Biology subjects

Yoshii, T.

Publications and source records attributed to Yoshii, T..

10 recordsLinked to original sources

bioRxiv2026

HPV-Associated Tonsillar Intraepithelial Neoplasia and Oral High-Risk HPV mRNA as a Candidate Biomarker

Early detection of human papillomavirus (HPV)-associated oropharyngeal cancer is an unmet need, as its premalignant lesions remain unestablished. We hypothesized that such lesions exist in individuals with oral high-risk HPV (HR-HPV) mRNA. We preoperatively screened 1,180 individuals undergoing tonsillectomy due to benign conditions and detected five with oral HR-HPV mRNA. Serial sectioning of the entire excised tonsils identified HPV-associated intraepithelial lesions in three of these five individuals. A similar lesion was identified in an additional individual with oral HPV16 infection with unknown oral HR-HPV mRNA status. Intraepithelial lesions in two individuals were HPV16-associated and showed moderate-to-severe atypia, whereas those in the other two individuals were associated with other HR-HPV and showed minimal-to-mild atypia. Based on HPV life cycle, the former were classified as transforming lesions and the latter as productive-to-intermediate lesions. Spatial transcriptomic analysis revealed molecular profiles intermediate between those of normal epithelium and HPV-associated oropharyngeal cancer. These findings establish the first evidence for HPV-associated tonsillar premalignant lesions and suggest oral HR-HPV mRNA as a candidate biomarker.

cancer biology↗

bioRxiv2026

THERM-D Uncovers Distinct Neural Mechanisms Separating Morning and Evening Body Temperature Rhythms in Drosophila

Animal body temperature rises throughout the day and peaks in the evening, a pattern conserved across diurnal endotherms and ectotherms. However, the mechanisms driving the robust body temperature rhythms (BTR) remain largely unclear. Here, we developed a machine learning-based platform, temperature homeostasis evaluation of rhythmicity in model Drosophila (THERM-D), enabling continuous, high-throughput analyses of BTR. Using THERM-D, we identified robust BTR patterns reflecting flies morning and evening behaviors and revealed the function of CRYPTOCHROME (CRY)-negative clock neurons. About half of all clock neurons lack CRY, yet their function was unclear. Newly developed Gal4 drivers targeting CRY-negative neurons demonstrated that these neurons control the morning temperature rise without affecting evening BTR. The data suggests that separate clock circuits regulate morning and evening BTR. Thus, THERM-D elucidated the role of CRY-negative clock neurons, which are specialized for BTR regulation and distinct from the circuits controlling sleep-wake cycles.

neuroscience↗

bioRxiv2025

Ion transport peptide regulates body water balance via a receptor guanylyl cyclase in the Drosophila hindgut

Maintaining internal water balance, including ionic and osmotic balance, is critical for animal development and survival. In insects, internal water balance is regulated through the Malpighian tubules and the hindgut, which transport water and ions across their epithelia under the regulation of multiple peptide hormones. One of these, ion transport peptide (ITP), a member of the highly conserved crustacean hyperglycemic hormone superfamily among ecdysozoans, is an anti-diuretic hormone in insects, but its mechanism of action remains largely unclear. Here, we show that the short amidated isoform of ITP (saITP), secreted from brain neurosecretory cells, regulates water absorption via the receptor guanylyl cyclase (rGC) Gyc76C in the hindgut of the fruit fly Drosophila melanogaster. Both ITP and Gyc76C are evolutionarily conserved and are essential for larval survival in D. melanogaster, as mutation or knockdown of either gene results in early larval lethality. In Drosophila S2 cells, synthetic saITP increases intracellular cyclic GMP (cGMP) in a Gyc76C-dependent manner, an effect abolished by deletion of its putative ligand-binding domain. Using the fluorescent cGMP biosensor RedcGull in ex vivo-cultured hindguts, we found that saITP increases epithelial cGMP levels, and this response requires Gyc76C. Consistently, saITP promotes hindgut water reabsorption via Gyc76C. Thus, saITP acts via Gyc76C in a brain-hindgut neuroendocrine axis that regulates internal water balance during development. Our study provides new insight into the neuroendocrine control of osmoregulation in ecdysozoans and supports a broader role for rGCs in peptide-hormone signaling.

physiology↗

bioRxiv2025

Octopamine signaling from clock neurons plays dual roles in Drosophila long-term memory

