Biology subjects

Toh, H.

Publications and source records attributed to Toh, H..

14 recordsLinked to original sources

bioRxiv2026

Daylight, Daily Rhythms, and Downstream Physiology: A Translational Study in Diurnal Nile Grass Rats (Arvicanthis niloticus)

The circadian system evolved under natural light-dark cycles, while modern humans spend much of their time indoors under electric lighting that differs substantially from daylight in intensity, spectral composition, and temporal structure. How such lighting environments influence circadian system has not been systematically examined in a diurnal animal model under ecologically relevant conditions. In this study, we used the diurnal Nile grass rat (Arvicanthis niloticus) to assess daily locomotor rhythms across four lighting conditions designed to approximate common human exposure scenarios: rectangular daylight (D65-R; [~]5,600 lux), semi-sigmoidal daylight mimicking natural intensity dynamics (D65-S; matched peak intensity with [~]50% lower cumulative energy), fluorescent indoor light (F12; [~]150 lux), and fluorescent light supplemented with a one-hour midday daylight pulse (F12+D65-P). Using a within-subject design (n = 8), male grass rats were housed under each condition for two weeks. D65-R produced the highest daytime activity levels and the strongest day/night activity ratio, consistent with robust circadian entrainment. Despite matching peak intensity, D65-S did not yield comparable circadian outcomes, indicating that cumulative photon exposure, rather than peak intensity alone, contributes to entrainment strength. Notably, the addition of a one-hour midday daylight pulse (D65-P) partially increased circadian amplitude under otherwise fluorescent conditions, with higher periodogram amplitude relative to F12 alone. A separate cohort of males was exposed to D65-R or F12 for six weeks (n = 10/condition) to assess physiological outcomes, including metabolic and reproductive measures. Compared with the D65-R group, F12 group showed higher diabetic rate (10% vs. 40%) and reduced sperm mobility (45{+/-}6 vs. 19{+/-}1 %), consistent with potential downstream correlates of circadian rhythm disruption. Together, these findings demonstrate that lighting conditions characteristic of indoor environments produce weaker circadian organization than daylight-equivalent lighting in a diurnal rodent, which underscore the importance of light quality in shaping circadian rhythms and downstream physiological processes.

animal behavior and cognition↗

bioRxiv2026

A Multi-tissue Transcriptomic-Metabolomic Map Linking Maternal High-Fiber Diet to Reduced Offspring Type 2 Diabetes

BackgroundEarly-life nutritional exposures are increasingly recognized as critical determinants of long-term metabolic health, yet the molecular mechanisms linking maternal diet to offspring type 2 diabetes susceptibility remain incompletely understood. Experimental models are essential to disentangle maternal dietary effects from later-life metabolic influences. MethodsUsing the Nile rat, a genetically heterogeneous model of diet-induced diabetes, we quantified the impact of maternal high-fiber diet on offspring diabetes incidence using sex-stratified time-to-event analyses in 762 offspring. To identify molecular mediators, we performed transcriptomic profiling across 13 offspring tissues, independently contrasting maternal diet exposure and early-onset diabetes status. Overlapping differentially expressed genes were prioritized and evaluated for cardiometabolic associations in human whole-blood transcriptomic data from the GENE-FORECAST cohort. Untargeted plasma metabolomics was integrated to identify circulating metabolites associated with candidate genes. ResultsOffspring born to dams maintained on a high-fiber diet exhibited a markedly reduced risk of developing type 2 diabetes, with approximately 70% lower hazard of diabetes onset in both males and females compared with offspring from regular chow-fed dams. Multi-tissue transcriptomic analyses identified 147 genes differentially expressed in association with both maternal diet and early-onset diabetes, with most effects being tissue-specific. Asnsd1 uniquely showed consistent regulation across the aorta, brown adipose tissue, and skeletal muscle, with higher expression in offspring exposed to a high-fiber maternal diet and lower expression in offspring with early-onset diabetes. In human whole-blood transcriptomic data, ASNSD1 expression was significantly associated with blood pressure-related cardiometabolic traits, including hypertension, systolic blood pressure, and mean arterial pressure. In the animal model, circulating succinic acid was positively correlated with Asnsd1 expression in the aorta but not in other tissues. ConclusionsThis study provides a multi-tissue transcriptomic-metabolomic framework linking maternal high-fiber diet to reduced offspring type 2 diabetes risk. The findings identify ASNSD1 as a maternal diet-sensitive gene associated with diabetes susceptibility across multiple tissues and with cardiometabolic traits in humans, while highlighting tissue-specific relationships between gene expression and circulating metabolites. Together, these results offer mechanistic insight into how early-life nutrition can durably influence diabetes risk across the life course.

