Biology subjects

Tsuji, K.

Publications and source records attributed to Tsuji, K..

12 recordsLinked to original sources

bioRxiv2026

Viral infection patterns in ants are affected by colony structure and phylogenetic lineage

Across ant species, there are differences in how their societies are structured. Single-queened (monogynous) societies only have one reproducing queen in the colony, and new queens disperse and start colonies independently. In multiple-queened (polygynous) societies, the colony instead can contain several reproductive queens, and newborn queens often remain and reproduce within their natal colony. As a result, polygynous societies are comparatively larger, more genetically diverse, and can span large areas through several interconnected nests, whereas monogynous societies are typically smaller in scale. In this study, we investigated how these different social structures, as well as their phylogenetic lineage, affect the diversity (number of virus species per ant sample) and abundance (number of viral sequences per sample) of viruses in ants. We produced pooled RNA sequence libraries from 15 ant species, representing both monogynous and polygynous social structures, and the two largest ant subfamilies: Formicinae and Myrmicinae, with each library containing the RNA of up to 400 individual worker ants from a single population. We identified 168 virus species in total, of which 152 species were new to science. Out of these 168 viruses, 59 were active viruses based on the host immune response. We observed that polygynous ant species harbor a higher diversity of viruses and also tend to have higher virus abundance compared to monogynous species. Also, the ant subfamily Myrmicinae had a higher virus diversity than Formicinae. These findings highlight how social structure and evolutionary history shape viral diversity in ants.

genomics↗

bioRxiv2026

Multi-Omic Analyses of Dietary Fatty Acid-Microbe-Host Interactions Reveal Metaorganismal Lipid Metabolic Crosstalk Impacting Cardiometabolic Disease

Following a meal, our gut microbiome and human cells collaborate via metaorganismal metabolic circuits to produce diverse nutrient metabolites that systemically circulate to influence health and disease. Although there are now several examples of bacterial fiber-, amino acid-, and micronutrient-derived metabolites impacting cardiometabolic disease, very little is known in regards to how diet-microbe-host interactions impact lipid homeostasis. Here we address this by defining dietary fatty acid substrate availability in germ-free versus conventionally-raised mice coupled to deep multi-omic metabolic phenotyping. Our data demonstrate that the effects of dietary saturated (SFA), monounsaturated (MUFA), and polyunsaturated fatty acids (PUFA) on the host lipidome, transcriptome, proteome and metabolome are uniquely impacted by resident microbiota. Also, the hepatic levels of both pro-inflammatory and pro-resolving lipid mediators are strongly influenced by dietary fatty acid-microbe interactions. This study presents a unique resource to the nutrition and metabolism research community to advance our understanding of metaorganismal lipid metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/705588v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@4fc7e3org.highwire.dtl.DTLVardef@1cc1dc8org.highwire.dtl.DTLVardef@1b7648dorg.highwire.dtl.DTLVardef@12a8088_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG

biochemistry↗

bioRxiv2025

Claudin-1 Inhibitor PDS-0330 Ameliorates Diabetic Kidney Disease by Suppressing Src/Akt/mTOR Signaling Pathway in Podocytes

IntroductionRecent studies have reported that claudin-1, which is reactively expressed in malignant tumors and inflammatory diseases, plays an important role in disease progression. In diabetic kidney disease (DKD), upregulated expression of claudin-1 in podocytes has also been shown to contribute to disease progression. However, it remains unclear whether claudin-1 itself could be a therapeutic target in DKD. In this study, we investigated whether the claudin-1 inhibitor PDS-0330 could ameliorate DKD. MethodsFive-week-old male C57BL/6J mice were fed either a high-fat diet (HFD) or a normal diet (ND). At 15 weeks of age, PDS-0330 (Inh) or vehicle as control (Ctrl) was administered orally once per week for 4 weeks. At the end of the treatment period, blood, urine, and kidney samples were collected. In in vitro study, immortalized podocytes were treated with Inh or Ctrl and cultured for 48 hours in either normal glucose medium (5.5 mM; NG) or high glucose medium (25 mM; HG), after which proteins were extracted for analysis. ResultsMice fed an HFD showed significant increases in body weight and serum glucose levels compared with ND mice, and these parameters were not significantly affected by Inh treatment. HFD mice treated with Ctrl (HFD-Ctrl) exhibited significantly higher urinary albumin excretion than ND mice treated with Ctrl (ND-Ctrl), whereas the Inh-treated HFD mice (HFD-Inh) showed a significant reduction. Transmission electron microscopy revealed foot process effacement in HFD-Ctrl podocytes, which was markedly improved in HFD-Inh mice. Immunofluorescence staining demonstrated claudin-1 expression in podocytes of HFD mice. Furthermore, phospho-mTOR staining in podocytes was significantly increased in HFD-Ctrl compared with ND-Ctrl and was significantly attenuated in HFD-Inh. Western blot analysis of kidney samples revealed activation of the Src/Akt/mTOR signaling pathway in HFD-Ctrl mice, which was significantly reduced in HFD-Inh mice. In in vitro study, Ctrl-treated podocytes cultured in HG (HG-Ctrl) showed significant activation of Src/Akt/mTOR signaling compared with those in NG (NG-Ctrl). This activation was significantly suppressed in Inh-treated podocytes (HG-Inh). ConclusionThese findings suggest that podocyte claudin-1 could be a potential therapeutic target in DKD.