Circadian clock genes are best known for regulating circadian rhythms, but they also play crucial roles in memory processes. This suggests that memory is modulated by neural networks containing clock neurons, although the underlying mechanisms remain unclear. In Drosophila melanogaster, approximately 240 clock neurons are grouped into at least eight distinct clusters. Among them, the dorsal-lateral neurons (LNds) are required for maintaining long-term memory (LTM). In contrast, the neuropeptide Pigment-dispersing factor (Pdf), expressed in both small and large ventral-lateral neurons (s-LNvs and l-LNvs, respectively), functions as a circadian output signal and is also essential for maintaining LTM. In addition, Pdf-expressing neurons (hereafter, Pdf neurons) release neurotransmitters other than Pdf, which are involved in LTM consolidation. However, the specific transmitters used by LNds and Pdf neurons in LTM processing have remained unknown. Here, we show that octopamine signaling from LNds is essential for LTM maintenance, whereas octopamine in Pdf neurons is essential for LTM consolidation. Temporally restricted knockdown of Tyramine {beta} hydroxylase (Tbh), the gene encoding the enzyme required for octopamine synthesis, disrupted LTM maintenance when targeted in LNds, whereas it impaired LTM consolidation when targeted in Pdf neurons. Notably, Tbh knockdown in LNds or Pdf neurons had minimal effects on circadian behavioral rhythms or sleep. These findings reveal that octopamine released from specific subtypes of clock neurons independently regulates distinct phases of LTM in Drosophila. Author SummaryAnimal memory formed through learning is stabilized by a process called consolidation and becomes long-term memory (LTM), which can persist for extended periods. The fruit fly Drosophila melanogaster is widely used in memory research, enabling the discovery of key genes and signaling pathways. In addition, Drosophila has contributed significantly to circadian rhythm research through studies of clock neurons and clock genes. Notably, clock neurons have been implicated in LTM regulation, suggesting a potential link between circadian clock neurons and memory function. However, the neural network connecting these processes remains poorly understood. Identifying the neurotransmitters released from clock neurons is critical to clarifying how these neurons affect memory function. In this study, we show that octopamine, the fly equivalent of the vertebrate neurotransmitter norepinephrine, released from two distinct groups of clock neurons regulates different phases of LTM in Drosophila: one group supports consolidation, whereas the other supports maintenance. Our findings demonstrate that clock neurons play an active role in memory regulation, and they provide new insights into the neural circuitry that controls LTM.

neuroscience↗

bioRxiv2025

De novo chemo-optogenetics through rational small-molecule design and TRAP display

Optical control of biomolecules is a powerful technique for biological research, but current tools derived from natural proteins face significant limitations. Engineering these proteins to meet researchers needs remains challenging. In this study, we present a novel approach to the de novo creation of tailored chemo-optogenetic tools. This method combines the rational design of synthetic photo-switchable molecules with in vitro selection of artificial protein binders that specifically recognize a particular conformation of these molecules. We demonstrate the utility of this approach by generating artificial proteins that bind exclusively to the cis-form of designed azobenzene derivatives. The newly created pairs enable sustained protein activation with a single light pulse and allow for precise, reversible, and repeatable switching of cellular processes using two distinct wavelengths of light in mammalian cells. This de novo technique provides tailored synthetic photoswitch-protein binder pairs, expanding the potential for optical biomolecule manipulation.

synthetic biology↗

bioRxiv2023

Synaptic and peptidergic connectomes of the Drosophila circadian clock

The circadian clock and its output pathways play a pivotal role in optimizing daily processes. To obtain novel insights into how diverse rhythmic physiology and behaviors are orchestrated, we have generated the first comprehensive connectivity map of an animal circadian clock using the Drosophila FlyWire brain connectome. Intriguingly, we identified additional dorsal clock neurons, thus showing that the Drosophila circadian network contains [~]240 instead of 150 neurons. We also revealed extensive contralateral synaptic connectivity within the network and discovered novel indirect light input pathways to the clock neurons. Interestingly, we observed sparse monosynaptic connectivity between clock neurons and down-stream higher-order brain centers and neurosecretory cells known to regulate behavior and physiology. Therefore, we integrated single-cell transcriptomics and receptor mapping to decipher putative paracrine peptidergic signaling by clock neurons. Our analyses identified additional novel neuropeptides expressed in clock neurons and suggest that peptidergic signaling significantly enriches interconnectivity within the clock network.