developmental biology↗

bioRxiv2025

Multi-omics Integration with GWAS Unveils Molecular Mechanistic Insights for Type 2 Diabetes

BackgroundType 2 diabetes (T2D) is a complex metabolic disorder driven by genetic and environmental factors. While genome-wide association studies (GWAS) have identified numerous T2D-associated variants, many remain functionally uncharacterized. Integration of GWAS with molecular phenotyping offers a path to revealing biological relevance. We investigated the influence of GWAS-variants, including sub-threshold T2D-associated variants (GWAS p-value [≤] 0.0001), on gene and protein expression to assign functional relevance. MethodsGenetic variants associated with T2D in the GWAS Catalog and present in our whole-genome sequencing (WGS) data were used to perform expression quantitative trait loci (eQTL) analysis in 242 whole-blood mRNA-sequenced samples. The same variants were used to perform protein quantitative trait loci (pQTL) analysis in a set of 362 plasma samples profiled on the Olink platform. For each analysis, the datasets were randomly split into discovery and validation subsets. Associations between variants and mRNA or protein levels were tested by multiple linear regression, and only QTLs that reached a false discovery rate adjusted p-value [≤] 0.05 in the discovery dataset and replicated in the validation dataset (p [≤] 0.05) with same direction of effect were carried forward. QTL-linked mRNAs and proteins were subsequently evaluated for their relationship with T2D status to connect them with T2D pathophysiology. ResultsWe identified 1,291 eQTLs linked to 97 mRNAs and 1,273 pQTLs linked to 22 proteins. Among these, 10 mRNAs and 5 proteins were differentially expressed between non-diabetic and diabetic individuals. Notably, LPL, APOBR, APOM (lipid metabolism), NOTCH2, TREH ({beta}-cell/endocrine regulation), and HLA-A, OAS3 (immune response) converged on three biological axes central to T2D pathophysiology. The directionality of molecular effects was consistent with known disease mechanisms, including insulin resistance (LPL, APOBR), {beta}-cell stress (TREH, NOTCH2), and chronic inflammation (OAS3). ConclusionsOur findings indicate that variants falling below conventional GWAS significance thresholds can have demonstrable effects on gene expression and protein levels. This underscores the importance of prioritizing biological relevance alongside statistical significance, rather than relying solely on rigid p-value cutoffs.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗

bioRxiv2025

Chromosomal fusions and subsequent rearrangements shaped octopus genomes

Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the context of morphological innovation. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) has led to a substantial increase in the chromosome number and a new set of chromosomal homologies. Compared to typical molluscan or bilaterian genomes, ACCRE has enabled the origin of many novel regulatory regions in coleoid cephalopods. However, the discrepancies between extant octopodiform (octopus, [~]30 chromosomes) and decapodiform (squid and cuttlefish, [~]46 chromosomes) karyotypes and the direction of these evolutionary changes remain unexplained. Here we provide a draft genome assembly of the vampire squid Vampyroteuthis sp., the largest cephalopod genome sequenced to-date (over 10 gigabasepairs). Through syntenic comparisons, we infer that this basally branching octopodiform species shows partial retention of the chromosomal complement of Decapodiformes, indicating its more ancestral state and the derived nature of the octopod karyotype. Together with the analysis of a new chromosome-level assembly of the pelagic octopod Argonauta hians, we identified irreversible chromosomal fusion-with-mixing events followed by inter-chromosomal translocations in octopods. We show that this secondary reduction and mixing within octopod chromosomes has enabled the origin of a more entangled genomic configuration, shedding light onto the early evolutionary transitions within the clade. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement events in animal genomes. Significance statementHow changes to the ancient animal synteny result in novel chromosomal homologies is difficult to dissect due to the lack of intermediate states. Here we report that the genome of Vampyroteuthis, one of the largest animal genomes sequenced to-date (over 11 gigabasepairs), despite its phylogenetic position within the octopodiform cephalopods, partially retains squid and cuttlefish chromosomal complement, reflecting an ancestral karyotypic state that existed at the time of divergence between these cephalopod lineages. Our findings reveal karyotype reductions through chromosomal fusions were followed by inter-chromosomal translocations in octopods, leading to a more specialized genomic and gene regulatory architecture. These data show how chromosomal fusions can act as drivers of further inter-chromosomal rearrangements in animal genomes.