physiology↗

bioRxiv2025

Diversity of vector-dispersed microbes peaks at a landscape-defined intermediate rate of dispersal

Dispersal rate has long been considered a primary determinant of species diversity in ecological communities. However, this knowledge is mostly built on studies of organisms that disperse actively by themselves or passively via physical forces. For organisms that disperse passively via other organisms, the landscape matrix that affects their vectors should indirectly shape the diversity of the vectored, but this relationship remains poorly understood. We investigated landscape-dispersal-diversity relationships in nectar-inhabiting bacteria that disperse via flower-visiting insects. Field observation and experiments revealed that bacterial diversity and abundance peaked at an intermediate frequency of insect visits, which was in turn determined by the surrounding landscape characteristics observed at the 200-m radius scale. Based on this finding, we discuss the possibility that species diversity tends to be maximized at an intermediate dispersal rate, especially when habitat patches of vectored organisms constitute consumable resources for their vectors.

ecology↗

bioRxiv2025

Development and Validation of a Stem Cell-Based Kidney Organoid Platform for Nephrotoxicity Assessment

Background and hypothesisRecent cases of acute kidney injury (AKI) in Japan have been linked to the Beni-koji CholesteHelp supplement. Renal biopsies from affected patients revealed tubular damage, and puberulic acid was subsequently identified as a potential nephrotoxic contaminant. Recognizing the urgent need for a reliable in vitro nephrotoxicity testing platform, we hypothesized that a kidney organoid-based system could replicate nephrotoxic injury and help identify novel nephrotoxicants. In this study, we developed a screening model using kidney organoids derived from adult rat kidney stem (KS) cells and applied it to evaluate the toxicity of puberulic acid. MethodsKidney organoids were generated from KS cells and exposed to established nephrotoxicants, including cisplatin and gentamicin, to validate the model. The nephrotoxicity of puberulic acid was evaluated using both KS cell-derived organoids and wild-type mice. Nephrotoxicity was assessed by morphological changes, Kim-1 mRNA expression, transmission electron microscopy (TEM), and analysis of markers related to mitochondrial injury, oxidative stress, and apoptosis. ResultsThe kidney organoids reproduced morphological features of injury induced by known nephrotoxins and showed significant upregulation of Kim-1 mRNA. Puberulic acid-treated organoids displayed ultrastructural features consistent with acute tubular necrosis (ATN) and increased Kim-1 expression. In vivo, puberulic acid-exposed mice exhibited impaired renal function and histological findings consistent with ATN. Both in vitro and in vivo models revealed mitochondrial structural abnormalities and reduced expression of cytochrome c oxidase subunit IV (COX-IV). Additionally, oxidative stress and apoptotic markers, including 8-hydroxy-2-deoxyguanosine (8-OHdG) and cleaved caspase-3, were significantly elevated, suggesting that puberulic acid induces mitochondrial dysfunction and oxidative stress, leading to tubular cell death. ConclusionPuberulic acid-induced nephrotoxicity was demonstrated using our kidney organoid model. KS cell-derived kidney organoids provide a simple, reproducible, and rapid platform for nephrotoxicity assessment, which contribute to a reduction of animal use in toxicology research.

pharmacology and toxicology↗

bioRxiv2024

Wound-initiated hair regeneration by adhesive and shrinkable materials

Although there is a global demand for hair regrowth, particularly among middle-aged and older individuals, an effective hair growth technology has not yet been established1. Hair follicle neogenesis is restricted to the embryonic period, but hair regeneration accompanied by wound healing has been observed under some conditions2-4; however, the underlying mechanisms are unclear. Herein, we demonstrated that creating a wound without dermal defects effectively induced postneonatal hair follicle neogenesis. Separating the epidermis from the dermis by topical application of adhesive and shrinkable materials to mouse skin promoted epidermal regeneration, followed by new hair follicle formation. Hair follicle regeneration, accompanied by the upregulation of related genes, can be induced in mice, including middle-aged and aged mice, regardless of species, sex, skin location, or age. The cycle of the regenerated hair eventually synchronized with that of the surrounding physiological hairs. Our new hair regeneration technique based on reproduction of epidermis-dermis interactions provides a novel means to treat hair loss, including androgenetic alopecia.

cell biology↗

bioRxiv2024

Effects of unconscious tactile stimuli on autonomic nervous activity and afferent signal processing

