnormalities and subsequent behavioral alteration in offspring.

neuroscience↗

Relationships of trainee dentists’ empathy and communication characteristics with simulated patients’ assessment in medical interviews

ObjectivesWe aimed to clarify the characteristics of communication between trainee dentists and simulated patients (SPs) and to examine how the level of trainee dentists self-reported empathy influences assessment by SPs in medical interviews.\n\nMaterials and methodsThe study involved 100 trainee dentists at Okayama University Hospital and eight SPs. The trainee dentists conducted initial interviews with the SPs after completing the Japanese version of the Jefferson Scale of Empathy. Their interviews were recorded and analyzed using the Roter Interaction Analysis System. The SPs assessed the trainees communication immediately after each interview. The trainee dentists were classified into two groups (more positive and less positive groups) according to SP assessment scores.\n\nResultsCompared with the less positive trainees, the more positive trainees scored higher on the [Emotional expression] and lower on the [Medical data gathering] Roter Interaction Analysis System categories. There was no difference in [Dental data gathering] between the two groups. The SPs of more positive trainees had higher rates of [Positive talk] and [Emotional expression] and lower rates of [Medical information giving] and [Dental information giving]. The trainees with more positive ratings from SPs had significantly higher Jefferson Scale of Empathy total scores.\n\nConclusionThe results of this study suggest that responding to the SPs emotions is a relevant characteristic of dentist-SP communication to SPs positive assessment in medical interviews. Further, trainees self-reported empathy was related with the SPs assessment of trainees communication, which indicated that patient satisfaction can be improved by increasing the dentists empathy. Thus, an empathic attitude among dentists is a significant determinant of patient satisfaction.

scientific communication and education↗

Growing oocyte specific transcription-dependent de novo DNA methylation at the imprinted Zrsr1-DMR

Zrsr1 is a paternally expressed imprinted gene located in the first intron of Commd1, and the Zrsr1 promoter resides in a differentially methylated region (DMR) that is maternally methylated in the oocyte. However, a mechanism for the establishment of the methylation has remained obscure. Commd1 is transcribed in the opposite direction to Zrsr1 with predominant maternal expression, especially in the adult brain. In this study, we found Commed1 transcribed through the DMR in the growing oocyte. Zrsr1-DMR methylation was abolished by the prevention of Commd1 transcription. This result indicated that methylation at the Zrsr1-DMR was transcription-dependent.

molecular biology↗

Stepwise approach to oocyte depletion in Sry mutated XY female mice

Little is known regarding the mechanisms underlying infertility in male-to-female sex-reversed females. To gain a better understanding of germ cell dysfunction in this condition, we produced XYsry--females via the CRISPR/Cas9 system in C57BL/6 inbred strain mice. Mutant mice showed severe attrition of germ cells during foetal development, resulting in depletion of ovarian germ cells before sexual maturation. Comprehensive transcriptome analysis of embryonic day 13.5 primordial germ cells (PGCs) and postnatal day 1 oocytes demonstrated that XYsry--PGCs had already deviated from the developmental process at the mitotic stage. In addition, XYsry--oocytes resulted in meiotic disruption and developmental failure, and the genes related to these processes were significantly changed. This grievous disruption, which caused germ cell deterioration in XYsry--females, was shown to proceed from the germ cells themselves. These results provide novel insight into the germ cell depletion of sex-reversed mice as well as into disorders of sex differentiation in human, such as Swyer syndrome, wherein patients present as typical females albeit with an XY karyotype and infertile.

developmental biology↗