genomics↗

bioRxiv2025

Fluorescein Angiography Image-AI Based Early Diabetic Retinopathy Detection

Fluorescein angiography (FA) is widely regarded as the clinical gold standard for diagnosing diabetic retinopathy (DR), based on a range of observable symptoms, including microaneurysms, retinal hemorrhages, and vascular leakage. However, early detection of DR remains challenging, as these symptoms may not manifest simultaneously and are often too subtle to detect. Acellular capillary density is currently the only quantitative metric used to assess the risk and severity of DR, particularly in its early stages when these clinical symptoms are minimal or absent. Unfortunately, measuring acellular capillary density to detect pre-symptomatic diabetic retinopathy (DR) requires destructive techniques such as trypsin digest to remove non-vascular tissues, making it unsuitable for human patients, while current imaging techniques such as FA does not have resolution to quantify acellular capillary density, limiting the utility of non- invasive approaches for early detection of DR. In this study, we used Nile rat as a DR model to train an AI deep learning model based on FA images to detect retinas with acellular capillary density [≥]18 counts per mm{superscript 2}, which is considered as pre-symptomatic (before clinically observed DR symptoms) DR. Our model achieves an accuracy of 80.85%, with a sensitivity of 84.21%, specificity of 75.68%, and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.86. We also showed that integrating the duration of diabetes as a pre-knowledge into a Bayesian framework with real time AI-image prediction can enhance the prediction power with AUC of ROC of 0.9. Using the first sequenced Nile rat genome and our RNA-seq data, we identified 43 gene markers that signified a shift from a normal state to a transitional phase preceding early diabetic retinopathy (DR). While PDGF-B/PDGFR{beta} signaling is typically associated with pericyte loss and increased acellular capillary density, which are hallmarks of early DR, none of the identified markers were related to this pathway. Instead, three genes (Bcl2a1, Birc5, and Il20rb) out of these 43 biomarkers are associated with inflammation or response to inflammation suggesting that inflammation may contribute to the shift in acellular capillary density from <16 (normal) to 17-18 counts (transitional phase preceding early DR) per mm{superscript 2} before pericyte loss occurs, providing new insights into the early pathogenesis of DR. Author SummaryDiabetic retinopathy (DR) is a leading cause of vision loss worldwide. Early detection is critical to prevent progression, yet current diagnostic methods rely on symptoms that may appear too late. The density of acellular capillaries--tiny, non-functioning blood vessels in the retina--is a key early marker of DR, but measuring it requires destructive techniques that are not suitable for human patients. In this study, we used Nile rats, a rodent model that naturally develops diabetes and DR, to train an artificial intelligence (AI) model using fluorescein angiography (FA) images. Our AI system detects retinas with acellular capillary density at levels associated with pre- symptomatic DR with high accuracy. We further improved predictive power by integrating diabetes duration into a Bayesian framework. In addition, our transcriptomic study identified 43 markers associated with the transition from a normal state to a transitional phase preceding early diabetic retinopathy. Interestingly, none were linked to a well-known pathway involving pericyte loss, which has been thought to drive early DR. Instead, three markers (Bcl2a1, Birc5, and Il20rb) suggest inflammation may contribute to early changes before pericyte loss occurs. These findings offer a new perspective on the earliest stages of DR.

bioengineering↗

bioRxiv2024

A deletion at the X-linked ARHGAP36 gene locus is associated with the orange coloration of tortoiseshell and calico cats