Autonomic nervous system (ANS) is a mechanism that regulates our internal environment. In recent years, the interest in how tactile stimuli presented directly to the body affect ANS function and cortical processing in humans has been renewed. However, it is not yet clear how subtle tactile stimuli below the level of consciousness affect human heart rate and cortical processing. To examine this, subthreshold electrical stimuli were presented to the left forearm of 43 participants during an image-viewing task, and electrocardiogram (ECG) and electroencephalogram (EEG) data were collected. The changes in the R-wave interval of the ECG immediately after the subthreshold electrical presentation and heartbeat-evoked potential (HEP), the afferent signal processing of cardiac activity, were measured. The results showed that heart rate decelerated immediately after the presentation of subthreshold electrical stimuli. The HEP during stimulus presentation was amplified for participants with greater heart rate acceleration immediately after this deceleration. The magnitude of these effects depended on the type of the subthreshold tactile stimuli. The results suggest that even with subthreshold stimulation, the changes in autonomic activity associated with orienting response and related afferent signal processing differ depending on the clarity of the tactile stimuli.

neuroscience↗

bioRxiv2024

Bacteria in honeybee crops are decoupled from those in floral nectar and bee mouths

Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.

ecology↗

bioRxiv2024

AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning

Annotation of multiple regions of interest across the whole mouse brain is an indispensable process for quantitative evaluation of a multitude of study endpoints in neuroscience digital pathology. Prior experience and domain expert knowledge are the key aspects for image annotation quality and consistency. At present, image annotation is often achieved manually by certified pathologists or trained technicians, limiting the total throughput of studies performed at neuroscience digital pathology labs. It may also mean that less rigorous, less time-consuming methods of histopathological assessment are employed by non-pathologists, especially for early discovery and preclinical studies. To address these limitations and to meet the growing demand for image analysis in a pharmaceutical setting, we developed AnNoBrainer, an open-source software tool that leverages deep learning, image registration, and standard cortical brain templates to automatically annotate individual brain regions on 2D pathology slides. Application of AnNoBrainer to a published set of pathology slides from transgenic mice models of synucleinopathy revealed comparable accuracy, increased reproducibility, and a significant reduction ([~]50%) in time spent on brain annotation, quality control and labelling compared to trained scientists in pathology. Taken together, AnNoBrainer offers a rapid, accurate, and reproducible automated annotation of mouse brain images that largely meets the experts histopathological assessment standards (>85% of cases) and enables high-throughput image analysis workflows in digital pathology labs.

neuroscience↗

bioRxiv2023

Time-deterministic cryo-optical microscopy

We developed a technique to rapidly freeze biological systems during observation under an optical microscope, which allows for detailed optical observation at a precise time in the biological dynamics at high spatial resolution and quantifiability under low-temperature conditions. Our study further found that ion distributions and molecular conformations can be fixed in space and time, demonstrated by visualization of calcium waves rapid-frozen at an instant using fluorescent ion indicators. These results show that time-deterministic cryo-optical microscopy can suspend cellular dynamics while maintaining molecular and ionic states, allowing us to view cellular dynamics in a way that has not been possible before. One-Sentence SummaryRapid freezing of dynamic biological systems during optical observation presents time information to the fixed samples

biophysics↗

bioRxiv2021

RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of [~]22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP-dependent sRNAs possess 5- monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of RdRPs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP through the 3UTR that contains a target site of RdRP-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways. Author summaryRNA-dependent RNA Polymerases (RdRPs) are essential for biogenesis of small regulatory RNAs (sRNAs) in many organisms such as plants and fungi, but its general importance in animals besides nematodes remains controversial because experimental evidence is lacking. By using a tick cell line, we demonstrate that RdRP-dependent sRNAs are abundantly expressed and tick RdRPs regulate gene expression. These results indicate that ticks have unexpectedly complex sRNA biogenesis pathways that are essential for proper gene regulation. Interestingly, we show that RdRP negatively regulates immune response by changing expression of a gene that is essential in an immunity-related signaling pathway. Because ticks are important vectors of human and animal pathogens, studying the novel tick sRNA pathways and their effects on immune signaling may lead to a better understanding of vector-virus interactions.

molecular biology↗

bioRxiv2021

Comprehensive analysis of male-free reproduction in Monomorium triviale (Formicidae: Myrmicinae)

We report comprehensive evidence for obligatory thelytokous parthenogenesis in an ant Monomorium triviale. This species is characterized by distinct queen-worker dimorphism with strict reproductive division of labor: queens produce both workers and new queens without mating, whereas workers are completely sterile. We collected 333 nests of this species from 14 localities and three laboratory-reared populations in Japan. All wild queens dissected had no sperm in their spermathecae. Laboratory observation confirmed that virgin queens produced workers without mating. Furthermore, microsatellite genotyping showed identical heterozygous genotypes between mothers and their respective daughters, suggesting an extremely low probability of sexual reproduction. Microbial analysis detected no bacterial genera that are known to induce thelytokous parthenogenesis in Hymenoptera. Finally, the lack of variation in partial sequences of mitochondrial DNA among individuals sampled from across Japan suggests recent rapid spread or selective sweep. M. triviale would be a promising model system of superorganism-like adaptation through comparative analysis with well-studied sexual congeners, including the pharaoh ant M. pharaonis.

zoology↗