neuroscience↗

bioRxiv2021

A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation

Chemogenetic methods that enable the rapid translocation of specific signaling proteins in living cells using small molecules are powerful tools for manipulating and interrogating intracellular signaling networks. However, existing techniques rely on chemically induced dimerization of two protein components and have certain limitations, such as a lack of reversibility, bioorthogonality, and usability. Here, by expanding our self-localizing ligand-induced protein translocation (SLIPT) approach, we have developed a versatile chemogenetic system for plasma membrane (PM)-targeted protein translocation. In this system, a novel engineered Escherichia coli dihydrofolate reductase in which a hexalysine (K6) sequence is inserted in a loop region (iK6DHFR) is used as a universal protein tag for PM-targeted SLIPT. Proteins of interest that are fused to the iK6DHFR tag can be specifically recruited from the cytoplasm to the PM within minutes by addition of a myristoyl-O_SCPLOWDC_SCPLOW-Cys-tethered trimethoprim ligand (mDcTMP). We demonstrated the broad applicability and robustness of this engineered protein-synthetic ligand pair as a tool for the conditional activation of various types of signaling molecules, including protein and lipid kinases, small GTPases, heterotrimeric G proteins, and second messengers. In combination with a competitor ligand and a culture-medium flow chamber, we further demonstrated the application of the system for chemically manipulating protein localization in a reversible and repeatable manner to generate synthetic signal oscillations in living cells. The present bioorthogonal iK6DHFR/mDcTMP-based SLIPT system affords rapid, reversible, and repeatable control of the PM recruitment of target proteins, offering a versatile and easy-to-use chemogenetic platform for chemical and synthetic biology applications.

synthetic biology↗

bioRxiv2020

Synthetic protein condensates that recruit and release protein activity in living cells

Compartmentation of proteins into biomolecular condensates or membraneless organelles formed by phase separation is an emerging principle for the regulation of cellular processes. Creating synthetic condensates that accommodate specific intracellular proteins on demand would have various applications in chemical biology, cell engineering and synthetic biology. Here, we report the construction of synthetic protein condensates capable of recruiting and/or releasing proteins of interest in living mammalian cells in response to a small molecule or light. We first present chemogenetic protein-recruiting and -releasing condensates, which rapidly inhibited and activated signaling proteins, respectively. An optogenetic condensate system was successfully constructed that enables reversible release and sequestration of protein activity using light. This proof-of-principle work provides a new platform for chemogenetic and optogenetic control of protein activity in mammalian cells and represents a step towards tailor-made engineering of synthetic protein condensates with various functionalities.

synthetic biology↗

bioRxiv2020

Amplitude of circadian rhythms becomes weaker in the north, but there is no cline in the period of rhythm in a beetle

Many species show rhythmicity in activity, from the timing of flowering in plants to that of foraging behaviour in animals. The free-running periods and amplitude (sometimes called strength or power) of circadian rhythms are often used as indicators of biological clocks. Many reports have shown that these traits highly geographically variable, and interestingly, they often show latitudinal or altitudinal clines. In many cases, the higher the latitude is, the longer the free-running circadian period (i.e., period of rhythm) in insects and plants. However, reports of positive correlations between latitude or longitude and circadian rhythm traits, including free-running periods, the power of the rhythm and locomotor activity, are limited to certain taxonomic groups. Therefore, we collected a cosmopolitan stored-product pest species, the red flour beetle Tribolium castaneum, in various parts of Japan and examined its rhythm traits, including the power of the rhythm and period of the rhythm, which were calculated from locomotor activity. The analysis revealed that power was significantly lower for beetles collected in northern areas compared with southern areas in Japan. However, it is worth noting that the period of circadian rhythm did not show any clines; specifically, it did not vary among the sampling sites, despite the very large sample size (n = 1585). We discuss why these cline trends were observed in T. castaneum.

animal behavior and cognition↗

bioRxiv2020

Improved synthetic lipidation-based protein translocation system for SNAP-tag fusion proteins

The ability to artificially attach lipids to specific intracellular protein targets would be a valuable approach for controlling protein localization and function in cells. We recently devised a chemogenetic method in which a SNAP-tag fusion protein can be translocated from the cytoplasm to the plasma membrane by post-translationally and covalently conjugating a synthetic lipopeptide in cells. However, the first-generation system lacked general applicability. Herein, we present an improved synthetic lipidation system that enables efficient plasma membrane translocation of SNAP-tag fusion proteins in cells. This second-generation system is now applicable to the control of various cell-signaling molecules, offering a new and useful research tool in chemical biology and synthetic biology.

biochemistry↗