The X-linked orange (O) locus in domestic cats controls an unknown molecular mechanism that causes the suppression of black-brownish pigmentation in favor of orange coloration. The alternating black-brownish and orange patches seen in tortoiseshell and calico cats are considered as classic examples of the phenotypic expression of random X-chromosome inactivation (XCI) occurring in female mammals. However, the O gene in the cat genome has not been identified, and the genetic variation responsible for the orange coloration remains unknown. We report here that a 5.1-kilobase (kb) deletion within an intron of the X-linked ARHGAP36 gene, encoding a Rho GTPase activating protein, is closely and exclusively associated with orange coloration. The deleted region contains a highly conserved putative regulatory element, whose removal presumably cause altered ARHGAP36 expression. Notably, ARHGAP36 expression in cat skin tissues is linked to the suppression of many melanogenesis genes, potentially shifting pigment synthesis from eumelanin to pheomelanin. Furthermore, we find evidence that the gene undergoes XCI in female human and mouse cells, and XCI-dependent CpG island methylation consistent with random XCI in female domestic cats. The 5.1-kb deletion seems widespread in domestic cats with orange coat coloration, suggesting a single origin of this coat color phenotype.

genetics↗

bioRxiv2024

Cholesterol sulfate prevents maternal-fetal conflict by locally modulating immune reactivity

Although placental mammals are at high risk of maternal-fetal immune conflict, it is unclear how the semi-allogeneic fetus avoids rejection. Cholesterol sulfate (CS) is a bioactive metabolite that inhibits leukocyte migration and activation. This study investigated the roles and cells associated with CS in pregnant mice and humans. CS was sequentially produced by maternal-derived endometrial cells and fetal-derived placental trophoblasts before and after placentation. When mated with allogeneic males, CS-deficient mice showed increased fetal resorption rates under induced placental inflammation. This phenotype disappeared when the activity of the CS-producing enzyme was restored in the placenta. Placental CS levels were reduced in patients with "villitis of unknown etiology." Thus, we uncovered the spatiotemporal control of CS production and its relevance to local immunosuppression during pregnancy.

immunology↗

bioRxiv2024

BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures

Many midbrain dopaminergic neuron (mDA) differentiation protocols aimed at Parkinsons disease (PD) modeling and cell replacement therapy have been developed. However, comprehensive evaluations of the transcriptomic fidelity of these protocols at the single-cell level against a common in vivo reference have been lacking. To this end, we constructed an integrated human fetal whole-brain atlas and a midbrain subatlas to use as a standard of comparison. From the whole-brain atlas, we observed distinct brain-region-specific gene expression in most neural cell types, emphasizing the need to first evaluate in vitro protocols at the whole-brain level to identify midbrain-associated cells. These cells are then mapped to the midbrain subatlas for more refined neuronal subtype specification and trajectory analysis specific to the midbrain. We surveyed all publicly available single-cell datasets of human midbrain culture models and performed the two-tier mapping. Using this biologically-driven multi-resolution mapping strategy which we termed BrainSTEM (brain Single-cell Two tiEr Mapping), we confirmed the presence of multiple midbrain cell types ( on-target), but also a substantial proportion of cells associated with non-midbrain regions and subtypes ( off-target). This leads to an overall inflation of mDA presence, stemming from non-midbrain-associated cells, across all published protocols. BrainSTEM thus offers an unbiased framework for understanding the current state of midbrain models and aids the improvement of midbrain differentiation protocols for PD studies.

bioinformatics↗

bioRxiv2024

Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

Through symbiosis, subunits of chloroplastic complexes are encoded in distinct genomes in the nucleus and organelles. For plant cells to maintain the stoichiometry of subunits and respond to environmental cues, the orchestration of the nuclear and organellar gene expression systems is an essential task. However, the mechanism maintaining chloroplastic complexes remains largely enigmatic. Here, we simultaneously assessed the translatomes of the chloroplast and the cytoplasm via ribosome profiling and revealed the differential mechanisms employed by these two systems to cope with acute light/dark transitions: in chloroplasts, translational regulation is employed, whereas in the cytoplasm, control of the mRNA abundance is implemented. This strategy is widely conserved in land plants (Arabidopsis and the grass plant Brachypodium) and green algae (Chlamydomonas). The translational control in chloroplasts may be established based on organelle symbiosis; the primitive chloroplast in Glaucophyta (Cyanophora) was found to have already acquired translational control, whereas cyanobacteria (Synechocystis) control the mRNA abundance. Moreover, reduced plastoquinones and active cytosolic protein synthesis drive chloroplastic translation of the complex subunits in the light. Our work reveals an early origin of coordination of chloroplast and nuclear/cytoplasmic gene expression upon light exposure.

molecular biology↗

bioRxiv2023

CRISPR-based Genome Editing of a Diurnal Rodent, Nile Grass Rat (Arvicanthis niloticus)

Diurnal and nocturnal mammals have evolved distinct pathways to optimize survival for their chronotype-specific lifestyles. Conventional rodent models, being nocturnal, may not sufficiently recapitulate the biology of diurnal humans in health and disease. Although diurnal rodents are potentially advantageous for translational research, until recently, they have not been genetically tractable. Here, we address this major limitation by demonstrating the first successful CRISPR genome editing of the Nile grass rat (Arvicanthis niloticus), a valuable diurnal rodent. We establish methods for superovulation; embryo development, manipulation, and culture; and pregnancy maintenance to guide future genome editing of this and other diurnal rodent species.

genomics↗

bioRxiv2021

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

The Nile rat (Avicanthis niloticus) is an important animal model for biomedical research, including the study of diurnal rhythms and type 2 diabetes. Here, we report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3,613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including those that affect genes associated with type 2 diabetes and metabolic dysfunctions. These include 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. Our findings reflect the exceptional level of genomic detail present in this assembly, which will greatly expand the potential of the Nile rat as a model organism for genetic studies.

genomics↗

bioRxiv2020

Maternal high fiber diet protects offspring on diabetogenic diet in the Nile rat

Previous studies have reported that maternal malnutrition is linked to increased risk of developing type 2 diabetes in adulthood. Although several diabetic risk factors associated with early life environment have been identified, protective factors remain elusive. Here, we modulate the early life environment using a maternal high fiber diet to investigate whether the offspring are protected from type 2 diabetes. We examined the interplay between early life environment (maternal diet) and later life environment (offspring diet) using a longitudinal study with 671 Nile rats. We found that exposure to a high fiber maternal diet prior to weaning significantly lowers the risk of diet-induced diabetes in the offspring. Interestingly, offspring consuming a high fiber diet after weaning do not get diet-induced diabetes, even when exposed to a diabetogenic maternal diet. Here, we provide the first evidence that the protective effect of high fiber can be transmitted to the offspring through a maternal diet, which has important implications in diabetes prevention.

developmental biology↗

bioRxiv2020

Intracellular Group A Streptococcus induces Golgi fragmentation to impair host defenses through Streptolysin O and NAD-glycohydrolase

Group A Streptococcus (GAS; Streptococcus pyogenes) is a major human pathogen that causes streptococcal pharyngitis, skin and soft-tissue infections, and life-threatening conditions such as streptococcal toxic-shock syndrome. During infection, GAS not only invades diverse host cells, but also injects effector proteins such as NAD-glycohydrolase (Nga) into the host cells through a streptolysin O (SLO)-dependent mechanism without invading the cells; Nga and SLO are two major virulence factors that are associated with increased bacterial virulence. Here, we have shown that the invading GAS induces fragmentation of the Golgi complex and inhibits anterograde transport in the infected host cells through the secreted toxins SLO and Nga. GAS infection-induced Golgi fragmentation required both bacterial invasion and SLO-mediated Nga translocation into the host cytosol. The cellular Golgi network is critical for the sorting of surface molecules and thus is essential for epithelial barrier integrity and the immune response of macrophages to pathogens. In epithelial cells, inhibition of anterograde trafficking by invading GAS and Nga resulted in the redistribution of E-cadherin to the cytosol and an increase in bacterial translocation across the epithelial barrier. Moreover, in macrophages, interleukin-8 secretion in response to GAS infection was found to be suppressed by intracellular GAS and Nga. Our findings reveal a previously undescribed bacterial invasion-dependent function of Nga as well as a previously unrecognized GAS-host interaction that is associated GAS pathogenesis. ImportanceTwo prominent virulence factors of GAS, SLO and Nga, have been established to be linked to enhanced pathogenicity of prevalent GAS strains. Recent advances show that SLO and Nga are important for intracellular survival of GAS in epithelial cells and macrophages. Here, we found that invading GAS disrupt the Golgi complex in host cells by SLO and Nga. We showed that GAS-induced Golgi fragmentation requires bacterial invasion into host cells, SLO pore-formation activity, and Nga NADase activity. GAS-induced Golgi fragmentation resulted in the impairment of epithelial barrier and chemokine secretion in macrophages. This immune inhibition property of SLO and Nga by intracellular GAS indicates that the invasion of GAS is associated with virulence exerted by SLO and Nga.

microbiology↗